Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations
Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional eco...
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Uppsala universitet, Limnologi
2021
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ftuppsalauniv:oai:DiVA.org:uu-458706 2024-02-11T10:09:00+01:00 Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations Garcia, Sarahi L. Mehrshad, Maliheh Buck, Moritz Tsuji, Jackson M. Neufeld, Josh D. McMahon, Katherine D. Bertilsson, Stefan Greening, Chris Peura, Sari 2021 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-458706 https://doi.org/10.1128/mSystems.01196-20 eng eng Uppsala universitet, Limnologi Stockholm Univ, Dept Ecol Environm & Plant Sci, Sci Life Lab, Stockholm, Sweden Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden Univ Waterloo, Dept Biol, Waterloo, ON, Canada Univ Waterloo, Dept Biol, Waterloo, ON, Canada. Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI USA.;Univ Wisconsin, Dept Bacteriol, Madison, WI USA. Monash Univ, Biomed Discovery Inst, Dept Microbiol, Clayton, Vic, Australia. Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Sci Life Lab, Uppsala, Sweden. American Society for Microbiology mSystems, 2021, 6:3, orcid:0000-0002-8622-0308 orcid:0000-0002-1108-6888 orcid:0000-0001-6632-5324 orcid:0000-0001-7244-4709 orcid:0000-0002-7038-026X orcid:0000-0002-4265-1835 orcid:0000-0001-7616-0594 orcid:0000-0003-3892-8157 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-458706 doi:10.1128/mSystems.01196-20 PMID 33975970 ISI:000709811800011 info:eu-repo/semantics/openAccess Chlorobia freshwater photosynthetic bacteria planktonic Microbiology Mikrobiologi Article in journal info:eu-repo/semantics/article text 2021 ftuppsalauniv https://doi.org/10.1128/mSystems.01196-20 2024-01-17T23:32:00Z Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of ... Article in Journal/Newspaper Subarctic Uppsala University: Publications (DiVA) mSystems 6 3 |
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Open Polar |
collection |
Uppsala University: Publications (DiVA) |
op_collection_id |
ftuppsalauniv |
language |
English |
topic |
Chlorobia freshwater photosynthetic bacteria planktonic Microbiology Mikrobiologi |
spellingShingle |
Chlorobia freshwater photosynthetic bacteria planktonic Microbiology Mikrobiologi Garcia, Sarahi L. Mehrshad, Maliheh Buck, Moritz Tsuji, Jackson M. Neufeld, Josh D. McMahon, Katherine D. Bertilsson, Stefan Greening, Chris Peura, Sari Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations |
topic_facet |
Chlorobia freshwater photosynthetic bacteria planktonic Microbiology Mikrobiologi |
description |
Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of ... |
format |
Article in Journal/Newspaper |
author |
Garcia, Sarahi L. Mehrshad, Maliheh Buck, Moritz Tsuji, Jackson M. Neufeld, Josh D. McMahon, Katherine D. Bertilsson, Stefan Greening, Chris Peura, Sari |
author_facet |
Garcia, Sarahi L. Mehrshad, Maliheh Buck, Moritz Tsuji, Jackson M. Neufeld, Josh D. McMahon, Katherine D. Bertilsson, Stefan Greening, Chris Peura, Sari |
author_sort |
Garcia, Sarahi L. |
title |
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations |
title_short |
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations |
title_full |
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations |
title_fullStr |
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations |
title_full_unstemmed |
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations |
title_sort |
freshwater chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations |
publisher |
Uppsala universitet, Limnologi |
publishDate |
2021 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-458706 https://doi.org/10.1128/mSystems.01196-20 |
genre |
Subarctic |
genre_facet |
Subarctic |
op_relation |
mSystems, 2021, 6:3, orcid:0000-0002-8622-0308 orcid:0000-0002-1108-6888 orcid:0000-0001-6632-5324 orcid:0000-0001-7244-4709 orcid:0000-0002-7038-026X orcid:0000-0002-4265-1835 orcid:0000-0001-7616-0594 orcid:0000-0003-3892-8157 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-458706 doi:10.1128/mSystems.01196-20 PMID 33975970 ISI:000709811800011 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1128/mSystems.01196-20 |
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mSystems |
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6 |
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3 |
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1790608694146236416 |