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Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil. Extremophiles 2021; 26:6. [PMID: 34962596 DOI: 10.1007/s00792-021-01255-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/09/2021] [Indexed: 12/27/2022]
Abstract
Three halophilic archaeal strains, Gai1-5T, SEDH52T and SQT7-1T were isolated from Gaize salt lake and Xiadi salt lake in Tibet, and saline soil from Xinjiang, respectively. Phylogenetic analysis based on 16S rRNA gene and rpoB' gene sequences showed that these three strains formed different branches separating them from Haloprofundus halophilus NK23T (97.7-98.3% similarities for 16S rRNA gene and 94.7-94.8% similarities for rpoB' gene, respectively) and Haloprofundus marisrubri SB9T (94.7-96.4% similarities for 16S rRNA gene and 92.3-93.2% similarities for rpoB' gene, respectively). Several phenotypic characteristics distinguish the strains Gai1-5 T, SEDH52T and SQT7-1T from Haloprofundus halophilus NK23T and Haloprofundus marisrubri SB9T. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values among the three strains and current Haloprofundus members were in the range of 83.3-88.3% and 27.2-35.7%, respectively, far below the species boundary threshold values. The major polar lipids of three strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol sulphate (PGS), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), mannosyl glucosyl diether-phosphatidic acid (DGD-PA) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). These results showed that strains Gai1-5T (= CGMCC 1.16079T = JCM 33561T), SQT7-1T (= CGMCC 1.16063T = JCM 33553 T) and SEDH52T (= CGMCC 1.17434T) represented three novel species in the genus Haloprofundus, for which the names Haloprofundus salilacus sp. nov., Haloprofundus salinisoli sp. nov., and Haloprofundus halobius sp. nov. are proposed.
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Banda JF, Zhang Q, Ma L, Pei L, Du Z, Hao C, Dong H. Both pH and salinity shape the microbial communities of the lakes in Badain Jaran Desert, NW China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148108. [PMID: 34126487 DOI: 10.1016/j.scitotenv.2021.148108] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 05/27/2023]
Abstract
Badain Jaran Desert (BJD), characterized by extremely arid climate and tallest sand dunes in the world, is the second largest desert in China. Surprisingly, there are a large number of permanent lakes in this desert. At present, little is known about the composition and distribution of microbial communities in these desert lakes, which are an important bioresource and play a fundamental role in the elemental cycles of the lakes. In this study, the physicochemical characteristics and microbial communities of water samples from 15 lakes in BJD were comparatively investigated. The results showed that the lakes were rich in Na+, Cl-, CO32- and HCO3- while Ca2+ and Mg2+ were scarce, with pH 8.52-10.27 and salinity 1.05-478.70 g/L. Bacteria dominated exclusively in low saline lakes (salinity < 50 g/L) while archaea were predominant in hypersaline lakes (salinity > 250 g/L), which abundance increased along salinity gradient linearly. Genera Flavobacterium, Synechocystis and Roseobacter from phyla Bacteroidetes, Cyanobacteria, Alphaproteobacteria were the major members in low saline lakes whereas Halomonas, Aliidiomarina and Halopelagius from Gammaproteobacteria and Euryarchaeota were abundant in moderately saline lakes (salinity 50-250 g/L). The hypersaline lakes were predominated by extreme halophiles such as Halorubrum, Halohasta and Natronomonas from Euryarchaeota. The correlation among the microbes in the lakes was mainly positive, suggesting they can survive in the harsh environments through synergistic interactions. Statistical analyses indicated that physicochemical characteristics rather than spatial factors shaped the microbial communities in the desert lakes. The pH was the most important environmental factor controlling alpha diversity, while salinity was the major driver determining microbial community structure in BJD lakes. In contrast, geographic factors had no significant impact on the microbial community compositions.
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Affiliation(s)
- Joseph Frazer Banda
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Qin Zhang
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Linqiang Ma
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Lixin Pei
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Zerui Du
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Chunbo Hao
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China.
| | - Hailiang Dong
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China; Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 45056, USA
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Xu Y, Lv J, Xie C, Sun S, Ke L, Chen S. Halorubrum glutamatedens sp. nov., a Halophilic Archaeon Isolated from a Rock Salt. Curr Microbiol 2018; 76:52-56. [PMID: 30317405 DOI: 10.1007/s00284-018-1583-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/09/2018] [Indexed: 01/30/2023]
Abstract
An extremely halophilic archaeon, strain ZY8T, was isolated from a rock salt of Yunnan salt mine. It was able to grow at 12-30% (w/v) NaCl (optimum, 15-20%), pH 7.0-9.0 (optimum, pH 8.5), and 20-45 °C (optimum, 42 °C). Sequence similarity search of its 16S rRNA gene showed that strain ZY8T belonged to the genus Halorubrum, and it is closely related to species of H. aethiopicum SAH-A6T (98.6%), H. aquaticum EN-2T (98.6%), and H. halodurans Cb34T (98.5%), respectively. Strain ZY8T contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate as its major phospholipids, and a sulfated diglycosyl diether as its major glycolipid. The DNA G+C content was 66.7 mol%. DNA-DNA relatedness between strains ZY8T and closely related species were far below 70%. Based on the phenotypic and phylogenetic analyses, it is proposed that strain ZY8T represents a novel species of the genus Halorubrum, for which the name Halorubrum glutamatedens sp. nov. is proposed. The type strain is ZY8T (=CGMCC 1.16026T=NBRC 112866T).
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Affiliation(s)
- Yao Xu
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Jinting Lv
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Chizhen Xie
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Siqi Sun
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Lixia Ke
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China
| | - Shaoxing Chen
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, People's Republic of China. .,College of Life Sciences, Honghe University, No.1 Xuefu Road, Mengzi, 661100, Yunnan, People's Republic of China.
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Halorubrum aethiopicum sp. nov., an extremely halophilic archaeon isolated from commercial rock salt. Int J Syst Evol Microbiol 2018; 68:416-422. [DOI: 10.1099/ijsem.0.002525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Paul VG, Mormile MR. A case for the protection of saline and hypersaline environments: a microbiological perspective. FEMS Microbiol Ecol 2017; 93:3950317. [DOI: 10.1093/femsec/fix091] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/09/2017] [Indexed: 11/12/2022] Open
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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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Anderson IJ, DasSarma P, Lucas S, Copeland A, Lapidus A, Del Rio TG, Tice H, Dalin E, Bruce DC, Goodwin L, Pitluck S, Sims D, Brettin TS, Detter JC, Han CS, Larimer F, Hauser L, Land M, Ivanova N, Richardson P, Cavicchioli R, DasSarma S, Woese CR, Kyrpides NC. Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34. Stand Genomic Sci 2016; 11:70. [PMID: 27617060 PMCID: PMC5018182 DOI: 10.1186/s40793-016-0194-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/03/2016] [Indexed: 01/26/2023] Open
Abstract
Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.
