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Hernández-Zulueta J, Rubio-Bueno S, Zamora-Tavares MDP, Vargas-Ponce O, Rodríguez-Troncoso AP, Rodríguez-Zaragoza FA. Metabarcoding the Bacterial Assemblages Associated with Toxopneustes roseus in the Mexican Central Pacific. Microorganisms 2024; 12:1195. [PMID: 38930577 PMCID: PMC11205562 DOI: 10.3390/microorganisms12061195] [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: 05/28/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species' physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the T. roseus bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (Saprospiraceae, Flammeovirgaceae, and Xanthobacteraceae). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the Campylobacteraceae and Helicobacteraceae families was key to T. roseus' holobiont. However, the dominance of certain bacterial families, such as Enterobacteriaceae, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition.
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Affiliation(s)
- Joicye Hernández-Zulueta
- Departamento de Biología Celular y Molecular, Centro Universitario de Ciencias Biológicas y Agropecuarias (CUCBA), Universidad de Guadalajara, Zapopan 45200, Jalisco, Mexico;
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología Aplicada, Centro Universitario de Ciencias Biológicas y Agropecuarias (CUCBA), Universidad de Guadalajara, Zapopan 45200, Jalisco, Mexico
| | - Sharix Rubio-Bueno
- Programa de Maestría en Ciencias en Biosistemática y Manejo de Recursos Naturales y Agrícolas, Centro Universitario de Ciencias Biológicas y Agropecuarias (CUCBA), Universidad de Guadalajara, Zapopan 45200, Jalisco, Mexico;
| | - María del Pilar Zamora-Tavares
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg), Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias (CUCBA), Universidad de Guadalajara, Zapopan 45200, Jalisco, Mexico; (M.d.P.Z.-T.); (O.V.-P.)
| | - Ofelia Vargas-Ponce
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg), Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias (CUCBA), Universidad de Guadalajara, Zapopan 45200, Jalisco, Mexico; (M.d.P.Z.-T.); (O.V.-P.)
| | - Alma Paola Rodríguez-Troncoso
- Laboratorio de Ecología Marina, Centro Universitario de la Costa (CUCosta), Universidad de Guadalajara, Puerto Vallarta 48280, Jalisco, Mexico;
| | - Fabián A. Rodríguez-Zaragoza
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología Aplicada, Centro Universitario de Ciencias Biológicas y Agropecuarias (CUCBA), Universidad de Guadalajara, Zapopan 45200, Jalisco, Mexico
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2
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González-Aravena M, Perrois G, Font A, Cárdenas CA, Rondon R. Microbiome profile of the Antarctic clam Laternula elliptica. Braz J Microbiol 2024; 55:487-497. [PMID: 38157148 PMCID: PMC10920576 DOI: 10.1007/s42770-023-01200-1] [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: 05/11/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
The filter feeder clam Laternula elliptica is a key species in the Antarctic ecosystem. As a stenothermal benthic species, it has a poor capacity for adaptation to small temperature variations. Despite their ecological importance and sensitivity to climate change, studies on their microbiomes are lacking. The goal of this study was to characterize the bacterial communities of L. elliptica and the tissues variability of this microbiome to provide an initial insight of host-microbiota interactions. We investigated the diversity and taxonomic composition of bacterial communities of L. elliptica from five regions of the body using high-throughput 16S rRNA gene sequencing. The results showed that the microbiome of L. elliptica tended to differ from that of the surrounding seawater samples. However, there were no significant differences in the microbial composition between the body sites, and only two OTUs were present in all samples, being considered core microbiome (genus Moritella and Polaribacter). No significant differences were detected in diversity indexes among tissues (mean 626.85 for observed OTUs, 628.89 Chao1, 5.42 Shannon, and 0.87 Simpson). Rarefaction analysis revealed that most tissues reached a plateau of OTU number according to sample increase, with the exception of Siphon samples. Psychromonas and Psychrilyobacter were particularly abundant in L. elliptica whereas Fluviicola dominated seawater and siphons. Typical polar bacteria were Polaribacter, Shewanella, Colwellia, and Moritella. We detected the prevalence of pathogenic bacterial sequences, particularly in the family Arcobacteraceae, Pseudomonadaceae, and Mycoplasmataceae. The prokaryotic diversity was similar among tissues, as well as their taxonomic composition, suggesting a homogeneity of the microbiome along L. elliptica body. The Antarctic clam population can be used to monitor the impact of human activity in areas near Antarctic stations that discharge wastewater.
