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Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae
The goal of the present work was to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. The composition of the anaerobic oil-degrading methanogenic enrichment obtained from an oil reservoir was determined by 16S rRNA-based survey, and the facultatively anaerob...
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| Published in: | Microorganisms (Basel) 2022-02, Vol.10 (2), p.378 |
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| creator | Semenova, Ekaterina M Grouzdev, Denis S Sokolova, Diyana S Tourova, Tatiyana P Poltaraus, Andrey B Potekhina, Natalia V Shishina, Polina N Bolshakova, Maria A Avtukh, Alexander N Ianutsevich, Elena A Tereshina, Vera M Nazina, Tamara N |
| description | The goal of the present work was to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. The composition of the anaerobic oil-degrading methanogenic enrichment obtained from an oil reservoir was determined by 16S rRNA-based survey, and the facultatively anaerobic chemoorganotrophic bacterial strain HO-Ch2
was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2
grew optimally at 28 °C, pH 8.0, and 1-2% (
/
) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2
had 98.8% similarity with the sequence of
CF5-4
. The genomic DNA G + C content of strain HO-Ch2
was 73.4%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the genome of strain HO-Ch2
and
genomes were 79.8-82.0% and 20.5-22.2%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic, and chemotaxonomic characterization, we propose strain HO-Ch2
(= VKM Ac-2850
= KCTC 49656
) as the type strain of a new species within the genus
, with the name
sp. nov. Based on the phylogenomic analysis of 187 genomes of
we propose the taxonomic revision of the genera
and
and of the family
. We also propose the reclassification of
as
comb. nov.,
as
comb. nov.,
as
comb. nov., and the transfer of the genus
to the family
of the order
. |
| doi_str_mv | 10.3390/microorganisms10020378 |
| format | article |
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was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2
grew optimally at 28 °C, pH 8.0, and 1-2% (
/
) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2
had 98.8% similarity with the sequence of
CF5-4
. The genomic DNA G + C content of strain HO-Ch2
was 73.4%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the genome of strain HO-Ch2
and
genomes were 79.8-82.0% and 20.5-22.2%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic, and chemotaxonomic characterization, we propose strain HO-Ch2
(= VKM Ac-2850
= KCTC 49656
) as the type strain of a new species within the genus
, with the name
sp. nov. Based on the phylogenomic analysis of 187 genomes of
we propose the taxonomic revision of the genera
and
and of the family
. We also propose the reclassification of
as
comb. nov.,
as
comb. nov.,
as
comb. nov., and the transfer of the genus
to the family
of the order
.</description><identifier>ISSN: 2076-2607</identifier><identifier>EISSN: 2076-2607</identifier><identifier>DOI: 10.3390/microorganisms10020378</identifier><identifier>PMID: 35208832</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Actinotalea subterranea ; Actinotaleaceae ; Bacteria ; Biodegradation ; Biomass ; Crude oil ; Degradation ; Deoxyribonucleic acid ; DNA ; Gene amplification ; Gene sequencing ; Genera ; genome analysis ; Genomes ; Genomic analysis ; Hybridization ; Hydrocarbons ; Microorganisms ; New species ; Nucleotide sequence ; Nucleotides ; Oil ; Oil and gas fields ; oil field ; Oil fields ; Oil reservoirs ; Physiology ; polyphasic taxonomy ; Prokaryotes ; Reclassification ; rRNA 16S ; Salinity ; Sodium chloride ; Taxonomic revision ; Taxonomy</subject><ispartof>Microorganisms (Basel), 2022-02, Vol.10 (2), p.378</ispartof><rights>2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 by the authors. 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c508t-874abf35bfabd842745b700a8026618c3f65c0d5decd66b4ea214730c461aba13</citedby><cites>FETCH-LOGICAL-c508t-874abf35bfabd842745b700a8026618c3f65c0d5decd66b4ea214730c461aba13</cites><orcidid>0000-0002-1358-5146 ; 0000-0002-6586-2467 ; 0000-0003-3258-7961 ; 0000-0002-7344-4126</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2633027213/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2633027213?