DOCSLIB.ORG

Marine-Freshwater Prokaryotic Transitions Require Extensive Changes in the Predicted Proteome Pedro J

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Marine-Freshwater Prokaryotic Transitions Require Extensive Changes in the Predicted Proteome Pedro J Cabello-Yeves and Rodriguez-Valera Microbiome (2019) 7:117 https://doi.org/10.1186/s40168-019-0731-5 RESEARCH Open Access Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome Pedro J. Cabello-Yeves1 and Francisco Rodriguez-Valera1,2* Abstract Background: The adaptation of a marine prokaryote to live in freshwater environments or vice versa is generally believed to be an unusual and evolutionary demanding process. However, the reasons are not obvious given the similarity of both kinds of habitats. Results: We have found major differences at the level of the predicted metaproteomes of marine and freshwater habitats with more acidic values of the isoelectric points (pI) in marine microbes. Furthermore, by comparing genomes of marine-freshwater phylogenetic relatives, we have found higher pI values (basic shift) in the freshwater ones. This difference was sharper in secreted > cytoplasmic > membrane proteins. The changes are concentrated on the surface of soluble proteins. It is also detectable at the level of total amino acid composition and involves similarly core and flexible genome- encoded proteins. Conclusions: The marked changes at the level of protein amino acid composition and pI provide a tool to predict the preferred habitat of a culture or a metagenome-assembled genome (MAG). The exact physiological explanation for such variations in the pIs and electrostatic surface potentials is not known yet. However, these changes might reflect differences in membrane bioenergetics derived from the absence of significant Na+ concentrations in most freshwater habitats. In any case, the changes in amino acid composition in most proteins imply that a long evolutionary time is required to adapt from one type of habitat to the other. Keywords: Isoelectric point, Marine-freshwater transition, Metaproteome, Basic shift, Electrostatic surface potential Background more abundant in marine waters [4, 5]. Second, although One classic conundrum of microbiology, or actually of it might be an artifact of lack of coverage, there are biology at large, is the marked borderline that exists lower-level taxa that appear to be altogether absent in between freshwater and marine habitats [1]. Although one of the groups of habitats regardless of how abundant aquatic environments share many features and ecological they are in the other. Some relevant examples are acI parameters, the microbes found throughout both sys- Actinobacteria [6], Limnohabitans, and Polynucleobacter tems have different characteristics at several levels. First, Betaproteobacteria [7, 8], which dominate freshwater but although the major microbial taxa have representation are absent in marine habitats. LD12 Alphaproteobac- in both, the proportions of each are very different. For teria, including Ca. Fonsibacter [9–11], have only been instance, the phylum Actinobacteria and the class found also in freshwater and estuarine systems, although Betaproteobacteria are two notorious examples of taxa their relatives in the SAR11 clade are widespread in ma- that are more abundant in freshwater [2–4], while clas- rine habitats. On the other hand, Prochlorococcus species ses Alphaproteobacteria and Gammaproteobacteria are [12] or Gammaproteobacteria groups such as SAR86 [13] are found only in marine ecosystems. The ex- * Correspondence: [email protected] planation for such differences is not obvious considering 1Evolutionary Genomics Group, Departamento de Producción Vegetal y the similarity of aquatic pelagic habitats aside from the Microbiología, Universidad Miguel Hernández, San Juan de Alicante, 03550 Alicante, Spain salinity and the influence of terrestrially derived organic 2Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia matter [1]. On the other hand, there are reports of © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Cabello-Yeves and Rodriguez-Valera Microbiome (2019) 7:117 Page 2 of 12 multiple marine clades being detected, albeit in small their proteomes markedly displaced to acidic values numbers, in freshwater habitats [14–16], and the oppos- [28]. However, marine bacteria and archaea are ite is true for marine regions neighboring the continents, expected to be salt-out strategists, i.e., that keep most particularly near large estuaries like the Amazon on the inorganic salts (particularly Na+) outside the cell, Atlantic