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Efremova J, Mazzella V, Mirasole A, Teixidó N, Núñez-Pons L. Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO 2 vents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170171. [PMID: 38246375 DOI: 10.1016/j.scitotenv.2024.170171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.
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Affiliation(s)
- Jana Efremova
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
| | - Valerio Mazzella
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Alice Mirasole
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Núria Teixidó
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy; Laboratoire d'Océanographie de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
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von Hoyningen-Huene AJE, Bang C, Rausch P, Rühlemann M, Fokt H, He J, Jensen N, Knop M, Petersen C, Schmittmann L, Zimmer T, Baines JF, Bosch TCG, Hentschel U, Reusch TBH, Roeder T, Franke A, Schulenburg H, Stukenbrock E, Schmitz RA. The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions. Front Microbiol 2024; 15:1347422. [PMID: 38476944 PMCID: PMC10927989 DOI: 10.3389/fmicb.2024.1347422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.
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Affiliation(s)
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Hannover Medical School, Institute for Medical Microbiology and Hospital Epidemiology, Hannover, Germany
| | - Hanna Fokt
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jinru He
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Nadin Jensen
- Institute for General Microbiology, Kiel University, Kiel, Germany
| | - Mirjam Knop
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
| | - Carola Petersen
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lara Schmittmann
- Research Unit Ocean Dynamics, GEOMAR Helmholtz Institute for Ocean Research Kiel, Kiel, Germany
| | - Thorsten Zimmer
- Institute for General Microbiology, Kiel University, Kiel, Germany
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thomas C. G. Bosch
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ute Hentschel
- Marine Evolutionary Ecology, GEOMAR Helmholtz Center for Ocean Research, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thorsten B. H. Reusch
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thomas Roeder
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Kiel University, Kiel, Germany
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Díez-Vives C, Riesgo A. High compositional and functional similarity in the microbiome of deep-sea sponges. THE ISME JOURNAL 2024; 18:wrad030. [PMID: 38365260 PMCID: PMC10837836 DOI: 10.1093/ismejo/wrad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/18/2024]
Abstract
Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.
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Affiliation(s)
- Cristina Díez-Vives
- Department of Systems Biology, Centro Nacional de Biotecnología, c/ Darwin, 3, 28049 Madrid, Spain
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/José Gutiérrez Abascal 2, 28006 Madrid, Spain
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Moeller FU, Herbold CW, Schintlmeister A, Mooshammer M, Motti C, Glasl B, Kitzinger K, Behnam F, Watzka M, Schweder T, Albertsen M, Richter A, Webster NS, Wagner M. Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta. THE ISME JOURNAL 2023; 17:1208-1223. [PMID: 37188915 PMCID: PMC10356861 DOI: 10.1038/s41396-023-01420-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.
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Affiliation(s)
- Florian U Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Cherie Motti
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Bettina Glasl
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Katharina Kitzinger
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Institute of Pharmacy, Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, St Lucia, QLD, Australia
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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Maggioni F, Bell JJ, Pujo-Pay M, Shaffer M, Cerrano C, Lemonnier H, Letourneur Y, Rodolfo-Metalpa R. Sponge organic matter recycling: Reduced detritus production under extreme environmental conditions. MARINE POLLUTION BULLETIN 2023; 190:114869. [PMID: 37023545 DOI: 10.1016/j.marpolbul.2023.114869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Sponges are a key component of coral reef ecosystems and play an important role in carbon and nutrient cycles. Many sponges are known to consume dissolved organic carbon and transform this into detritus, which moves through detrital food chains and eventually to higher trophic levels via what is known as the sponge loop. Despite the importance of this loop, little is known about how these cycles will be impacted by future environmental conditions. During two years (2018 and 2020), we measured the organic carbon, nutrient recycling, and photosynthetic activity of the massive HMA, photosymbiotic sponge Rhabdastrella globostellata at the natural laboratory of Bouraké in New Caledonia, where the physical and chemical composition of seawater regularly change according to the tide. We found that while sponges experienced acidification and low dissolved oxygen at low tide in both sampling years, a change in organic carbon recycling whereby sponges stopped producing detritus (i.e., the sponge loop) was only found when sponges also experienced higher temperature in 2020. Our findings provide new insights into how important trophic pathways may be affected by changing ocean conditions.
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Affiliation(s)
- Federica Maggioni
- ENTROPIE, IRD, Université de la Réunion, CNRS, IFREMER, Université de Nouvelle-Calédonie, Nouméa 98800, New Caledonia; Labex ICONA International CO(2) Natural Analogues Network, JSPS, Japan.
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Mireille Pujo-Pay
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650 Banyuls-sur-Mer, France
| | - Megan Shaffer
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Carlo Cerrano
- Department of Life and Environmental Sciences (DiSVA), Polytechnic University of Marche, Ancona, Italy
| | - Hugues Lemonnier
- ENTROPIE, IRD, Université de la Réunion, CNRS, IFREMER, Université de Nouvelle-Calédonie, Nouméa 98800, New Caledonia
| | - Yves Letourneur
- ENTROPIE, IRD, Université de la Réunion, CNRS, IFREMER, Université de Nouvelle-Calédonie, Nouméa 98800, New Caledonia
| | - Riccardo Rodolfo-Metalpa
- ENTROPIE, IRD, Université de la Réunion, CNRS, IFREMER, Université de Nouvelle-Calédonie, Nouméa 98800, New Caledonia; Labex ICONA International CO(2) Natural Analogues Network, JSPS, Japan
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Ramírez GA, Bar-Shalom R, Furlan A, Romeo R, Gavagnin M, Calabrese G, Garber AI, Steindler L. Bacterial aerobic methane cycling by the marine sponge-associated microbiome. MICROBIOME 2023; 11:49. [PMID: 36899421 PMCID: PMC9999580 DOI: 10.1186/s40168-023-01467-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Methanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogenic archaea inhabiting the sulfate-depleted sediments. However, methane-oxidizing bacteria from the candidate phylum Binatota have recently been described and shown to be present in oxic shallow-water marine sponges, where sources of methane remain undescribed. RESULTS Here, using an integrative -omics approach, we provide evidence for sponge-hosted bacterial methane synthesis occurring in fully oxygenated shallow-water habitats. Specifically, we suggest methane generation occurs via at least two independent pathways involving methylamine and methylphosphonate transformations that, concomitantly to aerobic methane production, generate bioavailable nitrogen and phosphate, respectively. Methylphosphonate may be sourced from seawater continuously filtered by the sponge host. Methylamines may also be externally sourced or, alternatively, generated by a multi-step metabolic process where carnitine, derived from sponge cell debris, is transformed to methylamine by different sponge-hosted microbial lineages. Finally, methanotrophs specialized in pigment production, affiliated to the phylum Binatota, may provide a photoprotective function, closing a previously undescribed C1-metabolic loop that involves both the sponge host and specific members of the associated microbial community. CONCLUSION Given the global distribution of this ancient animal lineage and their remarkable water filtration activity, sponge-hosted methane cycling may affect methane supersaturation in oxic coastal environments. Depending on the net balance between methane production and consumption, sponges may serve as marine sources or sinks of this potent greenhouse gas. Video Abstract.
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Affiliation(s)
- Gustavo A Ramírez
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
- Present address: Department of Biological Sciences, California State University, Los Angeles, CA, USA
| | - Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
| | - Andrea Furlan
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
| | - Roberto Romeo
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale, Trieste, Italy
| | - Michelle Gavagnin
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
| | - Gianluca Calabrese
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel
| | - Arkadiy I Garber
- School of Life Science, Arizona State University, Tempe, AZ, USA
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, Israel.
