1
|
Hu Y, Ma X, Li XX, Tan S, Cheng M, Hou J, Cui HL. Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine. Extremophiles 2023; 27:9. [PMID: 37000350 DOI: 10.1007/s00792-023-01294-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023]
Abstract
Four extremely halophilic archaeal strains (ZJ2T, BND6T, DT87T, and YPL30T) were isolated from marine environments and a salt mine in China. The 16S rRNA and rpoB' gene sequence similarities among strains ZJ2T, BND6T, DT87T, YPL30T and the current species of Natrinema were 93.2-99.3% and 89.2-95.8%, respectively. Both phylogenetic and phylogenomic analyses revealed that strains ZJ2T, BND6T, DT87T, and YPL30T cluster with the Natrinema members. The overall genome-related indexes (ANI, isDDH, and AAI) among these four strains and the current species of genus Natrinema were 70-88%, 22-43% and 75-89%, respectively, clearly below the threshold values for species boundary. Strains ZJ2T, BND6T, DT87T, and YPL30T could be distinguished from the related species according to differential phenotypic characteristics. The major polar lipids of the four strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), and disulfated mannosyl glucosyl diether (S2-DGD). The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains ZJ2T (= CGMCC 1.18786 T = JCM 34918 T), BND6T (= CGMCC 1.18777 T = JCM 34909 T), DT87T (= CGMCC 1.18921 T = JCM 35420 T), and YPL30T (= CGMCC 1.15337 T = JCM 31113 T) represent four novel species of the genus Natrinema, for which the names, Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., and Natrinema zhouii sp. nov., are proposed.
Collapse
Affiliation(s)
- Yao Hu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Xue Ma
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Xin-Xin Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Shun Tan
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Mu Cheng
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China.
| |
Collapse
|
2
|
Bao CX, Li SY, Xin YJ, Hou J, Cui HL. Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov., Natrinema amylolyticum sp. nov. and Haloterrigena alkaliphila sp. nov., four extremely halophilic archaea isolated from salt mine, saline soil and salt lake. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005385] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four halophilic archaeal strains, YPL8T, SLN56T, LT61T and KZCA68T, were isolated from a salt mine, saline soil and a salt lake located in different regions of China. Sequence similarities of 16S rRNA and rpoB′ genes among strains YPL8T, SLN56T, LT61T and the current members of
Natrinema
were 94.1–98.2 % and 89.3–95.1 %, respectively, while these values among strain KZCA68T and the current members of
Haloterrigena
were 97.2–97.4 % and 91.7–91.9 %, respectively. The average nucleotide identity, in silico DNA–DNA hybridization and average amino acid identity values among these four strains and their closely related species were all lower than the threshold values for species boundary. All four strains were unable to hydrolyse casein, gelatin, or Tween 80. Strain YPL8T contained phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), disulfated mannosyl glucosyl diether (S2-DGD) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). Strain SLN56T contained PA, PG, phosphatidylglycerol sulphate (PGS), PGP-Me, S-DGD-1, S2-DGD and S-DGD-PA. Strain LT61T contained PA, PG, PGS, PGP-Me, S-DGD-1 and S2-DGD. The phospholipids of strain KZCA68T were PA, PG and PGP-Me. These results showed that strains YPL8T (=CGMCC 1.13883T=JCM 31181T), SLN56T (=CGMCC 1.14945T=JCM 30832T) and LT61T (=CGMCC 1.14942T=JCM 30668T) represent novel species of the genus
Natrinema
, for which the names, Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov. and Natrinema amylolyticum sp. nov. are proposed. Strain KZCA68T (=CGMCC 1.17211T=JCM 34158T) represents a novel species of
Haloterrigena
, for which the name Haloterrigena alkaliphila sp. nov. is proposed.
