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Kothe CI, Monnet C, Irlinger F, Virsolvy M, Frühling A, Neumann-Schaal M, Wolf J, Renault P. Halomonas citrativorans sp. nov., Halomonas casei sp. nov. and Halomonas colorata sp. nov., isolated from French cheese rinds. Int J Syst Evol Microbiol 2024; 74. [PMID: 38265421 DOI: 10.1099/ijsem.0.006234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
Eight Gram-stain-negative bacterial strains were isolated from cheese rinds sampled in France. On the basis of 16S rRNA gene sequence analysis, all isolates were assigned to the genus Halomonas. Phylogenetic investigations, including 16S rRNA gene studies, multilocus sequence analysis, reconstruction of a pan-genome phylogenetic tree with the concatenated core-genome content and average nucleotide identity (ANI) calculations, revealed that they constituted three novel and well-supported clusters. The closest relative species, determined using the whole-genome sequences of the strains, were Halomonas zhanjiangensis for two groups of cheese strains, sharing 82.4 and 93.1 % ANI, and another cluster sharing 92.2 % ANI with the Halomonas profundi type strain. The strains isolated herein differed from the previously described species by ANI values <95 % and several biochemical, enzymatic and colony characteristics. The results of phenotypic, phylogenetic and chemotaxonomic analyses indicated that the isolates belonged to three novel Halomonas species, for which the names Halomonas citrativorans sp. nov., Halomonas casei sp. nov. and Halomonas colorata sp. nov. are proposed, with isolates FME63T (=DSM 113315T=CIRM-BIA2430T=CIP 111880T=LMG 32013T), FME64T (=DSM 113316T=CIRM-BIA2431T=CIP 111877T=LMG 32015T) and FME66T (=DSM 113318T=CIRM-BIA2433T=CIP 111876T=LMG 32014T) as type strains, respectively.
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Affiliation(s)
- Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Christophe Monnet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France
| | - Françoise Irlinger
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France
| | - Mathieu Virsolvy
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Anja Frühling
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Pierre Renault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Xu L, Wei HM, Sun YN, Wu Q, Gao XY, Shen B, Sun JQ. Halomonas rhizosphaerae sp. nov. and Halomonas kalidii sp. nov., two novel moderate halophilic phenolic acid-degrading species isolated from saline soil. Syst Appl Microbiol 2024; 47:126488. [PMID: 38278082 DOI: 10.1016/j.syapm.2024.126488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/01/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
Four vanillic acid-degrading bacterial strains, named LR5S13T, LR5S20, and M4R5S39T and LN1S58, were isolated from Kalidium cuspidatum rhizosphere and bulk soils, respectively. Phylogenetic analysis based on 16S rRNA gene as well as core genome revealed that LR5S13T and LR5S20 clustered closely with each other and with Halomonas ventosae Al12T, and that the two strains shared the highest similarities (both 99.3 %) with H. ventosae Al12T, in contrast, M4R5S39T and LN1S58 clustered together and with Halomonas heilongjiangensis 9-2T, and the two strains shared the highest similarities (99.4 and 99.2 %, respectively) with H. heilongjiangensis 9-2T. The average nucleotides identities based on BLAST (ANIb) and digital DNA-DNA hybridization (dDDH) values of strains LR5S13T to LR5S20, and M4R5S39T to LN1S58, were both higher than the threshold values for delineation of a species. The ANIb and dDDH values of the four strains to their closely relatives were lower than the threshold values. All four strains take phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids, Summed Feature 8, Summed Feature 3, and C16:0 as the major fatty acids. Based on the phylogenetic and phenotypic results, the four strains should be classified as two novel Halomonas species. Therefore, Halomonas rhizosphaerae sp. nov. (type strain LR5S13T = KCTC 8016T = CGMCC 1.62049T) and Halomonas kalidii (type strain M4R5S39T = KCTC 8015T = CGMCC 1.62047T) are proposed. The geographical distribution analysis based on 16S rRNA gene revealed that the two novel species are widely distributed across the globe, specifically in highly saline habits, especially in Central and Eastern Asia.
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Affiliation(s)
- Lian Xu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China; Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Hua-Mei Wei
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Ye-Nan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Qi Wu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Xiao-Yan Gao
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Biao Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China.
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de la Haba RR, Arahal DR, Sánchez-Porro C, Chuvochina M, Wittouck S, Hugenholtz P, Ventosa A. A long-awaited taxogenomic investigation of the family Halomonadaceae. Front Microbiol 2023; 14:1293707. [PMID: 38045027 PMCID: PMC10690426 DOI: 10.3389/fmicb.2023.1293707] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 12/05/2023] Open
Abstract
The family Halomonadaceae is the largest family composed of halophilic bacteria, with more than 160 species with validly published names as of July 2023. Several classifications to circumscribe this family are available in major resources, such as those provided by the List of Prokaryotic names with Standing in Nomenclature (LPSN), NCBI Taxonomy, Genome Taxonomy Database (GTDB), and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), with some degree of disagreement between them. Moreover, regardless of the classification adopted, the genus Halomonas is not phylogenetically consistent, likely because it has been used as a catch-all for newly described species within the family Halomonadaceae that could not be clearly accommodated in other Halomonadaceae genera. In the past decade, some taxonomic rearrangements have been conducted on the Halomonadaceae based on ribosomal and alternative single-copy housekeeping gene sequence analysis. High-throughput technologies have enabled access to the genome sequences of many type strains belonging to the family Halomonadaceae; however, genome-based studies specifically addressing its taxonomic status have not been performed to date. In this study, we accomplished the genome sequencing of 17 missing type strains of Halomonadaceae species that, together with other publicly available genome sequences, allowed us to re-evaluate the genetic relationship, phylogeny, and taxonomy of the species and genera within this family. The approach followed included the estimate of the Overall Genome Relatedness Indexes (OGRIs) such as the average amino acid identity (AAI), phylogenomic reconstructions using amino acid substitution matrices customized for the family Halomonadaceae, and the analysis of clade-specific signature genes. Based on our results, we conclude that the genus Halovibrio is obviously out of place within the family Halomonadaceae, and, on the other hand, we propose a division of the genus Halomonas into seven separate genera and the transfer of seven species from Halomonas to the genus Modicisalibacter, together with the emendation of the latter. Additionally, data from this study demonstrate the existence of various synonym species names in this family.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - David R. Arahal
- Departament of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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Lee SD, Kim IS. Larsenimonas rhizosphaerae sp. nov., isolated from a tidal mudflat. Int J Syst Evol Microbiol 2023; 73. [PMID: 37339061 DOI: 10.1099/ijsem.0.005930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
A Gram-reaction-negative, aerobic, motile, rod-shaped bacterium, designated GH3-8T, was isolated from rhizosphere mudflats of halophytes on the seashore of Gangwha Island, Republic of Korea. Growth was observed at pH 4-10 (optimum, pH 7-8), at 4-40 °C (optimum, 37 °C) and in the presence of 0.5-20 % (w/v) NaCl (optimum, 4 %). The predominant respiratory quinone was Q-9. The major fatty acids were C18 : 1 ω7c, C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C12 : 0 3OH. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified phosphoglycoaminolipid, an unidentified glycoaminolipid, two unidentified phospholipids and two unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences exhibited that the isolate belonged to the family Halomonadaceae, with the most closely related species, Larsenimonas suaedae (98.1 % sequence similarity) and Larsenimonas salina (97.9 %). Sequence similarity values between the isolate and other representatives of the family Halomonadaceae were all below 95.3 %. The values of average nucleotide identity between strain GH3-8T and members of the genus Larsenimonas were 73.42 % with L. salina CCM 8464T and 72.38 % with L. suaedae DSM 22428T. Strain GH3-8T showed digital DNA-DNA hybridization values of 18.5-18.6 % with members of the genus Larsenimonas. Based on phenotypic and chemotaxonomic distinctiveness together with low overall genomic relatedness indices and phylogenetic data, the isolate is considered to represent a new species of the genus Larsenimonas, for which the name Larsenimonas rhizosphaerae sp. nov. is proposed, with the type strain GH3-8T (=KCTC 62127T=NBRC 113214T).
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Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju 63243, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea
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Li X, Lu H, Wang Q, Yang H, Yang H, Wu J, Huang H. Halomonas binhaiensis sp. nov., isolated from saline-alkali soil. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748689 DOI: 10.1099/ijsem.0.005652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A Gram-stain-negative, aerobic and rod-shaped bacterium, strain Y2R2T, was isolated from a saline-alkali soil sample collected from Binhai New Area, Tianjin, PR China. Growth of strain Y2R2T was observed at 10-45 °C (optimum, 30 °C), at pH 6.0-11.0 (optimum, pH 9.0) and in the presence of 0-15 % (w/v) NaCl (optimum, 9.0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Y2R2T was affiliated with the genus Halomonas and showed the highest similarity to Halomonas huangheensis BJGMM-B45T (99.0%) and Halomonas cupida DSM 4740T (98.4%). The digital DNA-DNA hybridization and average nucleotide identity values of 21.0-22.8 % and 73.3-75.7 % with the closely related species H. huangheensis BJGMM-B45T, H. cupida DSM 4740T, H. ventosae AL12T, H. stenophila N12T and H. litopenaei SYSU ZJ2214T were lower than the threshold recommended for species discrimination.The major respiratory quinone of strain Y2R2T was Q-9 and the major cellular fatty acids consisted of C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The DNA G+C content of strain Y2R2T was 57.0 mol%. On the basis of this polyphasic taxonomic study, strain Y2R2T is considered to represent a novel species of the genus Halomonas, for which the name Halomonas binhaiensis sp. nov. is proposed. The type strain is Y2R2T (=CGMCC 1.16974T=KCTC 72578T).
