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Wang J, Xie Z, Liu Y, Yan F, Cao J, Liu R, Wang L, Wei Y, Fang J. Complete genome sequence of a multiple-stress-tolerant bacterium Halomonas piezotolerans NBT06E8 T isolated from a deep-sea sediment sample of the New Britain Trench. 3 Biotech 2022; 12:236. [PMID: 35999911 PMCID: PMC9392676 DOI: 10.1007/s13205-022-03283-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 07/22/2022] [Indexed: 11/01/2022] Open
Abstract
Halomonas piezotolerans NBT06E8T is a Gram-stain-negative, moderately halophilic, piezotolerant, H2O2 and heavy metal-resistant bacterium, isolated from a deep-sea sediment sample collected from the New Britain Trench at depth of 8900 m. Growth of the strain was observed at 4-45 °C (optimum 30 °C), at pH 5-11 (optimum 8-9) and in 0.5-21% (w/v) NaCl (optimum 3-7%). The optimum pressure for growth was 0.1-30 MPa (megapascal) with tolerance up to 60 MPa. Under optimum growth conditions, the strain could tolerant 15 mM H2O2. Here, we report the complete genome of H. piezotolerans NBT06E8T, which consists of 3,945,801 bp (G + C content of 57.93%) with a single chromosome, 3509 protein-coding genes, 60 tRNAs and 6 rRNA operons. Genomic analysis revealed the capability of utilizing various carbon and nitrogen sources, the presence of multiple toxin-antitoxin systems and strain-specific type VI secretion system benefitting its adaptation to the oligotrophic hadal environments. Multiple respiratory chain components, especially the strain-specific anaerobic enzymes, could allow its survival in both surficial and buried sediments with variable oxygen concentrations. Gene function and metabolic pathway analysis showed that strain NBT06E8T encodes a series of genes related to high hydrostatic pressure tolerance, antioxidative stress and heavy metal resistance, which could also contribute to its deep-sea adaptation strategies. The complete genome sequence of H. piezotolerans NBT06E8T provides further insights into the stress adaptation strategies of deep-sea bacteria and potential biotechnological application of Halomonas species. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03283-3.
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Affiliation(s)
- Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237 People’s Republic of China
| | - Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
| | - Fangfang Yan
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
| | - Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237 People’s Republic of China
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813 USA
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Yan F, Fang J, Cao J, Wei Y, Liu R, Wang L, Xie Z. Halomonas piezotolerans sp. nov., a multiple-stress-tolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench. Int J Syst Evol Microbiol 2020; 70:2560-2568. [PMID: 32129736 DOI: 10.1099/ijsem.0.004069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A piezotolerant, H2O2-tolerant, heavy-metal-tolerant, slightly halophilic bacterium (strain NBT06E8T) was isolated from a deep-sea sediment sample collected from the New Britain Trench at depth of 8900 m. The strain was aerobic, motile, Gram-stain-negative, rod-shaped, oxidase-positive and catalase-positive. Growth of the strain was observed at 4-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 8-9) and in 0.5-21 % (w/v) NaCl (optimum, 3-7 %). The optimum pressure for growth was 0.1-30 MPa with tolerance up to 60 MPa. Under optimum growth conditions, the strain could tolerate 15 mM H2O2. Resuls of 16S rRNA gene sequence analysis showed that strain NBT06E8T is closely related to Halomonas aquamarina DSM 30161T (99.5%), Halomonas meridiana DSM 5425T (99.43%) and Halomonas axialensis Althf1T (99.35%). The digital DNA-DNA hybridization values between strain NBT06E8T and the three related type strains, H. aquamarina, H. meridiana and H. axialensis, were 30.5±2.4 %, 30.7±2.5% and 31.5±2.5 %, respectively. The average nucleotide identity values between strain NBT06E8T and the three related type strains were 86.26, 86.26 and 83.63 %, respectively. The major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The predominant respiratory quinone detected was ubiquinone-9 (Q-9). Based on its phenotypic and phylogenetic characteristics, we conclude that strain NBT06E8T represents a novel species of the genus Halomonas, for which the name Halomonas piezotolerans sp. nov. is proposed (type strain NBT06E8T= MCCC 1K04228T=KCTC 72680T).
