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Naitam MG, Ramakrishnan B, Grover M, Kaushik R. Rhizosphere-dwelling halophilic archaea: a potential candidate for alleviating salinity-associated stress in agriculture. Front Microbiol 2023; 14:1212349. [PMID: 37564293 PMCID: PMC10410454 DOI: 10.3389/fmicb.2023.1212349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023] Open
Abstract
Salinity is a serious environmental factor that impedes crop growth and drastically reduces yield. This study aimed to investigate the potential of halophilic archaea isolated from the Rann of Kutch to alleviate the negative impact of salinity on crop growth and yield. The halophilic archaea, which demonstrated high tolerance to salinity levels up to 4.5 M, were evaluated for their ability to promote plant growth in both salt-tolerant and salt-susceptible wheat cultivars. Our assessment focused on their capacity to solubilize essential nutrients, including phosphorus (14-61 mg L-1), potassium (37-78 mg L-1), and zinc (8-17 mg L-1), as well as their production of the phytohormone IAA (17.30 to 49.3 μg ml-1). To conduct the experiments, five wheat cultivars (two salt-tolerant and three salt-susceptible) were grown in triplicates using soft MS agar tubes (50 ml) and pots containing 10 kg of soil with an electrical conductivity (EC) of 8 dSm-1. Data were collected at specific time points: 21 days after sowing (DAS) for the MS agar experiment, 45 DAS for the pot experiment, and at the time of harvest. In the presence of haloarchaea, the inoculated treatments exhibited significant increases in total protein (46%), sugar (27%), and chlorophyll (31%) levels compared to the un-inoculated control. Furthermore, the inoculation led to an elevated accumulation of osmolyte proline (31.51%) and total carbohydrates (27.85%) while substantially reducing the activity of antioxidant enzymes such as SOD, catalase, and peroxidase by 57-76%, respectively. Notably, the inoculated treatments also showed improved plant vegetative growth parameters compared to the un-inoculated treatments. Interestingly, the positive effects of the halophilic archaea were more pronounced in the susceptible wheat cultivars than in the tolerant cultivars. These findings highlight the growth-promoting abilities of the halophilic archaeon Halolamina pelagica CDK2 and its potential to mitigate the detrimental effects of salinity. Consequently, further evaluation of this halophilic archaeon under field conditions is warranted to explore its potential use in the development of microbial inoculants.
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Affiliation(s)
- Mayur G. Naitam
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - B. Ramakrishnan
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Monendra Grover
- Center for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistical Research Institute, New Delhi, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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2
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Chen M, Conroy JL, Sanford RA, Wyman-Feravich DA, Chee-Sanford JC, Connor LM. Tropical lacustrine sediment microbial community response to an extreme El Niño event. Sci Rep 2023; 13:6868. [PMID: 37106028 PMCID: PMC10140070 DOI: 10.1038/s41598-023-33280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015-2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.
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Affiliation(s)
- Mingfei Chen
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jessica L Conroy
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Joanne C Chee-Sanford
- Department of Natural Resource and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA-ARS, Urbana, IL, USA
| | - Lynn M Connor
- Department of Natural Resource and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA-ARS, Urbana, IL, USA
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Najjari A, Boussetta A, Youssef N, Linares-Pastén JA, Mahjoubi M, Belloum R, Sghaier H, Cherif A, Ouzari HI. Physiological and genomic insights into abiotic stress of halophilic archaeon Natrinema altunense 4.1R isolated from a saline ecosystem of Tunisian desert. Genetica 2023; 151:133-152. [PMID: 36795306 PMCID: PMC9995536 DOI: 10.1007/s10709-023-00182-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023]
Abstract
Halophilic archaea are polyextremophiles with the ability to withstand fluctuations in salinity, high levels of ultraviolet radiation, and oxidative stress, allowing them to survive in a wide range of environments and making them an excellent model for astrobiological research. Natrinema altunense 4.1R is a halophilic archaeon isolated from the endorheic saline lake systems, Sebkhas, located in arid and semi-arid regions of Tunisia. It is an ecosystem characterized by periodic flooding from subsurface groundwater and fluctuating salinities. Here, we assess the physiological responses and genomic characterization of N. altunense 4.1R to UV-C radiation, as well as osmotic and oxidative stresses. Results showed that the 4.1R strain is able to survive up to 36% of salinity, up to 180 J/m2 to UV-C radiation, and at 50 mM of H2O2, a resistance profile similar to Halobacterium salinarum, a strain often used as UV-C resistant model. In order to understand the genetic determinants of N. altunense 4.1R survival strategy, we sequenced and analyzed its genome. Results showed multiple gene copies of osmotic stress, oxidative stress, and DNA repair response mechanisms supporting its survivability at extreme salinities and radiations. Indeed, the 3D molecular structures of seven proteins related to responses to UV-C radiation (excinucleases UvrA, UvrB, and UvrC, and photolyase), saline stress (trehalose-6-phosphate synthase OtsA and trehalose-phosphatase OtsB), and oxidative stress (superoxide dismutase SOD) were constructed by homology modeling. This study extends the abiotic stress range for the species N. altunense and adds to the repertoire of UV and oxidative stress resistance genes generally known from haloarchaeon.
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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, Tunisie
| | - Ayoub Boussetta
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Noha Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Javier A Linares-Pastén
- Department of Biotechnology, Faculty of Engineering, Lunds Tekniska Högskola (LTH), Lund University, P. O. Box 124, 22100, Lund, Sweden.
| | - Mouna Mahjoubi
- University of Manouba, ISBST, LR11-ES31 BVBGR, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Rahma Belloum
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Haitham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Ariana, Tunisia
| | - Ameur Cherif
- University of Manouba, ISBST, LR11-ES31 BVBGR, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Hadda Imene Ouzari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
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Archaeome in Colorectal Cancer: High Abundance of Methanogenic Archaea in Colorectal Cancer Patients. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2022. [DOI: 10.5812/ijcm-117843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: The importance of microbiome in the progression and development of colorectal cancer (CRC) has been discussed in the last decade. Like colon bacteria, other intestinal microorganisms, including archaea, could also be involved in the CRC progression, so it's important to work out the archaeal microbiome (archaeome) composition among CRC patients. Objectives: The aim of this study was to determine the archaeome composition of CRC and healthy controls based on age and gender. Methods: Total bacterial DNA was extracted from 30 biopsy samples (17 CRC and 13 healthy controls). Archaeome communities were profiled by 16S rRNA high throughput sequencing, then compared to clinicopathological features, including CRC patients’ gender and age. Results: In the CRC patients, archaeal methanogens including Methanobrevibacter (86%) and Methanomassiliicoccus (8%) were overrepresented at the genus level. In contrast in the healthy controls, only two genera of haloarchaea including Natronococcus (58%) and Haloterrigena (42%) were presented. The results showed that the number of archaeal genera in men is higher than women in both the CRC and healthy controls. moreover, our results showed that the most genera of archaea are present in the CRC-32-50 group, six archaeal genera. The differential abundance taxa analysis results showed significant differences between healthy controls and CRC patients (P ≤ 0.05). Conclusions: The high abundance of methanogens in the colon archaeome of CRC patients compared to healthy controls suggests that methanogens may be involved in CRC development.