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Affiliation(s)
- Xiaoyan Li
- Tianjin Agricultural University, Tianjin 300384, PR China
| | - Hegang Lu
- Tianjin Agricultural University, Tianjin 300384, PR China
| | - Qian Wang
- Tianjin Academy of Agricultural Sciences, Tianjin 300112, PR China
| | - Haixia Yang
- Tianjin Agricultural University, Tianjin 300384, PR China
| | - Hongpeng Yang
- Tianjin Agricultural University, Tianjin 300384, PR China
| | - Jiang Wu
- Tianjin Agricultural University, Tianjin 300384, PR China
| | - Haidong Huang
- Tianjin Agricultural University, Tianjin 300384, PR China
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Biswas J, Jana SK, Mandal S. Biotechnological impacts of Halomonas: a promising cell factory for industrially relevant biomolecules. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36253947 DOI: 10.1080/02648725.2022.2131961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
Abstract
Extremophiles are the most fascinating life forms for their special adaptations and ability to offer unique extremozymes or bioactive molecules. Halophiles, the natural inhabitants of hypersaline environments, are one among them. Halomonas are the common genus of halophilic bacteria. To support growth in unusual environments, Halomonas produces various hydrolytic enzymes, compatible solutes, biopolymers like extracellular polysaccharides (EPS) and polyhydroxy alkaloates (PHA), antibiotics, biosurfactants, pigments, etc. Many of such molecules are being produced in large-scale bioreactors for commercial use. However, the prospect of the remaining bioactive molecules with industrial relevance is far from their application. Furthermore, the genetic engineering of the respective gene clusters could open up a new path to bio-prospect these molecules by overproducing their products through heterologous expression. The present survey on Halomonas highlights their ecological diversity, application potential of the their various industrially relevant biomolecules and impact of these biomolecules on respective fields.
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Affiliation(s)
- Jhuma Biswas
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
| | - Santosh Kumar Jana
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
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Woods DF, Kozak IM, O'Gara F. Genome analysis and phenotypic characterization of Halomonas hibernica isolated from a traditional food process with novel quorum quenching and catalase activities. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36099016 DOI: 10.1099/mic.0.001238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Traditional food processes can utilize bacteria to promote positive organoleptic qualities and increase shelf life. Wiltshire curing has a vital bacterial component that has not been fully investigated from a microbial perspective. During the investigation of a Wiltshire brine, a culturable novel bacterium of the genus Halomonas was identified by 16S rRNA gene (MN822133) sequencing and analysis. The isolate was confirmed as representing a novel species (Halomonas hibernica B1.N12) using a housekeeping (HK) gene phylogenetic tree reconstruction with the selected genes 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA. The genome of the new isolate was sequenced and annotated and comparative genome analysis was conducted. Functional analysis revealed that the isolate has a unique phenotypic signature including high salt tolerance, a wide temperature growth range and substrate metabolism. Phenotypic and biochemical profiling demonstrated that H. hibernica B1.N12 possesses strong catalase activity which is an important feature for an industrial food processing bacterium, as it can promote an increased product shelf life and improve organoleptic qualities. Moreover, H. hibernica exhibits biocontrol properties based on its quorum quenching capabilities. Our work on this novel isolate advances knowledge on potential mechanistic interplays operating in complex microbial communities that mediate traditional food processes.
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Affiliation(s)
- David F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Iwona M Kozak
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
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Shang J, Xu L, Yang R, Zhao Y, Tang SK, Sun JQ. Halomonas alkalisoli sp. nov., a novel haloalkalophilic species from saline-alkaline soil, and reclassification of Halomonas daqingensis Wu et al. 2008 as a later heterotypic synonym of Halomonas desiderata Berendes et al. 1996. Syst Appl Microbiol 2022; 45:126351. [PMID: 35905572 DOI: 10.1016/j.syapm.2022.126351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 10/17/2022]
Abstract
Two Gram-stain-negative, strictly aerobic, moderately halophilic, non-spore-forming and rod-shaped bacteria, designated M5N1S17T and M5N1S15, were isolated from saline soil in Baotou, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered closely with Halomonas montanilacus PYC7WT and shared 99.1 and 99.3% sequence similarities, respectively. The average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm) values of the two strains with each other were 95.5% and 96.7%, respectively, while the ANIb and ANIm values between the two strains and 15 closer Halomonas species were 74.8-91.3% and 84.1-92.6%, respectively. The major polar lipids of M5N1S17T are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and an unidentified phospholipid. The major polar lipids of M5N1S15 are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids, and an unidentified lipid. The predominant ubiquinone in the two strains is Q-9. The major fatty acids of the two strains are C18:1ω6c and/or C18:1ω7c, C16:0, and C16:1ω7c and/or C16:1ω6c. Based on phylogenetic, phenotypic, and physiological results, strains M5N1S17T and M5N1S15 should be identified as a novel species of the genus Halomonas, for which Halomonas alkalisoli sp. nov. is proposed. The type strain is M5N1S17T (= CGMCC 1.19023T = KCTC 92130T). The phylogenetic trees showed that Halomonas daqingensis CGMCC 1.6443T clustered tightly with Halomonas desiderata FB2T, and the two strains shared >98.0% of ANI values with each other. Therefore, we propose the reclassification of H. daqingensis Wu et al. 2008 as a later heterotypic synonym of H. desiderata Berendes et al. 1996.
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Affiliation(s)
- Jia Shang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Rui Yang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Yang Zhao
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China.
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China.
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Bu X, Xia Z, Liu Z, Ren M, Wan C, Zhang L. Halomonas jincaotanensis sp. nov., isolated from the Pamir Plateau degrading polycyclic aromatic hydrocarbon. Arch Microbiol 2022; 204:398. [PMID: 35710957 DOI: 10.1007/s00203-022-03008-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 01/25/2023]
Abstract
A Gram-strain-negative, rod-shaped, aerobic bacterium, designated strain TRM 85114T, was isolated from the Jincaotan wetland in the Pamir Plateau of China. This strain grew optimally at 30 °C and pH 6.0 in the presence of 3% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TRM 85114T was affiliated with the genus Halomonas, and shared high sequence similarity with Halomonas korlensis XK1T (97.3%) and Halomonas tibetensis pyc13T (96.4%). Strain TRM 85114T contained C16:0 and C19:0 cyclo ω8c as primary cellular fatty acids, Q-9 as predominate respiratory quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipids of unknown structure containing glucosamine, unidentified aminophospholipids, unidentified lipids and three unidentified phospholipids as the major polar lipids. The complete genome of TRM 85114T comprised 3,902 putative genes with a total of 4,126,476 bp and a G + C content of 61.6%. The average nucleotide identity and digital DNA-DNA hybridization values between strain TRM 85114T and related type Halomonas strains of H. korlensis XK1T, H. tibetensis pyc13T, Chromohalobacter salexigens DSM 6768T, and Halomonas urumqiensis BZ-SZ-XJ27T were 75.4-88.9% and 22.9-39.2%, respectively. Based on phenotypic, chemotaxonomic, and molecular features, strain TRM 85114T represents a novel species of the genus Halomonas, for which the name is proposed as Halomonas jincaotanensis sp. nov.. The type strain is TRM 85114T (CCTCC AB 2021006T = LMG 32311T). The amount of 1-naphthylamine degradation by strain TRM 85114T reached up to 32.0 mg/L in 14 days.
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Affiliation(s)
- Xuying Bu
- State Key Laboratory Breeding Base for The Protection and Utilization of Biological Resources in Tarim Basin Co-funded By Xinjiang Corps and The Ministry of Science and Technology, College of Life Sciences and Technology, Tarim University, Alaer, 843300, Xinjiang, People's Republic of China
| | - Zhanfeng Xia
- State Key Laboratory Breeding Base for The Protection and Utilization of Biological Resources in Tarim Basin Co-funded By Xinjiang Corps and The Ministry of Science and Technology, College of Life Sciences and Technology, Tarim University, Alaer, 843300, Xinjiang, People's Republic of China
| | - Zhanwen Liu
- State Key Laboratory Breeding Base for The Protection and Utilization of Biological Resources in Tarim Basin Co-funded By Xinjiang Corps and The Ministry of Science and Technology, College of Life Sciences and Technology, Tarim University, Alaer, 843300, Xinjiang, People's Republic of China
| | - Min Ren
- State Key Laboratory Breeding Base for The Protection and Utilization of Biological Resources in Tarim Basin Co-funded By Xinjiang Corps and The Ministry of Science and Technology, College of Life Sciences and Technology, Tarim University, Alaer, 843300, Xinjiang, People's Republic of China.
| | - Chuanxing Wan
- State Key Laboratory Breeding Base for The Protection and Utilization of Biological Resources in Tarim Basin Co-funded By Xinjiang Corps and The Ministry of Science and Technology, College of Life Sciences and Technology, Tarim University, Alaer, 843300, Xinjiang, People's Republic of China
| | - Lili Zhang
- State Key Laboratory Breeding Base for The Protection and Utilization of Biological Resources in Tarim Basin Co-funded By Xinjiang Corps and The Ministry of Science and Technology, College of Life Sciences and Technology, Tarim University, Alaer, 843300, Xinjiang, People's Republic of China
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Wang L, Shao Z. Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis. Front Microbiol 2021; 12:652766. [PMID: 33815342 PMCID: PMC8014003 DOI: 10.3389/fmicb.2021.652766] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the "H. desiderata group." To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the "H. desiderata group," in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the "H. desiderata group," while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.
