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Mazzella V, Dell'Anno A, Etxebarría N, González-Gaya B, Nuzzo G, Fontana A, Núñez-Pons L. High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits. Commun Biol 2024; 7:422. [PMID: 38589605 PMCID: PMC11001883 DOI: 10.1038/s42003-024-06109-5] [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: 08/04/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.
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Affiliation(s)
- Valerio Mazzella
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Ischia Marine Centre, 80077, Ischia, Naples, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy
| | - Antonio Dell'Anno
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Néstor Etxebarría
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Belén González-Gaya
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia-Bld. 7, 80126, Napoli, Italy
| | - Laura Núñez-Pons
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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Efremova J, Mazzella V, Mirasole A, Teixidó N, Núñez-Pons L. Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO 2 vents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170171. [PMID: 38246375 DOI: 10.1016/j.scitotenv.2024.170171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.
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Affiliation(s)
- Jana Efremova
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
| | - Valerio Mazzella
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Alice Mirasole
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Núria Teixidó
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy; Laboratoire d'Océanographie de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
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3
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Turk-Kubo KA, Gradoville MR, Cheung S, Cornejo-Castillo FM, Harding KJ, Morando M, Mills M, Zehr JP. Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters. FEMS Microbiol Rev 2023; 47:fuac046. [PMID: 36416813 PMCID: PMC10719068 DOI: 10.1093/femsre/fuac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Mary R Gradoville
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Columbia River Inter-Tribal Fish Commission, Portland, OR, United States
| | - Shunyan Cheung
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Francisco M Cornejo-Castillo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
| | - Katie J Harding
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Marine Biology Research Division, Scripps Institute of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Michael Morando
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Matthew Mills
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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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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Lamb CE, Watts JEM. Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa. ENVIRONMENTAL MICROBIOME 2023; 18:52. [PMID: 37291644 DOI: 10.1186/s40793-023-00508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Marine sponges are diverse and functionally important members of marine benthic systems, well known to harbour complex and abundant symbiotic microorganisms as part of their species-specific microbiome. Changes in the sponge microbiome have previously been observed in relation to natural environmental changes, including nutrient availability, temperature and light. With global climate change altering seasonal temperatures, this study aims to better understand the potential effects of natural seasonal fluctuations on the composition and functions of the sponge microbiome. RESULTS Metataxonomic sequencing of two marine sponge species native to the U.K. (Hymeniacidon perlevis and Suberites massa) was performed at two different seasonal temperatures from the same estuary. A host-specific microbiome was observed in each species between both seasons. Detected diversity within S. massa was dominated by one family, Terasakiellaceae, with remaining dominant families also being detected in the associated seawater. H. perlevis demonstrated sponge specific bacterial families including aforementioned Terasakiellaceae as well as Sphingomonadaceae and Leptospiraceae with further sponge enriched families present. CONCLUSIONS To our knowledge, these results describe for the first time the microbial diversity of the temperate marine sponge species H. perlevis and S. massa using next generation sequencing. This analysis detected the presence of core sponge taxa identified in each sponge species was not changed by seasonal temperature alterations, however, there were shifts observed in overall community composition due to fluctuations in less abundant taxa, demonstrating that microbiome stability across seasons is likely to be host species specific.
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Affiliation(s)
| | - Joy E M Watts
- Centre for Enzyme Innovation, Portsmouth, UK.
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK.
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6
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Cleary DFR, Oliveira V, Gomes NCM, Bialecki A, de Voogd NJ. A comparison of free-living and sponge-associated bacterial communities from a remote oceanic island with a focus on calcareous sponges. FEMS Microbiol Ecol 2023; 99:7033423. [PMID: 36758964 PMCID: PMC10022632 DOI: 10.1093/femsec/fiad014] [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: 09/22/2022] [Revised: 01/16/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
Calcareous sponges are an often overlooked element of sponge communities. In contrast to most other sponges, calcareous sponges produce calcium carbonate spicules, as opposed to the siliceous spicules of most sponges. Here, we investigated the bacterial communities of 17 sponge species, including type and paratype specimens of recently described calcareous species, sampled off the remote island of Rodrigues, in the Indian Ocean. The main axis of variation in a PCO analysis of all samples separated noncalcareous sponge species, including Axinyssa aplysinoides, Cinachyrella aff. australiensis, Petrosia seychellensis, Ircinia aff. variabilis, Spongia ceylonensis, Plakinastrella aff. clipptertonensis, Agelas aff. ceylonica, Agelas aff. mauritiana, and Hyrtios erectus from calcareous sponges, the noncalcareous Biemna tubulata, sediment, and seawater. Overall, the bacterial communities of calcareous sponges revealed unique prokaryotic profiles with low abundances of several bacterial phyla, and relatively high abundances of other taxa, for example, the phyla Fibrobacterota, Proteobacteria, and the SAR324 clade, the class Alphaproteobacteria, and orders Cytophagales and Cyanobacteriales, although there was considerable variation among species. Calcareous sponges also had a high dominance of unknown bacterial operational taxonomic units (OTUs). Considering the unique nature of these communities, further studies are needed to better understand the environmental and ecological drivers of calcareous sponge-associated bacterial communities and their relevance as potential sources of novel microbes of biotechnological interest.
