1
|
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.
Collapse
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
| |
Collapse
|
2
|
Lee CJD, McMullan PE, O'Kane CJ, Stevenson A, Santos IC, Roy C, Ghosh W, Mancinelli RL, Mormile MR, McMullan G, Banciu HL, Fares MA, Benison KC, Oren A, Dyall-Smith ML, Hallsworth JE. NaCl-saturated brines are thermodynamically moderate, rather than extreme, microbial habitats. FEMS Microbiol Rev 2018; 42:672-693. [PMID: 29893835 DOI: 10.1093/femsre/fuy026] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/08/2018] [Indexed: 11/12/2022] Open
Abstract
NaCl-saturated brines such as saltern crystalliser ponds, inland salt lakes, deep-sea brines and liquids-of-deliquescence on halite are commonly regarded as a paradigm for the limit of life on Earth. There are, however, other habitats that are thermodynamically more extreme. Typically, NaCl-saturated environments contain all domains of life and perform complete biogeochemical cycling. Despite their reduced water activity, ∼0.755 at 5 M NaCl, some halophiles belonging to the Archaea and Bacteria exhibit optimum growth/metabolism in these brines. Furthermore, the recognised water-activity limit for microbial function, ∼0.585 for some strains of fungi, lies far below 0.755. Other biophysical constraints on the microbial biosphere (temperatures of >121°C; pH > 12; and high chaotropicity; e.g. ethanol at >18.9% w/v (24% v/v) and MgCl2 at >3.03 M) can prevent any cellular metabolism or ecosystem function. By contrast, NaCl-saturated environments contain biomass-dense, metabolically diverse, highly active and complex microbial ecosystems; and this underscores their moderate character. Here, we survey the evidence that NaCl-saturated brines are biologically permissive, fertile habitats that are thermodynamically mid-range rather than extreme. Indeed, were NaCl sufficiently soluble, some halophiles might grow at concentrations of up to 8 M. It may be that the finite solubility of NaCl has stabilised the genetic composition of halophile populations and limited the action of natural selection in driving halophile evolution towards greater xerophilicity. Further implications are considered for the origin(s) of life and other aspects of astrobiology.
Collapse
Affiliation(s)
- Callum J D Lee
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Phillip E McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Callum J O'Kane
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Inês C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Chayan Roy
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Rocco L Mancinelli
- BAER Institute, Mail Stop 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Melanie R Mormile
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65401, USA
| | - Geoffrey McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Horia L Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Mario A Fares
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de Valencia (CSIC-UV), Valencia, 46980, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Dublin, Ireland
| | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, WV 26506-6300, USA
| | - Aharon Oren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 9190401, Israel
| | - Mike L Dyall-Smith
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| |
Collapse
|
3
|
dC Rubin SS, Marín I, Gómez MJ, Morales EA, Zekker I, San Martín-Uriz P, Rodríguez N, Amils R. Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat. Environ Microbiol 2017; 19:3745-3754. [DOI: 10.1111/1462-2920.13876] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 07/16/2017] [Accepted: 07/24/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Sergio S. dC Rubin
- Centro Nacional de Investigaciones Biotecnológicas; CNIB; Bolivia
- Departamento de Biología Molecular; Universidad Autónoma de Madrid, Cantoblanco; Madrid 28049 Spain
| | - Irma Marín
- Departamento de Biología Molecular; Universidad Autónoma de Madrid, Cantoblanco; Madrid 28049 Spain
| | - Manuel J. Gómez
- Centro Nacional de Investigaciones Cardiovasculares, Melchor Fernández Almagro 3; Madrid 28029 Spain
| | - Eduardo A. Morales
- Centro Nacional de Investigaciones Biotecnológicas; CNIB; Bolivia
- Herbario Criptogámico; Universidad Católica Boliviana; Cochabamba Bolivia
| | - Ivar Zekker
- Institute of Chemistry; University of Tartu; Tartu Estonia
| | | | - Nuria Rodríguez
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz; Madrid 28055 Spain
| | - Ricardo Amils
- Centro Nacional de Investigaciones Biotecnológicas; CNIB; Bolivia
- Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz; Madrid 28055 Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM); Universidad Autónoma de Madrid; Madrid 28049 Spain
| |
Collapse
|
4
|
Gomariz M, Martínez-García M, Santos F, Rodriguez F, Capella-Gutiérrez S, Gabaldón T, Rosselló-Móra R, Meseguer I, Antón J. From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists. ISME JOURNAL 2014; 9:16-31. [PMID: 24926861 DOI: 10.1038/ismej.2014.95] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 05/08/2014] [Accepted: 05/10/2014] [Indexed: 11/09/2022]
Abstract
The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.
