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Liébana R, Viver T, Ramos-Barbero MD, Bustos-Caparros E, Urdiain M, López C, Amoozegar MA, Antón J, Rossello-Mora R. Extremely halophilic brine community manipulation shows higher robustness of microbiomes inhabiting human-driven solar saltern than naturally driven lake. mSystems 2024; 9:e0053824. [PMID: 38934645 DOI: 10.1128/msystems.00538-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Hypersaline ecosystems display taxonomically similar assemblages with low diversities and highly dense accompanying viromes. The ecological implications of viral infection on natural microbial populations remain poorly understood, especially at finer scales of diversity. Here, we sought to investigate the influence of changes in environmental physicochemical conditions and viral predation pressure by autochthonous and allochthonous viruses on host dynamics. For this purpose, we transplanted two microbiomes coming from distant hypersaline systems (solar salterns of Es Trenc in Spain and the thalassohaline lake of Aran-Bidgol lake in Iran), by exchanging the cellular fractions with the sterile-filtered accompanying brines with and without the free extracellular virus fraction. The midterm exposure (1 month) of the microbiomes to the new conditions showed that at the supraspecific taxonomic range, the assemblies from the solar saltern brine more strongly resisted the environmental changes and viral predation than that of the lake. The metagenome-assembled genomes (MAGs) analysis revealed an intraspecific transition at the ecotype level, mainly driven by changes in viral predation pressure, by both autochthonous and allochthonous viruses. IMPORTANCE Viruses greatly influence succession and diversification of their hosts, yet the effects of viral infection on the ecological dynamics of natural microbial populations remain poorly understood, especially at finer scales of diversity. By manipulating the viral predation pressure by autochthonous and allochthonous viruses, we uncovered potential phage-host interaction, and their important role in structuring the prokaryote community at an ecotype level.
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Affiliation(s)
- Raquel Liébana
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - María Dolores Ramos-Barbero
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
| | - Cristina López
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
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2
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La Cono V, Messina E, Reva O, Smedile F, La Spada G, Crisafi F, Marturano L, Miguez N, Ferrer M, Selivanova EA, Golyshina OV, Golyshin PN, Rohde M, Krupovic M, Merkel AY, Sorokin DY, Hallsworth JE, Yakimov MM. Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea. Microb Biotechnol 2023; 16:1803-1822. [PMID: 37317055 PMCID: PMC10443357 DOI: 10.1111/1751-7915.14272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/18/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Climate change, desertification, salinisation of soils and the changing hydrology of the Earth are creating or modifying microbial habitats at all scales including the oceans, saline groundwaters and brine lakes. In environments that are saline or hypersaline, the biodegradation of recalcitrant plant and animal polysaccharides can be inhibited by salt-induced microbial stress and/or by limitation of the metabolic capabilities of halophilic microbes. We recently demonstrated that the chitinolytic haloarchaeon Halomicrobium can serve as the host for an ectosymbiont, nanohaloarchaeon 'Candidatus Nanohalobium constans'. Here, we consider whether nanohaloarchaea can benefit from the haloarchaea-mediated degradation of xylan, a major hemicellulose component of wood. Using samples of natural evaporitic brines and anthropogenic solar salterns, we describe genome-inferred trophic relations in two extremely halophilic xylan-degrading three-member consortia. We succeeded in genome assembly and closure for all members of both xylan-degrading cultures and elucidated the respective food chains within these consortia. We provide evidence that ectosymbiontic nanohaloarchaea is an active ecophysiological component of extremely halophilic xylan-degrading communities (although by proxy) in hypersaline environments. In each consortium, nanohaloarchaea occur as ectosymbionts of Haloferax, which in turn act as scavenger of oligosaccharides produced by xylan-hydrolysing Halorhabdus. We further obtained and characterised the nanohaloarchaea-host associations using microscopy, multi-omics and cultivation approaches. The current study also doubled culturable nanohaloarchaeal symbionts and demonstrated that these enigmatic nano-sized archaea can be readily isolated in binary co-cultures using an appropriate enrichment strategy. We discuss the implications of xylan degradation by halophiles in biotechnology and for the United Nation's Sustainable Development Goals.
