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Seah BKB, Schwaha T, Volland JM, Huettel B, Dubilier N, Gruber-Vodicka HR. Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis. Proc Biol Sci 2018; 284:rspb.2017.0764. [PMID: 28701560 PMCID: PMC5524500 DOI: 10.1098/rspb.2017.0764] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/06/2017] [Indexed: 12/03/2022] Open
Abstract
Symbioses between eukaryotes and sulfur-oxidizing (thiotrophic) bacteria have convergently evolved multiple times. Although well described in at least eight classes of metazoan animals, almost nothing is known about the evolution of thiotrophic symbioses in microbial eukaryotes (protists). In this study, we characterized the symbioses between mouthless marine ciliates of the genus Kentrophoros, and their thiotrophic bacteria, using comparative sequence analysis and fluorescence in situ hybridization. Ciliate small-subunit rRNA sequences were obtained from 17 morphospecies collected in the Mediterranean and Caribbean, and symbiont sequences from 13 of these morphospecies. We discovered a new Kentrophoros morphotype where the symbiont-bearing surface is folded into pouch-like compartments, illustrating the variability of the basic body plan. Phylogenetic analyses revealed that all investigated Kentrophoros belonged to a single clade, despite the remarkable morphological diversity of these hosts. The symbionts were also monophyletic and belonged to a new clade within the Gammaproteobacteria, with no known cultured representatives. Each host morphospecies had a distinct symbiont phylotype, and statistical analyses revealed significant support for host–symbiont codiversification. Given that these symbioses were collected from two widely separated oceans, our results indicate that symbiotic associations in unicellular hosts can be highly specific and stable over long periods of evolutionary time.
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Affiliation(s)
- Brandon K B Seah
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Thomas Schwaha
- Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Jean-Marie Volland
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
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252
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Grimonprez A, Molza A, Laurent MC, Mansot JL, Gros O. Thioautotrophic ectosymbiosis in Pseudovorticella sp., a peritrich ciliate species colonizing wood falls in marine mangrove. Eur J Protistol 2018; 62:43-55. [DOI: 10.1016/j.ejop.2017.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 10/18/2022]
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253
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Reveillaud J, Anderson R, Reves-Sohn S, Cavanaugh C, Huber JA. Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity. MICROBIOME 2018; 6:19. [PMID: 29374496 PMCID: PMC5787263 DOI: 10.1186/s40168-018-0411-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/19/2018] [Indexed: 06/01/2023]
Abstract
BACKGROUND The microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR) in the Caribbean Sea were characterized using microscopy, phylogenetic analyses, and a metagenomic approach. RESULTS Bacteria, with a typical Gram negative cell envelope contained within membrane-bound vacuoles, were observed within the trophosome of both tubeworm species. Phylogenetic analysis of the 16S rRNA gene and ITS region suggested MCR individuals harbored highly similar endosymbionts that were > 98% identical, with the exception of two symbionts that showed a 60 bp insertion within the ITS region. All sequences from MCR endosymbionts formed a separate well-supported clade that diverged from those of symbionts of seep and vent vestimentiferans from the Pacific, Gulf of Mexico, and Mediterranean Sea. The metagenomes of the symbionts of two specimens of each tubeworm species were sequenced, and two distinct Gammaproteobacteria metagenome-assembled genomes (MAGs) of more than 4 Mbp assembled. An Average Nucleotide Identity (ANI) of 86.5% between these MAGs, together with distinct 16S rRNA gene and ITS sequences, indicate the presence of multiple endosymbiont phylotypes at the MCR, with one MAG shared between one Escarpia and two Lamellibrachia individuals, indicating these endosymbionts are not specific to either host species. Genes for sulfur and hydrogen oxidation, nitrate reduction (assimilatory and dissimilatory), glycolysis and the Krebs cycle, peptide, sugar, and lipid transporters, and both rTCA and CBB carbon fixation cycles were detected in the MAGs, highlighting key and shared functions with symbiont metagenomes of the vestimentiferans Riftia, Tevnia, and Ridgeia from the Pacific. The potential for a second hydrogen oxidation pathway (via a bidirectional hydrogenase), formate dehydrogenase, a catalase, and several additional peptide transporters were found exclusively in the MCR endosymbiont MAGs. CONCLUSIONS The present study adds new evidence that tubeworm endosymbionts can potentially switch from autotrophic to heterotrophic metabolism, or may be mixotrophic, presumably while free-living, and also suggests their versatile metabolic potential may enable both the host and symbionts to exploit a wide range of environmental conditions. Together, the marked gene content and sequence dissimilarity at the rRNA operon and whole genome level between vent and seep symbionts suggest these newly described endosymbionts from the MCR belong to a novel tubeworm endosymbiont genera, introduced as Candidatus Vondammii.
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Affiliation(s)
- Julie Reveillaud
- ASTRE, INRA, CIRAD, University of Montpellier, Montpellier, France.
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.
| | - Rika Anderson
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
- Department of Biology, Carleton College, Northfield, MN, USA
| | - Sintra Reves-Sohn
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Colleen Cavanaugh
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Julie A Huber
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
- Present Address: Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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254
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Milan M, Carraro L, Fariselli P, Martino ME, Cavalieri D, Vitali F, Boffo L, Patarnello T, Bargelloni L, Cardazzo B. Microbiota and environmental stress: how pollution affects microbial communities in Manila clams. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 194:195-207. [PMID: 29202271 DOI: 10.1016/j.aquatox.2017.11.019] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/13/2017] [Accepted: 11/26/2017] [Indexed: 06/07/2023]
Abstract
Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key, although still not fully understood, player that must be considered to assess the toxicity of environmental contaminants. Bacteria-dependent metabolism of xenobiotics may indeed modulate the host toxicity. Conversely, environmental variables (including pollution) may alter the microbial community and/or its metabolic activity leading to host physiological alterations that may contribute to their toxicity. Here, 16s rRNA gene amplicon sequencing has been applied to characterize the hepatopancreas microbiota composition of the Manila clam, Ruditapes philippinarum. The animals were collected in the Venice lagoon area, which is subject to different anthropogenic pressures, mainly represented by the industrial activities of Porto Marghera (PM). Seasonal and geographic differences in clam microbiotas were explored and linked to host response to chemical stress identified in a previous study at the transcriptome level, establishing potential interactions among hosts, microbes, and environmental parameters. The obtained results showed the recurrent presence of putatively detoxifying bacterial taxa in PM clams during winter and over-representation of several metabolic pathways involved in xenobiotic degradation, which suggested the potential for host-microbial synergistic detoxifying actions. Strong interaction between seasonal and chemically-induced responses was also observed, which partially obscured such potentially synergistic actions. Seasonal variables and exposure to toxicants were therefore shown to interact and substantially affect clam microbiota, which appeared to mirror host response to environmental variation. It is clear that understanding how animals respond to chemical stress cannot ignore a key component of such response, the microbiota.
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Affiliation(s)
- M Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - L Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - P Fariselli
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - M E Martino
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon, Lyon, France
| | - D Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - F Vitali
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - L Boffo
- Associazione "Vongola Verace di Chioggia", Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - B Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
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255
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Baldrighi E, Vanreusel A, Zeppilli D, Sandulli R, Segonzac M. Occurrence of Chromadorita regabi sp. nov. (Nematoda: Adenophorea), a nematode egg predator of Alvinocaris muricola (Crustacea: Decapoda: Caridea: Alvinocarididae) from a deep cold seep area of the Gulf of Guinea. THE EUROPEAN ZOOLOGICAL JOURNAL 2018. [DOI: 10.1080/24750263.2018.1498926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- E. Baldrighi
- Institut Carnot Ifremer-EDROME, Ifremer, Centre Brest, REM/EEP/LEP, Plouzané, France
| | - A. Vanreusel
- Marine Biology section, University of Gent, Gent, Belgium
| | - D. Zeppilli
- Institut Carnot Ifremer-EDROME, Ifremer, Centre Brest, REM/EEP/LEP, Plouzané, France
| | - R. Sandulli
- Department of Sciences and Technologies, Naples University ‘Parthenope’, Napoli, Italy
| | - M. Segonzac
- Institut Carnot Ifremer-EDROME, Ifremer, Centre Brest, REM/EEP/LEP, Plouzané, France
- Département Systématique et évolution, Muséum national d’Histoire naturelle, Paris, France
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256
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Roughgarden J, Gilbert SF, Rosenberg E, Zilber-Rosenberg I, Lloyd EA. Holobionts as Units of Selection and a Model of Their Population Dynamics and Evolution. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s13752-017-0287-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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257
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Life and death in facultative chemosymbioses: control of bacterial population dynamics in the Thyasiridae. Symbiosis 2017. [DOI: 10.1007/s13199-017-0525-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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258
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Diversity and characterization of bacteria associated with the deep-sea hydrothermal vent crab Austinograea sp. comparing with those of two shallow-water crabs by 16S ribosomal DNA analysis. PLoS One 2017; 12:e0187842. [PMID: 29121118 PMCID: PMC5679544 DOI: 10.1371/journal.pone.0187842] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/26/2017] [Indexed: 11/19/2022] Open
Abstract
For deep-sea hydrothermal vent crabs, recent investigations have revealed some epibiotic bacteria, but no study has described the bacterial community associated with the gill and intestine. In this study, the microbiota attached to the gill and intestine of the hydrothermal vent crab Austinograea sp. and two shallow-water crab species (Eriocheir sinensis and Portunus trituberculatus) were compared by high-throughput sequencing of 16S rDNA genes. The highest and lowest diversity in bacterial communities were observed in the gill and intestine of Austinograea sp., respectively. Non-metric multidimensional scaling (NMDS) analysis indicated that Austinograea sp. harbored a distinct microbial community. Operational taxonomic units (OTUs) for phylum Fusobacteria, class Epsilonproteobacteria, and genera Leucothrix, Polaribacter, Fusibacter, etc. were dominant in Austinograea sp. Of these, Leucothrix, Sulfurospirillum, and Arcobacter may be involved in oxidizing reduced sulfur compounds and sulfur metabolism; Marinomonas, Polaribacter adapted to the low temperature, and Fusibacter and Psychrilyobacter may survive well under hypoxic conditions. Bacteria commonly present in seawater were dominant in the gill, whereas anaerobic bacteria showed strikingly high abundance in the intestine. Interestingly, Firmicutes and Epsilonproteobacteria may complement each other in Austinograea sp., forming an internal environment. The diversified microbial community of Austinograea sp. reveals adaptation to the hydrothermal vent environment.
