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 method of making a synthetic consortium comprising:
 (a) obtaining two or more samples from at least two different sources, wherein each sample comprises a plurality of microbes;   (b) determining the microbial composition and abundance of the samples, wherein the abundance of each observed microbe is recorded for each sample;   (c) performing a correlation analysis of abundances of one microbe in the two or more samples to abundances of another microbe in the two or more samples;   (d) repeating step (iii) for at least one additional pair of microbes in said samples;   (e) identifying a group of two or more microbes, whose abundance correlation to one another is greater than to other microbes in the samples; and   (f) assembling a synthetic microbial consortium by physically combining at least two microbial cultures of the identified microbes.   
     
     
         54 . The method of  claim 53 , wherein at least one source comprises a carbonaceous source formation. 
     
     
         55 . The method of  claim 53 , further comprising testing whether the synthetic microbial consortium is able to perform a specific function or process of interest in a culture or in a sample. 
     
     
         56 . The method of  claim 53 , wherein at least one of the two different sources comprises a production water, a core, a cutting, an outcrop sample, or an enrichment culture. 
     
     
         57 . The method of  claim 54 , wherein the carbonaceous source or formation further comprise a coal formation, a peat, a lignite, a bituminous coal, an anthracite coal, a coal analogue or precursor, a heavy oil, asphaltenes, or an organic debris. 
     
     
         58 . The method of  claim 53 , wherein the microbial abundance for each microbe is log transformed. 
     
     
         59 . The method of  claim 53 , wherein the identifying a group of two or more microbes comprises a hierarchical cluster analysis of a microbial distribution across the samples. 
     
     
         60 . The method of  claim 53 , wherein the identifying a group of two or more microbes of the synthetic microbial consortium comprises at least one of the group consisting of:
 (a) a culture independent molecular survey,   (b) deducing from the abundance data in a culture independent survey, or   (c) using distance metrics.   
     
     
         61 . The method of  claim 60 , wherein the culture independent molecular survey comprises counting a number of copies of each distinct 16S rRNA gene sequence detected from each sample. 
     
     
         62 . The method of  claim 53 , wherein the correlation analysis is selected from at least one of the group consisting of:
 (a) Euclidean distance,   (b) Chi square,   (c) City block, or   (d) an ordination method.   
     
     
         63 . The method of  claim 62 , wherein the ordination method is selected from at least one of the group consisting of:
 (a) Principal Components Analysis (PCA),   (b) Bray-Curtis, or   (c) Nonmetric multidimensional scaling.   
     
     
         64 . The method of  claim 53 , wherein determining the microbial composition and abundance further comprises sequencing of all or a portion of an rRNA gene. 
     
     
         65 . The method of  claim 53 , wherein the abundance comprises a nucleic acid, DNA or RNA recorded for each sample. 
     
     
         66 . The method of  claim 53 , wherein the correlation analysis comprises a Pearson correlation. 
     
     
         67 . The method of  claim 53 , further comprising correlating the synthetic consortium to a biogeochemical process, or a metabolic intermediate or product. 
     
     
         68 . The method of  claim 53 , wherein the assembling the synthetic microbial consortium further comprises cultivating the microbes using different nutrient combinations to obtain single colonies. 
     
     
         69 . The method of  claim 53 , wherein assembling the synthetic microbial consortium further comprises cultivating the microbes using anaerobic methods conditions. 
     
     
         70 . The method of  claim 59 , wherein he hierarchical cluster analysis is performed using a hierarchical clustering algorithm, or a Ward's method. 
     
     
         71 . The method of  claim 55 , further comprising testing whether the assembled synthetic consortium is able to convert a carbonaceous substrate into a lower molecular weight product, wherein the method makes a synthetic consortium capable of converting a carbonaceous substrate into a lower molecular weight product by identifying a synthetic consortium or a group of synthetic consortia that can convert a carbonaceous substrate into a lower molecular weight product. 
     
     
         72 . The method of  claim 68 , wherein at least one of the medium formulations comprises a carbonaceous substrate. 
     
