Citation: | Fei Xu, Xiang Zeng, Yadong Gong, Zongze Shao. Thiosulfate oxidation and autotrophy potential by marine prevalent heterotrophic bacteria of genus Marinobacter[J]. Acta Oceanologica Sinica, 2024, 43(8): 89-97. doi: 10.1007/s13131-023-2263-x |
Aziz R K, Bartels D, Best A A, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics, 9: 75, doi: 10.1186/1471-2164-9-75
|
Behera B C, Patra M, Dutta S K, et al. 2014. Isolation and characterisation of sulphur oxidising bacteria from mangrove soil of Mahanadi River Delta and their sulphur oxidising ability. Journal of Applied & Environmental Microbiology, 2(1): 1–5, doi: 10.12691/jaem-2-1-1
|
Boroujeni S R, Kalbasi M, Asgharzadeh A, et al. 2021. Evaluating the potential of Halothiobacillus bacteria for sulfur oxidation and biomass production under saline soil. Geomicrobiology Journal, 38(1): 57–65, doi: 10.1080/01490451.2020.1809571
|
Camacho C, Coulouris G, Avagyan V, et al. 2009. BLAST+: architecture and applications. BMC Bioinformatics, 10: 421, doi: 10.1186/1471-2105-10-421
|
Chaudhary S, Tanvi, Dhanker R, et al. 2019. Different applications of sulphur oxidizing bacteria: a review. International Journal of Current Microbiology and Applied Sciences (IJCMAS), 8(11): 770–778, doi: 10.20546/ijcmas.2019.811.091
|
Chen Zhiwei, Koh M, Van Driessche G, et al. 1994. The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium. Science, 266(5184): 430–432, doi: 10.1126/science.7939681
|
Choi B R, Pham V H, Park S J, et al. 2009. Characterization of facultative sulfur-oxidizing Marinobacter sp. BR13 isolated from marine sediment of Yellow Sea, Korea. Journal of the Korean Society for Applied Biological Chemistry, 52(4): 309–314, doi: 10.3839/jksabc.2009.055
|
Cooper Z S, Rapp J Z, Shoemaker A M D, et al. 2022. Evolutionary divergence of Marinobacter strains in cryopeg brines as revealed by pangenomics. Frontiers in Microbiology, 13: 879116, doi: 10.3389/fmicb.2022.879116
|
Dahl C. 2015. Cytoplasmic sulfur trafficking in sulfur-oxidizing prokaryotes. IUBMB Life, 67(4): 268–274, doi: 10.1002/iub.1371
|
Dahl C. 2017. Sulfur metabolism in phototrophic bacteria. In: Hallenbeck P C, ed. Modern Topics in the Phototrophic Prokaryotes: Metabolism, Bioenergetics, and Omics. Cham: Springer, 27–66
|
Denkmann K, Grein F, Zigann R, et al. 2012. Thiosulfate dehydrogenase: a widespread unusual acidophilic c-type cytochrome. Environmental Microbiology, 14(10): 2673–2688, doi: 10.1111/j.1462-2920.2012.02820.x
|
Ding Wei, Wang Shougang, Qin Peng, et al. 2023. Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms. Nature Communications, 14(1): 2033, doi: 10.1038/s41467-023-37759-4
|
Dou Le, Zhang Mengyu, Pan Luqing, et al. 2022. Sulfide removal characteristics, pathways and potential application of a novel chemolithotrophic sulfide-oxidizing strain, Marinobacter sp. SDSWS8. Environmental Research, 212: 113176, doi: 10.1016/j.envres.2022.113176
|
Du Rui, Gao Di, Wang Yiting, et al. 2022. Heterotrophic sulfur oxidation of Halomonas titanicae SOB56 and its habitat adaptation to the hydrothermal environment. Frontiers in Microbiology, 13: 888833, doi: 10.3389/fmicb.2022.888833
|
Edgar R C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5): 1792–1797, doi: 10.1093/nar/gkh340
|
Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17(6): 368–376, doi: 10.1007/BF01734359
|
Fritz G, Roth A, Schiffer A, et al. 2002. Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-Å resolution. Proceedings of the National Academy of Sciences of the United States of America, 99(4): 1836–1841, doi: 10.1073/pnas.042664399
|
Gauthier M J, Lafay B, Christen R, et al. 1992. Marinobacter hydrocarbonoclasticus gen. nov. , sp. nov. , a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. International Journal of Systematic and Evolutionary Microbiology, 42(4): 568–576, doi: 10.1099/00207713-42-4-568
|
Ghosh W, Dam B. 2009. Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea. FEMS Microbiology Reviews, 33(6): 999–1043, doi: 10.1111/j.1574-6976.2009.00187.x
|
Griesbeck C, Schütz M, Schödl T, et al. 2002. Mechanism of sulfide-quinone reductase investigated using site-directed mutagenesis and sulfur analysis. Biochemistry, 41(39): 11552–11565, doi: 10.1021/bi026032b
