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Zhou J, Zheng Y, Hou L, Qi L, Mao T, Yin G, Liu M. Nitrogen input modulates the effects of coastal acidification on nitrification and associated N 2O emission. WATER RESEARCH 2024; 261:122041. [PMID: 38972235 DOI: 10.1016/j.watres.2024.122041] [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: 05/07/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
Abstract
Acidification of coastal waters, synergistically driven by increasing atmospheric carbon dioxide (CO2) and intensive land-derived nutrient inputs, exerts significant stresses on the biogeochemical cycles of coastal ecosystem. However, the combined effects of anthropogenic nitrogen (N) inputs and aquatic acidification on nitrification, a critical process of N cycling, remains unclear in estuarine and coastal ecosystems. Here, we showed that increased loading of ammonium (NH4+) in estuarine and coastal waters alleviated the inhibitory effect of acidification on nitrification rates but intensified the production of the potent greenhouse gas nitrous oxide (N2O), thus accelerating global climate change. Metatranscriptomes and natural N2O isotopic signatures further suggested that the enhanced emission of N2O may mainly source from hydroxylamine (NH2OH) oxidation rather than from nitrite (NO2-) reduction pathway of nitrifying microbes. This study elucidates how anthropogenic N inputs regulate the effects of coastal acidification on nitrification and associated N2O emissions, thereby enhancing our ability to predict the feedbacks of estuarine and coastal ecosystems to climate change and human perturbations.
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Affiliation(s)
- Jie Zhou
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China.
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
| | - Tieqiang Mao
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, China
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2
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Buschi E, Dell’Anno A, Tangherlini M, Candela M, Rampelli S, Turroni S, Palladino G, Esposito E, Martire ML, Musco L, Stefanni S, Munari C, Fiori J, Danovaro R, Corinaldesi C. Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome. SCIENCE ADVANCES 2024; 10:eadk9117. [PMID: 38905343 PMCID: PMC11192080 DOI: 10.1126/sciadv.adk9117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.
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Affiliation(s)
- Emanuela Buschi
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luigi Musco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica “Anton Dohrn,” Villa Comunale, Napoli, Italy
| | - Cristina Munari
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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3
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Signorini SG, Munari M, Federico L, Farè F, Fontana M, Caruso D, Freitas R, Paciello S, D'Aniello I, Gambi MC, Della Torre C. Living under natural conditions of ocean acidification entails energy expenditure and oxidative stress in a mussel species. MARINE POLLUTION BULLETIN 2024; 203:116470. [PMID: 38728956 DOI: 10.1016/j.marpolbul.2024.116470] [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: 03/27/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
We investigated the health conditions of the Mediterranean mussel Mytilus galloprovincialis recruited in the CO2 vents system of Castello Aragonese at Ischia Island (Mediterranean Sea). Individuals of M. galloprovincialis were sampled in three sites along the pH gradient (8.10, 7.7 and up to <7.4). Untargeted metabolomics and biochemical endpoints related to energetic metabolism, oxidative stress/damage, neurotoxicity and immune defense were analyzed. Corrosion of the valves occurred at low pH. A separation of the metabolome was observed along the pH gradient. Metabolites belonging to amino acids, nucleosides, lipids and organic osmolytes were significantly reduced in the organisms from the most acidified sites. The content of reactive oxygen species and the activity of glutathione peroxidase were reduced in organisms from the acidified sites compared to ambient pH, and no oxidative damage was induced. Overall results suggested the presence of an energy cost underpinning long-term survival in acidified conditions for this species.
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Affiliation(s)
- Silvia Giorgia Signorini
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marco Munari
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy; Department of Biology, Stazione Idrobiologica Umberto D'Ancona, University of Padova, Chioggia, Venice, Italy
| | - Lorenzo Federico
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Fiorenza Farè
- Unitech OMICs, Mass Spectrometry Facility, Università degli Studi di Milano, Milan, Italy
| | - Manuela Fontana
- Unitech OMICs, Mass Spectrometry Facility, Università degli Studi di Milano, Milan, Italy
| | - Donatella Caruso
- Unitech OMICs, Mass Spectrometry Facility, Università degli Studi di Milano, Milan, Italy; Department of Pharmacological and Molecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Rosa Freitas
- CESAM - Centre of Marine and Environmental Studies & Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Sofia Paciello
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Département de Sciences Biologiques, Université de Montréal, Montréal, Canada
| | - Ilaria D'Aniello
- Department of Biology, Stazione Idrobiologica Umberto D'Ancona, University of Padova, Chioggia, Venice, Italy
| | | | - Camilla Della Torre
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
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4
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Williams J, Pettorelli N, Hartmann AC, Quinn RA, Plaisance L, O'Mahoney M, Meyer CP, Fabricius KE, Knowlton N, Ransome E. Decline of a distinct coral reef holobiont community under ocean acidification. MICROBIOME 2024; 12:75. [PMID: 38627822 PMCID: PMC11022381 DOI: 10.1186/s40168-023-01683-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/28/2023] [Indexed: 04/19/2024]
Abstract
BACKGROUND Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome. RESULTS We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation. CONCLUSIONS We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract.
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Affiliation(s)
- Jake Williams
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Buckhurst Road, Ascot, SL5 7PY, UK
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Nathalie Pettorelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Aaron C Hartmann
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Laetitia Plaisance
- Laboratoire Evolution Et Diversité Biologique, CNRS/UPS, Toulouse, France
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Michael O'Mahoney
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Chris P Meyer
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | | | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Emma Ransome
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Buckhurst Road, Ascot, SL5 7PY, UK.
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Mazzella V, Dell'Anno A, Etxebarría N, González-Gaya B, Nuzzo G, Fontana A, Núñez-Pons L. High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits. Commun Biol 2024; 7:422. [PMID: 38589605 PMCID: PMC11001883 DOI: 10.1038/s42003-024-06109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.
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Affiliation(s)
- Valerio Mazzella
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Ischia Marine Centre, 80077, Ischia, Naples, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy
| | - Antonio Dell'Anno
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Néstor Etxebarría
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Belén González-Gaya
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia-Bld. 7, 80126, Napoli, Italy
| | - Laura Núñez-Pons
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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Li X, Qi M, Li Q, Wu B, Fu Y, Liang X, Yin G, Zheng Y, Dong H, Liu M, Hou L. Acidification Offset Warming-Induced Increase in N 2O Production in Estuarine and Coastal Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4989-5002. [PMID: 38442002 DOI: 10.1021/acs.est.3c10691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Global warming and acidification, induced by a substantial increase in anthropogenic CO2 emissions, are expected to have profound impacts on biogeochemical cycles. However, underlying mechanisms of nitrous oxide (N2O) production in estuarine and coastal sediments remain rarely constrained under warming and acidification. Here, the responses of sediment N2O production pathways to warming and acidification were examined using a series of anoxic incubation experiments. Denitrification and N2O production were largely stimulated by the warming, while N2O production decreased under the acidification as well as the denitrification rate and electron transfer efficiency. Compared to warming alone, the combination of warming and acidification decreased N2O production by 26 ± 4%, which was mainly attributed to the decline of the N2O yield by fungal denitrification. Fungal denitrification was mainly responsible for N2O production under the warming condition, while bacterial denitrification predominated N2O production under the acidification condition. The reduced site preference of N2O under acidification reflects that the dominant pathways of N2O production were likely shifted from fungal to bacterial denitrification. In addition, acidification decreased the diversity and abundance of nirS-type denitrifiers, which were the keystone taxa mediating the low N2O production. Collectively, acidification can decrease sediment N2O yield through shifting the responsible production pathways, partly counteracting the warming-induced increase in N2O emissions, further reducing the positive climate warming feedback loop.
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Affiliation(s)
- Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Mengting Qi
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Qiuxuan Li
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Boshuang Wu
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
| | - Yuxuan Fu
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
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Moreno-Pino M, Manrique-de-la-Cuba MF, López-Rodríguez M, Parada-Pozo G, Rodríguez-Marconi S, Ribeiro CG, Flores-Herrera P, Guajardo M, Trefault N. Unveiling microbial guilds and symbiotic relationships in Antarctic sponge microbiomes. Sci Rep 2024; 14:6371. [PMID: 38493232 PMCID: PMC10944490 DOI: 10.1038/s41598-024-56480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.
