1
|
Peters EE, Cahn JKB, Lotti A, Gavriilidou A, Steffens UAE, Loureiro C, Schorn MA, Cárdenas P, Vickneswaran N, Crews P, Sipkema D, Piel J. Distribution and diversity of 'Tectomicrobia', a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites. ISME COMMUNICATIONS 2023; 3:50. [PMID: 37248312 PMCID: PMC10227082 DOI: 10.1038/s43705-023-00259-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023]
Abstract
Genomic and functional analyses of bacterial sponge symbionts belonging to the uncultivated candidate genus 'Entotheonella' has revealed them as the prolific producers of bioactive compounds previously identified from their invertebrate hosts. These studies also suggested 'Entotheonella' as the first members of a new candidate phylum, 'Tectomicrobia'. Here we analyzed the phylogenetic structure and environmental distribution of this as-yet sparsely populated phylum-like lineage. The data show that 'Entotheonella' and other 'Tectomicrobia' are not restricted to marine habitats but widely distributed among terrestrial locations. The inferred phylogenetic trees suggest several intra-phylum lineages with diverse lifestyles. Of these, the previously described 'Entotheonella' lineage can be more accurately divided into at least three different candidate genera with the terrestrial 'Candidatus Prasianella', the largely terrestrial 'Candidatus Allonella', the 'Candidatus Thalassonella' comprising sponge-associated members, and the more widely distributed 'Candidatus Entotheonella'. Genomic characterization of 'Thalassonella' members from a range of sponge hosts did not suggest a role as providers of natural products, despite high genomic similarity to 'Entotheonella' regarding primary metabolism and implied lifestyle. In contrast, the analysis revealed a correlation between the revised 'Entotheonella' 16S rRNA gene phylogeny and a specific association with sponges and their natural products. This feature might serve as a discovery method to accelerate the identification of new chemically rich 'Entotheonella' variants, and led to the identification of the first 'Entotheonella' symbiont in a non-tetractinellid sponge, Psammocinia sp., indicating a wide host distribution of 'Entotheonella'-based chemical symbiosis.
Collapse
Affiliation(s)
- Eike E Peters
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Jackson K B Cahn
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Alessandro Lotti
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Ursula A E Steffens
- Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Paco Cárdenas
- Pharmacognosy, Department of Pharmaceutical Biosciences, BioMedical Center, Uppsala University, Husargatan 3, 75124, Uppsala, Sweden
| | - Nilani Vickneswaran
- Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland.
| |
Collapse
|
2
|
Sugden S, Holert J, Cardenas E, Mohn WW, Stein LY. Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges. THE ISME JOURNAL 2022; 16:2503-2512. [PMID: 35906397 PMCID: PMC9562138 DOI: 10.1038/s41396-022-01296-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.
Collapse
Affiliation(s)
- Scott Sugden
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada.
| | - Johannes Holert
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Erick Cardenas
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
3
|
Thomson T, Ellis JI, Fusi M, Prinz N, Bennett-Smith MF, Aylagas E, Carvalho S, Jones BH. The Right Place at the Right Time: Seasonal Variation of Bacterial Communities in Arid Avicennia marina Soils in the Red Sea Is Specific to Its Position in the Intertidal. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.845611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mangrove forests play an important role in facilitating biogeochemical pathways and cycling acting as blue carbon sinks. These services are primarily regulated by the activity of the soil microbiome. However, there is still limited research into spatial and temporal variation patterns of bacterial community assemblages in mangrove soils. This study investigated important ecological scales of microprocesses that govern microbial communities in an arid mangrove ecosystem. Shifts in microbial community composition were influenced by fluctuations in environmental factors within the mangrove forests of the Red Sea influenced by seasonal changes in sea level. Notably, in summer microbial communities in shrub sites differed significantly from the fringe and the winter samples, with lower alpha diversity yet a higher dominance of specialized species capable of surviving in extreme conditions. The onset of dispersal limitation and heterogenous selection and the reduction of drift are likely the main forces shaping community assemblages. Specifically, in summer lower mean tidal levels eliminate tidal inundation creating a harsh high salinity and high temperature environment with no tidal connection thereby influencing the onset of dispersal limitation. An increased understanding of the spatial and temporal variation of bacterial communities is critical when assessing delivery of ecosystem services and their role in soil biogeochemical processes.