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Affiliation(s)
| | | | - Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Centre for Bioinformatics and Computational BiologyUniversity of PretoriaPretoriaSouth Africa
| | | | | | | | | | - Noa Miguez
- Instituto de Catalisis y Petroleoquimica (ICP), CSICMadridSpain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSICMadridSpain
| | - Elena A. Selivanova
- Institute for Cellular and Intracellular SymbiosisUral Branch, Russian Academy of SciencesOrenburgRussia
| | | | | | - Manfred Rohde
- Central Facility for MicrobiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Mart Krupovic
- Institut PasteurUniversité Paris Cité, Archaeal Virology UnitParisFrance
| | - Alexander Y. Merkel
- Winogradsky Institute of MicrobiologyResearch Centre of Biotechnology, Russian Academy of SciencesMoscowRussia
| | - Dimitry Y. Sorokin
- Winogradsky Institute of MicrobiologyResearch Centre of Biotechnology, Russian Academy of SciencesMoscowRussia
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastNorthern IrelandUK
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3
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Rudneva II, Shaida VG, Shcherba AV. Features of the Interannual and Seasonal Dynamics of the Ecological State of Salt Lakes under the Arid Climate of Crimea. ARID ECOSYSTEMS 2022. [DOI: 10.1134/s2079096122030118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Solchaga JI, Busalmen JP, Nercessian D. Unraveling Anaerobic Metabolisms in a Hypersaline Sediment. Front Microbiol 2022; 13:811432. [PMID: 35369499 PMCID: PMC8966722 DOI: 10.3389/fmicb.2022.811432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the microbial diversity inhabiting hypersaline sediments is still limited. In particular, existing data about anaerobic hypersaline archaea and bacteria are scarce and refer to a limited number of genera. The approach to obtain existing information has been almost exclusively attempting to grow every organism in axenic culture on the selected electron acceptor with a variety of electron donors. Here, a different approach has been used to interrogate the microbial community of submerged hypersaline sediment of Salitral Negro, Argentina, aiming at enriching consortia performing anaerobic respiration of different electron acceptor compounds, in which ecological associations can maximize the possibilities of successful growth. Growth of consortia was demonstrated on all offered electron acceptors, including fumarate, nitrate, sulfate, thiosulfate, dimethyl sulfoxide, and a polarized electrode. Halorubrum and Haloarcula representatives are here shown for the first time growing on lactate, using fumarate or a polarized electrode as the electron acceptor; in addition, they are shown also growing in sulfate-reducing consortia. Halorubrum representatives are for the first time shown to be growing in nitrate-reducing consortia, probably thanks to reduction of N2O produced by other consortium members. Fumarate respiration is indeed shown for the first time supporting growth of Halanaeroarchaeum and Halorhabdus belonging to the archaea, as well as growth of Halanaerobium, Halanaerobaculum, Sporohalobacter, and Acetohalobium belonging to the bacteria. Finally, evidence is presented suggesting growth of nanohaloarchaea in anaerobic conditions.
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Affiliation(s)
- Juan Ignacio Solchaga
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
| | - Juan Pablo Busalmen
- Laboratorio de Bioelectroquímica, INTEMA - CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
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5
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Azpiazu-Muniozguren M, Perez A, Rementeria A, Martinez-Malaxetxebarria I, Alonso R, Laorden L, Gamboa J, Bikandi J, Garaizar J, Martinez-Ballesteros I. Fungal Diversity and Composition of the Continental Solar Saltern in Añana Salt Valley (Spain). J Fungi (Basel) 2021; 7:1074. [PMID: 34947056 PMCID: PMC8703443 DOI: 10.3390/jof7121074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 12/19/2022] Open
Abstract
The Añana Salt Valley in Spain is an active continental solar saltern formed 220 million years ago. To date, no fungal genomic studies of continental salterns have been published, although DNA metabarcoding has recently expanded researchers' ability to study microbial community structures. Accordingly, the aim of this present study was to evaluate fungal diversity using the internal transcribed spacer (ITS) metabarcoding at different locations along the saltern (springs, ponds, and groundwater) to describe the fungal community of this saline environment. A total of 380 fungal genera were detected. The ubiquity of Saccharomyces was observed in the saltern, although other halotolerant and halophilic fungi like Wallemia, Cladosporium, and Trimmatostroma were also detected. Most of the fungi observed in the saltern were saprotrophs. The fungal distribution appeared to be influenced by surrounding conditions, such as the plant and soil contact, cereal fields, and vineyards of this agricultural region.
