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Williams SE, Varliero G, Lurgi M, Stach JEM, Race PR, Curnow P. Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39073401 DOI: 10.1099/mic.0.001478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.
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Affiliation(s)
- Sam E Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Miguel Lurgi
- Department of Biosciences, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul R Race
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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2
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Esposito R, Federico S, Sonnessa M, Reddel S, Bertolino M, Ruocco N, Zagami G, Giovine M, Pozzolini M, Guida M, Zupo V, Costantini M. Characterizing the bacterial communities associated with Mediterranean sponges: a metataxonomic analysis. Front Microbiol 2024; 14:1295459. [PMID: 38274771 PMCID: PMC10808595 DOI: 10.3389/fmicb.2023.1295459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
The oceans cover over 70% of our planet, hosting a biodiversity of tremendous wealth. Sponges are one of the major ecosystem engineers on the seafloor, providing a habitat for a wide variety of species to be considered a good source of bioactive compounds. In this study, a metataxonomic approach was employed to describe the bacterial communities of the sponges collected from Faro Lake (Sicily) and Porto Paone (Gulf of Naples). Morphological analysis and amplification of the conserved molecular markers, including 18S and 28S (RNA ribosomal genes), CO1 (mitochondrial cytochrome oxidase subunit 1), and ITS (internal transcribed spacer), allowed the identification of four sponges. Metataxonomic analysis of sponges revealed a large number of amplicon sequence variants (ASVs) belonging to the phyla Proteobacteria, Cloroflexi, Dadabacteria, and Poribacteria. In particular, Myxilla (Myxilla) rosacea and Clathria (Clathria) toxivaria displayed several classes such as Alphaproteobacteria, Dehalococcoidia, Gammaproteobacteria, Cyanobacteria, and Bacteroidia. On the other hand, the sponges Ircinia oros and Cacospongia mollior hosted bacteria belonging to the classes Dadabacteriia, Anaerolineae, Acidimicrobiia, Nitrospiria, and Poribacteria. Moreover, for the first time, the presence of Rhizobiaceae bacteria was revealed in the sponge M. (Myxilla) rosacea, which was mainly associated with soil and plants and involved in biological nitrogen fixation.
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Affiliation(s)
- Roberta Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Serena Federico
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Napoli, Italy
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | | | | | - Marco Bertolino
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | - Nadia Ruocco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Calabria Marine Centre, Amendolara, Italy
| | - Giacomo Zagami
- Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, Messina, Italy
| | - Marco Giovine
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | - Marina Pozzolini
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genoa, Italy
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Valerio Zupo
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Ischia Marine Centre, Naples, Italy
| | - Maria Costantini
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Napoli, Italy
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Wei TS, Gao ZM, Gong L, Li QM, Zhou YL, Chen HG, He LS, Wang Y. Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp. Front Microbiol 2023; 14:1078171. [PMID: 36846759 PMCID: PMC9944714 DOI: 10.3389/fmicb.2023.1078171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/12/2023] [Indexed: 02/10/2023] Open
Abstract
Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus Bathydorus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. Bdellovibrio species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR-Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.
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Affiliation(s)
- Tao-Shu Wei
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,University of Chinese Academy of Sciences, Beijing, China
| | - Zhao-Ming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,*Correspondence: Zhao-Ming Gao ✉
| | - Lin Gong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Qing-Mei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ying-Li Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Hua-Guan Chen
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China,Yong Wang ✉
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4
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Quek ZBR, Ng JY, Jain SS, Long JXS, Lim SC, Tun K, Huang D. Low genetic diversity and predation threaten a rediscovered marine sponge. Sci Rep 2022; 12:22499. [PMID: 36577798 PMCID: PMC9797562 DOI: 10.1038/s41598-022-26970-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Discovered in 1819 in the tropical waters off Singapore, the magnificent Neptune's cup sponge Cliona patera (Hardwicke, 1820) was harvested for museums and collectors until it was presumed extinct worldwide for over a century since 1907. Recently in 2011, seven living individuals were rediscovered in Singapore with six relocated to a marine protected area in an effort to better monitor and protect the population, as well as to enhance external fertilisation success. To determine genetic diversity within the population, we sequenced the complete mitochondrial genomes and nuclear ribosomal DNA of these six individuals and found extremely limited variability in their genes. The low genetic diversity of this rediscovered population is confirmed by comparisons with close relatives of C. patera and could compromise the population's ability to recover from environmental and anthropogenic pressures associated with the highly urbanised coastlines of Singapore. This lack of resilience is compounded by severe predation which has been shrinking sponge sizes by up to 5.6% every month. Recovery of this highly endangered population may require ex situ approaches and crossbreeding with other populations, which are also rare.
