1
|
Galià-Camps C, Junkin L, Borrallo X, Carreras C, Pascual M, Turon X. Navigating spatio-temporal microbiome dynamics: Environmental factors and trace elements shape the symbiont community of an invasive marine species. MARINE POLLUTION BULLETIN 2024; 203:116477. [PMID: 38759466 DOI: 10.1016/j.marpolbul.2024.116477] [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: 11/26/2023] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024]
Abstract
The proliferation of marine invasive species is a mounting concern. While the role of microbial communities in invasive ascidian species is recognized, the role of seasonal shifts in microbiome composition remains largely unexplored. We sampled five individuals of the invasive ascidian Styela plicata quarterly from January 2020 to October 2021 in two harbours, examining gills, tunics, and surrounding water. By analysing Amplicon Sequence Variants (ASVs) and seawater trace elements, we found that compartment (seawater, tunic, or gills) was the primary differentiating factor, followed by harbour. Clear seasonal patterns were evident in seawater bacteria, less so in gills, and absent in tunics. We identified compartment-specific bacteria, as well as seasonal indicator ASVs and ASVs correlated with trace element concentrations. Among these bacteria, we found that Endozoicomonas, Hepatoplasma and Rhodobacteraceae species had reported functions which might be necessary for overcoming seasonality and trace element shifts. This study contributes to understanding microbiome dynamics in invasive holobiont systems, and the patterns found indicate a potential role in adaptation and invasiveness.
Collapse
Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain; Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain.
| | - Liam Junkin
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain.
| | - Xavier Borrallo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Xavier Turon
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Liu F, Ryu T, Ravasi T, Wang X, Wang G, Li Z. Niche-dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis. ENVIRONMENTAL MICROBIOME 2024; 19:22. [PMID: 38589941 PMCID: PMC11000336 DOI: 10.1186/s40793-024-00563-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Most researches on sponge holobionts focus primarily on symbiotic microbes, yet data at the level of the sponge hologenome are still relatively scarce. Understanding of the sponge host and its microbial gene expression profiles and the host-microbes interplay in different niches represents a key aspect of sponge hologenome. Using the Hawaiian demosponge Mycale grandis in different niches as a model, i.e. on rocks, on the surface of coral Porites compressa, under alga Gracilaria salicornia, we compared the bacterial and fungal community structure, functional gene diversity, expression pattern and the host transcriptome by integrating open-format (deep sequencing) and closed-format (GeoChip microarray) high-throughput techniques. RESULTS Little inter-niche variation in bacterial and fungal phylogenetic diversity was detected for M. grandis in different niches, but a clear niche-dependent variability in the functional gene diversity and expression pattern of M. grandis host and its symbiotic microbiota was uncovered by GeoChip microarray and transcriptome analyses. Particularly, sponge host genes related to innate immunity and microbial recognition showed a strong correlation with the microbial symbionts' functional gene diversity and transcriptional richness in different niches. The cross-niche variability with respect to the symbiont functional gene diversity and the transcriptional richness of M. grandis holobiont putatively reflects the interplay of niche-specific selective pressure and the symbiont functional diversity. CONCLUSIONS Niche-dependent gene expression profiles of M. grandis hologenome and the host-microbes interplay were suggested though little inter-niche variation in bacterial and fungal diversity was detected, particularly the sponge innate immunity was found to be closely related to the symbiotic microbes. Altogether, these findings provide novel insights into the black box of one sponge holobiont in different niches at the hologenome level.
Collapse
Affiliation(s)
- Fang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Taewoo Ryu
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan
| | - Xin Wang
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 32611, Gainesville, FL, USA
| | - Guangyi Wang
- School of Environmental Science and Engineering, Tianjin University, 300072, Tianjin, P. R. China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China.
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China.
| |
Collapse
|
5
|
Pankey MS, Gochfeld DJ, Gastaldi M, Macartney KJ, Clayshulte Abraham A, Slattery M, Lesser MP. Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin. Mol Ecol 2024; 33:e17321. [PMID: 38529721 DOI: 10.1111/mec.17321] [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: 05/31/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024]
Abstract
Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles.
Collapse
Affiliation(s)
- M S Pankey
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - D J Gochfeld
- National Center for Natural Products Research and Environmental Toxicology, University of Mississippi, University, Mississippi, USA
| | - M Gastaldi
- Escuela Superior de Ciencias Marinas-Universidad Nacional del Comahue, San Antonio Oeste, Río Negro, Argentina
| | - K J Macartney
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - A Clayshulte Abraham
- Division of Environmental Toxicology, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
- Division of Pharmacognosy, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
| | - M Slattery
- Division of Environmental Toxicology, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
- Division of Pharmacognosy, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
| | - M P Lesser
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Turon M, Ford M, Maldonado M, Sitjà C, Riesgo A, Díez-Vives C. Microbiome changes through the ontogeny of the marine sponge Crambe crambe. ENVIRONMENTAL MICROBIOME 2024; 19:15. [PMID: 38468324 DOI: 10.1186/s40793-024-00556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND Poriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge microbiome can be acquired from the surrounding environment (horizontal acquisition) or obtained from the parents during the reproductive process through a variety of mechanisms (vertical transfer), typically resulting in the presence of symbiotic microbes throughout all stages of sponge development. How and to what extent the different components of the microbiome are transferred to the developmental stages remain poorly understood. Here, we investigated the microbiome composition of a common, low-microbial-abundance, Atlantic-Mediterranean sponge, Crambe crambe, throughout its ontogeny, including adult individuals, brooded larvae, lecithotrophic free-swimming larvae, newly settled juveniles still lacking osculum, and juveniles with a functional osculum for filter feeding. RESULTS Using 16S rRNA gene analysis, we detected distinct microbiome compositions in each ontogenetic stage, with variations in composition, relative abundance, and diversity of microbial species. However, a particular dominant symbiont, Candidatus Beroebacter blanensis, previously described as the main symbiont of C. crambe, consistently occurred throughout all stages, an omnipresence that suggests vertical transmission from parents to offspring. This symbiont fluctuated in relative abundance across developmental stages, with pronounced prevalence in lecithotrophic stages. A major shift in microbial composition occurred as new settlers completed osculum formation and acquired filter-feeding capacity. Candidatus Beroebacter blanensis decreased significatively at this point. Microbial diversity peaked in filter-feeding stages, contrasting with the lower diversity of lecithotrophic stages. Furthermore, individual specific transmission patterns were detected, with greater microbial similarity between larvae and their respective parents compared to non-parental conspecifics. CONCLUSIONS These findings suggest a putative vertical transmission of the dominant symbiont, which could provide some metabolic advantage to non-filtering developmental stages of C. crambe. The increase in microbiome diversity with the onset of filter-feeding stages likely reflects enhanced interaction with environmental microbes, facilitating horizontal transmission. Conversely, lower microbiome diversity in lecithotrophic stages, prior to filter feeding, suggests incomplete symbiont transfer or potential symbiont digestion. This research provides novel information on the dynamics of the microbiome through sponge ontogeny, on the strategies for symbiont acquisition at each ontogenetic stage, and on the potential importance of symbionts during larval development.
Collapse
Affiliation(s)
- Marta Turon
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Madeline Ford
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Manuel Maldonado
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), c/Accés a la Cala St. Francesc, 14, 17300, Blanes, Spain
| | - Cèlia Sitjà
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), c/Accés a la Cala St. Francesc, 14, 17300, Blanes, Spain
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | - Cristina Díez-Vives
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
- Department of Systems Biology, Centro Nacional de Biotecnología, c/Darwin, 3, 28049, Madrid, Spain.
| |
Collapse
|
8
|
Stuij TM, Cleary DFR, Rocha RJM, Polónia ARM, Silva DAM, Louvado A, de Voogd NJ, Gomes NCM. Impacts of humic substances, elevated temperature, and UVB radiation on bacterial communities of the marine sponge Chondrilla sp. FEMS Microbiol Ecol 2024; 100:fiae022. [PMID: 38366951 PMCID: PMC10939426 DOI: 10.1093/femsec/fiae022] [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: 06/06/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVs potentially involved in recalcitrant organic matter degradation (e.g., the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and there were no significant interactive effects of HS, heat, and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems.
