Microbial diversity and activity in Southern California salterns and bitterns: analogues for remnant ocean worlds.
Journal
Environmental microbiology
ISSN: 1462-2920
Titre abrégé: Environ Microbiol
Pays: England
ID NLM: 100883692
Informations de publication
Date de publication:
07 2021
07 2021
Historique:
revised:
12
02
2021
received:
16
11
2020
accepted:
15
02
2021
pubmed:
24
2
2021
medline:
16
11
2021
entrez:
23
2
2021
Statut:
ppublish
Résumé
Concurrent osmotic and chaotropic stress make MgCl
Identifiants
pubmed: 33621409
doi: 10.1111/1462-2920.15440
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Sodium Chloride
451W47IQ8X
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
3825-3839Informations de copyright
© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.
Références
Altheide, T., Chevrier, V., Nicholson, C., and Denson, J. (2009) Experimental investigation of the stability and evaporation of sulfate and chloride brines on Mars. Earth Planet Sci Lett 282: 69-78.
Antón, J., Oren, A., Benlloch, S., Rodríguez-Valera, F., Amann, R., and Rosselló-Mora, R. (2002) Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the bacteria from saltern crystallizer ponds. Int J Syst Evol Microbiol 52: 485-491.
Ball, P., and Hallsworth, J.E. (2015) Water structure and chaotropicity: their uses, abuses and biological implications. Phys Chem Chem Phys 17: 8297-8305.
Benner, S.A. (2017) Detecting Darwinism from molecules in the Enceladus plumes, Jupiter's moons, and other planetary water lagoons. Astrobiology 17: 840-851.
Bolhuis, H., Martín-Cuadrado, A.B., Rosselli, R., Pašić, L., and Rodriguez-Valera, F. (2017) Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface. BMC Genomics 18: 510.
Bolhuis, H., Palm, P., Wende, A., Falb, M., Rampp, M., Rodriguez-Valera, F., et al. (2006) The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7: 169.
Bonete, M.J., Martínez-Espinosa, R.M., Pire, C., Zafrilla, B., and Richardson, D.J. (2008) Nitrogen metabolism in haloarchaea. Saline Syst 4: 9.
Borin, S., Crotti, E., Mapelli, F., Tamagnini, I., Corselli, C., and Daffonchio, D. (2008) DNA is preserved and maintains transforming potential after contact with brines of the deep anoxic hypersaline lakes of the eastern Mediterranean Sea. Saline Syst 4: 10.
Boucher, Y., Douady, C.J., Sharma, A.K., Kamekura, M., and Doolittle, W.F. (2004) Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J Bacteriol 186: 3980-3990.
Bowman, J.S., and Ducklow, H.W. (2015) Microbial communities can be described by metabolic structure: a general framework and application to a seasonally variable, depth-stratified microbial community from the coastal West Antarctic Peninsula. PLoS One 10: e013586.
Callahan, B.J., Mcmurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., and Holmes, S.P. (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13: 581-583.
Chatake, T., and Sunami, T. (2013) Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl2. J Inorg Biochem 124: 15-25.
Cray, J.A., Russell, J.T., Timson, D.J., Singhal, R.S., and Hallsworth, J.E. (2013) A universal measure of chaotropicity and kosmotropicity. Environ Microbiol 15: 287-296.
Cubillos, C.F., Paredes, A., Yáñez, C., Palma, J., Severino, E., Vejar, D., et al. (2019) Insights into the microbiology of the chaotropic brines of Salar de Atacama, Chile. Front Microbiol 10: 1611.
Dawson, K.S., Scheller, S., Dillon, J.G., and Orphan, V.J. (2016) Stable isotope phenotyping via cluster analysis of nanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment. Frontiers in Microbiology 7: 774.
Dekas, A.E., Parada, A.E., Mayali, X., Fuhrman, J.A., Wollard, J., Weber, P.K., and Pett-Ridge, J. (2019) Characterizing chemoautotrophy and heterotrophy in marine archaea and bacteria with single-cell multi-isotope nanoSIP. Front Microbiol 10: 2682.
Duda, V.I., Danilevich, V.N., Suzina, N.E., Shorokhova, A.P., Dmitriev, V.V., Mokhova, O.N., and Akimov, V.N. (2004) Changes in the fine structure of microbial cells induced by chaotropic salts. Microbiology 73: 341-349.
Ellis, B., Haaland, P., Hahne, F., Le Meur, N., Gopalakrishnan, N., Spidlen, J., et al. (2020) flowCore: Basic structures for flow cytometry data. R package version 2.0.1.
