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Bollati E, Hughes DJ, Suggett DJ, Raina JB, Kühl M. Microscale sampling of the coral gastrovascular cavity reveals a gut-like microbial community. Anim Microbiome 2024; 6:55. [PMID: 39380028 PMCID: PMC11460067 DOI: 10.1186/s42523-024-00341-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 09/18/2024] [Indexed: 10/10/2024] Open
Abstract
Animal guts contain numerous microbes, which are critical for nutrient assimilation and pathogen defence. While corals and other Cnidaria lack a true differentiated gut, they possess semi-enclosed gastrovascular cavities (GVCs), where vital processes such as digestion, reproduction and symbiotic exchanges take place. The microbiome harboured in GVCs is therefore likely key to holobiont fitness, but remains severely understudied due to challenges of working in these small compartments. Here, we developed minimally invasive methodologies to sample the GVC of coral polyps and characterise the microbial communities harboured within. We used glass capillaries, low dead volume microneedles, or nylon microswabs to sample the gastrovascular microbiome of individual polyps from six species of corals, then applied low-input DNA extraction to characterise the microbial communities from these microliter volume samples. Microsensor measurements of GVCs revealed anoxic or hypoxic micro-niches, which persist even under prolonged illumination with saturating irradiance. These niches harboured microbial communities enriched in putatively microaerophilic or facultatively anaerobic taxa, such as Epsilonproteobacteria. Some core taxa found in the GVC of Lobophyllia hemprichii from the Great Barrier Reef were also detected in conspecific colonies held in aquaria, indicating that these associations are unlikely to be transient. Our findings suggest that the coral GVC is chemically and microbiologically similar to the gut of higher Metazoa. Given the importance of gut microbiomes in mediating animal health, harnessing the coral "gut microbiome" may foster novel active interventions aimed at increasing the resilience of coral reefs to the climate crisis.
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Affiliation(s)
- Elena Bollati
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, 3000, Denmark.
| | - David J Hughes
- National Sea Simulator, Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - David J Suggett
- KAUST Coral Restoration Initiative (KCRI) and Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Michael Kühl
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, 3000, Denmark
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2
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Tischer M, Bleidorn C. Further evidence of low infection frequencies of Wolbachia in soil arthropod communities. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105641. [PMID: 39004260 DOI: 10.1016/j.meegid.2024.105641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/22/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Endosymbiotic Alphaproteobacteria of the genus Wolbachia are exclusively transferred maternally from mother to offspring, but horizontal transfer across species boundaries seems to be frequent as well. However, the (ecological) mechanisms of how these bacteria are transferred between distantly related arthropod hosts remain unclear. Based on the observation that species that are part of the same ecological community often also share similar Wolbachia strains, host ecology has been hypothesized as an important factor enabling transmission and a key factor in explaining the global distribution of Wolbachia lineages. In this study, we focus on the diversity and abundance of Wolbachia strains in soil arthropods, a so far rather neglected community. We screened 82 arthropod morphotypes collected in the beech forest (dominated by Fagus sp.) soil in the area of Göttingen in central Germany for the presence of Wolbachia. By performing a PCR screen with Wolbachia-MLST markers (coxA, dnaA, fbpA, ftsZ, gatB, and hcpA), we found a rather low infection frequency of 12,2%. Additionally, we performed metagenomic screening of pooled individuals from the same sampling site and could not find evidence that this low infection frequency is an artefact due to PCR-primer bias. Phylogenetic analyses of the recovered Wolbachia strains grouped them in three known supergroups (A, B, and E), with the first report of Wolbachia in Protura (Hexapoda). Moreover, Wolbachia sequences from the pseudoscorpion Neobisium carcinoides cluster outside the currently known supergroup diversity. Our screening supports results from previous studies that the prevalence of Wolbachia infections seems to be lower in soil habitats than in above-ground terrestrial habitats. The reasons for this pattern are not completely understood but might stem from the low opportunity of physical contact and the prevalence of supergroups that are less suited for horizontal transfer.
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Affiliation(s)
- Marta Tischer
- Department for Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany.
| | - Christoph Bleidorn
- Department for Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany.