Collapse
Affiliation(s)
- Tamara M Stuij
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Rui J M Rocha
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Davide A M Silva
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Antonio Louvado
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, the Netherlands
- Institute of Biology (IBL), Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Newton C M Gomes
- Department of Biology and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| |
Collapse
|
9
|
Freitas MAMD, Cunha-Ferreira IC, Leal CV, Fernandez JCC, Omachi CY, Campos LS, Masi BP, Krüger RH, Hajdu E, Thompson CC, Thompson FL. Microbiome diversity from sponges biogeographically distributed between South America and Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163256. [PMID: 37011689 DOI: 10.1016/j.scitotenv.2023.163256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
Sponges from South America and Antarctica are evolutionarily closely related. Specific symbiont signatures that could differentiate these two geographic regions are unknown. This study aimed to investigate the microbiome diversity of sponges from South America and Antarctica. In total 71 sponge specimens were analyzed (Antarctica: N = 59, 13 different species; South America: N = 12, 6 different species). Illumina 16S rRNA sequences were generated (2.88 million sequences; 40K ± 29K/sample). The most abundant symbionts were heterotrophic (94.8 %) and belonged mainly to Proteobacteria and Bacteroidota. EC94 was the most abundant symbiont and dominated the microbiome of some species (70-87 %), comprising at least 10 phylogroups. Each of the EC94 phylogroups was specific to one genus or species of sponge. Furthermore, South America sponges had higher abundance of photosynthetic microorganisms (2.3 %) and sponges from Antarctica, the highest abundance of chemosynthetic (5.5 %). Sponge symbionts may contribute to the function of their hosts. The unique features from each of these two regions (e.g., light, temperature, and nutrients) possibly stimulate distinct microbiome diversity from sponges biogeographically distributed across continents.
Collapse
Affiliation(s)
- Mayanne A M de Freitas
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Camille V Leal
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Julio C C Fernandez
- Department of Invertebrates, National Museum, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Claudia Y Omachi
- Laboratory of Environmental Indicators, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Lucia S Campos
- Department of Zoology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno P Masi
- Laboratory of Marine Ecology and Fishery Oceanography of the Amazon (LEMOPA), Socio environmental and Water Resources Institute (ISARH), Federal Rural University of the Amazon (UFRA), Belém, PA, Brazil
| | - Ricardo H Krüger
- Laboratory of Enzymology, Biology Institute, University of Brasília (UNB), Brasília, Brazil
| | - Eduardo Hajdu
- Laboratory of Environmental Indicators, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Cristiane C Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| |
Collapse
|
10
|
Gantt SE, Erwin PM. Effects of sponge-to-sponge contact on the microbiomes of three spatially competing Caribbean coral reef species. Microbiologyopen 2023; 12:e1354. [PMID: 37379422 DOI: 10.1002/mbo3.1354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 06/30/2023] Open
Abstract
Sponges perform important ecosystem functions, host diverse microbial symbiont communities (microbiomes), and have been increasing in density on Caribbean coral reefs over the last decade. Sponges compete for space in coral reef communities through both morphological and allelopathic strategies, but no studies of microbiome impacts during these interactions have been conducted. Microbiome alterations mediate spatial competition in other coral reef invertebrates and may similarly impact competitive outcomes for sponges. In this study, we characterized the microbiomes of three common Caribbean sponges (Agelas tubulata, Iotrochota birotulata, and Xestospongia muta) observed to naturally interact spatially in Key Largo, Florida (USA). For each species, replicate samples were collected from sponges in contact with neighbors at the site of contact (contact) and distant from the site of contact (no contact), and from sponges spatially isolated from neighbors (control). Next-generation amplicon sequencing (V4 region of 16S rRNA) revealed significant differences in microbial community structure and diversity among sponge species, but no significant effects were observed within sponge species across all contact states and competitor pairings, indicating no large community shifts in response to direct contact. At a finer scale, particular symbiont taxa (operational taxonomic units at 97% sequence identity, OTUs) were shown to decrease significantly in some interaction pairings, suggesting localized effects for specific sponge competitors. Overall, these results revealed that direct contact during spatial competition does not significantly alter microbial community composition or structure of interacting sponges, suggesting that allelopathic interactions and competitive outcomes are not mediated by microbiome damage or destabilization.
Collapse
Affiliation(s)
- Shelby E Gantt
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Patrick M Erwin
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| |
Collapse
|
11
|
Hardoim CCP, Hardoim PR, Lôbo-Hajdu G, Custódio MR, Thomas T. The microbiome of the sponge Aplysina caissara in two sites with different levels of anthropogenic impact. FEMS Microbiol Lett 2023; 370:fnad064. [PMID: 37401172 DOI: 10.1093/femsle/fnad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023] Open
Abstract
Despite the important roles that marine sponges play in ecosystem functioning and structuring, little is known about how the sponge holobiont responds to local anthropogenic impacts. Here we assess the influence of an impacted environment (Praia Preta) on the microbial community associated with the endemic sponge Aplysina caissara in comparison to a less-impacted area (Praia do Guaecá) from the coast of São Paulo state (Brazil, southwestern Atlantic coast). We hypothesized that the local anthropogenic impacts will change the microbiome of A. caissara and that the community assembly will be driven by a different process (i.e. deterministic versus stochastic) under distinct levels of impact. The microbiome at the amplicon sequence variants level was found to be statistically distinct between sponges from the different sites, and this was also seen for the microbial communities of the surrounding seawater and sediments. Microbial communities of A. caissara from both sites were found to be assembled by deterministic processes, even though the sites presented distinct anthropogenic impacts, showing a pivotal role of the sponge host in selecting its own microbiome. Overall, this study revealed that local anthropogenic impacts altered the microbiome of A. caissara; however, assembly processes are largely determined by the sponge host.
Collapse
Affiliation(s)
- Cristiane C P Hardoim
- São Paulo State University, Praça Infante Dom Henrique s/nº, Parque Bitaru, São Vicente, São Paulo, CEP 11.330-900, Brazil
- Graduate Program in Evolution and Diversity of the Federal University of ABC, Av. dos Estados, 5001, Bairro Bangu, Santo André, São Paulo, CEP 09210-580, Brazil
| | - Pablo R Hardoim
- São Paulo State University, Praça Infante Dom Henrique s/nº, Parque Bitaru, São Vicente, São Paulo, CEP 11.330-900, Brazil
| | - Gisele Lôbo-Hajdu
- Department of Genetics, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rua São Francisco Xavier, 524, Maracanã, Rio de Janeiro, CEP: 20550-013, Brazil
| | - Márcio R Custódio
- Department of Genetics, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rua São Francisco Xavier, 524, Maracanã, Rio de Janeiro, CEP: 20550-013, Brazil
- Department of Physiology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14 , 101, São Paulo, CEP 05508-090, Brazil
| | - Torsten Thomas
- Department of Genetics, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rua São Francisco Xavier, 524, Maracanã, Rio de Janeiro, CEP: 20550-013, Brazil
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|
12
|
de Menezes TA, de Freitas MAM, Lima MS, Soares AC, Leal C, Busch MDS, Tschoeke DA, de O Vidal L, Atella GC, Kruger RH, Setubal J, Vasconcelos AA, de Mahiques MM, Siegle E, Asp NE, Cosenza C, Hajdu E, de Rezende CE, Thompson CC, Thompson FL. Fluxes of the Amazon River plume nutrients and microbes into marine sponges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157474. [PMID: 35868367 DOI: 10.1016/j.scitotenv.2022.157474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/14/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km2 off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ13C and δ15N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.
Collapse
Affiliation(s)
- Tatiane A de Menezes
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Mayanne A M de Freitas
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Michele S Lima
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ana Carolina Soares
- Bioinformatics Laboratory, Department of Biochemistry, Institute of Chemistry, University of São Paulo (USP), São Paulo, Brazil
| | - Camille Leal
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Mileane de S Busch
- Laboratory of Lipids Biochemistry and Lipoprotein, Biochemistry Institute Leopoldo de Meis, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo A Tschoeke
- Biomedical Engineering Program - COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Luciana de O Vidal
- Environmental Sciences Laboratory, Biosciences and Biotechnology Center, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil; Department of Ecology and Marine Resources, Institute of Biosciences, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil
| | - Georgia C Atella
- Laboratory of Lipids Biochemistry and Lipoprotein, Biochemistry Institute Leopoldo de Meis, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ricardo H Kruger
- Laboratory of Enzymology, University of Brasilia (UNB), Brasilia, Brazil
| | - João Setubal
- Bioinformatics Laboratory, Department of Biochemistry, Institute of Chemistry, University of São Paulo (USP), São Paulo, Brazil
| | | | | | - Eduardo Siegle
- Oceanographic Institute (IO), University of São Paulo (USP), São Paulo, Brazil
| | - Nils Edvin Asp
- Federal University of Pará, Institute of Coastal Studies (IECOS), Bragança Campus, Bragança, PA, Brazil
| | - Carlos Cosenza
- Center of Technology - CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Eduardo Hajdu
- Department of Invertebrates, National Museum, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carlos E de Rezende
- Environmental Sciences Laboratory, Biosciences and Biotechnology Center, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil.
| | - Cristiane C Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Fabiano L Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| |
Collapse
|
13
|
Lesser MP, Sabrina Pankey M, Slattery M, Macartney KJ, Gochfeld DJ. Microbiome diversity and metabolic capacity determines the trophic ecology of the holobiont in Caribbean sponges. ISME COMMUNICATIONS 2022; 2:112. [PMID: 37938762 PMCID: PMC9723761 DOI: 10.1038/s43705-022-00196-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/24/2022] [Accepted: 10/31/2022] [Indexed: 06/18/2023]
Abstract
Sponges are increasingly recognized as an ecologically important taxon on coral reefs, representing significant biomass and biodiversity where sponges have replaced scleractinian corals. Most sponge species can be divided into two symbiotic states based on symbiont community structure and abundance (i.e., the microbiome), and are characterized as high microbial abundance (HMA) or low microbial abundance (LMA) sponges. Across the Caribbean, sponge species of the HMA or LMA symbiotic states differ in metabolic capacity, as well as their trophic ecology. A metagenetic analysis of symbiont 16 S rRNA and metagenomes showed that HMA sponge microbiomes are more functionally diverse than LMA microbiomes, offer greater metabolic functional capacity and redundancy, and encode for the biosynthesis of secondary metabolites. Stable isotope analyses showed that HMA and LMA sponges primarily consume dissolved organic matter (DOM) derived from external autotrophic sources, or live particulate organic matter (POM) in the form of bacterioplankton, respectively, resulting in a low degree of resource competition between these symbiont states. As many coral reefs have undergone phase shifts from coral- to macroalgal-dominated reefs, the role of DOM, and the potential for future declines in POM due to decreased picoplankton productivity, may result in an increased abundance of chemically defended HMA sponges on tropical coral reefs.
