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Galià-Camps C, Junkin L, Borrallo X, Carreras C, Pascual M, Turon X. Navigating spatio-temporal microbiome dynamics: Environmental factors and trace elements shape the symbiont community of an invasive marine species. MARINE POLLUTION BULLETIN 2024; 203:116477. [PMID: 38759466 DOI: 10.1016/j.marpolbul.2024.116477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024]
Abstract
The proliferation of marine invasive species is a mounting concern. While the role of microbial communities in invasive ascidian species is recognized, the role of seasonal shifts in microbiome composition remains largely unexplored. We sampled five individuals of the invasive ascidian Styela plicata quarterly from January 2020 to October 2021 in two harbours, examining gills, tunics, and surrounding water. By analysing Amplicon Sequence Variants (ASVs) and seawater trace elements, we found that compartment (seawater, tunic, or gills) was the primary differentiating factor, followed by harbour. Clear seasonal patterns were evident in seawater bacteria, less so in gills, and absent in tunics. We identified compartment-specific bacteria, as well as seasonal indicator ASVs and ASVs correlated with trace element concentrations. Among these bacteria, we found that Endozoicomonas, Hepatoplasma and Rhodobacteraceae species had reported functions which might be necessary for overcoming seasonality and trace element shifts. This study contributes to understanding microbiome dynamics in invasive holobiont systems, and the patterns found indicate a potential role in adaptation and invasiveness.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain; Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain.
| | - Liam Junkin
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain.
| | - Xavier Borrallo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Xavier Turon
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain.
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2
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Morrison SK, Erwin PM, López‐Legentil S. Effects of color variation and physiological state on ascidian microbiomes. Microbiologyopen 2024; 13:e1405. [PMID: 38481089 PMCID: PMC10938030 DOI: 10.1002/mbo3.1405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/31/2024] [Accepted: 02/29/2024] [Indexed: 03/17/2024] Open
Abstract
Ascidians, known for their color variation, host species-specific microbial symbiont communities. Some ascidians can also transition into a nonfiltering (resting) physiological state. Recent studies suggest that the microbial symbiont communities may vary across different physiological states and color morphs of the host. The colonial ascidian, Polyclinum constellatum, which exhibits several color morphs in the Caribbean Sea, periodically ceases its filtering activity. To investigate if color variation in P. constellatum is indicative of sibling speciation, we sequenced fragments of the ribosomal 18S rRNA and the mitochondrial cytochrome oxidase subunit I genes. Additionally, we sequenced a fragment of the 16S rRNA gene to characterize the microbial communities of two common color morphs (red and green) in colonies that were either actively filtering (active) or nonfiltering (resting). Phylogenetic analyses of both ascidian genes resulted in well-supported monophyletic clades encompassing all color variants of P. constellatum. Interestingly, no significant differences were observed among the microbial communities of the green and red morphs, suggesting that color variation in this species is a result of intraspecific variation. However, the host's physiological state significantly influenced the microbial community structure. Nonfiltering (resting) colonies hosted higher relative abundances of Kiloniella (Alphaproteobacteria) and Fangia (Gammaproteobacteria), while filtering colonies hosted more Reugeria (Alphaproteobacteria) and Endozoicomonas (Gammaproteobacteria). This study demonstrates that microbial symbiont communities serve as reliable indicators of the taxonomic state of their host and are strongly influenced by the host's feeding condition.
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Affiliation(s)
- Samantha K. Morrison
- Department of Biology & Marine Biology, Center for Marine ScienceUniversity of North Carolina WilmingtonWilmingtonNorth CarolinaUSA
| | - Patrick M. Erwin
- Department of Biology & Marine Biology, Center for Marine ScienceUniversity of North Carolina WilmingtonWilmingtonNorth CarolinaUSA
| | - Susanna López‐Legentil
- Department of Biology & Marine Biology, Center for Marine ScienceUniversity of North Carolina WilmingtonWilmingtonNorth CarolinaUSA
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3
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Yuliani D, Morishita F, Imamura T, Ueki T. Vanadium Accumulation and Reduction by Vanadium-Accumulating Bacteria Isolated from the Intestinal Contents of Ciona robusta. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:338-350. [PMID: 38451444 PMCID: PMC11043195 DOI: 10.1007/s10126-024-10300-4] [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: 10/20/2023] [Accepted: 02/28/2024] [Indexed: 03/08/2024]
Abstract
The sea squirt Ciona robusta (formerly Ciona intestinalis type A) has been the subject of many interdisciplinary studies. Known as a vanadium-rich ascidian, C. robusta is an ideal model for exploring microbes associated with the ascidian and the roles of these microbes in vanadium accumulation and reduction. In this study, we discovered two bacterial strains that accumulate large amounts of vanadium, CD2-88 and CD2-102, which belong to the genera Pseudoalteromonas and Vibrio, respectively. The growth medium composition impacted vanadium uptake. Furthermore, pH was also an important factor in the accumulation and localization of vanadium. Most of the vanadium(V) accumulated by these bacteria was converted to less toxic vanadium(IV). Our results provide insights into vanadium accumulation and reduction by bacteria isolated from the ascidian C. robusta to further study the relations between ascidians and microbes and their possible applications for bioremediation or biomineralization.
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Affiliation(s)
- Dewi Yuliani
- Laboratory of Molecular and Cellular Physiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 1-3-1 Kagamiyama, Hiroshima, 739-8526, Japan
- Chemistry Department, Faculty of Mathematics and Natural Sciences, State Islamic University of Malang, Malang, 65145, Indonesia
| | - Fumihiro Morishita
- Laboratory of Molecular and Cellular Physiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 1-3-1 Kagamiyama, Hiroshima, 739-8526, Japan
| | - Takuya Imamura
- Laboratory of Molecular and Cellular Physiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 1-3-1 Kagamiyama, Hiroshima, 739-8526, Japan
| | - Tatsuya Ueki
- Laboratory of Molecular and Cellular Physiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 1-3-1 Kagamiyama, Hiroshima, 739-8526, Japan.
