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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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Turon M, Ford M, Maldonado M, Sitjà C, Riesgo A, Díez-Vives C. Microbiome changes through the ontogeny of the marine sponge Crambe crambe. ENVIRONMENTAL MICROBIOME 2024; 19:15. [PMID: 38468324 DOI: 10.1186/s40793-024-00556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND Poriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge microbiome can be acquired from the surrounding environment (horizontal acquisition) or obtained from the parents during the reproductive process through a variety of mechanisms (vertical transfer), typically resulting in the presence of symbiotic microbes throughout all stages of sponge development. How and to what extent the different components of the microbiome are transferred to the developmental stages remain poorly understood. Here, we investigated the microbiome composition of a common, low-microbial-abundance, Atlantic-Mediterranean sponge, Crambe crambe, throughout its ontogeny, including adult individuals, brooded larvae, lecithotrophic free-swimming larvae, newly settled juveniles still lacking osculum, and juveniles with a functional osculum for filter feeding. RESULTS Using 16S rRNA gene analysis, we detected distinct microbiome compositions in each ontogenetic stage, with variations in composition, relative abundance, and diversity of microbial species. However, a particular dominant symbiont, Candidatus Beroebacter blanensis, previously described as the main symbiont of C. crambe, consistently occurred throughout all stages, an omnipresence that suggests vertical transmission from parents to offspring. This symbiont fluctuated in relative abundance across developmental stages, with pronounced prevalence in lecithotrophic stages. A major shift in microbial composition occurred as new settlers completed osculum formation and acquired filter-feeding capacity. Candidatus Beroebacter blanensis decreased significatively at this point. Microbial diversity peaked in filter-feeding stages, contrasting with the lower diversity of lecithotrophic stages. Furthermore, individual specific transmission patterns were detected, with greater microbial similarity between larvae and their respective parents compared to non-parental conspecifics. CONCLUSIONS These findings suggest a putative vertical transmission of the dominant symbiont, which could provide some metabolic advantage to non-filtering developmental stages of C. crambe. The increase in microbiome diversity with the onset of filter-feeding stages likely reflects enhanced interaction with environmental microbes, facilitating horizontal transmission. Conversely, lower microbiome diversity in lecithotrophic stages, prior to filter feeding, suggests incomplete symbiont transfer or potential symbiont digestion. This research provides novel information on the dynamics of the microbiome through sponge ontogeny, on the strategies for symbiont acquisition at each ontogenetic stage, and on the potential importance of symbionts during larval development.
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Affiliation(s)
- Marta Turon
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Madeline Ford
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Manuel Maldonado
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), c/Accés a la Cala St. Francesc, 14, 17300, Blanes, Spain
| | - Cèlia Sitjà
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), c/Accés a la Cala St. Francesc, 14, 17300, Blanes, Spain
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | - Cristina Díez-Vives
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
- Department of Systems Biology, Centro Nacional de Biotecnología, c/Darwin, 3, 28049, Madrid, Spain.
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3
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Freitas MAMD, Cunha-Ferreira IC, Leal CV, Fernandez JCC, Omachi CY, Campos LS, Masi BP, Krüger RH, Hajdu E, Thompson CC, Thompson FL. Microbiome diversity from sponges biogeographically distributed between South America and Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163256. [PMID: 37011689 DOI: 10.1016/j.scitotenv.2023.163256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
Sponges from South America and Antarctica are evolutionarily closely related. Specific symbiont signatures that could differentiate these two geographic regions are unknown. This study aimed to investigate the microbiome diversity of sponges from South America and Antarctica. In total 71 sponge specimens were analyzed (Antarctica: N = 59, 13 different species; South America: N = 12, 6 different species). Illumina 16S rRNA sequences were generated (2.88 million sequences; 40K ± 29K/sample). The most abundant symbionts were heterotrophic (94.8 %) and belonged mainly to Proteobacteria and Bacteroidota. EC94 was the most abundant symbiont and dominated the microbiome of some species (70-87 %), comprising at least 10 phylogroups. Each of the EC94 phylogroups was specific to one genus or species of sponge. Furthermore, South America sponges had higher abundance of photosynthetic microorganisms (2.3 %) and sponges from Antarctica, the highest abundance of chemosynthetic (5.5 %). Sponge symbionts may contribute to the function of their hosts. The unique features from each of these two regions (e.g., light, temperature, and nutrients) possibly stimulate distinct microbiome diversity from sponges biogeographically distributed across continents.
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Affiliation(s)
- Mayanne A M de Freitas
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Camille V Leal
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Julio C C Fernandez
- Department of Invertebrates, National Museum, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Claudia Y Omachi
- Laboratory of Environmental Indicators, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Lucia S Campos
- Department of Zoology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno P Masi
- Laboratory of Marine Ecology and Fishery Oceanography of the Amazon (LEMOPA), Socio environmental and Water Resources Institute (ISARH), Federal Rural University of the Amazon (UFRA), Belém, PA, Brazil
| | - Ricardo H Krüger
- Laboratory of Enzymology, Biology Institute, University of Brasília (UNB), Brasília, Brazil
| | - Eduardo Hajdu
- Laboratory of Environmental Indicators, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Cristiane C Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Polyhydroxyalkanoate (PHA) Biopolymer Synthesis by Marine Bacteria of the Malaysian Coral Triangle Region and Mining for PHA Synthase Genes. Microorganisms 2022; 10:microorganisms10102057. [PMID: 36296332 PMCID: PMC9607975 DOI: 10.3390/microorganisms10102057] [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] [Received: 08/27/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Polyhydroxyalkanoate (PHA), a biodegradable and plastic-like biopolymer, has been receiving research and industrial attention due to severe plastic pollution, resource depletion, and global waste issues. This has spurred the isolation and characterisation of novel PHA-producing strains through cultivation and non-cultivation approaches, with a particular interest in genes encoding PHA synthesis pathways. Since sea sponges and sediment are marine benthic habitats known to be rich in microbial diversity, sponge tissues (Xestospongia muta and Aaptos aaptos) and sediment samples were collected in this study from Redang and Bidong islands located in the Malaysian Coral Triangle region. PHA synthase (phaC) genes were identified from sediment-associated bacterial strains using a cultivation approach and from sponge-associated bacterial metagenomes using a non-cultivation approach. In addition, phylogenetic diversity profiling was performed for the sponge-associated bacterial community using 16S ribosomal ribonucleic acid (16S rRNA) amplicon sequencing to screen for the potential presence of PHA-producer taxa. A total of three phaC genes from the bacterial metagenome of Aaptos and three phaC genes from sediment isolates (Sphingobacterium mizutaii UMTKB-6, Alcaligenes faecalis UMTKB-7, Acinetobacter calcoaceticus UMTKB-8) were identified. Produced PHA polymers were shown to be composed of 5C to nC monomers, with previously unreported PHA-producing ability of the S. mizutaii strain, as well as a 3-hydroxyvalerate-synthesising ability without precursor addition by the A. calcoaceticus strain.
