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Uniacke-Lowe S, Stanton C, Hill C, Ross RP. The Marine Fish Gut Microbiome as a Source of Novel Bacteriocins. Microorganisms 2024; 12:1346. [PMID: 39065114 PMCID: PMC11278639 DOI: 10.3390/microorganisms12071346] [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: 05/16/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due to the unique environmental pressures these microbial communities experience, the bioactive molecules they produce often evolve unique adaptations that give them diverse structures and activities, differentiating them from terrestrial homologues. Of particular interest, due to their structural and functional diversity, are the ribosomally-synthesized antimicrobial peptides (bacteriocins). With increasing pressure from emerging antibiotic-resistant disease and industrial demand for novel therapeutics, the marine fish gut microbiome represents a relatively untapped resource of novel bacteriocins that could prove beneficial to human health and aquaculture. This review presents an overview of the marine fish gut microbiome and explores its potential as a source of bacteriocins for human health with considerations for applications and future research in this area.
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Affiliation(s)
- Shona Uniacke-Lowe
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
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2
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Lilli G, Sirot C, Campbell H, Hermand F, Brophy D, Flot JF, Graham CT, George IF. Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea. Anim Microbiome 2024; 6:32. [PMID: 38872229 PMCID: PMC11177387 DOI: 10.1186/s42523-024-00319-2] [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: 03/28/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Biogeography has been linked to differences in gut microbiota in several animals. However, the existence of such a relationship in fish is not clear yet. So far, it seems to depend on the fish species studied. However, most studies of fish gut microbiotas are based on single populations. In this study, we investigated the gut microbiota of fish from three wild populations of the two-banded sea bream Diplodus vulgaris (Geoffroy Saint-Hilaire, 1817) to determine whether its diversity, structure and potential functionality reflect the geographic origin of the fish, at large and small geographical scale. Additionally, we explored the host- and environmental-related factors explaining this relationship. RESULTS We showed that the taxonomy and potential functionality of the mucosa-associated gut microbiota of Diplodus vulgaris differ to varying degrees depending on the spatial scale considered. At large scale, we observed that both the taxonomical structure and the potential functionality of the fish microbiota differed significantly between populations. In contrast, the taxonomical diversity of the microbial community displayed a significant relationship with factors other than the geographic origin of the fish (i.e. sampling date). On the other hand, at small scale, the different composition and diversity of the microbiota differ according to the characteristics of the habitat occupied by the fish. Specifically, we identified the presence of Posidonia oceanica in the benthic habitat as predictor of both the microbiota composition and diversity. Lastly, we reported the enrichment of functions related to the metabolism of xenobiotics (i.e. drugs and 4-aminobenzoate) in a population and we indicated it as a potential target of future monitoring. CONCLUSIONS With this study, we confirmed the importance of investigating the gut microbiota of wild fish species using multiple populations, taking into account the different habitats occupied by the individuals. Furthermore, we underscored the use of the biodegradation potential of the gut microbiota as an alternative means of monitoring emerging contaminants in Mediterranean fish.
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Affiliation(s)
- Ginevra Lilli
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium.
| | - Charlotte Sirot
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), University of Perpignan, Perpignan, France
| | - Hayley Campbell
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Fanny Hermand
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Deirdre Brophy
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels - (IB)², 1050, Brussels, Belgium
| | - Conor T Graham
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Isabelle F George
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium
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3
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Varela JL, Nikouli E, Medina A, Papaspyrou S, Kormas K. The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean. Int Microbiol 2024:10.1007/s10123-024-00524-8. [PMID: 38740652 DOI: 10.1007/s10123-024-00524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterial metabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similar and were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.
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Affiliation(s)
- José Luis Varela
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece
| | - Antonio Medina
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Sokratis Papaspyrou
- Department of Biology, University of Cádiz, Puerto Real, 11510, Cádiz, Spain
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46, Volos, Greece.
- Agricultural Development Institute, University Research and Innovation Centre "IASON", Argonafton & Filellinon, 382 21, Volos, Greece.
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4
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Turk-Kubo KA, Gradoville MR, Cheung S, Cornejo-Castillo FM, Harding KJ, Morando M, Mills M, Zehr JP. Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters. FEMS Microbiol Rev 2023; 47:fuac046. [PMID: 36416813 PMCID: PMC10719068 DOI: 10.1093/femsre/fuac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Mary R Gradoville
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Columbia River Inter-Tribal Fish Commission, Portland, OR, United States
| | - Shunyan Cheung
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Francisco M Cornejo-Castillo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
| | - Katie J Harding
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Marine Biology Research Division, Scripps Institute of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Michael Morando
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Matthew Mills
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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5
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Vagelas I, Reizopoulou A, Exadactylos A, Madesis P, Karapetsi L, Michail G. Stalactites Core Prospect as Environmental "Microbial Ark": The Actinomycetota Diversity Paradigm, First Reported from a Greek Cave. Pol J Microbiol 2023; 72:155-168. [PMID: 37314357 DOI: 10.33073/pjm-2023-016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/15/2023] [Indexed: 06/15/2023] Open
Abstract
Speleothems found in caves worldwide are considered the natural libraries of paleontology. Bacteria found in these ecosystems are generally limited to Proteobacteria and Actinomycetota, but rare microbiome and "Dark Matter" is generally under-investigated and often neglected. This research article discusses, for the first time to our knowledge, the diachronic diversity of Actinomycetota entrapped inside a cave stalactite. The planet's environmental microbial community profile of different eras can be stored in these refugia (speleothems). These speleothems could be an environmental "Microbial Ark" storing rare microbiome and "Dark Matter" bacterial communities evermore.
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Affiliation(s)
- Ioannis Vagelas
- 2Laboratory of Plant Pathology, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Angeliki Reizopoulou
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Athanasios Exadactylos
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Panagiotis Madesis
- 3Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Lefkothea Karapetsi
- 3Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
- 4Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), Thessaloniki, Greece
| | - George Michail
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
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6
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Kokate PP, Bales E, Joyner D, Hazen TC, Techtmann SM. Biogeographic patterns in populations of marine Pseudoalteromonas atlantica isolates. FEMS Microbiol Lett 2023; 370:fnad081. [PMID: 37573136 DOI: 10.1093/femsle/fnad081] [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: 04/19/2023] [Revised: 07/14/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023] Open
Abstract
Intra-specific genomic diversity is well documented in microbes. The question, however, remains whether natural selection or neutral evolution is the major contributor to this diversity. We undertook this study to estimate genomic diversity in Pseudoalteromonas atlantica populations and whether the diversity, if present, could be attributed to environmental factors or distance effects. We isolated and sequenced twenty-three strains of P. atlantica from three geographically distant deep marine basins and performed comparative genomic analyses to study the genomic diversity of populations among these basins. Average nucleotide identity followed a strictly geographical pattern. In two out of three locations, the strains within the location exhibited >99.5% identity, whereas, among locations, the strains showed <98.11% identity. Phylogenetic and pan-genome analysis also reflected the biogeographical separation of the strains. Strains from the same location shared many accessory genes and clustered closely on the phylogenetic tree. Phenotypic diversity between populations was studied in ten out of twenty-three strains testing carbon and nitrogen source utilization and osmotolerance. A genetic basis for phenotypic diversity could be established in most cases but was apparently not influenced by local environmental conditions. Our study suggests that neutral evolution may have a substantial role in the biodiversity of P. atlantica.
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Affiliation(s)
- Prajakta P Kokate
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, United States
| | - Erika Bales
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Dominique Joyner
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Terry C Hazen
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, United States
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, United States
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7
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Gallet A, Yao EK, Foucault P, Bernard C, Quiblier C, Humbert JF, Coulibaly JK, Troussellier M, Marie B, Duperron S. Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast). Front Microbiol 2022; 13:963456. [PMID: 36246274 PMCID: PMC9556852 DOI: 10.3389/fmicb.2022.963456] [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: 06/07/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Aghien lagoon (Ivory Coast) is a eutrophic freshwater lagoon that harbors high biomasses of phytoplankton. Despite Increasing interest in fish gut microbiomes diversity and functions, little data is currently available regarding wild species from tropical west African lakes. Here, gut-associated bacterial communities are investigated in four fish species that are consumed by locale populations, namely the Cichlidae Hemichromis fasciatus, Tilapia guineensis and Sarotherodon melanotheron, and the Claroteidae Chrysichthys nigrodigitatus. Species-related differences are identified, that can be attributed to host phylogeny and diet. Important variations throughout the year are observed in T. guineensis and C. nigrodigitatus. This result emphasized the importance of time-series sampling and comparison with environmental variables even in tropical regions, that are not often conducted in wild populations. Effects of environmental factors (anthropogenic or not) on the microbiota and potential outcomes for fish health and populations sustainability need to be further explored. Interestingly, fish appear as major reservoirs of bacterial diversity, suggesting that they could contribute to the overall stability and resilience of bacterial communities present in the Aghien lagoon.