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4
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Estaque T, Basthard-Bogain S, Bianchimani O, Blondeaux V, Cheminée A, Fargetton M, Richaume J, Bally M. Investigating the outcomes of a threatened gorgonian in situ transplantation: Survival and microbiome diversity in Paramuricea clavata (Risso, 1827). MARINE ENVIRONMENTAL RESEARCH 2024; 196:106384. [PMID: 38320428 DOI: 10.1016/j.marenvres.2024.106384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/08/2024]
Abstract
Gorgonian octocorals are threatened by global and local stressors that can act synergistically to affect their health. In recent years, mass mortality events triggered by marine heatwaves have caused demographic declines in Mediterranean gorgonian populations that may lead to their collapse. Potential changes in microbiome composition under stressful conditions may further increase the susceptibility of the gorgonian holobiont to disease. Given the low recovery capacity of gorgonians, restoration approaches using transplantation are becoming an increasingly attractive option to counteract their decline. Here, we compared the survival and microbiome diversity of Paramuricea clavata colonies transplanted to sites differing in depth and local environmental conditions. Gorgonians sampled at a greater depth than the transplantation site were more likely to suffer necrosis after 1 year of monitoring. Gorgonian transplantation into environments disturbed by an anthropogenic source of pollution resulted in an imbalance of the microbiome with potential consequences on the success of restoration initiatives.
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Affiliation(s)
- Tristan Estaque
- Septentrion Environnement, Campus Nature Provence, Marseille, France.
| | | | | | - Vincent Blondeaux
- Septentrion Environnement, Campus Nature Provence, Marseille, France
| | - Adrien Cheminée
- Septentrion Environnement, Campus Nature Provence, Marseille, France
| | - Margaux Fargetton
- Septentrion Environnement, Campus Nature Provence, Marseille, France
| | - Justine Richaume
- Septentrion Environnement, Campus Nature Provence, Marseille, France
| | - Marc Bally
- Mediterranean Institute of Oceanography, Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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5
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Kültz D, Gardell AM, DeTomaso A, Stoney G, Rinkevich B, Rinkevich Y, Qarri A, Dong W, Luu B, Lin M. Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri). Proteomics 2024:e2300628. [PMID: 38400697 DOI: 10.1002/pmic.202300628] [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: 12/02/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
Botryllus schlosseri, is a model marine invertebrate for studying immunity, regeneration, and stress-induced evolution. Conditions for validating its predicted proteome were optimized using nanoElute® 2 deep-coverage LCMS, revealing up to 4930 protein groups and 20,984 unique peptides per sample. Spectral libraries were generated and filtered to remove interferences, low-quality transitions, and only retain proteins with >3 unique peptides. The resulting DIA assay library enabled label-free quantitation of 3426 protein groups represented by 22,593 unique peptides. Quantitative comparisons of single systems from a laboratory-raised with two field-collected populations revealed (1) a more unique proteome in the laboratory-raised population, and (2) proteins with high/low individual variabilities in each population. DNA repair/replication, ion transport, and intracellular signaling processes were distinct in laboratory-cultured colonies. Spliceosome and Wnt signaling proteins were the least variable (highly functionally constrained) in all populations. In conclusion, we present the first colonial tunicate's deep quantitative proteome analysis, identifying functional protein clusters associated with laboratory conditions, different habitats, and strong versus relaxed abundance constraints. These results empower research on B. schlosseri with proteomics resources and enable quantitative molecular phenotyping of changes associated with transfer from in situ to ex situ and from in vivo to in vitro culture conditions.
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Affiliation(s)
- Dietmar Kültz
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Alison M Gardell
- School of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington, USA
| | - Anthony DeTomaso
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Goleta, California, USA
| | - Greg Stoney
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Goleta, California, USA
| | - Baruch Rinkevich
- Israel Oceanography & Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Yuval Rinkevich
- Helmholtz Zentrum München, Regenerative Biology and Medicine Institute, Munich, Germany
| | - Andy Qarri
- Israel Oceanography & Limnological Research, National Institute of Oceanography, Haifa, Israel
- Helmholtz Zentrum München, Regenerative Biology and Medicine Institute, Munich, Germany
| | - Weizhen Dong
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Brenda Luu
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
| | - Mandy Lin
- Department of Animal Sciences & Genome Center, University of California Davis, Meyer Hall, Davis, California, USA
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Bauermeister A, Furtado LC, Ferreira EG, Moreira EA, Jimenez PC, Lopes NP, Araújo WL, Olchanheski LR, Monteiro da Cruz Lotufo T, Costa-Lotufo LV. Chemical and microbial diversity of a tropical intertidal ascidian holobiont. MARINE ENVIRONMENTAL RESEARCH 2024; 194:106303. [PMID: 38150785 DOI: 10.1016/j.marenvres.2023.106303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023]
Abstract
The tropical ascidian Eudistoma vannamei, endemic to the northeastern coast of Brazil, is considered a prolific source of secondary metabolites and hosts Actinomycetota that produce bioactive compounds. Herein, we used an omics approach to study the ascidian as a holobiont, including the microbial diversity through 16S rRNA gene sequencing and metabolite production using mass spectrometry-based metabolomics. Gene sequencing analysis revealed all samples of E. vannamei shared about 50% of the observed ASVs, and Pseudomonadota (50.7%), Planctomycetota (9.58%), Actinomycetota (10.34%), Bacteroidota (12.05%) were the most abundant bacterial phyla. Analysis of tandem mass spectrometry (MS/MS) data allowed annotation of compounds, including phospholipids, amino acids, and pyrimidine alkaloids, such as staurosporine, a member of a well-known chemical class recognized as a microbial metabolite. Isolated bacteria, mainly belonging to Streptomyces and Micromonospora genera, were cultivated and extracted with ethyl acetate. MS/MS analysis of bacterial extracts allowed annotation of compounds not detected in the ascidian tissue, including marineosin and dihydroergotamine, yielding about 30% overlapped ions between host and isolated bacteria. This study reveals E. vannamei as a rich source of microbial and chemical diversity and, furthermore, highlights the importance of omic tools for a comprehensive investigation of holobiont systems.
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Affiliation(s)
- Anelize Bauermeister
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil; Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Luciana Costa Furtado
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Elthon G Ferreira
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, CE, 60451-970, Brazil
| | - Eduarda Antunes Moreira
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | | | - Norberto Peporine Lopes
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Welington Luiz Araújo
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Luiz Ricardo Olchanheski
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-900, Brazil
| | | | - Leticia Veras Costa-Lotufo
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil.