Collapse
Affiliation(s)
- Chen-Xi Bao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Si-Ya Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Yu-Jie Xin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, 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
| |
Collapse
|
3
|
de la Haba RR, Minegishi H, Kamekura M, Shimane Y, Ventosa A. Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena. Front Microbiol 2021; 12:740909. [PMID: 34690986 PMCID: PMC8530250 DOI: 10.3389/fmicb.2021.740909] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/25/2021] [Indexed: 02/03/2023] Open
Abstract
The haloarchaeal genera Natrinema and Haloterrigena were described almost simultaneously by two different research groups and some strains studied separately were described as different species of these genera. Furthermore, the description of additional species were assigned to either Natrinema or Haloterrigena, mainly on the basis of the phylogenetic comparative analysis of single genes (16S rRNA gene and more recently rpoB’ gene), but these species were not adequately separated or assigned to the corresponding genus. Some studies suggested that the species of these two genera should be unified into a single genus, while other studies indicated that the genera should remain but some of the species should be reassigned. In this study, we have sequenced or collected the genomes of the type strains of species of Natrinema and Haloterrigena and we have carried out a comparative genomic analysis in order to clarify the controversy related to these two genera. The phylogenomic analysis based on the comparison of 525 translated single-copy orthologous genes and the Overall Genome Relatedness Indexes (i.e., AAI, POCP, ANI, and dDDH) clearly indicate that the species Haloterrigena hispanica, Haloterrigena limicola, Haloterrigena longa, Haloterrigena mahii, Haloterrigena saccharevitans, Haloterrigena thermotolerans, and Halopiger salifodinae should be transferred to the genus Natrinema, as Natrinema hispanicum, Natrinema limicola, Natrinema longum, Natrinema mahii, Natrinema saccharevitans, Natrinema thermotolerans, and Natrinema salifodinae, respectively. On the contrary, the species Haloterrigena turkmenica, Haloterrigena salifodinae, and Haloterrigena salina will remain as the only representative species of the genus Haloterrigena. Besides, the species Haloterrigena daqingensis should be reclassified as a member of the genus Natronorubrum, as Natronorubrum daqingense. At the species level, Haloterrigena jeotgali and Natrinema ejinorense should be considered as a later heterotypic synonyms of the species Haloterrigena (Natrinema) thermotolerans and Haloterrigena (Natrinema) longa, respectively. Synteny analysis and phenotypic features also supported those proposals.
Collapse
Affiliation(s)
- Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Hiroaki Minegishi
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, Kawagoe, Japan
| | | | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| |
Collapse
|
4
|
Novel haloarchaeon Natrinema thermophila having the highest growth temperature among haloarchaea with a large genome size. Sci Rep 2018; 8:7777. [PMID: 29773867 PMCID: PMC5958107 DOI: 10.1038/s41598-018-25887-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Environmental temperature is one of the most important factors for the growth and survival of microorganisms. Here we describe a novel extremely halophilic archaeon (haloarchaea) designated as strain CBA1119T isolated from solar salt. Strain CBA1119T had the highest maximum and optimal growth temperatures (66 °C and 55 °C, respectively) and one of the largest genome sizes among haloarchaea (5.1 Mb). It also had the largest number of strain-specific pan-genome orthologous groups and unique pathways among members of the genus Natrinema in the class Halobacteria. A dendrogram based on the presence/absence of genes and a phylogenetic tree constructed based on OrthoANI values highlighted the particularities of strain CBA1119T as compared to other Natrinema species and other haloarchaea members. The large genome of strain CBA1119T may provide information on genes that confer tolerance to extreme environmental conditions, which may lead to the discovery of other thermophilic strains with potential applications in industrial biotechnology.
Collapse
|
5
|
Rasooli M, Naghoni A, Amoozegar MA, Mirfeizi L, Moshtaghi Nikou M, Shahzadeh Fazeli SA, Minegishi H, Ventosa A. Natrinema soli sp. nov., a novel halophilic archaeon isolated from a hypersaline wetland. Int J Syst Evol Microbiol 2017. [PMID: 28650314 DOI: 10.1099/ijsem.0.001909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon, designated strain 5-3T, was isolated from a soil sample of Meighan wetland in Iran. Strain 5-3T was strictly aerobic, catalase-positive and oxidase-negative. Cells were Gram-stain-negative, non-motile and ovoid. Colonies of strain 5-3T were cream-coloured. The isolate showed optimum growth at 4.0 M NaCl, 40 °C and pH 7.0. The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two unknown phospholipids and three glycolipids (including one that was chromatographically identical to S2-DGD). The major respiratory quinone was menaquinone MK-8. The G+C content of the genomic DNA was 61.5 mol%. The closest relative was Natrinema salaciae JCM 17869T with 97.3 % similarity in the orthologous 16S rRNA gene sequence. Analysis of 16S rRNA and rpoB' gene sequences indicated that strain 5-3T is a member of the genus Natrinema in the family Natrialbaceae and forms a distinct cluster. On the basis of phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, a novel species of the family Natrialbaceae, Natrinema soli sp. nov., is proposed. The type strain is 5-3T (=IBRC-M 11063T=LMG 29247T).
