Compositions and methods for identifying and modifying carbonaceous compositions

Abstract

This invention generally relates to natural gas and methylotrophic energy generation, bio-generated fuels and microbiology. In alternative embodiments, the invention provides nutrient amendments and microbial compositions, e.g., consortia, that are both specifically optimized to stimulate methanogenesis, or for “methylotrophic” or other conversions. 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. The invention also provides methods for the evaluation of potentially damaging biomass formation and scale precipitation resulting from the addition of nutrient amendments. In other embodiments, the invention provides methods for simulating biogas in sub-surface conditions using a computational model.

What is claimed is: 
     
         1 .- 52 . (canceled) 
     
     
         53 . A composition comprising:
 a) at least two microorganism strains of Consort-ABS1; or   b) a synthetic consortium comprising at least two different microorganism strains, each strain comprising at least one 16S rRNA gene having 90% sequence identity to a nucleic acid sequence selected from the group consisting of SEQ ID N0:1, SEQ ID N0:2, SEQ ID N0:3, SEQ ID N0:4, SEQ ID N0:5, SEQ ID N0:6, SEQ ID N0:7, SEQ ID N0:8, SEQ ID N0:8, SEQ ID NO: 10, SEQ ID NO: 11 and SEQ ID NO: 12.   
     
     
         54 . The composition of  claim 53 , wherein at least one of the microorganisms comprises a member of the genus  Acetobacterium, Bacteriodetes , or  Spirochetes.    
     
     
         55 . The composition of  claim 53 , further comprising production water and a carbonaceous material of interest. 
     
     
         56 . The composition of  claim 55 , wherein the carbonaceous material comprises a coal formation, a peat, a lignite, a bituminous coal, an anthracite coal, a coal, a coal analogue, a coal precursor, a heavy oil, an asphaltene, an organic debris, or a chemical analogue. 
     
     
         57 . The composition of  claim 53 , wherein the composition is contained in situ in a subsurface excavation, an artificial structure, a landfill, or a subsurface carbonaceous reservoir or a subsurface carbonaceous source. 
     
     
         58 . The composition of  claim 53  further comprising a bioreactor, wherein the bioreactor comprises a sand-pack or a coal bioreactor. 
     
     
         59 . The bioreactor of  claim 58 , wherein the bioreactor comprises an environment optimized through a bioreactor-nutrient optimization test. 
     
     
         60 . The composition of  claim 53  further comprising a biogas, wherein the biogas comprises methane. 
     
     
         61 . The composition of  claim 60 , wherein nutrients are provided to enhance further biogas formation. 
     
     
         62 . The composition of  claim 61 , wherein the nutrients comprise a metal salt of compounds found in methylotrophic or bacterial enzymes, a non-inhibitory level of alternate electron acceptors such as iron, manganese, or other nutrients and a trace element identified by correlating nutrient abundance to microbial growth or methane production. 
     
     
         63 . The composition of  claim 58 , wherein an environmental parameter of the bioreactor is modified to enhance biogas formation. 
     
     
         64 . The composition of  claim 63 , wherein the microorganism strains or the environmental parameters in the bioreactor are manipulated for more efficient coal or kerogen biodegrading, or more efficient Cook Inlet methanol or methyl-generating, or for increasing the methanogenesis rates. 
     
     
         65 . The composition of  claim 53 , further comprising a methylotrophic substrate wherein the methylotropic substrate is under neutral to slightly alkaline conditions. 
     
     
         66 . The composition of  claim 53 , further comprising a fluid to slow a build up of fatty acids that would inhibit methanogenesis. 
     
     
         67 . The composition of  claim 65 , wherein a newly generated biogas is monitored from gas isotopes, using a  14 C-, a  13 C-, a  2 H- or a  3 H-enriched methanogenic substrate, wherein the methanogenic substrate comprises bicarbonate, lignin or aromatic monomers. 
     
     
         68 . A method for improving methylotrophic biogas formation in situ in a subsurface carbonaceous formation or an excavated carbonaceous source comprising administering a methanogenic organism to the subsurface carbonaceous formation or the excavated carbonaceous source. 
     
     
         69 . The method of  claim 68 , wherein the methanogenic organism comprises the composition of  claim 53 . 
     
     
         70 . The method of  claim 68 , wherein the methanogenic organism comprises a member of the Archaea family. 
     
     
         71 . The method of  claim 68 , wherein the methanogenic organism comprises an anaerobic organism, an autotroph or a chemoheterotroph. 
     