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Affiliation(s)
| | - Garance Perrois
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
- Tropical & Subtropical Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Rodolfo Rondon
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile.
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3
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Park JY, Jo JW, An YJ, Lee JJ, Kim BS. Alterations in sea urchin (Mesocentrotus nudus) microbiota and their potential contributions to host according to barren severity. NPJ Biofilms Microbiomes 2023; 9:83. [PMID: 37907565 PMCID: PMC10618176 DOI: 10.1038/s41522-023-00450-z] [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: 02/09/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
Sea urchins are biotic factors driving the decline of kelp forests in marine ecosystems. However, few studies have analyzed the microbiota of surviving sea urchins in barren regions with scarce diet resources. Here, we analyzed the microbiota in the pharynx and gut of the sea urchin Mesocentrotus nudus located along the coast of an expanding barren region in South Korea. The ecological adaptation of genera in sea urchins was predicted using the neutral assembly model. The pharynx and gut microbiota were different, and microbes in the surrounding habitats dispersed more to the pharynx than to the gut. The gut microbiota in sea urchins is altered by barren severity and plays different roles in host energy metabolism. These findings help to understand the microbiota in sea urchins according to urchin barren and its contribution to the survival of sea urchins in severe barren regions with limited macroalgae.
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Affiliation(s)
- Joon-Young Park
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Jae-Won Jo
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Yu-Jeong An
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Jin-Jae Lee
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Bong-Soo Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea.
- The Korean Institute of Nutrition, Hallym University, Chuncheon, Gangwon-do, Republic of Korea.
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4
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Marangon E, Uthicke S, Patel F, Marzinelli EM, Bourne DG, Webster NS, Laffy PW. Life-stage specificity and cross-generational climate effects on the microbiome of a tropical sea urchin (Echinodermata: Echinoidea). Mol Ecol 2023; 32:5645-5660. [PMID: 37724851 DOI: 10.1111/mec.17124] [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: 10/28/2022] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Microbes play a critical role in the development and health of marine invertebrates, though microbial dynamics across life stages and host generations remain poorly understood in most reef species, especially in the context of climate change. Here, we use a 4-year multigenerational experiment to explore microbe-host interactions under the Intergovernmental Panel on Climate Change (IPCC)-forecast climate scenarios in the rock-boring tropical urchin Echinometra sp. A. Adult urchins (F0 ) were exposed for 18 months to increased temperature and pCO2 levels predicted for years 2050 and 2100 under RCP 8.5, a period which encompassed spawning. After rearing F1 offspring for a further 2 years, spawning was induced, and F2 larvae were raised under current day and 2100 conditions. Cross-generational climate effects were also explored in the microbiome of F1 offspring through a transplant experiment. Using 16S rRNA gene sequence analysis, we determined that each life stage and generation was associated with a distinct microbiome, with higher microbial diversity observed in juveniles compared to larval stages. Although life-stage specificity was conserved under climate conditions projected for 2050 and 2100, we observed changes in the urchin microbial community structure within life stages. Furthermore, we detected a climate-mediated parental effect when juveniles were transplanted among climate treatments, with the parental climate treatment influencing the offspring microbiome. Our findings reveal a potential for cross-generational impacts of climate change on the microbiome of a tropical invertebrate species.
