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Wang W, Song W, Majzoub ME, Feng X, Xu B, Tao J, Zhu Y, Li Z, Qian PY, Webster NS, Thomas T, Fan L. Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont. Nat Commun 2024; 15:8205. [PMID: 39294150 PMCID: PMC11410982 DOI: 10.1038/s41467-024-52464-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 09/07/2024] [Indexed: 09/20/2024] Open
Abstract
Holobionts are highly organized assemblages of eukaryotic hosts, cellular microbial symbionts, and viruses, whose interactions and evolution involve complex biological processes. It is largely unknown which specific determinants drive similarity or individuality in genetic diversity between holobionts. Here, we combine short- and long-read sequencing and DNA-proximity-linkage technologies to investigate intraspecific diversity of the microbiomes, including host-resolved viruses, in individuals of a model marine sponge. We find strong impacts of the sponge host and the cellular hosts of viruses on strain-level organization of the holobiont, whereas substantial overlap in nucleotide diversity between holobionts suggests frequent exchanges of microbial cells and viruses at intrastrain level in the local sponge population. Immune-evasive arms races likely restricted virus-host co-evolution at the intrastrain level, generated holobiont-specific genome variations, and linked virus-host genetics through recombination. Our work shows that a decoupling of strain- and intrastrain-level interactions is a key factor in the genetic diversification of holobionts.
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Affiliation(s)
- Wenxiu Wang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Weizhi Song
- Center for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marwan E Majzoub
- Center for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Xiaoyuan Feng
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Bu Xu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jianchang Tao
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yuanqing Zhu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Minhang, Shanghai, China
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Nicole S Webster
- The Australian Antarctic Division, Kingston, Tasmania, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Torsten Thomas
- Center for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia.
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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2
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Zhang B, Xiao L, Lyu L, Zhao F, Miao M. Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists. MICROBIOME 2024; 12:96. [PMID: 38790063 PMCID: PMC11127453 DOI: 10.1186/s40168-024-01809-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates. RESULTS To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range. CONCLUSIONS As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.
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Affiliation(s)
- Bing Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Liwen Xiao
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liping Lyu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Fangqing Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - Miao Miao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
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3
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van der Sprong J, de Voogd NJ, McCormack GP, Sandoval K, Schätzle S, Voigt O, Erpenbeck D, Wörheide G, Vargas S. A novel target-enriched multilocus assay for sponges (Porifera): Red Sea Haplosclerida (Demospongiae) as a test case. Mol Ecol Resour 2024; 24:e13891. [PMID: 38010340 DOI: 10.1111/1755-0998.13891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 10/13/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
Abstract
With declining biodiversity worldwide, a better understanding of species diversity and their relationships is imperative for conservation and management efforts. Marine sponges are species-rich ecological key players on coral reefs, but their species diversity is still poorly understood. This is particularly true for the demosponge order Haplosclerida, whose systematic relationships are contentious due to the incongruencies between morphological and molecular phylogenetic hypotheses. The single gene markers applied in previous studies did not resolve these discrepancies. Hence, there is a high need for a genome-wide approach to derive a phylogenetically robust classification and understand this group's evolutionary relationships. To this end, we developed a target enrichment-based multilocus probe assay for the order Haplosclerida using transcriptomic data. This probe assay consists of 20,000 enrichment probes targeting 2956 ultraconserved elements in coding (i.e. exon) regions across the genome and was tested on 26 haplosclerid specimens from the Red Sea. Our target-enrichment approach correctly placed our samples in a well-supported phylogeny, in agreement with previous haplosclerid molecular phylogenies. Our results demonstrate the applicability of high-resolution genomic methods in a systematically complex marine invertebrate group and provide a promising approach for robust phylogenies of Haplosclerida. Subsequently, this will lead to biologically unambiguous taxonomic revisions, better interpretations of biological and ecological observations and new avenues for applied research, conservation and managing declining marine diversity.
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Affiliation(s)
- Joëlle van der Sprong
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicole Joy de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
| | - Grace Patricia McCormack
- Molecular Evolution and Systematics Laboratory, Zoology, School of Natural Sciences & Ryan Institute, University of Galway, Galway, Ireland
| | - Kenneth Sandoval
- Molecular Evolution and Systematics Laboratory, Zoology, School of Natural Sciences & Ryan Institute, University of Galway, Galway, Ireland
| | - Simone Schätzle
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Oliver Voigt
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Bavarian State Collections of Palaeontology and Geology, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
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4
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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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5
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O'Brien PA, Tan S, Frade PR, Robbins SJ, Engelberts JP, Bell SC, Vanwonterghem I, Miller DJ, Webster NS, Zhang G, Bourne DG. Validation of key sponge symbiont pathways using genome-centric metatranscriptomics. Environ Microbiol 2023; 25:3207-3224. [PMID: 37732569 DOI: 10.1111/1462-2920.16509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | | | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Microbiome Research, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, Tasmania, Australia
| | - Guojie Zhang
- Centre for Evolutionary & Organismal Biology and Women's Hospital, Zhejiang University, School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
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6
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Gavriilidou A, Avcı B, Galani A, Schorn MA, Ingham CJ, Ettema TJG, Smidt H, Sipkema D. Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle. THE ISME JOURNAL 2023; 17:1808-1818. [PMID: 37587369 PMCID: PMC10579324 DOI: 10.1038/s41396-023-01484-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 08/18/2023]
Abstract
Members of the candidate phylum Dadabacteria, recently reassigned to the phylum Candidatus Desulfobacterota, are cosmopolitan in the marine environment found both free-living and associated with hosts that are mainly marine sponges. Yet, these microorganisms are poorly characterized, with no cultured representatives and an ambiguous phylogenetic position in the tree of life. Here, we performed genome-centric metagenomics to elucidate their phylogenomic placement and predict the metabolism of the sponge-associated members of this lineage. Rank-based phylogenomics revealed several new species and a novel family (Candidatus Spongomicrobiaceae) within a sponge-specific order, named here Candidatus Nemesobacterales. Metabolic reconstruction suggests that Ca. Nemesobacterales are aerobic heterotrophs, capable of synthesizing most amino acids, vitamins and cofactors and degrading complex carbohydrates. We also report functional divergence between sponge- and seawater-associated metagenome-assembled genomes. Niche-specific adaptations to the sponge holobiont were evident from significantly enriched genes involved in defense mechanisms against foreign DNA and environmental stressors, host-symbiont interactions and secondary metabolite production. Fluorescence in situ hybridization gave a first glimpse of the morphology and lifestyle of a member of Ca. Desulfobacterota. Candidatus Nemesobacterales spp. were found both inside sponge cells centred around sponge nuclei and in the mesohyl of the sponge Geodia barretti. This study sheds light on the enigmatic group Ca. Nemesobacterales and their functional characteristics that reflect a symbiotic lifestyle.
