Ontology type: schema:ScholarlyArticle Open Access: True
2006-09-24
AUTHORSHéctor García Martín, Natalia Ivanova, Victor Kunin, Falk Warnecke, Kerrie W Barry, Alice C McHardy, Christine Yeates, Shaomei He, Asaf A Salamov, Ernest Szeto, Eileen Dalin, Nik H Putnam, Harris J Shapiro, Jasmyn L Pangilinan, Isidore Rigoutsos, Nikos C Kyrpides, Linda Louise Blackall, Katherine D McMahon, Philip Hugenholtz
ABSTRACTEnhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, “Candidatus Accumulibacter phosphatis.” The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of A. phosphatis in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the A. phosphatis genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems. More... »
PAGES1263-1269
http://scigraph.springernature.com/pub.10.1038/nbt1247
DOIhttp://dx.doi.org/10.1038/nbt1247
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1009864240
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/16998472
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"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Adaptation, Biological",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Betaproteobacteria",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genome, Bacterial",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Phosphorus",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Sewage",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Waste Disposal, Fluid",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Mart\u00edn",
"givenName": "H\u00e9ctor Garc\u00eda",
"id": "sg:person.01331500261.79",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01331500261.79"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Ivanova",
"givenName": "Natalia",
"id": "sg:person.01263456163.47",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01263456163.47"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Kunin",
"givenName": "Victor",
"id": "sg:person.01303474506.40",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01303474506.40"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Warnecke",
"givenName": "Falk",
"id": "sg:person.01354546246.01",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01354546246.01"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Barry",
"givenName": "Kerrie W",
"id": "sg:person.0707307031.57",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0707307031.57"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "IBM Research Division, Thomas J. Watson Research Center, P.O. Box 218, 10598, Yorktown Heights, New York, USA",
"id": "http://www.grid.ac/institutes/grid.481554.9",
"name": [
"IBM Research Division, Thomas J. Watson Research Center, P.O. Box 218, 10598, Yorktown Heights, New York, USA"
],
"type": "Organization"
},
"familyName": "McHardy",
"givenName": "Alice C",
"id": "sg:person.01041701425.67",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01041701425.67"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Advanced Wastewater Management Centre, University of Queensland, 4072, St. Lucia, Queensland, Australia",
"id": "http://www.grid.ac/institutes/grid.1003.2",
"name": [
"Advanced Wastewater Management Centre, University of Queensland, 4072, St. Lucia, Queensland, Australia"
],
"type": "Organization"
},
"familyName": "Yeates",
"givenName": "Christine",
"id": "sg:person.01213342430.35",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01213342430.35"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Civil and Environmental Engineering Department, University of Wisconsin-Madison, 1415 Engineering Drive, 53706, Madison, Wisconsin, USA",
"id": "http://www.grid.ac/institutes/grid.14003.36",
"name": [
"Civil and Environmental Engineering Department, University of Wisconsin-Madison, 1415 Engineering Drive, 53706, Madison, Wisconsin, USA"
],
"type": "Organization"
},
"familyName": "He",
"givenName": "Shaomei",
"id": "sg:person.01051647600.78",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01051647600.78"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Salamov",
"givenName": "Asaf A",
"id": "sg:person.01152110305.72",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01152110305.72"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Szeto",
"givenName": "Ernest",
"id": "sg:person.01346033555.69",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01346033555.69"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Dalin",
"givenName": "Eileen",
"id": "sg:person.01005302050.84",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01005302050.84"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Putnam",
"givenName": "Nik H",
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Shapiro",
"givenName": "Harris J",
"id": "sg:person.0773407605.04",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773407605.04"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Pangilinan",
"givenName": "Jasmyn L",
"id": "sg:person.01137753554.97",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01137753554.97"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "IBM Research Division, Thomas J. Watson Research Center, P.O. Box 218, 10598, Yorktown Heights, New York, USA",
"id": "http://www.grid.ac/institutes/grid.481554.9",
"name": [
"IBM Research Division, Thomas J. Watson Research Center, P.O. Box 218, 10598, Yorktown Heights, New York, USA"