     
         72 . The method of  claim 68 , wherein the methanogenic organism comprises a member of a genus selected from the group consisting of  Methanolobus, Methanobacterium, Methanothermobacter, Methanogenium, Methanogenium, Methanofollis, Methanoculleus, Methanocorpusculum, Methanococcus, Methanocalculus, Methanobrevibacter  and  Methanosarcina.    
     
     
         73 . The method of  claim 68 , wherein the methanogenic organism comprises the composition of  claim 53 , or an organism selected from the group consisting of:  Methanolobus bornbayensis; Methanolobus taylorii; Methanolobus profundi; Methanolobus zinderi; Methanobacterium bryantii; Methanobacterium formicum; Methanobrevibacter arboriphilicus; Methanobrevibacter gottschalkii; Methanobrevibacter ruminantium; Methanobrevibacter smithii; Methanocalculus chunghsingensis; Methanococcoides burtonii; Methanococcus aeolicus; Methanococcus deltae; Methanococcus jannaschii; Methanococcus maripaludis; Methanococcus vannielii; Methanocorpusculum labreanum; Methanoculleus bourgensis  ( Methanogenium olentangyi  &  Methanogenium bourgense );  Methanoculleus marisnigri; Methanofollis liminatans; Methanogenium cariaci; Methanogenium frigidum; Methanogenium organophilum; Methanogenium wolfei; Methanomicrobium mobile; Methanopyrus kandleri; Methanoregula boonei; Methanosaeta concilii; Methanosaeta thermophila; Methanosarcina acetivorans; Methanosarcina barkeri; Methanosarcina mazei; Methanosphaera stadtmanae; Methanospirillium hungatei; Methanothermobacter defluvii  ( Methanobacterium defluvii );  Methanothermobacter thermautotrophicus  ( Methanobacterium thermoautotrophicum );  Methanothermobacter thermoflexus  ( Methanobacterium thermoflexum );  Methanothermobacter wolfei  ( Methanobacterium wolfei ); and  Methanothrix sochngenii.    
     
     
         74 . The method of  claim 68 , wherein the methanogenic organism has been enriched using an optimal nutrient mix. 
     
     
         75 . The method of  claim 74 , wherein the subsurface carbonaceous formation is modified to have properties of the optimal nutrient mix. 
     
     
         76 . The method  claim 68 , wherein the subsurface carbonaceous formation comprises a coal formation, a peat, a lignite, a bituminous coal, an anthracite coal, a coal, a coal analogue, a coal precursor, a heavy oil, an asphaltene, or an organic debris. 
     
     
         77 . The method of  claim 68 , further comprising applying to the subsurface carbonaceous formation an optimal nutrient mix. 
     
     
         78 . The method of  claim 68 , further comprising modifying the subsurface carbonaceous formation to have properties of an optimal nutrient mix. 
     
     
         79 . The method of  claim 68 , wherein the methanogenic organism decreases an amount of another microorganism's processes that negatively affects the methylotrophic biogas formation. 
     
     
         80 . A method of enhancing methanogenic rates in a subsurface carbonaceous reservoir comprising injecting a methanogenic organism into the subsurface carbonaceous reservoir, wherein the methanogenic organism comprises the composition of  claim 53 , or a member of the Archea family. 
     
     
         81 . The method of  claim 80 , wherein the methanogenic organism is an anaerobe, an autotroph, or a chemotroph. 
     
     
         82 . The method of  claim 80 , wherein the methanogenic organism comprises a member of a genus selected from the group consisting of  Methanolobus, Methanobacterium, Methanothermobacter, Methanogenium, Methanogenium, Methanofollis, Methanoculleus, Methanocorpusculum, Methanococcus, Methanocalculus, Methanobrevibacter  and  Methanosarcina.    
     
     
         83 . The method of  claim 80 , wherein the methanogenic organism comprises an organism selected from the group consisting of:
   Methanolobus bornbayensis; Methanolobus taylorii; Methanolobus profundi; Methanolobus zinderi; Methanobacterium bryantii; Methanobacterium formicum; Methanobrevibacter arboriphilicus; Methanobrevibacter gottschalkii; Methanobrevibacter ruminantium; Methanobrevibacter smithii; Methanocalculus chunghsingensis; Methanococcoides burtonii; Methanococcus aeolicus; Methanococcus deltae; Methanococcus jannaschii; Methanococcus maripaludis; Methanococcus vannielii; Methanocorpusculum labreanum; Methanoculleus bourgensis  ( Methanogenium olentangyi  &  Methanogenium bourgense );  Methanoculleus marisnigri; Methanofollis liminatans; Methanogenium cariaci; Methanogenium frigidum; Methanogenium organophilum; Methanogenium wolfei; Methanomicrobium mobile; Methanopyrus kandleri; Methanoregula boonei; Methanosaeta concilii; Methanosaeta thermophila; Methanosarcina acetivorans; Methanosarcina barkeri; Methanosarcina mazei; Methanosphaera stadtmanae; Methanospirillium hungatei; Methanothermobacter defluvii  ( Methanobacterium defluvii );  Methanothermobacter thermautotrophicus  ( Methanobacterium thermoautotrophicum );  Methanothermobacter thermoflexus  ( Methanobacterium thermoflexum );  Methanothermobacter wolfei  ( Methanobacterium wolfei ); and  Methanothrix sochngenii.      
     