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Affiliation(s)
- Liping Wang
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- School of Environment, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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11
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Pandiyan K, Kushwaha P, Bagul SY, Chakdar H, Madhaiyan M, Krishnamurthi S, Kumar P, Karthikeyan N, Singh A, Kumar M, Singh UB, Saxena AK. Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India. Int J Syst Evol Microbiol 2020; 71. [PMID: 33351740 DOI: 10.1099/ijsem.0.004611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic, Gram-stain-negative, aerobic bacterium, strain D1-1T, belonging to the genus Halomonas, was isolated from soil sampled at Pentha beach, Odisha, India. Phylogenetic trees reconstructed based on 16S rRNA genes and multilocus sequence analysis of gyrB and rpoD genes revealed that strain D1-1T belonged to the genus Halomonas and was most closely related to Halomonas alimentaria YKJ-16T (98.1 %) followed by Halomonas ventosae Al12T (97.5 %), Halomonas sediminicola CPS11T (97.5 %), Halomonas fontilapidosi 5CRT (97.4 %) and Halomonas halodenitrificans DSM 735T (97.2 %) on the basis of 16S rRNA gene sequence similarity. Sequence identities with other species within the genus were lower than 97.0 %. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of 22.4-30 % and 79.5-85.4 % with close relatives of H. halodenitrificans DSM 735T, H. alimentaria YKJ-16T, H. ventosae Al12T and H. fontilapidosi 5CRT were lower than the threshold recommended for species delineation (70 % and 95-96 % for dDDH and ANI, respectively). Further, strain D1-1T formed yellow-coloured colonies; cells were rod-shaped, motile with optimum growth at 30 °C (range, 4-45 °C) and 2-8 % NaCl (w/v; grew up to 24 % NaCl). The major fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 0 and the main respiratory quinone was ubiquinone Q-9 in line with description of the genus. Based on its chemotaxonomic and phylogenetic characteristics and genome uniqueness, strain D1-1T represents a novel species in the genus Halomonas, for which we propose the name Halomonas icarae sp. nov., within the family Halomonadaceae. The type strain is D1-1T (=JCM 33602T=KACC 21317T=NAIMCC-B-2254T).
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Affiliation(s)
- Kuppusamy Pandiyan
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India.,Ginning Training Centre, ICAR - Central Institute for Research on Cotton Technology (CIRCOT), Nagpur, Maharashtra - 440023, India
| | - Prity Kushwaha
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Samadhan Y Bagul
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Hillol Chakdar
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Munusamy Madhaiyan
- Biomaterials and Biocatalysts, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Sector 39A, Chandigarh-160036, India
| | - Pravin Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Sector 39A, Chandigarh-160036, India
| | - Nanjappan Karthikeyan
- School of Water Stress Management, ICAR-National Institute for Abiotic Stress Management (NIASM), Baramati, Maharashtra - 413115, India.,ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Arjun Singh
- Regional Research Station, ICAR - Central Soil Salinity Research Institute (CSSRI), Lucknow, Uttar Pradesh - 226002, India.,ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Murugan Kumar
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Udai Bhan Singh
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
| | - Anil Kumar Saxena
- ICAR - National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh- 275103, India
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12
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Ramezani M, Pourmohyadini M, Nikou MM, Makzum S, Schumann P, Clermont D, Criscuolo A, Amoozegar MA, Kämpfer P, Spröer C. Halomonas lysinitropha sp. nov., a novel halophilic bacterium isolated from a hypersaline wetland. Int J Syst Evol Microbiol 2020; 70:6098-6105. [PMID: 33052803 DOI: 10.1099/ijsem.0.004504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We carried out a polyphasic taxonomic study on a new halophilic strain designated 3(2)T, isolated from Meighan wetland, Iran. Cells of the novel strain were Gram-stain-negative, non-hemolytic, catalase- and oxidase-positive, rod-shaped, non-endospore-forming and motile. Cell growth occurred at 3-15 % NaCl (w/v; optimum, 5 %), pH 7.0-9.0 (optimum, pH 7.5-8.0) and 15-35 °C (optimum, 30 °C). 16S rRNA gene sequence comparisons confirmed the affiliation of strain 3(2)T to the class Gammaproteobacteria and the genus Halomonas with highest similarity to Halomonas daqiaonensis YCSA28T (98.4 %) and Halomonas ventosae Al12T (97.9 %). Experimental and in silico DNA-DNA hybridization values were 42.7 and 35.1% with H. daqiaonensis IBRC-M 10931T and 48 and 35.2% with H. ventosae IBRC-M 10566T, respectively, and indicated that they are different members of the same genus. The genome of the type strain was characterized by a size of 3.83 Mbp with 63 scaffolds and a G+C content of 64.8 mol%. Moreover, the average nucleotide identity values against H. ventosae Al12T and H. daqiaonensis YCSA28T were 88.8 and 88.5 %, respectively. The predominant respiratory quinone was Q-9 (92 %) with Q-8 (8 %) as a minor component. Major fatty acids were C16 : 0 cyclo, C19 : 0 ω8c, C16 : 1 ω7c and/or iso-C15:0 2-OH, C12 : 0 3-OH and C18 : 1 ω7c. The polar lipid profile of the strain contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoaminoglycolipid and four unidentified phospholipids. According to our results, strain 3(2)T could be classified as a novel species in the genus Halomonas for which the name Halomonas lysinitropha sp. nov. is proposed. The type strain is 3(2)T (=IBRC M 10929T=LMG 29450T=CIP 111708T).
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Affiliation(s)
- Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
| | | | | | - Somaye Makzum
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | | | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique ‒ Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32 (IFZ), D-35392 Giessen, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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13
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Li X, Gan L, Hu M, Wang S, Tian Y, Shi B. Halomonas pellis sp. nov., a moderately halophilic bacterium isolated from wetsalted hides. Int J Syst Evol Microbiol 2020; 70:5417-5424. [DOI: 10.1099/ijsem.0.004426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A Gram-stain-negative, moderately halophilic strain, designated strain L5T, was isolated from wetsalted hides collected from Chengdu, south-west PR China. The cells were motile, facultative aerobic, short rod-shaped and non-endospore-forming. Growth of strain L5T occurred at pH 6–10 (optimum, pH 8), 10–45 °C (optimum, 30 °C) and in the presence of 1–17 % (w/v) NaCl (optimum, 10 %). Results of phylogenetic analyses based on 16S rRNA, gyrB and rpoD gene sequences and its genome revealed that strain L5T belonged to the genus
Halomonas
. Strain L5T was found to be most closely related to the type strains of
Halomonas saliphila
,
Halomonas lactosivorans
,
Halomonas kenyensis
,
Halomonas daqingensis
and
Halomonas desiderata
(98.8, 98.6, 98.3, 97.9 and 97.4 % 16S rRNA gene sequence similarity, respectively). The draft genome was approximately 4.2 Mb in size with a G+C content of 63.5 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization values among strain L5T and the selected
Halomonas
species were 83.3–88.9 % (ANIm), 71.1–87.3 % (ANIb) and 20.2–34.6 %, which are below the recommended cutoff values. Major fatty acids were C16 : 0, C16 : 1
ω7c, C18 : 1
ω7c and C19 : 0 cyclo ω8c and the predominant ubiquinone was Q-9, with minor ubiquinone Q-8 also present. The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, four unidentified aminophospholipids and three unidentified phospholipids. Based on the mentioned polyphasic taxonomic evidence, strain L5T represents a novel species within the genus
Halomonas
, for which Halomonas pellis sp. nov. is proposed. The type strain is L5T (=CGMCC 1.17335T=KCTC 72573T).
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Affiliation(s)
- Xiaoguang Li
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Longzhan Gan
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Mengyao Hu
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Shiting Wang
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
| | - Bi Shi
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
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14
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Ming H, Ji WL, Li M, Zhao ZL, Cheng LJ, Niu MM, Zhang LY, Wang Y, Nie GX. Halomonas lactosivorans sp. nov., isolated from salt-lake sediment. Int J Syst Evol Microbiol 2020; 70:3504-3512. [DOI: 10.1099/ijsem.0.004209] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A bacteria strain, designated CFH 90008T, was isolated from a salt lake sediment sample collected from Yuncheng city, Shanxi Province, PR China. Strain CFH 90008T was Gram-stain-negative, strictly aerobic, motile with lateral flagella and rod-shaped. Colonies were yellow, circular and smooth. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CFH 90008T belonged to the genus
Halomonas
, showing highest sequence similarity to
Halomonas daqingensis
DQD2-30T (98.6 %),
Halomonas saliphila
LCB169T (98.5 %),
Halomonas desiderata
FB2T (98.1 %) and
Halomonas kenyensis
AIR-2T (98.0 %). Good growth was observed at 10–50 °C, pH 6.0–9.0 and with NaCl concentration from 1.0 to 12.0 % (w/v). The predominant quinone was Q9. The major fatty acid (>10 %) was C18 : 1 ω7c, C16 : 0 and C16 : 1 ω7c. The genome of strain CFH 90008T was 4.36 Mbp with a genomic DNA G+C content of 66.7 mol%. Based on low average nucleotide identity and DNA–DNAhybridization results, chemotaxonomic characteristics, and differential physiological properties, strain CFH 90008T could not be classified into any recognized species of the genus
Halomonas
. Therefore, a new species, for which the name Halomonas lactosivorans sp. nov. is proposed. The type strain is CFH 90008T (=DSM 103220T=KCTC 52281T).
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Affiliation(s)
- Hong Ming
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Wei-li Ji
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Meng Li
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Zhuo-li Zhao
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Li-jiao Cheng
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Ming-ming Niu
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Ling-yu Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Yan Wang
- Synthetic Biology Engineering Lab of Henan Province, College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Guo-xing Nie
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
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15
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Li X, Chen J, Gan L, Tian Y, Shi B. Description of Salinicola corii sp. nov., a Halotolerant Bacterium Isolated from Wetsalted Hides. Curr Microbiol 2020; 77:1932-1938. [DOI: 10.1007/s00284-020-01989-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 04/08/2020] [Indexed: 10/24/2022]
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16
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Lu H, Xing P, Zhai L, Li H, Wu Q. Halomonas montanilacus sp. nov., isolated from hypersaline Lake Pengyanco on the Tibetan Plateau. Int J Syst Evol Microbiol 2020; 70:2859-2866. [DOI: 10.1099/ijsem.0.004109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, catalase- and oxidase-positive, aerobic, rod-shaped, motile strain (PYC7WT) was isolated from Lake Pengyanco on the Tibetan Plateau. Comparisons based on 16S rRNA gene sequences showed that strain PYC7WT belongs to the genus
Halomonas
, with
Halomonas malpeensis
YU-PRIM-29T and
Halomonas johnsoniae
T68687T as its closest neighbours (96.8 and 96.6 % 16S rRNA gene sequence similarity, respectively), and only 93.1 % 16S rRNA gene sequence similarity to
Halomonas elongata
ATCC 33173T. The predominant respiratory quinone of strain PYC7WT is Q-9, with Q-8 as a minor component. The major fatty acids are C18 : 1
ω6c and / or C18 : 1
ω7c, C16 : 0, C16 : 1
ω6c and/or C16 : 1
ω7c, and C12 : 0 3OH. The polar lipids of strain PYC7WT include phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. Genome sequencing revealed a genome size of 4.79 Mbp and a G+C content of 62.9 mol%. DNA–DNA hybridization values of strain PYC7WT showed 45, 30 and 38 % relatedness with
Halomonas johnsoniae
DSM 21197T,
Halomonas hamiltonii
DSM 21196T and
Halomonas stevensii
DSM 21198T, respectively. Combining phenotypic, biochemical, genotypic and DNA–DNA hybridization data, we propose that strain PYC7WT represents a novel species within the genus
Halomonas
and to have the name Halomonas montanilacus sp. nov.; PYC7WT (=CICC 24506T= KCTC 62529T) is the type strain.