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Affiliation(s)
- Mario Moreno-Pino
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Génesis Parada-Pozo
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
- Millenium Nucleus in Marine Agronomy of Seaweed Holobionts (MASH), Puerto Montt, Chile
| | | | | | - Patricio Flores-Herrera
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
| | - Mariela Guajardo
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, 8580745, Santiago, Chile.
- Millenium Nucleus in Marine Agronomy of Seaweed Holobionts (MASH), Puerto Montt, Chile.
- FONDAP Center IDEAL- Dynamics of High Latitude Marine Ecosystem, Valdivia, Chile.
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8
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Efremova J, Mazzella V, Mirasole A, Teixidó N, Núñez-Pons L. Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO 2 vents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170171. [PMID: 38246375 DOI: 10.1016/j.scitotenv.2024.170171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.
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Affiliation(s)
- Jana Efremova
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
| | - Valerio Mazzella
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Alice Mirasole
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Núria Teixidó
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy; Laboratoire d'Océanographie de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
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9
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Peng S, Ye L, Li Y, Wang F, Sun T, Wang L, Zhao J, Dong Z. Metagenomic insights into jellyfish-associated microbiome dynamics during strobilation. ISME COMMUNICATIONS 2024; 4:ycae036. [PMID: 38571744 PMCID: PMC10988111 DOI: 10.1093/ismeco/ycae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Host-associated microbiomes can play key roles in the metamorphosis of animals. Most scyphozoan jellyfish undergo strobilation in their life cycles, similar to metamorphosis in classic bilaterians. The exploration of jellyfish microbiomes may elucidate the ancestral mechanisms and evolutionary trajectories of metazoan-microbe associations and interactions during metamorphosis. However, current knowledge of the functional features of jellyfish microbiomes remains limited. Here, we performed a genome-centric analysis of associated microbiota across four successive life stages (polyp, early strobila, advanced strobila, and ephyra) during strobilation in the common jellyfish Aurelia coerulea. We observed shifts in taxonomic and functional diversity of microbiomes across distinct stages and proposed that the low microbial diversity in ephyra stage may be correlated with the high expression of the host-derived antimicrobial peptide aurelin. Furthermore, we recovered 43 high-quality metagenome-assembled genomes and determined the nutritional potential of the dominant Vibrio members. Interestingly, we observed increased abundances of genes related to the biosynthesis of amino acids, vitamins, and cofactors, as well as carbon fixation during the loss of host feeding ability, indicating the functional potential of Aurelia-associated microbiota to support the synthesis of essential nutrients. We also identified several potential mechanisms by which jellyfish-associated microbes establish stage-specific community structures and maintain stable colonization in dynamic host environments, including eukaryotic-like protein production, bacterial secretion systems, restriction-modification systems, and clustered regularly interspaced short palindromic repeats-Cas systems. Our study characterizes unique taxonomic and functional changes in jellyfish microbiomes during strobilation and provides foundations for uncovering the ancestral mechanism of host-microbe interactions during metamorphosis.
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Affiliation(s)
- Saijun Peng
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lijing Ye
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
| | - Yongxue Li
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanghan Wang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Sun
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
| | - Lei Wang
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
| | - Jianmin Zhao
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijun Dong
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Chai G, Li J, Li Z. The interactive effects of ocean acidification and warming on bioeroding sponge Spheciospongia vesparium microbiome indicated by metatranscriptomics. Microbiol Res 2024; 278:127542. [PMID: 37979302 DOI: 10.1016/j.micres.2023.127542] [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: 08/03/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
Global climate change will cause coral reefs decline and is expected to increase the reef erosion potential of bioeroding sponges. Microbial symbionts are essential for the overall fitness and survival of sponge holobionts in changing ocean environments. However, we rarely know about the impacts of ocean warming and acidification on bioeroding sponge microbiome. Here, the structural and functional changes of the bioeroding sponge Spheciospongia vesparium microbiome, as well as its recovery potential, were investigated at the RNA level in a laboratory system simulating 32 °C and pH 7.7. Based on metatranscriptome analysis, acidification showed no significant impact, while warming or simultaneous warming and acidification disrupted the sponge microbiome. Warming caused microbial dysbiosis and recruited potentially opportunistic and pathogenic members of Nesiotobacter, Oceanospirillaceae, Deltaproteobacteria, Epsilonproteobacteria, Bacteroidetes and Firmicutes. Moreover, warming disrupted nutrient exchange and molecular interactions in the sponge holobiont, accompanied by stimulation of virulence activity and anaerobic metabolism including denitrification and dissimilatory reduction of nitrate and sulfate to promote sponge necrosis. Particularly, the interaction between acidification and warming alleviated the negative effects of warming and enhanced the Rhodobacteraceae-driven ethylmalonyl-CoA pathway and sulfur-oxidizing multienzyme system. The microbiome could not recover during the experiment period after warming or combined stress was removed. This study suggests that warming or combined warming and acidification will irreversibly destabilize the S. vesparium microbial community structure and function, and provides insight into the molecular mechanisms of the interactive effects of acidification and warming on the sponge microbiome.
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Affiliation(s)
- Guangjun Chai
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinlong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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11
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Turnlund AC, Vanwonterghem I, Botté ES, Randall CJ, Giuliano C, Kam L, Bell S, O'Brien P, Negri AP, Webster NS, Lurgi M. Linking differences in microbial network structure with changes in coral larval settlement. ISME COMMUNICATIONS 2023; 3:114. [PMID: 37865659 PMCID: PMC10590418 DOI: 10.1038/s43705-023-00320-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/27/2023] [Accepted: 10/06/2023] [Indexed: 10/23/2023]
Abstract
Coral cover and recruitment have decreased on reefs worldwide due to climate change-related disturbances. Achieving reliable coral larval settlement under aquaculture conditions is critical for reef restoration programmes; however, this can be challenging due to the lack of reliable and universal larval settlement cues. To investigate the role of microorganisms in coral larval settlement, we undertook a settlement choice experiment with larvae of the coral Acropora tenuis and microbial biofilms grown for different periods on the reef and in aquaria. Biofilm community composition across conditioning types and time was profiled using 16S and 18S rRNA gene sequencing. Co-occurrence networks revealed that strong larval settlement correlated with diverse biofilm communities, with specific nodes in the network facilitating connections between modules comprised of low- vs high-settlement communities. Taxa associated with high-settlement communities were identified as Myxoccales sp., Granulosicoccus sp., Alcanivoraceae sp., unassigned JTB23 sp. (Gammaproteobacteria), and Pseudovibrio denitrificans. Meanwhile, taxa closely related to Reichenbachiella agariperforans, Pleurocapsa sp., Alcanivorax sp., Sneathiella limmimaris, as well as several diatom and brown algae were associated with low settlement. Our results characterise high-settlement biofilm communities and identify transitionary taxa that may develop settlement-inducing biofilms to improve coral larval settlement in aquaculture.
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Affiliation(s)
- Abigail C Turnlund
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, 4072, Australia
| | - Inka Vanwonterghem
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, 4072, Australia
| | - Emmanuelle S Botté
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Carly J Randall
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | | | - Lisa Kam
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Sara Bell
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Paul O'Brien
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, 4072, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Nicole S Webster
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, 4072, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Department of Climate Change, Energy, the Environment and Water, Australian Antarctic Division, Kingston, ACT, Australia
| | - Miguel Lurgi
- Department of Biosciences, Swansea University, Swansea, SA2 8PP, UK.
