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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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Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8878594/
https://www.ncbi.nlm.nih.gov/pubmed/35208832
http://dx.doi.org/10.3390/microorganisms10020378
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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_facet 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 Semenova, Ekaterina M.
collection PubMed
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(T) was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2(T) grew optimally at 28 °C, pH 8.0, and 1–2% (w/v) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2(T) had 98.8% similarity with the sequence of Actinotalea ferrariae CF5-4(T). The genomic DNA G + C content of strain HO-Ch2(T) was 73.4%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the genome of strain HO-Ch2(T) and Actinotalea 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(T) (= VKM Ac-2850(T) = KCTC 49656(T)) as the type strain of a new species within the genus Actinotalea, with the name Actinotalea subterranea sp. nov. Based on the phylogenomic analysis of 187 genomes of Actinobacteria we propose the taxonomic revision of the genera Actinotalea and Pseudactinotalea and of the family Actinotaleaceae. We also propose the reclassification of Cellulomonas carbonis as Actinotalea carbonis comb. nov., Cellulomonas bogoriensis as Actinotalea bogoriensis comb. nov., Actinotalea caeni as Pseudactinotalea caeni comb. nov., and the transfer of the genus Pseudactinotalea to the family Ruaniaceae of the order Ruaniales.
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spelling pubmed-88785942022-02-26 Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae 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. Microorganisms Article 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(T) was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2(T) grew optimally at 28 °C, pH 8.0, and 1–2% (w/v) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2(T) had 98.8% similarity with the sequence of Actinotalea ferrariae CF5-4(T). The genomic DNA G + C content of strain HO-Ch2(T) was 73.4%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the genome of strain HO-Ch2(T) and Actinotalea 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(T) (= VKM Ac-2850(T) = KCTC 49656(T)) as the type strain of a new species within the genus Actinotalea, with the name Actinotalea subterranea sp. nov. Based on the phylogenomic analysis of 187 genomes of Actinobacteria we propose the taxonomic revision of the genera Actinotalea and Pseudactinotalea and of the family Actinotaleaceae. We also propose the reclassification of Cellulomonas carbonis as Actinotalea carbonis comb. nov., Cellulomonas bogoriensis as Actinotalea bogoriensis comb. nov., Actinotalea caeni as Pseudactinotalea caeni comb. nov., and the transfer of the genus Pseudactinotalea to the family Ruaniaceae of the order Ruaniales. MDPI 2022-02-06 /pmc/articles/PMC8878594/ /pubmed/35208832 http://dx.doi.org/10.3390/microorganisms10020378 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/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/).
spellingShingle Article
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.
Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae
title Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae
title_full Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae
title_fullStr Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae
title_full_unstemmed Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae
title_short Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae
title_sort physiological and genomic characterization of actinotalea subterranea sp. nov. from oil-degrading methanogenic enrichment and reclassification of the family actinotaleaceae
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8878594/
https://www.ncbi.nlm.nih.gov/pubmed/35208832
http://dx.doi.org/10.3390/microorganisms10020378
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