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Cristi A, Parada-Pozo G, Morales-Vicencio F, Cárdenas CA, Trefault N. Variability in Host Specificity and Functional Potential of Antarctic Sponge-Associated Bacterial Communities. Front Microbiol 2022; 12:771589. [PMID: 35095792 PMCID: PMC8792898 DOI: 10.3389/fmicb.2021.771589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Sponge-associated microorganisms are essential for sponge survival. They play an important role in recycling nutrients and, therefore, in the maintenance of the ecosystem. These microorganisms are diverse, species-specific, and different from those in the surrounding seawater. Bacterial sponge symbionts have been extensively studied in the tropics; however, little is known about these microorganisms in sponges from high-latitude environments. Sponges can cover up to 80% of the benthos in Antarctica and are crucial architects for the marine food web. In this study, we present analyses of the bacterial symbionts of three sponges: Haliclona (Rhizoniera) sp., Hymeniacidon torquata, and Isodictya kerguelenensis from the Western Antarctic Peninsula (WAP) with the aim to determine variations on the specificity of the bacteria–sponge interactions and potential signatures on their predicted functional profiles. We use high-throughput 16S rRNA gene sequencing of 30 sponge individuals inhabiting South Bay (Palmer Archipelago, WAP) to describe their microbiome taxonomy and diversity and predict potential functional profiles based on this marker gene. Our work shows similar bacterial community composition profiles among the same sponge species, although the symbiotic relationship is not equally conserved among the three Antarctic sponges. The number of species-specific core operational taxonomic units (OTUs) of these Antarctic sponges was low, with important differences between the total abundance accounted for these OTUs. Only eight OTUs were shared between the three sponge species. Analyses of the functional potential revealed that despite the high host–symbiont specificity, the inferred functions are conserved among these microbiomes, although with differences in the abundance of specific functions. H. torquata showed the highest level of intra-specificity and a higher potential of pathways related to energy metabolism, metabolisms of terpenoids and polyketides, and biosynthesis of other secondary metabolites. Overall, this work shows variations in the specificity of the sponge-associated bacterial communities, differences in how hosts and symbionts establish their relations, and in their potential functional capabilities.
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Affiliation(s)
- Antonia Cristi
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Department of Marine Science, University of Otago, Dunedin, New Zealand
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Génesis Parada-Pozo
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Felipe Morales-Vicencio
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - César A. Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Nicole Trefault
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- *Correspondence: Nicole Trefault,
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8
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Waterworth SC, Parker-Nance S, Kwan JC, Dorrington RA. Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts. mBio 2021; 12:e0157721. [PMID: 34519538 PMCID: PMC8546597 DOI: 10.1128/mbio.01577-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022] Open
Abstract
The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.
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Affiliation(s)
- Samantha C. Waterworth
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Shirley Parker-Nance
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Environmental Observation Network, Elwandle Coastal Node, Gqeberha (Port Elizabeth), South Africa
| | - Jason C. Kwan
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Rosemary A. Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- South African Institute for Aquatic Biodiversity, Makhanda, South Africa
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Chekidhenkuzhiyil J, Anas A, Thomas P, Tharakan B, Nair S. Characterization of archaeal symbionts of sponges from the coral reef ecosystems of the Gulf of Mannar, Southeast coast of India. Saudi J Biol Sci 2021; 28:3783-3788. [PMID: 34220232 PMCID: PMC8241630 DOI: 10.1016/j.sjbs.2021.03.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/10/2021] [Accepted: 03/21/2021] [Indexed: 10/26/2022] Open
Abstract
Sponges accommodate a diverse group of microorganisms with varied metabolic capabilities. The bacterial associates of sponges are widely studied while our understanding of archaeal counterparts is scanty. In the present study, we report the archaeal associates of two sponges, Pseudoceratina purpurea (NCBI barcode: KX454492) and Cinachyra sp. (NCBI barcode: KX454495), found in the coral reef ecosystems of Gulf of Mannar, India. Archaea in the water column was predominated by members of class Halobacteria of Phylum Euryarchaeota (97%) followed by a minor fraction (3%) of Nitrosopumilus sp. of phylum Thaumarchaeota. Interestingly, Thaumarchaeota was identified as the sole archaeal population associated with the two sponges studied, among which Nitrosopumilus sp. occuppied 80 and 100% of the sequences in the clone library of P. purpurea and Cinachyra sp. respectively. Other archaea found in the P. purpurea were Nitrososphaera (10%) and unclassified ones (10%). The study identified Nitrosopumilus sp. as a unique symbiotic archaeon of sponges, P. purpurea and Cinachyra sp. The existence of host driven factors in selecting specific associates from a diverse group of archaea in the environment may need further investigations.
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Affiliation(s)
| | - Abdulaziz Anas
- CSIR-National Institute of Oceanography, Regional Centre, Cochin, Kerala 682 018, India
| | - P.A. Thomas
- Panachammoottil, Gandhipuram, Thiruvananthapuram, Kerala 695017, India
| | - Balu Tharakan
- CSIR-National Institute of Oceanography, Regional Centre, Cochin, Kerala 682 018, India
| | - Shanta Nair
- CSIR-National Institute of Oceanography, Regional Centre, Cochin, Kerala 682 018, India
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10
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Ketchum RN, Smith EG, Vaughan GO, McParland D, Al-Mansoori N, Burt JA, Reitzel AM. Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients. Mol Ecol 2021; 30:3869-3881. [PMID: 34008895 DOI: 10.1111/mec.15990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 01/03/2023]
Abstract
Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32℃ in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the temperature predictive ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and highlight specific microbial taxa putatively involved in the response to thermal environment.
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Affiliation(s)
- Remi N Ketchum
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Grace O Vaughan
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Dain McParland
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Noura Al-Mansoori
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - John A Burt
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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11
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Scanes E, Parker LM, Seymour JR, Siboni N, King WL, Danckert NP, Wegner KM, Dove MC, O'Connor WA, Ross PM. Climate change alters the haemolymph microbiome of oysters. MARINE POLLUTION BULLETIN 2021; 164:111991. [PMID: 33485019 DOI: 10.1016/j.marpolbul.2021.111991] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
The wellbeing of marine organisms is connected to their microbiome. Oysters are a vital food source and provide ecological services, yet little is known about how climate change such as ocean acidification and warming will affect their microbiome. We exposed the Sydney rock oyster, Saccostrea glomerata, to orthogonal combinations of temperature (24, 28 °C) and pCO2 (400 and 1000 μatm) for eight weeks and used amplicon sequencing of the 16S rRNA (V3-V4) gene to characterise the bacterial community in haemolymph. Overall, elevated pCO2 and temperature interacted to alter the microbiome of oysters, with a clear partitioning of treatments in CAP ordinations. Elevated pCO2 was the strongest driver of species diversity and richness and elevated temperature also increased species richness. Climate change, both ocean acidification and warming, will alter the microbiome of S. glomerata which may increase the susceptibility of oysters to disease.
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Affiliation(s)
- Elliot Scanes
- The University of Sydney, School of Life and Environmental Sciences, Camperdown, New South Wales 2006, Australia.
| | - Laura M Parker
- The University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington, New South Wales 2052, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - William L King
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia; Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nathan P Danckert
- The University of Sydney, School of Life and Environmental Sciences, Camperdown, New South Wales 2006, Australia
| | - K Mathias Wegner
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Coastal Ecology, Wadden Sea Station, List, Sylt 25992, Germany
| | - Michael C Dove
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, New South Wales 2316, Australia
| | - Wayne A O'Connor
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, New South Wales 2316, Australia
| | - Pauline M Ross
- The University of Sydney, School of Life and Environmental Sciences, Camperdown, New South Wales 2006, Australia
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12
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Filtering Activity and Nutrient Release by the Keratose Sponge Sarcotragus spinosulus Schmidt, 1862 (Porifera, Demospongiae) at the Laboratory Scale. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9020178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sponges are an important constituent of filter-feeder benthic communities, characterized by high ecological plasticity and abundance. Free bacteria constitute an important quota of their diet, making them excellent candidates in aquaculture microbial bioremediation, where bacteria can be a serious problem. Although there are studies on this topic, certain promising species are still under investigation. Here we report applied microbiological research on the filtering activity of Sarcotragus spinosulus on two different concentrations of the pathogenic bacterium Vibrio parahaemolyticus in a laboratory experiment. To evaluate the effects of the filtration on the surrounding nutrient load, the release of ammonium, nitrate, and phosphate was also measured. The results obtained showed the efficient filtration capability of S. spinosulus as able to reduce the Vibrio load with a maximum retention efficiency of 99.72% and 99.35% at higher and lower Vibrio concentrations, respectively, and remarkable values of clearance rates (average maximum value 45.0 ± 4.1 mL h−1 g DW−1) at the highest Vibrio concentration tested. The nutrient release measured showed low values for each considered nutrient category at less than 1 mg L−1 for ammonium and phosphate and less than 5 mg L−1 for nitrate. The filtering activity and nutrient release by S. spinosulus suggest that this species represents a promising candidate in microbial bioremediation, showing an efficient capability in removing V. parahaemolyticus from seawater with a contribution to the nutrient load.