Collapse
|
4
|
Taylor JA, Díez-Vives C, Nielsen S, Wemheuer B, Thomas T. Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts. Environ Microbiol 2022; 24:2299-2314. [PMID: 35229422 DOI: 10.1111/1462-2920.15962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/13/2022] [Accepted: 02/26/2022] [Indexed: 11/03/2022]
Abstract
The diversity and function of sponge-associated symbionts is now increasingly understood, however, we lack an understanding on how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here we performed a metatransciptomics analysis of three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidising Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidising archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our timeseries study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Jessica A Taylor
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Cristina Díez-Vives
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Shaun Nielsen
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| |
Collapse
|
5
|
Ansari N, Rokhbakhsh-Zamin F, Hassanshahian M, Hesni MA. The Occurrence of Crude Oil-Degrading Bacteria in Some Sponges Collected at the Persian Gulf: Ecological Importance and Biotechnological Application. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2014529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Nasrin Ansari
- Department of Microbiology, Kerman Branch, Islamic Azad University, Kerman, Iran
| | | | - Mehdi Hassanshahian
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Majid Askari Hesni
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| |
Collapse
|
6
|
Hassanshahian M, Amirinejad N, Askarinejad Behzadi M. Crude oil pollution and biodegradation at the Persian Gulf: A comprehensive and review study. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2020; 18:1415-1435. [PMID: 33312652 PMCID: PMC7721969 DOI: 10.1007/s40201-020-00557-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/29/2020] [Indexed: 06/01/2023]
Abstract
The Persian Gulf consider as the fundamental biological marine condition between the seas. There is a different assortment of marine life forms including corals, wipes, and fish in this marine condition. Mangrove timberlands are found all through this sea-going biological system. Sullying of the Persian Gulf to oil-based goods is the principle of danger to this marine condition and this contamination can effectively affect this differing marine condition. Numerous specialists examined the result of oil contamination on Persian Gulf marine creatures including corals sponges, bivalves, and fishes. These analysts affirmed this oil contamination on the Persian Gulf significantly diminished biodiversity. Diverse microorganisms fit to consume oil-based commodities detailed by various scientists from the Persian Gulf and their capacity to the debasement of unrefined petroleum has been examined. There has additionally been little exploration of cyanobacteria, yeast, and unrefined petroleum debasing organisms in this sea-going environment. Biosurfactants are amphipathic molecules that upgrade the disintegration of oil and increment their bioavailability to corrupt microscopic organisms. Additionally, biosurfactant-producing bacteria were discovered from the Persian Gulf, and the capability to degradation of crude oil in microscale was evaluated. The current review article aims to collect the finding of various researches performed in the Persian Gulf on oil pollution and crude-oil biodegradation. It is expected that by applying biological methods in combination with mechanical and chemical methods, the hazard consequences of crude-oil contamination on this important aquatic ecosystem at the world will be mitigated and a step towards preserving this diverse marine environment.
Collapse
Affiliation(s)
- Mehdi Hassanshahian
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Nazanin Amirinejad
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | | |
Collapse
|
7
|
Díez‐Vives C, Taboada S, Leiva C, Busch K, Hentschel U, Riesgo A. On the way to specificity - Microbiome reflects sponge genetic cluster primarily in highly structured populations. Mol Ecol 2020; 29:4412-4427. [PMID: 32931063 PMCID: PMC7756592 DOI: 10.1111/mec.15635] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
Most animals, including sponges (Porifera), have species-specific microbiomes. Which genetic or environmental factors play major roles structuring the microbial community at the intraspecific level in sponges is, however, largely unknown. In this study, we tested whether geographic location or genetic structure of conspecific sponges influences their microbial assembly. For that, we used three sponge species with different rates of gene flow, and collected samples along their entire distribution range (two from the Mediterranean and one from the Southern Ocean) yielding a total of 393 samples. These three sponge species have been previously analysed by microsatellites or single nucleotide polymorphisms, and here we investigate their microbiomes by amplicon sequencing of the microbial 16S rRNA gene. The sponge Petrosia ficiformis, with highly isolated populations (low gene flow), showed a stronger influence of the host genetic distance on the microbial composition than the spatial distance. Host-specificity was therefore detected at the genotypic level, with individuals belonging to the same host genetic cluster harbouring more similar microbiomes than distant ones. On the contrary, the microbiome of Ircinia fasciculata and Dendrilla antarctica - both with weak population structure (high gene flow) - seemed influenced by location rather than by host genetic distance. Our results suggest that in sponge species with high population structure, the host genetic cluster influence the microbial community more than the geographic location.