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Affiliation(s)
- Emma Marangon
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
| | - Sven Uthicke
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Frances Patel
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
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5
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Rodríguez-Barreras R, Dominicci-Maura A, Tosado-Rodríguez EL, Godoy-Vitorino F. The Epibiotic Microbiota of Wild Caribbean Sea Urchin Spines Is Species Specific. Microorganisms 2023; 11:391. [PMID: 36838357 PMCID: PMC9966300 DOI: 10.3390/microorganisms11020391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Caribbean sea urchins are marine invertebrates that have experienced a decline over the years. Studies on sea urchins have focused primarily on the microbiome of the coelomic fluid or the gut microbiota. In this study, the epibiota community associated with four wild Caribbean sea urchin species, Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum, was characterized for the first time. Using 57 sea urchin animal samples, we evaluated the influence of animal species, trophic niches, and geographical location on the composition of the epibiotic microbiota. We found significant differences in the bacterial biota among species and trophic niches, but not among geographical locations. L. variegatus exhibited the highest alpha diversity with high dominance of Fusobacteria, Planctomycetes, and Cyanobacteria, whereas T. ventricosus and D. antillarum were dominated by Firmicutes. T. ventricosus inhabiting the seagrass biotope dominated by Thalassia testudinum meadows had mostly Endozoicomonas. In contrast, samples located in the reef (dominated by corals and other reef builders) had a higher abundance of Kistimonas and Photobacterium. Our findings confirm that the epibiotic microbiota is species-specific, but also niche-dependent, revealing the trophic networks emerging from the organic matter being recycled in the seagrass and reef niches. As echinoids are important grazers of benthic communities, their microbiota will likely influence ecosystem processes.
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Affiliation(s)
- Ruber Rodríguez-Barreras
- Department of Biology, University of Puerto Rico, Mayagüez Campus, P.O. Box 9000, Mayagüez 00681-9000, Puerto Rico
| | - Anelisse Dominicci-Maura
- Department of Microbiology, University of Puerto Rico School of Medicine, Guillermo Arbona Main Building, San Juan 00936-5067, Puerto Rico
| | - Eduardo L. Tosado-Rodríguez
- Department of Microbiology, University of Puerto Rico School of Medicine, Guillermo Arbona Main Building, San Juan 00936-5067, Puerto Rico
| | - Filipa Godoy-Vitorino
- Department of Microbiology, University of Puerto Rico School of Medicine, Guillermo Arbona Main Building, San Juan 00936-5067, Puerto Rico
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Digestive Enzyme Activities and Gut Emptying Are Correlated with the Reciprocal Regulation of TRPA1 Ion Channel and Serotonin in the Gut of the Sea Urchin Strongylocentrotus intermedius. BIOLOGY 2022; 11:biology11040503. [PMID: 35453703 PMCID: PMC9028161 DOI: 10.3390/biology11040503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/17/2022]
Abstract
The energetic link in the benthic community is based on physiological characteristics of the low food absorption efficiency of sea urchins. Low food absorption efficiency of sea urchins is correlated with the activity of digestive enzymes and the duration of food in their gut. Thus, the digestive enzymes activities (pepsin and amylase enzyme activities) and gut emptying are important indicators in assessing nutrient digestion and absorption in sea urchins. In the present study, the relationship between these indicators and molecules related to digestive physiology were quantified in sea urchins. We found (1) an inter-regulatory relationship existed between Transient receptor potential cation channel, subfamily A, member 1 (TRPA1), and serotonin (5-hydroxytryptamine; 5-HT) in the gut of Strongylocentrotus intermedius; (2) digestive enzyme activities were negatively correlated with the TRPA1 and concentration of 5-HT in the gut of S. intermedius; (3) gut emptying rate was positively correlated with TRPA1 and concentration of 5-HT in the gut of S. intermedius. The present study revealed that the digestion and absorption of food are correlated with the TRPA1 and 5-HT in the gut of S. intermedius, which provides valuable information about the digestive physiology of sea urchins. This novel finding is relevant to understanding the low food digestibility of sea urchins. It also provides valuable information to the digestive physiology of sea urchins, which are key to maintaining the stability of food webs in the marine ecosystem.