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5
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Leal CV, Avelino-Alves D, Salazar V, Omachi C, Thompson C, Berlinck RGS, Hajdu E, Thompson F. Sponges present a core prokaryotic community stable across Tropical Western Atlantic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155145. [PMID: 35429557 DOI: 10.1016/j.scitotenv.2022.155145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/24/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Sponges are among the earliest lineages of metazoans, with first fossil records dated back to 890 million years ago. All sponge species present associations with microorganisms to some extension, which influence sponges' survival and adaptation. Sponge species can be divided into two categories, Low Microbial Abundance and High Microbial Abundance, depending on the abundance of the microbial community that they host. Monanchora arbuscula (a Low Microbial Abundance sponge species) and Xestospongia muta (a High Microbial Abundance sponge species) are sponges with widespread distribution in the Tropical Western Atlantic. Despite previous studies on the major features of these species, little is known whether M. arcuscula and X. muta prokaryotic communities are stable across vast geographic regions. We obtained a total of ~9.26 million 16S rRNA gene Illumina sequences for M. arbuscula samples collected at seven locations and for X. muta samples collected at three locations, corresponding to five ecoregions of the Caribbean and the Southwestern Atlantic (N = 105, 39 from M. arcuscula and 66 from X. muta). These samples reflected different ecological strategies for prokaryotic communities assembly, since the core prokaryotic communities of M. arbuscula are more heterotrophic and shared with different sources (corals, sponges, seawater, sediments), while X. muta has more significant photosynthetic prokaryotic communities, mainly outsourced from other sponges. Results of M. arbuscula and X. muta prokaryotic communities analysis demonstrate that both sponge species have core prokaryotic communities stable across a vast geographic area (> 8000 km), and the world's most notable coastal marine biogeographic filter, the Amazon River Mouth, in spite of the significant differences found among transient prokaryotic communities of both sponge species.
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Affiliation(s)
- Camille V Leal
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; SAGE-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Dhara Avelino-Alves
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Vinícius Salazar
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; SAGE-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Claudia Omachi
- Laboratório de Indicadores Ambientais, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Cristiane Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; SAGE-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970 São Carlos, SP, Brazil
| | - Eduardo Hajdu
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fabiano Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; SAGE-COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Krikech I, Ranjbar Jafarabadi A, Leermakers M, Le Pennec G, Cappello T, Ezziyyani M. Insights into bioaccumulation and bioconcentration of potentially toxic elements in marine sponges from the Northwestern Mediterranean coast of Morocco. MARINE POLLUTION BULLETIN 2022; 180:113770. [PMID: 35635883 DOI: 10.1016/j.marpolbul.2022.113770] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/28/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The present research aimed to investigate the concentrations and patterns of six potentially toxic elements (PTEs) in three common sponge species collected along the Moroccan Mediterranean coast, as well as their levels in ambient seawater and sediments. Distinct inter-species variability in PTEs bioaccumulation was observed among the three species, suggesting that sponges have distinct selectivity for assimilating PTEs from the surrounding environment. C. crambe had a higher enrichment capacity for Cu, As, Cr and Ni, while P. ficiformis and C. reniformis exhibited the highest concentration of Cd and Pb, respectively. Interestingly, a similar spatial distribution patterns of PTEs was observed in the three media, with high values occurring in Tangier and Al-Hoceima locations. Overall, our results confirm that sponges reliably reflect the bioavailability of PTEs in their immediate environment, especially C. crambe, whose PTE tissue contents were highly and positively correlated with the contents of all PTEs in the sediments.
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Affiliation(s)
- Imad Krikech
- Department of Life Sciences, Polydisciplinary Faculty of Larache, Abdelmalek Essaadi University, 745 BP, 92004 Larache, Morocco; Laboratoire de Biotechnologie et de Chimie Marines, Université de Bretagne Sud, EA 3884-IUEM, BP 92116, 56321 CS, Lorient, Brittany, France; Analytical, Environmental and Geochemistry (AMGC), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Ali Ranjbar Jafarabadi
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran, Iran
| | - Martine Leermakers
- Analytical, Environmental and Geochemistry (AMGC), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Gaël Le Pennec
- Laboratoire de Biotechnologie et de Chimie Marines, Université de Bretagne Sud, EA 3884-IUEM, BP 92116, 56321 CS, Lorient, Brittany, France
| | - Tiziana Cappello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Mohammed Ezziyyani
- Department of Life Sciences, Polydisciplinary Faculty of Larache, Abdelmalek Essaadi University, 745 BP, 92004 Larache, Morocco.
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Amelia TSM, Suaberon FAC, Vad J, Fahmi ADM, Saludes JP, Bhubalan K. Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:492-512. [PMID: 35567600 DOI: 10.1007/s10126-022-10130-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.
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Affiliation(s)
- Tan Suet May Amelia
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Ferr Angelus C Suaberon
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Johanne Vad
- Changing Oceans Research Group, School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Afiq Durrani Mohd Fahmi
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Jonel P Saludes
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
- Department of Chemistry, University of San Agustin, 5000, Iloilo City, Philippines
- Department of Science and Technology, Balik Scientist Program, Philippine Council for Health Research & Development (PCHRD), Bicutan, 1631, Taguig, Philippines
| | - Kesaven Bhubalan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
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8
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Anteneh YS, Yang Q, Brown MH, Franco CMM. Factors affecting the isolation and diversity of marine sponge-associated bacteria. Appl Microbiol Biotechnol 2022; 106:1729-1744. [PMID: 35103809 PMCID: PMC8882111 DOI: 10.1007/s00253-022-11791-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/24/2022]
Abstract
Abstract Marine sponges are an ideal source for isolating as yet undiscovered microorganisms with some sponges having about 50% of their biomass composed of microbial symbionts. This study used a variety of approaches to investigate the culturable diversity of the sponge-associated bacterial community from samples collected from the South Australian marine environment. Twelve sponge samples were selected from two sites and their bacterial population cultivated using seven different agar media at two temperatures and three oxygen levels over 3 months. These isolates were identified using microscopic, macroscopic, and 16S rRNA gene analysis. A total of 1234 bacterial colonies were isolated which consisted of four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, containing 21 genera. The diversity of the bacterial population was demonstrated to be influenced by the type of isolation medium, length of the incubation period and temperature, sponge type, and oxygen level. The findings of this study showed that marine sponges of South Australia can yield considerable bacterial culturable diversity if a comprehensive isolation strategy is implemented. Two sponges, with the highest and the lowest diversity of culturable isolates, were examined using next-generation sequencing to better profile the bacterial population. A marked difference in terms of phyla and genera was observed using culture-based and culture-independent approaches. This observed variation displays the importance of utilizing both methods to reflect a more complete picture of the microbial population of marine sponges. Key points Improved bacterial diversity due to long incubations, 2 temperatures, and 3 oxygen levels. Isolates identified by morphology, restriction digests, and 16S rRNA gene sequencing. At least 70% of culturable genera were not revealed by NGS methods.
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11791-8.
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Affiliation(s)
- Yitayal S Anteneh
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.,Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa, Ethiopia.,Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Melissa H Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Christopher M M Franco
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia. .,Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
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9
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Rusanova A, Fedorchuk V, Toshchakov S, Dubiley S, Sutormin D. An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics. Life (Basel) 2021; 12:25. [PMID: 35054418 PMCID: PMC8777954 DOI: 10.3390/life12010025] [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: 11/12/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 05/07/2023] Open
Abstract
Sponges are remarkable holobionts harboring extremely diverse microbial and viral communities. However, the interactions between the components within holobionts and between a holobiont and environment are largely unknown, especially for polar organisms. To investigate possible interactions within and between sponge-associated communities, we probed the microbiomes and viromes of cold-water sympatric sponges Isodictya palmata (n = 2), Halichondria panicea (n = 3), and Halichondria sitiens (n = 3) by 16S and shotgun metagenomics. We showed that the bacterial and viral communities associated with these White Sea sponges are species-specific and different from the surrounding water. Extensive mining of bacterial antiphage defense systems in the metagenomes revealed a variety of defense mechanisms. The abundance of defense systems was comparable in the metagenomes of the sponges and the surrounding water, thus distinguishing the White Sea sponges from those inhabiting the tropical seas. We developed a network-based approach for the combined analysis of CRISPR-spacers and protospacers. Using this approach, we showed that the virus-host interactions within the sponge-associated community are typically more abundant (three out of four interactions studied) than the inter-community interactions. Additionally, we detected the occurrence of viral exchanges between the communities. Our work provides the first insight into the metagenomics of the three cold-water sponge species from the White Sea and paves the way for a comprehensive analysis of the interactions between microbial communities and associated viruses.