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Affiliation(s)
- D F R Cleary
- Corresponding author. Institute of Environmental Sciences, CML, Leiden University Einsteinweg 2, 2333 CC Leiden, The Netherlands. E-mail:
| | - V Oliveira
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - N C M Gomes
- Department of Biology and CESAM, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - A Bialecki
- Laboratoire de Chimie et de Biotechnologie des Produits Naturels, Faculté des Sciences et Technologies, Université de La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France
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Sánchez-Suárez J, Villamil L, Coy-Barrera E, Díaz L. Cliona varians-Derived Actinomycetes as Bioresources of Photoprotection-Related Bioactive End-Products. Mar Drugs 2021; 19:674. [PMID: 34940673 PMCID: PMC8707384 DOI: 10.3390/md19120674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Sunscreen and sunblock are crucial skincare products to prevent photoaging and photocarcinogenesis through the addition of chemical filters to absorb or block ultraviolet (UV) radiation. However, several sunscreen and sunblock ingredients, mostly UV filters, have been associated with human and environmental safety concerns. Therefore, the exploration and discovery of promising novel sources of efficient and safer compounds with photoprotection-related activities are currently required. Marine invertebrates, particularly their associated microbiota, are promising providers of specialized metabolites with valuable biotechnological applications. Nevertheless, despite Actinobacteria members being a well-known source of bioactive metabolites, their photoprotective potential has been poorly explored so far. Hence, a set of methanolic extracts obtained from Cliona varians-derived actinomycetes was screened regarding their antioxidant and UV-absorbing capacities (i.e., photoprotection-related activities). The active extract-producing strains were identified and classified within genera Streptomyces, Micrococcus, Gordonia, and Promicromonospora. This is the first report of the isolation of these microorganisms from C. varians (an ecologically important Caribbean coral reef-boring sponge). The in vitro cytotoxicity on dermal fibroblasts of oxybenzone and the selected active extracts revealed that oxybenzone exerted a cytotoxic effect, whereas no cytotoxic effect of test extracts was observed. Accordingly, the most active (SPFi > 5, radical scavenging > 50%) and nontoxic (cell viability > 75%) extracts were obtained from Streptomyces strains. Finally, LC-MS-based characterization suggested a broad chemical space within the test strains and agreed with the reported streptomycetes' chemodiversity. The respective metabolite profiling exposed a strain-specific metabolite occurrence, leading to the recognition of potential hits. These findings suggest that marine Streptomyces produce photoprotectants ought to be further explored in skincare applications.
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Affiliation(s)
- Jeysson Sánchez-Suárez
- Doctorate in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
| | - Luisa Villamil
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Universidad Militar Nueva Granada, Cajicá 250247, Colombia;
| | - Luis Díaz
- Doctorate in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia;
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Oliveira BFR, Lopes IR, Canellas ALB, Muricy G, Dobson ADW, Laport MS. Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea. Microorganisms 2020; 8:microorganisms8121978. [PMID: 33322780 PMCID: PMC7764410 DOI: 10.3390/microorganisms8121978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 11/25/2020] [Indexed: 01/28/2023] Open
Abstract
Marine sponges are excellent examples of invertebrate–microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.