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Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
| | - Burak Avcı
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Anastasia Galani
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Colin J Ingham
- Hoekmine BV, Verenigingstraat 36, 3515GJ, Utrecht, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
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7
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Goffredi SK, Panossian B, Brzechffa C, Field N, King C, Moggioli G, Rouse GW, Martín-Durán JM, Henry LM. A dynamic epibiont community associated with the bone-eating polychaete genus Osedax. mBio 2023; 14:e0314022. [PMID: 37382438 PMCID: PMC10470745 DOI: 10.1128/mbio.03140-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/08/2023] [Indexed: 06/30/2023] Open
Abstract
Osedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-yr study, we reveal a dynamic, yet persistent, shift of Campylobacterales integrated into the epidermis of Osedax, which change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species of Osedax, which comprise 67% of the bacterial community on the trunk, appear initially dominated by the genus Arcobacter (at early time points <24 mo), the Sulfurospirillum at intermediate stages (~50 mo), and the Sulfurimonas at later stages (>140 mo) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests potential for a transition from heterotrophy to autotrophy and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free-living relatives, the Osedax epibiont genomes were enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein (ELP) domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms. IMPORTANCE Symbiotic associations are widespread in nature and we can expect to find them in every type of ecological niche. In the last twenty years, the myriad of functions, interactions and species comprising microbe-host associations has fueled a surge of interest and appreciation for symbiosis. During this 14-year study, we reveal a dynamic population of bacterial epibionts, integrated into the epidermis of 7 species of a deep-sea worm group that feeds exclusively on the remains of marine mammals. The bacterial genomes provide clues of a long evolutionary history with these enigmatic worms. On the host surface, they exchange genes and appear to undergo ecological succession, as the whale carcass habitat degrades over time, similar to what is observed for some free-living communities. These, and other annelid worms are important keystone species for diverse deep-sea environments, yet the role of attached external bacteria in supporting host health has received relatively little attention.
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Affiliation(s)
- Shana K. Goffredi
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Balig Panossian
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Camille Brzechffa
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Naomi Field
- Department of Biology, Occidental College, Los Angeles, California, USA
| | - Chad King
- Monterey Bay National Marine Sanctuary, Monterey, California, USA
| | - Giacomo Moggioli
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg W. Rouse
- Scripps Oceanography, University of California, La Jolla, California, USA
| | - José M. Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Lee M. Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
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8
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Botté ES, Bennett H, Engelberts JP, Thomas T, Bell JJ, Webster NS, Luter HM. Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis. ISME COMMUNICATIONS 2023; 3:53. [PMID: 37311801 PMCID: PMC10264452 DOI: 10.1038/s43705-023-00247-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/22/2023] [Accepted: 04/14/2023] [Indexed: 06/15/2023]
Abstract
Oceans are rapidly warming and acidifying in the context of climate change, threatening sensitive marine biota including coral reef sponges. Ocean warming (OW) and ocean acidification (OA) can impact host health and associated microbiome, but few studies have investigated these effects, which are generally studied in isolation, on a specific component of the holobiont. Here we present a comprehensive view of the consequences of simultaneous OW and OA for the tropical sponge Stylissa flabelliformis. We found no interactive effect on the host health or microbiome. Furthermore, OA (pH 7.6 versus pH 8.0) had no impact, while OW (31.5 °C versus 28.5 °C) caused tissue necrosis, as well as dysbiosis and shifts in microbial functions in healthy tissue of necrotic sponges. Major taxonomic shifts included a complete loss of archaea, reduced proportions of Gammaproteobacteria and elevated relative abundances of Alphaproteobacteria. OW weakened sponge-microbe interactions, with a reduced capacity for nutrient exchange and phagocytosis evasion, indicating lower representations of stable symbionts. The potential for microbially-driven nitrogen and sulphur cycling was reduced, as was amino acid metabolism. Crucially, the dysbiosis annihilated the potential for ammonia detoxification, possibly leading to accumulation of toxic ammonia, nutrient imbalance, and host tissue necrosis. Putative defence against reactive oxygen species was greater at 31.5 °C, perhaps as microorganisms capable of resisting temperature-driven oxidative stress were favoured. We conclude that healthy symbiosis in S. flabelliformis is unlikely to be disrupted by future OA but will be deeply impacted by temperatures predicted for 2100 under a "business-as-usual" carbon emission scenario.
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Affiliation(s)
- Emmanuelle S Botté
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
- Australian Institute of Marine Science, Townsville, Queensland, Australia.
| | - Holly Bennett
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Victoria University of Wellington, Wellington, New Zealand
- Cawthron Institute, Nelson, New Zealand
| | - J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - James J Bell
- Victoria University of Wellington, Wellington, New Zealand
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Australian Antarctic Division, Hobart, Tasmania, Australia
| | - Heidi M Luter
- Australian Institute of Marine Science, Townsville, Queensland, Australia.
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9
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Wei TS, Gao ZM, Gong L, Li QM, Zhou YL, Chen HG, He LS, Wang Y. Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp. Front Microbiol 2023; 14:1078171. [PMID: 36846759 PMCID: PMC9944714 DOI: 10.3389/fmicb.2023.1078171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/12/2023] [Indexed: 02/10/2023] Open
Abstract
Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus Bathydorus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. Bdellovibrio species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR-Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.