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13
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Haber M, Burgsdorf I, Handley KM, Rubin-Blum M, Steindler L. Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges. Front Microbiol 2021; 11:622824. [PMID: 33537022 PMCID: PMC7848895 DOI: 10.3389/fmicb.2020.622824] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
Sponges are among the oldest metazoans and their success is partly due to their abundant and diverse microbial symbionts. They are one of the few animals that have Thaumarchaeota symbionts. Here we compare genomes of 11 Thaumarchaeota sponge symbionts, including three new genomes, to free-living ones. Like their free-living counterparts, sponge-associated Thaumarchaeota can oxidize ammonia, fix carbon, and produce several vitamins. Adaptions to life inside the sponge host include enrichment in transposases, toxin-antitoxin systems and restriction modifications systems, enrichments previously reported also from bacterial sponge symbionts. Most thaumarchaeal sponge symbionts lost the ability to synthesize rhamnose, which likely alters their cell surface and allows them to evade digestion by the host. All but one archaeal sponge symbiont encoded a high-affinity, branched-chain amino acid transporter system that was absent from the analyzed free-living thaumarchaeota suggesting a mixotrophic lifestyle for the sponge symbionts. Most of the other unique features found in sponge-associated Thaumarchaeota, were limited to only a few specific symbionts. These features included the presence of exopolyphosphatases and a glycine cleavage system found in the novel genomes. Thaumarchaeota have thus likely highly specific interactions with their sponge host, which is supported by the limited number of host sponge species to which each of these symbionts is restricted.
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Affiliation(s)
- Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research Institute, Haifa, Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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14
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Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte. Antonie van Leeuwenhoek 2020; 114:95-112. [DOI: 10.1007/s10482-020-01503-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022]
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15
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Menaa F, Wijesinghe PAUI, Thiripuranathar G, Uzair B, Iqbal H, Khan BA, Menaa B. Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions. Mar Drugs 2020; 18:md18120641. [PMID: 33327517 PMCID: PMC7764995 DOI: 10.3390/md18120641] [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: 11/30/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023] Open
Abstract
Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)–microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.
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Affiliation(s)
- Farid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
- Correspondence: or
| | - P. A. U. I. Wijesinghe
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Gobika Thiripuranathar
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan;
| | - Haroon Iqbal
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China;
| | - Barkat Ali Khan
- Department of Pharmacy, Gomal University, Dera Ismail Khan 29050, Pakistan;
| | - Bouzid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
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16
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Kumar G, Radha V, Jagadeeshwari U, Sasikala C, Venkata Ramana C. Bacterial communities of sponges from the wetland ecosystem of Little Rann of Kutch, India with particular reference to Planctomycetes. 3 Biotech 2020; 10:478. [PMID: 33094088 PMCID: PMC7568738 DOI: 10.1007/s13205-020-02449-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022] Open
Abstract
Five sponge specimens belonging to the genera Spongilla and Ciocalypta were collected from Little Rann of Kutch (in Gujarat, India) and analysed for associated microbiomes. Critical analysis was done with respect to members of the phylum Planctomycetes, using two different strategies; 1. Culture-independent metagenomic approach and 2. culture-dependent anaerobic enrichment for anammox-planctomycetes. The 16S rRNA gene (V1-V3 region) amplicon metagenome analysis revealed significant divergence in bacterial diversity, including Planctomycetes among the sponges analysed. Community metagenomics revealed a total of 376 Operational Taxonomic Units (OTUs) belonging to 41 different phyla. OTUs belonging to Proteobacteria was the most abundant (38%) among the sponge analysed. The KEGG annotation predicted a total of 6909 KEGG orthologs (KOs); most of the KOs are associated with membrane transport, xenobiotic degradation, production of secondary metabolites, amino acid metabolism and carbohydrate metabolism. In the culture-dependent study, FISH analysis confirmed the association of anammox-planctomycetes with sponges. Partial 16S rRNA gene sequences of two planctomycetes (JC545, JC543) were cladding with those of uncultured Phycisphaerae class. The other three putative anammox bacteria (JC541, JC542, JC544) formed a different clade with "Candidatus Brocadia anammoxidans". These three putative bacteria believably represent new species/genus related to "Candidatus Brocadia".
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Affiliation(s)
- Gaurav Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
| | - Vaddavalli Radha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
| | - Uppadda Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085 India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085 India
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
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17
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Luter HM, Andersen M, Versteegen E, Laffy P, Uthicke S, Bell JJ, Webster NS. Cross-generational effects of climate change on the microbiome of a photosynthetic sponge. Environ Microbiol 2020; 22:4732-4744. [PMID: 32869905 DOI: 10.1111/1462-2920.15222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 01/04/2023]
Abstract
Coral reefs are facing increasing pressure from rising seawater temperatures and ocean acidification. Sponges have been proposed as possible winners in the face of climate change; however, little is known about the mechanisms underpinning their predicted tolerance. Here we assessed whether microbiome-mediated cross-generational acclimatization could enable the photosynthetic sponge Carteriospongia foliascens to survive under future climate scenarios. To achieve this, we first established the potential for vertical (cross-generational) transmission of symbionts. Sixty-four amplicon sequence variants accounting for >90% of the total C. foliascens microbial community were present across adult, larval and juvenile life stages, showing that a large proportion of the microbiome is vertically acquired and maintained. When C. foliascens were exposed to climate scenarios projected for 2050 and 2100, the host remained visibly unaffected (i.e. no necrosis/bleaching) and the overall microbiome was not significantly different amongst treatments in adult tissue, the respective larvae or recruits transplanted amongst climate treatments. However, indicator species analysis revealed that parental exposure to future climate scenarios altered the presence and abundance of a small suite of microbial taxa in the recruits, thereby revealing the potential for microbiome-mediated cross-generational acclimatization through both symbiont shuffling and symbiont switching within a vertically acquired microbiome.