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Natalicchio M, Birgel D, Dela Pierre F, Ziegenbalg S, Hoffmann-Sell L, Gier S, Peckmann J. Messinian bottom-grown selenitic gypsum: An archive of microbial life. GEOBIOLOGY 2022; 20:3-21. [PMID: 34296807 DOI: 10.1111/gbi.12464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Primary gypsum deposits, which accumulated in the Mediterranean Basin during the so-called Messinian salinity crisis (5.97-5.33 Ma), represent an excellent archive of microbial life. We investigated the molecular fossil inventory and the corresponding compound-specific δ13 C values of bottom-grown gypsum formed during the first stage of the crisis in four marginal basins across the Mediterranean (Nijar, Spain; Vena del Gesso, Italy; Heraklion, Crete; and Psematismenos, Cyprus). All studied gypsum samples contain intricate networks of filamentous microfossils, whose phylogenetic affiliation has been debated for a long time. Petrographic analysis, molecular fossil inventories (hydrocarbons, alcohols, and carboxylic acids), and carbon stable isotope patterns suggest that the mazes of filamentous fossils represent benthic microbial assemblages dominated by chemotrophic sulfide-oxidizing bacteria; in some of the samples, the body fossils are accompanied by lipids produced by sulfate-reducing bacteria. Abundant isoprenoid alcohols including diphytanyl glycerol diethers (DGDs) and glycerol dibiphytanyl glycerol tetraethers (GDGTs), typified by highly variable carbon stable isotope composition with δ13 C values spanning from -40 to -14‰, reveal the presence of planktic and benthic archaeal communities dwelling in Messinian paleoenvironments. The compound inventory of archaeal lipids indicates the existence of a stratified water column, with a normal marine to diluted upper water column and more saline deeper waters. This study documents the lipid biomarker inventory of microbial life preserved in ancient gypsum deposits, helping to reconstruct the widely debated conditions under which Messinian gypsum formed.
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Affiliation(s)
- Marcello Natalicchio
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Torino, Italy
| | - Daniel Birgel
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
| | - Francesco Dela Pierre
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Torino, Italy
| | | | | | - Susanne Gier
- Institut für Geologie, Universität Wien, Wien, Austria
| | - Jörn Peckmann
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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Lach J, Jęcz P, Strapagiel D, Matera-Witkiewicz A, Stączek P. The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools. Genes (Basel) 2021; 12:genes12111756. [PMID: 34828362 PMCID: PMC8619533 DOI: 10.3390/genes12111756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/18/2021] [Accepted: 10/30/2021] [Indexed: 02/06/2023] Open
Abstract
Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile's genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.
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Affiliation(s)
- Jakub Lach
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 93-338 Lodz, Poland; (P.J.); (P.S.)
- Biobank Lab, Department of Molecular Biophysics, Faculty of Environmental Protection, University of Lodz, 93-338 Lodz, Poland;
- Correspondence:
| | - Paulina Jęcz
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 93-338 Lodz, Poland; (P.J.); (P.S.)
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Environmental Protection, University of Lodz, 93-338 Lodz, Poland;
| | - Agnieszka Matera-Witkiewicz
- Screening Laboratory of Biological Activity Tests and Collection of Biological Material, Faculty of Pharmacy, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Paweł Stączek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 93-338 Lodz, Poland; (P.J.); (P.S.)
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Verma DK, Chaudhary C, Singh L, Sidhu C, Siddhardha B, Prasad SE, Thakur KG. Isolation and Taxonomic Characterization of Novel Haloarchaeal Isolates From Indian Solar Saltern: A Brief Review on Distribution of Bacteriorhodopsins and V-Type ATPases in Haloarchaea. Front Microbiol 2020; 11:554927. [PMID: 33362726 PMCID: PMC7755889 DOI: 10.3389/fmicb.2020.554927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/17/2020] [Indexed: 01/10/2023] Open
Abstract
Haloarchaea inhabit high salinity environments worldwide. They are a potentially rich source of crucial biomolecules like carotenoids and industrially useful proteins. However, diversity in haloarchaea present in Indian high salinity environments is poorly studied. In the present study, we isolated 12 haloarchaeal strains from hypersaline Kottakuppam, Tamil Nadu solar saltern in India. 16S rRNA based taxonomic characterization of these isolates suggested that nine of them are novel strains that belong to genera Haloarcula, Halomicrobium, and Haloferax. Transmission electron microscopy suggests the polymorphic nature of these haloarchaeal isolates. Most of the haloarchaeal species are known to be high producers of carotenoids. We were able to isolate carotenoids from all these 12 isolates. The UV-Vis spectroscopy-based analysis suggests that bacterioruberin and lycopene are the major carotenoids produced by these isolates. Based on the visual inspection of the purified carotenoids, the isolates were classified into two broad categories i.e., yellow and orange, attributed to the differences in the ratio of bacterioruberin and lycopene as confirmed by the UV-Vis spectral analysis. Using a PCR-based screening assay, we were able to detect the presence of the bacteriorhodopsin gene (bop) in 11 isolates. We performed whole-genome sequencing for three bop positive and one bop negative haloarchaeal isolates. Whole-genome sequencing, followed by pan-genome analysis identified multiple unique genes involved in various biological functions. We also successfully cloned, expressed, and purified functional recombinant bacteriorhodopsin (BR) from one of the isolates using Escherichia coli as an expression host. BR has light-driven proton pumping activity resulting in the proton gradient across the membrane, which is utilized by V-Type ATPases to produce ATP. We analyzed the distribution of bop and other accessory genes involved in functional BR expression and ATP synthesis in all the representative haloarchaeal species. Our bioinformatics-based analysis of all the sequenced members of genus Haloarcula suggests that bop, if present, is usually inserted between the genes coding for B and D subunits of the V-type ATPases operon. This study provides new insights into the genomic variations in haloarchaea and reports expression of new BR variant having good expression in functional form in E. coli.
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Affiliation(s)
- Dipesh Kumar Verma
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Chetna Chaudhary
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Latika Singh
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Chandni Sidhu
- MTCC-Microbial Type Culture Collection & Gene Bank, Council of Scientific and Industrial Research Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Senthil E Prasad
- Biochemical Engineering Research and Process Development Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
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Ruginescu R, Gomoiu I, Popescu O, Cojoc R, Neagu S, Lucaci I, Batrinescu-Moteau C, Enache M. Bioprospecting for Novel Halophilic and Halotolerant Sources of Hydrolytic Enzymes in Brackish, Saline and Hypersaline Lakes of Romania. Microorganisms 2020; 8:microorganisms8121903. [PMID: 33266166 PMCID: PMC7760675 DOI: 10.3390/microorganisms8121903] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 12/31/2022] Open
Abstract
Halophilic and halotolerant microorganisms represent promising sources of salt-tolerant enzymes that could be used in various biotechnological processes where high salt concentrations would otherwise inhibit enzymatic transformations. Considering the current need for more efficient biocatalysts, the present study aimed to explore the microbial diversity of five under- or uninvestigated salty lakes in Romania for novel sources of hydrolytic enzymes. Bacteria, archaea and fungi were obtained by culture-based approaches and screened for the production of six hydrolases (protease, lipase, amylase, cellulase, xylanase and pectinase) using agar plate-based assays. Moreover, the phylogeny of bacterial and archaeal isolates was studied through molecular methods. From a total of 244 microbial isolates, 182 (74.6%) were represented by bacteria, 22 (9%) by archaea, and 40 (16.4%) by fungi. While most bacteria synthesized protease and lipase, the most frequent hydrolase produced by fungi was pectinase. The archaeal isolates had limited hydrolytic activity, being able to produce only amylase and cellulase. Among the taxonomically identified isolates, the best hydrolytic activities were observed in halotolerant bacteria belonging to the genus Bacillus and in extremely halophilic archaea of the genera Haloterrigena and Halostagnicola. Therefore, the present study highlights that the investigated lakes harbor various promising species of microorganisms able to produce industrially valuable enzymes.
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Affiliation(s)
- Robert Ruginescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, P.O. Box 56-53, 060031 Bucharest, Romania; (I.G.); (O.P.); (R.C.); (S.N.); (I.L.); (C.B.-M.); (M.E.)
- Correspondence:
| | - Ioana Gomoiu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, P.O. Box 56-53, 060031 Bucharest, Romania; (I.G.); (O.P.); (R.C.); (S.N.); (I.L.); (C.B.-M.); (M.E.)
| | - Octavian Popescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, P.O. Box 56-53, 060031 Bucharest, Romania; (I.G.); (O.P.); (R.C.); (S.N.); (I.L.); (C.B.-M.); (M.E.)