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Affiliation(s)
- Tao-Shu Wei
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,University of Chinese Academy of Sciences, Beijing, China
| | - Zhao-Ming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,*Correspondence: Zhao-Ming Gao ✉
| | - Lin Gong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Qing-Mei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ying-Li Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Hua-Guan Chen
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China,Yong Wang ✉
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10
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Ide K, Nishikawa Y, Maruyama T, Tsukada Y, Kogawa M, Takeda H, Ito H, Wagatsuma R, Miyaoka R, Nakano Y, Kinjo K, Ito M, Hosokawa M, Yura K, Suda S, Takeyama H. Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral. MICROBIOME 2022; 10:220. [PMID: 36503599 PMCID: PMC9743535 DOI: 10.1186/s40168-022-01395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Endozoicomonas bacteria symbiosis with various marine organisms is hypothesized as a potential indicator of health in corals. Although many amplicon analyses using 16S rRNA gene have suggested the diversity of Endozoicomonas species, genome analysis has been limited due to contamination of host-derived sequences and difficulties in culture and metagenomic analysis. Therefore, the evolutionary and functional potential of individual Endozoicomonas species symbiotic with the same coral species remains unresolved. RESULTS In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genomes (SAGs) for uncultured coral-associated Endozoicomonas spp. We obtained seven novel Endozoicomonas genomes and quantitative bacterial composition from Acropora tenuis corals at four sites in Japan. Our quantitative 16S rRNA gene and comparative genomic analysis revealed that these Endozoicomonas spp. belong to different lineages (Clade A and Clade B), with widely varying abundance among individual corals. Furthermore, each Endozoicomonas species possessed various eukaryotic-like genes in clade-specific genes. It was suggested that these eukaryotic-like genes might have a potential ability of different functions in each clade, such as infection of the host coral or suppression of host immune pathways. These Endozoicomonas species may have adopted different host adaptation strategies despite living symbiotically on the same coral. CONCLUSIONS This study suggests that coral-associated Endozoicomonas spp. on the same species of coral have different evolutional strategies and functional potentials in each species and emphasizes the need to analyze the genome of each uncultured strain in future coral-Endozoicomonas relationships studies. Video Abstract.
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Affiliation(s)
- Keigo Ide
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Toru Maruyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yuko Tsukada
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masato Kogawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Hiroki Takeda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Haruka Ito
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Ryota Wagatsuma
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Rimi Miyaoka
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yoshikatsu Nakano
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
- Marine Science Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | - Michihiro Ito
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Kei Yura
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Shoichiro Suda
- Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan.
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11
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Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae. THE ISME JOURNAL 2022; 16:2725-2740. [PMID: 36042324 PMCID: PMC9666466 DOI: 10.1038/s41396-022-01305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/24/2022] [Accepted: 08/02/2022] [Indexed: 12/15/2022]
Abstract
Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host interactions thus far remain unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 18.7% of bacteria. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Candidatus Sororchlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Based on gene content, sponge-associated chlamydiae resemble members from the same family more than sponge-associated chlamydiae of other families, and have greater metabolic versatility than known chlamydial animal pathogens. Sponge-associated chlamydiae are also enriched in genes for degrading diverse compounds found in sponges. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an unexplored source of novel natural products. This finding suggests that Chlamydiae members may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of the Chlamydiae phylum on marine ecosystems.
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12
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Sugden S, Holert J, Cardenas E, Mohn WW, Stein LY. Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges. THE ISME JOURNAL 2022; 16:2503-2512. [PMID: 35906397 PMCID: PMC9562138 DOI: 10.1038/s41396-022-01296-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.
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Affiliation(s)
- Scott Sugden
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada.
| | - Johannes Holert
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Erick Cardenas
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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13
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Díez-Vives C, Koutsouveli V, Conejero M, Riesgo A. Global patterns in symbiont selection and transmission strategies in sponges. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1015592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sponges host dense and diverse communities of microbes (known as the microbiome) beneficial for the host nutrition and defense. Symbionts in turn receive shelter and metabolites from the sponge host, making their relationship beneficial for both partners. Given that sponge-microbes associations are fundamental for the survival of both, especially the sponge, such relationship is maintained through their life and even passed on to the future generations. In many organisms, the microbiome has profound effects on the development of the host, but the influence of the microbiome on the reproductive and developmental pathways of the sponges are less understood. In sponges, microbes are passed on to oocytes, sperm, embryos, and larvae (known as vertical transmission), using a variety of methods that include direct uptake from the mesohyl through phagocytosis by oocytes to indirect transmission to the oocyte by nurse cells. Such microbes can remain in the reproductive elements untouched, for transfer to offspring, or can be digested to make the yolky nutrient reserves of oocytes and larvae. When and how those decisions are made are fundamentally unanswered questions in sponge reproduction. Here we review the diversity of vertical transmission modes existent in the entire phylum Porifera through detailed imaging using electron microscopy, available metabarcoding data from reproductive elements, and macroevolutionary patterns associated to phylogenetic constraints. Additionally, we examine the fidelity of this vertical transmission and possible reasons for the observed variability in some developmental stages. Our current understanding in marine sponges, however, is that the adult microbial community is established by a combination of both vertical and horizontal (acquisition from the surrounding environment in each new generation) transmission processes, although the extent in which each mode shapes the adult microbiome still remains to be determined. We also assessed the fundamental role of filtration, the cellular structures for acquiring external microbes, and the role of the host immune system, that ultimately shapes the stable communities of prokaryotes observed in adult sponges.
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14
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Abstract
Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named "Candidatus Thermopylae lasonolidus," only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. IMPORTANCE While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small quantities by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations, which causes premature chromosome condensation, blebbing, cell contraction, and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anticancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing, identified genes likely responsible for LSA synthesis in an uncultured bacterium, and assembled the symbiont's genome. These insights provide future opportunities for heterologous expression and cultivation efforts that may minimize LSA's supply problem.
