Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, <i>Shewanella zhuhaiensis</i> sp. nov., Isolated from a Tidal Flat Sediment
A new, facultatively anaerobic, light-yellow, and rod-shaped bacterium designated as 3B26<sup>T</sup> isolated from Qi’ao Island’s tidal flat sediment was identified. Strain 3B26<sup>T</sup> can hydrolyze gelatin, aesculin, and skim milk. The major cellular fatty acids were i...
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MDPI AG
2023-11-01
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| Online Access: | https://www.mdpi.com/2076-2607/11/12/2870 |
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| author | Yang Liu Tao Pei Juan Du Honghui Zhu |
| author_facet | Yang Liu Tao Pei Juan Du Honghui Zhu |
| author_sort | Yang Liu |
| collection | DOAJ |
| description | A new, facultatively anaerobic, light-yellow, and rod-shaped bacterium designated as 3B26<sup>T</sup> isolated from Qi’ao Island’s tidal flat sediment was identified. Strain 3B26<sup>T</sup> can hydrolyze gelatin, aesculin, and skim milk. The major cellular fatty acids were identified as iso-C<sub>15:0</sub>, referred to as summed feature 3, and C<sub>16:0</sub>; the polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and phospholipid; and the quinones contained Q-7, Q-8, MK-7, and MMK7. The genomic size of strain 3B26<sup>T</sup> was 4,682,650 bp, and its genomic DNA G + C content was 54.8%. While a 16S rRNA gene-based phylogenetic analysis confirmed that strain 3B26<sup>T</sup> belongs to the genus <i>Shewanella</i>, both phylogenomic inference and genomic comparison revealed that strain 3B26<sup>T</sup> is distinguishable from its relatives, and digital DNA-DNA hybridization (dDDH) values of 24.4–62.6% and average nucleotide identities (ANIs) of 83.5–95.6% between them were below the 70% dDDH and 96% ANI thresholds for bacterial species delineation. Genomic functional analysis demonstrated that strain 3B26<sup>T</sup> possesses complete gene clusters of eicosapentaenoic acid biosynthesis and denitrification. Based on the evidence above, strain 3B26<sup>T</sup> is considered to represent a novel species of the genus <i>Shewanella</i>, and the name <i>Shewanella zhuhaiensis</i> sp. nov. (type strain 3B26<sup>T</sup> = GDMCC 1.2057<sup>T</sup> = KCTC 82339<sup>T</sup>) is proposed. |
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| spelling | doaj.art-86619e084370462f82d744c5741a933f2023-12-22T14:25:49ZengMDPI AGMicroorganisms2076-26072023-11-011112287010.3390/microorganisms11122870Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, <i>Shewanella zhuhaiensis</i> sp. nov., Isolated from a Tidal Flat SedimentYang Liu0Tao Pei1Juan Du2Honghui Zhu3Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, ChinaKey Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, ChinaKey Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, ChinaKey Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, ChinaA new, facultatively anaerobic, light-yellow, and rod-shaped bacterium designated as 3B26<sup>T</sup> isolated from Qi’ao Island’s tidal flat sediment was identified. Strain 3B26<sup>T</sup> can hydrolyze gelatin, aesculin, and skim milk. The major cellular fatty acids were identified as iso-C<sub>15:0</sub>, referred to as summed feature 3, and C<sub>16:0</sub>; the polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and phospholipid; and the quinones contained Q-7, Q-8, MK-7, and MMK7. The genomic size of strain 3B26<sup>T</sup> was 4,682,650 bp, and its genomic DNA G + C content was 54.8%. While a 16S rRNA gene-based phylogenetic analysis confirmed that strain 3B26<sup>T</sup> belongs to the genus <i>Shewanella</i>, both phylogenomic inference and genomic comparison revealed that strain 3B26<sup>T</sup> is distinguishable from its relatives, and digital DNA-DNA hybridization (dDDH) values of 24.4–62.6% and average nucleotide identities (ANIs) of 83.5–95.6% between them were below the 70% dDDH and 96% ANI thresholds for bacterial species delineation. Genomic functional analysis demonstrated that strain 3B26<sup>T</sup> possesses complete gene clusters of eicosapentaenoic acid biosynthesis and denitrification. Based on the evidence above, strain 3B26<sup>T</sup> is considered to represent a novel species of the genus <i>Shewanella</i>, and the name <i>Shewanella zhuhaiensis</i> sp. nov. (type strain 3B26<sup>T</sup> = GDMCC 1.2057<sup>T</sup> = KCTC 82339<sup>T</sup>) is proposed.https://www.mdpi.com/2076-2607/11/12/2870<i>Shewanella zhuhaiensis</i>taxonomynovel speciesgenome functional analysisphylogenetic analyses |
| spellingShingle | Yang Liu Tao Pei Juan Du Honghui Zhu Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, <i>Shewanella zhuhaiensis</i> sp. nov., Isolated from a Tidal Flat Sediment Microorganisms <i>Shewanella zhuhaiensis</i> taxonomy novel species genome functional analysis phylogenetic analyses |
| title | Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, <i>Shewanella zhuhaiensis</i> sp. nov., Isolated from a Tidal Flat Sediment |
| title_full | Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, <i>Shewanella zhuhaiensis</i> sp. nov., Isolated from a Tidal Flat Sediment |
| title_fullStr | Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, <i>Shewanella zhuhaiensis</i> sp. nov., Isolated from a Tidal Flat Sediment |
| title_full_unstemmed | Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, <i>Shewanella zhuhaiensis</i> sp. nov., Isolated from a Tidal Flat Sediment |
| title_short | Polyphasic Characterization and Genomic Insights into an Aerobic Denitrifying Bacterium, <i>Shewanella zhuhaiensis</i> sp. nov., Isolated from a Tidal Flat Sediment |
| title_sort | polyphasic characterization and genomic insights into an aerobic denitrifying bacterium i shewanella zhuhaiensis i sp nov isolated from a tidal flat sediment |
| topic | <i>Shewanella zhuhaiensis</i> taxonomy novel species genome functional analysis phylogenetic analyses |
| url | https://www.mdpi.com/2076-2607/11/12/2870 |
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