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Affiliation(s)
- Z. B. Randolph Quek
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Yale-NUS College, National University of Singapore, Singapore, Singapore
| | - Juat Ying Ng
- grid.4280.e0000 0001 2180 6431School of Design and Environment, National University of Singapore, Singapore, Singapore ,grid.467827.80000 0004 0620 8814National Biodiversity Centre, National Parks Board, Singapore, Singapore
| | - Sudhanshi S. Jain
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - J. X. Sean Long
- grid.462738.c0000 0000 9091 4551Republic Polytechnic, Singapore, Singapore
| | - Swee Cheng Lim
- grid.4280.e0000 0001 2180 6431Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Karenne Tun
- grid.467827.80000 0004 0620 8814National Biodiversity Centre, National Parks Board, Singapore, Singapore
| | - Danwei Huang
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Centre for Nature-Based Climate Solutions, National University of Singapore, Singapore, Singapore
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5
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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] [MESH Headings] [Grants] [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
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.
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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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6
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Ruocco N, Esposito R, Zagami G, Bertolino M, De Matteo S, Sonnessa M, Andreani F, Crispi S, Zupo V, Costantini M. Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis. Sci Rep 2021; 11:21151. [PMID: 34707182 PMCID: PMC8551288 DOI: 10.1038/s41598-021-00713-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Although the Mediterranean Sea covers approximately a 0.7% of the world's ocean area, it represents a major reservoir of marine and coastal biodiversity. Among marine organisms, sponges (Porifera) are a key component of the deep-sea benthos, widely recognized as the dominant taxon in terms of species richness, spatial coverage, and biomass. Sponges are evolutionarily ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. In the present work, we firstly aimed at exploring the biodiversity of marine sponges from four different areas of the Mediterranean: Faro Lake in Sicily and "Porto Paone", "Secca delle fumose", "Punta San Pancrazio" in the Gulf of Naples. Eight sponge species were collected from these sites and identified by morphological analysis and amplification of several conserved molecular markers (18S and 28S RNA ribosomal genes, mitochondrial cytochrome oxidase subunit 1 and internal transcribed spacer). In order to analyze the bacterial diversity of symbiotic communities among these different sampling sites, we also performed a metataxonomic analysis through an Illumina MiSeq platform, identifying more than 1500 bacterial taxa. Amplicon Sequence Variants (ASVs) analysis revealed a great variability of the host-specific microbial communities. Our data highlight the occurrence of dominant and locally enriched microbes in the Mediterranean, together with the biotechnological potential of these sponges and their associated bacteria as sources of bioactive natural compounds.
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Affiliation(s)
- Nadia Ruocco
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Roberta Esposito
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, Complesso Universitario Di Monte Sant’Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Giacomo Zagami
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | - Marco Bertolino
- grid.5606.50000 0001 2151 3065DISTAV, Università Degli Studi Di Genova, Corso Europa 26, 16132 Genoa, Italy
| | - Sergio De Matteo
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | | | | | - Stefania Crispi
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.5326.20000 0001 1940 4177Institute of Biosciences and BioResources Naples, National Research Council of Italy, Naples, Italy
| | - Valerio Zupo
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Maria Costantini
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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7
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Anteneh YS, Yang Q, Brown MH, Franco CMM. Antimicrobial Activities of Marine Sponge-Associated Bacteria. Microorganisms 2021; 9:171. [PMID: 33466936 PMCID: PMC7830929 DOI: 10.3390/microorganisms9010171] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 11/17/2022] Open
Abstract
The misuse and overuse of antibiotics have led to the emergence of multidrug-resistant microorganisms, which decreases the chance of treating those infected with existing antibiotics. This resistance calls for the search of new antimicrobials from prolific producers of novel natural products including marine sponges. Many of the novel active compounds reported from sponges have originated from their microbial symbionts. Therefore, this study aims to screen for bioactive metabolites from bacteria isolated from sponges. Twelve sponge samples were collected from South Australian marine environments and grown on seven isolation media under four incubation conditions; a total of 1234 bacterial isolates were obtained. Of these, 169 bacteria were tested in media optimized for production of antimicrobial metabolites and screened against eleven human pathogens. Seventy bacteria were found to be active against at least one test bacterial or fungal pathogen, while 37% of the tested bacteria showed activity against Staphylococcus aureus including methicillin-resistant strains and antifungal activity was produced by 21% the isolates. A potential novel active compound was purified possessing inhibitory activity against S. aureus. Using 16S rRNA, the strain was identified as Streptomyces sp. Our study highlights that the marine sponges of South Australia are a rich source of abundant and diverse bacteria producing metabolites with antimicrobial activities against human pathogenic bacteria and fungi.