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15
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Kelly JB, Carlson DE, Low JS, Thacker RW. Novel trends of genome evolution in highly complex tropical sponge microbiomes. MICROBIOME 2022; 10:164. [PMID: 36195901 PMCID: PMC9531527 DOI: 10.1186/s40168-022-01359-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism. RESULTS A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts' molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes. CONCLUSIONS These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes. Video Abstract.
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Affiliation(s)
- Joseph B Kelly
- Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany.
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.
| | - David E Carlson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Jun Siong Low
- Institute of Microbiology,ETH Zürich, Zürich, Switzerland
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Panama City, Republic of Panama
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16
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Taylor JA, Díez-Vives C, Nielsen S, Wemheuer B, Thomas T. Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts. Environ Microbiol 2022; 24:2299-2314. [PMID: 35229422 DOI: 10.1111/1462-2920.15962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/13/2022] [Accepted: 02/26/2022] [Indexed: 11/03/2022]
Abstract
The diversity and function of sponge-associated symbionts is now increasingly understood, however, we lack an understanding on how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here we performed a metatransciptomics analysis of three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidising Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidising archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our timeseries study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jessica A Taylor
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Cristina Díez-Vives
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Shaun Nielsen
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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17
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Sandoval K, McCormack GP. Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera. Mar Drugs 2022; 20:md20010074. [PMID: 35049929 PMCID: PMC8778704 DOI: 10.3390/md20010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
Actinoporins are proteinaceous toxins known for their ability to bind to and create pores in cellular membranes. This quality has generated interest in their potential use as new tools, such as therapeutic immunotoxins. Isolated historically from sea anemones, genes encoding for similar actinoporin-like proteins have since been found in a small number of other animal phyla. Sequencing and de novo assembly of Irish Haliclona transcriptomes indicated that sponges also possess similar genes. An exhaustive analysis of publicly available sequencing data from other sponges showed that this is a potentially widespread feature of the Porifera. While many sponge proteins possess a sequence similarity of 27.70–59.06% to actinoporins, they show consistency in predicted structure. One gene copy from H. indistincta has significant sequence similarity to sea anemone actinoporins and possesses conserved residues associated with the fundamental roles of sphingomyelin recognition, membrane attachment, oligomerization, and pore formation, indicating that it may be an actinoporin. Phylogenetic analyses indicate frequent gene duplication, no distinct clade for sponge-derived proteins, and a stronger signal towards actinoporins than similar proteins from other phyla. Overall, this study provides evidence that a diverse array of Porifera represents a novel source of actinoporin-like proteins which may have biotechnological and pharmaceutical applications.
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18
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Selberherr E, Penz T, König L, Conrady B, Siegl A, Horn M, Schmitz-Esser S. The life cycle-dependent transcriptional profile of the obligate intracellular amoeba symbiont Amoebophilus asiaticus. FEMS Microbiol Ecol 2022; 98:6499296. [PMID: 34999767 PMCID: PMC8831229 DOI: 10.1093/femsec/fiac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Free-living amoebae often harbor obligate intracellular bacterial symbionts. Amoebophilus (A.) asiaticus is a representative of a lineage of amoeba symbionts in the phylum Bacteroidota. Here, we analyse the transcriptome of A. asiaticus strain 5a2 at four time points during its infection cycle and replication within the Acanthamoeba host using RNA sequencing. Our results reveal a dynamic transcriptional landscape throughout different A. asiaticus life cycle stages. Many intracellular bacteria and pathogens utilize eukaryotic-like proteins (ELPs) for host cell interaction and the A. asiaticus 5a2 genome shows a particularly high abundance of ELPs. We show the expression of all genes encoding ELPs and found many ELPs to be differentially expressed. At the replicative stage of A. asiaticus, ankyrin repeat proteins and tetratricopeptide/Sel1-like repeat proteins were upregulated. At the later time points, high expression levels of a type 6 secretion system that likely prepares for a new infection cycle after lysing its host, were found. This study reveals comprehensive insights into the intracellular lifestyle of A. asiaticus and highlights candidate genes for host cell interaction. The results from this study have implications for other intracellular bacteria such as other amoeba-associated bacteria and the arthropod symbionts Cardinium forming the sister lineage of A. asiaticus.
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Affiliation(s)
- E Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - T Penz
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,current affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - L König
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - B Conrady
- Department of Veterinary and Animal Science, University of Copenhagen, Denmark
| | - A Siegl
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - M Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - S Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, USA
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19
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Moreno-Pino M, Ugalde JA, Valdés JH, Rodríguez-Marconi S, Parada-Pozo G, Trefault N. Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia. Front Microbiol 2021; 12:660779. [PMID: 34177840 PMCID: PMC8222686 DOI: 10.3389/fmicb.2021.660779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
Antarctic sponges harbor a diverse range of microorganisms that perform unique metabolic functions for nutrient cycles. Understanding how microorganisms establish functional sponge-microbe interactions in the Antarctic marine ecosystem provides clues about the success of these ancient animals in this realm. Here, we use a culture-dependent approach and genome sequencing to investigate the molecular determinants that promote a dual lifestyle in three bacterial genera Sporosarcina, Cellulophaga, and Nesterenkonia. Phylogenomic analyses showed that four sponge-associated isolates represent putative novel bacterial species within the Sporosarcina and Nesterenkonia genera and that the fifth bacterial isolate corresponds to Cellulophaga algicola. We inferred that isolated sponge-associated bacteria inhabit similarly marine sponges and also seawater. Comparative genomics revealed that these sponge-associated bacteria are enriched in symbiotic lifestyle-related genes. Specific adaptations related to the cold Antarctic environment are features of the bacterial strains isolated here. Furthermore, we showed evidence that the vitamin B5 synthesis-related gene, panE from Nesterenkonia E16_7 and E16_10, was laterally transferred within Actinobacteria members. Together, these findings indicate that the genomes of sponge-associated strains differ from other related genomes based on mechanisms that may contribute to the life in association with sponges and the extreme conditions of the Antarctic environment.
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Affiliation(s)
- Mario Moreno-Pino
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Juan A. Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Jorge H. Valdés
- Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Susana Rodríguez-Marconi
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Génesis Parada-Pozo
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
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20
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Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe. Mar Drugs 2021; 19:md19060298. [PMID: 34073758 PMCID: PMC8225149 DOI: 10.3390/md19060298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.