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3
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Cook LSJ, Briscoe AG, Fonseca VG, Boenigk J, Woodward G, Bass D. Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment. Trends Microbiol 2024:S0966-842X(24)00173-2. [PMID: 39164135 DOI: 10.1016/j.tim.2024.07.003] [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: 01/16/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 08/22/2024]
Abstract
Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.
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Affiliation(s)
- Lauren S J Cook
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Andrew G Briscoe
- Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; NatureMetrics, Surrey Research Park, Guildford GU2 7HJ, UK
| | - Vera G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Guy Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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4
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Buschi E, Dell’Anno A, Tangherlini M, Candela M, Rampelli S, Turroni S, Palladino G, Esposito E, Martire ML, Musco L, Stefanni S, Munari C, Fiori J, Danovaro R, Corinaldesi C. Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome. SCIENCE ADVANCES 2024; 10:eadk9117. [PMID: 38905343 PMCID: PMC11192080 DOI: 10.1126/sciadv.adk9117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.
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Affiliation(s)
- Emanuela Buschi
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luigi Musco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica “Anton Dohrn,” Villa Comunale, Napoli, Italy
| | - Cristina Munari
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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5
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Surmacz B, Stec D, Prus-Frankowska M, Buczek M, Michalczyk Ł, Łukasik P. Pinpointing the microbiota of tardigrades: What is really there? Environ Microbiol 2024; 26:e16659. [PMID: 38899728 DOI: 10.1111/1462-2920.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024]
Abstract
Microbiota are considered significant in the biology of tardigrades, yet their diversity and distribution remain largely unexplored. This is partly due to the methodological challenges associated with studying the microbiota of small organisms that inhabit microbe-rich environments. In our study, we characterized the microbiota of 31 species of cultured tardigrades using 16S rRNA amplicon sequencing. We employed various sample preparation strategies and multiple types of controls and estimated the number of microbes in samples using synthetic DNA spike-ins. We also reanalysed data from previous tardigrade microbiome studies. Our findings suggest that the microbial communities of cultured tardigrades are predominantly composed of bacterial genotypes originating from food, medium, or reagents. Despite numerous experiments, we found it challenging to identify strains that were enriched in certain tardigrades, which would have indicated likely symbiotic associations. Putative tardigrade-associated microbes rarely constituted more than 20% of the datasets, although some matched symbionts identified in other studies. We also uncovered serious contamination issues in previous tardigrade microbiome studies, casting doubt on some of their conclusions. We concluded that tardigrades are not universally dependent on specialized microbes. Our work underscores the need for rigorous safeguards in studies of the microbiota of microscopic organisms and serves as a cautionary tale for studies involving samples with low microbiome abundance.
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Affiliation(s)
- Bartłomiej Surmacz
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Daniel Stec
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Monika Prus-Frankowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Łukasz Michalczyk
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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6
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Lanzoni O, Szokoli F, Schrallhammer M, Sabaneyeva E, Krenek S, Doak TG, Verni F, Berendonk TU, Castelli M, Petroni G. "Candidatus Intestinibacterium parameciiphilum"-member of the "Candidatus Paracaedibacteraceae" family (Alphaproteobacteria, Holosporales) inhabiting the ciliated protist Paramecium. Int Microbiol 2024; 27:659-671. [PMID: 37615902 PMCID: PMC11144129 DOI: 10.1007/s10123-023-00414-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]
Abstract
Protists frequently host diverse bacterial symbionts, in particular those affiliated with the order Holosporales (Alphaproteobacteria). All characterised members of this bacterial lineage have been retrieved in obligate association with a wide range of eukaryotes, especially multiple protist lineages (e.g. amoebozoans, ciliates, cercozoans, euglenids, and nucleariids), as well as some metazoans (especially arthropods and related ecdysozoans). While the genus Paramecium and other ciliates have been deeply investigated for the presence of symbionts, known members of the family "Candidatus Paracaedibacteraceae" (Holosporales) are currently underrepresented in such hosts. Herein, we report the description of "Candidatus Intestinibacterium parameciiphilum" within the family "Candidatus Paracaedibacteraceae", inhabiting the cytoplasm of Paramecium biaurelia. This novel bacterium is almost twice as big as its relative "Candidatus Intestinibacterium nucleariae" from the opisthokont Nuclearia and does not present a surrounding halo. Based on phylogenetic analyses of 16S rRNA gene sequences, we identified six further potential species-level lineages within the genus. Based on the provenance of the respective samples, we investigated the environmental distribution of the representatives of "Candidatus Intestinibacterium" species. Obtained results are consistent with an obligate endosymbiotic lifestyle, with protists, in particular freshwater ones, as hosts. Thus, available data suggest that association with freshwater protists could be the ancestral condition for the members of the "Candidatus Intestinibacterium" genus.