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Affiliation(s)
- Maia Azpiazu-Muniozguren
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Alba Perez
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Aitor Rementeria
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain;
| | - Irati Martinez-Malaxetxebarria
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Rodrigo Alonso
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Lorena Laorden
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Javier Gamboa
- Biogenetics, Portal de Zurbano 3, 6-B, 01013 Vitoria-Gasteiz, Spain;
| | - Joseba Bikandi
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Javier Garaizar
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Ilargi Martinez-Ballesteros
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
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6
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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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7
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Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing. Microorganisms 2021; 9:microorganisms9071525. [PMID: 34361960 PMCID: PMC8304926 DOI: 10.3390/microorganisms9071525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 01/31/2023] Open
Abstract
Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate in these habitats in contrast to the domain Bacteria (1.38% of reads). Representatives of the phylum Euryarchaeota were detected as the most predominant, while 59.48% and 1.32% of reads, respectively, were assigned to 18 archaeal genera, 19 bacterial genera, 10 archaeal genera, and one bacterial genus that were determined to be present, with more than 1% sequences in the samples. They were the archaeal genera Haloquadratum, Haloarcula, Halorhabdus, Natronomonas, Halosimplex, Halomicrobium, Halorubrum, Halonotius, Halolamina, Halobacterium, and Salinibacter within the domain Bacteria. The genera Haloquadratum and Halorhabdus were found in all sampling sites. While Haloquadratum, Haloarcula, and Halorhabdus were the most abundant genera, two uncultured Tuz Lake Halobacteria (TLHs) 1 and 2 were detected in high abundance, and an additional uncultured haloarchaeal TLH-3 was found as a minor abundant uncultured taxon. Their future isolation in pure culture would permit us to expand our knowledge on hypersaline thalassohaline habitats, as well as their ecological role and biomedical and biotechnological potential applications.
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8
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Ramos-Barbero MD, Viver T, Zabaleta A, Senel E, Gomariz M, Antigüedad I, Santos F, Martínez-García M, Rosselló-Móra R, Antón J. Ancient saltern metagenomics: tracking changes in microbes and their viruses from the underground to the surface. Environ Microbiol 2021; 23:3477-3498. [PMID: 34110059 DOI: 10.1111/1462-2920.15630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 11/28/2022]
Abstract
Microbial communities in hypersaline underground waters derive from ancient organisms trapped within the evaporitic salt crystals and are part of the poorly known subterranean biosphere. Here, we characterized the viral and prokaryotic assemblages present in the hypersaline springs that dissolve Triassic-Keuper evaporite rocks and feed the Añana Salt Valley (Araba/Alava, Basque Country, Spain). Four underground water samples (around 23% total salinity) with different levels of exposure to the open air were analysed by means of microscopy and metagenomics. Cells and viruses in the spring water had lower concentrations than what are normally found in hypersaline environments and seemed to be mostly inactive. Upon exposure to the open air, there was an increase in activity of both cells and viruses as well as a selection of phylotypes. The underground water was inhabited by a rich community harbouring a diverse set of genes coding for retinal binding proteins. A total of 35 viral contigs from 15 to 104 kb, representing partial or total viral genomes, were assembled and their evolutionary changes through the spring system were followed by SNP analysis and metagenomic island tracking. Overall, both the viral and the prokaryotic assemblages changed quickly upon exposure to the open air conditions.