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12
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Bell JJ, Strano F, Broadribb M, Wood G, Harris B, Resende AC, Novak E, Micaroni V. Sponge functional roles in a changing world. ADVANCES IN MARINE BIOLOGY 2023; 95:27-89. [PMID: 37923539 DOI: 10.1016/bs.amb.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Sponges are ecologically important benthic organisms with many important functional roles. However, despite increasing global interest in the functions that sponges perform, there has been limited focus on how such functions will be impacted by different anthropogenic stressors. In this review, we describe the progress that has been made in our understanding of the functional roles of sponges over the last 15 years and consider the impacts of anthropogenic stressors on these roles. We split sponge functional roles into interactions with the water column and associations with other organisms. We found evidence for an increasing focus on functional roles among sponge-focused research articles, with our understanding of sponge-mediated nutrient cycling increasing substantially in recent years. From the information available, many anthropogenic stressors have the potential to negatively impact sponge pumping, and therefore have the potential to cause ecosystem level impacts. While our understanding of the importance of sponges has increased in the last 15 years, much more experimental work is required to fully understand how sponges will contribute to reef ecosystem function in future changing oceans.
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Affiliation(s)
- James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Manon Broadribb
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Gabriela Wood
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Ben Harris
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Anna Carolina Resende
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Emma Novak
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Valerio Micaroni
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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13
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Pérez-Llano Y, Yarzábal Rodríguez LA, Martínez-Romero E, Dobson ADW, Gunde-Cimerman N, Vasconcelos V, Batista-García RA. From friends to foes: fungi could be emerging marine sponge pathogens under global change scenarios. Front Microbiol 2023; 14:1213340. [PMID: 37670990 PMCID: PMC10476623 DOI: 10.3389/fmicb.2023.1213340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
Global change, experienced in the form of ocean warming and pollution by man-made goods and xenobiotics, is rapidly affecting reef ecosystems and could have devastating consequences for marine ecology. Due to their critical role in regulating marine food webs and trophic connections, sponges are an essential model for studying and forecasting the impact of global change on reef ecosystems. Microbes are regarded as major contributors to the health and survival of sponges in marine environments. While most culture-independent studies on sponge microbiome composition to date have focused on prokaryotic diversity, the importance of fungi in holobiont behavior has been largely overlooked. Studies focusing on the biology of sponge fungi are uncommon. Thus, our current understanding is quite limited regarding the interactions and “crosstalk” between sponges and their associated fungi. Anthropogenic activities and climate change may reveal sponge-associated fungi as novel emerging pathogens. Global change scenarios could trigger the expression of fungal virulence genes and unearth new opportunistic pathogens, posing a risk to the health of sponges and severely damaging reef ecosystems. Although ambitious, this hypothesis has not yet been proven. Here we also postulate as a pioneering hypothesis that manipulating sponge-associated fungal communities may be a new strategy to cope with the threats posed to sponge health by pathogens and pollutants. Additionally, we anticipate that sponge-derived fungi might be used as novel sponge health promoters and beneficial members of the resident sponge microbiome in order to increase the sponge's resistance to opportunistic fungal infections under a scenario of global change.
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Affiliation(s)
- Yordanis Pérez-Llano
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Center for Genomic Sciences, Autonomous National University of Mexico (UNAM), Cuernavaca, Morelos, Mexico
| | | | - Esperanza Martínez-Romero
- Center for Genomic Sciences, Autonomous National University of Mexico (UNAM), Cuernavaca, Morelos, Mexico
| | | | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty. University of Ljubljana, Ljubljana, Slovenia
| | - Vitor Vasconcelos
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- CIIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
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14
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Moeller FU, Herbold CW, Schintlmeister A, Mooshammer M, Motti C, Glasl B, Kitzinger K, Behnam F, Watzka M, Schweder T, Albertsen M, Richter A, Webster NS, Wagner M. Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta. THE ISME JOURNAL 2023; 17:1208-1223. [PMID: 37188915 PMCID: PMC10356861 DOI: 10.1038/s41396-023-01420-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.
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Affiliation(s)
- Florian U Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Cherie Motti
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bettina Glasl
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Institute of Pharmacy, Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, St Lucia, QLD, Australia
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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15
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Wang H, Sui Q, Zhao J, Sun X, Zhu L, Chen B, Qu K, Xia B. Ocean acidification enhances the embryotoxicity of CuO nanoparticles to Oryzias melastigma. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131361. [PMID: 37043857 DOI: 10.1016/j.jhazmat.2023.131361] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/18/2023] [Accepted: 04/02/2023] [Indexed: 05/03/2023]
Abstract
Concerns are raised towards individual effects of ocean acidification (OA) and engineered nanoparticles (NPs) on marine organisms. However, there are scarce studies regarding nanotoxicity under OA conditions. We investigated the combined effects of OA (pHs, 7.70 and 7.40) and CuO NPs on the embryotoxicity of marine medaka Oryzias melastigma and the bioavailability of CuO NPs in embryos. The results showed that OA alleviated the aggregation of CuO NPs and promoted the dissolution of CuO NPs in seawater (increased by 0.010 and 0.029 mg/L under pHs 7.70 and 7.40, respectively). Synergistic effects of OA with CuO NPs on medaka embryos were observed as indicated by much higher mortality and oxidative damage. Importantly, the enhanced toxicity of CuO NPs to medaka embryos under OA conditions mainly originated from the higher bioavailability of particulate CuO (e.g., 30.28 mg/kg at pH 7.40) rather than their released Cu2+ ions (e.g. 3.04 mg/kg at pH 7.40). The weaker aggregation of NPs under OA conditions resulted in higher penetration of individual particles (or small aggregates) into embryos through the micropyle and chorionic pores, causing enhanced bioavailability of NPs. The obtained results provided underlying insights into understanding the risk of NPs to marine ecosystem under OA conditions.
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Affiliation(s)
- Hao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Institute of Costal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), Ocean University of China, Qingdao 266100, China
| | - Qi Sui
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jian Zhao
- Institute of Costal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Xuemei Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Lin Zhu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Bijuan Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Keming Qu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Bin Xia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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16
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Botté ES, Bennett H, Engelberts JP, Thomas T, Bell JJ, Webster NS, Luter HM. Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis. ISME COMMUNICATIONS 2023; 3:53. [PMID: 37311801 PMCID: PMC10264452 DOI: 10.1038/s43705-023-00247-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/22/2023] [Accepted: 04/14/2023] [Indexed: 06/15/2023]
Abstract
Oceans are rapidly warming and acidifying in the context of climate change, threatening sensitive marine biota including coral reef sponges. Ocean warming (OW) and ocean acidification (OA) can impact host health and associated microbiome, but few studies have investigated these effects, which are generally studied in isolation, on a specific component of the holobiont. Here we present a comprehensive view of the consequences of simultaneous OW and OA for the tropical sponge Stylissa flabelliformis. We found no interactive effect on the host health or microbiome. Furthermore, OA (pH 7.6 versus pH 8.0) had no impact, while OW (31.5 °C versus 28.5 °C) caused tissue necrosis, as well as dysbiosis and shifts in microbial functions in healthy tissue of necrotic sponges. Major taxonomic shifts included a complete loss of archaea, reduced proportions of Gammaproteobacteria and elevated relative abundances of Alphaproteobacteria. OW weakened sponge-microbe interactions, with a reduced capacity for nutrient exchange and phagocytosis evasion, indicating lower representations of stable symbionts. The potential for microbially-driven nitrogen and sulphur cycling was reduced, as was amino acid metabolism. Crucially, the dysbiosis annihilated the potential for ammonia detoxification, possibly leading to accumulation of toxic ammonia, nutrient imbalance, and host tissue necrosis. Putative defence against reactive oxygen species was greater at 31.5 °C, perhaps as microorganisms capable of resisting temperature-driven oxidative stress were favoured. We conclude that healthy symbiosis in S. flabelliformis is unlikely to be disrupted by future OA but will be deeply impacted by temperatures predicted for 2100 under a "business-as-usual" carbon emission scenario.
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Affiliation(s)
- Emmanuelle S Botté
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
- Australian Institute of Marine Science, Townsville, Queensland, Australia.
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Victoria University of Wellington, Wellington, New Zealand
- Cawthron Institute, Nelson, New Zealand
| | - J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - James J Bell
- Victoria University of Wellington, Wellington, New Zealand
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Australian Antarctic Division, Hobart, Tasmania, Australia
| | - Heidi M Luter
- Australian Institute of Marine Science, Townsville, Queensland, Australia.
