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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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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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Dong Y, Li Y, Ge M, Takatsu T, Wang Z, Zhang X, Ding D, Xu Q. Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats. Microbiol Spectr 2023; 11:e0207323. [PMID: 37889056 PMCID: PMC10715168 DOI: 10.1128/spectrum.02073-23] [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: 05/17/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.
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Affiliation(s)
- Yue Dong
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yixuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Meiling Ge
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Tetsuya Takatsu
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Zongling Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Dewen Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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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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Masasa M, Kushmaro A, Nguyen D, Chernova H, Shashar N, Guttman L. Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin. Microbiol Spectr 2023; 11:e0051423. [PMID: 37097162 PMCID: PMC10269587 DOI: 10.1128/spectrum.00514-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
Dietary influence on the microbiome in algivorous sea urchins such as Tripneustes gratilla elatensis suggests a bacterial contribution to the digestion of fiber-rich seaweed. An ecological insight into the spatial arrangement in the gut bacterial community will improve our knowledge of host-microbe relations concerning the involved taxa, their metabolic repertoire, and the niches of activity. Toward this goal, we investigated the bacterial communities in the esophagus, stomach, and intestine of Ulva-fed sea urchins through 16S rRNA amplicon sequencing, followed by the prediction of their functional genes. We revealed communities with distinct features, especially those in the esophagus and intestine. The esophageal community was less diverse and was poor in food digestive or fermentation genes. In contrast, bacteria that can contribute to the digestion of the dietary Ulva were common in the stomach and intestine and consisted of genes for carbohydrate decomposition, fermentation, synthesis of short-chain fatty acids, and various ways of N and S metabolism. Bacteroidetes and Firmicutes were found as the main phyla in the gut and are presumably also necessary in food digestion. The abundant sulfate-reducing bacteria in the stomach and intestine from the genera Desulfotalea, Desulfitispora, and Defluviitalea may aid in removing the excess sulfate from the decomposition of the algal polysaccharides. Although these sea urchins were fed with Ulva, genes for the degradation of polysaccharides of other algae and plants were present in this sea urchin gut microbiome. We conclude that the succession of microbial communities along the gut obtained supports the hypothesis on bacterial contribution to food digestion. IMPORTANCE Alga grazing by the sea urchin Tripneustes gratilla elatensis is vital for nutrient recycling and constructing new reefs. This research was driven by the need to expand the knowledge of bacteria that may aid this host in alga digestion and their phylogeny, roles, and activity niches. We hypothesized alterations in the bacterial compositional structure along the gut and their association with the potential contribution to food digestion. The current spatial insight into the sea urchin's gut microbiome ecology is novel and reveals how distinct bacterial communities are when distant from each other in this organ. It points to keynote bacteria with genes that may aid the host in the digestion of the complex sulfated polysaccharides in dietary Ulva by removing the released sulfates and fermentation to provide energy. The gut bacteria's genomic arsenal may also help to gain energy from diets of other algae and plants.
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Affiliation(s)
- Matan Masasa
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev, Eilat, Israel
- Israel Oceanographic and Limnological Research, The National Center for Mariculture, Eilat, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dzung Nguyen
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev, Eilat, Israel
- Israel Oceanographic and Limnological Research, The National Center for Mariculture, Eilat, Israel
| | - Helena Chernova
- Israel Oceanographic and Limnological Research, The National Center for Mariculture, Eilat, Israel
| | - Nadav Shashar
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev, Eilat, Israel
| | - Lior Guttman
- Israel Oceanographic and Limnological Research, The National Center for Mariculture, Eilat, Israel
- Ben-Gurion University of the Negev, Department of Life Sciences, Beer-Sheva, Israel
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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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Significant Changes in Bacterial Communities Associated with Pocillopora Corals Ingestion by Crown-of-Thorns Starfish: An Important Factor Affecting the Coral’s Health. Microorganisms 2022; 10:microorganisms10020207. [PMID: 35208662 PMCID: PMC8879049 DOI: 10.3390/microorganisms10020207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 02/07/2023] Open
Abstract
Coral ingestion by crown-of-thorns starfish (COTS) is an important cause of coral reef degradation, although the impacts of COTS feeding on coral-associated microbial communities are not well understood. Therefore, in this study, we analyzed the coral tissue-weight, Symbiodiniaceae density (SD), bacterial community composition, and the predicted functions of bacterial genes associated with Pocillopora corals in healthy portions and feeding scars, following COTS feeding. Coral tissue-weight loss rate in the feeding scars was 71.3–94.95%. The SDs were significantly lower in the feeding scars, and the SD-loss rate was 92.05% ± 2.12%. The relative abundances of bacterial communities associated with Pocillopora corals after COTS feeding changed significantly and were almost completely reorganized at the phylum and genus levels. Analysis of the microbial metagenomic-functional capacities showed that numerous physiological functions of the coral-bacterial holobionts in the feeding scars were different, including amino acid metabolism, xenobiotic biodegradation and metabolism, lipid metabolism, membrane transport, signal transduction, and cell motility, and all these capacities could be corroborated based on metagenomic, transcriptomic or proteomic technologies. Overall, our research suggests that coral holobionts may be destroyed by COTS, and our findings imply that bacterial communities in feeding scars could affect the health of Pocillopora corals.