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Affiliation(s)
| | - Franziska Szokoli
- Department of Biology, University of Pisa, Pisa, Italy
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Martina Schrallhammer
- Mikrobiologie, Institut für Biologie II, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Elena Sabaneyeva
- Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sascha Krenek
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | | | - Franco Verni
- Department of Biology, University of Pisa, Pisa, Italy
| | - Thomas U Berendonk
- Institut für Hydrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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7
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Zhang B, Xiao L, Lyu L, Zhao F, Miao M. Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists. MICROBIOME 2024; 12:96. [PMID: 38790063 PMCID: PMC11127453 DOI: 10.1186/s40168-024-01809-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates. RESULTS To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range. CONCLUSIONS As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.
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Affiliation(s)
- Bing Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Liwen Xiao
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liping Lyu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Fangqing Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - Miao Miao
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Zoology, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
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8
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Defourneaux É, Herranz M, Armenteros M, Sørensen MV, Norenburg JL, Park T, Worsaae K. Circumtropical distribution and cryptic species of the meiofaunal enteropneust Meioglossus (Harrimaniidae, Hemichordata). Sci Rep 2024; 14:9296. [PMID: 38654022 DOI: 10.1038/s41598-024-57591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Hemichordata has always played a central role in evolutionary studies of Chordata due to their close phylogenetic affinity and shared morphological characteristics. Hemichordates had no meiofaunal representatives until the surprising discovery of a microscopic, paedomorphic enteropneust Meioglossus psammophilus (Harrimaniidae, Hemichordata) from the Caribbean in 2012. No additional species have been described since, questioning the broader distribution and significance of this genus. However, being less than a millimeter long and superficially resembling an early juvenile acorn worm, Meioglossus may easily be overlooked in both macrofauna and meiofauna surveys. We here present the discovery of 11 additional populations of Meioglossus from shallow subtropical and tropical coralline sands of the Caribbean Sea, Red Sea, Indian Ocean, and East China Sea. These geographically separated populations show identical morphology but differ genetically. Our phylogenetic reconstructions include four gene markers and support the monophyly of Meioglossus. Species delineation analyses revealed eight new cryptic species, which we herein describe using DNA taxonomy. This study reveals a broad circumtropical distribution, supporting the validity and ecological importance of this enigmatic meiobenthic genus. The high cryptic diversity and apparent morphological stasis of Meioglossus may exemplify a potentially common evolutionary 'dead-end' scenario, where groups with highly miniaturized and simplified body plan lose their ability to diversify morphologically.
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Affiliation(s)
- Éloïse Defourneaux
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark
| | - Maria Herranz
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark
- Area of Biodiversity and Conservation, Superior School of Experimental Science and Technology (ESCET), Rey Juan Carlos University, C/ Tulipán S/N, 28933, Mostoles, Madrid, Spain
| | - Maickel Armenteros
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Joel Montes Camarena S/N, 82040, Mazatlán, México
| | - Martin V Sørensen
- Natural History Museum Denmark, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Jon L Norenburg
- Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Taeseo Park
- Species Diversity Research Division, National Institute of Biological Resources, Hwangyeong-Ro 42, Incheon, 22689, South Korea
| | - Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark.