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Affiliation(s)
- Heidi M Luter
- Australian Institute of Marine Science, QLD, Townsville, Australia.,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Maria Andersen
- Australian Institute of Marine Science, QLD, Townsville, Australia.,AIMS@JCU, QLD, Townsville, Australia
| | - Elien Versteegen
- Australian Institute of Marine Science, QLD, Townsville, Australia.,AIMS@JCU, QLD, Townsville, Australia
| | - Patrick Laffy
- Australian Institute of Marine Science, QLD, Townsville, Australia
| | - Sven Uthicke
- Australian Institute of Marine Science, QLD, Townsville, Australia
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Nicole S Webster
- Australian Institute of Marine Science, QLD, Townsville, Australia.,Australian Centre for Ecogenomics, University of Queensland, QLD, Brisbane, Australia
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18
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Bayer K, Busch K, Kenchington E, Beazley L, Franzenburg S, Michels J, Hentschel U, Slaby BM. Microbial Strategies for Survival in the Glass Sponge Vazella pourtalesii. mSystems 2020; 5:e00473-20. [PMID: 32788407 PMCID: PMC7426153 DOI: 10.1128/msystems.00473-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/23/2020] [Indexed: 01/04/2023] Open
Abstract
Few studies have explored the microbiomes of glass sponges (Hexactinellida). The present study seeks to elucidate the composition of the microbiota associated with the glass sponge Vazella pourtalesii and the functional strategies of the main symbionts. We combined microscopic approaches with metagenome-guided microbial genome reconstruction and amplicon community profiling toward this goal. Microscopic imaging revealed that the host and microbial cells appeared within dense biomass patches that are presumably syncytial tissue aggregates. Based on abundances in amplicon libraries and metagenomic data, SAR324 bacteria, Crenarchaeota, Patescibacteria, and Nanoarchaeota were identified as abundant members of the V. pourtalesii microbiome; thus, their genomic potentials were analyzed in detail. A general pattern emerged in that the V. pourtalesii symbionts had very small genome sizes, in the range of 0.5 to 2.2 Mb, and low GC contents, even below those of seawater relatives. Based on functional analyses of metagenome-assembled genomes (MAGs), we propose two major microbial strategies: the "givers," namely, Crenarchaeota and SAR324, heterotrophs and facultative anaerobes, produce and partly secrete all required amino acids and vitamins. The "takers," Nanoarchaeota and Patescibacteria, are anaerobes with reduced genomes that tap into the microbial community for resources, e.g., lipids and DNA, likely using pilus-like structures. We posit that the existence of microbial cells in sponge syncytia together with the low-oxygen conditions in the seawater environment are factors that shape the unique compositional and functional properties of the microbial community associated with V. pourtalesii IMPORTANCE We investigated the microbial community of V. pourtalesii that forms globally unique, monospecific sponge grounds under low-oxygen conditions on the Scotian Shelf, where it plays a key role in its vulnerable ecosystem. The microbial community was found to be concentrated within biomass patches and is dominated by small cells (<1 μm). MAG analyses showed consistently small genome sizes and low GC contents, which is unusual compared to known sponge symbionts. These properties, as well as the (facultatively) anaerobic metabolism and a high degree of interdependence between the dominant symbionts regarding amino acid and vitamin synthesis, are likely adaptations to the unique conditions within the syncytial tissue of their hexactinellid host and the low-oxygen environment.
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Affiliation(s)
- Kristina Bayer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
| | - Ellen Kenchington
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Lindsay Beazley
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Sören Franzenburg
- Institute for Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Jan Michels
- Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Kiel, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
- Kiel University, Kiel, Germany
| | - Beate M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
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19
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Engelberts JP, Robbins SJ, de Goeij JM, Aranda M, Bell SC, Webster NS. Characterization of a sponge microbiome using an integrative genome-centric approach. THE ISME JOURNAL 2020; 14:1100-1110. [PMID: 31992859 PMCID: PMC7174397 DOI: 10.1038/s41396-020-0591-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 11/09/2022]
Abstract
Marine sponges often host diverse and species-specific communities of microorganisms that are critical for host health. Previous functional genomic investigations of the sponge microbiome have focused primarily on specific symbiont lineages, which frequently make up only a small fraction of the overall community. Here, we undertook genome-centric analysis of the symbiont community in the model species Ircinia ramosa and analyzed 259 unique, high-quality metagenome-assembled genomes (MAGs) that comprised 74% of the I. ramosa microbiome. Addition of these MAGs to genome trees containing all publicly available microbial sponge symbionts increased phylogenetic diversity by 32% within the archaea and 41% within the bacteria. Metabolic reconstruction of the MAGs showed extensive redundancy across taxa for pathways involved in carbon fixation, B-vitamin synthesis, taurine metabolism, sulfite oxidation, and most steps of nitrogen metabolism. Through the acquisition of all major taxa present within the I. ramosa microbiome, we were able to analyze the functional potential of a sponge-associated microbial community in unprecedented detail. Critical functions, such as carbon fixation, which had previously only been assigned to a restricted set of sponge-associated organisms, were actually spread across diverse symbiont taxa, whereas other essential pathways, such as ammonia oxidation, were confined to specific keystone taxa.
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Affiliation(s)
- J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Manuel Aranda
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Australian Institute of Marine Science, Townsville, QLD, Australia.
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20
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Steinert G, Busch K, Bayer K, Kodami S, Arbizu PM, Kelly M, Mills S, Erpenbeck D, Dohrmann M, Wörheide G, Hentschel U, Schupp PJ. Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida). Front Microbiol 2020; 11:716. [PMID: 32390977 PMCID: PMC7193145 DOI: 10.3389/fmicb.2020.00716] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/27/2020] [Indexed: 12/01/2022] Open
Abstract
In the present study, we profiled bacterial and archaeal communities from 13 phylogenetically diverse deep-sea sponge species (Demospongiae and Hexactinellida) from the South Pacific by 16S rRNA-gene amplicon sequencing. Additionally, the associated bacteria and archaea were quantified by real-time qPCR. Our results show that bacterial communities from the deep-sea sponges are mostly host-species specific similar to what has been observed for shallow-water demosponges. The archaeal deep-sea sponge community structures are different from the bacterial community structures in that they are almost completely dominated by a single family, which are the ammonia-oxidizing genera within the Nitrosopumilaceae. Remarkably, the archaeal communities are mostly specific to individual sponges (rather than sponge-species), and this observation applies to both hexactinellids and demosponges. Finally, archaeal 16s gene numbers, as detected by quantitative real-time PCR, were up to three orders of magnitude higher than in shallow-water sponges, highlighting the importance of the archaea for deep-sea sponges in general.
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Affiliation(s)
- Georg Steinert
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Kathrin Busch
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Kristina Bayer
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sahar Kodami
- German Center for Marine Biodiversity Research, Senckenberg Research Institute, Wilhelmshaven, Germany
| | - Pedro Martinez Arbizu
- German Center for Marine Biodiversity Research, Senckenberg Research Institute, Wilhelmshaven, Germany
| | - Michelle Kelly
- National Institute of Water and Atmospheric Research, Ltd., Auckland, New Zealand
| | - Sadie Mills
- National Institute of Water and Atmospheric Research, Ltd., Wellington, New Zealand
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Dohrmann
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrecht University of Kiel, Kiel, Germany
| | - Peter J. Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
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21
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Gutleben J, Loureiro C, Ramírez Romero LA, Shetty S, Wijffels RH, Smidt H, Sipkema D. Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients. Front Microbiol 2020; 11:175. [PMID: 32140143 PMCID: PMC7042410 DOI: 10.3389/fmicb.2020.00175] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
Sponge-associated bacteria possess biotechnologically interesting properties but as yet have largely evaded cultivation. Thus, "omics"-based information on the ecology and functional potential of sponge symbionts is awaiting its integration into the design of innovative cultivation approaches. To cultivate bacteria derived from the marine sponge Aplysina aerophoba, nine novel media formulations were created based on the predicted genomic potential of the prevalent sponge symbiont lineage Poribacteria. In addition, to maintain potential microbial metabolic interactions in vitro, a Liquid-Solid cultivation approach and a Winogradsky-column approach were applied. The vast majority of microorganisms in the inoculum appeared viable after cryopreservation of sponge specimen as determined by selective propidium monoazide DNA modification of membrane-compromised cells, however, only 2% of the initial prokaryotic diversity could be recovered through cultivation. In total, 256 OTUs encompassing seven prokaryotic phyla were cultivated. The diversity of the cultivated community was influenced by the addition of the antibiotic aeroplysinin-1 as well as by medium dilution, rather than carbon source. Furthermore, the Winogradsky-column approach reproducibly enriched distinct communities at different column depths, amongst which were numerous Clostridia and OTUs that could not be assigned to a known phylum. While some bacterial taxa such as Pseudovibrio and Ruegeria were recovered from nearly all applied cultivation conditions, others such as Bacteroidetes were specific to certain medium types. Predominant sponge-associated prokaryotic taxa remained uncultured, nonetheless, alternative cultivation approaches applied here enriched for previously uncultivated microbes.