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7
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Díaz-Díaz LM, Rodríguez-Villafañe A, García-Arrarás JE. The Role of the Microbiota in Regeneration-Associated Processes. Front Cell Dev Biol 2022; 9:768783. [PMID: 35155442 PMCID: PMC8826689 DOI: 10.3389/fcell.2021.768783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
The microbiota, the set of microorganisms associated with a particular environment or host, has acquired a prominent role in the study of many physiological and developmental processes. Among these, is the relationship between the microbiota and regenerative processes in various organisms. Here we introduce the concept of the microbiota and its involvement in regeneration-related cellular events. We then review the role of the microbiota in regenerative models that extend from the repair of tissue layers to the regeneration of complete organs or animals. We highlight the role of the microbiota in the digestive tract, since it accounts for a significant percentage of an animal microbiota, and at the same time provides an outstanding system to study microbiota effects on regeneration. Lastly, while this review serves to highlight echinoderms, primarily holothuroids, as models for regeneration studies, it also provides multiple examples of microbiota-related interactions in other processes in different organisms.
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Affiliation(s)
- Lymarie M Díaz-Díaz
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico
| | | | - José E García-Arrarás
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico
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D’Alessio S, Buckley KM, Kraev I, Hayes P, Lange S. Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin ( Strongylocentrotus purpuratus) Coelomic Fluid-Novel Insights into Echinodermata Biology. BIOLOGY 2021; 10:866. [PMID: 34571743 PMCID: PMC8464700 DOI: 10.3390/biology10090866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
The purple sea urchin (Strongylocentrotus purpuratus) is a marine invertebrate of the class Echinoidea that serves as an important research model for developmental biology, cell biology, and immunology, as well as for understanding regenerative responses and ageing. Peptidylarginine deiminases (PADs) are calcium-dependent enzymes that mediate post-translational protein deimination/citrullination. These alterations affect protein function and may also play roles in protein moonlighting. Extracellular vesicles (EVs) are membrane-bound vesicles that are released from cells as a means of cellular communication. Their cargo includes a range of protein and RNA molecules. EVs can be isolated from many body fluids and are therefore used as biomarkers in physiological and pathological responses. This study assessed EVs present in the coelomic fluid of the purple sea urchin (Strongylocentrotus purpuratus), and identified both total protein cargo as well as the deiminated protein cargo. Deiminated proteins in coelomic fluid EVs were compared with the total deiminated proteins identified in coelomic fluid to assess putative differences in deiminated protein targets. Functional protein network analysis for deiminated proteins revealed pathways for immune, metabolic, and gene regulatory functions within both total coelomic fluid and EVs. Key KEGG and GO pathways for total EV protein cargo furthermore showed some overlap with deimination-enriched pathways. The findings presented in this study add to current understanding of how post-translational deimination may shape immunity across the phylogeny tree, including possibly via PAD activity from microbiota symbionts. Furthermore, this study provides a platform for research on EVs as biomarkers in sea urchin models.
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Affiliation(s)
- Stefania D’Alessio
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
| | | | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Polly Hayes
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK; (S.D.); (P.H.)
- UCL EGA Institute for Women’s Health, Maternal and Fetal Medicine, London WC1E 6AU, UK
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9
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Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics. Curr Issues Mol Biol 2021; 43:978-995. [PMID: 34563039 PMCID: PMC8929034 DOI: 10.3390/cimb43020070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022] Open
Abstract
This paper describes the microbial community composition and genes for key metabolic genes, particularly the nitrogen fixation of the mucous-enveloped gut digesta of green (Lytechinus variegatus) and purple (Strongylocentrotus purpuratus) sea urchins by using the shotgun metagenomics approach. Both green and purple urchins showed high relative abundances of Gammaproteobacteria at 30% and 60%, respectively. However, Alphaproteobacteria in the green urchins had higher relative abundances (20%) than the purple urchins (2%). At the genus level, Vibrio was dominant in both green (~9%) and purple (~10%) urchins, whereas Psychromonas was prevalent only in purple urchins (~24%). An enrichment of Roseobacter and Ruegeria was found in the green urchins, whereas purple urchins revealed a higher abundance of Shewanella, Photobacterium, and Bacteroides (q-value < 0.01). Analysis of key metabolic genes at the KEGG-Level-2 categories revealed genes for amino acids (~20%), nucleotides (~5%), cofactors and vitamins (~6%), energy (~5%), carbohydrates (~13%) metabolisms, and an abundance of genes for assimilatory nitrogen reduction pathway in both urchins. Overall, the results from this study revealed the differences in the microbial community and genes designated for the metabolic processes in the nutrient-rich sea urchin gut digesta, suggesting their likely importance to the host and their environment.