coast of Brazil [17] or the Baltic Sea [18, 19]. maintaining a relatively salt-free cytoplasm [28]. Thus, the differences cannot be explained by physical The large change in this value detected in the fresh- isolation. Still, excluding some microbes that can survive water microbes mentioned above made us wonder if it and remain rare, such as Escherichia coli or Vibrio cho- could be a general phenomenon and what could be the lerae, there is no known example of microbes of the underlying reason for such a broad deviation. There is a same species (with > 95% average nucleotide identity, current database with pI calculations and amino acid ANI) being found in both types of aquatic environments. properties for more than > 5000 bacteria and archaea One problem to understand the real differences between [30], and prior studies identified a correlation between these two kinds of aquatic systems is the enormous diver- salinity and pIs of microbes [31]. However, there are no sity within each of them. Particularly, freshwater lakes vary studies comparing bona fide freshwater and salt-adapted in their trophic status (from oligotrophic to highly microbial predicted proteomes including hypothetical eutrophic) and other environmental parameters, all of them proteins derived from metagenomes. Here, filling this having profound implications in the taxonomic compo- gap, we have analyzed in detail some specific cases when sition. Recently, we were involved in the first metagenomic closely related microbes by whole genome comparisons study of Lake Baikal, Siberia, Russia [20]. This is the largest have been retrieved from marine and freshwater habi- and deepest (max. 1600 m, average 1300 m) lake on Earth tats; furthermore, there is metagenomic evidence (by re- [21], ultraoligotrophic and with relatively little influence cruitment of metagenomic reads) showing that they are from terrestrial sources (all features that make it similar to actually adapted to live in either one or the other envir- marine off-shore waters) while having very low salt content onment. We have also dissected these pI values depend- + - (dominated by Ca2 and HCO3 , being particularly low in ing on the localization of the proteins and used available Na+ and K+)[22–24]. Interestingly, we found some groups three-dimensional models to determine whether there with close relatives among bona fide marine lineages, in- was a preferential location of the charges. Our data cluding the first freshwater Pelagibacter-like (SAR11 clade) confirm that indeed the predicted proteins, regardless of metagenome-assembled genome (MAG) within the typic- location in the cell, accumulate fewer negative charges ally marine clade I [20]. In previous studies, we compared in prokaryotes coming from freshwater environments, the pI patterns of this SAR11 MAG [20]andafreshwater corresponding to a significant deviation in the amino Synechococcus [25] with their marine closest relatives and, acidic composition. This fact, among other conse- in spite of their relative phylogenetic proximity, noticed sig- quences, implies a large sequence variation that requires nificant differences in the global values of their predicted long evolutionary times to carry out the transition proteome pIs. between marine and freshwater habitats or vice versa. The variations in the global proteome pI plots of cells depend on the amino acid overall charge and Results have important implications on protein structure and Global pIs of metaproteomes from different aquatic properties [26]. It is generally accepted that prokary- habitats otic genomes have a bimodal shape with two maxima A global metagenomic approach was first used to assess [27], one at acidic pH corresponding largely to dis- if the changes in pI could be detected at the level of the solved proteins (cytoplasmic or secreted) and one at microbial community as a whole. Specifically, we used basic pH of the membrane proteins that have a basic metagenomic datasets from freshwater (Tous reservoir (positively charged) domain intracellularly to facilitate and Lake Baikal), brackish (Caspian Sea), and marine the generation of the proton motive force. In between (Mediterranean Sea) environments from similar depths, these two peaks, there is a minimum at ca. neutral which were assembled and annotated, taking all pre- values that correspond to the intracellular pH at which dicted and hypothetical proteins from contigs > 5 kb proteins of equivalent pI value would be the least and obtaining sets of more than 85,000 proteins for soluble. In salt-in halophiles, the alkaline peak nearly each environment (Fig.