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9
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Vijayan N, McAnulty SJ, Sanchez G, Jolly J, Ikeda Y, Nishiguchi MK, Réveillac E, Gestal C, Spady BL, Li DH, Burford BP, Kerwin AH, Nyholm SV. Evolutionary history influences the microbiomes of a female symbiotic reproductive organ in cephalopods. Appl Environ Microbiol 2024; 90:e0099023. [PMID: 38315021 PMCID: PMC10952459 DOI: 10.1128/aem.00990-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/09/2023] [Indexed: 02/07/2024] Open
Abstract
Many female squids and cuttlefishes have a symbiotic reproductive organ called the accessory nidamental gland (ANG) that hosts a bacterial consortium involved with egg defense against pathogens and fouling organisms. While the ANG is found in multiple cephalopod families, little is known about the global microbial diversity of these ANG bacterial symbionts. We used 16S rRNA gene community analysis to characterize the ANG microbiome from different cephalopod species and assess the relationship between host and symbiont phylogenies. The ANG microbiome of 11 species of cephalopods from four families (superorder: Decapodiformes) that span seven geographic locations was characterized. Bacteria of class Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were found in all species, yet analysis of amplicon sequence variants by multiple distance metrics revealed a significant difference between ANG microbiomes of cephalopod families (weighted/unweighted UniFrac, Bray-Curtis, P = 0.001). Despite being collected from widely disparate geographic locations, members of the family Sepiolidae (bobtail squid) shared many bacterial taxa including (~50%) Opitutae (Verrucomicrobia) and Ruegeria (Alphaproteobacteria) species. Furthermore, we tested for phylosymbiosis and found a positive correlation between host phylogenetic distance and bacterial community dissimilarity (Mantel test r = 0.7). These data suggest that closely related sepiolids select for distinct symbionts from similar bacterial taxa. Overall, the ANGs of different cephalopod species harbor distinct microbiomes and thus offer a diverse symbiont community to explore antimicrobial activity and other functional roles in host fitness.IMPORTANCEMany aquatic organisms recruit microbial symbionts from the environment that provide a variety of functions, including defense from pathogens. Some female cephalopods (squids, bobtail squids, and cuttlefish) have a reproductive organ called the accessory nidamental gland (ANG) that contains a bacterial consortium that protects eggs from pathogens. Despite the wide distribution of these cephalopods, whether they share similar microbiomes is unknown. Here, we studied the microbial diversity of the ANG in 11 species of cephalopods distributed over a broad geographic range and representing 15-120 million years of host divergence. The ANG microbiomes shared some bacterial taxa, but each cephalopod species had unique symbiotic members. Additionally, analysis of host-symbiont phylogenies suggests that the evolutionary histories of the partners have been important in shaping the ANG microbiome. This study advances our knowledge of cephalopod-bacteria relationships and provides a foundation to explore defensive symbionts in other systems.
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Affiliation(s)
- Nidhi Vijayan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Sarah J. McAnulty
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
- Graduate School of Integrated Science for Life, Hiroshima University, Hiroshima, Japan
| | - Jeffrey Jolly
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Yuzuru Ikeda
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of Ryukyus, Ryukyus, Japan
| | - Michele K. Nishiguchi
- Department of Molecular and Cell Biology, University of California, Merced, California, USA
| | - Elodie Réveillac
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS–La Rochelle Université, La Rochelle, France
| | - Camino Gestal
- Institute of Marine Research (IIM), CSIC, Vigo, Spain
| | - Blake L. Spady
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- U.S. National Oceanic and Atmospheric Administration, National Environmental Satellite Data and Information Service, Center for Satellite Applications and Research, Coral Reef Watch, College Park, Maryland, USA
| | - Diana H. Li
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, USA
| | - Benjamin P. Burford
- Institute of Marine Sciences, University of California, affiliated with the National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, California, USA
| | - Allison H. Kerwin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Biology, McDaniel College, Westminster, Maryland, USA
| | - Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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10
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Castelli M, Nardi T, Gammuto L, Bellinzona G, Sabaneyeva E, Potekhin A, Serra V, Petroni G, Sassera D. Host association and intracellularity evolved multiple times independently in the Rickettsiales. Nat Commun 2024; 15:1093. [PMID: 38321113 PMCID: PMC10847448 DOI: 10.1038/s41467-024-45351-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/18/2024] [Indexed: 02/08/2024] Open
Abstract
The order Rickettsiales (Alphaproteobacteria) encompasses multiple diverse lineages of host-associated bacteria, including pathogens, reproductive manipulators, and mutualists. Here, in order to understand how intracellularity and host association originated in this order, and whether they are ancestral or convergently evolved characteristics, we built a large and phylogenetically-balanced dataset that includes de novo sequenced genomes and a selection of published genomic and metagenomic assemblies. We perform detailed functional reconstructions that clearly indicates "late" and parallel evolution of obligate host-association in different Rickettsiales lineages. According to the depicted scenario, multiple independent horizontal acquisitions of transporters led to the progressive loss of biosynthesis of nucleotides, amino acids and other metabolites, producing distinct conditions of host-dependence. Each clade experienced a different pattern of evolution of the ancestral arsenal of interaction apparatuses, including development of specialised effectors involved in the lineage-specific mechanisms of host cell adhesion and/or invasion.
