Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of <i>Aliineobacillus hadale</i> Isolated from Challenger Deep Sediment of the Mariana Trench
Hadal zones account for the deepest 45% of oceanic depth range and play an important role in ocean biogeochemical cycles. As the least-explored aquatic habitat on earth, further investigation is still required to fully elucidate the microbial taxonomy, ecological significance, metabolic diversity, a...
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2025-01-01
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| author | Shaofeng Yang Jie Liu Yang Liu Weichao Wu Jiahua Wang Yuli Wei |
| author_facet | Shaofeng Yang Jie Liu Yang Liu Weichao Wu Jiahua Wang Yuli Wei |
| author_sort | Shaofeng Yang |
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| description | Hadal zones account for the deepest 45% of oceanic depth range and play an important role in ocean biogeochemical cycles. As the least-explored aquatic habitat on earth, further investigation is still required to fully elucidate the microbial taxonomy, ecological significance, metabolic diversity, and adaptation in hadal environments. In this study, a novel strain Lsc_1132<sup>T</sup> was isolated from sediment of the Mariana Trench at 10,954 m in depth. Strain Lsc_1132<sup>T</sup> contains heterogenous 16S rRNA genes, exhibiting the highest sequence similarities to the type strains of <i>Neobacillus drentensis</i> LMG 21831<sup>T</sup>, <i>Neobacillus dielmonensis</i>, <i>Neobacillus drentensis</i> NBRC 102427<sup>T</sup>, <i>Neobacillus rhizosphaerae</i>, and <i>Neobacillus soli</i> NBRC 102451<sup>T</sup>, with a range of 98.60–99.10% identity. The highest average nucleotide identity (ANI), the highest digital DNA-DNA hybridization (DDH) values, and the average amino acid identity (AAI) with <i>Neobacillus</i> sp. PS3-40 reached 73.5%, 21.4%, and 75.54%, respectively. The major cellular fatty acids of strain Lsc_1132<sup>T</sup> included iso-C<sub>15:0</sub>, Summed Feature 3 (C<sub>16:1</sub><i>ω</i>6c and/or C<sub>16:1</sub><i>ω7</i>c), iso-C<sub>17:0</sub>, anteiso-C<sub>15:0</sub>, and iso-C<sub>17:1</sub><i>ω</i>5c. The respiratory quinone of strains Lsc_1132<sup>T</sup> was MK-7. The G + C content of the genomic DNA was 40.9%. Based on the GTDB taxonomy and phenotypic data, strain Lsc_1132<sup>T</sup> could represent a novel species of a novel genus, proposed as <i>Aliineobacillus hadale</i> gen. nov. sp. nov. (type strain Lsc_1132<sup>T</sup> = MCCC 1K09620<sup>T</sup>). Metabolically, strain Lsc_1132<sup>T</sup> demonstrates a robust carbohydrate metabolism with many strain-specific sugar transporters. It also has a remarkable capacity for metabolizing amino acids and carboxylic acids. Genomic analysis reveals a streamlined genome in the organism, characterized by a significant loss of orthologous genes, including those involved in cytochrome c synthesis, aromatic compound degradation, and polyhydroxybutyrate (PHB) synthesis, which suggests its adaptation to low oxygen levels and oligotrophic conditions through alternative metabolic pathways. In addition, the reduced number of paralogous genes in strain Lsc_1132<sup>T</sup>, together with its high protein-coding gene density, may further contribute to streamlining its genome and enhancing its genomic efficiency. This research expands our knowledge of hadal microorganisms and their metabolic strategies for surviving in extreme deep-sea environments. |
| format | Article |
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| institution | Kabale University |
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| spelling | doaj-art-1b37426b458d4043bcc9883f378186f12025-01-24T13:42:46ZengMDPI AGMicroorganisms2076-26072025-01-0113113210.3390/microorganisms13010132Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of <i>Aliineobacillus hadale</i> Isolated from Challenger Deep Sediment of the Mariana TrenchShaofeng Yang0Jie Liu1Yang Liu2Weichao Wu3Jiahua Wang4Yuli Wei5College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, ChinaCollege of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, ChinaMarine Biomedical Science and Technology Innovation Platform of Lingang Special Area, Shanghai 201306, ChinaCollege of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, ChinaCollege of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, ChinaCollege