Fernández-Remolar, D.C., Chong-Díaz, G., Ruíz-Bermejo, M., Harir, M., Schmitt-Kopplin, P., Tziotis, D., et al. (2013) Molecular preservation in halite- and perchlorate-rich hypersaline subsurface deposits in the Salar Grande basin (Atacama Desert, Chile): implications for the search for molecular biomarkers on Mars. J Geophys Res Biogeosci 118: 922-939.
Fredrickson, J.K., Chandler, D.P., and Onstott, T.C. (1997) Potential for preservation of halobacteria and their macromolecular constituents in brine inclusions from bedded salt deposits. Proc SPIE 3111: 318-329.
Haft, D.H., DiCuccio, M., Badretdin, A., Brover, V., Chetvernin, V., O'Neill, K., et al. (2018) RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 46: D851-D860.
Hallsworth, J.E., Yakimov, M.M., Golyshin, P.N., Gillion, J.L.M., D'Auria, G., De Lima Alves, F., et al. (2007) Limits of life in MgCl2-containing environments: chaotropicity defines the window. Environ Microbiol 9: 801-813.
Harvie, C.E., Møller, N., and Weare, J.H. (1984) The prediction of mineral solubilities in natural waters: the Na-K-Mg-Ca-H-Cl-SO4-OH-HCO3-CO3-CO2-H2O system to high ionic strengths at 25°C. Geochim Cosmochim Acta 48: 723-751.
Krüger, M., Wolters, H., Gehre, M., Joye, S.B., and Richnow, H.H. (2008) Tracing the slow growth of anaerobic methane-oxidizing communities by 15N-labelling techniques. FEMS Microbiol Ecol 63: 401-411.
Luck, G., and Zimmer, C. (1972) Conformational aspects and reactivity of DNA: effects of manganese and magnesium ions on interaction with DNA. Eur J Biochem 29: 528-536.
Martin, T.D., Brockhoff, C.A., Creed, J.T., and EMMC Methods Work Group. (1994) Method 200.7: Determination of Metals and Trace Elements in Water and Wastes by Inductively Coupled Plasma-Atomic Emission Spectrometry. Revision 4.4, Cincinnati, OH: US EPA.
Matsen, F.A., Kodner, R.B., and Armbrust, E.V. (2010) pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11: 538.
Mongodin, E.F., Nelson, K.E., Daugherty, S., Deboy, R.T., Wister, J., Khouri, H., et al. (2005) The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and. Archaea 102: 18147-18152.
Narasingarao, P., Podell, S., Ugalde, J.A., Brochier-Armanet, C., Emerson, J.B., Brocks, J.J., et al. (2012) De novo metagenomic assembly reveals abundant novel major lineage of archaea in hypersaline microbial communities. ISME J 6: 81-93.
Nawrocki, E.P., and Eddy, S.R. (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29: 2933-2935.
Nazari-Sharabian, M., Aghababaei, M., Karakouzian, M., and Karami, M. (2020) Water on Mars-a literature review. Galaxies 8: 40.
Neveu, M., Hays, L.E., Voytek, M.A., New, M.H., and Schulte, M.D. (2018) The ladder of life detection. Astrobiology 18: 1375-1402.
Nordstrom, D.K., Plummer, L.N., Wigley, T.M.L., Wolery, T.J., Ball, J.W., Jenne, E.A., et al. (1979) A comparison of computerized chemical models for equilibrium calculations in aqueous systems. In Chemical Modeling in Aqueous Systems, Jenne, E.A. (ed). Washington, DC: American Chemical Society, pp. 857-892.
Oh, D., Porter, K., Russ, B., Burns, D., and Dyall-Smith, M. (2010) Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds. Extremophiles 14: 161-169.
Oksanen, J.F., Blanchet, G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., et al. (2019) vegan: Community Ecology Package. R package version 2.5-6.
Oren, A. (2011) Thermodynamic limits to microbial life at high salt concentrations. Environ Microbiol 13: 1908-1923.
Oren, A. (2013) Life in magnesium- and calcium-rich hypersaline environments: salt stress by chaotropic ions. In Polyextremophiles, Seckbach, J., Oren, A., and Stan-lotter, H. (eds): Dordrecht, Netherlands: Springer, pp. 215-232.
Papke, R.T., Corral, P., Ram-Mohan, N., de la Haba, R.R., Sánchez-Porro, C., Makkay, A., and Ventosa, A. (2015) Horizontal gene transfer, dispersal and haloarchaeal speciation. Life 5: 1405-1426.
Papke, R.T., Koenig, J.E., Rodríguez-Valera, F., and Doolittle, W.F. (2004) Frequent recombination in a saltern population of Halorubrum. Science 353: 1928-1930.
Paradis, E., and Schliep, K. (2019) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.