     
         84 . A method of creating a synthetic microbial composition to enhance methanogenic degradation of a carbonaceous substrate comprising:
 a) obtaining a sample from a subsurface carbonaceous substrate;   b) inoculating an enrichment culture with the sample, wherein the enrichment culture comprises as a carbon source a carbonaceous material of interest or a chemical analogue;   c) incubating the enrichment culture until growth of an organism is detected, wherein the organism is a member of a methanogenic community; and   d) introducing the organism into a subsurface formation.   
     
     
         85 . The method of  claim 84 , wherein the sample comprises a water sample or a production water sample. 
     
     
         86 . The method of  claim 84 , wherein the subsurface carbonaceous substrate comprises a coal formation, a peat, a lignite, a bituminous coal, an anthracite coal, a coal, a coal analogue, a coal precursor, a heavy oil, an asphaltene, or an organic debris. 
     
     
         87 . The method of  claim 84 , wherein introducing the organism into the subsurface formation comprises injection at a well head. 
     
     
         88 . The method of  claim 84 , further comprising passaging the enrichment culture into a fresh medium at least once. 
     
     
         89 . The method of  claim 84 , wherein the organism is co-injected into the subsurface formation with an optimized nutrient mix. 
     
     
         90 . A method for processing a heavy oil comprising:
 a) injecting the composition of  claim 53  or a composition comprising a methanogenic organism into a subsurface carbonaceous reservoir comprising a heavy oil, a bitumen, a tar-sand; or   b) contacting a heavy oil, a coal, a bitumen, a tar-sand, with the composition of  claim 53  or a composition comprising a methanogenic organism, wherein the contacting is in situ in a man-made reservoir, a product of manufacture, or an excavated heavy oil, a mined heavy oil, a drilled heavy oil, an isolated heavy oil, a bitumen, a tar-sand,   wherein the subsurface carbonaceous reservoir comprises a coal formation, a peat, a lignite, a bituminous coal, or an anthracite coal.   
     
     
         91 . The method of  claim 90 , wherein the methanogenic organism is an anaerobe, an autotroph, or a chemotroph. 
     
     
         92 . The method of  claim 90 , wherein the methanogenic organism comprises a member of a genus selected from the group consisting of  Methanolobus, Methanobacterium, Methanothermobacter, Methanogenium, Methanogenium, Methanofollis, Methanoculleus, Methanocorpusculum, Methanococcus, Methanocalculus, Methanobrevibacter  and  Methanosarcina.    
     
     
         93 . The method of  claim 90 , wherein the methanogenic organism comprises an organism selected from the group consisting of:
   Methanolobus bornbayensis; Methanolobus taylorii; Methanolobus profundi; Methanolobus zinderi; Methanobacterium bryantii; Methanobacterium formicum; Methanobrevibacter arboriphilicus; Methanobrevibacter gottschalkii; Methanobrevibacter ruminantium; Methanobrevibacter smithii; Methanocalculus chunghsingensis; Methanococcoides burtonii; Methanococcus aeolicus; Methanococcus deltae; Methanococcus jannaschii; Methanococcus maripaludis; Methanococcus vannielii; Methanocorpusculum labreanum; Methanoculleus bourgensis  ( Methanogenium olentangyi  &  Methanogenium bourgense );  Methanoculleus marisnigri; Methanofollis liminatans; Methanogenium cariaci; Methanogenium frigidum; Methanogenium organophilum; Methanogenium wolfei; Methanomicrobium mobile; Methanopyrus kandleri; Methanoregula boonei; Methanosaeta concilii; Methanosaeta thermophila; Methanosarcina acetivorans; Methanosarcina barkeri; Methanosarcina mazei; Methanosphaera stadtmanae; Methanospirillium hungatei; Methanothermobacter defluvii  ( Methanobacterium defluvii );  Methanothermobacter thermautotrophicus  ( Methanobacterium thermoautotrophicum );  Methanothermobacter thermoflexus  ( Methanobacterium thermoflexum );  Methanothermobacter wolfei  ( Methanobacterium wolfei ); and  Methanothrix sochngenii.      
     