Collapse
Affiliation(s)
- Mehrnoosh Rasooli
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Ali Naghoni
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Leila Mirfeizi
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | | | - Seyed Abolhassan Shahzadeh Fazeli
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran.,Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Hiroaki Minegishi
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, Kawagoe-shi, Saitama, Japan
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Halocin C8: an antimicrobial peptide distributed among four halophilic archaeal genera: Natrinema, Haloterrigena, Haloferax, and Halobacterium. Extremophiles 2017; 21:623-638. [DOI: 10.1007/s00792-017-0931-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/24/2017] [Indexed: 11/26/2022]
|
8
|
Cheng H, Huo YY, Hu J, Xu XW, Wu M. High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2 T. Stand Genomic Sci 2017; 12:25. [PMID: 28265340 PMCID: PMC5333441 DOI: 10.1186/s40793-017-0237-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 12/05/2016] [Indexed: 11/10/2022] Open
Abstract
Natrinema altunense strain AJ2T, a halophilic archaeal strain, was isolated from a high-altitude (3884 m) salt lake in Xinjiang, China. This strain requires at least 1.7 M NaCl to grow and can grow anaerobically in the presence of nitrate. To understand the genetics underlying its extreme phenotype, we de novo assembled the entire genome sequence of AJ2T (=CGMCC 1.3731T=JCM 12890T). We assembled 3,774,135 bp of a total of 4.4 Mb genome in only 20 contigs and noted its high GC content (64.6%). Subsequently we predicted the gene content and generated genome annotation to identify the relationship between the epigenetic characteristics and genomic features. The genome sequence contains 52 tRNA genes, 3 rRNA genes and 4,462 protein-coding genes, 3792 assigned as functional or hypothetical proteins in nr database. This Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession JNCS00000000. We performed a Bayesian (Maximum-Likelihood) phylogenetic analysis using 16S rRNA sequence and obtained its relationship to other strains in the Natrinema and Haloterrigena genera. We also confirmed the ANI value between every two species of Natrinema and Haloterrigena genera. In conclusion, our analysis furthered our understanding of the extreme-environment adapted strain AJ2T by characterizing its genome structure, gene content and phylogenetic placement. Our detailed case study will contribute to our overall understanding of why Natrinema strains can survive in such a high-altitude salt lake.
Collapse
Affiliation(s)
- Hong Cheng
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012 People’s Republic of China
- College of Life Sciences, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Ying-Yi Huo
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012 People’s Republic of China
| | - Jing Hu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Xue-Wei Xu
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012 People’s Republic of China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| |
Collapse
|
9
|
Chitin accelerates activation of a novel haloarchaeal serine protease that deproteinizes chitin-containing biomass. Appl Environ Microbiol 2014; 80:5698-708. [PMID: 25002433 DOI: 10.1128/aem.01196-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The haloarchaeon Natrinema sp. strain J7-2 has the ability to degrade chitin, and its genome harbors a chitin metabolism-related gene cluster that contains a halolysin gene, sptC. The sptC gene encodes a precursor composed of a signal peptide, an N-terminal propeptide consisting of a core domain (N*) and a linker peptide, a subtilisin-like catalytic domain, a polycystic kidney disease domain (PkdD), and a chitin-binding domain (ChBD). Here we report that the autocatalytic maturation of SptC is initiated by cis-processing of N* to yield an autoprocessed complex (N*-I(WT)), followed by trans-processing/degradation of the linker peptide, the ChBD, and N*. The resulting mature form (M(WT)) containing the catalytic domain and the PkdD showed optimum azocaseinolytic activity at 3 to 3.5 M NaCl, demonstrating salt-dependent stability. Deletion analysis revealed that the PkdD did not confer extra stability on the enzyme but did contribute to enzymatic activity. The ChBD exhibited salt-dependent chitin-binding capacity and mediated the binding of N*-I(WT) to chitin. ChBD-mediated chitin binding enhances SptC maturation by promoting activation of the autoprocessed complex. Our results also demonstrate that SptC is capable of removing proteins from shrimp shell powder (SSP) at high salt concentrations. Interestingly, N*-I(WT) released soluble peptides from SSP faster than did M(WT). Most likely, ChBD-mediated binding of the autoprocessed complex to chitin in SSP not only accelerates enzyme activation but also facilitates the deproteinization process by increasing the local protease concentration around the substrate. By virtue of these properties, SptC is highly attractive for use in preparation of chitin from chitin-containing biomass.