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7
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Hutchings B, López-Legentil S, Stefaniak LM, Nydam M, Erwin PM. Distinct microbial communities in an ascidian-crustacean symbiosis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13242. [PMID: 38383831 PMCID: PMC10881349 DOI: 10.1111/1758-2229.13242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024]
Abstract
Ascidians are marine invertebrates known to occasionally host symbiotic crustaceans. Although the microbiomes of both ascidians and free-living crustaceans have been characterized, there is no documentation of microbial communities in an ascidian-crustacean symbiosis. Samples of the solitary ascidian Ascidia sydneiensis and ambient seawater were collected in Belize. Four symbiotic amphipod crustaceans were retrieved from the branchial sac of the animal, and their microbiomes were compared with those from their ascidian host (tunic and branchial sac compartments) and seawater. Microbiome richness and diversity differed significantly between sample types, with amphipod microbiomes exhibiting significantly lower diversity than tunic and ambient seawater samples. Microbiome composition also differed significantly between sample types and among all pairwise comparisons, except for branchial sac and amphipod microbiomes. Differential operational taxonomic unit (OTU) analyses revealed that only 3 out of 2553 OTUs had significantly different relative abundances in amphipods compared with ascidian branchial sacs, whereas 72 OTUs differed between amphipod and tunic and 315 between amphipod and seawater samples. Thus, different body compartments of A. sydneiensis hosted distinct microbiomes, and symbiotic amphipods contained microbiomes resembling the region they inhabit (i.e., the branchial sac), suggesting that environmental filtering and co-evolutionary processes are determinants of microbiome composition within ascidian-crustacean symbioses.
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Affiliation(s)
- Brenna Hutchings
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Susanna López-Legentil
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Lauren M Stefaniak
- Department of Marine Science, Coastal Carolina University, Conway, South Carolina, USA
| | - Marie Nydam
- Department of Biology, SOKA University of America, Aliso Viejo, California, USA
| | - Patrick M Erwin
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
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8
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Galià-Camps C, Baños E, Pascual M, Carreras C, Turon X. Multidimensional variability of the microbiome of an invasive ascidian species. iScience 2023; 26:107812. [PMID: 37744040 PMCID: PMC10514470 DOI: 10.1016/j.isci.2023.107812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Animals, including invasive species, are complex entities consisting of a host and its associated symbionts (holobiont). The interaction between the holobiont components is crucial for the host's survival. However, our understanding of how microbiomes of invasive species change across different tissues, localities, and ontogenetic stages, is limited. In the introduced ascidian Styela plicata, we found that its microbiome is highly distinct and specialized among compartments (tunic, gill, and gut). Smaller but significant differences were also found across harbors, suggesting local adaptation, and between juveniles and adults. Furthermore, we found a correlation between the microbiome and environmental trace element concentrations, especially in adults. Functional analyses showed that adult microbiomes possess specific metabolic pathways that may enhance fitness during the introduction process. These findings highlight the importance of integrated approaches in studying the interplay between animals and microbiomes, as a first step toward understanding how it can affect the species' invasive success.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Elena Baños
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Department of Marine Ecology, Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Catalonia, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Catalonia, Spain
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Mioduchowska M, Pawłowska J, Mazanowski K, Weydmann-Zwolicka A. Contrasting Marine Microbial Communities of the Fram Strait with the First Confirmed Record of Cyanobacteria Prochlorococcus marinus in the Arctic Region. BIOLOGY 2023; 12:1246. [PMID: 37759645 PMCID: PMC10525857 DOI: 10.3390/biology12091246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
The seawater microbiome is crucial in marine ecosystems because of its role in food chains and biogeochemical cycles; thus, we studied the composition of the pelagic marine microbiome collected in the upper 50 m on the opposite sides of Fram Strait: Spitsbergen and Greenland shelves. We found out that it differed significantly, with salinity being the main environmental variable responsible for these differences. The Spitsbergen shelf was dominated by Atlantic Waters, with a rather homogenous water column in terms of salinity and temperature down to 300 m; hence, the marine microbial community was also homogenous at all sampled depths (0, 25, 50 m). On the contrary, stations on the Greenland shelf were exposed to different water masses of both Arctic and Atlantic origin, which resulted in a more diverse microbial community there. Unexpectedly, for the very first time, we identified cyanobacterium Prochlorococcus marinus in Arctic waters (Spitsbergen shelf, 75-77° N). Till now, the distribution of this cyanobacteria in oceans has been described only between 40° N and 40° S. Considering the accelerated rate of climate warming in the Arctic, our results indicated that the seawater microbiome can be viewed as an amplifier of global change and that the Atlantification is in progress.
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Affiliation(s)
- Monika Mioduchowska
- Department of Evolutionary Genetics and Biosystematics, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland
- Laboratory of Plankton Biology, Department of Marine Biology and Biotechnology, University of Gdansk, 81-378 Gdynia, Poland;
| | - Joanna Pawłowska
- Department of Paleoceanography, Institute of Oceanology Polish Academy of Sciences, 81-712 Sopot, Poland;
| | - Karol Mazanowski
- Laboratory of Plankton Biology, Department of Marine Biology and Biotechnology, University of Gdansk, 81-378 Gdynia, Poland;
| | - Agata Weydmann-Zwolicka
- Laboratory of Plankton Biology, Department of Marine Biology and Biotechnology, University of Gdansk, 81-378 Gdynia, Poland;
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Connelly MT, Snyder G, Palacio-Castro AM, Gillette PR, Baker AC, Traylor-Knowles N. Antibiotics reduce Pocillopora coral-associated bacteria diversity, decrease holobiont oxygen consumption and activate immune gene expression. Mol Ecol 2023; 32:4677-4694. [PMID: 37317893 DOI: 10.1111/mec.17049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
Corals are important models for understanding invertebrate host-microbe interactions; however, to fully discern mechanisms involved in these relationships, experimental approaches for manipulating coral-bacteria associations are needed. Coral-associated bacteria affect holobiont health via nutrient cycling, metabolic exchanges and pathogen exclusion, yet it is not fully understood how bacterial community shifts affect holobiont health and physiology. In this study, a combination of antibiotics (ampicillin, streptomycin and ciprofloxacin) was used to disrupt the bacterial communities of 14 colonies of the reef framework-building corals Pocillopora meandrina and P. verrucosa, originally collected from Panama and hosting diverse algal symbionts (family Symbiodiniaceae). Symbiodiniaceae photochemical efficiencies and holobiont oxygen consumption (as proxies for coral health) were measured throughout a 5-day exposure. Antibiotics altered bacterial community composition and reduced alpha and beta diversity, however, several bacteria persisted, leading to the hypothesis that these bacteria are either antibiotics resistant or occupy internal niches that are shielded from antibiotics. While antibiotics did not affect Symbiodiniaceae photochemical efficiency, antibiotics-treated corals had lower oxygen consumption rates. RNAseq revealed that antibiotics increased expression of Pocillopora immunity and stress response genes at the expense of cellular maintenance and metabolism functions. Together, these results reveal that antibiotic disruption of corals' native bacteria negatively impacts holobiont health by decreasing oxygen consumption and activating host immunity without directly impairing Symbiodiniaceae photosynthesis, underscoring the critical role of coral-associated bacteria in holobiont health. They also provide a baseline for future experiments that manipulate Pocillopora corals' symbioses by first reducing the diversity and complexity of coral-associated bacteria.