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Masasa M, Kushmaro A, Kramarsky-Winter E, Shpigel M, Barkan R, Golberg A, Kribus A, Shashar N, Guttman L. Mono-specific algal diets shape microbial networking in the gut of the sea urchin Tripneustes gratilla elatensis. Anim Microbiome 2021; 3:79. [PMID: 34782025 PMCID: PMC8594234 DOI: 10.1186/s42523-021-00140-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Algivorous sea urchins can obtain energy from a diet of a single algal species, which may result in consequent changes in their gut microbe assemblies and association networks. METHODS To ascertain whether such changes are led by specific microbes or limited to a specific region in the gut, we compared the microbial assembly in the three major gut regions of the sea urchin Tripneustes gratilla elatensis when fed a mono-specific algal diet of either Ulva fasciata or Gracilaria conferta, or an algal-free diet. DNA extracts from 5 to 7 individuals from each diet treatment were used for Illumina MiSeq based 16S rRNA gene sequencing (V3-V4 region). Niche breadth of each microbe in the assembly was calculated for identification of core, generalist, specialist, or unique microbes. Network analyzers were used to measure the connectivity of the entire assembly and of each of the microbes within it and whether it altered with a given diet or gut region. Lastly, the predicted metabolic functions of key microbes in the gut were analyzed to evaluate their potential contribution to decomposition of dietary algal polysaccharides. RESULTS Sea urchins fed with U. fasciata grew faster and their gut microbiome network was rich in bacterial associations (edges) and networking clusters. Bacteroidetes was the keystone microbe phylum in the gut, with core, generalist, and specialist representatives. A few microbes of this phylum were central hub nodes that maintained community connectivity, while others were driver microbes that led the rewiring of the assembly network based on diet type through changes in their associations and centrality. Niche breadth agreed with microbes' richness in genes for carbohydrate active enzymes and correlated Bacteroidetes specialists to decomposition of specific polysaccharides in the algal diets. CONCLUSIONS The dense and well-connected microbial network in the gut of Ulva-fed sea urchins, together with animal's rapid growth, may suggest that this alga was most nutritious among the experimental diets. Our findings expand the knowledge on the gut microbial assembly in T. gratilla elatensis and strengthen the correlation between microbes' generalism or specialism in terms of occurrence in different niches and their metabolic arsenal which may aid host nutrition.
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Affiliation(s)
- Matan Masasa
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev, Eilat Campus, Eilat, Israel.,Israel Oceanographic and Limnological Research, The National Center for Mariculture, P.O. Box 1212, 8811201, Eilat, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, 8410501, Beer-Sheva, Israel
| | - Esti Kramarsky-Winter
- Avram and Stella Goldstein-Goren, Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, 8410501, Beer-Sheva, Israel
| | - Muki Shpigel
- Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, 3498838, Haifa, Israel
| | - Roy Barkan
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev, Eilat Campus, Eilat, Israel.,Israel Oceanographic and Limnological Research, The National Center for Mariculture, P.O. Box 1212, 8811201, Eilat, Israel
| | - Alex Golberg
- Department of Environmental Studies, Tel Aviv University, P.O. Box 39040, 6997801, Tel Aviv, Israel
| | - Abraham Kribus
- School of Mechanical Engineering, Tel Aviv University, P.O. Box 39040, 6997801, Tel Aviv, Israel
| | - Nadav Shashar
- Marine Biology and Biotechnology Program, Department of Life Sciences, Ben-Gurion University of the Negev, Eilat Campus, Eilat, Israel
| | - Lior Guttman
- Israel Oceanographic and Limnological Research, The National Center for Mariculture, P.O. Box 1212, 8811201, Eilat, Israel.
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Zapata-Vívenes E, Bastidas M, Marcano LDV, Sonnenholzner-Varas J. Colorless spherule cells and lysozyme contribute to innate immunological responses in the sea urchin Lytechinus variegatus, exposed to bacterial challenge. FISH & SHELLFISH IMMUNOLOGY 2021; 117:253-261. [PMID: 34418557 DOI: 10.1016/j.fsi.2021.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
The sea urchin Lytechinus variegatus is considered a good candidate for aquaculture, but bacterial diseases are a major challenge in culture conditions. The innate immunological defenses of L. variegatus to bacterial challenges were assessed through hematology parameters, in vitro phagocytosis, lysozyme activity and total plasma protein concentrations in cell-free coelomic fluid. Adult sea urchins were inoculated with Microccocus lysodeikticus, Escherichia coli and Vibrio parahaemolyticus in the cavity coelomic. Filtrated and sterile seawater (FSW) injected and non-injected sea urchins were used as control groups. Righting time, external aspects and behavior of sea urchins were evaluated. Twenty-four hours post-inoculation, we found an increase in the population of colorless spherule cells (CLS), phagocytosis, and humoral responses in sea urchins challenged by bacterial inoculations. Righting time was not affected by the treatments and apparent external signs of disease were not observed at least during 96h post-inoculation. The immunological system of L. variegatus quickly eliminated pathogenic microorganisms. CLS and lysozyme activity cooperate in the immune defenses of L. variegatus, showing an extraordinary efficiency for adjusting the immune defenses under stress caused by microbes. We recommend that the cellular and humoral markers serve as routine tests to monitor health status in sea urchins.
