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Maslin M, Paix B, van der Windt N, Ambo-Rappe R, Debitus C, Gaertner-Mazouni N, Ho R, de Voogd NJ. Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial. Antonie Van Leeuwenhoek 2024; 117:65. [PMID: 38602593 PMCID: PMC11008079 DOI: 10.1007/s10482-024-01962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.
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Affiliation(s)
- Mathilde Maslin
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Benoît Paix
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
| | - Niels van der Windt
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
| | - Rohani Ambo-Rappe
- Faculty of Marine Science and Fisheries, Department of Marine Science, Hasanuddin University, Makassar, Indonesia
| | - Cécile Debitus
- IRD, Univ Brest, CNRS, Ifremer, LEMAR, 29280, Plouzané, France
| | | | - Raimana Ho
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
- Institute of Biology (IBL), Leiden University, 2333 BE, PO Box 9505, Leiden, the Netherlands.
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Cleary DFR, de Voogd NJ, Stuij TM, Swierts T, Oliveira V, Polónia ARM, Louvado A, Gomes NCM, Coelho FJRC. A Study of Sponge Symbionts from Different Light Habitats. MICROBIAL ECOLOGY 2023; 86:2819-2837. [PMID: 37597041 PMCID: PMC10640470 DOI: 10.1007/s00248-023-02267-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023]
Abstract
The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.
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Affiliation(s)
- D F R Cleary
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands.
| | - T M Stuij
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - T Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - V Oliveira
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Polónia
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A Louvado
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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Ribeiro B, Padua A, Oliveira BFRD, Puccinelli G, da Costa Fernandes F, Laport MS, Klautau M. Uncovering the Microbial Diversity of Two Exotic Calcareous Sponges. MICROBIAL ECOLOGY 2023; 85:737-746. [PMID: 35234997 DOI: 10.1007/s00248-022-01980-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Sponges-associated microorganisms play important roles in their health and ecology; consequently, they may be crucial in the successful adaptation of exotic species to novel environments. However, few studies have focused on the microbial diversity of exotic sponges, especially those with calcium carbonate spicules (class Calcarea). Therefore, this is the first in situ characterization of the microbiota of the exotic calcareous sponges Sycettusa hastifera and Paraleucilla magna. Our results suggest that S. hastifera has a more stable microbiota than P. magna, as there were no differences in its beta diversity among sampling sites. Conversely, P. magna showed significant differences in its microbial communities, perhaps related to its adhesion to artificial substrate and/or shellfish mariculture activities. Each sponge species presented a single dominant proteobacterial OTU potentially active in the nitrogen cycle, which could help sponge detoxification, especially in polluted areas where exotic species usually establish. Our results show the importance of assessing the microbial diversity to unveil host-microorganism relationships and suggest that these associated nitrogen-cycling microorganisms could favor the success of exotic sponges in new environments.
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Affiliation(s)
- Bárbara Ribeiro
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
| | - André Padua
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
- Departamento de Biologia Animal, Instituto de Ciências Biológicas E da Saúde, Universidade Federal Rural do Rio de Janeiro, Seropédica, 23897000, Brazil
| | - Bruno Francesco Rodrigues de Oliveira
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, 24210130, Brazil
| | - Gabriela Puccinelli
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
| | | | - Marinella Silva Laport
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil
| | - Michelle Klautau
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brazil.