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Genome Features of Asaia sp. W12 Isolated from the Mosquito Anopheles stephensi Reveal Symbiotic Traits. Genes (Basel) 2021; 12:genes12050752. [PMID: 34067621 PMCID: PMC8156966 DOI: 10.3390/genes12050752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/29/2023] Open
Abstract
Asaia bacteria commonly comprise part of the microbiome of many mosquito species in the genera Anopheles and Aedes, including important vectors of infectious agents. Their close association with multiple organs and tissues of their mosquito hosts enhances the potential for paratransgenesis for the delivery of antimalaria or antivirus effectors. The molecular mechanisms involved in the interactions between Asaia and mosquito hosts, as well as Asaia and other bacterial members of the mosquito microbiome, remain underexplored. Here, we determined the genome sequence of Asaia strain W12 isolated from Anopheles stephensi mosquitoes, compared it to other Asaia species associated with plants or insects, and investigated the properties of the bacteria relevant to their symbiosis with mosquitoes. The assembled genome of strain W12 had a size of 3.94 MB, the largest among Asaia spp. studied so far. At least 3585 coding sequences were predicted. Insect-associated Asaia carried more glycoside hydrolase (GH)-encoding genes than those isolated from plants, showing their high plant biomass-degrading capacity in the insect gut. W12 had the most predicted regulatory protein components comparatively among the selected Asaia, indicating its capacity to adapt to frequent environmental changes in the mosquito gut. Two complete operons encoding cytochrome bo3-type ubiquinol terminal oxidases (cyoABCD-1 and cyoABCD-2) were found in most Asaia genomes, possibly offering alternative terminal oxidases and allowing the flexible transition of respiratory pathways. Genes involved in the production of 2,3-butandiol and inositol have been found in Asaia sp. W12, possibly contributing to biofilm formation and stress tolerance.
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Nguyen M, Wemheuer B, Laffy PW, Webster NS, Thomas T. Taxonomic, functional and expression analysis of viral communities associated with marine sponges. PeerJ 2021; 9:e10715. [PMID: 33604175 PMCID: PMC7863781 DOI: 10.7717/peerj.10715] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022] Open
Abstract
Viruses play an essential role in shaping the structure and function of ecological communities. Marine sponges have the capacity to filter large volumes of ‘virus-laden’ seawater through their bodies and host dense communities of microbial symbionts, which are likely accessible to viral infection. However, despite the potential of sponges and their symbionts to act as viral reservoirs, little is known about the sponge-associated virome. Here we address this knowledge gap by analysing metagenomic and (meta-) transcriptomic datasets from several sponge species to determine what viruses are present and elucidate their predicted and expressed functionality. Sponges were found to carry diverse, abundant and active bacteriophages as well as eukaryotic viruses belonging to the Megavirales and Phycodnaviridae. These viruses contain and express auxiliary metabolic genes (AMGs) for photosynthesis and vitamin synthesis as well as for the production of antimicrobials and the defence against toxins. These viral AMGs can therefore contribute to the metabolic capacities of their hosts and also potentially enhance the survival of infected cells. This suggest that viruses may play a key role in regulating the abundance and activities of members of the sponge holobiont.
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Affiliation(s)
- Mary Nguyen
- Centre for Marine Science and Innovation & School of Biological & Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation & School of Biological & Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation & School of Biological & Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
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23
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de Oliveira BFR, Freitas-Silva J, Sánchez-Robinet C, Laport MS. Transmission of the sponge microbiome: moving towards a unified model. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:619-638. [PMID: 33048474 DOI: 10.1111/1758-2229.12896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Sponges have co-evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host-associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways. Both vertical transmission (VT) and horizontal transmission (HT) have different advantages and disadvantages in the life cycle of these invertebrates. However, a third mode of transmission, called leaky vertical transmission or mixed mode of transmission (MMT), which incorporates both VT and HT modes, has gained relevance and seems to be the most robust model. In that regard, the aim of this review is to present the evolving knowledge on these main modes of transmission of the sponge microbiome. Our conclusions lead us to suggest that MMT may be more common for all sponges, with its frequency varying across the transmission spectrum between species and the environment. This hybrid model supports the stable and specific transmission of these microbial partners and reinforces their assistance in the resilience of sponges over the years.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Jéssyca Freitas-Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Claudia Sánchez-Robinet
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
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24
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Abstract
Through coevolution with host cells, microorganisms have acquired mechanisms to avoid the detection by the host surveillance system and to use the cell's supplies to establish themselves. Indeed, certain pathogens have evolved proteins that imitate specific eukaryotic cell proteins, allowing them to manipulate host pathways, a phenomenon termed molecular mimicry. Bacterial "eukaryotic-like proteins" are a remarkable example of molecular mimicry. They are defined as proteins that strongly resemble eukaryotic proteins or that carry domains that are predominantly present in eukaryotes and that are generally absent from prokaryotes. The widest diversity of eukaryotic-like proteins known to date can be found in members of the bacterial genus Legionella, some of which cause a severe pneumonia in humans. The characterization of a number of these proteins shed light on their importance during infection. The subsequent identification of eukaryotic-like genes in the genomes of other amoeba-associated bacteria and bacterial symbionts suggested that eukaryotic-like proteins are a common means of bacterial evasion and communication, shaped by the continuous interactions between bacteria and their protozoan hosts. In this review, we discuss the concept of molecular mimicry using Legionella as an example and show that eukaryotic-like proteins effectively manipulate host cell pathways. The study of the function and evolution of such proteins is an exciting field of research that is leading us toward a better understanding of the complex world of bacterium-host interactions. Ultimately, this knowledge will teach us how host pathways are manipulated and how infections may possibly be tackled.
