1
|
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.
Collapse
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
| |
Collapse
|
2
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
ZHANG L, YANG Y, FENG S, LUO G, ZHANG M. Correlation between microbial communities changes and physicochemical indexes of Dazu Dongcai during different fermentation periods. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.93522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Ling ZHANG
- Chongqing University of Arts and Sciences, China; Chongqing Three Gorges University, China
| | - Yan YANG
- Chongqing University of Arts and Sciences, China; Chongqing Three Gorges University, China
| | - Shunxin FENG
- Chongqing University of Arts and Sciences, China
| | - Gen LUO
- Chongqing University of Arts and Sciences, China
| | - Meixia ZHANG
- Chongqing University of Arts and Sciences, China
| |
Collapse
|
5
|
Wenting R, Montazersaheb S, Khan SA, Kim HM, Tarhriz V, Hejazi MA, Hejazi MS, Jeon CO. Halomonas azerica sp. nov., Isolated from Urmia Lake in Iran. Curr Microbiol 2021; 78:3299-3306. [PMID: 34132870 DOI: 10.1007/s00284-021-02482-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/26/2021] [Indexed: 11/26/2022]
Abstract
A novel moderately halophilic, Gram-staining negative and facultative aerobic bacterium, designated as TBZ9T, was isolated from water of Urmia Lake in Azerbaijan region of Iran. The cells were found to be rod-shaped and motile, growing in the form of creamy, convex and shiny colonies. The strain could grow in the presence of NaCl at concentrations 1-17% (w/v) (optimum, 3%), temperatures 10-40 °C (optimum, 30 °C) and pH 6.0-11.0 (optimum, pH 7.0) on marine agar. Strain TBZ9T 16S rRNA gene sequence was related to the genus Halomonas showing highest similarities to Halomonas arcis AJ282T (98.4%), Halomonas songnenensis NEAU-ST10-39T (98.0%) and Halomonas lutescens Q1UT (97.8%). In the phylogenetic trees, strain TBZ9T formed a distinct branch closely related to a subclade inside the Halomonas genus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain TBZ9T and H. arcis AJ282T (20.0%, 74.0%) and H. songnenensis NEAU-ST10-39T (19.8%, 75.2%) indicated that TBZ9T represents a distinct species. Evaluation of fatty acid contents determined C10:0, C16:0, C12:0 3-OH, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) as major cellular fatty acids. The major quinone of strain TBZ9T was Q-9. Polar lipid patterns consisted of phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified phospholipids (PL) and four unidentified polar lipids (L). The average DNA G + C content of strain TBZ9T is 55.4 mol%. Results from phenotypic, chemotaxonomic and molecular analysis suggest that the strain TBZ9T represents a novel species within the genus Halomonas for which the name Halomonas azerica sp. nov. is proposed. The type strain is TBZ9T (= KACC 21783T = LMG 25775T).
Collapse
Affiliation(s)
- Ruan Wenting
- Department of Life Science, Chung Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Soheila Montazersaheb
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shehzad Abid Khan
- Department of Life Science, Chung Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Hyung Min Kim
- Department of Life Science, Chung Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amin Hejazi
- Branch for the Northwest and West Region, Agriculture Biotechnology Research Institute of Iran (ABRII), Tabriz, Iran
| | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Che Ok Jeon
- Department of Life Science, Chung Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea.
| |
Collapse
|
6
|
ODFM, an omics data resource from microorganisms associated with fermented foods. Sci Data 2021; 8:113. [PMID: 33879798 PMCID: PMC8058077 DOI: 10.1038/s41597-021-00895-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/23/2021] [Indexed: 11/08/2022] Open
Abstract
ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.
Collapse
|
7
|
Qiu X, Cao X, Xu G, Wu H, Tang X. Halomonas maris sp. nov., a moderately halophilic bacterium isolated from sediment in the southwest Indian Ocean. Arch Microbiol 2021; 203:3279-3285. [PMID: 33860341 DOI: 10.1007/s00203-021-02317-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/14/2021] [Accepted: 03/30/2021] [Indexed: 11/30/2022]
Abstract
A halophilic, Gram-staining-negative, rod-shaped, flagellated and motile bacterium, strain QX-1 T, was isolated from deep-sea sediment at a depth of 3332 m in the southwestern Indian Ocean. Strain QX-1 T growth was observed at 4-50 °C (optimum 37 °C), pH 5.0-11.0 (optimum pH 7.0), 3-25% NaCl (w/v; optimum 7%), and it did not grow without NaCl. A phylogenetic analysis based on the 16S rRNA gene placed strain QX-1 T in the genus Halomonas and most closely related to Halomonas sulfidaeris (97.9%), Halomonas zhaodongensis (97.8%), Halomonas songnenensis (97.6%), Halomonas hydrothermalis (97.4%), Halomonas subterranea (97.3%), Halomonas salicampi (97.1%), and Halomonas arcis (97.0%). DNA-DNA hybridization (< 26.5%) and average nucleotide identity values (< 83.5%) between strain QX-1 T and the related type strains meet the accepted criteria for a new species. The principal fatty acids (> 10%) of strain QX-1 T are C16:0 (25.5%), C17:0 cyclo (14.0%), C19:0 cyclo ω8c (18.7%), and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c, 18.1%). The polar lipids of strain QX-1 T are mainly diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipid, unidentified aminophospholipid, and five unidentified lipids. The main respiratory quinone is Q-9. The G + C content of its chromosomal DNA is 54.4 mol%. Its fatty acid profile, respiratory quinones, and G + C content also support the placement of QX-1 T in the genus Halomonas. These phylogenetic, phenotypic, and chemotaxonomic analyses indicate that QX-1 T is a novel species, for which the name Halomonas maris is proposed. The type strain is QX-1 T (= MCCC 1A17875T = KCTC 82198 T = NBRC 114670 T).