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Affiliation(s)
- Alison Gallet
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Eric Kouamé Yao
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Institut Pasteur de Côte d’Ivoire, Abidjan, Côte d’Ivoire
| | - Pierre Foucault
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Catherine Quiblier
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| | | | | | - Marc Troussellier
- MARBEC, Centre National de la Recherche Scientifique, Université Montpellier, IFREMER, IRD, Montpellier, France
| | - Benjamin Marie
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptation des Micro-Organismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
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8
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Escalas A, Avouac A, Belmaker J, Bouvier T, Clédassou V, Ferraton F, Rieuvilleneuve F, Rilov G, Rovirosa Mulet A, Shapiro Goldberg D, Villéger S. An invasive herbivorous fish (Siganus rivulatus) influences both benthic and planktonic microbes through defecation and nutrient excretion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156207. [PMID: 35636548 DOI: 10.1016/j.scitotenv.2022.156207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 03/23/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Direct and indirect impacts by invasive animals on plants and other animals through predation and competition have been evidenced in many ecosystems. For instance, the rabbitfish Siganus rivulatus, originating from the Red Sea, is now the most abundant species in costal habitats of South-Eastern Mediterranean Sea where it overgrazes algae. However, little is known about its impacts on microbes through release of metabolic wastes and feces. We used a mesocosm experiment to test the effect of S. rivulatus on planktonic and benthic microbial communities. Excretion of dissolved nutrients by fish resulted in higher concentrations of dissolved inorganic nitrogen (NH4, NO2/NO3). This increase in availability of N was associated with higher N content in macroalgae, higher biomass of phytoplankton, higher abundance of bacterioplankton and shift in the structure of planktonic bacterial communities. The feces released mostly under the shelters where the fish rest at night, led to significant increases in diversity of sediment bacterial communities and shifts in their structure. The impact of S. rivulatus on planktonic microbes was related to the indirect bottom-up effect induced by excreted dissolved nutrients while its effect on benthic microbes was due to the direct release of both organic matter and microbes present in feces. Overall, this first evidence of the impacts of invasive species on planktonic and benthic microbes highlights that ongoing changes in fish biodiversity could have ecosystem-wide consequences.
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Affiliation(s)
- Arthur Escalas
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France.
| | - Amandine Avouac
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France
| | - Jonathan Belmaker
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv-Yafo, Israel; The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Thierry Bouvier
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France
| | - Valentin Clédassou
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France
| | - Franck Ferraton
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France
| | | | - Gil Rilov
- National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, Israel
| | | | - Daphna Shapiro Goldberg
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Sébastien Villéger
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Montpellier, France.
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Ghotbi M, Kelting O, Blümel M, Tasdemir D. Gut and Gill-Associated Microbiota of the Flatfish European Plaice ( Pleuronectes platessa): Diversity, Metabolome and Bioactivity against Human and Aquaculture Pathogens. Mar Drugs 2022; 20:md20090573. [PMID: 36135762 PMCID: PMC9500656 DOI: 10.3390/md20090573] [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: 07/19/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Similar to other marine holobionts, fish are colonized by complex microbial communities that promote their health and growth. Fish-associated microbiota is emerging as a promising source of bioactive metabolites. Pleuronectes platessa (European plaice, plaice), a flatfish with commercial importance, is common in the Baltic Sea. Here we used a culture-dependent survey followed by molecular identification to identify microbiota associated with the gills and the gastrointestinal tract (GIT) of P. platessa, then profiled their antimicrobial activity and metabolome. Altogether, 66 strains (59 bacteria and 7 fungi) were isolated, with Proteobacteria being the most abundant phylum. Gill-associated microbiota accounted for higher number of isolates and was dominated by the Proteobacteria (family Moraxellaceae) and Actinobacteria (family Nocardiaceae), whereas Gram-negative bacterial families Vibrionaceae and Shewanellaceae represented the largest group associated with the GIT. The EtOAc extracts of the solid and liquid media cultures of 21 bacteria and 2 fungi representing the diversity of cultivable plaice-associated microbiota was profiled for their antimicrobial activity against three fish pathogens, human bacterial pathogen panel (ESKAPE) and two human fungal pathogens. More than half of all tested microorganisms, particularly those originating from the GIT epithelium, exhibited antagonistic effect against fish pathogens (Lactococcus garvieae, Vibrio ichthyoenteri) and/or human pathogens (Enterococcus faecium, methicillin-resistant Staphylococcus aureus). Proteobacteria represented the most active isolates. Notably, the solid media extracts displayed higher activity against fish pathogens, while liquid culture extracts were more active against human pathogens. Untargeted metabolomics approach using feature-based molecular networking showed the high chemical diversity of the liquid extracts that contained undescribed clusters. This study highlights plaice-associated microbiota as a potential source of antimicrobials for the control of human and the aquaculture-associated infections. This is the first study reporting diversity, bioactivity and chemical profile of culture-dependent microbiota of plaice.
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Affiliation(s)
- Marjan Ghotbi
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Ole Kelting
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
- Correspondence: ; Tel.: +49-431-600-4430
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10
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Sukmarini L. Marine Bacterial Ribosomal Peptides: Recent Genomics- and Synthetic Biology-Based Discoveries and Biosynthetic Studies. Mar Drugs 2022; 20:md20090544. [PMID: 36135733 PMCID: PMC9505594 DOI: 10.3390/md20090544] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/27/2022] Open
Abstract
Marine biodiversity is represented by an exceptional and ample array of intriguing natural product chemistries. Due to their extensive post-translational modifications, ribosomal peptides—also known as ribosomally synthesized and post-translationally modified peptides (RiPPs)—exemplify a widely diverse class of natural products, endowing a broad range of pharmaceutically and biotechnologically relevant properties for therapeutic or industrial applications. Most RiPPs are of bacterial origin, yet their marine derivatives have been quite rarely investigated. Given the rapid advancement engaged in a more powerful genomics approach, more biosynthetic gene clusters and pathways for these ribosomal peptides continue to be increasingly characterized. Moreover, the genome-mining approach in integration with synthetic biology techniques has markedly led to a revolution of RiPP natural product discovery. Therefore, this present short review article focuses on the recent discovery of RiPPs from marine bacteria based on genome mining and synthetic biology approaches during the past decade. Their biosynthetic studies are discussed herein, particularly the organization of targeted biosynthetic gene clusters linked to the encoded RiPPs with potential bioactivities.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Bogor, Km. 46, Cibinong 16911, West Java, Indonesia
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11
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Ramalingam V, Rajaram R, Archunan G, Padmanabhan P, Gulyás B. Structural Characterization, Antimicrobial, Antibiofilm, Antioxidant, Anticancer and Acute Toxicity Properties of N-(2-hydroxyphenyl)-2-phenazinamine From Nocardiopsis exhalans (KP149558). Front Cell Infect Microbiol 2022; 12:794338. [PMID: 35663469 PMCID: PMC9161293 DOI: 10.3389/fcimb.2022.794338] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
The present study aimed to isolate and identify potential drugs from marine actinomycete Nocardiopsis exhalans and screen them for biomedical applications. The cell-free culture of N. exhalans was extracted with ethyl acetate and the solvent extract showed six fractions in thin-layer chromatography. The fractions were subjected to column chromatography for purification and evaluated for activity against human clinical pathogens. Fraction 4 showed significant activity and was identified as N-(2-hydroxyphenyl)-2-phenazinamine (NHP) using spectral analyses. Further, NHP showed excellent biofilm inhibitory activity against human clinical pathogens Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. The in vitro antioxidant activity confirmed that NHP is scavenging the oxidative stress-enhancing molecules. The anti-proliferative activity of NHP against human breast cancer cells showed significant activity at 300 µg/ml and less cytotoxic activity against normal cells. Additionally, the toxicity assessment against zebrafish revealed that NHP does not cause any toxicity in the important organs. The results highlight N. exhalans as a promising candidate for the development of antibiotics with potential therapeutic applications.