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25
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Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts. ISME JOURNAL 2020; 15:503-519. [PMID: 33011742 DOI: 10.1038/s41396-020-00791-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 01/17/2023]
Abstract
The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured and uncharacterised Proteobacteria. Here we set out to characterise this group using metagenomics, in-depth phylogenetic analyses, metatranscriptomics, and fluorescence in situ hybridisation microscopy. We obtained five metagenome-assembled-genomes (MAGs) from different sponge species that, together with a previously published MAG (AqS2), comprise two families within a new gammaproteobacterial order that we named UTethybacterales. Members of this order share a heterotrophic lifestyle but vary in their predicted ability to use various carbon, nitrogen and sulfur sources, including taurine, spermidine and dimethylsulfoniopropionate. The deep branching of the UTethybacterales within the Gammaproteobacteria and their almost exclusive presence in sponges suggests they have entered a symbiosis with their host relatively early in evolutionary time and have subsequently functionally radiated. This is reflected in quite distinct lifestyles of various species of UTethybacterales, most notably their diverse morphologies, predicted substrate preferences, and localisation within the sponge tissue. This study provides new insight into the evolution of metazoan-bacteria symbiosis.
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26
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Pascelli C, Laffy PW, Botté E, Kupresanin M, Rattei T, Lurgi M, Ravasi T, Webster NS. Viral ecogenomics across the Porifera. MICROBIOME 2020; 8:144. [PMID: 33008461 PMCID: PMC7532657 DOI: 10.1186/s40168-020-00919-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/08/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea. RESULTS Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts. CONCLUSIONS Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts. Video Abstract.
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Affiliation(s)
- Cecília Pascelli
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
- James Cook University, Townsville, Australia
| | - Patrick W Laffy
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
| | - Emmanuelle Botté
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia
| | - Marija Kupresanin
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Miguel Lurgi
- Biosciences Department, University of Swansea, Swansea, Wales
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Nicole S Webster
- AIMS@JCU, Townsville, Queensland, Australia.
- Australian Institute of Marine Science, PMB No.3, Townsville MC, Townsville, Queensland, 4810, Australia.
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia.
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27
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Sizikov S, Burgsdorf I, Handley KM, Lahyani M, Haber M, Steindler L. Characterization of sponge-associated Verrucomicrobia: microcompartment-based sugar utilization and enhanced toxin-antitoxin modules as features of host-associated Opitutales. Environ Microbiol 2020; 22:4669-4688. [PMID: 32840024 DOI: 10.1111/1462-2920.15210] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022]
Abstract
Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free-living organisms or as symbionts of eukaryotic hosts. Little is known about host-associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto-Mediterranean sponge Petrosia ficiformis and three genomes from strains that we isolated from offshore seawater of the Eastern Mediterranean Sea. Phylogenomic analysis of these five strains indicated that they are all members of Verrucomicrobia subdivision 4, order Opitutales. We compared these novel sponge-associated and seawater-isolated genomes to closely related Verrucomicrobia. Genomic analysis revealed that Planctomycetes-Verrucomicrobia microcompartment gene clusters are enriched in the genomes of symbiotic Opitutales including sponge symbionts but not in free-living ones. We hypothesize that in sponge symbionts these microcompartments are used for degradation of l-fucose and l-rhamnose, which are components of algal and bacterial cell walls and therefore may be found at high concentrations in the sponge tissue. Furthermore, we observed an enrichment of toxin-antitoxin modules in symbiotic Opitutales. We suggest that, in sponges, verrucomicrobial symbionts utilize these modules as a defence mechanism against antimicrobial activity deriving from the abundant microbial community co-inhabiting the host.
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Affiliation(s)
- Sofia Sizikov
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kim Marie Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Matan Lahyani
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - 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, Czech Republic
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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28
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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: 73] [Impact Index Per Article: 18.3] [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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29
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Frank AC. Molecular host mimicry and manipulation in bacterial symbionts. FEMS Microbiol Lett 2019; 366:5342066. [PMID: 30877310 DOI: 10.1093/femsle/fnz038] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/18/2019] [Indexed: 12/17/2022] Open
Abstract
It is common among intracellular bacterial pathogens to use eukaryotic-like proteins that mimic and manipulate host cellular processes to promote colonization and intracellular survival. Eukaryotic-like proteins are bacterial proteins with domains that are rare in bacteria, and known to function in the context of a eukaryotic cell. Such proteins can originate through horizontal gene transfer from eukaryotes or, in the case of simple repeat proteins, through convergent evolution. Recent studies of microbiomes associated with several eukaryotic hosts suggest that similar molecular strategies are deployed by cooperative bacteria that interact closely with eukaryotic cells. Some mimics, like ankyrin repeats, leucine rich repeats and tetratricopeptide repeats are shared across diverse symbiotic systems ranging from amoebae to plants, and may have originated early, or evolved independently in multiple systems. Others, like plant-mimicking domains in members of the plant microbiome are likely to be more recent innovations resulting from horizontal gene transfer from the host, or from microbial eukaryotes occupying the same host. Host protein mimics have only been described in a limited set of symbiotic systems, but are likely to be more widespread. Systematic searches for eukaryote-like proteins in symbiont genomes could lead to the discovery of novel mechanisms underlying host-symbiont interactions.
