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Maslin M, Paix B, van der Windt N, Ambo-Rappe R, Debitus C, Gaertner-Mazouni N, Ho R, de Voogd NJ. Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial. Antonie Van Leeuwenhoek 2024; 117:65. [PMID: 38602593 PMCID: PMC11008079 DOI: 10.1007/s10482-024-01962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.
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Affiliation(s)
- Mathilde Maslin
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Benoît Paix
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
| | - Niels van der Windt
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
| | - Rohani Ambo-Rappe
- Faculty of Marine Science and Fisheries, Department of Marine Science, Hasanuddin University, Makassar, Indonesia
| | - Cécile Debitus
- IRD, Univ Brest, CNRS, Ifremer, LEMAR, 29280, Plouzané, France
| | | | - Raimana Ho
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
- Institute of Biology (IBL), Leiden University, 2333 BE, PO Box 9505, Leiden, the Netherlands.
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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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Papale M, Giannarelli S, Azzaro di Rosamarina M, Ghezzi L, Lo Giudice A, Rizzo C. Chemical and microbiological insights into two littoral Antarctic demosponge species: Haliclona ( Rhizoniera) dancoi (Topsent 1901) and Haliclona ( Rhizoniera) scotti (Kirkpatrick 1907). Front Microbiol 2024; 15:1341641. [PMID: 38404594 PMCID: PMC10884823 DOI: 10.3389/fmicb.2024.1341641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/29/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction Antarctic Porifera have gained increasing interest as hosts of diversified associated microbial communities that could provide interesting insights on the holobiome system and its relation with environmental parameters. Methods The Antarctic demosponge species Haliclona dancoi and Haliclona scotti were targeted for the determination of persistent organic pollutant (i. e., polychlorobiphenyls, PCBs, and polycyclic aromatic hydrocarbons, PAHs) and trace metal concentrations, along with the characterization of the associated prokaryotic communities by the 16S rRNA next generation sequencing, to evaluate possible relationships between pollutant accumulation (e.g., as a stress factor) and prokaryotic community composition in Antarctic sponges. To the best of our knowledge, this approach has been never applied before. Results Notably, both chemical and microbiological data on H. scotti (a quite rare species in the Ross Sea) are here reported for the first time, as well as the determination of PAHs in Antarctic Porifera. Both sponge species generally contained higher amounts of pollutants than the surrounding sediment and seawater, thus demonstrating their accumulation capability. The structure of the associated prokaryotic communities, even if differing at order and genus levels between the two sponge species, was dominated by Proteobacteria and Bacteroidota (with Archaea abundances that were negligible) and appeared in sharp contrast to communities inhabiting the bulk environment. Discussions Results suggested that some bacterial groups associated with H. dancoi and H. scotti were significantly (positively or negatively) correlated to the occurrence of certain contaminants.
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Affiliation(s)
- Maria Papale
- Institute of Polar Sciences, National Research Council, Messina, Italy
| | - Stefania Giannarelli
- Department of Chemical and Industrial Chemistry, University of Pisa, Pisa, Italy
| | | | - Lisa Ghezzi
- Department of Earth Sciences, University of Pisa, Pisa, Italy
| | | | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council, Messina, Italy
- Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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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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De Castro-Fernández P, Angulo-Preckler C, García-Aljaro C, Avila C, Cutignano A. A Chemo-Ecological Investigation of Dendrilla antarctica Topsent, 1905: Identification of Deceptionin and the Effects of Heat Stress and Predation Pressure on Its Terpene Profiles. Mar Drugs 2023; 21:499. [PMID: 37755112 PMCID: PMC10532619 DOI: 10.3390/md21090499] [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: 07/30/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Marine sponges usually host a wide array of secondary metabolites that play crucial roles in their biological interactions. The factors that influence the intraspecific variability in the metabolic profile of organisms, their production or ecological function remain generally unknown. Understanding this may help predict changes in biological relationships due to environmental variations as a consequence of climate change. The sponge Dendrilla antarctica is common in shallow rocky bottoms of the Antarctic Peninsula and is known to produce diterpenes that are supposed to have defensive roles. Here we used GC-MS to determine the major diterpenes in two populations of D. antarctica from two islands, Livingston and Deception Island (South Shetland Islands). To assess the potential effect of heat stress, we exposed the sponge in aquaria to a control temperature (similar to local), heat stress (five degrees higher) and extreme heat stress (ten degrees higher). To test for defence induction by predation pressure, we exposed the sponges to the sea star Odontaster validus and the amphipod Cheirimedon femoratus. Seven major diterpenes were isolated and identified from the samples. While six of them were already reported in the literature, we identified one new aplysulphurane derivative that was more abundant in the samples from Deception Island, so we named it deceptionin (7). The samples were separated in the PCA space according to the island of collection, with 9,11-dihydrogracilin A (1) being more abundant in the samples from Livingston, and deceptionin (7) in the samples from Deception. We found a slight effect of heat stress on the diterpene profiles of D. antarctica, with tetrahydroaplysulphurin-1 (6) and the gracilane norditerpene 2 being more abundant in the group exposed to heat stress. Predation pressure did not seem to influence the metabolite production. Further research on the bioactivity of D. antarctica secondary metabolites, and their responses to environmental changes will help better understand the functioning and fate of the Antarctic benthos.
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Affiliation(s)
- Paula De Castro-Fernández
- Department of Evolutionary Biology, Ecology and Environmental Sciences (BEECA), Faculty of Biology, Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain;
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain;
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Chimica Biomolecolare (ICB), 80078 Pozzuoli, Napoli, Italy;
| | - Carlos Angulo-Preckler
- Red Sea Research Center and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Cristina García-Aljaro
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain;
| | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences (BEECA), Faculty of Biology, Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain;
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain
| | - Adele Cutignano
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Chimica Biomolecolare (ICB), 80078 Pozzuoli, Napoli, Italy;
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El Samak M, Zakeer S, Hanora A, Solyman SM. Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community. Mar Genomics 2023; 70:101032. [PMID: 37084583 DOI: 10.1016/j.margen.2023.101032] [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: 02/22/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge Theonella sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.
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Affiliation(s)
- Manar El Samak
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt.
| | - Samar M Solyman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt; Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University- Elkantara branch, Egypt
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Bacteria Associated with Benthic Invertebrates from Extreme Marine Environments: Promising but Underexplored Sources of Biotechnologically Relevant Molecules. Mar Drugs 2022; 20:md20100617. [DOI: 10.3390/md20100617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Microbe–invertebrate associations, commonly occurring in nature, play a fundamental role in the life of symbionts, even in hostile habitats, assuming a key importance for both ecological and evolutionary studies and relevance in biotechnology. Extreme environments have emerged as a new frontier in natural product chemistry in the search for novel chemotypes of microbial origin with significant biological activities. However, to date, the main focus has been microbes from sediment and seawater, whereas those associated with biota have received significantly less attention. This review has been therefore conceived to summarize the main information on invertebrate–bacteria associations that are established in extreme marine environments. After a brief overview of currently known extreme marine environments and their main characteristics, a report on the associations between extremophilic microorganisms and macrobenthic organisms in such hostile habitats is provided. The second part of the review deals with biotechnologically relevant bioactive molecules involved in establishing and maintaining symbiotic associations.
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