Pett-Ridge, J., and Weber, P.K. (in press). NanoSIP: NanoSIMS applications for microbial biology. In Microbial Systems Biology: Methods and Protocols, 2nd ed, Navid, A. (ed): Totowa, NJ: Humana Press, pp. 375-408.
Pfaff, J.D. (1993) Method 300.0: Determination of Inorganic Anions by Ion Chromatography. Revision 2.1, Cincinnati, OH: U.S. EPA.
Polerecky, L., Adam, B., Milucka, J., Musat, N., Vagner, T., and Kuypers, M.M.M. (2012) Look@NanoSIMS-a tool for the analysis of nanoSIMS data in environmental microbiology. Environ Microbiol 14: 1009-1023.
Popa, R., Weber, P.K., Pett-Ridge, J., Finzi, J.A., Fallon, S.J., Hutcheon, I.D., et al. (2007) Carbon and nitrogen fixation and metabolite exchange in and between individual cells of Anabaena oscillarioides. ISME J 1: 354-360.
Ram Mohan, N., Fullmer, M.S., Makkay, A.M., Wheeler, R., Ventosa, A., Naor, A., et al. (2014) Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Front Microbiol 5: 143.
Robinson, J.L., Pyzyna, B., Atrasz, R.G., Henderson, C.A., Morrill, K.L., Burd, A.M., et al. (2005) Growth kinetics of extremely halophilic archaea (family Halobacteriaceae) as revealed by Arrhenius plots. J Bacteriol 187: 923-929.
Rodriguez-Brito, B., Li, L., Wegley, L., Furlan, M., Angly, F., Breitbart, M., et al. (2010) Viral and microbial community dynamics in four aquatic environments. ISME J 4: 739-751.
Sass, A.M., McKew, B.A., Sass, H., Fichtel, J., Timmis, K.N., and McGenity, T.J. (2008) Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments. Saline Syst 4: 8.
Sawyer, W.H., and Puckridge, J. (1973) The dissociation of proteins by chaotropic salts. J Biol Chem 248: 8429-8433.
Selinummi, J., Seppälä, J., Yli-Harja, O., and Puhakka, J.A. (2005) Software for quantification of labeled bacteria from digital microscope images by automated image analysis. Biotechniques 39: 859-862.
Serec, K., Dolanski Babić, S., Podgornik, R., and Tomić, S. (2016) Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study. Nucleic Acids Res 44: 8456-8464.
Stevenson, A., Cray, J.A., Williams, J.P., Santos, R., Sahay, R., Neuenkirchen, N., et al. (2015) Is there a common water-activity limit for the three domains of life? ISME J 9: 1333-1351.
Stevenson, A., Hamill, P.G., O'Kane, C.J., Kminek, G., Rummel, J.D., Voytek, M.A., et al. (2017) Aspergillus penicillioides differentiation and cell division at 0.585 water activity. Environ Microbiol 19: 687-697.
Stryhanyuk, H., Calabrese, F., Kümmel, S., Musat, F., Richnow, H.H., and Musat, N. (2018) Calculation of single cell assimilation rates from SIP-nanoSIMS-derived isotope ratios: a comprehensive approach. Front Microbiol 9: 2342.
Tosca, N.J., Knoll, A.H., and McLennan, S.M. (2008) Water activity and the challenge for life on early Mars. Science 320: 1204-1208.
Walters, W., Hyde, E.R., Berg-lyons, D., Ackermann, G., Humphrey, G., Parada, A., et al. (2015) Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 1: e0009-15.
Webb, S.J., Rabsatt, T., Erazo, N., and Bowman, J.S. (2019) Impacts of Zostera eelgrasses on microbial community structure in San Diego coastal waters. Elem Sci Anthr 7: 11.
Wolery, T.W. and Jarek, R.L. (2003) EQ3/6, version 8.0. Sandia National Laboratories.
Yakimov, M.M., La Cono, V., Spada, G.L., Bortoluzzi, G., Messina, E., Smedile, F., et al. (2015) Microbial community of the deep-sea brine Lake Kryos seawater-brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA. Environ Microbiol 17: 364-382.
Zajc, J., Džeroski, S., Kocev, D., Oren, A., Sonjak, S., Tkavc, R., and Gunde-Cimerman, N. (2014) Chaophilic or chaotolerant fungi: a new category of extremophiles? Front Microbiol 5: 708.
Zeder, M., Kohler, E., and Pernthaler, J. (2010) Automated quality assessment of autonomously acquired microscopic images of fluorescently stained bacteria. Cytom Part A 77A: 76-85.
Zhaxybayeva, O., Stepanauskas, R., Ram Mohan, N., and Papke, R.T. (2013) Cell sorting analysis of geographically separated hypersaline environments. Extremophiles 17: 265-275.