Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil.
Identifieur interne : 000140 ( Main/Exploration ); précédent : 000139; suivant : 000141Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil.
Auteurs : Andriy Sheremet [Canada] ; Gareth M. Jones [Canada] ; Jessica Jarett [États-Unis] ; Robert M. Bowers [États-Unis] ; Isaac Bedard [Canada] ; Cassandra Culham [Canada] ; Emiley A. Eloe-Fadrosh [États-Unis] ; Natalia Ivanova [États-Unis] ; Rex R. Malmstrom [États-Unis] ; Stephen E. Grasby [Canada] ; Tanja Woyke [États-Unis] ; Peter F. Dunfield [Canada]Source :
- Environmental microbiology [ 1462-2920 ] ; 2020.
Abstract
Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 108 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.
DOI: 10.1111/1462-2920.15054
PubMed: 32372527
Affiliations:
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Jones</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Jarett, Jessica" sort="Jarett, Jessica" uniqKey="Jarett J" first="Jessica" last="Jarett">Jessica Jarett</name><affiliation wicri:level="1"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation></author><author><name sortKey="Bowers, Robert M" sort="Bowers, Robert M" uniqKey="Bowers R" first="Robert M" last="Bowers">Robert M. Bowers</name><affiliation wicri:level="1"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation></author><author><name sortKey="Bedard, Isaac" sort="Bedard, Isaac" uniqKey="Bedard I" first="Isaac" last="Bedard">Isaac Bedard</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Culham, Cassandra" sort="Culham, Cassandra" uniqKey="Culham C" first="Cassandra" last="Culham">Cassandra Culham</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author><author><name sortKey="Eloe Fadrosh, Emiley A" sort="Eloe Fadrosh, Emiley A" uniqKey="Eloe Fadrosh E" first="Emiley A" last="Eloe-Fadrosh">Emiley A. Eloe-Fadrosh</name><affiliation wicri:level="1"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation></author><author><name sortKey="Ivanova, Natalia" sort="Ivanova, Natalia" uniqKey="Ivanova N" first="Natalia" last="Ivanova">Natalia Ivanova</name><affiliation wicri:level="1"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation></author><author><name sortKey="Malmstrom, Rex R" sort="Malmstrom, Rex R" uniqKey="Malmstrom R" first="Rex R" last="Malmstrom">Rex R. Malmstrom</name><affiliation wicri:level="1"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation></author><author><name sortKey="Grasby, Stephen E" sort="Grasby, Stephen E" uniqKey="Grasby S" first="Stephen E" last="Grasby">Stephen E. Grasby</name><affiliation wicri:level="1"><nlm:affiliation>Geological Survey of Canada, Calgary, Alberta, T2L 2A7, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Geological Survey of Canada, Calgary, Alberta, T2L 2A7</wicri:regionArea><wicri:noRegion>T2L 2A7</wicri:noRegion></affiliation></author><author><name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name><affiliation wicri:level="1"><nlm:affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598</wicri:regionArea><wicri:noRegion>94598</wicri:noRegion></affiliation></author><author><name sortKey="Dunfield, Peter F" sort="Dunfield, Peter F" uniqKey="Dunfield P" first="Peter F" last="Dunfield">Peter F. Dunfield</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4</wicri:regionArea><orgName type="university">Université de Calgary</orgName><placeName><settlement type="city">Calgary</settlement><region type="state">Alberta</region></placeName></affiliation></author></analytic><series><title level="j">Environmental microbiology</title><idno type="eISSN">1462-2920</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 10<sup>8</sup> cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32372527</PMID><DateRevised><Year>2020</Year><Month>08</Month><Day>18</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1462-2920</ISSN><JournalIssue CitedMedium="Internet"><Volume>22</Volume><Issue>8</Issue><PubDate><Year>2020</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Environmental microbiology</Title><ISOAbbreviation>Environ Microbiol</ISOAbbreviation></Journal><ArticleTitle>Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil.</ArticleTitle><Pagination><MedlinePgn>3143-3157</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/1462-2920.15054</ELocationID><Abstract><AbstractText>Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 10<sup>8</sup> cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.</AbstractText><CopyrightInformation>© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sheremet</LastName><ForeName>Andriy</ForeName><Initials>A</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-4530-0678</Identifier><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jones</LastName><ForeName>Gareth M</ForeName><Initials>GM</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-3627-9440</Identifier><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jarett</LastName><ForeName>Jessica</ForeName><Initials>J</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-8602-7348</Identifier><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bowers</LastName><ForeName>Robert M</ForeName><Initials>RM</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-0028-0407</Identifier><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bedard</LastName><ForeName>Isaac</ForeName><Initials>I</Initials><Identifier Source="ORCID">https://orcid.org/0000-0003-3625-2464</Identifier><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Culham</LastName><ForeName>Cassandra</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eloe-Fadrosh</LastName><ForeName>Emiley A</ForeName><Initials>EA</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-8162-1276</Identifier><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ivanova</LastName><ForeName>Natalia</ForeName><Initials>N</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-5802-9485</Identifier><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Malmstrom</LastName><ForeName>Rex R</ForeName><Initials>RR</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-4758-7369</Identifier><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grasby</LastName><ForeName>Stephen E</ForeName><Initials>SE</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-3910-4443</Identifier><AffiliationInfo><Affiliation>Geological Survey of Canada, Calgary, Alberta, T2L 2A7, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Woyke</LastName><ForeName>Tanja</ForeName><Initials>T</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-9485-5637</Identifier><AffiliationInfo><Affiliation>Department of Energy Joint Genome Institute, Walnut Creek CA, 94598, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dunfield</LastName><ForeName>Peter F</ForeName><Initials>PF</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-9319-4697</Identifier><AffiliationInfo><Affiliation>Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta, T2N 1N4, Canada.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><Agency>DOE Office of Science</Agency><Country></Country></Grant><Grant><GrantID>2019-06265</GrantID><Agency>Natural Sciences and Engineering Research Council of Canada</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Environ Microbiol</MedlineTA><NlmUniqueID>100883692</NlmUniqueID><ISSNLinking>1462-2912</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>08</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>04</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>04</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>5</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>5</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>5</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32372527</ArticleId><ArticleId 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Malmstrom</name><name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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