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Affiliation(s)
- Michael T Connelly
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Grace Snyder
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Ana M Palacio-Castro
- University of Miami Cooperative Institute for Marine and Atmospheric Studies, Miami, Florida, USA
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA
| | - Phillip R Gillette
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Andrew C Baker
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science, Miami, Florida, USA
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11
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Hyams Y, Rubin-Blum M, Rosner A, Brodsky L, Rinkevich Y, Rinkevich B. Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii. Front Microbiol 2023; 14:1072053. [PMID: 37323901 PMCID: PMC10264598 DOI: 10.3389/fmicb.2023.1072053] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Environmental perturbations evoke down-regulation of metabolism in some multicellular organisms, leading to dormancy, or torpor. Colonies of the urochordate Botrylloides leachii enter torpor in response to changes in seawater temperature and may survive for months as small vasculature remnants that lack feeding and reproductive organs but possess torpor-specific microbiota. Upon returning to milder conditions, the colonies rapidly restore their original morphology, cytology and functionality while harboring re-occurring microbiota, a phenomenon that has not been described in detail to date. Here we investigated the stability of B. leachii microbiome and its functionality in active and dormant colonies, using microscopy, qPCR, in situ hybridization, genomics and transcriptomics. A novel lineage of Endozoicomonas, proposed here as Candidatus Endozoicomonas endoleachii, was dominant in torpor animals (53-79% read abundance), and potentially occupied specific hemocytes found only in torpid animals. Functional analysis of the metagenome-assembled genome and genome-targeted transcriptomics revealed that Endozoicomonas can use various cellular substrates, like amino acids and sugars, potentially producing biotin and thiamine, but also expressing various features involved in autocatalytic symbiosis. Our study suggests that the microbiome can be linked to the metabolic and physiological states of the host, B. leachii, introducing a model organism for the study of symbioses during drastic physiological changes, such as torpor.
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Affiliation(s)
- Yosef Hyams
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, Israel
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Yuval Rinkevich
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, Munich, Germany
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
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12
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Maire J, Tandon K, Collingro A, van de Meene A, Damjanovic K, Gotze CR, Stephenson S, Philip GK, Horn M, Cantin NE, Blackall LL, van Oppen MJH. Colocalization and potential interactions of Endozoicomonas and chlamydiae in microbial aggregates of the coral Pocillopora acuta. SCIENCE ADVANCES 2023; 9:eadg0773. [PMID: 37196086 DOI: 10.1126/sciadv.adg0773] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
Corals are associated with a variety of bacteria, which occur in the surface mucus layer, gastrovascular cavity, skeleton, and tissues. Some tissue-associated bacteria form clusters, termed cell-associated microbial aggregates (CAMAs), which are poorly studied. Here, we provide a comprehensive characterization of CAMAs in the coral Pocillopora acuta. Combining imaging techniques, laser capture microdissection, and amplicon and metagenome sequencing, we show that (i) CAMAs are located in the tentacle tips and may be intracellular; (ii) CAMAs contain Endozoicomonas (Gammaproteobacteria) and Simkania (Chlamydiota) bacteria; (iii) Endozoicomonas may provide vitamins to its host and use secretion systems and/or pili for colonization and aggregation; (iv) Endozoicomonas and Simkania occur in distinct, but adjacent, CAMAs; and (v) Simkania may receive acetate and heme from neighboring Endozoicomonas. Our study provides detailed insight into coral endosymbionts, thereby improving our understanding of coral physiology and health and providing important knowledge for coral reef conservation in the climate change era.
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Affiliation(s)
- Justin Maire
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Allison van de Meene
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Katarina Damjanovic
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
| | - Cecilie Ravn Gotze
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
| | - Sophie Stephenson
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
| | - Gayle K Philip
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Neal E Cantin
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, PMB No 3, Townsville, QLD 4810, Australia
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13
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Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. THE ISME JOURNAL 2022; 16:1883-1895. [PMID: 35444262 PMCID: PMC9296628 DOI: 10.1038/s41396-022-01226-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.
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14
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Wada N, Hsu MT, Tandon K, Hsiao SSY, Chen HJ, Chen YH, Chiang PW, Yu SP, Lu CY, Chiou YJ, Tu YC, Tian X, Chen BC, Lee DC, Yamashiro H, Bourne DG, Tang SL. High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata. SCIENCE ADVANCES 2022; 8:eabo2431. [PMID: 35857470 PMCID: PMC9258956 DOI: 10.1126/sciadv.abo2431] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/13/2022] [Indexed: 05/29/2023]
Abstract
Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.
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Affiliation(s)
- Naohisa Wada
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Ming-Tsung Hsu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Silver Sung-Yun Hsiao
- Institute of Astronomy and Astrophysics, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Hsing-Ju Chen
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Yu-Hsiang Chen
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Jing Chiou
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Yung-Chi Tu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Der-Chuen Lee
- Institute of Earth Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Hideyuki Yamashiro
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, 4811 QLD, Australia
- Australian Institute of Marine Science, Townsville, 4810 QLD, Australia
- AIMS@JCU, Townsville, 4811 QLD, Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
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15
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Demko AM, Patin NV, Jensen PR. Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques. Environ Microbiol 2021; 23:6859-6875. [PMID: 34636122 DOI: 10.1111/1462-2920.15798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 09/28/2021] [Indexed: 01/04/2023]
Abstract
The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.