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Affiliation(s)
- Huibin Lu
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Lei Zhai
- China Center of Industrial Culture Collection (CICC), China National Research, Institute of Food and Fermentation Industries, Beijing 100015, PR China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Qinglong Wu
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
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17
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Kushwaha B, Jadhav I, Jadhav K. Halomonas sambharensis sp. nov., a Moderately Halophilic Bacterium Isolated from the Saltern Crystallizer Ponds of the Sambhar Salt Lake in India. Curr Microbiol 2020; 77:1125-1134. [PMID: 32002626 DOI: 10.1007/s00284-020-01892-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/18/2020] [Indexed: 01/26/2023]
Abstract
Two moderately halophilic strains SBS 10T and SSO 06 were isolated from the saltern crystallizer ponds of the hypersaline Sambhar Salt Lake in India. Strains were aerobic, Gram-stain-negative, and rod shaped. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that two strains belong to the genus Halomonas in the Gammaproteobacteria, with highest 16S rRNA gene sequence similarities with Halomonas gudaonensis LMG 23610T (98.2% similarity) and Halomonas campaniensis 5AGT (99.0% similarity). Strains grew optimally at 37 °C, pH 7.5-8.0 in the presence of 5-8% (w/v) NaCl. The major fatty acids of the strain SBS 10T were C18:1ω7c (54.37%), C16:0 (25.69%), C16:1 × 7c/C16:1 × 6c (13.28%), and C12:0 (1.21%). The G+C content was 63.6 mol % (Tm). Phenotypic features, fatty acids profile, and DNA G+C content supported placement of the strain SBS 10T in the genus Halomonas having distinct characteristics with related strains. Analysis of the housekeeping genes: gryB and rpoD and in silico DNA-DNA hybridization between the strain SBS 10T and its type strain Halomonas gudaonensis (LMG 23610T) further revealed the strain SBS 10T to be a distinct species. On the basis of the phenotypic, chemotaxonomic and phylogenetic analysis, the strain SBS 10T is considered to represent a novel species for which the name Halomonas sambharensis is proposed. The type strain is SBS 10T (= MTCC 12313T = LMG 30344T).
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Affiliation(s)
| | - Indrani Jadhav
- School of Life Sciences, Jaipur National University, Jaipur, India
| | - Kapilesh Jadhav
- School of Engineering and Technology, Jaipur National University, Jaipur, India.
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18
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Navarro-Torre S, Carro L, Rodríguez-Llorente ID, Pajuelo E, Caviedes MÁ, Igual JM, Klenk HP, Montero-Calasanz MDC. Halomonas radicis sp. nov., isolated from Arthrocnemum macrostachyum growing in the Odiel marshes(Spain) and emended descriptions of Halomonas xinjiangensis and Halomonas zincidurans. Int J Syst Evol Microbiol 2020; 70:220-227. [DOI: 10.1099/ijsem.0.003742] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Salvadora Navarro-Torre
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Calle Profesor García González, 2, 41012 Sevilla, Spain
| | - Lorena Carro
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Ignacio D. Rodríguez-Llorente
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Calle Profesor García González, 2, 41012 Sevilla, Spain
| | - Eloísa Pajuelo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Calle Profesor García González, 2, 41012 Sevilla, Spain
| | - Miguel Ángel Caviedes
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Calle Profesor García González, 2, 41012 Sevilla, Spain
| | - José M. Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences (SNES), Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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19
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Phytohalomonas tamaricis gen. nov., sp. nov., an endophytic bacterium isolated from Tamarix ramosissima roots growing in Kumtag desert. Arch Microbiol 2019; 202:143-151. [PMID: 31535159 DOI: 10.1007/s00203-019-01724-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/05/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
A gram-stain-negative, aerobic, non-spore-forming, rod-shaped, non-motile bacterium strain R4HLG17T was isolated from Tamarix ramosissima roots growing in Kumtag desert. The strain grew at salinities of 0-16% (w/v) NaCl (optimum 5-6%), pH 5-9 (optimum 7) and at 16-45 °C. Based on 16S rRNA gene sequence similarity, strain R4HLG17T belonged to the family Halomonadaceae and was most closely related to Halomonas lutea DSM 23508T(95.1%), followed by Halotalea alkalilenta AW-7T(94.8%), Salinicola acroporae S4-41T(94.8%), Salinicola halophilus CG4.1T(94.6%), and Larsenimonas salina M1-18T(94.4%). Multilocus sequence analysis (MLSA) based on the partial sequences of 16S rRNA, atpA, gyrB, rpoD, and secA genes indicated that the strain R4HLG17T formed an independent and monophyletic branch related to other genera of Halomonadaceae, supporting its placement as a new genus in this family. The draft genome of strain R4HLG17T was 3.6 Mb with a total G + C content of 55.1%. The average nucleotide identity to Halomonas lutea DSM 23508T was 83.5%. Q-9 was detected as the major respiratory quinone and summed feature 8 (C18:1ω7c/C18:1ω6c), summed feature 3 (C16:1ω7c/C16:1ω6c), and C16:0 as predominant cellular fatty acids. On the basis of chemotaxonomic, phylogenetic, and phenotypic evidence, strain R4HLG17T is concluded to represent a novel species of a new genus within Halomonadaceae, for which the name Phytohalomonas tamaricis gen. nov., sp. nov., is proposed. The type strain is R4HLG17T (=ACCC 19929T=KCTC 52415T).
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Fidalgo C, Proença DN, Morais PV, Henriques I, Alves A. The endosphere of the salt marsh plant Halimione portulacoides is a diversity hotspot for the genus Salinicola: description of five novel species Salinicola halimionae sp. nov., Salinicola aestuarinus sp. nov., Salinicola endophyticus sp. nov., Salinicola halophyticus sp. nov. and Salinicola lusitanus sp. nov. Int J Syst Evol Microbiol 2018; 69:46-62. [PMID: 30418109 DOI: 10.1099/ijsem.0.003061] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven endophytic strains were isolated from the halophyte Halimione portulacoides, collected from Ria de Aveiro, Portugal. To determine their exact taxonomic position, comparative analyses were performed with these strains and closely related type strains of Salinicola species. Genome sequencing and comparison indicated that five of the seven isolated strains comprised distinct and novel species (average nucleotide identity <0.95; in silico DNA-DNA hybridization <70 %; G+C difference >1 %). Multilocus sequence analysis was performed using gyrB, rpoD and 16S rRNA gene sequences from the novel and type strains to determine their phylogenetic positions. The novel strains are facultative anaerobes, mesophilic, facultative alkaliphic and halophilic, test positive for catalase and oxidase activities, for hydrolysis of Tween 20 and phosphate, for production of indole-3-acetic acid, but do not produce H2S. Ubiquinone UQ-9 is present in major amounts in all strains. The major fatty acids include C16 : 0 and the summed feature containing C18 : 1ω7c and/or C18 : 1ω6c. The DNA G+C content ranges from 60.6 to 65.8 mol%. Five strains were confirmed as new species belonging to the genus Salinicola, for which the names Salinicolahalimionae sp. nov. (type strain CPA60T=CECT 9338T=LMG 30107T), Salinicolaaestuarinus sp. nov. (type strain CPA62T=CECT 9339T=LMG 30108T), Salinicolaendophyticus sp. nov. (type strain CPA92T=CECT 9340T=LMG 30109T), Salinicolahalophyticus sp. nov. (type strain CR45T=CECT 9341T=LMG 30105T) and Salinicola lusitanus sp. nov. (type strain CR50T=CECT 9342T=LMG 30106T) are proposed.