Collapse
Affiliation(s)
- Michael P Lesser
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
| | - M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Marc Slattery
- Department of BioMolecular Sciences, Division of Pharmacognosy, University of Mississippi, Oxford, MS, 38677, USA
| | - Keir J Macartney
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
- University of Texas Rio Grande Valley, School of Earth, Environmental and Marine Sciences, Port Isabel, TX, 78958, USA
| | - Deborah J Gochfeld
- National Center for Natural Products Research, University of Mississippi, Oxford, MS, 38677, USA
| |
Collapse
|
14
|
Indraningrat AAG, Steinert G, Becking LE, Mueller B, de Goeij JM, Smidt H, Sipkema D. Sponge holobionts shift their prokaryotic communities and antimicrobial activity from shallow to lower mesophotic depths. Antonie Van Leeuwenhoek 2022; 115:1265-1283. [PMID: 35998007 PMCID: PMC9534810 DOI: 10.1007/s10482-022-01770-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/07/2022] [Indexed: 11/05/2022]
Abstract
In this study, we used 16S rRNA gene amplicon sequencing to investigate prokaryotic community composition of the Caribbean sponges Xestospongia muta and Agelas sventres from three depth ranges: < 30 m (shallow), 30–60 m (upper mesophotic), and 60–90 m (lower mesophotic). The prokaryotic community in shallow samples of X. muta was enriched in Cyanobacteria, Chloroflexota, and Crenarchaeota compared to samples from mesophotic depths, while mesophotic samples of X. muta were enriched in Acidobacteriota. For A. sventres, relative abundance of Acidobacteriota, Chloroflexota, and Gammaproteobacteria was higher in shallow samples, while Proteobacteria and Crenarchaeota were enriched in mesophotic A. sventres samples. Antimicrobial activity was evaluated by screening crude extracts of sponges against a set of Gram-positive and Gram-negative bacteria, a yeast, and an oomycete. Antibacterial activities from crude extracts of shallow sponge individuals were generally higher than observed from mesophotic individuals, that showed limited or no antibacterial activities. Conversely, the highest anti-oomycete activity was found from crude extracts of X. muta individuals from lower mesophotic depth, but without a clear pattern across the depth gradient. These results indicate that sponge-associated prokaryotic communities and the antimicrobial activity of sponges change within species across a depth gradient from shallow to mesophotic depth.
Collapse
Affiliation(s)
- Anak Agung Gede Indraningrat
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Faculty of Medicine and Health Sciences, Warmadewa University, Jln Terompong 24, 80235, Denpasar, Bali, Indonesia
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Leontine E Becking
- Marine Animal Ecology Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Wageningen Marine Research, Wageningen University and Research, Ankerpark 27, 1781 AG, Den Helder, The Netherlands
| | - Benjamin Mueller
- Department of Freshwater and Marine Ecology, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, The Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| |
Collapse
|
15
|
Happel L, Rondon R, Font A, González-Aravena M, Cárdenas CA. Stability of the Microbiome of the Sponge Mycale ( Oxymycale) acerata in the Western Antarctic Peninsula. Front Microbiol 2022; 13:827863. [PMID: 35444618 PMCID: PMC9014287 DOI: 10.3389/fmicb.2022.827863] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/21/2022] [Indexed: 01/04/2023] Open
Abstract
The sponge microbiome, especially in Low Microbial Abundance (LMA) species, is expected to be influenced by the local environment; however, contrasting results exist with evidence showing that host specificity is also important, hence suggesting that the microbiome is influenced by host-specific and environmental factors. Despite sponges being important members of Southern Ocean benthic communities, their relationships with the microbial communities they host remain poorly studied. Here, we studied the spatial and temporal patterns of the microbiota associated with the ecologically important LMA sponge M. acerata at sites along ∼400 km of the Western Antarctic Peninsula (WAP) to assess patterns in the core and variable microbial components of the symbiont communities of this sponge species. The analyses of 31 samples revealed that the microbiome of M. acerata is composed of 35 prokaryotic phyla (3 Archaea, 31 Bacteria, and one unaffiliated), being mainly dominated by Proteobacteria with Gammaproteobacteria as the most dominant class. The core community was composed of six prokaryotic OTUs, with gammaproteobacterial OTU (EC94 Family), showing a mean abundance over 65% of the total abundance. Despite some differences in rare OTUs, the core community did not show clear patterns in diversity and abundance associated with specific sites/environmental conditions, confirming a low variability in community structure of this species along the WAP. The analysis at small scale (Doumer Island, Palmer Archipelago) showed no differences in space and time in the microbiome M. acerata collected at sites around the island, sampled in three consecutive years (2016–2018). Our results highlight the existence of a low spatial and temporal variability in the microbiome of M. acerata, supporting previous suggestions based on limited studies on this and other Antarctic sponges.
Collapse
Affiliation(s)
- Lea Happel
- IMBRSea International Masters Program, Ghent University, Ghent, Belgium.,Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Bremerhaven, Germany
| | - Rodolfo Rondon
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | | | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile.,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| |
Collapse
|
16
|
González-Acosta B, Barraza A, Guadarrama-Analco C, Hernández-Guerrero CJ, Martínez-Díaz SF, Cardona-Félix CS, Aguila-Ramírez RN. Depth effect on the prokaryotic community assemblage associated with sponges from different rocky reefs. PeerJ 2022; 10:e13133. [PMID: 35411254 PMCID: PMC8994493 DOI: 10.7717/peerj.13133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/26/2022] [Indexed: 01/12/2023] Open
Abstract
Background Sponge microbiomes are essential for the function and survival of their host and produce biologically active metabolites, therefore, they are ideal candidates for ecological, pharmacologic and clinical research. Next-generation sequencing (NGS) has revealed that many factors, including the environment and host, determine the composition and structure of these symbiotic communities but the controls of this variation are not well described. This study assessed the microbial communities associated with two marine sponges of the genera Aplysina (Nardo, 1834) and Ircinia (Nardo, 1833) in rocky reefs from Punta Arena de la Ventana (Gulf of California) and Pichilingue (La Paz Bay) in the coast of Baja California Sur, México to determine the relative importance of environment and host in structuring the microbiome of sponges. Methods Specimens of Aplysina sp were collected by scuba diving at 10 m and 2 m; Ircinia sp samples were collected at 2 m. DNA of sponge-associated prokaryotes was extracted from 1 cm3 of tissue, purified and sent for 16S amplicon sequencing. Primer trimmed pair-ended microbial 16S rDNA gene sequences were merged using Ribosomal Database Project (RDP) Paired-end Reads Assembler. Chao1, Shannon and Simpson (alpha) biodiversity indices were estimated, as well permutational analysis of variance (PERMANOVA), and Bray-Curtis distances. Results The most abundant phyla differed between hosts. Those phyla were: Proteobacteria, Acidobacteria, Cyanobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes. In Ircinia sp the dominant phylum was Acidobacteria. Depth was the main factor influencing the microbial community, as analysis of similarities (ANOSIM) showed a significant difference between the microbial communities from different depths. Conclusion Microbial diversity analysis showed that depth was more important than host in structuring the Aplysina sp and Ircinia sp microbiome. This observation contrast with previous reports that the sponge microbiome is highly host specific.