Collapse
Affiliation(s)
- María Gomariz
- 1] Department of Materials, Optics and Electronics, University Miguel Hernández of Elche, Alicante, Spain [2] Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Manuel Martínez-García
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | | | | | - Toni Gabaldón
- 1] Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Spain
| | - Inmaculada Meseguer
- Department of Materials, Optics and Electronics, University Miguel Hernández of Elche, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| |
Collapse
|
5
|
Phylogeny and ecophysiological features of prokaryotes isolated from temporary saline tidal pools. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0693-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
6
|
Oren A. Life in Magnesium- and Calcium-Rich Hypersaline Environments: Salt Stress by Chaotropic Ions. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
7
|
Boujelben I, Yarza P, Almansa C, Villamor J, Maalej S, Antón J, Santos F. Virioplankton community structure in Tunisian solar salterns. Appl Environ Microbiol 2012; 78:7429-37. [PMID: 22904045 PMCID: PMC3457115 DOI: 10.1128/aem.01793-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 08/06/2012] [Indexed: 11/20/2022] Open
Abstract
The microbial community inhabiting Sfax solar salterns on the east coast of Tunisia has been studied by means of different molecular and culture-dependent tools that have unveiled the presence of novel microbial groups as well as a community structure different from that of other coastal hypersaline environments. We have focused on the study of the viral assemblages of these salterns and their changes along the salinity gradient and over time. Viruses from three ponds (C4, M1, and TS) encompassing salinities from moderately hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in May and October 2009 and analyzed by transmission electron microscopy (TEM) and pulsed-field gel electrophoresis (PFGE). Additionally, for all three October samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios, increased along the salinity gradient, with around 10(10) virus-like particles (VLPs)/ml in close-to-saturation ponds, which represents the highest viral concentration reported so far for aquatic systems. Four distinct morphologies could be observed with TEM (spherical, tailed, spindled, and filamentous) but with various proportions in the different samples. Metagenomic analyses indicated that every pond harbored a distinct viral assemblage whose G+C content could be roughly correlated with that of the active part of the microbial community that may have constituted the putative hosts. As previously reported for hypersaline metaviromes, most sequences did not have matches in the databases, although some were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide frequency analyses indicated that (i) factors additional to salinity could be structuring viral communities and (ii) every metavirome had unique gene contents and dinucleotide frequencies. Comparison with hypersaline metaviromes available in the databases indicated that the viral assemblages present in close-to-saturation environments located thousands of kilometers apart presented some common traits among them in spite of their differences regarding the putative hosts. A small core metavirome for close-to-saturation systems was found that contained 7 sequences of around 100 nucleotides (nt) whose function was not hinted at by in silico search results, although it most likely represents properties essential for hyperhalophilic viruses.
Collapse
Affiliation(s)
- Ines Boujelben
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Pablo Yarza
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Cristina Almansa
- Servicios Técnicos de Investigación (SSTTI), Unidad de Microscopía, Universidad de Alicante, Alicante, Spain
| | - Judith Villamor
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Sami Maalej
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
| | - Josefa Antón
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio Ramón Margalef, Universidad de Alicante, Alicante, Spain
| | - Fernando Santos
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| |
Collapse
|