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Kerem G, Yu X, Ismayi A, Teng B, Udduttula A, Liu C, Yu Z, Tohty D, Zhang JV, Ren PG. Small intestinal microbiota composition altered in obesity-T2DM mice with high salt fed. Sci Rep 2023; 13:8256. [PMID: 37217529 DOI: 10.1038/s41598-023-33909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Obesity has become a global concern because of increasing the risk of many diseases. Alterations in human gut microbiota have been proven to be associated with obesity, yet the mechanism of how the microbiota are altered by high salt diet (HSD) remains obscure. In this study, the changes of Small Intestinal Microbiota (SIM) in obesity-T2DM mice were investigated. High-throughput sequencing was applied for the jejunum microbiota analysis. Results revealed that high salt intake (HS) could suppress the body weight (B.W.) in some extent. In addition, significant T2DM pathological features were revealed in high salt-high food diet (HS-HFD) group, despite of relatively lower food intake. High-throughput sequencing analysis indicated that the F/B ratio in HS intake groups increased significantly (P < 0.001), whereas beneficial bacteria, such as lactic acid or short chain fatty acid producing bacteria, were significantly decreased in HS-HFD group (P < 0.01 or P < 0.05). Furthermore, Halorubrum luteum were observed in small intestine for the first time. Above results preliminary suggested that in obesity-T2DM mice, high dietary salt could aggravate the imbalance of composition of SIM to unhealthy direction.
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Affiliation(s)
- Goher Kerem
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiangfang Yu
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, China
| | - Aynur Ismayi
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bin Teng
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Anjaneyulu Udduttula
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chang Liu
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, China
| | - Zhongjia Yu
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, China
| | - Dilbar Tohty
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Jian V Zhang
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Guangdong Key Laboratory of Nanomedicine, Shenzhen, China
| | - Pei-Gen Ren
- Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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Najjari A, Stathopoulou P, Elmnasri K, Hasnaoui F, Zidi I, Sghaier H, Ouzari HI, Cherif A, Tsiamis G. Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia. BIOLOGY 2021; 10:biology10050397. [PMID: 34064384 PMCID: PMC8147861 DOI: 10.3390/biology10050397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/27/2022]
Abstract
A thorough assessment of the phylogenetic diversity and community structure of halophilic archaea from three halite-crystal salts, processed from two separated saline systems of Southern Tunisia has been performed using culture dependent and independent methods targeting different regions of 16S rRNA gene sequences including DGGE, 16S rRNA clone libraries and Illumina Miseq sequencing. Two samples, CDR (red halite-crystal salts) and CDW (white halite-crystal salts), were collected from Chott-Eljerid and one sample CDZ (white halite-crystal salts) from Chott Douz. Fourteen isolates were identified as Halorubrum, Haloferax, Haloarcula, and Halogeometricum genera members. Culture-independent approach revealed a high diversity of archaeal members present in all samples, represented by the Euryarchaeal phylum and the dominance of the Halobacteria class. Nanohaloarchaea were also identified only in white halite samples based on metagenomic analysis. In fact, a total of 61 genera were identified with members of the Halorhabdus, Halonotius, Halorubrum, Haloarcula, and unclassified. Halobacteriaceae were shared among all samples. Unexpected diversity profiles between samples was observed where the red halite crust sample was considered as the most diverse one. The highest diversity was observed with Miseq approach, nevertheless, some genera were detected only with 16S rRNA clone libraries and cultured approaches.
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Affiliation(s)
- Afef Najjari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
- Correspondence:
| | - Panagiota Stathopoulou
- Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece; (P.S.); (G.T.)
| | - Khaled Elmnasri
- Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; (K.E.); (H.S.); (A.C.)
| | - Faten Hasnaoui
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
| | - Ines Zidi
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
| | - Haitham Sghaier
- Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; (K.E.); (H.S.); (A.C.)
- Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), 2020 Sidi Thabet, Tunisia
| | - Hadda Imene Ouzari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia; (F.H.); (I.Z.); (H.I.O.)
| | - Ameur Cherif
- Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia; (K.E.); (H.S.); (A.C.)
| | - George Tsiamis
- Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece; (P.S.); (G.T.)