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259
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Medina-Silva R, Oliveira RR, Trindade FJ, Borges LGA, Lopes Simão TL, Augustin AH, Valdez FP, Constant MJ, Simundi CL, Eizirik E, Groposo C, Miller DJ, da Silva PR, Viana AR, Ketzer JMM, Giongo A. Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water. Antonie van Leeuwenhoek 2017; 111:533-550. [PMID: 29110156 DOI: 10.1007/s10482-017-0975-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/31/2017] [Indexed: 11/27/2022]
Abstract
As the depth increases and the light fades in oceanic cold seeps, a variety of chemosynthetic-based benthic communities arise. Previous assessments reported polychaete annelids belonging to the family Siboglinidae as part of the fauna at cold seeps, with the 'Vestimentifera' clade containing specialists that depend on microbial chemosynthetic endosymbionts for nutrition. Little information exists concerning the microbiota of the external portion of the vestimentiferan trunk wall. We employed 16S rDNA-based metabarcoding to describe the external microbiota of the chitin tubes from the vestimentiferan Escarpia collected from a chemosynthetic community in a cold seep area at the southwestern Atlantic Ocean. The most abundant operational taxonomic unit (OTU) belonged to the family Pirellulaceae (phylum Planctomycetes), and the second most abundant OTU belonged to the order Methylococcales (phylum Proteobacteria), composing an average of 21.1 and 15.4% of the total reads on tubes, respectively. These frequencies contrasted with those from the surrounding environment (sediment and water), where they represent no more than 0.1% of the total reads each. Moreover, some taxa with lower abundances were detected only in Escarpia tube walls. These data constitute on the first report of an epibiont microbial community found in close association with external surface of a cold-seep metazoan, Escarpia sp., from a chemosynthetic community in the southwestern Atlantic Ocean.
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Affiliation(s)
- Renata Medina-Silva
- Instituto do Petróleo e dos Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rafael R Oliveira
- Instituto do Petróleo e dos Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda J Trindade
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiz G A Borges
- Instituto do Petróleo e dos Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Taiz L Lopes Simão
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adolpho H Augustin
- Instituto do Petróleo e dos Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda P Valdez
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcelo J Constant
- Instituto do Petróleo e dos Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Carolina L Simundi
- Instituto do Petróleo e dos Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Eduardo Eizirik
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Claudia Groposo
- Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Mello - CENPES, PETROBRAS, Rio de Janeiro, Brazil
| | - Dennis J Miller
- Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Mello - CENPES, PETROBRAS, Rio de Janeiro, Brazil
| | - Priscila Reis da Silva
- Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Mello - CENPES, PETROBRAS, Rio de Janeiro, Brazil
| | | | - João M M Ketzer
- Instituto do Petróleo e dos Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriana Giongo
- Instituto do Petróleo e dos Recursos Naturais, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil. .,, Av. Ipiranga, 6681 Prédio 96J Sala 501-04, Porto Alegre, RS, Brazil.
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260
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Jakubowicz M, Hryniewicz K, Belka Z. Mass occurrence of seep-specific bivalves in the oldest-known cold seep metazoan community. Sci Rep 2017; 7:14292. [PMID: 29085054 PMCID: PMC5662593 DOI: 10.1038/s41598-017-14732-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/16/2017] [Indexed: 12/03/2022] Open
Abstract
One of the most striking features of modern chemosynthesis-based ecosystems surrounding methane seeps is the presence of abundant chemosymbiotic bivalves. However, such accumulations have rarely been reported from Palaeozoic to mid-Mesozoic seeps, and it is widely thought that general trends in the evolution of chemosynthetic communities paralleled those typifying most marine environments, with the bivalve prevalence starting in the Mesozoic and with Palaeozoic seeps being dominated by brachiopods. Here, we report a discovery of bivalve clusters in the oldest-known methane seep that hosted metazoan fauna, dated to the late Silurian. We identify the bivalves, externally very similar to modern chemosymbiotic forms, as members of the extinct family Modiomorphidae, known previously from a younger, Devonian seep. The bivalves inhabited the seep at a stage of increased fluid flow, when they co-occurred with atrypid brachiopods, and display a set of morphological characteristics suggesting a seep-obligate lifestyle. We conclude that bivalves colonised chemosynthesis-based ecosystems at least as early as brachiopods and apparently first developed specialized lineages able to thrive in seep-related habitats for a prolonged period of time. Rather than being simple ecological successors of brachiopods, rich bivalve communities represent an ancient and recurring theme in the evolution of chemosynthetic assemblages.
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Affiliation(s)
- Michal Jakubowicz
- Institute of Geoecology and Geoinformation, Adam Mickiewicz University, ul. B. Krygowskiego 10, 61-680, Poznań, Poland.
| | - Krzysztof Hryniewicz
- Institute of Paleobiology, Polish Academy of Sciences, ul. Twarda 51/55, 00-818, Warszawa, Poland
| | - Zdzislaw Belka
- Isotope Laboratory, Adam Mickiewicz University, ul. B. Krygowskiego 10, 61-680, Poznań, Poland
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261
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Brune A. Co-evolution of marine worms and their chemoautotrophic bacterial symbionts: unexpected host switches explained by ecological fitting? Mol Ecol 2017; 25:2964-6. [PMID: 27373707 DOI: 10.1111/mec.13688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/02/2016] [Indexed: 11/29/2022]
Abstract
Mutualistic associations of bacteria and invertebrates are widespread and encompass an enormous diversity on the side of both partners. The advantages gained from the symbiosis favour reciprocal adaptations that increase the stability of the association and can lead to codiversification of symbiont and host. While numerous examples of a strictly vertical transfer of the symbionts from parent to offspring among intracellular associations abound, little is known about the fidelity of the partners in extracellular associations, where symbionts colonize the surface or body cavity of their host. In this issue of Molecular Ecology, Zimmermann et al. () investigated the evolutionary history of the symbiotic association between a monophyletic clade of sulphur-oxidizing Gammaproteobacteria and two distantly related lineages of marine worms (nematodes and annelids). The study supports the surprising conclusion that partner fidelity does not necessarily increase with the intimacy of the association. Ectosymbionts on the cuticle of the nematodes seem to be cospeciating with their hosts, whereas endosymbionts housed in the body cavity of the annelids must have originated multiple times, probably by host switching, from ectosymbionts of sympatric nematodes. This excellent case study on the evolutionary history of invertebrate-microbe interactions supports the emerging concept that the co-evolutionary processes shaping such mutualistic symbioses include both codiversification and ecological fitting.
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Affiliation(s)
- A Brune
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
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262
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Wagner-Döbler I. Biofilm transplantation in the deep sea. Mol Ecol 2017; 25:1905-7. [PMID: 27169388 DOI: 10.1111/mec.13612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/02/2016] [Accepted: 03/08/2016] [Indexed: 11/29/2022]
Abstract
A gold rush is currently going on in microbial ecology, which is powered by the possibility to determine the full complexity of microbial communities through next-generation sequencing. Accordingly, enormous efforts are underway to describe microbiomes worldwide, in humans, animals, plants, soil, air and the ocean. While much can be learned from these studies, only experiments will finally unravel mechanisms. One of the key questions is how a microbial community is assembled from a pool of bacteria in the environment, and how it responds to change - be it the increase in CO2 concentration in the ocean, or antibiotic treatment of the gut microbiome. The study by Zhang et al. () in this issue is one of the very few that approaches this problem experimentally in the natural environment. The authors selected a habitat which is both extremely interesting and difficult to access. They studied the Thuwal Seep in the Red Sea at 850 m depth and used a remotely operated vehicle (ROV) to place a steel frame carrying substrata for biofilm growth into the brine pool and into the adjacent normal bottom water (NBW). Biofilms were allowed to develop for 3 days, and then those that had been growing in the brine pool were transported to normal bottom water and stayed there for another 3 days, and vice versa. The 'switched' biofilms were then compared with their source communities by metagenome sequencing. Strikingly, both 'switched' biofilms were now dominated by the same two species. These species were able to cope with conditions in both source ecosystems, as shown by assembly of their genomes and detection of expression of key genes. The biofilms had adapted to environmental change, rather than to brine pools or NBW. The study shows both the resilience and adaptability of biofilm communities and has implications for microbial ecology in general and even for therapeutic approaches such as transplantation of faecal microbiomes.