Load more

Recommended publications
  • Seasonal Fluctuations in Ionic Concentrations Drive Microbial Succession in a Hypersaline Lake Community
    The ISME Journal (2014) 8, 979–990 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community Sheila Podell1, Joanne B Emerson2,3, Claudia M Jones2, Juan A Ugalde1, Sue Welch4, Karla B Heidelberg5, Jillian F Banfield2,6 and Eric E Allen1,7 1Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA; 2Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA; 3Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA; 4School of Earth Sciences, Byrd Polar Research Center, Ohio State University, Columbus, OH, USA; 5Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; 6Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA and 7Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA Microbial community succession was examined over a two-year period using spatially and temporally coordinated water chemistry measurements, metagenomic sequencing, phylogenetic binning and de novo metagenomic assembly in the extreme hypersaline habitat of Lake Tyrrell, Victoria, Australia. Relative abundances of Haloquadratum-related sequences were positively correlated with co-varying concentrations of potassium, magnesium and sulfate,
    [Show full text]
  • The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts
    biomolecules Review The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts Laura Matarredona ,Mónica Camacho, Basilio Zafrilla , María-José Bonete and Julia Esclapez * Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; [email protected] (L.M.); [email protected] (M.C.); [email protected] (B.Z.); [email protected] (M.-J.B.) * Correspondence: [email protected]; Tel.: +34-965-903-880 Received: 31 July 2020; Accepted: 24 September 2020; Published: 29 September 2020 Abstract: Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations.
    [Show full text]
  • Community Respiration Studies in Saltern Crystallizer Ponds
    Vol. 56: 255–261, 2009 AQUATIC MICROBIAL ECOLOGY Printed September 2009 doi: 10.3354/ame01298 Aquat Microb Ecol Published online May 19, 2009 Contribution to AME Special 2 ‘Progress and perspectives in aquatic primary productivity’ OPENPEN ACCESSCCESS Community respiration studies in saltern crystallizer ponds Mareike Warkentin1, Rhena Schumann1, Aharon Oren2,* 1Department of Biological Sciences, Applied Ecology, University of Rostock, Albert-Einstein-Strasse 3, 18059 Rostock, Germany 2The Institute of Life Sciences, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, Jerusalem, Israel ABSTRACT: To measure community respiration by the heterotrophic Archaea (dominated by Halo- quadratum) and Bacteria (Salinibacter) in the NaCl-saturated crystallizer brines of the solar salterns in Eilat, Israel, and to obtain information on the substrates preferred by the community as energy sources, we used 2 complementary approaches: monitoring of changes in oxygen concentration using planar optode sensors in short (up to 30 min) experiments, and long-term (up to 40–50 h) incubations using Winkler titration to assess changes in oxygen levels. Respiration rates measured were ~3 fmol cell–1 h–1. Respiration was markedly stimulated by glycerol, dihydroxyacetone and pyruvate, but not by yeast extract, succinate, and fumarate. These findings are discussed in view of genomic informa- tion on the dominant heterotrophic organisms in the community as well as the outcome of earlier studies on the behavior of halophilic prokaryotes in situ and in laboratory cultures. Despite the low in situ respiration rate, the oxygen uptake studies added information on the activities of the heterotro- phic communities in salt-saturated ecosystems and on the substrates metabolized by the microorgan- isms present.
    [Show full text]
  • Diversity of Haloquadratum and Other Haloarchaea in Three, Geographically Distant, Australian Saltern Crystallizer Ponds
    Extremophiles (2010) 14:161–169 DOI 10.1007/s00792-009-0295-6 ORIGINAL PAPER Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds Dickson Oh • Kate Porter • Brendan Russ • David Burns • Mike Dyall-Smith Received: 13 October 2009 / Accepted: 1 December 2009 / Published online: 20 December 2009 Ó The Author(s) 2009. This article is published with open access at Springerlink.com Abstract Haloquadratum walsbyi is frequently a domi- were present at all three sites and, overall, 98% of the nant member of the microbial communities in hypersaline Haloquadratum-related sequences displayed B2% diver- waters. 16S rRNA gene sequences indicate that divergence gence from that of the type strain. While haloarchaeal within this species is very low but relatively few sites have diversity at each site was relatively low (9–16 OTUs), been examined, particularly in the southern hemisphere. seven phylogroups (clones and/or isolates) and 4 different The diversity of Haloquadratum was examined in three clones showed B90% sequence identity to classified taxa, coastal, but geographically distant saltern crystallizer and appear to represent novel genera. Six of these branched ponds in Australia, using both culture-independent and together in phylogenetic tree reconstructions, forming a culture-dependent methods. Two 97%-OTU, comprising clade (MSP8-clade) whose members were only distantly Haloquadratum- and Halorubrum-related sequences, were related to classified taxa. Such sequences have only rarely shared by all three sites, with the former OTU representing been previously detected but were found at all three Aus- about 40% of the sequences recovered at each site. tralian crystallizers.
