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Scoma A. Functional groups in microbial ecology: updated definitions of piezophiles as suggested by hydrostatic pressure dependence on temperature. THE ISME JOURNAL 2021; 15:1871-1878. [PMID: 33782568 PMCID: PMC8245400 DOI: 10.1038/s41396-021-00930-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 02/01/2021] [Accepted: 02/08/2021] [Indexed: 02/01/2023]
Affiliation(s)
- Alberto Scoma
- grid.7048.b0000 0001 1956 2722Engineered Microbial Systems Laboratory (EMS-Lab), Department of Biological and Chemical Engineering (BCE), Aarhus University, Aarhus N, Denmark ,grid.7048.b0000 0001 1956 2722Section of Microbiology, Department of Biology, Aarhus University, Aarhus C, Denmark
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2
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Kim M, Lee KE, Cha IT, Kim ET, Park SJ. Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment. Curr Microbiol 2021; 78:3321-3327. [PMID: 34170378 DOI: 10.1007/s00284-021-02576-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/14/2021] [Indexed: 11/25/2022]
Abstract
A Gram-stain-negative, rod-shaped, and strictly aerobic bacterium designated strain G2-bT was isolated from the marine sediment around Jeju Island, South Korea. Strain G2-bT was found to be catalase- and oxidase-positive, white-pigmented, motile with polar flagellum, and to grow optimally at 25 °C, pH 7.0 in the presence of 4% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain G2-bT belongs to the genus Salinimonas and was closely related Salinimonas sediminis N102T (96.7% sequence similarity), Salinimonas iocasae KX18D6T (95.4%), Salinimonas lutimaris DPSR-4T (94.7%), and Salinimonas chungwhensis BH030046T (94.6%). Strain G2-bT possessed ubiquinone 8 as the sole respiratory quinone, summed feature 3 and summed feature 8 as the major fatty acids, and phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genome size and G + C content of the strain G2-bT were determined to be 3,765,169 bp, and 49.7%, respectively, as a complete circular genome. Based on the genomic analyses (e.g., average nucleotide identity and digital DNA-DNA hybridization), the strain G2-BT likely represents a new species in the genus Salinimonas, for which we propose to name this novel bacterium Salinimonas marina sp. nov., and the type strain is designated G2-BT (= KCTC 72817T = VTCC 910110T).
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Eui Tae Kim
- Department of Microbiology and Immunology, Jeju National University School of Medicine, Aran 13-15, Jeju, 63241, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea.
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3
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Gago JF, Viver T, Urdiain M, Pastor S, Kämpfer P, Ferreira E, Rossello-Mora R. Description of three new Alteromonas species Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. isolated from marine environments, and proposal for reclassification of the genus Salinimonas as Alteromonas. Syst Appl Microbiol 2021; 44:126226. [PMID: 34171620 DOI: 10.1016/j.syapm.2021.126226] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 11/26/2022]
Abstract
In the course of a bioprospective study of marine prokaryotes for cosmetic purposes, four strains, MD_567T, MD_652T, MD_674 and PS_109T, were isolated that 16S rRNA gene affiliation indicated could represent three new species within the family Alteromonadaceae. A thorough phylogenetic, genomic and phenotypic taxonomic study confirmed that the isolates could be classified as three new taxa for which we propose the names Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. In addition, the consistent monophyletic nature of the members of the genera Alteromonas and Salinimonas showed that both taxa should be unified, and therefore we also propose the reclassification of the genus Salinimonas within Alteromonas, as well as new combinations for the species of the former. As the specific epithets profundi and sediminis are already used for Alteromonas species, we created the nomina nova "Alteromonas alteriprofundi" nom. nov. and Alteromonas alterisediminis nom. nov. to accommodate the new names for "Salinimonas profundi" and Salinimonas sediminis. Whole genome comparisons also allowed us to detect the unexpected codification of aromatic hydrocarbon biodegradative compounds, such as benzoate and catechol, whose activity was then demonstrated phenotypically. Finally, the high genomic identity between the type strains of Alteromonas stellipolaris and Alteromonas addita indicated that the latter is a junior heterotypic synonym of Alteromonas stellipolaris.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Lipotrue S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | | | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
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Su HN, Zhang YZ. Lifestyle of bacteria in deep sea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:15-17. [PMID: 33006410 DOI: 10.1111/1758-2229.12891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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Zhang DF, Cui XW, Li WJ, Zhang XM, Xue HP, Huang JK, Zhang AH. Description of Salinimonas profundi sp. nov., a deep-sea bacterium harboring a transposon Tn6333. Antonie van Leeuwenhoek 2021; 114:69-81. [DOI: 10.1007/s10482-020-01501-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/17/2020] [Indexed: 11/28/2022]
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Xue J, Fang J, Zhang H, Wei Y, Wang L, Liu R, Cao J. Complete genome sequence of a piezophilic bacterium Salinimonas sediminis N102 T, isolated from deep-sea sediment of the New Britain Trench. Mar Genomics 2020; 56:100807. [PMID: 33632424 DOI: 10.1016/j.margen.2020.100807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/22/2023]
Abstract
Salinimonas sediminis N102T is a cold-adapted, slightly halophilic piezophile isolated from deep-sea sediment (4700 m) of the New Britain Trench. In this study, we report the complete genome sequence of S. sediminis N102T, which is comprised of 4,440,293 base pairs with a mean G + C content of 48.2 mol%. The complete genome harbors 3851 predicted protein-coding genes, 70 tRNA genes and 15 rRNA genes. Abundant genes in the genome were predicted to be linked to bacterial deep-sea lifestyle. The complete genome sequence of S. sediminis N102T provides insights into the microbial adaptation strategies to the deep-sea environment.
