Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea.

Hang Yu,Ramsunder Iyer,Silvan Scheller,Robert L Hettich,Patricia L Tavormina,Karuna Chourey,Connor T Skennerton,Biswarup Mukhopadhyay,Shawn E Mcglynn,Victoria J Orphan,Dwi Susanti

doi:10.3389/fmicb.2018.02917

Abstract

Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F420-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.

Highlights

The anaerobic oxidation of methane (AOM) is an important biogeochemical process in the global carbon cycle, and is the primary sink for methane in anoxic ocean sediments (Reeburgh, 2007)
Methanoperedens recovered from freshwater environments showed a more expanded genetic capacity to reduce sulfate compared to the marine ANME lineages (ANME-1b, ANME-2a, ANME-2b, and ANME-2c) that perform AOM coupled sulfate reduction with deltaproteobacterial partners (Figure 1)
This study focuses on the genetic potential of sulfate reduction to sulfide in the marine ANME lineages

Summary

Introduction

The anaerobic oxidation of methane (AOM) is an important biogeochemical process in the global carbon cycle, and is the primary sink for methane in anoxic ocean sediments (Reeburgh, 2007). A new ANME-1b genome (CONS3730B06UFb1), estimated to be 90% complete and 2.4% contamination by CheckM software package v1.0.6 using the taxonomy workflow and the Euryarchaeota set of markers (Parks et al, 2015), was obtained from methane seep sediment at Hydrate Ridge, United States (ID 3730; Supplementary Table 3) using activity-based cell sorting method in a previous study (Hatzenpichler et al, 2016).

Results

Conclusion