- Molecular Biology Center, Institute of Interdisciplinary Research in Bio-Nano-Sciences, Babes-Bolyai-University, 42 Treboniu Laurian St., 400271 Cluj-Napoca, Romania
| | - Roxana Cojoc
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, P.O. Box 56-53, 060031 Bucharest, Romania; (I.G.); (O.P.); (R.C.); (S.N.); (I.L.); (C.B.-M.); (M.E.)
| | - Simona Neagu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, P.O. Box 56-53, 060031 Bucharest, Romania; (I.G.); (O.P.); (R.C.); (S.N.); (I.L.); (C.B.-M.); (M.E.)
| | - Ioana Lucaci
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, P.O. Box 56-53, 060031 Bucharest, Romania; (I.G.); (O.P.); (R.C.); (S.N.); (I.L.); (C.B.-M.); (M.E.)
| | - Costin Batrinescu-Moteau
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, P.O. Box 56-53, 060031 Bucharest, Romania; (I.G.); (O.P.); (R.C.); (S.N.); (I.L.); (C.B.-M.); (M.E.)
| | - Madalin Enache
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, P.O. Box 56-53, 060031 Bucharest, Romania; (I.G.); (O.P.); (R.C.); (S.N.); (I.L.); (C.B.-M.); (M.E.)
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Moopantakath J, Imchen M, Siddhardha B, Kumavath R. 16s rRNA metagenomic analysis reveals predominance of Crtl and CruF genes in Arabian Sea coast of India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140699. [PMID: 32679495 DOI: 10.1016/j.scitotenv.2020.140699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.
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Affiliation(s)
- Jamseel Moopantakath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India
| | - Madangchanok Imchen
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Ranjith Kumavath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India.
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Mani K, Taib N, Hugoni M, Bronner G, Bragança JM, Debroas D. Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India. Front Microbiol 2020; 11:1891. [PMID: 33013726 PMCID: PMC7461921 DOI: 10.3389/fmicb.2020.01891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 07/20/2020] [Indexed: 11/26/2022] Open
Abstract
The microbial fluctuations along an increasing salinity gradient during two different salt production phases – initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes on Illumina MiSeq platform. Elemental analysis of the brine samples showed high concentration of sodium (Na+) and chloride (Cl–) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea transited from sediment to brine while Bacteria transited from brine to sediment with increasing salinity. Frequency of Archaea was found to be significantly enriched even in low and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum, Haloarcula, Halorhabdus, and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence frequency of Halorubrum, and Halorhabdus decreased while Haloarcula, Haloplanus, and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes, Proteobacteria, and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira, Desulfovermiculus, and Marinobacter were selectively present in sediments. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame.
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Affiliation(s)
- Kabilan Mani
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Zuarinagar, India.,Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
| | - Najwa Taib
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Gisele Bronner
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Judith M Bragança
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Zuarinagar, India
| | - Didier Debroas
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, Clermont-Ferrand, France
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11
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Kim JY, Whon TW, Lim MY, Kim YB, Kim N, Kwon MS, Kim J, Lee SH, Choi HJ, Nam IH, Chung WH, Kim JH, Bae JW, Roh SW, Nam YD. The human gut archaeome: identification of diverse haloarchaea in Korean subjects. MICROBIOME 2020; 8:114. [PMID: 32753050 PMCID: PMC7409454 DOI: 10.1186/s40168-020-00894-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/17/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is available. RESULTS We surveyed the archaeome of faecal samples collected from 897 East Asian subjects living in South Korea. In total, 42.47% faecal samples were positive for archaeal colonisation; these were subsequently subjected to archaeal 16S rRNA gene deep sequencing and real-time quantitative polymerase chain reaction-based abundance estimation. The mean archaeal relative abundance was 10.24 ± 4.58% of the total bacterial and archaeal abundance. We observed extensive colonisation of haloarchaea (95.54%) in the archaea-positive faecal samples, with 9.63% mean relative abundance in archaeal communities. Haloarchaea were relatively more abundant than methanogens in some samples. The presence of haloarchaea was also verified by fluorescence in situ hybridisation analysis. Owing to large inter-individual variations, we categorised the human gut archaeome into four archaeal enterotypes. CONCLUSIONS The study demonstrated that the human gut archaeome is indigenous, responsive, and functional, expanding our understanding of the archaeal signature in the gut of human individuals. Video Abstract.
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Affiliation(s)
- Joon Yong Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Tae Woong Whon
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Mi Young Lim
- Research Group of Healthcare, Research Division of Food Functionality, Korea Food Research Institute, Jeollabuk-do, 55365 Republic of Korea
| | - Yeon Bee Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Namhee Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Min-Sung Kwon
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Juseok Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Se Hee Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - In-Hyun Nam
- Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132 Republic of Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Research Division of Food Functionality, Korea Food Research Institute, Jeollabuk-do, 55365 Republic of Korea
| | - Jung-Ha Kim
- Department of Family Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, 06973 Republic of Korea
| | - Jin-Woo Bae
- Department of Biology, Kyung Hee University, Seoul, 02447 Republic of Korea
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755 Republic of Korea
| | - Young-Do Nam
- Research Group of Healthcare, Research Division of Food Functionality, Korea Food Research Institute, Jeollabuk-do, 55365 Republic of Korea
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12
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Verma A, Pal Y, Kumar P, Krishnamurthi S. Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil. Int J Syst Evol Microbiol 2020; 70:3693-3700. [DOI: 10.1099/ijsem.0.004222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A novel archaeal strain designated as SPP-AMP-1T was isolated from saltpan soil, using the serial dilution method on a halophilic archaeal medium supplemented with ampicillin. Cells were both rod-shaped and pleomorphic in nature, non-motile, unable to produce acid from a variety of sugars or grow anaerobically with different substrates (l-arginine) and electron acceptors (DMSO, nitrate). Optimal growth was observed at 42 °C, 3.4–4.2 M NaCl and pH 7.2. Cells did not lyse in distilled water and grew in the absence of Mg2+ ions. Phylogenetic analysis based on the sequences of 16S rRNA gene, amino acid sequence of β′-subunit of RNA polymerase and 400 conserved proteins retrieved from the whole genome assemblies showed that strain SPP-AMP-1T was distantly related to any existing genera within the family
Halobacteriaceae
. MK-8 was the only quinone detected. Polar lipid analysis showed a unique combination of diethyl derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, glycosyl-mannosyl-glucosyl diether and sulphated glycosyl-mannosyl-glucosyl diether as the major lipids. The G+C content of genomic DNA is 57.7 mol%. The phenotypic, phylogenetic and genomic data supported the concept of the novel genus status of strain SPP-AMP-1T in the family
Halobacteriaceae
for which the name Halocatena pleomorpha gen. nov., sp. nov., is proposed; the type strain is SPP-AMP-1T (=JCM 31368T=KCTC 4276T=MTCC 12579T).
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Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Yash Pal
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Pravin Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
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Surviving salt fluctuations: stress and recovery in Halobacterium salinarum, an extreme halophilic Archaeon. Sci Rep 2020; 10:3298. [PMID: 32094390 PMCID: PMC7040004 DOI: 10.1038/s41598-020-59681-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/04/2019] [Indexed: 11/18/2022] Open
Abstract
Halophilic proteins subjected to below about 15% salt in vitro denature through misfolding, aggregation and/or precipitation. Halobacteria, however, have been detected in environments of fluctuating salinity such as coastal salterns and even around fresh water springs in the depths of the Dead Sea. In order to identify the underlying mechanisms of low salt survival, we explored the reactivation capacity of Halobacterium (Hbt) salinarum sub-populations after incubation in low salt media and recovery in physiological salt. Respiratory oxygen consumption was assessed in stressed cells and cell viability was estimated by Live/Dead staining and flow cytometry. In vivo neutron scattering experiments showed that the recovery of Hbt salinarum sub-populations exposed to severe low salt conditions is related to a rapid retrieval of functional molecular dynamics in the proteome. In the hypothesis that the observations on Hbt salinarum have wider relevance, they could be of key ecological significance for the dispersion of extremophiles when environmental fluctuations become severe.