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Affiliation(s)
- Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Sudarshan Shetty
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - René H. Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University, Wageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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22
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Pawlik JR, McMurray SE. The Emerging Ecological and Biogeochemical Importance of Sponges on Coral Reefs. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:315-337. [PMID: 31226028 DOI: 10.1146/annurev-marine-010419-010807] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
With the decline of reef-building corals on tropical reefs, sponges have emerged as an important component of changing coral reef ecosystems. Seemingly simple, sponges are highly diverse taxonomically, morphologically, and in terms of their relationships with symbiotic microbes, and they are one of nature's richest sources of novel secondary metabolites. Unlike most other benthic organisms, sponges have the capacity to disrupt boundary flow as they pump large volumes of seawater into the water column. This seawater is chemically transformed as it passes through the sponge body as a consequence of sponge feeding, excretion, and the activities of microbial symbionts, with important effects on carbon and nutrient cycling and on the organisms in the water column and on the adjacent reef. In this review, we critically evaluate developments in the recently dynamic research area of sponge ecology on tropical reefs and provide a perspective for future studies.
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Affiliation(s)
- Joseph R Pawlik
- Department of Biology and Marine Biology and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina 28409, USA; ,
| | - Steven E McMurray
- Department of Biology and Marine Biology and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina 28409, USA; ,
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23
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Achlatis M, Pernice M, Green K, de Goeij JM, Guagliardo P, Kilburn MR, Hoegh-Guldberg O, Dove S. Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter. Proc Biol Sci 2019; 286:20192153. [PMID: 31795848 DOI: 10.1098/rspb.2019.2153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known, however, about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most other invertebrates. Here, we examine the cellular capacity for direct processing of DOM, and the fate of the processed matter, inside a dinoflagellate-hosting bioeroding sponge that is prominent on Indo-Pacific coral reefs. Integrating transmission electron microscopy with nanoscale secondary ion mass spectrometry, we track 15N- and 13C-enriched DOM over time at the individual cell level of an intact sponge holobiont. We show initial high enrichment in the filter-feeding cells of the sponge, providing visual evidence of their capacity to process DOM through pinocytosis without mediation of resident bacteria. Subsequent enrichment of the endosymbiotic dinoflagellates also suggests sharing of host nitrogenous wastes. Our results shed light on the physiological mechanism behind the ecologically important ability of sponges to cycle DOM via the recently described sponge loop.
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Affiliation(s)
- Michelle Achlatis
- School of Biological Sciences, Coral Reef Ecosystems Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland 4072, Australia.,Global Change Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Kathryn Green
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, University of Amsterdam, Institute for Biodiversity and Ecosystem Dynamics, 1090 GE Amsterdam, The Netherlands
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Matthew R Kilburn
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ove Hoegh-Guldberg
- School of Biological Sciences, Coral Reef Ecosystems Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland 4072, Australia.,Global Change Institute, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sophie Dove
- School of Biological Sciences, Coral Reef Ecosystems Laboratory, The University of Queensland, St Lucia, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland 4072, Australia
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24
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Zhang F, Jonas L, Lin H, Hill RT. Microbially mediated nutrient cycles in marine sponges. FEMS Microbiol Ecol 2019; 95:5582607. [DOI: 10.1093/femsec/fiz155] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/04/2019] [Indexed: 01/05/2023] Open
Abstract
ABSTRACTEfficient nutrient cycles mediated by symbiotic microorganisms with their hosts are vital to support the high productivity of coral reef ecosystems. In these ecosystems, marine sponges are important habitat-forming organisms in the benthic community and harbor abundant microbial symbionts. However, few studies have reviewed the critical microbially mediated nutrient cycling processes in marine sponges. To bridge this gap, in this review article, we summarize existing knowledge and recent advances in understanding microbially mediated carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles in sponges, propose a conceptual model that describes potential interactions and constraints in the major nutrient cycles, and suggest that shifting redox state induced by animal behavior like sponge pumping can exert great influence on the activities of symbiotic microbial communities. Constraints include the lack of knowledge on spatial and temporal variations and host behavior; more studies are needed in these areas. Sponge microbiomes may have a significant impact on the nutrient cycles in the world’s coral reef ecosystems.
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Affiliation(s)
- Fan Zhang
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Lauren Jonas
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Hanzhi Lin
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
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25
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Moeller FU, Webster NS, Herbold CW, Behnam F, Domman D, Albertsen M, Mooshammer M, Markert S, Turaev D, Becher D, Rattei T, Schweder T, Richter A, Watzka M, Nielsen PH, Wagner M. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. Environ Microbiol 2019; 21:3831-3854. [PMID: 31271506 PMCID: PMC6790972 DOI: 10.1111/1462-2920.14732] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022]
Abstract
Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.
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Affiliation(s)
- Florian U. Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Nicole S. Webster
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Craig W. Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Daryl Domman
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Stephanie Markert
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Dmitrij Turaev
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Dörte Becher
- Institute of Microbiology, Microbial ProteomicsUniversity of GreifswaldGreifswaldGermany
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
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26
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In situ determination of Si, N, and P utilization by the demosponge Tethya citrina: A benthic-chamber approach. PLoS One 2019; 14:e0218787. [PMID: 31283799 PMCID: PMC6613687 DOI: 10.1371/journal.pone.0218787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/11/2019] [Indexed: 11/23/2022] Open
Abstract
Sponges consume dissolved silicon (DSi) to build their skeletons. Few studies have attempted to quantify DSi utilization by these organisms and all available determinations come from laboratory measurements. Here we measured DSi consumption rates of the sponge Tethya citrina in its natural habitat, conducting 24h incubations in benthic chambers. Sponges consumed DSi at an average rate of 0.046 ± 0.018 μmol h-1 mL-1 when DSi availability in its habitat was 8.3 ± 1.8 μM. Such DSi consumption rates significantly matched the values predicted by a kinetic model elsewhere developed previously for this species through laboratory incubations. These results support the use of laboratory incubations as a suitable approach to learn about DSi consumption. During the field incubations, utilization of other dissolved inorganic nutrients by this low-microbial-abundance (LMA) sponge was also measured. The sponges were net sources of ammonium (-0.043 ± 0.031 μmol h-1 mL-1), nitrate (-0.063 ± 0.031 μmol h-1 mL-1), nitrite (-0.007 ± 0.003 μmol h-1 mL-1), and phosphate (-0.004 ± 0.005 μmol h-1 mL-1), in agreement with the general pattern in other LMA species. The detected effluxes were among the lowest reported for sponges, which agreed with the low respiration rates characterizing this species (0.35 ± 0.11 μmol-O2 h-1 mL-1). Despite relatively low flux, the dense population of T. citrina modifies the availability of dissolved inorganic nutrients in the demersal water of its habitat, contributing up to 14% of nitrate and nitrite stocks. Through these effects, the bottom layer contacting the benthic communities where siliceous LMA sponges abound can be partially depleted in DSi, but can benefit from inputs of N and P dissolved inorganic nutrients that are critical to primary producers.
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27
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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
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28
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Functional annotation of operome from Methanothermobacter thermautotrophicus ΔH: An insight to metabolic gap filling. Int J Biol Macromol 2018; 123:350-362. [PMID: 30445075 DOI: 10.1016/j.ijbiomac.2018.11.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/10/2018] [Accepted: 11/12/2018] [Indexed: 12/16/2022]
Abstract
Methanothermobacter thermautotrophicus ΔH (MTH) is a potential methanogen known to reduce CO2 with H2 for producing methane biofuel in thermophilic digesters. The genome of this organism contains ~50.5% conserved hypothetical proteins (HPs; operome) whose function is still not determined precisely. Here, we employed a combined bioinformatics approach to annotate a precise function to HPs and categorize them as enzymes, binding proteins, and transport proteins. Results of our study show that 315 (35.6%) HPs have exhibited well-defined functions contributing imperative roles in diverse cellular metabolism. Some of them are responsible for stress-response mechanisms and cell cycle, membrane transport, and regulatory processes. The genome-neighborhood analysis found five important gene clusters (dsr, ehb, kaiC, cmr, and gas) involving in the energetic metabolism and defense systems. MTH operome contains 223 enzymes with 15 metabolic subsystems, 15 cell cycle proteins, 17 transcriptional regulators and 33 binding proteins. Functional annotation of its operome is thus more fundamental to a profound understanding of the molecular and cellular machinery at systems-level.