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Affiliation(s)
- Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Tiago Nardi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | | | - Greta Bellinzona
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Elena Sabaneyeva
- Department of Cytology and Histology, Saint Petersburg State University, Petersburg, Russia
| | - Alexey Potekhin
- Department of Microbiology, Saint Petersburg State University, Petersburg, Russia
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | | | | | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
- IRCCS Policlinico San Matteo, Pavia, Italy.
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11
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Mazel F, Pitteloud C, Guisan A, Pellissier L. Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets. ISME COMMUNICATIONS 2024; 4:ycad013. [PMID: 38374896 PMCID: PMC10875604 DOI: 10.1093/ismeco/ycad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024]
Abstract
Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Camille Pitteloud
- Département de la mobilité, du territoire et de l'environnement, Service des forêts, de la nature et du paysage, Sion 1950, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne 1015, Switzerland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
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12
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Bacci G, Meriggi N, Cheng CLY, Ng KH, Iannucci A, Mengoni A, Cavalieri D, Cannicci S, Fratini S. Species-specific gill's microbiome of eight crab species with different breathing adaptations. Sci Rep 2023; 13:21033. [PMID: 38030652 PMCID: PMC10687215 DOI: 10.1038/s41598-023-48308-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023] Open
Abstract
Transitions to physically different environments, such as the water-to-land transition, proved to be the main drivers of relevant evolutionary events. Brachyuran crabs evolved remarkable morphological, behavioral, and physiological adaptations to terrestrial life. Terrestrial species evolved new respiratory structures devoted to replace or support the gills, a multifunctional organ devoted to gas exchanges, ion-regulation and nitrogen excretion. It was hypothesized that microorganisms associated with respiratory apparatus could have facilitated the processes of osmoregulation, respiration, and elimination of metabolites along this evolutionary transition. To test if crab species with different breathing adaptations may host similar microbial communities on their gills, we performed a comparative targeted-metagenomic analysis, selecting two marine and six terrestrial crabs belonging to different families and characterised by different breathing adaptations. We analysed anterior and posterior gills separately according to their different and specific roles. Regardless of their terrestrial or marine adaptations, microbial assemblages were strongly species-specific indicating a non-random association between the host and its microbiome. Significant differences were found in only two terrestrial species when considering posterior vs. anterior gills, without any association with species-specific respiratory adaptations. Our results suggest that all the selected species are strongly adapted to the ecological niche and specific micro-habitat they colonise.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Christine L Y Cheng
- The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, Hong Kong SAR, People's Republic of China
| | - Ka Hei Ng
- The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, Hong Kong SAR, People's Republic of China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, Hong Kong SAR, People's Republic of China
| | - Alessio Iannucci
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Duccio Cavalieri
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
| | - Stefano Cannicci
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy.
- The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, Hong Kong SAR, People's Republic of China.
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy.
| | - Sara Fratini
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
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13
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Holt CC, Dhaliwal S, Na I, Mtawali M, Boscaro V, Keeling P. Spatial compartmentalisation of bacteria in phoronid microbiomes. Sci Rep 2023; 13:18612. [PMID: 37903823 PMCID: PMC10616082 DOI: 10.1038/s41598-023-45652-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/22/2023] [Indexed: 11/01/2023] Open
Abstract
The phylum Phoronida comprises filter-feeding invertebrates that live in a protective tube sometimes reinforced with particulate material from the surrounding environments. Animals with these characteristics make promising candidate hosts for symbiotic bacteria, given the constant interactions with various bacterial colonizers, yet phoronids are one of the very few animal phyla with no available microbiome data whatsoever. Here, by sequencing the V4 region of the 16S rRNA gene, we compare bacterial microbiomes in whole phoronids, including both tube and living tissues, with those associated exclusively to the isolated tube and/or the naked animal inside. We also compare these communities with those from the surrounding water. Phoronid microbiomes from specimens belonging to the same colony but collected a month apart were significantly different, and bacterial taxa previously reported in association with invertebrates and sediment were found to drive this difference. The microbiomes associated with the tubes are very similar in composition to those isolated from whole animals. However, just over half of bacteria found in whole specimens are also found both in tubes and naked specimens. In conclusion, phoronids harbour bacterial microbiomes that differ from those in the surrounding water, but the composition of those microbiomes is not stable and appears to change in the same colony over a relatively short time frame. Considering individual spatial/anatomical compartments, the phoronid tube contributes most to the whole-animal microbiome.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, Canada.
