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Cheng M, Li XX, Hou J, Cui HL. Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov., Halophilic Archaea Isolated from Coastal and Inland Saline Soil. Curr Microbiol 2024; 81:194. [PMID: 38806737 DOI: 10.1007/s00284-024-03746-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/19/2024] [Indexed: 05/30/2024]
Abstract
Four halophilic archaeal strains, BCD28T, BND7T, PSR21T, and PSRA2T, were isolated from coastal and inland saline soil, respectively. The 16S rRNA and rpoB' gene sequence similarities among these four strains and current species of Halomarina were 95.9-96.6% and 86.9-90.3%, respectively. Phylogenetic and phylogenomic analyses revealed that these four strains tightly cluster with the current species of the genus Halomarina. The AAI, ANI, and dDDH values among these four strains and current species of Halomarina were 65.3-68.4%, 75.8-77.7%, and 20.3-22.0%, respectively, clearly below the threshold values for species demarcation. Strains BCD28T, BND7T, PSR21T, and PSRA2T could be differentiated from the current species of Halomarina based on the comparison of diverse phenotypic characteristics. The major polar lipids of these four strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), and four to five glycolipids. Phosphatidylglycerol sulfate (PGS) was only detected in strain BND7T. The phenotypic, phylogenetic, and genome-based analyses suggested that strains BCD28T (= CGMCC 1.18776T = JCM 34908T), BND7T (= CGMCC 1.18778T = JCM 34910T), PSR21T (= CGMCC 1.17027T = JCM 34147T), and PSRA2T (= CGMCC 1.17214T = JCM 34148T) represent four novel species of the genus Halomarina, for which the names Halomarina litorea sp. nov., Halomarina pelagica sp. nov., Halomarina halobia sp. nov., and Halomarina ordinaria sp. nov. are proposed.
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Affiliation(s)
- Mu Cheng
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou, Zhenjiang, 212013, People's Republic of China
| | - Xin-Xin Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou, Zhenjiang, 212013, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou, Zhenjiang, 212013, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou, Zhenjiang, 212013, People's Republic of China.
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2
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Cui C, Han D, Hou J, Cui HL. Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486319 DOI: 10.1099/ijsem.0.005984] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
Currently, there are four mainstream taxonomic opinions on the classification of the class Halobacteria at the family and order levels. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria (ICSP), List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Centre for Biotechnology Information (NCBI) adopted taxonomies have three to four orders and up to eight families, while the Genome Taxonomy Database (GTDB) taxonomy proposes only one order with nine families. To resolve the taxonomic inconsistency, phylogenomic analyses based on concatenated single-copy orthologous proteins and 122 concatenated conserved single-copy marker proteins were conducted to infer the taxonomic status of the current representatives of the class Halobacteria at the family and order levels. The current 76 genera with validly published names of the class Halobacteria were able to be assigned into eight families in one order. On the basis of these results, it is proposed that the current species with validly published names of the class Halobacteria should be remerged into the order Halobacteriales, then assigned to eight families, Haladaptataceae, Haloarculaceae, Halobacteriaceae, Halococcaceae, Haloferacaceae, Natronoarchaeaceae, Natrialbaceae and Halorubellaceae. Thus, Haladaptataceae fam. nov. is described based on Haladaptatus, Halomicrococcus and Halorussus and Halorubellaceae fam. nov. is proposed incorporating Haloarchaeobius and Halorubellus, respectively.
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Affiliation(s)
- Can Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Dong Han
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
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3
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Chen M, Conroy JL, Sanford RA, Wyman-Feravich DA, Chee-Sanford JC, Connor LM. Tropical lacustrine sediment microbial community response to an extreme El Niño event. Sci Rep 2023; 13:6868. [PMID: 37106028 PMCID: PMC10140070 DOI: 10.1038/s41598-023-33280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015-2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.
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Affiliation(s)
- Mingfei Chen
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jessica L Conroy
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Joanne C Chee-Sanford
- Department of Natural Resource and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA-ARS, Urbana, IL, USA
| | - Lynn M Connor
- Department of Natural Resource and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA-ARS, Urbana, IL, USA
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4
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Tang SK, Zhi XY, Zhang Y, Makarova KS, Liu BB, Zheng GS, Zhang ZP, Zheng HJ, Wolf YI, Zhao YR, Jiang SH, Chen XM, Li EY, Zhang T, Chen PR, Feng YZ, Xiang MX, Lin ZQ, Shi JH, Chang C, Zhang X, Li R, Lou K, Wang Y, Chang L, Yin M, Yang LL, Gao HY, Zhang ZK, Tao TS, Guan TW, He FC, Lu YH, Cui HL, Koonin EV, Zhao GP, Xu P. Cellular differentiation into hyphae and spores in halophilic archaea. Nat Commun 2023; 14:1827. [PMID: 37005419 PMCID: PMC10067837 DOI: 10.1038/s41467-023-37389-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/14/2023] [Indexed: 04/04/2023] Open
Abstract
Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea.