Collapse
Affiliation(s)
| | - Sergi Taboada
- Departamento de Ciencias de la VidaEU‐US Marine Biodiversity GroupUniversidad de AlcaláAlcalá de HenaresSpain
- Departamento de Biología (Zoología)Universidad Autónoma de MadridFacultad de CienciasMadridSpain
| | - Carlos Leiva
- Department of Life SciencesThe Natural History MuseumLondonUK
- Department of Genetics, Microbiology and StatisticsFaculty of BiologyUniversity of BarcelonaBarcelonaSpain
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research KielResearch Unit Marine SymbiosesKielGermany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research KielResearch Unit Marine SymbiosesKielGermany
| | - Ana Riesgo
- Department of Life SciencesThe Natural History MuseumLondonUK
- Department of Biodiversity and Evolutionary BiologyMuseo Nacional de Ciencias Naturales de Madrid (CSIC)MadridSpain
| |
Collapse
|
8
|
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.
Collapse
|
9
|
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.
Collapse
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
| | | |
Collapse
|
10
|
A horizon scan of priorities for coastal marine microbiome research. Nat Ecol Evol 2019; 3:1509-1520. [PMID: 31636428 DOI: 10.1038/s41559-019-0999-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 09/05/2019] [Indexed: 12/21/2022]
Abstract
Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the 'microbiome') and the environment or their hosts - termed the 'holobiont'. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research.
Collapse
|
11
|
Feng G, Zhang F, Banakar S, Karlep L, Li Z. Analysis of functional gene transcripts suggests active CO2 assimilation and CO oxidation by diverse bacteria in marine sponges. FEMS Microbiol Ecol 2019; 95:5513993. [DOI: 10.1093/femsec/fiz087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/08/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Guofang Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200240, China
| | - Fengli Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200240, China
| | - Shivakumar Banakar
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200240, China
| | - Liisi Karlep
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Ehitajate 5, Tallinn 19086, Estonia
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200240, China
| |
Collapse
|
12
|
Kuo J, Yang YT, Lu MC, Wong TY, Sung PJ, Huang YS. Antimicrobial activity and diversity of bacteria associated with Taiwanese marine sponge Theonella swinhoei. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1414-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
13
|
Van Duyl FC, Mueller B, Meesters EH. Spatio-temporal variation in stable isotope signatures (δ 13C and δ 15N) of sponges on the Saba Bank. PeerJ 2018; 6:e5460. [PMID: 30128208 PMCID: PMC6097495 DOI: 10.7717/peerj.5460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/26/2018] [Indexed: 12/02/2022] Open
Abstract
Sponges are ubiquitous on coral reefs, mostly long lived and therefore adaptive to changing environmental conditions. They feed on organic matter withdrawn from the passing water and they may harbor microorganisms (endosymbionts), which contribute to their nutrition. Their diets and stable isotope (SI) fractionation determine the SI signature of the sponge holobiont. Little is known of spatio–temporal variations in SI signatures of δ13C and δ15N in tropical sponges and whether they reflect variations in the environment. We investigated the SI signatures of seven common sponge species with different functional traits and their potential food sources between 15 and 32 m depth along the S-SE and E-NE side of the Saba Bank, Eastern Caribbean, in October 2011 and October 2013. SI signatures differed significantly between most sponge species, both in mean values and in variation, indicating different food preferences and/or fractionation, inferring sponge species-specific isotopic niche spaces. In 2011, all sponge species at the S-SE side were enriched in d13C compared to the E-NE side. In 2013, SI signatures of sponges did not differ between the two sides and were overall lighter in δ13C and δ15N than in 2011. Observed spatio–temporal changes in SI in sponges could not be attributed to changes in the SI signatures of their potential food sources, which remained stable with different SI signatures of pelagic (particulate organic matter (POM): δ13C −24.9‰, δ15N +4.3‰) and benthic-derived food (macroalgae: δ13C −15.4‰, δ15N +0.8‰). Enriched δ13C signatures in sponges at the S-SE side in 2011 are proposed to be attributed to predominantly feeding on benthic-derived C. This interpretation was supported by significant differences in water mass constituents between sides in October 2011. Elevated NO3 and dissolved organic matter concentrations point toward a stronger reef signal in reef overlying water at the S-SE than N-NE side of the Bank in 2011. The depletions of δ13C and δ15N in sponges in October 2013 compared to October 2011 concurred with significantly elevated POM concentrations. The contemporaneous decrease in δ15N suggests that sponges obtain their N mostly from benthic-derived food with a lower δ15N than pelagic food. Average proportional feeding on available sources varied between sponge species and ranged from 20% to 50% for benthic and 50% to 80% for pelagic-derived food, assuming trophic enrichment factors of 0.5‰ ± sd 0.5 for δ13C and 3‰ ± sd 0.5 for δ15N for sponges. We suggest that observed variation of SI in sponges between sides and years were the result of shifts in the proportion of ingested benthic- and pelagic-derived organic matter driven by environmental changes. We show that sponge SI signatures reflect environmental variability in space and time on the Saba Bank and that SI of sponges irrespective of their species-specific traits move in a similar direction in response to these environmental changes.