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Affiliation(s)
- Irene Wagner-Döbler
- Helmholz-Centre for Infection Research (HZI), Inhoffenstr. 7, 39124, Braunschweig, Germany
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263
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Cleary DFR, Polónia ARM. Bacterial and archaeal communities inhabiting mussels, sediment and water in Indonesian anchialine lakes. Antonie Van Leeuwenhoek 2017; 111:237-257. [PMID: 29027059 DOI: 10.1007/s10482-017-0944-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/13/2017] [Indexed: 11/24/2022]
Abstract
Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding 'open water' marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.
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Affiliation(s)
- D F R Cleary
- CESAM and Department of Biology, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- CESAM and Department of Biology, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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264
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Kohl KD, Dearing MD. With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology-An Introduction to the Symposium. Integr Comp Biol 2017; 57:669-673. [PMID: 28992098 DOI: 10.1093/icb/icx103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The role that host-associated microbes play in animal biology is gaining attention in comparative biology. Numerous research groups study the roles that microbes play in human health and nutrition, or in enhancing the production of agricultural animals. However, inclusion of host-associated microbes into research questions of integrative and comparative biology has lagged behind. We hosted a symposium to bring together top researchers in the field of host-associated microbes who also incorporate aspects of integrative and comparative biology. In this introduction, we highlight recent research demonstrating the profound roles that host-associated microbes play in many aspects of animal biology, such as immune function, endocrinology, and even behavior. It is our hope that integrative and comparative biologists will begin to include aspects of host-associated microbes into their research programs, enhancing both the fields of comparative biology and host-microbe interactions.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
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265
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López-Madrigal S, Gil R. Et tu, Brute? Not Even Intracellular Mutualistic Symbionts Escape Horizontal Gene Transfer. Genes (Basel) 2017; 8:genes8100247. [PMID: 28961177 PMCID: PMC5664097 DOI: 10.3390/genes8100247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/14/2017] [Accepted: 09/22/2017] [Indexed: 01/21/2023] Open
Abstract
Many insect species maintain mutualistic relationships with endosymbiotic bacteria. In contrast to their free-living relatives, horizontal gene transfer (HGT) has traditionally been considered rare in long-term endosymbionts. Nevertheless, meta-omics exploration of certain symbiotic models has unveiled an increasing number of bacteria-bacteria and bacteria-host genetic transfers. The abundance and function of transferred loci suggest that HGT might play a major role in the evolution of the corresponding consortia, enhancing their adaptive value or buffering detrimental effects derived from the reductive evolution of endosymbionts’ genomes. Here, we comprehensively review the HGT cases recorded to date in insect-bacteria mutualistic consortia, and discuss their impact on the evolutionary success of these associations.
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Affiliation(s)
- Sergio López-Madrigal
- Biologie Fonctionnelle Insectes et Interactions, UMR203 BF2I, INRA, INSA-Lyon, Université de Lyon, 69100 Villeurbanne, France.
| | - Rosario Gil
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC, 46980 Paterna (València), Spain.
- Departament de Genètica, Universitat de València, Dr. Moliner, 50, 46100 Burjassot (València), Spain.
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266
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An Overview on Marine Sponge-Symbiotic Bacteria as Unexhausted Sources for Natural Product Discovery. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040040] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Microbial symbiotic communities of marine macro-organisms carry functional metabolic profiles different to the ones found terrestrially and within surrounding marine environments. These symbiotic bacteria have increasingly been a focus of microbiologists working in marine environments due to a wide array of reported bioactive compounds of therapeutic importance resulting in various patent registrations. Revelations of symbiont-directed host specific functions and the true nature of host-symbiont interactions, combined with metagenomic advances detecting functional gene clusters, will inevitably open new avenues for identification and discovery of novel bioactive compounds of biotechnological value from marine resources. This review article provides an overview on bioactive marine symbiotic organisms with specific emphasis placed on the sponge-associated ones and invites the international scientific community to contribute towards establishment of in-depth information of the environmental parameters defining selection and acquisition of true symbionts by the host organisms.
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267
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Hydrothermal activity, functional diversity and chemoautotrophy are major drivers of seafloor carbon cycling. Sci Rep 2017; 7:12025. [PMID: 28931949 PMCID: PMC5607325 DOI: 10.1038/s41598-017-12291-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 09/07/2017] [Indexed: 11/09/2022] Open
Abstract
Hydrothermal vents are highly dynamic ecosystems and are unusually energy rich in the deep-sea. In situ hydrothermal-based productivity combined with sinking photosynthetic organic matter in a soft-sediment setting creates geochemically diverse environments, which remain poorly studied. Here, we use comprehensive set of new and existing field observations to develop a quantitative ecosystem model of a deep-sea chemosynthetic ecosystem from the most southerly hydrothermal vent system known. We find evidence of chemosynthetic production supplementing the metazoan food web both at vent sites and elsewhere in the Bransfield Strait. Endosymbiont-bearing fauna were very important in supporting the transfer of chemosynthetic carbon into the food web, particularly to higher trophic levels. Chemosynthetic production occurred at all sites to varying degrees but was generally only a small component of the total organic matter inputs to the food web, even in the most hydrothermally active areas, owing in part to a low and patchy density of vent-endemic fauna. Differences between relative abundance of faunal functional groups, resulting from environmental variability, were clear drivers of differences in biogeochemical cycling and resulted in substantially different carbon processing patterns between habitats.
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268
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Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora. Curr Biol 2017; 27:2763-2773.e5. [DOI: 10.1016/j.cub.2017.08.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/12/2017] [Accepted: 08/03/2017] [Indexed: 01/03/2023]
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269
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Gros O. First description of a new uncultured epsilon sulfur bacterium colonizing marine mangrove sediment in the Caribbean: Thiovulum sp. strain karukerense. FEMS Microbiol Lett 2017; 364:4067810. [DOI: 10.1093/femsle/fnx172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/04/2017] [Indexed: 01/06/2023] Open
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270
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Wasmund K, Mußmann M, Loy A. The life sulfuric: microbial ecology of sulfur cycling in marine sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:323-344. [PMID: 28419734 PMCID: PMC5573963 DOI: 10.1111/1758-2229.12538] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.
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Affiliation(s)
- Kenneth Wasmund
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
| | - Marc Mußmann
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
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271
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McCuaig B, Liboiron F, Dufour SC. The bivalve Thyasira cf. gouldi hosts chemoautotrophic symbiont populations with strain level diversity. PeerJ 2017; 5:e3597. [PMID: 28761786 PMCID: PMC5533157 DOI: 10.7717/peerj.3597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/29/2017] [Indexed: 11/20/2022] Open
Abstract
Invertebrates from various marine habitats form nutritional symbioses with chemosynthetic bacteria. In chemosynthetic symbioses, both the mode of symbiont transmission and the site of bacterial housing can affect the composition of the symbiont population. Vertically transmitted symbionts, as well as those hosted intracellularly, are more likely to form clonal populations within their host. Conversely, symbiont populations that are environmentally acquired and extracellular may be more likely to be heterogeneous/mixed within host individuals, as observed in some mytilid bivalves. The symbionts of thyasirid bivalves are also extracellular, but limited 16S rRNA sequencing data suggest that thyasirid individuals contain uniform symbiont populations. In a recent study, Thyasira cf. gouldi individuals from Bonne Bay, Newfoundland, Canada were found to host one of three 16S rRNA phylotypes of sulfur-oxidizing gammaproteobacteria, suggesting environmental acquisition of symbionts and some degree of site-specificity. Here, we use Sanger sequencing of both 16S RNA and the more variable ribulose-1,5-bisphosphate carboxylase (RuBisCO) PCR products to further examine Thyasira cf. gouldi symbiont diversity at the scale of host individuals, as well as to elucidate any temporal or spatial patterns in symbiont diversity within Bonne Bay, and relationships with host OTU or size. We obtained symbiont 16S rRNA and RuBisCO Form II sequences from 54 and 50 host individuals, respectively, during nine sampling trips to three locations over four years. Analyses uncovered the same three closely related 16S rRNA phylotypes obtained previously, as well as three divergent RuBisCO phylotypes; these were found in various pair combinations within host individuals, suggesting incidents of horizontal gene transfer during symbiont evolution. While we found no temporal patterns in phylotype distribution or relationships with host OTU or size, some spatial effects were noted, with some phylotypes only found within particular sampling sites. The sequencing also revealed symbiont populations within individual hosts that appeared to be a mixture of different phylotypes, based on multiple base callings at divergent sites. This work provides further evidence that Thyasira cf. gouldi acquires its symbionts from the environment, and supports the theory that hosts can harbour symbiont populations consisting of multiple, closely related bacterial phylotypes.