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Affiliation(s)
- Vaikundamoorthy Ramalingam
- Centre for Natural Products and Traditional Knowledge, Indian Institute of Chemical Technology, Hyderabad, India
- DNA Barcoding and Marine Genomics Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, India
- *Correspondence: Vaikundamoorthy Ramalingam, ; Parasuraman Padmanabhan,
| | - Rajendran Rajaram
- DNA Barcoding and Marine Genomics Lab, Department of Marine Science, Bharathidasan University, Tiruchirappalli, India
| | - Govindaraju Archunan
- Department of Animal Science, Bharathidasan University Tiruchirappalli, Tamil Nadu, India
- Dean of Research, Marudupandiyar College, Thanjavur, India
| | - Parasuraman Padmanabhan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Cognitive Neuroimaging Centre, Nanyang Technological University, Nanyang Technological University, Singapore, Singapore
- Imaging Probe Development Platform (IPDP), Nanyang Technological University, Singapore, Singapore
- *Correspondence: Vaikundamoorthy Ramalingam, ; Parasuraman Padmanabhan,
| | - Balázs Gulyás
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Cognitive Neuroimaging Centre, Nanyang Technological University, Nanyang Technological University, Singapore, Singapore
- Imaging Probe Development Platform (IPDP), Nanyang Technological University, Singapore, Singapore
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12
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Yang H, Wu J, Du H, Zhang H, Li J, Wei Q. Quantifying the Colonization of Environmental Microbes in the Fish Gut: A Case Study of Wild Fish Populations in the Yangtze River. Front Microbiol 2022; 12:828409. [PMID: 35250916 PMCID: PMC8891936 DOI: 10.3389/fmicb.2021.828409] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/28/2021] [Indexed: 01/10/2023] Open
Abstract
In aquatic animals, gut microbial communities shift with host development and living environments. Understanding the mechanism by which the environment impacts the gut microbial communities of aquatic animals is crucial for assessing and managing aquatic ecosystem health. Here, we proposed a simplified framework for the colonization and dynamics of gut microbial communities. Then, to quantify the colonization of environmental microbes in the wild fish gut, the current study used 16S rRNA gene amplicon sequencing to obtain the structure of the water environmental microbial community and the gut microbial community in 10 wild fish populations (Leiocassis crassilabris, Leiocassis longirostris, Pelteobagrus vachelli, Silurus asotus, Siniperca chuatsi, Coilia brachygnathus, Aristichthys nobilis, Hypophthalmichthys molitrix, Coreius heterodon, and Xenocypris argentea) from the Wuhan section of the Yangtze River, and the relationship of these microbial communities was analyzed. The results identified that in most individuals, approximately 80% of gut microbes [at the operational taxonomic unit (OTU) level] were shared with the water environmental microbial community (except for individuals of Siniperca chuatsi and Coilia brachygnathus, approximately 74%). In approximately 80% of individuals, more than 95% of microbial species (OTUs) in the gut were transient. For fish species, more than 99% of microbial species (OTUs) that were introduced into the gut were transient. Nearly 79% of OTUs and 89% of species of water environmental microbes could be introduced into the fish gut. Driven by the introduction of transient microbes, fishes with similar feeding habits had similar gut microbial communities. The results indicated that for adult wild fishes, most gut microbiota were transient from the environmental microbiota that were related to fish feeding habits. We therefore encourage future research to focus on environmental microbiota monitoring and management to promote the better conservation of aquatic animals. It was important to note that, because of various influence factors, interspecific differences and individual variations on gut microbial community characteristics, the quantification of gut microbes in the current work was approximate rather than accurate. We hope that more comparable research could be conducted to outline the quantitative characteristics of the relationship between gut microbial community and aquatic environment microbial community as soon as possible.
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Affiliation(s)
- Haile Yang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jinming Wu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Hui Zhang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Junyi Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Qiwei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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13
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Jin X, Chen Z, Shi Y, Gui J, Zhao Z. Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus. Microb Biotechnol 2022; 15:683-702. [PMID: 33393737 PMCID: PMC8867974 DOI: 10.1111/1751-7915.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 02/06/2023] Open
Abstract
Environmental bacteria have a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to the disturbance from environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon the hindgut microbiota of cultured fugu. Consequently, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, implying a reduced stability upon bacterial disturbance from feed. Moreover, quantitative ecological analyses indicated that homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts in the context of lower degree of disturbance. While the disturbance peaked, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Our findings emphasized the intricate linkage between feed and gut microbiota and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.
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Affiliation(s)
- Xingkun Jin
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
| | - Ziwei Chen
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
| | - Yan Shi
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
| | - Jian‐Fang Gui
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
- State Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of HydrobiologyThe Innovation Academy of Seed DesignChinese Academy of SciencesWuhan430072China
| | - Zhe Zhao
- Department of Marine BiologyCollege of OceanographyHohai UniversityNanjing210098China
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14
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Escalas A, Troussellier M, Melayah D, Bruto M, Nicolas S, Bernard C, Ader M, Leboulanger C, Agogué H, Hugoni M. Strong reorganization of multi-domain microbial networks associated with primary producers sedimentation from oxic to anoxic conditions in an hypersaline lake. FEMS Microbiol Ecol 2021; 97:6464137. [PMID: 34918080 DOI: 10.1093/femsec/fiab163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/14/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the role of microbial interactions in the functioning of natural systems is often impaired by the levels of complexity they encompass. In this study, we used the relative simplicity of an hypersaline crater lake hosting only microbial organisms (Dziani Dzaha) to provide a detailed analysis of the microbial networks including the three domains of life. We identified two main ecological zones, one euphotic and oxic zone in surface, where two phytoplanktonic organisms produce a very high biomass, and one aphotic and anoxic deeper zone, where this biomass slowly sinks and undergoes anaerobic degradation. We highlighted strong differences in the structure of microbial communities from the two zones and between the microbial consortia associated with the two primary producers. Primary producers sedimentation was associated with a major reorganization of the microbial network at several levels: global properties, modules composition, nodes and links characteristics. We evidenced the potential dependency of Woesearchaeota to the primary producers' exudates in the surface zone, and their disappearance in the deeper anoxic zone, along with the restructuration of the networks in the anoxic zone toward the decomposition of the organic matter. Altogether, we provided an in-depth analysis of microbial association network and highlighted putative changes in microbial interactions supporting the functioning of the two ecological zones in this unique ecosystem.
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Affiliation(s)
- Arthur Escalas
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Marc Troussellier
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Delphine Melayah
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Maxime Bruto
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Sébastien Nicolas
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Cécile Bernard
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, CP 39, 75005 Paris, France
| | - Magali Ader
- Université de Paris, Institut de physique du globe de Paris, CNRS, 75005 Paris, France
| | - Christophe Leboulanger
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Hélène Agogué
- Littoral Environnement et Sociétés (LIENSs) UMR 7266 CNRS -La Rochelle Université, 17000 La Rochelle, France
| | - Mylène Hugoni
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France.,Institut Universitaire de France (IUF)
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15
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Michail G, Karapetsi L, Madesis P, Reizopoulou A, Vagelas I. Metataxonomic Analysis of Bacteria Entrapped in a Stalactite's Core and Their Possible Environmental Origins. Microorganisms 2021; 9:microorganisms9122411. [PMID: 34946013 PMCID: PMC8705861 DOI: 10.3390/microorganisms9122411] [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: 10/26/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 02/02/2023] Open
Abstract
Much is known about microbes originally identified in caves, but little is known about the entrapment of microbes (bacteria) in stalactites and their possible environmental origins. This study presents data regarding the significant environmental distribution of prokaryotic bacterial taxa of a Greek stalactite core. We investigated the involvement of those bacteria communities in stalactites using a metataxonomic analysis approach of partial 16S rRNA genes. The metataxonomic analysis of stalactite core material revealed an exceptionally broad ecological spectrum of bacteria classified as members of Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and other unclassified bacteria. We concluded that (i) the bacterial transport process is possible through water movement from the upper ground cave environment, forming cave speleothems such as stalactites, (ii) bacterial genera such as Polaromonas, Thioprofundum, and phylum Verrucomicrobia trapped inside the stalactite support the paleoecology, paleomicrobiology, and paleoclimate variations, (iii) the entrapment of certain bacteria taxa associated with water, soil, animals, and plants such as Micrococcales, Propionibacteriales, Acidimicrobiales, Pseudonocardiales, and α-, β-, and γ-Proteobacteria.
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Affiliation(s)
- George Michail
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
- Correspondence:
| | - Lefkothea Karapetsi
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (L.K.); (P.M.)
- Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), 57001 Thessaloniki, Greece
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (L.K.); (P.M.)
- Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), 57001 Thessaloniki, Greece
| | | | - Ioannis Vagelas
- Department of Agriculture Crop Production and Rural Environment, University of Thessaly, 38446 Volos, Greece;
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16
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Huang Z, Hou D, Zhou R, Zeng S, Xing C, Wei D, Deng X, Yu L, Wang H, Deng Z, Weng S, Ning D, Xiao C, Yan Q, Zhou J, He Z, He J. Environmental Water and Sediment Microbial Communities Shape Intestine Microbiota for Host Health: The Central Dogma in an Anthropogenic Aquaculture Ecosystem. Front Microbiol 2021; 12:772149. [PMID: 34795658 PMCID: PMC8593368 DOI: 10.3389/fmicb.2021.772149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/08/2021] [Indexed: 12/22/2022] Open
Abstract
From increasing evidence has emerged a tight link among the environment, intestine microbiota, and host health status; moreover, the microbial interaction in different habitats is crucial for ecosystems. However, how the environmental microbial community assembly governs the intestinal microbiota and microbial communities of multiple habitats contribute to the metacommunity remain elusive. Here, we designed two delicate experiments from temporal and spatial scales in a shrimp culture pond ecosystem (SCPE). Of the SCPE metacommunity, the microbial diversity was mainly contributed to by the diversity of–βIntraHabitats and βInterHabitats, and water and sediment communities had a large contribution to the shrimp intestine community as shown by SourceTracker and Sloan neutral community model analyses. Also, phylogenetic bin-based null model results show that microbial assembly of three habitats in the SCPE appeared to be largely driven by stochastic processes. These results enrich our understanding of the environment–intestinal microbiota–host health closely linked relationship, making it possible to be the central dogma for an anthropogenic aquaculture ecosystem. Our findings enhance the mechanistic understanding of microbial assembly in the SCPE for further analyzing metacommunities, which has important implications for microbial ecology and animal health.
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Affiliation(s)
- Zhijian Huang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Renjun Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chengguang Xing
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongdong Wei
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xisha Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lingfei Yu
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Wang
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhixuan Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, School of Civil Engineering and Environmental Sciences, The University of Oklahoma, Norman, OK, United States
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Jizhong Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, School of Civil Engineering and Environmental Sciences, The University of Oklahoma, Norman, OK, United States
| | - Zhili He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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17
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Hörstmann C, Buttigieg PL, John U, Raes EJ, Wolf-Gladrow D, Bracher A, Waite AM. Microbial diversity through an oceanographic lens: refining the concept of ocean provinces through trophic-level analysis and productivity-specific length scales. Environ Microbiol 2021; 24:404-419. [PMID: 34766422 DOI: 10.1111/1462-2920.15832] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023]
Abstract
In the marine realm, microorganisms are responsible for the bulk of primary production, thereby sustaining marine life across all trophic levels. Longhurst provinces have distinct microbial fingerprints; however, little is known about how microbial diversity and primary productivity change at finer spatial scales. Here, we sampled the Atlantic Ocean from south to north (~50°S-50°N), every ~0.5° latitude. We conducted measurements of primary productivity, chlorophyll-a and relative abundance of 16S and 18S rRNA genes, alongside analyses of the physicochemical and hydrographic environment. We analysed the diversity of autotrophs, mixotrophs and heterotrophs, and noted distinct patterns among these guilds across provinces with high and low chlorophyll-a conditions. Eukaryotic autotrophs and prokaryotic heterotrophs showed a shared inter-province diversity pattern, distinct from the diversity pattern shared by mixotrophs, cyanobacteria and eukaryotic heterotrophs. Additionally, we calculated samplewise productivity-specific length scales, the potential horizontal displacement of microbial communities by surface currents to an intrinsic biological rate (here, specific primary productivity). This scale provides key context for our trophically disaggregated diversity analysis that we could relate to underlying oceanographic features. We integrate this element to provide more nuanced insights into the mosaic-like nature of microbial provincialism, linking diversity patterns to oceanographic transport through primary production.
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Affiliation(s)
- Cora Hörstmann
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany.,Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, Germany
| | | | - Uwe John
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Eric J Raes
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Dieter Wolf-Gladrow
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany
| | - Astrid Bracher
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Science, Bremerhaven, Germany.,Institute of Environmental Physics, University of Bremen, Bremen, Germany
| | - Anya M Waite
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada
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18
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Osvatic JT, Wilkins LGE, Leibrecht L, Leray M, Zauner S, Polzin J, Camacho Y, Gros O, van Gils JA, Eisen JA, Petersen JM, Yuen B. Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups. Proc Natl Acad Sci U S A 2021; 118:e2104378118. [PMID: 34272286 PMCID: PMC8307296 DOI: 10.1073/pnas.2104378118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the ocean, most hosts acquire their symbionts from the environment. Due to the immense spatial scales involved, our understanding of the biogeography of hosts and symbionts in marine systems is patchy, although this knowledge is essential for understanding fundamental aspects of symbiosis such as host-symbiont specificity and evolution. Lucinidae is the most species-rich and widely distributed family of marine bivalves hosting autotrophic bacterial endosymbionts. Previous molecular surveys identified location-specific symbiont types that "promiscuously" form associations with multiple divergent cooccurring host species. This flexibility of host-microbe pairings is thought to underpin their global success, as it allows hosts to form associations with locally adapted symbionts. We used metagenomics to investigate the biodiversity, functional variability, and genetic exchange among the endosymbionts of 12 lucinid host species from across the globe. We report a cosmopolitan symbiont species, Candidatus Thiodiazotropha taylori, associated with multiple lucinid host species. Ca. T. taylori has achieved more success at dispersal and establishing symbioses with lucinids than any other symbiont described thus far. This discovery challenges our understanding of symbiont dispersal and location-specific colonization and suggests both symbiont and host flexibility underpin the ecological and evolutionary success of the lucinid symbiosis.
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Affiliation(s)
- Jay T Osvatic
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Laetitia G E Wilkins
- Genome and Biomedical Sciences Facility, Genome Center, University of California, Davis, CA 95616
- Department of Symbiosis, Max Planck Institute for Marine Microbiology, 28209 Bremen, Germany
| | - Lukas Leibrecht
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Republic of Panama
| | - Sarah Zauner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Julia Polzin
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Yolanda Camacho
- Centro de Investigación en Ciencias del Mar y Limnología, Escuela de Biología, Universidad de Costa Rica, San Pedro 11501-2060, Costa Rica
| | - Olivier Gros
- UMR 7205, Institut de Systématique, Évolution, Biodiversité, Equipe Biologie de la Mangrove, Département de Biologie, Université des Antilles, 97159 Pointe-à-Pitre Cedex, Guadeloupe
| | - Jan A van Gils
- Royal Netherlands Institute for Sea Research,1790 AB Den Burg, The Netherlands
| | - Jonathan A Eisen
- Genome and Biomedical Sciences Facility, Genome Center, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
- Department of Medical Microbiology and Immunology, University of California, Davis, CA 95616
| | - Jillian M Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria;
| | - Benedict Yuen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria;
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19
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The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View. BIOLOGY 2021; 10:biology10070651. [PMID: 34356506 PMCID: PMC8301382 DOI: 10.3390/biology10070651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022]
Abstract
Simple Summary This interdisciplinary study, conducted by experts in evolutionary biology, ecology, ecosystem studies, arts, medicine, forensic analyses, agriculture, law, and philosophy of science describe how microbiome studies are convergently affecting the concepts and practices of diverse fields and practices, that now consider microbiomes within their legitimate scope. Consequently, it describes what seems to be an ongoing pluridisciplinary epistemic revolution, with the potential to fundamentally change how we understand the world through an ecologization of pre-existing concepts, a greater focus on interactions, the use of multi-scalar interaction networks as explanatory frameworks, the reconceptualization of the usual definitions of individuals, and a de-anthropocentrification of our perception of phenomena. Abstract Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An ‘epistemic revolution induced by microbiome studies’ seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use openly multi-scalar interaction networks as an explanatory framework to investigate phenomena to acknowledge the causal effects of microbiomes, (iv) a reconceptualization of the usual definitions of which individuals are worth considering as an explanans or as an explanandum by a given field, which result in a fifth strong trend, namely (v) a de-anthropocentrification of our perception of the world.
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Pascoal F, Costa R, Magalhães C. The microbial rare biosphere: current concepts, methods and ecological principles. FEMS Microbiol Ecol 2021; 97:5974270. [PMID: 33175111 DOI: 10.1093/femsec/fiaa227] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1049-001, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, CA 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, CA 94720 Berkeley, USA
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,School of Science, University of Waikato, Gate 1, Knighton Road 3240, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Steele Ocean Sciences Building, Dalhousie University 1355 Oxford St., B3H4R2 Halifax, NS, Canada
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21
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Thompson AW, Ward AC, Sweeney CP, Sutherland KR. Host-specific symbioses and the microbial prey of a pelagic tunicate (Pyrosoma atlanticum). ISME COMMUNICATIONS 2021; 1:11. [PMID: 36721065 PMCID: PMC9723572 DOI: 10.1038/s43705-021-00007-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/12/2021] [Accepted: 02/24/2021] [Indexed: 02/03/2023]
Abstract
Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. This is the first study of the marine microorganisms associated with pyrosomes undertaken to improve the understanding of pyrosome biology, the impact of pyrosome blooms on marine microbial systems, and microbial symbioses with marine animals. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry. We found that pyrosomes harbor a microbiome distinct from the surrounding seawater, which was dominated by a few novel taxa. In addition to the dominant taxa, numerous more rare pyrosome-specific microbial taxa were recovered. Multiple bioluminescent taxa were present in pyrosomes, which may be a source of the iconic pyrosome luminescence. We also discovered free-living marine microorganisms in association with pyrosomes, suggesting that pyrosome feeding impacts all microbial size classes but preferentially removes larger eukaryotic taxa. This study demonstrates that microbial symbionts and microbial prey are central to pyrosome biology. In addition to pyrosome impacts on higher trophic level marine food webs, the work suggests that pyrosomes also alter marine food webs at the microbial level through feeding and seeding of the marine microbial communities with their symbionts. Future efforts to predict pyrosome blooms, and account for their ecosystem impacts, should consider pyrosome interactions with marine microbial communities.
