301
|
Seston SL, Beinart RA, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ. Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes. Front Microbiol 2016; 7:1074. [PMID: 27486438 PMCID: PMC4949241 DOI: 10.3389/fmicb.2016.01074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/27/2016] [Indexed: 12/26/2022] Open
Abstract
Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.
Collapse
Affiliation(s)
| | - Roxanne A Beinart
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Abigail C Shockey
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| |
Collapse
|
302
|
Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches. Appl Environ Microbiol 2016; 82:4682-4695. [PMID: 27235430 DOI: 10.1128/aem.00611-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/18/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED By combining genomics and isotope imaging analysis using high-resolution secondary ion mass spectrometry (NanoSIMS), we examined the function and evolution of Bacteroidales ectosymbionts of the protist Barbulanympha from the hindguts of the wood-eating cockroach Cryptocercus punctulatus In particular, we investigated the structure of ectosymbiont genomes, which, in contrast to those of endosymbionts, has been little studied to date, and tested the hypothesis that these ectosymbionts fix nitrogen. Unlike with most obligate endosymbionts, genome reduction has not played a major role in the evolution of the Barbulanympha ectosymbionts. Instead, interaction with the external environment has remained important for this symbiont as genes for synthesis of transporters, outer membrane proteins, lipopolysaccharides, and lipoproteins have been retained. The ectosymbiont genome carried two complete operons for nitrogen fixation, a urea transporter, and a urease, indicating the availability of nitrogen as a driving force behind the symbiosis. NanoSIMS analysis of C. punctulatus hindgut symbionts exposed in vivo to (15)N2 supports the hypothesis that Barbulanympha ectosymbionts are capable of nitrogen fixation. This genomic and in vivo functional investigation of protist ectosymbionts highlights the diversity of evolutionary forces and trajectories that shape symbiotic interactions. IMPORTANCE The ecological and evolutionary importance of symbioses is increasingly clear, but the overall diversity of symbiotic interactions remains poorly explored. In this study, we investigated the evolution and nitrogen fixation capabilities of ectosymbionts attached to the protist Barbulanympha from the hindgut of the wood-eating cockroach Cryptocercus punctulatus In addressing genome evolution of protist ectosymbionts, our data suggest that the ecological pressures influencing the evolution of extracellular symbionts clearly differ from intracellular symbionts and organelles. Using NanoSIMS analysis, we also obtained direct imaging evidence of a specific hindgut microbe playing a role in nitrogen fixation. These results demonstrate the power of combining NanoSIMS and genomics tools for investigating the biology of uncultivable microbes. This investigation paves the way for a more precise understanding of microbial interactions in the hindguts of wood-eating insects and further exploration of the diversity and ecological significance of symbiosis between microbes.
Collapse
|
303
|
Kroer P, Kjeldsen KU, Nyengaard JR, Schramm A, Funch P. A Novel Extracellular Gut Symbiont in the Marine Worm Priapulus caudatus (Priapulida) Reveals an Alphaproteobacterial Symbiont Clade of the Ecdysozoa. Front Microbiol 2016; 7:539. [PMID: 27199899 PMCID: PMC4844607 DOI: 10.3389/fmicb.2016.00539] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 04/01/2016] [Indexed: 11/29/2022] Open
Abstract
Priapulus caudatus (phylum Priapulida) is a benthic marine predatory worm with a cosmopolitan distribution. In its digestive tract we detected symbiotic bacteria that were consistently present in specimens collected over 8 years from three sites at the Swedish west coast. Based on their 16S rRNA gene sequence, these symbionts comprise a novel genus of the order Rickettsiales (Alphaproteobacteria). Electron microscopy and fluorescence in situ hybridization (FISH) identified them as extracellular, elongate bacteria closely associated with the microvilli, for which we propose the name “Candidatus Tenuibacter priapulorum”. Within Rickettsiales, they form a phylogenetically well-defined, family-level clade with uncultured symbionts of marine, terrestrial, and freshwater arthropods. Cand. Tenuibacter priapulorum expands the host range of this candidate family from Arthropoda to the entire Ecdysozoa, which may indicate an evolutionary adaptation of this bacterial group to the microvilli-lined guts of the Ecdysozoa.
Collapse
Affiliation(s)
- Paul Kroer
- Section for Genetics, Ecology, and Evolution, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Kasper U Kjeldsen
- Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Jens R Nyengaard
- Stereology and Electron Microscopy Laboratory, Department of Clinical Medicine, Centre for Stochastic Geometry and Advanced Bioimaging, Aarhus University Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Peter Funch
- Section for Genetics, Ecology, and Evolution, Department of Bioscience, Aarhus University Aarhus, Denmark
| |
Collapse
|
304
|
Nakajima Y, Shinzato C, Khalturina M, Nakamura M, Watanabe H, Satoh N, Mitarai S. The mitochondrial genome sequence of a deep-sea, hydrothermal vent limpet, Lepetodrilus nux, presents a novel vetigastropod gene arrangement. Mar Genomics 2016; 28:121-126. [PMID: 27102631 DOI: 10.1016/j.margen.2016.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 01/27/2023]
Abstract
While mitochondrial (mt) genomes are used extensively for comparative and evolutionary genomics, few mt genomes of deep-sea species, including hydrothermal vent species, have been determined. The Genus Lepetodrilus is a major deep-sea gastropod taxon that occurs in various deep-sea ecosystems. Using next-generation sequencing, we determined nearly the complete mitochondrial genome sequence of Lepetodrilus nux, which inhabits hydrothermal vents in the Okinawa Trough. The total length of the mitochondrial genome is 16,353bp, excluding the repeat region. It contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, typical of most metazoan genomes. Compared with other vetigastropod mt genome sequences, L. nux employs a novel mt gene arrangement. Other novel arrangements have been identified in the vetigastropod, Fissurella volcano, and in Chrysomallon squamiferum, a neomphaline gastropod; however, all three gene arrangements are different, and Bayesian inference suggests that each lineage diverged independently. Our findings suggest that vetigastropod mt gene arrangements are more diverse than previously realized.
Collapse
Affiliation(s)
- Yuichi Nakajima
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Mariia Khalturina
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Masako Nakamura
- School of Marine Science and Technology, Tokai University, Shimizu, Shizuoka 424-8610, Japan
| | - Hiromi Watanabe
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| |
Collapse
|
305
|
Montanaro J, Gruber D, Leisch N. Improved ultrastructure of marine invertebrates using non-toxic buffers. PeerJ 2016; 4:e1860. [PMID: 27069800 PMCID: PMC4824901 DOI: 10.7717/peerj.1860] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/09/2016] [Indexed: 01/25/2023] Open
Abstract
Many marine biology studies depend on field work on ships or remote sampling locations where sophisticated sample preservation techniques (e.g., high-pressure freezing) are often limited or unavailable. Our aim was to optimize the ultrastructural preservation of marine invertebrates, especially when working in the field. To achieve chemically-fixed material of the highest quality, we compared the resulting ultrastructure of gill tissue of the mussel Mytilus edulis when fixed with differently buffered EM fixatives for marine specimens (seawater, cacodylate and phosphate buffer) and a new fixative formulation with the non-toxic PHEM buffer (PIPES, HEPES, EGTA and MgCl2). All buffers were adapted for immersion fixation to form an isotonic fixative in combination with 2.5% glutaraldehyde. We showed that PHEM buffer based fixatives resulted in equal or better ultrastructure preservation when directly compared to routine standard fixatives. These results were also reproducible when extending the PHEM buffered fixative to the fixation of additional different marine invertebrate species, which also displayed excellent ultrastructural detail. We highly recommend the usage of PHEM-buffered fixation for the fixation of marine invertebrates.
Collapse
Affiliation(s)
- Jacqueline Montanaro
- OCUVAC—Center of Ocular Inflammation and Infection, Laura Bassi Centers of Expertise, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Daniela Gruber
- Core Facility Cell Imaging and Ultrastructure Research, University of Vienna, Vienna, Austria
| | - Nikolaus Leisch
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| |
Collapse
|
306
|
Abstract
The hologenome concept of evolution postulates that the holobiont (host plus symbionts) with its hologenome (host genome plus microbiome) is a level of selection in evolution. Multicellular organisms can no longer be considered individuals by the classical definitions of the term. Every natural animal and plant is a holobiont consisting of the host and diverse symbiotic microbes and viruses. Microbial symbionts can be transmitted from parent to offspring by a variety of methods, including via cytoplasmic inheritance, coprophagy, direct contact during and after birth, and the environment. A large number of studies have demonstrated that these symbionts contribute to the anatomy, physiology, development, innate and adaptive immunity, and behavior and finally also to genetic variation and to the origin and evolution of species. Acquisition of microbes and microbial genes is a powerful mechanism for driving the evolution of complexity. Evolution proceeds both via cooperation and competition, working in parallel.
