METHODS OF CREATING SYNTHETIC CONSORTIA OF MICROORGANISMS RELATED APPLICATIONS The present application is a divisional application of Australian Application No. 5 2011268263, which is incorporated in its entirety herein by reference. This International (PCT) Patent Application claims benefit of priority to United States Provisional Patent Application Serial No. (USSN) 61/355,488 filed June 16, 2010, and USSN 61/495,815 filed June 10, 2011, both of which are expressly incorporated by reference herein in their entirety for all purposes. 0 FIELD OF THE INVENTION Any discussion of the prior art throughout the specification should in no way be considered as an admission that such prior art is widely known or forms part of common general knowledge in the field. This invention generally relates to natural gas and methylotrophic energy generation, 5 bio-generated fuels and microbiology. In alternative embodiments, the invention provides compositions and methods for methanol-utilizing methanogenesis, or "methylotrophic" conversion, including utilizing methylamines and other methyl-containing intermediates. In alternative embodiments, the invention provides nutrient amendments and microbial compositions that are both specifically optimized to stimulate methanogenesis from coal or 0 other subsurface carbonaceous materials. In alternative embodiments, the invention provides methods to develop nutrient amendments and microbial compositions that are both specifically optimized to stimulate methanogenesis in a given reservoir. BACKGROUND OF THE INVENTION The methanogenic degradation of subsurface carbonaceous material is of significant 25 commercial interest for a variety of reasons including production of natural gas (including methane). Methane is a predominant end-product of anaerobic microbially-mediated organic matter decomposition following a variety of carbon-pathways and intermediate steps. Recent technological advances have enabled characterization of microbial communities and the biogeochemical processes that take place in the subsurface. These 30 processes generally occur under non-ideal conditions due to limiting nutrients and sub-optimal microbial community structure. Under normal sub-surface conditions, microbial gas formed in 1 these natural "bioreactors" is generated at very slow rates due to limited nutrients and/or other environmental conditions, e.g., suboptimal water chemistry, pH, salinity and the like. SUMMARY In alternative embodiments, the invention provides compositions, bioreactors, 5 reservoirs, products of manufacture, fluids or muds, or synthetic consortiums (e.g., la manufactured groups of organisms) comprising a plurality of microorga nism strains, wherein the microorganism strains comprise: (a) at least two, three, ftour, five, six, seven, eight, nine, ten or eleven or all twelve of the nicroorganism strains of ConsoruABS I; or 5 (b) a group (or "consortiumn" of different nicroorgan isnm strains comprising at least two, three, four, five, six, seven, eight, nine, ten, eleven or twelve different nicroorganism strains, each strain comprising at least one 6 rRN A gene or nucleic acid sequence selected from the group con\isting of a nucleic acid having at least about 90%, 91%, 92%., 93%,s 94%, 95%, 96%, 97%, 98%, 99% or 100% (complete) sequence identity to SEQ ID NO: 1, SEQ ID 10 NO:2 SEQ ID NO:3 SEQ ID. NO:4, SEQ TD NO:5, SEQ 1D NO:6, SEQ 1D NO:?, SEQ 1D NO:8, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: i and SEQ ID NO: 12, or (c) a group (or "consortium") of different microorganism strains consisting of at least two, three, four, five, six, seven. eigat, nine, ten, eleven or twelve different microorganism strains, each strain comprising at least one I (S rRN A gene or nucleic acid sequence selected 15 from the group con\isti ng ofa nucleic acid having at least about 90%, 91%, 92%., 93%, 94%, 95%, 96%, 97%, 9 % A or 100% (complete) sequence identity to SEQ ID NO: 1, SEQ ID NO:2 SEQ ID NO:3 SIQ ID NO:4, SEQ TD N0:5, SEQ 1D N0:6, SEQ fD NO:?, SEQ 11 NO:8, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO:l I and SEQ ID NO: 12, wherein optionally each member of the group (or "'consortium") of different 20 nicroorganisn strains is a different microorganism strain, or each member of the group (or consortiumn") of different microorganism strains has a different 16S rRNA gene or nucleic acid sequence, and optionally the at least one I 6S rRNA gene or nucleic acid sequence comprises a subsequence (a portion) of a 16S rRN.A sequence that optionally includes (comprises) the fifth 25 and sixth variable (V5 and V6) regions of a 16S rRNA gene, and optionally the reservoir is an in sim, subsurface reservoir, a surface reservoir, a synthetic reservoir or an excavated reservoir, In alternative embodiments of the compositions, bioreactors, reservoirs, products of manufacture, fluids, muds and/or synthetic consortiums: 30 (i) at least 1, 2, 3, 4, 5. 6. 7, 8, 9, 10, 11 or all 12 of the nicroorganisn strains cornprise a member of the genus Acerobcae ium, a member of tile genus Bacteroidees and/or a member of the genus Spirchaexes; or 2 ii) at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 of the microorganism strai s comprise a member of the genus .4crobterium, a member of the genus Bacteroidees and a member of the genus Spiochaetes. In altenative embodiments, the invention provides methods of identifying and/Uor 5 characterizin one or more microbes in a subsurface methanogenic nicroblal community, or identifying and/or charactcrizing a nutrient composition that is customized for a specific subsurface methanoenic microbial community, comprising: ta) obtaining or providing one or a set of samples from a subsurface carbonaceous form nation orfrations, 10 wherein optionally the samples comprise a production water, or the samples are taken from a core, cuttings or outcrop sample and optionally the subsurface carbonaceous firmation or formations comprises a coal formation or a. peat, or a lignite, or a bituminous coal, or an anthracite coal, or a volcanic ash, or a lignite or a lignin or lignin-comprising composition, a coal or a coal analogue(s) or a 15 precursor(s) thereof, heavy oil, asphaltenes, and/or an organic debris; (b) determining and/or chamterizing the microbial composition, or the methanogen ic strains (e.g, a phylogenetic analysis) of the sample or samples, wherein optionally all or substantially most of the microbes in the staple or samples are characterized or identified, 20 or optionally all or substantially most of the methanogenic microbes (the methanogens, or nethanogenic strains) in the sample or samples are characterized or identified; and (c) (i) identifying and/or characterizing one or more microbes in the sample or samples that are the most (or relatively more) methanogenic, 25 idenmifying and/or characterizing one or more microbes in the sample or samples that are the most abundant methanogens, identifving and/or characterizing one or more microbes in the sample or samples whose distributions are (or distribution is) correlated with that of most other methanogens in the sample, or whose distributions are (or distribution is) correlated with the highest level of 30 methanogenesis in the sample, and/or identifying unfavorable endenmtic microbes or conditions showing negative correlation to biogas formation; or 3 (ii) applying to the sample or samples a plurality of(a variety of) nutrients mixes anod determining a consensus and/or optiral (optimal for methanogenesis) nutrient mix, wherein optionally tie consensus and/or optional nutrient nix is at least initially based upon known requirements of methanogenic microbes, r r associated with $ methanogen ic microbes, and/or field observations of s ubsurface methanogenie environments, and optionally the sample or samples comprise a subset of the microbial composition of the sample or samples of step (b), or a subset of the nethanogenic organisms identified or characterized in step (b), or a set of metnhanogen oranisms identified or characterized in 10 and optionally the consensus and/or optimal nutrient mix is also designed to decrease the amount of other (non-methanogenic bacterial processes affecting biogas formation, or to provide an environment unfavorable to endemic microbes or conditions that show a negative correlation to biogas (e,g.r, methane) formation. In alternative embodiments, the methods further comprise introducing the consensus 15 or optimal nutrient mix of 3(c)(ii) to a rethanogenic microbial conuunity; wherein optionally the methanogenic microbial community is in situ in subsurface rnethanogenic microbial community, In alternative emubodi ments., the microbial compose ition of step 3(b) is determined and or characterized by nucleic acid (e.g, DNA, RNA) sequencing all or a portion of an rRNA 20 gene; or a 16S rRNA geneI. In ateatve embodiments. the microbial co.mrposition of step 3(b) is determined by a chemical, microbiological or any analytical method. In alternative embodiments, the chemical or microbiological analytical method comprises a fatty acid methyl ester analysis, a membrane lipid analysis andior a cultivation dependent method. 25 In alternative embodiments, the methanogenie organisms (methanogenic strains) comprise one or more members of the Archaea fainily, or are anaerobic organisms, or are autotrophs or chenoheterotrophs; or the mnethanogeni orgaiMnismS comprise one or more members of a genus selected from the group consisting of Metmhanolobus,M .eihanothermobacter Methanogenium, Methanogenium, Methanofolis. Methaoculieus. 31 Methianocorpuscuum, Methanococcus, Meetanocalcuu,. Methanobrevibacter and /ethanosarcina; or the methanogenic organisms (mefhanogenic strains) comprise or consist of at least one synthetic consortium of the invention, or one or more members selected front the group consisting of: 4 / Methabno/obus brnbayensis 0 MthAItanolobus taorI -WMenhanolobus prollfmdi * Methnobiu w zinder * Mi eaobacteriwn jormicrum e Methanocbrevibacter arript(hilicu~s *o .- srwh 04Iany * Methanalcbis chunghsingensis elehanococcus eliu * Mecthanococcu s detae 15 * Methancccus jcianhil e Methanotocus aripais * Melhanoegicoc vonniei W Mechanocopuscuu a breanum i Mthanuoculu bourgeCt?(nns (-Me'thannu oientangyvi &.A-euhanogenium 20 bourgense) - Mehancullus arisniri * Medkanofbiis limintrans * Methianugenium- cariaci' e Mekthanagenuiumf?<Yjgidwnf 25 W Methnogenium ognplum 4 Methanogenum an"e I en pyu kanodeinstwivezo ovde ltoso a1me ceno-tc M thaoregCustma e b onei imlfra pcfcsbu-ao drba 4-5 a,/ obaiin a)P-r o ,t fs'Tl .famceo nw Subuf 30 * Mt huansaet council e M-e hano saetas trophila'' * MVethansar in':mz 35 aoehaousphaiora sadtineret e Me/ti-hnohermoblactdefu (Methanobacterium deftuv-l ) * Me ?thauniP thhob ar thermurohicus (AMthanobceriumn- themnnatotro phicum) * Methaunother mobactr thrmofeus ( Me-thanbacterium thermolexum) 40) * Mtihanot/ermobter woli (.M/thanobacteriumn vvoi/i) ,ad * Methanwothnrxscnei In ahemative. ~ tmodintvs. the invention provides methods of deternining a nint composition that is cusTtoized or otmlfr a specific subsurface methanogen ic microbial community comprisg the following steps: 45 a, obtaining a samipie or a set of samples from one or more subsurface carbonaceous tonnation(s) of in terest, 5 wherein optionally the subsurface carbonaceous formation or formations comprises a coal formation, or a peat, or a lignite, or a bituminous coal, or an anthracite coal, or a coal analogues) or a precursor(s) thereof, a heavy oil, asphaltenes, and/or an organic debris; 5 b. determining or characterizing the microbial composition of the methanogenic microbial community of the samplernples; and C, growing or culturing one or more enrichment cultures of all or a subset of the microbial composition on a carbonaceous substrate, a chemical analog, a methanogenic substrate or a combination thereof, 10 wherein optionally the enrichment cultures are designed to distinguish different methanogenic pathways, and (0 identify ing and/or characterizing one or more methanogens grown or cultured in the enrichment culture or cultures whose distribution strongly correlates with a high methanogenes is rate; and/or 15 (ii) identifying one or more microbes present in the sample or samples whose distribution correlates with that of a inethanogen in the sample, or whose distribution correlates with that of a methangen(s) identified in step (i In alternative embodiments the methods further comprise designing a nutrient mix for optimizing growth of the mcthanogens) an d/or optimizing methanogenic activity, 20 wherein optionally the nutrient mix is at least initially based on one or more requirements, or a range of requirements, of methanoge nic microbes or microbes associated with methanogens as identified through literature searches, field observations of subsurface methanogen ic environments and/or cultivation experiments, and optionally the nutrient mix is als dg to decrease the amount of other (non 25 methanogenic) bacterial processes negatively affecting biogas formation, In alternative embodiments the methods further evaluating the effect of nutrient concentration variations on mrethanogenesis rates in test cultures using endemic carbonaceous substrates. In alternative embodiments the methods further comprise introducing the nutrient mix to a methanogenic microbial co.mmunity wherein optionally the methanogenic microbial 30 community is in sin in a subsurface carbonaceous formation. In alternative embodiments the samples comprise a production water, or the samples are taken from a cure sample. 6 In arnative embodiments, the invention provides methods for improving methylotrophic biogas formation in situ in a subsurface carbonaceous formnation comprising: (a) administering one or more mehne organisms identified in a method of the invention, or at least one synthetic consortium of the invention, to the subsurface 5 carbonaceous formation or formatonsor (b1) administering one or more methanogeni organisrns, wherein optionally the methanogeme organisms comprise one or nore mnimbers of the Archea family, or are anaerobic organisms or are autotrophs or chemohtrotrophs, and optionally the methanogenic organisms comprise one or more members of a genus 10 selected fr..m the group consisting of Methano/obus, tkhanobacerium, Methanothermocbacw tfer etanogen/in, Mehanagenium, MethanojoIs, Methanwc/Ieus, MeAtha nocCrpuscuum, Met~hanoccoccus, Mehaocalculus AMethanubrvibacter and tzannsarcna, and optionally the methanogenic organisms conmprise: at least one synthetic 15 consortium of the invention, or one or more members selected from the group consisting of: a Me>thanolobis payrii a Methzanotbus ron i a M.ehano/obus 01onderi 20 a Methanobacterium bryai l * Me.thanbacterium formicum~ a Met/hanobre v/bacr abr ipiis e Mtethanobrwevibacte hotisc'halkii A Methanobretibact unniu 25 a Methanobresivicer smithii' a MCefhanocacus chunngngensi's e Mtethncoccox:idres burtonii a Methanzococcus Osewius a Me'thanococcus deltae 30 a Mthanoccrcus j an narsh a Mtethanococcus maripaludis a Mfethatnococcus uie icf a Methanocorpusuban hi!breanum a Mefthanocu/leu~s buorss (Mlethnocgenium olentan gvi & Metthainagenim a Met hanocull1eus maPrf snigri a Metanogeniumn cariaci 40 a Mh genium organophilum a Miethanogeniumi wollei a Meahanomi cobum mobile 7 e Mithanoyruskandieri ' Methanoregula boorne * M/eanaosaeta coinc ilii * Methanosaeta thrmpila * Methanosarcina barker i e Meh'ancarctina mazei * Mlethanosphaera stadt marne * Mlharnosirlsm 0 hungat( SMletaznotheroacter thermautotrophI(iu (Metha~nobteium a thermoautotrophicumn) * Meiharnthrmobaik cer 1 w nhro/aexu's (Mtethanfobacte rum thermoflexumor) AMehanothermobacter wle Mehnohaterum ?vlj , n 15 wherein optionally the one or more mnthanogeic organisms have been enriched using the consensus andior optimal nutrient nix ideified i a. rethod of ie invention, wherein optionally the subsurface carbonacous fonmation is modified to have properties more like or similar to ow morc property's of the optimal nutrient -mix 20 and optionally the subsurface carbonaceous formation or forimations comprises a coal formation, or a peat, or a lignite, or a bitauinous coal, or an anthracite coal, or a coal or a coal analogue(s) or a precursor(s) thereof, heavy oil, asphalenes, andor an ornanic debris. In alternative cmbodiumnts, he invemntion provides methods for improving metylotrophic biogas formation in situ in a subsurface carbonaceous formation or formations 25 comprising: (a) (I administering one or more methanogenic organisms identiifd in a method of the invention, or at least one synthetic consortium of the invention, to the subsurface carbonaceous formation or fornations., wherein optionally the subsurface carbonaceous formation or fomnations comprises a 30 coal formation, or a peat, a lign ite, or a bituminous coal, or an anthracite coal, a coal or a coal analogue(s) or a precurswors) thereof. heavy oil, asphahenes, and/or an organic debris, or 2)administring one or more nethnogtenie organisms, wherein o ptionally tei methanogeic organisms comprise one or more members of the Archaea family, or are anaerobic organisms, or are autotrophs or chemoheterotrophs, 35 and optionally the methanogenic organisms comprise one or more members of a gcenus selected from the group consisting of Methanolobs, anobactium, Mehnteroatr MetA~hanazgenhum, M.ethaOS'ngenium, Methano/ois, Mthdanoculieuss, Methanocarupusculum, Metihanococcus, Melthanocalculus, MAenhanobrev..ibsacter and 8 Methanos arcana. or rhe methanogenic organisms comprise: at least one synthetic consortum of the invention, or one or more members selected from the group consisting of: SMthaLus bnba yensis A Aethanolobus tylori 5 e Meth-Wanlobs poud e Menthanolobu4s zinderi a nethanbacterium bryanlii * Mirtkanobacterium form icuml a Methanobrevibaer; ar~fbihilicu 10 . Metnobrevibacer ganschaikll A Methanobrevibacter ruminantium a Methanabrerihacter smith * Mit han ocaliuhs ch;mghsingensis * Mthanococcoides burtonii 15 ae Mehanococcus awolicus a netacoccus deltae * MVjrtkan ococcus jan naschri 2 -tlanococusJ maripa/udis e AMethanococcus i'annelii 20 W Methacopscun labreanu m * Meithanoculhmus borg ~ensis (M!ethanogeniwn oletantgt'i & AMethancgenimn V Melhanocauleus mi k Menthanofolis ina tans 25 3Mthansogenwim cariaci * Meths~anogeicniu organpilumnt a Meth anagenmn wouei 30 a Mthxarapy'rus k ardieri SMthcnoreigulal oone a Methcmanosaeta co'ncili * Methanasacta thermeopbha * Mthxanosarcina acr.evon~s 35 * Mecthmnosarcina barkeri SMethnanosarcina maze; , Methnospaer stadtmanaei o a nmanosrillum hungaei a Meihanothermobacter deuvii (Me/t hanobacerium detyui) 40 a Methanothermobacmcr hrmautotrophicus (iMthanobtefrium therm uorohcm a M1emhanothermob~tdac/er Ihe;rmo/texus (Methanobacternum thermoftexum) a Mthlanthermobacter wol/el (Metihanacteriumt wvoli), ande a Mthbanothrix schsngen; or (b) the method of (a), fAther comfprising: 9 (i) applying (before, during and/or after ad ministering the organisns) to the subsurface carbonaceous formation an optimal nutrient mix, or the optimal nutrient mix identified in any of claims 3 to 15; (ii) modifying beforee, during and/or after administering the organisms) the 5 subsurface carbonaceous formation to have properties more like or smilar to o or more properties of the optimal nutrient "mix; or (iii) a combination of both i) and (ii). In alternative embodiments of the methods, the nethanogenic organisms and/or nutrient mix can (are designed to) decrease the amount of other (non-methanogenic) bacterial 10 processes negatively affecting biogas formation, wherein optionally bacterial processes affecting sulfate-reduction and bi hydrogen consumption via acetogenesis or non methanogenic hvdrogenotrophic pathways are reduced. In alternative embodiments, the invention provides methods of enhancing methanogenic rates in subsurface carbonaceous reservoirs comprising injecting one or more 15 methanogenic organisms into the subsurface carbonaceous reservoir, wherein the one or more methanuoenic org-anisms comprise: at least one synthetic consortium of the invention, one or more members of the Arcnhaa family, or are anaerobic organisms, or are autotrophs or chemoheterotrophs, wherein optionallv the subsurface carbonaceous reservoir r comprises a coal formation, 20 or a peat, or a lignite, or a bituninous coal, or an anthracite coal, a coal or a coal analogue(s) or a precursor(s) thereof heavy oil, asphalenes, and/or an organic debris. In alternative embodiments of the methods, one or more methanogeni organisms comprise one or more members of a genus selected from the group consisting of Methanoiobus, Mehanobacteriumr, Metrhantrobacter, Methanogeniumt Mehageum 25 Methanofois, Methanoculleus, Methanocors Methanococcus, Methanocalcidus, MethanobrevIbacter and A hanosarcina, or the one or more methanogenic or ganisms comprise: at least one synthetic consortium of the invention, or one or more members selected from the group consisting of: a Me thanoloburs bornbayensis 30 a Meti hanuPolms tayIori SAMethanolou zinder a ethanccbacterium bfranti 35 a Methanobrevlbacter arboriphilicus a Metihanobrev'ibacter gotschakii 104 c' M~t etorevibact r'umnantium t Methanol rev! bacter smthii * Methano ~calcuus chun ghsingensis * M etococoide bu1rtonii 5 MiLhanococcus aeoticus SMthtanoc'ccus tdelae e Methanococcuts janniaschni * Methanococcus maripaludIis 10 eMtaoopsua araa * Mtethanoculieuds borgenis (iMthano geniwn olentan gv! & M/ehanogeniumt bourgenses * Mthtiantotcue marngri SMehanoibllis liiiatins 15 * Me'thangenium car'aci e /l Mehnaget~nwnft?<iidwn * Methanngeniwn organ4£ophZinn * Mtthanogenium wol'tei 20 e Mthranopyrus andleri * Me~thanoregula boone * Meithanosaeta tconiitU * Mectanosaeta thermeophila I AMtnsarcina aevra dns 25 * AMIetha nsetrcina barker! 