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Affiliation(s)
- Bruno F. R. Oliveira
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
| | - Isabelle R. Lopes
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Anna L. B. Canellas
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Guilherme Muricy
- Laboratório de Biologia de Porifera, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940040, Brazil;
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
- Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - Marinella S. Laport
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
- Correspondence:
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de Oliveira BFR, Freitas-Silva J, Sánchez-Robinet C, Laport MS. Transmission of the sponge microbiome: moving towards a unified model. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:619-638. [PMID: 33048474 DOI: 10.1111/1758-2229.12896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Sponges have co-evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host-associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways. Both vertical transmission (VT) and horizontal transmission (HT) have different advantages and disadvantages in the life cycle of these invertebrates. However, a third mode of transmission, called leaky vertical transmission or mixed mode of transmission (MMT), which incorporates both VT and HT modes, has gained relevance and seems to be the most robust model. In that regard, the aim of this review is to present the evolving knowledge on these main modes of transmission of the sponge microbiome. Our conclusions lead us to suggest that MMT may be more common for all sponges, with its frequency varying across the transmission spectrum between species and the environment. This hybrid model supports the stable and specific transmission of these microbial partners and reinforces their assistance in the resilience of sponges over the years.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Jéssyca Freitas-Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Claudia Sánchez-Robinet
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
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Mote S, Gupta V, De K, Nanajkar M, Damare SR, Ingole B. Bacterial diversity associated with a newly described bioeroding sponge, Cliona thomasi, from the coral reefs on the West Coast of India. Folia Microbiol (Praha) 2020; 66:203-211. [PMID: 33140282 DOI: 10.1007/s12223-020-00830-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022]
Abstract
The bacterial diversity associated with eroding sponges belonging to the Cliona viridis species complex is scarcely known. Cliona thomasi described from the West Coast of India is a new introduction to the viridis species complex. In this study, we determined the bacterial diversity associated with C. thomasi using next-generation sequencing. The results revealed the dominance of Proteobacteria followed by Cyanobacteria, Actinobacteria and Firmicutes. Among Proteobacteria, the Alphaproteobacteria were found to be the most dominant class. Furthermore, at the genus level, Rhodothalassium were highly abundant followed by Endozoicomonas in sponge samples. The beta-diversity and species richness measures showed remarkably lower diversity in Cliona thomasi than the ambient environment. The determined lower bacterial diversity in C. thomasi than the environmental samples, thus, categorized it as a low microbial abundance (LMA). Functional annotation of the C. thomasi-associated bacterial community indicates their possible role in photo-autotrophy, aerobic nitrification, coupling of sulphate reduction and sulphide oxidization. The present study unveils the bacterial diversity in bioeroding C. thomasi, which is a crucial step to determine the functions of the sponge holobiont in coral reef ecosystem.
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Affiliation(s)
- Sambhaji Mote
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India.,Department of Marine Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Vishal Gupta
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India. .,School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Kalyan De
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India.,School of Earth, Ocean, and Atmospheric Sciences, Goa University, Taleigao, Goa, India
| | - Mandar Nanajkar
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India
| | - Samir R Damare
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India
| | - Baban Ingole
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India.
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11
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León-Zayas R, McCargar M, Drew JA, Biddle JF. Microbiomes of fish, sediment and seagrass suggest connectivity of coral reef microbial populations. PeerJ 2020; 8:e10026. [PMID: 33005496 PMCID: PMC7513772 DOI: 10.7717/peerj.10026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/02/2020] [Indexed: 11/20/2022] Open
Abstract
The benthic environments of coral reefs are heavily shaped by physiochemical factors, but also the ecological interactions of the animals and plants in the reef ecosystem. Microbial populations may be shared within the ecosystem of sediments, seagrasses and reef fish. In this study, we hypothesize that coral reef and seagrass environments share members of the microbial community that are rare in some habitats and enriched in others, and that animals may integrate this connectivity. We investigated the potential connectivity between the microbiomes of sediments, seagrass blades and roots (Syringodium isoetifolium), and a seagrass-specialist parrotfish (C. spinidens) guts in reef areas of Fiji. We contrasted these with sediment samples from the Florida Keys, gut samples from surgeonfish (A. nigricauda, Acanthurinae sp. unknown, C. striatus), and ocean water microbiomes from the Atlantic, Pacific and Indian Oceans to test the robustness of our characterizations of microbiome environments. In general, water, sediment and fish gut samples were all distinct microbiomes. Sediment microbiomes were mostly similar between Fiji and Florida, but also showed some regional similarities. In Fiji, we show connectivity of a shared microbiome between seagrass, fish and sediments. Additionally, we identified an environmental reservoir of a surgeonfish symbiont, Epulopiscium. The connection of these ecosystem components suggests that the total microbiome of these environments may vary as their animal inhabitants shift in a changing ocean.