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Affiliation(s)
- Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Bing-Bing Liu
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Guo-Song Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhen-Peng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 201203, China
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Yu-Rong Zhao
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Song-Hao Jiang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Xi-Ming Chen
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - En-Yuan Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Pei-Ru Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Yu-Zhou Feng
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ming-Xian Xiang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Zhi-Qian Lin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Jia-Hui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Xue Zhang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, China
| | - Rui Li
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Kai Lou
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Yun Wang
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Science, Urumqi, 830091, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Min Yin
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Ling-Ling Yang
- Yunnan Institute of Microbiology, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Hui-Ying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Zhong-Kai Zhang
- Biotechnology and Genetic Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Tian-Shen Tao
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China
| | - Tong-Wei Guan
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039, China
| | - Fu-Chu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China
| | - Yin-Hua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
| | - Guo-Ping Zhao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200032, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, 102206, China.
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Hebei, 071002, China.
- Department of Microbiology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China.
- Guizhou University, School of Medicine, Guiyang, 550025, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.
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5
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Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt. J Microbiol 2022; 60:899-904. [DOI: 10.1007/s12275-022-2137-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 10/17/2022]
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6
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Zhao W, Ma X, Liu X, Jian H, Zhang Y, Xiao X. Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal Vent. Front Microbiol 2020; 11:2081. [PMID: 33013758 PMCID: PMC7511516 DOI: 10.3389/fmicb.2020.02081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/07/2020] [Indexed: 11/13/2022] Open
Abstract
Hyperthermophiles, living in environments above 80°C and usually coupling with multi-extreme environmental stresses, have drawn great attention due to their application potential in biotechnology and being the primitive extant forms of life. Studies on their survival and adaptation mechanisms have extended our understanding on how lives thrive under extreme conditions. During these studies, the "cross-stress" behavior in various organisms has been observed between the extreme high temperature and other environmental stresses. Despite the broad observation, the global view of the cross-stress behavior remains unclear in hyperthermophiles, leaving a knowledge gap in our understanding of extreme adaptation. In this study, we performed a global quantitative proteomic analysis under extreme temperatures, pH, hydrostatic pressure (HP), and salinity on an archaeal strain, Thermococcus eurythermalis A501, which has outstanding growth capability on a wide range of temperatures (50-100°C), pH (4-9), and HPs (0.1-70 MPa), but a narrow range of NaCl (1.0-5.0 %, w/v). The proteomic analysis (79.8% genome coverage) demonstrated that approximately 61.5% of the significant differentially expressed proteins (DEPs) responded to multiple stresses. The responses to most of the tested stresses were closely correlated, except the responses to high salinity and low temperature. The top three enriched universal responding processes include the biosynthesis and protection of macromolecules, biosynthesis and metabolism of amino acids, ion transport, and binding activities. In addition, this study also revealed that the specific dual-stress responding processes, such as the membrane lipids for both cold and HP stresses and the signal transduction for both hyperosmotic and heat stresses, as well as the sodium-dependent energetic processes might be the limiting factor of the growth range in salinity. The present study is the first to examine the global cross-stress responses in a piezophilic hyperthermophile at the proteomic level. Our findings provide direct evidences of the cross-stress adaptation strategy (33.5% of coding-genes) to multiple stresses and highlight the specific and unique responding processes (0.22-0.63% of coding genes for each) to extreme temperature, pH, salinity, and pressure, which are highly relevant to the fields of evolutionary biology as well as next generation industrial biotechnology (NGIB).
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Affiliation(s)
- Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaopan Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoxia Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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7
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Verma A, Pal Y, Kumar P, Krishnamurthi S. Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil. Int J Syst Evol Microbiol 2020; 70:3693-3700. [DOI: 10.1099/ijsem.0.004222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A novel archaeal strain designated as SPP-AMP-1T was isolated from saltpan soil, using the serial dilution method on a halophilic archaeal medium supplemented with ampicillin. Cells were both rod-shaped and pleomorphic in nature, non-motile, unable to produce acid from a variety of sugars or grow anaerobically with different substrates (l-arginine) and electron acceptors (DMSO, nitrate). Optimal growth was observed at 42 °C, 3.4–4.2 M NaCl and pH 7.2. Cells did not lyse in distilled water and grew in the absence of Mg2+ ions. Phylogenetic analysis based on the sequences of 16S rRNA gene, amino acid sequence of β′-subunit of RNA polymerase and 400 conserved proteins retrieved from the whole genome assemblies showed that strain SPP-AMP-1T was distantly related to any existing genera within the family
Halobacteriaceae
. MK-8 was the only quinone detected. Polar lipid analysis showed a unique combination of diethyl derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, glycosyl-mannosyl-glucosyl diether and sulphated glycosyl-mannosyl-glucosyl diether as the major lipids. The G+C content of genomic DNA is 57.7 mol%. The phenotypic, phylogenetic and genomic data supported the concept of the novel genus status of strain SPP-AMP-1T in the family
Halobacteriaceae
for which the name Halocatena pleomorpha gen. nov., sp. nov., is proposed; the type strain is SPP-AMP-1T (=JCM 31368T=KCTC 4276T=MTCC 12579T).