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17
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Zhou J, Zheng Y, Hou L, An Z, Chen F, Liu B, Wu L, Qi L, Dong H, Han P, Yin G, Liang X, Yang Y, Li X, Gao D, Li Y, Liu Z, Bellerby R, Liu M. Effects of acidification on nitrification and associated nitrous oxide emission in estuarine and coastal waters. Nat Commun 2023; 14:1380. [PMID: 36914644 PMCID: PMC10011576 DOI: 10.1038/s41467-023-37104-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
In the context of an increasing atmospheric carbon dioxide (CO2) level, acidification of estuarine and coastal waters is greatly exacerbated by land-derived nutrient inputs, coastal upwelling, and complex biogeochemical processes. A deeper understanding of how nitrifiers respond to intensifying acidification is thus crucial to predict the response of estuarine and coastal ecosystems and their contribution to global climate change. Here, we show that acidification can significantly decrease nitrification rate but stimulate generation of byproduct nitrous oxide (N2O) in estuarine and coastal waters. By varying CO2 concentration and pH independently, an expected beneficial effect of elevated CO2 on activity of nitrifiers ("CO2-fertilization" effect) is excluded under acidification. Metatranscriptome data further demonstrate that nitrifiers could significantly up-regulate gene expressions associated with intracellular pH homeostasis to cope with acidification stress. This study highlights the molecular underpinnings of acidification effects on nitrification and associated greenhouse gas N2O emission, and helps predict the response and evolution of estuarine and coastal ecosystems under climate change and human activities.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China. .,School of Geographic Sciences, East China Normal University, Shanghai, 200241, China. .,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China. .,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China.
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China.
| | - Zhirui An
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Li Wu
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China.,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China.,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Yi Yang
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China.,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China
| | - Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, East China Normal University, Shanghai, 200241, China
| | - Ye Li
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China.,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China
| | - Zhanfei Liu
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, 78373, USA
| | - Richard Bellerby
- Norwegian Institute for Water Research, Thormøhlensgt 53D, 5006, Bergen, Norway
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China. .,Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China. .,Key Laboratory of Spatial-temporal Big Data Analysis and Application of Natural Resources in Megacities, Ministry of Natural Resources, Shanghai, 200241, China.
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18
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Engelberts JP, Robbins SJ, Herbold CW, Moeller FU, Jehmlich N, Laffy PW, Wagner M, Webster NS. Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta. Environ Microbiol 2023; 25:646-660. [PMID: 36480164 PMCID: PMC10947273 DOI: 10.1111/1462-2920.16302] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host-microbe interactions and provide a basis for in-depth physiological experiments.
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Affiliation(s)
- Joan Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - Steven J. Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | - Craig W. Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Florian U. Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Nico Jehmlich
- Department of Molecular Systems BiologyHelmholtz‐Centre for Environmental Research – UFZLeipzigGermany
| | - Patrick W. Laffy
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Nicole S. Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
- Australian Antarctic DivisionKingstonTasmaniaAustralia
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19
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Chou PH, Hu MY, Guh YJ, Wu GC, Yang SH, Tandon K, Shao YT, Lin LY, Chen C, Tseng KY, Wang MC, Zhang CM, Han BC, Lin CC, Tang SL, Jeng MS, Chang CF, Tseng YC. Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents. Proc Biol Sci 2023; 290:20221973. [PMID: 36629118 PMCID: PMC9832567 DOI: 10.1098/rspb.2022.1973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/17/2022] [Indexed: 01/12/2023] Open
Abstract
The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.
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Affiliation(s)
- Pei-Hsuan Chou
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan County, Taiwan
| | - Marian Y. Hu
- Institute of Physiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Ying-Jey Guh
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan County, Taiwan
| | - Guan-Chung Wu
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans National Taiwan Ocean University, Keelung, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei City, Taiwan
| | - Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Yi-Ta Shao
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Li-Yih Lin
- Department of Life Science, National Taiwan Normal University, Taipei City, Taiwan
| | - Chi Chen
- Doctoral Degree Program in Marine Biotechnology, National Taiwan Ocean University and Academia Sinica, Taipei City, Taiwan
| | - Kuang-Yu Tseng
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Min-Chen Wang
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan County, Taiwan
| | - Cheng-Mao Zhang
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Bor-Cheng Han
- School of Public Health, Taipei Medical College, Taipei, Taiwan
| | - Ching-Chun Lin
- Biomedical Translation Research Center, Academia Sinica, Taipei City, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Ming-Shiou Jeng
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Ching-Fong Chang
- Center of Excellence for the Oceans National Taiwan Ocean University, Keelung, Taiwan
| | - Yung-Che Tseng
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan County, Taiwan
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20
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Bell JJ, Smith RO, Micaroni V, Strano F, Balemi CA, Caiger PE, Miller KI, Spyksma AJP, Shears NT. Marine heat waves drive bleaching and necrosis of temperate sponges. Curr Biol 2023; 33:158-163.e2. [PMID: 36462506 DOI: 10.1016/j.cub.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/13/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Marine heat waves (MHWs) are extended periods of excessively warm water1 that are increasing in frequency, duration, intensity, and impact, and they likely represent a greater threat to marine ecosystems than the more gradual increases in sea surface temperature.2,3,4 Sponges are major and important components of global benthic marine communities,5,6,7 with earlier studies identifying tropical sponges as potential climate change "winners."8,9,10,11 In contrast, cold-water sponges may be less tolerant to predicted ocean warming and concurrent MHWs. Here, we report how a series of unprecedented MHWs in New Zealand have impacted millions of sponges at a spatial scale far greater than previously reported anywhere in the world. We reported sponge tissue necrosis12 and bleaching (symbiont loss/dysfunction),13 which have been previously associated with temperature stress,6,12,14 for three common sponge species across multiple biogeographical regions, with the severity of impact being correlated with MHW intensity. Given the ecological importance of sponges,15 their loss from these rocky temperate reefs will likely have important ecosystem-level consequences.
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Affiliation(s)
- James J Bell
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand.
| | - Robert O Smith
- Department of Marine Science, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Valerio Micaroni
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Celia A Balemi
- Leigh Marine Laboratory, Institute of Marine Science, University of Auckland, P.O. Box 349, Auckland, New Zealand
| | - Paul E Caiger
- Leigh Marine Laboratory, Institute of Marine Science, University of Auckland, P.O. Box 349, Auckland, New Zealand
| | - Kelsey I Miller
- Leigh Marine Laboratory, Institute of Marine Science, University of Auckland, P.O. Box 349, Auckland, New Zealand
| | - Arie J P Spyksma
- Leigh Marine Laboratory, Institute of Marine Science, University of Auckland, P.O. Box 349, Auckland, New Zealand
| | - Nick T Shears
- Leigh Marine Laboratory, Institute of Marine Science, University of Auckland, P.O. Box 349, Auckland, New Zealand
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21
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Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts. Microbiol Res 2022; 265:127183. [PMID: 36108440 DOI: 10.1016/j.micres.2022.127183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/24/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022]
Abstract
Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.
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22
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Harnessing solar power: photoautotrophy supplements the diet of a low-light dwelling sponge. THE ISME JOURNAL 2022; 16:2076-2086. [PMID: 35654830 PMCID: PMC9381825 DOI: 10.1038/s41396-022-01254-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 01/07/2023]
Abstract
The ability of organisms to combine autotrophy and heterotrophy gives rise to one of the most successful nutritional strategies on Earth: mixotrophy. Sponges are integral members of shallow-water ecosystems and many host photosynthetic symbionts, but studies on mixotrophic sponges have focused primarily on species residing in high-light environments. Here, we quantify the contribution of photoautotrophy to the respiratory demand and total carbon diet of the sponge Chondrilla caribensis, which hosts symbiotic cyanobacteria and lives in low-light environments. Although the sponge is net heterotrophic at 20 m water depth, photosynthetically fixed carbon potentially provides up to 52% of the holobiont’s respiratory demand. When considering the total mixotrophic diet, photoautotrophy contributed an estimated 7% to total daily carbon uptake. Visualization of inorganic 13C- and 15N-incorporation using nanoscale secondary ion mass spectrometry (NanoSIMS) at the single-cell level confirmed that a portion of nutrients assimilated by the prokaryotic community was translocated to host cells. Photoautotrophy can thus provide an important supplemental source of carbon for sponges, even in low-light habitats. This trophic plasticity may represent a widespread strategy for net heterotrophic sponges hosting photosymbionts, enabling the host to buffer against periods of nutritional stress.