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Affiliation(s)
- Anne W Thompson
- Department of Biology, Portland State University, Portland, OR, USA.
| | - Anna C Ward
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR, USA
| | - Carey P Sweeney
- Department of Biology, Portland State University, Portland, OR, USA
| | - Kelly R Sutherland
- Oregon Institute of Marine Biology, University of Oregon, Eugene, OR, USA
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22
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Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 2021; 9:e10911. [PMID: 33665032 PMCID: PMC7916533 DOI: 10.7717/peerj.10911] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/16/2021] [Indexed: 12/19/2022] Open
Abstract
Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
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Affiliation(s)
- Simon M Dittami
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Enrique Arboleda
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Arite Bigalke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, Nantes, France
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ulisse Cardini
- Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Johan Decelle
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France
| | | | - Damien Eveillard
- Laboratoire des Sciences Numériques de Nantes (LS2N), Université de Nantes, CNRS, Nantes, France
| | - Claire M M Gachon
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, United Kingdom
| | - Sarah M Griffiths
- School of Science and the Environment, Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Ehsan Kayal
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - François H Lallier
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Ezequiel M Marzinelli
- Ecology and Environment Research Centre, The University of Sydney, Sydney, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Sydney Institute of Marine Science, Mosman, Australia
| | | | - Laura Núñez Pons
- Section Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Soizic Prado
- Molecules of Communication and Adaptation of Microorganisms (UMR 7245), National Museum of Natural History, CNRS, Paris, France
| | - José Pintado
- Instituto de Investigaciones Marinas, CSIC, Vigo, Spain
| | - Mahasweta Saha
- Benthic Ecology, Helmholtz Center for Ocean Research, Kiel, Germany.,Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - Marc-André Selosse
- National Museum of Natural History, Département Systématique et Evolution, Paris, France.,Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Derek Skillings
- Philosophy Department, University of Pennsylvania, Philadelphia, United States of America
| | - Willem Stock
- Laboratory of Protistology & Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinichi Sunagawa
- Dept. of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH, Zürich, Switzerland
| | - Eve Toulza
- IHPE, Univ. de Montpellier, CNRS, IFREMER, UPDV, Perpignan, France
| | - Alexey Vorobev
- CEA - Institut de Biologie François Jacob, Genoscope, Evry, France
| | - Catherine Leblanc
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Fabrice Not
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
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Streptococcal Infections in Marine Mammals. Microorganisms 2021; 9:microorganisms9020350. [PMID: 33578962 PMCID: PMC7916692 DOI: 10.3390/microorganisms9020350] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 02/07/2021] [Indexed: 01/28/2023] Open
Abstract
Marine mammals are sentinels for the marine ecosystem and threatened by numerous factors including infectious diseases. One of the most frequently isolated bacteria are beta-hemolytic streptococci. However, knowledge on ecology and epidemiology of streptococcal species in marine mammals is very limited. This review summarizes published reports on streptococcal species, which have been detected in marine mammals. Furthermore, we discuss streptococcal transmission between and adaptation to their marine mammalian hosts. We conclude that streptococci colonize and/or infect marine mammals very frequently, but in many cases, streptococci isolated from marine mammals have not been further identified. How these bacteria disseminate and adapt to their specific niches can only be speculated due to the lack of respective research. Considering the relevance of pathogenic streptococci for marine mammals as part of the marine ecosystem, it seems that they have been neglected and should receive scientific interest in the future.
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24
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Neu AT, Hughes IV, Allen EE, Roy K. Decade-scale stability and change in a marine bivalve microbiome. Mol Ecol 2021; 30:1237-1250. [PMID: 33432685 DOI: 10.1111/mec.15796] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]
Abstract
Predicting how populations and communities of organisms will respond to anthropogenic change is of paramount concern in ecology today. For communities of microorganisms, however, these predictions remain challenging, primarily due to data limitations. Information about long-term dynamics of host-associated microbial communities, in particular, is lacking. In this study, we use well-preserved and freshly collected samples of soft tissue from a marine bivalve host, Donax gouldii, at a single site to quantify the diversity and composition of its microbiome over a decadal timescale. Site-level measurements of temperature, salinity and chlorophyll a allowed us to test how the microbiome of this species responded to two natural experiments: a seasonal increase in temperature and a phytoplankton bloom. Our results show that ethanol-preserved tissue can provide high-resolution information about temporal trends in compositions of host-associated microbial communities. Specifically, we found that the richness of amplicon sequence variants (ASVs) associated with D.gouldii did not change significantly over time despite increases in water temperature (+1.6°C due to seasonal change) and chlorophyll a concentration (more than ninefold). The phylogenetic composition of the communities, on the other hand, varied significantly between all collection years, with only six ASVs persisting over our sampling period. Overall, these results suggest that the diversity of microbial taxa associated with D.gouldii has remained stable over time and in response to seasonal environmental change over the course of more than a decade, but such stability is underlain by substantial turnover in the composition of the microbiome.
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Affiliation(s)
- Alexander T Neu
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ian V Hughes
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.,Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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25
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Gould AL, Fritts-Penniman A, Gaisiner A. Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish. Front Ecol Evol 2021; 9:630207. [PMID: 34485316 PMCID: PMC8412414 DOI: 10.3389/fevo.2021.630207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Symbiotic relationships between bioluminescent bacteria and fishes have evolved multiple times across hundreds of fish taxa, but relatively little is known about the specificity of these associations and how stable they are over host generations. This study describes the degree of specificity of a bioluminescent symbiosis between cardinalfishes in the genus Siphamia and luminous bacteria in the Vibrio family. Primarily using museum specimens, we investigated the codivergence of host and symbiont and test for patterns of divergence that correlate with both biogeography and time. Contrary to expectations, we determined that the light organ symbionts of all 14 Siphamia species examined belong to one genetic clade of Photobacterium mandapamensis (Clade II), indicating that the association is highly specific and conserved throughout the host genus. Thus, we did not find evidence of codivergence among hosts and symbionts. We did observe that symbionts hosted by individuals sampled from colder water regions were more divergent, containing more than three times as many single nucleotide polymorphisms than the rest of the symbionts examined. Overall, our findings indicate that the symbiosis between Siphamia fishes and P. mandapamensis Clade II has been highly conserved across host taxa and over a broad geographic range despite the facultative nature of the bacterial symbiont. We also present a new approach to simultaneously recover genetic information from a bacterial symbiont and its vertebrate host from formalin-fixed specimens, enhancing the utility of museum collections.
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Affiliation(s)
- Alison L. Gould
- California Academy of Sciences, San Francisco, CA, United States
| | | | - Ana Gaisiner
- California Academy of Sciences, San Francisco, CA, United States
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26
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Takeshita N, Watanabe T, Ishida-Kuroki K, Sekizaki T. Transition of microbiota in chicken cecal droppings from commercial broiler farms. BMC Vet Res 2021; 17:10. [PMID: 33407476 PMCID: PMC7789685 DOI: 10.1186/s12917-020-02688-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 11/23/2020] [Indexed: 11/11/2022] Open
Abstract
Background Chickens are major sources of human nutrition worldwide, but the chicken intestinal microbiota can be a source of bacterial infection. The microbiota has potential to regulate the colonization of pathogens by competitive exclusion, production of antimicrobial compounds, and stimulation of the mucosal immune system. But information on the microbiota in commercial broiler chickens is limited because of the difficulty of conducting studies at commercial farms. To obtain fundamental information that can be used to control pathogens in chickens, we determined the 6-week dynamics of microbiota in chicken cecal droppings from commercial broiler farms. Results Cecal droppings from four chickens were collected once a week from 1 to 6 weeks of age at three commercial broiler farms. A total of 168 samples were collected from 7 flocks and subjected to 16S rRNA amplicon sequencing. Despite the farms have distinctly different climate conditions, the microbiota in the same growth stages were similar among farms. Moreover, as the chickens grew and the feed types were switched, the richness and diversity of the microbiota gradually increased and convergence of the composition of the microbiota was apparent. Notably, minor bacterial taxa (i.e. OTUs with relative abundance < 0.05%) within the microbiota were changed by the chicken age, switching of feed types, and presence of Campylobacter. In particular, the effects of switching of feed types on the microbiota were larger than the effects of age and Campylobacter. Conclusions Irrespective of the locations of the farms, the microbiota of chicken cecum, especially minor bacteria, was successively changed more affected by feed types than by ages. Switching of feed types inducing the alteration of the microbiota may be associated with the colonization of pathogens in the chicken gut. These results will also help with extrapolation of studies in experimental animals to those in the commercial farms. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-020-02688-7.