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Affiliation(s)
- Bonita McCuaig
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - France Liboiron
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
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272
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Heywood JL, Chen C, Pearce DA, Linse K. Bacterial communities associated with the Southern Ocean vent gastropod, Gigantopelta chessoia: indication of horizontal symbiont transfer. Polar Biol 2017. [DOI: 10.1007/s00300-017-2148-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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273
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Fisher RM, Henry LM, Cornwallis CK, Kiers ET, West SA. The evolution of host-symbiont dependence. Nat Commun 2017; 8:15973. [PMID: 28675159 PMCID: PMC5500886 DOI: 10.1038/ncomms15973] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/15/2017] [Indexed: 11/09/2022] Open
Abstract
Organisms across the tree of life form symbiotic partnerships with microbes for metabolism, protection and resources. While some hosts evolve extreme dependence on their symbionts, others maintain facultative associations. Explaining this variation is fundamental to understanding when symbiosis can lead to new higher-level individuals, such as during the evolution of the eukaryotic cell. Here we perform phylogenetic comparative analyses on 106 unique host-bacterial symbioses to test for correlations between symbiont function, transmission mode, genome size and host dependence. We find that both transmission mode and symbiont function are correlated with host dependence, with reductions in host fitness being greatest when nutrient-provisioning, vertically transmitted symbionts are removed. We also find a negative correlation between host dependence and symbiont genome size in vertically, but not horizontally, transmitted symbionts. These results suggest that both function and population structure are important in driving irreversible dependence between hosts and symbionts.
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Affiliation(s)
- Roberta M Fisher
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085-1087, 1081 HV Amsterdam, The Netherlands.,Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Lee M Henry
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - E Toby Kiers
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085-1087, 1081 HV Amsterdam, The Netherlands
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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274
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Chamberland VF, Latijnhouwers KRW, Huisman J, Hartmann AC, Vermeij MJA. Costs and benefits of maternally inherited algal symbionts in coral larvae. Proc Biol Sci 2017; 284:20170852. [PMID: 28659451 PMCID: PMC5489732 DOI: 10.1098/rspb.2017.0852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/26/2017] [Indexed: 12/21/2022] Open
Abstract
Many marine invertebrates provide their offspring with symbionts. Yet the consequences of maternally inherited symbionts on larval fitness remain largely unexplored. In the stony coral Favia fragum (Esper 1797), mothers produce larvae with highly variable amounts of endosymbiotic algae, and we examined the implications of this variation in symbiont density on the performance of F. fragum larvae under different environmental scenarios. High symbiont densities prolonged the period that larvae actively swam and searched for suitable settlement habitats. Thermal stress reduced survival and settlement success in F. fragum larvae, whereby larvae with high symbiont densities suffered more from non-lethal stress and were five times more likely to die compared with larvae with low symbiont densities. These results show that maternally inherited algal symbionts can be either beneficial or harmful to coral larvae depending on the environmental conditions at hand, and suggest that F. fragum mothers use a bet-hedging strategy to minimize risks associated with spatio-temporal variability in their offspring's environment.
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Affiliation(s)
- Valérie F Chamberland
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH Amsterdam, The Netherlands
- SECORE International, 4673 Northwest Parkway, Hilliard, OH 43026, USA
- CARMABI Foundation, PO Box 2090, Piscaderabaai z/n, Willemstad, Curaçao
| | - Kelly R W Latijnhouwers
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH Amsterdam, The Netherlands
| | - Jef Huisman
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH Amsterdam, The Netherlands
| | - Aaron C Hartmann
- Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Avenue NW, Washington, DC 20560, USA
- San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Mark J A Vermeij
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 700, 1098 XH Amsterdam, The Netherlands
- CARMABI Foundation, PO Box 2090, Piscaderabaai z/n, Willemstad, Curaçao
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275
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Oono R, Rasmussen A, Lefèvre E. Distance decay relationships in foliar fungal endophytes are driven by rare taxa. Environ Microbiol 2017. [PMID: 28640496 DOI: 10.1111/1462-2920.13799] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Foliar fungal endophytes represent a diverse and species-rich plant microbiome. Their biogeography provides essential clues to their cryptic relationship with hosts and the environment in which they disperse. We present species composition, diversity, and dispersal patterns of endophytic fungi associated with needles of Pinus taeda trees across regional scales in the absence of strong environmental gradients as well as within individual trees. An empirical designation of rare and abundant taxa enlightens us on the structure of endophyte communities. We report multiple distance-decay patterns consistent with effects of dispersal limitation, largely driven by community changes in rare taxa, those taxonomic units that made up less than 0.31% of reads per sample on average. Distance-decay rates and community structure also depended on specific classes of fungi and were predominantly influenced by rare members of Dothideomycetes. Communities separated by urban areas also revealed stronger effects of distance on community similarity, confirming that host density and diversity plays an important role in symbiont biogeography, which may ultimately lead to a mosaic of functional diversity as well as rare species diversity across landscapes.
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Affiliation(s)
- Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Anna Rasmussen
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Emilie Lefèvre
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708, USA
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276
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277
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Ho PT, Park E, Hong SG, Kim EH, Kim K, Jang SJ, Vrijenhoek RC, Won YJ. Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents. BMC Evol Biol 2017; 17:121. [PMID: 28558648 PMCID: PMC5450337 DOI: 10.1186/s12862-017-0966-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/12/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Chemolithoautotrophic primary production sustains dense invertebrate communities at deep-sea hydrothermal vents and hydrocarbon seeps. Symbiotic bacteria that oxidize dissolved sulfur, methane, and hydrogen gases nourish bathymodiolin mussels that thrive in these environments worldwide. The mussel symbionts are newly acquired in each generation via infection by free-living forms. This study examined geographical subdivision of the thiotrophic endosymbionts hosted by Bathymodiolus mussels living along the eastern Pacific hydrothermal vents. High-throughput sequencing data of 16S ribosomal RNA encoding gene and fragments of six protein-coding genes of symbionts were examined in the samples collected from nine vent localities at the East Pacific Rise, Galápagos Rift, and Pacific-Antarctic Ridge. RESULTS Both of the parapatric sister-species, B. thermophilus and B. antarcticus, hosted the same numerically dominant phylotype of thiotrophic Gammaproteobacteria. However, sequences from six protein-coding genes revealed highly divergent symbiont lineages living north and south of the Easter Microplate and hosted by these two Bathymodiolus mussel species. High heterogeneity of symbiont haplotypes among host individuals sampled from the same location suggested that stochasticity associated with initial infections was amplified as symbionts proliferated within the host individuals. The mussel species presently contact one another and hybridize along the Easter Microplate, but the northern and southern symbionts appear to be completely isolated. Vicariance associated with orogeny of the Easter Microplate region, 2.5-5.3 million years ago, may have initiated isolation of the symbiont and host populations. Estimates of synonymous substitution rates for the protein-coding bacterial genes examined in this study were 0.77-1.62%/nucleotide/million years. CONCLUSIONS Our present study reports the most comprehensive population genetic analyses of the chemosynthetic endosymbiotic bacteria based on high-throughput genetic data and extensive geographical sampling to date, and demonstrates the role of the geographical features, the Easter Microplate and geographical distance, in the intraspecific divergence of this bacterial species along the mid-ocean ridge axes in the eastern Pacific. Altogether, our results provide insights into extrinsic and intrinsic factors affecting the dispersal and evolution of chemosynthetic symbiotic partners in the hydrothermal vents along the eastern Pacific Ocean.
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Affiliation(s)
- Phuong-Thao Ho
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, 03760, Korea
| | - Eunji Park
- Division of EcoScience, Ewha Womans University, Seoul, 03760, Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Eun-Hye Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Kangchon Kim
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, 03760, Korea
| | - Sook-Jin Jang
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, 03760, Korea
| | | | - Yong-Jin Won
- Interdisciplinary Program of EcoCreative, The Graduate School, Ewha Womans University, Seoul, 03760, Korea. .,Division of EcoScience, Ewha Womans University, Seoul, 03760, Korea.
