scholarly journals Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) and the Blue Mussel (Mytilus edulis): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities

mSphere ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Melissa L. Pierce ◽  
J. Evan Ward
Keyword(s):  
Microbial Community ◽  
Temporal Variation ◽  
Microbial Communities ◽  
Mytilus Edulis ◽  
Crassostrea Virginica ◽  
Blue Mussel ◽  
Eastern Oyster ◽  
Content Type ◽  
Marine Aggregate ◽  
Gut Microbial Community

ABSTRACT Gut microbial community structure was evaluated for two species of bivalve molluscs, the eastern oyster (Crassostrea virginica) and the blue mussel (Mytilus edulis) collected from Long Island Sound, Connecticut, over the course of a year. These bivalves utilize a shared feeding mechanism, which may result in similar gut microbial communities. Their particle diet, marine aggregates, and surrounding environment, aggregate-free seawater (AFSW), were also collected for comparison. Due to the suspension-feeding activities of bivalves, the potential for aggregate- and AFSW-associated microbiota to influence their microbial communities may be significant. Both taxonomic and functional diversity of the samples were assessed. 16S rRNA gene amplicon sequencing indicated that oysters and mussels maintained similar, but not identical, gut microbiomes, with some temporal variation. Throughout the year, bivalve species had gut microbial community compositions that were more similar to one another than to aggregates. Within a month, bivalves shared on average a quarter of their total operational taxonomic units (OTUs) with each other and a 10th of their total OTUs with aggregates. During months with warm water temperatures, individuals within each of the four sample types had similar alpha diversity, but again, temporal variation was observed. On a functional level, bivalve gut microbial communities exhibited variation attributed to host species and season. Unlike oysters, mussel gut bacterial communities maintained high richness and evenness values throughout the year, even when values for the particle diet and AFSW were reduced. Overall, a core gut bivalve microbiome was present, and it was partially influenced by the marine aggregate microbial community. IMPORTANCE This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment.

scholarly journals Extracellular Vesicles and Post-Translational Protein Deimination Signatures in Mollusca—The Blue Mussel (Mytilus edulis), Soft Shell Clam (Mya arenaria), Eastern Oyster (Crassostrea virginica) and Atlantic Jacknife Clam (Ensis leei)

Biology ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 416
Author(s):  
Timothy J. Bowden ◽  
Igor Kraev ◽  
Sigrun Lange
Keyword(s):  
Mytilus Edulis ◽  
Crassostrea Virginica ◽  
Blue Mussel ◽  
Binding Protein ◽  
Pdz Domain ◽  
Eastern Oyster ◽  
Mya Arenaria ◽  
Beta Catenin ◽  
Soft Shell Clam ◽  
Soft Shell

Oysters and clams are important for food security and of commercial value worldwide. They are affected by anthropogenic changes and opportunistic pathogens and can be indicators of changes in ocean environments. Therefore, studies into biomarker discovery are of considerable value. This study aimed at assessing extracellular vesicle (EV) signatures and post-translational protein deimination profiles of hemolymph from four commercially valuable Mollusca species, the blue mussel (Mytilus edulis), soft shell clam (Mya arenaria), Eastern oyster (Crassostrea virginica), and Atlantic jacknife clam (Ensis leei). EVs form part of cellular communication by transporting protein and genetic cargo and play roles in immunity and host–pathogen interactions. Protein deimination is a post-translational modification caused by peptidylarginine deiminases (PADs), and can facilitate protein moonlighting in health and disease. The current study identified hemolymph-EV profiles in the four Mollusca species, revealing some species differences. Deiminated protein candidates differed in hemolymph between the species, with some common targets between all four species (e.g., histone H3 and H4, actin, and GAPDH), while other hits were species-specific; in blue mussel these included heavy metal binding protein, heat shock proteins 60 and 90, 2-phospho-D-glycerate hydrolyase, GTP cyclohydrolase feedback regulatory protein, sodium/potassium-transporting ATPase, and fibrinogen domain containing protein. In soft shell clam specific deimination hits included dynein, MCM3-associated protein, and SCRN. In Eastern oyster specific deimination hits included muscle LIM protein, beta-1,3-glucan-binding protein, myosin heavy chain, thaumatin-like protein, vWFA domain-containing protein, BTB domain-containing protein, amylase, and beta-catenin. Deiminated proteins specific to Atlantic jackknife clam included nacre c1q domain-containing protein and PDZ domain-containing protein In addition, some proteins were common as deiminated targets between two or three of the Bivalvia species under study (e.g., EP protein, C1q domain containing protein, histone H2B, tubulin, elongation factor 1-alpha, dominin, extracellular superoxide dismutase). Protein interaction network analysis for the deiminated protein hits revealed major pathways relevant for immunity and metabolism, providing novel insights into post-translational regulation via deimination. The study contributes to EV characterization in diverse taxa and understanding of roles for PAD-mediated regulation of immune and metabolic pathways throughout phylogeny.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Temporal Variation in Fecundity and Spawning in the Eastern Oyster,Crassostrea virginica, in the Piankatank River, Virginia

2014 ◽  
Vol 33 (1) ◽  
pp. 167-176 ◽  
Author(s):  
Roger Mann ◽  
Melissa Southworth ◽  
Ryan B. Carnegie ◽  
Rita K. Crockett
Keyword(s):  
Temporal Variation ◽  
Crassostrea Virginica ◽  
Eastern Oyster

scholarly journals Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea)

2016 ◽  
Vol 82 (12) ◽  
pp. 3440-3449 ◽  
Author(s):  
Tiffany C. Delport ◽  
Michelle L. Power ◽  
Robert G. Harcourt ◽  
Koa N. Webster ◽  
Sasha G. Tetu
Keyword(s):  
Microbial Community ◽  
Marine Mammals ◽  
Animal Health ◽  
Sea Lion ◽  
Content Type ◽  
Sea Lions ◽  
Neophoca Cinerea ◽  
Australian Sea Lion ◽  
Captive Populations ◽  
Gut Microbial Community

ABSTRACTGut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (Neophoca cinerea), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla:Firmicutes,Proteobacteria,Bacteroidetes,Actinobacteria, andFusobacteria. The phylumFirmicuteswas dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), whileProteobacteriacontributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial familiesClostridiaceaeandRuminococcaceaewere more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species.IMPORTANCEThe Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study of the fecal microbiota of a large number of Australian sea lions from geographically diverse wild and captive populations. Colony location and captivity were found to influence the gut microbial community compositions of these animals. Our findings significantly extend the baseline knowledge of marine mammal gut microbiome composition and variability.

scholarly journals Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
Nastassia V. Patin ◽  
Michelle Schorn ◽  
Kristen Aguinaldo ◽  
Tommie Lincecum ◽  
Bradley S. Moore ◽  
...  
Keyword(s):  
Microbial Community ◽  
Secondary Metabolites ◽  
Microbial Communities ◽  
Community Composition ◽  
Marine Sediments ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Next Generation ◽  
Content Type ◽  
Predatory Bacteria

ABSTRACT Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

scholarly journals Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Ryan A. Blaustein ◽  
Graciela L. Lorca ◽  
Julie L. Meyer ◽  
Claudio F. Gonzalez ◽  
Max Teplitski
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Sequencing ◽  
Symptom Severity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
The Core ◽  
Symptom Progression

ABSTRACTStable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused byLiberibacter asiaticus,Liberibacter americanus, andLiberibacter africanus. The microbial communities of leaves (n= 94) and roots (n= 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance ofLiberibacterspp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship betweenLiberibacterspp. and members of theBurkholderiaceae,Micromonosporaceae, andXanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCEThis study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.

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