    [Show full text]
  • Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks
    Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks Orland Gonzalez M¨unchen, 2009 Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks Orland Gonzalez Dissertation an der Fakult¨at f¨ur Mathematik, Informatik und Statistik der Ludwig-Maximilians-Universit¨at M¨unchen vorgelegt von Orland Gonzalez aus Manila M¨unchen, den 02.03.2009 Erstgutachter: Prof. Dr. Ralf Zimmer Zweitgutachter: Prof. Dr. Dieter Oesterhelt Tag der m¨undlichen Pr¨ufung: 21.01.2009 Contents Summary xiii Zusammenfassung xvi 1 Introduction 1 2 The Halophilic Archaea 9 2.1NaturalEnvironments............................. 9 2.2Taxonomy.................................... 11 2.3PhysiologyandMetabolism.......................... 14 2.3.1 Osmoadaptation............................ 14 2.3.2 NutritionandTransport........................ 16 2.3.3 Motility and Taxis ........................... 18 2.4CompletelySequencedGenomes........................ 19 2.5DynamicsofBlooms.............................. 20 2.6Motivation.................................... 21 3 The Metabolism of Halobacterium salinarum 23 3.1TheModelArchaeon.............................. 24 3.1.1 BacteriorhodopsinandOtherRetinalProteins............ 24 3.1.2 FlexibleBioenergetics......................... 26 3.1.3 Industrial Applications ......................... 27 3.2IntroductiontoMetabolicReconstructions.................. 27 3.2.1 MetabolismandMetabolicPathways................. 27 3.2.2 MetabolicReconstruction....................... 28 3.3Methods....................................
    [Show full text]
  • Characterization of Heterotrophic Prokaryote Subgroups in the Sfax Coastal Solar Salterns by Combining flow Cytometry Cell Sorting and Phylogenetic Analysis
    Extremophiles (2011) 15:347–358 DOI 10.1007/s00792-011-0364-5 ORIGINAL PAPER Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis Hana Trigui • Salma Masmoudi • Ce´line Brochier-Armanet • Aude Barani • Ge´rald Gre´gori • Michel Denis • Sam Dukan • Sami Maalej Received: 25 January 2011 / Accepted: 1 March 2011 / Published online: 20 March 2011 Ó The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Here, we combined flow cytometry (FCM) and and low nucleic acid content (LNA) prokaryotes. Next, we phylogenetic analyses after cell sorting to characterize the performed a taxonomic analysis of the bacterial and dominant groups of the prokaryotic assemblages inhabiting archaeal communities comprising the two most populated two ponds of increasing salinity: a crystallizer pond (TS) clusters by phylogenetic analyses of 16S rRNA gene clone with a salinity of 390 g/L, and the non-crystallizer pond library. We show for the first time that the presence of (M1) with a salinity of 200 g/L retrieved from the solar HNA and LNA content cells could also be extended to the saltern of Sfax in Tunisia. As expected, FCM analysis archaeal populations. Archaea were detected in all M1 and enabled the resolution of high nucleic acid content (HNA) TS samples, whereas representatives of Bacteria were detected only in LNA for M1 and HNA for TS. Although most of the archaeal sequences remained undetermined, Communicated by A. Oren. other clones were most frequently affiliated to Haloquad- ratum and Halorubrum.