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Affiliation(s)
- Rosa León-Zayas
- Department of Biology, Willamette University, Salem, OR, USA
| | - Molly McCargar
- Department of Biological Sciences, Fordham University Bronx, NY, NY, USA
| | - Joshua A. Drew
- Environmental Science and Forestry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Jennifer F. Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
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12
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Cleary DFR, Polónia ARM, Reijnen BT, Berumen ML, de Voogd NJ. Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea. MICROBIAL ECOLOGY 2020; 80:103-119. [PMID: 31932882 DOI: 10.1007/s00248-019-01465-w] [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: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.
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Affiliation(s)
- D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - B T Reijnen
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, The Netherlands
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13
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Helber SB, Steinert G, Wu YC, Rohde S, Hentschel U, Muhando CA, Schupp PJ. Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis. FEMS Microbiol Ecol 2020; 95:5369420. [PMID: 30830220 DOI: 10.1093/femsec/fiz026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/02/2019] [Indexed: 11/13/2022] Open
Abstract
Sponges are one of the most dominant organisms in marine ecosystems. One reason for their success is their association with microorganisms that are besides the host itself responsible for the chemical defence. Sponge abundances have been increasing on coral reefs in the Western Indian Ocean (WIO) and are predicted to increase further with rising anthropogenic impacts on coral reefs. However, there is a paucity of information on chemical ecology of sponges from the WIO and their prokaryotic community composition. We used a combination of Illumina sequencing and a predictive metagenomic analysis to (i) assess the prokaryotic community composition of sponges from Zanzibar, (ii) predict the presence of KEGG metabolic pathways responsible for bioactive compound production and (iii) relate their presence to the degree of observed chemical defence in their respective sponge host. We found that sponges from Zanzibar host diverse prokaryotic communities that are host species-specific. Sponge-species and respective specimens that showed strong chemical defences in previous studies were also predicted to be highly enriched in various pathways responsible for secondary metabolite production. Hence, the combined sequencing and predictive metagenomic approach proved to be a useful indicator for the metabolic potential of sponge holobionts.
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Affiliation(s)
- Stephanie B Helber
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany.,Leibniz Center for Tropical Marine Research (ZMT) GmbH, Fahrenheitstr. 6, 28359 Bremen, Germany
| | - Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Yu-Chen Wu
- GEOMAR Helmholtz Centre for Ocean Research, Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Sven Rohde
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Christopher A Muhando
- Institute of Marine Sciences (IMS), Mizingani Road, P.O Box 668, Stonetown, Zanzibar, Tanzania
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Carl von Ossietzky University of Oldenburg, Ammerländer Heeerstr. 231, 26129 Oldenburg, Germany
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14
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Pawlik JR, McMurray SE. The Emerging Ecological and Biogeochemical Importance of Sponges on Coral Reefs. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:315-337. [PMID: 31226028 DOI: 10.1146/annurev-marine-010419-010807] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
With the decline of reef-building corals on tropical reefs, sponges have emerged as an important component of changing coral reef ecosystems. Seemingly simple, sponges are highly diverse taxonomically, morphologically, and in terms of their relationships with symbiotic microbes, and they are one of nature's richest sources of novel secondary metabolites. Unlike most other benthic organisms, sponges have the capacity to disrupt boundary flow as they pump large volumes of seawater into the water column. This seawater is chemically transformed as it passes through the sponge body as a consequence of sponge feeding, excretion, and the activities of microbial symbionts, with important effects on carbon and nutrient cycling and on the organisms in the water column and on the adjacent reef. In this review, we critically evaluate developments in the recently dynamic research area of sponge ecology on tropical reefs and provide a perspective for future studies.
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Affiliation(s)
- Joseph R Pawlik
- Department of Biology and Marine Biology and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina 28409, USA; ,
| | - Steven E McMurray
- Department of Biology and Marine Biology and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina 28409, USA; ,
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15
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Zhang F, Jonas L, Lin H, Hill RT. Microbially mediated nutrient cycles in marine sponges. FEMS Microbiol Ecol 2019; 95:5582607. [DOI: 10.1093/femsec/fiz155] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/04/2019] [Indexed: 01/05/2023] Open
Abstract
ABSTRACTEfficient nutrient cycles mediated by symbiotic microorganisms with their hosts are vital to support the high productivity of coral reef ecosystems. In these ecosystems, marine sponges are important habitat-forming organisms in the benthic community and harbor abundant microbial symbionts. However, few studies have reviewed the critical microbially mediated nutrient cycling processes in marine sponges. To bridge this gap, in this review article, we summarize existing knowledge and recent advances in understanding microbially mediated carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles in sponges, propose a conceptual model that describes potential interactions and constraints in the major nutrient cycles, and suggest that shifting redox state induced by animal behavior like sponge pumping can exert great influence on the activities of symbiotic microbial communities. Constraints include the lack of knowledge on spatial and temporal variations and host behavior; more studies are needed in these areas. Sponge microbiomes may have a significant impact on the nutrient cycles in the world’s coral reef ecosystems.