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Affiliation(s)
- A Carolin Frank
- Life and Environmental Sciences, 5200 North Lake Rd, University of California Merced, Merced, CA 95343, USA.,Sierra Nevada Research Institute, School of Natural Sciences, 5200 North Lake Rd, University of California Merced, Merced, CA 95343, USA
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30
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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: 25] [Impact Index Per Article: 5.0] [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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31
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Burgsdorf I, Handley KM, Bar-Shalom R, Erwin PM, Steindler L. Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont. mSystems 2019; 4:e00057-19. [PMID: 31086829 PMCID: PMC6506613 DOI: 10.1128/msystems.00057-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/02/2019] [Indexed: 02/06/2023] Open
Abstract
"Candidatus Synechococcus feldmannii" is a facultative intracellular symbiont of the Atlanto-Mediterranean sponge Petrosia ficiformis. Genomic information of sponge-associated cyanobacteria derives thus far from the obligate and extracellular symbiont "Candidatus Synechococcus spongiarum." Here we utilized a differential methylation-based approach for bacterial DNA enrichment combined with metagenomics to obtain the first draft genomes of "Ca. Synechococcus feldmannii." By comparative genomics, we revealed that some genomic features (e.g., iron transport mediated by siderophores, eukaryotic-like proteins, and defense mechanisms, like CRISPR-Cas [clustered regularly interspaced short palindromic repeats-associated proteins]) are unique to both symbiont types and absent or rare in the genomes of taxonomically related free-living cyanobacteria. These genomic features likely enable life under the conditions found inside the sponge host. Interestingly, there are many genomic features that are shared by "Ca. Synechococcus feldmannii" and free-living cyanobacteria, while they are absent in the obligate symbiont "Ca. Synechococcus spongiarum." These include genes related to cell surface structures, genetic regulation, and responses to environmental stress, as well as the composition of photosynthetic genes and DNA metabolism. We speculate that the presence of these genes confers on "Ca. Synechococcus feldmannii" its facultative nature (i.e., the ability to respond to a less stable environment when free-living). Our comparative analysis revealed that distinct genomic features depend on the nature of the symbiotic interaction: facultative and intracellular versus obligate and extracellular. IMPORTANCE Given the evolutionary position of sponges as one of the earliest phyla to depart from the metazoan stem lineage, studies on their distinct and exceptionally diverse microbial communities should yield a better understanding of the origin of animal-bacterium interactions. While genomes of several extracellular sponge symbionts have been published, the intracellular symbionts have, so far, been elusive. Here we compare the genomes of two unicellular cyanobacterial sponge symbionts that share an ancestor but followed different evolutionary paths-one became intracellular and the other extracellular. Counterintuitively, the intracellular cyanobacteria are facultative, while the extracellular ones are obligate. By sequencing the genomes of the intracellular cyanobacteria and comparing them to the genomes of the extracellular symbionts and related free-living cyanobacteria, we show how three different cyanobacterial lifestyles are reflected by adaptive genomic features.
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Affiliation(s)
- 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
| | - Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Patrick M. Erwin
- Department of Biology and Marine Biology, Centre for Marine Science, University of North Carolina—Wilmington, Wilmington, North Carolina, USA
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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32
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Rubin-Blum M, Antony CP, Sayavedra L, Martínez-Pérez C, Birgel D, Peckmann J, Wu YC, Cardenas P, MacDonald I, Marcon Y, Sahling H, Hentschel U, Dubilier N. Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts. THE ISME JOURNAL 2019; 13:1209-1225. [PMID: 30647460 PMCID: PMC6474228 DOI: 10.1038/s41396-019-0346-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/16/2018] [Accepted: 12/20/2018] [Indexed: 01/26/2023]
Abstract
Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host-symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.
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Affiliation(s)
- Maxim Rubin-Blum
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
- Israel Limnology and Oceanography Research, Tel Shikmona, 3108000, Haifa, Israel.
| | - Chakkiath Paul Antony
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Lizbeth Sayavedra
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Clara Martínez-Pérez
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Daniel Birgel
- Institute for Geology, Center for Earth System Research and Sustainability, University of Hamburg, 20146, Hamburg, Germany
| | - Jörn Peckmann
- Institute for Geology, Center for Earth System Research and Sustainability, University of Hamburg, 20146, Hamburg, Germany
| | - Yu-Chen Wu
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105, Kiel, Germany
| | - Paco Cardenas
- Department of Medicinal Chemistry, Pharmacognosy, BioMedical Centre, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ian MacDonald
- Florida State University, POB 3064326, Tallahassee, FL, 32306, USA
| | - Yann Marcon
- Wegener Institute Helmholtz Centre for Polar and Marine Research, HGF-MPG Group for Deep Sea Ecology and Technology, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Heiko Sahling
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105, Kiel, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany.
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Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria. Sci Rep 2019; 9:1999. [PMID: 30760820 PMCID: PMC6374434 DOI: 10.1038/s41598-019-38737-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/09/2019] [Indexed: 02/07/2023] Open
Abstract
Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness – were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.
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O'Brien PA, Webster NS, Miller DJ, Bourne DG. Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts. mBio 2019; 10:e02241-18. [PMID: 30723123 PMCID: PMC6428750 DOI: 10.1128/mbio.02241-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
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Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade. mSystems 2018; 3:mSystems00150-18. [PMID: 30637337 PMCID: PMC6306507 DOI: 10.1128/msystems.00150-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/29/2018] [Indexed: 01/25/2023] Open
Abstract
Chloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought. Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for “Candidatus Poribacteria” and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCEChloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.
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36
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Evolution of the main skeleton-forming genes in sponges (phylum Porifera) with special focus on the marine Haplosclerida (class Demospongiae). Mol Phylogenet Evol 2018; 131:245-253. [PMID: 30502904 DOI: 10.1016/j.ympev.2018.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/26/2018] [Accepted: 11/19/2018] [Indexed: 01/14/2023]
Abstract
The skeletons of sponges (Phylum Porifera) are comprised of collagen, often embedded with small siliceous structures (spicules) arranged in various forms to provide strength and flexibility. The main proteins responsible for the formation of the spicules in demosponges are the silicateins, which are related to the cathepsins L of other animals. While the silicatein active site, necessary for the formation of biosilica crystals, is characterized by the amino acids SHN, different variants of the silicatein genes have been found, some that retain SHN at the active site and some that don't. As part of an effort to further understand skeleton formation in marine sponges of the order Haplosclerida, a search for all silicatein variants were made in Irish species representing the main clades of this large sponge group. For this task, transcriptomes were sequenced and de novo assembled from Haliclona oculata, H. simulans and H. indistincta. Silicatein genes were identified from these and all available genomes and transcriptomes from Porifera. These were analysed along with all complete silicateins from GenBank. Silicateins were only found in species belonging to the class Demospongiae but excluding Keratosa and Verongimorpha and there was significant duplication and diversity of these genes. Silicateins showing SHN at the active site were polyphyletic. Indeed silicatein sequences were divided into six major clades (CHNI, CHNII, CHNIII, SHNI, SHNII and C/SQN). In those clades where haplosclerids were well represented the silicatein phylogeny reflected previous ribosomal and mitochondrial topologies. The most basal silicatein clade (CHNI) contained sequences only from marine haplosclerids and freshwater sponges while one silicatein from H. indistincta was more related to cathepsins L (outgroup) than to the overall silicatein clade indicating the presence of an old silicatein or an intermediary form. This data could suggest that marine haplosclerids were one of the first groups of extant demosponges to acquire silicatein genes. Furthermore, we suggest that the paucity of spicule types in this group may be due to their single copy of SHNI variants, and the lack of a silintaphin gene.