- Hakai Institute, Heriot Bay, Canada.
| | - Sahib Dhaliwal
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Ina Na
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Mahara Mtawali
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada.
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14
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Pushpakumara BLDU, Tandon K, Willis A, Verbruggen H. The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis. MICROBIAL ECOLOGY 2023; 86:2032-2046. [PMID: 37002423 PMCID: PMC10497448 DOI: 10.1007/s00248-023-02209-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.
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Affiliation(s)
| | - Kshitij Tandon
- School of Biosciences, University of Melbourne, Victoria, 3010, Australia
| | - Anusuya Willis
- Australian National Algae Culture Collection, CSIRO, Tasmania, 7000, Victoria, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Victoria, 3010, Australia
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15
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Abalde S, Tellgren-Roth C, Heintz J, Vinnere Pettersson O, Jondelius U. The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes. Front Genet 2023; 14:1244493. [PMID: 37829276 PMCID: PMC10565955 DOI: 10.3389/fgene.2023.1244493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group's main clades and whose origin has been dated more than 400 million years ago. Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades. Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system. Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.
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Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Christian Tellgren-Roth
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Julia Heintz
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
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16
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Buschi E, Dell’Anno A, Tangherlini M, Stefanni S, Lo Martire M, Núñez-Pons L, Avila C, Corinaldesi C. Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean. Front Microbiol 2023; 14:1234725. [PMID: 37799611 PMCID: PMC10548270 DOI: 10.3389/fmicb.2023.1234725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Abstract
Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.
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Affiliation(s)
- Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat, University of Barcelona, Barcelona, Catalonia, Spain
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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17
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Ishaq SL, Turner SM, Lee G, Tudor MS, MacRae JD, Hamlin H, Bouchard D. Water temperature and disease alters bacterial diversity and cultivability from American lobster ( Homarus americanus) shells. iScience 2023; 26:106606. [PMID: 37128602 PMCID: PMC10148122 DOI: 10.1016/j.isci.2023.106606] [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: 11/16/2022] [Revised: 02/15/2023] [Accepted: 03/31/2023] [Indexed: 05/03/2023] Open
Abstract
The American lobster, Homarus americanus, is an economically valuable and ecologically important crustacean along the North Atlantic coast of North America. Populations in southern locations have declined in recent decades due to increasing ocean temperatures and disease, and these circumstances are progressing northward. We monitored 57 adult female lobsters, healthy and shell diseased, under three seasonal temperature cycles for a year, to track shell bacterial communities using culturing and 16S rRNA gene sequencing, progression of epizootic shell disease using visual assessment, and antimicrobial activity of hemolymph. The richness of bacterial taxa present, evenness of abundance, and community similarity between lobsters was affected by water temperature at the time of sampling, water temperature over time based on seasonal temperature regimes, shell disease severity, and molt stage. Several bacteria were prevalent on healthy lobster shells but missing or less abundant on diseased shells, although some bacteria were found on all shells regardless of health status.