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Affiliation(s)
- Edgar Zapata-Vívenes
- Grupo de Biología y Cultivo de Equinodermos, Departamento de Acuicultura, Pesca y Recursos Naturales Renovables, Facultad de Ciencias Veterinarias, Universidad Técnica de Manabí, Ecuador.
| | - Mariángel Bastidas
- Departamento de Bioanálisis, Escuela de Ciencias, Núcleo de Sucre, Universidad de Oriente, Venezuela.
| | - Leida Del Valle Marcano
- Laboratorio de Bioquímica y Ecotoxicología, Departamento de Biología, Escuela de Ciencias, Núcleo de Sucre, Universidad de Oriente, Venezuela.
| | - Jorge Sonnenholzner-Varas
- Grupo de Biología y Cultivo de Equinodermos, Departamento de Acuicultura, Pesca y Recursos Naturales Renovables, Facultad de Ciencias Veterinarias, Universidad Técnica de Manabí, Ecuador.
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10
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Rodríguez-Barreras R, Tosado-Rodríguez EL, Godoy-Vitorino F. Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins. PeerJ 2021; 9:e12084. [PMID: 34540373 PMCID: PMC8415288 DOI: 10.7717/peerj.12084] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/07/2021] [Indexed: 11/20/2022] Open
Abstract
Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species' guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.
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Affiliation(s)
| | - Eduardo L Tosado-Rodríguez
- Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, School of Medicine, San Juan, Puerto Rico, USA
| | - Filipa Godoy-Vitorino
- Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, School of Medicine, San Juan, Puerto Rico, USA
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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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12
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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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13
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Ballarin L, Karahan A, Salvetti A, Rossi L, Manni L, Rinkevich B, Rosner A, Voskoboynik A, Rosental B, Canesi L, Anselmi C, Pinsino A, Tohumcu BE, Jemec Kokalj A, Dolar A, Novak S, Sugni M, Corsi I, Drobne D. Stem Cells and Innate Immunity in Aquatic Invertebrates: Bridging Two Seemingly Disparate Disciplines for New Discoveries in Biology. Front Immunol 2021; 12:688106. [PMID: 34276677 PMCID: PMC8278520 DOI: 10.3389/fimmu.2021.688106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022] Open
Abstract
The scopes related to the interplay between stem cells and the immune system are broad and range from the basic understanding of organism's physiology and ecology to translational studies, further contributing to (eco)toxicology, biotechnology, and medicine as well as regulatory and ethical aspects. Stem cells originate immune cells through hematopoiesis, and the interplay between the two cell types is required in processes like regeneration. In addition, stem and immune cell anomalies directly affect the organism's functions, its ability to cope with environmental changes and, indirectly, its role in ecosystem services. However, stem cells and immune cells continue to be considered parts of two branches of biological research with few interconnections between them. This review aims to bridge these two seemingly disparate disciplines towards much more integrative and transformative approaches with examples deriving mainly from aquatic invertebrates. We discuss the current understanding of cross-disciplinary collaborative and emerging issues, raising novel hypotheses and comments. We also discuss the problems and perspectives of the two disciplines and how to integrate their conceptual frameworks to address basic equations in biology in a new, innovative way.
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Affiliation(s)
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli, Mersin, Turkey
| | - Alessandra Salvetti
- Department of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Pisa, Italy
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Pisa, Italy
| | - Lucia Manni
- Department of Biology, University of Padua, Padua, Italy
| | - Baruch Rinkevich
- Department of Biology, Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Amalia Rosner
- Department of Biology, Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Ayelet Voskoboynik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States
- Department of Biology, Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Regenerative Medicine and Stem Cells, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Laura Canesi
- Department of Earth Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Chiara Anselmi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States
| | - Annalisa Pinsino
- Institute for Biomedical Research and Innovation, National Research Council, Palermo, Italy
| | - Begüm Ece Tohumcu
- Middle East Technical University, Institute of Marine Sciences, Erdemli, Mersin, Turkey
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andraž Dolar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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14
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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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15
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Dong Y, Li Y, He P, Wang Z, Fan S, Zhang Z, Zhang X, Xu Q. Gut Microbial Composition and Diversity in Four Ophiuroid Species: Divergence Between Suspension Feeder and Scavenger and Their Symbiotic Microbes. Front Microbiol 2021; 12:645070. [PMID: 33815331 PMCID: PMC8017295 DOI: 10.3389/fmicb.2021.645070] [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: 01/07/2021] [Accepted: 02/19/2021] [Indexed: 12/31/2022] Open
Abstract
Gut microbiota have important roles in the survival and adaptation of the host. Ophiuroids, as the worldwide dominant benthos, have ecological roles in benthic-pelagic coupling in the sea floor. However, little is known about the composition and diversity of their gut microbiota and its potential functions in benthic ecosystems. In present study, we preformed 16S rRNA sequencing and function analysis in four dominant species (Stegophiura sladeni, Ophiopholis mirabilis, Ophiura sarsii vadicola, and Ophiura kinbergi) with two feeding types (suspension feeding/herbivores and scavenger/carnivores) from the Yellow Sea, China. Results showed that 56 phyla and 569 genera of microbiota were identified among ophiuroid guts. Multivariate and diversity analyses showed that the ophiuroid gut microbiota were independent and have higher biodiversity to the sediment microbial in the Yellow Sea. Phyla Proteobacteria, Firmicutes, Tenericutes, and Bacteroidetes were the dominant bacteria, with more than 80% abundance among the four ophiuroid species. A comparison among the gut microbial compositions among four ophiuroids showed the similarity of two offshore carnivore ophiuroids (S. sladeni and O. sarsii vadicola) and variation in the dominant microbiota types of three nearshore ophiuroids (S. sladeni, O. mirabilis, and O. kinbergi). The functional analysis revealed the significant differences of the environment-related expression in S. sladeni gut microbiota between nearshore and offshore environments. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional annotation showed the significant divergence of metabolism pathways between two nearshore species, the herbivores O. mirabilis and carnivores S. sladeni, such as the Lipid metabolism, Carbohydrate metabolism, and Metabolism of cofactors and vitamins. The homolog search and phylogenetic analysis identified the first gut symbiotic Candidatus Hepatoplasma in S. sladeni with important roles for the nutrient metabolisms. Overall, our study reported the comprehensive data of ophiuroid gut microbiota, while the functional microbiome provides insight into the physiology and environmental adaptation in ophiuroids.