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29
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Baquiran JIP, Conaco C. Sponge-microbe partnerships are stable under eutrophication pressure from mariculture. MARINE POLLUTION BULLETIN 2018; 136:125-134. [PMID: 30509793 DOI: 10.1016/j.marpolbul.2018.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 06/09/2023]
Abstract
Sponges harbor a great diversity of symbiotic microorganisms. However, environmental stresses can affect this partnership and influence the health and abundance of the host sponges. In Bolinao, Pangasinan, Philippines, chronic input of organic materials from mariculture activities contributes to a eutrophic coastal environment. To understand how these conditions might affect sponge-microbial partnerships, transplantation experiments were conducted with the marine sponge Gelliodes obtusa. High-throughput sequencing of 16S rRNA revealed that the associated microbial community of the sponges did not exhibit significant shifts after six weeks of transplantation at a eutrophic fish farm site compared to sponges grown at a coral reef or a seagrass area. However, sponges at the fish farm revealed higher abundance of the amoA gene, suggesting that microbiome members are responsive to increased ammonium levels at the site. The stable association between G. obtusa and its microbiome indicates that the sponge holobiont can withstand eutrophication pressure from mariculture.
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Affiliation(s)
- Jake Ivan P Baquiran
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines.
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30
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Kiran GS, Sekar S, Ramasamy P, Thinesh T, Hassan S, Lipton AN, Ninawe AS, Selvin J. Marine sponge microbial association: Towards disclosing unique symbiotic interactions. MARINE ENVIRONMENTAL RESEARCH 2018; 140:169-179. [PMID: 29935729 DOI: 10.1016/j.marenvres.2018.04.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/01/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Sponges are sessile benthic filter-feeding animals, which harbor numerous microorganisms. The enormous diversity and abundance of sponge associated bacteria envisages sponges as hot spots of microbial diversity and dynamics. Many theories were proposed on the ecological implications and mechanism of sponge-microbial association, among these, the biosynthesis of sponge derived bioactive molecules by the symbiotic bacteria is now well-indicated. This phenomenon however, is not exhibited by all marine sponges. Based on the available reports, it has been well established that the sponge associated microbial assemblages keep on changing continuously in response to environmental pressure and/or acquisition of microbes from surrounding seawater or associated macroorganisms. In this review, we have discussed nutritional association of sponges with its symbionts, interaction of sponges with other eukaryotic organisms, dynamics of sponge microbiome and sponge-specific microbial symbionts, sponge-coral association etc.
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Affiliation(s)
- G Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
| | - Sivasankari Sekar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Pasiyappazham Ramasamy
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | | | - Saqib Hassan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Anuj Nishanth Lipton
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - A S Ninawe
- Department of Biotechnology, Ministry of Science and Technology, New Delhi, India
| | - Joseph Selvin
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
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31
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Dat TTH, Steinert G, Thi Kim Cuc N, Smidt H, Sipkema D. Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam. PeerJ 2018; 6:e4970. [PMID: 29900079 PMCID: PMC5995103 DOI: 10.7717/peerj.4970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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32
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Feng G, Sun W, Zhang F, Orlić S, Li Z. Functional Transcripts Indicate Phylogenetically Diverse Active Ammonia-Scavenging Microbiota in Sympatric Sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:131-143. [PMID: 29423641 DOI: 10.1007/s10126-018-9797-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/19/2017] [Indexed: 05/06/2023]
Abstract
Symbiotic ammonia scavengers contribute to effective removal of ammonia in sponges. However, the phylogenetic diversity and in situ activity of ammonia-scavenging microbiota between different sponge species are poorly addressed. Here, transcribed ammonia monooxygenase genes (amoA), hydrazine synthase genes (hzsA), and glutamine synthetase genes (glnA) were analyzed to reveal the active ammonia-scavenging microbiota in the sympatric sponges Theonella swinhoei, Plakortis simplex, and Phakellia fusca, and seawater. Archaeal amoA and bacterial glnA transcripts rather than bacterial amoA, hzsA, and archaeal glnA transcripts were detected in the investigated sponges and seawater. The transcribed amoA genes were ascribed to two Thaumarchaeota ecotypes, while the transcribed glnA genes were interspersed among the lineages of Cyanobacteria, Tectomicrobia, Poribacteria, Alpha-, Beta-, Gamma-, and Epsilonproteobacteria. In addition, transcribed abundances of archaeal amoA and bacterial glnA genes in these sponges have been quantified, showing significant variation among the investigated sponges and seawater. The transcriptome-based qualitative and quantitative analyses clarified the different phylogenetic diversity and transcription expression of functional genes related to microbially mediated ammonia scavenging in different sympatric sponges, contributing to the understanding of in situ active ecological functions of sponge microbial symbionts in holobiont nitrogen cycling.
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Affiliation(s)
- Guofang Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China
| | - Wei Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China
| | - Fengli Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China
| | - Sandi Orlić
- Ruđer Bošković Institute, Bijeničkacesta 54, 10000, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean region-STIM, Bijeničkacesta 54, 10000, Zagreb, Croatia
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China.
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Pita L, Rix L, Slaby BM, Franke A, Hentschel U. The sponge holobiont in a changing ocean: from microbes to ecosystems. MICROBIOME 2018; 6:46. [PMID: 29523192 PMCID: PMC5845141 DOI: 10.1186/s40168-018-0428-1] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as "nested ecosystems." In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.
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Affiliation(s)
- L. Pita
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - L. Rix
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - B. M. Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - A. Franke
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - U. Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts-University of Kiel (CAU), Kiel, Germany
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Karimi E, Ramos M, Gonçalves JMS, Xavier JR, Reis MP, Costa R. Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium. Front Microbiol 2017; 8:2499. [PMID: 29312205 PMCID: PMC5735121 DOI: 10.3389/fmicb.2017.02499] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022] Open
Abstract
Current knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis “endosymbiome” as a distinct consortium of uncultured prokaryotes displaying a likely “sit-and-wait” strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe–microbe and host–microbe gene transfer amenability.
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Affiliation(s)
- Elham Karimi
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Miguel Ramos
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Jorge M S Gonçalves
- Fisheries, Biodiversity and Conservation Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Joana R Xavier
- Department of Biology and K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Margarida P Reis
- Faculty of Science and Technology, University of Algarve, Faro, Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of Algarve, Faro, Portugal.,Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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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.
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Moitinho-Silva L, Steinert G, Nielsen S, Hardoim CCP, Wu YC, McCormack GP, López-Legentil S, Marchant R, Webster N, Thomas T, Hentschel U. Predicting the HMA-LMA Status in Marine Sponges by Machine Learning. Front Microbiol 2017; 8:752. [PMID: 28533766 PMCID: PMC5421222 DOI: 10.3389/fmicb.2017.00752] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n = 19) and LMA (n = 17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species. The largest proportion of microbiome variation was explained by the host identity. Several phyla, classes, and OTUs were found differentially abundant in either group, which were considered “HMA indicators” and “LMA indicators.” Machine learning algorithms (classifiers) were trained to predict the HMA-LMA status of sponges. Among nine different classifiers, higher performances were achieved by Random Forest trained with phylum and class abundances. Random Forest with optimized parameters predicted the HMA-LMA status of additional 135 sponge species (1,232 specimens) without a priori knowledge. These sponges were grouped in four clusters, from which the largest two were composed of species consistently predicted as HMA (n = 44) and LMA (n = 74). In summary, our analyses shown distinct features of the microbial communities associated with HMA and LMA sponges. The prediction of the HMA-LMA status based on the microbiome profiles of sponges demonstrates the application of machine learning to explore patterns of host-associated microbial communities.