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Kalwasińska A, Deja-Sikora E, Szabó A, Felföldi T, Kosobucki P, Brzezinska MS, Walczak M. Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:842-854. [PMID: 30481711 DOI: 10.1016/j.scitotenv.2018.11.246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
This paper presents study on the microbiome of a unique extreme environment - saline and alkaline lime, a by-product of soda ash and table salt production in Janikowo, central Poland. High-throughput 16S rDNA amplicon sequencing was used to reveal the structure of bacterial and archaeal communities in the lime samples, taken from repository ponds differing in salinity (2.3-25.5% NaCl). Surprisingly abundant and diverse bacterial communities were discovered in this extreme environment. The most important geochemical drivers of the observed microbial diversity were salinity, calcium ions, nutrients, and water content. The bacterial and archaeal communities in saline, alkaline lime were similar to those found in natural haloalkaline environments. Although the archaeal contribution to the whole microbial community was lower than 4%, the four archaeal genera Natronomonas, Halorubrum, Halobellus, and Halapricum constituted the core microbiome of saline, alkaline lime - a set of OTUs (> 0.1% of total archaeal relative abundance) present in all samples under study. The high proportion of novel, unclassified archaeal and bacterial sequences (not identified at 97% similarity level) in the 16S rRNA gene libraries indicated that potentially new genera, especially within the class of Thermoplasmata inhabit this unique environment.
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Affiliation(s)
- Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland.
| | - Edyta Deja-Sikora
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland; Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Attila Szabó
- Department of Microbiology, ELTE Eötvös Loránd University, PázmányPéterstny. 1/c. H-1117 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, PázmányPéterstny. 1/c. H-1117 Budapest, Hungary
| | - Przemysław Kosobucki
- Department of Food Analysis and Environmental Protection, Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland
| | - Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Maciej Walczak
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
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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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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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Siliakus MF, van der Oost J, Kengen SWM. Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure. Extremophiles 2017; 21:651-670. [PMID: 28508135 PMCID: PMC5487899 DOI: 10.1007/s00792-017-0939-x] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 04/29/2017] [Indexed: 12/30/2022]
Abstract
The cytoplasmic membrane of a prokaryotic cell consists of a lipid bilayer or a monolayer that shields the cellular content from the environment. In addition, the membrane contains proteins that are responsible for transport of proteins and metabolites as well as for signalling and energy transduction. Maintenance of the functionality of the membrane during changing environmental conditions relies on the cell's potential to rapidly adjust the lipid composition of its membrane. Despite the fundamental chemical differences between bacterial ester lipids and archaeal ether lipids, both types are functional under a wide range of environmental conditions. We here provide an overview of archaeal and bacterial strategies of changing the lipid compositions of their membranes. Some molecular adjustments are unique for archaea or bacteria, whereas others are shared between the two domains. Strikingly, shared adjustments were predominantly observed near the growth boundaries of bacteria. Here, we demonstrate that the presence of membrane spanning ether-lipids and methyl branches shows a striking relationship with the growth boundaries of archaea and bacteria.
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Affiliation(s)
- Melvin F Siliakus
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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7
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Chen S, Liu HC, Zhou J, Xiang H. Haloparvum sedimenti gen. nov., sp. nov., a member of the family Haloferacaceae. Int J Syst Evol Microbiol 2016; 66:2327-2334. [PMID: 27001607 DOI: 10.1099/ijsem.0.001033] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaeal strains, DYS4T and Y2, were isolated from rock salt of the Jiangcheng Salt Mine, Yunnan province, China. Cells of the two strains were non-motile, pleomorphic rods and Gram-stain-negative. The cells produced light red-pigmented colonies. Strains DYS4T and Y2 required 2.6-3.4 M NaCl, pH 7.5- 8.0 and 42 ºC in aerobic conditions for optimal growth. Mg2+ was required for growth. The major polar lipids of both strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. An unidentified minor glycolipid spot was present for strains DYS4T and Y2, which differentiates them from the closely related species of the genera Halorubrum and Halopenitus. The lipid core of the glycolipid was sn-2,3-diphytanylglycerol (C20C20). The sequence similarity of the 16S rRNA gene demonstrated that the closest relatives of strains DYS4T and Y2 were Halorubrum aidingense 31-hongT (94.1 % and 93.6 % 16S rRNA gene sequence similarity to DYS4T and Y2, respectively) and Halopenitus salinus SKJ47T (93.4% and 93.1%). Phylogenetic analysis of the 16S rRNA gene and the rpoB' gene revealed that strains DYS4T and Y2 formed an independent lineage closely related to the genera Halorubrum and Halopenitus. The DNA G+C contents of strains DYS4T and Y2 were 68.2 and 67.0 mol%, respectively. The DNA-DNA relatedness value between strains DYS4T and Y2 was 90.0 ± 0.5%, while that between strain DYS4T and other closest relatives was less than 26 % (19 ± 0.7 % for Halorubrum aidingense 31-hongT and 25 ± 0.3% for Halopenitus salinus SKJ47T). The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains DYS4T and Y2 (=CGMCC 1.15000=JCM 30892) represent a novel species of a new genus within the family Haloferacaceae, for which the name Haloparvum sedimenti gen. nov., sp. nov. is proposed. The type strain of the type species is DYS4T (=CGMCC 1.14998T=JCM 30891T).