3 Mutien osarcina maenti * AM easphaera stadtmnanae * Methn onsprilliu hungate * M/ethanothermqobacter dcuvt mth ctanobctriumri deluil ) 30 * Me0thanot) o hrmo ate r th rattrophics ( Methanobacterium 0 teutotronphium * Mexhanothermiobactcr thnnoflexus tv Mtethnohcacterliwn thermtto/lexum ) SMetnothtetrmcaecter wioil (aMthanrobactetimn woI) , ad * Meth'anothix sthcngenreo In alternative enodiments, the inmen tionprovides o mpositions, formuattions, oruids, 35 nmds, or nutrient mixes for enhancing mnethanogenic rates in subsurf ace carbonaceons reserve oirs comprising: (i) one or mfore methanoge nie organisms selected from the group consisting of1a member of the Archea family, an anaerobic organismi an autotroph, a chemtoheterotrophi or a combination thereof; 40) (11) at least one synthetic consortium of the invention., or (ii.) the one or more methanoge organisms of (i) d a consensus andior optimal nutrient nix identified in a method of the invention, 11 wherein optionally the subsurface carbonaceous reservoir comprises a coal formation, or a peat, or a lignite, or a bituminous coal, or an anthracite coal, a coal or a coal anliogue~s) or a precmsor(s)ihereof, heavy oil, asqmhan oJrr an organic debris, In alternative embodiments, the one or more methanogenic organisms comprise one or 5 more members of a genus selected from the group consisting of Mehanolobus, Methanobacterium, thanoikermobact Methanogenh Afnk khanokki/is, lethanocu Methanocorqpustulum, Mv1nethancoccus, Methncalcou5s, Mljethaniobrevibac'rr and Methnosarcina, or the one or more methanogenc organisms comprise one or more members sekcted from the group consistig of: 10 - Methanlobus bornbayensis * Me hanolobus iraulori N Methanolobus projkndi a .! Melhanolbus Zinderi 2 Mehanbacteriu b yant 1 5 a Methanobacteriumformicum#0 SMethanobribactr arihus 2 Methanobrevibacter gtishaikll * Methanobrevibacter rUqjinan7tiumf 20 a Methanroacuhus husn get,3<nf3(l75s a M~ethasnococo /dsnhrtonii e Mehanococcus aus SMethnococcusr deltae ;UMethancocu ja.N nac awac 25 a Me/hanococcus msarcipudts e Methano cosvniii a Mtohuanculs 'U b)ourges (Metfrhanageniumn olentangv'i &i M(ethnangenium? 40 'bouense 30 * Mtethanocuileus marisnigri a Methagnofbi/is liminatans a Me'thanngeniun Caraci a Me'thanognipu~ oraopiu * Mexhanous P~ kandleri 45 Mehnoeul nei a Methanoseai concli1 40) a Methannsaeta thermboph i/ a MeP/hanosarcina brk~eri a Methanosarcina mazei? a Mhanks~ osphaera srtdtm0 aa 45 a -kMetanospirillium hsungoari 12 c' Meth~nothemobcter de/hivii (AMethanobaeriurn defhii~) e . Methan othermlo bacter thermatotrophiclus (MAethanob~acteriumi thermoauWtrpicumI) * Met hanothermobhacter thermoj)/exus (Mthanobacterimn therm otiexuin) AiMethanothermobacter wof.(Mthnhceim avili j ,an 5 Mktkanothrcix che In alternative embudi mens, the invention provides methods of creating a microbial composition to enhance niethanogenic degradation of carbonaceous substrates comprising the following steps: a, obtaining a sample from a subsurface carbonaceous 1Ofoatioii(S) of interest, 10 wherein optionally the sample comprises a water sample, or a production water sample; and optionally the subsuraIe carbonaceous formation(s) Comprises a coal frmbnatioin, or a peat, or a inite, or a bituminous coal. or an anthracite coal, or a coal or a coal analogue(s) or a precursor(s) thereof, heavy oil, asphaltenes, and/or an 15 organic debris, b. using die sample to inoculate an enrichinent culture comprising a carbonaceous material of interest, and/or a chemical analogue thereof, as carbon source; c. incubating the enrichment eoture until growth of an organism is detected, wherein opuonally the organism is a member of a methanogenic community; and 20 d, introducing the cells detected in (c) into a subsurface formation, wherein optionally the cells are introduced by a method comprising injection at a. well head. In alternative embodiments, the enrichment culture is massaged into fresh med.hum at least one tine. In alternative enbodnients., the cells are co-injected into the subsurface formation with an optimized nutrient inux 25 In alternative embodi-ments, the invention provides products of manufacture fluids, muds, bioreactors or surfer or subsurface reservoii, for generating a biogas comprising: (a) production water, (b) a carbonaceous material of interest and/or a chemical analogue thereof as a carbon source; and (c) a Composition or a otmuration, fluid ornutrient mix of the invention, or at least one synthetic consortium of the invention, In alternative 30 embodiments,. the carbonaceous material or carbon source comprises or further comprises a coal, a bituminous coal, an anthracite coal, a volcanic ash, or a lignite or a lignin or lignin comprising composition, a coal or a coal analogues or a precursors thereof, neavy oil, asp henes, and/or an organic debris. 13 In alternative embodiments, the product of manufacture, fluid, mud, reservoir or bioreactor is contained in siu in a subsurface excavation or is contained in an artificial structure, or the product of manufacture or bioreactor is placed in or contained in a landfill or a subsurface carbonaceous reservoir or source. In alternative embodiments, the product of 5 manufacture or bioreactor is a sand-pack bioreactor or a coal bioreactor. In aternative embodiments, the biogas comprises methane, or thew biogas mainly (or substantial) comprises methane, In alternative embodiments, the following parameters are controlled and/or modified in the product of manufacture or bioreactor: i) type of organic matter (plant vs algae derived), 10 ii) thermal maturity of organic matter (level of aromnaicity and hence recalcitrance), iii) formation water chemistrv (i.e, salinity, pH, inorganic and organic water chemistry), iv) temperature, and v) presence of appropriate syntropic bacterial community able to provide specific methanogenic substrates., In alternative embodiments, nutrients to enhance biogas formation are provided to the 15 product of manufacture or bioreactor, In alternative embodiruents, the nutrients to enhance biogas formation comprise metal salts of compounds found in methylotrophic/bacteriai enzymes, non-inhibitory level of alternate electron acceptors such as iron, manganese, or other nutriens and trace enemnts identified by correlating nutrient abundance to microbial growth/methane production. 20 In alternative embodiments, the. environmental parameters in the bioreactor are modified to enhance b iogas formati on. in altenative embodiments, the environmental parameters comprisefor-mation or composition of water, pHf of water (e.g higher p 1 H to the optimal range of the microbial association from culture experiments at the reservoir temperature), 25 In alternative embodiments, tIe microbial populations andor the environmental parameters in the bioreactor are manipulated or shifted towards more efficient coal/kerogen biodegrading, or more efficient Cook Inlet methanol/methyl-generating, or for increasing the methanogenesis rates, In alternative embodiments, the products of manufacture., fluids, muds, reservoirs, 30 bioreactois or surface or subsurface renservoirs comprise use of methylotrophic (methanol and other methyl-providing) substrates under neutral to sigihtly alkaline conditions to enhance biogas formation, wherein optionally the sI ightly alkaline conditions comprise conditions of between about p1H T5 to 9, or at least about pH 7.5, p-I 8, p. 8,5, or p 1-19. 14 in alternative embodiments, the products of manufacture., fluids, muds, reservoirs, bioreactors or surface or subsurface reservoirs comprise use o1 compose tons and/or fluids to prevent or slow build up of volatile fatty acids such as propionic acid and/or to prevent or slow a pH drop that would inhibit methanogenesis. 5 In alternative embodiments, a nutrient mixture or composition, or the compositions and/or fluids, are introduced into a product of manufacture., flaud or bioreactor or a bioreactor reservoir through injection of a single bou or through a continuous process. In alternative emitbodi ments, niewly generated biogas is monitored andor traced from gas isotopes, using ic- TC~ H~ or THenriched methanogenic substrates, and optionally the methanogenic 10 substrates coimprise bicarbonate, lignn and/or aromatic monomers, In alternative embodiments, the invention provides methods for improving methylotrophic biogas formation in stu in a subsurface source or formation or an isolated, mined or excavated carbonaceous source or formation, comprising (a) administering to or contacting the subsurface source or formation or isolated, 15 mined or excavated carbotnaceous source or formation; at least one synthetic consortium of the invention, or one or more methanogenic organisms identified i a method of the invention, or (b) administering to or contacting the subsurface source or formation or isolated, mined or excavated carbonaceous source or formation: one or more methanogenic organisms, wherein optionally the methanogenic organisms comprise one or more members of the 20 Arhaea family, or are anaerobic organisns, or are autotrophs or chemoheterotrophs, and optionally the methanogeni organisms comprise one or more members of a genus selected from the group consisting of Mlethanolob us, Meth anobacterium, Mecthanothennobacter, Memhanogenimn Methanageniumi, Methanobolli, Merthancculius, Methanocor pusculum, AMethaniococcus, *Methanocalculus, Methanobrevibhaacter and 25 Merhanosarcina, or the mehanogenie organisms comprise one or more members selected from the group consisting of; a Mldhanolbs bornbavensi e~ Mehnoou 1aylorii a Methanzolobus provihnd 30 Methanohbs zindeal a Mkihanobacterium bantil a Methrkanobtreviac ar oiphiclicus SMetchanbre'viacter gous.chalkii 35 a Mehanobre vitbacrer ru ntium a Methanob rev/ibater smithii SMVelhanoca culus chunghsingensis 15 ce Methanococcodes burton ii SMetanococusa oli isMethanococcus ehae SMethnococcus jaInnasc 5 Medhancccus m hahipaludis * MethanI0ococcus 'aniii e M/etanocoruscuan sabreanum * AMethanculkeus bourges s (Methanogenium o/entanypi &utMethanogeim 10) * Mtthancullens~ minenigri * 4/ Methanfolis liminatans * Methangenium car ic 20 ehageumOrgnophilum 15 * Metharnogenium wo/fe * Methzanopyrus kaniier'i * Mikcanoregula boone'i * Me'~tnosaetcociiflii 20 e Meth'asaeta thermopjh i/a * ihanasarcina barkeri - Methanosacinamae * Mevthanorsphat'ra stat/manate 25 11-.Mtaoprlimhnae * -A - I c 5 ~, . - . . , * Metaofthermobati~5ctr U dehi (M/ethanobacltium deflu vii) a Mitihanothtermob acter therma utontvophicus t/Mohanoateium termloattrophicum) * Mefthan~fothennlhobate~r ifC therm oxs &/etni~hanobacterum *th ermoiexum) * M.edhanothermoacct vwolti {Mthainoba~cK'tri u /olei) , n 30 Methanantrx .schngenii wherein optionally the one or more iethanogenc, orlanisms have been enriched using the consensus and/or optimal nutrent rix identied in any of claims 3 to 15, or the cOmposition, formulation, fluid or nutrient mix of any of claims 22 to 24, 35 wherein optionally the subsurface carbonaceous formation is modified to have properties more like or similar to one or more properties of the opt imil nutrient mix and optionally the subsurface carbonaceous formation or formations corifses a coal formation, or a peat, or a lignite, or a bituminous coal, or an anthracite coat In ahermative embodiments, the invention provides methods for processing a heavy oil, 40 or decreasing the viscosity of a heavy oil by converting high molecule arweight hydrocarbons into lower umolcular weight hydrocarbons, or convetna heavy oil, a bitmein, a tar-sand, or equivalents, to a les viscou\ fim, or to a gaseou\ fight gas, gas ardvor diesel product, wherein optionally ie Les viscouS forn of the heavy oil, bitumn., tar-sand or equivalents comprises substantially from CI to about C24 hydrocarbons, csnprising: 16 (a) injecting: at least one synthetic consortium of the invention, and/or one or more methanogenic organisms, into a subsurface carbonaceous reservoir comprising a heavy oil, a bitumen, a tars-and, or equivalents, or (b) contacting the heavy oil, a coal, a. bitumen, a tars-and, or equivalent with: at least 5 one synthetic consortium of the invention, or a composition comprising one or more methanogeni organisms, wherein optionally the contacting is insiu g in a ground formation or a subsurface carbonaceous reservoir), or a man-made reservoir or product of manufacture, or all excavated, mined, drilled or isolated heavy oil,. bitumen, tar-sand, or equivalent, 10 wherein the one or more methaiogenic organisms comprise one or more members of the Archaca family, or are anaerobic organisms, or are autotrophs or chemoheterotrophs, wherein optionally the subsurfae carbonaceus reservoir comprises a coal formation, or a peat, or a. ignite, or a bituminous coal, or an anthracite coal. In alternative embodiments of the methods, the one or more nethanogenic organisms 15 comprise one or more members of a gemus selected from the group consistiun of MAfehanobus, Mehanbate Mthanoerm .Methanotbiis, Methnoculieus,~ Methanocorpuscu/um, Metrhanococcus, Merhanocalcubos, Methaobrei.'acte'r and hanosarna, or the one or more methanugenic oranisms comprise one or more members selected from the group consisting of: 20 a Mk/hanolobus bnb 'aensis a Methnoobus aylorii a Methanzolobus prtvnd a Mthano/obus tzinderi A Mhi hanobacuterium bryantai 25 a M~ethanobaceriumnnfarmicum a Metanobretibacter arborlphjiicus a Methannbrevbacter gou.bcha/kii a MAehanobrev/'acter ruminantium a Mehanob rev/bater smithi 30 aA Mehanocalculus chunghsinge.nis a Mthdanooccoides burtonii a Mexhanococcus aeicu 14s a .ethanofccus dtintu a Mthanococcus jannaschi 35 a Methanacoccus maripaldi a Mexhanococcus va;nieli a M hanocoaruuum labreawnum a AMethancueus bourgen'sis (I1Metnogenium 0lenani z & thanogenium bosrgense 40 a thanocutleus marisnin 17 ce Methanofilis niinasans SMfetanagsenhum craci 5 Iethanogenumig * Mevthaneittani ornophilu * Methanosicrobiwn mobile et)Methanoyrusrturndleri / Methargua ~boonsI * M erkansarta concian 10 a Methnaetae theropin hila vninpoiosnooscilrs-lgal4tga poe's Me tnsarinias acetioas r rmusifc mttrrc 'rai Ca * Miktanosphaeta staatmanae 15 * M/ etnospiril/tan hungateic * Me'taothermtobaczer de/iic (Medumoater'ium'-f defluii ail/ItMeflo-than o ter o o thermauittrophks)is (.iMerthaUn ob arorium thlermoautotrophicwnn 2 Meikanctherm obat the Procedurm /one (Meanobactt rim r exw Tntn{4ctn i * Mth/anothermobsacter wol/i (Mtanobateiumf woliki) and 20 e Metanothrix sascheni In alterntve emfbodimts the in ventionl provides methods comprising anine id process for oputimizin biogas generation from subsurfae organic matter-rich formations (coal and/or oter org/anic--containn rocks), comprising one or more, or afl, the folwn seps: 25 (a) a microbial collection proce dure conduct to acquing both deep micro!il community surneys (DNA/RNA analyses) and cultured isolates of key living microorganisms; (b) dentification of specific targot micro-bial associations capable of rapidly transforinng organic matter to biogas, using empirical correlation of the microbial profiling data (e.g, from 454pyrosequencing) to key geochemiai parameters using an integrated 30 mu!tscpinary data-set; C) simul taneous identification otunifavorabie endemic microbes or conditions showing negative correlation to biogas formation, as identified in 6b above; (d) use of microbial evaluation toos, to further identifvfic active microbes critical to biogas growth (or inhibition) out of the empirically identified microbial targets; 35 (e) rock characterization of both indigenou organic carbon-rich substrates and inorganic mIneralogy affecting the water-ncta recipe composutifor enhanced biogas formation and section of substrate rocks: (f) further optimization of the proposed injectate water chemistry from a- matrix of laboratory enrichment experiments to promote subsurface biogas production without 40 activating dceterious microbial effects at the reservoir temperature of the target field) and 18 subsequent flow-through core experiments using the water-injectate recipe on targeted rock cores; (g) geochemical modeling of the solution stability to account for undesired precipitation of minerals due to interactions between in-situ formation vater, the injectate and 5 in--situ mineral phases; (h) modeling fluid transport within the reservoir structure and delivery mechanisms to successfully spread the water-soluble amendments and cultured microbes to the target formations; (i) modeling of transport of the newly generated microbial mrtethane within the 10 reservoir towards the gas colunum and the producing wells; (j) field implementation of the biogas production process; and/or (k) fild monitoring of biogas production and collateral icrobial/water changes, In alternative embodiments, the invention provides netods of transforming a carbonaceous substrate, a carbonaceous material or a carbon source into a lower molecular 15 weight (MW) compound using a synthetic microbial consoria coprisin g the steps of: a. Providing a plurality of samples that comprise a carbonaceous substrate and microbial communities; b, Determining the of'the microbial community in each sample; c. identifying a consortium (a grouping) of microbes whose abundance correlates 20 with transformaion of the carbonaceous substrate; d, Assembling a synthetic consortium by combining individual pure cultures in a strain collection; e. Combining the synthetic consortium with a carbonaceous substrate to convert n to a higher value and lower molecular weight product; 25 and optionally the samples are enrichment cultures incubated with the carbonaceous substrate. In alternative embodiments of the method, the carbonaceous substrate, carbonaceous material or carbon source comprises or father comprises a coal, a bituminou's coal, an antraciute coal, a volcanic ash. or a ignite or a liginin 01 Or inn-c prising conlpositon, a coal 30 or a coal analogues or a precursors ther.fc Iheavy oil., asphatcnes, and/or an organic debris, In alternative embodiients the invention provide methods for increasing or stinulating a coal to methane conversion rate, comprising: 19 (a) injecting: at least one synthetic consortium of the invention, andor one or more methanogenic organisms, into an isolated (e.g. out of ground, mind or excavated) or a subsurface carbonaceous or coal reservoir or a source comprising a coal, a bitumen, a tar-sand or an equivalent, or 5 (b) eontacling the isolated or subsurface carbonaceous or coal reservoir, or coal bitumen, a tar-sand, or equivalent, with: at least one synthetic consorntum of the invention, or a composition comprising one or more methanogenic orgaiismts, wherein optionally the contacting is in ' it (e,g., in a ground formation or a subsurface carbonaceous reservoir), or a nan-nade reservoir or product of nianufature, 10 wherein the one or more methanogenic organisms comprise one or more members of the Archaca family, or are anaerobic organisms, or are autotrophs or chemoheterotrophs, wherein option ally the subsurfae carbonaceus reservoir comprises a coal formation, or a peat, or a. ignite, or a bituminous coal, or an anthracite coal. in alternative embodiments, wherein the one or more methanogenic organisms 15 comprise one or more members of a gemus selected from the group consisung of Methlanolobus, Meitanoactum MethanthembatrMthngeimMthngeim Methanotb6iis, Methanoculieus Metanocpusculum, Mthanococcus, Mehanocalcuis, Methanorevcterand hanosarcna, or the one or more methanogenic organisms comprise one or more members selected from the group consisting of: 20 a M/hanoiobus bornbw aensis w Methlobus layio0ii a Methanolobus prov Andi a Metuhanoos ziner a Met/hanobacteriumn bytrNis 25 a Mefthtanobacteriumforminicum a Mehanobrevihacter atrbipcfhilics SMethzannbrevibkacter .mgouchakii a Melhanobreibacter rumnanim a Methanobevibacter smithii 30 a hanocalcuhus chnghstnge.nis SMethano Iscoccodes blutoni a Mehanococcus aeol(itcu0s a Meth/ hanococcus delt? a Methanmococcus jannaschil 35 a Methanococcus maripaludis a Mehanococcuus vaniii a M/hanccrpusculum llabreanum a Metjhuinoculle~s YbouiI1SIs ( Methanogeium lenangv I & thanogenium /boursgense) 40 a thanocuiheus misnigri 20 ce Methanofi lis uinatans # Metanagenum carc 5 Iethanogenpum igidum * Metchanosgenicn (or(anpi o * Methanopyrusrndlend i thebloanreuia o lnornetio ll*l dtktwings Isntile decito bo'w Othe fotre' oCs an dvalt 4 Z Meckanosarrta contile Al Me haolsn bareriptlI plclol -edhri r eeyopcs * Miktanosphaera statmanae 15 i n thro anospilin hunase e Metanothermobacer detluviikS (Medumoacteriu def/uviia Methnoertmob ac th if vJ7pbe Wertooph uh (vehobs ahcvtriu rthermoautopvthicum * Mikanother mbate thermo7llexus (Mth~aobactenium thermollexwn~n ) * Mth/anothermob~arcr wofi (Mt// habaceriu wodl), and 20 e Meuhanothrix sw chngenIi The. details of one o ro oe embhodimnts of th nvnin are et frt in the acoma nying drawings and the description below. Other features, objects, and advantages of the in vention will be apparent front the description and drawings, and fronm the claims. All publications, patents, patent applications cited herein are heeb'xpressly 25 incorporated by reference for all purposes, Nevertheless, it will be understood that various modifications may be made without departing front thet spirit and scope of the invention, Other features, objects and advantages of the invention will be apparent front die description and drawings, and from the claims. BRIEF DESCRIPTION OF TIE DRAWINGS 30 The drawings set forth herein are illustrative of embodinents of the invention and are not meant to limit the scope of the invention as encompassed by the claims. Reference will now be made in detail to various exemplary enbodmnents of the invention, examples of which are illustrated in the accompanying drawings, The folklowing detailed description iN provided to give the reader a bettcr understanding of crtflain details of aspects and mbodiments of the 35 invention, and should not be interpreted as a [in nation ol th scope of the invention, A more complete understandig of the present invention and benefits thereof mtay be acquired by referring to the follow description taken in conjunction with the accompanying drawings in which: 21 FIG I graphically illustrates the Rank abundance plot of 16S rRNA gene sequences isolated from production water of gas wells from the Cook Inlet, Alaska. DNA sequences belonging to the genus Merhanoobus are shown as highlighted bars, The relative proportions of ethanoes iat utilize oe Or mIr of the three mefhanogenic patihways ar indicated 5 (inset). FIG 2: graphically illustrates the Distribution of Archaeal populations along pH gradient (bottom panel) in the Cook Inlet wells. Note high pH and high methane production rates typically coincide with significant ftacti on of Methanolobus. igh positive corrciation between field-ieasured pH-1 of formation water and Methno lbus population (data log 10 transformed and Z-scored) is indicated in the inset. FIG. 3: graphically illustrates Methanogenesis rates from coallignin/lignin monomers and f-actions of methanogen s split into substrate-specific categories. Microbial populations fom two wells with largest fraction of obligae. methylmethanol utilizers (40-3 and 21-5) obtained highest rates of methanogenesis expressed as ml of CH per L of medium per day. 15 Wells 21-1 2i-4, and 40-1 