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Mukhtar S, Ahmad S, Bashir A, Mehnaz S, Mirza MS, Malik KA. Identification of plasmid encoded osmoregulatory genes from halophilic bacteria isolated from the rhizosphere of halophytes. Microbiol Res 2019; 228:126307. [DOI: 10.1016/j.micres.2019.126307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/25/2019] [Accepted: 08/02/2019] [Indexed: 12/27/2022]
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15
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Spatial distribution of prokaryotic communities in hypersaline soils. Sci Rep 2019; 9:1769. [PMID: 30741985 PMCID: PMC6370769 DOI: 10.1038/s41598-018-38339-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 12/20/2018] [Indexed: 11/29/2022] Open
Abstract
Increasing salinization in wetland systems is a major threat to ecosystem services carried out by microbial communities. Thus, it is paramount to understand how salinity drives both microbial community structures and their diversity. Here we evaluated the structure and diversity of the prokaryotic communities from a range of highly saline soils (EC1:5 from 5.96 to 61.02 dS/m) from the Odiel Saltmarshes and determined their association with salinity and other soil physicochemical features by analyzing 16S rRNA gene amplicon data through minimum entropy decomposition (MED). We found that these soils harbored unique communities mainly composed of halophilic and halotolerant taxa from the phyla Euryarchaeota, Proteobacteria, Balneolaeota, Bacteroidetes and Rhodothermaeota. In the studied soils, several site-specific properties were correlated with community structure and individual abundances of particular sequence variants. Salinity had a secondary role in shaping prokaryotic communities in these highly saline samples since the dominant organisms residing in them were already well-adapted to a wide range of salinities. We also compared ESV-based results with OTU-clustering derived ones, showing that, in this dataset, no major differences in ecological outcomes were obtained by the employment of one or the other method.
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16
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Isolation and culturing of protease- and lipase-producing Halococcus agarilyticus GUGFAWS-3 from marine Haliclona sp. inhabiting the rocky intertidal region of Anjuna in Goa, India. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1391-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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17
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Zhou J, Song X, Zhang CY, Chen GF, Lao YM, Jin H, Cai ZH. Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea. MICROBIAL ECOLOGY 2018; 76:592-609. [PMID: 29442157 DOI: 10.1007/s00248-018-1150-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
A central goal in marine microecology is to understand the ecological factors shaping spatiotemporal microbial patterns and the underlying processes. We hypothesized that abiotic and/or biotic interactions are probably more important for explaining the distribution patterns of marine bacterioplankton than environmental filtering. In this study, surface seawater samples were collected about 7000 miles from the Mediterranean Sea, transecting the North Atlantic Ocean, to the Brazilian marginal sea. In bacterial biosphere, SAR11, SAR86, Rhodobacteraceae, and Rhodospiriaceae were predominant in the Mediterranean Sea; Prochlorococcus was more frequent in Atlantic Ocean; whereas in the Brazilian coastal sea, the main bacterial members were Synechococcus and SAR11. With respect to archaea, Euryarchaeota were predominant in the Atlantic Ocean and Thaumarchaeota in the Mediterranean Sea. With respect to the eukaryotes, Syndiniales, Spumellaria, Cryomonadida, and Chlorodendrales were predominant in the open ocean, while diatoms and microzooplankton were dominant in the coastal sea. Distinct clusters of prokaryotes and eukaryotes displayed clear spatial heterogeneity. Among the environmental parameters measured, temperature and salinity were key factors controlling bacterial and archaeal community structure, respectively, whereas N/P/Si contributed to eukaryotic variation. The relative contribution of environmental parameters to the microbial distribution pattern was 45.2%. Interaction analysis showed that Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the keystone taxa within the positive-correlation network, while Thermoplasmata was the main contributor in the negative-correlation network. Our study demonstrated that microbial communities are co-governed by environmental filtering and biotic interactions, which are the main deterministic driving factors modulating the spatiotemporal patterns of marine plankton synergistically at the regional or global levels.
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Affiliation(s)
- Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen University Town, Room 905, Marine Building, Xili Town, Shenzhen, 518055, Guangdong Province, People's Republic of China
| | - Xiao Song
- The Department of Life Science, Tsinghua University, Beijing, People's Republic of China
| | - Chun-Yun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, Shangdong Province, People's Republic of China
| | - Guo-Fu Chen
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, Shangdong Province, People's Republic of China.
| | - Yong-Min Lao
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen University Town, Room 905, Marine Building, Xili Town, Shenzhen, 518055, Guangdong Province, People's Republic of China
| | - Hui Jin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen University Town, Room 905, Marine Building, Xili Town, Shenzhen, 518055, Guangdong Province, People's Republic of China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen University Town, Room 905, Marine Building, Xili Town, Shenzhen, 518055, Guangdong Province, People's Republic of China.
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18
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Khelaifia S, Caputo A, Andrieu C, Cadoret F, Armstrong N, Michelle C, Lagier JC, Djossou F, Fournier PE, Raoult D. Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut. Extremophiles 2018; 22:485-498. [PMID: 29435649 PMCID: PMC5862939 DOI: 10.1007/s00792-018-1011-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/05/2018] [Indexed: 12/22/2022]
Abstract
By applying the culturomics concept and using culture conditions containing a high salt concentration, we herein isolated the first known halophilic archaeon colonizing the human gut. Here we described its phenotypic and biochemical characterization as well as its genome annotation. Strain Arc-HrT (= CSUR P0974 = CECT 9307) was mesophile and grew optimally at 37 °C and pH 7. Strain Arc-HrT was also extremely halophilic with an optimal growth observed at 15% NaCl. It showed gram-negative cocci, was strictly aerobic, non-motile and non-spore-forming, and exhibited catalase and oxidase activities. The 4,015,175 bp long genome exhibits a G + C% content of 65.36% and contains 3911 protein-coding and 64 predicted RNA genes. PCR-amplified 16S rRNA gene of strain Arc-HrT yielded a 99.2% sequence similarity with Haloferax prahovense, the phylogenetically closest validly published species in the Haloferax genus. The DDH was of 50.70 ± 5.2% with H. prahovense, 53.70 ± 2.69% with H. volcanii, 50.90 ± 2.64% with H. alexandrinus, 52.90 ± 2.67% with H. gibbonsii and 54.30 ± 2.70% with H. lucentense. The data herein represented confirm strain Arc-HrT as a unique species and consequently we propose its classification as representative of a novel species belonging to the genus Haloferax, as Haloferax massiliense sp. nov.
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Affiliation(s)
- Saber Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France.
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Claudia Andrieu
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Frederique Cadoret
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Nicholas Armstrong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Caroline Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Felix Djossou
- Infectious and Tropical Diseases Department, Centre Hospitalier Andrée-Rosemon, Cayenne, French Guiana
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Gunde-Cimerman N, Plemenitaš A, Oren A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol Rev 2018. [DOI: 10.1093/femsre/fuy009] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 1, SI-1000 Ljubljana, Slovenia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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Abstract
Lake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg−1 salinity brine, a red ~180 g kg−1 salinity brine and a white ~300 g kg−1 salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities.
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21
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Halomarina salina sp. nov., isolated from a marine solar saltern. Antonie van Leeuwenhoek 2016; 109:1121-6. [DOI: 10.1007/s10482-016-0714-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/10/2016] [Indexed: 11/26/2022]
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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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Sanni GO, Coulon F, McGenity TJ. Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15230-15247. [PMID: 25869427 DOI: 10.1007/s11356-015-4313-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Mudflats are ecologically important habitats that are susceptible to oil pollution, but intervention is difficult in these fine-grained sediments, and so clean-up usually relies on natural attenuation. Therefore, we investigated the impact of crude oil on the bacterial, diatom and archaeal communities within the upper parts of the diatom-dominated sediment and the biofilm that detached from the surface at high tide. Biodegradation of petroleum hydrocarbons was rapid, with a 50 % decrease in concentration in the 0-2-mm section of sediment by 3 days, indicating the presence of a primed hydrocarbon-degrading community. The biggest oil-induced change was in the biofilm that detached from the sediment, with increased relative abundance of several types of diatom and of the obligately hydrocarbonoclastic Oleibacter sp., which constituted 5 % of the pyrosequences in the oiled floating biofilm on day 3 compared to 0.6 % in the non-oiled biofilm. Differences in bacterial community composition between oiled and non-oiled samples from the 0-2-mm section of sediment were only significant at days 12 to 28, and the 2-4-mm-sediment bacterial communities were not significantly affected by oil. However, specific members of the Chromatiales were detected (1 % of sequences in the 2-4-mm section) only in the oiled sediment, supporting other work that implicates them in anaerobic hydrocarbon degradation. Unlike the Bacteria, the archaeal communities were not significantly affected by oil. In fact, changes in community composition over time, perhaps caused by decreased nutrient concentration and changes in grazing pressure, overshadowed the effect of oil for both Bacteria and Archaea. Many obligate hydrocarbonoclastic and generalist oil-degrading bacteria were isolated, and there was little correspondence between the isolates and the main taxa detected by pyrosequencing of sediment-extracted DNA, except for Alcanivorax, Thalassolituus, Cycloclasticus and Roseobacter spp., which were detected by both methods.