Collapse
|
307
|
Zimmermann J, Wentrup C, Sadowski M, Blazejak A, Gruber-Vodicka HR, Kleiner M, Ott JA, Cronholm B, De Wit P, Erséus C, Dubilier N. Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla. Mol Ecol 2016; 25:3203-23. [PMID: 26826340 DOI: 10.1111/mec.13554] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/23/2015] [Accepted: 01/19/2016] [Indexed: 12/21/2022]
Abstract
The level of integration between associated partners can range from ectosymbioses to extracellular and intracellular endosymbioses, and this range has been assumed to reflect a continuum from less intimate to evolutionarily highly stable associations. In this study, we examined the specificity and evolutionary history of marine symbioses in a group of closely related sulphur-oxidizing bacteria, called Candidatus Thiosymbion, that have established ecto- and endosymbioses with two distantly related animal phyla, Nematoda and Annelida. Intriguingly, in the ectosymbiotic associations of stilbonematine nematodes, we observed a high degree of congruence between symbiont and host phylogenies, based on their ribosomal RNA (rRNA) genes. In contrast, for the endosymbioses of gutless phallodriline annelids (oligochaetes), we found only a weak congruence between symbiont and host phylogenies, based on analyses of symbiont 16S rRNA genes and six host genetic markers. The much higher degree of congruence between nematodes and their ectosymbionts compared to those of annelids and their endosymbionts was confirmed by cophylogenetic analyses. These revealed 15 significant codivergence events between stilbonematine nematodes and their ectosymbionts, but only one event between gutless phallodrilines and their endosymbionts. Phylogenetic analyses of 16S rRNA gene sequences from 50 Cand. Thiosymbion species revealed seven well-supported clades that contained both stilbonematine ectosymbionts and phallodriline endosymbionts. This closely coupled evolutionary history of marine ecto- and endosymbionts suggests that switches between symbiotic lifestyles and between the two host phyla occurred multiple times during the evolution of the Cand. Thiosymbion clade, and highlights the remarkable flexibility of these symbiotic bacteria.
Collapse
Affiliation(s)
- Judith Zimmermann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Cecilia Wentrup
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.,Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Miriam Sadowski
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Anna Blazejak
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | | | - Manuel Kleiner
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.,Department of Geoscience, University of Calgary, Calgary, 2500 University Drive, AB, T2N 1N4, Canada
| | - Jörg A Ott
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Bodil Cronholm
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05, Stockholm, Sweden
| | - Pierre De Wit
- Department of Marine Sciences, Sven Lovén Centre for Marine Sciences Tjärnö, University of Gothenburg, Hättebäcksvägen 7, SE-452 96, Strömstad, Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.,Faculty of Biology/Chemistry, University of Bremen, Bibliothekstrasse 1, D-28359, Bremen, Germany
| |
Collapse
|
308
|
Bacterial Community Associated with Organs of Shallow Hydrothermal Vent Crab Xenograpsus testudinatus near Kuishan Island, Taiwan. PLoS One 2016; 11:e0150597. [PMID: 26934591 PMCID: PMC4774926 DOI: 10.1371/journal.pone.0150597] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/16/2016] [Indexed: 01/21/2023] Open
Abstract
Shallow-water hydrothermal vents off Kueishan Island (northeastern Taiwan) provide a unique, sulfur-rich, highly acidic (pH 1.75-4.6) and variable-temperature environment. In this species-poor habitat, the crab Xenograpsus testudinatus is dominant, as it mainly feeds on zooplankton killed by sulfurous plumes. In this study, 16S ribosomal RNA gene amplicon pyrosequencing was used to investigate diversity and composition of bacteria residing in digestive gland, gill, stomach, heart, and mid-gut of X. testudinatus, as well as in surrounding seawater. Dominant bacteria were Gamma- and Epsilonproteobacteria that might be capable of autotrophic growth by oxidizing reduced sulfur compounds and are usually resident in deep-sea hydrothermal systems. Dominant bacterial OTUs in X. testudinatus had both host and potential organ specificities, consistent with a potential trophic symbiotic relationship (nutrient transfer between host and bacteria). We inferred that versatile ways to obtain nutrients may provide an adaptive advantage for X. testudinatus in this demanding environment. To our knowledge, this is the first study of bacterial communities in various organs/tissues of a crustacean in a shallow-water hydrothermal system, and as such, may be a convenient animal model for studying these systems.
Collapse
|
309
|
Lokmer A, Kuenzel S, Baines JF, Wegner KM. The role of tissue-specific microbiota in initial establishment success of Pacific oysters. Environ Microbiol 2016; 18:970-87. [DOI: 10.1111/1462-2920.13163] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 11/27/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Ana Lokmer
- Helmholtz Centre for Polar and Marine Research; Alfred Wegener Institute; Coastal Ecology; Wadden Sea Station Sylt; List Sylt Germany
| | - Sven Kuenzel
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 D-24306 Plön Germany
| | - John F. Baines
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 D-24306 Plön Germany
- Institute for Experimental Medicine; Christian-Albrechts-University of Kiel; Arnold-Heller-Strasse 3 D-24105 Kiel Germany
| | - Karl Mathias Wegner
- Helmholtz Centre for Polar and Marine Research; Alfred Wegener Institute; Coastal Ecology; Wadden Sea Station Sylt; List Sylt Germany
| |
Collapse
|
310
|
Patra AK, Kwon YM, Kang SG, Fujiwara Y, Kim SJ. The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida. Mar Genomics 2016; 26:63-71. [PMID: 26776396 DOI: 10.1016/j.margen.2015.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/30/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022]
Abstract
The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions.
Collapse
Affiliation(s)
- Ajit Kumar Patra
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea.
| | - Yong Min Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea.
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea.
| | - Yoshihiro Fujiwara
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan.
| | - Sang-Jin Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea; National Marine Biodiversity Institute of Korea, Seocheon 325-902, Republic of Korea.
| |
Collapse
|
311
|
Meisterhans G, Raymond N, Girault E, Lambert C, Bourrasseau L, de Montaudouin X, Garabetian F, Jude-Lemeilleur F. Structure of Manila Clam (Ruditapes philippinarum) Microbiota at the Organ Scale in Contrasting Sets of Individuals. MICROBIAL ECOLOGY 2016; 71:194-206. [PMID: 26311127 DOI: 10.1007/s00248-015-0662-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/10/2015] [Indexed: 06/04/2023]
Abstract
Marine invertebrate microbiota has a key function in host physiology and health. To date, knowledge about bivalve microbiota is poorly documented except public health concerns. This study used a molecular approach to characterize the microbiota associated with the bivalve Manila clam (Ruditapes philippinarum) by determining (1) the difference among organs either or not under the influence of host habitat, (2) small-scale variability of microbiota, and (3) the experimental response of the Manila clam microbiota submitted to different lateral transmissions. These questions were investigated by sampling two groups of individuals living in contrasting habitats and carrying out a transplant experiment. Manila clam microbiota (i.e., bacterial community structure) was determined at organ-scale (gills, gut, and a pool of remaining tissues) by capillary electrophoresis DNA fingerprinting (CE fingerprinting). The Manila clam microbiota structure differed among organs indicating a selection of Manila clam microbiota at organ scale. Habitat strongly influenced gill and gut microbiota. In contrast, microbiota associated with remaining tissues was similar between group individuals suggesting that these communities are mostly autochthonous, i.e., Manila clam specific. Transplant experiment showed that improving living condition did not induce any change in microbiota associated with remaining tissues. In contrast, the reduction in individual habitat quality led to individuals in declining health as strongly suggested by the increase in phagocytosis activity and decrease in condition index together with the change in internal organ microbiota. This study provides a first description of the Manila clam holobiont which can withstand disturbance and respond opportunistically to improved environmental conditions.
Collapse
Affiliation(s)
- Guillaume Meisterhans
- Université de Bordeaux, UMR 5805 EPOC, F-33120, Arcachon, France.
- CNRS, UMR 5805 EPOC, F-33120, Arcachon, France.
- Freshwater Institute, Fisheries and Oceans Canada, Winnipeg, MB, R3T 2N6, Canada.
| | - Natalie Raymond
- Université de Bordeaux, UMR 5805 EPOC, F-33120, Arcachon, France
- CNRS, UMR 5805 EPOC, F-33120, Arcachon, France
| | - Emilie Girault
- Université de Bordeaux, UMR 5805 EPOC, F-33120, Arcachon, France
- CNRS, UMR 5805 EPOC, F-33120, Arcachon, France
| | - Christophe Lambert
- LEMAR UMR 6539, Unité Mixte UBO/CNRS/IFREMER/IRD, IUEM, Place Nicolas Copernic, F-29280, Plouzané, France
| | - Line Bourrasseau
- Université de Bordeaux, UMR 5805 EPOC, F-33120, Arcachon, France
- CNRS, UMR 5805 EPOC, F-33120, Arcachon, France
| | - Xavier de Montaudouin
- Université de Bordeaux, UMR 5805 EPOC, F-33120, Arcachon, France
- CNRS, UMR 5805 EPOC, F-33120, Arcachon, France
| | - Frédéric Garabetian
- Université de Bordeaux, UMR 5805 EPOC, F-33120, Arcachon, France
- CNRS, UMR 5805 EPOC, F-33120, Arcachon, France
| | - Florence Jude-Lemeilleur
- Université de Bordeaux, UMR 5805 EPOC, F-33120, Arcachon, France
- CNRS, UMR 5805 EPOC, F-33120, Arcachon, France
| |
Collapse
|
312
|
Laming SR, Szafranski KM, Rodrigues CF, Gaudron SM, Cunha MR, Hilário A, Le Bris N, Duperron S. Fickle or Faithful: The Roles of Host and Environmental Context in Determining Symbiont Composition in Two Bathymodioline Mussels. PLoS One 2015; 10:e0144307. [PMID: 26710314 PMCID: PMC4692436 DOI: 10.1371/journal.pone.0144307] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/15/2015] [Indexed: 11/24/2022] Open
Abstract
The Mediterranean Sea and adjoining East Atlantic Ocean host a diverse array of small-sized mussels that predominantly live on sunken, decomposing organic remains. At least two of these, Idas modiolaeformis and Idas simpsoni, are known to engage in gill-associated symbioses; however, the composition, diversity and variability of these symbioses with changing habitat and location is poorly defined. The current study presents bacterial symbiont assemblage data, derived from 454 pyrosequencing carried out on replicate specimens of these two host species, collected across seven sample sites found in three oceanographic regions in the Mediterranean and East Atlantic. The presence of several bacterial OTUs in both the Mediterranean Sea and eastern Atlantic suggests that similar symbiont candidates occur on both sides of the Strait of Gibraltar. The results reveal markedly different symbiotic modes in the two species. Idas modiolaeformis displays high symbiont diversity and flexibility, with strong variation in symbiont composition from the East Mediterranean to the East Atlantic. Idas simpsoni displays low symbiont diversity but high symbiont fidelity, with a single dominant OTU occurring in all specimens analysed. These differences are argued to be a function of the host species, where subtle differences in host evolution, life-history and behaviour could partially explain the observed patterns. The variability in symbiont compositions, particularly in Idas modiolaeformis, is thought to be a function of the nature, context and location of the habitat from which symbiont candidates are sourced.