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Affiliation(s)
- Mª Dolores Ramos-Barbero
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (IMEDEA; CSIC-UIB), Esporles, Illes Balears, 07190, Spain
| | - Ane Zabaleta
- Hydro-Environmental Processes Group, Geology Department, Science and Technology Faculty, University of the Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Ece Senel
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain.,Department of Biology, Institute of Graduate Programs, Eskisehir Technical University, Yunusemre Campus, Eskisehir, 26470, Turkey
| | - María Gomariz
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Iñaki Antigüedad
- Hydro-Environmental Processes Group, Geology Department, Science and Technology Faculty, University of the Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Manuel Martínez-García
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (IMEDEA; CSIC-UIB), Esporles, Illes Balears, 07190, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
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9
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Huby TJC, Clark DR, McKew BA, McGenity TJ. Extremely halophilic archaeal communities are resilient to short-term entombment in halite. Environ Microbiol 2021; 23:3370-3383. [PMID: 31919959 PMCID: PMC8359394 DOI: 10.1111/1462-2920.14913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
Some haloarchaea avoid the harsh conditions present in evaporating brines by entombment in brine inclusions within forming halite crystals, where a subset of haloarchaea survives over geological time. However, shifts in the community structure of halite-entombed archaeal communities remain poorly understood. Therefore, we analysed archaeal communities from in situ hypersaline brines collected from Trapani saltern (Sicily) and their successional changes in brines versus laboratory-grown halite over 21 weeks, using high-throughput sequencing. Haloarchaea were dominant, comprising >95% of the archaeal community. Unexpectedly, the OTU richness of the communities after 21 weeks was indistinguishable from the parent brine and overall archaeal abundance in halite showed no clear temporal trends. Furthermore, the duration of entombment was less important than the parent brine from which the halite derived in determining the community composition and relative abundances of most genera in halite-entombed communities. These results show that halite-entombed archaeal communities are resilient to entombment durations of up to 21 weeks, and that entombment in halite may be an effective survival strategy for near complete communities of haloarchaea. Additionally, the dominance of 'halite specialists' observed in ancient halite must occur over periods of years, rather than months, hinting at long-term successional dynamics in this environment.
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Affiliation(s)
- Tom J. C. Huby
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Dave R. Clark
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Boyd A. McKew
- School of Life SciencesUniversity of EssexColchesterEssexUK
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10
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Martínez JM, Escudero C, Rodríguez N, Rubin S, Amils R. Subsurface and surface halophile communities of the chaotropic Salar de Uyuni. Environ Microbiol 2021; 23:3987-4001. [PMID: 33511754 DOI: 10.1111/1462-2920.15411] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/04/2023]
Abstract
Salar de Uyuni (SdU) is the biggest athalosaline environment on Earth, holding a high percentage of the known world Li reserves. Due to its hypersalinity, temperature and humidity fluctuations, high exposure to UV radiation, and its elevated concentration of chaotropic agents like MgCl2 , LiCl and NaBr, SdU is considered a polyextreme environment. Here, we report the prokaryotic abundance and diversity of 46 samples obtained in different seasons and geographical areas. The identified bacterial community was found to be more heterogeneous than the archaeal community, with both communities varying geographically. A seasonal difference has been detected for archaea. Salinibacter, Halonotius and Halorubrum were the most abundant genera in Salar de Uyuni. Different unclassified archaea were also detected. In addition, the diversity of two subsurface samples obtained at 20 and 80 m depth was evaluated and compared with the surface data, generating an evolutionary record of a multilayer hypersaline ecosystem.
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Affiliation(s)
- José M Martínez
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (CBMSO, CSIC-UAM), Cantoblanco, Madrid, 28049, Spain
| | - Cristina Escudero
- Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, 28055, Spain
| | - Nuria Rodríguez
- Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, 28055, Spain
| | - Sergio Rubin
- Université Catholique de Louvain, Earth and Life Institute, Georges Lamaitre Center for Earth and Climate Research, Gante, Belgium.,Centro Nacional de Investigaciones Biotecnológicas, CNIB, Cochabamba, Bolivia
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (CBMSO, CSIC-UAM), Cantoblanco, Madrid, 28049, Spain.,Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, 28055, Spain
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11
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Abstract
The brines of natural salt lakes with total salt concentrations exceeding 30% are often colored red by dense communities of halophilic microorganisms. Such red brines are found in the north arm of Great Salt Lake, Utah, in the alkaline hypersaline lakes of the African Rift Valley, and in the crystallizer ponds of coastal and inland salterns where salt is produced by evaporation of seawater or some other source of saline water. Red blooms were also reported in the Dead Sea in the past. Different types of pigmented microorganisms may contribute to the coloration of the brines. The most important are the halophilic archaea of the class Halobacteria that contain bacterioruberin carotenoids as well as bacteriorhodopsin and other retinal pigments, β-carotene-rich species of the unicellular green algal genus Dunaliella and bacteria of the genus Salinibacter (class Rhodothermia) that contain the carotenoid salinixanthin and the retinal protein xanthorhodopsin. Densities of prokaryotes in red brines often exceed 2-3×107 cells/mL. I here review the information on the biota of the red brines, the interactions between the organisms present, as well as the possible roles of the red halophilic microorganisms in the salt production process and some applied aspects of carotenoids and retinal proteins produced by the different types of halophiles inhabiting the red brines.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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12
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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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13
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Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China. PLoS One 2020; 15:e0236006. [PMID: 32649724 PMCID: PMC7351256 DOI: 10.1371/journal.pone.0236006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
Halophiles are relatively unexplored as potential sources of novel species.