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Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Cristiane C P Hardoim
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Yu-Chen Wu
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel and Christian-Albrechts UniversityKiel, Germany
| | - Grace P McCormack
- Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland GalwayGalway, Ireland
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, and Center for Marine Science, University of North CarolinaWilmington, NC, USA
| | - Roman Marchant
- Centre for Translational Data Science, School of Information Technologies, University of SydneySydney, NSW, Australia
| | - Nicole Webster
- Australian Institute of Marine ScienceTownsville, QLD, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of QueenslandSt. Lucia, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, University of New South WalesSydney, NSW, Australia.,School of Biological, Earth and Environmental Sciences, University of New South WalesSydney, NSW, Australia
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel and Christian-Albrechts UniversityKiel, Germany
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Matcher GF, Waterworth SC, Walmsley TA, Matsatsa T, Parker‐Nance S, Davies‐Coleman MT, Dorrington RA. Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts. Microbiologyopen 2017; 6:e00417. [PMID: 27781403 PMCID: PMC5387304 DOI: 10.1002/mbo3.417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 01/13/2023] Open
Abstract
The Latrunculiidae are a family of cold water sponges known for their production of bioactive pyrroloiminoquinone alkaloids. Previously it was shown that the bacterial community associated with a Tsitsikamma sponge species comprises unusual bacterial taxa and is dominated by a novel Betaproteobacterium. Here, we have characterized the bacterial communities associated with six latrunculid species representing three genera (Tsitsikamma, Cyclacanthia, and Latrunculia) as well as a Mycale species, collected from Algoa Bay on the South African southeast coast. The bacterial communities of all seven sponge species were dominated by a single Betaproteobacterium operational taxonomic unit (OTU0.03 ), while a second OTU0.03 was dominant in the Mycale sp. The Betaproteobacteria OTUs from the different latrunculid sponges are closely related and their phylogenetic relationship follows that of their hosts. We propose that the latrunculid Betaproteobacteria OTUs are members of a specialized group of sponge symbionts that may have coevolved with their hosts. A single dominant Spirochaetae OTU0.03 was present in the Tsitsikamma and Cyclacanthia sponge species, but absent from the Latrunculia and Mycale sponges. This study sheds new light on the interactions between latrunculid sponges and their bacterial communities and may point to the potential involvement of dominant symbionts in the biosynthesis of the bioactive secondary metabolites.
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Affiliation(s)
- Gwynneth F. Matcher
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | | | - Tara A. Walmsley
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
- Department of BiotechnologyVaal University of TechnologyVanderbijlparkSouth Africa
| | - Tendayi Matsatsa
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Shirley Parker‐Nance
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Michael T. Davies‐Coleman
- Department of ChemistryRhodes UniversityGrahamstownSouth Africa
- Faculty of Natural ScienceUniversity of the Western CapeCape TownSouth Africa
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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.
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Li Z, Wang Y, Li J, Liu F, He L, He Y, Wang S. Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:659-671. [PMID: 27819120 DOI: 10.1007/s10126-016-9725-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 10/14/2016] [Indexed: 05/20/2023]
Abstract
Sponges host complex symbiotic communities, but to date, the whole picture of the metabolic potential of sponge microbiota remains unclear, particularly the difference between the shallow-water and deep-sea sponge holobionts. In this study, two completely different sponges, shallow-water sponge Theonella swinhoei from the South China Sea and deep-sea sponge Neamphius huxleyi from the Indian Ocean, were selected to compare their whole symbiotic communities and metabolic potential, particularly in element transformation. Phylogenetically diverse bacteria, archaea, fungi, and algae were detected in both shallow-water sponge T. swinhoei and deep-sea sponge N. huxleyi, and different microbial community structures were indicated between these two sponges. Metagenome-based gene abundance analysis indicated that, though the two sponge microbiota have similar core functions, they showed different potential strategies in detailed metabolic processes, e.g., in the transformation and utilization of carbon, nitrogen, phosphorus, and sulfur by corresponding microbial symbionts. This study provides insight into the putative metabolic potentials of the microbiota associated with the shallow-water and deep-sea sponges at the whole community level, extending our knowledge of the sponge microbiota's functions, the association of sponge- microbes, as well as the adaption of sponge microbiota to the marine environment.
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Affiliation(s)
- Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.
| | - Yuezhu Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China
| | - Jinlong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Fang Liu
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Liming He
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Ying He
- Laboratory of Marine Oceanography, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Shenyue Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China
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Horn H, Slaby BM, Jahn MT, Bayer K, Moitinho-Silva L, Förster F, Abdelmohsen UR, Hentschel U. An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes. Front Microbiol 2016; 7:1751. [PMID: 27877161 PMCID: PMC5099237 DOI: 10.3389/fmicb.2016.01751] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/19/2016] [Indexed: 11/18/2022] Open
Abstract
Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes. Specifically, clustered regularly interspaced short palindromic repeats, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defense is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. This study contributes to an understanding of the evolutionary arms race between viruses/phages and bacterial genomes and it sheds light on the bacterial defenses that have evolved in the context of the sponge holobiont.
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Affiliation(s)
- Hannes Horn
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of WürzburgWürzburg, Germany
| | - Beate M Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of WürzburgWürzburg, Germany
| | - Martin T Jahn
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of WürzburgWürzburg, Germany
| | - Kristina Bayer
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Lucas Moitinho-Silva
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW, Australia
| | - Frank Förster
- Department of Bioinformatics, University of WürzburgWürzburg, Germany; Center for Computational and Theoretical Biology, University of WürzburgWürzburg, Germany
| | - Usama R Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of WürzburgWürzburg, Germany; Department of Pharmacognosy, Faculty of Pharmacy, Minia UniversityMinia, Egypt
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean ResearchKiel, Germany; Christian-Albrechts-Universität zu KielKiel, Germany
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41
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Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment. Mar Genomics 2016; 29:69-80. [DOI: 10.1016/j.margen.2016.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 12/17/2022]
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Imhoff JF. New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment. Microorganisms 2016; 4:microorganisms4020019. [PMID: 27681913 PMCID: PMC5029485 DOI: 10.3390/microorganisms4020019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 12/11/2022] Open
Abstract
During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.
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Affiliation(s)
- Johannes F Imhoff
- GEOMAR Helmholtz-Zentrum für Ozeanforschung, Düsternbrooker Weg 20, D-24105 Kiel, Germany.
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43
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Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei. Sci Rep 2016; 6:24966. [PMID: 27113140 PMCID: PMC4844951 DOI: 10.1038/srep24966] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/06/2016] [Indexed: 01/06/2023] Open
Abstract
Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei.
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Abstract
A paradigm shift has recently transformed the field of biological science; molecular advances have revealed how fundamentally important microorganisms are to many aspects of a host’s phenotype and evolution. In the process, an era of “holobiont” research has emerged to investigate the intricate network of interactions between a host and its symbiotic microbial consortia. Marine sponges are early-diverging metazoa known for hosting dense, specific, and often highly diverse microbial communities. Here we synthesize current thoughts about the environmental and evolutionary forces that influence the diversity, specificity, and distribution of microbial symbionts within the sponge holobiont, explore the physiological pathways that contribute to holobiont function, and describe the molecular mechanisms that underpin the establishment and maintenance of these symbiotic partnerships. The collective genomes of the sponge holobiont form the sponge hologenome, and we highlight how the forces that define a sponge’s phenotype in fact act on the genomic interplay between the different components of the holobiont.