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Affiliation(s)
- Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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16
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Matos A, Antunes A. Symbiotic Associations in Ascidians: Relevance for Functional Innovation and Bioactive Potential. Mar Drugs 2021; 19:370. [PMID: 34206769 PMCID: PMC8303170 DOI: 10.3390/md19070370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022] Open
Abstract
Associations between different organisms have been extensively described in terrestrial and marine environments. These associations are involved in roles as diverse as nutrient exchanges, shelter or adaptation to adverse conditions. Ascidians are widely dispersed marine invertebrates associated to invasive behaviours. Studying their microbiomes has interested the scientific community, mainly due to its potential for bioactive compounds production-e.g., ET-73 (trabectedin, Yondelis), an anticancer drug. However, these symbiotic interactions embrace several environmental and biological functions with high ecological relevance, inspiring diverse biotechnological applications. We thoroughly reviewed microbiome studies (microscopic to metagenomic approaches) of around 171 hosts, worldwide dispersed, occurring at different domains of life (Archaea, Bacteria, Eukarya), to illuminate the functions and bioactive potential of associated organisms in ascidians. Associations with Bacteria are the most prevalent, namely with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria and Planctomycetes phyla. The microbiomes of ascidians belonging to Aplousobranchia order have been the most studied. The integration of worldwide studies characterizing ascidians' microbiome composition revealed several functions including UV protection, bioaccumulation of heavy metals and defense against fouling or predators through production of natural products, chemical signals or competition. The critical assessment and characterization of these communities is extremely valuable to comprehend their biological/ecological role and biotechnological potential.
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Affiliation(s)
- Ana Matos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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17
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Evans JS, Erwin PM, Sihaloho HF, López‐Legentil S. Cryptic genetic lineages of a colonial ascidian host distinct microbiomes. ZOOL SCR 2021. [DOI: 10.1111/zsc.12482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- James S. Evans
- Department of Biology & Marine Biology Center for Marine Science University of North Carolina Wilmington Wilmington NC USA
| | - Patrick M. Erwin
- Department of Biology & Marine Biology Center for Marine Science University of North Carolina Wilmington Wilmington NC USA
| | - Hendra F. Sihaloho
- Department of Biology & Marine Biology Center for Marine Science University of North Carolina Wilmington Wilmington NC USA
| | - Susanna López‐Legentil
- Department of Biology & Marine Biology Center for Marine Science University of North Carolina Wilmington Wilmington NC USA
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18
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The bacterial composition associated with Atriolum robustum, a common ascidian from Xisha coral reef, China. Symbiosis 2021. [DOI: 10.1007/s13199-020-00742-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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The Ascidian-Derived Metabolites with Antimicrobial Properties. Antibiotics (Basel) 2020; 9:antibiotics9080510. [PMID: 32823633 PMCID: PMC7460354 DOI: 10.3390/antibiotics9080510] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022] Open
Abstract
Among the sub-phylum of Tunicate, ascidians represent the most abundant class of marine invertebrates, with 3000 species by heterogeneous habitat, that is, from shallow water to deep sea, already reported. The chemistry of these sessile filter-feeding organisms is an attractive reservoir of varied and peculiar bioactive compounds. Most secondary metabolites isolated from ascidians stand out for their potential as putative therapeutic agents in the treatment of several illnesses like microbial infections. In this review, we present and discuss the antibacterial activity shown by the main groups of ascidian-derived products, such as sulfur-containing compounds, meroterpenes, alkaloids, peptides, furanones, and their derivatives. Moreover, the direct evidence of a symbiotic association between marine ascidians and microorganisms shed light on the real producers of many extremely potent marine natural compounds. Hence, we also report the antibacterial potential, joined to antifungal and antiviral activity, of metabolites isolated from ascidian-associate microorganisms by culture-dependent methods.
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20
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Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago , Antarctica. Mar Drugs 2020; 18:md18060298. [PMID: 32498449 PMCID: PMC7345734 DOI: 10.3390/md18060298] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 01/04/2023] Open
Abstract
Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.
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21
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Cleary DFR, Polónia ARM, Huang YM, Swierts T. Compositional variation between high and low prokaryotic diversity coral reef biotopes translates to different predicted metagenomic gene content. Antonie van Leeuwenhoek 2019; 113:563-587. [PMID: 31802337 DOI: 10.1007/s10482-019-01364-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
Abstract
In a previous study, we identified host species that housed high and low diversity prokaryotic communities. In the present study, we expand on this and assessed the prokaryotic communities associated with seawater, sediment and 11 host species from 7 different phyla in a Taiwanese coral reef setting. The host taxa sampled included hard, octo- and black corals, molluscs, bryozoans, flatworms, fish and sea urchins. There were highly significant differences in composition among host species and all host species housed distinct communities from those found in seawater and sediment. In a hierarchical clustering analysis, samples from all host species, with the exception of the coral Galaxea astreata, formed significantly supported clusters. In addition to this, the coral G. astreata and the bryozoan Triphyllozoon inornatum on the one hand and the coral Tubastraea coccinea, the hermit crab Calcinus laevimanus and the flatworm Thysanozoon nigropapillosum on the other formed significantly supported clusters. In addition to composition, there were highly pronounced differences in richness and evenness among host species from the most diverse species, the bryozoan T. inornatum at 2518 ± 240 OTUs per 10,000 sequences to the least diverse species, the octocoral Cladiella sp. at 142 ± 14 OTUs per 10,000 sequences. In line with the differences in composition, there were significant differences in predicted metagenomic gene counts among host species. Furthermore, there were pronounced compositional and predicted functional differences between high diversity hosts (Liolophura japonica, G. astreata, T. coccinea, C. laevimanus, T. inornatum) and low diversity hosts (Antipathes sp., Pomacentrus coelestis, Modiolus auriculatus, T. nigropapillosum, Cladiella sp. and Diadema savigny). In particular, we found that all tested low diversity hosts were predicted to be enriched for the phosphotransferase system compared to high diversity hosts.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Ana Rita M Polónia
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Yusheng M Huang
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, Penghu, Taiwan.,Department of Marine Recreation, University of Science and Technology, Penghu, Taiwan
| | - Thomas Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands
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22
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Alex A, Antunes A. Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses. Microorganisms 2019; 7:microorganisms7120635. [PMID: 31801294 PMCID: PMC6955870 DOI: 10.3390/microorganisms7120635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/19/2019] [Accepted: 11/27/2019] [Indexed: 11/29/2022] Open
Abstract
The most recently described bacterial members of the genus Endozoicomonas have been found in association with a wide variety of marine invertebrates. Despite their ubiquity in the host holobiont, limited information is available on the molecular genomic signatures of the symbiotic association of Endozoicomonas with marine sponges. Here, we generated a draft genome of Endozoicomonas sp. OPT23 isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative genomics analyses. Genome-specific analysis and metabolic pathway comparison of the members of the genus Endozoicomonas revealed the presence of gene clusters encoding for unique metabolic features, such as the utilization of carbon sources through lactate, L-rhamnose metabolism, and a phenylacetic acid degradation pathway in Endozoicomonas sp. OPT23. Moreover, the genome harbors genes encoding for eukaryotic-like proteins, such as ankyrin repeats, tetratricopeptide repeats, and Sel1 repeats, which likely facilitate sponge-bacterium attachment. The genome also encodes major secretion systems and homologs of effector molecules that seem to enable the sponge-associated bacterium to interact with the sponge and deliver the virulence factors for successful colonization. In conclusion, the genome analysis of Endozoicomonas sp. OPT23 revealed the presence of adaptive genomic signatures that might favor their symbiotic lifestyle within the sponge host.