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,25732,27903,27904,36991,36992,44569,53769,53771,74872</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35208832$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Semenova, Ekaterina M</creatorcontrib><creatorcontrib>Grouzdev, Denis S</creatorcontrib><creatorcontrib>Sokolova, Diyana S</creatorcontrib><creatorcontrib>Tourova, Tatiyana P</creatorcontrib><creatorcontrib>Poltaraus, Andrey B</creatorcontrib><creatorcontrib>Potekhina, Natalia V</creatorcontrib><creatorcontrib>Shishina, Polina N</creatorcontrib><creatorcontrib>Bolshakova, Maria A</creatorcontrib><creatorcontrib>Avtukh, Alexander N</creatorcontrib><creatorcontrib>Ianutsevich, Elena A</creatorcontrib><creatorcontrib>Tereshina, Vera M</creatorcontrib><creatorcontrib>Nazina, Tamara N</creatorcontrib><title>Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae</title><title>Microorganisms (Basel)</title><addtitle>Microorganisms</addtitle><description>The goal of the present work was to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. The composition of the anaerobic oil-degrading methanogenic enrichment obtained from an oil reservoir was determined by 16S rRNA-based survey, and the facultatively anaerobic chemoorganotrophic bacterial strain HO-Ch2
was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2
grew optimally at 28 °C, pH 8.0, and 1-2% (
/
) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2
had 98.8% similarity with the sequence of
CF5-4
. The genomic DNA G + C content of strain HO-Ch2
was 73.4%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the genome of strain HO-Ch2
and
genomes were 79.8-82.0% and 20.5-22.2%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic, and chemotaxonomic characterization, we propose strain HO-Ch2
(= VKM Ac-2850
= KCTC 49656
) as the type strain of a new species within the genus
, with the name
sp. nov. Based on the phylogenomic analysis of 187 genomes of
we propose the taxonomic revision of the genera
and
and of the family
. We also propose the reclassification of
as
comb. nov.,
as
comb. nov.,
as
comb. nov., and the transfer of the genus
to the family
of the order
.</description><subject>Actinotalea subterranea</subject><subject>Actinotaleaceae</subject><subject>Bacteria</subject><subject>Biodegradation</subject><subject>Biomass</subject><subject>Crude oil</subject><subject>Degradation</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Gene amplification</subject><subject>Gene sequencing</subject><subject>Genera</subject><subject>genome analysis</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Hybridization</subject><subject>Hydrocarbons</subject><subject>Microorganisms</subject><subject>New species</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Oil</subject><subject>Oil and gas fields</subject><subject>oil field</subject><subject>Oil fields</subject><subject>Oil reservoirs</subject><subject>Physiology</subject><subject>polyphasic taxonomy</subject><subject>Prokaryotes</subject><subject>Reclassification</subject><subject>rRNA 16S</subject><subject>Salinity</subject><subject>Sodium chloride</subject><subject>Taxonomic revision</subject><subject>Taxonomy</subject><issn>2076-2607</issn><issn>2076-2607</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptUttu1DAQjRCIVqW_UFnihZddfIkd5wWpWtpSqagIwbM1sZ3EK8de7Gyl5Zv4SNztRVuEXzyaOXOOZ3yq6ozgJWMt_jg5nWJMAwSXp0wwppg18lV1THEjFlTg5vVBfFSd5rzG5bSESU7eVkeMUywlo8fVn2_jLrvo4-A0eATBoCsbYlFAqxES6Nkm9xtmFwOKPTrXswtxBm8B5W1XignCfbxZohDvlqhPcUK3zi8-2yGBcWFAX-08QoiDDYX0IiSnx8mGea_13WoPObu-qD9pzKNFlzA5vzuU0xbsu-pNDz7b08f7pPp5efFj9WVxc3t1vTq_WWiO5byQTQ1dz3jXQ2dkTZuadw3GIDEVgkjNesE1NtxYbYToaguU1A3DuhYEOiDspLp-4DUR1mqT3ARppyI4tU-UzStIs9PeKsG4aGpqTWtpzWQLtcVgMAfJTFvUCtenB67Ntpus0WXyBP4F6ctKcKMa4p2SspG8rQvBh0eCFH9tbZ7V5LK23pfFx21WVLDyq5xQXqDv_4Gu4zaFsqo9CtOGElZQ4gFVTJRzsv3zYwhW9_5S__dXaTw7HOW57clN7C9q-9Pb</recordid><startdate>20220206</startdate><enddate>20220206</enddate><creator>Semenova, Ekaterina M</creator><creator>Grouzdev, Denis S</creator><creator>Sokolova, Diyana S</creator><creator>Tourova, Tatiyana P</creator><creator>Poltaraus, Andrey B</creator><creator>Potekhina, Natalia V</creator><creator>Shishina, Polina N</creator><creator>Bolshakova, Maria A</creator><creator>Avtukh, Alexander N</creator><creator>Ianutsevich, Elena A</creator><creator>Tereshina, Vera M</creator><creator>Nazina, Tamara N</creator><general>MDPI AG</general><general>MDPI</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7T7</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-1358-5146</orcidid><orcidid>https://orcid.org/0000-0002-6586-2467</orcidid><orcidid>https://orcid.org/0000-0003-3258-7961</orcidid><orcidid>https://orcid.org/0000-0002-7344-4126</orcidid></search><sort><creationdate>20220206</creationdate><title>Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae</title><author>Semenova, Ekaterina M ; Grouzdev, Denis S ; Sokolova, Diyana S ; Tourova, Tatiyana P ; Poltaraus, Andrey B ; Potekhina, Natalia V ; Shishina, Polina N ; Bolshakova, Maria A ; Avtukh, Alexander N ; Ianutsevich, Elena A ; Tereshina, Vera M ; Nazina, Tamara N</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c508t-874abf35bfabd842745b700a8026618c3f65c0d5decd66b4ea214730c461aba13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Actinotalea