Collapse
|
10
|
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)).
Collapse
Affiliation(s)
- Wen-Jiao Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
11
|
Albuquerque L, Taborda M, La Cono V, Yakimov M, da Costa MS. Natrinema salaciae sp. nov., a halophilic archaeon isolated from the deep, hypersaline anoxic Lake Medee in the Eastern Mediterranean Sea. Syst Appl Microbiol 2012; 35:368-73. [DOI: 10.1016/j.syapm.2012.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 06/19/2012] [Accepted: 06/21/2012] [Indexed: 10/28/2022]
|
12
|
Feng J, Liu B, Zhang Z, Ren Y, Li Y, Gan F, Huang Y, Chen X, Shen P, Wang L, Tang B, Tang XF. The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements. PLoS One 2012; 7:e41621. [PMID: 22911826 PMCID: PMC3402447 DOI: 10.1371/journal.pone.0041621] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Accepted: 06/22/2012] [Indexed: 11/19/2022] Open
Abstract
Natrinema sp. J7-2 is an extreme haloarchaeon capable of growing on synthetic media without amino acid supplements. Here we report the complete genome sequence of Natrinema sp. J7-2 which is composed of a 3,697,626-bp chromosome and a 95,989-bp plasmid pJ7-I. This is the first complete genome sequence of a member of the genus Natrinema. We demonstrate that Natrinema sp. J7-2 can use gluconate, glycerol, or acetate as the sole carbon source and that its genome encodes complete metabolic pathways for assimilating these substrates. The biosynthetic pathways for all 20 amino acids have been reconstructed, and we discuss a possible evolutionary relationship between the haloarchaeal arginine synthetic pathway and the bacterial lysine synthetic pathway. The genome harbors the genes for assimilation of ammonium and nitrite, but not nitrate, and has a denitrification pathway to reduce nitrite to N2O. Comparative genomic analysis suggests that most sequenced haloarchaea employ the TrkAH system, rather than the Kdp system, to actively uptake potassium. The genomic analysis also reveals that one of the three CRISPR loci in the Natrinema sp. J7-2 chromosome is located in an integrative genetic element and is probably propagated via horizontal gene transfer (HGT). Finally, our phylogenetic analysis of haloarchaeal genomes provides clues about evolutionary relationships of haloarchaea.
Collapse
Affiliation(s)
- Jie Feng
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Ziqian Zhang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yan Ren
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yang Li
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Fei Gan
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yuping Huang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Xiangdong Chen
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Ping Shen
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, People's Republic of China
| | - Bing Tang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
- * E-mail: (BT); (X-FT)
| | - Xiao-Feng Tang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, People's Republic of China
- * E-mail: (BT); (X-FT)
| |
Collapse
|
13
|
Shimane Y, Hatada Y, Minegishi H, Mizuki T, Echigo A, Miyazaki M, Ohta Y, Usami R, Grant WD, Horikoshi K. Natronoarchaeum mannanilyticum gen. nov., sp. nov., an aerobic, extremely halophilic archaeon isolated from commercial salt. Int J Syst Evol Microbiol 2010; 60:2529-2534. [DOI: 10.1099/ijs.0.016600-0] [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
Strain YSM-123T was isolated from commercial salt made from Japanese seawater in Niigata prefecture. Optimal NaCl and Mg2+ concentrations for growth were 4.0–4.5 M and 5 mM, respectively. The isolate was a mesophilic and slightly alkaliphilic haloarchaeon, whose optimal growth temperature and pH were 37 °C and pH 8.0–9.0. Phylogenetic analysis based on 16S rRNA gene sequence analysis suggested that strain YSM-123T is a member of the phylogenetic group defined by the family Halobacteriaceae, but there were low similarities to type strains of other genera of this family (≤90 %); for example, Halococcus (similarity <89 %), Halostagnicola (<89 %), Natronolimnobius (<89 %), Halobiforma (<90 %), Haloterrigena (<90 %), Halovivax (<90 %), Natrialba (<90 %), Natronobacterium (<90 %) and Natronococcus (<90 %). The G+C content of the DNA was 63 mol%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, disulfated diglycosyl diether and an unknown glycolipid. On the basis of the data presented, we propose that strain YSM-123T should be placed in a new genus and species, Natronoarchaeum mannanilyticum gen. nov., sp. nov. The type strain of Natronoarchaeum mannanilyticum is strain YSM-123T (=JCM 16328T =CECT 7565T).