from FG. 2 not shown due to little or no methane production. FIQG 4: is a Schematic of an exemplary process of this invention for creating optiniized chemical recipe for enhanced microbial methanogenesis, FIG. 5: is a Schematic of an exemplary process of this invention for creating optimized nutrient and microbial mixes or comnostions, e fg nutrient and microbial mixes or 20 compositions of the invention. FI. 6: graphically illustrates a Visual representation. of formation water ad justment to the optimized recipe, Example formation water composition co-produced from one of the Cook Inlet gas wells Required adjustment of parameters is represented by arrows, FIG. 7: graphically illustrates an Example of optimization methane production from 25 Cook Inlet rock material by varying single sparameter in sand--pack incubations (total methane produced after 6 weeks of incubation), FiG 8: graphically illustrates a Comparison of methane production rate from Cook. inlet rock material without and with optimized nutrient addition, Production water from 40--3 well Production of methane without nutrient addition is significantly slower after 42 days of 30 incubation. Each data point represents a triplicate set of sand pack tubes. FIG. 9: graphically illustrates a Methane production from the Cook. Inlet rock. material; sand-pack incubations using cell additions of the Cook Inlet consortia grovn on mixture of the Cook inlet coal. lignin and iigninmonomers: FIG. 9(a) addition of microbial consortium 22 frm the same well and grown on c ni,''nmones mixture l40--3 had the highest rate, see Fig, 3, hence this consortiun was used as inoculurn) enhances the methanogencsis rate over tubes with optimized chemical recipe only, but no cell additions: FIG 9(b) addition of coallignnign in monomers mixture-grown consortium to formation 5 water from well that originally had very low methane production (FIG, 3), Note that adding coalliinlignin monomersgrown consortia to production water from diffrent basin (California) also successfullv increases methane production from the same rock material Each data point represents a triplicate set of sand pack tubes, FIG, 10: graphically illustrates Introduction of a pure MeThanolobus taylorl culure 10 increases methane production in model sand pack incubations. Each data point represents a triplicate set of sand pack tubes, FIG, 11: schematically illustrates an exemplary mechanism or method of the invention for enhancement of biogas generationi in a highly permeable formation with predominantly dispersed organic debris and thin bedded coals; in one embodiment, injection of nutrient 15 amended injectate into the water leg down dip and/or into production-induced water leg stimulates biogas generation and migration updifp towards gas cap and production well FIG. 12: is a Schematic representation of an exenplary method of the invention comprising nutrient and microbe injection in a field application, FIG, I2 A) Representation of well infection system including existing injection water systems, concentrated nutrient storage 20 tank, nutrient mixing tank, and injection line for injecting dilute nutrient mixture. FIG, 12(B) One example of a Batch Mixing tank A and Storage tank B for storage and mixing of concentrated nutrient solutions up to 250 bbs per batch. FIG 13: graphically illustrates Field imeasurements of redox potential (black bars) and oxygen satiratioin (gray bars) of produced water from Various producing wells and front the 25 vacuum truck which collects watcr from al) wells for disposal into injection well FIG, 14: graphically illustrates Test results of effectiveness and concentration of sodium hypochlorite (NaCCl) required to control bionass formation in injections fine and injection well-bore: FIG, 14A, Level of biomass before treatment with O6% NaOCI solution at various oxygen levels and nutrient conditions; FIG. 14B, Level of biomnass immediately 30 after treatment with 0,6% NaOC] solution at various oxygen levels and nutrient conditions., CFU/mL = Colony-forming units per milliliter. FIG. 15: graphically illustrates Biomass development in an exemplary (lx) concentration nutrient recipe of the invention, and in an exemplary "excess (25x.) 23 concentration nutrient recipe" of the invention: FIG. 15A. Biomass level over tine in cultures incubated at OC and 20*C in 25 excess concentration nutrient recipe; FIG, 13, Biomass level in cultures incubated at 25C in standard (1x) concentration of recipe. CFU/mL Colony-formiug units per milliliter, 5 FIG. 16: A schematic illustration representation ot a three-dimensional geocellular model showing the biodenradable coal fraction in one layer. Lighter color indicates a higher percentage of biodegradable coal. Arrow in picture points North. This model was used to simulate the vokune and flow of bioenic generated from the addition of optimized nutrients and microbial additions. 10 FIG, 17: graphically illustrates the results from simulation of multiple biogas generation rates/volumes compositions and methods of tin t showingtracer concentration observed at the mon itoring wed ovcr time, starting at 5 months after start of gas injection, Travel time between injection well and monitor well is reduced with higher biogas generation rates/volnumes, 15 FIG. 18: graphically illustrates Level of trace compounds in monosodium phosphate from two different commercial vendois. FIQG 19: graphically illustrates Effect of NaOCi solution in absence (A)and presence (Bot oxygen on viability of microbial population. CFU/mL = Colony-forming units per milliliter, 20 FiG 20: graphically illustrates Development of biomass in (A) concentrated nutrient solution (25x) and (B) standard convention on of nutrient (lx), CFi/mnL =Colony-forming units per milliliter. FIG. 21: graphically illustrates graphically illustrates Effect of oxygen-scavenging compounds on redox potential of produced water previously exposed to oxygen. 25 _mV=millivohs, FIG 22: is a Schenma describing an exemplary method of the invention (or a method used to make a composition of theinvention) comprising steps of finding, assembling and deploying a synthetic consortium of microbes. FIG, 23: illustrates a Two-di.mensional cluster analysis of I 6S rRNA genes from 30 biogenic gas samples, The numerical values in each cell of the array represent the number of times a specific 165 rRNA gene sequence was identified in that sample. The values in the first column are the sum of the occurrences of each sequence in all samples (Note, this view is truncated and does not include all of the samples or all of the sequences identified). Each 24 column in the array represents a single sample. Each row in the array is a unique 16S rRNA gene sequence which serves as a proxy for a unique microbe. The columns are rearranged (clustered according to the microbial community present in that sample such that samples with similar microbial coimnunities are grouped together The rows are chistered according 5 to the abundance distribution of each sequence across the samples. Thus, sequences with similar distributions are grouped, FIGE. 24: graphically illustrates Methane production in sandpacks incubations supplemented with additional cells including the exemplary "Consort -ABS" composition of the invention, 10 DETAILED DESCRIPTION Turning now to the detailed description of the arrangement or arrangements of the one or more embodiments of the invention, it should be understood that the inventive features and concepts may be manifested in other arrangements and that the scope of the invention is not limited to the embodiments described or illustrated The scope of the invention is intended 15 only to be limited by the scope of the claims that follow. The invention provides compositions and methods for commercial hboa, e.g. methane, production. In ahernative embodiments, the invention provides compositions and methods for methanol-atilizin methanogenesis, or "methylotrophie"-conversion, including utilizing methylam lines and other methybcontaining intermediates. 20 The inventors have successfully demonstrated master, commercial biogas (e.g, methane) Production rates tnder highly favomble laboratory conditions by enhancing the microbial environment, e.g. by varying pH, mlicrobe and nutrient s upplemren tation of water. The in ventors have demonstrated that biogenic gas fields in the Cook Inlet (Alaska) have a surprisingly significant contribution from a third, equally important and often disregarded 25 pathway *- methanoutilizing methanogenesis, or "methylotrophic"-conversion, which also can include substrates such as methylamines and other methy-containing intermediates, In ahernative embodiments the invention provides compositions and methods comprising use of methano utiizing methanogenesis, which also can iclude use of substrates such. as methyl amines and other methy-containig intermediates. 30 in alternaive embodiments the invention provides an integrated process for optimization of biogas (e.g, methane) generation in subsurface organic matter-ich formations (eg, man made formations, such as landfills, or natural formations such as Coal formations, shale, sandstone or limestone with organic debris or oil) via the methylotrophic pathway, 25 in alternative embodients the ultimate goal of this biogas application is to extend the productive field-life of sub-surface biogenic-gas assets, In alternative embodiments, field implementation of biogas production is based on an integrated microbiasubstrate characterization, including all or sorme of the following steps: ( I) a microbial collection 5 procedure conducive to both deep microbial community surveys (DNA/RNA analyses), cuturing and isolation of living m;croorgaisins; (2) identification of specific target microbial associations capable of rapid transformnation of subsurface organic matter to biogas via e.g. the methylotrophic pathway, using enmpiriea correlation of indcrobial profiling tin alternative embodiments using pyrosequencing) data to key geochemical parameters and targeted 10 incubaions (e.g. with lignin or other coal-anaiogues or precursors); (3 simultaneous identification of unfavorable endemic microbes or conditions showing negative correlation to biogas formation usinc the same information as in step #2; (4) formation characterization of both indigenous organic carbon-rich substrates and inorgamic mineralogy affecting the water injectate composition for biogas formation (including core-water-microbe experiments); (5) 15 optimization of an injectate water chemistry (especially 'water pH and essential nutrients) and microbiology (selected isolates or pregrown successful communitis obtaining high methanogenesis rates with targeted coal and coal anal .gues) to promote subsurfico biogas production at the reervoir temperature of the target field); (6) investigation and modeling of delivery mechanisms to successfully spread the water-soluble amendments and cultured 20 microbes to the target formations; and (7) field inplemen station of any one or all of these steps in e.g., a biogas production process, In alternative embodiments, the compositions and methods of the invention identify, mimic and/or manipulate the combination of parameters that resul tin the specificity of a methanogen ic pathway in the subsurface, including e.g, any one or a combination of 25 parameters, for example: i) type of organic matter (e.g., plant versus (vs) algae derived), ii) thermal maturity of organic matter (eg, level of aromaticity and hence recalcitrance), iii) formation water chemistry (e.g., salinity, pH, inorganic and organic water chemistry), iv) temperature, and v) presence of appropriate syntrophic bacterial community ablto provide specific methanogenicsubstrates. 30 In alternative embodiments. the invention provides compositions, e.g, nutrient mixes, and methods of enhancing biogenic methane production through the creation of customized nutrient amendments (e.g. supplements, mixes and the like), wherein the compositions and methods can be used to specifically stimutilate (or inhibit, as appropriate) functionally 26 importan constituents of a microbial community responsible for biogas formation (or responsible for inhibition of optimal biogas production), In alternative embodiments, the invention provides microbial compositions (including bioreactors, which include subsurface reservoirs) to augment microorganisms involved in the methanogenic degradation of 5 recalcitrant organic matter or to introduce new microbial functionalitie into a reservoir to initiate or stinlulate this process. In alternative embodiments, the invention can identify a microbial community present in a subsurface carbonaceous reservoir, e-g., by nucleic acid (e.g., DNA, RNA) characterization, e. g.bv nucleic acid sequencing, hybridization, PCR and the like, to 10 determine or characterize the microbes present (optionally including their relative abundance); and in alternative embodiments a customized nutrient mixture of the invention comprises, or is based on: (1) published nutrient reoquirenent values that are weighted toward the more abundant and important (relative to the targeted methainogenic pathway) organisms; and (2), field observations about specific reservoir conditions (e.g, water chemistry, well production, 15 etc,). In alternative embodiments, the resulting customized nutrient composition of the invention is introduced to a reservoir through an injection process at the well head, or is used in a bioreactor of the invention. In alternative embodim.ents, a bioreactor of the invention includes any subsurface space or reservoir, such as a man-made subsurface reservoir. Organisms that participate in a given biogeochemical process or pathway make up 20 consortia and might be expected to be coordinately distributed in the environment. In other words, the members of a given consortium will tend to be found together. The degree to which these microbes are found together is expected to be a function of the obligate nature of their metabolic relationship. For example, two syntrophic organisms that only utilize a single carbon substrate and that were absolutely dependent upon. each other to metabolize fie 25 substrate would display the strongest coordinated distribution since neither partner could exist orr proliferate without the other (eg.. sulfate reducing bacteria with anaerobic methane oxidizers or potentially a methanol producing bacterum with obigate .methylotrophic methanogen such as aethanwobus), In other cases where two syntrophic organisms had similar dependencies upon one another for a given substrate, but had additional substrates that 30 they could utilize indepenidently of the syntrophic partner, would display a much less tightly inked environmental distribution. The organisms of this latter example are expected to have a coordinated distribution among environments where syntrophy was necessary fbr 27 netabolism of the prevaing' substrates. An example of this sittiaon 1, iin stibsurlace accuiniations of coal This tendency of members of a given co'sorium to be found together is an attribute that can be used to identify microbes that work together in a given biodegradative process 5 such as the conversion of Coal into methane (Ashbv 2003). By identifying the key microbial players that perform a process of interest in a particular environment, they can be specifically re-introduced into an environment to enhance the rate and specificity of said process. In alternative s embodiments, a consortium is a group of tw or mor e a plurality of) microorganims IN tat participate in a common ecological or biosynthetic or iodegradative 10 process, e.g., a biogeochenical process. During biogentic gas formationmicrobes can participate in the same biogeochemical process or metabolic pathway. Oftentimaes, these microbes are able to perform distinct steps of the same t.bolc biochemical or biodegradaive pathway, In some embodiments, te term consortium" defines a group of (a plurality of) microorganisms that participate in the same biogeochemical cycle, such as the 15 conversion of a coal to a methane, or biodegradation of a heavy oil; and in alternative embodiment consortiuns of the invention are used to convert a coal, or a coal analogues) or a pirecl'sois) and the like to a methane, or biodegrade an ol or a heavy oil and the like, in other erobodiments, therm "consortium" is defined as a group of microorganisms that participate in a unified set of biochemical reactions such as in biogeochemiical cycles, 20 In alternative sbodiments species describes a taxononic rank of an i anisnrn alternative embody iments species aclassifed based on traits such as similarity of DNA, notphology or ecological niche, In alternative, embodiments species ae grouped using statistical analysis of DNA sequenes or markers to deren the relatedness of two or more bacterial or Archaeal microorganisms, in one embodiment, two or 1oe orgaSnis are 25 classified as members of the same species when an alignment of' the 16S rRNA gene sequences reveals about 5% or less difference (95%O identity) at the nucleoide level, about 4% or less difference (96% identity at the nTuclestide level, about 3% or less difference (97% identity) at the nucotide lvel, about 2% or less difference (98% identity) at the nucleotide level, or about 1% or less difference (99% identity) a' the nicleotide level, 30 In altrnative eimibodiments, synthetic consortium are a set of microbes where each one exists $i pure culture and are combined to form a defined mixture or consortium of microbes that can perform a particular, useful ftIction. In one embodiment, a synthetic consortium comprises two or more cultured species available from commercial and/or unique isolated 28 cultures where the cultured species are selected to perform complementary processes in a geochemuical or biogenic gas pathway, In one embodiment, a synthetic consortium of microbes comprises two or more uncultured species that are combined by physical means where the culured species are selected to perform complementary processes in a geochemical 5 or biogenic gas pathway. In aternative embodiments, syntrophs are organisms that utilize products from another organisnl In one embodiment, two or more microbes may be dependent upon each other to perform a biochemical reaction, generate an essential product, or produce a substrate or cofactor. 10 In alternative embodiments, biochemical and geochemical compositions undergo one or more chemical transfornmat-ions, In one embodiment, a substrate is transformed when it undergoes a biochemical reaction through the action of enzymes produced by biological organisms, for example, by practicing a method of this invention, in another embodimen, the transformation involves one or more catabolic reactions where the result of the process or 15 pathway is reduction in the molecular weight of the substrate. In aternative embodiments, upgrading heavy oil as used herein describes the process of lowering the boiling point of a composition that may include e-avy crude oil, biumen, tars, and other high viscosity hydrocarbons, The vscosit of crude oil or tar usually by reducing the molecular weight of its constituents, increasing aromatic components, removing volatile 20 fatty acids, increasing the igas to oil (GOR) ratio, addition of solvents, increasing the hvdronen content, and other processes where viscosity is decreased. In one embodiment the viscosity of the heavy oil is decreased by converting high molecular weight hydrocarbons into lower molecular weight hydrocarbons. In another embodiment, heavy oils, bitumens, tarsands and the like are converted to less viscous or gaseous light gas, gas and diesel range products from 25 CI -C24 hydrocarbons, Idntifyi R Cimd its Members In one embodiment, the composition of microbial communities is determined or profiled from samples that have been in contact with coal or other carbonaceous material of interest. These samples will include environmental samplecs such as production water, 30 formation water, core samples, drill cuttings, water, sediment or soit Optimally, the samples would contain the same carbonaceous material that was the subject of investigation to find microbes capable of transforming into a higher value product. For example, samples Would be chosen that contained coal that had a similar level of maturity as that in the target basin. 29 In another embodiment, the microbial comm mtes present inl these samples are used to inoculate cttures comprising a carbon source., essential nutrients cluding vitamins, trace metals and a source of phosphorus, sulfur and nitrogen), and optionally including a buffer to maintain pH., a reducing agent (sodium sulfide, sodium dithionite, dithiothreitol, thioglycollate 5 or cysteine) a redox indicator (e.g. resazurin or methylene blue) and a terminal electron acceptor (e.g, oxygen, nitrate, sulfate, Fe(III), Mn(IV), carbon dioxide, or anthraquinone disulfonate (AQDS)). Anaerobic culture conditions, enrichment methods and mediun formulatons are widely known to those skilled in the art arnd may be practiced in a varitv of ways such as those described by Shelton and Tiedje (Shelton and Tiedje 1984), The carbon 10 source for the enrichnien ts would be of the same type such as coal or asphaltenes as described above. Ifri an aternative embodiment, the enrichment cultures are maintained in serum vials. At various time points in their incubation, the enrichment cultures would be tested for growth and metabolism Cell growth is assayed by microscopic cell counts or by measuring optical 15 density at 55S1 or 600 rnm wavelength in a spectrophotomueter. Metabolism is measured by gas production where the volume of gras produced is determined with a pressure transducer (Shelton and Tiedje 1984) and the type of gas(e,g. CH4, H2, or C02) is determined by gas chromatography, The transfer of elctrons to AQDS and the resulting color change from clear to orange, can also be used as a measure of metabolic activity. Additionally, consumption of 20 the carbonaceous substrate can indicate metabolic activity. In vet another embodiment, DNA is extracted from the enrichment cultures to characterize the microbial community at fte beginning of incubation and after growth and/or metabolism is detected, This community analysis can be done repeatedly to characterize community changes during the period of incubation and can be tracked together with the 25 geochemical changes of the medium and gaseous headspace, After the enrichment cultures exhaust nutrients as evidenced by a reduction in growth rate or metabolic activity, the cultures are optionally passaged into fresh medium using a dilution factor such as I ml of original culture diluted into 100 mis of fresh medium The methods described above to determine growth and metabolism are repeated for subsequent passages. This exercise of repeated 30 growth and transfer to fresh medium can also be performed in bioreactors, fermenters or chemostats and will have the effect of diluting away ('washing out') members of the community that are not involved in metabolizing the target substrate. At the same time consortium members that are involved in metabolizing the substrate will become established 30 if they are able to increase their cell numbers to offset their dilution during culture passagig or through the outflow of mcdi um in a chemostat. An exmrplary method of the invention for determining the microbial community composition can comprise any of the methods kiown to those skilled in the art; such as, eg 5 DNA sequencing of all or a portion of 16S rRNA genes, by hybridization of sample derived DNA to immobilized oligonucleotides or PCR generated probes (ie. DNA microarravs)quantitative PCR (qPCR) analysis, separation of DNA fragments such as terminal restriction fragment length polymorlhism (T-RFLP) analysis or by nonO-DNA-based methods such as fatty acid methyl ester (FAM) analysis. For iNA-based profiling methods, 10 ge'nomic DNA is isolated by any of a number of methods or commercially available kits that would result in the efficient recovery of DNA with a minimal level of introduced bias. For DNA sequence profiling of 16S rRNA genes, umiversaP primers can be utilized to PCR amplify a portion of the gene that includes variable regions. Limiting the number of PCR cycles can reduce biases and artifacts that might occur. 