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23
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Bell JJ, Shaffer M, Luter HM, Mana R, Rodolfo-Metalpa R. Phototrophic sponge productivity may not be enhanced in a high CO 2 world. GLOBAL CHANGE BIOLOGY 2022; 28:4900-4911. [PMID: 35662355 DOI: 10.1111/gcb.16235] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Sponges are major components of benthic communities across the world and have been identified as potential "winners" on coral reefs in the face of global climate change as result of their tolerance to ocean warming and acidification (OA). Previous studies have also hypothesised that photosymbiont-containing sponges might have higher productivity under future OA conditions as a result of photosymbionts having increased access to CO2 and subsequently greater carbon production. Here we test this hypothesis for a widespread and abundant photosymbiont-containing sponge species Lamellodysidea herbacea at a CO2 seep in Papua New Guinea simulating OA conditions. We found seep sponges had relatively higher cyanobacterial abundance, chlorophyll concentrations and symbiont photosynthetic efficiency than non-seep sponges, and a three-fold higher sponge abundance at the seep site. However, while gross oxygen production was the same for seep and non-seep sponges, seep sponge dark respiration rates were higher and instantaneous photosynthesis: respiration (P:R) ratios were lower. We show that while photosymbiont containing sponges may not have increased productivity under OA, they are able to show flexibility in their relationships with microbes and offset increased metabolic costs associated with climate change associated stress.
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Affiliation(s)
- James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Megan Shaffer
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Heidi M Luter
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Ralph Mana
- School of Natural and Physical Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Riccardo Rodolfo-Metalpa
- ENTROPIE, IRD, Université de la Réunion, CNRS, IFREMER, Université de Nouvelle-Calédonie, Nouméa, New Caledonia
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24
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Carrier TJ, Maldonado M, Schmittmann L, Pita L, Bosch TCG, Hentschel U. Symbiont transmission in marine sponges: reproduction, development, and metamorphosis. BMC Biol 2022; 20:100. [PMID: 35524305 PMCID: PMC9077847 DOI: 10.1186/s12915-022-01291-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.
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Affiliation(s)
- Tyler J Carrier
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
- Zoological Institute, University of Kiel, Kiel, Germany.
| | - Manuel Maldonado
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | | | - Lucía Pita
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | | | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Zoological Institute, University of Kiel, Kiel, Germany
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25
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Wu L, An Z, Zhou J, Chen F, Liu B, Qi L, Yin G, Dong H, Liu M, Hou L, Zheng Y. Effects of Aquatic Acidification on Microbially Mediated Nitrogen Removal in Estuarine and Coastal Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5939-5949. [PMID: 35465670 DOI: 10.1021/acs.est.2c00692] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Acidification of estuarine and coastal waters is anticipated to influence nitrogen (N) removal processes, which are critical pathways for eliminating excess N from these ecosystems. We found that denitrification rates decreased significantly under acidified conditions (P < 0.05), which reduced by 41-53% in estuarine and coastal sediments under an approximately 0.3 pH reduction of the overlying water. However, the N removal rates through the anaerobic ammonium oxidation (anammox) process were concomitantly promoted under the same acidification conditions (increased by 47-109%, P < 0.05), whereas the total rates of N loss were significantly inhibited by aquatic acidification (P < 0.05), as denitrification remained the dominant N removal pathway. More importantly, the emission of nitrous oxide (N2O) from estuarine and coastal sediments was greatly stimulated by aquatic acidification (P < 0.05). Molecular analyses further demonstrated that aquatic acidification also altered the functional microbial communities in estuarine and coastal sediments; and the abundance of denitrifiers was significantly reduced (P < 0.05), while the abundance of anammox bacteria remained relatively stable. Collectively, this study reveals the effects of acidification on N removal processes and the underlying mechanisms and suggests that the intensifying acidification in estuarine and coastal waters might reduce the N removal function of these ecosystems, exacerbate eutrophication, and accelerate global climate change.
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Affiliation(s)
- Li Wu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Zhirui An
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
| | - Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
| | - Yanling Zheng
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
- State Key Laboratory of Estuarine and Coastal Research, Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education & Shanghai, East China Normal University, Shanghai 200241, China
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26
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Marine Sponge Endosymbionts: Structural and Functional Specificity of the Microbiome within
Euryspongia arenaria
Cells. Microbiol Spectr 2022; 10:e0229621. [PMID: 35499324 PMCID: PMC9241883 DOI: 10.1128/spectrum.02296-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Sponge microbiomes are typically profiled by analyzing the community DNA of whole tissues, which does not distinguish the taxa residing within sponge cells from extracellular microbes. To uncover the endosymbiotic microbiome, we separated the sponge cells to enrich the intracellular microbes. The intracellular bacterial community of sponge Euryspongia arenaria was initially assessed by amplicon sequencing, which indicated that it hosts three unique phyla not found in the extracellular and bulk tissue microbiomes. These three phyla account for 66% of the taxonomically known genera in the intracellular microbiome. The shotgun metagenomic analysis extended the taxonomic coverage to viruses and eukaryotes, revealing the most abundant signature taxa specific to the intracellular microbiome. Functional KEGG pathway annotation demonstrated that the endosymbiotic microbiome hosted the greatest number of unique gene orthologs. The pathway profiles distinguished the intra- and extracellular microbiomes from the tissue and seawater microbiomes. Carbohydrate-active enzyme analysis further discriminated each microbiome based on their representative and dominant enzyme families. One pathway involved in digestion system and family esterase had a consistently higher level in intracellular microbiome and could statistically differentiate the intracellular microbiome from the others, suggesting that triacylglycerol lipases could be the key functional component peculiar to the endosymbionts. The identified higher abundance of lipase-related eggNOG categories further supported the lipid-hydrolyzing metabolism of endosymbiotic microbiota. Pseudomonas members, reported as lipase-producing bacteria, were only in the endosymbiotic microbiome, meanwhile Pseudomonas also showed a greater abundance intracellularly. Our study aided a comprehensive sponge microbiome that demonstrated the taxonomic and functional specificity of endosymbiotic microbiota. IMPORTANCE Sponges host abundant microbial symbionts that can produce an impressive number of novel bioactive metabolites. However, knowledge on intracellular (endosymbiotic) microbiota is scarce. We characterize the composition and function of the endosymbiotic microbiome by separation of sponge cells and enrichment of intracellular microbes. We uncover a noteworthy number of taxa exclusively in the endosymbiotic microbiome. We unlock the unique pathways and enzymes of endosymbiotic taxa. This study achieves a more comprehensive sponge microbial community profile, which demonstrates the structural and functional specificity of the endosymbiotic microbiome. Our findings not only open the possibility to reveal the low abundant and the likely missed microbiota when directly sequencing the sponge bulk tissues, but also warrant future in-depth exploration within single sponge cells.