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Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Yash Pal
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Pravin Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
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8
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Kırtel O, Versluys M, Van den Ende W, Toksoy Öner E. Fructans of the saline world. Biotechnol Adv 2018; 36:1524-1539. [DOI: 10.1016/j.biotechadv.2018.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 06/08/2018] [Accepted: 06/14/2018] [Indexed: 10/28/2022]
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9
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Hou J, Zhao YJ, Zhu L, Cui HL. Salinirubellus salinus gen. nov., sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2018; 68:1874-1878. [DOI: 10.1099/ijsem.0.002757] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Yang-Jie Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Lin Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
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10
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Zhou Y, Li Y, Lü ZZ, Cui HL. Halomarina rubra sp. nov., isolated from a marine solar saltern. Arch Microbiol 2017; 199:1431-1435. [PMID: 28779470 DOI: 10.1007/s00203-017-1420-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/27/2017] [Accepted: 07/29/2017] [Indexed: 10/19/2022]
Abstract
Halophilic archaeal strain ZS-47-ST was isolated from Zhoushan marine solar saltern, China. Cells were pleomorphic, stained Gram-negative, and formed red-pigmented colonies on agar plate. Strain ZS-47-ST was able to grow at 20-50 °C (optimum 37 °C), at 0.9-4.8 M NaCl (optimum 3.4 M), at 0.005-1.0 M MgCl2 (optimum 0.03 M), and at pH 5.5-9.5 (optimum pH 6.5-7.5). The cells lysed in distilled water and the minimal NaCl concentration to prevent cell-lysis was 5% (w/v). The major polar lipids were C20C20 and C20C25 diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, glucosyl mannosyl glucosyl diether, and three unidentified glycolipids. The 16S rRNA gene and rpoB' gene of strain ZS-47-ST were phylogenetically related to the corresponding genes of Halomarina oriensis JCM 16495T (98.57 and 92.94% similarities, respectively) and Halomarina salina CGMCC 1.12543T (97.96 and 93.65% similarities, respectively). The DNA G + C content of strain ZS-47-ST was 64.6 mol % (T m). The phenotypic, chemotaxonomic, and phylogenetic properties suggested that strain ZS-47-ST (=CGMCC 1.12563T = JCM 30037T) represents a new species of Halomarina, for which the name Halomarina rubra sp. nov. is proposed.
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Affiliation(s)
- Yao Zhou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Yang Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Zhen-Zhen Lü
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China.
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11
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Amoozegar MA, Siroosi M, Atashgahi S, Smidt H, Ventosa A. Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. MICROBIOLOGY-SGM 2017; 163:623-645. [PMID: 28548036 DOI: 10.1099/mic.0.000463] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Halophilic archaea, also referred to as haloarchaea, dominate hypersaline environments. To survive under such extreme conditions, haloarchaea and their enzymes have evolved to function optimally in environments with high salt concentrations and, sometimes, with extreme pH and temperatures. These features make haloarchaea attractive sources of a wide variety of biotechnological products, such as hydrolytic enzymes, with numerous potential applications in biotechnology. The unique trait of haloarchaeal enzymes, haloenzymes, to sustain activity under hypersaline conditions has extended the range of already-available biocatalysts and industrial processes in which high salt concentrations inhibit the activity of regular enzymes. In addition to their halostable properties, haloenzymes can also withstand other conditions such as extreme pH and temperature. In spite of these benefits, the industrial potential of these natural catalysts remains largely unexplored, with only a few characterized extracellular hydrolases. Because of the applied impact of haloarchaea and their specific ability to live in the presence of high salt concentrations, studies on their systematics have intensified in recent years, identifying many new genera and species. This review summarizes the current status of the haloarchaeal genera and species, and discusses the properties of haloenzymes and their potential industrial applications.