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Affiliation(s)
- Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Frédéric Coulon
- School of Energy, Environment and Agrifood, Cranfield University, Building 40, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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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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Kanekar PP, Kulkarni SO, Kanekar SP, Shouche Y, Jani K, Sharma A. Exploration of a haloarchaeon, Halostagnicola larsenii, isolated from rock pit sea water, West Coast of Maharashtra, India, for the production of bacteriorhodopsin. J Appl Microbiol 2015; 118:1345-56. [PMID: 25727916 DOI: 10.1111/jam.12784] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/24/2015] [Accepted: 02/24/2015] [Indexed: 01/11/2023]
Abstract
AIMS The aim of the present investigation was to isolate haloarchaea from rock pit sea water, West Coast of India and to explore their potential in the production of bacteriorhodopsin (BR) which converts light energy into electrical energy. METHODS AND RESULTS Haloarchaeal strains were isolated from rock pit sea water samples collected from Rock garden, Malvan, West Coast of India. Based on morphological, physiological and biochemical characteristics, and 16S rRNA gene sequencing, all the 11 strains were identified as Halostagnicola larsenii. All the strains require at least 1·5 mol l(-1) NaCl for growth; grow optimally in the range of 3·5-5·2 mol l(-1) NaCl. BR was detected in all the strains ranging from 0·035 to 0·258 g l(-1) . All 11 strains showed conversion of light energy into electrical energy in the range of 0·7-44·2 mV, when exposed to sunlight. CONCLUSIONS A haloarchaeon, Hst. larsenii is isolated from rock pit sea water and demonstrated to have BR that converted light energy into electrical energy. SIGNIFICANCE AND IMPACT OF THE STUDY The present investigation is presumably the first report of the isolation of Hst. larsenii from low salinity environment and its potential in production of BR. The haloarchaeon could be explored for the generation of electrical energy.
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Affiliation(s)
- P P Kanekar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Pune, India
| | - S O Kulkarni
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Pune, India
| | - S P Kanekar
- Microbial Sciences Divison, MACS-Agharkar Research Institute, Pune, India
| | - Y Shouche
- Microbial Culture Collection (MCC), National Centre for Cell Science (NCCS), Pune, India
| | - K Jani
- Microbial Culture Collection (MCC), National Centre for Cell Science (NCCS), Pune, India
| | - A Sharma
- Microbial Culture Collection (MCC), National Centre for Cell Science (NCCS), Pune, India
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General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Youssef NH, Savage-Ashlock KN, McCully AL, Luedtke B, Shaw EI, Hoff WD, Elshahed MS. Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales. ISME JOURNAL 2013; 8:636-649. [PMID: 24048226 DOI: 10.1038/ismej.2013.165] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 11/09/2022]
Abstract
We investigated the mechanisms of osmoadaptation in the order Halobacteriales, with special emphasis on Haladaptatus paucihalophilus, known for its ability to survive in low salinities. H. paucihalophilus genome contained genes for trehalose synthesis (trehalose-6-phosphate synthase/trehalose-6-phosphatase (OtsAB pathway) and trehalose glycosyl-transferring synthase pathway), as well as for glycine betaine uptake (BCCT family of secondary transporters and QAT family of ABC transporters). H. paucihalophilus cells synthesized and accumulated ∼1.97-3.72 μmol per mg protein of trehalose in a defined medium, with its levels decreasing with increasing salinities. When exogenously supplied, glycine betaine accumulated intracellularly with its levels increasing at higher salinities. RT-PCR analysis strongly suggested that H. paucihalophilus utilizes the OtsAB pathway for trehalose synthesis. Out of 83 Halobacteriales genomes publicly available, genes encoding the OtsAB pathway and glycine betaine BCCT family transporters were identified in 38 and 60 genomes, respectively. Trehalose (or its sulfonated derivative) production and glycine betaine uptake, or lack thereof, were experimentally verified in 17 different Halobacteriales species. Phylogenetic analysis suggested that trehalose synthesis is an ancestral trait within the Halobacteriales, with its absence in specific lineages reflecting the occurrence of gene loss events during Halobacteriales evolution. Analysis of multiple culture-independent survey data sets demonstrated the preference of trehalose-producing genera to saline and low salinity habitats, and the dominance of genera lacking trehalose production capabilities in permanently hypersaline habitats. This study demonstrates that, contrary to current assumptions, compatible solutes production and uptake represent a common mechanism of osmoadaptation within the Halobacteriales.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Kristen N Savage-Ashlock
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,3Present address: Department of Biology, Georgia State University, Atlanta, Georgia
| | - Alexandra L McCully
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,4Present address: Department of Biology, Indiana University, Bloomington IN
| | - Brandon Luedtke
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,5Present address: US Department of Agriculture, Agricultural Research Service, Roman L. Hruska Meat Animal Research Center, Clay Center, NE 68933-0166
| | - Edward I Shaw
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Department of Chemistry, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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Oueriaghli N, Béjar V, Quesada E, Martínez-Checa F. Molecular ecology techniques reveal both spatial and temporal variations in the diversity of archaeal communities within the athalassohaline environment of Rambla Salada, Spain. MICROBIAL ECOLOGY 2013; 66:297-311. [PMID: 23354292 DOI: 10.1007/s00248-013-0176-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 01/01/2013] [Indexed: 05/04/2023]
Abstract
We have studied the distribution of the archaeal communities in Rambla Salada (Murcia, Spain) over three different seasons and observed the influence upon them of the environmental variables, salinity, pH, oxygen and temperature. Samples were collected from three representative sites in order to gain an insight into the archaeal population of the rambla as a whole. Denaturing gradient gel electrophoresis patterns and diversity indexes indicate that the diversity of the archaeal community in Rambla Salada changed mainly according to the season. We found no significant differences between the types of sample studied: watery sediments and soils. The upwelling zone showed most diversity in its archaeal community. The overall archaeal community was composed mainly of Halobacteriales and Thermoplasmatales, accounting for 72.6 and 12.1 % of the total, respectively. Haloarcula was the most abundant genus, being present at all three sites during all three seasons. Some few Crenarchaeota were always found, mainly at low-salinity levels. Ordination canonical correspondence analysis demonstrated that salinity affected the structure of the community significantly, whilst pH, oxygen and temperature did so to a lesser extent. Most Halobacteriales correlated positively with salinity and pH, whilst Thermoplasmatales correlated negatively with both salinity and pH and positively with temperature and oxygen. The archaeal community with the highest diversity was sampled during June 2006, the season with the highest salt concentration. Catalyzed reporter deposition-fluorescence in situ hybridization showed that the percentage of archaea in Rambla Salada compared to the total number of microorganisms (as measured by DAPI) ranged from 11.1 to 16.7 %. Our research group had isolated the most abundant taxon, Haloarcula, previously in Rambla Salada using classical culture techniques, but on this occasion, using culture-independent methods, we were also able to identify some phylotypes, Halorubrum, Methanolobus, Natronomonas, Halomicrobium, Halobacterium, Halosimplex, uncultured Thermoplasmatales and uncultured Crenarchaeota, that had remained undetected during our earlier studies in this habitat.