Collapse
Affiliation(s)
- Sven R. Laming
- Sorbonne Universités, UPMC Université Paris 06, UMR7208 Laboratoire biologie des organismes et écosystèmes aquatiques (UPMC CNRS MNHM IRD CAEN), 7 quai St Bernard, Paris, France
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
| | - Kamil M. Szafranski
- Sorbonne Universités, UPMC Université Paris 06, UMR7208 Laboratoire biologie des organismes et écosystèmes aquatiques (UPMC CNRS MNHM IRD CAEN), 7 quai St Bernard, Paris, France
| | - Clara F. Rodrigues
- Sorbonne Universités, UPMC Université Paris 06, UMR7208 Laboratoire biologie des organismes et écosystèmes aquatiques (UPMC CNRS MNHM IRD CAEN), 7 quai St Bernard, Paris, France
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
| | - Sylvie M. Gaudron
- Sorbonne Universités, UPMC Université Paris 06, UMR7208 Laboratoire biologie des organismes et écosystèmes aquatiques (UPMC CNRS MNHM IRD CAEN), 7 quai St Bernard, Paris, France
| | - Marina R. Cunha
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
| | - Ana Hilário
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
| | - Nadine Le Bris
- Sorbonne Universités, UPMC Banyuls, UMR8222 Laboratoire d'Ecogéochimie des Environnements Benthiques (UPMC CNRS), Station marine de Banyuls, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Sébastien Duperron
- Sorbonne Universités, UPMC Université Paris 06, UMR7208 Laboratoire biologie des organismes et écosystèmes aquatiques (UPMC CNRS MNHM IRD CAEN), 7 quai St Bernard, Paris, France
- Institut Universitaire de France, Paris, France
- * E-mail:
| |
Collapse
|
313
|
Georgieva MN, Wiklund H, Bell JB, Eilertsen MH, Mills RA, Little CTS, Glover AG. A chemosynthetic weed: the tubeworm Sclerolinum contortum is a bipolar, cosmopolitan species. BMC Evol Biol 2015; 15:280. [PMID: 26667806 PMCID: PMC4678467 DOI: 10.1186/s12862-015-0559-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sclerolinum (Annelida: Siboglinidae) is a genus of small, wiry deep-sea tubeworms that depend on an endosymbiosis with chemosynthetic bacteria for their nutrition, notable for their ability to colonise a multitude of reducing environments. Since the early 2000s, a Sclerolinum population has been known to inhabit sediment-hosted hydrothermal vents within the Bransfield Strait, Southern Ocean, and whilst remaining undescribed, it has been suggested to play an important ecological role in this ecosystem. Here, we show that the Southern Ocean Sclerolinum population is not a new species, but more remarkably in fact belongs to the species S. contortum, first described from an Arctic mud volcano located nearly 16,000 km away. RESULTS Our new data coupled with existing genetic studies extend the range of this species across both polar oceans and the Gulf of Mexico. Our analyses show that the populations of this species are structured on a regional scale, with greater genetic differentiation occurring between rather than within populations. Further details of the external morphology and tube structure of S. contortum are revealed through confocal and SEM imaging, and the ecology of this worm is discussed. CONCLUSIONS These results shed further insight into the plasticity and adaptability of this siboglinid group to a range of reducing conditions, and into the levels of gene flow that occur between populations of the same species over a global extent.
Collapse
Affiliation(s)
- Magdalena N Georgieva
- Life Sciences Department, Natural History Museum, London, UK.
- School of Earth and Environment, University of Leeds, Leeds, UK.
| | - Helena Wiklund
- Life Sciences Department, Natural History Museum, London, UK.
| | - James B Bell
- Life Sciences Department, Natural History Museum, London, UK.
- School of Geography, University of Leeds, Leeds, UK.
| | - Mari H Eilertsen
- Centre for Geobiology, University of Bergen, Bergen, Norway.
- Department of Biology, University of Bergen, Bergen, Norway.
| | - Rachel A Mills
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK.
| | | | - Adrian G Glover
- Life Sciences Department, Natural History Museum, London, UK.
| |
Collapse
|
314
|
Laming SR, Duperron S, Gaudron SM, Hilário A, Cunha MR. Adapted to change: The rapid development of symbiosis in newly settled, fast-maturing chemosymbiotic mussels in the deep sea. MARINE ENVIRONMENTAL RESEARCH 2015; 112:100-112. [PMID: 26275834 DOI: 10.1016/j.marenvres.2015.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 06/04/2023]
Abstract
Symbioses between microbiota and marine metazoa occur globally at chemosynthetic habitats facing imminent threat from anthropogenic disturbance, yet little is known concerning the role of symbiosis during early development in chemosymbiotic metazoans: a critical period in any benthic species' lifecycle. The emerging symbiosis of Idas (sensu lato) simpsoni mussels undergoing development is assessed over a post-larval-to-adult size spectrum using histology and fluorescence in situ hybridisation (FISH). Post-larval development shows similarities to that of both heterotrophic and chemosymbiotic mussels. Data from newly settled specimens confirm aposymbiotic, planktotrophic larval development. Sulphur-oxidising (SOX) symbionts subsequently colonise multiple exposed, non-ciliated epithelia shortly after metamorphosis, but only become abundant on gills as these expand with greater host size. This wide-spread bathymodiolin recorded from sulphidic wood, bone and cold-seep habitats, displays a suite of adaptive traits that could buffer against anthropogenic disturbance.
Collapse
Affiliation(s)
- Sven R Laming
- Sorbonne Universités, Université Paris 06, UMR7208 Laboratoire biologie des organismes et écosystèmes aquatiques (UPMC CNRS MNHM IRD CAEN), 7 quai St Bernard, 75005 Paris, France; Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal.
| | - Sébastien Duperron
- Sorbonne Universités, Université Paris 06, UMR7208 Laboratoire biologie des organismes et écosystèmes aquatiques (UPMC CNRS MNHM IRD CAEN), 7 quai St Bernard, 75005 Paris, France; Institut Universitaire de France, Paris, France
| | - Sylvie M Gaudron
- Sorbonne Universités, Université Paris 06, UMR7208 Laboratoire biologie des organismes et écosystèmes aquatiques (UPMC CNRS MNHM IRD CAEN), 7 quai St Bernard, 75005 Paris, France
| | - Ana Hilário
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
| | - Marina R Cunha
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
| |
Collapse
|
315
|
Salem H, Florez L, Gerardo N, Kaltenpoth M. An out-of-body experience: the extracellular dimension for the transmission of mutualistic bacteria in insects. Proc Biol Sci 2015; 282:20142957. [PMID: 25740892 DOI: 10.1098/rspb.2014.2957] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Across animals and plants, numerous metabolic and defensive adaptations are a direct consequence of symbiotic associations with beneficial microbes. Explaining how these partnerships are maintained through evolutionary time remains one of the central challenges within the field of symbiosis research. While genome erosion and co-cladogenesis with the host are well-established features of symbionts exhibiting intracellular localization and transmission, the ecological and evolutionary consequences of an extracellular lifestyle have received little attention, despite a demonstrated prevalence and functional importance across many host taxa. Using insect-bacteria symbioses as a model, we highlight the diverse routes of extracellular symbiont transfer. Extracellular transmission routes are unified by the common ability of the bacterial partners to survive outside their hosts, thereby imposing different genomic, metabolic and morphological constraints than would be expected from a strictly intracellular lifestyle. We emphasize that the evolutionary implications of symbiont transmission routes (intracellular versus extracellular) do not necessarily correspond to those of the transmission mode (vertical versus horizontal), a distinction of vital significance when addressing the genomic and physiological consequences for both host and symbiont.
Collapse
Affiliation(s)
- Hassan Salem
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura Florez
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Nicole Gerardo
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Martin Kaltenpoth
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| |
Collapse
|
316
|
Kiel S. Did shifting seawater sulfate concentrations drive the evolution of deep-sea methane-seep ecosystems? Proc Biol Sci 2015; 282:20142908. [PMID: 25716797 DOI: 10.1098/rspb.2014.2908] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The origin and evolution of the faunas inhabiting deep-sea hydrothermal vents and methane seeps have been debated for decades. These faunas rely on a local source of sulfide and other reduced chemicals for nutrition, which spawned the hypothesis that their evolutionary history is independent from that of photosynthesis-based food chains and instead driven by extinction events caused by deep-sea anoxia. Here I use the fossil record of seep molluscs to show that trends in body size, relative abundance and epifaunal/infaunal ratios track current estimates of seawater sulfate concentrations through the last 150 Myr. Furthermore, the two main faunal turnovers during this time interval coincide with major changes in seawater sulfate concentrations. Because sulfide at seeps originates mostly from seawater sulfate, variations in sulfate concentrations should directly affect the base of the food chain of this ecosystem and are thus the likely driver of the observed macroecologic and evolutionary patterns. The results imply that the methane-seep fauna evolved largely independently from developments and mass extinctions affecting the photosynthesis-based biosphere and add to the growing body of evidence that the chemical evolution of the oceans had a major impact on the evolution of marine life.