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Affiliation(s)
- Fangfang Yan
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Junwei Cao
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yuli Wei
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Rulong Liu
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Li Wang
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Zhe Xie
- 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
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Finore I, Gioiello A, Leone L, Orlando P, Romano I, Nicolaus B, Poli A. Aeribacillus composti sp. nov., a thermophilic bacillus isolated from olive mill pomace compost. Int J Syst Evol Microbiol 2017; 67:4830-4835. [PMID: 28984237 DOI: 10.1099/ijsem.0.002391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, endospore-forming, thermophilic bacterium, strain N.8T, was isolated from the curing step of an olive mill pomace compost sample, collected at the Composting Experimental Centre (CESCO, Salerno, Italy). Strain N.8T, based on 16S rRNA gene sequence similarities, was most closely related to Aeribacillus pallidus strain H12T (=DSM 3670T) (99.8 % similarity value) with a 25 % DNA-DNA relatedness value. Cells were rod-shaped, non-motile and grew optimally at 60 °C and pH 9.0, forming cream colonies. Strain N.8 was able to grow on medium containing up to 9.0 % (w/v) NaCl with an optimum at 6.0 % (w/v) NaCl. The cellular membrane contained MK-7, and C16 : 0 (48.4 %), iso-C17 : 0 (19.4 %) and anteiso-C17 : 0 (14.6 %) were the major cellular fatty acids. The DNA G+C content was 40.5 mol%. Based on phenotypic characteristics, 16S rRNA gene sequences, DNA-DNA hybridization values and chemotaxonomic characteristics, strain N.8T represents a novel species of the genus Aeribacillus, for which the name Aeribacillus composti sp. nov. is proposed. The type strain is N.8T (=KCTC 33824T=JCM 31580T).
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Affiliation(s)
- Ilaria Finore
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Alessia Gioiello
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Luigi Leone
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Pierangelo Orlando
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Applied Sciences and Intelligent Systems (I.S.A.S.I.), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Ida Romano
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Barbara Nicolaus
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Annarita Poli
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
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Oren A. Reclassification of Halomonas caseinilytica Wu et al. 2008 as a later synonym of Halomonas sinaiensis—Comments on the proposal by Hwang et al., Antonie van Leeuwenhoek 109:1345–1352, 2016. Antonie van Leeuwenhoek 2016; 110:171. [DOI: 10.1007/s10482-016-0776-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 09/25/2016] [Indexed: 11/25/2022]
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Reclassification of Halomonas caseinilytica Wu et al. 2008 as a later synonym of Halomonas sinaiensis Romano et al. 2007, and emendation of the species description. Antonie van Leeuwenhoek 2016; 109:1345-52. [PMID: 27418263 DOI: 10.1007/s10482-016-0733-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
Abstract
The taxonomic relationship between Halomonas sinaiensis DSM 18067(T) and Halomonas caseinilytica JCM 14802(T) has not been established, despite the high similarity (99.6 %) of their 16S rRNA gene sequences. To clarify their taxonomic positions, a polyphasic approach was applied to both type strains. Genomic relatedness analyses between H. sinaiensis DSM 18067(T) and H. caseinilytica JCM 14802(T) resulted in an average nucleotide identity of 99.5 % and an estimated DNA-DNA hybridization of 96.1 % by the genome-to-genome distance calculator, indicating that they belong to a single species. Phenotypic and chemotaxonomic characteristics showed no pronounced differences between the two type strains. Based on the results of this polyphasic study, it is proposed that H. caseinilytica JCM 14802(T) is a later heterotypic synonym of H. sinaiensis DSM 18067(T). An emended description for the species H. sinaiensis is given.
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Liu W, Zhang G, Xian W, Yang J, Yang L, Xiao M, Jiang H, Li WJ. Halomonas xiaochaidanensis sp. nov., isolated from a salt lake sediment. Arch Microbiol 2016; 198:761-6. [PMID: 27177899 DOI: 10.1007/s00203-016-1235-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/16/2016] [Accepted: 05/05/2016] [Indexed: 11/30/2022]
Abstract
A short-rod-shaped moderately halophilic bacterium, designated CUG 00002(T), was isolated from the sediment of Xiaochaidan salt lake in Qinghai Province, China by using R2A medium. The cells were Gram-staining negative, aerobic, forming creamy and circular colonies with diameters of 2-3 mm on R2A agar when incubated at 30 °C for 3 days. 16S rRNA gene-based phylogenetic analysis indicated that strain CUG 00002(T) belonged to the genus Halomonas in the class Gammaproteobacteria, showing highest sequence similarity of 97.1 and 96.7 % to Halomonas mongoliensis Z-7009(T) (=DSM 17332=VKM B2353) and Halomonas shengliensis SL014B-85(T) (=CGMCC 1.6444(T)=LMG 23897(T)), respectively. The predominant isoprenoid quinone was ubiquinone-9 (Q9), and the major fatty acids were C16:0, summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (comprising C18:1 ω7c or C18:1 ω6c). The genomic DNA G+C content of strain CUG 00002(T) was 61.8 mol%. The above characteristics were consistent with the placement of the organism in the genus Halomonas. The level of DNA-DNA relatedness between CUG 00002(T) and its most closely related strain H. mongoliensis Z-7009(T) was 41.0 ± 1.6 %. Based on the results of phenotypic, phylogenetic and biochemical analyses, strain CUG 00002(T) represents a novel species of the genus Halomonas, for which the name Halomonas xiaochaidanensis sp. nov. is proposed. The type strain is CUG 00002(T) (=CCTCC AB 2014152(T)=KCTC 42685(T)).