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Morley SA, Berman J, Barnes DKA, de Juan Carbonell C, Downey RV, Peck LS. Extreme Phenotypic Plasticity in Metabolic Physiology of Antarctic Demosponges. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2015.00157] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Rua CPJ, Gregoracci GB, Santos EO, Soares AC, Francini-Filho RB, Thompson F. Potential metabolic strategies of widely distributed holobionts in the oceanic archipelago of St Peter and St Paul (Brazil). FEMS Microbiol Ecol 2015; 91:fiv043. [PMID: 25873456 DOI: 10.1093/femsec/fiv043] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2015] [Indexed: 11/13/2022] Open
Abstract
Sponges are one of the most complex symbiotic communities and while the taxonomic composition of associated microbes has been determined, the biggest challenge now is to uncover their functional role in symbiosis. We investigated the microbiota of two widely distributed sponge species, regarding both their taxonomic composition and their functional roles. Samples of Didiscus oxeata and Scopalina ruetzleri were collected in the oceanic archipelago of St Peter and St Paul and analysed through metagenomics. Sequences generated by 454 pyrosequencing and Ion Torrent were taxonomically and functionally annotated on the MG-RAST server using the GenBank and SEED databases, respectively. Both communities exhibit equivalence in core functions, interestingly played by the most abundant taxa in each community. Conversely, the microbial communities differ in composition, taxonomic diversity and potential metabolic strategies. Functional annotation indirectly suggests differences in preferential pathways of carbon, nitrogen and sulphur metabolisms, which may indicate different metabolic strategies.
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Affiliation(s)
- Cintia P J Rua
- Av. Carlos Chagas Filho, s/nº - CCS - Instituto de Biologia, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Gustavo B Gregoracci
- Av. Alm. Saldanha da Gama, 89 - Departamento de Ciências do Mar, Universidade Federal de São Paulo (UNIFESP), Santos, CEP 11030-400, Brazil
| | - Eidy O Santos
- Av. Nossa Senhora das Graças, 50 - Divisão de Metrologia Aplicada a Ciências da Vida (DIMAV), Instituto Nacional de Metrologia, Normalização e Qualidade Industrial (INMETRO), Xerém, CEP 25250-020, Brazil
| | - Ana Carolina Soares
- Av. Carlos Chagas Filho, s/nº - CCS - Instituto de Biologia, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, CEP 21941-599, Brazil
| | - Ronaldo B Francini-Filho
- Rua da Mangueira, s/nº - Centro de Ciências Aplicadas e Educação, Departamento de Engenharia e Meio Ambiente, Campus IV - Litoral Norte - Universidade Federal da Paraíba (UFPB), Rio Tinto, PB, CEP 58297-000, Brazil
| | - Fabiano Thompson
- Av. Carlos Chagas Filho, s/nº - CCS - Instituto de Biologia, Lab de Microbiologia - Bloco A (Anexo) A3 - sl 102, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, CEP 21941-599, Brazil
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Zhang Y, Chen L, Sun R, Dai T, Tian J, Wen D. Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China. Appl Microbiol Biotechnol 2015; 99:4495-507. [DOI: 10.1007/s00253-014-6352-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/19/2014] [Accepted: 12/21/2014] [Indexed: 12/11/2022]
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Cuvelier ML, Blake E, Mulheron R, McCarthy PJ, Blackwelder P, Thurber RLV, Lopez JV. Two distinct microbial communities revealed in the sponge Cinachyrella. Front Microbiol 2014; 5:581. [PMID: 25408689 PMCID: PMC4219487 DOI: 10.3389/fmicb.2014.00581] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/15/2014] [Indexed: 11/25/2022] Open
Abstract
Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial) belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1) with lower diversity (Shannon-Weiner index: 3.73 ± 0.22) and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25). Hosts' 28S rRNA gene sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences) present in low abundance or below detection limits (<0.07%) in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria, and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5 and 22.4% of SG1 and SG2's total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters.
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Affiliation(s)
- Marie L. Cuvelier
- Biological Sciences Department, Florida International UniversityMiami, FL, USA
| | - Emily Blake
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
| | - Rebecca Mulheron
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
| | - Peter J. McCarthy
- Marine Biomedical and Biotechnology Research, Harbor Branch Oceanographic Institute, Florida Atlantic UniversityFort Pierce, FL, USA
| | - Patricia Blackwelder
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
- Marine Geosciences, Rosenstiel School of Marine and Atmospheric Science, University of MiamiMiami, FL, USA
| | | | - Jose V. Lopez
- Oceanographic Center, Nova Southeastern UniversityDania Beach, FL, USA
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Zhang F, Pita L, Erwin PM, Abaid S, López-Legentil S, Hill RT. Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality. FEMS Microbiol Ecol 2014; 90:699-707. [DOI: 10.1111/1574-6941.12427] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 09/02/2014] [Accepted: 09/10/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Fan Zhang
- Institute of Marine and Environmental Technology (IMET); University of Maryland Center for Environmental Science (UMCES); Baltimore MD USA
| | - Lucía Pita
- Department of Animal Biology; Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona (UB); Barcelona Spain
| | - Patrick M. Erwin
- Department of Biology & Marine Biology; Center for Marine Science; University of North Carolina Wilmington; Wilmington NC USA
| | - Summara Abaid
- Institute of Marine and Environmental Technology (IMET); University of Maryland Center for Environmental Science (UMCES); Baltimore MD USA
| | - Susanna López-Legentil
- Department of Animal Biology; Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona (UB); Barcelona Spain
- Department of Biology & Marine Biology; Center for Marine Science; University of North Carolina Wilmington; Wilmington NC USA
| | - Russell T. Hill
- Institute of Marine and Environmental Technology (IMET); University of Maryland Center for Environmental Science (UMCES); Baltimore MD USA
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Gloeckner V, Wehrl M, Moitinho-Silva L, Gernert C, Schupp P, Pawlik JR, Lindquist NL, Erpenbeck D, Wörheide G, Hentschel U. The HMA-LMA dichotomy revisited: an electron microscopical survey of 56 sponge species. THE BIOLOGICAL BULLETIN 2014; 227:78-88. [PMID: 25216505 DOI: 10.1086/bblv227n1p78] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been long recognized. In the present study, 56 sponge species from three geographic regions (greater Caribbean, Mediterranean, Red Sea) were investigated by transmission electron microscopy for the presence of microorganisms in the mesohyl matrix. Additionally, bacterial enumeration by DAPI-counting was performed on a subset of samples. Of the 56 species investigated, 28 were identified as belonging to the HMA and 28 to the LMA category. The sponge orders Agelasida and Verongida consisted exclusively of HMA species, and the Poecilosclerida were composed only of LMA sponges. Other taxa contained both types of microbial associations (e.g., marine Haplosclerida, Homoscleromorpha, Dictyoceratida), and a clear phylogenetic pattern could not be identified. For a few sponge species, an intermediate microbial load was determined, and the microscopy data did not suffice to reliably determine HMA or LMA status. To experimentally determine the HMA or LMA status of a sponge species, we therefore recommend a combination of transmission electron microscopy and 16S rRNA gene sequence data. This study significantly expands previous reports on microbial abundances in sponge tissues and contributes to a better understanding of the HMA-LMA dichotomy in sponge-microbe symbioses.
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Affiliation(s)
- Volker Gloeckner
- Julius-von-Sachs Institute for Biological Sciences, Department of Botany II, University of Wuerzburg, Julius-von-Sachs Platz 3, 97082 Wuerzburg, Germany
| | - Markus Wehrl
- Julius-von-Sachs Institute for Biological Sciences, Department of Botany II, University of Wuerzburg, Julius-von-Sachs Platz 3, 97082 Wuerzburg, Germany
| | - Lucas Moitinho-Silva
- Julius-von-Sachs Institute for Biological Sciences, Department of Botany II, University of Wuerzburg, Julius-von-Sachs Platz 3, 97082 Wuerzburg, Germany
| | - Christine Gernert
- Julius-von-Sachs Institute for Biological Sciences, Department of Botany II, University of Wuerzburg, Julius-von-Sachs Platz 3, 97082 Wuerzburg, Germany
| | - Peter Schupp
- Carl-von-Ossietzky University Oldenburg, Institute for Chemistry and Biology of the Marine Environment (ICBM), Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Joseph R Pawlik
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, North Carolina, USA
| | - Niels L Lindquist
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, & GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany; and
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, & GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany; and SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333 München, Germany
| | - Ute Hentschel
- Julius-von-Sachs Institute for Biological Sciences, Department of Botany II, University of Wuerzburg, Julius-von-Sachs Platz 3, 97082 Wuerzburg, Germany;
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