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Delgadillo-Ordoñez N, Raimundo I, Barno AR, Osman EO, Villela H, Bennett-Smith M, Voolstra CR, Benzoni F, Peixoto RS. Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients-A Systematic Review. Microorganisms 2022; 10:microorganisms10122340. [PMID: 36557593 PMCID: PMC9787610 DOI: 10.3390/microorganisms10122340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/12/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
The Red Sea is a suitable model for studying coral reefs under climate change due to its strong environmental gradient that provides a window into future global warming scenarios. For instance, corals in the southern Red Sea thrive at temperatures predicted to occur at the end of the century in other biogeographic regions. Corals in the Red Sea thrive under contrasting thermal and environmental regimes along their latitudinal gradient. Because microbial communities associated with corals contribute to host physiology, we conducted a systematic review of the known diversity of Red Sea coral-associated bacteria, considering geographic location and host species. Our assessment comprises 54 studies of 67 coral host species employing cultivation-dependent and cultivation-independent techniques. Most studies have been conducted in the central and northern Red Sea, while the southern and western regions remain largely unexplored. Our data also show that, despite the high diversity of corals in the Red Sea, the most studied corals were Pocillopora verrucosa, Dipsastraea spp., Pleuractis granulosa, and Stylophora pistillata. Microbial diversity was dominated by bacteria from the class Gammaproteobacteria, while the most frequently occurring bacterial families included Rhodobacteraceae and Vibrionaceae. We also identified bacterial families exclusively associated with each of the studied coral orders: Scleractinia (n = 125), Alcyonacea (n = 7), and Capitata (n = 2). This review encompasses 20 years of research in the Red Sea, providing a baseline compendium for coral-associated bacterial diversity.
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Affiliation(s)
- Nathalia Delgadillo-Ordoñez
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Inês Raimundo
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Adam R. Barno
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Eslam O. Osman
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Helena Villela
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Morgan Bennett-Smith
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Christian R. Voolstra
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Francesca Benzoni
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Raquel S. Peixoto
- Marine Microbiomes Laboratory, Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Correspondence:
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Haydon TD, Suggett DJ, Siboni N, Kahlke T, Camp EF, Seymour JR. Temporal Variation in the Microbiome of Tropical and Temperate Octocorals. MICROBIAL ECOLOGY 2022; 83:1073-1087. [PMID: 34331071 DOI: 10.1007/s00248-021-01823-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.
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Affiliation(s)
- Trent D Haydon
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - David J Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Tim Kahlke
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Emma F Camp
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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Ortiz P, Quiroga E, Montero P, Hamame M, Betti F. Trophic structure of benthic communities in a Chilean fjord (45°S) influenced by salmon aquaculture: Insights from stable isotopic signatures. MARINE POLLUTION BULLETIN 2021; 173:113149. [PMID: 34813999 DOI: 10.1016/j.marpolbul.2021.113149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Benthic marine food webs, which recycle organic matter and sustain unique biodiversity, are an important component of estuarine Patagonian fjords; however, these may be heavily influenced by salmon farming activities. Under the above conditions, this study collected several food sources (sediment organic matter, suspended particulate organic matter, macroalgae) and 26 benthic invertebrate species, and analyzed them using a Bayesian mixing model. Briefly, carbon and nitrogen stable isotopes analyses revealed that the highly variable isotopic niche widths respond to food supplies from marine and terrestrial organic matter. In addition, particulate and dissolved waste from salmon farming activities were found to modify isotopic composition ratios in many suspension feeders. Particularly, our results indicate high δ15N values in the sponge Cliona chilensis and the encrusting coral Incrustatus comauensis, which appear to be potential ecological indicators for evaluating stoichiometry imbalances and trace organic pollution sources in fjord environments.
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Affiliation(s)
- Paula Ortiz
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Moraleda 16, Coyhaique 5951601, Chile.
| | - Eduardo Quiroga
- Pontificia Universidad Católica de Valparaíso, Escuela de Ciencias del Mar, Avenida Universidad 330, Curauma, Valparaíso, Chile; Centro de Investigación Oceanográfica COPAS Sur-Austral, Universidad de Concepción, Concepción, Chile
| | - Paulina Montero
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Moraleda 16, Coyhaique 5951601, Chile; Centro de Investigación Oceanográfica COPAS Sur-Austral, Universidad de Concepción, Concepción, Chile
| | - Madeleine Hamame
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Moraleda 16, Coyhaique 5951601, Chile
| | - Federico Betti
- Department of Earth, Environment and Life Sciences, Università degli Studi di Genova, Genova, Italy
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