Collapse
Affiliation(s)
- Bárbara González-Acosta
- Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
| | - Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
| | - César Guadarrama-Analco
- Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
| | | | | | | | - Ruth Noemí Aguila-Ramírez
- Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
| |
Collapse
|
17
|
Madden AA, Oliverio AM, Kearns PJ, Henley JB, Fierer N, Starks PTB, Wolfe BE, Romero LM, Lattin CR. Chronic stress and captivity alter the cloacal microbiome of a wild songbird. J Exp Biol 2022; 225:274791. [DOI: 10.1242/jeb.243176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/07/2022] [Indexed: 11/20/2022]
Abstract
There are complex interactions between an organism's microbiome and its response to stressors, often referred to as the “gut-brain axis;” however, the ecological relevance of this axis in wild animals remains poorly understood. Here, we used a chronic mild stress protocol to induce stress in wild-caught house sparrows (Passer domesticus), and compared microbial communities among stressed animals, those recovering from stress, captive controls (unstressed), and a group not brought into captivity. We assessed changes in microbial communities and abundance of shed microbes by culturing cloacal samples on multiple media to select for aerobic and anaerobic bacteria and fungi. We complemented this with cultivation-independent 16S and ITS rRNA gene amplification and sequencing, pairing these results with host physiological and immune metrics, including body mass change, relative spleen mass, and plasma corticosterone concentrations. We found significant effects of stress and captivity on the house sparrow microbiomes, with stress leading to an increased relative abundance of endotoxin-producing bacteria— a possible mechanism for the hyperinflammatory response observed in captive avians. While we found evidence that the microbiome community partially recovers after stress cessation, animals may lose key taxa, and the abundance of endotoxin-producing bacteria persists. Our results suggest an overall link between chronic stress, host immune system, and the microbiome, with the loss of potentially beneficial taxa (e.g., lactic acid bacteria), and an increase in endotoxin-producing bacteria due to stress and captivity. Ultimately, consideration of the host's microbiome may be useful when evaluating the impact of stressors on individual and population health.
Collapse
Affiliation(s)
- Anne A. Madden
- Department of Biology, Tufts University, Medford, MA 02155, USA
- The Microbe Institute, Everett, MA, 02149, USA
| | - Angela M. Oliverio
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
- Yale School of the Environment, Yale University, 195 Prospect St., New Haven, CT, 06511, USA
| | | | - Jessica B. Henley
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | | | | | | | - Christine R. Lattin
- Department of Biology, Tufts University, Medford, MA 02155, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| |
Collapse
|
18
|
Cristi A, Parada-Pozo G, Morales-Vicencio F, Cárdenas CA, Trefault N. Variability in Host Specificity and Functional Potential of Antarctic Sponge-Associated Bacterial Communities. Front Microbiol 2022; 12:771589. [PMID: 35095792 PMCID: PMC8792898 DOI: 10.3389/fmicb.2021.771589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Sponge-associated microorganisms are essential for sponge survival. They play an important role in recycling nutrients and, therefore, in the maintenance of the ecosystem. These microorganisms are diverse, species-specific, and different from those in the surrounding seawater. Bacterial sponge symbionts have been extensively studied in the tropics; however, little is known about these microorganisms in sponges from high-latitude environments. Sponges can cover up to 80% of the benthos in Antarctica and are crucial architects for the marine food web. In this study, we present analyses of the bacterial symbionts of three sponges: Haliclona (Rhizoniera) sp., Hymeniacidon torquata, and Isodictya kerguelenensis from the Western Antarctic Peninsula (WAP) with the aim to determine variations on the specificity of the bacteria–sponge interactions and potential signatures on their predicted functional profiles. We use high-throughput 16S rRNA gene sequencing of 30 sponge individuals inhabiting South Bay (Palmer Archipelago, WAP) to describe their microbiome taxonomy and diversity and predict potential functional profiles based on this marker gene. Our work shows similar bacterial community composition profiles among the same sponge species, although the symbiotic relationship is not equally conserved among the three Antarctic sponges. The number of species-specific core operational taxonomic units (OTUs) of these Antarctic sponges was low, with important differences between the total abundance accounted for these OTUs. Only eight OTUs were shared between the three sponge species. Analyses of the functional potential revealed that despite the high host–symbiont specificity, the inferred functions are conserved among these microbiomes, although with differences in the abundance of specific functions. H. torquata showed the highest level of intra-specificity and a higher potential of pathways related to energy metabolism, metabolisms of terpenoids and polyketides, and biosynthesis of other secondary metabolites. Overall, this work shows variations in the specificity of the sponge-associated bacterial communities, differences in how hosts and symbionts establish their relations, and in their potential functional capabilities.
Collapse
Affiliation(s)
- Antonia Cristi
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Department of Marine Science, University of Otago, Dunedin, New Zealand
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Génesis Parada-Pozo
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Felipe Morales-Vicencio
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - César A. Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Nicole Trefault
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- *Correspondence: Nicole Trefault,
| |
Collapse
|
19
|
Ruocco N, Esposito R, Zagami G, Bertolino M, De Matteo S, Sonnessa M, Andreani F, Crispi S, Zupo V, Costantini M. Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis. Sci Rep 2021; 11:21151. [PMID: 34707182 PMCID: PMC8551288 DOI: 10.1038/s41598-021-00713-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Although the Mediterranean Sea covers approximately a 0.7% of the world's ocean area, it represents a major reservoir of marine and coastal biodiversity. Among marine organisms, sponges (Porifera) are a key component of the deep-sea benthos, widely recognized as the dominant taxon in terms of species richness, spatial coverage, and biomass. Sponges are evolutionarily ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. In the present work, we firstly aimed at exploring the biodiversity of marine sponges from four different areas of the Mediterranean: Faro Lake in Sicily and "Porto Paone", "Secca delle fumose", "Punta San Pancrazio" in the Gulf of Naples. Eight sponge species were collected from these sites and identified by morphological analysis and amplification of several conserved molecular markers (18S and 28S RNA ribosomal genes, mitochondrial cytochrome oxidase subunit 1 and internal transcribed spacer). In order to analyze the bacterial diversity of symbiotic communities among these different sampling sites, we also performed a metataxonomic analysis through an Illumina MiSeq platform, identifying more than 1500 bacterial taxa. Amplicon Sequence Variants (ASVs) analysis revealed a great variability of the host-specific microbial communities. Our data highlight the occurrence of dominant and locally enriched microbes in the Mediterranean, together with the biotechnological potential of these sponges and their associated bacteria as sources of bioactive natural compounds.
Collapse
Affiliation(s)
- Nadia Ruocco
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Roberta Esposito
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, Complesso Universitario Di Monte Sant’Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Giacomo Zagami
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | - Marco Bertolino
- grid.5606.50000 0001 2151 3065DISTAV, Università Degli Studi Di Genova, Corso Europa 26, 16132 Genoa, Italy
| | - Sergio De Matteo
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | | | | | - Stefania Crispi
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.5326.20000 0001 1940 4177Institute of Biosciences and BioResources Naples, National Research Council of Italy, Naples, Italy
| | - Valerio Zupo
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Maria Costantini
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| |
Collapse
|
20
|
Waterworth SC, Parker-Nance S, Kwan JC, Dorrington RA. Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts. mBio 2021; 12:e0157721. [PMID: 34519538 PMCID: PMC8546597 DOI: 10.1128/mbio.01577-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022] Open
Abstract
The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.
Collapse
Affiliation(s)
- Samantha C. Waterworth
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Shirley Parker-Nance
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Environmental Observation Network, Elwandle Coastal Node, Gqeberha (Port Elizabeth), South Africa
| | - Jason C. Kwan
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Rosemary A. Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Institute for Aquatic Biodiversity, Makhanda, South Africa
| |
Collapse
|
21
|
Campana S, Demey C, Busch K, Hentschel U, Muyzer G, de Goeij JM. Marine sponges maintain stable bacterial communities between reef sites with different coral to algae cover ratios. FEMS Microbiol Ecol 2021; 97:fiab115. [PMID: 34351429 PMCID: PMC8378938 DOI: 10.1093/femsec/fiab115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022] Open
Abstract
Marine sponges play a major ecological role in recycling resources on coral reef ecosystems. The cycling of resources may largely depend on the stability of the host-microbiome interactions and their susceptibility to altered environmental conditions. Given the current coral to algal phase shift on coral reefs, we investigated whether the sponge-associated bacterial communities of four sponge species, with either high or low microbial abundances (HMA and LMA), remain stable at two reefs sites with different coral to algae cover ratios. Additionally, we assessed the bacterial community composition of two of these sponge species before and after a reciprocal transplantation experiment between the sites. An overall stable bacterial community composition was maintained across the two sites in all sponge species, with a high degree of host-specificity. Furthermore, the core bacterial communities of the sponges remained stable also after a 21-day transplantation period, although a minor shift was observed in less abundant taxa (< 1%). Our findings support the conclusion that host identity and HMA-LMA status are stronger traits in shaping bacterial community composition than habitat. Nevertheless, long-term microbial monitoring of sponges along with benthic biomass and water quality assessments are needed for identifying ecosystem tolerance ranges and tipping points in ongoing coral reef phase shifts.