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278
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Identification and gene expression of multiple peptidoglycan recognition proteins (PGRPs) in the deep-sea mussel Bathymodiolus azoricus , involvement in symbiosis? Comp Biochem Physiol B Biochem Mol Biol 2017; 207:1-8. [DOI: 10.1016/j.cbpb.2017.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/20/2017] [Accepted: 02/09/2017] [Indexed: 11/17/2022]
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279
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Peptides, Peptidomimetics, and Polypeptides from Marine Sources: A Wealth of Natural Sources for Pharmaceutical Applications. Mar Drugs 2017; 15:md15040124. [PMID: 28441741 PMCID: PMC5408270 DOI: 10.3390/md15040124] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 01/07/2023] Open
Abstract
Nature provides a variety of peptides that are expressed in most living species. Evolutionary pressure and natural selection have created and optimized these peptides to bind to receptors with high affinity. Hence, natural resources provide an abundant chemical space to be explored in peptide-based drug discovery. Marine peptides can be extracted by simple solvent extraction techniques. The advancement of analytical techniques has made it possible to obtain pure peptides from natural resources. Extracted peptides have been evaluated as possible therapeutic agents for a wide range of diseases, including antibacterial, antifungal, antidiabetic and anticancer activity as well as cardiovascular and neurotoxin activity. Although marine resources provide thousands of possible peptides, only a few peptides derived from marine sources have reached the pharmaceutical market. This review focuses on some of the peptides derived from marine sources in the past ten years and gives a brief review of those that are currently in clinical trials or on the market.
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280
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Discovery of chemoautotrophic symbiosis in the giant shipworm Kuphus polythalamia (Bivalvia: Teredinidae) extends wooden-steps theory. Proc Natl Acad Sci U S A 2017; 114:E3652-E3658. [PMID: 28416684 DOI: 10.1073/pnas.1620470114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The "wooden-steps" hypothesis [Distel DL, et al. (2000) Nature 403:725-726] proposed that large chemosynthetic mussels found at deep-sea hydrothermal vents descend from much smaller species associated with sunken wood and other organic deposits, and that the endosymbionts of these progenitors made use of hydrogen sulfide from biogenic sources (e.g., decaying wood) rather than from vent fluids. Here, we show that wood has served not only as a stepping stone between habitats but also as a bridge between heterotrophic and chemoautotrophic symbiosis for the giant mud-boring bivalve Kuphus polythalamia This rare and enigmatic species, which achieves the greatest length of any extant bivalve, is the only described member of the wood-boring bivalve family Teredinidae (shipworms) that burrows in marine sediments rather than wood. We show that K. polythalamia harbors sulfur-oxidizing chemoautotrophic (thioautotrophic) bacteria instead of the cellulolytic symbionts that allow other shipworm species to consume wood as food. The characteristics of its symbionts, its phylogenetic position within Teredinidae, the reduction of its digestive system by comparison with other family members, and the loss of morphological features associated with wood digestion indicate that K. polythalamia is a chemoautotrophic bivalve descended from wood-feeding (xylotrophic) ancestors. This is an example in which a chemoautotrophic endosymbiosis arose by displacement of an ancestral heterotrophic symbiosis and a report of pure culture of a thioautotrophic endosymbiont.
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281
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Sun J, Zhang Y, Xu T, Zhang Y, Mu H, Zhang Y, Lan Y, Fields CJ, Hui JHL, Zhang W, Li R, Nong W, Cheung FKM, Qiu JW, Qian PY. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nat Ecol Evol 2017; 1:121. [PMID: 28812709 DOI: 10.1038/s41559-017-0121] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/16/2017] [Indexed: 01/08/2023]
Abstract
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro-benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilizing protein structures and removing toxic substances from cells, are highly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The innate immune system of B. platifrons is considerably more complex than that of other lophotrochozoan species, including M. philippinarum, with substantial expansion and high expression levels of gene families that are related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons shows methanotrophy, assimilatory sulfate reduction and ammonia metabolic pathways in the symbionts, providing energy and nutrients, which allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.
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Affiliation(s)
- Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.,Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yu Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Science, Shenzhen University, Shenzhen, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yi Lan
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Christopher J Fields
- High Performance Computing in Biology, Roy J. Carver Biotechnology Centre, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jerome Ho Lam Hui
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong, China
| | - Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Wenyan Nong
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong, China
| | - Fiona Ka Man Cheung
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.,HKUST-CAS Joint Laboratory, Sanya Institute of Deep Sea Science and Engineering, Sanya 572000, China
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282
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Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge. mSystems 2017; 2:mSystems00184-16. [PMID: 28345060 PMCID: PMC5361782 DOI: 10.1128/msystems.00184-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/09/2017] [Indexed: 12/20/2022] Open
Abstract
Sponges and their symbionts are important players in the biogeochemical cycles of marine environments. As a unique habitat within marine ecosystems, cold seeps have received considerable interest in recent years. This study explores the lifestyle of a new symbiotic SOB in a cold seep sponge. The results demonstrate that both this sponge symbiont and endosymbionts in deep-sea clams employ similar strategies of genome reduction. However, this bacterium has retained unique functions for immunity and defense. Thus, the functional features are determined by both the symbiotic relationship and host type. Moreover, analyses of the genome of an AOA suggest that microbes play different roles in biochemical cycles in the sponge body. Our findings provide new insights into invertebrate-associated bacteria in cold seep environments. As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored “differential coverage binning” method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed “Gsub”) may represent a new deep-sea SOB group. Microscopic observations suggest that Gsub is probably an extracellular symbiont. Gsub has complete sulfide oxidation and carbon fixation pathways, suggesting a chemoautotrophic lifestyle. Comparative genomics with other sponge-associated SOB and free-living SOB revealed significant genome reduction in Gsub, characterized by the loss of genes for carbohydrate metabolism, motility, DNA repair, and osmotic stress response. Intriguingly, this scenario of genome reduction is highly similar to those of the endosymbionts in deep-sea clams. However, Gsub has retained genes for phage defense and protein secretion, with the latter potentially playing a role in interactions with the sponge host. In addition, we recovered the genome of an ammonia-oxidizing archaeon (AOA), which may carry out ammonia oxidation and carbon fixation within the sponge body. IMPORTANCE Sponges and their symbionts are important players in the biogeochemical cycles of marine environments. As a unique habitat within marine ecosystems, cold seeps have received considerable interest in recent years. This study explores the lifestyle of a new symbiotic SOB in a cold seep sponge. The results demonstrate that both this sponge symbiont and endosymbionts in deep-sea clams employ similar strategies of genome reduction. However, this bacterium has retained unique functions for immunity and defense. Thus, the functional features are determined by both the symbiotic relationship and host type. Moreover, analyses of the genome of an AOA suggest that microbes play different roles in biochemical cycles in the sponge body. Our findings provide new insights into invertebrate-associated bacteria in cold seep environments.