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Affiliation(s)
- Nahid Oueriaghli
- Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071, Granada, Spain
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Vasileiadis S, Puglisi E, Arena M, Cappa F, van Veen JA, Cocconcelli PS, Trevisan M. Soil microbial diversity patterns of a lowland spring environment. FEMS Microbiol Ecol 2013; 86:172-84. [DOI: 10.1111/1574-6941.12150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/09/2013] [Accepted: 05/21/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sotirios Vasileiadis
- Institute of Agricultural and Environmental Chemistry; Universitá Cattolica del Sacro Cuore; Piacenza; Italy
| | - Edoardo Puglisi
- Institute of Microbiology; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - Maria Arena
- Institute of Agricultural and Environmental Chemistry; Universitá Cattolica del Sacro Cuore; Piacenza; Italy
| | - Fabrizio Cappa
- Institute of Microbiology; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | | | - Pier S. Cocconcelli
- Institute of Microbiology; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - Marco Trevisan
- Institute of Agricultural and Environmental Chemistry; Universitá Cattolica del Sacro Cuore; Piacenza; Italy
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Williams D, Gogarten JP, Papke RT. Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol Evol 2013; 4:1223-44. [PMID: 23160063 PMCID: PMC3542582 DOI: 10.1093/gbe/evs098] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In vitro studies of the haloarchaeal genus Haloferax have demonstrated
their ability to frequently exchange DNA between species, whereas rates of homologous
recombination estimated from natural populations in the genus Halorubrum
are high enough to maintain random association of alleles between five loci. To quantify
the effects of gene transfer and recombination of commonly held (relaxed core) genes
during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history
of 21 genomes representing all major groups. Using a novel algorithm and a concatenated
ribosomal protein phylogeny as a reference, we created a directed horizontal genetic
transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed
that 90% of testable HGTs were by direct homologous replacement, rather than
nonhomologous integration followed by a loss. Network analysis revealed an inverse
log-linear relationship between HGT frequency and ribosomal protein evolutionary distance
that is maintained across the deepest divergences in Halobacteria. We use this
mathematical relationship to estimate the total transfers and amino acid substitutions
delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core
genes of each genome, we conservatively estimate that 11–20% of their
evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer
and homologous recombination of relaxed core genes between members of the class
Halobacteria disrupts the coevolution of genes; however, the generation of new
combinations of divergent but functionally related genes may lead to adaptive phenotypes
not available through cumulative mutations and recombination within a single
population.
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Affiliation(s)
- David Williams
- Department of Molecular and Cell Biology, University of Connecticut, CT, USA
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Shimoshige H, Yamada T, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Usami R. Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt. Int J Syst Evol Microbiol 2013; 63:861-866. [DOI: 10.1099/ijs.0.037432-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, strains MGY-184T and MGY-205, were isolated from sea salt produced in Japan and rock salt imported from Bolivia, respectively. Both strains were pleomorphic, non-motile, Gram-negative and required more than 5 % (w/v) NaCl for growth, with optimum at 9–12 %, in the presence of 2 % (w/v) MgCl2 . 6H2O. In the presence of 18 % (w/v) MgCl2 . 6H2O, however, both strains showed growth even at 1.0 % (w/v) NaCl. Both strains possessed two 16S rRNA genes (rrnA and rrnB), and they revealed closest similarity to
Halobaculum gomorrense
JCM 9908T, the single species with a validly published name of the genus
Halobaculum
, with similarity of 97.8 %. The rrnA and rrnB genes of both strains were 100 % similar. The rrnA genes were 97.6 % similar to the rrnB genes in both strains. DNA G+C contents of strains MGY-184T and MGY-205 were 67.0 and 67.4 mol%, respectively. Polar lipid analysis revealed that the two strains contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester derived from C20C20 archaeol. The DNA–DNA hybridization value between the two strains was 70 % and both strains showed low levels of DNA–DNA relatedness (48–50 %) with
Halobaculum gomorrense
JCM 9908T. Physiological and biochemical characteristics allowed differentiation of strains MGY-184T and MGY-205 from
Halobaculum gomorrense
JCM 9908T. Therefore, strains MGY-184T and MGY-205 represent a novel species of the genus
Halobaculum
, for which the name Halobaculum magnesiiphilum sp. nov. is proposed; the type strain is MGY-184T ( = JCM 17821T = KCTC 4100T).
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Affiliation(s)
- Hirokazu Shimoshige
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Tomoaki Yamada
- Department of Biological Applied Chemistry, Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Hiroaki Minegishi
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Akinobu Echigo
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
| | - Yasuhiro Shimane
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Masahiro Kamekura
- Halophiles Research Institute, 677-1 Shimizu, Noda, Chiba 278-0043, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ron Usami
- Graduate School of Interdisciplinary New Science, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
- Bio-Nano Electronics Research Centre, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan
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Zhaxybayeva O, Stepanauskas R, Mohan NR, Papke RT. Cell sorting analysis of geographically separated hypersaline environments. Extremophiles 2013; 17:265-75. [PMID: 23358730 DOI: 10.1007/s00792-013-0514-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 01/04/2013] [Indexed: 11/27/2022]
Abstract
Biogeography of microbial populations remains to be poorly understood, and a novel technique of single cell sorting promises a new level of resolution for microbial diversity studies. Using single cell sorting, we compared saturated NaCl brine environments (32-35 %) of the South Bay Salt Works in Chula Vista in California (USA) and Santa Pola saltern near Alicante (Spain). Although some overlap in community composition was detected, both samples were significantly different and included previously undiscovered 16S rRNA sequences. The community from Chula Vista saltern had a large bacterial fraction, which consisted of diverse Bacteroidetes and Proteobacteria. In contrast, Archaea dominated Santa Pola's community and its bacterial fraction consisted of the previously known Salinibacter lineages. The recently reported group of halophilic Archaea, Nanohaloarchaea, was detected at both sites. We demonstrate that cell sorting is a useful technique for analysis of halophilic microbial communities, and is capable of identifying yet unknown or divergent lineages. Furthermore, we argue that observed differences in community composition reflect restricted dispersal between sites, a likely mechanism for diversification of halophilic microorganisms.
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Affiliation(s)
- Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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Dave BP, Soni A. Diversity of Halophilic Archaea at Salt Pans Around Bhavnagar Coast, Gujarat. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s40011-012-0124-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chen S, Tulloss RE, Liu Y, Feng B, Zhao Z, Yang ZL. Lateral gene transfer occurring in haloarchaea: an interpretative imitation study. World J Microbiol Biotechnol 2012; 28:2913-8. [PMID: 22806731 DOI: 10.1007/s11274-012-1101-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 06/06/2012] [Indexed: 11/26/2022]
Abstract
Lateral gene transfer (LGT) plays an important role in the molecular evolution of haloarchaea. Polyethylene glycol-mediated LGT in haloarchaea has been demonstrated in the laboratory, yet few explanations have been put forward for the apparently common, natural occurrence of plentiful plasmids within haloarchaeal cells. In this study, LGT was induced in two genera of haloarchaea, Haloferax and Halorubrum, by modification of salt concentration of media-a factor that may vary naturally in native haloarchaeal habitat. Minimal growth salt concentrations (MGSCs) of four strains of haloarchaea from these two genera were established, and transformations using two circular double-stranded DNAs (dsDNAs), pSY1 and pWL102, were then produced in media at strain-appropriate MGSCs. The four strains of haloarchaea were transformed successfully by both kinds of dsDNAs with an efficiency of 10(2)-10(3) transformants per microgram dsDNA. The transformation under reduced salt concentration may be an imitation of natural LGT of dsDNA into haloarchaea when salinity in normally hypersaline environments is altered by sudden introduction of fresh water--for example, by rainfall, snow-melt, or flooding--providing a reasonable interpretation for haloarchaea being naturally richer in plasmids than any other known organisms.
