Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics

Hannah D Schweitzer,Robin Gerlach,Elliott P Barnhart,Danielle Goudeau,Alfred B Cunningham,Heidi J Smith,Rex R Malmstrom,Luke J Mckay,Matthew W Fields

doi:10.1038/s41522-022-00267-2

Abstract

Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways was observed but with a predominance of aerobic dioxygenases. The putative low-molecular-weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study—subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes—offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.

Highlights

The terrestrial subsurface contains the majority of Earth’s organic carbon (~90%)[1], and much of the carbon can be converted to methane under anaerobic conditions through biogasification
Coal is a heterogeneous and highly complex hydrocarbon consisting of polycyclic aromatic hydrocarbons, alkylated benzenes, and long and short-chain n-alkanes[3], and despite the recalcitrant nature of coal, degradation by microbial consortia has been shown in a variety of coal formations[4,5,6]
DsrA genes have been detected in acetate-amended methane-producing coal seams, and these results suggest organisms with dsrA may play an important role in syntrophic biogasification in the absence of sulfate[41]

Summary

Introduction

The terrestrial subsurface contains the majority of Earth’s organic carbon (~90%)[1], and much of the carbon can be converted to methane under anaerobic conditions through biogasification (i.e., biological decomposition of organic matter into methane and secondary gases). To further investigate the dominant methanogenic populations in the low-sulfate coal seams, the BONCAT-FACS active (BONCAT +) metagenome from the FG-L coal seam was analyzed and resulted in 24 MAGs (Fig. 4, Supplementary Data 4).

Results

Conclusion