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Affiliation(s)
- Yue Dong
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yixuan Li
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Peiqing He
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Zongling Wang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shiliang Fan
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | | | - Xuelei Zhang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qinzeng Xu
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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16
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Undaria pinnatifida exudates trigger shifts in seawater chemistry and microbial communities from Atlantic Patagonian coasts. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02471-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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The bacterial composition associated with Atriolum robustum, a common ascidian from Xisha coral reef, China. Symbiosis 2021. [DOI: 10.1007/s13199-020-00742-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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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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19
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Sea Cucumber Intestinal Regeneration Reveals Deterministic Assembly of the Gut Microbiome. Appl Environ Microbiol 2020; 86:AEM.00489-20. [PMID: 32358014 DOI: 10.1128/aem.00489-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/28/2020] [Indexed: 01/08/2023] Open
Abstract
The gut microbiome has far-reaching effects on host organism health, so understanding the processes that underlie microbial community assembly in the developing gut is a current research priority. Here, a holothurian (also known as sea cucumber; phylum Echinodermata) host is explored as a promising model system for studying the assembly of the gut microbiome. Holothurians have a unique capacity for evisceration (expulsion of the internal organs), followed by rapid regeneration of the gut, decoupling host ontogeny from gut tissue development and permitting experimental manipulation of the gut microbiome in mature host individuals. Here, evisceration was induced in the sea cucumber Sclerodactyla briareus, and regenerating stomach and intestine microbiomes were characterized before and on days 0, 13, 17, and 20 after evisceration using Illumina sequencing of 16S rRNA genes. Regenerating stomach and intestine tissues had microbial communities significantly different from those of mature tissues, with much higher alpha diversity and evenness of taxa in regenerating tissues. Despite immersion in a diverse pool of sediment and seawater microbes in flowthrough seawater aquaria, regenerating gut microbiomes differed at each stage of regeneration and displayed a highly similar community structure among replicates, providing evidence for deterministic host selection of a specific microbial consortium. Moreover, regenerating gut tissues acquired a microbiome that likely conferred energetic and immune advantages to the sea cucumber host, including microbes that can fix carbon and degrade invading pathogens.IMPORTANCE The gut microbiome is pertinent to many aspects of animal health, and there is a great need for natural but tractable experimental systems to examine the processes shaping gut microbiome assembly. Here, the holothurian (sea cucumber) Sclerodactyla briareus was explored as an experimental system to study microbial colonization in the gut, as S. briareus individuals have the ability to completely eviscerate and rapidly regenerate their digestive organs. After induced evisceration, microbial community assembly was characterized over 20 days in regenerating animals. This study demonstrated that colonization of the sea cucumber gut was deterministic; despite immersion in a diverse consortium of environmental microbes, a specific subset of microbes proliferated in the gut, including taxa that likely conferred energetic and immune advantages to the host. Sea cucumbers have the potential to revolutionize our understanding of gut microbiome assembly, as rapid and repeatable gut tissue regeneration provides a promising and tractable experimental system.
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20
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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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21
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Woodhams DC, Bletz MC, Becker CG, Bender HA, Buitrago-Rosas D, Diebboll H, Huynh R, Kearns PJ, Kueneman J, Kurosawa E, LaBumbard BC, Lyons C, McNally K, Schliep K, Shankar N, Tokash-Peters AG, Vences M, Whetstone R. Host-associated microbiomes are predicted by immune system complexity and climate. Genome Biol 2020; 21:23. [PMID: 32014020 PMCID: PMC6996194 DOI: 10.1186/s13059-019-1908-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors. RESULTS Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate. CONCLUSIONS Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.