15 In one embodiment, the microbial comnmnunty comtiposition profile data detenrined through the use of culture independent, molecular surveys described above, optionally in the form of number of copies of each disinct 16S rRNA gene sequence detected from each sample-, is then analyzed to detect the distribution patterns of microbes amongst the samples tested, As indicated above, microbes that participate in the same biodegradative or nmeabolic 20 pathway and thus, members of a common microbial consortium will tend to be found together in the environment (including samples derived therefrom), This relationship can also be deduced from abundance data in culture independent surveys (Ashby 2003), In one embodiment, to identify potential relationships that exist between environmental microbes as indicated by their tendency to be coordinately distributed in the 25 environment, the data is first log transformed. Log transformation tends to make microbial distribution data more normally distributed which may result from the logarithmic nature of microbial growth. Log transformed microbial distribution data can then be compared between different 16S rRNA gene sequence detected using correlation analysis (eg Pearson), Operationally, a distance matrix is constructed where the distribution of every sequence is 30 correlated with that of every other sequence. The results can then be graphically represented using hierarchical clustering algorithms such as Ward's method, Computer software programs are widely available to perform this analysis such as PC--ORD (Gleneden Beach, OR), This exercise will reveal groups of sequences that tend to be found together (see 31 example below). Comparison of the distribution of the group as a whole to the transformation or metabolic activity observed in the samples (or enrichment cultures) will provide furiber evidence as to the metabolic functional capability fh consortium. In alternative embodiments, the members of a consortium are identified from 5 microbial community surveys using distance metrics that include Euclidean distance, Chi square, city block, and ordination methods that include PCA, Bray-Curtis, and nonmetric multidimensional scaling (NMS or NMDS). LiiinConsortium to Enhance iransfrmnatn Rate ofa Carboaceous Substrate In alternative embodiments, consortium of microbes to be utilized to enhance 10 methanogenesis rates can be prepared by nmutipie strategies. One approach involves systematically isolatingin pure culture all of the members of the consortium of interest, The individual consortium members are then combined into a synthetic consortium which can tmen be tested for metabolism of the substrate of interest and/or utilized for the commercial scale conversion of a carbonaceous substrate in to a higher value-lower molecular weight product. 15 in alernative embodiments, methods and medium formations for isolating environmental microbes in pure form comprise those known in the art, In alternative embodiments,. fr consortia that would ultunately be deployed in the subsurface where oxygen is absent, anaerobic cultivation methods are used. Samples or enrichment cultures that possess the microbes of interest are diluted and plated onto a variety of solid medium 20 containing different nutrient combinations to obtain single colonies, At least one of the medium formulations should contain the carbonaceous substrate of interest. Parameters such as salt concentration and pH should be as consistent as possible with the original sample wherc the organisms of interest were present or adjusted to optimize growth of targeted microbes and enhancement of targeted metabolic process, Oftentimes environmental 25 microbes are difficult, if not impossible, to cultivate and their isolation requires the use of alternative strtegies such as dilute nutrients and different medium solidifying agents (e.g, see Connon and Giovannoni 2002: Sait, Hiiugenholtz et al. 2002). In alternative embodiments, microbial colonies that appear on plates following incubation should be picked and re-streaked onto fresh medium at a low enough density to 30 obtain new, well resolved colonies. This colony purification procedure can be repeated to reduce the risk of colonies being comprised of multiple species. The resulting colonies should display a uniform morphology consistent with a homogenous population of organisms, in alternative embodiments, a colony is picked and grown up either in liquid culture or as a patch 32 on the same medium type. The resulting culture is then frozen at -- 80"C and/or freeze dried for archival purposes. DNA from the cells from the same culture is extracted for identification by sequencing its 168 rRNA gene. In alternative embodiments, a second approach is to utilize enrichment cultures as 5 described above to select for a consortum with the properties of interest while at the same tine selecting against microbes that do not participate in the process. This approach is utilized when some members of the consortium of interest cannot be cultivated in pure form. Organisms that are expected to fidl into this category include obligate syntrophs which by definition cannot be grown in pure culture in the absence of their syntrophic partner. While 10 this approach is not as prefenable as the pure culture route that can produce a community of exactly the members desired, it can lead to a highly enriched culture for the organisms with the metabolic potential of interest. Such successful ctilture might be further tested to identify tightly bomd syntrophic associations, Subsequent cultivation may allow isolation of these tight associations, their phylogenetic confirmation by DNA extraction, and their storage for 15 further lab and commercial use. In alternative embodiments, additional methods of assembling a synthetic consortiun of the invention involve physically separating cells present in a sample using methods such as fluorescence activated cell sorting (FACS), The cells of interest can be specifically labeled with fluorescent labeled probes and fluorescent in situ hybridization (FISH) without using 20 fixatives, Other methods to physically separate cells of interest include optical tweezers or through the use of antibodies that specifically recognize determinants on the cell of interests surface, In aternative embodiments. synthetic consortium of the invention comprise a mixture of CelS each derived from pure isolates or a highly enriched consortium, which optionally can 25 be derived from a selective growth, and then optionally can then be introduced into a subsurfee reservoir or other environment containing the carbonaceous substrate of interest, where optionally the consortium has been selected for growth and metabolic performance under the specific environmental conditions with the goal to convert the substrate to a higher value product. 30 One embodiment provides methods for increasing commercial biogas production in a sub-surface environment, it another embodiment the invention provides an integrated process for optimization of biogas generation inchiding methane in subsurface organic matter-rich formations including man made frmations, such as landfills, surface or subsurface 33 bioreactors (in alternative embodiments, a bioreactor of the invention or a bioreactor used to practice the invention includes any subsurface space or reservoir, such as a manmmade subsurface reservoir) and the like., or natural formations such as shale, coal, oil sands, bitumen, tar, oil, sandstone and I inestone with ogan ic debris or other hydrocarbon rich 5 formations via the methylotrophic pathway, Methods for analysis and understanding of subsurftee microbial communities responsible for conversion of coal and coal-like substrates into methane, and for controlling geochemical conditions are provided. This, in alternative embodiments., coimpositions and methods to stimulate subsurface methanogenesis pathways and to enhance the rates oftbiogas formation are provided. 10 In alternative embodiments, methods of the invention for increasing biogas production extend the productive field-life of ub-surface biogenic-gas assets. In alternative embodiments, field imrplementation of biogas production is based on an integrated microbial substrate characterization, including all or some of the following steps: (1) a microbial collection procedure. conducive to both deep microbial community surveys (DNAIRNA 15 anialyses), culturing and isolation of living microorganisms; (2) identification of specific target microbial associations capable of mpid transformation of subsurface organic matter to biogas via e.g. the methyltrophic pathway, using empirical correlation of microbial profiling (in alternative embodiments using pyrosequencing) data to key geochemical parameters and targeted incubations (eg, with lignin or other coal-analogues or precursors; (3) simul laneous 20 idenitificaton of unfavorable endemic microbes or conditions showing negative correlation to biogas formation using the same information as in step #12; (4) formation characterization of both indigenous oranic carbon-rich substrates and inorganic mineralogy affecting the injectati-water composition for biogas formation (including core-water-microbe experiments); (5) optimization of an injectate water chemistry (especially w-ater pH. and essential nutrients) 25 and microbiology (selected isolates or pre-grown successfit communities obtaining high mnehadnogenesis rates with targeted coal and coal analogues) to promote subsurface biogas production at the reservoir temperature of the target. field ; (6) investigation and .modeling of delivery mechanisms to successfully spread the water-soluble amendments and cultured iicrobes to the target formations; and (7) field mplementation of any one or all of these steps 30 in e. a biogas production process. In other embodiments the invention may include., evaluation of the potential for biomass formation and scale precipitation associated with adding amendments and cultured microbes to existing field conditions; simulation of biogas in a sub-surface reservoir using a computational model; mitoring injectedfluids, biogas, and 34 changes in the microbial community: or field inplementation of any one or all of these steps in eg., a biogas production process. in alternative embodiments, the conmpositions and methods of the invention identify, mimic and/or manipulate a combination of parameters that result in the speci ofa 5 methanogenic pathway in the sub-surfhac, including e. any one or a combination of parameters, for example: 0 type of organic nattor (cg. plant vs algae derived), ii) tlienral maturity of organic matter (level of aromaticity and hence recalcitrance), iii) formation water chemistry (i.c. salinity, pH, inorganic and organic water chemistry), iv) temperature, and v) presence of appropriate syntrophic baceril community able to provide specific methanogenic 10 substrates In alternative embodiments. the invention provides compositions, e.g., nutrient mixes, and methods of enhancing biogenic methane production through the catio of custom d intrient amendments (eg. supplements, mixes and the like), wherein the compositions and methods can be used to specifically stinlate (or inhibit, as appropriate) functionally 15 i mportait constituents of a microbial comnunitv responsible for biogas formation (or responsible for inhibition of opturial biogas production), In alternative emibodieniits, the invention provides microbial compositions includingg bioreactors to augment microorganisms involved in the metlhanogenic degradation of recalcitrant organic matter or to introduce new microbial functionalities into a reservoir to initiate or stimulate this process. 20 In alternative embodiments, the. invention can identify a microbial community present in a subsurface carbonaceous reservoir, e.g, by nucleic acid (e.g.. DNA, RNA) characterization, eg. by sequencing, hybridization, PCR and the like, to determine or characterize the microbes present (optionally including their relative abundance); and in alternative embodiments' a customized nutrient mixture provided comprises, or is based on: 25 (1) published nutrient requirement values that are weighted toward the more abundant and important (relative to the targeted methanogenic pathway) organisms; and (2), field observations about specific reservoir conditions (e~g. water chemistry, well production, etc.). In alternative embodiments, the resulting customized nutrient composition of the invention is introduced to a reservoir through an injection process at the well head, or is used in a 30 bioreactor of the invention, In alternative embodiments, the resulting customized nutrient composition is used in a bioreactor, optimized through a bioreactor-nutrient optimization test, and/or introduced to a 35 reservoir through an injection process atbthe well head as requirek to optimin bogas production in the bioreactor and/or in the hydrocarbon formation. In another embodiment, the invention characterizes, e..g, by sequencing., hybridization, PCR and the like, microbial communities present in a subsurface carbonaceous reservoir. in 5 one embodiment, a custonized nutrient mixture is determined based oni published nutrient requirement values alone that is weighted toward the more abundant and important organisms. The resulting customized nutrient composition used in a bioreactor, optimized through a bioreactor-nutrient optimzation test, and/or introduced to a reservoir through an ijection process at the well head as required to optimize biogas production in a bioreactor and/or in a 10 hydrocarbon formation. In alternative e mbodiments, the invention characterizes. e., by nucleic acid sequencing, hybridization, PCR and the like, microbial comunitics present in a subsurface carbonaceous reservoir, The resulting customized nutrient mixture of the invention can be determined based on published nutrient requirement values. 15 1n another embodiment, nutrient formulations that were developed for one reservoir are utilized for another reservoir with similar properies suchei as geological history, geochemistry, source of carbon and inicrobial coniunnity composition. In alternative embodiments, the rate of methanogenesis in a subsurface reservoir harboring coal and other recalcitrant organic carbon sources is increased by introduction of 20 one or more members of a genus selected from the group consisting of Methn bu Mehanobacterian, MhnhmaeMhn num, MthanogeniumnMehanofo zlis, Mfehanocu leus, Methan ocat usc11un, Mehanococcus, Methanocalcdus, Methanobrcvbaerv and Methanosacna (as pure or nearly pure culture, e.g, greater than about 70%, 80%, 90%, or 95% of cells, are from one particular genus) through injection at 25 the well bead, The cells may be provided as cultures, cell pellets (such as obtained through centrifugati on or filtration , or lyophilized preparations that are reconstituted, In alternative embodiments, Methanolobus. Mebhoacrium, Methanothermobacter, Methanogenium, Aexhanogenium, Methanofolii, M e hanocuies, Mehan'corpuscutum, AMethanococ cus, Methanacalculus, Mehanobrevibacter and/or 30 Methanosarina cells (e.. as pure, substantially pure or1 nearly pure culture, e.g.. greater than about 50%, 60%,70%, 75%, 80%, 85%, 90%, or 95% or more of cells in culture) (e., in a nutrient nix, a fuid, or composition, e.g, a mud) are introduced into a subsurface 36 reservoir or deposit, or isolated, mined or excavated source, e.g., that has (comprises) gas, coal, oil, heavy oil, tar-sand, bitumen and the like. In alernative embodiments. Methanolobus.Mthanobacerimn Methaun othermobacter, Methaognium~f Oi, MethanogeniumCMthnflIs, Mthan~2ocuieus, $ Me/thaqncorpuscudum, Methanccccus, Mt'rhanocalculus. Me/t hanobrev/ibucter andort Methanosarcina cells (optionally e.g, as pure, substantially pure, or nearly pure culture, e.g. greater than about 50%, 6(%W 70%, 75%, 80%, 85%, 90%. or 95% or more of cells in culture) are delivered to the subsurface reservoir or deposit, or isolated, mined or excavated source, through injection as enrichment cultures, where optionally they comprise a substantial or 10 signaificnt portion of the total number of cells, e qg., enivalent to at least about 1%, 5%, 10%, 5 20%, 25%, 30% or 35% or more by cell number. In alternative embodiments, Methanolobus, Methaobcterium, ethanothermobacter, Me/hanogenum, Methnogentum, Aethano/oks Methanoculkeu, Mehanocorpusculum, Aethanocccus, Mthanocalculus, Met-hanobevibacer and/or 15 MeThanosarna cel (eIg., as pure, substantially pure, or nearly pure culture, e.g. greater than about 50% 6 , 70%, 75%, 80%, 85%, 90% or 95% or more of cells in culture) are used in a bioreactor, fluid, composition or product of manufacture of the invention. In alternative embodiments, the invention also provides methods to enrich or select for endemic organisms capable of converting a catbonaceous material of interest that can then be 20 re-injected inu a formation to enhance methanogenesis rates, or inhibit or decrease endemic organisms that inhibit or decrease biogas formation. In one embodiment, this process of the invention is useful because it sclets fur the most important organisms required for the entire degradative nethanogenic pathway from a Pool of organisms that are already selected (e.g, through natural selection) for growth under reservoir conditions. These methods also can be 25 used to enrich an environment of a bioreactor of the invention. In alternative embodiments, cells present in production water are used to inoculate enrichment cultures containing defined medium (mineral salts, trace metals, vitamins), where the only carbon source (above trace levels) is provided as the reservoir carbonaceous material and/or chemical analogues thereof, Growth of the cultures is monitored by measuring changes 30 in headspace pressure (e.g, as described by Shelon and Tiedje 194) and methane production (e.g, using C|FID as described by Strapoc e! at, 2008) and in increased numbers of cells present that resuls in increased turbidity, Once a significant amount of growth is detected, the culture is passaged into fresh medium (e.g, about I to I 00-fold dilution). This procedure can 37 be repeated indefinitely. These procedures are well known to those skilled in the art and are described in detail in general microbiology textbooks (e.g, Manual of Environmental Microbiology, 3rd edIn Hirst, CJ, Crawford, RL, Garland, J.L, ipson, D.A., Mills, A.L., and Stetzenbach, LD. Washington, DC, USA: ASM Press, pp. 1063-110 7i. Prior to injection 5 into the reservoir the culture can be passagced into a large capacity fermenter to produce large munber of cells, These methods also can be used to produce a bioreactor of the invention. In alternative embodiments, cells present in production water are used to inoculate enrichment cultures containing defined medium (mineral salts, tried metals. vitamins) produced water, or nu trient-amended produced water, where the only carbon source provided 10 is a chemical analogue or multiple analogues of the reservoir carbonaceous material, in this embodiment, use of tested chemical analogues allows faster bionmass growth, e.g, prior inijction into the reservoir, of the Cultures than in cultures using oly the reservoir carbonaceous material. In yet another embodiment, cels present in production Water are used to inoculate enrichment cultures containing defi ned medium supplemented with a customized 15 nutrient mix where the only carbon source (above trace levels) is provided as the reservoir carbonaceous material The cells can be inoculated into enrihnmem cultures of a bioreactor of the invention, In alternative enbodiments, cells isolated from or microbial consortia tound in other formations, basins or environments are used to inoculate enrich mert cultures containing 20 defined medium or target produced water supplemented with a customized nutrient mix where the only carbon source (above trace levels) is provided as the target reservoir carbonaceous material or analogue of thereof or carbonaceous material from other reservoir or basin. The cells can be inoculated into enrichment cultures of a bioreactor of the invention or the target reservoir or other reservoir or basin, 25 In alternative embodiments, the cells produced from the aforementioned enrichmen ts or fermenter are lyophilized for storage and transport to the well site where they are mixed with water and customized nutrient formulations immediately prior to injection, The cells would be lyophilized in the presence of reducing agents to protect the methanogens and other obligate anaerobes from oxidation during storage and injection, These cells also can be 30 inoculated into enrichment cultures of a bioreactor of the invention. In alternative embodiments the invention provides methods for analysis and u-nderstanding of subsurface microbial communities responsible for conversion of coal and coal-like substrates into methane, and for controlling gcochemical conditions, Thus, in 38 alernative embodinents, the invention, conpositions and wthods of the i-nntio are used to stimulate preferred subsurface methanogenesis pafhwavys and to enhance the rates of biogas frnatiton, In alternative embodiments, compositions and methods of the invention supply 5 deficient nutrients (e.g, enhanced metal salts of compounds found in methylotrophic/bacterial enzymes, non-inhibitory level of alternate electron acceptors such as iron, manganese, or other mtrients and trace elements identified by correlating nutrient abundance to microbial growth/mtethane production) and/or niodifying some parameters of the fornation water (e.g, higher pH to the optimal range of the microbial association Ifrom ncuture experiments at the 10 reservoir temperature can shift microbial populations of all wells towards more efficient coa/kerogen biodegrading (ei., in Beluga methanol/methyl-generating) and increase the metanogenesis rates. In alternative embodiments, compositions and methods of the invention comprise use if subsurface exploitation of methylotrophic (e.g, methanol and other methyl-contain ing 15 substrates under neutral to slightly alkaline conditions to enhanced biogas formation. in alternative embodiments, methods of the invention identify: (a) key and fastest operating microbial pathway for subsurface biogas formation and (b) ranges of key environmental geochemical parameters that stimulate this pathway thus enabling a means to optimize subsurfie biogas-production rates and generate a positive offset to the gas field's 20 production decline. In alternative embodiments, careful stimulation of the subsurface bioreactor (by inspecting and adjusting chemistry and microbiology of co-produced and reinjected water) ensures potential long te rm stable rmethane production rate ti0's of years), owing to vastness of accessible organic matter (organic debris and bedded coals) in the subsurface. 