Collapse
Affiliation(s)
- Steffen Kiel
- Georg-August-Universität Göttingen, Geoscience Center, Geobiology Group, Goldschmidtstraße 3, Göttingen 37077, Germany Department for Geodynamics and Sedimentology, Universität Wien, Althanstrasse 14, Vienna 1090, Austria
| |
Collapse
|
317
|
Gil R, Peretó J. Small genomes and the difficulty to define minimal translation and metabolic machineries. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
318
|
Kiel S, Hansen BT. Cenozoic Methane-Seep Faunas of the Caribbean Region. PLoS One 2015; 10:e0140788. [PMID: 26468887 PMCID: PMC4607474 DOI: 10.1371/journal.pone.0140788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 09/30/2015] [Indexed: 11/29/2022] Open
Abstract
We report new examples of Cenozoic cold-seep communities from Colombia, Cuba, the Dominican Republic, Trinidad, and Venezuela, and attempt to improve the stratigraphic dating of Cenozoic Caribbean seep communities using strontium isotope stratigraphy. Two seep faunas are distinguished in Barbados: the late Eocene mudstone-hosted ‘Joes River fauna’ consists mainly of large lucinid bivalves and tall abyssochrysoid gastropods, and the early Miocene carbonate-hosted ‘Bath Cliffs fauna’ containing the vesicomyid Pleurophopsis, the mytilid Bathymodiolus and small gastropods. Two new Oligocene seep communities from the Sinú River basin in Colombia consist of lucinid bivalves including Elongatolucina, thyasirid and solemyid bivalves, and Pleurophopsis. A new early Miocene seep community from Cuba includes Pleurophopsis and the large lucinid Meganodontia. Strontium isotope stratigraphy suggests an Eocene age for the Cuban Elmira asphalt mine seep community, making it the oldest in the Caribbean region. A new basal Pliocene seep fauna from the Dominican Republic is characterized by the large lucinid Anodontia (Pegophysema). In Trinidad we distinguish two types of seep faunas: the mudstone-hosted Godineau River fauna consisting mainly of lucinid bivalves, and the limestone-hosted Freeman’s Bay fauna consisting chiefly of Pleurophopsis, Bathymodiolus, and small gastropods; they are all dated as late Miocene. Four new seep communities of Oligocene to Miocene age are reported from Venezuela. They consist mainly of large globular lucinid bivalves including Meganodontia, and moderately sized vesicomyid bivalves. After the late Miocene many large and typical ‘Cenozoic’ lucinid genera disappeared from the Caribbean seeps and are today known only from the central Indo-Pacific Ocean. We speculate that the increasingly oligotrophic conditions in the Caribbean Sea after the closure of the Isthmus of Panama in the Pliocene may have been unfavorable for such large lucinids because they are only facultative chemosymbiotic and need to derive a significant proportion of their nutrition from suspended organic matter.
Collapse
Affiliation(s)
- Steffen Kiel
- Georg-August-Universität Göttingen, Geoscience Center, Geobiology Group, Goldschmidtstr. 3, 37077, Göttingen, Germany
- Naturhistoriska riksmuseet, Department of Palaeobiology, Box 500 07, 104 05, Stockholm, Sweden
- * E-mail:
| | - Bent T. Hansen
- Georg-August-Universität Göttingen, Geoscience Center, Department of Isotope Geology, Goldschmidtstr. 3, 37077, Göttingen, Germany
| |
Collapse
|
319
|
van Gils JA, Ahmedou Salem MV. Validating the Incorporation of 13C and 15N in a Shorebird That Consumes an Isotopically Distinct Chemosymbiotic Bivalve. PLoS One 2015; 10:e0140221. [PMID: 26458005 PMCID: PMC4601768 DOI: 10.1371/journal.pone.0140221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 09/23/2015] [Indexed: 11/18/2022] Open
Abstract
The wealth of field studies using stable isotopes to make inferences about animal diets require controlled validation experiments to make proper interpretations. Despite several pleas in the literature for such experiments, validation studies are still lagging behind, notably in consumers dwelling in chemosynthesis-based ecosystems. In this paper we present such a validation experiment for the incorporation of 13C and 15N in the blood plasma of a medium-sized shorebird, the red knot (Calidris canutus canutus), consuming a chemosymbiotic lucinid bivalve (Loripes lucinalis). Because this bivalve forms a symbiosis with chemoautotrophic sulphide-oxidizing bacteria living inside its gill, the bivalve is isotopically distinct from 'normal' bivalves whose food has a photosynthetic basis. Here we experimentally tested the hypothesis that isotope discrimination and incorporation dynamics are different when consuming such chemosynthesis-based prey. The experiment showed that neither the isotopic discrimination factor, nor isotopic turnover time, differed between birds consuming the chemosymbiotic lucinid and a control group consuming a photosynthesis-based bivalve. This was true for 13C as well as for 15N. However, in both groups the 15N discrimination factor was much higher than expected, which probably had to do with the birds losing body mass over the course of the experiment.
Collapse
Affiliation(s)
- Jan A. van Gils
- NIOZ Royal Netherlands Institute for Sea Research, 1790 AB Den Burg, The Netherlands
- * E-mail:
| | - Mohamed Vall Ahmedou Salem
- EBIOME Ecobiologie Marine et Environnement, Département de Biologie, Université des Sciences, de Technologie et de Médecine, B.P. 880, Nouakchott, Mauritania
- Laboratoire de Biologie Appliquée et Pathologie, Département de Biologie, Faculté des Science, B.P. 2121, Tetouan, Morocco
- Parc National du Banc d’Arguin, B.P. 5355, Nouakchott, Mauritania
| |
Collapse
|
320
|
Koyama S, Nishi S, Tokuda M, Uemura M, Ishikawa Y, Seya T, Chow S, Ise Y, Hatada Y, Fujiwara Y, Tsubouchi T. Electrical Retrieval of Living Microorganisms from Cryopreserved Marine Sponges Using a Potential-Controlled Electrode. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:678-92. [PMID: 26242755 PMCID: PMC4540769 DOI: 10.1007/s10126-015-9651-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/06/2015] [Indexed: 05/19/2023]
Abstract
The purpose of this study was to develop a novel electrical retrieval method (ER method) for living sponge-associated microorganisms from marine sponges frozen at -80 °C. A -0.3-V vs. Ag/AgCl constant potential applied for 2 h at 9 °C induced the attachment of the sponge-associated microorganisms to an indium tin oxide/glass (ITO) or a gallium-doped zinc oxide/glass (GZO) working electrode. The electrically attached microorganisms from homogenized Spirastrella insignis tissues had intact cell membranes and showed intracellular dehydrogenase activity. Dead microorganisms were not attracted to the electrode when the homogenized tissues were autoclaved for 15 min at 121 °C before use. The electrically attached microorganisms included cultivable microorganisms retrieved after detachment from the electrode by application of a 9-MHz sine-wave potential. Using the ER method, we obtained 32 phyla and 72 classes of bacteria and 3 archaea of Crenarchaeota thermoprotei, Marine Group I, and Thaumarchaeota incertae sedis from marine sponges S. insignis and Callyspongia confoederata. Employment of the ER method for extraction and purification of the living microorganisms holds potential of single-cell cultivation for genome, transcriptome, proteome, and metabolome analyses of bioactive compounds producing sponge-associated microorganisms.
Collapse
Affiliation(s)
- Sumihiro Koyama
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan,
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
321
|
Marzinelli EM, Campbell AH, Zozaya Valdes E, Vergés A, Nielsen S, Wernberg T, de Bettignies T, Bennett S, Caporaso JG, Thomas T, Steinberg PD. Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography. Environ Microbiol 2015; 17:4078-88. [PMID: 26148974 DOI: 10.1111/1462-2920.12972] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 11/30/2022]
Abstract
Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.
Collapse
Affiliation(s)
- Ezequiel M Marzinelli
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Sydney Institute of Marine Science (SIMS), 19 Chowder Bay Road, Mosman, NSW, 2088, Australia
| | - Alexandra H Campbell
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Sydney Institute of Marine Science (SIMS), 19 Chowder Bay Road, Mosman, NSW, 2088, Australia
| | - Enrique Zozaya Valdes
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Adriana Vergés
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Sydney Institute of Marine Science (SIMS), 19 Chowder Bay Road, Mosman, NSW, 2088, Australia
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Thomas Wernberg
- UWA Oceans Institute & School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Thibaut de Bettignies
- UWA Oceans Institute & School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - Scott Bennett
- UWA Oceans Institute & School of Plant Biology, University of Western Australia, Crawley, WA, 6009, Australia
| | - J Gregory Caporaso
- Center for Microbial Genetics and Genomics, Northern Arizona University, 1298 S Knoles Drive, PO Box 4073, Flagstaff, AZ, 86011-4073, USA
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Peter D Steinberg
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Sydney Institute of Marine Science (SIMS), 19 Chowder Bay Road, Mosman, NSW, 2088, Australia
- Advanced Environmental Biotechnology Centre, Nanyang Technical University, Singapore, 637551, Singapore
| |
Collapse
|
322
|
Ikuta T, Takaki Y, Nagai Y, Shimamura S, Tsuda M, Kawagucci S, Aoki Y, Inoue K, Teruya M, Satou K, Teruya K, Shimoji M, Tamotsu H, Hirano T, Maruyama T, Yoshida T. Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population. ISME JOURNAL 2015; 10:990-1001. [PMID: 26418631 PMCID: PMC4796938 DOI: 10.1038/ismej.2015.176] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 11/09/2022]
Abstract
Chemosynthetic symbiosis is one of the successful systems for adapting to a wide range of habitats including extreme environments, and the metabolic capabilities of symbionts enable host organisms to expand their habitat ranges. However, our understanding of the adaptive strategies that enable symbiotic organisms to expand their habitats is still fragmentary. Here, we report that a single-ribotype endosymbiont population in an individual of the host vent mussel, Bathymodiolus septemdierum has heterogeneous genomes with regard to the composition of key metabolic gene clusters for hydrogen oxidation and nitrate reduction. The host individual harbours heterogeneous symbiont subpopulations that either possess or lack the gene clusters encoding hydrogenase or nitrate reductase. The proportions of the different symbiont subpopulations in a host appeared to vary with the environment or with the host's development. Furthermore, the symbiont subpopulations were distributed in patches to form a mosaic pattern in the gill. Genomic heterogeneity in an endosymbiont population may enable differential utilization of diverse substrates and confer metabolic flexibility. Our findings open a new chapter in our understanding of how symbiotic organisms alter their metabolic capabilities and expand their range of habitats.