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Affiliation(s)
- Nachiko Takeshita
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takayasu Watanabe
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.,Present Address: Department of Chemistry, Nihon University School of Dentistry, Kanda-Surugadai 1-8-13, Chiyoda-ku, Tokyo, 101-8310, Japan
| | - Kasumi Ishida-Kuroki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tsutomu Sekizaki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
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27
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Mestre M, Höfer J. The Microbial Conveyor Belt: Connecting the Globe through Dispersion and Dormancy. Trends Microbiol 2020; 29:482-492. [PMID: 33281016 DOI: 10.1016/j.tim.2020.10.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022]
Abstract
Despite the recent increase in knowledge concerning microorganisms, the processes determining their global distribution and functioning have not been disentangled. Microbial dormant stages are adapted to endure specific adverse conditions related to their dispersion path, suggesting that dispersion is not entirely a stochastic process. Long-term dormancy enhances microbial dispersion, promoting the ubiquity of microorganisms. The evidence leads us to propose that there is a global, recurrent, and spatially cyclical dispersion of microorganisms that we have called the Microbial Conveyor Belt. These dispersion cycles directly influence the distribution of microorganisms, the global cycling of inorganic and organic matter, and thus the Earth system's functioning.
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Affiliation(s)
- Mireia Mestre
- Centro de Investigación Oceanográfica COPAS Sur-Austral, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile; Centro FONDAP de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile.
| | - Juan Höfer
- Centro FONDAP de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile; Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile; Centro de Investigación y Formación San Ignacio de Huinay, Huinay, Chile.
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28
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Panteli N, Mastoraki M, Nikouli E, Lazarina M, Antonopoulou E, Kormas KA. Imprinting statistically sound conclusions for gut microbiota in comparative animal studies: A case study with diet and teleost fishes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100738. [PMID: 32896688 DOI: 10.1016/j.cbd.2020.100738] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Despite the technical progress in high-throughput sequencing technologies, defining the sample size which is capable of yielding representative inferences in metabarcoding analysis still remains debatable. The present study addresses the influence of individual variability in assessing dietary effects on fish gut microbiota parameters and estimates the biological sample size that is sufficient to imprint a statistically secure outcome. European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata) were fed three alternative animal protein diets and a fishmeal control diet. Gut microbiota data from 12 individuals per diet, derived from Illumina sequencing of the V3-V4 region of the 16S rRNA gene, were randomized in all possible combinations of n-1 individuals. Results in this study showcased that increasing the sample size can limit the prevalence of individuals with high microbial load on the outcome and can ensure the statistical confidence required for an accurate validation of dietary-induced microbe shifts. Inter-individual variability was evident in the four dietary treatments where consequently misleading inferences arose from insufficient biological replication. These findings have critical implications for the design of future metabarcoding studies and highlight the urgency in selecting an adequate sample size able to safely elucidate the dietary effects on fish gut microbial communities.
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Affiliation(s)
- Nikolas Panteli
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Maria Mastoraki
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Maria Lazarina
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece.
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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Biagi E, Caroselli E, Barone M, Pezzimenti M, Teixido N, Soverini M, Rampelli S, Turroni S, Gambi MC, Brigidi P, Goffredo S, Candela M. Patterns in microbiome composition differ with ocean acidification in anatomic compartments of the Mediterranean coral Astroides calycularis living at CO 2 vents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:138048. [PMID: 32251879 DOI: 10.1016/j.scitotenv.2020.138048] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
Coral microbiomes, the complex microbial communities associated with the different anatomic compartments of the coral, provide important functions for the host's survival, such as nutrient cycling at the host's surface, prevention of pathogens colonization, and promotion of nutrient uptake. Microbiomes are generally referred to as plastic entities, able to adapt their composition and functionality in response to environmental change, with a possible impact on coral acclimatization to phenomena related to climate change, such as ocean acidification. Ocean sites characterized by natural gradients of pCO2 provide models for investigating the ability of marine organisms to acclimatize to decreasing seawater pH. Here we compared the microbiome of the temperate, shallow water, non-symbiotic solitary coral Astroides calycularis that naturally lives at a volcanic CO2 vent in Ischia Island (Naples, Italy), with that of corals living in non-acidified sites at the same island. Bacterial DNA associated with the different anatomic compartments (mucus, tissue and skeleton) of A. calycularis was differentially extracted and a total of 68 samples were analyzed by 16S rRNA gene sequencing. In terms of phylogenetic composition, the microbiomes associated with the different coral anatomic compartments were different from each other and from the microbial communities of the surrounding seawater. Of all the anatomic compartments, the mucus-associated microbiome differed the most between the control and acidified sites. The differences detected in the microbial communities associated to the three anatomic compartments included a general increase in subdominant bacterial groups, some of which are known to be involved in different stages of the nitrogen cycle, such as potential nitrogen fixing bacteria and bacteria able to degrade organic nitrogen. Our data therefore suggests a potential increase of nitrogen fixation and recycling in A. calycularis living close to the CO2 vent system.
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Affiliation(s)
- Elena Biagi
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Erik Caroselli
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032 Fano, Pesaro Urbino, Italy
| | - Monica Barone
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Martina Pezzimenti
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Nuria Teixido
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, 181 chemin du Lazaret, F-06230 Villefranche-sur-Mer, France; Villa Dohrn-Benthic Ecology Center, Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80077 Ischia (Naples), Italy
| | - Matteo Soverini
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Simone Rampelli
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Silvia Turroni
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Maria Cristina Gambi
- Villa Dohrn-Benthic Ecology Center, Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80077 Ischia (Naples), Italy
| | - Patrizia Brigidi
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Stefano Goffredo
- Marine Science Group, Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032 Fano, Pesaro Urbino, Italy.
| | - Marco Candela
- Unit of Holobiont Microbiome and Microbiome Engineering (HolobioME), Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, viale Adriatico 1/N, 61032 Fano, Pesaro Urbino, Italy.
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30
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Diversity of Trichoderma spp. in Marine Environments and Their Biological Potential for Sustainable Industrial Applications. SUSTAINABILITY 2020. [DOI: 10.3390/su12104327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms are regarded as a sustainable source of biologically active molecules. Among them, Trichoderma spp. have been an attractive source of biological compounds. However, the study of marine-derived Trichoderma has developed slowly because of the difficulty in isolating the fungi. In our study, 30 strains of marine-derived Trichoderma were identified through the translation elongation factor 1-alpha (EF1α) sequences, and their biological activities, such as antioxidant activity by ABTS and DPPH assays, antifungal activity against Asteromyces cruciatus and Lindra thalassiae, and tyrosinase inhibition activity, were investigated. As a result, the 30 marine Trichoderma species were classified into 21 taxa, including three new species candidates. Three strains of T. asperellum showed the highest ABTS radical scavenging activity and antifungal activity. T. bissettii SFC20170821-M05 and T. guizhouense SFC20180619-M23 showed notable DPPH radical scavenging activity and tyrosinase inhibition activity, respectively. This study showed the potential of marine-derived Trichoderma as a source of bioactive compounds.
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31
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Chiarello M, Auguet JC, Graham NAJ, Claverie T, Sucré E, Bouvier C, Rieuvilleneuve F, Restrepo-Ortiz CX, Bettarel Y, Villéger S, Bouvier T. Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes. Proc Biol Sci 2020; 287:20200642. [PMID: 32396801 DOI: 10.1098/rspb.2020.0642] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However, the diversity of such microbiomes is mostly described in a few coral species and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the total microbial diversity of coral reefs could be important, yet potentially vulnerable to the loss of animal species. Analysis of the surface microbiome from 74 taxa, including teleost fishes, hard and soft corals, crustaceans, echinoderms, bivalves and sponges, revealed that more than 90% of their prokaryotic phylogenetic richness was specific and not recovered in surrounding plankton. Estimate of the total richness associated with coral reef animal surface microbiomes reached up to 2.5% of current estimates of Earth prokaryotic diversity. Therefore, coral reef animal surfaces should be recognized as a hotspot of marine microbial diversity. Loss of the most vulnerable reef animals expected under present-day scenarios of reef degradation would induce an erosion of 28% of the prokaryotic richness, with unknown consequences on coral reef ecosystem functioning.