25 In altermative embodiments, the invention provides a specific int egrted process for microbe discovery (including syntrophic associations between organic-matter degrading bacteria and gas-)roducing Archaea) and an optimization strategy for developing a supplemental water injectate promoting biogas growth and minimizing deleterious effects. In alternative embodiments, the invention can assess the formation of carbon mass and 30 characterize the geochemical bio-convertibility of organic matter, and follow-up enrichment 10 experiments on indigenous formations required for potentially successful field implementation. Amendments can be extremely cost-effetive, 39 In alternative embodiments, cOmpositions and methods provided can be practiced to enhance and produce natural gases from certain Cook Inlet fields which contain biogenic methane almost exclusively. In alternative embodiments., conpositions and methods provided can be used to enhance microbial communities that are still active at present day in both the 5 Beluga and Sterling formations, degrading complex organic matter to simpler compounds that in turn can be biologically transformed to methane. Thin coals and dispersed organic debris in the sand-dominated fluvial system are easily accessible for microbial attack, Faster rates of biodegradation and methanogenesi can be achieved by selecting for specific microbial populations through adjusting the chemistry of formation waters (i.e. p-I, Eh, as well as trace 10 elements and nutrients such as Mo, Ni, phosphate, ammonia, etc.), Several parameters of Cook inlet microbial communities including 16S rRNA gene profiling, metagenomics analysis, cultivati on screens and geochemical ana lysis were studied in the lab for potential future field implementation, Both the Behuga and Sterling formations are excellent candidates for a field pilot for enhancement of microbial methane generation, 15 These formations have low reservoir temperatures, association of organic matter within and adjacent to highly porous and permeable sands with organic debris and nutritious volcanic ash, and reasonably good lateral connectivity within the Sterling formation reservoirs, DNA, culturing, and geochemistry of Cook Inlet microbial associations were studied in the lab for potential future field implementation, Both the Beluga and Sterling formations 20 are excellent candidates for a field Pilot for enhancement of biogas, These fornations have low reservoir temperatures,. association of organic matter within and adjacent to highly porous and permeable sands with organic debris and nutritious volcanic ash, and reasonably good lateral connectivity within the Sterling formation reservoirs, In alternative embodiments, the term "'carbonaceous" is defined as any rock contain ing 25 organic carbon (carbonaceous rocks s-uich as coal, shale, sandstone or limestone with organic debris or oil) with a total organic carbon (TOC) content >0,5 weight % (wt. ). In alternative embodiments., the. term "coal" is defined as a readily combustible rock containing >50 v, % TOC, in alternative embodiments, the term "correlation" is defined as the relationship or 30 degree of similarity between two variables. Correlation analyses may be performed by any method or calculation known in the art. Correlation analyses for R and R may be performed as described by M. J. Schmidt in Understanding and Using Statistics, 1975 (D, C, Health and Company) pages 131-147. The degree of correlation for R is defined as follows: 40 LO Perfect 0-0.99 High 0.5-0,7 Moderate 0.3~05 Low 5 0.1-0,3 Negiigible in alternative embodiments, the term "field observation" is defied as the set of res. rv oir pa rameters that include: gas composition and isotopes, water chemistry, pH, salinity, Eh redoxx potential , temperature, depth, production paramnete and history, description and characterizatin of the trmation, description, saupling, or analyses of core, cuttings or 10 outcrop rock material. In alternative embodiments, the term "production water" is defined as water recovered co--produced with any petroleum or hydrocarbon products at the well head, in aiternaive mbodim s, the term "recalirant organic matter" is defined as any organic matter that i' generally r"sistant to biodegradation by fy action of microorganims, 15 cg, highly aromatic coaIs, In alternative embodiments, the term "chemical analogue" is defines as specific chemical compound or compounds of structure and bond types representative of the target carbonaceous material Such chemicallV defined analogune has known chemical structure, is commercially available and can be used as a surrogate for faster growth of targeted 20 consortium, In aternative embodiments, biogenic gas formation is modeled in one or mo sub.urfaceN formations, Biogenic gas formation i determiing changes in the tor.mation composition and gas formation as biogenic growth occurs, Modeling includes estimating changes in organic matter comment in the formation, volume of gas generated during 25 bio genc growth an destination of potential. gas flow paths through the formation and. travel time ofl biogas from bigenesis o production, based on a geological characterization and model of the formaton, In alternative ermbodiments, careful sample collection of gases and the co-produced water at the well-head improved idenification of microbial communities associated with 30 potentially commercial geochenical processes and was facilitated by proper treatment of water samples to preserve microbes and water clhermistrv during transit to an d storage at the laboratory. About IL of non-filtered water was collected for DNA extraction and 16S r-RNA gene profiling using pyrosequencing. Additional water samples were collected in 160 TL 41 serum bottles for enrichment (amended with, resazurin and sodium sulfide with blue butyl stoppers). Another L5L. of water was filtered on -site usig 02:2 pm pore size fibters, Fiftered water samples were split for variety of subsequent analyses including inorgai fixed with HO(, anions) and orgailc chemistry (volatile fatty acids - amended with 5 benzalkonium chloride, alcohols), Well-head gas samples were taken for molecular and isotopic composition of the gas using e.g, ISOTUBESI' (IsoTech). In addition the field p-f. Eh1 salinity, temperature of the waters, alkalinity (via titration), and/or other properties were measured as soon as possible after water collection, In alternative embodiments, an integrated (wide and deep) screening of both geocherical and microbiological environmental properties 10 was used to characterize subsurface microbial environments; hus, providing an accurate background for the composition of the reservoir. In another embodiment, genomic DNA is extracted from samples of a subsurfae carbonaceous reservoir of interest, Geno.mic DNA may be extracted from the samples by any of a number of commercially available kits (e., POWERSOIUMJ' available from MoBio 15 Laboratories Inc. (Carlsbad, CA) or FASTDNAT 1 M kit by Q Biogene) or by methods ordinarily known by those skilled in the art of environmental microbiology. The microbial coutmmni ties resident in the reservoir samples are profiled (or inventoried) by determining the DNA sequence of a portion of the 16S rRNA genes present. This geoc is widely used as an indicator, or barcode for a given microbial species (Pace, 1997), The I 6S rRNA genes arc 20 recovered from genonic DNA through PC.R. amplification using primers that are designed to conserved regions with the gene, Such priners are well known in the art, For example, the primers TX9 and 1391 R (e.g , see Ashby, Rine et al 2007, see list below) amplify an approximately 600 base-pair region of the 16S rRNA gene that includes the fifth through eighth variable (V5-V8) regions. The DNA sequence of the resulting 16S rRNA amplicon 25 may be determined using any available technology including, but not limited to, Sanger, or 'next generation technologies such as those available from Roche, ABI, illumrina, ion Torrent or Pacific Biosciences, Determination of the number of times each sequence occurs in a sample provides an indication of the microbial community structure ( e.g., see Ashby, Rine el al 2007). The abundance of each sequence identified from a given sample can be compared 30 with that of every other sequence to identify sequences that show significant correlations to one another. These sequences are likely to be members of the same consortium and participate in common biogeochcmical process (Ashby 20(03 _ The microbial communities mray also be characterized by sequencing genes other than the 16S rRNA genes or even by random shotgun 42 sequencing of genomic fragments by methods that are well known in the art, (Venter, Reninugton et a/ 2004), The microbial communities may also be characterized by cultivation dependent approaches that are well known in the art. For example, this approach may identify organisms through metabolic capabilities, morphological considerations and Gram stains. 5 Total count of microbial sequences in the Cook Inlet gas field was dominated by Methanotobus (Fig. 1i). In one embodiment, specific target microbial Bacteria-Archaea as soc iations favorable for biogas production are identified through an integpratedng strategy that allowed for the search across biological and geochemical parameters for en vironmental 10 correlations between microbe associations and key chemical processes with potential commercial value. For the purpones of high-guradin enhanced biomethane production, the correlations have been based on two specific microbial enrichments of the Cook Inlet formaton waters with: (a) common methanogenic substrates (combination of CtIF acetate, methanol substrates) to gauge the general health of the endemie methanogenic community and 15 (13) with lignin/lignin monomeasupplemented Cook inlet coals/organic rmatter-rich sandstone enrichments to simulate further the bacterial breakdown of organic macromolecules to specific substrates vital to the growth of key Archaeal methanogens. Statistical correlation of geochemical data from the formation water and the microbial distribution data (expressed as Z score values of log-tansformed 16S rRNA gene sequence occurrence data) has successfully 20 identified microbial associations and potential syntrophies as well as their affiliation to specific ranges of geochemical parameters (ie pH, salinity, temperature, trace metals, gas isotopic composition. Sequence occurrence and geochemistrvy data from multiple wells and/or basins can be used. For the Cook Inlet gas fields, 16S rRNA gene pyrosequencing data integrated with these two biogas-production datasets clarly show that methanol and other 25 methyl-containing species are the most efficient substrates for biogas formation via the methylotrophic pathway, The highest methane production rate corresponded to highest tormation-water pHJ and was dominated by methiano/methyl utiizing genus Methanolobus (FIG, 2). The correlations of 16S rRNA sequence data achieved with new generation 454 sequencr also pointed out specific microbial associations and potential syntrophies between 30 different microbial groups, For example, Family Merhanosarcinaceae (Class ethan-omicrobia) is capable of utilizing methyl-containing compounds (i.e methiylami nes) as substrates for methanogenesis and the main Cook Inlet methanogens belong to this family: Methanolabus and Methanosarcina. 43 Lab experiments were able to determine the ability of microbial cultures or microbes present in produced water to convert different types of organic matter (OM) to methane: (a) subsurface OM (2 types of coal, (b) coal-mimicking substrates I.e. ignin mix, 0.4 nUL*d, yield up to i15% mass to mass), and (c) biowaste materials (i.e. refinery sludge, biocoals, up to 5 0.9 mL/Ld) urthermore, molybdenum (MIo) (good correlation with methanogenesis rate), nickel (Nit tungsten (W) phosphi e and amunia were considered as important nutrients, Additionally, the methylotrophic biogas formation correlated with neutral to slightly alkaline conditions in the ftrmation waters (FIG, 2, pH greater than 7,2 with an optimum approximately 7.5), Methanogenesis rate is measured usin a pressure transducer and 10 GC/FID. Alternatively, rates of intermediate steps can be measured, by inhibiting methanogens (i.e. with BESA) and. analyzing the enrichment water chemistrv including volatile fatty acids (VFA's), alcohols and the like, Similarly, substrate material (i.e. coal, oil sands, bitumen, and the like) can be characterized before and after enrichment (i.e. conversion to methane) for chemical structure (ie. NMR., FTEIR) The bacterial break-down' polymers of 15 macromolecular subsurface OM (the rate limiting step) can be also enriched by using: (a) potential synthetic syntrophic microbial associations inferred from this research or (b) by armending an enrichmem of indigenous microbial populations (i e, on coal or coal analogues). In another embodiment, unfavorable endemic bacteria or environmental conditions affecting biogas formation were identified, Endemic bacteria that did not produce methane, 20 environment unfavorable to endemic microbes that did produce methane., or conditions that show a negative correlation to biogas (eg., methane) formation were identified, The inteCgrated data from microbial DNA., geochemistry, and biogas production via enrichment. experiments are also used to find negative correlations, indicating possible specific microbes or environmental conditions deleterious to biogas formation. Negative correlation within 25 DNA sequences and against geochemistry are also taker. into account as potential microbial rivalry/inhibition and toxicity/unfavorable chemical conditions (i.e. igh propionate concentrations of nitrate or sulfaut reducing bacteria, typically inhibiting methanogens, respectively, Potential risk of fouling of the bioreactor including production hydrogen sulfide and accumulation no-reactive acidic products is an important element of 30 the targeted injectate-water recipe, such that biogas formation by tie methylotrophic pathway is optimized for their essential growth substrates without impeding production due to other factors, For example, microbial populations derived from the Cook Inlet subsurface waters are also tested for the extent of mnicrobial removal of individual VFAs and retardation of 44 microbial pathways leading to potential VFA buildup (and lowered pH to tnfavorable acidic coiiditions). NIicrobial populations from most of the wells were capable of stochiometric conversion of butyrate and acetate to CH 4 within a few months. In contrast propionate was not degraded in any of the samples and its buildup in a subsurfae bioreactor has a likely 5 deleterious impact on biogas production by the methylotrophic pathway, Therefore, in some enbodiments, potential stimulation of propionate generation via supplemental inIjectate-water must be avoided. In addition, the introduction of certain anions such as sulfate and nitrate is to be avoided. in one embodiment, injection zone placement and injectate water composition were 10 determined based on formation characterization in organic carbon-rich formations and through inorganic moineralogy. The carbonaceous substrate is as important as the microbial comimitv in achieving biogas formation at economically significant rates. Our work shows a relationship between biogas rate and substrate thermal maturity (meaure by vitrinite reflectance or another geochemical parameter expressed in vitrinite-reflectance equivalencee. 15 Furthermore, the formations targeted for stimulated biogas growth must have sticient organic mass, contain microbial enzyme-accessible chemical-bond types, and also allow for fluid injectability at sufficiently meaninful rates. Thus, in alternative embodiments, methods of the invention can comprise geochenmical characterization of: (a) the mineralogy (e.g, content of the nutritious volcanic ash clays using XRD their chemical composition and ion 20 exchange potential usig SEM/EDS, association with organic matter particles using thin sections and SEM), (b) organic matter (functional groups and bond type distribution using NMR, TOC, ROCK-EVALTm pyrolvsis, organic petrography including vitrinite reflectance and OM fluorescence), and (c) correlation of organic-content ofcore samples, to well-logs for biogas resourcing, and formation-evaluation of fluid flow (porosity, permeability, swelling). 25 In addition, clays and other minerals within the organic matter-rich formations can be studied for ion exchange, Potential interactions between any proposed injectate and indigenous tormation water can be evaluated using advanced physical-emical and transport modeling. In another embodiment, injeetate water chemistry is optimized for biogas production enhancement. Methods of the invention comprise use of geochemical correlations with 30 desired microbial associations to optimize biogas-formation rate/yield by chemistry adjustment; this information is used to make a injectate-water recipe used to practice this invention, including the use of p'H- buffrs., The highest biogas-formation on an ideal substrate medimn (combirati on of C(OA, acetate, methanol) and highest biogas production rate on a 45 ignin/lignin monomers-upplemented Cook inlet coal-lignin enrichment has been achieved by the methy/methanolpathway associated microbial community derived exchsively fhorim wells with p>7.23 (FIG, 2)5 strongly imiplying higher pH as an alternative condition (neutral slightly alkaline) and an important basic makeup of injc tate- water recipes of this invention. 5 Thus, in another embodiment, compositions and methods comprise use of relatively alkaline (high) pH nutrients, injectate-water, liquid recipes and the like, and use of buffers biasing an alkaline (high) pH. In alternative enbodiments, injeetate water may also include spplenmentation with the best performing microbes on target substrate or its chemical analogae, even if derived front different environetm (e. another oil or CBM basin), that 10 performed well in the enrichments, For the targeted fields, the indigenous mineralogy, orgnic matter, porosity structure are likely to affect the growth of Iethanogenic robes, and in some cases, microbial biofilm (e.g, via surface adhesion and mining nutritious mineralogy due to the presence of clays, volcanic ash, and/or organic debris) under the supplemented water conditions, Therefore, the targeted microbial community and favorable environment 15 (e.g., optimized pH., supplemental macro-- and micro-nutrients, vitamins) may be adjusted for inte'ractions with the native organic-containng formations (FIG 6), in addition, undesirable dissolution or precipitation of mineral phases potentially harmful to the microbes or the reservoir quality can be assessed; eg, tested using cMical modeling, PHREEQC --- mineral solubility changes caused by interactions of formation water and minerals with the injectate. 20 A minimalistic approach can be used to favorably enhance the tar geted biogas-torming bacterial-archacal microbial association, whie not promoting over-enhanced growth of other microbes not important to the biogas formation process (i.e., to avoid water injction delivery problems due to biofilm plugging around well injectors). In one embodiment, customized nutrient amen-doents are provided. A nutrient mix 25 customized for a specific microbial community, which eg, can be developed by the following steps (FiG, 4 and 5); 1. Transform microbial. 16S rRNA gene sequence count data for all samples including adding a small value to each sequence count (e~g. add 1/10th of the lowest value observed to every sequence count, thus avoiding taking log of zero; log20 transform 30 sequence counts and determine Z-scores (for a given sequence in a given well, by subtracting the mean value of the occurrence of a given sequence in all wells examined and dividing the resulting number by the standard deviation of the same an-ay) 46 2. Determine correlation of the distribution of all sequences to distribution of target sequences, eg, domirant methangens responsible for leading methanogenic pathway (tested experimentally with coal/li gunin in monomers incubations, e.g. donating Methanolobus sequence using transformed data) to obtain Pearson correlation coefficients iRa and Rb. 5 3, Sort sequences based on their R values. Select sequences with R higher than cut oft value (e.g. 0.70). Subsequenly, remove sequences with low counts (e~g. 300) with small contribution to the community and having the sequence count iu a range of potential sequencing error. 4. Remaining sequences forim so called Consoitium, consisting of bacteria (b) and 10 Archaca (a) related or similarly distributed to the selected dominant methanogen, Correlations to sum of several grouped sequences (e.g. syntrophic microorganisms) can be also used. 5. 16S rRNA gene sequences in the Consortium are identified by comparison to annotated DNA sequence database (eg. NCBI), 15 6. Nutrient and growth condition (e.g. pH., Cl-, NH4+, etc.) requirements for of each of ie selected microbial genus or inicrobial strains was determined using information from publicly available literatures and in certain cases using information from the German Resource Center for Biological Materials. From this, an optimal Recipe Concentration (CR) of each element (e,g. Mg) or condition (e.g pI) X for each Consortium nenber (a or b) was 20 obtained, 7. Final Recipe Concentration (C, ) of given element or condition (X) for entire Consortium is obtained by using following equation (I ) Cs, f x C x fNC x: * +h x *C' x x 25 Where C. is the final recipe concentration of element X for a value or condition X., e.g. p11; C is a literature-based recipe concentration of element or condition X; Sand j are optional weighting parameters for bacteria vs Archaca in a population of targeted well, formation, and/or incubation conditions: j" is the fraction of bacterial sequence ni out of total bacterial sequence count within the consortium; , 30 is the fraction of archaeal sequence m out of total archaeal sequence count within the consortium; fy is the Pearson correlation coefficient of a bacterial sequence n to selected dominant sequence (e.g. main metnanogen) or grouped sequences (e.g. 47 syntrophic association); and is th1e Pearson correlation coefficient of an archaeai sequence m to selected dominant sequence (e.g. main methanopen) or grouped sequences te. g, syntrophic association If condi tions for Archaea and bacteria are equal both f and f parameters are equal to O.S If however, Archaea or bacteria are 5 dominant in a formation or injectate, or if Arehaea or bacteria are more critical or rate limitng, .. or f, can be adjusted to account for differences in consortium population, overall activity, or other factors dependent upon the specific process or conditions in the targeted well, formation, and/or incubation, 8. Final calculated C' values contribute to the final recipe (FR), 10 9. Additional minor adjustments of the calculated paraueters are tested one parameter at a time while maintaining other parameters, In one embodimem changes are assessed in a iand-pack bioreactor (Table 1, FIG 7), 10, Subtract all amendments (X) present in the formation water (FW) to obtain an adjusted final recipe (AFR) for the curont well conditions (FIG, 6), 15 .1 .1. Small adjustments to the AFR. may be made to accommodate charge balance, icrease chemical stability, and ensure no precipitation occurs during mixing, storage, injection or uider donation conditions. Chemical stability may be calculated using