Collapse
Affiliation(s)
- Tetsuro Ikuta
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yukiko Nagai
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Miwako Tsuda
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shinsuke Kawagucci
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yui Aoki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Koji Inoue
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Morimi Teruya
- Okinawa Industrial Technology Center, 12-2 Suzaki, Uruma, Okinawa, Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Hinako Tamotsu
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan.,Okinawa Science and Technology Promotion Center (OSTC), 112-18 Asahimachi, Naha, Okinawa, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| |
Collapse
|
323
|
Sayavedra L, Kleiner M, Ponnudurai R, Wetzel S, Pelletier E, Barbe V, Satoh N, Shoguchi E, Fink D, Breusing C, Reusch TBH, Rosenstiel P, Schilhabel MB, Becher D, Schweder T, Markert S, Dubilier N, Petersen JM. Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. eLife 2015; 4:e07966. [PMID: 26371554 PMCID: PMC4612132 DOI: 10.7554/elife.07966] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/14/2015] [Indexed: 01/06/2023] Open
Abstract
Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable 'arsenal' of TRGs.
Collapse
Affiliation(s)
| | - Manuel Kleiner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ruby Ponnudurai
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Silke Wetzel
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Eric Pelletier
- Genoscope - Centre National de Séquençage, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
- Metabolic Genomics Group, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
- University of Évry-Val d'Essonne, Evry, France
| | - Valerie Barbe
- Genoscope - Centre National de Séquençage, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Dennis Fink
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Corinna Breusing
- Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Thorsten BH Reusch
- Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | | | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, Bremen, Germany
| | | |
Collapse
|
324
|
Ohbayashi T, Takeshita K, Kitagawa W, Nikoh N, Koga R, Meng XY, Tago K, Hori T, Hayatsu M, Asano K, Kamagata Y, Lee BL, Fukatsu T, Kikuchi Y. Insect's intestinal organ for symbiont sorting. Proc Natl Acad Sci U S A 2015; 112:E5179-88. [PMID: 26324935 PMCID: PMC4577176 DOI: 10.1073/pnas.1511454112] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Symbiosis has significantly contributed to organismal adaptation and diversification. For establishment and maintenance of such host-symbiont associations, host organisms must have evolved mechanisms for selective incorporation, accommodation, and maintenance of their specific microbial partners. Here we report the discovery of a previously unrecognized type of animal organ for symbiont sorting. In the bean bug Riptortus pedestris, the posterior midgut is morphologically differentiated for harboring specific symbiotic bacteria of a beneficial nature. The sorting organ lies in the middle of the intestine as a constricted region, which partitions the midgut into an anterior nonsymbiotic region and a posterior symbiotic region. Oral administration of GFP-labeled Burkholderia symbionts to nymphal stinkbugs showed that the symbionts pass through the constricted region and colonize the posterior midgut. However, administration of food colorings revealed that food fluid enters neither the constricted region nor the posterior midgut, indicating selective symbiont passage at the constricted region and functional isolation of the posterior midgut for symbiosis. Coadministration of the GFP-labeled symbiont and red fluorescent protein-labeled Escherichia coli unveiled selective passage of the symbiont and blockage of E. coli at the constricted region, demonstrating the organ's ability to discriminate the specific bacterial symbiont from nonsymbiotic bacteria. Transposon mutagenesis and screening revealed that symbiont mutants in flagella-related genes fail to pass through the constricted region, highlighting that both host's control and symbiont's motility are involved in the sorting process. The blocking of food flow at the constricted region is conserved among diverse stinkbug groups, suggesting the evolutionary origin of the intestinal organ in their common ancestor.
Collapse
Affiliation(s)
- Tsubasa Ohbayashi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Kazutaka Takeshita
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; Bioproduction Research Institute, Hokkaido Center, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan
| | - Wataru Kitagawa
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; Bioproduction Research Institute, Hokkaido Center, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan
| | - Naruo Nikoh
- Department of Liberal Arts, The Open University of Japan, Chiba 261-8586, Japan
| | - Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Kanako Tago
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, Tsukuba 305-8604, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8569, Japan
| | - Masahito Hayatsu
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, Tsukuba 305-8604, Japan
| | - Kozo Asano
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; Bioproduction Research Institute, Hokkaido Center, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan
| | - Bok Luel Lee
- Global Research Laboratory, College of Pharmacy, Pusan National University, Pusan 609-735, Korea
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Yoshitomo Kikuchi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; Bioproduction Research Institute, Hokkaido Center, National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan;
| |
Collapse
|
325
|
Har JY, Helbig T, Lim JH, Fernando SC, Reitzel AM, Penn K, Thompson JR. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression. Front Microbiol 2015; 6:818. [PMID: 26388838 PMCID: PMC4557100 DOI: 10.3389/fmicb.2015.00818] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/27/2015] [Indexed: 01/08/2023] Open
Abstract
We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing <85% identity with cultivated strains, and two γ-Proteobacterial ribotypes sharing >99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat.
Collapse
Affiliation(s)
- Jia Y Har
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Tim Helbig
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Ju H Lim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Samodha C Fernando
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte Charlotte, NC, USA
| | - Kevin Penn
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - Janelle R Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| |
Collapse
|
326
|
West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci U S A 2015; 112:10112-9. [PMID: 25964342 PMCID: PMC4547252 DOI: 10.1073/pnas.1421402112] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven't taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved.
Collapse
Affiliation(s)
- Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; Magdalen College, Oxford OX1 4AU, United Kingdom;
| | - Roberta M Fisher
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Andy Gardner
- School of Biology, University of St. Andrews, Dyers Brae, St. Andrews KY16 9TH, United Kingdom; and
| | - E Toby Kiers
- Institute of Ecological Sciences, Faculty of Earth and Life Sciences, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands
| |
Collapse
|
327
|
Flood BE, Jones DS, Bailey JV. Sedimenticola thiotaurini sp. nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens. Int J Syst Evol Microbiol 2015; 65:2522-2530. [DOI: 10.1099/ijs.0.000295] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A marine facultative anaerobe, strain SIP-G1T, was isolated from salt marsh sediments, Falmouth, MA, USA. Phylogenetic analysis of its 16S rRNA gene sequence indicated that it belongs to an unclassified clade of Gammaproteobacteria that includes numerous sulfur-oxidizing bacteria that are endosymbionts of marine invertebrates endemic to sulfidic habitats. Strain SIP-G1T is a member of the genus Sedimenticola, of which there is one previously described isolate, Sedimenticola selenatireducens AK4OH1T. S. selenatireducens AK4OH1T was obtained for further characterization and comparison with strain SIP-G1T. The two strains were capable of coupling the oxidation of thiosulfate, tetrathionate, elemental sulfur and sulfide to autotrophic growth and they produced sulfur inclusions as metabolic intermediates. They showed varying degrees of O2 sensitivity, but when provided amino acids or peptides as a source of energy, they appeared more tolerant of O2 and exhibited concomitant production of elemental sulfur inclusions. The organic substrate preferences and limitations of these two organisms suggest that they possess an oxygen-sensitive carbon fixation pathway(s). Organic acids may be used to produce NADPH through the TCA cycle and are used in the formation of polyhydroxyalkanoates. Cell-wall-deficient morphotypes appeared when organic compounds (especially acetate) were present in excess and reduced sulfur was absent. Levels of DNA–DNA hybridization (∼47 %) and phenotypic characterization indicate that strain SIP-G1T represents a separate species within the genus Sedimenticola, for which the name Sedimenticola thiotaurini sp. nov. is proposed. The type strain is SIP-G1T ( = ATCC BAA-2640T = DSM 28581T). The results also justify emended descriptions of the genus Sedimenticola and of S. selenatireducens.
Collapse
Affiliation(s)
- Beverly E. Flood
- Department of Earth Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel S. Jones
- Department of Earth Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jake V. Bailey
- Department of Earth Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| |
Collapse
|
328
|
Abstract
Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.
Collapse
Affiliation(s)
- Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kevin R. Theis
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| |
Collapse
|
329
|
Panão I, Carrascosa C, Jaber JR, Raposo A. Puffer fish and its consumption: To eat or not to eat? FOOD REVIEWS INTERNATIONAL 2015. [DOI: 10.1080/87559129.2015.1075213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
330
|
Fujiyoshi S, Tateno H, Watsuji T, Yamaguchi H, Fukushima D, Mino S, Sugimura M, Sawabe T, Takai K, Sawayama S, Nakagawa S. Effects of Hemagglutination Activity in the Serum of a Deep-Sea Vent Endemic Crab, Shinkaia Crosnieri, on Non-Symbiotic and Symbiotic Bacteria. Microbes Environ 2015. [PMID: 26212518 PMCID: PMC4567561 DOI: 10.1264/jsme2.me15066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In deep-sea hydrothermal environments, most invertebrates associate with dense populations of symbiotic microorganisms in order to obtain nutrition. The molecular interactions between deep-sea animals and environmental microbes, including their symbionts, have not yet been elucidated in detail. Hemagglutinins/lectins, which are carbohydrate-binding proteins, have recently been reported to play important roles in a wide array of biological processes, including the recognition and control of non-self materials. We herein assessed hemagglutination activity in the serum of a deep-sea vent endemic crab, Shinkaia crosnieri, which harbors chemosynthetic epibionts on its plumose setae. Horse and rabbit erythrocytes were agglutinated using this serum (opt. pH 7.5 and opt. temperature 15°C). Agglutinating activity was inhibited by eight kinds of sugars and several divalent cations, did not require any divalent metal ions, and remained detectable even after heating the serum at 100°C for 30 min. By using fluorescently labeled serum, we demonstrated that deep-sea crab serum components bound to the epibionts even in the presence of sugars. This study represents the first immunological assessment of a deep-sea vent endemic crab and demonstrated the possibility of a non-lectin-mediated symbiont-host interaction.
