Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published March 17, 2023 | Supplemental Material + Submitted
Report Open

Physiological adaptation of sulfate reducing bacteria in syntrophic partnership with anaerobic methanotrophic archaea

Abstract

Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we explore the metabolic adaptation of four syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a and Seep-SRB1g) from a phylogenomics perspective, tracing the evolution of conserved proteins in the syntrophic SRB clades, and comparing the genomes of syntrophic SRB to their nearest evolutionary neighbors in the phylum Desulfobacterota. We note several examples of gain, loss or biochemical adaptation of proteins within pathways involved in extracellular electron transfer, electron transport chain, nutrient sharing, biofilm formation and cell adhesion. We demonstrate that the metabolic adaptations in each of these syntrophic clades are unique, suggesting that they have independently evolved, converging to a syntrophic partnership with ANME. Within the clades we also investigated the specialization of different syntrophic SRB species to partnerships with different ANME clades, using metagenomic sequences obtained from ANME and SRB partners in individual consortia after fluorescent-sorting of cell aggregates from anaerobic sediments. In one instance of metabolic adaptation to different partnerships, we show that Seep-SRB1a partners of ANME-2c appear to lack nutritional auxotrophies, while the related Seep-SRB1a partners of a different methanotrophic archaeal lineage, ANME-2a, are missing the cobalamin synthesis pathway, suggesting that the Seep-SRB1a partners of ANME-2a may have a nutritional dependence on its partner. Together, our paired genomic analysis of AOM consortia highlights the specific adaptation and diversification of syntrophic SRB clades linked to their associated ANME lineages.

Additional Information

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. We thank the DOE and the Moore Foundation for funding this research (Principle Investigator: Dr. Victoria J. Orphan). We acknowledge the Dalio Foundation and Woods Hole Oceanographic Institute for supporting the NA091 research cruise to South Pescadero Basin on E/V Nautilus operated by the Ocean Exploration Trust in October-November 2017. The work (Award doi: 10.46936/fics.proj.2017.49956/60006219) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. We would also like to thank Magdalena Mayr for her thoughtful comments on this manuscript and Fernanda Jimenez-Otero for sharing her thoughts and expertise in the field of extracellular electron transfer. We are also grateful to Alon Philosof, Aditi Narayan, Kriti Sharma and James Hemp for many productive discussions on broad scientific questions in microbial ecology and evolution, metabolism and scientific writing that lent itself to the framing of this manuscript. The authors have declared no competing interest.

Attached Files

Submitted - 2022.11.23.517749v1.full.pdf

Supplemental Material - media-1.pdf

Supplemental Material - media-2.zip

Supplemental Material - media-3.xlsx

Supplemental Material - media-4.xlsx

Files

media-2.zip
Files (30.9 MB)
Name Size Download all
md5:73f341c7aeaf63ad8008890d1be8fa7c
624.5 kB Preview Download
md5:087dd8d17722fe85b4ff760c08bb2bb0
9.6 MB Preview Download
md5:d003192f419f938e28d4ab7ccc24f377
8.5 MB Download
md5:e978a56b9315fc0171024d52d1142503
3.0 MB Preview Download
md5:fc470a4ffa5d1ffdb64bc49daad66f42
9.2 MB Download

Additional details

Created:
August 20, 2023
Modified:
December 13, 2023