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Affiliation(s)
| | - Priya DasSarma
- Institute of Marine and Environmental Technology, Columbus Center, University of Maryland School of Medicine, University System of Maryland, Baltimore, MD 21202 USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Eileen Dalin
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - David C Bruce
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - David Sims
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Thomas S Brettin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - John C Detter
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Cliff S Han
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Frank Larimer
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, CA 94598 USA ; Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | | | | | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052 Australia
| | - Shiladitya DasSarma
- Institute of Marine and Environmental Technology, Columbus Center, University of Maryland School of Medicine, University System of Maryland, Baltimore, MD 21202 USA
| | - Carl R Woese
- B103 Chemical and Life Sciences Laboratory, University of Illinois at Urbana-Champaign, MC-110, 601 South Goodwin Avenue, Urbana, IL 61801 USA
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Corral P, de la Haba RR, Sánchez-Porro C, Ali Amoozegar M, Thane Papke R, Ventosa A. Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake. Int J Syst Evol Microbiol 2015; 66:435-444. [PMID: 26537912 DOI: 10.1099/ijsem.0.000738] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, strains Cb34T and C170, belonging to the genus Halorubrum, were isolated from the brine of the hypersaline lake Aran-Bidgol in Iran. Cells of the two strains were motile, pleomorphic rods, stained Gram-variable and produced red-pigmented colonies. Strains Cb34T and C170 required 25 % (w/v) salts, pH 7.0 and 37 °C for optimal growth under aerobic conditions; 0.3 M Mg2+ was required. Cells of both isolates were lysed in distilled water and hypotonic treatment with < 10 % NaCl provoked cell lysis. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that these two strains were closely related to Halorubrum cibi B31T (98.8 %) and other members of the genus Halorubrum. In addition, studies based on the rpoB' gene revealed that strains Cb34T and C170 are placed among the species of Halorubrum and are closely related to Halorubrum cibi B31T, with rpoB' gene sequence similarity less than or equal to 95.7 %. The polar lipid patterns of both strains consisted of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The DNA G+C content was 62.1-62.4 mol%. DNA-DNA hybridization studies confirmed that strains Cb34T and C170 constitute a distinct species. Data obtained in this study show that the two strains represent a novel species, for which the name Halorubrum halodurans sp. nov. is proposed. The type strain is Cb34T ( = CECT 8745T = IBRC-M 10233T).
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Affiliation(s)
- Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Mohammad Ali Amoozegar
- Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Kondo Y, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Takahashi-Ando N, Fukushima Y, Yoshida Y, Usami R. Halorubrum gandharaense sp. nov., an alkaliphilic haloarchaeon from commercial rock salt. Int J Syst Evol Microbiol 2015; 65:2345-2350. [DOI: 10.1099/ijs.0.000261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, pleomorphic rod-shaped, orange–red-pigmented, facultatively aerobic and haloalkaliphilic archaeon, strain MK13-1T, was isolated from commercial rock salt imported from Pakistan. The NaCl, pH and temperature ranges for growth of strain MK13-1T were 3.0–5.2 M NaCl, pH 8.0–11.0 and 15–50 °C, respectively. Optimal growth occurred at 3.2–3.4 M NaCl, pH 9.0–9.5 and 45 °C. Addition of Mg2+ was not required for growth. The major polar lipids of the isolate were C20C20 and C20C25 archaeol derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Glycolipids were not detected. The DNA G+C content was 64.1 mol%. The 16S rRNA gene sequence of strain MK13-1T was most closely related to those of the species of the genus Halorubrum, Halorubrum luteum CECT 7303T (95.9 % similarity), Halorubrum alkaliphilum JCM 12358T (95.3 %), Halorubrum kocurii JCM 14978T (95.3 %) and Halorubrum lipolyticum JCM 13559T (95.3 %). The rpoB′ gene sequence of strain MK13-1T had < 90 % sequence similarity to those of other members of the genus Halorubrum. Based on the phylogenetic analysis and phenotypic characterization, strain MK13-1T may represent a novel species of the genus Halorubrum, for which the name Halorubrum gandharaense sp. nov. is proposed, with the type strain MK13-1T ( = JCM 17823T = CECT 7963T).
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Affiliation(s)
- Yusuke Kondo
- Department of Biological Applied Chemistry, Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Hiroaki Minegishi
- Department of Biological Applied Chemistry, Graduate School of Engineering, 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
| | - Akinobu Echigo
- Department of Biological Applied Chemistry, Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15, Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Masahiro Kamekura
- Halophiles Research Institute, 677-1 Shimizu, Noda-shi, Chiba 278-0043, Japan
| | - Takashi Itoh
- RIKEN BioResource Center, 3-1-1 Koyadai, Tukuba-shi, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- RIKEN BioResource Center, 3-1-1 Koyadai, Tukuba-shi, Ibaraki 305-0074, Japan
| | - Naoko Takahashi-Ando
- Department of Biological Applied Chemistry, Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Yasumasa Fukushima
- Department of Biological Applied Chemistry, Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Yasuhiko Yoshida
- Department of Biological Applied Chemistry, Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
| | - Ron Usami
- Department of Biological Applied Chemistry, Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe-shi, Saitama 350-8585, Japan
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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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Extracellular Proteases from Halophilic and Haloalkaliphilic Bacteria: Occurrence and Biochemical Properties. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2015. [DOI: 10.1007/978-3-319-14595-2_16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Halorubrum halophilum sp. nov., an extremely halophilic archaeon isolated from a salt-fermented seafood. Antonie van Leeuwenhoek 2014; 105:603-12. [PMID: 24442192 DOI: 10.1007/s10482-014-0115-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
A novel, red-pigmented, pleomorphic and short rod-shaped haloarchaeon, designated B8(T), was isolated from a salt-fermented seafood. Strain B8(T) was found to be able to grow at 20-45 °C, in the presence of 15-30 % (w/v) NaCl and at pH 7.0-9.0. The optimum requirements were found to be a temperature range of 35-40 °C, pH 8.0 and the presence of 25 % NaCl. The cells of strain B8(T) were observed to be Gram-staining negative and lysed in distilled water. Anaerobic growth did not occur in the presence of nitrate, L-arginine, dimethyl sulfoxide or trimethylamine N-oxide. The catalase and oxidase activities were found to be positive and nitrate was reduced in aerobic conditions. Tween 20, 40 and 80 were found to be hydrolyzed, whereas casein, gelatin and starch were not hydrolyzed. Indole or H2S was not formed and urease activity was not detected. A phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain B8(T) is most closely related to members of the genus Halorubrum in the family Halobacteriaceae. Strain B8(T) was found to have three 16S rRNA genes, rrnA, rrnB and rrnC; similarities between the 16S rRNA gene sequences are 99.0-99.8 %. Strain B8(T) shared 99.0 % 16S rRNA gene sequence similarity with Halorubrum (Hrr.) lipolyticum JCM 13559(T) and Hrr. saccharovorum DSM 1137(T), 98.8 % with Hrr. kocurii JCM 14978(T), 98.3 % with Hrr. lacusprofundi DSM 5036(T), 98.0 % with Hrr. arcis JCM 13916(T), 97.7 % with Hrr. aidingense JCM 13560(T) and 97.0 % with Hrr. aquaticum JCM 14031(T), as well as 93.7-96.5 % with other type strains in the genus Halorubrum. The RNA polymerase subunit B' gene sequence similarity of strain B8(T) with Hrr. kocurii JCM 14978(T) is 97.2 % and lower with other members of the genus Halorubrum. DNA-DNA hybridization experiments showed that strain B8(T) shared equal or lower than 50 % relatedness with reference species in the genus Halorubrum. The genomic DNA G+C content of strain B8(T) was determined to be 64.6 mol%. The major isoprenoid quinone of strain B8(T) was identified as menaquinone-8 and the major polar lipids as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether and an unidentified phospholipid. Based on this polyphasic taxonomic study, strain B8(T) is considered to represent a new species in the genus Halorubrum, for which the name Hrr. halophilum sp. nov. is proposed. The type strain is B8(T) (=JCM 18963(T) = CECT 8278(T)).
