Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep

Xiyang Dong,Martin Fowler,Oyeboade Adebayo,Ian A Lewis,Anirban Chakraborty,Carmen Li,Chris Greening,Ryan A Groves,Stuart Matthews,Natasha M Morrison,Adam Macdonald,Scott H Wang,Jayne E Rattray,Casey R J Hubert,Daisuke Mayumi,D Calvin Campbell,Jamie Webb

doi:10.1038/s41467-020-19648-2

Abstract

At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.

Highlights

IntroductionGaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface
At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface
We provide strong evidence supporting that (i) hydrocarbons are thermogenic and experience biodegradation upon migration up into surface sediment layers; (ii) these processes are actively performed in the cold deep sea by bacteria and archaea through diverse biochemical mechanisms; and (iii) the microbiome catalysing anaerobic hydrocarbon degradation at different depths is dependent on metabolic adaptations for different redox regimes

Summary

Introduction

Gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Long-chain alkanes can be metabolized in syntrophic partnerships, e.g., by bacteria in the genera Despite this progress, it remains uncertain whether anaerobic hydrocarbon-degrading isolates or consortia studied in enrichment cultures play these roles in situ in deep sea sediments. Most genome-resolved metagenomic studies have focused on hydrothermally influenced sediments that are rich in hydrocarbons, e.g., Guaymas Basin in the Gulf of California[26,27,28] These studies have provided insights into the phylogenetic diversity and functional capabilities of potential hydrocarbon-degrading microorganisms, including the discovery of Ca. Helarchaeota from the Asgard superphylum with the potential for hydrocarbon oxidation using methyl-CoM reductase-like enzymes[28]. Based on satellite and seismic reflection data, this area shows strong evidence for seepage of thermogenic hydrocarbons with occurrences of high‐pressure diapirs, polygonal faults, pockmarks, and gas chimneys[31]

Methods

Results

Conclusion