Collapse
Affiliation(s)
- Xu Qiu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.,School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Xiaorong Cao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Guangxin Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Huangming Wu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| |
Collapse
|
8
|
Zhang C, Zhang J, Liu D. Biochemical changes and microbial community dynamics during spontaneous fermentation of Zhacai, a traditional pickled mustard tuber from China. Int J Food Microbiol 2021; 347:109199. [PMID: 33878643 DOI: 10.1016/j.ijfoodmicro.2021.109199] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Zhacai is a traditional fermented vegetable that has been consumed in China for centuries. It is currently manufactured by spontaneous fermentation and therefore mostly relies on the activities of autochthonous microorganisms. Here, we characterized microbial community dynamics and associated biochemical changes in 12% salted Zhacai during a 90-day spontaneous fermentation process using high-throughput sequencing and chromatography-based approaches to identify associations between microorganisms and fermentation characteristics. Amplicon sequencing targeting bacterial 16S rRNA genes revealed that bacterial communities were dominated by halophilic bacteria (HAB, i.e., Halomonas and Idiomarina) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) after 30 days of fermentation. In addition, the relative abundances of the fungal genera Debaryomyces, Sterigmatomyces, and Sporidiobolus increased as fermentation progressed. Concomitantly, pH decreased while titratable acidity increased during fermentation, along with associated variation in biochemical profiles. Overall, the levels of organic acids (i.e., lactic and acetic acid), free amino acids (i.e., alanine, lysine, and glutamic acid), and volatiles (i.e., alcohols, esters, aldehydes, and ketones) increased in mature Zhacai. In addition, the abundances of Lactobacillus-related species, Halomonas spp., Idiomarina loihiensis, as well as that of the yeast Debaryomyces hansenii, were strongly correlated with increased concentrations of organic acids, amino acids, biogenic amines, and volatiles. This study provides new detailed insights into the succession of microbial communities and their potential roles in Zhacai fermentation.
Collapse
Affiliation(s)
- Chengcheng Zhang
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jianming Zhang
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Daqun Liu
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| |
Collapse
|
9
|
Qiu X, Yu L, Cao X, Wu H, Xu G, Tang X. Halomonas sedimenti sp. nov., a Halotolerant Bacterium Isolated from Deep-Sea Sediment of the Southwest Indian Ocean. Curr Microbiol 2021; 78:1662-1669. [PMID: 33651187 DOI: 10.1007/s00284-021-02425-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
A Gram-staining-negative, aerobic, flagellated, motile, rod-shaped, halophilic bacterium QX-2T was isolated from the deep-sea sediment of the Southwest Indian Ocean at a depth of 2699 m. Growth of the QX-2T bacteria was observed at 4-50 °C (optimum 30 °C), pH 5.0-12.0 (optimum pH 6.0) and 0%-30% NaCl (w/v) [optimum 4% (w/v)]. 16S rRNA gene sequencing revealed that strain QX-2T has the closest relationship with Halomonas titanicae DSM 22872T (98.2%). Phylogeny analysis classified the strain QX-2T into the genus Halomonas. The average nucleotide identity and DNA-DNA hybridization values between strain QX-2T and related type strains were lower than the currently accepted new species definition standards. Principal fatty acids (> 10%) determined were C16:0 (12.41%), C12:0-3OH (25.15%), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c, 11.55%) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c, 16.06%). Identified polar lipids in strain QX-2T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipid, unidentified aminophospholipid and five unidentified lipids (L1-L5). The main respiratory quinone was Q-9. The content of DNA G+C was determined to be 54.34 mol%. The results of phylogenetic analysis, phenotypic analysis and chemotaxonomic studies showed that strain QX-2T represents a novel species within the genus Halomonas, for which the name Halomonas sedimenti sp. nov. is proposed, with the type strain QX-2T (MCCC 1A17876T = KCTC 82199T).