Collapse
Affiliation(s)
- Sara Campana
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
| | - Celine Demey
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
| | - Kathrin Busch
- Department of Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Ute Hentschel
- Department of Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
- CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
| |
Collapse
|
22
|
Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte. Antonie van Leeuwenhoek 2020; 114:95-112. [DOI: 10.1007/s10482-020-01503-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022]
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
Díez‐Vives C, Taboada S, Leiva C, Busch K, Hentschel U, Riesgo A. On the way to specificity - Microbiome reflects sponge genetic cluster primarily in highly structured populations. Mol Ecol 2020; 29:4412-4427. [PMID: 32931063 PMCID: PMC7756592 DOI: 10.1111/mec.15635] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
Most animals, including sponges (Porifera), have species-specific microbiomes. Which genetic or environmental factors play major roles structuring the microbial community at the intraspecific level in sponges is, however, largely unknown. In this study, we tested whether geographic location or genetic structure of conspecific sponges influences their microbial assembly. For that, we used three sponge species with different rates of gene flow, and collected samples along their entire distribution range (two from the Mediterranean and one from the Southern Ocean) yielding a total of 393 samples. These three sponge species have been previously analysed by microsatellites or single nucleotide polymorphisms, and here we investigate their microbiomes by amplicon sequencing of the microbial 16S rRNA gene. The sponge Petrosia ficiformis, with highly isolated populations (low gene flow), showed a stronger influence of the host genetic distance on the microbial composition than the spatial distance. Host-specificity was therefore detected at the genotypic level, with individuals belonging to the same host genetic cluster harbouring more similar microbiomes than distant ones. On the contrary, the microbiome of Ircinia fasciculata and Dendrilla antarctica - both with weak population structure (high gene flow) - seemed influenced by location rather than by host genetic distance. Our results suggest that in sponge species with high population structure, the host genetic cluster influence the microbial community more than the geographic location.
Collapse
Affiliation(s)
| | - Sergi Taboada
- Departamento de Ciencias de la VidaEU‐US Marine Biodiversity GroupUniversidad de AlcaláAlcalá de HenaresSpain
- Departamento de Biología (Zoología)Universidad Autónoma de MadridFacultad de CienciasMadridSpain
| | - Carlos Leiva
- Department of Life SciencesThe Natural History MuseumLondonUK
- Department of Genetics, Microbiology and StatisticsFaculty of BiologyUniversity of BarcelonaBarcelonaSpain
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research KielResearch Unit Marine SymbiosesKielGermany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research KielResearch Unit Marine SymbiosesKielGermany
| | - Ana Riesgo
- Department of Life SciencesThe Natural History MuseumLondonUK
- Department of Biodiversity and Evolutionary BiologyMuseo Nacional de Ciencias Naturales de Madrid (CSIC)MadridSpain
| |
Collapse
|
25
|
Papale M, Rizzo C, Fani R, Bertolino M, Costa G, Paytuví-Gallart A, Schiaparelli S, Michaud L, Azzaro M, Lo Giudice A. Exploring the Diversity and Metabolic Profiles of Bacterial Communities Associated With Antarctic Sponges (Terra Nova Bay, Ross Sea). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
26
|
O'Brien PA, Tan S, Yang C, Frade PR, Andreakis N, Smith HA, Miller DJ, Webster NS, Zhang G, Bourne DG. Diverse coral reef invertebrates exhibit patterns of phylosymbiosis. THE ISME JOURNAL 2020; 14:2211-2222. [PMID: 32444811 PMCID: PMC7608455 DOI: 10.1038/s41396-020-0671-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023]
Abstract
Microbiome assemblages of plants and animals often show a degree of correlation with host phylogeny; an eco-evolutionary pattern known as phylosymbiosis. Using 16S rRNA gene sequencing to profile the microbiome, paired with COI, 18S rRNA and ITS1 host phylogenies, phylosymbiosis was investigated in four groups of coral reef invertebrates (scleractinian corals, octocorals, sponges and ascidians). We tested three commonly used metrics to evaluate the extent of phylosymbiosis: (a) intraspecific versus interspecific microbiome variation, (b) topological comparisons between host phylogeny and hierarchical clustering (dendrogram) of host-associated microbial communities, and (c) correlation of host phylogenetic distance with microbial community dissimilarity. In all instances, intraspecific variation in microbiome composition was significantly lower than interspecific variation. Similarly, topological congruency between host phylogeny and the associated microbial dendrogram was more significant than would be expected by chance across all groups, except when using unweighted UniFrac distance (compared with weighted UniFrac and Bray-Curtis dissimilarity). Interestingly, all but the ascidians showed a significant positive correlation between host phylogenetic distance and associated microbial dissimilarity. Our findings provide new perspectives on the diverse nature of marine phylosymbioses and the complex roles of the microbiome in the evolution of marine invertebrates.
Collapse
Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Chentao Yang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Pedro R Frade
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Nikos Andreakis
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Hillary A Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David J Miller
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia.
- Australian Institute of Marine Science, Townsville, QLD, Australia.
- AIMS@JCU, Townsville, QLD, Australia.
| |
Collapse
|
27
|
Molecular Network and Culture Media Variation Reveal a Complex Metabolic Profile in Pantoea cf. eucrina D2 Associated with an Acidified Marine Sponge. Int J Mol Sci 2020; 21:ijms21176307. [PMID: 32878176 PMCID: PMC7504411 DOI: 10.3390/ijms21176307] [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: 08/05/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
The Gram-negative Pantoea eucrina D2 was isolated from the marine sponge Chondrosia reniformis. Sponges were collected in a shallow volcanic vents system in Ischia island (South Italy), influenced by CO2 emissions and lowered pH. The chemical diversity of the secondary metabolites produced by this strain, under different culture conditions, was explored by a combined approach including molecular networking, pure compound isolation and NMR spectroscopy. The metabolome of Pantoea cf. eucrina D2 yielded a very complex molecular network, allowing the annotation of several metabolites, among them two biosurfactant clusters: lipoamino acids and surfactins. The production of each class of metabolites was highly dependent on the culture conditions, in particular, the production of unusual surfactins derivatives was reported for the first time from this genus; interestingly the production of these metabolites only arises by utilizing inorganic nitrogen as a sole nitrogen source. Major components of the extract obtained under standard medium culture conditions were isolated and identified as N-lipoamino acids by a combination of 1D and 2D NMR spectroscopy and HRESI-MS analysis. Assessment of the antimicrobial activity of the pure compounds towards some human pathogens, indicated a moderate activity of leucine containing N-lipoamino acids towards Staphylococcus aureus, Staphylococcus epidermidis and a clinical isolate of the emerging food pathogen Listeria monocytogenes.
Collapse
|
28
|
Gökalp M, Kooistra T, Rocha MS, Silva TH, Osinga R, Murk AJ, Wijgerde T. The Effect of Depth on the Morphology, Bacterial Clearance, and Respiration of the Mediterranean Sponge Chondrosia reniformis (Nardo, 1847). Mar Drugs 2020; 18:E358. [PMID: 32664196 PMCID: PMC7401281 DOI: 10.3390/md18070358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 11/16/2022] Open
Abstract
To support the successful application of sponges for water purification and collagen production, we evaluated the effect of depth on sponge morphology, growth, physiology, and functioning. Specimens of Eastern Mediterranean populations of the sponge Chondrosia reniformis (Nardo, 1847) (Demospongiae, Chondrosiida, Chondrosiidae) were reciprocally transplanted between 5 and 20 m depth within the Kaş-Kekova Marine Reserve Area. Control sponges at 5 m had fewer but larger oscula than their conspecifics at 20 m, and a significant inverse relationship between the osculum density and size was found in C. reniformis specimens growing along a natural depth gradient. Sponges transplanted from 20 to 5 m altered their morphology to match the 5 m control sponges, producing fewer but larger oscula, whereas explants transplanted from 5 to 20 m did not show a reciprocal morphological plasticity. Despite the changes in morphology, the clearance, respiration, and growth rates were comparable among all the experimental groups. This indicates that depth-induced morphological changes do not affect the overall performance of the sponges. Hence, the potential for the growth and bioremediation of C. reniformis in mariculture is not likely to change with varying culture depth. The collagen content, however, was higher in shallow water C. reniformis compared to deeper-growing sponges, which requires further study to optimize collagen production.
Collapse
Affiliation(s)
- Mert Gökalp
- Marine Animal Ecology Group, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands; (T.K.); (R.O.); (A.J.M.); (T.W.)
| | - Tjitske Kooistra
- Marine Animal Ecology Group, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands; (T.K.); (R.O.); (A.J.M.); (T.W.)
| | - Miguel Soares Rocha
- 3B’s Research Group, I3Bs–Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal; (M.S.R.); (T.H.S.)
- ICVS/3B’s–PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Tiago H. Silva
- 3B’s Research Group, I3Bs–Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal; (M.S.R.); (T.H.S.)
- ICVS/3B’s–PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Ronald Osinga
- Marine Animal Ecology Group, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands; (T.K.); (R.O.); (A.J.M.); (T.W.)
| | - AlberTinka J. Murk
- Marine Animal Ecology Group, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands; (T.K.); (R.O.); (A.J.M.); (T.W.)
| | - Tim Wijgerde
- Marine Animal Ecology Group, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands; (T.K.); (R.O.); (A.J.M.); (T.W.)
