Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface

Emma Bell,Rizlan Bernier-Latmani,Chen Qian,Weili Xiong,Robert L Hettich,Johannes Alneberg,Tiina Lamminmäki,Manon Frutschi

doi:10.1038/s41396-022-01207-w

Abstract

Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic environments remain unclear. In the deep crystalline bedrock of the Fennoscandian Shield at Olkiluoto, Finland, opposing gradients of abiotic methane and ancient seawater-derived sulfate create a terrestrial sulfate-methane transition zone (SMTZ). We used chemical and isotopic data coupled to genome-resolved metaproteogenomics to demonstrate active life and, for the first time, provide direct evidence of active anaerobic oxidation of methane (AOM) in a deep terrestrial bedrock. Proteins from Methanoperedens (formerly ANME-2d) are readily identifiable despite the low abundance (≤1%) of this genus and confirm the occurrence of AOM. This finding is supported by 13C-depleted dissolved inorganic carbon. Proteins from Desulfocapsaceae and Desulfurivibrionaceae, in addition to 34S-enriched sulfate, suggest that these organisms use inorganic sulfur compounds as both electron donor and acceptor. Zerovalent sulfur in the groundwater may derive from abiotic rock interactions, or from a non-obligate syntrophy with Methanoperedens, potentially linking methane and sulfur cycles in Olkiluoto groundwater. Finally, putative episymbionts from the candidate phyla radiation (CPR) and DPANN archaea represented a significant diversity in the groundwater (26/84 genomes) with roles in sulfur and carbon cycling. Our results highlight AOM and sulfur disproportionation as active metabolisms and show that methane and sulfur fuel microbial activity in the deep terrestrial subsurface.

Highlights

Microbial cells in the subsurface comprise a significant proportion of the global prokaryotic biomass [1]
Stable isotopes and metaproteomics show that active anaerobic oxidation of methane (AOM) occurs Cell counts in this environment and that sulfate-reducing bacteria (SRB) and Cells in the groundwater were fixed in paraformaldehyde at a final sulfur-disproportionating bacteria (SDB) are active
Bins belonging to Patescibacteria (50/238) were checked for completeness and contamination with the Candidate Phyla Radiation (CPR; Patescibacteria) custom 43 gene marker set in CheckM [57] and clustered into groups (ANI 99%) with FastANI [58]

Summary

INTRODUCTION

Microbial cells in the subsurface comprise a significant proportion of the global prokaryotic biomass [1]. The engineering of stable bedrock formations for industrial purposes (spent nuclear fuel disposal, underground storage of gases, geothermal energy production, oil and gas recovery) alters the subsurface ecosystem causing biogeochemical changes that impact microbial community activity and function [12, 13]. Has proposed, but not demonstrated, widespread AOM in crystalline bedrock environments This hypothesis was based on the detection of ANME from the archaeal family Methanoperedenaceae (formerly ANME-2d) in groundwater from granitic bedrock in both Finland [21, 25] and Japan [26,27,28]. Enrichment experiments using deep groundwater suggest Methanoperedenaceae conduct sulfate-dependent AOM in the terrestrial subsurface [27, 36]. Stable isotopes and metaproteomics show that active AOM occurs Cell counts in this environment and that sulfate-reducing bacteria (SRB) and Cells in the groundwater were fixed in paraformaldehyde at a final sulfur-disproportionating bacteria (SDB) are active.

MATERIALS AND METHODS

Bell et al 3

RESULTS

DISCUSSION