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Affiliation(s)
- Anastasiia Rusanova
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (A.R.); (S.D.)
| | - Victor Fedorchuk
- The Faculty of Geology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Stepan Toshchakov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia;
| | - Svetlana Dubiley
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (A.R.); (S.D.)
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Dmitry Sutormin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (A.R.); (S.D.)
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
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10
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Waterworth SC, Parker-Nance S, Kwan JC, Dorrington RA. Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts. mBio 2021; 12:e0157721. [PMID: 34519538 PMCID: PMC8546597 DOI: 10.1128/mbio.01577-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022] Open
Abstract
The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.
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Affiliation(s)
- Samantha C. Waterworth
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Shirley Parker-Nance
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Environmental Observation Network, Elwandle Coastal Node, Gqeberha (Port Elizabeth), South Africa
| | - Jason C. Kwan
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Rosemary A. Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Institute for Aquatic Biodiversity, Makhanda, South Africa
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11
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Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte. Antonie van Leeuwenhoek 2020; 114:95-112. [DOI: 10.1007/s10482-020-01503-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022]
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12
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Berlinck RGS, Bernardi DI, Fill T, Fernandes AAG, Jurberg ID. The chemistry and biology of guanidine secondary metabolites. Nat Prod Rep 2020; 38:586-667. [PMID: 33021301 DOI: 10.1039/d0np00051e] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2017-2019Guanidine natural products isolated from microorganisms, marine invertebrates and terrestrial plants, amphibians and spiders, represented by non-ribosomal peptides, guanidine-bearing polyketides, alkaloids, terpenoids and shikimic acid derived, are the subject of this review. The topics include the discovery of new metabolites, total synthesis of natural guanidine compounds, biological activity and mechanism-of-action, biosynthesis and ecological functions.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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13
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Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts. ISME JOURNAL 2020; 15:503-519. [PMID: 33011742 DOI: 10.1038/s41396-020-00791-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 01/17/2023]
Abstract
The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured and uncharacterised Proteobacteria. Here we set out to characterise this group using metagenomics, in-depth phylogenetic analyses, metatranscriptomics, and fluorescence in situ hybridisation microscopy. We obtained five metagenome-assembled-genomes (MAGs) from different sponge species that, together with a previously published MAG (AqS2), comprise two families within a new gammaproteobacterial order that we named UTethybacterales. Members of this order share a heterotrophic lifestyle but vary in their predicted ability to use various carbon, nitrogen and sulfur sources, including taurine, spermidine and dimethylsulfoniopropionate. The deep branching of the UTethybacterales within the Gammaproteobacteria and their almost exclusive presence in sponges suggests they have entered a symbiosis with their host relatively early in evolutionary time and have subsequently functionally radiated. This is reflected in quite distinct lifestyles of various species of UTethybacterales, most notably their diverse morphologies, predicted substrate preferences, and localisation within the sponge tissue. This study provides new insight into the evolution of metazoan-bacteria symbiosis.
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14
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Yang Q, Franco CMM, Lin HW, Zhang W. Untapped sponge microbiomes: structure specificity at host order and family levels. FEMS Microbiol Ecol 2020; 95:5554005. [PMID: 31494678 DOI: 10.1093/femsec/fiz136] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/22/2019] [Indexed: 12/12/2022] Open
Abstract
Sponges are complex holobionts in which the structure of the microbiome has seldom been characterized above the host species level. The hypothesis tested in this study is that the structure of the sponge microbiomes is specific to the host at the order and family levels. This was done by using 33 sponge species belonging to 19 families representing five orders. A combination of three primer sets covering the V1-V8 regions of the 16S rRNA gene provided a more comprehensive coverage of the microbiomes. Both the diversity and structure of sponge microbiomes were demonstrated to be highly specific to the host phylogeny at the order and family levels. There are always dominant operational taxonomic units (OTUs) (relative abundance >1%) shared between microbial communities of sponges within the same family or order, but these shared OTUs showed high levels of dissimilarity between different sponge families and orders. The unique OTUs for a particular sponge family or order could be regarded as their 'signature identity'. 70%-87% of these unique OTUs (class level) are unaffiliated and represent a vast resource of untapped microbiota. This study contributes to a deeper understanding on the concept of host-specificity of sponge microbiomes and highlights a hidden reservoir of sponge-associated microbial resources.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia 5042, Australia
| | - Hou-Wen Lin
- Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei Zhang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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15
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Bovio E, Sfecci E, Poli A, Gnavi G, Prigione V, Lacour T, Mehiri M, Varese GC. The culturable mycobiota associated with the Mediterranean sponges Aplysina cavernicola, Crambe crambe and Phorbas tenacior. FEMS Microbiol Lett 2019; 366:5710934. [PMID: 31960895 DOI: 10.1093/femsle/fnaa014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 01/20/2020] [Indexed: 01/15/2023] Open
Abstract
Marine fungi are part of the huge and understudied biodiversity hosted in the sea. To broaden the knowledge on fungi inhabiting the Mediterranean Sea and their role in sponge holobiont, three sponges namely Aplysina cavernicola, Crambe crambe and Phorbas tenacior were collected in Villefranche sur Mer, (France) at about 25 m depth. The fungal communities associated with the sponges were isolated using different techniques to increase the numbers of fungi isolated. All fungi were identified to species level giving rise to 19, 13 and 3 species for P. tenacior, A. cavernicola and C. crambe, respectively. Of note, 35.7% and 50.0% of the species detected were either reported for the first time in the marine environment or in association with sponges. The mini-satellite analysis confirmed the uniqueness of the mycobiota of each sponge, leading to think that the sponge, with its metabolome, may shape the microbial community.