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Affiliation(s)
- Fan Zhang
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Lauren Jonas
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Hanzhi Lin
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
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16
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Cleary DFR, Swierts T, Coelho FJRC, Polónia ARM, Huang YM, Ferreira MRS, Putchakarn S, Carvalheiro L, van der Ent E, Ueng JP, Gomes NCM, de Voogd NJ. The sponge microbiome within the greater coral reef microbial metacommunity. Nat Commun 2019; 10:1644. [PMID: 30967538 PMCID: PMC6456735 DOI: 10.1038/s41467-019-09537-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 03/18/2019] [Indexed: 02/03/2023] Open
Abstract
Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan.
| | - Thomas Swierts
- Marine Biodiversity, 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
| | - Francisco J R C Coelho
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Yusheng M Huang
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
- Department of Marine Recreation, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
| | - Marina R S Ferreira
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Sumaitt Putchakarn
- Institute of Marine Science, Burapha University, Chon Buri, 20131, Thailand
| | - Luis Carvalheiro
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Esther van der Ent
- Marine Biodiversity, 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
| | - Jinn-Pyng Ueng
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
- Department of Aquaculture, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
| | - Newton C M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Marine Biodiversity, 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
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17
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Ferrier‐Pagès C, Leal MC. Stable isotopes as tracers of trophic interactions in marine mutualistic symbioses. Ecol Evol 2019; 9:723-740. [PMID: 30680151 PMCID: PMC6342181 DOI: 10.1002/ece3.4712] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/17/2018] [Accepted: 10/26/2018] [Indexed: 12/31/2022] Open
Abstract
Mutualistic nutritional symbioses are widespread in marine ecosystems. They involve the association of a host organism (algae, protists, or marine invertebrates) with symbiotic microorganisms, such as bacteria, cyanobacteria, or dinoflagellates. Nutritional interactions between the partners are difficult to identify in symbioses because they only occur in intact associations. Stable isotope analysis (SIA) has proven to be a useful tool to highlight original nutrient sources and to trace nutrients acquired by and exchanged between the different partners of the association. However, although SIA has been extensively applied to study different marine symbiotic associations, there is no review taking into account of the different types of symbiotic associations, how they have been studied via SIA, methodological issues common among symbiotic associations, and solutions that can be transferred from one type of association with another. The present review aims to fill such gaps in the scientific literature by summarizing the current knowledge of how isotopes have been applied to key marine symbioses to unravel nutrient exchanges between partners, and by describing the difficulties in interpreting the isotopic signal. This review also focuses on the use of compound-specific stable isotope analysis and on statistical advances to analyze stable isotope data. It also highlights the knowledge gaps that would benefit from future research.
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Affiliation(s)
| | - Miguel Costa Leal
- MARE – Marine and Environmental Sciences CentreFaculdade de Ciências da Universidade de LisboaLisbonPortugal
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18
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Cleary DFR, Polónia ARM, de Voogd NJ. Bacterial Communities Inhabiting the Sponge Biemna fortis, Sediment and Water in Marine Lakes and the Open Sea. MICROBIAL ECOLOGY 2018; 76:610-624. [PMID: 29470608 DOI: 10.1007/s00248-018-1156-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
Marine lakes are small bodies of landlocked seawater that are isolated from the open sea and have been shown to house numerous rare and unique taxa. The environmental conditions of the lakes are also characterised by lower pH and salinity and higher temperatures than generally found in the open sea. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach and a predictive metagenomic approach (PICRUSt) to examine bacterial composition and function in three distinct biotopes (sediment, water and the sponge species Biemna fortis) in three habitats (two marine lakes and the open sea) of the Berau reef system, Indonesia. Both biotope and habitat were significant predictors of higher taxon abundance and compositional variation. Most of the variation in operational taxonomic unit (OTU) composition was related to the biotope (42% for biotope alone versus 9% for habitat alone and 15% combined). Most OTUs were also restricted to a single biotope (1047 for B. fortis, 6120 for sediment and 471 for water). Only 98 OTUs were shared across all three biotopes. Bacterial communities from B. fortis, sediment and water samples were, however, also distinct in marine lake and open sea habitats. This was evident in the abundance of higher bacterial taxa. For example, the phylum Cyanobacteria was significantly more abundant in samples from marine lakes than from the open sea. This difference was most pronounced in the sponge B. fortis. In line with the compositional differences, there were pronounced differences in predicted relative gene count abundance among biotopes and habitats. Of particular interest was the predicted enrichment in B. fortis from the marine lakes for pathways including DNA replication and repair and the glutathione metabolism. This may facilitate adaptation of host and microbes to life in 'stressful' low pH, low salinity and/or high temperature environments such as those encountered in marine lakes.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology, CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Ana R M Polónia
- Department of Biology, CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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19
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Van Duyl FC, Mueller B, Meesters EH. Spatio-temporal variation in stable isotope signatures (δ 13C and δ 15N) of sponges on the Saba Bank. PeerJ 2018; 6:e5460. [PMID: 30128208 PMCID: PMC6097495 DOI: 10.7717/peerj.5460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/26/2018] [Indexed: 12/02/2022] Open
Abstract
Sponges are ubiquitous on coral reefs, mostly long lived and therefore adaptive to changing environmental conditions. They feed on organic matter withdrawn from the passing water and they may harbor microorganisms (endosymbionts), which contribute to their nutrition. Their diets and stable isotope (SI) fractionation determine the SI signature of the sponge holobiont. Little is known of spatio–temporal variations in SI signatures of δ13C and δ15N in tropical sponges and whether they reflect variations in the environment. We investigated the SI signatures of seven common sponge species with different functional traits and their potential food sources between 15 and 32 m depth along the S-SE and E-NE side of the Saba Bank, Eastern Caribbean, in October 2011 and October 2013. SI signatures differed significantly between most sponge species, both in mean values and in variation, indicating different food preferences and/or fractionation, inferring sponge species-specific isotopic niche spaces. In 2011, all sponge species at the S-SE side were enriched in d13C compared to the E-NE side. In 2013, SI signatures of sponges did not differ between the two sides and were overall lighter in δ13C and δ15N than in 2011. Observed spatio–temporal changes in SI in sponges could not be attributed to changes in the SI signatures of their potential food sources, which remained stable with different SI signatures of pelagic (particulate organic matter (POM): δ13C −24.9‰, δ15N +4.3‰) and benthic-derived food (macroalgae: δ13C −15.4‰, δ15N +0.8‰). Enriched δ13C signatures in sponges at the S-SE side in 2011 are proposed to be attributed to predominantly feeding on benthic-derived C. This interpretation was supported by significant differences in water mass constituents between sides in October 2011. Elevated NO3 and dissolved organic matter concentrations point toward a stronger reef signal in reef overlying water at the S-SE than N-NE side of the Bank in 2011. The depletions of δ13C and δ15N in sponges in October 2013 compared to October 2011 concurred with significantly elevated POM concentrations. The contemporaneous decrease in δ15N suggests that sponges obtain their N mostly from benthic-derived food with a lower δ15N than pelagic food. Average proportional feeding on available sources varied between sponge species and ranged from 20% to 50% for benthic and 50% to 80% for pelagic-derived food, assuming trophic enrichment factors of 0.5‰ ± sd 0.5 for δ13C and 3‰ ± sd 0.5 for δ15N for sponges. We suggest that observed variation of SI in sponges between sides and years were the result of shifts in the proportion of ingested benthic- and pelagic-derived organic matter driven by environmental changes. We show that sponge SI signatures reflect environmental variability in space and time on the Saba Bank and that SI of sponges irrespective of their species-specific traits move in a similar direction in response to these environmental changes.
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Affiliation(s)
- Fleur C Van Duyl
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, The Netherlands
| | - Benjamin Mueller
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, The Netherlands.,Department for Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, The Netherlands
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20
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Pita L, Rix L, Slaby BM, Franke A, Hentschel U. The sponge holobiont in a changing ocean: from microbes to ecosystems. MICROBIOME 2018; 6:46. [PMID: 29523192 PMCID: PMC5845141 DOI: 10.1186/s40168-018-0428-1] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as "nested ecosystems." In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.