Collapse
Affiliation(s)
- Fleur C Van Duyl
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, The Netherlands
| | - Benjamin Mueller
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, The Netherlands.,Department for Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, The Netherlands
| | | |
Collapse
|
14
|
Mehbub MF, Tanner JE, Barnett SJ, Bekker J, Franco CMM, Zhang W. A controlled aquarium system and approach to study the role of sponge-bacteria interactions using Aplysilla rosea and Vibrio natriegens. Sci Rep 2018; 8:11801. [PMID: 30087404 PMCID: PMC6081443 DOI: 10.1038/s41598-018-30295-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/23/2018] [Indexed: 11/09/2022] Open
Abstract
Sponge-bacteria interactions are very important due to their ecological and biological significance. To understand the impact of interactions between sponges and bacteria (both associated with and external to sponges) on sponge-associated microbial diversity, sponge metabolite profiles and bioactivity, we used a controlled aquarium system and designed an experimental approach that allows the study of sponge-bacteria interactions in a well-defined manner. To test the feasibility of this approach, this system was used to study the interaction between a sponge Aplysilla rosea and a marine bacterium commonly found in seawater, Vibrio natriegens. Sponge explants were exposed to V. natriegens, at 5 × 106 cfu/ml, and changes were monitored for 48 hours. Pyro-sequencing revealed significant shifts in microbial communities associated with the sponges after 24 to 48 hours. Both the control (sponge only without added bacteria) and Vibrio-exposed sponges showed a distinct shift in bacterial diversity and abundance with time. Vibrio exposure significantly increased bacterial diversity, the abundance of a number of taxa compared to control sponges. The result experimentally supports the notion of dynamic and concerted responses by the sponge when interacting with a bacterium, and demonstrates the feasibility of using this controlled aquarium system for the study of sponge-bacteria interactions.
Collapse
Affiliation(s)
- Mohammad F Mehbub
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
| | - Jason E Tanner
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
- SARDI Aquatic Sciences, 2 Hamra Avenue, West Beach, SA, 5024, Adelaide, Australia
| | - Stephen J Barnett
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
| | - Jan Bekker
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
| | - Wei Zhang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Adelaide, Australia.
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Astudillo-García C, Slaby BM, Waite DW, Bayer K, Hentschel U, Taylor MW. Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges. Environ Microbiol 2017; 20:561-576. [DOI: 10.1111/1462-2920.13965] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/20/2017] [Accepted: 10/19/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Carmen Astudillo-García
- School of Biological Sciences; University of Auckland; Auckland New Zealand
- Institute of Marine Science, University of Auckland; Auckland New Zealand
| | - Beate M. Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences, University of Würzburg; Würzburg Germany
| | - David W. Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences; The University of Queensland; QLD, St Lucia Australia
| | - Kristina Bayer
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- Christian-Albrechts-Universität zu Kiel; Kiel Germany
| | - Michael W. Taylor
- School of Biological Sciences; University of Auckland; Auckland New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland; New Zealand
| |
Collapse
|
17
|
An Overview on Marine Sponge-Symbiotic Bacteria as Unexhausted Sources for Natural Product Discovery. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040040] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Microbial symbiotic communities of marine macro-organisms carry functional metabolic profiles different to the ones found terrestrially and within surrounding marine environments. These symbiotic bacteria have increasingly been a focus of microbiologists working in marine environments due to a wide array of reported bioactive compounds of therapeutic importance resulting in various patent registrations. Revelations of symbiont-directed host specific functions and the true nature of host-symbiont interactions, combined with metagenomic advances detecting functional gene clusters, will inevitably open new avenues for identification and discovery of novel bioactive compounds of biotechnological value from marine resources. This review article provides an overview on bioactive marine symbiotic organisms with specific emphasis placed on the sponge-associated ones and invites the international scientific community to contribute towards establishment of in-depth information of the environmental parameters defining selection and acquisition of true symbionts by the host organisms.
