Ontology type: schema:ScholarlyArticle Open Access: True
2021-06-09
AUTHORSKristopher Kieft, Zhichao Zhou, Rika E. Anderson, Alison Buchan, Barbara J. Campbell, Steven J. Hallam, Matthias Hess, Matthew B. Sullivan, David A. Walsh, Simon Roux, Karthik Anantharaman
ABSTRACTMicrobial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides fundamental insights on the distribution, diversity, and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations. More... »
PAGES3503
http://scigraph.springernature.com/pub.10.1038/s41467-021-23698-5
DOIhttp://dx.doi.org/10.1038/s41467-021-23698-5
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1138725549
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/34108477
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Microbiology",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Amino Acid Motifs",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Bacteriophages",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Caudovirales",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Ecosystem",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Energy Metabolism",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Environmental Microbiology",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genes, Viral",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genetic Variation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genome, Viral",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Metagenomics",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Oxidation-Reduction",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Phylogeny",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Protein Domains",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Sulfur",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Thiosulfates",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Viral Proteins",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Department of Bacteriology, University of Wisconsin\u2013Madison, Madison, WI, USA",
"id": "http://www.grid.ac/institutes/grid.14003.36",
"name": [
"Department of Bacteriology, University of Wisconsin\u2013Madison, Madison, WI, USA"
],
"type": "Organization"
},
"familyName": "Kieft",
"givenName": "Kristopher",
"id": "sg:person.07704021365.64",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07704021365.64"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Bacteriology, University of Wisconsin\u2013Madison, Madison, WI, USA",
"id": "http://www.grid.ac/institutes/grid.14003.36",
"name": [
"Department of Bacteriology, University of Wisconsin\u2013Madison, Madison, WI, USA"
],
"type": "Organization"
},
"familyName": "Zhou",
"givenName": "Zhichao",
"id": "sg:person.01257470070.21",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01257470070.21"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Biology Department, Carleton College, Northfield, MN, USA",
"id": "http://www.grid.ac/institutes/grid.253692.9",
"name": [
"Biology Department, Carleton College, Northfield, MN, USA"
],
"type": "Organization"
},
"familyName": "Anderson",
"givenName": "Rika E.",
"id": "sg:person.01121552430.56",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01121552430.56"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Microbiology, University of Tennessee, Knoxville, TN, USA",
"id": "http://www.grid.ac/institutes/grid.411461.7",
"name": [
"Department of Microbiology, University of Tennessee, Knoxville, TN, USA"
],
"type": "Organization"
},
"familyName": "Buchan",
"givenName": "Alison",
"id": "sg:person.01052747630.13",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01052747630.13"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Biological Sciences, Life Science Facility, Clemson University, Clemson, SC, USA",
"id": "http://www.grid.ac/institutes/grid.26090.3d",
"name": [
"Department of Biological Sciences, Life Science Facility, Clemson University, Clemson, SC, USA"
],
"type": "Organization"
},
"familyName": "Campbell",
"givenName": "Barbara J.",
"id": "sg:person.01277036215.21",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01277036215.21"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada",
"id": "http://www.grid.ac/institutes/grid.17091.3e",
"name": [
"Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada",
"Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, BC, Canada",
"Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada",
"Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada",
"ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada"
],
"type": "Organization"
},
"familyName": "Hallam",
"givenName": "Steven J.",
"id": "sg:person.01116336612.76",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01116336612.76"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Animal Science, University of California Davis, Davis, CA, USA",
"id": "http://www.grid.ac/institutes/grid.27860.3b",
"name": [
"Department of Animal Science, University of California Davis, Davis, CA, USA"
],
"type": "Organization"
},
"familyName": "Hess",
"givenName": "Matthias",
"id": "sg:person.0771255275.49",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0771255275.49"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Microbiology, The Ohio State University, Columbus, OH, USA",
"id": "http://www.grid.ac/institutes/grid.261331.4",
"name": [
"Department of Microbiology, The Ohio State University, Columbus, OH, USA"
],
"type": "Organization"
},
"familyName": "Sullivan",
"givenName": "Matthew B.",
"id": "sg:person.01040164115.34",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01040164115.34"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Groupe de recherche interuniversitaire en limnologie, Department of Biology, Concordia University, Montr\u00e9al, QC, Canada",
"id": "http://www.grid.ac/institutes/grid.410319.e",
"name": [
"Groupe de recherche interuniversitaire en limnologie, Department of Biology, Concordia University, Montr\u00e9al, QC, Canada"
],
"type": "Organization"
},
"familyName": "Walsh",
"givenName": "David A.",
"id": "sg:person.0616627526.18",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0616627526.18"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA",
"id": "http://www.grid.ac/institutes/None",
"name": [
"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA"
],
"type": "Organization"
},
"familyName": "Roux",
"givenName": "Simon",
"id": "sg:person.01326704035.18",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01326704035.18"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Bacteriology, University of Wisconsin\u2013Madison, Madison, WI, USA",
"id": "http://www.grid.ac/institutes/grid.14003.36",
"name": [
"Department of Bacteriology, University of Wisconsin\u2013Madison, Madison, WI, USA"
],
"type": "Organization"
},
"familyName": "Anantharaman",
"givenName": "Karthik",
"id": "sg:person.0714252516.09",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714252516.09"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1186/s13059-016-0997-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050687712",
"https://doi.org/10.1186/s13059-016-0997-x"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2105-8-209",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020623557",