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Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (A.Al.); (A.An.); Tel.: +351-22-340-1813 (A.Al.); +351-22-340-1813 (A.An.)
| | - Agostino Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (A.Al.); (A.An.); Tel.: +351-22-340-1813 (A.Al.); +351-22-340-1813 (A.An.)
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23
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Rossbach S, Cardenas A, Perna G, Duarte CM, Voolstra CR. Tissue-Specific Microbiomes of the Red Sea Giant Clam Tridacna maxima Highlight Differential Abundance of Endozoicomonadaceae. Front Microbiol 2019; 10:2661. [PMID: 31849854 PMCID: PMC6901920 DOI: 10.3389/fmicb.2019.02661] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 10/31/2019] [Indexed: 02/01/2023] Open
Abstract
Giant clams (subfamily Tridacninae) are prevalent members of coral reef communities and engage in symbioses with algal photosymbionts of the family Symbiodiniaceae, similar to their scleractinian coral counterparts. However, we know little about their associated bacterial microbiome members. Here, we explored bacterial community diversity of digestive system, gill, and mantle tissues associated with the giant clam Tridacna maxima across a cross-shelf gradient (inshore, midshore, and offshore reef sites) in the central Red Sea using 16S rRNA gene amplicon sequencing. Different tissues harbor spatially stable and distinct microbial communities. Notably, diverse assemblages of bacteria affiliated to the family Endozoicomonadaceae were prevalent in all tissues, but particularly abundant in gills and to a lesser extent in digestive tissues. Besides Endozoicomonadaceae, bacteria in the families Pasteurellaceae, Alteromonadaceae, and Comamonadaceae were common associates, depending on the tissue queried. Taxonomy-based functional inference identified processes related to nitrogen cycling (among others) to be enriched in giant clam tissues and contributed by Endozoicomonadaceae. Our study highlights the tissue-specificity and broad taxonomic range of Endozoicomonadaceae associates, similar to other marine invertebrates, and suggests their contribution to nitrogen-related pathways. The investigation of bivalve-associated microbiome communities provides an important addition to the pathogen-focused studies for commercially important bivalves (e.g., oysters).
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Affiliation(s)
- Susann Rossbach
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anny Cardenas
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gabriela Perna
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
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24
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Evans JS, Erwin PM, Shenkar N, López-Legentil S. A comparison of prokaryotic symbiont communities in nonnative and native ascidians from reef and harbor habitats. FEMS Microbiol Ecol 2019; 94:5056155. [PMID: 30052904 DOI: 10.1093/femsec/fiy139] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/17/2018] [Indexed: 11/14/2022] Open
Abstract
Harbor systems represent passive gateways for the introduction of nonnative ascidians that compete with the surrounding benthos and may spread through localized dispersal, even populating adjacent natural reefs. To investigate the potential role of microbial symbionts in the success of ascidian introductions and spread, we evaluated the host-specificity of prokaryotic communities within two ascidian species commonly found off the North Carolina coast. Replicate samples of the native ascidian Eudistoma capsulatum, the nonnative ascidian Distaplia bermudensis and seawater were collected from artificial (harbor) and natural reef substrates. Prokaryotic communities in seawater samples and ascidian tunics were characterized via next-generation sequencing of partial 16S rRNA gene sequences. Ascidian microbiomes clustered strongly in response to host species, with significant differences in community structure between the two species and seawater. Further, symbiont community structure differed significantly between E. capsulatumindividuals collected from artificial and natural habitats, though this was not the case for D. bermudensis. These findings suggested that some ascidian species possess stable microbial symbiont communities that allow them to thrive in a wide range of habitats, while other species rely on the restructuring of their microbial communities with specific symbionts (e.g. Chelativorans) to survive under particular environmental conditions such as increased pollution.
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Affiliation(s)
- James S Evans
- Department of Biology and Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington NC 28409, USA
| | - Patrick M Erwin
- Department of Biology and Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington NC 28409, USA
| | - Noa Shenkar
- School of Zoology, and The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington NC 28409, USA
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25
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Hooper PM, Ross SH, Feist SW, Cano I. Shedding and survival of an intracellular pathogenic Endozoicomonas-like organism infecting king scallop Pecten maximus. DISEASES OF AQUATIC ORGANISMS 2019; 134:167-173. [PMID: 31120042 DOI: 10.3354/dao03375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Lyme Bay marine protected area (MPA) hosts a valuable population of king scallop Pecten maximus L. Recently, an Endozoicomonas-like organism (ELO), infecting host gill epithelial tissue, was associated with king scallop mass mortality events within the Lyme Bay MPA. Currently, very little is known about its transmission and survival outside the host. In this investigation, animals collected outside of reported mortality events showed high levels of ELO infection. Gill tissue disruption and the release of bacteria into the interlamellar space was seen histologically, suggesting shedding of ELO from host animals. To investigate pathogen survival outside the host, infected scallops were maintained in static water for a 24 h period, and then removed. Over the subsequent 8 d, water samples were collected and the quantity of ELO 16S rRNA transcript was measured by TaqManTM quantitative PCR (qPCR). The 16S rRNA transcript quantity was stable outside the host for 6 d before bacteria survival declined 2 logs (7.9 × 108 16S rRNA to 2.3 × 106 transcripts), suggesting that ELO can survive independently outside the host organism. The ELO-specific qPCR probe can therefore be used in future field studies of ELO prevalence within the environment and fauna of the Lyme Bay MPA.