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Affiliation(s)
- 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
| | - Maryam Siroosi
- 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
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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Halomarina salina sp. nov., isolated from a marine solar saltern. Antonie van Leeuwenhoek 2016; 109:1121-6. [DOI: 10.1007/s10482-016-0714-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/10/2016] [Indexed: 11/26/2022]
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Gupta RS, Naushad S, Fabros R, Adeolu M. A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov. Antonie van Leeuwenhoek 2016; 109:565-87. [PMID: 26837779 DOI: 10.1007/s10482-016-0660-2] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/28/2016] [Indexed: 12/11/2022]
Abstract
The evolutionary interrelationships between the archaeal organisms which comprise the class Halobacteria have proven difficult to elucidate using traditional phylogenetic tools. The class currently contains three orders. However, little is known about the family level relationships within these orders. In this work, we have completed a comprehensive comparative analysis of 129 sequenced genomes from members of the class Halobacteria in order to identify shared molecular characteristics, in the forms of conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which can provide reliable evidence, independent of phylogenetic trees, that the species from the groups in which they are found are specifically related to each other due to common ancestry. Here we present 20 CSIs and 31 CSPs which are unique characteristics of infra-order level groups of genera within the class Halobacteria. We also present 40 CSIs and 234 CSPs which are characteristic of Haloarcula, Halococcus, Haloferax, or Halorubrum. Importantly, the CSIs and CSPs identified here provide evidence that the order Haloferacales contains two main groups, one consisting of Haloferax and related genera supported by four CSIs and five CSPs and the other consisting of Halorubrum and related genera supported by four CSPs. We have also identified molecular characteristics that suggest that the polyphyletic order Halobacteriales contains at least two large monophyletic clusters of organisms in addition to the polyphyletic members of the order, one cluster consisting of Haloarcula and related genera supported by ten CSIs and nineteen CSPs and the other group consisting of the members of the genus Halococcus supported by nine CSIs and 23 CSPs. We have also produced a highly robust phylogenetic tree based on the concatenated sequences of 766 proteins which provide additional support for the relationships identified by the CSIs and CSPs. On the basis of the phylogenetic analyses and the identified conserved molecular characteristics presented here, we propose a division of the order Haloferacales into two families, an emended family Haloferacaceae and Halorubraceae fam. nov. and a division of the order Halobacteriales into three families, an emended family Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada.
| | - Sohail Naushad
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Reena Fabros
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
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Patterns and determinants of halophilic archaea (class halobacteria) diversity in tunisian endorheic salt lakes and sebkhet systems. Appl Environ Microbiol 2015; 81:4432-41. [PMID: 25911472 DOI: 10.1128/aem.01097-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/17/2015] [Indexed: 12/13/2022] Open
Abstract
We examined the diversity and community structure of members of the halophilic Archaea (class Halobacteria) in samples from central and southern Tunisian endorheic salt lakes and sebkhet (also known as sebkha) systems using targeted 16S rRNA gene diversity survey and quantitative PCR (qPCR) approaches. Twenty-three different samples from four distinct locations exhibiting a wide range of salinities (2% to 37%) and physical characteristics (water, salt crust, sediment, and biofilm) were examined. A total of 4,759 operational taxonomic units at the 0.03 (species-level) cutoff (OTU0.03s) belonging to 45 currently recognized genera were identified, with 8 to 43 genera (average, 30) identified per sample. In spite of the large number of genera detected per sample, only a limited number (i.e., 2 to 16) usually constituted the majority (≥80%) of encountered sequences. Halobacteria diversity showed a strong negative correlation to salinity (Pearson correlation coefficient = -0.92), and community structure analysis identified salinity, rather than the location or physical characteristics of the sample, as the most important factor shaping the Halobacteria community structure. The relative abundance of genera capable of biosynthesis of the compatible solute(s) trehalose or 2-sulfotrehalose decreased with increasing salinities (Pearson correlation coefficient = -0.80). Indeed, qPCR analysis demonstrated that the Halobacteria otsB (trehalose-6-phosphatase)/16S rRNA gene ratio decreases with increasing salinities (Pearson correlation coefficient = -0.87). The results highlight patterns and determinants of Halobacteria diversity at a previously unexplored ecosystem and indicate that genera lacking trehalose biosynthetic capabilities are more adapted to growth in and colonization of hypersaline (>25% salt) ecosystems than trehalose producers.