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Yang Q, Franco CMM, Lin HW, Zhang W. Untapped sponge microbiomes: structure specificity at host order and family levels. FEMS Microbiol Ecol 2020; 95:5554005. [PMID: 31494678 DOI: 10.1093/femsec/fiz136] [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: 02/27/2019] [Accepted: 08/22/2019] [Indexed: 12/12/2022] Open
Abstract
Sponges are complex holobionts in which the structure of the microbiome has seldom been characterized above the host species level. The hypothesis tested in this study is that the structure of the sponge microbiomes is specific to the host at the order and family levels. This was done by using 33 sponge species belonging to 19 families representing five orders. A combination of three primer sets covering the V1-V8 regions of the 16S rRNA gene provided a more comprehensive coverage of the microbiomes. Both the diversity and structure of sponge microbiomes were demonstrated to be highly specific to the host phylogeny at the order and family levels. There are always dominant operational taxonomic units (OTUs) (relative abundance >1%) shared between microbial communities of sponges within the same family or order, but these shared OTUs showed high levels of dissimilarity between different sponge families and orders. The unique OTUs for a particular sponge family or order could be regarded as their 'signature identity'. 70%-87% of these unique OTUs (class level) are unaffiliated and represent a vast resource of untapped microbiota. This study contributes to a deeper understanding on the concept of host-specificity of sponge microbiomes and highlights a hidden reservoir of sponge-associated microbial resources.
Collapse
Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia 5042, Australia
| | - Hou-Wen Lin
- Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei Zhang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Xia X, Ki Leung S, Cheung S, Zhang S, Liu H. Rare bacteria in seawater are dominant in the bacterial assemblage associated with the Bloom-forming dinoflagellate Noctiluca scintillans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:135107. [PMID: 31818556 DOI: 10.1016/j.scitotenv.2019.135107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/19/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
Noctiluca scintillans is a bloom-forming dinoflagellate, which is widely distributed in the global coastal seas. Associated bacteria have been proven to be essential for the survival and growth of zooplanktons. However, the diversity and function of bacteria associated with Noctiluca scintillans are under studied and largely unknown. Here, we examined the diversity and function of bacteria associated with field-acquired and laboratory-maintained Noctiluca cells. Our results showed that the bacterial communities associated with the laboratory-maintained Noctiluca were dominated by Rhodobacterales, whereas those associated with the field-acquired Noctiluca varied over time. In addition, major Noctiluca-associated bacteria had low relative abundance in the ambient environment. We also observed that when field-acquired Noctiluca were cultivated with a mono-species food source, there was a shift in the associated bacterial communities. Metagenomic analysis showed that genes involved in DNA replication/repair and osmotic regulation were more abundant than other genes in the Noctiluca-associated bacterial community. Furthermore, the associated bacteria were able to degrade various complex carbohydrates and actively participate in the nitrogen cycle in their host cells. In addition, a draft genome of the Rickettsiaceae strain was recovered, and we showed that the genome did not contain genes encoding hexokinase and phosphoglucomutase, two key enzymes involved in glucose utilization. Instead, the primary energy sources of this bacteria were shown to be glutamate, glutamine and pyruvate, which might be obtained from the host. We suggest that in return, the Rickettsiaceae strain is likely to provide cofactors and amino acids to the host. This study highlights the spatial and temporal complexity of bacterial communities associated with Noctiluca, and provides valuable insights into the interaction between a host and its associated bacteria.
Collapse
Affiliation(s)
- Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), PR China.
| | - Sze Ki Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shunyan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shuwen Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou, PR China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
| |
Collapse
|
33
|
Cárdenas CA, Font A, Steinert G, Rondon R, González-Aravena M. Temporal Stability of Bacterial Communities in Antarctic Sponges. Front Microbiol 2019; 10:2699. [PMID: 31824467 PMCID: PMC6883807 DOI: 10.3389/fmicb.2019.02699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/07/2019] [Indexed: 11/18/2022] Open
Abstract
Marine sponges host dense, diverse, and species-specific microbial communities around the globe; however, most of the current knowledge is restricted to species from tropical and temperate waters. Only recently, some studies have assessed the microbiome of a few Antarctic sponges; however, contrary to low mid-latitude sponges, the knowledge about temporal (stability) patterns in the bacterial communities of Antarctic sponges is absent. Here, we studied the temporal patterns of bacterial communities in the Antarctic sponges Mycale (Oxymycale) acerata, Isodictya sp., Hymeniacidon torquata, and Tedania (Tedaniopsis) wellsae that were tagged in situ and monitored during three austral summers over a 24-month period. By using amplicon sequencing of the bacterial 16S rRNA gene we found that the microbiome differed between species. In general, bacterial communities were dominated by gammaproteobacterial OTUs; however, M. acerata showed the most distinct pattern, being dominated by a single betaproteobacterial OTU. The analysis at OTU level (defined at 97% sequence similarity) showed a highly stable bacterial community through time, despite the abnormal seawater temperatures (reaching 3°C) and rates of temperature increase of 0.15°C day-1 recorded in austral summer 2017. Sponges were characterized by a small core bacterial community that accounted for a high percentage of the abundance. Overall, no consistent changes in core OTU abundance were recorded for all studied species, confirming a high temporal stability of the microbiome. In addition, predicted functional pathway profiles showed that the most abundant pathways among all sponges belonged mostly to metabolism pathway groups (e.g., amino acid, carbohydrate, energy, and nucleotide). The predicted functional pathway patterns differed among the four sponge species. However, no clear temporal differences were detected supporting what was found in terms of the relatively stable composition of the bacterial communities.
Collapse
Affiliation(s)
- César A. Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Rodolfo Rondon
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | | |
Collapse
|
34
|
Estrada A, Hughey MC, Medina D, Rebollar EA, Walke JB, Harris RN, Belden LK. Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling. PeerJ 2019; 7:e7044. [PMID: 31275740 PMCID: PMC6590418 DOI: 10.7717/peerj.7044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/27/2019] [Indexed: 12/28/2022] Open
Abstract
The amphibian skin microbiome has been the focus of recent studies aiming to better understand the role of these microbial symbionts in host defense against disease. However, host-associated microbial communities are complex and dynamic, and changes in their composition and structure can influence their function. Understanding temporal variation of bacterial communities on amphibian skin is critical for establishing baselines from which to improve the development of mitigation techniques based on probiotic therapy and provides long-term host protection in a changing environment. Here, we investigated whether microbial communities on amphibian skin change over time at a single site. To examine this, we collected skin swabs from two pond-breeding species of treefrogs, Agalychnis callidryas and Dendropsophus ebraccatus, over 4 years at a single lowland tropical pond in Panamá. Relative abundance of operational taxonomic units (OTUs) based on 16S rRNA gene amplicon sequencing was used to determine bacterial community diversity on the skin of both treefrog species. We found significant variation in bacterial community structure across long and short-term time scales. Skin bacterial communities differed across years on both species and between seasons and sampling days only in D. ebraccatus. Importantly, bacterial community structures across days were as variable as year level comparisons. The differences in bacterial community were driven primarily by differences in relative abundance of key OTUs and explained by rainfall at the time of sampling. These findings suggest that skin-associated microbiomes are highly variable across time, and that for tropical lowland sites, rainfall is a good predictor of variability. However, more research is necessary to elucidate the significance of temporal variation in bacterial skin communities and their maintenance for amphibian conservation efforts.
Collapse
Affiliation(s)
- Angie Estrada
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Myra C Hughey
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jenifer B Walke
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Smithsonian Tropical Research Institute, Balboa, Ancón, Panamá, Panamá
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Sacristán‐Soriano O, Winkler M, Erwin P, Weisz J, Harriott O, Heussler G, Bauer E, West Marsden B, Hill A, Hill M. Ontogeny of symbiont community structure in two carotenoid-rich, viviparous marine sponges: comparison of microbiomes and analysis of culturable pigmented heterotrophic bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:249-261. [PMID: 30761773 PMCID: PMC6850349 DOI: 10.1111/1758-2229.12739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Marine sponges harbour diverse communities of microbes. Mechanisms used to establish microbial symbioses in sponges are poorly understood, and the relative contributions of horizontal and vertical transmission are unknown for most species. We examined microbial communities in adults and larvae of carotenoid-rich Clathria prolifera and Halichondria bowerbanki from the mid-Atlantic region of the eastern United States. We sequenced microbiomes from larvae and their mothers and seawater (16S rRNA gene sequencing), and compared microbial community characteristics between species and ambient seawater. The microbial communities in sponges were significantly different than those found in seawater, and each species harboured a distinctive microbiome. Larval microbiomes exhibited significantly lower richness compared with adults, with both sponges appearing to transfer to larvae a particular subset of the adult microbiome. We also surveyed culturable bacteria isolated from larvae of both species. Due to conspicuous coloration of adults and larvae, we focused on pigmented heterotrophic bacteria. We found that the densities of bacteria, in terms of colony-forming units and pigmented heterotrophic bacteria, were higher in larvae than in seawater. We identified a common mode of transmission (vertical and horizontal) of microbes in both sponges that might differ between species.