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Affiliation(s)
- Elena Bovio
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy.,University Nice Côte d'Azur, CNRS, Nice Institute of Chemistry, UMR 7272, Marine Natural Products Team, Nice 60103, France
| | - Estelle Sfecci
- University Nice Côte d'Azur, CNRS, Nice Institute of Chemistry, UMR 7272, Marine Natural Products Team, Nice 60103, France
| | - Anna Poli
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Giorgio Gnavi
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Valeria Prigione
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | | | - Mohamed Mehiri
- University Nice Côte d'Azur, CNRS, Nice Institute of Chemistry, UMR 7272, Marine Natural Products Team, Nice 60103, France
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Turin, Viale Mattioli 25, 10125 Turin, Italy
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16
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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: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/07/2019] [Indexed: 11/18/2022] Open
Abstract
Marine sponges host dense, diverse, and species-specific microbial communities around the globe; however, most of the current knowledge is restricted to species from tropical and temperate waters. Only recently, some studies have assessed the microbiome of a few Antarctic sponges; however, contrary to low mid-latitude sponges, the knowledge about temporal (stability) patterns in the bacterial communities of Antarctic sponges is absent. Here, we studied the temporal patterns of bacterial communities in the Antarctic sponges Mycale (Oxymycale) acerata, Isodictya sp., Hymeniacidon torquata, and Tedania (Tedaniopsis) wellsae that were tagged in situ and monitored during three austral summers over a 24-month period. By using amplicon sequencing of the bacterial 16S rRNA gene we found that the microbiome differed between species. In general, bacterial communities were dominated by gammaproteobacterial OTUs; however, M. acerata showed the most distinct pattern, being dominated by a single betaproteobacterial OTU. The analysis at OTU level (defined at 97% sequence similarity) showed a highly stable bacterial community through time, despite the abnormal seawater temperatures (reaching 3°C) and rates of temperature increase of 0.15°C day-1 recorded in austral summer 2017. Sponges were characterized by a small core bacterial community that accounted for a high percentage of the abundance. Overall, no consistent changes in core OTU abundance were recorded for all studied species, confirming a high temporal stability of the microbiome. In addition, predicted functional pathway profiles showed that the most abundant pathways among all sponges belonged mostly to metabolism pathway groups (e.g., amino acid, carbohydrate, energy, and nucleotide). The predicted functional pathway patterns differed among the four sponge species. However, no clear temporal differences were detected supporting what was found in terms of the relatively stable composition of the bacterial communities.
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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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17
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Kinase-Based Screening of Marine Natural Extracts Leads to the Identification of a Cytotoxic High Molecular Weight Metabolite from the Mediterranean Sponge Crambe tailliezi. Mar Drugs 2019; 17:md17100569. [PMID: 31600933 PMCID: PMC6836018 DOI: 10.3390/md17100569] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 12/18/2022] Open
Abstract
Regulated cell death (RCD) results from the activation of one or more signal transduction modules both in physiological or pathological conditions. It is now established that RCD is involved in numerous human diseases, including cancer. As regulated cell death processes can be modulated by pharmacological tools, the research reported here aims to characterize new marine compounds acting as RCD modulators. Protein kinases (PKs) are key signaling actors in various RCDs notably through the control of either mitosis (e.g., the PKs Aurora A and B) or necroptosis (e.g., RIPK1 and RIPK3). From the primary screening of 27 various extracts of marine organisms collected in the Mediterranean Sea, an extract and subsequently a purified high molecular weight compound dubbed P3, were isolated from the marine sponge Crambe tailliezi and characterized as a selective inhibitor of PKs Aurora A and B. Furthermore, P3 was shown to induce apoptosis and to decrease proliferation and mitotic index of human osteosarcoma U-2 OS cells.
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18
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Gantt SE, McMurray SE, Stubler AD, Finelli CM, Pawlik JR, Erwin PM. Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges. MICROBIOME 2019; 7:124. [PMID: 31466521 PMCID: PMC6716902 DOI: 10.1186/s40168-019-0739-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 08/19/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sponges are important suspension-feeding members of reef communities, with the collective capacity to overturn the entire water column on shallow Caribbean reefs every day. The sponge-loop hypothesis suggests that sponges take up dissolved organic carbon (DOC) and, via assimilation and shedding of cells, return carbon to the reef ecosystem as particulate organic carbon (POC). Sponges host complex microbial communities within their tissues that may play a role in carbon and nutrient cycling within the sponge holobiont. To investigate this relationship, we paired microbial community characterization (16S rRNA analysis, Illumina Mi-Seq platform) with carbon (DOC, POC) and nutrient (PO4, NOx, NH4) flux data (specific filtration rate) for 10 common Caribbean sponge species at two distant sites (Florida Keys vs. Belize, ~ 1203 km apart). RESULTS Distance-based linear modeling revealed weak relationships overall between symbiont structure and carbon and nutrient flux, suggesting that the observed differences in POC, DOC, PO4, and NOx flux among sponges are not caused by variations in the composition of symbiont communities. In contrast, significant correlations between symbiont structure and NH4 flux occurred consistently across the dataset. Further, several individual symbiont taxa (OTUs) exhibited relative abundances that correlated with NH4 flux, including one OTU affiliated with the ammonia-oxidizing genus Cenarchaeum. CONCLUSIONS Combined, these results indicate that microbiome structure is uncoupled from sponge carbon cycling and does not explain variation in DOC uptake among Caribbean coral reef sponges. Accordingly, differential DOC assimilation by sponge cells or stable microbiome components may ultimately drive carbon flux in the sponge holobiont.
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Affiliation(s)
- Shelby E Gantt
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Steven E McMurray
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Amber D Stubler
- Biology Department, Occidental College, 1600 Campus Road, Los Angeles, CA, 90041, USA
| | - Christopher M Finelli
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Joseph R Pawlik
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Patrick M Erwin
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA.
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19
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Yang Q, Franco CMM, Zhang W. Uncovering the hidden marine sponge microbiome by applying a multi-primer approach. Sci Rep 2019; 9:6214. [PMID: 30996336 PMCID: PMC6470215 DOI: 10.1038/s41598-019-42694-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/05/2019] [Indexed: 02/07/2023] Open
Abstract
Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, 5042, Australia.,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Wei Zhang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, 5042, Australia. .,Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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20
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Cleary DFR, Swierts T, Coelho FJRC, Polónia ARM, Huang YM, Ferreira MRS, Putchakarn S, Carvalheiro L, van der Ent E, Ueng JP, Gomes NCM, de Voogd NJ. The sponge microbiome within the greater coral reef microbial metacommunity. Nat Commun 2019; 10:1644. [PMID: 30967538 PMCID: PMC6456735 DOI: 10.1038/s41467-019-09537-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 03/18/2019] [Indexed: 02/03/2023] Open
Abstract
Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan.
| | - Thomas Swierts
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands
| | - Francisco J R C Coelho
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Ana R M Polónia
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Yusheng M Huang
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
- Department of Marine Recreation, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
| | - Marina R S Ferreira
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Sumaitt Putchakarn
- Institute of Marine Science, Burapha University, Chon Buri, 20131, Thailand
| | - Luis Carvalheiro
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Esther van der Ent
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands
| | - Jinn-Pyng Ueng
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
- Department of Aquaculture, National Penghu University of Science and Technology, 300 Liu-Ho Rd., Magong City, Penghu 880, Taiwan
| | - Newton C M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
- CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Nicole J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands
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21
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Silva SBL, Oberhänsli F, Tribalat MA, Genta-Jouve G, Teyssié JL, Dechraoui-Bottein MY, Gallard JF, Evanno L, Poupon E, Thomas OP. Insights into the Biosynthesis of Cyclic Guanidine Alkaloids from Crambeidae Marine Sponges. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Siguara B. L. Silva
- UMR Géoazur; Université Nice Sophia Antipolis; CNRS, IRD, Observatoire de la Côte d'Azur; 250 rue Albert Einstein 06560 Valbonne France
- Pharmacognosie et Chimie des Substances Naturelles; BioCIS; Université Paris-Sud; Université Paris-Saclay; CNRS; 92290 Châtenay-Malabry France
| | - François Oberhänsli
- Radioecology Laboratory; International Atomic Energy Agency-Environment Laboratories; MC 98012 Monaco
| | - Marie-Aude Tribalat
- UMR Géoazur; Université Nice Sophia Antipolis; CNRS, IRD, Observatoire de la Côte d'Azur; 250 rue Albert Einstein 06560 Valbonne France
| | - Grégory Genta-Jouve
- Laboratoire de Chimie-Toxicologie Analytique et Cellulaire (C-TAC) UMR CNRS 8638 COMETE; Université Paris-Descartes; 4, avenue de l'Observatoire 75006 Paris France
| | - Jean-Louis Teyssié
- Radioecology Laboratory; International Atomic Energy Agency-Environment Laboratories; MC 98012 Monaco
| | | | - Jean-François Gallard
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301; Université Paris-Saclay; 1, avenue de la Terrasse 91198 Gif-sur-Yvette France
| | - Laurent Evanno
- Pharmacognosie et Chimie des Substances Naturelles; BioCIS; Université Paris-Sud; Université Paris-Saclay; CNRS; 92290 Châtenay-Malabry France
| | - Erwan Poupon
- Pharmacognosie et Chimie des Substances Naturelles; BioCIS; Université Paris-Sud; Université Paris-Saclay; CNRS; 92290 Châtenay-Malabry France
| | - Olivier P. Thomas
- UMR Géoazur; Université Nice Sophia Antipolis; CNRS, IRD, Observatoire de la Côte d'Azur; 250 rue Albert Einstein 06560 Valbonne France
- Marine Biodiscovery; School of Chemistry and Ryan Institute; National University of Ireland Galway (NUI Galway); University Road H91 TK33 Galway Ireland
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22
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García-Bonilla E, Brandão PFB, Pérez T, Junca H. Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida). MICROBIAL ECOLOGY 2019; 77:25-36. [PMID: 29766224 DOI: 10.1007/s00248-018-1201-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.
