Taxonomic Description and Complete Genome Sequencing of <i>Pseudomonas silvicola</i> sp. nov. Isolated from <i>Cunninghamia laceolata</i>
The <i>Pseudomonas</i> strain T1-3-2<sup>T</sup> isolated from the cone of <i>Cunninghamia laceolata</i> exhibited growth-promoting and antifungal activity. Strain T1-3-2<sup>T</sup> was characterized by a polyphasic taxonomy and complete genome sequen...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-05-01
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| Series: | Forests |
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| Online Access: | https://www.mdpi.com/1999-4907/14/6/1089 |
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| author | Longyan Tian Yanfeng Zhang Hua Yang Qian Zhao Hualong Qiu Jinzhu Xu Changsheng Qin |
| author_facet | Longyan Tian Yanfeng Zhang Hua Yang Qian Zhao Hualong Qiu Jinzhu Xu Changsheng Qin |
| author_sort | Longyan Tian |
| collection | DOAJ |
| description | The <i>Pseudomonas</i> strain T1-3-2<sup>T</sup> isolated from the cone of <i>Cunninghamia laceolata</i> exhibited growth-promoting and antifungal activity. Strain T1-3-2<sup>T</sup> was characterized by a polyphasic taxonomy and complete genome sequencing analysis to explore its taxonomic position and biocontrol potentials fully. The results revealed that strain T1-3-2<sup>T</sup> shares a high degree of similarity with <i>Pseudomonas eucalypticola</i> and is distinct from any known <i>Pseudomonas</i> species. The G + C content was 61.65%, and the difference was greater than 1 compared to “<i>P. eucalypticola</i>”. Additionally, values of the average nucleotide identity blast (ANIb), average nucleotide identity MUMmer (ANIm), and DNA-DNA hybridization (DDH) between T1-3-2<sup>T</sup> and its closest known related species, “<i>P. eucalypticola</i>”, were below the thresholds necessary for species delineation. Furthermore, the T1-3-2<sup>T</sup> strain exhibited the distinctions with the multiple polar flagella and the specific quinone system with MK8 compared with that of “<i>P. eucalypticola</i>”. Collectively, these findings affirm the designation of strain T1-3-2<sup>T</sup> as a new <i>Pseudomonas</i> species, proposed to be named <i>Pseudomonas silvicola</i>, with T1-3-2<sup>T</sup> as the type strain. Genomic analyses revealed strain T1-3-2<sup>T</sup> contains three circular DNA contigs, including a 7,613,303 bp chromosome and two plasmids (952,764 bp and 84,880 bp). Bioinformatics analyses further offered potential insight into the molecular mechanisms whereby this strain can promote plant growth and control disease, revealing encoded genes related to antibiotic and secondary metabolite production, the uptake and biosynthesis of siderophores, and pyoverdine biosynthesis. These genomic data offer a valuable foundation for future efforts to apply the T1-3-2<sup>T</sup> strain in research contexts. |
| first_indexed | 2024-03-11T02:27:40Z |
| format | Article |
| id | doaj.art-710b6419bee644d3acc008d60af88259 |
| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-11T02:27:40Z |
| publishDate | 2023-05-01 |
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| spelling | doaj.art-710b6419bee644d3acc008d60af882592023-11-18T10:26:13ZengMDPI AGForests1999-49072023-05-01146108910.3390/f14061089Taxonomic Description and Complete Genome Sequencing of <i>Pseudomonas silvicola</i> sp. nov. Isolated from <i>Cunninghamia laceolata</i>Longyan Tian0Yanfeng Zhang1Hua Yang2Qian Zhao3Hualong Qiu4Jinzhu Xu5Changsheng Qin6Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Eco-Engineering Polytechnic, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaThe <i>Pseudomonas</i> strain T1-3-2<sup>T</sup> isolated from the cone of <i>Cunninghamia laceolata</i> exhibited growth-promoting and antifungal activity. Strain T1-3-2<sup>T</sup> was characterized by a polyphasic taxonomy and complete genome sequencing analysis to explore its taxonomic position and biocontrol potentials fully. The results revealed that strain T1-3-2<sup>T</sup> shares a high degree of similarity with <i>Pseudomonas eucalypticola</i> and is distinct from any known <i>Pseudomonas</i> species. The G + C content was 61.65%, and the difference was greater than 1 compared to “<i>P. eucalypticola</i>”. Additionally, values of the average nucleotide identity blast (ANIb), average nucleotide identity MUMmer (ANIm), and DNA-DNA hybridization (DDH) between T1-3-2<sup>T</sup> and its closest known related species, “<i>P. eucalypticola</i>”, were below the thresholds necessary for species delineation. Furthermore, the T1-3-2<sup>T</sup> strain exhibited the distinctions with the multiple polar flagella and the specific quinone system with MK8 compared with that of “<i>P. eucalypticola</i>”. Collectively, these findings affirm the designation of strain T1-3-2<sup>T</sup> as a new <i>Pseudomonas</i> species, proposed to be named <i>Pseudomonas silvicola</i>, with T1-3-2<sup>T</sup> as the type strain. Genomic analyses revealed strain T1-3-2<sup>T</sup> contains three circular DNA contigs, including a 7,613,303 bp chromosome and two plasmids (952,764 bp and 84,880 bp). Bioinformatics analyses further offered potential insight into the molecular mechanisms whereby this strain can promote plant growth and control disease, revealing encoded genes related to antibiotic and secondary metabolite production, the uptake and biosynthesis of siderophores, and pyoverdine biosynthesis. These genomic data offer a valuable foundation for future efforts to apply the T1-3-2<sup>T</sup> strain in research contexts.https://www.mdpi.com/1999-4907/14/6/1089<i>Pseudomonas</i>taxonomic descriptiongenome |
| spellingShingle | Longyan Tian Yanfeng Zhang Hua Yang Qian Zhao Hualong Qiu Jinzhu Xu Changsheng Qin Taxonomic Description and Complete Genome Sequencing of <i>Pseudomonas silvicola</i> sp. nov. Isolated from <i>Cunninghamia laceolata</i> Forests <i>Pseudomonas</i> taxonomic description genome |
| title | Taxonomic Description and Complete Genome Sequencing of <i>Pseudomonas silvicola</i> sp. nov. Isolated from <i>Cunninghamia laceolata</i> |
| title_full | Taxonomic Description and Complete Genome Sequencing of <i>Pseudomonas silvicola</i> sp. nov. Isolated from <i>Cunninghamia laceolata</i> |
| title_fullStr | Taxonomic Description and Complete Genome Sequencing of <i>Pseudomonas silvicola</i> sp. nov. Isolated from <i>Cunninghamia laceolata</i> |
| title_full_unstemmed | Taxonomic Description and Complete Genome Sequencing of <i>Pseudomonas silvicola</i> sp. nov. Isolated from <i>Cunninghamia laceolata</i> |
| title_short | Taxonomic Description and Complete Genome Sequencing of <i>Pseudomonas silvicola</i> sp. nov. Isolated from <i>Cunninghamia laceolata</i> |
| title_sort | taxonomic description and complete genome sequencing of i pseudomonas silvicola i sp nov isolated from i cunninghamia laceolata i |
| topic | <i>Pseudomonas</i> taxonomic description genome |
| url | https://www.mdpi.com/1999-4907/14/6/1089 |
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