Collapse
|
18
|
Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks. Sci Rep 2017; 7:2542. [PMID: 28566699 PMCID: PMC5451456 DOI: 10.1038/s41598-017-02656-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 04/18/2017] [Indexed: 12/24/2022] Open
Abstract
Sponges (Porifera) are abundant and diverse members of benthic filter feeding communities in most marine ecosystems, from the deep sea to tropical reefs. A characteristic feature is the associated dense and diverse prokaryotic community present within the sponge mesohyl. Previous molecular genetic studies revealed the importance of host identity for the community composition of the sponge-associated microbiota. However, little is known whether sponge host-specific prokaryotic community patterns observed at 97% 16S rRNA gene sequence similarity are consistent at high taxonomic ranks (from genus to phylum level). In the present study, we investigated the prokaryotic community structure and variation of 24 sponge specimens (seven taxa) and three seawater samples from Sweden. Results show that the resemblance of prokaryotic communities at different taxonomic ranks is consistent with patterns present at 97% operational taxonomic unit level.
Collapse
|
19
|
Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila. Sci Rep 2017; 7:43247. [PMID: 28233813 PMCID: PMC5324122 DOI: 10.1038/srep43247] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/20/2017] [Indexed: 11/08/2022] Open
Abstract
Microbial symbionts in sponges are ubiquitous, forming complex and highly diverse host-specific communities. Conspecific sponges display remarkable stability in their symbiont communities, both spatially and temporally, yet extreme fluctuations in environmental factors can cause shifts in host-symbiont associations. We previously demonstrated that the marine sponge Hymeniacidon heliophila displayed significant community-level differences in microbial symbiont diversity, structure and composition when sampled from intertidal and subtidal environments. Here, we conducted a 70-day reciprocal transplant experiment to directly test the effect of tidal exposure on the microbiome of H. heliophila, using next-generation Illumina sequencing of 16S rRNA gene sequences to characterize symbiont communities. While sponges transplanted between habitats displayed shifts in microbial communities after 70 days, temporal variation was the dominant factor affecting microbial community composition. Further, we identified core symbionts that persisted across these spatio-temporal scales and used a metagenomic approach to show that these dominant members of the microbiome of H. heliophila represent nitrogen cycling taxa that have the potential to contribute to a diverse array of nitrogen transformations in the sponge holobiont. Together, these results indicate that despite moderate spatio-temporal shifts in symbiont composition, core symbiont functions (e.g. nitrogen cycling) can be maintained in sponge microbiomes through functional redundancy.
Collapse
|
20
|
The role of sponge-bacteria interactions: the sponge Aplysilla rosea challenged by its associated bacterium Streptomyces ACT-52A in a controlled aquarium system. Appl Microbiol Biotechnol 2016; 100:10609-10626. [PMID: 27717966 DOI: 10.1007/s00253-016-7878-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/05/2016] [Accepted: 09/16/2016] [Indexed: 10/20/2022]
Abstract
Sponge-associated bacteria play a critical role in sponge biology, metabolism and ecology, but how they interact with their host sponges and the role of these interactions are poorly understood. This study investigated the role of the interaction between the sponge Aplysilla rosea and its associated actinobacterium, Streptomyces ACT-52A, in modifying sponge microbial diversity, metabolite profile and bioactivity. A recently developed experimental approach that exposes sponges to bacteria of interest in a controlled aquarium system was improved by including the capture and analysis of secreted metabolites by the addition of an absorbent resin in the seawater. In a series of controlled aquaria, A. rosea was exposed to Streptomyces ACT-52A at 106 cfu/ml and monitored for up to 360 h. Shifts in microbial communities associated with the sponges occurred within 24 to 48 h after bacterial exposure and continued until 360 h, as revealed by TRFLP. The metabolite profiles of sponge tissues also changed substantially as the microbial community shifted. Control sponges (without added bacteria) and Streptomyces ACT-52A-exposed sponges released different metabolites into the seawater that was captured by the resin. The antibacterial activity of compounds collected from the seawater increased at 96 and 360 h of exposure for the treated sponges compared to the control group due to new compounds being produced and released. Increased antibacterial activity of metabolites from treated sponge tissue was observed only at 360 h, whereas that of control sponge tissue remained unchanged. The results demonstrate that the interaction between sponges and their associated bacteria plays an important role in regulating secondary metabolite production.