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Affiliation(s)
- Douglas C. Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Molly C. Bletz
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - C. Guilherme Becker
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Hayden A. Bender
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Daniel Buitrago-Rosas
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Hannah Diebboll
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Roger Huynh
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Patrick J. Kearns
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Jordan Kueneman
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Building – 401, 0843-03092 Panamá, Panama
| | - Emmi Kurosawa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | | | - Casandra Lyons
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Kerry McNally
- School for the Environment, University of Massachusetts, Boston, MA 02125 USA
- Animal Health Department, New England Aquarium, Boston, MA 02110 USA
| | - Klaus Schliep
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Nachiket Shankar
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Amanda G. Tokash-Peters
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, RN1, Butare, Rwanda
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Ross Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
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22
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Schuh NW, Carrier TJ, Schrankel CS, Reitzel AM, Heyland A, Rast JP. Bacterial Exposure Mediates Developmental Plasticity and Resistance to Lethal Vibrio lentus Infection in Purple Sea Urchin (Strongylocentrotus purpuratus) Larvae. Front Immunol 2020; 10:3014. [PMID: 31993052 PMCID: PMC6971090 DOI: 10.3389/fimmu.2019.03014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/09/2019] [Indexed: 12/27/2022] Open
Abstract
Exposure to and colonization by bacteria during development have wide-ranging beneficial effects on animal biology but can also inhibit growth or cause disease. The immune system is the prime mediator of these microbial interactions and is itself shaped by them. Studies using diverse animal taxa have begun to elucidate the mechanisms underlying the acquisition and transmission of bacterial symbionts and their interactions with developing immune systems. Moreover, the contexts of these associations are often confounded by stark differences between "wild type" microbiota and the bacterial communities associated with animals raised in conventional or germ-free laboratories. In this study, we investigate the spatio-temporal kinetics of bacterial colonization and associated effects on growth and immune function in larvae of the purple sea urchin (Strongylocentrotus purpuratus) as a model for host-microbe interactions and immune system development. We also compare the host-associated microbiota of developing embryos and larvae raised in natural seawater or exposed to adult-associated bacteria in the laboratory. Bacteria associated with zygotes, embryos, and early larvae are detectable with 16S amplicon sequencing, but 16S-FISH indicates that the vast majority of larval bacterial load is acquired after feeding begins and is localized to the gut lumen. The bacterial communities of laboratory-cultured embryos are significantly less diverse than the natural microbiota but recapitulate its major components (Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes), suggesting that biologically relevant host-microbe interactions can be studied in the laboratory. We also demonstrate that bacterial exposure in early development induces changes in morphology and in the immune system. In the absence of bacteria, larvae grow larger at the 4-arm stage. Additionally, bacteria-exposed larvae are significantly more resistant to lethal infection with the larva-associated pathogen Vibrio lentus suggesting that early exposure to high levels of microbes, as would be expected in natural conditions, affects the immune state in later larvae. These results expand our knowledge of microbial influences on early sea urchin development and establish a model in which to study the interactions between the developing larval immune system and the acquisition of larval microbiota.
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Affiliation(s)
- Nicholas W Schuh
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Tyler J Carrier
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Catherine S Schrankel
- Department of Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada.,Department of Immunology, University of Toronto, Toronto, ON, Canada.,Marine Biology Research Division, Scripps Institute of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Andreas Heyland
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Jonathan P Rast
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada.,Department of Immunology, University of Toronto, Toronto, ON, Canada.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States.,Emory Vaccine Center, Emory University, Atlanta, GA, United States
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23
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Lawrence JM, Lawrence AL, Watts SA. Ingestion, digestion, and digestibility of regular sea urchins. DEVELOPMENTS IN AQUACULTURE AND FISHERIES SCIENCE 2020. [DOI: 10.1016/b978-0-12-819570-3.00009-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Cleary DFR, Polónia ARM, Huang YM, Swierts T. Compositional variation between high and low prokaryotic diversity coral reef biotopes translates to different predicted metagenomic gene content. Antonie van Leeuwenhoek 2019; 113:563-587. [PMID: 31802337 DOI: 10.1007/s10482-019-01364-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
Abstract
In a previous study, we identified host species that housed high and low diversity prokaryotic communities. In the present study, we expand on this and assessed the prokaryotic communities associated with seawater, sediment and 11 host species from 7 different phyla in a Taiwanese coral reef setting. The host taxa sampled included hard, octo- and black corals, molluscs, bryozoans, flatworms, fish and sea urchins. There were highly significant differences in composition among host species and all host species housed distinct communities from those found in seawater and sediment. In a hierarchical clustering analysis, samples from all host species, with the exception of the coral Galaxea astreata, formed significantly supported clusters. In addition to this, the coral G. astreata and the bryozoan Triphyllozoon inornatum on the one hand and the coral Tubastraea coccinea, the hermit crab Calcinus laevimanus and the flatworm Thysanozoon nigropapillosum on the other formed significantly supported clusters. In addition to composition, there were highly pronounced differences in richness and evenness among host species from the most diverse species, the bryozoan T. inornatum at 2518 ± 240 OTUs per 10,000 sequences to the least diverse species, the octocoral Cladiella sp. at 142 ± 14 OTUs per 10,000 sequences. In line with the differences in composition, there were significant differences in predicted metagenomic gene counts among host species. Furthermore, there were pronounced compositional and predicted functional differences between high diversity hosts (Liolophura japonica, G. astreata, T. coccinea, C. laevimanus, T. inornatum) and low diversity hosts (Antipathes sp., Pomacentrus coelestis, Modiolus auriculatus, T. nigropapillosum, Cladiella sp. and Diadema savigny). In particular, we found that all tested low diversity hosts were predicted to be enriched for the phosphotransferase system compared to high diversity hosts.