PHREEQCQ
1
T
1 - PH.IIRE..QCP-0, or PH.AST softwvare frorn USGS and others, AQUACHEMTI m from Waterloo, Inc., ROCKWARE.:M, as well as other programs are also available to analyze 20 water salinity and precipitation under various conditions. The nutrient composition may be introduced to the reservoir through inlection of a single bolus, through a coninuous (e g a bleed in) process, or a pulsed process. The AFR may be amended dependent upon the changes in Ie production water, nethane production, 25 and/or microbial composition over time. The same methods used to re-inject produced water into well may be used to inict/re-i-nj ct a \mixture of produced water and nutrient concentrate. In another embodiment, the final water inijectate is delivered to the target formation to induce or increase biogas production. Field implementation, delivery of the designed injectate, 30 may be improved where good well-to-well connecivitv exists through highly ermeable continuous fArmation intervals. Core description, geophysical logs, and permeability/porosity data may be used to idenuifv target wells, optimze infection intervals, and improve biogenic gas production. For sandstone containing dispersed organic debris, injection of supplemented 48 water may be applied to the: (a) near- water leg or (b) previously depleted gas-bearing zones, in the same formation down--dip ftrom the free-gas zone (FIG, i1), Consequently, new microbial gas formed in the water leg nigrates upwards to column, supplementing Ohe overall gas reserves. Nevertheless, converting these large resources of sub-surface organic 5 matter require that the injectate--water supplement contact a large volume of the formation, without choking off injection around the well-bore due to biofilin growth, Therefore, an important consideration prior to implementation is investigation of the use of time-release substances or near-well toxic concentrations to prevent biofilm phigging, followed up by bInch testing on target tormations. In an alternative enbodienit, the incthods involve 10 continuous inijecuon of nutrients at final concentration (e. bleed in of concentrated nutrients into produced water-disposal well), Another option is delivery of nutrients with the fracturing fuids used often during comlpletionletion of gas producing wells. in alternative embodiments, tracing ejected water migration, biogas formation and changes in microbial communities are critical to benchmarkingz- sus Water migration can 15 be traced using water soluble geocherical tracers (i.e. stable or radio isotopically labeled ions such as C or C carbonatc and "iodine or chlorine, bromide, N Iewlv geicrated biogas can be traced fron gas isotopes, using "C, -H or 314 enriched methanogenic substrates, including bicarbonate, lignin and aromatic monomers, AdditionalIy, production profile of nearby producing wells can be observed together with gas to water ratio, gas pressure, 20 production. rates, and gas dryness, Bioiass tracers of newly grown microbes can be also used, including "C, C, t H or t H-iabeled organic compounds (i1e, lignin monomers, DNA, amino acids, bacteriophage, or other coal analogues. i.e. aromatic substrates listed in Example 4), t"N-enriched ammonia. Monitoring will. also include microbial community changes through RNA/DNA profiling, RNA/DNA yields 25 In another embodiment, chemical analogs of subsurface organic matter-containing rocks allow for quick growth of biomnass in microbial consortia that can be re-injcted, e.g., when the optimized nutrient mix is identified. For low thernai maturity coals, a lignin monomer mixture has been used to benchmark high methane producing consortia capable of the critical depolymerization step (FIG 3). Coal depolymerization is thought to be rate 30 limiting in the coal biogasification process. For higher maturity coals (about 06 to L.4% Ro) aromatic analogs are tested as surrogates for biogas formation, including biphenyl 4-methanol, methoxy bipheni 1,1,-biphenyl, methyl, dimethyl, phenanthrene, and other compounds that mimic degraded coal monomers. 49 In one embodiment, a biogenic gas formation is assessed by developing a facies model, determining formation parameters and distributing these parameters for each facies in a geocellular model. This geocellular model can then be used to simulate and history match any previous gas/water production to validate the model, and then to simulate future biogenic 5 gas production with nutrient optimization. As biogenic gas production continues, the initial model may be updated based on current production trends with optimized nutrient formulations, One or more geocellular models may be developed using numerous formation modeling techniques including ECLIPSE'M, GEOFINDIQf" from Schlumberger, MPS (Multipie-Point Statistics), FDM (Facies Distribution Modeling) and other geocellular 10 modeling techniques and programs, inuoding techniques and tools developed in house or by independent programmers, Formation parameters can include %TOC (total organic carbon), density, porosity, permeability, pressure distribution, saturation (gas, water, fluid, oil, etc.) conductivity, impedance, continuity, flow rate or velocit., volume, compressibility, thickness, fluid viscosity, and other properties. Formation parameters may be measured directly or 15 indirectly through well logging, measured through core samples and analysis, or esiated based on various formation properties, Formation properties imay be distributed by estimating from one sample well to the next, interpolatin, or applied by simulation algorithms including Kriging, stochastic simulation, Markov Chain Monte Carlo distribution, and the like, as well as combinations of these methods. Biogenic gas production can be simulated using STARS T 51 20 Ifrom. Computer Model ing Group, Ltd, JEWELSUITES from Balker Huges, BASINMOD 53 m from Platte River. or other reservoir simulation software as well as programs designed and developed in house or by independent programmers, Some software may incorporate both geocellular modeling and reservoir simulation. In another embodiment, a geocellular model is developed as described above and used 25 to test as flow, travel time, and continuity of the reservoir against variabilities in key formation parameters, which may be the result of limited or conficing geological data. Once these key parameter variabilities are identified, the reservoir analysis may be simplfied. In one embodiment, the travel time for biogenic gas in the reservoir was determined by modeling the biogenic gas production rate as actual gas injection into an injection well This allowed for 30 multiple variations of the key parameters in the geocell ular model to be simulated significantly faster than would be possible with a reservoir model which included the full biogenic gas production, This quick method helped to define the possible range in gas travel time based on variabilities in formation parameters and to identify which formaion 50 parameters are mos influential on gas travel time and require further investigation to narrow their variabili in another embodiment, risk analysis is used to identify potential risks, evaluate risk severity and probability, propose possible mitigation strategies, demsn tests for each risk, and 5 test each risk and putative preventive action. Potential risks associated with biogenic gas production can be identified from product suppliers, through water acquisition, to nutrient injection, to microbe growth and biofilm formation. In one embodiment, potential risks include inmuities in one or more of the nutrients, additives, treatments, water, or other feedstreans; contamination with oxygen, sulfur, or other comipounds; contamination with one 10 or mtore microbes; scaing in di injection line, wellihore and/or formation; biofilm formation in the mixing tank, storage tank, injection line, welbore and/or fonnation; sludge formation In the mixing tank and/r storage tan; biocorrosion in the mixing tank, storage tank, and/or injection line; formation of hydrogen sulfide (H2S) oxygen rmoval, biomass plugging; and the like, eithu individwlly or in coniunetion with other risks. Some risks may contribute to or 15 correlate- with other risks, for example sludge formation in the storage tank and biofihn formation in the direction line may both be the related to increased bionass in the storage tank, Additionally, in some embodimen ts, enriehmlient of bacterial cultures using analogues to target subsurface organic material including lignin and lignin monomers, soluble 20 hydrocarbons, other soluble substrates that mimic the composition of the hydrocarbon formation are used to enhance microbial growth in vitro. Models' components of the hydrocarbon formation using simple monomers identified in produced water and/or through decomposition of formaion samples provides a ready source of soluble substrates for microbial growth and selection assays. This innovative approach to rapid microbial growth 25 and selection allows deveopment of chemical and microbial optimized amendments for the targeted methanounic pathway' and for enhanced methnogenesi rate. Amendments were tested under Current fid conditions developed to evaluate the potential fo bniomss formation and scale precipitatati rulting from the addition of amendments, xhich cold create operational problus in the gas poduction and water injection tecilities in the field. 30 implementation of any enhanced bioas producing proc ess nust include the combined optimization of the reward (biogas formation) versus the risk factors (deleterious effects to overall gas production, corrosion/scabing, or gas quality), 51 The inventon provides kits comprising compositions and methods of the invention, including instructions for use thereof, In alternative embodients, the invention provides kits comprising a composition (e.g. a nutrient composition), product of manufacture (eg. a bioreaetor), or mixture (e.g, a nutrient mixture) or culture of cells of the invention; wherein 5 optionally the kit further comprises instructions for practicing a method or the iventon. The following examples of certain embodiments of the invention are given. Each example is provided by way of explanation of the invention, One of many embodiments of the invention, and the following ex amples should not be read to limit, or ecfine, the scopc of the invention, 10 EXAMPLES EXAME :identification of Akdzcwoiobus-at a fo n "'enigrad n of coalgand olter recalcitrant organi matter This Example describes the identification of Methanolobus spp. as rmor contributor to methanocenic degradation of coal and other recalcitrant organic matter in subsurface gas 15 reservoirs. Production water was collected from the separator unit at the well head from a ninmer of gas wells from the Beluga River Unit on the Cook Inlet of Alaska. A portion of the water sample designated for microbiological analysis was maintained anaerobically in sterile containers supplemented with cysteine and resazurin (redox indicator) under an argon 20 headspace. The samples were shipped cold to Taxon's facility in California by express delivery. Genomic DNA was isolated from celi pellets obtained by centrifugin g the production water at 4,004) x g for 30 miin at 4'C. The pellets were resuspended in phosphate buffer and transferred to bead beating tubes. Total genomic D: A was extracted by a bead beating 25 procedure as described (A shby, Rine er al 2007), A portion of the 16S rRNA genes were PCR-amplified using the primers TX9/!139 fr, followed by agarose purification of the amplicons. The amplicons were amplified a second time using fi.n primers to incorporate the A and B adapters in addition to barcodes that enabled multiplexing of samples into a. single run. 30 The 16S rRNA gene amplicots were sequerted on a Roche 454mll sequencer using Titanium chemistry and standard shotgun sequencing kits following the manufacturer's protocoL Profiles were created by documenting the number of times each unique sequence occurred in each sample, Sequences corresponding to those of Methanolobus spp, were 52 observed to be dominant members of the Cook Inlet subsurface communities (see FI ). Annotation of the sequences was performed by BLAST comparisons (Alchul, Madden et al 1997) to the Genbank database, EXAMPLE 2: -tibnmulation of methanouci derdation W1 coat' il recalcitrant organlic matter Minmodel sandpack bioreactors 1w adrhna: custormzeo nutrient amteridmtettts, of' the intVlitiofl In order to create a culture condition hiat approximated the rock matrix found in the sub-surface gas reservoir, carbonaceous material recovered front core samples were mixed in the natural in situ ratios with sand in anaerobic tubes fitted with solid rubber stoppers that 10 were crimp sealed. Specifically, ASTM grade sand (1 7,8 g, U.S, Silica Company) was added into 1 ml polypropylene conical tubes which was followed by addition of carbonaceous materials ( g67 g each of coal, sandstone with organic debris, and volcanic ash, to represet Cook Inlet gas-bearing formation) that are derived from Miocene aged rocks (i.e. core samples) from the 15 Beluga gas field in Alaska., USA Conical tubes representing control set-up was amended with 22. 88g of sand but without adding the carbonaceous materials, The mixture in the conical tubes was homogenized fir 10 s with a vortex mixer, and all the materials above including several aliquot of sterile 3,5 g sands were transferred into an anaerobic chamber that has been equilibrated with an atmosphere of hydrogen., carbon dioxide and nitrogen (5:5:90% 20 v/v, respectively), Then, the caps on the conical tubes were loosely opened in order to create anaerobic condition in the tubes. All experimental procedures from this point were carried out inside the anaerobic chamber. After 24 h the mixture in the conical tubes that contained sand and carbonaceous materials was transferred into sterile glass tubes (15 nL) that was previously stored in the 25 anaerobic chamber. This mixture of sand and carbonaceous materials was then overlaid with 3,5 g aliquot of sand to create a ~1 cn upper layer that is free of carbonaceous materials. The carbon-free mixture in the control conical tubes was also decanted into sterile test tubes but in this case it was not overlaid with another layer of sand. The orifice of each of the tube was capped with sterile stoppers and crimped-sealed with metal caps, All the tubes and its content 30 were autoclaved for 20 min at 120. The conditions fOr the experimental investigation are stated below: i. Sand - unamended produced water from the targeted gas field 53 ii, Sand/carbonaceous materials (organic rich rocks from targeted formations) + unamended produced water (FIG. 8) iii. Sandcatrbonaceous naterials + standard nutrient atmded produced 'water based on lab experiments (1st order) and literature search ind order) as shown in FIG, 5, 5 Step 5 fresulhs of sand pack experiments shown on FIG. 8) iv. Sand carbmaceons materials + standard nutrient amended produced water (FIG. 5, step 5) in which specific nutrient parameters were varied individually or in groups v. Sand/carbonceous materials coal/lignin-grown enrichments + optimized nutrient amended produced water (FIG. 5, Step II); Table> Stok soltton used to oeirfrsndpcaelr mas Mineral nuret rplnIn~ dP 5dtion>Pe vitamins';hv sou uOlmcl (mg/m) NaCi/KCL,5844/7455 Na-natriraeat,1500 p-Aminobetnzoate 50 Na2SO4 1011 | FeCI14HIO, 200 Biotin, 20 NH4C, 29.99 MnCh4110, 100 Cyanocobalamin, 5 IgCh, 5, 7 NaWO12 H2O, 20 Folic, 20 Na2HPO4/TNaH-i/PO 4 , | Co(I.6H1 00 Lipoic acid, $0 553 6/479 |ZnCh,5 Nicotinie acid, 50 CuC 2HNI0,2 Pyridoxine-HCL 100 HB0, 5 Thiunine iCl, 50 Nao()2H110,10 IttRiboflavit, 50 Na2SeO I7 Ca-Pantothenic acid, 50 NiCI> 6H0,24 a, Roh etcal 2006 b, Zinder, SI-, Technviques .n Micr~obia~l Ecology, p113-i134 10 Stock solutions listed in Table I were used to prepare set of solutions for nutrient additions to the sand pack experiments wit varyitng nutrient concentrations. The final optirzd mutrient concentrations (mM) and the amount ofthe constituents in the standard optimized nutrient amended produced water finali pH 7,5) was: NaC-CI, 100 mM; NHC, 5,6 M; P4, 78 m ; Mg 2 mM SO 0; 1 ml Trace element solution, lx; I m] vitamn 15 solution, ix (Table4- 1) The pH:t and concentration of NaC IKGl, NH4 PO 4 , Mg SO> , trace elemetnt soldution, and vi tamin so.luton, Ix Te tubes iteh produced water with ligntn/coal grown enrichment were separately prepared by addition of conenatr atd stock culture of cells, wich were stored ftrozen at 80*C and duawed prior to use" 'The fintat volume of nutrient and/oir cell amended produced water and the munan-ended 20) produced water in all the tubes (i.e. tubes with sand andI carbonaceous materials, and tubes with sand only) was 20 nml, All transfers into the tubes was done using a 20 gauge-6 inches 54 BD spinal needle which allow the transfer of the mixtures at the bottom of the tube which allowed good distribution ofthe equiibrated mixture throughout the sand-packed tubes. All experimental and con tol sand-packed tubes were prepared in triplicates, and the tubes were capped with freshly prepared sterile 20 mm septum stopper which were crimped-sealed. The 5 atmosphere in the headspace of all the tubes was replaced N2 (100% v v) and they were immediately incubated at 204C. Table 2: r anamer xvaria bil BiLNK 2 4 5 2 NaC KC 0 5 ) 00 00 00 3' SO~ 0 T 3__ ____ 3___ 4 N___ .6 7 l 0 5 0 .6 s 0 6 M. 0 0 0 Vixu X X,\ Recipe optiization used a matrix of parametea variability (Table 2 PI to P8) to define eiht variable parameters ard vO to v5 represent tested values of each parameter. Each tube was composed using the standard values of each parameter (highlighted) except for one 10 which was varied, In this round of sand pack experiments included 23 tubes plus blanks (all in triplicates;), Initial methanogen cultivation tests of production water ftron the Beluga gas field revealed that Methanolobus had a salt optinmm of 16 gafiter when grown on methanol and trimnetlianine (TMA) Nevertheless, when the same production water was tested for salt 15 optima using endemic coal as a substrate, the sal opim n was found to be 4 gdier, This result revealed that the salt requirements of the entire degradative pathway must be considered when designing consensus nutrient mixes. EXAMPLE 3: Stimulation of mehngnedetradation off co al and recalcitrant oran te 20 Akthanolbu aorii was added to sand pack tubes amended with target (Cook Inlet) coal organic debris/olcanie ash, and optimized nutrient additions suspended in filter sterilized, target production water, Rates of methane production were stimulated with addition of 1f Tayloi (FIG. I ). 