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Affiliation(s)
- Cátia Fidalgo
- 1Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | | | - Paula V Morais
- 2CEMMPRE, University of Coimbra, 3030-788 Coimbra, Portugal
- 3Department of Life Sciences, FCTUC, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Isabel Henriques
- 1Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Artur Alves
- 1Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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Isolation and characterization of halophilic bacteria producing exopolymers with emulsifying and antioxidant activities. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.10.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Lu HB, Xing P, Zhai L, Phurbu D, Tang Q, Wu QL. Halomonas tibetensis sp. nov., isolated from saline lakes on Tibetan Plateau. J Microbiol 2018; 56:493-499. [DOI: 10.1007/s12275-018-8076-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/19/2018] [Accepted: 05/08/2018] [Indexed: 10/14/2022]
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Gan L, Long X, Zhang H, Hou Y, Tian J, Zhang Y, Tian Y. Halomonas saliphila sp. nov., a moderately halophilic bacterium isolated from a saline soil. Int J Syst Evol Microbiol 2018; 68:1153-1159. [DOI: 10.1099/ijsem.0.002644] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Longzhan Gan
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Xiufeng Long
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Heming Zhang
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yanyan Hou
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Jiewei Tian
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and PeKing Union Medical College, Beijing 100050, PR China
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
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de la Haba RR, Corral P, Sánchez-Porro C, Infante-Domínguez C, Makkay AM, Amoozegar MA, Ventosa A, Papke RT. Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure. Front Microbiol 2018; 9:512. [PMID: 29662474 PMCID: PMC5890160 DOI: 10.3389/fmicb.2018.00512] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/06/2018] [Indexed: 11/13/2022] Open
Abstract
To gain a better understanding of how divergence occurs, and how taxonomy can benefit from studying natural populations, we isolated and examined 25 closely related Halorubrum strains obtained from different hypersaline communities and compared them to validly named species and other reference strains using five taxonomic study approaches: phylogenetic analysis using the 16S rRNA gene and multilocus sequencing analysis (MLSA), polar lipid profiles (PLP), average nucleotide identity (ANI) and DNA-DNA hybridization (DDH). 16S rRNA gene sequence could not differentiate the newly isolated strains from described species, while MLSA grouped strains into three major clusters. Two of those MLSA clusters distinguished candidates for new species. The third cluster with concatenated sequence identity equal to or greater than 97.5% was comprised of strains from Aran-Bidgol Lake (Iran) and solar salterns in Namibia and Spain, and two previously described species isolated from Mexico and Algeria. PLP and DDH analyses showed that Aran-Bidgol strains formed uniform populations, and that strains isolated from other geographic locations were heterogeneous and divergent, indicating that they may constitute different species. Therefore, applying only sequencing approaches and similarity cutoffs for circumscribing species may be too conservative, lumping concealed diversity into a single taxon. Further, our data support the interpretation that local populations experience unique evolutionary homogenization pressures, and once relieved of insular constraints (e.g., through migration) are free to diverge.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Carmen Infante-Domínguez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Andrea M. Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Mohammad A. Amoozegar
- Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
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25
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Kämpfer P, Rekha PD, Busse HJ, Arun AB, Priyanka P, Glaeser SP. Halomonas malpeensis sp. nov., isolated from rhizosphere sand of a coastal sand dune plant. Int J Syst Evol Microbiol 2018; 68:1037-1046. [PMID: 29458496 DOI: 10.1099/ijsem.0.002616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-endospore-forming organism, isolated from the rhizosphere sand of a coastal sand dune plant was studied for its taxonomic position. On the basis of 16S rRNA gene sequence similarity comparisons, strain YU-PRIM-29T was grouped within the genus Halomonas and was most closely related to Halomonas johnsoniae (97.5 %). The 16S rRNA gene sequence similarity to other Halomonas species was <97.5 %. Strain YU-PRIM-29T grew optimally at 28 °C (growth range, 10-36 °C), at a pH of 7-9 (growth range, pH 5.5-12.0) and in the presence of 0.5 to 5 % (w/v) NaCl (growth up to 20 % NaCl). The fatty acid profile from whole-cell hydrolysates supported the allocation of the strain to the genus Halomonas. The fatty acids C18 : 1ω7c and C16 : 0 were found as major compounds, followed by the hydroxylated fatty acid C12 : 0 3-OH. The quinone system consisted predominantly of ubiquinone Q-9. The polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In the polyamine pattern, spermidine was the predominant compound. The DNA G+C content was 64.8 mol%. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain YU-PRIM-29T from its closest-related species. Hence, YU-PRIM-29T represents a new species of the genus Halomonas, for which we propose the name Halomonas malpeensis sp. nov., with YU-PRIM-29T (=LMG 28855T=CCM 8737T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - P D Rekha
- Yenepoya Research Center, Yenepoya University, Mangalore 18, Karnataka State, India
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, Wien, Austria
| | - A B Arun
- Yenepoya Research Center, Yenepoya University, Mangalore 18, Karnataka State, India
| | - P Priyanka
- Yenepoya Research Center, Yenepoya University, Mangalore 18, Karnataka State, India
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Vahed SZ, Forouhandeh H, Tarhriz V, Chaparzadeh N, Hejazi MA, Jeon CO, Hejazi MS, Lee Y. Halomonas tabrizica sp. nov., a novel moderately halophilic bacterium isolated from Urmia Lake in Iran. Antonie van Leeuwenhoek 2018; 111:1139-1148. [DOI: 10.1007/s10482-018-1018-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/12/2018] [Indexed: 11/30/2022]
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Oguntoyinbo FA, Cnockaert M, Cho GS, Kabisch J, Neve H, Bockelmann W, Wenning M, Franz CMAP, Vandamme P. Halomonas nigrificans sp. nov., isolated from cheese. Int J Syst Evol Microbiol 2017; 68:371-376. [PMID: 29231158 DOI: 10.1099/ijsem.0.002515] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped Proteobacteria isolate, MBT G8648T, was obtained from an acid curd cheese called Quargel. The isolate was moderately salt tolerant and motile, with numerous peritrichous flagella. The 16S rRNA gene sequence analysis indicated that the strain belongs to the genus Halomonas, with 98.42 % 16S rRNA gene sequence similarity with Halomonas titanicae BH1T as nearest related neighbour. Further comparative sequence analysis of secA and gyrB genes, as well as physiological and biochemical tests, revealed that this bacterium formed a taxon well-separated from its nearest neighbours and other established Halomonas species. Thus, the strain represents a new species, for which the name Halomonas nigrificans sp. nov. is proposed, with strain MBT G8648T (=LMG 29097T =DSM 105749T) as type strain.
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Affiliation(s)
- Folarin A Oguntoyinbo
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Margo Cnockaert
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Jan Kabisch
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Wilhelm Bockelmann
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Mareike Wenning
- Lehrstuhl für Mikrobielle Ökologie, ZIEL-Institute for Food and Health, Technische Universität München, Weihenstephaner Berg 3, D-85354 Freising, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Str. 1, 24103 Kiel, Germany
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
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Koh HW, Rani S, Kim SJ, Moon E, Nam SW, Rhee SK, Park SJ. Halomonas aestuarii sp. nov., a moderately halophilic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2017; 67:4298-4303. [PMID: 28126041 DOI: 10.1099/ijsem.0.001824] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain Hb3T was isolated from a tidal flat in Jeollabuk-do Gunsan, Republic of Korea. Cells were Gram-stain-negative, oxidase- and catalase-positive, rod-shaped and motile. The strain grew optimally at 25-35 °C, at pH 6.0-6.5 and with 3.0-10.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Hb3T belonged to the genus Halomonas. Strain Hb3T was related most closely to Halomonas ventosae Al12T (98.6 % 16S rRNA gene sequence similarity), Halomonas denitrificans M29T (98.6 %) and Halomonas saccharevitans AJ275T (98.4 %). Moreover, multilocus sequence analysis using the gyrB, rpoD and secA genes supported the phylogenetic position of strain Hb3T. The genomic G+C content of strain Hb3T was 67.9 mol%. DNA-DNA hybridization values for strain Hb3T versus H. ventosae Al12T, H. denitrificans M29T and H. saccharevitans AJ275T were 38.0, 54.5 and 47.4 %, respectively. The major quinone was ubiquinone Q-9 and the major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and C19 : 0 cyclo ω8c. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, amino lipid, six unidentified phospholipids and an unidentified lipid comprised the polar lipid profile. On the basis of the data presented in this report, strain Hb3T represents a novel species of the genus Halomonas. The name Halomonas aestuarii sp. nov. is proposed for this novel species. The type strain is Hb3T (=KCTC 52253T=JCM 31415T).
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Affiliation(s)
- Heyon-Woo Koh
- Department of Biology, Jeju National University, Jejudaehak-ro 102, Jeju 63243, Republic of Korea
| | - Sundas Rani
- Department of Biology, Jeju National University, Jejudaehak-ro 102, Jeju 63243, Republic of Korea
| | - So-Jeong Kim
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Donam 2-gil, Sangju 37242, Republic of Korea.,Present address: Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, 124 Gwahak-ro, Daejeon, 34132, Republic of Korea
| | - Eunyoung Moon
- Division of Electron Microscopic Research, Korea Basic Science Institute, 169-148 Gwahak-ro, Yuseong-gu, Daejeon 34133, Republic of Korea
| | - Seung Won Nam
- Bioresources Culture Collection Division, Nakdonggang National Institute of Biological Resources, Donam 2-gil, Sangju 37242, Republic of Korea
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jejudaehak-ro 102, Jeju 63243, Republic of Korea
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López-Hermoso C, de la Haba RR, Sánchez-Porro C, Papke RT, Ventosa A. Assessment of MultiLocus Sequence Analysis As a Valuable Tool for the Classification of the Genus Salinivibrio. Front Microbiol 2017; 8:1107. [PMID: 28690592 PMCID: PMC5479898 DOI: 10.3389/fmicb.2017.01107] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/31/2017] [Indexed: 01/15/2023] Open
Abstract
The genus Salinivibrio includes obligatory halophilic bacteria and is commonly isolated from hypersaline habitats and salted food products. They grow optimally between 7.5 and 10% salts and are facultative anaerobes. Currently, this genus comprises four species, one of them, S. costicola, with three subspecies. In this study we isolated and characterized an additional 70 strains from solar salterns located in different locations. Comparative 16S rRNA gene sequence analysis identified these strains as belonging to the genus Salinivibrio but could not differentiate strains into species-like groups. To achieve finer phylogenetic resolution, we carried out a MultiLocus Sequence Analysis (MLSA) of the new isolates and the type strains of the species of Salinivibrio based on the individual as well as concatenated sequences of four housekeeping genes: gyrB, recA, rpoA, and rpoD. The strains formed four clearly differentiated species-like clusters called phylogroups. All of the known type and subspecies strains were associated with one of these clusters except S. sharmensis. One phylogroup had no previously described species coupled to it. Further DNA–DNA hybridization (DDH) experiments with selected representative strains from these phylogroups permitted us to validate the MLSA study, correlating the species level defined by the DDH (70%) with a 97% cut-off for the concatenated MLSA gene sequences. Based on these criteria, the novel strains forming phylogroup 1 could constitute a new species while strains constructing the other three phylogroups are members of previously recognized Salinivibrio species. S. costicola subsp. vallismortis co-occurs with S. proteolyticus in phylogroup 4, and separately from other S. costicola strains, indicating its need for reclassification. On the other hand, genome fingerprinting analysis showed that the environmental strains do not form clonal populations and did not cluster according to their site of cultivation. In future studies regarding the classification and identification of new Salinivibrio strains we recommend the following strategy: (i) initial partial sequencing of the 16S rRNA gene for genus-level identification; (ii) sequencing and concatenation of the four before mentioned housekeeping genes for species-level discrimination; (iii) DDH experiments, only required when the concatenated MLSA similarity values among a new isolate and other Salinivibrio strains are above the 97% cut-off.