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Affiliation(s)
- L. Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - L. Rix
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - B. M. Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - A. Franke
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - U. Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts-University of Kiel (CAU), Kiel, Germany
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21
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Cleary DFR, Polónia ARM, de Voogd NJ. Prokaryote composition and predicted metagenomic content of two Cinachyrella Morphospecies and water from West Papuan Marine Lakes. FEMS Microbiol Ecol 2017; 94:4693832. [DOI: 10.1093/femsec/fix175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 12/03/2017] [Indexed: 01/08/2023] Open
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22
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Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean. ISME JOURNAL 2017; 11:2356-2367. [PMID: 28742073 DOI: 10.1038/ismej.2017.97] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/31/2017] [Accepted: 05/12/2017] [Indexed: 11/08/2022]
Abstract
Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day-1) occurred in coastal surface waters and lowest detectable rates (~0.2 nM day-1) were found in the anoxic region of offshore stations. BNF was not detectable in most samples from oxygen-depleted waters. The composition of the N2-fixing assemblage was investigated by sequencing of nifH genes. The diazotrophic assemblage in surface waters contained mainly Proteobacterial sequences (Cluster I nifH), while both Proteobacterial sequences and sequences with high identities to those of anaerobic microbes characterized as Clusters III and IV type nifH sequences were found in the anoxic waters. Our results indicate modest input of N through BNF in oxygen-depleted zones mainly due to the activity of proteobacterial diazotrophs.
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23
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Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks. Sci Rep 2017; 7:2542. [PMID: 28566699 PMCID: PMC5451456 DOI: 10.1038/s41598-017-02656-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 04/18/2017] [Indexed: 12/24/2022] Open
Abstract
Sponges (Porifera) are abundant and diverse members of benthic filter feeding communities in most marine ecosystems, from the deep sea to tropical reefs. A characteristic feature is the associated dense and diverse prokaryotic community present within the sponge mesohyl. Previous molecular genetic studies revealed the importance of host identity for the community composition of the sponge-associated microbiota. However, little is known whether sponge host-specific prokaryotic community patterns observed at 97% 16S rRNA gene sequence similarity are consistent at high taxonomic ranks (from genus to phylum level). In the present study, we investigated the prokaryotic community structure and variation of 24 sponge specimens (seven taxa) and three seawater samples from Sweden. Results show that the resemblance of prokaryotic communities at different taxonomic ranks is consistent with patterns present at 97% operational taxonomic unit level.
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24
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The Assimilation of Diazotroph-Derived Nitrogen by Scleractinian Corals Depends on Their Metabolic Status. mBio 2017; 8:mBio.02058-16. [PMID: 28074021 PMCID: PMC5241398 DOI: 10.1128/mbio.02058-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tropical corals are associated with a diverse community of dinitrogen (N2)-fixing prokaryotes (diazotrophs) providing the coral an additional source of bioavailable nitrogen (N) in oligotrophic waters. The overall activity of these diazotrophs changes depending on the current environmental conditions, but to what extent it affects the assimilation of diazotroph-derived N (DDN) by corals is still unknown. Here, in a series of 15N2 tracer experiments, we directly quantified DDN assimilation by scleractinian corals from the Red Sea exposed to different environmental conditions. We show that DDN assimilation strongly varied with the corals’ metabolic status or with phosphate availability in the water. The very autotrophic shallow-water (~5 m) corals showed low or no DDN assimilation, which significantly increased under elevated phosphate availability (3 µM). Corals that depended more on heterotrophy (i.e., bleached and deep-water [~45 m] corals) assimilated significantly more DDN, which contributed up to 15% of the corals’ N demand (compared to 1% in shallow corals). Furthermore, we demonstrate that a substantial part of the DDN assimilated by deep corals was likely obtained from heterotrophic feeding on fixed N compounds and/or diazotrophic cells in the mucus. Conversely, in shallow corals, the net release of mucus, rich in organic carbon compounds, likely enhanced diazotroph abundance and activity and thereby the release of fixed N to the pelagic and benthic reef community. Overall, our results suggest that DDN assimilation by corals varies according to the environmental conditions and is likely linked to the capacity of the coral to acquire nutrients from seawater. Tropical corals are associated with specialized bacteria (i.e., diazotrophs) able to transform dinitrogen (N2) gas into a bioavailable form of nitrogen, but how much of this diazotroph-derived nitrogen (DDN) is assimilated by corals under different environmental conditions is still unknown. Here, we used 15N2 labeling to trace the fate of DDN within the coral symbiosis. We show that DDN is assimilated by both the animal host and the endosymbiotic algae. In addition, the amount of assimilated DDN was significantly greater in mesophotic, bleached, or phosphorus-enriched corals than in surface corals, which almost did not take up this nitrogen form. DDN can thus be of particular importance for the nutrient budget of corals whenever they are limited by the availability of other forms of dissolved nutrients.