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10
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Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution. PLoS Biol 2021; 19:e3001322. [PMID: 34411089 PMCID: PMC8376202 DOI: 10.1371/journal.pbio.3001322] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions. This Essay argues that in order to truly understand how marine hosts benefit from the immense diversity of microbes, we need to expand towards long-term, multi-disciplinary research focussing on few areas of the world’s ocean that we refer to as “natural experiments,” where processes can be studied at scales that far exceed those captured in laboratory experiments.
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11
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Uthicke S, Patel F, Petrik C, Watson SA, Karelitz SE, Lamare MD. Cross-generational response of a tropical sea urchin to global change and a selection event in a 43-month mesocosm study. GLOBAL CHANGE BIOLOGY 2021; 27:3448-3462. [PMID: 33901341 DOI: 10.1111/gcb.15657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/09/2021] [Accepted: 04/17/2021] [Indexed: 06/12/2023]
Abstract
Long-term experimental investigations of transgenerational plasticity (TGP) and transgenerational acclimatization to global change are sparse in marine invertebrates. Here, we test the effect of ocean warming and acidification over a 25-month period of Echinometra sp. A sea urchins whose parents were acclimatized at ambient or one of two near-future (projected mid and end of the 21st century) climate scenarios for 18 months. Several parameters linked to performance exhibited strong effects of future ocean conditions at 9 months of age. The Ambient-Ambient group (A-A, both F0 and F1 at ambient conditions) was significantly larger (21%) and faster in righting response (31%) compared to other groups. A second set of contrasts revealed near-future scenarios caused significant negative parental carryover effects. Respiration at 9 months was depressed by 59% when parents were from near-future climate conditions, and righting response was slowed by 28%. At 10 months, a selective pathogenic mortality event led to significantly higher survival rates of A-A urchins. Differences in size and respiration measured prior to the mortality were absent after the event, while a negative parental effect on righting (29% reduction) remained. The capacity to spawn at the end of the experiment was higher in individuals with ambient parents (50%) compared to other groups (21%) suggesting persistent parental effects. Obtaining different results at different points in time illustrates the importance of longer term and multigeneration studies to investigate effects of climate change. Given some animals in all groups survived the pathogenic event and that effects on physiology (but not behavior) among groups were eliminated after the mortality, we suggest that similar events could constitute selective sweeps, allowing genetic adaptation. However, given the observed negative parental effects and reduced potential for population replenishment, it remains to be determined if selection would be sufficiently rapid to rescue this species from climate change effects.