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27
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Taylor JA, Díez-Vives C, Nielsen S, Wemheuer B, Thomas T. Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts. Environ Microbiol 2022; 24:2299-2314. [PMID: 35229422 DOI: 10.1111/1462-2920.15962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/13/2022] [Accepted: 02/26/2022] [Indexed: 11/03/2022]
Abstract
The diversity and function of sponge-associated symbionts is now increasingly understood, however, we lack an understanding on how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here we performed a metatransciptomics analysis of three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidising Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidising archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our timeseries study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jessica A Taylor
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Cristina Díez-Vives
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Shaun Nielsen
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Zhang S, Song W, Nothias LF, Couvillion SP, Webster N, Thomas T. Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts. MICROBIOME 2022; 10:22. [PMID: 35105377 PMCID: PMC8805237 DOI: 10.1186/s40168-021-01220-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Sponges are ancient sessile metazoans, which form with their associated microbial symbionts a complex functional unit called a holobiont. Sponges are a rich source of chemical diversity; however, there is limited knowledge of which holobiont members produce certain metabolites and how they may contribute to chemical interactions. To address this issue, we applied non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) and gas chromatography mass spectrometry (GC-MS) to either whole sponge tissue or fractionated microbial cells from six different, co-occurring sponge species. RESULTS Several metabolites were commonly found or enriched in whole sponge tissue, supporting the notion that sponge cells produce them. These include 2-methylbutyryl-carnitine, hexanoyl-carnitine and various carbohydrates, which may be potential food sources for microorganisms, as well as the antagonistic compounds hymenialdisine and eicosatrienoic acid methyl ester. Metabolites that were mostly observed or enriched in microbial cells include the antioxidant didodecyl 3,3'-thiodipropionate, the antagonistic compounds docosatetraenoic acid, and immune-suppressor phenylethylamide. This suggests that these compounds are mainly produced by the microbial members in the sponge holobiont, and are potentially either involved in inter-microbial competitions or in defenses against intruding organisms. CONCLUSIONS This study shows how different chemical functionality is compartmentalized between sponge hosts and their microbial symbionts and provides new insights into how chemical interactions underpin the function of sponge holobionts. Video abstract.
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Affiliation(s)
- Shan Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052 Australia
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, 2052 Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, 2052 Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052 Australia
| | - Louis-Félix Nothias
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA USA
| | - Sneha P. Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, 2052 Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052 Australia
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29
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Posadas N, Baquiran JIP, Nada MAL, Kelly M, Conaco C. Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions. THE ISME JOURNAL 2022; 16:58-67. [PMID: 34218251 PMCID: PMC8692459 DOI: 10.1038/s41396-021-01050-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
The sponge-associated microbial community contributes to the overall health and adaptive capacity of the sponge holobiont. This community is regulated by the environment and the immune system of the host. However, little is known about the effect of environmental stress on the regulation of host immune functions and how this may, in turn, affect sponge-microbe interactions. In this study, we compared the bacterial diversity and immune repertoire of the demosponge, Neopetrosia compacta, and the calcareous sponge, Leucetta chagosensis, under varying levels of acidification and warming stress based on climate scenarios predicted for 2100. Neopetrosia compacta harbors a diverse microbial community and possesses a rich repertoire of scavenger receptors while L. chagosensis has a less diverse microbiome and an expanded range of pattern recognition receptors and immune response-related genes. Upon exposure to RCP 8.5 conditions, the microbiome composition and host transcriptome of N. compacta remained stable, which correlated with high survival (75%). In contrast, tissue necrosis and low survival (25%) of L. chagosensis was accompanied by microbial community shifts and downregulation of host immune-related pathways. Meta-analysis of microbiome diversity and immunological repertoire across poriferan classes further highlights the importance of host-microbe interactions in predicting the fate of sponges under future ocean conditions.
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Affiliation(s)
- Niño Posadas
- grid.11134.360000 0004 0636 6193Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Jake Ivan P. Baquiran
- grid.11134.360000 0004 0636 6193Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Michael Angelou L. Nada
- grid.11134.360000 0004 0636 6193Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Michelle Kelly
- grid.419676.b0000 0000 9252 5808National Institute of Water and Atmospheric Research, Ltd., Auckland, New Zealand
| | - Cecilia Conaco
- grid.11134.360000 0004 0636 6193Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
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30
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Burgsdorf I, Sizikov S, Squatrito V, Britstein M, Slaby BM, Cerrano C, Handley KM, Steindler L. Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool. THE ISME JOURNAL 2021; 16:1163-1175. [PMID: 34876682 PMCID: PMC8941161 DOI: 10.1038/s41396-021-01165-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 10/30/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023]
Abstract
Marine sponges host a wide diversity of microorganisms, which have versatile modes of carbon and energy metabolism. In this study we describe the major lithoheterotrophic and autotrophic processes in 21 microbial sponge-associated phyla using novel and existing genomic and transcriptomic datasets. We show that the main microbial carbon fixation pathways in sponges are the Calvin–Benson–Bassham cycle (energized by light in Cyanobacteria, by sulfur compounds in two orders of Gammaproteobacteria, and by a wide range of compounds in filamentous Tectomicrobia), the reductive tricarboxylic acid cycle (used by Nitrospirota), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (active in Thaumarchaeota). Further, we observed that some sponge symbionts, in particular Acidobacteria, are capable of assimilating carbon through anaplerotic processes. The lithoheterotrophic lifestyle was widespread and CO oxidation is the main energy source for sponge lithoheterotrophs. We also suggest that the molybdenum-binding subunit of dehydrogenase (encoded by coxL) likely evolved to benefit also organoheterotrophs that utilize various organic substrates. Genomic potential does not necessarily inform on actual contribution of autotrophs to light and dark carbon budgets. Radioisotope assays highlight variability in the relative contributions of photo- and chemoautotrophs to the total carbon pool across different sponge species, emphasizing the importance of validating genomic potential with physiology experimentation.
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Affiliation(s)
- I Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - S Sizikov
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - V Squatrito
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - M Britstein
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - B M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - C Cerrano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - K M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - L Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
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Abstract
Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.
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32
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Sweet M, Villela H, Keller-Costa T, Costa R, Romano S, Bourne DG, Cárdenas A, Huggett MJ, Kerwin AH, Kuek F, Medina M, Meyer JL, Müller M, Pollock FJ, Rappé MS, Sere M, Sharp KH, Voolstra CR, Zaccardi N, Ziegler M, Peixoto R. Insights into the Cultured Bacterial Fraction of Corals. mSystems 2021; 6:e0124920. [PMID: 34156291 PMCID: PMC8269258 DOI: 10.1128/msystems.01249-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite their putative importance, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable bacteria isolated from corals originating from tropical, temperate, and cold-water habitats. A total of 3,055 isolates from 52 studies were considered by our metasurvey. Of these, 1,045 had full-length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterium-coral symbioses among the strains. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features-not previously described for coral-bacterium symbioses-potentially involved in host colonization and host-symbiont recognition, antiviral defense mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning and guide the selection of probiotic candidates to promote coral resilience and improve holistic and customized reef restoration and rehabilitation efforts. IMPORTANCE Our paper is the first study to synthesize currently available but decentralized data of cultured microbes associated with corals. We were able to collate 3,055 isolates across a number of published studies and unpublished collections from various laboratories and researchers around the world. This equated to 1,045 individual isolates which had full-length 16S rRNA gene sequences, after filtering of the original 3,055. We also explored which of these had genomes available. Originally, only 36 were available, and as part of this study, we added a further 38-equating to 74 in total. From this, we investigated potential genetic signatures that may facilitate a host-associated lifestyle. Further, such a resource is an important step in the selection of probiotic candidates, which are being investigated for promoting coral resilience and potentially applied as a novel strategy in reef restoration and rehabilitation efforts. In the spirit of open access, we have ensured this collection is available to the wider research community through the web site http://isolates.reefgenomics.org/ with the hope many scientists across the globe will ask for access to these cultures for future studies.