Collapse
Affiliation(s)
- So Fujiyoshi
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
331
|
Kleiner M, Wentrup C, Holler T, Lavik G, Harder J, Lott C, Littmann S, Kuypers MMM, Dubilier N. Use of carbon monoxide and hydrogen by a bacteria–animal symbiosis from seagrass sediments. Environ Microbiol 2015; 17:5023-35. [PMID: 26013766 PMCID: PMC4744751 DOI: 10.1111/1462-2920.12912] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 05/19/2015] [Indexed: 11/23/2022]
Abstract
The gutless marine worm Olavius algarvensis lives in symbiosis with chemosynthetic bacteria that provide nutrition by fixing carbon dioxide (CO2) into biomass using reduced sulfur compounds as energy sources. A recent metaproteomic analysis of the O. algarvensis symbiosis indicated that carbon monoxide (CO) and hydrogen (H2) might also be used as energy sources. We provide direct evidence that the O. algarvensis symbiosis consumes CO and H2. Single cell imaging using nanoscale secondary ion mass spectrometry revealed that one of the symbionts, the γ3‐symbiont, uses the energy from CO oxidation to fix CO2. Pore water analysis revealed considerable in‐situ concentrations of CO and H2 in the O. algarvensis environment, Mediterranean seagrass sediments. Pore water H2 concentrations (89–2147 nM) were up to two orders of magnitude higher than in seawater, and up to 36‐fold higher than previously known from shallow‐water marine sediments. Pore water CO concentrations (17–51 nM) were twice as high as in the overlying seawater (no literature data from other shallow‐water sediments are available for comparison). Ex‐situ incubation experiments showed that dead seagrass rhizomes produced large amounts of CO. CO production from decaying plant material could thus be a significant energy source for microbial primary production in seagrass sediments.
Collapse
Affiliation(s)
- Manuel Kleiner
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
- Department of Geoscience University of Calgary 2500 University Drive Calgary AB T2N 1N4 Canada
| | - Cecilia Wentrup
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
- Department of Microbiology and Ecosystem Science Division of Microbial Ecology University of Vienna Althanstr. 14 A‐1090 Vienna Austria
| | - Thomas Holler
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Jens Harder
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Christian Lott
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
- Elba Field Station HYDRA Institute for Marine Sciences Via del Forno 80 Campo nell'Elba LI 57034 Italy
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Marcel M. M. Kuypers
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| |
Collapse
|
332
|
Breusing C, Johnson SB, Tunnicliffe V, Vrijenhoek RC. Population structure and connectivity in Indo-Pacific deep-sea mussels of the Bathymodiolus septemdierum complex. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0750-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
333
|
Tame A, Yoshida T, Ohishi K, Maruyama T. Phagocytic activities of hemocytes from the deep-sea symbiotic mussels Bathymodiolus japonicus, B. platifrons, and B. septemdierum. FISH & SHELLFISH IMMUNOLOGY 2015; 45:146-156. [PMID: 25804489 DOI: 10.1016/j.fsi.2015.03.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 03/02/2015] [Accepted: 03/14/2015] [Indexed: 06/04/2023]
Abstract
Deep-sea mytilid mussels harbor symbiotic bacteria in their gill epithelial cells that are horizontally or environmentally transmitted to the next generation of hosts. To understand the immune defense system in deep-sea symbiotic mussels, we examined the hemocyte populations of the symbiotic Bathymodiolus mussel species Bathymodiolus japonicus, Bathymodiolus platifrons, and Bathymodiolus septemdierum, and characterized three types of hemocytes: agranulocytes (AGs), basophilic granulocytes (BGs), and eosinophilic granulocytes (EGs). Of these, the EG cells were the largest (diameter, 8.4-10.0 μm) and had eosinophilic cytoplasm with numerous eosinophilic granules (diameter, 0.8-1.2 μm). Meanwhile, the BGs were of medium size (diameter, 6.7-8.0 μm) and contained small basophilic granules (diameter, 0.3-0.4 μm) in basophilic cytoplasm, and the AGs, the smallest of the hemocytes (diameter, 4.8-6.0 μm), had basophilic cytoplasm lacking granules. A lectin binding assay revealed that concanavalin A bound to all three hemocyte types, while wheat germ agglutinin bound exclusively to EGs and BGs. The total hemocyte population densities within the hemolymph of all three Bathymodiolus mussel species were similar (8.4-13.3 × 10(5) cells/mL), and the percentages of circulating AGs, BGs, and EGs in the hemolymph of these organisms were 44.7-48.5%, 14.3-17.6%, and 34.3-41.0%, respectively. To analyze the functional differences between these hemocytes, the phagocytic activity and post-phagocytic phagosome-lysosome fusion events were analyzed in each cell type using a fluorescent Alexa Fluor(®) 488-conjugated Escherichia coli bioparticle and a LysoTracker(®) lysosomal marker, respectively. While the AGs exhibited no phagocytic activity, both types of granulocytes were phagocytic. Of the three hemocyte types, the EGs exhibited the highest level of phagocytic activity as well as rapid phagosome-lysosome fusion, which occurred within 2 h of incubation. Meanwhile, the BGs showed lower phagocytic activity and lower rates of phagosome-lysosome fusion than the EGs. These findings indicate that the two types of granulocyte play distinct roles in the defense system.
Collapse
Affiliation(s)
- Akihiro Tame
- Department of Technical Services, Marine Works Japan Ltd., Oppama Higashi-cho, Yokosuka-shi, Kanagawa 237-0063, Japan; School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan; Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Takao Yoshida
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan; Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Kazue Ohishi
- Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan; Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan.
| |
Collapse
|
334
|
Affiliation(s)
- E Toby Kiers
- Institute of Ecological Sciences, Vrije Universiteit, 1081 HV Amsterdam, Netherlands.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| |
Collapse
|
335
|
Complete Genome Sequence of Sedimenticola thiotaurini Strain SIP-G1, a Polyphosphate- and Polyhydroxyalkanoate-Accumulating Sulfur-Oxidizing Gammaproteobacterium Isolated from Salt Marsh Sediments. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00671-15. [PMID: 26089430 PMCID: PMC4472907 DOI: 10.1128/genomea.00671-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report the closed genome sequence of Sedimenticola thiotaurini strain SIP-G1 and an unnamed plasmid obtained through PacBio sequencing with 100% consensus concordance. The genome contained several distinctive features not found in other published Sedimenticola genomes, including a complete nitrogen fixation pathway, a complete ethanolamine degradation pathway, and an alkane-1-monooxygenase.
Collapse
|
336
|
Abouna S, Gonzalez-Rizzo S, Grimonprez A, Gros O. First Description of Sulphur-Oxidizing Bacterial Symbiosis in a Cnidarian (Medusozoa) Living in Sulphidic Shallow-Water Environments. PLoS One 2015; 10:e0127625. [PMID: 26011278 PMCID: PMC4444309 DOI: 10.1371/journal.pone.0127625] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 04/17/2015] [Indexed: 01/18/2023] Open
Abstract
Background Since the discovery of thioautotrophic bacterial symbiosis in the giant tubeworm Riftia pachyptila, there has been great impetus to investigate such partnerships in other invertebrates. In this study, we present the occurrence of a sulphur-oxidizing symbiosis in a metazoan belonging to the phylum Cnidaria in which this event has never been described previously. Methodology/Principal Findings Scanning Electron Microscope (SEM), Transmission Electron Microscope (TEM) observations and Energy-dispersive X-ray spectroscopy (EDXs) analysis, were employed to unveil the presence of prokaryotes population bearing elemental sulphur granules, growing on the body surface of the metazoan. Phylogenetic assessments were also undertaken to identify this invertebrate and microorganisms in thiotrophic symbiosis. Our results showed the occurrence of a thiotrophic symbiosis in a cnidarian identified as Cladonema sp. Conclusions/Significance This is the first report describing the occurrence of a sulphur-oxidizing symbiosis in a cnidarian. Furthermore, of the two adult morphologies, the polyp and medusa, this mutualistic association was found restricted to the polyp form of Cladonema sp.
Collapse
Affiliation(s)
- Sylvie Abouna
- Institut de Biologie Paris-Seine, UMR 7138—Evolution Paris-Seine, Equipe Biologie de la Mangrove. Université des Antilles et de la Guyane, UFR des Sciences Exactes et Naturelles, Département de Biologie, BP 592. 97159 Pointe-à-Pitre cedex, Guadeloupe, France
| | - Silvina Gonzalez-Rizzo
- Institut de Biologie Paris-Seine, UMR 7138—Evolution Paris-Seine, Equipe Biologie de la Mangrove. Université des Antilles et de la Guyane, UFR des Sciences Exactes et Naturelles, Département de Biologie, BP 592. 97159 Pointe-à-Pitre cedex, Guadeloupe, France
| | - Adrien Grimonprez
- Institut de Biologie Paris-Seine, UMR 7138—Evolution Paris-Seine, Equipe Biologie de la Mangrove. Université des Antilles et de la Guyane, UFR des Sciences Exactes et Naturelles, Département de Biologie, BP 592. 97159 Pointe-à-Pitre cedex, Guadeloupe, France
| | - Olivier Gros
- Institut de Biologie Paris-Seine, UMR 7138—Evolution Paris-Seine, Equipe Biologie de la Mangrove. Université des Antilles et de la Guyane, UFR des Sciences Exactes et Naturelles, Département de Biologie, BP 592. 97159 Pointe-à-Pitre cedex, Guadeloupe, France
- C3MAG, UFR des Sciences Exactes et Naturelles, Université des Antilles et de la Guyane, BP 592. 97159 Pointe-à-Pitre, Guadeloupe (French West Indies)
- * E-mail:
| |
Collapse
|
337
|
Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater. ISME JOURNAL 2015; 9:2657-70. [PMID: 25885564 DOI: 10.1038/ismej.2015.61] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/16/2015] [Accepted: 03/18/2015] [Indexed: 11/08/2022]
Abstract
Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.