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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: 122] [Impact Index Per Article: 12.2] [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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Youssef NH, Rinke C, Stepanauskas R, Farag I, Woyke T, Elshahed MS. Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'. ISME JOURNAL 2014; 9:447-60. [PMID: 25083931 DOI: 10.1038/ismej.2014.141] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/22/2014] [Accepted: 07/01/2014] [Indexed: 11/09/2022]
Abstract
The archaeal phylum 'Diapherotrites' was recently proposed based on phylogenomic analysis of genomes recovered from an underground water seep in an abandoned gold mine (Homestake mine in Lead, SD, USA). Here we present a detailed analysis of the metabolic capabilities and genomic features of three single amplified genomes (SAGs) belonging to the 'Diapherotrites'. The most complete of the SAGs, Candidatus 'Iainarchaeum andersonii' (Cand. IA), had a small genome (∼1.24 Mb), short average gene length (822 bp), one ribosomal RNA operon, high coding density (∼90.4%), high percentage of overlapping genes (27.6%) and low incidence of gene duplication (2.16%). Cand. IA genome possesses limited catabolic capacities that, nevertheless, could theoretically support a free-living lifestyle by channeling a narrow range of substrates such as ribose, polyhydroxybutyrate and several amino acids to acetyl-coenzyme A. On the other hand, Cand. IA possesses relatively well-developed anabolic capabilities, although it remains auxotrophic for several amino acids and cofactors. Phylogenetic analysis suggests that the majority of Cand. IA anabolic genes were acquired from bacterial donors via horizontal gene transfer. We thus propose that members of the 'Diapherotrites' have evolved from an obligate symbiotic ancestor by acquiring anabolic genes from bacteria that enabled independent biosynthesis of biological molecules previously acquired from symbiotic hosts. 'Diapherotrites' 16S rRNA genes exhibit multiple mismatches with the majority of archaeal 16S rRNA primers, a fact that could be responsible for their observed rarity in amplicon-generated data sets. The limited substrate range, complex growth requirements and slow growth rate predicted could be responsible for its refraction to isolation.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | | | - Ibrahim Farag
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Halapricum salinum gen. nov., sp. nov., an extremely halophilic archaeon isolated from non-purified solar salt. Antonie van Leeuwenhoek 2014; 105:979-86. [PMID: 24677144 DOI: 10.1007/s10482-014-0156-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/12/2014] [Indexed: 10/25/2022]
Abstract
A halophilic archaeal strain, designated CBA1105(T), was isolated from non-purified solar salt. Strain CBA1105(T) was found to have three 16S rRNA genes, rrnA, rrnB and rrnC; similarities between the 16S rRNA gene sequences were 99.5-99.7 %. The phylogenetic analysis of the 16S rRNA gene sequences showed that strain CBA1105(T) forms a distinct clade with the strains of the closely related genera, Halorientalis and Halorhabdus, with similarities of 94.2 % and 93.9-94.2 %, respectively. Multilocus sequence analysis confirmed that strain CBA1105(T) is closely related to the genus Halorhabdus or Halorientalis. Growth of the strain was observed in 15-30 % NaCl (w/v; optimum 20 %), at 30-45 °C (optimum 37 °C) and pH 7.0-8.0 (optimum pH 7.0) and with 0-0.5 M MgCl2·6H2O (optimum 0.05-0.2 M). The cells of the strain were observed to be Gram-stain negative and pleomorphic with coccoid or ovoid-shape. The cells lysed in distilled water. Tweens 20, 40 and 80 were found to be hydrolysed but starch, casein and gelatine were not. The cells were unable to reduce nitrate under aerobic conditions. Assays for indole formation and urease activity were negative and no growth was observed under anaerobic conditions. Cells were found to be able to utilize L-glutamate, D-glucose, L-maltose, D-mannose and sucrose as sole carbon sources. The polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, unidentified glycolipids and an unidentified phospholipid. The G+C content of strain CBA1105(T) was determined to be 66.0 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that the strain represents a novel species of a novel genus within the family Halobacteriaceae, for which the name Halapricum salinum is proposed with CBA1105(T) (= KCTC 4202(T) = JCM 19729(T)) as the type strain.