    [Show full text]
  • Sculpting the Bacterial Cell Review
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Current Biology 19, R812–R822, September 15, 2009 ª2009 Elsevier Ltd All rights reserved DOI 10.1016/j.cub.2009.06.033 Sculpting the Bacterial Cell Review William Margolin tuberculosis is a pleomorphic rod that often branches or swells at the poles; Staphylococcus aureus is a sphere, Prokaryotes come in a wide variety of shapes, determined and Streptococcus pneumoniae is ovoid, with pointed polar largely by natural selection, physical constraints, and caps. Then there are even more interesting ones, including patterns of cell growth and division. Because of their Streptomyces, which form fungi-like mycelial mats and aerial relative simplicity, bacterial cells are excellent models for hyphae; Caulobacter crescentus, which forms a curved rod how genes and proteins can directly determine mor- like V. cholerae but with tapered ends and a polar stalk at phology. Recent advances in cytological methods for one end. Archaea also have diverse shapes. While they bacteria have shown that distinct cytoskeletal filaments generally have similar shapes and sizes as bacteria, either composed of actin and tubulin homologs are important round or rod-like, one extreme thermophile (Haloquadratum for guiding growth patterns of the cell wall in bacteria, walsbyi) forms flat squares. Some bacteria are tiny rods, and that the glycan strands that constitute the wall are such as Bdellovibrio bacteriovorus, which hunts and invades generally perpendicular to the direction of growth. This other bacteria and grows in their cytoplasm. Others are cytoskeleton-directed cell wall patterning is strikingly remi- hundreds of microns long and over 20 microns wide, such niscent of how plant cell wall growth is regulated by micro- as Epulopiscium fishelsoni.
    [Show full text]
  • Microbial Drivers of Methane Emissions from Unrestored Industrial Salt Ponds ✉ Jinglie Zhou1, Susanna M
    www.nature.com/ismej ARTICLE OPEN Microbial drivers of methane emissions from unrestored industrial salt ponds ✉ Jinglie Zhou1, Susanna M. Theroux1,2, Clifton P. Bueno de Mesquita 1, Wyatt H. Hartman1, Ye Tian3 and Susannah G. Tringe 1,4 © The Author(s) 2021 Wetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions. The ISME Journal; https://doi.org/10.1038/s41396-021-01067-w INTRODUCTION methylamine, or dimethylsulfide (methylotrophic methanogen- Wetlands are land areas saturated or covered with water and are a esis) [8].
    [Show full text]
  • Halosarcina Pallida Gen. Nov., Sp. Nov., a Halophilic Archaeon from a Low-Salt, Sulfide-Rich Spring
    International Journal of Systematic and Evolutionary Microbiology (2008), 58, 856–860 DOI 10.1099/ijs.0.65398-0 Halosarcina pallida gen. nov., sp. nov., a halophilic archaeon from a low-salt, sulfide-rich spring Kristen N. Savage,1 Lee R. Krumholz,1 Aharon Oren2 and Mostafa S. Elshahed3 Correspondence 1Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA Mostafa S. Elshahed 2The Institute of Life Sciences and the Moshe Shilo Minerva Center for Marine Biogeochemistry, [email protected] The Hebrew University of Jerusalem, Jerusalem, Israel 3Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA A novel halophilic archaeon, strain BZ256T, was isolated from Zodletone Spring, a sulfide- and sulfur-rich spring in south-western Oklahoma, USA. Cells were non-motile, non-flagellated cocci that divided along two axes, resulting in the formation of sarcina-like clusters. Strain BZ256T grew at salt concentrations ranging from 1.3 to 4.3 M NaCl, with optimum growth at approximately + 3.4 M, and required at least 1 mM Mg2 for growth. The pH range for growth was 5.0 to at least 8.5, and the temperature range for growth was 25–45 6C. The two diether phospholipids that are typical of members of the order Halobacteriales, namely phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, were present in strain BZ256T, as were two glycolipids chromatographically identical to S-DGD-1 and DGD-1. The 16S rRNA gene sequence of strain BZ256T showed 96.8 % similarity to that of the type strain of Halogeometricum borinquense, the closest recognized species within the order Halobacteriales.