However, little is known about the culturable bacterial diversity thrive in
hypersaline lakes. In this work, a total of 343 bacteria from sediment samples
of Aiding Lake, China, were isolated using nine different media supplemented
with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria
recovered from the different media varied, indicating the need to optimize the
isolation conditions. The results showed an unexpected level of bacterial
diversity, with four phyla (Actinobacteria,
Firmicutes, Proteobacteria, and
Rhodothermaeota), fourteen orders
(Actinopolysporales, Alteromonadales,
Bacillales, Balneolales,
Chromatiales, Glycomycetales,
Jiangellales, Micrococcales,
Micromonosporales, Oceanospirillales,
Pseudonocardiales, Rhizobiales,
Streptomycetales, and
Streptosporangiales), including 17 families, 43 genera
(including two novel genera), and 71 species (including four novel species). The
predominant phyla included Actinobacteria and Firmicutes and the predominant
genera included Actinopolyspora,
Gracilibacillus, Halomonas,
Nocardiopsis, and Streptomyces. To our
knowledge, this is the first time that members of phylum
Rhodothermaeota were identified in sediment samples from a
salt lake.
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14
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Chen S, Xu Y, Helfant L. Geographical Isolation, Buried Depth, and Physicochemical Traits Drive the Variation of Species Diversity and Prokaryotic Community in Three Typical Hypersaline Environments. Microorganisms 2020; 8:microorganisms8010120. [PMID: 31963126 PMCID: PMC7022874 DOI: 10.3390/microorganisms8010120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 01/08/2023] Open
Abstract
The prokaryotic community composition, species diversity and the distribution patterns at various taxonomic levels in a salt lake (Chaka salt lake), solar salterns (Taipei saltworks and Dongfang saltworks), and salt mines (Yuanyongjing salt mine, Xiangyan salt mine, and Dinyuan salt mine) were investigated using clone library or Illumina MiSeq sequencing. The clone library approach revealed that the salt lake harbors low species diversity (H’ = 0.98) as compared to the solar saltern (H’ = 4.36) and salt mine (H’ = 3.57). The dominant group in the salt lake is a species from the genus Haloparvum which constitutes about 85% of the total sequences analyzed. The species diversities in salt salterns and salt mines are richer than in the salt lake, and the dominant group is less significant in terms of total percentage. High-throughput sequencing showed that geographical isolation greatly impacted on the microbial community (phyla level) and species diversity (operational taxonomic units (OTUs) level) of salt mines. Species of the genus Natronomonas are found in all three types of environments investigated. In addition, the microbial community and species diversity of different stratums of the salt mine are very similar. Furthermore, species of the genus Halorubrum flourish in the newest stratum of salt mine and have become the dominant group. This study provides some new knowledge on the species diversity and prokaryotic community composition of three typical hypersaline environments.
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Affiliation(s)
- Shaoxing Chen
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, China
- College of Life Sciences, Honghe University, No.1 Xuefu Road, Mengzi 661100, China
- Correspondence: ; Tel.: +86-553-3869297
| | - Yao Xu
- College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu 241000, China
| | - Libby Helfant
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA;
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15
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Almeida E, Dias TV, Ferraz G, Carvalho MF, Lage OM. Culturable bacteria from two Portuguese salterns: diversity and bioactive potential. Antonie van Leeuwenhoek 2019; 113:459-475. [PMID: 31720916 DOI: 10.1007/s10482-019-01356-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 11/29/2022]
Abstract
Salterns are extreme environments, where the high salt concentration is the main limitation to microbial growth, along with solar radiation, temperature and pH. These selective pressures might lead to the acquisition of unique genetic adaptations that can manifest in the production of interesting natural products. The present study aimed at obtaining the culturable microbial diversity from two Portuguese salterns located in different geographic regions. A total of 190 isolates were retrieved and identified as belonging to 30 genera distributed among 4 phyla-Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. Specifically, members of the genus Bacillus were the most frequently isolated from both salterns and all actinobacterial isolates belong to the rare members of this group. The molecular screening of NRPS and PKS-I genes allowed the detection of 38 isolates presenting PKS-I, 25 isolates presenting NRPS and 23 isolates presenting both types of biosynthetic genes. Sequencing of randomly selected amplicons revealed similarity with known PKS-I and NRPS genes or non-annotated hypothetical proteins. This study is the first contribution on the culturable bacterial diversity of Portuguese salterns and on their bioactive potential. Ultimately, these findings provide a novel contribution to improve the understanding on the microbial diversity of salterns.