     
         94 . A method for optimizing subsurface biogas generation from a subsurface organic matter-rich formation comprising:
 a) collecting a microbe from a deep microbial community and a cultured isolate of a key living microorganism;   b) identifying a specific target microbial association capable of rapidly transforming organic matter to biogas, wherein the identifying comprises using an empirical correlation of a microbial profiling data to a key geochemical parameter using an integrated multi-disciplinary data-set;   c) identifying a negative correlation to subsurface biogas generation comprising a simultaneous unfavorable endemic microbe or condition;   d) identifying a specific active microbe critical to subsurface biogas generation from the specific target microbial association of b);   e) characterizing an indigenous organic carbon-rich substrate and an inorganic mineralogy affecting a water-injectate recipe composition for enhanced subsurface biogas generation and a selection of a substrate rock;   f) optimizing the water-injectate recipe composition using a matrix of laboratory enrichment experiments that promote subsurface biogas generation without activating a deleterious microbial effect at a reservoir temperature of a target field and a subsequent flow-through core experiment using the water-injectate recipe composition on a targeted rock core;   g) modeling of a solution stability to account for an undesired precipitation of minerals due to interactions between an in-situ formation water, the water-injectate recipe composition and an in-situ mineral phase;   h) modeling a fluid transport within a reservoir structure and a delivery mechanism to successfully spread a water-soluble amendment and a cultured microbe to a target formation;   i) modeling of a transport of a newly generated microbial methane within the reservoir structure towards a gas column and a producing well;   j) implementing a biogas generation process in a field; and   k) monitoring biogas generation and collateral microbial or water changes in the field.   
     
     
         95 . A method of transforming a carbonaceous substrate using a synthetic microbial consortia comprising:
 a) providing a plurality of samples, wherein each sample comprises a carbonaceous substrate and a microbial community;   b) determining the composition of the microbial community in each sample;   c) identifying a consortium of microbes whose abundance correlates with a transformation of the carbonaceous substrate;   d) assembling a synthetic consortium by combining individual pure cultures into a strain collection; and   e) combining the synthetic consortium with a carbonaceous substrate to convert the carbonaceous substrate to a higher value and a lower molecular weight product.   
     
     
         96 . The method of  claim 95 , wherein the carbonaceous substrate comprises a coal, a bituminous coal, an anthracite coal, a volcanic ash, a lignite, a lignin, lignin-comprising composition, a coal analogue, a coal precursor, a heavy oil, an asphaltene, or an organic debris. 
     
     
         97 . The method of  claim 95 , wherein the methanogenic organism is an anaerobe, an autotroph, or a chemotroph. 
     
     
         98 . The method of  claim 95 , wherein the methanogenic organism comprises a members of a genus selected from the group consisting of  Methanolobus, Methanobacterium, Methanothermobacter, Methanogenium, Methanogenium, Methanofollis, Methanoculleus, Methanocorpusculum, Methanococcus, Methanocalculus, Methanobrevibacter  and  Methanosarcina.    
     
     
         99 . The method of  claim 95 , wherein the methanogenic organism comprises an organism selected from the group consisting of:
   Methanolobus bornbayensis; Methanolobus taylorii; Methanolobus profundi; Methanolobus zinderi; Methanobacterium bryantii; Methanobacterium formicum; Methanobrevibacter arboriphilicus; Methanobrevibacter gottschalkii; Methanobrevibacter ruminantium; Methanobrevibacter smithii; Methanocalculus chunghsingensis; Methanococcoides burtonii; Methanococcus aeolicus; Methanococcus deltae; Methanococcus jannaschii; Methanococcus maripaludis; Methanococcus vannielii; Methanocorpusculum labreanum; Methanoculleus bourgensis  ( Methanogenium olentangyi  &  Methanogenium bourgense );  Methanoculleus marisnigri; Methanofollis liminatans; Methanogenium cariaci; Methanogenium frigidum; Methanogenium organophilum; Methanogenium wolfei; Methanomicrobium mobile; Methanopyrus kandleri; Methanoregula boonei; Methanosaeta concilii; Methanosaeta thermophila; Methanosarcina acetivorans; Methanosarcina barkeri; Methanosarcina mazei; Methanosphaera stadtmanae; Methanospirillium hungatei; Methanothermobacter defluvii  ( Methanobacterium defluvii );  Methanothermobacter thermautotrophicus  ( Methanobacterium thermoautotrophicum );  Methanothermobacter thermoflexus  ( Methanobacterium thermoflexum );  Methanothermobacter wolfei  ( Methanobacterium wolfei ); and  Methanothrix sochngenii.