55 Model sand pack bioreactors were set up as described in Example 2, Briefiy, carbonaceous materials (0,167g each of coal, sandstone with organic debris, and volcanic ash) from Cook Inlet core samples were mixed in the natural in situ ratios with 17.8g of sand (US, Silica Company, AST.M grade) in Himgate tubes (1 8 X 150mm fitted wiIih blue., byl rubber 5 stoppers, The components had been transferred into an anaerobic chamber, which is where assembly of the tubes and inoculations with microorganisms tookcplace. The tubes containing carbonaceous matcrial/sand were overlayed with pure sand, stoppered and crimped with ahiminmm caps, and then autoclaved for 20 minutes at 1:20*C, Sterile sand pack tubes were brought back into the anaerobic chamber. Standard 10 optimized nutrient conditions were used (see Example 2') and the final solutions, which also contained gas field production water amended with endogenous microorganisms +- M. taylori, were introduced into the tubes using a 20 gauge six inch spinal needle. Mthanuuolbums tavlof! (#9005) was purchased from the Deutsche Sam lung von Mikroorganisnen und Ze lkuturen GmnbH (DSM Bm raunschweli Germany and grown in 15 liquid culture using established techniques. The minimal essential medium (MEM-1) may he used as described by Zinder, S. H1, in "Techniques in Microbial Ecology". The NIEM- I was supplemented with trimethylamine 8 g/L sodium chloride, and mercapoethane sulfonic acid (Coenzyn M), as well as the following antibiotics: vancomycin, streptomycin, kanamycin, penicillin G. M, taylorii was grown with a iutrogen hcadspace at room temperature, shaking, 20 until turbid, Frozen stocks (~04C) of the organism were made b-v mixing turbid cultures with a 2X stock solution of freezing medium (final concentration 20%, glycerol in MEN-1) For the sand pack inoculations, a concentrated frozen stock (I. 8mL) was thawed, added to reduced anaerobic mineral medium (i{AM.Mi and washed once to remove glycerol and antibiotics. The cells were resuspended in production water plus nutrients before inoculation into sand 25 pack tubes, The amount of cells added was indeterminate, All experimental conditions were performed in triplicate. After inoculation, the atmosphere in the headspaces of all. tubes was replaced with nitrogen, and the tubes were 5 incubated at 20*C EXAMPLE 4:, Synthetic Cnoi of the inve-ntio-n 30 This example describes an exemplary method of making a composition of the invention, a synthetic consornia, and eg. the so-called "Consort-ABS I" composition of the invention. 56 A collection of production watersamples from biogenic gas reservoir (Cook Inlet) was profiled and analyzed to test whether two-dimensional custer analysis of 16S rRNA gene sequences would reveal the presence of a consortiumr of sequences (where the sequences serve as a proxy for the eorrespondin robe) whose abundance distribution among the samples 5 as a group corresponded to mtethtanogenesis activity. To isolate total genomic DNA., production water samples (250-500 inls) were filtered through a 47 mm 0,2 pm pore size Durapore membrane filter (Millipore, Billerica, MA). Using a sterile scalpel, fliers weresliced into 96 egtual sized portions and transferred equally into two 2.0 ml screw cap centrifuge tubes containing ceramic beads obtained from CeroGlass 10 (Columbia, TN). The bead-beating matrix consisted of one 4-mm glass bead (GSM-40), 0.75 g L4- to I .6-mm zirconium silicate beads (SLZ- 15), and LO g 0,07- to 0.125-mm zirconiutmn silicate beads (BSL-) I )in 1 ml phosphate buffer (180 mM sodium phosphate, 18 mM EDTA, pH 8, Cells were disrupted in a -astprep F20 instrument as previously described (A shby, Rine et al. 2007), Total genomic DNA was purified by centrifhging the lysed cells at 15 13,200 x g for 5 mini at 4C. The supernatants were transferred to 1.5 mi centrifuge tubes and 250 i of 2M potassium acetate pH. 5.3 was added, The tubes were mixed by rotating end over-end and were centrifuged as above. The resulting genonic DNA was purified on QlAprep Plasmid Spin columns (Qiagen, Valencia, CA) according to the manufacturer's instructions, 20 A portion of the 16S rRNA gene was amplified using the TX9/1f391 primers as previously described (Ashby, Rin. t al 2007) Amplicons were agarose gel purified and quantitated using SYBR green (Invitrogen, Carlsbad, CA) A second round of PCR was performed using fusion primers that incorporated the 'A' and 'B' 454 pyrosequencing adapters onto the- 5' ends of the TX9/1391 primers, respectively, The forward fusion primer 25 also included variable length barcodes that enabled rultiplexing multiple samples into a single 454 sequencing run. These amplicons were PAE purified and quantitated prior to combining into one composite library. The resulting libray was sequenced using the standard 454 Life Sciences Lib-L emulsion PCR. protocol and Titanium chemistry sequencing (M.argulies, Egholm et al 2005), Sequences that passed the instrument QC filters were also 30 subjected to additional filters that required all bases be Q20 or higher and the average of all bases in any read to be Q25 or greater. Furthermore, the TX9 primer was trimmed off of the 5' end and the sequences were trimmed on the 3' end at a. conserved site distal to the V6 57 region (ca position 1067, E. coli mnbering). The final seque-nces were approimateiv 250 bp fi length and included the V5 aud V6 ogos The seq emc abundance da as it'j tranwtXornud C ( d clustered using Pearson correlation as the dislace metric and WXaM 'N reabh& for hr'r''chical ivhrterin, 'T'he ejdusteings wa porn~mo tedim uuo. heoftware program f ( ORD. ispeeono of the data re-vealed thle organuzatlon of cequu"lces m~wo groups xitone part icular group soiga 2 rong association with hioen ic pas san-ples (FIG. 23), ThiAs presurmptiveconot was comnprismd oif 12 distinct sequence-s defived from three generaicldn.crbabum .&wewkser nd j1rocaeea Thais consortium was labeled ComnrAISi. The 12 t0 sequecnces (the so-caled "CoisoitAB1S1 ") are; AACG( TAAt AC6A( GCA'lCiEiAACTAAC AA CAAi s tj C 1 -5 (CC' ACA A6CAC' A(iATC-TCCYP'FT..TAATTX.(IAA(,iCAAC,CiAA(iAAC C I 1' C( AT CT(Js AC A-C" [C'TC'T( kAA'JCTOF.'AGA( AVC{ ACT~kCCC-[- CC:CQ-,,C:5 A.CAQi A.GA : M3 13C T 20 \VATCt WId t1CI i ALCOCAACF3TTOAAACTCAA At. AATCOACOiGCG(I C(JCAK-A( k \(CGG \((utx . ITGTT F-TAAVJCXI(.(AAG -CAAC -C> '. x xCC'II-AC(-'(f rTfl' (3 4ATCCTCTG Nt' A AXCC -. AAC-ATT(fliC'(t-TTTCCCTTC-:i(iO (.AC' .AG(z-(AAAC AC-iCT 25 CACCCGTi1AA&(AsA -'Ts .kslT.(A(KiTCW T( ,C''CssA(S(CTC AA-s s(Vt O C T' 'CCCAAT ~ T X Th CVs'. C UB \ACA:A'T *GAO AC I I " *'CT"CX'CIC AAC A6 ,kj: AN 'C AGOT' 30 ,k' I C:C j.C:'G " N VAI UAsflC AG6Oiss ( sut.A'K'NTC\CTB CUCOCNCTAACICAAT C.C XC'AAx UC Aut 3(KA( .AttTs 'CII NTT ATTC&AAkGCAA{ GCtAAGA'ACCFTACt'As.'s 1N5 (n Tot CAUICCtT AA K (s :,Alt. iA(-i(i-TA-'-T--t.KTAuT35TC.t.'(iQCiCA( ' 'C((' t.TC'-C'kt'T.A-AC S A <I' ~AiCACT CFCCCTGGGs3 x UAtA(sAC CGtCAAOGTTO AANACTC'A A Att A ATT&I ,AC'C-i(i(st'A 40 ( :TGt..3A TCtTC TO-At. C 4C Tt-iAC-iA(I'ATC.ANtA(CTTTt"'C'CT"CI(it(iC t Af(iA.iAC-A(.xss-.i'T C ',st (C,' TA.,(iTi( ~CT(,C (iT?('iiA,.--T-Ai(' (' f -TAA:AC SF0 II) NO 4 kcei'sbaeters ustkz-('-:T.A-:.A( , 58 SEt) T NQ.:7i ,BAeoaewrium CACCAGCTAAACGAiXI'AOFTAOTAC.l'(it-FO (C(iATACAA-r-,TCA(iTOCOC'-ACACAAG (iAA .'1 C CCC.( . R~A A (AC~iT) ICyAAC TTAAAQAAAC "i ',AATTO--,V.'C AC( t GA 10GCC CGCAVCAA(YC{4'FA 4 N h.AA (ii,(iTTTFCACAA CCiA(jAA(.C:UAOACCIFTACCAC 20) sOC.- ICA:,k3A ' .(CA(5A . "-((,pCj "AJ A 10>7 iCTI N AATATAC(JCACICACCCCAC CI( 30 CTOCi tICACAOTAAN C(0 NAT( i (31 NTAC( Va (ita S,C(ICCICAC--AiAACC:CA-.AOC( AAA-AC2 35~ (sEA iC:TN( ACJ-kC VCA('i(C -isAsC C C xL I \V T I A T(AACCAAA(3TT(}AACIT dua C ha V. qri - thC C N\VIi{}AAAICt 14 IC Cothm had 45 -ntazts Aiot}CRheCA MV stran' CONo wit I I l -/ Vt V tiOandCIi (X Cla~ 3) th 4sri C t4 VUsU NYTAANbSA rt ( coioC>314, 316 32N3,tAOAA 325, 3 1, 339, r N57 362 CO 368 ( 372,(Ji NCCW 39,NCC4C,57, 5-71IIC'1CA5x l 646,s4ti650 661, 2A',VT NAOAIITGSCG 674 N-75 C-, IC9 It0 It,2 684AC6 69 T96 45 711>CIC 4, 1 , - 7 4 ? ( , ,,, -i 4. 'S SEQ Ic aod l'crforlc1SHes oc nldn pinrs ucoieqo"e C CAA~'N NC.a I :A<NiC7 t sI*TCCOTTAAOA ( e4LaC59NA including SEQ ID NO. 1,2, 3 4, 5, 6, 7 8 9 10, , or 12, may be used to identify strains in a consortium. Table 3. Strain information from members of the Consort-ABSI synthetic consortium C600 Strain 454 V5V6 Genus SEQ ID NO 368 372 646 TxN 6-01 cocr 1 650 6174 722)- xvv6-0h'1090 ceobactrimv2 316, 331, 3>5 3 62 5;Y, 649 T P'tt: 4Uobau ir tn3 684 714 724 TXvsv i6 0 4 tobceru 4 675, 679 680 Tx 0139 Acetobacterium 5 650 67 721Tv. PVy0,f 2156 Actbctru 6 339 357 6500 674 "722 T Acetobatr7 677 Tx1v-02M6 Bctemdte 314 325 557 561, 71 587, 591, 662, B& vtv,& .sctemidees 12 686 694 696 712 -733, '734 661 62 71 14, 717 41 Txtv-05 BaCte it, 10 3 462 669 t 72 6 Txvv000568 A Bactidees 485 393 386xv 0 9r s 9 Each of these rains was thawed from the strain library (stored at -80OC), and patched ot in an anaerobic camber onto the following ruedium plate types: 5 Strains 571, 587, 591, 71, 722, 724, 726, 733, 734, and 741 on Anaerobic Agar; Strains 14, 16, 323,32, 331,)339, 357, '62, 462, 485, 646, 649, 650, 661, 662 674 675. 677, 679, 680, 682, 684, and 6R6 on Brucela 1lood Agar Struins 368, 372, 386, 393, 537, 557, 561, 694, 696, 711, 712, and 7 14 on Tryptic Soy Agarose. After 14 days of growth on. solid media, te patches were picked in an anaerobic 10 chamber and transferred to liquid media: Annrobic Broth, Brucella Broth, and Tryptic Soy Broth, After 20 days of growth, a Consortium mixture Wa prepared by pipctting 301pl of each strain into a sterile anaerobic conical, producing 9ml of mixture. To this mix, 9m1 of a 2X freezing mcdiun was added: 2Xi. Brucella Broth, 30% glycerol, 0,05% sodium sulfide. The mix was then frozen at -80"C for storage. 15 On the day of Sand Pack inoculation, 4nl of the Consortium mixture was thawed and then washed via centrifugation to remove any residual freezing medium by centrifuging the mixture at 4'C, at 201 x g for 20 minutes followed by removing and discarding the supernatant, The pellet was resspendei in I ml of production wa t eby inverting several times. This preparation served as the inoculum for the Consor-ABS I addition in the 20 sandpack. experiment, 60 Sandpack tubes were set up to test the effect of a synthetic consortium (Consort ABS I1 on the coal to methane conversin rate in. gas well production water icubated with coal and other endogenous potentIal subsurface substrates comprising sandstone with organic debris and volcanic ash, This experiment would in effect be supplementing the native 5 microbes present in the production water with the Consort-ABS I consortium. Since Consort ABS I did not contain a nethanogen a source of methylkotrophic methanogens (Methanolobus sp ) was included in the experiment. Approximately 17.8 g of US. Silica Company's ASTM graded sand was added to a sterile 15 ml polypropylene conical tube (22.88 g was added to each no carbon substrate 10 controls), Approximately 0. 167 g of each carbon substrate mixture (coal, volcanic ash., and sandstone with organic debris) were weighed out and added to the sand in each conical tube. To create the carbon substrate mixtures, coal, volcanic ash and organic debris each of which had been obtained from four different Cook inlet core samples were combined , Each conical tube was vortexed for 10 see to homogenize the carbon and sand mixture, Additional 3,5 g 15 aiqicuots of sand were weighed into weigh paper packets for each of the conical tubes. All conical tubes with t'he carbon and sand mixtures (as well as the all sand controls), the packets of sand, and 1 \ x 150I mm glass Balch tubes { Belico No, 2048001 50) that were previously washed with Sparkleen 1, rinsed with deionized water and drid were brought into an anaerobic chamber filled with 5%Ha and %XO. balanced with N. The caps to the 20 conical tubes were unscrewed and loosely replaced in the chamber to allow gas exchange. These materials remained in the chamber for at least two days before assembly. To assemble the sand pack tubes, each carbon and sand mixture was gently poured into a test tube in the chamber and an aliquot of sand was added to the top to create a top layer (approximately I" height) with no carbon substrate. Each tube was capped with a rubber 25 stopper, over which a metal cap was crimped. The assembled tubes were autoclaved on fast exhaust for 20 minutes and immediately brought back into the anaerobic chamber, Sand uck2- Cell Additions: To maintain the same concentration of nutrient addition between all cell addition treatments, 45.5 ml of the standard nutrient additions solution descr bed previously was mixed 30 with 154,5 ml of sterile (0.2am filtered) production water (40~3) for a final volume of 200 ml. The standard nutrient mix was assembled such that the final concentrations in the sandpack. incubations would be: sodium phosphate, pH 7,5, 7,8 mM; NaCl-KCi, 100 iM; NHACi, 5.6 mM; MgCl , 2 nl.M; and Ix trace metals and vitamin solution. Three sand pack tubes (with 61 carbon substrate) were inoculated as no cell blanks with 5,5 nil each of only this mixture using the same method previously described. The remainig 1 83.5 ml of the production water and nutrient mixture was inoculated with 1.22 mil of cells (40~3) thawed anaerobically from frozen stock (previously stored at -80C) for a i 15Ox cell dilution. Three sand pack tubes 5 with carbon substrates and three tubes with only sand (no carbon) were inoculated with this production water nutrients and endogenous cells (40~3). The remaining inoculated production water with nutrients was split into seven aliquots of 17.5 mnl each in sterile $0 ml conical tubes, Additional cells ftom different sources were added to each conical tube to create the various cell addition treatment inocula. To remove 10 any freezing media, frozen stocks (~804C) of cell addition types were spun at 3000 x g for 20 min. The supernatant was removed, and the cells were anaerobically resuspended in I ml of sterile (02 am filtered) production water (40 -3). Cell additions grown in antibiotics were also washed and anaerobically resuspended in sterile production water, A 250 pl aliqluot of the resuspended cells were removed and loaded into a 96 well plate. OD readings of each cell 15 addition type includingg the end ogenous cells, 40-3) were taken at 550 un on a Biotek Epoch plate reader, [he volune of cells to add to each 17,5 ni aliquot was determined based on their OD reading using the following formula; .....................- 6) "a.12m1 20 OD(cell addition) where 0.12 mil is ie volume of the endogenous cells added per 17.5 ml aliquot (15Ox dilution), Based on the OD readings, the following volumes of resuspended celis were added to each 17-5 ml treatment al iquot, and inverted to -mix: 'No Cell Additions': None 'Methanogens Only': 0.14 ml Mgcn I and 0,23 ml Mcn2 'ConsortABSI + Methanogen' 0.7 ml Consort-ABS1 and 0.14 ml Mgen aund 0.23 Mgen2 25 Three sand pack tubes (with carbon substrates) were inoculated for each cell addition treatment using a venting method. in. an anaerobic chamber, the tubes were opened and a 6" sterile spinal needle was gently pushed through ite sand mixture to the bottom with its plug inside. The plug was removed. leaving the needle in the sand as a vent and 5,5 ml of the corresponding cell addition inocula mixture was added to the top of the sand with a 5 ml 30 serological pipet, The liquid inocula slowly saturated the sand mixture from the top until it reached the bottom, Once saturated, the needle was slowly removed, leaving a thin layer of 62 liquid at the top of the sand, 'Te same needle was used for each replicate within a cell treatment Once inoculated, the tubes were capped and crimped, the headspaces were replaced, and they were stored at 20*C as previously described, Descrptio cit Addtitions; 5 1. 40-3 at cells that are endogenous to the production water used in the sand pack experiments, The cells were isolated by centrifuging the production water, anaerobically, at 3000 X g for 22 minutes at 4"C. The supernatant was removed and the cells were resuspended in standard freezing mdium containing Bceella broth, 0.05% sodium sulfide, and 15% glycerol, They were then stored at (-80"C) until needed. 10 iL Mgen I is an enrichment culture that was cultured from production water frn Beluga well (404). The previously frozen cells were inoculated into methanogen enrichment medium, MIEM trimethylanine + 16g/L NaCI, sodium sulfide, and antibiotics tvancomycin. streptovcin, kanamycin, penicillin G) and incubated for several months before it was determined that the culture was making methane, It has been sequenced using 454 sequencing 15 technology and shown to contain a high proportion of Methandobus. It was frozen until needed. I.L Mgen2 is a highly purified metianogen culture (that contains more than one species) derived from production water 40-3 The previously frozen cells from this Beluga well were inoculated into MEM+ petone + sodiurn acetate - mnethanol-trethylamine + 20 sodium format + antibiotics (kanamycin, vancomycin, ampicillin) + sodium sulfide, and the culture in the serum vial was given a hydrogen overpressure. After a month the culture was shown to produce methane, An aliquot was then placed in a "Cellan Roll Vial" in order to isolate single colonies, The composition of the ge 1 lan roll vial was the same as the liquid culture except that no antibiotics were used and the gelling agent added was 0.7% gelan. A 25 single colony was plucked from the vial after incubation for one month and it was resuspended in liquid medium of the same composition as described above. After two weeks this highly purified culture was shown to produce methane. This culture was used directly in the sand packs. IV, Consort-ABSI: 12 sequences were identified from the 454 sequence data as 30 chstering across multiple samples from biogenic gas wells when sorted by abundance, and were therefore selected as candidates for a Consortium mixture. At various time points dur-ing incubation of the sand pack tubes, a portion of the headspace was removed to determine the amount of gas produced using a pressure transducer 63 The amount of methane produced wars determined by gas chromatography analysis of headspace samples including a correction for the total volume of gas produced, The rate of conversion of coal to methane began to increase at 42 days in the Consort-ABS 1 plus Methanogen and the No Cell Addition sand pack incubations (FIG, 24). interestingly, 5 incubations supplemented with Methanogens alone appea red to detract from the iethanogenic rate. The h highest coal to methane rates fromi any of the conditions tested were observed in the Conort--ABS i plus Methanogens from 70 days onward and these differences were stabistically sigificant, EXAMPLE 5 Creating Iniectates comprised of microbes capable of enhanced methamoienic 10 degradatin of ogicsubstae Microbial consortia derived from target (Cook Inlet) production water were select vely enriched with specific chemical compounds which are analogues to target subsurface organic matter (PIC. I 0) This method allows relatively rapid growth. of biomass in microbial consortia thait could be re-injected, e.g, with the optimized nutrient mix. The coal/lignin 15 degrading consortium was derived from target gas field production water, and is composed of rnicroorgarnsrns that were enriched on lignin (S-oMAumCH lignin monomers, and Cook Inlet gas field coalt The Ilignin monomers that were tested were: ferulic acid, tannic acid, quinic acid, and shikimic acid, which are representative compounds typical to low maturity coals, e,g. Beluga and Sterling formation organic matter thermal maturity averages at 0,33% 20 of R 0 To obtain the consortia used for inoculation into sand pack tubes, enrichment cultures werc established previously, assayed for pressure and methane production, passaged into medium of the same composition, and then frozen at -80*C. To prepare the parent cultures the ignin and liglnin like compounds were added to RAMIM-Fresh medium (Shelton and Tiedje 25 1984) along with a mixture of coals, Final concentration for all lignin and lignin-like compounds combined was 50mg/L The seven rock. types, originating from target basins were ground together using a mortar and pestle, and 0.9g of the mixture was allocated anaerobically into each vial of RAMM-F, Production water (3-4mL) from target sites, which had been kept anaerobic, was inoculated into the vials, and a nitrogen headspace was provided. The vials 30 were incubated in the dark, shaking, at room temperature for several months, During the incubation the headspace gases were assayed and the production water-consortia that produced high volumes of methane gas were noted. These corresponded to the same production waters used in the sand pack experiments described herein, Aliquots of these 64 cultures were inoculated into fresh medium of the samte composition to obtain P1 culures, These culures were then incubated and monitored as described above. Frozen aliquots of the parent (PO) and passaged (P1) cultures were obtained by nixing the liquid cultures with 2X freezing medium (30% glyceroL 2X. RA.M.M-F). The coal-degrading consortia used in the 5 sand pack tube, was a frozen P1 aliquot (2mL that was thawed, and then added to RAMM-F medium, washed once, and resuspended in production water. Th1le coal froun the original coal/gnin enrichment was not removed. 