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Affiliation(s)
- Eduarda Almeida
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal. .,Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Porto, Portugal.
| | - Teresa Vale Dias
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Gonçalo Ferraz
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Maria F Carvalho
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Porto, Portugal
| | - Olga M Lage
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Porto, Portugal
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16
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Glamoclija M, Ramirez S, Sirisena K, Widanagamage I. Subsurface Microbial Ecology at Sediment-Groundwater Interface in Sulfate-Rich Playa; White Sands National Monument, New Mexico. Front Microbiol 2019; 10:2595. [PMID: 31781077 PMCID: PMC6861310 DOI: 10.3389/fmicb.2019.02595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/25/2019] [Indexed: 01/23/2023] Open
Abstract
The hypersaline sediment and groundwater of playa lake, Lake Lucero, at the White Sands National Monument in New Mexico were examined for microbial community composition, geochemical gradients, and mineralogy during the dry season along a meter and a half depth profile of the sediment vs. the groundwater interface. Lake Lucero is a highly dynamic environment, strongly characterized by the capillary action of the groundwater, the extreme seasonality of the climate, and the hypersalinity. Sediments are predominantly composed of gypsum with minor quartz, thenardite, halite, quartz, epsomite, celestine, and clays. Geochemical analysis has revealed the predominance of nitrates over ammonium in all of the analyzed samples, indicating oxygenated conditions throughout the sediment column and in groundwater. Conversely, the microbial communities are primarily aerobic, gram-negative, and are largely characterized by their survival adaptations. Halophiles and oligotrophs are ubiquitous for all the samples. The very diverse communities contain methanogens, phototrophs, heterotrophs, saprophytes, ammonia-oxidizers, sulfur-oxidizers, sulfate-reducers, iron-reducers, and nitrifiers. The microbial diversity varied significantly between groundwater and sediment samples as their temperature adaptation inferences that revealed potential psychrophiles inhabiting the groundwater and thermophiles and mesophiles being present in the sediment. The dynamism of this environment manifests in the relatively even character of the sediment hosted microbial communities, where significant taxonomic distinctions were observed. Therefore, sediment and groundwater substrates are considered as separate ecological entities. We hope that the variety of the discussed playa environments and the microorganisms may be considered a useful terrestrial analog providing valuable information to aid future astrobiological explorations.
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Affiliation(s)
- Mihaela Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States
| | - Steven Ramirez
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States
| | - Kosala Sirisena
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States.,Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, United States.,Department of Environmental Technology, Faculty of Technology, University of Colombo, Colombo, Sri Lanka
| | - Inoka Widanagamage
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States.,Department of Geology and Geological Engineering, The University of Mississippi, Oxford, MS, United States
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17
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McGonigle JM, Bernau JA, Bowen BB, Brazelton WJ. Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats. mSphere 2019; 4:e00378-19. [PMID: 31462415 PMCID: PMC6714890 DOI: 10.1128/msphere.00378-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022] Open
Abstract
We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape.IMPORTANCE Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.