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Zhang WJ, Han D, Qiu XX, Zhao ML, Mou YZ, Cui HL, Li ZR. Halobellus rarus sp. nov., a halophilic archaeon from an inland salt lake of China. Antonie van Leeuwenhoek 2013; 104:377-84. [PMID: 23828176 DOI: 10.1007/s10482-013-9960-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 06/24/2013] [Indexed: 11/25/2022]
Abstract
Two halophilic archaeal strains, YC21(T) and YC77, were isolated from an inland salt lake of China. Both have pleomorphic rod-shaped cells that lyse in distilled water, stain Gram-negative and form red-pigmented colonies. They are neutrophilic, require at least 2.1 M NaCl for growth under the optimum growth temperature of 37 °C. The major polar lipids of the two strains were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), two major glycolipids (GL1 and GL2) chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1), respectively. Trace amounts of two unidentified lipids (GL0-1 and GL0-2) were also detected. The 16S rRNA gene sequences of the two strains are 99.9 % identical, show 94.0-98.9 % similarity to the closest relative members of Halobellus of the family Halobacteriaceae. The rpoB' gene similarity between strains YC21(T) and YC77 is 99.8 % and show 90.3-95.3 % similarity to the closest relative members of Halobellus. The DNA G+C content of strains YC21(T) and YC77 were 66.1 and 66.2 mol%, respectively. The DNA-DNA hybridization value between strain YC20(T) and strain YC77 was 89 %, and the two strains showed low DNA-DNA relatedness with Halobellus limi TBN53(T), the most related member of Halobellus. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains YC21(T) and YC77 represent a novel species of the genus Halobellus, for which the name Halobellus rarus sp. nov. is proposed. The type strain is YC21(T) (=CGMCC 1.12121(T) = JCM 18362(T)).
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Affiliation(s)
- Wen-Jiao Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, People's Republic of China
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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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Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S. Characterization of Halorubrum sfaxense sp. nov., a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia. Int J Microbiol 2011; 2011:240191. [PMID: 21754938 PMCID: PMC3132631 DOI: 10.1155/2011/240191] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 03/02/2011] [Accepted: 03/31/2011] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon, strain ETD6, was isolated from a marine solar saltern in Sfax, Tunisia. Analysis of the 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genus Halorubrum among the family Halobacteriaceae, with a close relationship to Hrr. xinjiangense (99.77% of identity). However, value for DNA-DNA hybridization between strain ETD6 and Hrr.xinjiangense were about 24.5%. The G+C content of the genomic DNA was 65.1 mol% (T(m)). Strain ETD6 grew in 15-35% (w/v) NaCl. The temperature and pH ranges for growth were 20-55°C and 6-9, respectively. Optimal growth occurred at 25% NaCl, 37°C, and pH 7.4. The results of the DNA hybridization against Hrr. xinjiangense and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain ETD6 from other Hrr. species. Therefore, strain ETD6 represents a novel species of the genus Halorubrum, for which the name Hrr. sfaxense sp. nov. is proposed. The Genbank EMBL-EBI accession number is GU724599.
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Affiliation(s)
- Hana Trigui
- Laboratoire de Chimie Bactérienne, Aix Marseille Université, UPR 9043-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
- Laboratoire de Microbiologie, Faculté des Sciences de Sfax, BP802, Sfax 3000, Tunisia
| | - Salma Masmoudi
- Laboratoire de Microbiologie, Faculté des Sciences de Sfax, BP802, Sfax 3000, Tunisia
| | - Céline Brochier-Armanet
- Laboratoire de Chimie Bactérienne, Aix Marseille Université, UPR 9043-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Sami Maalej
- Laboratoire de Microbiologie, Faculté des Sciences de Sfax, BP802, Sfax 3000, Tunisia
| | - Sam Dukan
- Laboratoire de Chimie Bactérienne, Aix Marseille Université, UPR 9043-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Halorubrum aquaticum sp. nov., an archaeon isolated from hypersaline lakes. Int J Syst Evol Microbiol 2011; 61:1144-1148. [DOI: 10.1099/ijs.0.025015-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two halophilic archaea, strains EN-2T and SH-4, were isolated from the saline lakes Erliannor and Shangmatala, respectively, in Inner Mongolia, China. Cells were strictly aerobic, motile rods. Colonies were red. Strains EN-2T and SH-4 were able to grow at 25–50 °C (optimum 35–40 °C), with 2.5–5.0 M NaCl (optimum 3.4 M NaCl) and at pH 6.0–9.0 (optimum pH 7.5). MgCl2 was not required for growth. Cells lysed in distilled water and the lowest NaCl concentration that prevented cell lysis was 12 % (w/v). On the basis of 16S rRNA gene sequence analysis, strains EN-2T and SH-4 were closely related to Halorubrum cibi B31T (97.9 and 98.0 % similarity, respectively), Hrr. tibetense 8W8T (97.3 and 97.7 %), Hrr. alkaliphilum DZ-1T (96.8 and 97.1 %), Hrr. luteum CGSA15T (96.8 and 97.0 %) and Hrr. lipolyticum 9-3T (96.8 and 97.0 %). DNA–DNA hybridization showed that strains EN-2T and SH-4 did not belong to the same species as any of these strains (≤45 % DNA–DNA relatedness) but that they are members of the same species (>70 % DNA–DNA relatedness). Polar lipid analysis revealed that strains EN-2T and SH-4 contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated diglycosyl diethers and several unidentified glycolipids. The DNA G+C content of both isolates was 62.1 mol%. It was concluded that strains EN-2T and SH-4 represent a novel species of the genus Halorubrum, for which the name Halorubrum aquaticum sp. nov. is proposed. The type strain is EN-2T ( = CECT 7174T = CGMCC 1.6377T = JCM 14031T).