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Affiliation(s)
- Wen Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Guojing Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Wendong Xian
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Lingling Yang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China.
| | - Wen-Jun Li
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China. .,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Zhang S, Pan J, Lu W, Yan Y, Wang H, Wiegel J, Zhao B. Halomonas urumqiensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkaline lake. Int J Syst Evol Microbiol 2016; 66:1962-1969. [PMID: 26873696 DOI: 10.1099/ijsem.0.000975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic, aerobic bacterium, strain BZ-SZ-XJ27T, belonging to the genus Halomonas, was isolated from a saline-alkaline lake in the Xinjiang Uyghur Autonomous Region of China. Phylogenetic analysis based on 16S rRNA gene sequences and a multilocus sequence analysis using the 16S rRNA, gyrB and rpoD genes demonstrated that strain BZ-SZ-XJ27T represents a member of the genus Halomonas. On the basis of 16S rRNA gene sequence similarity, the closest relatives were Halomonas campaniensis 5AGT, H. fontilapidosi 5CRT, H. korlensis XK1T and H. sinaiensis ALO SharmT, with similarities of 96.2-97.2 %. DNA-DNA hybridization with H. korlensis CGMCC 1.6981T (the nearest phylogenetic neighbour) and H. campaniensis DSM 15293T (the highest 16S rRNA gene sequence similarity) showed relatedness values of 53 and 38 %, respectively, demonstrating the separateness of the three taxa. The bacterium stained Gram-negative and the cells were motile and rod-shaped. The strain formed creamy-white colonies and grew under optimal conditions of 1.42 M Na+ (range 0.22-4.32 M Na+), pH 8.0-8.5 (range pH 6.0-10.0) and 39 °C (range 4-43 °C). The dominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 36.6 %), C16 : 0 (25.9 %) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 21.2 %). The dominant polar lipids were two unknown phospholipids, phosphatidylethanolamine and phosphatidylglycerol, and the main respiratory quinones were ubiquinone 9 (Q-9; 89 %) and ubiquinone 8 (Q-8; 10 %). The genomic DNA G+C content was 61.7 ± 0.8 mol% (Tm). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BZ-SZ-XJ27T is proposed to represent a novel species, Halomonas urumqiensis sp. nov., within the genus Halomonas of the family Halomonadaceae. The type strain is BZ-SZ-XJ27T ( = JCM 30202T = CGMCC 1.12917T).
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Affiliation(s)
- Shanshan Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jiao Pan
- College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Weidong Lu
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Haisheng Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jurgen Wiegel
- Department of Microbiology, University of Georgia, Athens, GA 306021, USA
| | - Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Halomonas heilongjiangensis sp. nov., a novel moderately halophilic bacterium isolated from saline and alkaline soil. Antonie van Leeuwenhoek 2015; 108:403-13. [DOI: 10.1007/s10482-015-0493-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/24/2015] [Indexed: 10/23/2022]
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9
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Mustafa GA, Abd-Elgawad A, Abdel-Haleem AM, Siam R. Egypt's Red Sea coast: phylogenetic analysis of cultured microbial consortia in industrialized sites. Front Microbiol 2014; 5:363. [PMID: 25157243 PMCID: PMC4127681 DOI: 10.3389/fmicb.2014.00363] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/27/2014] [Indexed: 11/13/2022] Open
Abstract
The Red Sea possesses a unique geography, and its shores are rich in mangrove, macro-algal and coral reef ecosystems. Various sources of pollution affect Red Sea biota, including microbial life. We assessed the effects of industrialization on microbes along the Egyptian Red Sea coast at eight coastal sites and two lakes. The bacterial communities of sediment samples were analyzed using bacterial 16S rDNA pyrosequencing of V6-V4 hypervariable regions. The taxonomic assignment of 131,402 significant reads to major bacterial taxa revealed five main bacterial phyla dominating the sampled sites: Proteobacteria (68%), Firmicutes (13%), Fusobacteria (12%), Bacteriodetes (6%), and Spirochetes (0.03%). Further analysis revealed distinct bacterial consortia that primarily included (1) marine Vibrio spp.-suggesting a "marine Vibrio phenomenon"; (2) potential human pathogens; and (3) oil-degrading bacteria. We discuss two divergent microbial consortia that were sampled from Solar Lake West near Taba/Eilat and Saline Lake in Ras Muhammad; these consortia contained the highest abundance of human pathogens and no pathogens, respectively. Our results draw attention to the effects of industrialization on the Red Sea and suggest the need for further analysis to overcome the hazardous effects observed at the impacted sites.