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Affiliation(s)
- Patrick M Hooper
- International Centre of Excellence for Aquatic Animal Health, Cefas Weymouth Laboratory, Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK
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26
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Features of a novel protein, rusticalin, from the ascidian Styela rustica reveal ancestral horizontal gene transfer event. Mob DNA 2019; 10:4. [PMID: 30675192 PMCID: PMC6339383 DOI: 10.1186/s13100-019-0146-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/02/2019] [Indexed: 12/18/2022] Open
Abstract
Background The transfer of genetic material from non-parent organisms is called horizontal gene transfer (HGT). One of the most conclusive cases of HGT in metazoans was previously described for the cellulose synthase gene in ascidians. Results In this study we identified a new protein, rusticalin, from the ascidian Styela rustica and presented evidence for its likely origin by HGT. Discernible homologues of rusticalin were found in placozoans, coral, and basal Chordates. Rusticalin was predicted to consist of two distinct regions, an N-terminal domain and a C-terminal domain. The N-terminal domain comprises two cysteine-rich repeats and shows remote similarity to the tick carboxypeptidase inhibitor. The C-terminal domain shares significant sequence similarity with bacterial MD peptidases and bacteriophage A500 L-alanyl-D-glutamate peptidase. A possible transfer of the C-terminal domain by bacteriophage was confirmed by an analysis of noncoding sequences of C. intestinalis rusticalin-like gene, which was found to contain a sequence similar to the bacteriophage A500 recombination site. Moreover, a sequence similar to the bacteriophage recombination site was found to be adjacent to the cellulose synthase catalytic subunit gene in the genome of Streptomices sp., the donor of ascidian cellulose synthase. Conclusions The C-terminal domain of rusticalin and rusticalin-like proteins is likely to be horizontally transferred by the bacteriophage A500. A common mechanism involving bacteriophage mediated gene transfer can be proposed for at least two HGT events in ascidians.
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27
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Evans JS, López-Legentil S, Erwin PM. Comparing Two Common DNA Extraction Kits for the Characterization of Symbiotic Microbial Communities from Ascidian Tissue. Microbes Environ 2018; 33:435-439. [PMID: 30487350 PMCID: PMC6308000 DOI: 10.1264/jsme2.me18031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/01/2018] [Indexed: 11/30/2022] Open
Abstract
Various DNA extraction methods are often used interchangeably for the characterization of microbial communities despite indications that different techniques produce disparate results. The microbiomes of two ascidian species were herein characterized using two common DNA extraction kits, the DNeasy Blood and Tissue Kit (Qiagen) and the PowerSoil DNA Isolation Kit (Mo Bio Laboratories), followed by next-generation (Illumina) sequencing of partial 16S rRNA genes. Significant differences were detected in microbial community diversity and structure between ascidian species, but not between kits, suggesting similar recovery of biological variation and low technical variation between the two extraction methods for ascidian microbiome characterization.
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Affiliation(s)
- James S. Evans
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington5600 Marvin K. Moss Lane, Wilmington NC 28409United States of America
| | - Susanna López-Legentil
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington5600 Marvin K. Moss Lane, Wilmington NC 28409United States of America
| | - Patrick M. Erwin
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington5600 Marvin K. Moss Lane, Wilmington NC 28409United States of America
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28
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Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species. ISME JOURNAL 2018; 13:902-920. [PMID: 30518817 PMCID: PMC6461927 DOI: 10.1038/s41396-018-0318-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 10/23/2018] [Accepted: 11/04/2018] [Indexed: 12/28/2022]
Abstract
Lucinidae clams harbor gammaproteobacterial thioautotrophic gill endosymbionts that are environmentally acquired. Thioautotrophic lucinid symbionts are related to metabolically similar symbionts associated with diverse marine host taxa and fall into three distinct phylogenetic clades. Most studies on the lucinid–bacteria chemosymbiosis have been done with seagrass-dwelling hosts, whose symbionts belong to the largest phylogenetic clade. In this study, we examined the taxonomy and functional repertoire of bacterial endosymbionts at an unprecedented resolution from Phacoides pectinatus retrieved from mangrove-lined coastal sediments, which are underrepresented in chemosymbiosis studies. The P. pectinatus thioautotrophic endosymbiont expressed metabolic gene variants for thioautotrophy, respiration, and nitrogen assimilation distinct from previously characterized lucinid thioautotrophic symbionts and other marine symbionts. At least two other bacterial species with different metabolisms were also consistently identified in the P. pectinatus gill microbiome, including a Kistimonas-like species and a Spirochaeta-like species. Bacterial transcripts involved in adhesion, growth, and virulence and mixotrophy were highly expressed, as were host-related hemoglobin and lysozyme transcripts indicative of sulfide/oxygen/CO2 transport and bactericidal activity. This study suggests the potential roles of P. pectinatus and its gill microbiome species in mangrove sediment biogeochemistry and offers insights into host and microbe metabolisms in the habitat.