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Affiliation(s)
- Julia M McGonigle
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Jeremiah A Bernau
- Department of Geology and Geophysics, University of Utah, Salt Lake City, Utah, USA
| | - Brenda B Bowen
- Department of Geology and Geophysics, University of Utah, Salt Lake City, Utah, USA
| | - William J Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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18
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Martin‐Cuadrado A, Senel E, Martínez‐García M, Cifuentes A, Santos F, Almansa C, Moreno‐Paz M, Blanco Y, García‐Villadangos M, Cura MÁG, Sanz‐Montero ME, Rodríguez‐Aranda JP, Rosselló‐Móra R, Antón J, Parro V. Prokaryotic and viral community of the sulfate‐rich crust from Peñahueca ephemeral lake, an astrobiology analogue. Environ Microbiol 2019; 21:3577-3600. [DOI: 10.1111/1462-2920.14680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ece Senel
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
- Department of BiologyGraduate School of Sciences, Eskisehir Technical University Yunusemre Campus, Eskisehir 26470 Turkey
| | - Manuel Martínez‐García
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Ana Cifuentes
- Department of Ecology and Marine Resources, Marine Microbiology GroupMediterranean Institute for Advanced Studies (IMEDEA, CSIC‐UIB) Esporles Spain
| | - Fernando Santos
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Cristina Almansa
- Research Technical Services (SSTTI), Microscopy UnitUniversity of Alicante Alicante Spain
| | - Mercedes Moreno‐Paz
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
| | - Yolanda Blanco
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
| | | | | | | | | | - Ramon Rosselló‐Móra
- Department of BiologyGraduate School of Sciences, Eskisehir Technical University Yunusemre Campus, Eskisehir 26470 Turkey
| | - Josefa Antón
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Víctor Parro
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
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19
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Archaeal communities in the deep-sea sediments of the South China Sea revealed by Illumina high-throughput sequencing. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01477-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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20
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Mizuno CM, Prajapati B, Lucas‐Staat S, Sime‐Ngando T, Forterre P, Bamford DH, Prangishvili D, Krupovic M, Oksanen HM. Novel haloarchaeal viruses from Lake Retba infecting
Haloferax
and
Halorubrum
species. Environ Microbiol 2019; 21:2129-2147. [DOI: 10.1111/1462-2920.14604] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Carolina M. Mizuno
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Bina Prajapati
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - Soizick Lucas‐Staat
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Telesphore Sime‐Ngando
- CNRS UMR 6023, Université Clermont‐AuvergneLaboratoire "Microorganismes: Génome et Environnement" (LMGE) F‐63000, Clermont‐Ferrand France
| | - Patrick Forterre
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Dennis H. Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - David Prangishvili
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
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21
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Uritskiy G, DiRuggiero J. Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome. Genes (Basel) 2019; 10:genes10030220. [PMID: 30875864 PMCID: PMC6471235 DOI: 10.3390/genes10030220] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/25/2022] Open
Abstract
In the past decades, the study of microbial life through shotgun metagenomic sequencing has rapidly expanded our understanding of environmental, synthetic, and clinical microbial communities. Here, we review how shotgun metagenomics has affected the field of halophilic microbial ecology, including functional potential reconstruction, virus–host interactions, pathway selection, strain dispersal, and novel genome discoveries. However, there still remain pitfalls and limitations from conventional metagenomic analysis being applied to halophilic microbial communities. Deconvolution of halophilic metagenomes has been difficult due to the high G + C content of these microbiomes and their high intraspecific diversity, which has made both metagenomic assembly and binning a challenge. Halophiles are also underrepresented in public genome databases, which in turn slows progress. With this in mind, this review proposes experimental and analytical strategies to overcome the challenges specific to the halophilic microbiome, from experimental designs to data acquisition and the computational analysis of metagenomic sequences. Finally, we speculate about the potential applications of other next-generation sequencing technologies in halophilic communities. RNA sequencing, long-read technologies, and chromosome conformation assays, not initially intended for microbiomes, are becoming available in the study of microbial communities. Together with recent analytical advancements, these new methods and technologies have the potential to rapidly advance the field of halophile research.
