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Lo Giudice A, Papale M, Rizzo C, Giannarelli S, Caruso G, Aspholm PE, Maimone G, Azzaro M. First report on pollutant accumulation and associated microbial communities in the freshwater sponge Spongilla lacustris (Linnaeus, 1759) from the sub-Arctic Pasvik River (Norway). WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e11039. [PMID: 38787335 DOI: 10.1002/wer.11039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
This explorative study was aimed at first characterizing the sponge Spongilla lacustris (Linnaeus, 1759) from the sub-Arctic Pasvik River (Northern Fennoscandia), in terms of associated microbial communities and pollutant accumulation. Persistent organic pollutants were determined in sponge mesohyl tissues, along with the estimation of the microbial enzymatic activity rates, prokaryotic abundance and morphometric traits, and the analysis of the taxonomic bacterial diversity by next-generation sequencing techniques. The main bacterial groups associated with S. lacustris were Alphaproteobacteria and Gammaproteobacteria, followed by Chloroflexi and Acidobacteria. The structure of the S. lacustris-associated bacterial communities was in sharp contrast to those of the bacterioplankton, being statistically close to those found in sediments. Dieldrin was measured at higher concentrations in the sponge tissues (3.1 ± 0.4 ng/g) compared to sediment of the same site (0.04 ± 0.03 ng/g). Some taxonomic groups were possibly related to the occurrence of certain contaminants, as was the case of Patescibacteria and dieldrin. Obtained results substantially contribute to the still scarce knowledge of bacterial community diversity, activities, and ecology in freshwater sponges. PRACTITIONER POINTS: Microbial community associated with Spongilla lacustris is probably shaped by the occurrence of certain contaminants, mainly dieldrin and heavy metals. A higher accumulation of dieldrin in the sponge mesohyl tissues than in sediment was determined. S. lacustris is suggested as sponge species to be used as a sentinel of pesticide pollution in the Pasvik River. S. lacustris, living in tight contact with soft substrates, harbored communities more similar to sediment than water communities.
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Affiliation(s)
- Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
| | - Maria Papale
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
| | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
- Department of Marine Biotechnology, Zoological Station "Anton Dohrn", Messina, Italy
| | - Stefania Giannarelli
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Gabriella Caruso
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
| | | | - Giovanna Maimone
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
| | - Maurizio Azzaro
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
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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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Ratnawati SE, Kuuliala L, Verschuere N, Cnockaert M, Vandamme P, Devlieghere F. The exploration of dominant spoilage bacteria in blue mussels (Mytilus edulis) stored under different modified atmospheres by MALDI-TOF MS in combination with 16S rRNA sequencing. Food Microbiol 2024; 118:104407. [PMID: 38049269 DOI: 10.1016/j.fm.2023.104407] [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: 06/30/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 12/06/2023]
Abstract
Few studies have addressed species-level identification of spoilage bacteria in blue mussels packed under modified atmospheres (MAs). We investigated the effect of MAs and seasons on the tentative species-level of dominant spoilage bacteria in blue mussels. Summer (s) and winter (w) blue mussels were stored at 4 °C in the atmospheres (%CO2/O2/N2): A40s (30/40/30), B60s (40/60/0), C60s (0/60/40), A40w (30/40/30), and D75w (25/75/0). In total, 122 culturable isolates were obtained at the final stage of shelf life, when mortality was high (56-100%) and total psychrotrophic bacteria counted >7 log CFU g-1. Biochemical properties were analyzed using gram reactions, catalase and oxidase activities, and salt tolerance tests. Culturable isolates were identified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16 S rRNA gene sequence analysis. Spoilage potential tests were investigated by evaluating protease, lipase, and fermentation activities as well as gas and H2S production. The culturable isolates showed tolerance to varied salt concentrations. Psychromonas arctica, Pseudoalteromonas elyakovii, and Shewanella frigidimarina were dominating in specific MAs. Winter blue mussels resulted in a higher variation of spoilage bacteria, including S. frigidimarina, S. vesiculosa, S. polaris, Micrococcus luteus, Paeniglutamicibacter terrestris sp. nov., and Alteromonas sp.
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Affiliation(s)
- S E Ratnawati
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - L Kuuliala
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Research Unit Knowledge-based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - N Verschuere
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - M Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - P Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - F Devlieghere
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Lo Giudice A, Rizzo C. Freshwater Sponges as a Neglected Reservoir of Bacterial Biodiversity. Microorganisms 2023; 12:25. [PMID: 38257852 PMCID: PMC10819713 DOI: 10.3390/microorganisms12010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Freshwater sponges (Spongillida: Demospongiae), including more than 240 described species, are globally distributed in continental waters (except for Antarctica), where they cover both natural and artificial surfaces. However, fragmentary studies have targeted their microbiome, making it difficult to test hypotheses about sponge-microbe specificity and metabolic relationships, along with the environmental factors playing key roles in structuring the associated microbial communities. To date, particular attention has been paid to sponges (family Lubomirskiidae) that are endemic to Lake Baikal. Few other freshwater sponge species (e.g., Ephydatia spp., Eunapius spp., and Spongilla lacustris), from lakes and rivers spanning from Europe to South and North America, have been targeted for microbiological studies. Representatives of the phyla Proteobacteria, Bacteroidetes, and Actinobacteria largely predominated, and high differences were reported between the microbiome of freshwater and marine sponges. Several bacterial strains isolated from freshwater sponges can produce bioactive compounds, mainly showing antibiotic activities, with potential application in biotechnology. Understanding the roles played by sponge microbiomes in freshwater ecosystems is still in its infancy and has yet to be clarified to disentangle the ecological and evolutionary significance of these largely under-investigated microbial communities. This review was aimed at providing the main available information on the composition and biotechnological potential of prokaryotic communities associated with healthy freshwater sponges, as a neglected component of the global sponge microbiome, to stimulate researchers interested in the field.
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Affiliation(s)
- Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR.ISP), Spianata S. Raineri 86, 98122 Messina, Italy;
| | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council (CNR.ISP), Spianata S. Raineri 86, 98122 Messina, Italy;
- Zoological Station “Anton Dohrn”, Department of Ecosustainable Marine Biotechnology, Villa Pace, Contrada Porticatello, 98168 Messina, Italy
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Graffius S, Garzón JFG, Zehl M, Pjevac P, Kirkegaard R, Flieder M, Loy A, Rattei T, Ostrovsky A, Zotchev SB. Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris. Microbiol Spectr 2023; 11:e0435322. [PMID: 36728429 PMCID: PMC10100984 DOI: 10.1128/spectrum.04353-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023] Open
Abstract
Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.
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Affiliation(s)
- Sophie Graffius
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
| | | | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Rasmus Kirkegaard
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Mathias Flieder
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational System Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Andrew Ostrovsky
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, Geozentrum, University of Vienna, Vienna, Austria
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sergey B. Zotchev
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
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