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Affiliation(s)
- Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Helena Villela
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB), University of Lisbon, Lisbon, Portugal
- Instituto Superior Técnico (IST), University of Lisbon, Lisbon, Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), University of Lisbon, Lisbon, Portugal
- Instituto Superior Técnico (IST), University of Lisbon, Lisbon, Portugal
- Department of Energy, Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefano Romano
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, Australia
- Australian Institute of Marine Science, Townsville, Australia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Megan J. Huggett
- School of Environmental and Life Sciences, The University of Newcastle, Ourimbah, NSW, Australia
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | | | - Felicity Kuek
- Australian Institute of Marine Science, Townsville, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Julie L. Meyer
- Soil and Water Sciences Department, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Moritz Müller
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak Campus, Kuching, Sarawak, Malaysia
| | - F. Joseph Pollock
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Hawaii and Palmyra Programs, The Nature Conservancy, Honolulu, Hawaii, USA
| | - Michael S. Rappé
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA
| | - Mathieu Sere
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Koty H. Sharp
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, USA
| | | | - Nathan Zaccardi
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Raquel Peixoto
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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33
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O'Brien PA, Andreakis N, Tan S, Miller DJ, Webster NS, Zhang G, Bourne DG. Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts. Mol Ecol 2021; 30:3768-3782. [PMID: 34060182 DOI: 10.1111/mec.16006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group. Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle key microbial interactions that occur within complex microbiomes and reveal long-standing, essential microbial symbioses in coral reef invertebrates.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Nikos Andreakis
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Qld, Australia.,College of Public Health, Medical and Veterinary Sciences, 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, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia
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34
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Robbins SJ, Song W, Engelberts JP, Glasl B, Slaby BM, Boyd J, Marangon E, Botté ES, Laffy P, Thomas T, Webster NS. A genomic view of the microbiome of coral reef demosponges. THE ISME JOURNAL 2021; 15:1641-1654. [PMID: 33469166 PMCID: PMC8163846 DOI: 10.1038/s41396-020-00876-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 01/30/2023]
Abstract
Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.
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Affiliation(s)
- S J Robbins
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - W Song
- Centre for Marine Science & Innovation, University of New South Wales, Kensington, NSW, 2052, Australia
| | - J P Engelberts
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - B Glasl
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - B M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - J Boyd
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia
| | - E Marangon
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, 4810, Australia
| | - E S Botté
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - P Laffy
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - T Thomas
- Centre for Marine Science & Innovation, University of New South Wales, Kensington, NSW, 2052, Australia
| | - N S Webster
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia.
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35
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Hudspith M, Rix L, Achlatis M, Bougoure J, Guagliardo P, Clode PL, Webster NS, Muyzer G, Pernice M, de Goeij JM. Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis. MICROBIOME 2021; 9:44. [PMID: 33583434 PMCID: PMC7883440 DOI: 10.1186/s40168-020-00984-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/16/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea. RESULTS The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome. CONCLUSIONS Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract.
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Affiliation(s)
- Meggie Hudspith
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura Rix
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Michelle Achlatis
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Peta L. Clode
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
- The UWA Oceans Institute, The University of Western Australia, Perth, Australia
- The UWA School of Biological Sciences, The University of Western Australia, Perth, Australia
| | - Nicole S. Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Mathieu Pernice
- Climate Change Cluster (C3), Faculty of Science, University of Technology, Sydney, Australia
| | - Jasper M. de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
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36
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Li C, Zhang X, Wei L, Wei D, Chen Z, Cao Z, Zhao Q, Chang CC. Molecular biological methods in environmental engineering. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2020; 92:1786-1793. [PMID: 32762138 DOI: 10.1002/wer.1432] [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: 03/03/2020] [Revised: 07/08/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Microbes are sensitive to environmental changes and can respond in a short time. Genomics, proteomics, transcriptomics, metabolomics, and multigroup association are used to characterize the composition, function, and metabolism of microorganisms, and to evaluate the environment according to the changes in microorganisms, which has important reference and guiding significance of environmental monitoring, management, and repair. In this paper, the application of molecular biological methods to study environmental microorganisms in the fields of wastewater treatment, pollution control, soil improvement, and environmental monitoring in 2019 is reviewed.
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Affiliation(s)
- Chunying Li
- School of Energy and Civil Engineering, Harbin University of Commerce, Harbin, China
| | - Xinxin Zhang
- Guangzhou HKUST Fok Ying Tung Research Institute, Guangzhou, China
| | - Li Wei
- Guangzhou HKUST Fok Ying Tung Research Institute, Guangzhou, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Dong Wei
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Zhongxi Chen
- Daqing Oil-field Design and Research Institute, Daqing, China
| | - Zhenkun Cao
- Daqing Oil-field Design and Research Institute, Daqing, China
| | - Qiushi Zhao
- Daqing Oil-field Design and Research Institute, Daqing, China
| | - Chein-Chi Chang
- Department of Engineering and Technical Services, DC Water and Sewer Authority, Washington, DC, USA
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37
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Luter HM, Andersen M, Versteegen E, Laffy P, Uthicke S, Bell JJ, Webster NS. Cross-generational effects of climate change on the microbiome of a photosynthetic sponge. Environ Microbiol 2020; 22:4732-4744. [PMID: 32869905 DOI: 10.1111/1462-2920.15222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 01/04/2023]
Abstract
Coral reefs are facing increasing pressure from rising seawater temperatures and ocean acidification. Sponges have been proposed as possible winners in the face of climate change; however, little is known about the mechanisms underpinning their predicted tolerance. Here we assessed whether microbiome-mediated cross-generational acclimatization could enable the photosynthetic sponge Carteriospongia foliascens to survive under future climate scenarios. To achieve this, we first established the potential for vertical (cross-generational) transmission of symbionts. Sixty-four amplicon sequence variants accounting for >90% of the total C. foliascens microbial community were present across adult, larval and juvenile life stages, showing that a large proportion of the microbiome is vertically acquired and maintained. When C. foliascens were exposed to climate scenarios projected for 2050 and 2100, the host remained visibly unaffected (i.e. no necrosis/bleaching) and the overall microbiome was not significantly different amongst treatments in adult tissue, the respective larvae or recruits transplanted amongst climate treatments. However, indicator species analysis revealed that parental exposure to future climate scenarios altered the presence and abundance of a small suite of microbial taxa in the recruits, thereby revealing the potential for microbiome-mediated cross-generational acclimatization through both symbiont shuffling and symbiont switching within a vertically acquired microbiome.
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Affiliation(s)
- Heidi M Luter
- Australian Institute of Marine Science, QLD, Townsville, Australia.,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Maria Andersen
- Australian Institute of Marine Science, QLD, Townsville, Australia.,AIMS@JCU, QLD, Townsville, Australia
| | - Elien Versteegen
- Australian Institute of Marine Science, QLD, Townsville, Australia.,AIMS@JCU, QLD, Townsville, Australia
| | - Patrick Laffy
- Australian Institute of Marine Science, QLD, Townsville, Australia
| | - Sven Uthicke
- Australian Institute of Marine Science, QLD, Townsville, Australia
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Nicole S Webster
- Australian Institute of Marine Science, QLD, Townsville, Australia.,Australian Centre for Ecogenomics, University of Queensland, QLD, Brisbane, Australia
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38
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de Oliveira BFR, Carr CM, Dobson ADW, Laport MS. Harnessing the sponge microbiome for industrial biocatalysts. Appl Microbiol Biotechnol 2020; 104:8131-8154. [PMID: 32827049 DOI: 10.1007/s00253-020-10817-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Clodagh M Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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39
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Bell JJ, McGrath E, Kandler NM, Marlow J, Beepat SS, Bachtiar R, Shaffer MR, Mortimer C, Micaroni V, Mobilia V, Rovellini A, Harris B, Farnham E, Strano F, Carballo JL. Interocean patterns in shallow water sponge assemblage structure and function. Biol Rev Camb Philos Soc 2020; 95:1720-1758. [PMID: 32812691 DOI: 10.1111/brv.12637] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 01/04/2023]
Abstract
Sponges are a major component of benthic ecosystems across the world and fulfil a number of important functional roles. However, despite their importance, there have been few attempts to compare sponge assemblage structure and ecological functions across large spatial scales. In this review, we examine commonalities and differences between shallow water (<100 m) sponges at bioregional (15 bioregions) and macroregional (tropical, Mediterranean, temperate, and polar) scales, to provide a more comprehensive understanding of sponge ecology. Patterns of sponge abundance (based on density and area occupied) were highly variable, with an average benthic cover between ~1 and 30%. Sponges were generally found to occupy more space (percentage cover) in the Mediterranean and polar macroregions, compared to temperate and tropical macroregions, although sponge densities (sponges m-2 ) were highest in temperate bioregions. Mean species richness standardised by sampling area was similar across all bioregions, except for a few locations that supported very high small-scale biodiversity concentrations. Encrusting growth forms were generally the dominant sponge morphology, with the exception of the Tropical West Atlantic, where upright forms dominated. Annelids and Arthropods were the most commonly reported macrofauna associated with sponges across bioregions. With respect to reproduction, there were no patterns in gametic development (hermaphroditism versus gonochorism), although temperate, tropical, and polar macroregions had an increasingly higher percentage of viviparous species, respectively, with viviparity being the sole gamete development mechanism reported for polar sponges to date. Seasonal reproductive timing was the most common in all bioregions, but continuous timing was more common in the Mediterranean and tropical bioregions compared to polar and temperate bioregions. We found little variation across bioregions in larval size, and the dominant larval type across the globe was parenchymella. No pattens among bioregions were found in the limited information available for standardised respiration and pumping rates. Many organisms were found to predate sponges, with the abundance of sponge predators being higher in tropical systems. While there is some evidence to support a higher overall proportion of phototrophic species in the Tropical Austalian bioregion compared to the Western Atlantic, both also have large numbers of heterotrophic species. Sponges are important spatial competitors across all bioregions, most commonly being reported to interact with anthozoans and algae. Even though the available information was limited for many bioregions, our analyses demonstrate some differences in sponge traits and functions among bioregions, and among macroregions. However, we also identified similarities in sponge assemblage structure and function at global scales, likely reflecting a combination of regional- and local-scale biological and physical processes affecting sponge assemblages, along with common ancestry. Finally, we used our analyses to highlight geographic bias in past sponge research, and identify gaps in our understanding of sponge ecology globally. By so doing, we identified key areas for future research on sponge ecology. We hope that our study will help sponge researchers to consider bioregion-specific features of sponge assemblages and key sponge-mediated ecological processes from a global perspective.