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Caton TM, Caton IR, Witte LR, Schneegurt MA. Archaeal diversity at the great salt plains of Oklahoma described by cultivation and molecular analyses. MICROBIAL ECOLOGY 2009; 58:519-528. [PMID: 19306116 PMCID: PMC4066810 DOI: 10.1007/s00248-009-9507-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 02/22/2009] [Indexed: 05/27/2023]
Abstract
The Great Salt Plains of Oklahoma is a natural inland terrestrial hypersaline environment that forms evaporite crusts of mainly NaCl. Previous work described the bacterial community through the characterization of 105 isolates from 46 phylotypes. The current report describes the archaeal community through both microbial isolation and culture-independent techniques. Nineteen distinct archaea were isolated, and ten were characterized phenetically. Included were isolates phylogenetically related to Haloarcula, Haloferax, Halorubrum, Haloterrigena, and Natrinema. The isolates were aerobic, non-motile, Gram-negative organisms and exhibited little capacity for fermentation. All of the isolates were halophilic, with most requiring at least 15% salinity for growth, and all grew at 30% salinity. The isolates were mainly mesothermic and could grow at alkaline pH (8.5). A 16S rRNA gene library was generated by polymerase chain reaction amplification of direct soil DNA extracts, and 200 clones were sequenced and analyzed. At 99% and 94% sequence identity, 36 and 19 operational taxonomic units (OTUs) were detected, respectively, while 53 and 22 OTUs were estimated by Chao1, respectively. Coverage was relatively high (100% and 59% at 89% and 99% sequence identity, respectively), and the Shannon Index was 3.01 at 99% sequence identity, comparable to or somewhat lower than hypersaline habitats previously studied. Only sequences from Euryarchaeota in the Halobacteriales were detected, and the strength of matches to known sequences was generally low, most near 90% sequence identity. Large clusters were observed that are related to Haloarcula and Halorubrum. More than two-thirds of the sequences were in clusters that did not have close relatives reported in public databases.
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Affiliation(s)
- T M Caton
- Department of Biological Sciences, Wichita State University, Box 26, 1845 Fairmount, Wichita, KS 67260, USA
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Archaeosomes made of Halorubrum tebenquichense total polar lipids: a new source of adjuvancy. BMC Biotechnol 2009; 9:71. [PMID: 19678953 PMCID: PMC2739508 DOI: 10.1186/1472-6750-9-71] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Accepted: 08/13/2009] [Indexed: 11/10/2022] Open
Abstract
Background Archaeosomes (ARC), vesicles prepared from total polar lipids (TPL) extracted from selected genera and species from the Archaea domain, elicit both antibody and cell-mediated immunity to the entrapped antigen, as well as efficient cross priming of exogenous antigens, evoking a profound memory response. Screening for unexplored Archaea genus as new sources of adjuvancy, here we report the presence of two new Halorubrum tebenquichense strains isolated from grey crystals (GC) and black mood (BM) strata from a littoral Argentinean Patagonia salt flat. Cytotoxicity, intracellular transit and immune response induced by two subcutaneous (sc) administrations (days 0 and 21) with BSA entrapped in ARC made of TPL either form BM (ARC-BM) and from GC (ARC-GC) at 2% w/w (BSA/lipids), to C3H/HeN mice (25 μg BSA, 1.3 mg of archaeal lipids per mouse) and boosted on day 180 with 25 μg of bare BSA, were determined. Results DNA G+C content (59.5 and 61.7% mol BM and GC, respectively), 16S rDNA sequentiation, DNA-DNA hybridization, arbitrarily primed fingerprint assay and biochemical data confirmed that BM and GC isolates were two non-previously described strains of H. tebenquichense. Both multilamellar ARC mean size were 564 ± 22 nm, with -50 mV zeta-potential, and were not cytotoxic on Vero cells up to 1 mg/ml and up to 0.1 mg/ml of lipids on J-774 macrophages (XTT method). ARC inner aqueous content remained inside the phago-lysosomal system of J-774 cells beyond the first incubation hour at 37°C, as revealed by pyranine loaded in ARC. Upon subcutaneous immunization of C3H/HeN mice, BSA entrapped in ARC-BM or ARC-GC elicited a strong and sustained primary antibody response, as well as improved specific humoral immunity after boosting with the bare antigen. Both IgG1 and IgG2a enhanced antibody titers could be demonstrated in long-term (200 days) recall suggesting induction of a mixed Th1/Th2 response. Conclusion We herein report the finding of new H. tebenquichense non alkaliphilic strains in Argentinean Patagonia together with the adjuvant properties of ARC after sc administration in mice. Our results indicate that archaeosomes prepared with TPL from these two strains could be successfully used as vaccine delivery vehicles.
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Mancinelli RL, Landheim R, Sánchez-Porro C, Dornmayr-Pfaffenhuemer M, Gruber C, Legat A, Ventosa A, Radax C, Ihara K, White MR, Stan-Lotter H. Halorubrum chaoviator sp. nov., a haloarchaeon isolated from sea salt in Baja California, Mexico, Western Australia and Naxos, Greece. Int J Syst Evol Microbiol 2009; 59:1908-13. [PMID: 19567575 DOI: 10.1099/ijs.0.000463-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three halophilic isolates, strains Halo-G*T, AUS-1 and Naxos II, were compared. Halo-G* was isolated from an evaporitic salt crystal from Baja California, Mexico, whereas AUS-1 and Naxos II were isolated from salt pools in Western Australia and the Greek island of Naxos, respectively. Halo-G*T had been exposed previously to conditions of outer space and survived 2 weeks on the Biopan facility. Chemotaxonomic and molecular comparisons suggested high similarity between the three strains. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains clustered with Halorubrum species, showing sequence similarities of 99.2-97.1%. The DNA-DNA hybridization values of strain Halo-G*T and strains AUS-1 and Naxos II are 73 and 75%, respectively, indicating that they constitute a single species. The DNA relatedness between strain Halo-G*T and the type strains of 13 closely related species of the genus Halorubrum ranged from 39 to 2%, suggesting that the three isolates constitute a different genospecies. The G+C content of the DNA of the three strains was 65.5-66.5 mol%. All three strains contained C20C20 derivatives of diethers of phosphatidylglycerol, phosphatidylglyceromethylphosphate and phosphatidylglycerolsulfate, together with a sulfated glycolipid. On the basis of these results, a novel species that includes the three strains is proposed, with the name Halorubrum chaoviator sp. nov. The type strain is strain Halo-G*T (=DSM 19316T=NCIMB 14426T=ATCC BAA-1602T).