Collapse
|
21
|
Souza DT, Genuário DB, Silva FSP, Pansa CC, Kavamura VN, Moraes FC, Taketani RG, Melo IS. Analysis of bacterial composition in marine sponges reveals the influence of host phylogeny and environment. FEMS Microbiol Ecol 2016; 93:fiw204. [PMID: 27702764 DOI: 10.1093/femsec/fiw204] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/14/2016] [Accepted: 10/02/2016] [Indexed: 01/10/2023] Open
Abstract
Bacterial communities associated with sponges are influenced by environmental factors; however, some degree of genetic influence of the host on the microbiome is also expected. In this work, 16S rRNA gene amplicon sequencing revealed diverse bacterial phylotypes based on the phylogenies of three tropical sponges (Aplysina fulva, Aiolochroia crassa and Chondrosia collectrix). Despite their sympatric occurrence, the studied sponges presented different bacterial compositions that differed from those observed in seawater. However, lower dissimilarities in bacterial communities were observed within sponges from the same phylogenetic group. The relationships between operational taxonomic units (OTUs) recovered from the sponges and database sequences revealed associations among sequences from unrelated sponge species and sequences retrieved from diverse environmental samples. In addition, one Proteobacteria OTU retrieved from A. fulva was identical to sequences previously reported from A. fulva specimens collected along the Brazilian coast. Based on these results, we conclude that bacterial communities associated with marine sponges are shaped by host identity, while environmental conditions seem to be less important in shaping symbiont communities. This is the first study to assess bacterial communities associated with marine sponges in the remote St. Peter and St. Paul Archipelago using amplicon sequencing of the 16S rRNA gene.
Collapse
Affiliation(s)
- Danilo T Souza
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Diego B Genuário
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| | - Fabio Sérgio P Silva
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Camila C Pansa
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
- College of Agriculture 'Luiz de Queiroz', University of São Paulo, 13418-900, Piracicaba, SP, Brazil
| | - Vanessa N Kavamura
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| | - Fernando C Moraes
- Rio de Janeiro Botanical Garden Research Institute, 22460-030, Rio de Janeiro, RJ, Brazil
- National Museum, Federal University of Rio de Janeiro, 20940-040, Rio de Janeiro, RJ, Brazil
| | - Rodrigo G Taketani
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| | - Itamar S Melo
- Environmental Microbiology Laboratory, Embrapa Environment, 13820-000, Jaguariúna, SP, Brazil
| |
Collapse
|
22
|
Steinert G, Taylor MW, Deines P, Simister RL, de Voogd NJ, Hoggard M, Schupp PJ. In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity. PeerJ 2016; 4:e1936. [PMID: 27114882 PMCID: PMC4841226 DOI: 10.7717/peerj.1936] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/23/2016] [Indexed: 01/03/2023] Open
Abstract
Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges, Rhabdastrella globostellata, Callyspongia sp., Rhaphoxya sp., and Acanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant for Callyspongia sp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges.