'he amount of cells added vas indeterminate. Taruet basin pr-oduction water Target basin (California) production water was collected and kept anaerobic until used 10 for sand pack experiments, The sand pack. tubes were assembled exactly as described in Example 3 except that for these experiments, California production water and endogenous 10 microbes were amended with standard optinized nutrients at the concenirations described in Table 2. Cook inlet coal/volcanic ash/sandstone with organic debris was used in these sand pack tubes, The coal-lignin consortium derived from Cook Inlet 40-5 production water, as 15 described in Example 4, was added to enhance methanogenesis rate (FIG. 10b), Identification of methanol-utlizing methanogenesis or "methylotrophic conversion, provided nwroutes to increased biogenic gas production. Identification of the dominant gas production pathway given the combination of micro.bial organisms, hydrocarbon substrate, and formation water chemistry allows for increased biogas production rates, better utilization 20 of reservoir hytdrocarbon, greaer overall biogen ic gas production and a longer life tor biogenic gias reservoirs EXAMPLE 6. Biogasification R isk Analysis Applying a biogasification risk analysis process in the field (e.g. biopiugging and excess biomass development. oxygen-driven microbial corrosion in injection lines, bio-siudge 25 development in injection tanks, inorganic scaie formation, field-wide redox status of productionnection water, etc), was proposed in order to identify problems that could arise during field operations, A scheme for injection of the optimized nutrient recipe was also used to idmify some of the potential problems (FIG. 12), The scheme is made up of 2 separate tanks (A and B). Tank A is to be used for mixing concentrated stock solution of the optimized 30 nutrient recipe, while tank B is to be used fIr storing nutrient solution received fromt tank A. The scheme also includes ports for sample removal, and injection pumps to control flow of solutions exiting both tanks. According to thescherne, nutrient solution exiting tank B is to be 65 mixed with injection water at appropriate. ratio in order to achieve the desired concentration of nutrient cononents in the final mixture that is to be injected into the reservoir. Further, understanding of the travel lenIgth and the corrsponding travel time of solution from the point of nixtlue to the point of entry into the reservoir helped clari fy the likelihood of excess 5 biomass formation, bioplugging, and oxygenv-driven bio-corrosion along the injection line and in the well-bore, The potential for biological and inorgan shiidge forination and accumulation in the mixing and storage tanks was evaluated. The tests carried out included chemical analysis of reagent samples, field-wide redox measurement; biomass control with sodium hypochlorite (NaOCl) solution; slude treatment; as well as scale frrnation and 10 mlodeling, The purity of chemical reagents to be used for developing solution of nutrient recipe was con firmed by analyzing test samples of reagents that was obtained from selected commercial vendors. The analytical tests carried out incl ude ion chromatoraphy (IC), inductively coupled plasma mass spectromnetry (iCPMS) and inductively coupled plasma 15 atomic emission spectroscopy (ICP-AES). The overall objective of the analysis is to determine the level of purity of the reagents, as well as identify level of certain elements (e.g. sulrfu) in the reagents which may pose potential problems if introduced imo the reservoir, This allows identification of the appropriate vendor supplying purer forms of the required chemical reagents (FIC 18), 20 The procedures to test the effectiveness, and the minimum dose, of NaOCl that is required to eliminate biomass in the injiection line and injection well-bore during the field biogasification process are the following, The initial population of microbes in production water, placed in ttbes that were to be incubated under defined oxygen saturation conditions was determined either by direct counting of cells using a Petroff Hausser bacterial counting 25 chamber, or by counting the colony forming uni ts (CF U/mL) of microorganisms that developed on specialized media after incubation for specific period. The population of microbes that were present in the incubated tubes (also with added carbon source-coal and nutrient additions) was determined over time after methane was detected in the headspace of the tubes, Thereafter, the same tubes were amended with different concentrations (0,6%, 30 0.3%, 0. i.10. , 0.03% and 0%) of NaOC solution followed by incubation of the tubes for 23 hours to allow the biomolecuie-oxidizing action of the solution to come to appreciable completion Immediately after this, the population of viable microbes (ite, CPU/iL) in the NaOCL-a.mended tubes was determined by plating a specific volume of 66 the cuhure on defmed solid medium, All the concentrations ofNaOC solution that was tested were effective in inactivinlg microorgarnisms in the utCient solution irrespective ofi the presence or absence of oxygen (F IC 19). The potential for biomnass production and accunulation in nutrient sohtion in the 5 mixing tank, storage tanks, and injection line was evaluated as fIllows. Production water was amended with specific concentrations of specially selected nutrients. To mimic the concentration to be used for the storage tanks, the production water was ar mded with excess concentration (i.e. 25x) of nutrients, while nutrients amended into production water at lower concentrations (lx) minic the concentration of nutrients in solution entering the injection line, 10 The nutrientamended water was transferred into test tubes, and the initial population of microbes in the water in these tubes was determined. Thereafter, the tubes were incubated at 10, 20, or 25*C for different periods (9 and 30 days for Ix concentration; 7, 16, and 28 and 50 days for 25x concentration) to allow growth of microbes and development of appropriate amount of biomass in the tubes if any.The pulation of microbes that developed after 15 incubation was determined using the direct counting procedure (i.e. CFU/mtL), Bionass levels dropped after 50 days of incubation in the concentrated 25x nutrient solution (FIG. 20) although there was an initial increase in biomnass level after seven days, Biomass level in the Ix nutrients recipe increased over time (0 -- 30 days), suggesting that the nutrient solution once in the injection line and injection well-bore may support the development of biomass in 20 the zones,. The effectiveness of any one or combination of compounds with an imine or quinone funeti on al group to remove oxygen from oxygeln-exposedproduction water was tested. The imine solutions may contain one or more imine oxygen scavengers including hydrazines, methylimines, ethylimi nes, propylimines, butylimines, diethylhydroxylamine (DEHA), 25 aikeneimines like hydroxyalkylhydroxyhunne, phenyinediamines, aminoguanidine, carbohydrazide, and the like, The quinone solutions may contain one or more quinone oxygen scavengers including hydroquinone, orthoquinone, semi quinone. pyrroloquinolin-qiinone (PQQ), methyIhydroquinone and the like. Other non-sulfir containing oxygen scavengers may also be used like aldehydes, carboxylic acids like acetic acid and tartronic acid, 30 carbohydroxide, erythorbate, cobalt, methylethylketoximne (MEKOfand the like. The extent of oxygen removal was determined by measuring the change in redox potential of nutrient amended (i.e. Ix concentration) production water that was previously exposed to atmospheric oxygen, The concentration of the oxygen scavenging compounds that was tested is shown in 67 Table 4. The results from thns test show that the compounds were effective in reducing oxygen saturation level in the produced water (FiG, 2 1A). lable 4: Covos 00on rotnrooce water amned wit two oxe-cavnin eonipounld\ SonditioNs A | B (C D E F G Composition" Water Water Water, Water Water, Water, Water, and nutrients nutiets. nutrients nutrints utrints nutrients, nutrients 34 mg o 34 ig of 68 mng of 136 mg 170 mg 204 m imine nine + Wine + of i c of X of imine L"9 mg .8 mng + 7.4 mng 9.3 mig + I L-2 of of of of 1g of qumowne qumone qumnene qumon quinon Fmal concentration of inine and qunone m I L of aqueous nutrient solution FieId measurement of redox potential tORP) and oxygen saturation level, in produced water and injection water, determined if ORP and oxygen saturation level in the produced water and injection water vary in water obtained from wells or facilities across the field. Measurement was done using a YSl 6920 V2 sonde (YSI, Ohio,. USA) which also allowed simultaneous evaluation of multiple parneters in water samples that were collected from the well-heads or water storage tanks direct, According to the in formation generated during the field sampling the ORP and oxygen saturation level vary across the field however water 10 collected directly front the well-heads exhibits lower ORP and oxygen level in comparison to water collected from storage. tanks receiving water from the respective wells. Water collected from vacuum trucks that are transferring produced water from producing wells to the injection well in dhe field had the highest ORP> and oxygen level (FIG.22 B), The effectiveness of defmed concentration of chemical reagents (NaOCI and acid) to 15 act individually or complimentarily in dissolving sludge material that was collected from an on-site storage tank was determined by adding 10 mL of 6% NaOCI solution to -2-3 g of sludge sample, This was then mixed by a vortex m-nixer for 30 sec. The mixture was then incubated at room. temperature for 10, 30 or 60 rmin. Thereafter, the mixture was filtered through a pre-washed (uinig 10 L of 6% NaOCI solution fodlowed by 10 nL deionized 20 water) and pre--weighed 50 pm filter. Then, 10 mL of deonized water was used to wash excess NaOCI solution. The filter and any residue that was left was then weighed. Alternatively, the filter with residue was exposed to 10 mL of 2N HCl for 10 minutes before filtration and washing with 10 mL deionized vater, In all cases the amount of residue left on thc filter after treatments was compared to the amount prior to treatment and the percent difference in weight 25 was estimated (Table 5), Results show that NaOC solution was very effective in dissolving 68 sludge material and that treatment with acid 1C1 solution) alone was not as effective, H1-owever, treatment of sludge with NaOCI prior to treatment with acid increased dissolution of the sludge materials, mnost likely due to increased accessibility of the inorganic particles that are trapped within the sludge to acid after NaOCI treatment. I able 5, Efiheof N40I solution and acid treatment on- dissolution of tank derived sk udte m~aterial Incubation time Sludge Weight After NaOCI After NaOCi Total (min) (g (Ag) and HCI dissolved 10 2 5 2 0,331 U 93 88S4 30 2.26 0 174 0.166 92,6 60 2,80 0.120 0107 962 5 Finally, the tendency for inorganic scale tornmation in a solution that contained specific volume of produced water and defined amount of imtrient recipe was determined by a combination of bench tests and chemical modeling of scale formation. The proceduires include: thermodynamic prediction modeling using ScALECunMTr 3,1 OLI Systems) in order to calculate scale formation by the inixtures; anal ysis of solid filtrate collected by passing 10 produced water through a 0.45 HV filter, and in which the solids were vacuum dried, weghed and subjected to FTIR and XRD/XRF in order to identify its composition; bottle tests using filtered (0.22 pm) produced water and nutrient recipe in which the major constituents in the recipe were added into the produced water followed by manual swirling of the mixture followed by incubation at stationary position for appropriate period and further analysis by 15 inductivelv coupled plasma (ICP); bottle test at 80T by filtration of produced water with 0.45 un and 0.22 pn fihers, and, thereafter, ammonium phosphates and vitamin solution were equilibrated at SOF and then added into the produced water that was also equilibrated at a similar temperature to achieve the defined concentrations of nutrient components. The mixtures were then incubated overnight on a shaker (85 rpm) at SOT After that the mixtures 20 were then filtered and analyzed by ICP in order to determine phos phate concentration in the solution; kinetics of generation of calcium phosphate solids at different initial calcium concentration was determined by kinetic turbidity measurement, Then 125 pL of the different concentrated stock. solutions of Calcitum was added individually into 2.5 nL of synthetic produced water-nutrient solution placed in cuvettes. The absorbance of the mixtures was read 25 at 500 nm with a VARIAN CARY -Vis 1(000 SpectroIhotometer, In all cases, samples in the~ cuvettes were stirred during incubation at 47 and 8OT. 69 Thermodynamic modeling showed tat there is the likelihood for inorganic scale formation in produced water-recipe mixture, suggesting that the final composition of optimized nutrient recipe is determined after careful consideration of the composition of the scale forming compounds that precipitates in the mixture, This .thod predicted the most 5 likely inorganic mineral scale based on the saturation index (SI) of the identified compounds. Caicium-containing compounds were identified as most likely inorganic mineral scale. In agreement with th rsut of thermodynamics prediction, addition of nutrients into the produced water led to depletion of calcium in the produced water-nutrient recipe mixture as determined by ICP. Results also shows precipitation of some calcium-containing compounds 10 may cause depletion f other essential nutrients in the produced water-nutrient recipe mixture. LXA-NI L E 7: ReevorSiuation' of lBio) as Simulation of biogas in the sub-surface reservoir requires the ability to model the flow of ntrient & microbe amended fluids and methane tlrrough porous media, as well as the ability to represent microbial generation of methane through chemical reactions, To 1$ accomplish these tasks, computational modeling software was used, incorporating methane generation rates as derived from laboratory testing and a geoceliular model which adequately represents the geologic variability inherent in the reservoir. The generation of methane front microbial processes is represented through a series of chemical reactions involving the following components: microbes, nutrients, and biodegradable coal volume in the sub-surface, 20 Sub-surfiae microbe and nutrient volumes are determined from current conditions in the sub surface, as analyzed from produced water samples, and assumed volumes of nutrient/mierobe amendments to be injected into the sub-surface. Biodegradable coal volume in the sub-surface reservoir may be calculated from petrophysica interpretation of coals observed in well logs and total organic carbon (TOC) measurements of sub-surface core samples for each lithology/ 25 and/or faces expected to be contacted by injected fluids. Coal votime is then discounted based on the both the fraction of the coal that is biodegradable and on the accessibility of these biodegradable coals to microbes ina the sub-surface, i,g lithologies or faces with lower porosity or permeability will. be difficult for microbes to move through, and, therefore, access the available organic matter, as compared to lithologies and/or faces with higher 30 porosity/permcability (Fable 6), The fraction of accessible biodegradable coal can then be populated tirougiout the geocelluar model based on the lithology/facies distribution previously defined for that model (FIG, I 6) 70 L- contentBk based (1OC- Accessibi degradabl coal, based) in Coal beds + e coal Wo- e & Bio Vol diswminate disseminate fraction degradtb accessible degradabI Model fratio id form, Vol d csal, Vol Permeabilit basedd on e coal coal e coal VoL Faces m fraction fratior y pennd fraction fracton % of rock Flood ph;n 0:60 0.046 036 nterm6eiarte 00 0250 0 25 3S29 t vey lw Alvindot 03 00 0.046 0.46 MM I 0 e 0 225 0 158 2305 d chatme to o1w0 Crev'sse 100 0.113 0.213 nnediate 0.225 0 169 3,600 spla W0 060 0.045 ,65 good 0,90 0 200 O J80 1176 * 4or abn dod1 chamei rnc tion, floodplain was 'ued b eaus the 2 oa Ihaie a a kely include in the log-derived coast have Very hih TOC) 5 The Nub-surface sinmlation of biogas as, described abov is high l y dependent on understanding how applicable the methane generation rates fromn laboratory testing are to the sub-surfice. Given the large degree of uncertainty in this understanding, it is desirable to test multiple methane generation rates in onder to understand the range of possible methane volumes generated and the travel time of miethanie generatecd near the injection well-bores to 10 the producing and/or monitoring well-bores, In order to quickly test munliple scenarios, a simplied simulatin approch can be used to mimi-nic t he simulation described above, while significantly decreasing the' computer processing time required for simulation. For this simulation, a range of potential biogas generation ra te in the sub-surftace are calculated by upscaing the biogas generation rates observed in laboratory experiments to he estimated rock 15 and fluid vohins expected in the sub-surfaee These mtiple rates may be further rmodified up or down by scaling factors to represent possible unknown co nditions in the sub-surface and give a wider variation in potential outcomes,. These various rats are then represented as gas injection rates into the injection well-bore. Simulation of methane flow trom inject well bore to producing/monitoring wel-bores can then be done using standard flow simulation 20 software. Adding a small volum of a ga isotope tracer (described below) to the gas inaction then allows the gas travel tinmne from injection well-bore to producingmonitoring wellbore to be quickly estimated for multiple bogas generation rates. The simulation results shown in FIG, 17 are based on an 18-month inj eton of gas at various rates, representing the total 71 volume of biogas expected to be generated dring the 18-month period. Once the tracer detection nimit is estabi ished, the gas travel time from injection wellbore to producing/mitoring wellbore can be determined for the various biogas generation rates, This method can also be used to quickly test various reservoir properties with uncertainties 5 that may also affect the gas movement through the reservoir. This will assist in identifing reservoir properties which may need further investigation to narrow key uncertainties and in determining the appropriate length of time necessary for monitoring to detect newly generated bio gas. EXAMPLE 8: Mim4icking of Coal Monomer 10 Modeling microbial growth in a reservoir is difficult because the subterranean carbon sources often have differing chemical compositions, limited surface area, microbial growth is restricted, and reaction conditions including pressures and temperatures are hard to replicate in vitro, In order to quickly identify growth fetors that improve ncrobial growth in situ, a niethod of growing microbial cultures in vitro was requirel that both mimicked the 15 subterranean formation and increased surfiace area to allow for faster reaction times. Monomers were identified for various subternean carbonaceous formations that nimcked the cheiical-bond structures present within the targeted formation substrate. in addition o water environment, microbial associations are likely to be partially controlled by the substrate chemistry. 20 Chemical compositions that mimic substrate chemistry are readily available arnd may be identified based on the sticture and composition ot tIe carbon compounds in the reservoir in some examples the substrates are selected from syringic acid; syringic acid methyl ester; dimethyl phenol; 2,4--dinethyl phenol; guaiaol; protocatechuic acid; vanillic acid; isovanillic acid: caffibic acid; ferulic acid: isoferilic acid; dbenzofuran; 8-amino 2~naphthanol; 7 25 methoxy counmarin; biphenyl 4-methanol; 1,'-biphenyl methyl; methoxy biphenyl; 3 mecthoxy b ydimetyl phenan three; dimethyl fluoranfhene; dimethylnapththalene; dinethyl anthraene; acetylene; diacetylenc ; vinylacetylene; methyl naphthalene; trimethyl naphthalene; 7-ethyl- I4-dimethylazulene; trimer-3~methoxy-4 benzyloxy-aipha-2-methoxyphenoxy b-hydroxypropiophenone; composition derived from 30 the basic structure of lignin or kerogen; or other hydrocarbons found in the subterranean carbonaceous formation. Addition of these substrates to an aqueous culture, sand-pack bioreactor, or as an additive to other growth media provides a method to identify 72 tmicroorganismns that will preferentially degrade a carbonaceous substrate, candor generate biogas from the carbonaceous substrate, Table. 7: Carbonaceous, Lb .nialiko uroqeue Vitrinite Reflectance Sana mp)I e Location(s) Ra uk (%R- ononiers Ligni te/sub~ Coal A A aska bituminous 033 qmmue acid shikme acid __________ __________ _________ WrieC acid, krulc cli Volatile Coal B Utah Mit6 btununous -- - - -- - - - .__ _ _ _ _ ................. -------- _ syingic acid; dimehyl phenol, 8-amnino 2-naphthanol; 7 aethoxy coumarin; biphenyl 4 Hihmebhanol; metho'xy biphe nyl; voltij e ,'biphenvl me thyl dimethy coai C Nnsw M o menanthrene dinethyl A thiorarthene; and tomer-3 methoxy4ben zyloxy-alpha-i2 methoxyphenoxy)-B~ syringic. acid; dimehyl phenol; 8-amino 2-aphhanol; 7 mtanhoxy COin; bipheny 4 ethanol; methoxy biphel;v Mfedmmun Coal D New Mexico volatile 1. 10 1 bpheav itik I dUcik hienous nanth dimethyl luorathene; and inmer-3 methoxysvbenzylox-alIpha/ methoxyphenxy)~B _________ ______________hydroxyprlfloiopheno Europe. North humic, fibric, hernic, sapric America syringic, quiic., shikimic Peat New Peat <03 panic, and/or firuhi acids, as Zealand well as coinpositions listed Asia, below Malaysia Europe, North Lignlin carbonyl, carboxyl, America, amidi, cstr, phenoic. Aasia ", alcohoie, ketone, aldehyde,. Australia, benznoid paraffinic, naphthenic India aid aromatic hydrocarbon Coal wo n Svunu -- 038-0.6 bitumous 73 Vitrinite Reflectance Sample LocationIs) Rank (%RK) Monomers Brazil, igh Coal Illinois. volatile 4511 Indiana bitminowi Ned.ium Coal volatile 1 I5S Low Coa volatie .5 9 ________ _____________ bitninnous ________ Semn Coal ~L9 2, 5 Cowl_______ I____ _ anthracite (2 ) _________ nthgracit e ~~~0 _______________________ The discussion of any rernce is not an adnission that it is prior art to the present invention, especially any reference that may have a publication date after the priority (late of this application. At ih s-ame time, each and every claim below is hereby ineoporated into this detailed description or specificaton as additional emubodniments of the present invention. 5 Although the systems and processes described herein have been described in detail, it should be understood that various changes, substitutions, and alterations can be nade without departing from the spirit and scope of the invention as defined by the following claims. Those skilled in the art may be able to study the preferred embodiments and identify other ways to practice tie invention that are not exactly as described herein, It is the intent of the inventors 10 that variations and equivalents of the invention are within the scope of the claims while the desciption, abstract and drawings are not to be iCd to limit the scope of the invention. The hive-ntion is specifically intended to be as broad as the claims below and their equivalents, REFERENCES All references, publications, patents, patent applicatins cited herein are hereby expressly 15 incorporated by reference for all purposes. The discussion of any reference is not an admission that it is prior art to the present invention, especially any reference that may have a publication data after the Priority date of tis application. Incorporated references are listed again here for convenene: (3US4826769, US8484503f4,I US6143534, Menger et at. "Microbial process for producing 20 me thane from coal." R ei Energy 1nc, (1985). 74 2, US5845032, Srivastava and Walia, "Biological production of hunie acid and clean 25 fuels fron coal," (1998). 3, US5424195, Volkwein, "Metod for in situ biological conversion of coal to nethane" U S Dept, Interior, (1990), 5 4. 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