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Affiliation(s)
- Shaoxing Chen
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Mani K, Salgaonkar BB, Braganca JM. Culturable halophilic archaea at the initial and crystallization stages of salt production in a natural solar saltern of Goa, India. AQUATIC BIOSYSTEMS 2012; 8:15. [PMID: 22747590 PMCID: PMC3444409 DOI: 10.1186/2046-9063-8-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 06/13/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND Goa is a coastal state in India and salt making is being practiced for many years. This investigation aimed in determining the culturable haloarchaeal diversity during two different phases of salt production in a natural solar saltern of Ribandar, Goa. Water and sediment samples were collected from the saltern during pre-salt harvesting phase and salt harvesting phase. Salinity and pH of the sampling site was determined. Isolates were obtained by plating of the samples on complex and synthetic haloarchaeal media. Morphology of the isolates was determined using Gram staining and electron microscopy. Response of cells to distilled water was studied spectrophotometrically at 600nm. Molecular identification of the isolates was performed by sequencing the 16S rRNA. RESULTS Salinity of salt pans varied from 3-4% (non-salt production phase) to 30% (salt production phase) and pH varied from 7.0-8.0. Seven haloarchaeal strains were isolated from water and sediment samples during non-salt production phase and seventeen haloarchaeal strains were isolated during the salt production phase. All the strains stained uniformly Gram negative. The orange-red acetone extract of the pigments showed similar spectrophotometric profile with absorption maxima at 393, 474, 501 and 535 nm. All isolates obtained from the salt dilute phase were grouped within the genus Halococcus. This was validated using both total lipid profiling and 16S rRNA data sequencing. The isolates obtained from pre-salt harvesting phase were resistant to lysis. 16S rRNA data showed that organisms belonging to Halorubrum, Haloarcula, Haloferax and Halococcus genera were obtained during the salt concentrated phase. The isolates obtained from salt harvesting phase showed varied lysis on suspension in distilled water and /or 3.5% NaCl. CONCLUSION Salterns in Goa are transiently operated during post monsoon season from January to May. During the pre-salt harvesting phase, all the isolates obtained belonged to Halococcus sp. During the salt harvesting phase, isolates belonging to Halorubrum, Haloarcula, Haloferax and Halococcus genera were obtained. This study clearly indicates that Halococcus sp. dominates during the low salinity conditions.
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Affiliation(s)
- Kabilan Mani
- Department of Biological Sciences, BITS PILANI, K K Birla Goa Campus, NH 17 B, Zuarinagar, Sancoale, Goa 403 726, India
| | - Bhakti B Salgaonkar
- Department of Biological Sciences, BITS PILANI, K K Birla Goa Campus, NH 17 B, Zuarinagar, Sancoale, Goa 403 726, India
| | - Judith M Braganca
- Department of Biological Sciences, BITS PILANI, K K Birla Goa Campus, NH 17 B, Zuarinagar, Sancoale, Goa 403 726, India
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Carbonero F, Oakley BB, Hawkins RJ, Purdy KJ. Genotypic distribution of a specialist model microorganism, Methanosaeta, along an estuarine gradient: does metabolic restriction limit niche differentiation potential? MICROBIAL ECOLOGY 2012; 63:856-864. [PMID: 22183047 DOI: 10.1007/s00248-011-9993-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/02/2011] [Indexed: 05/31/2023]
Abstract
A reductionist ecological approach of using a model genus was adopted in order to understand how microbial community structure is driven by metabolic properties. The distribution along an estuarine gradient of the highly specialised genus Methanosaeta was investigated and compared to the previously determined distribution of the more metabolically flexible Desulfobulbus. Methanosaeta genotypic distribution along the Colne estuary (Essex, UK) was determined by DNA- and RNA-based denaturing gradient gel electrophoresis and 16S rRNA gene sequence analyses. Methanosaeta distribution was monotonic, with a consistently diverse community and no apparent niche partitioning either in DNA or RNA analyses. This distribution pattern contrasts markedly with the previously described niche partitioning and sympatric differentiation of the model generalist, Desulfobulbus. To explain this difference, it is hypothesised that Methanosaeta's strict metabolic needs limit its adaptation potential, thus populations do not partition into spatially distinct groups and so do not appear to be constrained by gross environmental factors such as salinity. Thus, at least for these two model genera, it appears that metabolic flexibility may be an important factor in spatial distribution and this may be applicable to other microbes.
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Andrei AŞ, Banciu HL, Oren A. Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems. FEMS Microbiol Lett 2012; 330:1-9. [DOI: 10.1111/j.1574-6968.2012.02526.x] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/10/2012] [Accepted: 02/11/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Adrian-Ştefan Andrei
- Department of Experimental Biology, Faculty of Biology and Geology; Babeş-Bolyai University; Cluj-Napoca; Romania
| | - Horia Leonard Banciu
- Department of Experimental Biology, Faculty of Biology and Geology; Babeş-Bolyai University; Cluj-Napoca; Romania
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences and the Moshe Shilo Minerva Center for Marine Biogeochemistry; The Hebrew University of Jerusalem; Jerusalem; Israel
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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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Potential for industrial products from the halophilic Archaea. J Ind Microbiol Biotechnol 2011; 38:1635-47. [PMID: 21853327 DOI: 10.1007/s10295-011-1021-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Accepted: 07/20/2011] [Indexed: 10/17/2022]
Abstract
The halophilic Archaea are a group of microorganisms that have not been extensively considered for biotechnological applications. This review describes some of the enzymes and products and the potential applications of this unique group of microorganisms to various industrial processes. Specifically, the characteristics of the glycosyl hydrolases, lipases and esterases, proteases, biopolymers and surfactants, as well as some miscellaneous other activities will be described.
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Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper SD, Porat I, Klenk HP, Ivanova N, Kyrpides N. Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. PLoS One 2011; 6:e20237. [PMID: 21633497 PMCID: PMC3102087 DOI: 10.1371/journal.pone.0020237] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 04/15/2011] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis. METHODOLOGY/PRINCIPAL FINDINGS We report here the comparative analysis of five newly sequenced haloarchaeal genomes with five previously published ones. Whole genome trees based on protein sequences provide strong support for deep relationships between the ten organisms. Using a soft clustering approach, we identified 887 protein clusters present in all halophiles. Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature. Four of the halophiles were isolated from water, and four were isolated from soil or sediment. Although there are few habitat-specific clusters, the soil/sediment halophiles tend to have greater capacity for polysaccharide degradation, siderophore synthesis, and cell wall modification. Halorhabdus utahensis and Haloterrigena turkmenica encode over forty glycosyl hydrolases each, and may be capable of breaking down naturally occurring complex carbohydrates. H. utahensis is specialized for growth on carbohydrates and has few amino acid degradation pathways. It uses the non-oxidative pentose phosphate pathway instead of the oxidative pathway, giving it more flexibility in the metabolism of pentoses. CONCLUSIONS These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism. Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.
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Affiliation(s)
- Iain Anderson
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
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43
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Inoue K, Itoh T, Ohkuma M, Kogure K. Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium. Int J Syst Evol Microbiol 2011; 61:942-946. [DOI: 10.1099/ijs.0.020677-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel halophilic archaeon, strain KeC-11T, was isolated from a seawater aquarium at the Ocean Research Institute, University of Tokyo, Japan. The strain was aerobic, Gram-negative and chemo-organotrophic, growing optimally at 37 °C, at pH 7.0–8.0 and in 2.7 M (16 %) NaCl. The strain required at least 10 mM magnesium ions for growth. Cells of strain KeC-11T were non-motile and generally irregular coccoids or discoids. The DNA G+C content of the isolate was 67.7 mol%. Phylogenetic tree reconstructions indicated that it was distantly related to the other recognized members of the family Halobacteriaceae, with the closest relative being Natronomonas pharaonis GabaraT (91 % sequence similarity). The strain contained C20C20 and C20C25 diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, a glycolipid chromatographically identical to the glycosyl-mannosyl-glucosyl diether (TGD-2) and at least one unidentified glycolipid. Phenotypic characterization and phylogenetic data support the placement of isolate KeC-11T in a novel species in a new genus within the family Halobacteriaceae, for which the name Halomarina oriensis gen. nov., sp. nov. is proposed; the type strain is KeC-11T ( = JCM 16495T = KCTC 4074T).