Collapse
Affiliation(s)
- Georg Steinert
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg, Wilhelmshaven, Germany; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland , Auckland , New Zealand
| | - Peter Deines
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Rachel L Simister
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | | | - Michael Hoggard
- School of Biological Sciences, University of Auckland , Auckland , New Zealand
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg , Wilhelmshaven , Germany
| |
Collapse
|
23
|
Luter HM, Widder S, Botté ES, Abdul Wahab M, Whalan S, Moitinho-Silva L, Thomas T, Webster NS. Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens. PeerJ 2015; 3:e1435. [PMID: 26713229 PMCID: PMC4690404 DOI: 10.7717/peerj.1435] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/03/2015] [Indexed: 01/07/2023] Open
Abstract
Sponges are well known for hosting dense and diverse microbial communities, but how these associations vary with biogeography and environment is less clear. Here we compared the microbiome of an ecologically important sponge species, Carteriospongia foliascens, over a large geographic area and identified environmental factors likely responsible for driving microbial community differences between inshore and offshore locations using co-occurrence networks (NWs). The microbiome of C. foliascens exhibited exceptionally high microbial richness, with more than 9,000 OTUs identified at 97% sequence similarity. A large biogeographic signal was evident at the OTU level despite similar phyla level diversity being observed across all geographic locations. The C. foliascens bacterial community was primarily comprised of Gammaproteobacteria (34.2% ± 3.4%) and Cyanobacteria (32.2% ± 3.5%), with lower abundances of Alphaproteobacteria, Bacteroidetes, unidentified Proteobacteria, Actinobacteria, Acidobacteria and Deltaproteobacteria. Co-occurrence NWs revealed a consistent increase in the proportion of Cyanobacteria over Bacteroidetes between turbid inshore and oligotrophic offshore locations, suggesting that the specialist microbiome of C. foliascens is driven by environmental factors.
Collapse
Affiliation(s)
- Heidi M Luter
- NAMRA and the Research Institute for the Environment & Livelihoods, Charles Darwin University , Darwin, Northern Territory , Australia
| | - Stefanie Widder
- CUBE, Department of Microbiology and Ecosystem Science, University of Vienna , Vienna , Austria
| | - Emmanuelle S Botté
- Australian Institute of Marine Science , Townsville, Queensland , Australia
| | | | - Stephen Whalan
- Marine Ecology Research Centre, School of Environment, Science and Engineering,Southern Cross University , Lismore, New South Wales , Australia
| | - Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences,University of New South Wales , Sydney, New South Wales , Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences,University of New South Wales , Sydney, New South Wales , Australia
| | - Nicole S Webster
- Australian Institute of Marine Science , Townsville, Queensland , Australia
| |
Collapse
|
24
|
Intraspecific Variation in Microbial Symbiont Communities of the Sun Sponge, Hymeniacidon heliophila, from Intertidal and Subtidal Habitats. Appl Environ Microbiol 2015; 82:650-8. [PMID: 26567307 DOI: 10.1128/aem.02980-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/07/2015] [Indexed: 11/20/2022] Open
Abstract
Sponges host diverse and complex communities of microbial symbionts that display a high degree of host specificity. The microbiomes of conspecific sponges are relatively constant, even across distant locations, yet few studies have directly examined the influence of abiotic factors on intraspecific variation in sponge microbial community structure. The contrast between intertidal and subtidal environments is an ideal system to assess the effect of environmental variation on sponge-microbe symbioses, producing two drastically different environments on a small spatial scale. Here, we characterized the microbial communities of individual intertidal and subtidal Hymeniacidon heliophila sponges, ambient seawater, and sediment from a North Carolina oyster reef habitat by partial (Illumina sequencing) and nearly full-length (clone libraries) 16S rRNA gene sequence analyses. Clone library sequences were compared to H. heliophila symbiont communities from the Gulf of Mexico and Brazil, revealing strong host specificity of dominant symbiont taxa across expansive geographic distances. Sediment and seawater samples yielded clearly distinct microbial communities from those found in H. heliophila. Despite the close proximity of the sponges sampled, significant differences between subtidal and intertidal sponges in the diversity, structure, and composition of their microbial communities were detected. Differences were driven by changes in the relative abundance of a few dominant microbial symbiont taxa, as well as the presence or absence of numerous rare microbial taxa. These findings suggest that extreme abiotic fluctuations, such as periodic air exposure in intertidal habitats, can drive intraspecific differences in complex host-microbe symbioses.