Collapse
Affiliation(s)
- Xu Qiu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.,School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Libo Yu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Xiaorong Cao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Huangming Wu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Guangxin Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| |
Collapse
|
10
|
Yan F, Fang J, Cao J, Wei Y, Liu R, Wang L, Xie Z. Halomonas piezotolerans sp. nov., a multiple-stress-tolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench. Int J Syst Evol Microbiol 2020; 70:2560-2568. [PMID: 32129736 DOI: 10.1099/ijsem.0.004069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A piezotolerant, H2O2-tolerant, heavy-metal-tolerant, slightly halophilic bacterium (strain NBT06E8T) was isolated from a deep-sea sediment sample collected from the New Britain Trench at depth of 8900 m. The strain was aerobic, motile, Gram-stain-negative, rod-shaped, oxidase-positive and catalase-positive. Growth of the strain was observed at 4-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 8-9) and in 0.5-21 % (w/v) NaCl (optimum, 3-7 %). The optimum pressure for growth was 0.1-30 MPa with tolerance up to 60 MPa. Under optimum growth conditions, the strain could tolerate 15 mM H2O2. Resuls of 16S rRNA gene sequence analysis showed that strain NBT06E8T is closely related to Halomonas aquamarina DSM 30161T (99.5%), Halomonas meridiana DSM 5425T (99.43%) and Halomonas axialensis Althf1T (99.35%). The digital DNA-DNA hybridization values between strain NBT06E8T and the three related type strains, H. aquamarina, H. meridiana and H. axialensis, were 30.5±2.4 %, 30.7±2.5% and 31.5±2.5 %, respectively. The average nucleotide identity values between strain NBT06E8T and the three related type strains were 86.26, 86.26 and 83.63 %, respectively. The major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The predominant respiratory quinone detected was ubiquinone-9 (Q-9). Based on its phenotypic and phylogenetic characteristics, we conclude that strain NBT06E8T represents a novel species of the genus Halomonas, for which the name Halomonas piezotolerans sp. nov. is proposed (type strain NBT06E8T= MCCC 1K04228T=KCTC 72680T).
Collapse
Affiliation(s)
- Fangfang Yan
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jiasong Fang
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Junwei Cao
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Yuli Wei
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Rulong Liu
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Li Wang
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, PR China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
| |
Collapse
|
11
|
Khan SA, Zununi Vahed S, Forouhandeh H, Tarhriz V, Chaparzadeh N, Hejazi MA, Jeon CO, Hejazi MS. Halomonas urmiana sp. nov., a moderately halophilic bacterium isolated from Urmia Lake in Iran. Int J Syst Evol Microbiol 2020; 70:2254-2260. [PMID: 32039745 DOI: 10.1099/ijsem.0.004005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In the course of screening halophilic bacteria in Urmia Lake in Iran, which is being threatened by dryness, a novel Gram-negative, moderately halophilic, heterotrophic and short rod-shaped bacteria was isolated and characterized. The bacterium was isolated from a water specimen and designated as TBZ3T. Colonies were found to be creamy yellow, with catalase- and oxidase-positive activities. The growth of strain TBZ3T was observed to be at 10-45 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0.5-20 % (w/v) NaCl (optimum, 7.5 %). Strain TBZ3T contained C16 : 0, cyclo-C19 : 0 ω8c, summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c) as major fatty acids and ubiquinone-9 as the only respiratory isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid, unidentified phospholipid and unidentified polar lipids were detected as the major polar lipids. Strain TBZ3T was found to be most closely related to Halomonas saccharevitans AJ275T , Halomonas denitrificans M29T and Halomonas sediminicola CPS11T with the 16S rRNA gene sequence similarities of 98.93, 98.15 and 97.60 % respectively and in phylogenetic analysis strain TBZ3T grouped with Halomonas saccharevitans AJ275T contained within a large cluster within the genus Halomonas. Based on phenotypic, chemotaxonomic and molecular properties, strain TBZ3T represents a novel species of the Halomonas genus, for which the name Halomonas urmiana sp. nov. is proposed. The type strain is TBZ3T (=DSM 22871T=LMG 25416T).
Collapse
Affiliation(s)
- Shehzad Abid Khan
- Department of Life Science, Chung Ang University, Seoul 06974, Republic of Korea
| | | | - Haleh Forouhandeh
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nader Chaparzadeh
- Department of Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mohammad Amin Hejazi
- Branch for the Northwest and West Region, Agriculture Biotechnology Research Institute of Iran (ABRII), Tabriz, Iran
| | - Che Ok Jeon
- Department of Life Science, Chung Ang University, Seoul 06974, Republic of Korea
| | - Mohammad Saeid Hejazi
- School of Advanced Biomedical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|