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Affiliation(s)
- Erika García-Bonilla
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT 11, Chía, 250008, Colombia
| | - Pedro F B Brandão
- Laboratorio de Microbiología Ambiental y Aplicada, Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Avenida Carrera 30 No. 45-03, Bogotá, Colombia
| | - Thierry Pérez
- Station Marine d'Endoume SME - IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, UMR 7263 CNRS, Aix-Marseille Université, IRD, Avignon Université, Rue Batterie des Lions, 13007, Marseille, France
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT 11, Chía, 250008, Colombia.
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Silva SBL, Oberhänsli F, Tribalat MA, Genta-Jouve G, Teyssié JL, Dechraoui-Bottein MY, Gallard JF, Evanno L, Poupon E, Thomas OP. Insights into the Biosynthesis of Cyclic Guanidine Alkaloids from Crambeidae Marine Sponges. Angew Chem Int Ed Engl 2018; 58:520-525. [DOI: 10.1002/anie.201809539] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 10/22/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Siguara B. L. Silva
- UMR Géoazur; Université Nice Sophia Antipolis; CNRS, IRD, Observatoire de la Côte d'Azur; 250 rue Albert Einstein 06560 Valbonne France
- Pharmacognosie et Chimie des Substances Naturelles; BioCIS; Université Paris-Sud; Université Paris-Saclay; CNRS; 92290 Châtenay-Malabry France
| | - François Oberhänsli
- Radioecology Laboratory; International Atomic Energy Agency-Environment Laboratories; MC 98012 Monaco
| | - Marie-Aude Tribalat
- UMR Géoazur; Université Nice Sophia Antipolis; CNRS, IRD, Observatoire de la Côte d'Azur; 250 rue Albert Einstein 06560 Valbonne France
| | - Grégory Genta-Jouve
- Laboratoire de Chimie-Toxicologie Analytique et Cellulaire (C-TAC) UMR CNRS 8638 COMETE; Université Paris-Descartes; 4, avenue de l'Observatoire 75006 Paris France
| | - Jean-Louis Teyssié
- Radioecology Laboratory; International Atomic Energy Agency-Environment Laboratories; MC 98012 Monaco
| | | | - Jean-François Gallard
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301; Université Paris-Saclay; 1, avenue de la Terrasse 91198 Gif-sur-Yvette France
| | - Laurent Evanno
- Pharmacognosie et Chimie des Substances Naturelles; BioCIS; Université Paris-Sud; Université Paris-Saclay; CNRS; 92290 Châtenay-Malabry France
| | - Erwan Poupon
- Pharmacognosie et Chimie des Substances Naturelles; BioCIS; Université Paris-Sud; Université Paris-Saclay; CNRS; 92290 Châtenay-Malabry France
| | - Olivier P. Thomas
- UMR Géoazur; Université Nice Sophia Antipolis; CNRS, IRD, Observatoire de la Côte d'Azur; 250 rue Albert Einstein 06560 Valbonne France
- Marine Biodiscovery; School of Chemistry and Ryan Institute; National University of Ireland Galway (NUI Galway); University Road H91 TK33 Galway Ireland
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24
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Knobloch S, Jóhannsson R, Marteinsson V. Bacterial diversity in the marine spongeHalichondria paniceafrom Icelandic waters and host-specificity of its dominant symbiont “CandidatusHalichondribacter symbioticus”. FEMS Microbiol Ecol 2018; 95:5173036. [DOI: 10.1093/femsec/fiy220] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/07/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Stephen Knobloch
- Microbiology Group, Department of Research and Innovation, Matís ohf., Vinlandsleid 12, 113 Reykjavik, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Saemundargata 2, 101 Reykjavík, Iceland
| | - Ragnar Jóhannsson
- Marine and Freshwater Research Institute, Hafrannsóknastofnun, Skúlagata 4, 101 Reykjavik, Iceland
| | - Viggó Marteinsson
- Microbiology Group, Department of Research and Innovation, Matís ohf., Vinlandsleid 12, 113 Reykjavik, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Saemundargata 2, 101 Reykjavik, Iceland
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25
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Cárdenas CA, González-Aravena M, Font A, Hestetun JT, Hajdu E, Trefault N, Malmberg M, Bongcam-Rudloff E. High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas. PeerJ 2018; 6:e4935. [PMID: 29892508 PMCID: PMC5994334 DOI: 10.7717/peerj.4935] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/19/2018] [Indexed: 01/07/2023] Open
Abstract
Sponges belonging to genus Mycale are common and widely distributed across the oceans and represent a significant component of benthic communities in term of their biomass, which in many species is largely composed by bacteria. However, the microbial communities associated with Mycale species inhabiting different geographical areas have not been previously compared. Here, we provide the first detailed description of the microbiota of two Mycale species inhabiting the sub-Antarctic Magellan region (53°S) and the Western Antarctic Peninsula (62-64°S), two geographically distant areas (>1,300 km) with contrasting environmental conditions. The sponges Mycale (Aegogropila) magellanica and Mycale (Oxymycale) acerata are both abundant members of benthic communities in the Magellan region and in Antarctica, respectively. High throughput sequencing revealed a remarkable similarity in the microbiota of both sponge species, dominated by Proteobacteria and Bacteroidetes, with both species sharing more than 74% of the OTUs. In contrast, 16% and 10% of the OTUs were found only in either M. magellanica or M. acerata, respectively. Interestingly, despite slight differences in the relative abundance, the most dominant OTUs were present in both species, whereas the unique OTUs had very low abundances (less than 1% of the total abundance). These results show a significant overlap among the microbiota of both Mycale species and also suggest the existence of a low level of specificity of the most dominant symbiont groups.