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Affiliation(s)
- Junyi Xue
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
| | - Hongge Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.
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Zhang H, Wang H, Cao L, Chen H, Wang M, Lian C, Zhong Z, Li C. Salinimonas iocasae sp. nov., a halophilic bacterium isolated from a polychaete tube in a hydrothermal field. Int J Syst Evol Microbiol 2020; 70:3899-3904. [DOI: 10.1099/ijsem.0.004258] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic bacterium, designated strain KX18D6T, was isolated from the tube of the polychaete Paralvinella hessleri collected from a hydrothermal field located in the Okinawa Trough. Strain KX18D6T was Gram-stain-negative, rod-shaped, facultatively anaerobic, motile, oxidase- and catalase-positive, and grew optimally at 30–35 °C, pH 7.0 and in the presence of 3–5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KX18D6T grouped with the members of the genus
Salinimonas
, including
Salinimonas chungwhensis
BH030046T (97.7 % sequence similarity),
Salinimonas lutimaris
DPSR-4T (97.2 %) and
Salinimonas sediminis
N102T (96.4 %). Genome sequencing of strain KX18D6T revealed a genome size of 4.16 Mb and a DNA G+C content of 47.3 mol%. Genomic average nucleotide identity (orthoANI) values of strain KX18D6T with
S. chungwhensis
DSM 16280T,
S. lutimaris
KCTC 23464T and
S. sediminis
N102T were 76.2, 73.1 and 73.2 %, respectively, while the in silico DNA–DNA hybridization (GGDC) values for strain KX18D6T with these strains were 25.3, 17.7 and 18.0 %, respectively. The major fatty acids were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The predominant respiratory quinone was ubiquinone 8, and the predominant polar lipids were phosphatidylethanolamine and phosphatidylglycerol. On the basis of comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain KX18D6T (=KCTC 72464T=MCCC 1K03884T) is clearly distinguishable from the type strains of species of the genus
Salinimonas
and is considered to represent a novel species of the genus
Salinimonas
, for which the name Salinimonas iocasae sp. nov. is proposed.
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Affiliation(s)
- Huan Zhang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
| | - Hao Wang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
| | - Lei Cao
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
| | - Hao Chen
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
| | - Minxiao Wang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
| | - Chao Lian
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
| | - Zhaoshan Zhong
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Key Laboratory of Marine Ecology and Environmental Sciences, Chinese Academy of Sciences, Qingdao 266071, PR China
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Cao J, Ding W, Lai Q, Wei Y, Liu R, Wang L, Fang J. Alteromonas indica Lin et al. 2018 is a later heterotypic synonym of Salinimonas sediminis Cao et al. 2018. Int J Syst Evol Microbiol 2019; 69:1423-1425. [PMID: 30843786 DOI: 10.1099/ijsem.0.003329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alteromonas indica IO390401T was compared with Salinimonas sediminis N102T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of A. indica IO390401T shared high similarity (99.9 %) with that of S. sediminis N102T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Salinimonas. Whole genomic comparison between the two strains revealed an average nucleotide identity of 99.2 % and a digital DNA-DNA hybridization estimate of 92.6 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking difference in metabolic, physiological or chemotaxonomic features. Therefore, we propose Alteromonas indica as a later heterotypic synonym of Salinimonas sediminis.
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Affiliation(s)
- Junwei Cao
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.,2National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
| | - Wanzhen Ding
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.,2National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
| | - Qiliang Lai
- 3State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, The Third Institute of State Oceanic Administration; Collaborative Innovation Center of Marine Biological Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Yuli Wei
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.,2National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
| | - Rulong Liu
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.,2National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
| | - Li Wang
- 1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.,2National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- 5Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA.,4Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China.,1Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
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