     
         73 . The method of  claim 53  wherein the microbial culture is selected from at least one of the group consisting of:
 (a) a pure culture, 
 (b) a nearly pure culture, 
 (c) an enrichment culture, or 
 (d) a type strain. 
 
     
     
         74 . A method of identifying and making a synthetic microbial consortium comprising:
 (a) obtaining a plurality of samples comprising microbes;   (b) determining the abundances of a plurality of microbes in the plurality of samples, wherein the abundance of each microbe is recorded for each sample;   (c) compiling a numerical abundance of an environmental parameter of said plurality of samples;   (d) performing a correlation analysis of the abundance of one microbe in said plurality of samples to the abundance of the environmental parameter in said plurality of samples wherein the correlation analysis provides a comparison between the abundance of the microbe to the abundance of the environmental parameter;   (e) repeating step (d) for at least one additional microbe in said plurality samples;   (f) identifying at least two microbes whose correlation to the environmental parameter is greater than other microbes in said plurality of samples   (g) obtaining microbial cultures of at least two identified microbes; and   (h) combining the microbial cultures of the identified microbes identified in step   (f), thereby making a synthetic consortium.   
     
     
         75 . The method of  claim 74 , wherein the environmental parameter comprises a biochemical process, or a metabolic intermediate or a product. 
     
     
         76 . The method of  claim 74 , further comprising performing a hierarchical cluster analysis of the correlations. 
     
     
         77 . The method of  claim 53 , further comprising constructing a distance matrix. 
     
     
         78 . The method of  claim 74  wherein the microbial culture is selected from at least one of the group consisting of:
 (a) a pure culture, 
 (b) a nearly pure culture, 
 (c) an enrichment culture, or 
 (d) a type strain. 
 
     
     
         79 . The method of  claim 74 , wherein at least one sample comprises a carbonaceous source or formation. 
     
     
         80 . The method of  claim 74 , wherein at least one sample comprises a production water, a core, a cutting, an outcrop sample, or an enrichment culture. 
     
     
         81 . The method of  claim 79 , wherein the carbonaceous source or formation further comprises a coal formation, a peat, a lignite, a bituminous coal, an anthracite coal, a coal analogue or precursor, a heavy oil, asphaltenes, or an organic debris. 
     
     
         82 . The method of  claim 74 , wherein the abundance for each microbe is log transformed. 
     
     
         83 . The method of  claim 74 , wherein the identifying a group of two or more microbes of the synthetic consortium comprises at least one of the group consisting of:
 (a) a culture independent molecular survey,   (b) deducing from the abundance data in a culture independent survey, or   (c) using distance metrics.   
     
     
         84 . The method of  claim 83 , wherein the culture independent molecular survey comprises counting a number of copies of distinct 16S rRNA gene sequence detected from each sample. 
     
     
         85 . The method of  claim 74 , wherein the correlation analysis is selected from at least one of the group consisting of:
 (a) Euclidean distance,   (b) Chi square,   (c) City block, or   (d) an ordination method.   
     
     
         86 . The method of  claim 85 , wherein the ordination method is selected from at least one of the group consisting of:
 (a) Principal Components Analysis,   (b) Bray-Curtis, or   (c) Nonmetric multidimensional scaling.   
     
     
         87 . The method of  claim 74 , wherein determining the abundances of a plurality of microbes further comprises sequencing of at least a portion of an rRNA gene. 
     
     
         88 . The method of  claim 87 , wherein the abundance comprises a nucleic acid, DNA or RNA recorded for each sample. 
     
     
         89 . The method of  claim 74 , wherein the correlation analysis comprises a Pearson correlation. 
     
     
         90 . The method of  claim 74 , wherein the obtaining microbial cultures of at least two identified microbes further comprises cultivating the microbes using different nutrient combinations to obtain single colonies. 
     
     
         91 . The method of  claim 74 , wherein the obtaining microbial cultures of at least two identified microbes further comprises cultivating the microbes using anaerobic methods. 
     
     
         92 . The method of  claim 76 , wherein the hierarchical cluster analysis is performed using a hierarchical clustering algorithm, or a Ward's method. 
     
     
         93 . The method of  claim 68 , wherein at least one of the nutrient combinations comprises a carbonaceous substrate.