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37
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Knobloch S, Jóhannsson R, Marteinsson V. Bacterial diversity in the marine spongeHalichondria paniceafrom Icelandic waters and host-specificity of its dominant symbiont “CandidatusHalichondribacter symbioticus”. FEMS Microbiol Ecol 2018; 95:5173036. [DOI: 10.1093/femsec/fiy220] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/07/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Stephen Knobloch
- Microbiology Group, Department of Research and Innovation, Matís ohf., Vinlandsleid 12, 113 Reykjavik, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Saemundargata 2, 101 Reykjavík, Iceland
| | - Ragnar Jóhannsson
- Marine and Freshwater Research Institute, Hafrannsóknastofnun, Skúlagata 4, 101 Reykjavik, Iceland
| | - Viggó Marteinsson
- Microbiology Group, Department of Research and Innovation, Matís ohf., Vinlandsleid 12, 113 Reykjavik, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Saemundargata 2, 101 Reykjavik, Iceland
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38
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Renard E, Leys SP, Wörheide G, Borchiellini C. Understanding Animal Evolution: The Added Value of Sponge Transcriptomics and Genomics: The disconnect between gene content and body plan evolution. Bioessays 2018; 40:e1700237. [PMID: 30070368 DOI: 10.1002/bies.201700237] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/22/2018] [Indexed: 02/06/2023]
Abstract
Sponges are important but often-neglected organisms. The absence of classical animal traits (nerves, digestive tract, and muscles) makes sponges challenging for non-specialists to work with and has delayed getting high quality genomic data compared to other invertebrates. Yet analyses of sponge genomes and transcriptomes currently available have radically changed our understanding of animal evolution. Sponges are of prime evolutionary importance as one of the best candidates to form the sister group of all other animals, and genomic data are essential to understand the mechanisms that control animal evolution and diversity. Here we review the most significant outcomes of current genomic and transcriptomic analyses of sponges, and discuss limitations and future directions of sponge transcriptomic and genomic studies.
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Affiliation(s)
- Emmanuelle Renard
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France.,Aix Marseille Univ., CNRS, UMR 7288, IBDM, Marseille, France
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Bavarian State Collection for Paleontology and Geology, Munich, Germany
| | - Carole Borchiellini
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, UMR 7263, Mediterranean Institute of Marine and Continental Biodiversity and Ecology (IMBE), Station Marine d'Endoume, Marseille, France
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39
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Díez-Vives C, Esteves AIS, Costa R, Nielsen S, Thomas T. Detecting signatures of a sponge-associated lifestyle in bacterial genomes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:433-443. [PMID: 29707906 DOI: 10.1111/1758-2229.12655] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Sponges interact with diverse and rich communities of bacteria that are phylogenetically often distinct from their free-living counterparts. Recent genomics and metagenomic studies have indicated that bacterial sponge symbionts also have distinct functional features from free-living bacteria; however, it is unclear, if such genome-derived functional signatures are common and present in different symbiont taxa. We therefore compared here a large set of genomes from cultured (Pseudovibrio, Ruegeria and Aquimarina) and yet-uncultivated (Synechococcus) bacteria found in either sponge-associated or free-living sources. Our analysis revealed only very few genera-specific functions that could be correlated with a sponge-associated lifestyle. Using different sets of sponge-associated and free-living bacteria for each genus, we could however show that the functions identified as 'sponge-associated' are dependent on the reference comparison being made. Using simulation approaches, we show how this influences the robustness of identifying functional signatures and how evolutionary divergence and genomic adaptation can be distinguished. Our results highlight the future need for robust comparative analyses to define genomic signatures of symbiotic lifestyles, whether it is for symbionts of sponges or other host organisms.
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Affiliation(s)
- Cristina Díez-Vives
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Ana I S Esteves
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (IBB), IST, Universidade de Lisboa, Lisbon, Portugal
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
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40
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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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41
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BluePharmTrain: Biology and Biotechnology of Marine Sponges. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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42
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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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43
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Moitinho-Silva L, Díez-Vives C, Batani G, Esteves AIS, Jahn MT, Thomas T. Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics. THE ISME JOURNAL 2017; 11:1651-1666. [PMID: 28338677 PMCID: PMC5520145 DOI: 10.1038/ismej.2017.25] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/10/2017] [Accepted: 01/19/2017] [Indexed: 12/21/2022]
Abstract
Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales. Gene expression was estimated by mapping C. concentrica metatranscriptomic reads. Our analyses indicated that CcPhy is heterotrophic, while CcNi and CcThau are chemolithoautotrophs. CcPhy expressed many transporters for the acquisition of dissolved organic compounds, likely available through the sponge's filtration activity and symbiotic carbon fixation. Coupled nitrification by CcThau and CcNi was reconstructed, supported by the observed close proximity of the cells in fluorescence in situ hybridization. CcPhy facultative anaerobic respiration and assimilation by diatoms may consume the resulting nitrate. Transcriptional analysis of diatom and sponge functions indicated that these organisms are likely sources of organic compounds, for example, creatine/creatinine and dissolved organic carbon, for other members of the symbiosis. Our results suggest that organic nitrogen compounds, for example, creatine, creatinine, urea and cyanate, fuel the nitrogen cycle within the sponge. This study provides an unprecedented view of the metabolic interactions within sponge-microbe symbiosis, bridging the gap between cell- and community-level knowledge.
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Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Cristina Díez-Vives
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Giampiero Batani
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Ana IS Esteves
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Martin T Jahn
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
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