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Cui HL, Qiu XX. Salinarubrum litoreum gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from Chinese marine solar salterns. Antonie van Leeuwenhoek 2013; 105:135-41. [DOI: 10.1007/s10482-013-0061-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/17/2013] [Indexed: 10/26/2022]
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Youssef NH, Savage-Ashlock KN, McCully AL, Luedtke B, Shaw EI, Hoff WD, Elshahed MS. Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales. ISME JOURNAL 2013; 8:636-649. [PMID: 24048226 DOI: 10.1038/ismej.2013.165] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 11/09/2022]
Abstract
We investigated the mechanisms of osmoadaptation in the order Halobacteriales, with special emphasis on Haladaptatus paucihalophilus, known for its ability to survive in low salinities. H. paucihalophilus genome contained genes for trehalose synthesis (trehalose-6-phosphate synthase/trehalose-6-phosphatase (OtsAB pathway) and trehalose glycosyl-transferring synthase pathway), as well as for glycine betaine uptake (BCCT family of secondary transporters and QAT family of ABC transporters). H. paucihalophilus cells synthesized and accumulated ∼1.97-3.72 μmol per mg protein of trehalose in a defined medium, with its levels decreasing with increasing salinities. When exogenously supplied, glycine betaine accumulated intracellularly with its levels increasing at higher salinities. RT-PCR analysis strongly suggested that H. paucihalophilus utilizes the OtsAB pathway for trehalose synthesis. Out of 83 Halobacteriales genomes publicly available, genes encoding the OtsAB pathway and glycine betaine BCCT family transporters were identified in 38 and 60 genomes, respectively. Trehalose (or its sulfonated derivative) production and glycine betaine uptake, or lack thereof, were experimentally verified in 17 different Halobacteriales species. Phylogenetic analysis suggested that trehalose synthesis is an ancestral trait within the Halobacteriales, with its absence in specific lineages reflecting the occurrence of gene loss events during Halobacteriales evolution. Analysis of multiple culture-independent survey data sets demonstrated the preference of trehalose-producing genera to saline and low salinity habitats, and the dominance of genera lacking trehalose production capabilities in permanently hypersaline habitats. This study demonstrates that, contrary to current assumptions, compatible solutes production and uptake represent a common mechanism of osmoadaptation within the Halobacteriales.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Kristen N Savage-Ashlock
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,3Present address: Department of Biology, Georgia State University, Atlanta, Georgia
| | - Alexandra L McCully
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,4Present address: Department of Biology, Indiana University, Bloomington IN
| | - Brandon Luedtke
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,5Present address: US Department of Agriculture, Agricultural Research Service, Roman L. Hruska Meat Animal Research Center, Clay Center, NE 68933-0166
| | - Edward I Shaw
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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Minegishi H, Shimane Y, Echigo A, Ohta Y, Hatada Y, Kamekura M, Maruyama T, Usami R. Thermophilic and halophilic β-agarase from a halophilic archaeon Halococcus sp. 197A. Extremophiles 2013; 17:931-9. [PMID: 23949137 PMCID: PMC3824881 DOI: 10.1007/s00792-013-0575-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/30/2013] [Indexed: 11/28/2022]
Abstract
An agar-degrading archaeon Halococcus sp. 197A was isolated from a solar salt sample. The agarase was purified by hydrophobic column chromatography using a column of TOYOPEARL Phenyl-650 M. The molecular mass of the purified enzyme, designated as Aga-HC, was ~55 kDa on both SDS-PAGE and gel-filtration chromatography. Aga-HC released degradation products in the order of neoagarohexose, neoagarotetraose and small quantity of neoagarobiose, indicating that Aga-HC was a β-type agarase. Aga-HC showed a salt requirement for both stability and activity, being active from 0.3 M NaCl, with maximal activity at 3.5 M NaCl. KCl supported similar activities as NaCl up to 3.5 M, and LiCl up to 2.5 M. These monovalent salts could not be substituted by 3.5 M divalent cations, CaCl2 or MgCl2. The optimal pH was 6.0. Aga-HC was thermophilic, with optimum temperature of 70 °C. Aga-HC retained approximately 90 % of the initial activity after incubation for 1 hour at 65-80 °C, and retained 50 % activity after 1 hour at 95 °C. In the presence of additional 10 mM CaCl2, approximately 17 % remaining activity was detected after 30 min at 100 °C. This is the first report on agarase purified from Archaea.
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Affiliation(s)
- Hiroaki Minegishi
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe, Saitama, 350-8585, Japan,
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Ma B, Gong J. A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils. World J Microbiol Biotechnol 2013; 29:2325-34. [DOI: 10.1007/s11274-013-1399-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
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Polyextremophiles and the Constraints for Terrestrial Habitability. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Cui HL, Yang X, Zhou YG, Liu HC, Zhou PJ, Dyall-Smith ML. Halobellus limi sp. nov. and Halobellus salinus sp. nov., isolated from two marine solar salterns. Int J Syst Evol Microbiol 2012; 62:1307-1313. [PMID: 22661071 DOI: 10.1099/ijs.0.032169-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two halophilic archaea, strains TBN53(T) and CSW2.24.4(T), were characterized to elucidate their taxonomic status. Strain TBN53(T) was isolated from the Taibei marine solar saltern near Lianyungang city, Jiangsu province, China, whereas strain CSW2.24.4(T) was isolated from a saltern crystallizer in Victoria, Australia. Cells of the two strains were pleomorphic, stained Gram-negative and produced red-pigmented colonies. Strain TBN53(T) was able to grow at 25-55 °C (optimum 45 °C), with 1.4-5.1 M NaCl (optimum 2.6-3.9 M NaCl), with 0-1.0 M MgCl(2) (optimum 0-0.1 M MgCl(2)) and at pH 5.5-9.5 (optimum pH 7.0), whereas strain CSW2.24.4(T) was able to grow at 25-45 °C (optimum 37 °C), with 2.6-5.1 M NaCl (optimum 3.4 M NaCl), with 0.01-0.7 M MgCl(2) (optimum 0.05 M MgCl(2)) and at pH 5.5-9.5 (optimum pH 7.0-7.5). Cells of the two isolates lysed in distilled water. The minimum NaCl concentrations that prevented cell lysis were 8 % (w/v) for strain TBN53(T) and 12 % (w/v) for strain CSW2.24.4(T). The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate, with two glycolipids chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. Trace amounts of other unidentified lipids were also detected. On the basis of 16S rRNA gene sequence analysis, strains TBN53(T) and CSW2.24.4(T) showed 94.1 % similarity to each other and were closely related to Halobellus clavatus TNN18(T) (95.0 and 94.7 % similarity, respectively). Levels of rpoB' gene sequence similarity between strains TBN53(T) and CSW2.24.4(T), and between these strains and Halobellus clavatus TNN18(T) were 88.5, 88.5 and 88.1 %, respectively. The DNA G+C contents of strains TBN53(T) and CSW2.24.4(T) were 69.2 and 67.0 mol%, respectively. The level of DNA-DNA relatedness between strain TBN53(T) and strain CSW2.24.4(T) was 25 %, and these two strains showed low levels of DNA-DNA relatedness with Halobellus clavatus TNN18(T) (30 and 29 % relatedness, respectively). Based on these phenotypic, chemotaxonomic and phylogenetic properties, two novel species of the genus Halobellus are proposed to accommodate these two strains, Halobellus limi sp. nov. (type strain TBN53(T) = CGMCC 1.10331(T) = JCM 16811(T)) and Halobellus salinus sp. nov. (type strain CSW2.24.4(T) = DSM 18730(T) = CGMCC 1.10710(T) = JCM 14359(T)).
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Affiliation(s)
- Heng-Lin Cui
- School of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xin Yang
- School of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Yu-Guang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Pei-Jin Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Mike L Dyall-Smith
- Department of Membrane Biochemistry, Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
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Phylogenetic diversities and community structure of members of the extremely halophilic Archaea (order Halobacteriales) in multiple saline sediment habitats. Appl Environ Microbiol 2011; 78:1332-44. [PMID: 22179255 DOI: 10.1128/aem.07420-11] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We investigated the phylogenetic diversity and community structure of members of the halophilic Archaea (order Halobacteriales) in five distinct sediment habitats that experience various levels of salinity and salinity fluctuations (sediments from Great Salt Plains and Zodletone Spring in Oklahoma, mangrove tree sediments in Puerto Rico, sediment underneath salt heaps in a salt-processing plant, and sediments from the Great Salt Lake northern arm) using Halobacteriales-specific 16S rRNA gene primers. Extremely diverse Halobacteriales communities were encountered in all habitats, with 27 (Zodletone) to 37 (mangrove) different genera identified per sample, out of the currently described 38 Halobacteriales genera. With the exception of Zodletone Spring, where the prevalent geochemical conditions are extremely inhospitable to Halobacteriales survival, habitats with fluctuating salinity levels were more diverse than permanently saline habitats. Sequences affiliated with the recently described genera Halogranum, Halolamina, Haloplanus, Halosarcina, and Halorientalis, in addition to the genera Halorubrum, Haloferax, and Halobacterium, were among the most abundant and ubiquitous genera, suggesting a wide distribution of these poorly studied genera in saline sediments. The Halobacteriales sediment communities analyzed in this study were more diverse than and completely distinct from communities from typical hypersaline water bodies. Finally, sequences unaffiliated with currently described genera represented a small fraction of the total Halobacteriales communities, ranging between 2.5% (Zodletone) to 7.0% (mangrove and Great Salt Lake). However, these novel sequences were characterized by remarkably high levels of alpha and beta diversities, suggesting the presence of an enormous, yet-untapped supply of novel Halobacteriales genera within the rare biosphere of various saline ecosystems.
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Cui HL, Yang X, Mou YZ. Salinarchaeum laminariae gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from salted brown alga Laminaria. Extremophiles 2011; 15:625-31. [PMID: 21901373 DOI: 10.1007/s00792-011-0393-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 08/22/2011] [Indexed: 11/29/2022]
Abstract
Halophilic archaeal strains R26(T) and R22 were isolated from the brown alga Laminaria produced at Dalian, Liaoning Province, China. Cells from the two strains were pleomorphic rods and Gram negative, and colonies were red pigmented. Strains R26(T) and R22 were able to grow at 20-50°C (optimum 37°C) in 1.4-5.1 M NaCl (optimum 3.1-4.3 M) at pH 5.5-9.5 (optimum pH 8.0-8.5) and neither strain required Mg(2+) for growth. Cells lyse in distilled water and the minimum NaCl concentration required to prevent cell lysis was 8% (w/v) for strain R26(T) and 12% (w/v) for strain R22. The major polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and minor phosphatidylglycerol sulfate; glycolipids were not detected. Phylogenetic analyses based on 16S rRNA genes and rpoB' genes revealed that strains R26(T) and R22 formed a distinct clade with the closest relative, Natronoarchaeum mannanilyticum. The DNA G+C content of strains R26(T) and R22 was 65.8 and 66.4 mol%, respectively. The DNA-DNA hybridization value between strains R26(T) and R22 was 89%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that the strains R26(T) and R22 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Salinarchaeum laminariae gen. nov., sp. nov. is proposed. The type strain is R26(T) (type strain R26(T) = CGMCC 1.10590(T) = JCM 17267(T), reference strain R22 = CGMCC 1.10589).
