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Predominance of Methanomicrobiales and diverse hydrocarbon–degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome–resolved metabolisms

Journal Article · · Environmental Microbiology
 [1];  [2];  [1]
  1. National Energy Technology Lab. (NETL), Pittsburgh, PA (United States)
  2. National Energy Technology Lab. (NETL), Pittsburgh, PA (United States); Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); GFZ German Research Centre for Geosciences, Potsdam, Brandenburg (Germany)
Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin. Our analyses resulted in the recovery of over 40 metagenome-assembled genomes (MAGs) from eight coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. Further, the data presented herein provides novel insights into Appalachian Basin coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.
Research Organization:
National Energy Technology Laboratory (NETL), Pittsburgh, PA, Morgantown, WV, and Albany, OR (United States)
Sponsoring Organization:
USDOE; USDOE Office of Fossil Energy and Carbon Management (FECM)
Grant/Contract Number:
89243318CFE000003
OSTI ID:
1958774
Alternate ID(s):
OSTI ID: 1897297
Journal Information:
Environmental Microbiology, Journal Name: Environmental Microbiology Journal Issue: 12 Vol. 24; ISSN 1462-2912
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English

References (72)

Environmental Constraints that Limit Methanogenesis book January 2018
Biochemistry of the Anaerobic Degradation of Non-Methane Alkanes book January 2010
Anaerobic Degradation of Aromatic Hydrocarbons book January 2010
Diversity and Common Principles in Enzymatic Activation of Hydrocarbons book January 2010
Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers journal April 2012
Several ways one goal—methanogenesis from unconventional substrates journal June 2020
Biodegradation and bioremediation of hydrocarbons in extreme environments journal September 2001
Basic local alignment search tool journal October 1990
Coalbed methane in the Ruhr Basin, Germany: a renewable energy resource? journal November 2004
Microbial diversity of western Canadian subsurface coal beds and methanogenic coal enrichment cultures journal May 2010
The effect of coal oxidation on methane production and microbial community structure in Powder River Basin coal journal August 2013
Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals journal January 2015
Enhanced microbial coalbed methane generation: A review of research, commercial activity, and remaining challenges journal July 2015
Characterizing microbial communities dedicated for conversion of coal to methane in situ and ex situ journal July 2015
Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed journal May 2016
Changes in microbial communities and associated water and gas geochemistry across a sulfate gradient in coal beds: Powder River Basin, USA journal January 2019
Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams journal February 2019
Organic intermediates in the anaerobic biodegradation of coal to methane under laboratory conditions journal September 2010
Microbial methanogenesis in subsurface oil and coal journal November 2013
Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common journal September 2013
Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers journal August 2014
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea journal August 2017
Fast and sensitive taxonomic classification for metagenomics with Kaiju journal April 2016
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity journal February 2016
Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales journal September 2016
Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation journal October 2018
Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane journal October 2021
Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics journal February 2022
Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams journal November 2019
Pathways for degradation of lignin in bacteria and fungi journal January 2011
Global patterns in bacterial diversity journal June 2007
Library preparation methodology can influence genomic and functional predictions in human microbiome research journal October 2015
QUAST: quality assessment tool for genome assemblies journal February 2013
Prokka: rapid prokaryotic genome annotation journal March 2014
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database journal November 2019
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 journal October 2013
DRAM for distilling microbial metabolism to automate the curation of microbiome function journal August 2020
Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site. journal September 2000
The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill b journal November 2002
Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge journal August 2009
Methanocalculus taiwanensis sp. nov., isolated from an estuarine environment journal September 2002
Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan journal January 2004
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities journal January 2007
Methanosalsum natronophilum sp. nov., and Methanocalculus alkaliphilus sp. nov., haloalkaliphilic methanogens from hypersaline soda lakes journal October 2015
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal May 2015
metaSPAdes: a new versatile metagenomic assembler journal March 2017
Evolution of proline biosynthesis: enzymology, bioinformatics, genetics, and transcriptional regulation: Proline biosynthesis journal November 2014
Ethylene-induced stomatal closure in Arabidopsis occurs via AtrbohF-mediated hydrogen peroxide synthesis journal September 2006
Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil: Epsilonproteobacteria in a biodegraded oil sands reservoir journal August 2011
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics journal October 2015
Methane production from coal by a single methanogen journal October 2016
Stimulation of Methane Generation from Nonproductive Coal by Addition of Nutrients or a Microbial Consortium journal September 2010
Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities journal September 2015
Methane-Producing Microbial Community in a Coal Bed of the Illinois Basin journal February 2008
Salinity Constraints on Subsurface Archaeal Diversity and Methanogenesis in Sedimentary Rock Rich in Organic Matter journal April 2007
Complete Genome Sequence of Methanoregula formicica SMSP T , a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge Blanket Reactor journal October 2014
Evaluating the Information Content of Shallow Shotgun Metagenomics journal October 2018
phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes journal October 2020
Methanocalculus natronophilus sp. nov., a new alkaliphilic hydrogenotrophic methanogenic archaeon from a soda lake, and proposal of the new family Methanocalculaceae journal November 2013
Biogeochemistry of Microbial Coal-Bed Methane journal May 2011
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
The RAST Server: Rapid Annotations using Subsystems Technology journal January 2008
Microbial life at high salt concentrations: phylogenetic and metabolic diversity journal January 2008
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data journal May 2011
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data journal January 2015
Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea journal March 2008
Geochemical signature of formation waters associated with coalbed methane journal April 2003
Evolutionary history influences the salinity preference of bacterial taxa in wetland soils journal October 2015
Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA journal November 2015
Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well journal June 2016
Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient journal September 2016
PhyloPythiaS+ : a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes journal January 2016

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