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Halorubrum cibi sp. nov., an extremely halophilic archaeon from salt-fermented seafood. J Microbiol 2009; 47:162-6. [DOI: 10.1007/s12275-009-0016-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 03/20/2009] [Indexed: 10/20/2022]
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Oren A, Arahal DR, Ventosa A. Emended descriptions of genera of the family Halobacteriaceae. Int J Syst Evol Microbiol 2009; 59:637-42. [DOI: 10.1099/ijs.0.008904-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Pesenti PT, Sikaroodi M, Gillevet PM, Sánchez-Porro C, Ventosa A, Litchfield CD. Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA. Int J Syst Evol Microbiol 2009; 58:2710-5. [PMID: 19060045 DOI: 10.1099/ijs.0.2008/002410-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A motile, rod-shaped, pink-pigmented, extremely halophilic archaeon, strain SF3-213(T), was isolated from a crystallizer pond at the Cargill Solar Salt Plant, Newark, California (USA). Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genus Halorubrum, with a close relationship to Halorubrum trapanicum NRC 34021(T) (98.6 % similarity), Halorubrum sodomense ATCC 33755(T) (98.3 %) and Halorubrum xinjiangense AS 1.3527(T) (98.2 %). The polar lipids of strain SF3-213(T) were C(20)C(20) derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a sulfated diglycosyl-diether. Strain SF3-213(T) grew in 2.5-5.0 M NaCl. The temperature and pH ranges for growth were 25-42 degrees C and 6.8-8.5, respectively. Optimal growth occurred at 3.5-4.5 M NaCl, 37 degrees C and pH 7.3. Mg(2+) was required for growth. The DNA G+C content was 69.4 mol%. DNA-DNA hybridization values lower than 70 % were obtained between strain SF3-213(T) and the closely related species of the genus Halorubrum. Based on the data presented in this study, strain SF3-213(T) represents a novel species for which the name Halorubrum californiense sp. nov. is proposed; the type strain is SF3-213(T) (=CECT 7256(T)=DSM 19288(T)=JCM 14715(T)).
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Affiliation(s)
- Peter T Pesenti
- Department of Environmental Science and Policy, George Mason University, Manassas, VA 20110, USA
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Gutiérrez MC, Castillo AM, Pagaling E, Heaphy S, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halorubrum kocurii sp. nov., an archaeon isolated from a saline lake. Int J Syst Evol Microbiol 2008; 58:2031-5. [PMID: 18768599 DOI: 10.1099/ijs.0.65840-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, neutrophilic, rod-shaped, extremely halophilic archaeon, designated strain BG-1(T), was isolated from a salt lake, Lake Bagaejinnor, in Inner Mongolia, China. Strain BG-1(T) was able to grow at 25-55 degrees C, required at least 2.5 M NaCl for growth (with an optimum at 3.4 M NaCl) and grew at pH 6.0-9.0 (with an optimum at pH 7.5). Hypotonic treatment with less than 2.0 M NaCl caused cell lysis. Phylogenetic analysis of the almost-complete 16S rRNA gene sequence positioned the isolate within the genus Halorubrum in the family Halobacteriaceae. Strain BG-1(T) was most closely related to Halorubrum aidingense 31-hong(T) (98.8% sequence similarity), Halorubrum saccharovorum NCIMB 2081(T) (98.6%), Halorubrum lacusprofundi ACAM 34(T) (98.6%) and Halorubrum lipolyticum 9-3(T) (98.4%). However, values for DNA-DNA hybridization between strain BG-1(T) and the most closely related members of the genus Halorubrum were below 40%. Analysis of the polar lipids of strain BG-1(T) revealed the presence of mannosyl-2-sulfate-(1-4)-glycosyl-archaeol, the main glycolipid found in neutrophilic species of the genus Halorubrum. The G+C content of the genomic DNA was 69.4 mol% (T(m)). Comparison of the phenotypic characteristics of the strain with those of Halorubrum species supported the conclusion that BG-1(T) represents a novel species within this genus, for which the name Halorubrum kocurii sp. nov. is proposed. The type strain is BG-1(T) (=CECT 7322(T) =CGMCC 1.7018(T) =JCM 14978(T)).
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Affiliation(s)
- M C Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
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Hu L, Pan H, Xue Y, Ventosa A, Cowan DA, Jones BE, Grant WD, Ma Y. Halorubrum luteum sp. nov., isolated from Lake Chagannor, Inner Mongolia, China. Int J Syst Evol Microbiol 2008; 58:1705-8. [PMID: 18599720 DOI: 10.1099/ijs.0.65700-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon, strain CGSA15(T), was isolated from water of Lake Chagannor in China. The strain grew optimally at 33-37 degrees C, pH 9.5-10.0 and 4.0-4.3 M NaCl. The major polar lipids were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. The genomic DNA G+C content of strain CGSA15(T) was 60.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CGSA15(T) was a member of the genus Halorubrum and was related most closely to Halorubrum alkaliphilum AS 1.3528(T) (96.1 % similarity) and Halorubrum tibetense AS 1.3239(T) (96.9 %). Levels of DNA-DNA relatedness between strain CGSA15(T) and Hrr. alkaliphilum AS 1.3528(T) and Hrr. tibetense AS 1.3239(T) were 36.7 and 28.9 %, respectively. According to the phenotypic and genotypic data presented, strain CGSA15(T) is considered to represent a novel species of the genus Halorubrum, for which the name Halorubrum luteum sp. nov. is proposed. The type strain is CGSA15(T) (=CGMCC 1.6783(T) =CECT 7303(T)).
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Affiliation(s)
- Lingfei Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Castillo AM, Gutiérrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halorubrum ejinorense sp. nov., isolated from Lake Ejinor, Inner Mongolia, China. Int J Syst Evol Microbiol 2007; 57:2538-2542. [DOI: 10.1099/ijs.0.65241-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon, strain EJ-32T, was isolated from water from Lake Ejinor in Inner Mongolia, China. The taxonomy of strain EJ-32T was studied by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain EJ-32T was shown to be phylogenetically related to Halorubrum coriense (97.9 %), Halorubrum trapanicum (97.9 %), Halorubrum sodomense (97.8 %), Halorubrum tebenquichense (97.8 %), Halorubrum xinjiangense (97.6 %), Halorubrum terrestre (97.4 %), Halorubrum distributum (97.1 %) and Halorubrum saccharovorum (96.4 %). Strain EJ-32T was found to be neutrophilic, non-motile and Gram-negative. It grew in medium containing saturation concentrations of NaCl and did not require magnesium for optimal growth. The G+C content of the DNA is 64.0 mol%. Values for DNA–DNA hybridization with respect to phylogenetically related Halorubrum species were ≤49 %, indicating that EJ-32T constitutes a different genospecies. The data show that strain EJ-32T represents a novel species of the genus Halorubrum, for which the name Halorubrum ejinorense sp. nov. is proposed. The type strain is EJ-32T (=CECT 7194T=CGMCC 1.6782T=JCM 14265T).