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Affiliation(s)
- Yitayal S. Anteneh
- 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 9086, Ethiopia
| | - Qi Yang
- 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;
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Melissa H. Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia;
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Oliveira BFR, Lopes IR, Canellas ALB, Muricy G, Dobson ADW, Laport MS. Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea. Microorganisms 2020; 8:E1978. [PMID: 33322780 PMCID: PMC7764410 DOI: 10.3390/microorganisms8121978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 11/25/2020] [Indexed: 01/28/2023] Open
Abstract
Marine sponges are excellent examples of invertebrate-microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.
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Affiliation(s)
- Bruno F. R. Oliveira
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
| | - Isabelle R. Lopes
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Anna L. B. Canellas
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Guilherme Muricy
- Laboratório de Biologia de Porifera, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940040, Brazil;
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
- Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - Marinella S. Laport
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
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9
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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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10
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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: 11] [Impact Index Per Article: 2.2] [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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Vicente J, Ríos JA, Zea S, Toonen RJ. Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean. PeerJ 2019; 7:e6371. [PMID: 30746308 PMCID: PMC6368163 DOI: 10.7717/peerj.6371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/28/2018] [Indexed: 11/20/2022] Open
Abstract
Neopetrosia proxima (Porifera: Demospongiae: Haplosclerida) is described as a morphologically variable sponge common on shallow reefs of the Caribbean. However, the range of morphological and reproductive variation within putative N. proxima led us to hypothesize that such variability may be indicative of cryptic species rather than plasticity. Using DNA sequences and morphological characters we confirmed the presence of three previously undescribed species of Neopetrosia. Morphological differences of each new congener were best resolved by partial gene sequences of the mitochondrial cytochrome oxidase subunit 1 over nuclear ones (18S rRNA and 28S rRNA). Several new characters for Neopetrosia were revealed by each new species. For example, N. dendrocrevacea sp. nov. and N. cristata sp. nov. showed the presence of grooves on the surface of the sponge body that converge at the oscula, and a more disorganized skeleton than previously defined for the genus. N. sigmafera sp. nov. adds the (1) presence of sigma microscleres, (2) significantly wider/longer oxeas (>200 μm), and (3) the presence of parenchymella larvae. Sampling of conspecifics throughout several locations in the Caribbean revealed larger spicules in habitats closer to the continental shelf than those in remote island locations. Our study highlights the importance of integrating molecular and morphological systematics for the discrimination of new Neopetrosia spp. despite belonging to one of several polyphyletic groups (families, genera) within the current definition of the order Haplosclerida.
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Affiliation(s)
- Jan Vicente
- University of Hawai‘i at Mānoa, Hawai‘i Institute of Marine Biology, Kāne‘ohe, HI, USA
| | - Jaime Andrés Ríos
- Universidad Nacional de Colombia—Sede Bogotá—Departamento de Biología, Ciudad Universitaria, Bogotá, Colombia
| | - Sven Zea
- Universidad Nacional de Colombia—Sede Caribe—Instituto de Estudios en Ciencias del Mar–CECIMAR, c/o INVEMAR, Rodadero Sur, Playa Salguero, Santa Marta, Colombia
| | - Robert J. Toonen
- University of Hawai‘i at Mānoa, Hawai‘i Institute of Marine Biology, Kāne‘ohe, HI, USA
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