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Affiliation(s)
- Daniel F R Cleary
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Ana Rita M Polónia
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Yusheng M Huang
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, Penghu, Taiwan.,Department of Marine Recreation, University of Science and Technology, Penghu, Taiwan
| | - Thomas Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands
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25
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Microbial Diversity of the Red Sea Urchin Loxechinus albus during Controlled Farming in Puerto Montt, Chile, Using 16S rRNA Gene Amplicon Sequencing. Microbiol Resour Announc 2019; 8:8/42/e00851-19. [PMID: 31624162 PMCID: PMC6797527 DOI: 10.1128/mra.00851-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Loxechinus albus is a shallow-water sea urchin, and its distribution is related to the cold water of the Southern Hemisphere. Recently, bacterial communities, also called microbiota, in sea urchins have started being explored. In this report, we have characterized the surface, testa, and gonad microbiota using 16S rRNA sequencing. Loxechinus albus is a shallow-water sea urchin, and its distribution is related to the cold water of the Southern Hemisphere. Recently, bacterial communities, also called microbiota, in sea urchins have started being explored. In this report, we have characterized the surface, testa, and gonad microbiota using 16S rRNA sequencing.
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26
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Hakim JA, Morrow CD, Watts SA, Bej AK. High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of naturally occurring and laboratory aquaculture green sea urchins Lytechinus variegatus. Data Brief 2019; 26:104405. [PMID: 31528670 PMCID: PMC6742851 DOI: 10.1016/j.dib.2019.104405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 02/01/2023] Open
Abstract
We present high-throughput amplicon sequence (HTS) datasets of the microbial metacommunity DNA of the gut tissue and the gut digesta of naturally occurring (n = 3) and laboratory aquaculture (n = 2) green sea urchins, Lytechinus variegatus. The HTS datasets were generated on an Illumina MiSeq by targeting the amplicons of the V4 region of the 16S rRNA gene. After the raw sequences were quality checked and filtered, 88% of the sequence reads were subjected to bioinformatics analyses to generate operation taxonomic units (OTUs), which were then verified for saturation by using rarefaction analysis at a 3% sequence variation. Further, the OTUs were randomly subsampled to the minimum sequence count values. Then, the FASTA-formatted representative sequences of the microbiota were assigned taxonomic identities through multiple databases using the SILVA ACT: Alignment, Classification and Tree Service (www.arb-silva.de/aligner). The HTS datasets of this metagenome can be accessed from the BioSample Submission Portal (https://www.ncbi.nlm.nih.gov/bioproject/) under the BioProject IDs PRJNA291441 and PRJNA326427.
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Affiliation(s)
- Joseph A. Hakim
- Department of Biology, The University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA
| | - Stephen A. Watts
- Department of Biology, The University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA
| | - Asim K. Bej
- Department of Biology, The University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA
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27
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Yao Q, Yu K, Liang J, Wang Y, Hu B, Huang X, Chen B, Qin Z. The Composition, Diversity and Predictive Metabolic Profiles of Bacteria Associated With the Gut Digesta of Five Sea Urchins in Luhuitou Fringing Reef (Northern South China Sea). Front Microbiol 2019; 10:1168. [PMID: 31191489 PMCID: PMC6546719 DOI: 10.3389/fmicb.2019.01168] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/07/2019] [Indexed: 11/18/2022] Open
Abstract
Sea urchins strongly affect reef ecology, and the bacteria associated with their gut digesta have not been well studied in coral reefs. In the current study, we analyze the bacterial composition of five sea urchin species collected from Luhuitou fringing reef, namely Stomopneustes variolaris, Diadema setosum, Echinothrix calamaris, Diadema savignyi, and Tripneustes gratilla, using high-throughput 16S rRNA gene-based pyrosequencing. Propionigenium, Prolixibacter, and Photobacterium were found to be the dominant bacterial genera in all five species. Interestingly, four sea urchin species, including S. variolaris, D. setosum, E. calamaris, and D. savignyi, displayed a higher mean total abundance of the three bacterial genera (69.72 ± 6.49%) than T. gratilla (43.37 ± 13.47%). Diversity analysis indicated that the gut digesta of sea urchin T. gratilla displayed a higher bacterial α-diversity compared with the other four species. PCoA showed that the four groups representing D. setosum, D. savignyi, E. calamaris, and S. variolaris were overlapping, but distant from the group representing T. gratilla. Predictive metagenomics performed by PICRUSt revealed that the abundances of genes involved in amino acid metabolism and metabolism of terpenoid and polyketide were higher in T. gratilla, while those involved in carbohydrate metabolism were higher in the other four sea urchin species. Therefore, our results indicated that the composition, diversity and predictive metabolic profiles of bacteria associated with the gut digesta of T. gratilla were significantly different from those of the other four sea urchin species in Luhuitou fringing reef.