Collapse
Affiliation(s)
- Oriol Sacristán‐Soriano
- Department of BiologyUniversity of RichmondRichmondVAUSA
- Marine Ecology DepartmentCentro de Estudios Avanzados de Blanes (CEAB, CSIC)BlanesSpain
| | - Marina Winkler
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | - Patrick Erwin
- Department of Biology and Marine Biology, Center for Marine ScienceUniversity of North CarolinaWilmingtonNCUSA
| | - Jeremy Weisz
- Department of BiologyLinfield CollegeMcMinnvilleORUSA
| | | | - Gary Heussler
- Department of BiologyFairfield UniversityFairfieldCTUSA
| | - Emily Bauer
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | | | - April Hill
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | - Malcolm Hill
- Department of BiologyUniversity of RichmondRichmondVAUSA
| |
Collapse
|
37
|
Knobloch S, Jóhannsson R, Marteinsson V. Bacterial diversity in the marine spongeHalichondria paniceafrom Icelandic waters and host-specificity of its dominant symbiont “CandidatusHalichondribacter symbioticus”. FEMS Microbiol Ecol 2018; 95:5173036. [DOI: 10.1093/femsec/fiy220] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/07/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Stephen Knobloch
- Microbiology Group, Department of Research and Innovation, Matís ohf., Vinlandsleid 12, 113 Reykjavik, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Saemundargata 2, 101 Reykjavík, Iceland
| | - Ragnar Jóhannsson
- Marine and Freshwater Research Institute, Hafrannsóknastofnun, Skúlagata 4, 101 Reykjavik, Iceland
| | - Viggó Marteinsson
- Microbiology Group, Department of Research and Innovation, Matís ohf., Vinlandsleid 12, 113 Reykjavik, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Saemundargata 2, 101 Reykjavik, Iceland
| |
Collapse
|
38
|
Turon M, Cáliz J, Garate L, Casamayor EO, Uriz MJ. Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges. Sci Rep 2018; 8:15201. [PMID: 30315194 PMCID: PMC6185911 DOI: 10.1038/s41598-018-33545-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/25/2018] [Indexed: 02/08/2023] Open
Abstract
We studied the core bacterial communities of 19 sponge species from Nha Trang Bay (Central Vietnam), with particular emphasis on the contribution of planktonic seawater bacteria to the sponge core microbiomes. To ensure consistent sponge-microbe associations and accurate identification of planktonic bacteria transmitted from seawater, we were very restrictive with the definition of the sponge core microbiomes (present in all the replicates), and with the identification of valid biological 16S rRNA gene sequences (100% sequence identity) that belonged to potentially different bacterial taxa. We found a high overlap (>50% relative abundance) between the sponge species core microbiome and the seawater bacterial core in ca. a half of the studied species, including representatives of both, HMA and LMA sponges. From our restrictive analysis, we point to horizontal transmission as a relevant way of symbiont acquisition in sponges. Some species-specific recognition mechanisms may act in sponges to enrich specific seawater bacteria in their tissues. These mechanisms would allow the maintenance of bacterial communities in a species across geographical ranges. Moreover, besides contrasting preferences in bacteria selection from seawater, divergent physiological traits may also account for the different microbiomes in species of HMA and LMA sponges.
Collapse
Affiliation(s)
- Marta Turon
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain.
| | - Joan Cáliz
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain
| | - Leire Garate
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain
| | - Emilio O Casamayor
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain
| | - Maria J Uriz
- Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala St. Francesc, Blanes, Girona, 17300, Spain.
| |
Collapse
|
39
|
Dat TTH, Steinert G, Thi Kim Cuc N, Smidt H, Sipkema D. Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam. PeerJ 2018; 6:e4970. [PMID: 29900079 PMCID: PMC5995103 DOI: 10.7717/peerj.4970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.
Collapse
Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
40
|
Cárdenas CA, González-Aravena M, Font A, Hestetun JT, Hajdu E, Trefault N, Malmberg M, Bongcam-Rudloff E. High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas. PeerJ 2018; 6:e4935. [PMID: 29892508 PMCID: PMC5994334 DOI: 10.7717/peerj.4935] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/19/2018] [Indexed: 01/07/2023] Open
Abstract
Sponges belonging to genus Mycale are common and widely distributed across the oceans and represent a significant component of benthic communities in term of their biomass, which in many species is largely composed by bacteria. However, the microbial communities associated with Mycale species inhabiting different geographical areas have not been previously compared. Here, we provide the first detailed description of the microbiota of two Mycale species inhabiting the sub-Antarctic Magellan region (53°S) and the Western Antarctic Peninsula (62-64°S), two geographically distant areas (>1,300 km) with contrasting environmental conditions. The sponges Mycale (Aegogropila) magellanica and Mycale (Oxymycale) acerata are both abundant members of benthic communities in the Magellan region and in Antarctica, respectively. High throughput sequencing revealed a remarkable similarity in the microbiota of both sponge species, dominated by Proteobacteria and Bacteroidetes, with both species sharing more than 74% of the OTUs. In contrast, 16% and 10% of the OTUs were found only in either M. magellanica or M. acerata, respectively. Interestingly, despite slight differences in the relative abundance, the most dominant OTUs were present in both species, whereas the unique OTUs had very low abundances (less than 1% of the total abundance). These results show a significant overlap among the microbiota of both Mycale species and also suggest the existence of a low level of specificity of the most dominant symbiont groups.
Collapse
Affiliation(s)
- César A. Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | | | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - Jon T. Hestetun
- Marine Biodiversity Group, Department of Biology, University of Bergen, Bergen, Norway
| | - Eduardo Hajdu
- Museu Nacional, Departamento de Invertebrados, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Maja Malmberg
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
41
|
Exploring the diversity-stability paradigm using sponge microbial communities. Sci Rep 2018; 8:8425. [PMID: 29849034 PMCID: PMC5976656 DOI: 10.1038/s41598-018-26641-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
A key concept in theoretical ecology is the positive correlation between biodiversity and ecosystem stability. When applying this diversity-stability concept to host-associated microbiomes, the following questions emerge: (1) Does microbial diversity influence the stability of microbiomes upon environmental fluctuations? (2) Do hosts that harbor high versus low microbial diversity differ in their stress response? To test the diversity-stability concept in host-associated microbiomes, we exposed six marine sponge species with varying levels of microbial diversity to non-lethal salinity disturbances and followed their microbial composition over time using 16S rRNA gene amplicon sequencing. No signs of sponge stress were evident following salinity amendment and microbiomes exhibited compositional resistance irrespective of their microbial diversity. Compositional stability of the sponge microbiome manifests itself at distinct host taxonomic and host microbial diversity groups, with (1) stable host genotype-specific microbiomes at oligotype-level; (2) stable host species-specific microbiomes at genus-level; and (3) stable and specific microbiomes at phylum-level for hosts with high versus low microbial diversity. The resistance of sponge microbiomes together with the overall stability of sponge holobionts upon salinity fluctuations suggest that the stability-diversity concept does not appear to hold for sponge microbiomes and provides further evidence for the widely recognized environmental tolerance of sponges.
Collapse
|
42
|
Ramsby BD, Hoogenboom MO, Whalan S, Webster NS. Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge. Mol Ecol 2018; 27:2124-2137. [PMID: 29473977 DOI: 10.1111/mec.14544] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 01/08/2023]
Abstract
Bioeroding sponges break down calcium carbonate substratum, including coral skeleton, and their capacity for reef erosion is expected to increase in warmer and more acidic oceans. However, elevated temperature can disrupt the functionally important microbial symbionts of some sponge species, often with adverse consequences for host health. Here, we provide the first detailed description of the microbial community of the bioeroding sponge Cliona orientalis and assess how the community responds to seawater temperatures incrementally increasing from 23°C to 32°C. The microbiome, identified using 16S rRNA gene sequencing, was dominated by Alphaproteobacteria, including a single operational taxonomic unit (OTU; Rhodothalassium sp.) that represented 21% of all sequences. The "core" microbial community (taxa present in >80% of samples) included putative nitrogen fixers and ammonia oxidizers, suggesting that symbiotic nitrogen metabolism may be a key function of the C. orientalis holobiont. The C. orientalis microbiome was generally stable at temperatures up to 27°C; however, a community shift occurred at 29°C, including changes in the relative abundance and turnover of microbial OTUs. Notably, this microbial shift occurred at a lower temperature than the 32°C threshold that induced sponge bleaching, indicating that changes in the microbiome may play a role in the destabilization of the C. orientalis holobiont. C. orientalis failed to regain Symbiodinium or restore its baseline microbial community following bleaching, suggesting that the sponge has limited ability to recover from extreme thermal exposure, at least under aquarium conditions.
Collapse
Affiliation(s)
- Blake D Ramsby
- College of Science and Engineering and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Qld, Australia
| | - Mia O Hoogenboom
- College of Science and Engineering and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Steve Whalan
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Qld, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, Australia
| |
Collapse
|
43
|
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.