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Affiliation(s)
- Sven Uthicke
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Frances Patel
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - Chelsea Petrik
- Australian Institute of Marine Science, Townsville, Qld, Australia
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research and Restoration, Sarasota, FL, USA
| | - Sue-Ann Watson
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum Network, Townsville, Qld, Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Sam E Karelitz
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Miles D Lamare
- Department of Marine Science, University of Otago, Dunedin, New Zealand
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The Gut Microbiota of Naturally Occurring and Laboratory Aquaculture Lytechinus variegatus Revealed Differences in the Community Composition, Taxonomic Co-Occurrence, and Predicted Functional Attributes. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1020016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sea urchins, in many instances, are collected from the wild, maintained in the laboratory aquaculture environment, and used as model animals for various scientific investigations. It has been increasingly evident that diet-driven dysbiosis of the gut microbiome could affect animal health and physiology, thereby impacting the outcome of the scientific studies. In this study, we compared the gut microbiome between naturally occurring (ENV) and formulated diet-fed laboratory aquaculture (LAB) sea urchin Lytechinus variegatus by amplicon sequencing of the V4 region of the 16S rRNA gene and bioinformatics tools. Overall, the ENV gut digesta had higher taxa richness with an abundance of Propionigenium, Photobacterium, Roseimarinus, and Flavobacteriales. In contrast, the LAB group revealed fewer taxa richness, but noticeable abundances of Arcobacter, Agarivorans, and Shewanella. However, Campylobacteraceae, primarily represented by Arcobacter spp., was commonly associated with the gut tissues of both ENV and LAB groups whereas the gut digesta had taxa from Gammaproteobacteria, particularly Vibrio spp. Similarly, the co-occurrence network displayed taxonomic organizations interconnected by Arcobacter and Vibrio as being the key taxa in gut tissues and gut digesta, respectively. Predicted functional analysis of the gut tissues microbiota of both ENV and LAB groups showed a higher trend in energy-related metabolisms, whereas amino acids, carbohydrate, and lipid metabolisms heightened in the gut digesta. This study provides an outlook of the laboratory-formulated diet-fed aquaculture L. variegatus gut microbiome and predicted metabolic profile as compared to the naturally occurring animals, which should be taken into consideration for consistency, reproducibility, and translatability of scientific studies.
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Ketchum RN, Smith EG, Vaughan GO, McParland D, Al-Mansoori N, Burt JA, Reitzel AM. Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients. Mol Ecol 2021; 30:3869-3881. [PMID: 34008895 DOI: 10.1111/mec.15990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 01/03/2023]
Abstract
Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32℃ in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the temperature predictive ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and highlight specific microbial taxa putatively involved in the response to thermal environment.
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Affiliation(s)
- Remi N Ketchum
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Grace O Vaughan
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Dain McParland
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Noura Al-Mansoori
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - John A Burt
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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Pan Y, Ren Q, Chen P, Wu J, Wu Z, Zhang G. Insight Into Microbial Community Aerosols Associated With Electronic Waste Handling Facilities by Culture-Dependent and Culture-Independent Methods. Front Public Health 2021; 9:657784. [PMID: 33889561 PMCID: PMC8055949 DOI: 10.3389/fpubh.2021.657784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/10/2021] [Indexed: 11/13/2022] Open
Abstract
Airborne microorganisms in the waste associated environments are more active and complex compared to other places. However, the diversity and structure of airborne bacteria in waste-associated environments are still not clearly understood. The purpose of this study was to assess airborne bacterial community in electronic waste dismantling site and a waste transfer station based on culture-dependent and culture-independent methods. A total of 229 isolates were obtained from four airborne sites collected from residential area, electronic industrial park, and office area in or near an electronic waste dismantling site and a waste transfer station in Southern China in the morning, afternoon, and evening. Most of the isolates were isolated from air for the first time and 14 potentially novel species were identified by Sanger sequencing. Bacterial communities in waste-associated bioaerosols were predominated by Proteobacteria and Bacteroidetes. Abundant genera (>1%) included Paracaedibacteraceae (uncultured EF667926), Ralstonia, Chroococcidiopsis, Chitinophagaceae (uncultured FN428761), Sphingobium, and Heliimonas. One-third of the species in these genera were uncultured approximately. Differences community structure existed in airborne bacterial diversity among different sampling sites. These results showed that waste-associated environments have unique bacterial diversity. Further studies on such environments could provide new insights into bacterial community.