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Affiliation(s)
- Clara López-Hermoso
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaSevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaSevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaSevilla, Spain
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, StorrsCT, United States
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of SevillaSevilla, Spain
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Zhao GY, Zhao LY, Xia ZJ, Zhu JL, Liu D, Liu CY, Chen XL, Zhang YZ, Zhang XY, Dai MX. Salinicola tamaricis sp. nov., a heavy-metal-tolerant, endophytic bacterium isolated from the halophyte Tamarix chinensis Lour. Int J Syst Evol Microbiol 2017; 67:1813-1819. [PMID: 28604335 DOI: 10.1099/ijsem.0.001868] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped bacterium, strain F01T, was isolated from leaves of Tamarix chinensis Lour. The isolate grew optimally at 30 °C, at pH 7.0 and with 5.0 % (w/v) NaCl, and showed a high tolerance to manganese, lead, nickel, ferrous ions and copper ions. The major fatty acids were C18 : 1ω7c and C16 : 0, and the predominant respiratory quinone was Q-9. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminoglycolipids and phospholipids. The DNA G+C content was 65.8 %. Based on multilocus phylogenetic analysis, strain F01T belonged to the genus Salinicola, with highest 16S rRNA gene sequence similarity to Salinicola peritrichatus CGMCC 1.12381T (97.7 %). The level of DNA-DNA hybridization between strain F01T and closely related Salinicola strains was well below 70 %. According to the phenotypic, genetic and chemotaxonomic data, strain F01T is considered to represent a novel species in the genus Salinicola, for which the name Salinicola tamaricis sp. nov. is proposed. The type strain is F01T (=CCTCC AB 2015304T=KCTC 42855T).
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Affiliation(s)
- Guo-Yan Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, Jinan 250014, PR China.,College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Li-Ya Zhao
- Shandong Provincial Key Laboratory of Plant Stress Research, Jinan 250014, PR China.,College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Zhi-Jie Xia
- Shandong Provincial Key Laboratory of Plant Stress Research, Jinan 250014, PR China.,College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Jin-Lei Zhu
- Shandong Provincial Key Laboratory of Plant Stress Research, Jinan 250014, PR China.,College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Di Liu
- Shandong Provincial Key Laboratory of Plant Stress Research, Jinan 250014, PR China.,College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Chun-Yue Liu
- Shandong Provincial Key Laboratory of Plant Stress Research, Jinan 250014, PR China.,College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Mei-Xue Dai
- Shandong Provincial Key Laboratory of Plant Stress Research, Jinan 250014, PR China.,College of Life Science, Shandong Normal University, Jinan 250014, PR China
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Williamson A, De Santi C, Altermark B, Karlsen C, Hjerde E. Complete genome sequence of Halomonas sp. R5-57. Stand Genomic Sci 2016; 11:62. [PMID: 27610212 PMCID: PMC5015195 DOI: 10.1186/s40793-016-0192-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/31/2016] [Indexed: 05/31/2024] Open
Abstract
The marine Arctic isolate Halomonas sp. R5-57 was sequenced as part of a bioprospecting project which aims to discover novel enzymes and organisms from low-temperature environments, with potential uses in biotechnological applications. Phenotypically, Halomonas sp. R5-57 exhibits high salt tolerance over a wide range of temperatures and has extra-cellular hydrolytic activities with several substrates, indicating it secretes enzymes which may function in high salinity conditions. Genome sequencing identified the genes involved in the biosynthesis of the osmoprotectant ectoine, which has applications in food processing and pharmacy, as well as those involved in production of polyhydroxyalkanoates, which can serve as precursors to bioplastics. The percentage identity of these biosynthetic genes from Halomonas sp. R5-57 and current production strains varies between 99 % for some to 69 % for others, thus it is plausible that R5-57 may have a different production capacity to currently used strains, or that in the case of PHAs, the properties of the final product may vary. Here we present the finished genome sequence (LN813019) of Halomonas sp. R5-57 which will facilitate exploitation of this bacterium; either as a whole-cell production host, or by recombinant expression of its individual enzymes.
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Affiliation(s)
- Adele Williamson
- Department of Chemistry, UiT- The Arctic University of Norway, N-9019 Tromsø, Norway
| | - Concetta De Santi
- Department of Chemistry, UiT- The Arctic University of Norway, N-9019 Tromsø, Norway
| | - Bjørn Altermark
- Department of Chemistry, UiT- The Arctic University of Norway, N-9019 Tromsø, Norway
| | - Christian Karlsen
- Department of Chemistry, UiT- The Arctic University of Norway, N-9019 Tromsø, Norway
- Division of Aquaculture, Nofima AS, PO Box 210, Ås, N-1431 Norway
| | - Erik Hjerde
- Department of Chemistry, UiT- The Arctic University of Norway, N-9019 Tromsø, Norway
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Pistricoccus aurantiacus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a shark. Antonie van Leeuwenhoek 2016; 109:1593-1603. [PMID: 27566710 DOI: 10.1007/s10482-016-0760-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 08/20/2016] [Indexed: 12/30/2022]
Abstract
A novel Gram-stain negative, non-motile, moderately halophilic, facultatively anaerobic and spherical bacterium designated strain SS9T was isolated from the gill homogenate of a shark. Cells of SS9T were observed to be 0.8-1.2 μm in diameter. The strain was found to grow optimally at 33 °C, pH 7.0-8.0 and in the presence of 6.0 % (w/v) NaCl. On the basis of 16S rRNA gene phylogeny, strain SS9T can be affiliated with the family Halomonadaceae and is closely related to Chromohalobacter marismortui NBRC 103155T (95.6 % sequence similarity), Halomonas ilicicola SP8T (95.6 %) and Chromohalobacter salexigens DSM 3043T (95.5 %). Multilocus sequence analysis of strain SS9T using the housekeeping genes 16S rRNA, 23S rRNA, gyrB, rpoD and secA revealed the strain's distinct phylogenetic position, separate from other known genera of the family Halomonadaceae. Strain SS9T was found to contain ubiquinone-9 (Q-9) as the predominant ubiquinone and C18:1 ω7c, C16:0 and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) as the major fatty acids. The major polar lipids of strain SS9T were identified as phosphatidylglycerol and phosphatidylethanolamine. The DNA G + C content of strain SS9T was determined to be 60.4 mol%. It is evident from phylogenetic, genotypic, phenotypic and chemotaxonomic results that strain SS9T represents a novel species in a new genus, for which the name Pistricoccus aurantiacus gen. nov., sp. nov. is proposed. The type strain is SS9T (=KCTC 42586T = MCCC 1H00111T).
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Wang T, Wei X, Xin Y, Zhuang J, Shan S, Zhang J. Halomonas lutescens sp. nov., a halophilic bacterium isolated from a lake sediment. Int J Syst Evol Microbiol 2016; 66:4697-4704. [PMID: 27514670 DOI: 10.1099/ijsem.0.001413] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, Gram-stain-negative, facultatively anaerobic, halophilic bacterium, designated strain Q1UT, was isolated from a sediment sample collected from Qinghai Lake, PR China. The cells of the strain were short rod-shaped (0.2-0.3×0.6-2.5 µm) and non-motile. Strain Q1UT formed yellowish colonies and grew at temperatures of 2-37 °C (optimum 30-33 °C), at pH 6.0-9.0 (optimum pH 7.0) and in the presence of 0-20 % (w/v) NaCl (optimum 7.5 %). The major cellular fatty acids were C18 : 1ω7c (58.6 %), C16 : 1ω7c and/or C16 : 1ω6c (14.8 %) and C16 : 0 (10.1 %). The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown phospholipid and unknown lipids. The genomic DNA G+C content was 61.5 mol%, and the predominant respiratory ubiquinone Q-9. Based on phylogenetic analysis of the 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences, the isolate was found to belong to the genus Halomonas in the class Gammaproteobacteria. The most closely related species were Halomonas venusta DSM 4743T (98.3 % 16S rRNA sequence similarity), Halomonas songnenensis DSM 25870T (98.2 %) and Halomonas hydrothermalis DSM 15725T (98.2 %). DNA-DNA relatedness values between strain Q1UT and the type strains of eight other species of the genus Halomonas ranged from 21.3 % to 10.1 %. On the basis of phenotypic, phylogenetic and chemotaxonomic analyses, and DNA-DNA hybridization relatedness values, strain Q1UT is considered to represent a novel species of the genus Halomonas; the name Halomonas lutescens sp. nov. is proposed. The type strain is Q1UT (=CGMCC 1.15122T=KCTC 42517T).
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Affiliation(s)
- Tianying Wang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Xuexin Wei
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Junli Zhuang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Shuangquan Shan
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Jianli Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
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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: 0.2] [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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Xia ZJ, Wu HZ, Cui CX, Chen Q, Zhao GY, Wang HX, Dai MX. Larsenimonas suaedae sp. nov., a moderately halophilic, endophytic bacterium isolated from the halophyte Suaeda salsa. Int J Syst Evol Microbiol 2016; 66:2952-2958. [PMID: 27129697 DOI: 10.1099/ijsem.0.001126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic, Gram-stain-negative, non-endospore-forming endophytic bacterium designated strain ST307T was isolated from the euhalophyte Suaeda salsa in Dongying, China. Strain ST307T was aerobic, rod-shaped, motile and orange-yellow-pigmented. The organism grew at NaCl concentrations of 0.6-20 % (w/v) (optimum 5-6 %, w/v), at temperatures of 5-45 °C (optimum 35 °C) and at pH 5-9 (optimum pH 7-8). It accumulated poly-β-hydroxybutyric acid and produced exopolysaccharides. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. The predominant lipoquinone was ubiquinone Q-9. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, a glycoaminolipid and a phosphoglycoaminolipid. The DNA G+C content was 60.5 mol%. Phylogenetic analyses of 16S rRNA gene sequences and concatenated atpA, rpoD and secA gene sequences revealed that the strain represents a member of the genus Larsenimonas. The closest related type strain was Larsenimonas salina M1-18T. Mean DNA-DNA relatedness values between strain ST307T and the related species L. salina M1-18T, Chromohalobacter beijerinckii DSM 7218T, C. canadensis DSM 6769T, C. israelensis DSM 6768T, C. marismortui CGMCC 1.2321T, C. nigrandesensis DSM 14323T, C. salexigens DSM 3043T and C. sarecensis DSM 15547T were 15±2-45±1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain ST307T clearly represents a novel species of the genus Larsenimonas. The name Larsenimonassuaedae sp. nov. is proposed, with ST307T (=CGMCC 1.8902T=DSM 22428T) as the type strain.