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Jingkou District, Zhenjiang, People's Republic of China.
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Shimane Y, Hatada Y, Minegishi H, Echigo A, Nagaoka S, Miyazaki M, Ohta Y, Maruyama T, Usami R, Grant WD, Horikoshi K. Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt. Int J Syst Evol Microbiol 2010; 61:2266-2270. [PMID: 20952548 DOI: 10.1099/ijs.0.025064-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain YSM-79(T) was isolated from commercial salt made from seawater in Yonaguni island, Okinawa, Japan. The strain is an aerobic, Gram-negative, chemo-organotrophic and extremely halophilic archaeon. Cells are short rods that lyse in distilled water. Growth occurs at 1.5-5.3 M NaCl (optimum 2.5-3.0 M), pH 5.0-8.8 (optimum pH 5.2-6.3) and 20-55 °C (optimum 40 °C). Mg²⁺ is required for growth, with maximum growth at 200-300 mM Mg²⁺. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, sulfated diglycosyl diether-1 and five unidentified glycolipids. The G+C content of the DNA was 64 mol%. On the basis of 16S rRNA gene sequence analysis, strain YSM-79(T) was determined to be a member of the family Halobacteriaceae, with the closest related genus being Halobacterium (94 % sequence identity). In addition, the rpoB' gene sequence of strain YSM-79(T) had <88 % sequence similarity to those of other members of the family Halobacteriaceae. The results of phenotypic, chemotaxonomic and phylogenetic analysis suggested that strain YSM-79(T) should be placed in a new genus, Salarchaeum gen. nov., as a representative of Salarchaeum japonicum sp. nov. The type strain is YSM-79(T) ( = JCM 16327(T) = CECT 7563(T)).
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Affiliation(s)
- Yasuhiro Shimane
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Hiroaki Minegishi
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Akinobu Echigo
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Syuhei Nagaoka
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Masayuki Miyazaki
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yukari Ohta
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Ron Usami
- Bio-Nano Electronics Research Center, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - William D Grant
- Department of Infection, Immunity and Inflammation, University of Leicester, Maurice Shock Medical Sciences Building, Leicester LE1 9HN, UK
| | - Koki Horikoshi
- Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan.,Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
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Cui HL, Gao X, Yang X, Xu XW. Halolamina pelagica gen. nov., sp. nov., a new member of the family Halobacteriaceae. Int J Syst Evol Microbiol 2010; 61:1617-1621. [PMID: 20693359 DOI: 10.1099/ijs.0.026799-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaeal strains, TBN21(T) and TBN49, were isolated from the Taibei marine solar saltern near Lianyungang city, Jiangsu province, China. Cells of the two strains were pleomorphic and gram-negative and colonies were red. Strains TBN21(T) and TBN49 were able to grow at 25-50 °C (optimum 37 °C), at 1.4-5.1 M NaCl (optimum 3.4-3.9 M) and at pH 5.5-9.5 (optimum pH 7.0-7.5) and neither strain required Mg(2+) for growth. Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). The major polar lipids of the two strains were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and eight glycolipids; three of these glycolipids (GL3, GL4 and GL5) were chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1), galactosyl mannosyl glucosyl diether (TGD-1) and mannosyl glucosyl diether (DGD-1), respectively. Phylogenetic analysis revealed that strains TBN21(T) and TBN49 formed a distinct clade with their closest relative, Halobaculum gomorrense JCM 9908(T) (89.0-89.5 % 16S rRNA gene sequence similarity). The DNA G+C contents of strains TBN21(T) and TBN49 were 64.8 and 62.7 mol%, respectively. DNA-DNA hybridization between strains TBN21(T) and TBN49 was 90.1 %. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains TBN21(T) and TBN49 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halolamina pelagica gen. nov., sp. nov. is proposed. The type strain of Halolamina pelagica is TBN21(T) ( = CGMCC 1.10329(T) = JCM 16809(T)).
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Affiliation(s)
- Heng-Lin Cui
- School of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xia Gao
- School of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xin Yang
- School of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xue-Wei Xu
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
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