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29
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Qi W, Cascarano MC, Schlapbach R, Katharios P, Vaughan L, Seth-Smith HMB. Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity. Genome Biol Evol 2018; 10:1363-1374. [PMID: 29726925 PMCID: PMC6007542 DOI: 10.1093/gbe/evy092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2018] [Indexed: 02/06/2023] Open
Abstract
Endozoicomonas bacteria are generally beneficial symbionts of diverse marine invertebrates including reef-building corals, sponges, sea squirts, sea slugs, molluscs, and Bryozoans. In contrast, the recently reported Ca. Endozoicomonas cretensis was identified as a vertebrate pathogen, causing epitheliocystis in fish larvae resulting in massive mortality. Here, we described the Ca. E. cretensis draft genome, currently undergoing genome decay as evidenced by massive insertion sequence (IS element) expansion and pseudogene formation. Many of the insertion sequences are also predicted to carry outward-directed promoters, implying that they may be able to modulate the expression of neighbouring coding sequences (CDSs). Comparative genomic analysis has revealed many Ca. E. cretensis-specific CDSs, phage integration and novel gene families. Potential virulence related CDSs and machineries were identified in the genome, including secretion systems and related effector proteins, and systems related to biofilm formation and directed cell movement. Mucin degradation would be of importance to a fish pathogen, and many candidate CDSs associated with this pathway have been identified. The genome may reflect a bacterium in the process of changing niche from symbiont to pathogen, through expansion of virulence genes and some loss of metabolic capacity.
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Affiliation(s)
- Weihong Qi
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Maria Chiara Cascarano
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Lloyd Vaughan
- Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland.,Pathovet AG, Tagelswangen, Switzerland
| | - Helena M B Seth-Smith
- Functional Genomics Center Zurich, University of Zurich, Switzerland.,Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
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30
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Chen L, Hu JS, Xu JL, Shao CL, Wang GY. Biological and Chemical Diversity of Ascidian-Associated Microorganisms. Mar Drugs 2018; 16:md16100362. [PMID: 30275404 PMCID: PMC6212887 DOI: 10.3390/md16100362] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 11/16/2022] Open
Abstract
Ascidians are a class of sessile filter-feeding invertebrates, that provide unique and fertile niches harboring various microorganisms, such as bacteria, actinobacteria, cyanobacteria and fungi. Over 1000 natural products, including alkaloids, cyclic peptides, and polyketides, have been isolated from them, which display diverse properties, such as antibacterial, antifungal, antitumor, and anti-inflammatory activities. Strikingly, direct evidence has confirmed that ~8% of natural products from ascidians are actually produced by symbiotic microorganisms. In this review, we present 150 natural products from microorganisms associated with ascidians that have been reported up to 2017.
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Affiliation(s)
- Lei Chen
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Jin-Shuang Hu
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Jia-Lei Xu
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Chang-Lun Shao
- Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
| | - Guang-Yu Wang
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
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31
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Creasy A, Rosario K, Leigh BA, Dishaw LJ, Breitbart M. Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism ( Ciona robusta). Viruses 2018; 10:v10080404. [PMID: 30065169 PMCID: PMC6116155 DOI: 10.3390/v10080404] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system used to study gut microbial interactions, this study investigated ssDNA phages found in the Ciona gut. We identified 258 Microviridae genomes, which were dominated by novel members of the Gokushovirinae subfamily, but also represented several proposed phylogenetic groups (Alpavirinae, Aravirinae, Group D, Parabacteroides prophages, and Pequeñovirus) and a novel group. Comparative analyses between Ciona specimens with full and cleared guts, as well as the surrounding water, indicated that Ciona retains a distinct and highly diverse community of ssDNA phages. This study significantly expands the known diversity within the Microviridae family and demonstrates the promise of Ciona as a model system for investigating their role in animal health.
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Affiliation(s)
- Alexandria Creasy
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Brittany A Leigh
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Larry J Dishaw
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
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32
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Neave MJ, Apprill A, Ferrier-Pagès C, Voolstra CR. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Appl Microbiol Biotechnol 2016; 100:8315-24. [PMID: 27557714 PMCID: PMC5018254 DOI: 10.1007/s00253-016-7777-0] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 02/01/2023]
Abstract
Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.
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Affiliation(s)
- Matthew J Neave
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Amy Apprill
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | | | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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33
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Schreiber L, Kjeldsen KU, Obst M, Funch P, Schramm A. Description of Endozoicomonas ascidiicola sp. nov., isolated from Scandinavian ascidians. Syst Appl Microbiol 2016; 39:313-8. [PMID: 27344411 DOI: 10.1016/j.syapm.2016.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/20/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
Abstract
Two gram-negative, facultative anaerobic, chemoorganoheterotrophic, motile and rod-shaped bacteria, strains AVMART05(T) and KASP37, were isolated from ascidians (Tunicata, Ascidiaceae) of the genus Ascidiella collected at Gullmarsfjord, Sweden. The strains are the first cultured representatives of an ascidian-specific lineage within the genus Endozoicomonas (Gammaproteobacteria, Oceanospirillales, Hahellaceae). Both strains feature three distinct 16S rRNA gene paralogs, with identities of 98.9-99.1% (AVMART05(T)) and 97.7-98.8% (KASP37) between paralogs. The strains are closely related to Endozoicomonas atrinae and Endozoicomonas elysicola, with which they share 97.3-98.0% 16S rRNA gene sequence identity. Digital DNA-DNA hybridization, average nucleotide identity, and tetra-nucleotide correlation analysis indicate that both strains belong to a single species distinct from their closest relatives. Both strains feature similar DNA G+C contents of 46.70mol% (AVMART05(T)) and 44.64mol% (KASP37). The fatty acid patterns of AVMART05(T) and KASP37 are most similar to those of Endozoicomonas euniceicola and Endozoicomonas gorgoniicola. Based on the polyphasic approach, we propose the species Endozoicomonas ascidiicola sp. nov. to accommodate the newly isolated strains. E. ascidiicola sp. nov. is represented by the type strain AVMART05(T) (=DSM 100913(T)=LMG 29095(T)) and strain KASP37 (=DSM 100914=LMG 29096).
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Affiliation(s)
- Lars Schreiber
- Center for Geomicrobiology & Section for Microbiology, Department of Bioscience, Aarhus University, Denmark.
| | - Kasper Urup Kjeldsen
- Center for Geomicrobiology & Section for Microbiology, Department of Bioscience, Aarhus University, Denmark
| | - Matthias Obst
- Systematics and Biodiversity, Department of Biological and Environmental Sciences, Göteborg University, Sweden
| | - Peter Funch
- Section for Genetics, Ecology, and Evolution, Department of Bioscience, Aarhus University, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology & Section for Microbiology, Department of Bioscience, Aarhus University, Denmark
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