Collapse
|
338
|
Szafranski KM, Deschamps P, Cunha MR, Gaudron SM, Duperron S. Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria. Front Microbiol 2015; 6:162. [PMID: 25774156 PMCID: PMC4343019 DOI: 10.3389/fmicb.2015.00162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/12/2015] [Indexed: 11/13/2022] Open
Abstract
Reducing conditions with elevated sulfide and methane concentrations in ecosystems such as hydrothermal vents, cold seeps or organic falls, are suitable for chemosynthetic primary production. Understanding processes driving bacterial diversity, colonization and dispersal is of prime importance for deep-sea microbial ecology. This study provides a detailed characterization of bacterial assemblages colonizing plant-derived substrates using a standardized approach over a geographic area spanning the North-East Atlantic and Mediterranean. Wood and alfalfa substrates in colonization devices were deployed for different periods at 8 deep-sea chemosynthesis-based sites in four distinct geographic areas. Pyrosequencing of a fragment of the 16S rRNA-encoding gene was used to describe bacterial communities. Colonization occurred within the first 14 days. The diversity was higher in samples deployed for more than 289 days. After 289 days, no relation was observed between community richness and deployment duration, suggesting that diversity may have reached saturation sometime in between. Communities in long-term deployments were different, and their composition was mainly influenced by the geographical location where devices were deployed. Numerous sequences related to horizontally-transmitted chemosynthetic symbionts of metazoans were identified. Their potential status as free-living forms of these symbionts was evaluated based on sequence similarity with demonstrated symbionts. Results suggest that some free-living forms of metazoan symbionts or their close relatives, such as Epsilonproteobacteria associated with the shrimp Rimicaris exoculata, are efficient colonizers of plant substrates at vents and seeps.
Collapse
Affiliation(s)
- Kamil M Szafranski
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7208, Adaptation aux Milieux Extrêmes Paris, France ; UMR MNHN UPMC CNRS IRD UCBN 7208, Biologie des Organismes Aquatiques et Ecosystèmes Paris, France
| | - Philippe Deschamps
- UMR8079 Unité d'Ecologie, Systématique et Evolution, CNRS Université Paris-Sud 11 Orsay, France
| | - Marina R Cunha
- Departamento de Biologia and CESAM, Universidade de Aveiro Aveiro, Portugal
| | - Sylvie M Gaudron
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7208, Adaptation aux Milieux Extrêmes Paris, France ; UMR MNHN UPMC CNRS IRD UCBN 7208, Biologie des Organismes Aquatiques et Ecosystèmes Paris, France
| | - Sébastien Duperron
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7208, Adaptation aux Milieux Extrêmes Paris, France ; UMR MNHN UPMC CNRS IRD UCBN 7208, Biologie des Organismes Aquatiques et Ecosystèmes Paris, France ; Institut Universitaire de France Paris, France
| |
Collapse
|
339
|
Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems. PLoS One 2015; 10:e0119284. [PMID: 25760332 PMCID: PMC4356598 DOI: 10.1371/journal.pone.0119284] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/26/2015] [Indexed: 12/02/2022] Open
Abstract
Chemolithoautotrophic iron-oxidizing bacteria play an essential role in the global iron cycle. Thus far, the majority of marine iron-oxidizing bacteria have been identified as Zetaproteobacteria, a novel class within the phylum Proteobacteria. Marine iron-oxidizing microbial communities have been found associated with volcanically active seamounts, crustal spreading centers, and coastal waters. However, little is known about the presence and diversity of iron-oxidizing communities at hydrothermal systems along the slow crustal spreading center of the Mid-Atlantic Ridge. From October to November 2012, samples were collected from rust-colored mats at three well-known hydrothermal vent systems on the Mid-Atlantic Ridge (Rainbow, Trans-Atlantic Geotraverse, and Snake Pit) using the ROV Jason II. The goal of these efforts was to determine if iron-oxidizing Zetaproteobacteria were present at sites proximal to black smoker vent fields. Small, diffuse flow venting areas with high iron(II) concentrations and rust-colored microbial mats were observed at all three sites proximal to black smoker chimneys. A novel, syringe-based precision sampler was used to collect discrete microbial iron mat samples at the three sites. The presence of Zetaproteobacteria was confirmed using a combination of 16S rRNA pyrosequencing and single-cell sorting, while light micros-copy revealed a variety of iron-oxyhydroxide structures, indicating that active iron-oxidizing communities exist along the Mid-Atlantic Ridge. Sequencing analysis suggests that these iron mats contain cosmopolitan representatives of Zetaproteobacteria, but also exhibit diversity that may be uncommon at other iron-rich marine sites studied to date. A meta-analysis of publically available data encompassing a variety of aquatic habitats indicates that Zetaproteobacteria are rare if an iron source is not readily available. This work adds to the growing understanding of Zetaproteobacteria ecology and suggests that this organism is likely locally restricted to iron-rich marine environments but may exhibit wide-scale geographic distribution, further underscoring the importance of Zetaproteobacteria in global iron cycling.
Collapse
|
340
|
Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes. Antonie van Leeuwenhoek 2015; 107:821-34. [PMID: 25563637 DOI: 10.1007/s10482-014-0375-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/30/2014] [Indexed: 10/24/2022]
Abstract
In the present study, we sampled bacterial communities associated with mussels inhabiting two distinct coastal marine ecosystems in Kalimantan, Indonesia, namely, marine lakes and coastal mangroves. We used 16S rRNA gene pyrosequencing and predicted metagenomic analysis to compare microbial composition and function. Marine lakes are small landlocked bodies of seawater isolated to varying degrees from the open sea environment. They contain numerous endemic taxa and represent natural laboratories of speciation. Our primary goals were to (1) use BLAST search to identify closely related organisms to dominant bacterial OTUs in our mussel dataset and (2) to compare bacterial communities and enrichment in the predicted bacterial metagenome among lakes. Our sequencing effort yielded 3553 OTUs belonging to 44 phyla, 99 classes and 121 orders. Mussels in the largest marine lake (Kakaban) and the coastal mangrove habitat were dominated by bacteria belonging to the phylum Proteobacteria whereas smaller lakes, located on the island of Maratua, were dominated by bacteria belonging to the phyla Firmicutes and Tenericutes. The single most abundant OTU overall was assigned to the genus Mycoplasma. There were several significant differences among locations with respect to metabolic pathways. These included enrichment of xenobiotic biodegradation pathways in the largest marine lake and coastal mangrove. These locations were also the most enriched with respect to nitrogen metabolism. The presence of genes related to isoquinoline alkaloids, polyketides, hydrolases, mono and dioxygenases in the predicted analysis of functional pathways is an indication that the bacterial communities of Brachidontes mussels may be potentially important sources of new marine medicines and enzymes of industrial interest. Future work should focus on measuring how mussel microbial communities influence nutrient dynamics within the marine lake environment and isolating microbes with potential biotechnological applications.
Collapse
|
341
|
Characterization of Bacterial Symbionts in Deep-Sea Fauna: Protocols for Sample Conditioning, Fluorescence In Situ Hybridization, and Image Analysis. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_73] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
342
|
Cysteine dioxygenase and cysteine sulfinate decarboxylase genes of the deep-sea mussel Bathymodiolus septemdierum: possible involvement in hypotaurine synthesis and adaptation to hydrogen sulfide. Amino Acids 2014; 47:571-8. [PMID: 25501502 DOI: 10.1007/s00726-014-1891-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022]
Abstract
It has been suggested that invertebrates inhabiting deep-sea hydrothermal vent areas use the sulfinic acid hypotaurine, a precursor of taurine, to protect against the toxicity of hydrogen sulfide contained in the seawater from the vent. In this protective system, hypotaurine is accumulated in the gill, the primary site of sulfide exposure. However, the pathway for hypotaurine synthesis in mollusks has not been identified. In this study, we screened for the mRNAs of enzymes involved in hypotaurine synthesis in the deep-sea mussel Bathymodiolus septemdierum and cloned cDNAs encoding cysteine dioxygenase and cysteine sulfinate decarboxylase. As mRNAs encoding cysteamine dioxygenase and cysteine lyase were not detected, the cysteine sulfinate pathway is suggested to be the major pathway of hypotaurine and taurine synthesis. The two genes were found to be expressed in all the tissues examined, but the gill exhibited the highest expression. The mRNA level in the gill was not significantly changed by exposure to sulfides or thiosulfate. These results suggests that the gill of B. septemdierum maintains high levels of expression of the two genes regardless of ambient sulfide level and accumulates hypotaurine continuously to protect against sudden exposure to high level of sulfide.