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Affiliation(s)
- Qiucui Yao
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China.,College of Forestry, Guangxi University, Nanning, China.,Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Teachers Education University, Nanning, China
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Yinghui Wang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Baoqing Hu
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Teachers Education University, Nanning, China
| | - Xueyong Huang
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Guangxi University, Nanning, China.,School of Marine Sciences, Guangxi University, Nanning, China
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28
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Brink M, Rhode C, Macey BM, Christison KW, Roodt-Wilding R. Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla. Mar Genomics 2019; 47:100675. [PMID: 30962029 DOI: 10.1016/j.margen.2019.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 12/31/2022]
Abstract
Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.
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Affiliation(s)
- M Brink
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag X1, Stellenbosch, Western Cape 7602, South Africa
| | - C Rhode
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag X1, Stellenbosch, Western Cape 7602, South Africa
| | - B M Macey
- Department of Agriculture, Forestry and Fisheries, Aquaculture Research, Private Bag X2, Roggebaai, Western Cape 8012, South Africa
| | - K W Christison
- Department of Agriculture, Forestry and Fisheries, Aquaculture Research, Private Bag X2, Roggebaai, Western Cape 8012, South Africa; Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - R Roodt-Wilding
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag X1, Stellenbosch, Western Cape 7602, South Africa.
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29
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O'Brien PA, Webster NS, Miller DJ, Bourne DG. Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts. mBio 2019; 10:e02241-18. [PMID: 30723123 PMCID: PMC6428750 DOI: 10.1128/mbio.02241-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
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30
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Pagán-Jiménez M, Ruiz-Calderón JF, Dominguez-Bello MG, García-Arrarás JE. Characterization of the intestinal microbiota of the sea cucumber Holothuria glaberrima. PLoS One 2019; 14:e0208011. [PMID: 30699110 PMCID: PMC6353073 DOI: 10.1371/journal.pone.0208011] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/09/2018] [Indexed: 12/26/2022] Open
Abstract
High-throughput 16S rRNA gene sequencing has been used to identify the intestinal microbiota of many animal species, but that of marine invertebrate organisms remains largely unknown. There are only a few high-throughput sequencing studies on the intestinal microbiota of echinoderms (non-vertebrate Deuterostomes). Here we describe the intestinal microbiota of the sea cucumber Holothuria glaberrima, an echinoderm, well-known for its remarkable power of regeneration. We characterized the microbiota from the anterior descending intestine, the medial intestine (these two comprise the small intestine) and the posterior descending intestine (or large intestine), using pyrosequencing to sequence the V4 region of the 16S rRNA gene. We compared animals in their natural marine environment and in sea-water aquaria. A total of 8,172 OTU's were grouped in 10 bacterial phyla, 23 classes, 44 orders, 83 families, 127 genera and 1 group of unknown bacteria, present across the digestive tract of 10 specimens. The results showed that the anterior intestine is dominated by Proteobacteria (61%) and Bacteroidetes (22%), the medium intestine is similar but with lower Bacteroidetes (4%), and the posterior intestine was remarkably different, dominated by Firmicutes (48%) and Bacteroidetes (35%). The structure of the community changed in animals kept in aquaria, which had a general dominance of Firmicutes and Bacteroidetes, regardless the intestinal segment. Our results evidence that in the natural sea environment, there is intestinal segment differentiation in the microbiota of H. glaberrima, which is lost in artificial conditions. This is relevant for physiological studies, such as mechanisms of digestive regeneration, which might be affected by the microbiota.
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Affiliation(s)
- María Pagán-Jiménez
- Biology Department, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico
| | - Jean F. Ruiz-Calderón
- Biology Department, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico
| | | | - José E. García-Arrarás
- Biology Department, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico
- * E-mail:
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31
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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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32
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Wenzel MA, Douglas A, Piertney SB. Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons). PLoS One 2018; 13:e0202212. [PMID: 30157257 PMCID: PMC6114722 DOI: 10.1371/journal.pone.0202212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/29/2018] [Indexed: 02/05/2023] Open
Abstract
The increasingly recognised effects of microbiomes on the eco-evolutionary dynamics of their hosts are promoting a view of the "hologenome" as an integral host-symbiont evolutionary entity. For example, sex-ratio distorting reproductive parasites such as Wolbachia are well-studied pivotal drivers of invertebrate reproductive processes, and more recent work is highlighting novel effects of microbiome assemblages on host mating behaviour and developmental incompatibilities that underpin or reinforce reproductive isolation processes. However, examining the hologenome and its eco-evolutionary effects in natural populations is challenging because microbiome composition is considerably influenced by environmental factors. Here we illustrate these challenges in a sympatric species complex of intertidal isopods (Jaera albifrons spp.) with pervasive sex-ratio distortion and ecological and behavioural reproductive isolation mechanisms. We deep-sequence the bacterial 16S rRNA gene among males and females collected in spring and summer from two coasts in north-east Scotland, and examine microbiome composition with a particular focus on reproductive parasites. Microbiomes of all species were diverse (overall 3,317 unique sequences among 3.8 million reads) and comprised mainly Proteobacteria and Bacteroidetes taxa typical of the marine intertidal zone, in particular Vibrio spp. However, we found little evidence of the reproductive parasites Wolbachia, Rickettsia, Spiroplasma and Cardinium, suggesting alternative causes of sex-ratio distortion. Notwithstanding, a significant proportion of the variance in microbiome composition among samples was explained by sex (14.1 %), nested within geographic (26.9 %) and seasonal (39.6 %) variance components. The functional relevance of this sex signal was difficult to ascertain given the absence of reproductive parasites, the ephemeral nature of the species assemblages and substantial environmental variability. These results establish the Jaera albifrons species complex as an intriguing system for examining the effects of microbiomes on reproductive processes and speciation, and highlight the difficulties associated with snapshot assays of microbiome composition in dynamic and complex environments.