Collapse
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
| | - Toru Mizuki
- 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
| | - 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
| | - 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, Room 144, Maurice Shock Medical Sciences Building, Leicester, 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
| |
Collapse
|
14
|
Tapingkae W, Tanasupawat S, Itoh T, Parkin KL, Benjakul S, Visessanguan W, Valyasevi R. Natrinema gari sp. nov., a halophilic archaeon isolated from fish sauce in Thailand. Int J Syst Evol Microbiol 2008; 58:2378-83. [DOI: 10.1099/ijs.0.65644-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
15
|
Romano I, Poli A, Finore I, Huertas FJ, Gambacorta A, Pelliccione S, Nicolaus G, Lama L, Nicolaus B. Haloterrigena hispanica sp. nov., an extremely halophilic archaeon from Fuente de Piedra, southern Spain. Int J Syst Evol Microbiol 2007; 57:1499-1503. [PMID: 17625183 DOI: 10.1099/ijs.0.64895-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon belonging to the order Halobacteriales was isolated from Fuente de Piedra salt lake, Spain. This strain, designated FP1T, was a pleomorphic coccoid, neutrophilic and required at least 15 % (w/v) NaCl for growth. Strain FP1T grew at 37–60 °C, with optimal growth at 50 °C. Mg2+ was not required, but growth was observed with up to 10 % (w/v) MgSO4. Polar lipid analysis revealed the presence of mannose-6-sulfate(1-2)-glucose glycerol diether as a major glycolipid. Both C20C20 and C20C25 core lipids were present. The genomic DNA G+C content was 62.0 mol%. Phylogenetic analysis based on comparison of 16S rRNA gene sequences demonstrated that the isolate was most closely related to species of the genus Haloterrigena. DNA–DNA reassociation values between strain FP1T and the most closely related species of the genus Haloterrigena (Haloterrigena thermotolerans, Haloterrigena saccharevitans and Haloterrigena limicola) were lower than 29 %. It is therefore considered that strain FP1T represents a novel species of the genus Haloterrigena, for which the name Haloterrigena hispanica sp. nov. is proposed. The type strain is FP1T (=DSM 18328T=ATCC BAA-1310T).
Collapse
MESH Headings
- Base Composition
- DNA, Archaeal/chemistry
- DNA, Archaeal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Glycolipids/analysis
- Halobacteriaceae/chemistry
- Halobacteriaceae/classification
- Halobacteriaceae/isolation & purification
- Halobacteriaceae/physiology
- Magnesium Chloride/metabolism
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Spain
- Temperature
- Water Microbiology
Collapse
Affiliation(s)
- Ida Romano
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Annarita Poli
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Ilaria Finore
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - F Javier Huertas
- CSIC, Estacion Experimental del Zaidin, Department of Earth Sciences and Environmental Chemistry, Profesor Albareda 1, 18008 Granada, Spain
| | - Agata Gambacorta
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Salvatore Pelliccione
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Giancarlo Nicolaus
- Istituto di Ricerche di Biologia Molecolare Angeletti IRBM, Pomezia, Roma, Italy
| | - Licia Lama
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Barbara Nicolaus
- Istituto di Chimica Biomolecolare, Comprensorio ex Olivetti, via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| |
Collapse
|