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283
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Kerwin AH, Nyholm SV. Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs. Environ Microbiol 2017; 19:1463-1475. [DOI: 10.1111/1462-2920.13665] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/07/2016] [Accepted: 01/02/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Allison H. Kerwin
- Department of Molecular and Cell Biology; University of Connecticut; CT 06269 USA
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology; University of Connecticut; CT 06269 USA
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284
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Thornhill DJ, Howells EJ, Wham DC, Steury TD, Santos SR. Population genetics of reef coral endosymbionts (Symbiodinium
, Dinophyceae). Mol Ecol 2017; 26:2640-2659. [DOI: 10.1111/mec.14055] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 01/02/2023]
Affiliation(s)
- D. J. Thornhill
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies; Auburn University; 101 Rouse Life Sciences Building Auburn AL 36849 USA
| | - E. J. Howells
- Center for Genomics and Systems Biology; New York University Abu Dhabi; PO Box 129188 Abu Dhabi United Arab Emirates
| | - D. C. Wham
- Department of Biology; Pennsylvania State University; 208 Mueller Laboratory University Park PA 16802 USA
| | - T. D. Steury
- School of Forestry and Wildlife Sciences; Auburn University; 3301 Forestry and Wildlife Building Auburn AL 36849 USA
| | - S. R. Santos
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies; Auburn University; 101 Rouse Life Sciences Building Auburn AL 36849 USA
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285
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Chen C, Uematsu K, Linse K, Sigwart JD. By more ways than one: Rapid convergence at hydrothermal vents shown by 3D anatomical reconstruction of Gigantopelta (Mollusca: Neomphalina). BMC Evol Biol 2017; 17:62. [PMID: 28249568 PMCID: PMC5333402 DOI: 10.1186/s12862-017-0917-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/17/2017] [Indexed: 02/03/2023] Open
Abstract
Background Extreme environments prompt the evolution of characteristic adaptations. Yet questions remain about whether radiations in extreme environments originate from a single lineage that masters a key adaptive pathway, or if the same features can arise in parallel through convergence. Species endemic to deep-sea hydrothermal vents must accommodate high temperature and low pH. The most successful vent species share a constrained pathway to successful energy exploitation: hosting symbionts. The vent-endemic gastropod genus Gigantopelta, from the Southern and Indian Oceans, shares unusual features with a co-occurring peltospirid, the ‘scaly-foot gastropod’ Chrysomallon squamiferum. Both are unusually large for the clade and share other adaptive features such as a prominent enlarged trophosome-like oesophageal gland, not found in any other vent molluscs. Results Transmission electron microscopy confirmed endosymbiont bacteria in the oesophageal gland of Gigantopelta, as also seen in Chrysomallon. They are the only known members of their phylum in vent ecosystems hosting internal endosymbionts; other vent molluscs host endosymbionts in or on their gills, or in the mantle cavity. A five-gene phylogenetic reconstruction demonstrated that Gigantopelta and Chrysomallon are not phylogenetically sister-taxa, despite their superficial similarity. Both genera have specialist adaptations to accommodate internalised endosymbionts, but with anatomical differences that indicate separate evolutionary origins. Hosting endosymbionts in an internal organ within the host means that all resources required by the bacteria must be supplied by the animal, rather than directly by the vent fluid. Unlike Chrysomallon, which has an enlarged oesophageal gland throughout post-settlement life, the oesophageal gland in Gigantopelta is proportionally much smaller in juveniles and the animals likely undergo a trophic shift during ontogeny. The circulatory system is hypertrophied in both but the overall size is smaller in Gigantopelta. In contrast with Chrysomallon, Gigantopelta possesses true ganglia and is gonochoristic. Conclusions Key anatomical differences between Gigantopelta and Chrysomallon demonstrate these two genera acquired a similar way of life through independent and convergent adaptive pathways. What appear to be the holobiont’s adaptations to an extreme environment, are driven by optimising bacteria’s access to vent nutrients. By comparing Gigantopelta and Chrysomallon, we show that metazoans are capable of rapidly and repeatedly evolving equivalent anatomical adaptations and close-knit relationships with chemoautotrophic bacteria, achieving the same end-product through parallel evolutionary trajectories. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0917-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chong Chen
- Marine Laboratory, Queen's University Belfast, 12-13 The Strand, Portaferry, Northern Ireland. .,Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Katsuyuki Uematsu
- Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka, 237-0063, Japan
| | - Katrin Linse
- British Antarctic Survey, High Cross, Cambridge, UK
| | - Julia D Sigwart
- Marine Laboratory, Queen's University Belfast, 12-13 The Strand, Portaferry, Northern Ireland.,Berkeley, Museum of Paleontology, University of California, VLSB 1101, Berkeley, CA, 94720, USA
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286
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Wang R, Seyedsayamdost MR. Opinion: Hijacking exogenous signals to generate new secondary metabolites during symbiotic interactions. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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287
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López-García P, Eme L, Moreira D. Symbiosis in eukaryotic evolution. J Theor Biol 2017; 434:20-33. [PMID: 28254477 DOI: 10.1016/j.jtbi.2017.02.031] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/19/2017] [Accepted: 02/25/2017] [Indexed: 01/27/2023]
Abstract
Fifty years ago, Lynn Margulis, inspiring in early twentieth-century ideas that put forward a symbiotic origin for some eukaryotic organelles, proposed a unified theory for the origin of the eukaryotic cell based on symbiosis as evolutionary mechanism. Margulis was profoundly aware of the importance of symbiosis in the natural microbial world and anticipated the evolutionary significance that integrated cooperative interactions might have as mechanism to increase cellular complexity. Today, we have started fully appreciating the vast extent of microbial diversity and the importance of syntrophic metabolic cooperation in natural ecosystems, especially in sediments and microbial mats. Also, not only the symbiogenetic origin of mitochondria and chloroplasts has been clearly demonstrated, but improvement in phylogenomic methods combined with recent discoveries of archaeal lineages more closely related to eukaryotes further support the symbiogenetic origin of the eukaryotic cell. Margulis left us in legacy the idea of 'eukaryogenesis by symbiogenesis'. Although this has been largely verified, when, where, and specifically how eukaryotic cells evolved are yet unclear. Here, we shortly review current knowledge about symbiotic interactions in the microbial world and their evolutionary impact, the status of eukaryogenetic models and the current challenges and perspectives ahead to reconstruct the evolutionary path to eukaryotes.
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Affiliation(s)
- Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France.
| | - Laura Eme
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada NS B3H 4R2
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
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288
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Miyamoto N, Yoshida MA, Koga H, Fujiwara Y. Genetic mechanisms of bone digestion and nutrient absorption in the bone-eating worm Osedax japonicus inferred from transcriptome and gene expression analyses. BMC Evol Biol 2017; 17:17. [PMID: 28086748 PMCID: PMC5237233 DOI: 10.1186/s12862-016-0844-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 12/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bone-eating worms of the genus Osedax (Annelida, Siboglinidae) have adapted to whale fall environments by acquiring a novel characteristic called the root, which branches and penetrates into sunken bones. The worms lack a digestive tract and mouth opening, and it has been suggested that Osedax degrade vertebrate bones and uptake nutrients through acidification and secretion of enzymes from the root. Symbiotic bacteria in the root tissue may have a crucial role in the metabolism of Osedax. However, the molecular mechanisms and cells responsible for bone digestion and nutrient uptake are still unclear, and information on the metabolic interaction between Osedax and symbiotic bacteria is limited. RESULTS We compared transcriptomes from three different RNA samples from the following tissues: trunk + palps, root + ovisac, and larva + male. A Pfam domain enrichment analysis revealed that protease- and transporter-related genes were enriched in the root + ovisac specific genes compared with the total transcriptome. Through targeted gene annotation we found gene family expansions resulting in a remarkably large number of matrix metalloproteinase (mmp) genes in the Osedax compared with other invertebrates. Twelve of these Osedax mmp genes were expressed in the root epidermal cells. Genes encoding various types of transporters, including amino acid, oligopeptide, bicarbonate, and sulfate/carboxylate transporters, were also expressed in root epidermal cells. In addition, amino acid and other metabolite transporter genes were expressed in bacteriocytes. These protease and transporter genes were first expressed in root tissues at the juvenile stage, when the root starts to develop. CONCLUSIONS The expression of various proteinase and transporter genes in the root epidermis supports the theory that the root epidermal cells are responsible for bone digestion and subsequent nutrient uptake. Expression of transporter genes in the host bacteriocytes suggests the presence of metabolic interaction between Osedax and symbiotic bacteria.
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Affiliation(s)
- Norio Miyamoto
- Japan Agency for Marine-Earth Science and Techonology, Yokosuka, Kanagawa, Japan.
| | - Masa-Aki Yoshida
- National Institute of Genetics, Mishima, Shizuoka, Japan.,Postodoctral research fellow, Japanese Society for Promotion of Science, Tokyo, Japan
| | - Hiroyuki Koga
- Postodoctral research fellow, Japanese Society for Promotion of Science, Tokyo, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshihiro Fujiwara
- Japan Agency for Marine-Earth Science and Techonology, Yokosuka, Kanagawa, Japan
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289
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Petersen JM. Ecology and Fisheries: Dark Carbon on Your Dinner Plate. Curr Biol 2016; 26:R1277-R1279. [PMID: 27997838 DOI: 10.1016/j.cub.2016.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chemosynthetic primary production by symbiotic microbes powers entire ecosystems in the remote deep sea. New research shows that in shallow waters chemosynthetic symbioses can contribute substantially to a vital economic resource - lobster fisheries in the Caribbean Sea.
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Affiliation(s)
- Jillian M Petersen
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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290
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Johnson SB, Krylova EM, Audzijonyte A, Sahling H, Vrijenhoek RC. Phylogeny and origins of chemosynthetic vesicomyid clams. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1252438] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shannon B. Johnson
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
| | - Elena M. Krylova
- P.P. Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovskii prospect 36, 117997 Moscow, Russia
| | - Asta Audzijonyte
- Fisheries and Environmental Management Group, Department of Environmental Sciences, University of Helsinki, Viikinaari 2, P.O. Box 65, FIN-00014, Finland
| | - Heiko Sahling
- MARUM – Center for Marine Environment Sciences and Faculty of Geosciences, University of Bremen, Klagenfurter Str., 28359 Bremen, Germany
| | - Robert C. Vrijenhoek
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
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291
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Caribbean Spiny Lobster Fishery Is Underpinned by Trophic Subsidies from Chemosynthetic Primary Production. Curr Biol 2016; 26:3393-3398. [PMID: 27939312 DOI: 10.1016/j.cub.2016.10.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/16/2016] [Accepted: 10/19/2016] [Indexed: 11/22/2022]
Abstract
The Caribbean spiny lobster, Panulirus argus, is one of the most valuable fisheries commodities in the Central American region, directly employing 50,000 people and generating >US$450 million per year [1]. This industry is particularly important to small island states such as The Bahamas, which exports more lobster than any other country in the region [1]. Several factors contribute to this disproportionally high productivity, principally the extensive shallow-water banks covered in seagrass meadows [2], where fishermen deploy artificial shelters for the lobsters to supplement scarce reef habitat [3]. The surrounding seabed communities are dominated by lucinid bivalve mollusks that live among the seagrass root system [4, 5]. These clams host chemoautotrophic bacterial symbionts in their gills that synthesize organic matter using reduced sulfur compounds, providing nutrition to their hosts [6]. Recent studies have highlighted the important role of the lucinid clam symbiosis in maintaining the health and productivity of seagrass ecosystems [7, 8], but their biomass also represents a potentially abundant, but as yet unquantified, food source to benthic predators [9]. Here we undertake the first analysis of Caribbean spiny lobster diet using a stable isotope approach (carbon, nitrogen, and sulfur) and show that a significant portion of their food (∼20% on average) is obtained from chemosynthetic primary production in the form of lucinid clams. This nutritional pathway was previously unrecognized in the spiny lobster's diet, and these results are the first empirical evidence that chemosynthetic primary production contributes to the productivity of commercial fisheries stocks.