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Affiliation(s)
- Marius A. Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alex Douglas
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Stuart B. Piertney
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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Brothers CJ, Van Der Pol WJ, Morrow CD, Hakim JA, Koo H, McClintock JB. Ocean warming alters predicted microbiome functionality in a common sea urchin. Proc Biol Sci 2018; 285:20180340. [PMID: 29925614 PMCID: PMC6030520 DOI: 10.1098/rspb.2018.0340] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/29/2018] [Indexed: 01/05/2023] Open
Abstract
The microbiome of sea urchins plays a role in maintaining digestive health and innate immunity. Here, we investigated the effects of long-term (90 day) exposure to elevated seawater temperatures on the microbiome of the common, subtropical sea urchin Lytechinus variegatus The community composition and diversity of microbes varied according to the type of sample collected from the sea urchin (seawater, feed, intestines, coelomic fluid, digested pellet and faeces), with the lowest microbial diversity (predominately the order Campylobacterales) located in the intestinal tissue. Sea urchins exposed to near-future seawater temperatures maintained the community structure and diversity of microbes associated with their tissues. However, marginal, non-significant shifts in microbial community structure with elevated temperature resulted in significant changes in predicted metagenomic functions such as membrane transport and amino acid and carbohydrate metabolism. The predicted changes in key metabolic categories suggest that near-future climate-induced increases in seawater temperature could shift microbial community function and impact sea urchin digestive and immune physiology.
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Affiliation(s)
- Cecilia J Brothers
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - William J Van Der Pol
- Biomedical Informatics, Center for Clinical and Translational Science, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Casey D Morrow
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joseph A Hakim
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hyunmin Koo
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - James B McClintock
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Schram JB, Kobelt JN, Dethier MN, Galloway AWE. Trophic Transfer of Macroalgal Fatty Acids in Two Urchin Species: Digestion, Egestion, and Tissue Building. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00083] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Mente E, Nikouli E, Antonopoulou E, Martin SAM, Kormas KA. Core versus diet-associated and postprandial bacterial communities of the rainbow trout ( Oncorhynchus mykiss) midgut and faeces. Biol Open 2018; 7:bio.034397. [PMID: 29776922 PMCID: PMC6031335 DOI: 10.1242/bio.034397] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This study investigated the impact of different dietary ingredients, with different protein/lipid sources, on midgut and faeces bacteria community structures just before feeding and 3 h after feeding a single meal to individual rainbow trout (Oncorhynchus mykiss). Fish were kept in experimental rearing facilities and fed ad libitum twice daily for 5 weeks. Fish were fed three different commercial diets, which contained variations of high or low marine fishmeal/fish oil content. DNA was extracted from midgut and faeces samples for analysis of their bacterial 16S rRNA gene diversity by targeting the V3-V4 region with 454 pyrosequencing. A total of 332 unique bacterial operational taxonomic units (OTUs) were revealed in all samples. However, each sample was dominated (>80% relative abundance) by 2–14 OTUs, with the single most dominant OTU having >30% dominance, indicating that only a few bacteria were fundamental in terms of relative abundance in each treatment. Fifteen OTUs occurred in all samples (core microbiota). The majority of these OTUs belonged to the Proteobacteria, Firmicutes or Tenericutes, and were associated with other animal gut environments. The faecal material and the midgut samples had few overlaps in their shared OTUs. A postprandial response in the gut bacterial community structure 3 h after feeding highlights how dietary stimulation induces structural changes in the microbiota profiles in the established gut bacteria. This study showed that feeding O. mykiss different diets and even single meals lead to perturbations in the established gut bacteria of O. mykiss. Summary: The gut bacterial microbiome of rainbow trout contains a few core bacterial taxa and has little overlap with its faeces. Bacterial communities can change even 3 h after feeding.
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Affiliation(s)
- Eleni Mente
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece.,School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Samuel A M Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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Abstract
Larvae are a diverse set of postembryonic life forms distinct from juveniles or adults that have evolved in many animal phyla. Echinoids (sea urchins and sand dollars) generate rapidly developing, morphologically simple, and optically transparent larvae and are a well-established model system supported by a broad array of genomic resources, experimental approaches, and imaging techniques. As such, they provide a unique opportunity to study postembryonic processes such as endocrine signaling, immunity, host-microbe interactions, and regeneration. Here we review a broad array of literature focusing on these important processes in sea urchin larvae, providing support for the claim that they represent excellent experimental study systems. Specifically, there is strong evidence emerging that endocrine signaling, immunity, and host-microbe interactions play major roles in larval development and physiology. Future research should take advantage of sea urchin larvae as a model to study these processes in more detail.
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Koo H, Hakim JA, Morrow CD, Andersen DT, Bej AK. Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Next-Generation Sequencing and Bioinformatics Tools. J Microbiol Methods 2018. [DOI: 10.1016/bs.mim.2018.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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