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Affiliation(s)
- Yimin Pan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Qiaoqiao Ren
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Pei Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jiguo Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zhendong Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Guoxia Zhang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
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Faddetta T, Ardizzone F, Faillaci F, Reina C, Palazzotto E, Strati F, De Filippo C, Spinelli G, Puglia AM, Gallo G, Cavalieri V. Composition and geographic variation of the bacterial microbiota associated with the coelomic fluid of the sea urchin Paracentrotus lividus. Sci Rep 2020; 10:21443. [PMID: 33293569 PMCID: PMC7723044 DOI: 10.1038/s41598-020-78534-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 11/19/2020] [Indexed: 12/26/2022] Open
Abstract
In the present work, culture-based and culture-independent investigations were performed to determine the microbiota structure of the coelomic fluid of Mediterranean sea urchin Paracentrotus lividus individuals collected from two distinct geographical sites neighboring a high-density population bay and a nature reserve, respectively. Next Generation Sequencing analysis of 16S rRNA gene (rDNA) showed that members of the Proteobacteria, Bacteroidetes and Fusobacteria phyla, which have been previously reported to be commonly retrieved from marine invertebrates, dominate the overall population of microorganisms colonizing this liquid tissue, with minority bacterial genera exhibiting remarkable differences among individuals. Our results showed that there is a correlation between microbiota structure and geographical location of the echinoderm collection site, highlighting over-representation of metagenomic functions related to amino acid and bioactive peptides metabolism in specimens inhabiting the nature reserve. Finally, we also described the developmental delay and aberrations exhibited by sea urchin embryos exposed to distinct bacterial isolates, and showed that these defects rely upon hydrophilic compound(s) synthesized by the bacterial strains assayed. Altogether, our findings lay the groundwork to decipher the relationships of bacteria with sea urchins in their aquatic environment, also providing an additional layer of information to understand the biological roles of the coelomic fluid.
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Affiliation(s)
- Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Francesco Ardizzone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Francesca Faillaci
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Chiara Reina
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Piazza Delle Cliniche 2, 90127, Palermo, Italy
| | - Emilia Palazzotto
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Francesco Strati
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello, 16, 20139, Milano, Italy
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Moruzzi, 1, 56124, Pisa, Italy
| | - Giovanni Spinelli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy.
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Hylander BL, Repasky EA. Temperature as a modulator of the gut microbiome: what are the implications and opportunities for thermal medicine? Int J Hyperthermia 2020; 36:83-89. [PMID: 31795833 DOI: 10.1080/02656736.2019.1647356] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
There is substantial research being conducted on the relationships between the gut microbiome, the immune response and health and disease. Environmental temperature and heat stress are known to modify the gut microbiome. Changes in core temperature have been linked, in multiple phyla, to altered microbiome composition and function. This raises the question of whether local/regional or whole body thermal therapies which target tumors in the abdomen, peritoneal cavity, or pelvis influence the gut microbiome. To date, there is little information on whether thermal therapy exerts positive or negative effects on the microbiome. This is an intriguing question since there is growing interest in the immunological impact of various thermal therapies. The goal of this brief review is to highlight research on how environmental conditions, particularly temperature (internal as well as external temperatures) influences the gut microbiome. Given the potential for temperature shifts to modulate gut microbe function and composition, it is likely that various forms of thermal therapy, including hyperthermic intraperitoneal chemotherapy (HIPEC), deep regional, and whole body hyperthermia influence the microbiome in ways that are currently not appreciated. More research is needed to determine whether thermal therapy induced changes in the microbiome occur, and whether they are beneficial or detrimental to the host. Currently, although approaches to microbiome modification such as dietary intervention, fecal transfer, probiotics and prebiotics are being developed, the potential of temperature manipulation has, as yet, not been explored. Therefore, new research could reveal whether perturbations of the microbiome composition that have negative health consequences (dysbiosis) could be an important target for treatment by thermal medicine.
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Affiliation(s)
- Bonnie L Hylander
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Elizabeth A Repasky
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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Frankel-Bricker J, Song MJ, Benner MJ, Schaack S. Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature. MICROBIAL ECOLOGY 2020; 79:731-742. [PMID: 31377832 PMCID: PMC7176607 DOI: 10.1007/s00248-019-01412-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/04/2019] [Indexed: 05/09/2023]
Abstract
Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism's biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any differences in genotype- or population-specific microbial communities, and to assess whether the microbiota varied among temperatures. Our study is similar to a recent comparison of the microbial communities among D. magna genotypes raised in different temperatures published by Sullam et al. (Microb Ecol 76(2):506-517, 2017), and as such represents one of the first examples of a reproducible result in microbiome research. Like the previous study, we find evidence for a strong effect of temperature on the microbiome of D. magna, although across a much smaller temperature range representing potential near-future climates. In addition, we find evidence that the microbiomes of D. magna genotypes from different regions are distinct, even years after being brought into the laboratory. Finally, our results highlight a potentially common finding in the expanding area of microbiome research-differences among treatments are not necessarily observed in the most abundant taxonomic groups. This highlights the importance of considering sampling scheme and depth of coverage when characterizing the microbiome, as different experimental designs can significantly impact taxon-specific results, even when large-scale effects are reproduced.