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Affiliation(s)
- A. M. Castillo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M. C. Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M. Kamekura
- Noda Institute for Scientific Research, 399 Noda, Noda-shi, Chiba-ken 278-0037, Japan
| | - Y. Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, People's Republic of China
| | - Y. Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, People's Republic of China
| | - D. A. Cowan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - B. E. Jones
- Genencor International BV, Archimedesweg 30, 2333 CN Leiden, The Netherlands
| | - W. D. Grant
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - A. Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Enache M, Itoh T, Fukushima T, Usami R, Dumitru L, Kamekura M. Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences. Int J Syst Evol Microbiol 2007; 57:2289-2295. [PMID: 17911299 DOI: 10.1099/ijs.0.65190-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B′ gene (rpoB′) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family Halobacteriaceae. Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera Natrialba, Natronococcus, Halobiforma, Natronobacterium, Natronorubrum, Natrinema/Haloterrigena and Natronolimnobius formed a monophyletic group in all trees. In the RpoB′ protein tree, the alkaliphilic species Natrialba chahannaoensis, Natrialba hulunbeirensis and Natrialba magadii formed a tight group, while the neutrophilic species Natrialba asiatica formed a separate group with species of the genera Natronorubrum and Natronolimnobius. Species of the genus Natronorubrum were split into two groups in both the rpoB′ gene and protein trees. The most important advantage of the use of the rpoB′ gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family Halobacteriaceae. All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The rpoB′ gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the Halobacteriaceae.
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Affiliation(s)
- Madalin Enache
- Institute of Biology, Romanian Academy, Splaiul Independentei 296, PO Box 56-53, Bucharest 060031, Romania
- Japan Collection of Micro-organisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Takashi Itoh
- Japan Collection of Micro-organisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Tadamasa Fukushima
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Ron Usami
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Lucia Dumitru
- Institute of Biology, Romanian Academy, Splaiul Independentei 296, PO Box 56-53, Bucharest 060031, Romania
| | - Masahiro Kamekura
- Halophiles Research Institute, 677-1 Shimizu, Noda, Chiba 278-0043, Japan
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27
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Xu XW, Wu YH, Zhang HB, Wu M. Halorubrum arcis sp. nov., an extremely halophilic archaeon isolated from a saline lake on the Qinghai–Tibet Plateau, China. Int J Syst Evol Microbiol 2007; 57:1069-1072. [PMID: 17473261 DOI: 10.1099/ijs.0.64921-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, neutrophilic and extremely halophilic archaeon (strain AJ201T), isolated from Ayakekum salt lake on the Qinghai–Tibet Plateau, was investigated by a polyphasic approach. The DNA G+C content of strain AJ201Twas 65.7 mol%. The major polar lipid profile and phylogenetic analysis based on 16S rRNA gene sequences supported the allocation of the strain to the genusHalorubrum. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain AJ201Tfrom closely related species. Therefore, strain AJ201Trepresents a novel species of the genusHalorubrum, for which the nameHalorubrum arcissp. nov. is proposed. The type strain is strain AJ201T(=CGMCC 1.5343T=JCM 13916T).
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Affiliation(s)
- Xue-Wei Xu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Yue-Hong Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Hui-Bin Zhang
- Altun Mountain National Nature Reserve Administrative, Kuerle 841000, People's Republic of China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
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28
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Castillo AM, Gutiérrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halorubrum orientale sp. nov., a halophilic archaeon isolated from Lake Ejinor, Inner Mongolia, China. Int J Syst Evol Microbiol 2007; 56:2559-2563. [PMID: 17082390 DOI: 10.1099/ijs.0.64420-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A motile, pleomorphic, red-pigmented archaeon, strain EJ-52T, was isolated from water from Lake Ejinor, a saline lake in Inner Mongolia, China. Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genus Halorubrum, being most closely related to Halorubrum saccharovorum ATCC 29252T (96.1% sequence similarity), Halorubrum lacusprofundi JCM 8891T (95.9%), Halorubrum tibetense AS 1.3239T (95.2%), Halorubrum alcaliphilum AS 1.3528T (95.2%) and Halorubrum vacuolatum JCM 9060T (95.1%). The polar lipids of strain EJ-52T were C20C20 derivatives of phosphatidylglycerol phosphate and phosphatidylglycerol phosphate methyl ester and a sulfated diglycosyl diether. Strain EJ-52T requires at least 2.5 M NaCl for growth and grows optimally at 3.4 M NaCl. The strain grows at 25-50 degrees C, with optimal growth occurring at 35-45 degrees C. Mg2+ is not required. The DNA G+C content is 64.2 mol%. On the basis of the data obtained in this study, strain EJ52T represents a novel species, for which the name Halorubrum orientale sp. nov. is proposed. The type strain is EJ-52T (=CECT 7145T=JCM 13889T=CGMCC 1.6295T).
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MESH Headings
- Base Composition
- China
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Halobacteriaceae/classification
- Halobacteriaceae/cytology
- Halobacteriaceae/isolation & purification
- Halobacteriaceae/physiology
- Lipids/analysis
- Lipids/chemistry
- Magnesium/metabolism
- Molecular Sequence Data
- Movement
- Phylogeny
- Pigments, Biological/analysis
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/analysis
- Sodium Chloride/metabolism
- Temperature
- Water Microbiology
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Affiliation(s)
- A M Castillo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M C Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M Kamekura
- Noda Institute for Scientific Research, 399 Noda, Noda-shi, Chiba-ken 278-0037, Japan
| | - Y Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, China
| | - Y Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, China
| | - D A Cowan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - B E Jones
- Genencor International BV, Archimedesweg 30, 2333 CN Leiden, The Netherlands
| | - W D Grant
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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29
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Ozcan B, Cokmus C, Coleri A, Caliskan M. Characterization of extremely halophilic Archaea isolated from saline environment in different parts of Turkey. Microbiology (Reading) 2006. [DOI: 10.1134/s002626170606018x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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30
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Castillo AM, Gutiérrez MC, Kamekura M, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halovivax asiaticus gen. nov., sp. nov., a novel extremely halophilic archaeon isolated from Inner Mongolia, China. Int J Syst Evol Microbiol 2006; 56:765-770. [PMID: 16585691 DOI: 10.1099/ijs.0.63954-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain EJ-46T, a novel pleomorphic, aerobic, extremely halophilic member of the Archaea was isolated from sediment of the saline Lake Ejinor, in Inner Mongolia, China. This organism was neutrophilic and required at least 15 % (2.5 M) NaCl for growth. MgCl2 was not required. The isolate was able to grow at pH 6.0-9.0. Optimum growth occurred in media containing 20 % (3.4 M) NaCl at pH 7.0-7.5. Polar lipid analysis revealed the presence of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 glycerol diethers. Four glycolipids were detected, one of which may be novel. The DNA G+C content was 60.3 mol%. 16S rRNA gene analysis revealed that strain EJ-46T was a member of the phylogenetic group defined by the family Halobacteriaceae, and the highest 16S rRNA gene similarity values of 94.9 and 94.8 % were obtained with the haloalkaliphilic species of the genus Natronococcus, Natronococcus occultus and Natronococcus amylolyticus, respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the novel isolate should be classified as representing a new genus and species, for which the name Halovivax asiaticus gen. nov., sp. nov. is proposed. The type strain is EJ-46T (=CGMCC 1.4248T = CECT 7098T).