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Affiliation(s)
- Gherman Uritskiy
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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22
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Ramos‐Barbero MD, Martínez JM, Almansa C, Rodríguez N, Villamor J, Gomariz M, Escudero C, Rubin SDC, Antón J, Martínez‐García M, Amils R. Prokaryotic and viral community structure in the singular chaotropic salt lake Salar de Uyuni. Environ Microbiol 2019; 21:2029-2042. [DOI: 10.1111/1462-2920.14549] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/19/2019] [Accepted: 01/29/2019] [Indexed: 02/01/2023]
Affiliation(s)
| | - José M. Martínez
- Department of Virology and Microbiology, Centro de Biología Molecular Severo OchoaUniversidad Autónoma de Madrid (CBMSO, CSIC‐UAM) Cantoblanco, 28049 Madrid Spain
| | - Cristina Almansa
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - Nuria Rodríguez
- Department of Planetology and HabitabilityCentro de Astrobiología (CAB, INTA‐CSIC) 28055 Torrejón de Ardoz Spain
| | - Judith Villamor
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - María Gomariz
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - Cristina Escudero
- Department of Virology and Microbiology, Centro de Biología Molecular Severo OchoaUniversidad Autónoma de Madrid (CBMSO, CSIC‐UAM) Cantoblanco, 28049 Madrid Spain
| | - Sergio dC Rubin
- Department of Virology and Microbiology, Centro de Biología Molecular Severo OchoaUniversidad Autónoma de Madrid (CBMSO, CSIC‐UAM) Cantoblanco, 28049 Madrid Spain
- Université catholique de LouvainEarth and Life Institute, Georges Lemaître Centre for Earth and Climate Research Belgium
| | - Josefa Antón
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - Manuel Martínez‐García
- Department of Physiology, Genetics and MicrobiologyUniversidad de Alicante Alicante Spain
| | - Ricardo Amils
- Department of Virology and Microbiology, Centro de Biología Molecular Severo OchoaUniversidad Autónoma de Madrid (CBMSO, CSIC‐UAM) Cantoblanco, 28049 Madrid Spain
- Department of Planetology and HabitabilityCentro de Astrobiología (CAB, INTA‐CSIC) 28055 Torrejón de Ardoz Spain
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23
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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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Viver T, Orellana L, González-Torres P, Díaz S, Urdiain M, Farías ME, Benes V, Kaempfer P, Shahinpei A, Ali Amoozegar M, Amann R, Antón J, Konstantinidis KT, Rosselló-Móra R. Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano. Syst Appl Microbiol 2018; 41:198-212. [DOI: 10.1016/j.syapm.2017.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/22/2017] [Accepted: 12/23/2017] [Indexed: 01/08/2023]
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25
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Vera-Gargallo B, Ventosa A. Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain). Genes (Basel) 2018. [PMID: 29518047 PMCID: PMC5867873 DOI: 10.3390/genes9030152] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hypersaline environments encompass aquatic and terrestrial habitats. While only a limited number of studies on the microbial diversity of saline soils have been carried out, hypersaline lakes and marine salterns have been thoroughly investigated, resulting in an aquatic-biased knowledge about life in hypersaline environments. To improve our understanding of the assemblage of microbes thriving in saline soils, we assessed the phylogenetic diversity and metabolic potential of the prokaryotic community of two hypersaline soils (with electrical conductivities of ~24 and 55 dS/m) from the Odiel saltmarshes (Spain) by metagenomics. Comparative analysis of these soil databases with available datasets from salterns ponds allowed further identification of unique and shared traits of microbial communities dwelling in these habitats. Saline soils harbored a more diverse prokaryotic community and, in contrast to their aquatic counterparts, contained sequences related to both known halophiles and groups without known halophilic or halotolerant representatives, which reflects the physical heterogeneity of the soil matrix. Our results suggest that Haloquadratum and certain Balneolaeota members may preferentially thrive in aquatic or terrestrial habitats, respectively, while haloarchaea, nanohaloarchaea and Salinibacter may be similarly adapted to both environments. We reconstructed 4 draft genomes related to Bacteroidetes, Balneolaeota and Halobacteria and appraised their metabolism, osmoadaptation strategies and ecology. This study greatly improves the current understanding of saline soils microbiota.
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Affiliation(s)
- Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
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Han R, Zhang X, Liu J, Long Q, Chen L, Liu D, Zhu D. Microbial community structure and diversity within hypersaline Keke Salt Lake environments. Can J Microbiol 2017; 63:895-908. [PMID: 28850799 DOI: 10.1139/cjm-2016-0773] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3-V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%-58.35% relative abundance), Lactococcus (9.52%-10.51%), and Oceanobacillus (8.82%-9.88%) within the Firmicutes phylum (74.81%-80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai-Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg2+, Cl-, Na+, and K+) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.
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Affiliation(s)
- Rui Han
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.,b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Xin Zhang
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Jing Liu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Qifu Long
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
| | - Laisheng Chen
- b Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Deli Liu
- a Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Derui Zhu
- c Research Center of Basic Medical Sciences, Qinghai University Medical College, Xining, Qinghai 810016, People's Republic of China
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