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Affiliation(s)
- Suzanne L. Ishaq
- School of Food and Agriculture, University of Maine, Orono, Maine 04469, USA
- Aquaculture Research Institute, University of Maine, Orono, Maine 04469, USA
- Corresponding author
| | - Sarah M. Turner
- Aquaculture Research Institute, University of Maine, Orono, Maine 04469, USA
- Cooperative Extension, University of Maine, Orono, Maine 04469, USA
| | - Grace Lee
- Department of Neuroscience, Bowdoin College, Brunswick, ME 04011, USA
- Boston Children’s Hospital, Boston, MA 02115, USA
| | - M. Scarlett Tudor
- Aquaculture Research Institute, University of Maine, Orono, Maine 04469, USA
- Cooperative Extension, University of Maine, Orono, Maine 04469, USA
| | - Jean D. MacRae
- Department of Civil and Environmental Engineering, University of Maine, Orono, Maine 04469, USA
| | - Heather Hamlin
- Aquaculture Research Institute, University of Maine, Orono, Maine 04469, USA
- School of Marine Sciences, University of Maine, Orono, Maine 04469, USA
| | - Deborah Bouchard
- Aquaculture Research Institute, University of Maine, Orono, Maine 04469, USA
- Cooperative Extension, University of Maine, Orono, Maine 04469, USA
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18
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Parr McQueen J, Gattoni K, Gendron E, Schmidt S, Sommers P, Porazinska DL. External and Internal Microbiomes of Antarctic Nematodes are Distinct, but More Similar to each other than the Surrounding Environment. J Nematol 2023; 55:20230004. [PMID: 36969543 PMCID: PMC10035304 DOI: 10.2478/jofnem-2023-0004] [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: 08/02/2022] [Indexed: 03/11/2023] Open
Abstract
Host-associated microbiomes have primarily been examined in the context of their internal microbial communities, but many animal species also contain microorganisms on external host surfaces that are important to host physiology. For nematodes, single strains of bacteria are known to adhere to the cuticle (e.g., Pasteuria penetrans), but the structure of a full external microbial community is uncertain. In prior research, we showed that internal gut microbiomes of nematodes (Plectus murrayi, Eudorylaimus antarcticus) and tardigrades from Antarctica's McMurdo Dry Valleys were distinct from the surrounding environment and primarily driven by host identity. Building on this work, we extracted an additional set of individuals containing intact external microbiomes and amplified them for 16S and 18S rRNA metabarcoding. Our results showed that external bacterial microbiomes were more diverse than internal microbiomes, but less diverse than the surrounding environment. Host-specific bacterial compositional patterns were observed, and external microbiomes were most similar to their respective internal microbiomes. However, external microbiomes were more influenced by the environment than the internal microbiomes were. Non-host eukaryotic communities were similar in diversity to internal eukaryotic communities, but exhibited more stochastic patterns of assembly compared to bacterial communities, suggesting the lack of a structured external eukaryotic microbiome. Altogether, we provide evidence that nematode and tardigrade cuticles are inhabited by robust bacterial communities that are substantially influenced by the host, albeit less so than internal microbiomes are.
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Affiliation(s)
- J. Parr McQueen
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| | - K. Gattoni
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| | - E.M.S. Gendron
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| | - S.K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309Colorado BoulderUSA
| | - P. Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309Colorado BoulderUSA
| | - D. L. Porazinska
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
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19
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Holt CC, Boscaro V, Van Steenkiste NWL, Herranz M, Mathur V, Irwin NAT, Buckholtz G, Leander BS, Keeling PJ. Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi. MICROBIOME 2022; 10:161. [PMID: 36180959 PMCID: PMC9523941 DOI: 10.1186/s40168-022-01363-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis, yet eukaryotic microbiome sequencing is rarely undertaken, with much of the focus on bacteria. To explore the importance of microscopic marine invertebrates as potential symbiont reservoirs, we used a phylogenetic-focused approach to analyze the host-associated eukaryotic microbiomes of 220 animal specimens spanning nine different animal phyla. RESULTS Our data expanded the traditional host range of several microbial taxa and identified numerous undescribed lineages. A lack of comparable reference sequences resulted in several cryptic clades within the Apicomplexa and Ciliophora and emphasized the potential for microbial invertebrates to harbor novel protistan and fungal diversity. CONCLUSIONS Microscopic marine invertebrates, spanning a wide range of animal phyla, host various protist and fungal sequences and may therefore serve as a useful resource in the detection and characterization of undescribed symbioses. Video Abstract.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, Canada.
- Hakai Institute, Heriot Bay, Canada.
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
| | - Niels W L Van Steenkiste
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Maria Herranz
- Department of Botany, University of British Columbia, Vancouver, Canada
- Hakai Institute, Heriot Bay, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Gracy Buckholtz
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada.
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