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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
| | - Jon T. Hestetun
- Marine Biodiversity Group, Department of Biology, University of Bergen, Bergen, Norway
| | - Eduardo Hajdu
- Museu Nacional, Departamento de Invertebrados, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Maja Malmberg
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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26
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Feng G, Sun W, Zhang F, Orlić S, Li Z. Functional Transcripts Indicate Phylogenetically Diverse Active Ammonia-Scavenging Microbiota in Sympatric Sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:131-143. [PMID: 29423641 DOI: 10.1007/s10126-018-9797-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/19/2017] [Indexed: 05/06/2023]
Abstract
Symbiotic ammonia scavengers contribute to effective removal of ammonia in sponges. However, the phylogenetic diversity and in situ activity of ammonia-scavenging microbiota between different sponge species are poorly addressed. Here, transcribed ammonia monooxygenase genes (amoA), hydrazine synthase genes (hzsA), and glutamine synthetase genes (glnA) were analyzed to reveal the active ammonia-scavenging microbiota in the sympatric sponges Theonella swinhoei, Plakortis simplex, and Phakellia fusca, and seawater. Archaeal amoA and bacterial glnA transcripts rather than bacterial amoA, hzsA, and archaeal glnA transcripts were detected in the investigated sponges and seawater. The transcribed amoA genes were ascribed to two Thaumarchaeota ecotypes, while the transcribed glnA genes were interspersed among the lineages of Cyanobacteria, Tectomicrobia, Poribacteria, Alpha-, Beta-, Gamma-, and Epsilonproteobacteria. In addition, transcribed abundances of archaeal amoA and bacterial glnA genes in these sponges have been quantified, showing significant variation among the investigated sponges and seawater. The transcriptome-based qualitative and quantitative analyses clarified the different phylogenetic diversity and transcription expression of functional genes related to microbially mediated ammonia scavenging in different sympatric sponges, contributing to the understanding of in situ active ecological functions of sponge microbial symbionts in holobiont nitrogen cycling.
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Affiliation(s)
- Guofang Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China
| | - Wei Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China
| | - Fengli Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China
| | - Sandi Orlić
- Ruđer Bošković Institute, Bijeničkacesta 54, 10000, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean region-STIM, Bijeničkacesta 54, 10000, Zagreb, Croatia
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China.
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27
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Gantt SE, López-Legentil S, Erwin PM. Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor. FEMS Microbiol Lett 2018; 364:3833132. [PMID: 28520957 DOI: 10.1093/femsle/fnx105] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/16/2017] [Indexed: 01/04/2023] Open
Abstract
Marine sponges have been shown to harbor diverse microbial symbiont communities that play key roles in host functioning, yet little is known about how anthropogenic disturbances impact sponge-microbe interactions. The Mediterranean sponge Crambe crambe is known to accumulate heavy metals in polluted harbors. In this study, we investigated whether the microbiome of C. crambe differed between sponges inhabiting a polluted harbor in Blanes (Spain) and a nearby (<1 km) natural environment. Triplicate sponge and ambient seawater samples were collected from each site and the microbial composition of each sample was determined by 16S rRNA gene sequence analysis (Illumina Hi-Seq platform). No significant differences in the diversity or structure of microbial communities in C. crambe were detected between habitats, while a significant difference in community structure was observed in ambient seawater inside and outside of the polluted harbor. The microbiome of C. crambe was clearly differentiated from free-living seawater microbes and dominated by Proteobacteria, specifically a single betaproteobacterium that accounted for >86% of all sequence reads. These results indicate that sponge microbiomes exhibit greater stability and pollution tolerance than their free-living microbial counterparts, potentially mitigating the effects of pollutants on coastal marine communities.
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Affiliation(s)
- Shelby E Gantt
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA
| | - Patrick M Erwin
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409, USA
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28
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Chaib De Mares M, Sipkema D, Huang S, Bunk B, Overmann J, van Elsas JD. Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera. Front Microbiol 2017; 8:2560. [PMID: 29326681 PMCID: PMC5742488 DOI: 10.3389/fmicb.2017.02560] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/11/2017] [Indexed: 02/01/2023] Open
Abstract
Sponges are engaged in intimate symbioses with a diversity of microorganisms from all three domains of life, namely Bacteria, Archaea and Eukarya. Sponges have been well studied and categorized for their bacterial communities, some displaying a high microbial abundance (HMA), while others show low microbial abundance (LMA). However, the associated Archaea and Eukarya have remained relatively understudied. We assessed the bacterial, archaeal and eukaryotic diversities in the LMA sponge species Dysidea avara and Dysidea etheria by deep amplicon sequencing, and compared the results to those in the HMA sponges Aplysina aerophoba and Aplysina cauliformis. D. avara and A. aerophoba are sympatric in the Mediterranean Sea, while D. etheria and A. cauliformis are sympatric in the Caribbean Sea. The bacterial communities followed a host-specific pattern, with host species identity explaining most of the variation among samples. We identified OTUs shared by the Aplysina species that support a more ancient association of these microbes, before the split of the two species studied here. These shared OTUs are suitable targets for future studies of the microbial traits that mediate interactions with their hosts. Even though the archaeal communities were not as rich as the bacterial ones, we found a remarkable diversification and specificity of OTUs of the family Cenarchaeaceae and the genus Nitrosopumilus in all four sponge species studied. Similarly, the differences in fungal communities were driven by sponge identity. The structures of the communities of small eukaryotes such as dinophytes and ciliophores (alveolates), and stramenopiles, could not be explained by either sponge host, sponge genus or geographic location. Our analyses suggest that the host specificity that was previously described for sponge bacterial communities also extends to the archaeal and fungal communities, but not to other microbial eukaryotes.
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Affiliation(s)
- Maryam Chaib De Mares
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Sixing Huang
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,German Centre of Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,German Centre of Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Jan Dirk van Elsas
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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29
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Ternon E, Perino E, Manconi R, Pronzato R, Thomas OP. How Environmental Factors Affect the Production of Guanidine Alkaloids by the Mediterranean Sponge Crambe crambe. Mar Drugs 2017. [PMID: 28621725 PMCID: PMC5484131 DOI: 10.3390/md15060181] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Most marine sponges are known to produce a large array of low molecular-weight metabolites which have applications in the pharmaceutical industry. The production of so-called specialized metabolites may be closely related to environmental factors. In this context, assessing the contribution of factors like temperature, nutrients or light to the metabolomes of sponges provides relevant insights into their chemical ecology as well as the supply issue of natural sponge products. The sponge Crambe crambe was chosen as a model due to its high content of specialized metabolites belonging to polycyclic guanidine alkaloids (PGA). First results were obtained with field data of both wild and farmed specimens collected in two seasons and geographic areas of the North-Western Mediterranean. Then, further insights into factors responsible for changes in the metabolism were gained with sponges cultivated under controlled conditions in an aquarium. Comparative metabolomics showed a clear influence of the seasons and to a lesser extent of the geography while no effect of depth or farming was observed. Interestingly, sponge farming did not limit the production of PGA, while ex situ experiments did not show significant effects of several abiotic factors on the specialized metabolome at a one-month time scale. Some hypotheses were finally proposed to explain the very limited variations of PGA in C. crambe placed under different environmental conditions.
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Affiliation(s)
- Eva Ternon
- Université Côte d'Azur, CNRS, OCA, IRD, Géoazur, 250 rue Albert Einstein, 06560 Valbonne, France.
| | - Erica Perino
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Corso Europa 26, 16132 Genoa, Italy.
| | - Renata Manconi
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Via Muroni 25, 07100 Sassari, Italy.
| | - Roberto Pronzato
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Corso Europa 26, 16132 Genoa, Italy.
| | - Olivier P Thomas
- Université Côte d'Azur, CNRS, OCA, IRD, Géoazur, 250 rue Albert Einstein, 06560 Valbonne, France.