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Affiliation(s)
- Ghada A Mustafa
- Biotechnology Graduate Program, Biology Department and YJ-Science and Technology Research Center, American University in Cairo New Cairo, Egypt
| | - Amr Abd-Elgawad
- Tourism Development Authority, Ministry of Tourism Cairo, Egypt
| | - Alyaa M Abdel-Haleem
- Biotechnology Graduate Program, Biology Department and YJ-Science and Technology Research Center, American University in Cairo New Cairo, Egypt
| | - Rania Siam
- Biotechnology Graduate Program, Biology Department and YJ-Science and Technology Research Center, American University in Cairo New Cairo, Egypt
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Characterization of a native cellulase activity from an anaerobic thermophilic hydrogen-producing bacterium Thermosipho sp. strain 3. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-013-0792-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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11
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Xu L, Xu XW, Meng FX, Huo YY, Oren A, Yang JY, Wang CS. Halomonas zincidurans sp. nov., a heavy-metal-tolerant bacterium isolated from the deep-sea environment. Int J Syst Evol Microbiol 2013; 63:4230-4236. [PMID: 23811134 DOI: 10.1099/ijs.0.051656-0] [Citation(s) in RCA: 25] [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 Gram-stain-negative, aerobic, rod-like, motile by peritrichous flagella and moderately halophilic bacterium, designated strain B6(T), was isolated a deep-sea sediment collected from the South Atlantic Ocean. The isolate grew with 0.5-15 % (w/v) NaCl, at 4-37 °C and pH 5.0-8.5 and showed a high tolerance to zinc, manganese, cobalt and copper ions. The major fatty acids were C16 : 0, C19 : 0 cyclo ω8c, C12 : 0 3-OH and C12 : 0. The predominant ubiquinone was Q-9. The genomic DNA G+C content was 61.1 mol%. Phylogenetic analysis based on 16S rRNA gene comparisons indicated that strain B6(T) belonged to the genus Halomonas, and the closest relative was Halomonas xinjiangensis TRM 0175(T) (96.1 %). Based upon the phenotypic, chemotaxonomic and genetic data, strain B6(T) represents a novel species from the genus Halomonas, for which the name Halomonas zincidurans sp. nov. is proposed. The type strain is B6(T) ( = CGMCC 1.12450(T) = JCM 18472(T)).
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Affiliation(s)
- Lin Xu
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Fan-Xu Meng
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Ying-Yi Huo
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Aharon Oren
- Department of Plant and Environmental Sciences, the Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jun-Yi Yang
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Chun-Sheng Wang
- Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
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Potential for plant growth promotion of rhizobacteria associated with Salicornia growing in Tunisian hypersaline soils. BIOMED RESEARCH INTERNATIONAL 2013; 2013:248078. [PMID: 23781499 PMCID: PMC3679824 DOI: 10.1155/2013/248078] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 12/05/2022]
Abstract
Soil salinity and drought are among the environmental stresses that most severely affect plant growth and production around the world. In this study the rhizospheres of Salicornia plants and bulk soils were collected from Sebkhet and Chott hypersaline ecosystems in Tunisia. Depiction of bacterial microbiome composition by Denaturing Gradient Gel Electrophoresis unveiled the occurrence of a high bacterial diversity associated with Salicornia root system. A large collection of 475 halophilic and halotolerant bacteria was established from Salicornia rhizosphere and the surrounding bulk soil, and the bacteria were characterized for the resistance to temperature, osmotic and saline stresses, and plant growth promotion (PGP) features. Twenty Halomonas strains showed resistance to a wide set of abiotic stresses and were able to perform different PGP activities in vitro at 5% NaCl, including ammonia and indole-3-acetic acid production, phosphate solubilisation, and potential nitrogen fixation. By using a gfp-labelled strain it was possible to demonstrate that Halomonas is capable of successfully colonising Salicornia roots in the laboratory conditions. Our results indicated that the culturable halophilic/halotolerant bacteria inhabiting salty and arid ecosystems have a potential to contribute to promoting plant growth under the harsh salinity and drought conditions. These halophilic/halotolerant strains could be exploited in biofertilizer formulates to sustain crop production in degraded and arid lands.