Collapse
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
| |
Collapse
|
44
|
Gantt SE, López-Legentil S, Erwin PM. Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor. FEMS Microbiol Lett 2018; 364:3833132. [PMID: 28520957 DOI: 10.1093/femsle/fnx105] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/16/2017] [Indexed: 01/04/2023] Open
Abstract
Marine sponges have been shown to harbor diverse microbial symbiont communities that play key roles in host functioning, yet little is known about how anthropogenic disturbances impact sponge-microbe interactions. The Mediterranean sponge Crambe crambe is known to accumulate heavy metals in polluted harbors. In this study, we investigated whether the microbiome of C. crambe differed between sponges inhabiting a polluted harbor in Blanes (Spain) and a nearby (<1 km) natural environment. Triplicate sponge and ambient seawater samples were collected from each site and the microbial composition of each sample was determined by 16S rRNA gene sequence analysis (Illumina Hi-Seq platform). No significant differences in the diversity or structure of microbial communities in C. crambe were detected between habitats, while a significant difference in community structure was observed in ambient seawater inside and outside of the polluted harbor. The microbiome of C. crambe was clearly differentiated from free-living seawater microbes and dominated by Proteobacteria, specifically a single betaproteobacterium that accounted for >86% of all sequence reads. These results indicate that sponge microbiomes exhibit greater stability and pollution tolerance than their free-living microbial counterparts, potentially mitigating the effects of pollutants on coastal marine communities.
Collapse
Affiliation(s)
- Shelby E Gantt
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA
| | - Patrick M Erwin
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA
| |
Collapse
|
45
|
Coelho FJRC, Cleary DFR, Gomes NCM, Pólonia ARM, Huang YM, Liu LL, de Voogd NJ. Sponge Prokaryote Communities in Taiwanese Coral Reef and Shallow Hydrothermal Vent Ecosystems. MICROBIAL ECOLOGY 2018; 75:239-254. [PMID: 28699015 DOI: 10.1007/s00248-017-1023-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
Previously, it was believed that the prokaryote communities of typical 'low-microbial abundance' (LMA) or 'non-symbiont harboring' sponges were merely subsets of the prokaryote plankton community. Recent research has, however, shown that these sponges are dominated by particular clades of Proteobacteria or Cyanobacteria. Here, we expand on this research and assess the composition and putative functional profiles of prokaryotic communities from LMA sponges collected in two ecosystems (coral reef and hydrothermal vent) from vicinal islands of Taiwan with distinct physicochemical conditions. Six sponge species identified as Acanthella cavernosa (Bubarida), Echinodictyum asperum, Ptilocaulis spiculifer (Axinellida), Jaspis splendens (Tetractinellida), Stylissa carteri (Scopalinida) and Suberites sp. (Suberitida) were sampled in coral reefs in the Penghu archipelago. One sponge species provisionally identified as Hymeniacidon novo spec. (Suberitida) was sampled in hydrothermal vent habitat. Each sponge was dominated by a limited set of operational taxonomic units which were similar to sequences from organisms previously obtained from other LMA sponges. There was a distinct bacterial community between sponges collected in coral reef and in hydrothermal vents. The putative functional profile revealed that the prokaryote community from sponges collected in hydrothermal vents was significantly enriched for pathways related to DNA replication and repair.
Collapse
Affiliation(s)
- F J R C Coelho
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Pólonia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Y M Huang
- Department of Marine Recreation, National Penghu University of Science and Technology, Penghu, Taiwan
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - L-L Liu
- Department of Oceanography, National Sun Yet-Sen University, Kaohsiung, Taiwan
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, the Netherlands.
| |
Collapse
|
46
|
Moitinho-Silva L, Steinert G, Nielsen S, Hardoim CCP, Wu YC, McCormack GP, López-Legentil S, Marchant R, Webster N, Thomas T, Hentschel U. Predicting the HMA-LMA Status in Marine Sponges by Machine Learning. Front Microbiol 2017; 8:752. [PMID: 28533766 PMCID: PMC5421222 DOI: 10.3389/fmicb.2017.00752] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species. The largest proportion of microbiome variation was explained by the host identity. Several phyla, classes, and OTUs were found differentially abundant in either group, which were considered “HMA indicators” and “LMA indicators.” Machine learning algorithms (classifiers) were trained to predict the HMA-LMA status of sponges. Among nine different classifiers, higher performances were achieved by Random Forest trained with phylum and class abundances. Random Forest with optimized parameters predicted the HMA-LMA status of additional 135 sponge species (1,232 specimens) without a priori knowledge. These sponges were grouped in four clusters, from which the largest two were composed of species consistently predicted as HMA (n = 44) and LMA (n = 74). In summary, our analyses shown distinct features of the microbial communities associated with HMA and LMA sponges. The prediction of the HMA-LMA status based on the microbiome profiles of sponges demonstrates the application of machine learning to explore patterns of host-associated microbial communities.
Collapse
Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Cristiane C P Hardoim
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Yu-Chen Wu
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel and Christian-Albrechts UniversityKiel, Germany
| | - Grace P McCormack
- Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland GalwayGalway, Ireland
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, and Center for Marine Science, University of North CarolinaWilmington, NC, USA
| | - Roman Marchant
- Centre for Translational Data Science, School of Information Technologies, University of SydneySydney, NSW, Australia
| | - Nicole Webster
- Australian Institute of Marine ScienceTownsville, QLD, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of QueenslandSt. Lucia, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel and Christian-Albrechts UniversityKiel, Germany
| |
Collapse
|
47
|
Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila. Sci Rep 2017; 7:43247. [PMID: 28233813 PMCID: PMC5324122 DOI: 10.1038/srep43247] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/20/2017] [Indexed: 11/08/2022] Open
Abstract
Microbial symbionts in sponges are ubiquitous, forming complex and highly diverse host-specific communities. Conspecific sponges display remarkable stability in their symbiont communities, both spatially and temporally, yet extreme fluctuations in environmental factors can cause shifts in host-symbiont associations. We previously demonstrated that the marine sponge Hymeniacidon heliophila displayed significant community-level differences in microbial symbiont diversity, structure and composition when sampled from intertidal and subtidal environments. Here, we conducted a 70-day reciprocal transplant experiment to directly test the effect of tidal exposure on the microbiome of H. heliophila, using next-generation Illumina sequencing of 16S rRNA gene sequences to characterize symbiont communities. While sponges transplanted between habitats displayed shifts in microbial communities after 70 days, temporal variation was the dominant factor affecting microbial community composition. Further, we identified core symbionts that persisted across these spatio-temporal scales and used a metagenomic approach to show that these dominant members of the microbiome of H. heliophila represent nitrogen cycling taxa that have the potential to contribute to a diverse array of nitrogen transformations in the sponge holobiont. Together, these results indicate that despite moderate spatio-temporal shifts in symbiont composition, core symbiont functions (e.g. nitrogen cycling) can be maintained in sponge microbiomes through functional redundancy.
Collapse
|
48
|
Pita L, Fraune S, Hentschel U. Emerging Sponge Models of Animal-Microbe Symbioses. Front Microbiol 2016; 7:2102. [PMID: 28066403 PMCID: PMC5179597 DOI: 10.3389/fmicb.2016.02102] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/12/2016] [Indexed: 12/30/2022] Open
Abstract
Sponges have a significant impact on marine benthic communities, they are of biotechnological interest owing to their production of bioactive natural compounds, and they promise to provide insights into conserved mechanisms of host–microbe interactions in basal metazoans. The natural variability of sponge-microbe associations across species and environments provides a meaningful ecological and evolutionary framework to investigate animal-microbial symbiosis through experimentation in the field and also in aquaria. In addition, next-generation sequencing technologies have shed light on the genomic repertoire of the sponge host and revealed metabolic capacities and symbiotic lifestyle features of their microbiota. However, our understanding of symbiotic mechanisms is still in its infancy. Here, we discuss the potential and limitations of the sponge-microbe symbiosis as emerging models for animal-associated microbiota.
Collapse
Affiliation(s)
- Lucia Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Sebastian Fraune
- Zoological Institute, Christian-Albrechts-University of Kiel (CAU), Kiel Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Christian-Albrechts-University of Kiel (CAU), KielGermany
| |
Collapse
|
49
|
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.
Collapse
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
| |
Collapse
|
50
|
Steinert G, Taylor MW, Deines P, Simister RL, de Voogd NJ, Hoggard M, Schupp PJ. In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity. PeerJ 2016; 4:e1936. [PMID: 27114882 PMCID: PMC4841226 DOI: 10.7717/peerj.1936] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/23/2016] [Indexed: 01/03/2023] Open
Abstract
Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges, Rhabdastrella globostellata, Callyspongia sp., Rhaphoxya sp., and Acanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant for Callyspongia sp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges.
Collapse
Affiliation(s)
- Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg, Wilhelmshaven, Germany; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland , Auckland , New Zealand
| | - Peter Deines
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Rachel L Simister
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | | | - Michael Hoggard
- School of Biological Sciences, University of Auckland , Auckland , New Zealand
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg , Wilhelmshaven , Germany
| |
Collapse
|