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Affiliation(s)
- Zhi-Jie Xia
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Hong-Zhen Wu
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Chun-Xiao Cui
- Medical College, Shandong Xiehe University, Jinan 250107, PR China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Guo-Yan Zhao
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Hai-Xia Wang
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Mei-Xue Dai
- College of Life Science, Shandong Normal University, Jinan 250014, PR 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: 1.1] [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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Raju K, Sekar J, Vaiyapuri Ramalingam P. Salinicola rhizosphaerae sp. nov., isolated from the rhizosphere of the mangrove Avicennia marina L. Int J Syst Evol Microbiol 2016; 66:1074-1079. [DOI: 10.1099/ijsem.0.000837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kathiravan Raju
- Microbiology Department, M.S. Swaminathan Research Foundation, 3rd Cross Street, Taramani Institutional Area, Chennai 600113, India
| | - Jegan Sekar
- Microbiology Department, M.S. Swaminathan Research Foundation, 3rd Cross Street, Taramani Institutional Area, Chennai 600113, India
| | - Prabavathy Vaiyapuri Ramalingam
- Microbiology Department, M.S. Swaminathan Research Foundation, 3rd Cross Street, Taramani Institutional Area, Chennai 600113, India
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Meyer JL, Dillard BA, Rodgers JM, Ritchie KB, Paul VJ, Teplitski M. Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata. Stand Genomic Sci 2015; 10:75. [PMID: 26451236 PMCID: PMC4597393 DOI: 10.1186/s40793-015-0069-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/28/2015] [Indexed: 11/24/2022] Open
Abstract
Members of the gammaproteobacterial genus Halomonas are common in marine environments. Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microbiota of reef-building corals. Halomonas meridiana strain R1t3 was isolated from the surface mucus layer of the scleractinian coral Acropora palmata in 2005 from the Florida Keys. This strain was chosen for genome sequencing to provide insight into the role of commensal heterotrophic bacteria in the coral holobiont. The draft genome consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397 protein-coding genes.
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Affiliation(s)
- Julie L Meyer
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA
| | - Brian A Dillard
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA
| | - John M Rodgers
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA
| | | | | | - Max Teplitski
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, FL USA ; Smithsonian Marine Station, Fort Pierce, FL USA
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Ntougias S, Lapidus A, Copeland A, Reddy TBK, Pati A, Ivanova NN, Markowitz VM, Klenk HP, Woyke T, Fasseas C, Kyrpides NC, Zervakis GI. High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea. Stand Genomic Sci 2015; 10:52. [PMID: 26380640 PMCID: PMC4572670 DOI: 10.1186/s40793-015-0052-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 07/28/2015] [Indexed: 12/28/2022] Open
Abstract
Members of the genus Halotalea (family Halomonadaceae) are of high significance since they can tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and are involved in the degradation of industrial effluents. Here, the characteristics and the permanent-draft genome sequence and annotation of Halotalea alkalilenta AW-7(T) are described. The microorganism was sequenced as a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project at the DOE Joint Genome Institute, and it is the only strain within the genus Halotalea having its genome sequenced. The genome is 4,467,826 bp long and consists of 40 scaffolds with 64.62 % average GC content. A total of 4,104 genes were predicted, comprising of 4,028 protein-coding and 76 RNA genes. Most protein-coding genes (87.79 %) were assigned to a putative function. Halotalea alkalilenta AW-7(T) encodes the catechol and protocatechuate degradation to β-ketoadipate via the β-ketoadipate and protocatechuate ortho-cleavage degradation pathway, and it possesses the genetic ability to detoxify fluoroacetate, cyanate and acrylonitrile. An emended description of the genus Halotalea Ntougias et al. 2007 is also provided in order to describe the delayed fermentation ability of the type strain.
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Affiliation(s)
- Spyridon Ntougias
- />Laboratory of Wastewater Management and Treatment Technologies, Department of Environmental Engineering, Democritus University of Thrace, Xanthi, Greece
| | - Alla Lapidus
- />Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- />Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Alex Copeland
- />Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA
| | - T. B. K. Reddy
- />Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA
| | - Amrita Pati
- />Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA
| | - Natalia N. Ivanova
- />Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA
| | - Victor M. Markowitz
- />Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Hans-Peter Klenk
- />Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- />Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA
| | - Constantinos Fasseas
- />Electron Microscopy Laboratory, Agricultural University of Athens, Athens, Greece
| | - Nikos C. Kyrpides
- />Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA USA
- />Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Georgios I. Zervakis
- />Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
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Comparative 16S rRNA signatures and multilocus sequence analysis for the genus Salinicola and description of Salinicola acroporae sp. nov., isolated from coral Acropora digitifera. Antonie van Leeuwenhoek 2015; 108:59-73. [PMID: 25944083 DOI: 10.1007/s10482-015-0464-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/24/2015] [Indexed: 10/23/2022]
Abstract
A novel Gram-negative, aerobic, motile marine bacterium, strain S4-41(T), was isolated from mucus of the coral Acropora digitifera from the Andaman Sea. Heterotrophic growth was observed in 0-25 % NaCl, at 15-45 °C and pH 4.5-9. In phylogenetic trees, strain S4-41(T) was grouped within the genus Salinicola but formed a separate branch distant from a cluster composed of Salinicola salarius M27(T) and Salinicola socius SMB35(T). DNA-DNA relatedness between strain S4-41(T) and these reference strains were well below 70 %. Q-9 was the sole respiratory quinone. The DNA G+C content was determined to be 63.6 mol%. Based on a polyphasic analysis, strain S4-41(T) is concluded to represent a novel species in the genus Salinicola for which the name Salinicola acroporae sp. nov. is proposed. The type strain is S4-41(T) (=JCM 30412(T) = LMG 28587(T)). Comparative 16S rRNA analysis of the genera Salinicola, Kushneria, Chromohalobacter and Cobetia revealed the presence of genus specific sequence signatures. Multilocus sequence analysis based on concatenated sequences of rRNAs (16S and 23S) and four protein coding housekeeping genes (atpA, gyrB, secA, rpoD) was found to be unnecessary for phylogenetic studies of the genus Salinicola.
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Glaeser SP, Kämpfer P. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 2015; 38:237-45. [PMID: 25959541 DOI: 10.1016/j.syapm.2015.03.007] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 11/17/2022]
Abstract
To obtain a higher resolution of the phylogenetic relationships of species within a genus or genera within a family, multilocus sequence analysis (MLSA) is currently a widely used method. In MLSA studies, partial sequences of genes coding for proteins with conserved functions ('housekeeping genes') are used to generate phylogenetic trees and subsequently deduce phylogenies. However, MLSA is not only suggested as a phylogenetic tool to support and clarify the resolution of bacterial species with a higher resolution, as in 16S rRNA gene-based studies, but has also been discussed as a replacement for DNA-DNA hybridization (DDH) in species delineation. Nevertheless, despite the fact that MLSA has become an accepted and widely used method in prokaryotic taxonomy, no common generally accepted recommendations have been devised to date for either the whole area of microbial taxonomy or for taxa-specific applications of individual MLSA schemes. The different ways MLSA is performed can vary greatly for the selection of genes, their number, and the calculation method used when comparing the sequences obtained. Here, we provide an overview of the historical development of MLSA and critically review its current application in prokaryotic taxonomy by highlighting the advantages and disadvantages of the method's numerous variations. This provides a perspective for its future use in forthcoming genome-based genotypic taxonomic analyses.
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Affiliation(s)
- Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany.
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Gupta RS, Naushad S, Baker S. Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov. Int J Syst Evol Microbiol 2014; 65:1050-1069. [PMID: 25428416 DOI: 10.1099/ijs.0.070136-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Halobacteria constitute one of the largest groups within the Archaea. The hierarchical relationship among members of this large class, which comprises a single order and a single family, has proven difficult to determine based upon 16S rRNA gene trees and morphological and physiological characteristics. This work reports detailed phylogenetic and comparative genomic studies on >100 halobacterial (haloarchaeal) genomes containing representatives from 30 genera to investigate their evolutionary relationships. In phylogenetic trees reconstructed on the basis of 32 conserved proteins, using both neighbour-joining and maximum-likelihood methods, two major clades (clades A and B) encompassing nearly two-thirds of the sequenced haloarchaeal species were strongly supported. Clades grouping the same species/genera were also supported by the 16S rRNA gene trees and trees for several individual highly conserved proteins (RpoC, EF-Tu, UvrD, GyrA, EF-2/EF-G). In parallel, our comparative analyses of protein sequences from haloarchaeal genomes have identified numerous discrete molecular markers in the form of conserved signature indels (CSI) in protein sequences and conserved signature proteins (CSPs) that are found uniquely in specific groups of haloarchaea. Thirteen CSIs in proteins involved in diverse functions and 68 CSPs that are uniquely present in all or most genome-sequenced haloarchaea provide novel molecular means for distinguishing members of the class Halobacteria from all other prokaryotes. The members of clade A are distinguished from all other haloarchaea by the unique shared presence of two CSIs in the ribose operon protein and small GTP-binding protein and eight CSPs that are found specifically in members of this clade. Likewise, four CSIs in different proteins and five other CSPs are present uniquely in members of clade B and distinguish them from all other haloarchaea. Based upon their specific clustering in phylogenetic trees for different gene/protein sequences and the unique shared presence of large numbers of molecular signatures, members of clades A and B are indicated to be distinct from all other haloarchaea because of their uniquely shared evolutionary histories. Based upon these results, it is proposed that clades A and B be recognized as two new orders, Natrialbales ord. nov. and Haloferacales ord. nov., within the class Halobacteria, containing the novel families Natrialbaceae fam. nov. and Haloferacaceae fam. nov. Other members of the class Halobacteria that are not members of these two orders will remain part of the emended order Halobacteriales in an emended family Halobacteriaceae.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Sohail Naushad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Sheridan Baker
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
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Larsenia salina gen. nov., sp. nov., a new member of the family Halomonadaceae based on multilocus sequence analysis. Syst Appl Microbiol 2014; 37:480-7. [DOI: 10.1016/j.syapm.2014.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/22/2014] [Accepted: 07/31/2014] [Indexed: 11/24/2022]
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44
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Li C, Lai Q, Li G, Liu Y, Sun F, Shao Z. Multilocus sequence analysis for the assessment of phylogenetic diversity and biogeography in hyphomonas bacteria from diverse marine environments. PLoS One 2014; 9:e101394. [PMID: 25019154 PMCID: PMC4096408 DOI: 10.1371/journal.pone.0101394] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 06/06/2014] [Indexed: 11/19/2022] Open
Abstract
Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus.