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292
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Tobler M, Passow CN, Greenway R, Kelley JL, Shaw JH. The Evolutionary Ecology of Animals Inhabiting Hydrogen Sulfide–Rich Environments. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032418] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydrogen sulfide (H2S) is a respiratory toxicant that creates extreme environments tolerated by few organisms. H2S is also produced endogenously by metazoans and plays a role in cell signaling. The mechanisms of H2S toxicity and its physiological functions serve as a basis to discuss the multifarious strategies that allow animals to survive in H2S-rich environments. Despite their toxicity, H2S-rich environments also provide ecological opportunities, and complex selective regimes of covarying abiotic and biotic factors drive trait evolution in organisms inhabiting H2S-rich environments. Furthermore, adaptation to H2S-rich environments can drive speciation, giving rise to biodiversity hot spots with high levels of endemism in deep-sea hydrothermal vents, cold seeps, and freshwater sulfide springs. The diversity of H2S-rich environments and their inhabitants provides ideal systems for comparative studies of the effects of a clear-cut source of selection across vast geographic and phylogenetic scales, ultimately informing our understanding of how environmental stressors affect ecological and evolutionary processes.
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Affiliation(s)
- Michael Tobler
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | | | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Jennifer H. Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078
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293
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Petersen JM, Kemper A, Gruber-Vodicka H, Cardini U, van der Geest M, Kleiner M, Bulgheresi S, Mußmann M, Herbold C, Seah BKB, Antony CP, Liu D, Belitz A, Weber M. Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation. Nat Microbiol 2016; 2:16195. [PMID: 27775707 PMCID: PMC6872982 DOI: 10.1038/nmicrobiol.2016.195] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/07/2016] [Indexed: 12/04/2022]
Abstract
Chemosynthetic symbioses are partnerships between invertebrate animals
and chemosynthetic bacteria. The latter are the primary producers, providing most of
the organic carbon needed for the animal host's nutrition. We sequenced genomes of
the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species
encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic
symbiont was previously known to be capable of nitrogen fixation. We detected
nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and
proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric
nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability
to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic
habitats, where nitrogen availability often limits primary productivity. The chemosynthetic symbionts of the bivalve Loripes lucinalis and nematode Laxus
oneistus are found to encode nitrogen fixation genes, with evidence for
active nitrogen fixation.
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Affiliation(s)
- Jillian M Petersen
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria.,Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Anna Kemper
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Ulisse Cardini
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Matthijs van der Geest
- Centre for Marine Biodiversity, Exploitation and Conservation (MARBEC), UMR 9190, IRD-IFREMER-CNRS-UM, Université de Montpellier, Montpellier Cedex 5 34095, France.,Department of Coastal Systems and Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Manuel Kleiner
- Department of Geoscience, University of Calgary, 2500 University Drive Northwest, Alberta T2N 1N4, Canada
| | - Silvia Bulgheresi
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Marc Mußmann
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Craig Herbold
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Brandon K B Seah
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Chakkiath Paul Antony
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Dan Liu
- Department of Geoscience, University of Calgary, 2500 University Drive Northwest, Alberta T2N 1N4, Canada
| | - Alexandra Belitz
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Miriam Weber
- HYDRA Institute for Marine Sciences, Elba Field Station, Campo nell'Elba, Livorno 54037, Italy
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294
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Kopac SM, Klassen JL. Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche. Front Microbiol 2016; 7:1647. [PMID: 27818648 PMCID: PMC5073103 DOI: 10.3389/fmicb.2016.01647] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/04/2016] [Indexed: 11/18/2022] Open
Abstract
Virtually all multicellular organisms host a community of symbionts composed of mutualistic, commensal, and pathogenic microbes, i.e., their microbiome. The mechanism of selection on host-microbe assemblages remains contentious, particularly regarding whether selection acts differently on hosts and their microbial symbionts. Here, we attempt to reconcile these viewpoints using a model that describes how hosts and their microbial symbionts alter each other's niche and thereby fitness. We describe how host-microbe interactions might change the shape of the host niche and/or reproductive rates within it, which are directly related to host fitness. A host may also alter the niche of a symbiotic microbe, although this depends on the extent to which that microbe is dependent on the host for reproduction. Finally, we provide a mathematical model to test whether interactions between hosts and microbes are necessary to describe the niche of either partner. Our synthesis highlights the phenotypic effects of host-microbe interactions while respecting the unique lifestyles of each partner, and thereby provides a unified framework to describe how selection might act on a host that is associated with its microbiome.
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Affiliation(s)
| | - Jonathan L. Klassen
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT, USA
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295
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Ozawa G, Shimamura S, Takaki Y, Yokobori SI, Ohara Y, Takishita K, Maruyama T, Fujikura K, Yoshida T. Updated mitochondrial phylogeny of Pteriomorph and Heterodont Bivalvia, including deep-sea chemosymbiotic Bathymodiolus mussels, vesicomyid clams and the thyasirid clam Conchocele cf. bisecta. Mar Genomics 2016; 31:43-52. [PMID: 27720682 DOI: 10.1016/j.margen.2016.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/22/2016] [Accepted: 09/22/2016] [Indexed: 10/20/2022]
Abstract
The mitochondrial genomes of bivalves have often been used for comparative genomics and for resolving phylogenetic relationships. More than 100 bivalve complete mitochondrial genomes have been sequenced to date. However, few mitochondrial genomes have been reported for deep-sea chemosymbiotic bivalves, which belong to the subclasses Pteriomorphia and Heterodonta. In the present study, we sequenced the mitochondrial genomes of eight deep-sea chemosymbiotic bivalve species: three species of Bathymodiolus mussels (B. japonicus, B. platifrons, and B. septemdierum), four species of vesicomyid clams (Abyssogena mariana, A. phaseoliformis, Isorropodon fossajaponicum, and Phreagena okutanii, all of which were formerly classified in the genus Calyptogena), and one species of thyasirid clam (Conchocele cf. bisecta). With a few exceptions, these mitochondrial genomes contained genes that are typical of metazoans: 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The major non-coding region with a high A+T content of each genome, which contained tandem repeats and hairpins, was hypothesized to function as a control region. The phylogenetic trees of Pteriomorphia and Heterodonta were reconstructed based on the concatenated sequences of 14 shared genes. Bathymodiolus formed a monophyletic clade with asymbiotic Mytilidae mussels, the vesicomyid clams formed a monophyly that was sister to the Veneridae, and C. cf. bisecta branched basally in the Heterodonta. It is known that the gene orders of mitochondrial genomes vary among bivalves. To examine whether gene order variation exhibits phylogenetic signals, tree topologies based on the minimum number of gene rearrangements were reconstructed for two clades (superfamily Tellinoidea, which includes the Psammobiidae, Semelidae, Solecurtidae, and Tellinidae; and the clade comprising the Myidae, Mactridae, Arcticidae, Vesicomyidae, and Veneridae) with high statistical support in sequence-based phylogenies. The resulting tree topologies were almost identical to those of the sequence-based trees. Our present findings suggest that the evolution of bivalves could be precisely traced back through the analysis of mitochondrial genomes, and that such an analysis could contribute to understanding bivalve evolution and diversity.
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Affiliation(s)
- Genki Ozawa
- Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Shigeru Shimamura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Shin-Ichi Yokobori
- Laboratory of Cellular Biochemistry, Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
| | - Yasuhiko Ohara
- Hydrographic and Oceanographic Department of Japan, 3-1-1, Kasumigaseki, Chiyoda-ku, Tokyo 100-8932, Japan.
| | - Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Katsunori Fujikura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Takao Yoshida
- Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
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296
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Assié A, Borowski C, van der Heijden K, Raggi L, Geier B, Leisch N, Schimak MP, Dubilier N, Petersen JM. A specific and widespread association between deep-sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:805-813. [PMID: 27428292 DOI: 10.1111/1758-2229.12442] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/13/2016] [Indexed: 06/06/2023]
Abstract
Bathymodiolus mussels dominate animal communities at many hydrothermal vents and cold seeps. Essential to the mussels' ecological and evolutionary success is their association with symbiotic methane- and sulfur-oxidizing gammaproteobacteria, which provide them with nutrition. In addition to these well-known gammaproteobacterial endosymbionts, we found epsilonproteobacterial sequences in metatranscriptomes, metagenomes and 16S rRNA clone libraries as well as by polymerase chain reaction screening of Bathymodiolus species sampled from vents and seeps around the world. These epsilonproteobacterial sequences were closely related, indicating that the association is highly specific. The Bathymodiolus-associated epsilonproteobacterial 16S rRNA sequences were at most 87.6% identical to the closest cultured relative, and 91.2% identical to the closest sequences in public databases. This clade therefore represents a novel family within the Epsilonproteobacteria. Fluorescence in situ hybridization and transmission electron microscopy showed that the bacteria are filamentous epibionts associated with the gill epithelia in two Bathymodiolus species. In animals that host highly specific symbioses with one or a few types of endosymbionts, other less-abundant members of the microbiota can be easily overlooked. Our work highlights how widespread and specific associations with less-abundant microbes can be. Possibly, these microbes play an important role in the survival and health of their animal hosts.
