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Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions

Fincker, Maeva and Huber, Julie A. and Orphan, Victoria J. and Rappé, Michael S. and Teske, Andreas and Spormann, Alfred M. (2020) Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions. Environmental Microbiology, 22 (8). pp. 3188-3204. ISSN 1462-2912. https://resolver.caltech.edu/CaltechAUTHORS:20200506-150820782

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Abstract

Uncultured members of the Chloroflexi phylum are highly enriched in numerous subseafloor environments. Their metabolic potential was evaluated by reconstructing 31 Chloroflexi genomes from six different subseafloor habitats. The near ubiquitous presence of enzymes of the Wood–Ljungdahl pathway, electron bifurcation, and ferredoxin‐dependent transport‐coupled phosphorylation indicated anaerobic acetogenesis was central to their catabolism. Most of the genomes simultaneously contained multiple degradation pathways for complex carbohydrates, detrital protein, aromatic compounds, and hydrogen, indicating the coupling of oxidation of chemically diverse organic substrates to ubiquitous CO₂ reduction. Such pathway combinations may confer a fitness advantage in subseafloor environments by enabling these Chloroflexi to act as primary fermenters and acetogens in one microorganism without the need for syntrophic H₂ consumption. While evidence for catabolic oxygen respiration was limited to two phylogenetic clusters, the presence of genes encoding putative reductive dehalogenases throughout the phylum expanded the phylogenetic boundary for potential organohalide respiration past the Dehalococcoidia class.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1111/1462-2920.15061DOIArticle
ORCID:
AuthorORCID
Huber, Julie A.0000-0002-4790-7633
Orphan, Victoria J.0000-0002-5374-6178
Rappé, Michael S.0000-0002-9829-251X
Teske, Andreas0000-0001-8702-3800
Spormann, Alfred M.0000-0001-5103-9704
Additional Information:© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd. Issue Online: 17 August 2020; Version of Record online: 04 June 2020; Accepted manuscript online: 05 May 2020; Manuscript accepted: 03 May 2020; Manuscript revised: 29 April 2020; Manuscript received: 23 February 2020. The authors thank Benjamin J. Tully for his help accessing the C‐DEBI server on which part of the analysis was run. The authors thank Connor Skennerton for his work on the Santa Monica Mounds samples as well as the members of the Spormann Group for their helpful comments. Data from the Mid‐Cayman Rise were based upon work supported by the Schmidt Ocean Institute during cruise FX008‐2013 aboard R/V Falkor. The authors thank Julie Reveillaud and Rika Anderson for providing sequence data. Data for the White Oak River were based upon work supported by the US Department of Energy and a European Research Council DARCLIFE grant; the authors thank Cassandre Lazar and Brett Baker for their work on the samples. Data for the Guaymas Basin were based upon work supported by NSF Biological Oceanography grants; the authors thank Nina Dombrowski, Kiley Seitz for their work on the samples. Data from the Juan de Fuca Ridge flank were based on work supported by the National Science Foundation grants MCB‐0604014 and OCE‐1260723 during cruise AT18‐07 aboard the R/V Atlantis; the authors thank Sean Jungbluth for initial sequence analysis. This work was funded by the US National Science Foundation through the Center for Deep Dark Energy Biosphere Investigations. This is C‐DEBI contribution number 531.
Funders:
Funding AgencyGrant Number
Department of Energy (DOE)UNSPECIFIED
European Research Council (ERC)DARCLIFE
NSFMCB-0604014
NSFOCE-1260723
Other Numbering System:
Other Numbering System NameOther Numbering System ID
C‐DEBI531
Issue or Number:8
Record Number:CaltechAUTHORS:20200506-150820782
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200506-150820782
Official Citation:Fincker, M., Huber, J.A., Orphan, V.J., Rappé, M.S., Teske, A. and Spormann, A.M. (2020), Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions. Environ Microbiol, 22: 3188-3204. https://doi.org/10.1111/1462-2920.15061
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:103049
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:06 May 2020 22:21
Last Modified:11 Dec 2020 23:02

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