Collapse
|
343
|
Wentrup C, Wendeberg A, Schimak M, Borowski C, Dubilier N. Forever competent: deep‐sea bivalves are colonized by their chemosynthetic symbionts throughout their lifetime. Environ Microbiol 2014; 16:3699-713. [DOI: 10.1111/1462-2920.12597] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 08/08/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Cecilia Wentrup
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Annelie Wendeberg
- Department of Environmental Microbiology UFZ, Helmholtz Centre for Environmental Research Permoserstrasse 15 Leipzig 04318 Germany
| | - Mario Schimak
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Christian Borowski
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Nicole Dubilier
- Department of Symbiosis Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| |
Collapse
|
344
|
Beinart RA, Nyholm SV, Dubilier N, Girguis PR. Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic, γ-Proteobacterial symbionts. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:656-664. [PMID: 25756119 DOI: 10.1111/1758-2229.12183] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Associations between bacteria from the γ-Proteobacterial order Oceanospirillales and marine invertebrates are quite common. Members of the Oceanospirillales exhibit a diversity of interactions with their various hosts, ranging from the catabolism of complex compounds that benefit host growth to attacking and bursting host nuclei. Here, we describe the association between a novel Oceanospirillales phylotype and the hydrothermal vent snail Alviniconcha. Alviniconcha typically harbour chemoautotrophic γ- or ε-Proteobacterial symbionts inside their gill cells. Via fluorescence in situ hybridization and transmission electron microscopy, we observed an Oceanospirillales phylotype (named AOP for ‘Alviniconcha Oceanospirillales phylotype’) in membrane-bound vacuoles that were separate from the known γ- or ε-Proteobacterial symbionts. Using quantitative polymerase chain reaction, we surveyed 181 Alviniconcha hosting γ-Proteobacterial symbionts and 102 hosting ε-Proteobacterial symbionts, and found that the population size of AOP was always minor relative to the canonical symbionts (median 0.53% of the total quantified 16S rRNA genes). Additionally, we detected AOP more frequently in Alviniconcha hosting γ-Proteobacterial symbionts than in those hosting ε-Proteobacterial symbionts (96% and 5% of individuals respectively). The high incidence of AOP in γ-Proteobacteria hosting Alviniconcha implies that it could play a significant ecological role either as a host parasite or as an additional symbiont with unknown physiological capacities.
Collapse
|
345
|
Degnan SM. Think laterally: horizontal gene transfer from symbiotic microbes may extend the phenotype of marine sessile hosts. Front Microbiol 2014; 5:638. [PMID: 25477875 PMCID: PMC4237138 DOI: 10.3389/fmicb.2014.00638] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/06/2014] [Indexed: 12/31/2022] Open
Abstract
Since the origin of the animal kingdom, marine animals have lived in association with viruses, prokaryotes and unicellular eukaryotes, often as symbionts. This long and continuous interaction has provided ample opportunity not only for the evolution of intimate interactions such as sharing of metabolic pathways, but also for horizontal gene transfer (HGT) of non-metazoan genes into metazoan genomes. The number of demonstrated cases of inter-kingdom HGT is currently small, such that it is not yet widely appreciated as a significant player in animal evolution. Sessile marine invertebrates that vertically inherit bacterial symbionts, that have no dedicated germ line, or that bud or excise pluripotent somatic cells during their life history may be particularly receptive to HGT from their symbionts. Closer scrutiny of the growing number of genomes being accrued for these animals may thus reveal HGT as a regular source of novel variation that can function to extend the host phenotype metabolically, morphologically, or even behaviorally. Taxonomic identification of symbionts will help to address the intriguing question of whether past HGT events may constrain contemporary symbioses.
Collapse
Affiliation(s)
- Sandie M Degnan
- Marine Genomics Lab, School of Biological Sciences, The University of Queensland Brisbane, QLD, Australia
| |
Collapse
|
346
|
Pérez-Rodríguez I, Bolognini M, Ricci J, Bini E, Vetriani C. From deep-sea volcanoes to human pathogens: a conserved quorum-sensing signal in Epsilonproteobacteria. ISME JOURNAL 2014; 9:1222-34. [PMID: 25397946 DOI: 10.1038/ismej.2014.214] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/27/2014] [Accepted: 10/01/2014] [Indexed: 12/27/2022]
Abstract
Chemosynthetic Epsilonproteobacteria from deep-sea hydrothermal vents colonize substrates exposed to steep thermal and redox gradients. In many bacteria, substrate attachment, biofilm formation, expression of virulence genes and host colonization are partly controlled via a cell density-dependent mechanism involving signal molecules, known as quorum sensing. Within the Epsilonproteobacteria, quorum sensing has been investigated only in human pathogens that use the luxS/autoinducer-2 (AI-2) mechanism to control the expression of some of these functions. In this study we showed that luxS is conserved in Epsilonproteobacteria and that pathogenic and mesophilic members of this class inherited this gene from a thermophilic ancestor. Furthermore, we provide evidence that the luxS gene is expressed--and a quorum-sensing signal is produced--during growth of Sulfurovum lithotrophicum and Caminibacter mediatlanticus, two Epsilonproteobacteria from deep-sea hydrothermal vents. Finally, we detected luxS transcripts in Epsilonproteobacteria-dominated biofilm communities collected from deep-sea hydrothermal vents. Taken together, our findings indicate that the epsiloproteobacterial lineage of the LuxS enzyme originated in high-temperature geothermal environments and that, in vent Epsilonproteobacteria, luxS expression is linked to the production of AI-2 signals, which are likely produced in situ at deep-sea vents. We conclude that the luxS gene is part of the ancestral epsilonproteobacterial genome and represents an evolutionary link that connects thermophiles to human pathogens.
Collapse
Affiliation(s)
- Ileana Pérez-Rodríguez
- 1] Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA [2] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Marie Bolognini
- 1] Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA [2] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Jessica Ricci
- 1] Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA [2] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Elisabetta Bini
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Costantino Vetriani
- 1] Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA [2] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| |
Collapse
|
347
|
Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton ILG, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 2014; 15:924. [PMID: 25342549 PMCID: PMC4287430 DOI: 10.1186/1471-2164-15-924] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. RESULTS Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. CONCLUSIONS The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jonathan A Eisen
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, 4081 Biological Laboratories, Cambridge, MA 02138, USA.
| | | |
Collapse
|
348
|
Mori K, Suzuki KI, Yamaguchi K, Urabe T, Hanada S. Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from a deep-sea hydrothermal field, and an emended description of the genus Thiohalomonas. Int J Syst Evol Microbiol 2014; 65:235-241. [PMID: 25336721 DOI: 10.1099/ijs.0.070599-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, obligately chemolithoautotrophic, sulfur-oxidizing bacterial strain, designated strain gps52(T), was isolated from a rock sample collected near the hydrothermal vents of the Suiyo Seamount in the Pacific Ocean. The cells possessed a Gram-stain-negative-type cell wall and contained menaquinone-8(H4) and menaquinone-9(H4) as respiratory quinones, and C16 : 1ω7c, C16 : 0 and C18 : 1ω7c as major cellular fatty acids. Neither storage compounds nor extensive internal membranes were observed in the cells. Strain gps52(T) grew using carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as electron acceptor. Optimal growth was observed at 32 °C, pH 6.5 and with 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain gps52(T) belongs to the family Ectothiorhodospiraceae and is different from any other known bacteria, with sequence similarities of less than 93 %. Based on phenotypic and phylogenetic findings, the isolate is considered to represent a novel genus and species in the family Ectothiorhodospiraceae, and the name Thiogranum longum gen. nov., sp. nov. is proposed. The type strain is gps52(T) ( = NBRC 101260(T) = DSM 19610(T)). An emended description of the genus Thiohalomonas is also proposed.
Collapse
Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ken-Ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kaoru Yamaguchi
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tetsuro Urabe
- Department of Earth and Planetary Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Hanada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| |
Collapse
|
349
|
Bik HM. Deciphering diversity and ecological function from marine metagenomes. THE BIOLOGICAL BULLETIN 2014; 227:107-116. [PMID: 25411370 DOI: 10.1086/bblv227n2p107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Metagenomic sequencing now represents a common, powerful approach for investigating diversity and functional relationships in marine ecosystems. High-throughput datasets generated from random fragments of environmental DNA can provide a less biased view of organismal abundance (versus PCR-based amplicon sequencing) and enable novel exploration of microbial genomes by recovering genome assemblies from uncultured species, identifying ecological functions, and reconstructing metabolic pathways. This review highlights the current state of knowledge in marine metagenomics, focusing on biological insights gained from recent environmental studies and detailing commonly employed methods for data collection and analysis.
Collapse
Affiliation(s)
- Holly M Bik
- UC Davis Genome Center, University of California-Davis, One Shields Ave, Davis, California 95616
| |
Collapse
|
350
|
Garcia JR, Gerardo NM. The symbiont side of symbiosis: do microbes really benefit? Front Microbiol 2014; 5:510. [PMID: 25309530 PMCID: PMC4176458 DOI: 10.3389/fmicb.2014.00510] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/10/2014] [Indexed: 11/24/2022] Open
Abstract
Microbial associations are integral to all eukaryotes. Mutualism, the interaction of two species for the benefit of both, is an important aspect of microbial associations, with evidence that multicellular organisms in particular benefit from microbes. However, the microbe’s perspective has largely been ignored, and it is unknown whether most microbial symbionts benefit from their associations with hosts. It has been presumed that microbial symbionts receive host-derived nutrients or a competition-free environment with reduced predation, but there have been few empirical tests, or even critical assessments, of these assumptions. We evaluate these hypotheses based on available evidence, which indicate reduced competition and predation are not universal benefits for symbionts. Some symbionts do receive nutrients from their host, but this has not always been linked to a corresponding increase in symbiont fitness. We recommend experiments to test symbiont fitness using current experimental systems of symbiosis and detail considerations for other systems. Incorporating symbiont fitness into symbiosis research will provide insight into the evolution of mutualistic interactions and cooperation in general.
Collapse
Affiliation(s)
- Justine R Garcia
- Gerardo Lab, Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, GA USA
| | - Nicole M Gerardo
- Gerardo Lab, Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, GA USA
| |
Collapse
|