subterranea</topic><topic>Actinotaleaceae</topic><topic>Bacteria</topic><topic>Biodegradation</topic><topic>Biomass</topic><topic>Crude oil</topic><topic>Degradation</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Gene amplification</topic><topic>Gene sequencing</topic><topic>Genera</topic><topic>genome analysis</topic><topic>Genomes</topic><topic>Genomic analysis</topic><topic>Hybridization</topic><topic>Hydrocarbons</topic><topic>Microorganisms</topic><topic>New species</topic><topic>Nucleotide sequence</topic><topic>Nucleotides</topic><topic>Oil</topic><topic>Oil and gas fields</topic><topic>oil field</topic><topic>Oil fields</topic><topic>Oil reservoirs</topic><topic>Physiology</topic><topic>polyphasic taxonomy</topic><topic>Prokaryotes</topic><topic>Reclassification</topic><topic>rRNA 16S</topic><topic>Salinity</topic><topic>Sodium chloride</topic><topic>Taxonomic revision</topic><topic>Taxonomy</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Semenova, Ekaterina M</creatorcontrib><creatorcontrib>Grouzdev, Denis S</creatorcontrib><creatorcontrib>Sokolova, Diyana S</creatorcontrib><creatorcontrib>Tourova, Tatiyana P</creatorcontrib><creatorcontrib>Poltaraus, Andrey B</creatorcontrib><creatorcontrib>Potekhina, Natalia V</creatorcontrib><creatorcontrib>Shishina, Polina N</creatorcontrib><creatorcontrib>Bolshakova, Maria A</creatorcontrib><creatorcontrib>Avtukh, Alexander N</creatorcontrib><creatorcontrib>Ianutsevich, Elena A</creatorcontrib><creatorcontrib>Tereshina, Vera M</creatorcontrib><creatorcontrib>Nazina, Tamara N</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>Biological Sciences</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Environmental Science Collection</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Microorganisms (Basel)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Semenova, Ekaterina M</au><au>Grouzdev, Denis S</au><au>Sokolova, Diyana S</au><au>Tourova, Tatiyana P</au><au>Poltaraus, Andrey B</au><au>Potekhina, Natalia V</au><au>Shishina, Polina N</au><au>Bolshakova, Maria A</au><au>Avtukh, Alexander N</au><au>Ianutsevich, Elena A</au><au>Tereshina, Vera M</au><au>Nazina, Tamara N</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae</atitle><jtitle>Microorganisms (Basel)</jtitle><addtitle>Microorganisms</addtitle><date>2022-02-06</date><risdate>2022</risdate><volume>10</volume><issue>2</issue><spage>378</spage><pages>378-</pages><issn>2076-2607</issn><eissn>2076-2607</eissn><abstract>The goal of the present work was to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. The composition of the anaerobic oil-degrading methanogenic enrichment obtained from an oil reservoir was determined by 16S rRNA-based survey, and the facultatively anaerobic chemoorganotrophic bacterial strain HO-Ch2
was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2
grew optimally at 28 °C, pH 8.0, and 1-2% (
/
) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2
had 98.8% similarity with the sequence of
CF5-4
. The genomic DNA G + C content of strain HO-Ch2
was 73.4%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the genome of strain HO-Ch2
and
genomes were 79.8-82.0% and 20.5-22.2%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic, and chemotaxonomic characterization, we propose strain HO-Ch2
(= VKM Ac-2850
= KCTC 49656
) as the type strain of a new species within the genus
, with the name
sp. nov. Based on the phylogenomic analysis of 187 genomes of
we propose the taxonomic revision of the genera
and
and of the family
. We also propose the reclassification of
as
comb. nov.,
as
comb. nov.,
as
comb. nov., and the transfer of the genus
to the family
of the order
.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>35208832</pmid><doi>10.3390/microorganisms10020378</doi><orcidid>https://orcid.org/0000-0002-1358-5146</orcidid><orcidid>https://orcid.org/0000-0002-6586-2467</orcidid><orcidid>https://orcid.org/0000-0003-3258-7961</orcidid><orcidid>https://orcid.org/0000-0002-7344-4126</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 2076-2607 |
| ispartof | Microorganisms (Basel), 2022-02, Vol.10 (2), p.378 |
| issn | 2076-2607 2076-2607 |
| language | eng |
| recordid | cdi_doaj_primary_oai_doaj_org_article_6356742ed9e24389a4e0ad05a83d9661 |
| source | Publicly Available Content Database; PubMed Central |
| subjects | Actinotalea subterranea Actinotaleaceae Bacteria Biodegradation Biomass Crude oil Degradation Deoxyribonucleic acid DNA Gene amplification Gene sequencing Genera genome analysis Genomes Genomic analysis Hybridization Hydrocarbons Microorganisms New species Nucleotide sequence Nucleotides Oil Oil and gas fields oil field Oil fields Oil reservoirs Physiology polyphasic taxonomy Prokaryotes Reclassification rRNA 16S Salinity Sodium chloride Taxonomic revision Taxonomy |
| title | Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae |
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