- Marine Biodiscovery, School of Chemistry, National University of Ireland Galway, University Road, H91 TK33 Galway, Ireland.
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30
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Reverter M, Sasal P, Tapissier-Bontemps N, Lecchini D, Suzuki M. Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems. FEMS Microbiol Ecol 2017; 93:3738480. [DOI: 10.1093/femsec/fix051] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 04/17/2017] [Indexed: 12/26/2022] Open
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31
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Matcher GF, Waterworth SC, Walmsley TA, Matsatsa T, Parker‐Nance S, Davies‐Coleman MT, Dorrington RA. Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts. Microbiologyopen 2017; 6:e00417. [PMID: 27781403 PMCID: PMC5387304 DOI: 10.1002/mbo3.417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 01/13/2023] Open
Abstract
The Latrunculiidae are a family of cold water sponges known for their production of bioactive pyrroloiminoquinone alkaloids. Previously it was shown that the bacterial community associated with a Tsitsikamma sponge species comprises unusual bacterial taxa and is dominated by a novel Betaproteobacterium. Here, we have characterized the bacterial communities associated with six latrunculid species representing three genera (Tsitsikamma, Cyclacanthia, and Latrunculia) as well as a Mycale species, collected from Algoa Bay on the South African southeast coast. The bacterial communities of all seven sponge species were dominated by a single Betaproteobacterium operational taxonomic unit (OTU0.03 ), while a second OTU0.03 was dominant in the Mycale sp. The Betaproteobacteria OTUs from the different latrunculid sponges are closely related and their phylogenetic relationship follows that of their hosts. We propose that the latrunculid Betaproteobacteria OTUs are members of a specialized group of sponge symbionts that may have coevolved with their hosts. A single dominant Spirochaetae OTU0.03 was present in the Tsitsikamma and Cyclacanthia sponge species, but absent from the Latrunculia and Mycale sponges. This study sheds new light on the interactions between latrunculid sponges and their bacterial communities and may point to the potential involvement of dominant symbionts in the biosynthesis of the bioactive secondary metabolites.
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Affiliation(s)
- Gwynneth F. Matcher
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | | | - Tara A. Walmsley
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
- Department of BiotechnologyVaal University of TechnologyVanderbijlparkSouth Africa
| | - Tendayi Matsatsa
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Shirley Parker‐Nance
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Michael T. Davies‐Coleman
- Department of ChemistryRhodes UniversityGrahamstownSouth Africa
- Faculty of Natural ScienceUniversity of the Western CapeCape TownSouth Africa
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32
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A Place to Call Home: An Analysis of the Bacterial Communities in Two Tethya rubra Samaai and Gibbons 2005 Populations in Algoa Bay, South Africa. Mar Drugs 2017; 15:md15040095. [PMID: 28346340 PMCID: PMC5408241 DOI: 10.3390/md15040095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/08/2017] [Accepted: 03/16/2017] [Indexed: 11/26/2022] Open
Abstract
Sponges are important sources of bioactive secondary metabolites. These compounds are frequently synthesized by bacterial symbionts, which may be recruited from the surrounding seawater or transferred to the sponge progeny by the parent. In this study, we investigated the bacterial communities associated with the sponge Tethya rubra Samaai and Gibbons 2005. Sponge specimens were collected from Evans Peak and RIY Banks reefs in Algoa Bay, South Africa and taxonomically identified by spicule analysis and molecular barcoding. Crude chemical extracts generated from individual sponges were profiled by ultraviolet high performance liquid chromatography (UV-HPLC) and subjected to bioactivity assays in mammalian cells. Next-generation sequencing analysis of 16S rRNA gene sequences was used to characterize sponge-associated bacterial communities. T. rubra sponges collected from the two locations were morphologically and genetically indistinguishable. Chemical extracts from sponges collected at RIY banks showed mild inhibition of the metabolic activity of mammalian cells and their UV-HPLC profiles were distinct from those of sponges collected at Evans Peak. Similarly, the bacterial communities associated with sponges from the two locations were distinct with evidence of vertical transmission of symbionts from the sponge parent to its embryos. We conclude that these distinct bacterial communities may be responsible for the differences observed in the chemical profiles of the two Algoa Bay T. rubra Samaai and Gibbons 2005 populations.
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33
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Endosymbiotic calcifying bacteria across sponge species and oceans. Sci Rep 2017; 7:43674. [PMID: 28262822 PMCID: PMC5337934 DOI: 10.1038/srep43674] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/27/2017] [Indexed: 11/17/2022] Open
Abstract
From an evolutionary point of view, sponges are ideal targets to study marine symbioses as they are the most ancient living metazoans and harbour highly diverse microbial communities. A recently discovered association between the sponge Hemimycale columella and an intracellular bacterium that generates large amounts of calcite spherules has prompted speculation on the possible role of intracellular bacteria in the evolution of the skeleton in early animals. To gain insight into this purportedly ancestral symbiosis, we investigated the presence of symbiotic bacteria in Mediterranean and Caribbean sponges. We found four new calcibacteria OTUs belonging to the SAR116 in two orders (Poecilosclerida and Clionaida) and three families of Demospongiae, two additional OTUs in cnidarians and one more in seawater (at 98.5% similarity). Using a calcibacteria targeted probe and CARD-FISH, we also found calcibacteria in Spirophorida and Suberitida and proved that the calcifying bacteria accumulated at the sponge periphery, forming a skeletal cortex, analogous to that of siliceous microscleres in other demosponges. Bacteria-mediated skeletonization is spread in a range of phylogenetically distant species and thus the purported implication of bacteria in skeleton formation and evolution of early animals gains relevance.
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34
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Ternon E, Zarate L, Chenesseau S, Croué J, Dumollard R, Suzuki MT, Thomas OP. Spherulization as a process for the exudation of chemical cues by the encrusting sponge C. crambe. Sci Rep 2016; 6:29474. [PMID: 27381941 PMCID: PMC4933965 DOI: 10.1038/srep29474] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/20/2016] [Indexed: 01/07/2023] Open
Abstract
Ecological interactions in the marine environment are now recognized to be partly held by chemical cues produced by marine organisms. In particular, sponges are sessile animals thought to rely on the bioactive substances they synthesize to ensure their development and defense. However, the mechanisms leading the sponges to use their specialized metabolites as chemical cues remain unknown. Here we report the constant release of bioactive polycyclic guanidinic alkaloids by the Mediterranean sponge Crambe crambe into the dissolved and the particulate phases using a targeted metabolomics study. These compounds were proven to be stored into already described specialized (spherulous) sponge cells and dispersed into the water column after release through the sponge exhaling channels (oscula), leading to a chemical shield surrounding the sponge. Low concentrations of these compounds were demonstrated to have teratogenic effects on embryos of a common sea squirt (ascidian). This mechanism of action called spherulization may therefore contribute to the ecological success of encrusting sponges that need to extend their substrate cover to expand.