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Haber M, Shefer S, Giordano A, Orlando P, Gambacorta A, Ilan M. Aureivirga marina gen. nov., sp. nov., a marine bacterium isolated from the Mediterranean sponge Axinella verrucosa. Int J Syst Evol Microbiol 2013; 63:1089-1095. [DOI: 10.1099/ijs.0.043257-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, VI.14 and VIII.04T, were isolated from the Mediterranean sponge Axinella verrucosa collected off the Israeli coast near Sdot Yam. The non-motile, aerobic, Gram-negative isolates were oxidase-negative and catalase-positive, and formed golden-brown colonies on marine agar 2216. The pigment was neither diffusible nor flexirubin-like. Strain VIII.04T grew at 15–37 °C, at pH 6.0–9.0, in the presence of 20–50 g NaCl l−1 and 20–80 g sea salts l−1, The spectrum was narrower for strain VI.14, with growth at pH 7.0–8.0. and in the presence of 30–50 g NaCl l−1 and 30–70 g sea salts l−1. The predominant fatty acid (>50 %) in both strains was iso-C15 : 0, and the major respiratory quinone was MK-6. The DNA G+C content was 30.7 and 31.1 mol% for VIII.04T and VI.14, respectively. Results from 16S rRNA sequence similarity and phylogenetic analyses indicated that both strains are closely related to members of the family
Flavobacteriaceae
within the phylum
Bacteroidetes
, with as much as 91.7 % 16S rRNA sequence similarity. On the basis of data from the polyphasic analysis, we suggest that the strains represent a novel species in a new genus within the family
Flavobacteriaceae
, for which the name Aureivirga marina gen. nov., sp. nov. is proposed. Strain VIII.04T ( = ATCC BAA-2394T = LMG 26721T) is the type strain of Aureivirga marina.
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Affiliation(s)
- Markus Haber
- Department of Zoology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Sigal Shefer
- Department of Zoology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Assunta Giordano
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, 80078 Pozzuoli, Napoli, Italy
| | - Pierangelo Orlando
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, 80131 Napoli, Italy
| | - Agata Gambacorta
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, 80078 Pozzuoli, Napoli, Italy
| | - Micha Ilan
- Department of Zoology, Tel Aviv University, 69978 Tel Aviv, Israel
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14
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Spanò A, Gugliandolo C, Lentini V, Maugeri TL, Anzelmo G, Poli A, Nicolaus B. A Novel EPS-Producing Strain of Bacillus licheniformis Isolated from a Shallow Vent Off Panarea Island (Italy). Curr Microbiol 2013; 67:21-9. [DOI: 10.1007/s00284-013-0327-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/16/2013] [Indexed: 11/24/2022]
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15
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List of new names and new combinations previously effectively, but not validly, published – Validation List No. 141. Int J Syst Evol Microbiol 2011. [DOI: 10.1099/ijs.0.036640-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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16
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Salinivibrio sharmensis sp. nov., a novel haloalkaliphilic bacterium from a saline lake in Ras Mohammed Park (Egypt). Extremophiles 2011; 15:213-20. [DOI: 10.1007/s00792-010-0349-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
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17
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A halotolerant Alcanivorax sp. strain with potential application in saline soil remediation. Appl Microbiol Biotechnol 2010; 90:305-12. [PMID: 21153810 DOI: 10.1007/s00253-010-3049-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 11/27/2010] [Accepted: 11/28/2010] [Indexed: 11/27/2022]
Abstract
Biodegradation of petroleum compounds in saline environments seems intricate and needs more attention. In this study, tetracosane was used to enrich alkane-degrading bacteria from oil-contaminated saline soils. Among the isolates, strain Qtet3, with the highest 16s rRNA gene sequence similarity to Alcanivorax dieselolei B-5(T), was able to grow at a wide range of NaCl concentrations and was shown by GC analysis to degrade more than 90% of tetracosane in 10 days. This strain has at least two alkB genes and could grow on crude oil and diesel fuel, and utilize various pure aliphatic hydrocarbon substrates (from C(12) to C(34)). Highly hydrophobic cell surfaces and lack of significant surface tension reduction in the media suggest that the main mechanism of the cells for accessing substrate is to attach directly to hydrocarbon particles. Application of this strain for remediating crude oil-contaminated soils irrigated with defined saline water demonstrated that this halotolerant bacterium could survive and grow in saline soils irrigated with NaCl solutions up to 5% w/v, with the highest hydrocarbon degradation of 26.1% observed at 2.5% NaCl. This strain is promising for future industrial applications especially in bioremediation of saline soils and wastes.