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Affiliation(s)
- James J Bell
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Emily McGrath
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.,Cawthron Institute, 98 Halifax St E, The Wood, Nelson, 7010, New Zealand
| | - Nora M Kandler
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Joseph Marlow
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K
| | - Sandeep S Beepat
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Ramadian Bachtiar
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Megan R Shaffer
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Charlotte Mortimer
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Valerio Micaroni
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Valeria Mobilia
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Alberto Rovellini
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Benjamin Harris
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Elizabeth Farnham
- Ministry of Primary Industries, PO Box 2526, Wellington, New Zealand
| | - Francesca Strano
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - José Luis Carballo
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (UNAM), Avenida Joel Montes Camarena, s/n. apartado postal 811, Mazatlán, 82000, Mexico
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40
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Vanwonterghem I, Webster NS. Coral Reef Microorganisms in a Changing Climate. iScience 2020; 23:100972. [PMID: 32208346 PMCID: PMC7096749 DOI: 10.1016/j.isci.2020.100972] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 01/09/2023] Open
Abstract
Coral reefs are one of the most diverse and productive ecosystems on the planet, yet they have suffered tremendous losses due to anthropogenic disturbances and are predicted to be one of the most adversely affected habitats under future climate change conditions. Coral reefs can be viewed as microbially driven ecosystems that rely on the efficient capture, retention, and recycling of nutrients in order to thrive in oligotrophic waters. Microorganisms play vital roles in maintaining holobiont health and ecosystem resilience under environmental stress; however, they are also key players in positive feedback loops that intensify coral reef decline, with cascading effects on biogeochemical cycles and marine food webs. There is an urgent need to develop a fundamental understanding of the complex microbial interactions within coral reefs and their role in ecosystem acclimatization, and it is important to include microorganisms in reef conservation in order to secure a future for these unique environments.
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Affiliation(s)
- Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia
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41
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Glasl B, Robbins S, Frade PR, Marangon E, Laffy PW, Bourne DG, Webster NS. Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes. ISME JOURNAL 2020; 14:1435-1450. [PMID: 32123297 PMCID: PMC7242418 DOI: 10.1038/s41396-020-0622-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 01/06/2023]
Abstract
Microbially mediated processes contribute to coral reef resilience yet, despite extensive characterisation of microbial community variation following environmental perturbation, the effect on microbiome function is poorly understood. We undertook metagenomic sequencing of sponge, macroalgae and seawater microbiomes from a macroalgae-dominated inshore coral reef to define their functional potential and evaluate seasonal shifts in microbially mediated processes. In total, 125 high-quality metagenome-assembled genomes were reconstructed, spanning 15 bacterial and 3 archaeal phyla. Multivariate analysis of the genomes relative abundance revealed changes in the functional potential of reef microbiomes in relation to seasonal environmental fluctuations (e.g. macroalgae biomass, temperature). For example, a shift from Alphaproteobacteria to Bacteroidota-dominated seawater microbiomes occurred during summer, resulting in an increased genomic potential to degrade macroalgal-derived polysaccharides. An 85% reduction of Chloroflexota was observed in the sponge microbiome during summer, with potential consequences for nutrition, waste product removal, and detoxification in the sponge holobiont. A shift in the Firmicutes:Bacteroidota ratio was detected on macroalgae over summer with potential implications for polysaccharide degradation in macroalgal microbiomes. These results highlight that seasonal shifts in the dominant microbial taxa alter the functional repertoire of host-associated and seawater microbiomes, and highlight how environmental perturbation can affect microbially mediated processes in coral reef ecosystems.
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Affiliation(s)
- Bettina Glasl
- Australian Institute of Marine Science, Townsville, QLD, Australia. .,College of Science and Engineering, James Cook University, Townsville, QLD, Australia. .,AIMS@JCU, Townsville, QLD, Australia.
| | - Steven Robbins
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Pedro R Frade
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Emma Marangon
- Australian Institute of Marine Science, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Townsville, QLD, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, 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
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42
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Fiore CL, Jarett JK, Steinert G, Lesser MP. Trait-Based Comparison of Coral and Sponge Microbiomes. Sci Rep 2020; 10:2340. [PMID: 32047192 PMCID: PMC7012828 DOI: 10.1038/s41598-020-59320-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/27/2020] [Indexed: 12/27/2022] Open
Abstract
Corals and sponges harbor diverse microbial communities that are integral to the functioning of the host. While the taxonomic diversity of their microbiomes has been well-established for corals and sponges, their functional roles are less well-understood. It is unclear if the similarities of symbiosis in an invertebrate host would result in functionally similar microbiomes, or if differences in host phylogeny and environmentally driven microhabitats within each host would shape functionally distinct communities. Here we addressed this question, using metatranscriptomic and 16S rRNA gene profiling techniques to compare the microbiomes of two host organisms from different phyla. Our results indicate functional similarity in carbon, nitrogen, and sulfur assimilation, and aerobic nitrogen cycling. Additionally, there were few statistical differences in pathway coverage or abundance between the two hosts. For example, we observed higher coverage of phosphonate and siderophore metabolic pathways in the star coral, Montastraea cavernosa, while there was higher coverage of chloroalkane metabolism in the giant barrel sponge, Xestospongia muta. Higher abundance of genes associated with carbon fixation pathways was also observed in M. cavernosa, while in X. muta there was higher abundance of fatty acid metabolic pathways. Metagenomic predictions based on 16S rRNA gene profiling analysis were similar, and there was high correlation between the metatranscriptome and metagenome predictions for both hosts. Our results highlight several metabolic pathways that exhibit functional similarity in these coral and sponge microbiomes despite the taxonomic differences between the two microbiomes, as well as potential specialization of some microbially based metabolism within each host.
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Affiliation(s)
- Cara L Fiore
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, School of Marine Science and Ocean Engineering, Durham, NH, USA.
- Appalachian State University, Biology Department, Boone, NC, USA.
| | - Jessica K Jarett
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, School of Marine Science and Ocean Engineering, Durham, NH, USA
- AnimalBiome, Oakland, CA, USA
| | - Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University Oldenburg, Wilhelmshaven, Germany
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Symbioses, Kiel, Germany
| | - Michael P Lesser
- University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, School of Marine Science and Ocean Engineering, Durham, NH, USA
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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: 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: 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.
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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
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