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25
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Souza DT, Genuário DB, Silva FSP, Pansa CC, Kavamura VN, Moraes FC, Taketani RG, Melo IS. Analysis of bacterial composition in marine sponges reveals the influence of host phylogeny and environment. FEMS Microbiol Ecol 2016; 93:fiw204. [PMID: 27702764 DOI: 10.1093/femsec/fiw204] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/14/2016] [Accepted: 10/02/2016] [Indexed: 01/10/2023] Open
Abstract
Bacterial communities associated with sponges are influenced by environmental factors; however, some degree of genetic influence of the host on the microbiome is also expected. In this work, 16S rRNA gene amplicon sequencing revealed diverse bacterial phylotypes based on the phylogenies of three tropical sponges (Aplysina fulva, Aiolochroia crassa and Chondrosia collectrix). Despite their sympatric occurrence, the studied sponges presented different bacterial compositions that differed from those observed in seawater. However, lower dissimilarities in bacterial communities were observed within sponges from the same phylogenetic group. The relationships between operational taxonomic units (OTUs) recovered from the sponges and database sequences revealed associations among sequences from unrelated sponge species and sequences retrieved from diverse environmental samples. In addition, one Proteobacteria OTU retrieved from A. fulva was identical to sequences previously reported from A. fulva specimens collected along the Brazilian coast. Based on these results, we conclude that bacterial communities associated with marine sponges are shaped by host identity, while environmental conditions seem to be less important in shaping symbiont communities. This is the first study to assess bacterial communities associated with marine sponges in the remote St. Peter and St. Paul Archipelago using amplicon sequencing of the 16S rRNA gene.
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Affiliation(s)
- Danilo T Souza
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Diego B Genuário
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| | - Fabio Sérgio P Silva
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Camila C Pansa
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Vanessa N Kavamura
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| | - Fernando C Moraes
- Rio de Janeiro Botanical Garden Research Institute, 22460-030, Rio de Janeiro, RJ, Brazil
- National Museum, Federal University of Rio de Janeiro, 20940-040, Rio de Janeiro, RJ, Brazil
| | - Rodrigo G Taketani
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| | - Itamar S Melo
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
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26
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Ribes M, Calvo E, Movilla J, Logares R, Coma R, Pelejero C. Restructuring of the sponge microbiome favors tolerance to ocean acidification. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:536-544. [PMID: 27264698 DOI: 10.1111/1758-2229.12430] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Ocean acidification is increasing and affects many marine organisms. However, certain sponge species can withstand low-pH conditions. This may be related to their complex association with microbes. We hypothesized that species with greater microbial diversity may develop functional redundancy that could enable the holobiont to survive even if particular microbes are lost at low-pH conditions. We evaluated the effects of acidification on the growth and associated microbes of three ubiquitous Mediterranean sponges by exposing them to the present pH level and that predicted for the year 2100. We found marked differences among the species in the acquisition of new microbes, being high in Dysidea avara, moderate in Agelas oroides and null in Chondrosia reniformis; however, we did not observe variation in the overall microbiome abundance, richness or diversity. The relative abilities to alter the microbiomes contributes to survivorship in an OA scenario as demonstrated by lowered pH severely affecting the growth of C. reniformis, halving that of A. oroides, and unaffecting D. avara. Our results indicate that functional stability of the sponge holobiont to withstand future OA is species-specific and is linked to the species' ability to use horizontal transmission to modify the associated microbiome to adapt to environmental change.
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Affiliation(s)
- M Ribes
- Institut de Ciències del Mar, ICM-CSIC, Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalunya, 08003, Spain
| | - E Calvo
- Institut de Ciències del Mar, ICM-CSIC, Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalunya, 08003, Spain
| | - J Movilla
- Institut de Ciències del Mar, ICM-CSIC, Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalunya, 08003, Spain
| | - R Logares
- Institut de Ciències del Mar, ICM-CSIC, Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalunya, 08003, Spain
| | - R Coma
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accès Cala Sant Francesc 14, Blanes, Girona, Catalunya, 17300, Spain
| | - C Pelejero
- Institut de Ciències del Mar, ICM-CSIC, Passeig Marítim de la Barceloneta 37-49, Barcelona, Catalunya, 08003, Spain
- Institució Catalana de Recerca i Estudis Avançats, ICREA, Barcelona, Catalunya, 08010, Spain
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