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Affiliation(s)
- Adrien Assié
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Christian Borowski
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | | | - Luciana Raggi
- CIGoM, Instituto de Biotecnologia, UNAM, Av. Universidad 2001, C.P.62210, Cuernavaca, Morelos, Mexico
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Nikolaus Leisch
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Mario P Schimak
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
- MARUM, University of Bremen, Germany
| | - Jillian M Petersen
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, 28359, Germany
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, 1090, Austria
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297
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van Kessel MAHJ, Mesman RJ, Arshad A, Metz JR, Spanings FAT, van Dalen SCM, van Niftrik L, Flik G, Wendelaar Bonga SE, Jetten MSM, Klaren PHM, Op den Camp HJM. Branchial nitrogen cycle symbionts can remove ammonia in fish gills. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:590-594. [PMID: 27040730 DOI: 10.1111/1758-2229.12407] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/18/2016] [Indexed: 06/05/2023]
Abstract
Knowledge of the mechanisms by which fish excrete their metabolic nitrogenous waste and insights into nitrogen cycling in aquaculture systems is of utmost importance to improve the sustainable commercial production of fish. In fish, most nitrogenous waste is excreted via the gills as ammonia, a potentially toxic nitrogenous compound. In this study; activity assays, physiological experiments, molecular analysis and microscopy were used to show that the gills of fish harbor a unique combination of hitherto overlooked nitrogen-cycle microorganisms that can theoretically detoxify excreted ammonia by converting it into inert dinitrogen gas. By doing so, these microorganisms may benefit from the ammonia supply by the host and prevent the build-up of this compound to toxic concentrations. This novel relationship between vertebrates and microorganisms may shed new light on nitrogen handling by ammonotelic fish species.
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Affiliation(s)
- Maartje A H J van Kessel
- Departments of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
- Organismal Animal Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Rob J Mesman
- Departments of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Arslan Arshad
- Departments of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Juriaan R Metz
- Organismal Animal Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - F A Tom Spanings
- Organismal Animal Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Stephanie C M van Dalen
- Organismal Animal Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Laura van Niftrik
- Departments of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Gert Flik
- Organismal Animal Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Sjoerd E Wendelaar Bonga
- Ecology and Ecophysiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Departments of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Peter H M Klaren
- Organismal Animal Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Departments of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
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298
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Affiliation(s)
- Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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299
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Portail M, Olu K, Dubois SF, Escobar-Briones E, Gelinas Y, Menot L, Sarrazin J. Food-Web Complexity in Guaymas Basin Hydrothermal Vents and Cold Seeps. PLoS One 2016; 11:e0162263. [PMID: 27683216 PMCID: PMC5040445 DOI: 10.1371/journal.pone.0162263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 08/20/2016] [Indexed: 11/29/2022] Open
Abstract
In the Guaymas Basin, the presence of cold seeps and hydrothermal vents in close proximity, similar sedimentary settings and comparable depths offers a unique opportunity to assess and compare the functioning of these deep-sea chemosynthetic ecosystems. The food webs of five seep and four vent assemblages were studied using stable carbon and nitrogen isotope analyses. Although the two ecosystems shared similar potential basal sources, their food webs differed: seeps relied predominantly on methanotrophy and thiotrophy via the Calvin-Benson-Bassham (CBB) cycle and vents on petroleum-derived organic matter and thiotrophy via the CBB and reductive tricarboxylic acid (rTCA) cycles. In contrast to symbiotic species, the heterotrophic fauna exhibited high trophic flexibility among assemblages, suggesting weak trophic links to the metabolic diversity of chemosynthetic primary producers. At both ecosystems, food webs did not appear to be organised through predator-prey links but rather through weak trophic relationships among co-occurring species. Examples of trophic or spatial niche differentiation highlighted the importance of species-sorting processes within chemosynthetic ecosystems. Variability in food web structure, addressed through Bayesian metrics, revealed consistent trends across ecosystems. Food-web complexity significantly decreased with increasing methane concentrations, a common proxy for the intensity of seep and vent fluid fluxes. Although high fluid-fluxes have the potential to enhance primary productivity, they generate environmental constraints that may limit microbial diversity, colonisation of consumers and the structuring role of competitive interactions, leading to an overall reduction of food-web complexity and an increase in trophic redundancy. Heterogeneity provided by foundation species was identified as an additional structuring factor. According to their biological activities, foundation species may have the potential to partly release the competitive pressure within communities of low fluid-flux habitats. Finally, ecosystem functioning in vents and seeps was highly similar despite environmental differences (e.g. physico-chemistry, dominant basal sources) suggesting that ecological niches are not specifically linked to the nature of fluids. This comparison of seep and vent functioning in the Guaymas basin thus provides further supports to the hypothesis of continuity among deep-sea chemosynthetic ecosystems.
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Affiliation(s)
- Marie Portail
- Laboratoire Environnement Profond, REM/EEP, Institut Carnot Ifremer EDROME, Centre de Bretagne, Plouzané, France
- * E-mail:
| | - Karine Olu
- Laboratoire Environnement Profond, REM/EEP, Institut Carnot Ifremer EDROME, Centre de Bretagne, Plouzané, France
| | - Stanislas F. Dubois
- Laboratoire Ecologie Benthique, DYNECO, Ifremer, Centre de Bretagne, Plouzané, France
| | - Elva Escobar-Briones
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City D.F., Mexico
| | - Yves Gelinas
- GEOTOP and Chemistry and Biochemistry Department, Concordia University, Montréal, Québec, Canada
| | - Lénaick Menot
- Laboratoire Environnement Profond, REM/EEP, Institut Carnot Ifremer EDROME, Centre de Bretagne, Plouzané, France
| | - Jozée Sarrazin
- Laboratoire Environnement Profond, REM/EEP, Institut Carnot Ifremer EDROME, Centre de Bretagne, Plouzané, France
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300
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A Novel Colonial Ciliate Zoothamnium ignavum sp. nov. (Ciliophora, Oligohymenophorea) and Its Ectosymbiont Candidatus Navis piranensis gen. nov., sp. nov. from Shallow-Water Wood Falls. PLoS One 2016; 11:e0162834. [PMID: 27683199 PMCID: PMC5040259 DOI: 10.1371/journal.pone.0162834] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/29/2016] [Indexed: 12/04/2022] Open
Abstract
Symbioses between ciliate hosts and prokaryote or unicellular eukaryote symbionts are widespread. Here, we report on a novel ciliate species within the genus Zoothamnium Bory de St. Vincent, 1824, isolated from shallow-water sunken wood in the North Adriatic Sea (Mediterranean Sea), proposed as Zoothamnium ignavum sp. nov. We found this ciliate species to be associated with a novel genus of bacteria, here proposed as “Candidatus Navis piranensis” gen. nov., sp. nov. The descriptions of host and symbiont species are based on morphological and ultrastructural studies, the SSU rRNA sequences, and in situ hybridization with symbiont-specific probes. The host is characterized by alternate microzooids on alternate branches arising from a long, common stalk with an adhesive disc. Three different types of zooids are present: microzooids with a bulgy oral side, roundish to ellipsoid macrozooids, and terminal zooids ellipsoid when dividing or bulgy when undividing. The oral ciliature of the microzooids runs 1¼ turns in a clockwise direction around the peristomial disc when viewed from inside the cell and runs into the infundibulum, where it makes another ¾ turn. The ciliature consists of a paroral membrane (haplokinety), three adoral membranelles (polykineties), and one stomatogenic kinety (germinal kinety). One circular row of barren kinetosomes is present aborally (trochal band). Phylogenetic analyses placed Z. ignavum sp. nov. within the clade II of the polyphyletic family Zoothamniidae (Oligohymenophorea). The ectosymbiont was found to occur in two different morphotypes, as rods with pointed ends and coccoid rods. It forms a monophyletic group with two uncultured Gammaproteobacteria within an unclassified group of Gammaproteobacteria, and is only distantly related to the ectosymbiont of the closely related peritrich Z. niveum (Hemprich and Ehrenberg, 1831) Ehrenberg, 1838.
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