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Affiliation(s)
- A M Castillo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M C Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - M Kamekura
- Noda Institute for Scientific Research, 399 Noda, Noda-shi, Chiba-ken 278-0037, Japan
| | - Y Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, China
| | - D A Cowan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - B E Jones
- Genencor International BV, Archimedesweg 30, 2333 CN Leiden, The Netherlands
| | - W D Grant
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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31
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Cui HL, Tohty D, Zhou PJ, Liu SJ. Halorubrum lipolyticum sp. nov. and Halorubrum aidingense sp. nov., isolated from two salt lakes in Xin-Jiang, China. Int J Syst Evol Microbiol 2006; 56:1631-1634. [PMID: 16825640 DOI: 10.1099/ijs.0.64305-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, strains 9-3(T) and 31-hong(T), were isolated from Aibi salt lake and Aiding salt lake in Xin-Jiang, China. Their morphology, physiology, biochemical features, polar lipid compositions and 16S rRNA gene sequences were characterized in order to elucidate their taxonomic status. The results from this study indicated that strains 9-3(T) and 31-hong(T) are members of the genus Halorubrum. Their physiological properties and polar lipid compositions are clearly different from those of the currently described species of Halorubrum. DNA-DNA relatedness values for strain 9-3(T) with respect to its closely related neighbours Halorubrum saccharovorum JCM 8865(T) and Halorubrum lacusprofundi JCM 8891(T) were 51.6 and 25.1 %, respectively, DNA-DNA relatedness values for strain 31-hong(T) with respect to its closely related neighbours Hrr. saccharovorum JCM 8865(T) and Hrr. lacusprofundi JCM 8891(T) were 29.4 and 44.9 %, respectively, and DNA-DNA relatedness between strains 9-3(T) and 31-hong(T) was 54 %. Thus, two novel species of the genus Halorubrum are proposed, Halorubrum lipolyticum sp. nov. (type strain 9-3(T)=CGMCC 1.5332(T)=JCM 13559(T)) and Halorubrum aidingense sp. nov. (type strain 31-hong(T)=CGMCC 1.2670(T)=JCM 13560(T)).
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- China
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Halobacteriaceae/classification
- Halobacteriaceae/genetics
- Halobacteriaceae/isolation & purification
- Halobacteriaceae/physiology
- Lipids/analysis
- Lipids/chemistry
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Water Microbiology
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Affiliation(s)
- Heng-Lin Cui
- Graduate University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, People's Republic of China
| | - Dilbr Tohty
- College of Life Sciences, Xin-Jiang Normal University, Urumqi 830053, People's Republic of China
| | - Pei-Jin Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, People's Republic of China
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32
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Kharroub K, Quesada T, Ferrer R, Fuentes S, Aguilera M, Boulahrouf A, Ramos-Cormenzana A, Monteoliva-Sánchez M. Halorubrum ezzemoulense sp. nov., a halophilic archaeon isolated from Ezzemoul sabkha, Algeria. Int J Syst Evol Microbiol 2006; 56:1583-1588. [PMID: 16825633 DOI: 10.1099/ijs.0.64272-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel extremely halophilic archaeon was isolated from Ezzemoul sabkha, Algeria. The strain, designated 5.1(T), was neutrophilic, motile and Gram-negative. At least 15 % (w/v) NaCl was required for growth. The isolate grew at pH 6.5-9.0, with optimum growth at pH 7.0-7.5. Mg(2+) was required for growth. Polar lipids were C(20)C(20) derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, and phosphatidylglycerol sulfate and sulfated diglycosyl diether. The genomic DNA G+C content of strain 5.1(T) was 61.9 mol% (T(m)). Phylogenetic analysis based on comparison of 16S rRNA gene sequences revealed that strain 5.1(T) clustered with Halorubrum species. The results of DNA-DNA hybridization and biochemical tests allowed genotypic and phenotypic differentiation of strain 5.1(T) from other Halorubrum species. The name Halorubrum ezzemoulense sp. nov. (type strain 5.1(T)=CECT 7099(T)=DSM 17463(T)) is proposed.
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MESH Headings
- Algeria
- Bacterial Typing Techniques
- Base Composition
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Halobacteriaceae/chemistry
- Halobacteriaceae/classification
- Halobacteriaceae/isolation & purification
- Halobacteriaceae/physiology
- Hydrogen-Ion Concentration
- Lipids/chemistry
- Lipids/isolation & purification
- Molecular Sequence Data
- Movement
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/pharmacology
- Water Microbiology
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Affiliation(s)
- Karima Kharroub
- Institut de Nutrition de l'Alimentation et des Technologies Agro-Alimentaires, Université Mentouri, Constantine, Algeria
- Departamento de Microbiologia, Facultad de Farmacia, Campus Universitario de Cartuja s/n 18071, Granada, Spain
| | - Teresa Quesada
- Departamento de Microbiologia, Facultad de Farmacia, Campus Universitario de Cartuja s/n 18071, Granada, Spain
| | - Raquel Ferrer
- Departamento de Microbiologia, Facultad de Farmacia, Campus Universitario de Cartuja s/n 18071, Granada, Spain
| | - Susana Fuentes
- Departamento de Microbiologia, Facultad de Farmacia, Campus Universitario de Cartuja s/n 18071, Granada, Spain
| | - Margarita Aguilera
- Departamento de Microbiologia, Facultad de Farmacia, Campus Universitario de Cartuja s/n 18071, Granada, Spain
| | - Abdrahmane Boulahrouf
- Institut des Sciences de la Nature, Faculté des Sciences, Université Mentouri, Constantine, Algeria
| | - Alberto Ramos-Cormenzana
- Departamento de Microbiologia, Facultad de Farmacia, Campus Universitario de Cartuja s/n 18071, Granada, Spain
| | - Mercedes Monteoliva-Sánchez
- Departamento de Microbiologia, Facultad de Farmacia, Campus Universitario de Cartuja s/n 18071, Granada, Spain
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33
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Castillo AM, Gutiérrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A. Halostagnicola larsenii gen. nov., sp. nov., an extremely halophilic archaeon from a saline lake in Inner Mongolia, China. Int J Syst Evol Microbiol 2006; 56:1519-1524. [PMID: 16825623 DOI: 10.1099/ijs.0.64286-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain XH-48T was isolated from the sediment of Lake Xilinhot, a saline lake in Inner Mongolia (China). The organism is pleomorphic, neutrophilic and requires at least 2.5 M (15 %) NaCl, but not MgCl2, for growth; it exhibits optimal growth at 3.4 M (20 %) NaCl. The G+C content of its DNA is 61 mol%. 16S rRNA gene sequence analysis revealed that strain XH-48T is a member of the family Halobacteriaceae, but there were low levels of similarity with other members of this family. The highest sequence similarity values (94.5 and 93.3 %) were obtained with the 16S rRNA genes of Natrialba aegyptiaca and Natrialba asiatica, respectively. Polar lipid analyses revealed that strain XH-48T contains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C20C20 and C20C25 glycerol diethers, and two unidentified glycolipids. On the basis of the data obtained, the novel isolate cannot be classified within any recognized genus. Strain XH-48T should be placed within a novel genus and species within the family Halobacteriaceae, order Halobacteriales, for which the name Halostagnicola larsenii gen. nov., sp. nov. is proposed. The type strain of Halostagnicola larsenii is strain XH-48T (=DSM 17691T=CGMCC 1.5338T=JCM 13463T=CECT 7116T).