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18
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Romano I, Dipasquale L, Orlando P, Lama L, d’Ippolito G, Pascual J, Gambacorta A. Thermoanaerobacterium thermostercus sp. nov., a new anaerobic thermophilic hydrogen-producing bacterium from buffalo-dung. Extremophiles 2010; 14:233-40. [DOI: 10.1007/s00792-010-0303-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 01/27/2010] [Indexed: 11/28/2022]
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19
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Bowers KJ, Mesbah NM, Wiegel J. Biodiversity of poly-extremophilic Bacteria: does combining the extremes of high salt, alkaline pH and elevated temperature approach a physico-chemical boundary for life? SALINE SYSTEMS 2009; 5:9. [PMID: 19930649 PMCID: PMC2785825 DOI: 10.1186/1746-1448-5-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 11/23/2009] [Indexed: 11/10/2022]
Abstract
Bacterial microorganisms that grow optimally at Na+ concentrations of 1.7 M, or the equivalent of 10% (w/v) NaCl, and greater are considered to be extreme halophiles. This review focuses on the correlation between the extent of alkaline pH and elevated temperature optima and the extent of salt tolerance of extremely halophilic eubacteria; the focus is on those with alkaline pH optima, above 8.5, and elevated temperature optima, above 50°C. If all three conditions are required for optimal growth, these microorganisms are termed "poly-extremophiles". However, only a very few extreme halophiles able to grow optimally under alkaline conditions as well as at elevated temperatures have been isolated so far. Therefore the question is: do the combined extreme growth conditions of the recently isolated poly-extremophiles, i.e., anaerobic halophilic alkalithermophiles, approach a physico-chemical boundary for life? These poly-extremophiles are of interest, as their adaptive mechanisms give insight into organisms' abilities to survive in environments which were previously considered prohibitive to life, as well as to possible properties of early evolutionary and extraterrestrial life forms.
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Affiliation(s)
- Karen J Bowers
- Department of Microbiology, University of Georgia, Athens, GA, USA.
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20
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Poli A, Romano I, Cordella P, Orlando P, Nicolaus B, Ceschi Berrini C. Anoxybacillus thermarum sp. nov., a novel thermophilic bacterium isolated from thermal mud in Euganean hot springs, Abano Terme, Italy. Extremophiles 2009; 13:867-74. [PMID: 19710998 DOI: 10.1007/s00792-009-0274-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 08/03/2009] [Indexed: 10/20/2022]
Abstract
A novel aerobe thermophilic endospore-forming bacterium designated strain AF/04(T) was isolated from thermal mud located in Euganean hot springs, Abano Terme, Padova, Italy. Strain AF/04(T) was Gram-positive, motile, rod-shaped, occurring in pairs, or filamentous. The isolate grew between 55 and 67 degrees C (optimum 65 degrees C) and at pH 6.0-7.5 (optimum pH 7.2). The strain was aerobic and grew on maltose, trehalose, and sodium acetate as sole carbon sources. The G + C content of DNA was 53.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AF/04(T) falls within the genus Anoxybacillus. Levels of 16S rRNA gene sequence similarity between strain AF/04(T) and the type strains of recognized Anoxybacillus species ranged from 95 to 99%. Chemotaxonomic data (major isoprenoid quinone-menaquinone-7; major fatty acid iso-C15:0 and anteiso-C17:0) supported the affiliation of strain AF/04(T) to the genus Anoxybacillus. Based on phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence analysis and DNA-DNA hybridization data, it was proposed that strain AF/04(T) (=DSM 17141(T) = ATCC BAA 1156(T)) should be placed in the genus Anoxybacillus as the type strain of a novel species, Anoxybacillus thermarum sp. nov.
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Affiliation(s)
- Annarita Poli
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078, Pozzuoli (Naples), Italy.
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