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Affiliation(s)
- Eva Ternon
- Université Nice Sophia Antipolis, Institut de Chimie de Nice, UMR 7272 CNRS, Faculté des Sciences, Parc Valrose, 06108 NICE Cedex 2, France
| | - Lina Zarate
- Université Nice Sophia Antipolis, Institut de Chimie de Nice, UMR 7272 CNRS, Faculté des Sciences, Parc Valrose, 06108 NICE Cedex 2, France
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Sandrine Chenesseau
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale, Station Marine d’Endoume, rue de la Batterie des Lions, 13007 Marseille, France
| | - Julie Croué
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Rémi Dumollard
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Marcelino T. Suzuki
- Sorbonne Universités, UPMC Univ Paris 06 and CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Olivier P. Thomas
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale, Station Marine d’Endoume, rue de la Batterie des Lions, 13007 Marseille, France
- National University of Ireland Galway, Marine Biodiscovery, School of Chemistry, University Road, Galway, Ireland
- Université Côte d’Azur, CNRS, OCA, IRD, Géoazur, 250 rue Albert Einstein, 06560 Valbonne, France
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Sfecci E, Lacour T, Amade P, Mehiri M. Polycyclic Guanidine Alkaloids from Poecilosclerida Marine Sponges. Mar Drugs 2016; 14:E77. [PMID: 27070629 PMCID: PMC4849081 DOI: 10.3390/md14040077] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/26/2016] [Accepted: 04/01/2016] [Indexed: 01/09/2023] Open
Abstract
Sessile marine sponges provide an abundance of unique and diversified scaffolds. In particular, marine guanidine alkaloids display a very wide range of biological applications. A large number of cyclic guanidine alkaloids, including crambines, crambescins, crambescidins, batzelladines or netamins have been isolated from Poecilosclerida marine sponges. In this review, we will explore the chemodiversity of tri- and pentacyclic guanidine alkaloids. NMR and MS data tools will also be provided, and an overview of the wide range of bioactivities of crambescidins and batzelladines derivatives will be given.
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Affiliation(s)
- Estelle Sfecci
- Nice Institute of Chemistry, Marine Natural Product Team, University Nice Sophia Antipolis, Parc Valrose, 28 avenue de Valrose, 06108 Nice Cedex 02, France.
| | | | - Philippe Amade
- Nice Institute of Chemistry, Marine Natural Product Team, University Nice Sophia Antipolis, Parc Valrose, 28 avenue de Valrose, 06108 Nice Cedex 02, France.
| | - Mohamed Mehiri
- Nice Institute of Chemistry, Marine Natural Product Team, University Nice Sophia Antipolis, Parc Valrose, 28 avenue de Valrose, 06108 Nice Cedex 02, France.
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36
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Berlinck RGS, Romminger S. The chemistry and biology of guanidine natural products. Nat Prod Rep 2016; 33:456-90. [DOI: 10.1039/c5np00108k] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The present review discusses the isolation, structure determination, synthesis, biosynthesis and biological activities of secondary metabolites bearing a guanidine group.
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Affiliation(s)
| | - Stelamar Romminger
- Instituto de Química de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
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37
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Erwin PM, Coma R, López-Sendino P, Serrano E, Ribes M. Stable symbionts across the HMA-LMA dichotomy: low seasonal and interannual variation in sponge-associated bacteria from taxonomically diverse hosts. FEMS Microbiol Ecol 2015; 91:fiv115. [DOI: 10.1093/femsec/fiv115] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2015] [Indexed: 12/13/2022] Open
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Yang Q, Franco CMM, Zhang W. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification. Appl Microbiol Biotechnol 2015; 99:8731-40. [PMID: 26245685 DOI: 10.1007/s00253-015-6875-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 11/26/2022]
Abstract
Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
- Centre for Marine Drugs, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200240, China.
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39
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Alex A, Antunes A. Pyrosequencing characterization of the microbiota from Atlantic intertidal marine sponges reveals high microbial diversity and the lack of co-occurrence patterns. PLoS One 2015; 10:e0127455. [PMID: 25992625 PMCID: PMC4439068 DOI: 10.1371/journal.pone.0127455] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/15/2015] [Indexed: 11/19/2022] Open
Abstract
Sponges are ancient metazoans that host diverse and complex microbial communities. Sponge-associated microbial diversity has been studied from wide oceans across the globe, particularly in subtidal regions, but the microbial communities from intertidal sponges have remained mostly unexplored. Here we used pyrosequencing to characterize the microbial communities in 12 different co-occurring intertidal marine sponge species sampled from the Atlantic coast, revealing a total of 686 operational taxonomic units (OTUs) at 97% sequence similarity. Taxonomic assignment of 16S ribosomal RNA tag sequences estimated altogether 26 microbial groups, represented by bacterial (75.5%) and archaeal (22%) domains. Proteobacteria (43.4%) and Crenarchaeota (20.6%) were the most dominant microbial groups detected in all the 12 marine sponge species and ambient seawater. The Crenarchaeota microbes detected in three Atlantic Ocean sponges had a close similarity with Crenarchaeota from geographically separated subtidal Red Sea sponges. Our study showed that most of the microbial communities observed in sponges (73%) were also found in the surrounding ambient seawater suggesting possible environmental acquisition and/or horizontal transfer of microbes. Beyond the microbial diversity and community structure assessments (NMDS, ADONIS, ANOSIM), we explored the interactions between the microbial communities coexisting in sponges using the checkerboard score (C-score). Analyses of the microbial association pattern (co-occurrence) among intertidal sympatric sponges revealed the random association of microbes, favoring the hypothesis that the sponge-inhabiting microbes are recruited from the habitat mostly by chance or influenced by environmental factors to benefit the hosts.
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Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050–123, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo, Alegre, 4169–007, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050–123, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo, Alegre, 4169–007, Porto, Portugal
- * E-mail:
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40
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Gutiérrez MH, Galand PE, Moffat C, Pantoja S. Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord. Environ Microbiol 2015; 17:3882-97. [PMID: 25856307 DOI: 10.1111/1462-2920.12872] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 04/02/2015] [Accepted: 04/02/2015] [Indexed: 01/30/2023]
Abstract
Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.
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Affiliation(s)
- Marcelo H Gutiérrez
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile
| | - Pierre E Galand
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, F-66650, Banyuls sur Mer, France
| | - Carlos Moffat
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile.,Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Silvio Pantoja
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile
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de Voogd NJ, Cleary DFR, Polónia ARM, Gomes NCM. Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia. FEMS Microbiol Ecol 2015; 91:fiv019. [PMID: 25764467 DOI: 10.1093/femsec/fiv019] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2015] [Indexed: 11/12/2022] Open
Abstract
In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change.
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Affiliation(s)
- Nicole J de Voogd
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands Institute for Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, the Netherlands
| | - Daniel F R Cleary
- Departamento de Biologia, CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Ana R M Polónia
- Departamento de Biologia, CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Departamento de Biologia, CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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Marine sponge derived natural products between 2001 and 2010: trends and opportunities for discovery of bioactives. Mar Drugs 2014; 12:4539-77. [PMID: 25196730 PMCID: PMC4145330 DOI: 10.3390/md12084539] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/07/2014] [Accepted: 07/15/2014] [Indexed: 12/20/2022] Open
Abstract
Marine sponges belonging to the phylum Porifera (Metazoa), evolutionarily the oldest animals are the single best source of marine natural products. The present review presents a comprehensive overview of the source, taxonomy, country of origin or geographical position, chemical class, and biological activity of sponge-derived new natural products discovered between 2001 and 2010. The data has been analyzed with a view to gaining an outlook on the future trends and opportunities in the search for new compounds and their sources from marine sponges.
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43
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Fuerst JA. Diversity and biotechnological potential of microorganisms associated with marine sponges. Appl Microbiol Biotechnol 2014; 98:7331-47. [DOI: 10.1007/s00253-014-5861-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/21/2014] [Accepted: 05/21/2014] [Indexed: 12/13/2022]
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