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Affiliation(s)
- Kentaro Inoue
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazuhiro Kogure
- Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan
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44
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Phylogenetic characterization of archaea in saltpan sediments. Indian J Microbiol 2011; 51:132-7. [PMID: 22654153 DOI: 10.1007/s12088-011-0125-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 07/06/2009] [Indexed: 10/18/2022] Open
Abstract
A study was undertaken to investigate the presence of archaeal diversity in saltpan sediments of Goa, India by 16S rDNA-dependent molecular phylogeny. Small subunit rRNA (16S rDNA) from saltpan sediment metagenome were amplified by polymerase chain reaction (PCR) using primers specific to the domain archaea. 10 unique phylotypes were obtained by PCR based RFLP of 16S rRNA genes using endonuclease Msp 1, which was most suitable to score the genetic diversity. These phylotypes spanned a wide range within the domain archaea including both crenarchaeota and euryarcheaota. None of the retrieved crenarchaeota sequences could be grouped with previously cultured crenarchaeota however; two sequences were related with haloarchaea. Most of the sequences determined were closely related to the sequences that had been previously obtained from metagenome of a variety of marine environments. The phylogenetic study of a site investigated for the first time revealed the presence of low archaeal population but showed yet unclassified species, may specially adapted to the salt pan sediment of Goa.
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Sayeh R, Birrien JL, Alain K, Barbier G, Hamdi M, Prieur D. Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches. Extremophiles 2010; 14:501-14. [PMID: 20835839 DOI: 10.1007/s00792-010-0327-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 08/25/2010] [Indexed: 10/19/2022]
Abstract
Prokaryotic diversities of 12 geothermal hot springs located in Northern, Central and Southern Tunisia were investigated by culture-based and molecular approaches. Enrichment cultures for both aerobic and anaerobic microorganisms were successfully obtained at temperatures ranging from 50 to 75°C. Fourteen strains including four novel species were cultivated and assigned to the phyla Firmicutes (9), Thermotogae (2), Betaproteobacteria (1), Synergistetes (1) and Bacteroidetes (1). Archaeal or universal oligonucleotide primer sets were used to generate 16S rRNA gene libraries. Representative groups included Proteobacteria, Firmicutes, Deinococcus-Thermus, Thermotogae, Synergistetes, Bacteroidetes, Aquificae, Chloroflexi, candidate division OP9 in addition to other yet unclassified strains. The archaeal library showed a low diversity of clone sequences belonging to the phyla Euryarchaeota and Crenarchaeota. Furthermore, we confirmed the occurrence of sulfate reducers and methanogens by amplification and sequencing of dissimilatory sulfite reductase (dsrAB) and methyl coenzyme M reductase α-subunit (mcrA) genes. Altogether, we discuss the diverse prokaryotic communities arising from the 12 geothermal hot springs studied and relate these findings to the physico-chemical features of the hot springs.
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Affiliation(s)
- Raja Sayeh
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, UBO-CNRS-IFREMER, Place Nicolas Copernic, 29280, Plouzané, France.
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Cui HL, Gao X, Yang X, Xu XW. Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Extremophiles 2010; 14:493-9. [PMID: 20824294 DOI: 10.1007/s00792-010-0329-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 08/25/2010] [Indexed: 11/24/2022]
Abstract
Two halophilic archaeal strains TBN4(T) and TBN5 were isolated from Taibei marine solar saltern in Jiangsu, China. Both strains showed light red-pigmented colonies and their cells were rod, motile and Gram-stain-negative. They were able to grow at 25-50°C (optimum 37°C), at 1.4-4.3 M NaCl (optimum 2.1 M NaCl), at 0-1.0 M MgCl(2) (optimum 0.005 M MgCl(2)) and at pH 6.0-9.0 (optimum pH 7.0). Their cells lyse in distilled water and minimal NaCl concentration to prevent cell lysis is 8% (w/v). The major polar lipids of the two strains were PG (phosphatidylglycerol), PGP-Me (phosphatidylglycerol phosphate methyl ester), PGS (phosphatidylglycerol sulfate) and five glycolipids chromatographically identical to S-TGD-1 (sulfated galactosyl mannosyl glucosyl diether), S-DGD-1 (sulfated mannosyl glucosyl diether), TGD-1 (galactosyl mannosyl glucosyl diether), DGD-1 (mannosyl glucosyl diether) and DGD-2 (an unknown diglycosyl diether). Phylogenetic analysis revealed that TBN4(T) and strain TBN5 formed a distinct clade with genus Haladaptatus (showing 90.0-90.9% 16S rRNA gene similarities). The DNA G + C content of strain TBN4(T) and strain TBN5 are 66.1 and 65.4 mol%, respectively. The DNA-DNA hybridization value between strain TBN4(T) and strain TBN5 was 94.3%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain TBN4(T) and strain TBN5 represent a novel species in a new genus within the family Halobacteriaceae, for which the name Halorussus rarus gen. nov., sp. nov. is proposed. The type strain is TBN4(T) (=CGMCC 1.10122(T) = JCM 16429(T)).
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China.
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Oxley APA, Lanfranconi MP, Würdemann D, Ott S, Schreiber S, McGenity TJ, Timmis KN, Nogales B. Halophilic archaea in the human intestinal mucosa. Environ Microbiol 2010; 12:2398-410. [PMID: 20438582 DOI: 10.1111/j.1462-2920.2010.02212.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The human gastrointestinal tract microbiota, despite its key roles in health and disease, remains a diverse, variable and poorly understood entity. Current surveys reveal a multitude of undefined bacterial taxa and a low diversity of methanogenic archaea. In an analysis of the microbiota in colonic mucosal biopsies from patients with inflammatory bowel disease we found 16S rDNA sequences representing a phylogenetically rich diversity of halophilic archaea from the Halobacteriaceae (haloarchaea), including novel phylotypes. As the human colon is not considered a salty environment and haloarchaea are described as extreme halophiles, we evaluated and further discarded the possibility that these sequences originated from pre-colonoscopy saline lavage solutions. Furthermore, aerobic enrichment cultures prepared from a patient biopsy at low salinity (2.5% NaCl) yielded haloarchaeal sequence types. Microscopic observation after fluorescence in situ hybridization provided evidence of the presence of viable archaeal cells in these cultures. These results prove the survival of haloarchaea in the digestive system and suggest that they may be members of the mucosal microbiota, even if present in low numbers in comparison with methanogenic archaea. Investigation of a potential physiological basis of this association may lead to new insights into gastrointestinal health and disease.
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Affiliation(s)
- Andrew P A Oxley
- Environmental Microbiology Laboratory, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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Halobacterium salinarum strain MMD047-A low-salt adapted member of the Halobacteriaceae? BIOTECHNOL BIOPROC E 2010. [DOI: 10.1007/s12257-009-2001-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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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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Cui HL, Gao X, Sun FF, Dong Y, Xu XW, Zhou YG, Liu HC, Oren A, Zhou PJ. Halogranum rubrum gen. nov., sp. nov., a halophilic archaeon isolated from a marine solar saltern. Int J Syst Evol Microbiol 2009; 60:1366-1371. [PMID: 19671729 DOI: 10.1099/ijs.0.014928-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, strains RO2-11(T) and HO2-1, were isolated from two Chinese marine solar salterns, Rudong solar saltern and Haimen solar saltern, respectively. Cells of the two strains were polymorphic and Gram-stain-negative; colonies were red-pigmented. The two strains grew at NaCl concentrations of 2.6-4.3 M (optimum 3.9 M) and required at least 0.1 M Mg2+ for growth. They were able to grow over a pH range of 6.0-8.0 and a temperature range of 20-50 degrees C, with optimal pH of 7.5 and optimal temperature of 37 degrees C. The major polar lipids of strain RO2-11(T) and strain HO2-1 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three glycolipids, two of them chromatographically identical to S-DGD-1 and DGD-1, the third unidentified. The 16S rRNA gene sequence similarity of strain RO2-11(T) and strain HO2-1 was 99.3 % and highest sequence similarity with the closest relative (Haloferax larsenii) was 91.4 %. Based on the data obtained, the two isolates could not be classified in any recognized genus of the family Halobacteriaceae. Strain RO2-11(T) and strain HO2-1 are thus considered to represent a novel species of a new genus within the family Halobacteriaceae, for which the name Halogranum rubrum gen. nov., sp. nov. is proposed. The type strain is RO2-11(T) (=CGMCC 1.7738(T) =JCM 15772(T)).
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xia Gao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Fang-Fang Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Ying Dong
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xue-Wei Xu
- Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Yu-Guang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Aharon Oren
- Institute of Life Sciences, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Pei-Jin Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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