Collapse
|
25
|
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
|
26
|
Microbial Diversity and Putative Diazotrophy in High- and Low-Microbial-Abundance Mediterranean Sponges. Appl Environ Microbiol 2015; 81:5683-93. [PMID: 26070678 DOI: 10.1128/aem.01320-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/02/2015] [Indexed: 01/12/2023] Open
Abstract
Microbial communities associated with marine sponges carry out nutrient transformations essential for benthic-pelagic coupling; however, knowledge about their composition and function is still sparse. We evaluated the richness and diversity of prokaryotic assemblages associated with three high-microbial-abundance (HMA) and three low-microbial-abundance (LMA) sympatric Mediterranean sponges to address their stability and uniqueness. Moreover, to examine functionality and because an imbalance between nitrogen ingestion and excretion has been observed for some of these species, we sequenced nitrogenase genes (nifH) and measured N2 fixation. The prokaryotic communities in the two sponge types did not differ in terms of richness, but the highest diversity was found in HMA sponges. Moreover, the discrete composition of the communities in the two sponge types relative to that in the surrounding seawater indicated that horizontal transmission and vertical transmission affect the microbiomes associated with the two sponge categories. nifH genes were found in all LMA species and sporadically in one HMA species, and about half of the nifH gene sequences were common between the different sponge species and were also found in the surrounding water, suggesting horizontal transmission. (15)N2-enriched incubations showed that N2 fixation was measurable in the water but was not associated with the sponges. Also, the analysis of the isotopic ratio of (15)N to (14)N in sponge tissue indicated that N2 fixation is not an important source of nitrogen in these Mediterranean sponges. Overall, our results suggest that compositional and functional features differ between the prokaryotic communities associated with HMA and LMA sponges, which may affect sponge ecology.
Collapse
|
27
|
Croué J, West NJ, Escande ML, Intertaglia L, Lebaron P, Suzuki MT. A single betaproteobacterium dominates the microbial community of the crambescidine-containing sponge Crambe crambe. Sci Rep 2014; 3:2583. [PMID: 24002533 PMCID: PMC3761228 DOI: 10.1038/srep02583] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/12/2013] [Indexed: 11/09/2022] Open
Abstract
Crambe crambe is a marine sponge that produces high concentrations of the pharmacologically significant pentacyclic guanidine alkaloids (PGAs), Crambescines and Crambescidines. Although bio-mimetic chemical synthesis of PGAs suggests involvement of microorganisms in their biosynthesis, there are conflicting reports on whether bacteria are associated with this sponge or not. Using 16S rRNA gene pyrosequencing we show that the associated bacterial community of C. crambe is dominated by a single bacterial species affiliated to the Betaproteobacteria. Microscopy analysis of sponge tissue sections using a specific probe and in situ hybridization confirmed its dominance in the sponge mesohyl and a single microbial morphology was observed by transmission electron microscopy. If confirmed the presence of a simple bacteria community in C. crambe makes this association a very pertinent model to study sponge-bacteria interactions and should allow further research into the possible implication of bacteria in PGA biosynthesis.
Collapse
Affiliation(s)
- Julie Croué
- 1] UPMC Univ. Paris 06, UMR 7621, LOMIC, UMR 7232, BIOM, UMS 2348 (Plate-forme Bio2Mar), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France [2] CNRS, UMR 7621, LOMIC, F-66650, Observatoire Océanologique, Banyuls-sur-Mer, France
| | | | | | | | | | | |
Collapse
|
28
|
Cárdenas CA, Bell JJ, Davy SK, Hoggard M, Taylor MW. Influence of environmental variation on symbiotic bacterial communities of two temperate sponges. FEMS Microbiol Ecol 2014; 88:516-27. [PMID: 24617641 DOI: 10.1111/1574-6941.12317] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/27/2014] [Accepted: 03/03/2014] [Indexed: 11/30/2022] Open
Abstract
Sponges are an important component of temperate subtidal marine ecosystems, with a range of important functional roles and extensive symbiotic relationships with microorganisms. However, much remains unknown about their relationships with these symbiotic microorganisms, and specifically, the role that these symbionts play in sponge physiology, feeding and adaptation to local environmental conditions. Changes in environmental factors may alter relationships between sponges and their symbionts, which could conceivably influence the abundance and distribution patterns of some temperate sponge species. Here, we analyzed the effect of transplantation of sponges between different habitats to test the effect of changes in environmental conditions on the stability of the bacterial communities in specimens of Tethya bergquistae and Ecionemia alata, based on pyrosequencing of amplified 16S rRNA genes. Bacterial communities differed markedly between the two host species. While some morphological changes were observed in transplanted sponges, transplantation had little overall effect on sponge-associated bacterial communities at either phylum or 97%-OTU level. Our results show the importance of host species and also the stability of sponge-associated bacterial communities under environmental variation.
Collapse
Affiliation(s)
- César A Cárdenas
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | | | | | | |
Collapse
|