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Affiliation(s)
- Marlène Chiarello
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | - Nicholas A J Graham
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster LA1 4YQ, UK
| | - Thomas Claverie
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France.,Département Sciences et Technologie, Centre Universitaire de Formation et de Recherche de Mayotte, Route nationale 3, BP53, 97660 Dembeni, France
| | - Elliott Sucré
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France.,Département Sciences et Technologie, Centre Universitaire de Formation et de Recherche de Mayotte, Route nationale 3, BP53, 97660 Dembeni, France
| | - Corinne Bouvier
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | | | - Yvan Bettarel
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Sébastien Villéger
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Thierry Bouvier
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
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32
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Xia X, Ki Leung S, Cheung S, Zhang S, Liu H. Rare bacteria in seawater are dominant in the bacterial assemblage associated with the Bloom-forming dinoflagellate Noctiluca scintillans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:135107. [PMID: 31818556 DOI: 10.1016/j.scitotenv.2019.135107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/19/2019] [Accepted: 10/20/2019] [Indexed: 06/10/2023]
Abstract
Noctiluca scintillans is a bloom-forming dinoflagellate, which is widely distributed in the global coastal seas. Associated bacteria have been proven to be essential for the survival and growth of zooplanktons. However, the diversity and function of bacteria associated with Noctiluca scintillans are under studied and largely unknown. Here, we examined the diversity and function of bacteria associated with field-acquired and laboratory-maintained Noctiluca cells. Our results showed that the bacterial communities associated with the laboratory-maintained Noctiluca were dominated by Rhodobacterales, whereas those associated with the field-acquired Noctiluca varied over time. In addition, major Noctiluca-associated bacteria had low relative abundance in the ambient environment. We also observed that when field-acquired Noctiluca were cultivated with a mono-species food source, there was a shift in the associated bacterial communities. Metagenomic analysis showed that genes involved in DNA replication/repair and osmotic regulation were more abundant than other genes in the Noctiluca-associated bacterial community. Furthermore, the associated bacteria were able to degrade various complex carbohydrates and actively participate in the nitrogen cycle in their host cells. In addition, a draft genome of the Rickettsiaceae strain was recovered, and we showed that the genome did not contain genes encoding hexokinase and phosphoglucomutase, two key enzymes involved in glucose utilization. Instead, the primary energy sources of this bacteria were shown to be glutamate, glutamine and pyruvate, which might be obtained from the host. We suggest that in return, the Rickettsiaceae strain is likely to provide cofactors and amino acids to the host. This study highlights the spatial and temporal complexity of bacterial communities associated with Noctiluca, and provides valuable insights into the interaction between a host and its associated bacteria.
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Affiliation(s)
- Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), PR China.
| | - Sze Ki Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shunyan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shuwen Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, College of Life Science, South China Normal University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou, PR China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
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33
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Chen ML, Becraft ED, Pachiadaki M, Brown JM, Jarett JK, Gasol JM, Ravin NV, Moser DP, Nunoura T, Herndl GJ, Woyke T, Stepanauskas R. Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. Front Microbiol 2020; 11:376. [PMID: 32226422 PMCID: PMC7081726 DOI: 10.3389/fmicb.2020.00376] [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: 11/19/2019] [Accepted: 02/20/2020] [Indexed: 12/31/2022] Open
Abstract
Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.
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Affiliation(s)
- Michael L Chen
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, Williams College, Williamstown, MA, United States
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, University of North Alabama, Florence, AL, United States
| | - Maria Pachiadaki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Jessica K Jarett
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Josep M Gasol
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.,Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
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34
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Bastaraud A, Cecchi P, Handschumacher P, Altmann M, Jambou R. Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17020480. [PMID: 31940838 PMCID: PMC7013806 DOI: 10.3390/ijerph17020480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022]
Abstract
A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.
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Affiliation(s)
- Alexandra Bastaraud
- Laboratoire d’Hygiène des Aliments et de l’Environnement, Institut Pasteur de Madagascar, BP 1274, Antananarivo 101, Madagascar;
| | - Philippe Cecchi
- MARBEC (IRD, IFREMER, UM2 and CNRS), University Montpellier, 34095 Montpellier, France;
- Centre de Recherche Océanologique (CRO), Abidjan BPV 18, Ivory Coast
| | - Pascal Handschumacher
- IRD UMR 912 SESSTIM, INSERM-IRD-Université de Marseille II, 13000 Marseille, France;
| | - Mathias Altmann
- ISPED Université Victor Segalen Bordeaux II, 146 rue Leo Saignat, 33076 Bordeaux cedex, France;
| | - Ronan Jambou
- Département de Parasitologie et des insectes vecteurs, Institut Pasteur Paris, 75015 Paris, France
- Correspondence: ; Tel.: +33-622-10-72-96
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35
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Gould AL, Dunlap PV. Shedding Light on Specificity: Population Genomic Structure of a Symbiosis Between a Coral Reef Fish and Luminous Bacterium. Front Microbiol 2019; 10:2670. [PMID: 31824455 PMCID: PMC6879551 DOI: 10.3389/fmicb.2019.02670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/01/2019] [Indexed: 11/13/2022] Open
Abstract
All organisms depend on symbiotic associations with bacteria for their success, yet how these interspecific interactions influence the population structure, ecology, and evolution of microbial symbionts is not well understood. Additionally, patterns of genetic variation in interacting species can reveal ecological traits that are important to gene flow and co-evolution. In this study, we define patterns of spatial and temporal genetic variation of a coral reef fish, Siphamia tubifer, and its luminous bacterial symbiont, Photobacterium mandapamensis in the Okinawa Islands, Japan. Using restriction site-associated sequencing (RAD-Seq) methods, we show that populations of the facultative light organ symbiont of S. tubifer exhibit genetic structure at fine spatial scales of tens of kilometers despite the absence of physical barriers to dispersal and in contrast to populations of the host fish. These results suggest that the host’s behavioral ecology and environmental interactions between host and symbiont help to structure symbiont populations in the region, consequently fostering the specificity of the association between host generations. Our approach also revealed several symbiont genes that were divergent between host populations, including hfq and a homolog of varS, both of which play a role in host association in Vibrio cholerae. Overall, this study highlights the important role that a host animal can play in structuring the distribution of its bacterial symbiont, particularly in highly connected marine environments, thereby promoting specificity of the symbiosis between host generations.
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Affiliation(s)
- Alison L Gould
- Department of Ichthyology, California Academy of Sciences, San Francisco, CA, United States.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Paul V Dunlap
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
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36
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Kormas KA. Editorial for the Special Issue: Gut Microorganisms of Aquatic Animals. Microorganisms 2019; 7:E377. [PMID: 31546574 PMCID: PMC6843498 DOI: 10.3390/microorganisms7100377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 11/17/2022] Open
Abstract
Since the introduction of the term holobiont [...].
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Affiliation(s)
- Konstantinos Ar Kormas
- Department of Ichthyology & Aquatic Environment Faculty of Agricultural Sciences, University of Thessaly, Volos 382 21, Greece.
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37
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Dale H, Solan M, Lam P, Cunliffe M. Sediment microbial assemblage structure is modified by marine polychaete gut passage. FEMS Microbiol Ecol 2019; 95:5426820. [DOI: 10.1093/femsec/fiz047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/02/2019] [Indexed: 01/13/2023] Open
Affiliation(s)
- Harriet Dale
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Martin Solan
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Phyllis Lam
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Marine Biology and Ecology Research Group, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
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38
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Hakim JA, Schram JB, Galloway AWE, Morrow CD, Crowley MR, Watts SA, Bej AK. The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence. Microorganisms 2019; 7:E35. [PMID: 30691133 PMCID: PMC6406795 DOI: 10.3390/microorganisms7020035] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/13/2019] [Accepted: 01/21/2019] [Indexed: 12/13/2022] Open
Abstract
The sea urchin Strongylocentrotus purpuratus (order Camarodonta, family Strongylocentrotidae) can be found dominating low intertidal pool biomass on the southern coast of Oregon, USA. In this case study, three adult sea urchins were collected from their shared intertidal pool, and the bacteriome of their pharynx, gut tissue, and gut digesta, including their tide pool water and algae, was determined using targeted high-throughput sequencing (HTS) of the 16S rRNA genes and bioinformatics tools. Overall, the gut tissue demonstrated Arcobacter and Sulfurimonas (Epsilonproteobacteria) to be abundant, whereas the gut digesta was dominated by Psychromonas (Gammaproteobacteria), Propionigenium (Fusobacteria), and Flavobacteriales (Bacteroidetes). Alpha and beta diversity analyses indicated low species richness and distinct microbial communities comprising the gut tissue and digesta, while the pharynx tissue had higher richness, more closely resembling the water microbiota. Predicted functional profiles showed Kyoto Encyclopedia of Genes and Genomes (KEGG) Level-2 categories of energy metabolism, membrane transport, cell motility, and signal transduction in the gut tissue, and the gut digesta represented amino acid, carbohydrate, vitamin and cofactor metabolisms, and replication and repair. Co-occurrence network analysis showed the potential relationships and key taxa, such as the highly abundant Arcobacter and Propionigenium, influencing population patterns and taxonomic organization between the gut tissue and digesta. These results demonstrate a trend of microbial community integration, allocation, predicted metabolic roles, and taxonomic co-occurrence patterns in the S. purpuratus gut ecosystem.