"https://doi.org/10.1186/1471-2105-8-209"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt.3988",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1092237583",
"https://doi.org/10.1038/nbt.3988"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41564-020-0779-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1130291027",
"https://doi.org/10.1038/s41564-020-0779-9"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nrmicro1750",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049635150",
"https://doi.org/10.1038/nrmicro1750"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12985-019-1120-1",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1111836920",
"https://doi.org/10.1186/s12985-019-1120-1"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41396-018-0289-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1107583446",
"https://doi.org/10.1038/s41396-018-0289-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/bf00177193",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023913878",
"https://doi.org/10.1007/bf00177193"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41579-019-0270-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1122306771",
"https://doi.org/10.1038/s41579-019-0270-x"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s40168-018-0541-1",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1106998933",
"https://doi.org/10.1186/s40168-018-0541-1"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41396-019-0580-z",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1123778524",
"https://doi.org/10.1038/s41396-019-0580-z"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.1923",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1006541515",
"https://doi.org/10.1038/nmeth.1923"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41396-017-0043-3",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1100592784",
"https://doi.org/10.1038/s41396-017-0043-3"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ismej.2015.81",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023964718",
"https://doi.org/10.1038/ismej.2015.81"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ismej.2017.126",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1090891867",
"https://doi.org/10.1038/ismej.2017.126"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms15892",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1086119384",
"https://doi.org/10.1038/ncomms15892"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41564-018-0190-y",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1105584553",
"https://doi.org/10.1038/s41564-018-0190-y"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ismej.2012.78",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014417998",
"https://doi.org/10.1038/ismej.2012.78"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2013-14-11-r123",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024924860",
"https://doi.org/10.1186/gb-2013-14-11-r123"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2105-11-119",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1026423599",
"https://doi.org/10.1186/1471-2105-11-119"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.3176",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023901695",
"https://doi.org/10.1038/nmeth.3176"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41587-019-0100-8",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1113937265",
"https://doi.org/10.1038/s41587-019-0100-8"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s40168-020-00867-0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1128385853",
"https://doi.org/10.1186/s40168-020-00867-0"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41396-018-0078-0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1101059542",
"https://doi.org/10.1038/s41396-018-0078-0"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature06130",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029540629",
"https://doi.org/10.1038/nature06130"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature04111",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042267725",
"https://doi.org/10.1038/nature04111"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature19366",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012162698",
"https://doi.org/10.1038/nature19366"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/424741a",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031785841",
"https://doi.org/10.1038/424741a"
],
"type": "CreativeWork"
}
],
"datePublished": "2021-06-09",
"datePublishedReg": "2021-06-09",
"description": "Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides fundamental insights on the distribution, diversity, and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.",
"genre": "article",
"id": "sg:pub.10.1038/s41467-021-23698-5",
"inLanguage": "en",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.9605964",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2998996",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.6938881",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1043282",
"issn": [
"2041-1723"
],
"name": "Nature Communications",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "12"
}
],
"keywords": [
"auxiliary metabolic genes",
"auxiliary metabolism",
"sulfur metabolism",
"diverse phage populations",
"measurable fitness benefits",
"microbial sulfur metabolism",
"freshwater lakes",
"fitness benefits",
"metabolic genes",
"phage populations",
"gene abundance",
"ecosystem biogeochemistry",
"biogeochemical configurations",
"expression profiles",
"biogeochemical cycling",
"host cells",
"phages",
"ecology",
"viral contribution",
"metabolism",
"oxidation of sulfur",
"fundamental insights",
"genes",
"microbes",
"hydrothermal environments",
"global scale",
"diversity",
"abundance",
"bacteriophages",
"biogeochemistry",
"lakes",
"cells",
"cycling",
"insights",
"sensitive response",
"thiosulfate",
"evidence",
"population",
"environment",
"sulfur",
"Ocean",
"oxidation",
"response",
"significant contribution",
"sulfur concentration",
"profile",
"contribution",
"distribution",
"concentration",
"study",
"retention",
"ramifications",
"scale",
"benefits",
"necessity",
"configuration"
],
"name": "Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages",
"pagination": "3503",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1138725549"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/s41467-021-23698-5"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"34108477"
]
}
],
"sameAs": [
"https://doi.org/10.1038/s41467-021-23698-5",
"https://app.dimensions.ai/details/publication/pub.1138725549"
],
"sdDataset": "articles",
"sdDatePublished": "2022-05-10T10:26",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220509/entities/gbq_results/article/article_878.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1038/s41467-021-23698-5"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41467-021-23698-5'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41467-021-23698-5'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-021-23698-5'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41467-021-23698-5'
This table displays all metadata directly associated to this object as RDF triples.
401 TRIPLES
22 PREDICATES
127 URIs
90 LITERALS
23 BLANK NODES