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Genomic Evidence for Phototrophic Oxidation of Small Alkanes in a Member of the Chloroflexi Phylum

Ward, Lewis M. and Shih, Patrick M. and Hemp, James and Kakegawa, Takeshi and Fischer, Woodward W. and McGlynn, Shawn E. (2019) Genomic Evidence for Phototrophic Oxidation of Small Alkanes in a Member of the Chloroflexi Phylum. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20190923-100935684

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Abstract

Recent genomic and microcosm based studies revealed a wide diversity of previously unknown microbial processes involved in alkane and methane metabolism. Here we described a new bacterial genome from a member of the Chloroflexi phylum—termed here Candidatus Chlorolinea photoalkanotrophicum—with cooccurring pathways for phototrophy and the oxidation of methane and/or other small alkanes. Recovered as a metagenome-assembled genome from microbial mats in an iron-rich hot spring in Japan, Ca. ‘C. photoalkanotrophicum’ forms a new lineage within the Chloroflexi phylum and expands the known metabolic diversity of this already diverse clade. Ca. ‘C. photoalkanotrophicum’ appears to be metabolically versatile, capable of phototrophy (via a Type 2 reaction center), aerobic respiration, nitrite reduction, oxidation of carbon monoxide, oxidation and incorporation of carbon from methane and/or other short-chain alkanes such as propane, and potentially carbon fixation via a novel pathway composed of hybridized components of the serine cycle and the 3-hydroxypropionate bi-cycle. The biochemical network of this organism is constructed from components from multiple organisms and pathways, further demonstrating the modular nature of metabolic machinery and the ecological and evolutionary importance of horizontal gene transfer in the establishment of novel pathways.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/531582DOIDiscussion Paper
ORCID:
AuthorORCID
Ward, Lewis M.0000-0002-9290-2567
Shih, Patrick M.0000-0002-2119-3345
Hemp, James0000-0001-7193-0553
Kakegawa, Takeshi0000-0003-1627-1385
Fischer, Woodward W.0000-0002-8836-3054
McGlynn, Shawn E.0000-0002-8199-7011
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. bioRxiv preprint first posted online Jan. 26, 2019. LMW acknowledges support from NASA NESSF (#NNX16AP39H), NSF (#OISE 1639454), NSF GROW (#DGE 1144469), the Earth-Life Science Institute Origins Network (EON), and the Agouron Institute. P.M.S. was supported by The Branco Weiss Fellowship - Society in Science from ETH Zurich. WWF acknowledges the generous support of the Caltech Center for Environment Microbe Interactions, NASA Exobiology (#NNX16AJ57G), and the Simons Foundation Collaboration on the Origins of Life (SCOL). SEM is supported by NSF Award 1724300, JSPS KAKENHI Grant Number 18H01325, and the Astrobiology Center Program of the National Institutes of Natural Sciences (grant no. AB311013).
Group:Caltech Center for Environmental Microbial Interactions (CEMI)
Funders:
Funding AgencyGrant Number
NASA Earth and Space Science FellowshipNNX16AP39H
NSFOISE-1639454
NSF Graduate Research FellowshipDGE-1144469
Earth-Life Science Institute Origins Network (EON)UNSPECIFIED
Agouron InstituteUNSPECIFIED
ETH ZurichUNSPECIFIED
Caltech Center for Environmental Microbial Interactions (CEMI)UNSPECIFIED
NASANNX16AJ57G
Simons FoundationUNSPECIFIED
NSFEF-1724300
Japan Society for the Promotion of Science (JSPS)18H01325
National Institutes of Natural Sciences of JapanAB311013
Subject Keywords:lateral gene transfer, metagenomics, photosynthesis, greenhouse gas, propanotrophy, photoalkanotrophy
Record Number:CaltechAUTHORS:20190923-100935684
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190923-100935684
Official Citation:Genomic Evidence for Phototrophic Oxidation of Small Alkanes in a Member of the Chloroflexi Phylum. Lewis M. Ward, Patrick M. Shih, James Hemp, Takeshi Kakegawa, Woodward W. Fischer, Shawn E. McGlynn. bioRxiv 531582; doi: https://doi.org/10.1101/531582
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:98793
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:23 Sep 2019 17:32
Last Modified:03 Oct 2019 21:44

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