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Affiliation(s)
- Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.
| | - Julie B Schram
- Oregon Institute of Marine Biology, University of Oregon, 63466 Boat Basin Rd, Charleston, OR 97420, USA.
| | - Aaron W E Galloway
- Oregon Institute of Marine Biology, University of Oregon, 63466 Boat Basin Rd, Charleston, OR 97420, USA.
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA.
| | - Michael R Crowley
- Department of Genetics, Heflin Center Genomics Core, School of Medicine, University of Alabama at Birmingham, 705 South 20th Street, Birmingham, AL 35294, USA.
| | - Stephen A Watts
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA.
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39
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Clarke LJ, Suter L, King R, Bissett A, Deagle BE. Antarctic Krill Are Reservoirs for Distinct Southern Ocean Microbial Communities. Front Microbiol 2019; 9:3226. [PMID: 30697197 PMCID: PMC6340936 DOI: 10.3389/fmicb.2018.03226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Host-associated bacterial communities have received limited attention in polar habitats, but are likely to represent distinct nutrient-rich niches compared to the surrounding environment. Antarctic krill (Euphausia superba) are a super-abundant species with a circumpolar distribution, and the krill microbiome may make a substantial contribution to marine bacterial diversity in the Southern Ocean. We used high-throughput sequencing of the bacterial 16S ribosomal RNA gene to characterize bacterial diversity in seawater and krill tissue samples from four locations south of the Kerguelen Plateau, one of the most productive regions in the Indian Sector of the Southern Ocean. Krill-associated bacterial communities were distinct from those of the surrounding seawater, with different communities inhabiting the moults, digestive tract and faecal pellets, including several phyla not detected in the surrounding seawater. Digestive tissues from many individuals contained a potential gut symbiont (order: Mycoplasmoidales) shown to improve survival on a low quality diet in other crustaceans. Antarctic krill swarms thus influence Southern Ocean microbial communities not only through top-down grazing of eukaryotic cells and release of nutrients into the water column, but also by transporting distinct microbial assemblages horizontally via migration and vertically via sinking faecal pellets and moulted exuviae. Changes to Antarctic krill demographics or distribution through fishing pressure or climate-induced range shifts will also influence the composition and dispersal of Southern Ocean microbial communities.
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Affiliation(s)
- Laurence J Clarke
- Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, TAS, Australia
| | - Léonie Suter
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Robert King
- Australian Antarctic Division, Kingston, TAS, Australia
| | - Andrew Bissett
- Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia
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40
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Nikouli E, Meziti A, Antonopoulou E, Mente E, Kormas KA. Gut Bacterial Communities in Geographically Distant Populations of Farmed Sea Bream ( Sparus aurata) and Sea Bass ( Dicentrarchus labrax). Microorganisms 2018; 6:microorganisms6030092. [PMID: 30200504 PMCID: PMC6164763 DOI: 10.3390/microorganisms6030092] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 01/21/2023] Open
Abstract
This study investigated the profile of the autochthonous gut bacterial communities in adult individuals of Sparus aurata and Dicentrarchus labrax reared in sea cages in five distantly located aquaculture farms in Greece and determine the impact of geographic location on them in order to detect the core gut microbiota of these commercially important fish species. Data analyses resulted in no significant geographic impact in the gut microbial communities within the two host species, while strong similarities between them were also present. Our survey revealed the existence of a core gut microbiota within and between the two host species independent of diet and geographic location consisting of the Delftia, Pseudomonas, Pelomonas, Propionibacterium, and Atopostipes genera.
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Affiliation(s)
- Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos 384 46, Greece.
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos 384 46, Greece.
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki 541 24, Greece.
| | - Eleni Mente
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos 384 46, Greece.
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos 384 46, Greece.
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41
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Campos P, Guivernau M, Prenafeta-Boldú FX, Cardona L. Fast acquisition of a polysaccharide fermenting gut microbiome by juvenile green turtles Chelonia mydas after settlement in coastal habitats. MICROBIOME 2018; 6:69. [PMID: 29636094 PMCID: PMC5894180 DOI: 10.1186/s40168-018-0454-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 04/02/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Tetrapods do not express hydrolases for cellulose and hemicellulose assimilation, and hence, the independent acquisition of herbivory required the establishment of new endosymbiotic relationships between tetrapods and microbes. Green turtles (Chelonia mydas) are one of the three groups of marine tetrapods with an herbivorous diet and which acquire it after several years consuming pelagic animals. We characterized the microbiota present in the feces and rectum of 24 young wild and captive green turtles from the coastal waters of Brazil, with curved carapace length ranging from 31.1 to 64.7 cm, to test the hypotheses that (1) the ontogenetic dietary shift after settlement is followed by a gradual change in the composition and diversity of the gut microbiome, (2) differences exist between the composition and diversity of the gut microbiome of green turtles from tropical and subtropical regions, and (3) the consumption of omnivorous diets modifies the gut microbiota of green turtles. RESULTS A genomic library of 2,186,596 valid bacterial 16S rRNA reads was obtained and these sequences were grouped into 6321 different operational taxonomic units (at 97% sequence homology cutoff). The results indicated that most of the juvenile green turtles less than 45 cm of curved carapace length exhibited a fecal microbiota co-dominated by representatives of the phyla Bacteroidetes and Firmicutes and high levels of Clostridiaceae, Prophyromonas, Ruminococaceae, and Lachnospiraceae within the latter phylum. Furthermore, this was the only microbiota profile found in wild green turtles > 45 cm CCL and in most of the captive green turtles of any size feeding on a macroalgae/fish mixed diet. Nevertheless, microbial diversity increased with turtle size and was higher in turtles from tropical than from subtropical regions. CONCLUSIONS These results indicate that juvenile green turtles from the coastal waters of Brazil had the same general microbiota, regardless of body size and origin, and suggest a fast acquisition of a polysaccharide fermenting gut microbiota by juvenile green turtles after settlement into coastal habitats.
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Affiliation(s)
- Patricia Campos
- IRBio and Department of Evolutionary Biology, Ecology and Environmental Science, Faculty of Biology, University of Barcelona, Avenida Diagonal 643, 08028 Barcelona, Spain
| | - Miriam Guivernau
- GIRO, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, E-08140 Caldes de Montbui, Barcelona, Spain
| | - Francesc X. Prenafeta-Boldú
- GIRO, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, E-08140 Caldes de Montbui, Barcelona, Spain
| | - Luis Cardona
- IRBio and Department of Evolutionary Biology, Ecology and Environmental Science, Faculty of Biology, University of Barcelona, Avenida Diagonal 643, 08028 Barcelona, Spain
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42
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KleinJan H, Jeanthon C, Boyen C, Dittami SM. Exploring the Cultivable Ectocarpus Microbiome. Front Microbiol 2017; 8:2456. [PMID: 29312170 PMCID: PMC5732352 DOI: 10.3389/fmicb.2017.02456] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/27/2017] [Indexed: 01/08/2023] Open
Abstract
Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.
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Affiliation(s)
- Hetty KleinJan
- Sorbonne Universités, CNRS-UPMC, Station Biologique de Roscoff, UMR8227, Integrative Biology of Marine Models, Roscoff, France
| | - Christian Jeanthon
- CNRS, Station Biologique de Roscoff, UMR7144, Adaptation et Diversité en Milieu Marin, Roscoff, France.,Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, UMR7144, Adaptation et Diversité en Milieu Marin, Roscoff, France
| | - Catherine Boyen
- Sorbonne Universités, CNRS-UPMC, Station Biologique de Roscoff, UMR8227, Integrative Biology of Marine Models, Roscoff, France
| | - Simon M Dittami
- Sorbonne Universités, CNRS-UPMC, Station Biologique de Roscoff, UMR8227, Integrative Biology of Marine Models, Roscoff, France
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Escalas A, Troussellier M, Yuan T, Bouvier T, Bouvier C, Mouchet MA, Flores Hernandez D, Ramos Miranda J, Zhou J, Mouillot D. Functional diversity and redundancy across fish gut, sediment and water bacterial communities. Environ Microbiol 2017; 19:3268-3282. [PMID: 28618142 DOI: 10.1111/1462-2920.13822] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 06/07/2017] [Indexed: 11/26/2022]
Abstract
This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.
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Affiliation(s)
- Arthur Escalas
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Marc Troussellier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Thierry Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Corinne Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Maud A Mouchet
- UMR 7204 CESCO, Muséum d'Histoire Naturelle, 55 rue Buffon, Paris, 75005, France
| | - Domingo Flores Hernandez
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Julia Ramos Miranda
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - David Mouillot
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
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