of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, ChinaHadal zones account for the deepest 45% of oceanic depth range and play an important role in ocean biogeochemical cycles. As the least-explored aquatic habitat on earth, further investigation is still required to fully elucidate the microbial taxonomy, ecological significance, metabolic diversity, and adaptation in hadal environments. In this study, a novel strain Lsc_1132<sup>T</sup> was isolated from sediment of the Mariana Trench at 10,954 m in depth. Strain Lsc_1132<sup>T</sup> contains heterogenous 16S rRNA genes, exhibiting the highest sequence similarities to the type strains of <i>Neobacillus drentensis</i> LMG 21831<sup>T</sup>, <i>Neobacillus dielmonensis</i>, <i>Neobacillus drentensis</i> NBRC 102427<sup>T</sup>, <i>Neobacillus rhizosphaerae</i>, and <i>Neobacillus soli</i> NBRC 102451<sup>T</sup>, with a range of 98.60–99.10% identity. The highest average nucleotide identity (ANI), the highest digital DNA-DNA hybridization (DDH) values, and the average amino acid identity (AAI) with <i>Neobacillus</i> sp. PS3-40 reached 73.5%, 21.4%, and 75.54%, respectively. The major cellular fatty acids of strain Lsc_1132<sup>T</sup> included iso-C<sub>15:0</sub>, Summed Feature 3 (C<sub>16:1</sub><i>ω</i>6c and/or C<sub>16:1</sub><i>ω7</i>c), iso-C<sub>17:0</sub>, anteiso-C<sub>15:0</sub>, and iso-C<sub>17:1</sub><i>ω</i>5c. The respiratory quinone of strains Lsc_1132<sup>T</sup> was MK-7. The G + C content of the genomic DNA was 40.9%. Based on the GTDB taxonomy and phenotypic data, strain Lsc_1132<sup>T</sup> could represent a novel species of a novel genus, proposed as <i>Aliineobacillus hadale</i> gen. nov. sp. nov. (type strain Lsc_1132<sup>T</sup> = MCCC 1K09620<sup>T</sup>). Metabolically, strain Lsc_1132<sup>T</sup> demonstrates a robust carbohydrate metabolism with many strain-specific sugar transporters. It also has a remarkable capacity for metabolizing amino acids and carboxylic acids. Genomic analysis reveals a streamlined genome in the organism, characterized by a significant loss of orthologous genes, including those involved in cytochrome c synthesis, aromatic compound degradation, and polyhydroxybutyrate (PHB) synthesis, which suggests its adaptation to low oxygen levels and oligotrophic conditions through alternative metabolic pathways. In addition, the reduced number of paralogous genes in strain Lsc_1132<sup>T</sup>, together with its high protein-coding gene density, may further contribute to streamlining its genome and enhancing its genomic efficiency. This research expands our knowledge of hadal microorganisms and their metabolic strategies for surviving in extreme deep-sea environments.https://www.mdpi.com/2076-2607/13/1/132genome streamlining<i>Bacillota</i>genomic comparisonMariana Trench |
| spellingShingle | Shaofeng Yang Jie Liu Yang Liu Weichao Wu Jiahua Wang Yuli Wei Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of <i>Aliineobacillus hadale</i> Isolated from Challenger Deep Sediment of the Mariana Trench Microorganisms genome streamlining <i>Bacillota</i> genomic comparison Mariana Trench |
| title | Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of <i>Aliineobacillus hadale</i> Isolated from Challenger Deep Sediment of the Mariana Trench |
| title_full | Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of <i>Aliineobacillus hadale</i> Isolated from Challenger Deep Sediment of the Mariana Trench |
| title_fullStr | Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of <i>Aliineobacillus hadale</i> Isolated from Challenger Deep Sediment of the Mariana Trench |
| title_full_unstemmed | Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of <i>Aliineobacillus hadale</i> Isolated from Challenger Deep Sediment of the Mariana Trench |
| title_short | Comparative Genomics Reveals Evidence of the Genome Reduction and Metabolic Potentials of <i>Aliineobacillus hadale</i> Isolated from Challenger Deep Sediment of the Mariana Trench |
| title_sort | comparative genomics reveals evidence of the genome reduction and metabolic potentials of i aliineobacillus hadale i isolated from challenger deep sediment of the mariana trench |
| topic | genome streamlining <i>Bacillota</i> genomic comparison Mariana Trench |
| url | https://www.mdpi.com/2076-2607/13/1/132 |
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