    [Show full text]
  • Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S Rrna Amplicon Sequencing
    microorganisms Article Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing Can Akpolat 1 , Ana Beatriz Fernández 2 , Pinar Caglayan 1 , Baris Calli 3 , Meral Birbir 1,* and Antonio Ventosa 4,* 1 Department of Biology, Faculty of Arts and Sciences, Marmara University, 34722 Istanbul, Turkey; [email protected] (C.A.); [email protected] (P.C.) 2 Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Publica de Navarra, Multilva, 31006 Navarra, Spain; [email protected] 3 Department of Environmental Engineering, Faculty of Engineering, Marmara University, 34722 Istanbul, Turkey; [email protected] 4 Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41004 Sevilla, Spain * Correspondence: [email protected] (M.B.); [email protected] (A.V.); Tel.: +90-216-777-3200 (M.B.); +34-954-556-765 (A.V.) 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% Citation: Akpolat, C.; Fernández, and 1.32% of reads, respectively, were assigned to 18 archaeal genera, 19 bacterial genera, 10 archaeal A.B.; Caglayan, P.; Calli, B.; Birbir, M.; genera, and one bacterial genus that were determined to be present, with more than 1% sequences in Ventosa, A.
    [Show full text]
  • Marine Microbial Diversity and Its Role in Ecosystem Functioning and Environmental Change May 2012 Marine Board
    Position Paper 17 Marine Microbial Diversity and its role in Ecosystem Functioning and Environmental Change May 2012 Marine Board The Marine Board provides a pan-European platform for its member organisations to develop common pri- orities, to advance marine research, and to bridge the gap between science and policy in order to meet future marine science challenges and opportunities. The Marine Board was established in 1995 to facilitate enhanced cooperation between European marine sci- ence organisations (both research institutes and research funding agencies) towards the development of a com- mon vision on the research priorities and strategies for marine science in Europe. In 2012, the Marine Board represents 34 Member Organisations from 20 countries. The marine Board provides the essential components for transferring knowledge for leadership in marine research in Europe. Adopting a strategic role, the Marine Board serves its member organisations by providing a forum within which marine research policy advice to national agencies and to the European Commission is developed, with the objective of promoting the establishment of the European Marine Research Area. www.marineboard.eu Cover photograph credits: Left: Research Vessel lowering a rosette with Niskin bottles to obtain seawater samples (courtesy, Lucas Stal) Right from top to bottom: Fluorescence in situ hybridisation picture of a marine water sample stained with a probe specific for Bacteria (courtesy, Frank Oliver Glöckner); Marine microbiologist working in the laboratory (courtesy, Frank Oliver Glöckner and Anna Klindworth); Example of a microorganism culture on a laboratory Petri dish (courtesy, Frank Oliver Glöckner); Image of an alga using Scanning Electron Microscopy (SEM). (courtesy, Ruth-Anne Sandaa).
    [Show full text]
  • High Level of Intergenera Gene Exchange Shapes the Evolution of Haloarchaea in an Isolated Antarctic Lake
    High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake Matthew Z. DeMaerea, Timothy J. Williamsa, Michelle A. Allena, Mark V. Browna,b, John A. E. Gibsonc, John Richa, Federico M. Lauroa, Michael Dyall-Smithd, Karen W. Davenporte, Tanja Woykef, Nikos C. Kyrpidesf, Susannah G. Tringef, and Ricardo Cavicchiolia,1 aSchool of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia; bEvolution and Ecology Research Centre, The University of New South Wales, NSW 2052, Australia; cInstitute of Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, Australia; dCharles Sturt University, Wagga Wagga, NSW 2678, Australia; eDepartment of Energy Joint Genome Institute Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545; and fDepartment of Energy Joint Genome Institute, Walnut Creek, CA 94598 Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved September 5, 2013 (received for review April 17, 2013) Deep Lake in Antarctica is a globally isolated, hypersaline system have noted the ability of H. lacusprofundi, and a recent isolate, that remains liquid at temperatures down to −20 °C. By analyzing tADL (14), to form aggregates and biofilms at either high or low metagenome data and genomes of four isolates we assessed ge- temperatures (13, 15, 16), the only studies addressing adaptive nome variation and patterns of gene exchange to learn how the responses are those linking the production of unsaturated diether lake community evolved. The lake is completely and uniformly membrane lipids to cold adaptation in H. lacusprofundi (3, 17). dominated by haloarchaea, comprising a hierarchically structured, Various mechanisms that alter genetic composition have been low-complexity community that differs greatly to temperate and reported in haloarchaea, including archaeal viruses, conjugative plasmids, genome rearrangements mediated by transposons, and tropical hypersaline environments.
    [Show full text]