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Affiliation(s)
- Jonas Frankel-Bricker
- Department of Biology, Reed College, Portland, OR, 97202, USA
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - Michael J Song
- University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Maia J Benner
- Department of Biology, Reed College, Portland, OR, 97202, USA
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, 97202, USA.
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Schwob G, Cabrol L, Poulin E, Orlando J. Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii. Front Microbiol 2020; 11:308. [PMID: 32184772 PMCID: PMC7058685 DOI: 10.3389/fmicb.2020.00308] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/11/2020] [Indexed: 12/25/2022] Open
Abstract
Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition and putative functional capacity, evaluating its differentiation among the gut content and the gut tissue in comparison with the external sediment. Additionally, we aimed to define a core gut microbiota between A. agassizii populations to identify potential keystone bacterial taxa. Our results show that the diversity and the composition of the microbiota, at both genetic and predicted functional levels, were mostly driven by the sample type, and to a lesser extent by the population location. Specific bacterial taxa, belonging mostly to Planctomycetacia and Spirochaetia, were differently enriched in the gut content and the gut tissue, respectively. Predictive functional profiles revealed higher abundance of specific pathways, as the sulfur cycle in the gut content and the amino acid metabolism, in the gut tissue. Further, the definition of a core microbiota allowed to obtain evidence of specific localization of bacterial taxa and the identification of potential keystone taxa assigned to the Desulfobacula and Spirochaeta genera as potentially host selected. The ecological relevance of these keystone taxa in the host metabolism is discussed.
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Affiliation(s)
- Guillaume Schwob
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Léa Cabrol
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
| | - Elie Poulin
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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A horizon scan of priorities for coastal marine microbiome research. Nat Ecol Evol 2019; 3:1509-1520. [PMID: 31636428 DOI: 10.1038/s41559-019-0999-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 09/05/2019] [Indexed: 12/21/2022]
Abstract
Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the 'microbiome') and the environment or their hosts - termed the 'holobiont'. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research.
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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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Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling. Sci Rep 2018; 8:16476. [PMID: 30405146 PMCID: PMC6220307 DOI: 10.1038/s41598-018-34697-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/24/2018] [Indexed: 12/19/2022] Open
Abstract
The recent outbreak of Sea Star Wasting Disease (SSWD) is one of the largest marine epizootics in history, but the host-associated microbial community changes specific to disease progression have not been characterized. Here, we sampled the microbiomes of ochre sea stars, Pisaster ochraceus, through time as animals stayed healthy or became sick and died with SSWD. We found community-wide differences in the microbiomes of sick and healthy sea stars, changes in microbial community composition through disease progression, and a decrease in species richness of the microbiome in late stages of SSWD. Known beneficial taxa (Pseudoalteromonas spp.) decreased in abundance at symptom onset and through disease progression, while known pathogenic (Tenacibaculum spp.) and putatively opportunistic bacteria (Polaribacter spp. and Phaeobacter spp.) increased in abundance in early and late disease stages. Functional profiling revealed microbes more abundant in healthy animals performed functions that inhibit growth of other microbes, including pathogen detection, biosynthesis of secondary metabolites, and degradation of xenobiotics. Changes in microbial composition with disease onset and progression suggest that a microbial imbalance of the host could lead to SSWD or be a consequence of infection by another pathogen. This work highlights the importance of the microbiome in SSWD and also suggests that a healthy microbiome may help confer resistance to SSWD.
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