],
"type": "Organization"
},
"familyName": "Rigoutsos",
"givenName": "Isidore",
"id": "sg:person.01366001022.42",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366001022.42"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Kyrpides",
"givenName": "Nikos C",
"id": "sg:person.01230412614.56",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01230412614.56"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Advanced Wastewater Management Centre, University of Queensland, 4072, St. Lucia, Queensland, Australia",
"id": "http://www.grid.ac/institutes/grid.1003.2",
"name": [
"Advanced Wastewater Management Centre, University of Queensland, 4072, St. Lucia, Queensland, Australia"
],
"type": "Organization"
},
"familyName": "Blackall",
"givenName": "Linda Louise",
"id": "sg:person.01364066674.36",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01364066674.36"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Civil and Environmental Engineering Department, University of Wisconsin-Madison, 1415 Engineering Drive, 53706, Madison, Wisconsin, USA",
"id": "http://www.grid.ac/institutes/grid.14003.36",
"name": [
"Civil and Environmental Engineering Department, University of Wisconsin-Madison, 1415 Engineering Drive, 53706, Madison, Wisconsin, USA"
],
"type": "Organization"
},
"familyName": "McMahon",
"givenName": "Katherine D",
"id": "sg:person.01007375500.45",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007375500.45"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA",
"id": "http://www.grid.ac/institutes/grid.451309.a",
"name": [
"DOE Joint Genome Institute, 2800 Mitchell Drive, 94598, Walnut Creek, California, USA"
],
"type": "Organization"
},
"familyName": "Hugenholtz",
"givenName": "Philip",
"id": "sg:person.01055510700.73",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01055510700.73"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1007/bf02010434",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1017265226",
"https://doi.org/10.1007/bf02010434"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1023/a:1020538429009",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021635466",
"https://doi.org/10.1023/a:1020538429009"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature02340",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023089166",
"https://doi.org/10.1038/nature02340"
],
"type": "CreativeWork"
}
],
"datePublished": "2006-09-24",
"datePublishedReg": "2006-09-24",
"description": "Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, \u201cCandidatus Accumulibacter phosphatis.\u201d The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of A. phosphatis in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the A. phosphatis genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems.",
"genre": "article",
"id": "sg:pub.10.1038/nbt1247",
"inLanguage": "en",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.3041993",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1115214",
"issn": [
"1087-0156",
"1546-1696"
],
"name": "Nature Biotechnology",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "10",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "24"
}
],
"keywords": [
"metagenomic analysis",
"common functional theme",
"Candidatus Accumulibacter phosphatis",
"systems-level understanding",
"EBPR sludge",
"EBPR metabolic models",
"inferred metabolism",
"phylogenetic overlap",
"evolutionary dynamics",
"environmental adaptation",
"Accumulibacter phosphatis",
"functional themes",
"same species",
"metabolic models",
"dominant organisms",
"sludge communities",
"uncultured bacterium",
"metabolic level",
"biological phosphorus removal",
"cultivation requirements",
"biological systems",
"EBPR",
"apparent lack",
"genome",
"metagenomics",
"habitats",
"economic relevance",
"organisms",
"species",
"bacterium",
"phosphorus removal",
"metabolism",
"community",
"adaptation",
"dominance",
"present study",
"insights",
"mechanism",
"analysis",
"overlap",
"hypothesis",
"understanding",
"sludge",
"blueprint",
"dynamics",
"levels",
"light",
"relevance",
"process",
"lifestyle",
"spite",
"lack",
"study",
"removal",
"industrial processes",
"comparison",
"system",
"requirements",
"model",
"controversy",
"themes"
],
"name": "Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities",
"pagination": "1263-1269",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1009864240"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/nbt1247"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"16998472"
]
}
],
"sameAs": [
"https://doi.org/10.1038/nbt1247",
"https://app.dimensions.ai/details/publication/pub.1009864240"
],
"sdDataset": "articles",
"sdDatePublished": "2022-05-20T07:23",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220519/entities/gbq_results/article/article_428.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1038/nbt1247"
}
]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/nbt1247'
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/nbt1247'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt1247'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nbt1247'
This table displays all metadata directly associated to this object as RDF triples.
295 TRIPLES
22 PREDICATES
96 URIs
85 LITERALS
13 BLANK NODES