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Affiliation(s)
- Chongping Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guizhen Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, the Third Institute of State Oceanic Administration, Xiamen, China
- Collaborative Innovation Center of Marine Biological Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- * E-mail:
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45
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Kim KK, Lee JS, Stevens DA. Microbiology and epidemiology of Halomonas species. Future Microbiol 2014; 8:1559-73. [PMID: 24266356 DOI: 10.2217/fmb.13.108] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Halomonas has been organized as a genus since 1980, and comprises halophilic and/or halotolerant Gram-negative aerobic bacteria, typically found in saline environments. The genus is enlarging: at present, 76 species are taxonomically recognized, with more to be added. Increasing industrial uses have been found, largely in bioremediation and the production of desirable compounds. Originally seen as environmental contaminants, pathogenicity was initially not recognized; however, disease in algae, animals and humans has now been described. As the biotechnological use of these species increases, and the ability to isolate and recognize them improves, one might expect further pathogenic encounters with humans to be described.
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Affiliation(s)
- Kwang Kyu Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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46
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Jiang J, Pan Y, Hu S, Zhang X, Hu B, Huang H, Hong S, Meng J, Li C, Wang K. Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils. Int J Syst Evol Microbiol 2014; 64:1662-1669. [DOI: 10.1099/ijs.0.056499-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic bacterium (strain NEAU-ST10-39T) was isolated from saline and alkaline soils in the oilfield of Daqing City, Heilongjiang Province, China. The strain was strictly aerobic, Gram-stain-negative, rod-shaped and motile by peritrichous flagella. Its colonies were yellow. It grew at NaCl concentrations of 0.2–15 % (w/v) (optimum 4 %, w/v), at temperatures of 4–40 °C (optimum 35 °C) and at pH 5–10 (optimum pH 7). It did not produce acids from sugars or alcohols. Its DNA G+C content was 57.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD gene sequences indicated that it belonged to the genus
Halomonas
in the class
Gammaproteobacteria
. The most phylogenetically related species were
Halomonas axialensis
,
Halomonas meridiana
and
Halomonas aquamarina
, whose types shared 98.3 % (16S rRNA), 82.7 % (gyrB) and 83.9–84.5 % (rpoD) sequence similarity with strain NEAU-ST10-39T. The results of DNA–DNA hybridization assays showed 20±2 %–50±1 % relatedness between strain NEAU-ST10-39T and the most closely related species including
Halomonas axialensis
DSM 15723T,
Halomonas meridiana
DSM 5425T,
Halomonas aquamarina
DSM 30161T,
Halomonas johnsoniae
DSM 21197T,
Halomonas stevensii
DSM 21198T,
Halomonas nanhaiensis
CCTCC AB 2012911T,
Halomonas hamiltonii
DSM 21196T and
Halomonas arcis
CGMCC 1.6494T. The major fatty acids were C18 : 1ω7c (47.2 %), C16 : 1ω7c and/or C16 : 1ω6c (18.9 %) and C16 : 0 (16.3 %), the only respiratory quinone detected was ubiquinone 9 and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and three unknown lipids. The new isolate is proposed to represent a novel species with the name Halomonas songnenensis sp. nov., NEAU-ST10-39T ( = CGMCC 1.12152T = DSM 25870T) being the type strain.
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Affiliation(s)
- Juquan Jiang
- Department of Microbiology and Biotechnology, Northeast Agricultural University, and Key Laboratory of Soybean Biology of Ministry of Education, Harbin 150030, PR China
| | - Yuanyuan Pan
- Department of Microbiology and Biotechnology, Northeast Agricultural University, and Key Laboratory of Soybean Biology of Ministry of Education, Harbin 150030, PR China
| | - Shaoxin Hu
- Maize Research Center, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Xiaoxia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Baozhong Hu
- Department of Microbiology and Biotechnology, Northeast Agricultural University, and Key Laboratory of Soybean Biology of Ministry of Education, Harbin 150030, PR China
| | - Haipeng Huang
- Department of Microbiology and Biotechnology, Northeast Agricultural University, and Key Laboratory of Soybean Biology of Ministry of Education, Harbin 150030, PR China
| | - Shan Hong
- Department of Microbiology and Biotechnology, Northeast Agricultural University, and Key Laboratory of Soybean Biology of Ministry of Education, Harbin 150030, PR China
| | - Jing Meng
- Department of Microbiology and Biotechnology, Northeast Agricultural University, and Key Laboratory of Soybean Biology of Ministry of Education, Harbin 150030, PR China
| | - Cheng Li
- Department of Microbiology and Biotechnology, Northeast Agricultural University, and Key Laboratory of Soybean Biology of Ministry of Education, Harbin 150030, PR China
| | - Kaibiao Wang
- Department of Microbiology and Biotechnology, Northeast Agricultural University, and Key Laboratory of Soybean Biology of Ministry of Education, Harbin 150030, PR China
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47
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Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP, Papke RT. Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Front Microbiol 2014; 5:143. [PMID: 24782838 PMCID: PMC3988388 DOI: 10.3389/fmicb.2014.00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 03/19/2014] [Indexed: 01/29/2023] Open
Abstract
Halobacteria require high NaCl concentrations for growth and are the dominant inhabitants of hypersaline environments above 15% NaCl. They are well-documented to be highly recombinogenic, both in frequency and in the range of exchange partners. In this study, we examine the genetic and genomic variation of cultured, naturally co-occurring environmental populations of Halobacteria. Sequence data from multiple loci (~2500 bp) identified many closely and more distantly related strains belonging to the genera Halorubrum and Haloarcula. Genome fingerprinting using a random priming PCR amplification method to analyze these isolates revealed diverse banding patterns across each of the genera and surprisingly even for isolates that are identical at the nucleotide level for five protein coding sequenced loci. This variance in genome structure even between identical multilocus sequence analysis (MLSA) haplotypes indicates that accumulation of genomic variation is rapid: faster than the rate of third codon substitutions.
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Affiliation(s)
- Nikhil Ram Mohan
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Matthew S Fullmer
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Andrea M Makkay
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Ryan Wheeler
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, University of Seville Seville, Spain
| | - Adit Naor
- Molecular Microbiology and Biotechnology, Tel Aviv University Tel Aviv, Israel
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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48
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Amouric A, Liebgott PP, Joseph M, Brochier-Armanet C, Lorquin J. Halomonas olivaria sp. nov., a moderately halophilic bacterium isolated from olive-processing effluents. Int J Syst Evol Microbiol 2013; 64:46-54. [PMID: 24030688 DOI: 10.1099/ijs.0.049007-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic, Gram-stain-negative, non-sporulating bacterium designed as strain TYRC17(T) was isolated from olive-processing effluents. The organism was a straight rod, motile by means of peritrichous flagella and able to respire both oxygen and nitrate. Growth occurred with 0-25 % (w/v) NaCl (optimum, 7 %), at pH 5-11 (optimum, pH 7.0) and at 4-50 °C (optimally at 35 °C). It accumulated poly-β-hydroxyalkanoate granules and produced exopolysaccharides. The predominant fatty acids were C18 : 1ω7c, C16 : 1ω7c and C16 : 0. Ubiquinone 9 (Q-9) was the only respiratory quinone. The DNA G+C content of TYRC17(T) was 53.9 mol%. Phylogenetic analyses of 16S rRNA gene sequences revealed that the strain represents a member of the genus Halomonas and more precisely of the subgroup containing Halomonas sulfidaeris, H. titanicae, H. variabilis, H. zhanjiangensis, H. alkaliantarctica, H. boliviensis and H. neptunia. TYRC17(T) showed high 16S-rRNA sequence identities in particular with the three last species listed (99.4-99.5 %). A multilocus sequence analysis (MLSA) using the 23S rRNA, gyrB, rpoD and secA genes allowed clarifying the phylogenetic position of TYRC17(T). This, combined with the level of DNA-DNA hybridization between TYRC17(T) and its closest relatives ranging from 21.6 % to 48.4 %, indicated that TYRC17(T) did not represent any of these species. On the basis of phenotypic and genotypic characteristics, and also genomic and phylogenetic evidence, it was concluded that strain TYRC17(T) represented a novel species of the genus Halomonas. The name Halomonas olivaria sp. nov. is proposed with TYRC17(T) ( = DSM 19074(T) = CCUG 53850B(T)) as the type strain.
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Affiliation(s)
- Agnès Amouric
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille
| | - Pierre-Pol Liebgott
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille
| | - Manon Joseph
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 Boulevard du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Jean Lorquin
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 13288 Marseille
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49
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Halomonas zhaodongensis sp. nov., a slightly halophilic bacterium isolated from saline–alkaline soils in Zhaodong, China. Antonie van Leeuwenhoek 2013; 104:685-94. [DOI: 10.1007/s10482-013-9976-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/14/2013] [Indexed: 11/29/2022]
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50
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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: 2.1] [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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