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Affiliation(s)
- Shaoxing Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University Key Laboratory of Crop High Quality and High Effective Cultivation and Safety Control in Yunnan Province, Honghe University, Mengzi 66110, Yunnan, China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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de la Vega M, Sayago A, Ariza J, Barneto AG, León R. Characterization of a bacterioruberin-producing Haloarchaea isolated from the marshlands of the Odiel river in the southwest of Spain. Biotechnol Prog 2016; 32:592-600. [DOI: 10.1002/btpr.2248] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 02/08/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Marta de la Vega
- Dept. of Chemistry; Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR) and CEICAMBIO, University of Huelva; Huelva Spain
| | - Ana Sayago
- Dept. of Chemistry; Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR) and CEICAMBIO, University of Huelva; Huelva Spain
| | - José Ariza
- Dept. of Chemistry; Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR) and CEICAMBIO, University of Huelva; Huelva Spain
| | - Agustín G. Barneto
- Dept. of Chemistry; Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR) and CEICAMBIO, University of Huelva; Huelva Spain
| | - Rosa León
- Dept. of Chemistry; Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR) and CEICAMBIO, University of Huelva; Huelva Spain
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Simachew A, Lanzén A, Gessesse A, Øvreås L. Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond. MICROBIAL ECOLOGY 2016; 71:326-338. [PMID: 26408190 DOI: 10.1007/s00248-015-0675-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
The effect of salinity on prokaryotic community diversity in Abijata-Shalla Soda Ash Concentration Pond system was investigated by using high-throughput 16S rRNA gene 454 pyrosequencing. Surface water and brine samples from five sites spanning a salinity range of 3.4 % (Lake Abijata) to 32 % (SP230F, crystallizer pond) were analyzed. Overall, 33 prokaryotic phyla were detected, and the dominant prokaryotic phyla accounted for more than 95 % of the reads consisting of Planctomycetes, Bacteroidetes, candidate division TM7, Deinococcus-Thermus, Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota. Diversity indices indicated that operational taxonomic unit (OTU) richness decreases drastically with increasing salinity in the pond system. A total of 471 OTUs were found at 3.4 % salinity whereas 49 OTUs were detected in pond SP211 (25 % salinity), and only 19 OTUs in the crystallization pond at 32 % salinity (SP230F). Along the salinity gradient, archaeal community gradually replaced bacterial community. Thus, archaeal community accounted for 0.4 % in Lake Abijata while 99.0 % in pond SP230F. This study demonstrates that salinity appears to be the key environmental parameter in structuring the prokaryotic communities of haloalkaline environments. Further, it confirmed that the prokaryotic diversity in Lake Abijata is high and it harbors taxa with low or no phylogenetic similarities to existing prokaryotic taxa and thus represents novel microorganisms.
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Affiliation(s)
| | - Anders Lanzén
- Department of Ecology and Natural Resources, NEIKER-Tecnalia, Derio, Spain
| | | | - Lise Øvreås
- Department of Biology, University of Bergen, Bergen, Norway
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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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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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Bowers KJ, Wiegel J. Temperature and pH optima of extremely halophilic archaea: a mini-review. Extremophiles 2011; 15:119-28. [DOI: 10.1007/s00792-010-0347-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 12/08/2010] [Indexed: 11/25/2022]
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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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