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MESH Headings
- Aerobiosis
- Anaerobiosis
- Base Composition
- China
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Enzymes/analysis
- Genes, rRNA
- Geologic Sediments/microbiology
- Halobacteriaceae/classification
- Halobacteriaceae/cytology
- Halobacteriaceae/genetics
- Halobacteriaceae/isolation & purification
- Halobacteriaceae/physiology
- Lipids/chemistry
- Lipids/isolation & purification
- Magnesium Chloride/metabolism
- Microscopy, Phase-Contrast
- Molecular Sequence Data
- Mongolia
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Water Microbiology
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Affiliation(s)
- A M Castillo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - M C Gutiérrez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - M Kamekura
- Noda Institute for Scientific Research, 399 Noda, Noda-shi, Chiba-ken 278-0037, Japan
| | - Y Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, P. R. China
| | - Y Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100080 Beijing, P. R. China
| | - D A Cowan
- Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - B E Jones
- Genencor International BV, Archimedesweg 30, 2333 CN Leiden, The Netherlands
| | - W D Grant
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - A Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
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Abstract
The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.
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Affiliation(s)
- Bonnie Chaban
- Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada
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35
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36
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Feng J, Zhou P, Zhou YG, Liu SJ, Warren-Rhodes K. Halorubrum alkaliphilum sp. nov., a novel haloalkaliphile isolated from a soda lake in Xinjiang, China. Int J Syst Evol Microbiol 2005; 55:149-152. [PMID: 15653868 DOI: 10.1099/ijs.0.63320-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel haloalkaliphilic archaeon, strain DZ-1T, was isolated from a soda lake in Xinjiang, China. The taxonomy of strain DZ-1T was studied by polyphasic methods. According to 16S rRNA gene sequence similarity, strain DZ-1T was phylogenetically related to Halorubrum tibetense (97.5 %), Halorubrum vacuolatum (95.7 %) and Halorubrum saccharovorum (95.9 %). Strain DZ-1T was able to grow at 20-44 degrees C and was also physiologically different from the above-mentioned species with respect to assimilation of sugars and utilization of organic acids. The DNA G+C content of strain DZ-1T was 62.1 mol% (Tm). The DNA-DNA relatedness of strain DZ-1T to H. tibetense and H. vacuolatum was 22 and 13 %, respectively. It was concluded that strain DZ-1T represents a novel species of the genus Halorubrum, for which the name Halorubrum alkaliphilum (type strain, DZ-1T=AS 1.3528T=JCM 12358T) is proposed.
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Affiliation(s)
- Jie Feng
- State Key Laboratory for Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, PR China
| | - Peijin Zhou
- State Key Laboratory for Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, PR China
| | - Yu-Guang Zhou
- State Key Laboratory for Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory for Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Haidian, Beijing 100080, PR China
| | - Kimberly Warren-Rhodes
- Ecosystem Sciences Division, Department of Environmental Science, Policy and Management, University of California at Berkeley, CA 94720, USA
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37
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Feng J, Zhou PJ, Liu SJ. Halorubrum xinjiangense sp. nov., a novel halophile isolated from saline lakes in China. Int J Syst Evol Microbiol 2005; 54:1789-1791. [PMID: 15388744 DOI: 10.1099/ijs.0.63209-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon, strain BD-1T, was isolated from Xiao-Er-Kule Lake in Xinjiang, China. The taxonomy of strain BD-1T was studied by polyphasic methods. According to 16S rRNA gene sequence similarity, strain BD-1T was phylogenetically related to Halorubrum trapanicum (98.4 %), Halorubrum sodomense (98.0 %), Halorubrum distributum (97.8 %) and Halorubrum coriense (97.3 %). Strain BD-1T is able to grow at 10 degrees C and further differs physiologically from the above species in the assimilation of sugars. The G + C content of DNA is 68.0 % (Tm). The DNA-DNA relatedness values to Hrr. trapanicum and Hrr. distributum are 47 and 24 %, respectively. It is concluded that strain BD-1T represents a novel species of the genus Halorubrum, for which the name Halorubrum xinjiangense sp. nov. is proposed. The type strain is BD-1T (= AS 1.3527T = JCM 12388T).
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MESH Headings
- Base Composition
- Carbohydrate Metabolism
- China
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Growth Inhibitors/pharmacology
- Halobacteriaceae/classification
- Halobacteriaceae/genetics
- Halobacteriaceae/isolation & purification
- Halobacteriaceae/physiology
- Hydrogen-Ion Concentration
- Magnesium/metabolism
- Molecular Sequence Data
- Movement
- Nucleic Acid Hybridization
- Phosphatidylglycerols/analysis
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic/pharmacology
- Sequence Analysis, DNA
- Temperature
- Water Microbiology
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Affiliation(s)
- Jie Feng
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Pei-Jin Zhou
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Shuang-Jiang Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
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38
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Itoh T, Yamaguchi T, Zhou P, Takashina T. Natronolimnobius baerhuensis gen. nov., sp. nov. and Natronolimnobius innermongolicus sp. nov., novel haloalkaliphilic archaea isolated from soda lakes in Inner Mongolia, China. Extremophiles 2004; 9:111-6. [PMID: 15841343 DOI: 10.1007/s00792-004-0426-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 10/01/2004] [Indexed: 11/26/2022]
Abstract
Three novel isolates of haloalkaliphilic archaea, strains IHC-005T, IHC-010, and N-1311T, from soda lakes in Inner Mongolia, China, were characterized to elucidate their taxonomic positions. The three strains were aerobic, Gram-negative chemoorganotrophs growing optimally at 37-45 degrees C, pH 9.0-9.5, and 15-20% NaCl. Cells of strains IHC-005T/IHC-010 were motile rods, while those of strain N-1311T were non-motile pleomorphic flats or cocci. The three strains contained diphytanyl and phytanyl-sesterterpanyl diether derivatives of phosphatidylglycerol and phosphatidylglycerophosphate methyl ester. No glycolipids were detected. On phylogenetic analysis of 16S rRNA gene sequences, they formed an independent cluster in the Natro group of the family Halobacteriaceae. Comparison of their morphological, physiological, and biochemical properties, DNA G + C content and 16S rRNA gene sequences, and DNA-DNA hybridization study support the view that strains IHC-005T/IHC-010 and strain N-1311T represent separate species. Therefore, we propose Natronolimnobius baerhuensis gen. nov., sp. nov. for strains IHC-005T (=CGMCC 1.3597T =JCM 12253T)/IHC-010 (=CGMCC 1.3598 = JCM 12254) and Natronolimnobius innermongolicus sp. nov. for N-1311T (=CGMCC 1.2124T =JCM 12255T).
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Affiliation(s)
- Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan.
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