|
Handley K M, Hery M, Lloyd J R. 2009. Marinobacter santoriniensis sp. nov. , an arsenate-respiring and arsenite-oxidizing bacterium isolated from hydrothermal sediment. International Journal of Systematic and Evolutionary Microbiology, 59(Pt 4): 886–892, doi: 10.1099/ijs.0.003145-0
|
Handley K M, Lloyd J R. 2013. Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species. Frontiers in Microbiology, 4: 136, doi: 10.3389/fmicb.2013.00136
|
He Yang, Zeng Xiang, Xu Fei, et al. 2023. Diversity of mixotrophic neutrophilic thiosulfate- and iron-oxidizing bacteria from deep-sea hydrothermal vents. Microorganisms, 11(1): 100, doi: 10.3390/microorganisms11010100
|
Hensen D, Sperling D, Trüper H G, et al. 2006. Thiosulphate oxidation in the phototrophic sulphur bacterium Allochromatium vinosum. Molecular Microbiology, 62(3): 794–810, doi: 10.1111/j.1365-2958.2006.05408.x
|
Houghton J L, Foustoukos D I, Flynn T M, et al. 2016. Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistry. Environmental Microbiology, 18(9): 3057–3072, doi: 10.1111/1462-2920.13232
|
Kumar S, Stecher G, Li Michael, et al. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6): 1547–1549, doi: 10.1093/molbev/msy096
|
Lian Fengbai, Chen Xuyang, Jiang Shan, et al. 2021. Marinobacter orientalis sp. nov. , a thiosulfate-oxidizing bacterium isolated from a marine solar saltern. Antonie van Leeuwenhoek, 114(6): 765–775,doi: 10.1007/s10482-021-01556-0
|
Montes M J, Bozal N, Mercadé E. 2008. Marinobacter guineae sp. nov. , a novel moderately halophilic bacterium from an Antarctic environment. International Journal of Systematic and Evolutionary Microbiology, 58(Pt 6): 1346–1349, doi: 10.1099/ijs.0.65298-0
|
Na S I, Kim Y O, Yoon S H, et al. 2018. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. Journal of Microbiology, 56(4): 280–285, doi: 10.1007/s12275-018-8014-6
|
Pott A S, Dahl C. 1998. Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Microbiology, 144(Pt 7): 1881–1894, doi: 10.1099/00221287-144-7-1881
|
Rana K, Rana N, Singh B. 2020. Applications of sulfur oxidizing bacteria. In: Salwan R, Sharma V, eds. Physiological and Biotechnological Aspects of Extremophiles. London: Academic Press, 131–136.
|
Randolph T G. 1944. Blood studies in allergy: I. The direct counting chamber determination of eosinophils by propylene glycol aqueous stains. Journal of Allergy, 15(2): 89–96, doi: 10.1016/S0021-8707(44)90155-3
|
Ruby E G, Wirsen C O, Jannasch H W. 1981. Chemolithotrophic sulfur-oxidizing bacteria from the galapagos rift hydrothermal vents. Applied and Environmental Microbiology, 42(2): 317–324, doi: 10.1128/aem.42.2.317-324.1981
|
Teske A, Brinkhoff T, Muyzer G, et al. 2000. Diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. Applied and Environmental Microbiology, 66(8): 3125–3133, doi: 10.1128/AEM.66.8.3125-3133.2000
|
Trifinopoulos J, Nguyen L T, von Haeseler A, et al. 2016. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44(W1): W232–W235, doi: 10.1093/nar/gkw256
|
Wasmund K, Mussmann M, Loy A. 2017. The life sulfuric: microbial ecology of sulfur cycling in marine sediments. Environmental Microbiology Reports, 9(4): 323–344, doi: 10.1111/1758-2229.12538
|
Watanabe T, Kojima H, Umezawa K, et al. 2019. Genomes of neutrophilic sulfur-oxidizing chemolithoautotrophs representing 9 proteobacterial species from 8 genera. Frontiers in Microbiology, 10: 316, doi: 10.3389/fmicb.2019.00316
|
Wu Zhengchao, Li Qian P, Ge Zaiming, et al. 2021. Impacts of biogenic polyunsaturated aldehydes on metabolism and community composition of particle-attached bacteria in coastal hypoxia. Biogeosciences, 18(3): 1049–1065, doi: 10.5194/bg-18-1049-2021
|
Xie Jianmin, Chen Yuerong, Cai Guanjing, et al. 2023. Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees. Nucleic Acids Research, 51(W1): W587–W592, doi: 10.1093/nar/gkad359
|
Zhang Yu, Zhong Xianchun, Xu Wei, et al. 2020. Marinobacter vulgaris sp. nov. , a moderately halophilic bacterium isolated from a marine solar saltern. International Journal of Systematic and Evolutionary Microbiology, 70(1): 450–456, doi: 10.1099/ijsem.0.003774
|
Xu Fei Supplementary material.zip |