Microbial Ecology of the Bivalvia, with an Emphasis on the Family Ostreidae

Pierce, Melissa L.; Ward, J. Evan

doi:10.2983/035.037.0410

Cited by 67 publications

(57 citation statements)

References 144 publications

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“…The microbiome of wild shellfish is influenced by a variety of environmental conditions (King et al, 2012;Chauhan et al, 2014;Lokmer and Wegner, 2015;Pierce et al, 2016;Pierce and Ward, 2018;Stevick et al, 2019), and linking specific environmental conditions to microbiome composition may be interesting. For example, we determined that the Desulfobulbaceae and Halieaceae families contributed to the differences between clams harvested from different geographic sites.…”

Section: Discussionmentioning

confidence: 99%

“…The microbiome of shellfish such as mussels, oysters, and clams varies based on geographic location, season, temperature, salinity, and other environmental conditions (King et al, 2012;Chauhan et al, 2014;Lokmer and Wegner, 2015;Pierce et al, 2016;Pierce and Ward, 2018;Stevick et al, 2019). As filter feeders, the microbiome of shellfish is thought to be heavily influenced based on which bacteria are consumed from the environment (Trabal et al, 2012); although, the microbiome of shellfish can be significantly different from surrounding seawater, indicating that host-microbiome interactions are also important (Vezzulli et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Exploring the Potential of the Microbiome as a Marker of the Geographic Origin of Fresh Seafood

et al. 2020

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Geographic food fraud-misrepresenting the geographic origin of a food item, is very difficult to detect, and therefore this type of fraud tends to go undetected. This potentially negatively impacts the health of Canadians and economic success of our seafood industry. Surveillance studies have shown that up to a significant portion of commercially sold seafood items in Canada are mislabeled or otherwise misrepresented in some way. The current study aimed to determine if the microbiome of fresh shellfish could be used as an accurate marker of harvest location. Total DNA was extracted from the homogenate of 25 batches of fresh soft-shell clams (Mya arenaria) harvested in 2015 and 2018 from two locations on the East Coast of Canada and the microbiome of each homogenate was characterized using 16S rRNA targeted amplicon sequencing. Clams harvested from Nova Scotia in both years had a higher abundance of Proteobacteria and Acidobacteria (p < 0.05), but a lower abundance of Actinobacteria (p < 0.05) than those from Quebec. Alpha-diversity also differed significantly between sites. Samples harvested from Nova Scotia had greater diversity (p < 0.0001) than those from Quebec. Beta-diversity analysis showed that the microbial community composition was significantly different between the samples from Nova Scotia and Quebec and indicated that 16S rRNA targeted amplicon sequencing might be an effective tool for elucidating the geographic origin of unprocessed shellfish. To evaluate if the microbiome of shellfish experiences a loss of microbial diversity during processing and storagewhich would limit the ability of this technique to link retail samples to geographic origin, 10 batches of retail clams purchased from grocery stores were also examined. Microbial diversity and species richness was significantly lower in retail clams, and heavily dominated by Proteobacteria, a typical spoilage organism for fresh seafood, this may make determining the geographic origin of seafood items more difficult in retail clams than in freshly harvested clams.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Exploring the Potential of the Microbiome as a Marker of the Geographic Origin of Fresh Seafood

et al. 2020

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“…Microscopic observations of oyster tissue homogenates reveal 10 5 times more bacteria per gram of tissue than can be determined by quantification from culture on agar plates, indicating that a great proportion of the oyster microbiome cannot be cultivated by standard procedures (Romero and Espejo 2001;Fernandez-Piquer et al 2012). Molecular techniques are providing new insights into the diversity of microbiota associated with oysters (Romero and Espejo 2001;Hernandez-Zarate and Olmos-Soto 2006;Green and Barnes 2010;Fernandez-Piquer et al 2012;Pierce and Ward 2018). In this regard, sequencing of the bacterial 16S rRNA gene is a common approach which requires bacterial DNA extraction from oyster tissues (Romero et al 2002;Hernandez-Zarate and Olmos-Soto 2006;Mardis 2008;King et al 2012;Lokmer et al 2016a).…”

Section: Introductionmentioning

confidence: 99%

The role of tissue type, sampling and nucleic acid purification methodology on the inferred composition of Pacific oyster ( Crassostrea gigas ) microbiome

Pathirana

McPherson

Whittington

et al. 2019

J of Applied Microbiology

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Aims This study evaluated methods to sample and extract nucleic acids from Pacific oysters to accurately determine the microbiome associated with different tissues. Methods and Results Samples were collected from haemolymph, gill, gut and adductor muscle, using swabs and homogenates of solid tissues. Nucleic acids were extracted from fresh and frozen samples using three different commercial kits. The bacterial DNA yield varied between methods (P < 0·05) and each tissue harboured a unique microbiota, except for gill and muscle. Higher bacterial DNA yields were obtained by swabbing compared to tissue homogenates and from fresh tissues compared to frozen tissues, without impacting the bacterial community composition estimated by 16S rRNA gene (V1–V3 region) sequencing. Despite the higher bacterial DNA yields with QIAamp® DNA Microbiome Kit, the E.Z.N.A.® Mollusc DNA Kit identified twice as many operational taxonomic units (OTUs) and eliminated PCR inhibition from gut tissues. Conclusions Sampling and nucleic acid purification substantially affected the quantity and diversity of bacteria identified in Pacific oyster microbiome studies and a fit‐for‐purpose strategy is recommended. Significance and Impact of the Study Accurate identification of Pacific oyster microbial diversity is instrumental for understanding the polymicrobial aetiology of Pacific oyster mortality diseases which greatly impact oyster production.

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“…Despite a surge of interest in this research focus, very few invertebrate microbiomes have been studied, with the notable exception of insects. Among marine organisms, marine bivalves, especially oysters because of their economic value, are part of the few marine invertebrates of which microbial community has been studied [56][57][58][59]. In this study, we tested the influence of different benthic species assemblages on the microbial community and health of giant clams under two environmental contexts, by the concomitant analysis of the clams' bacterial and algal microbiome.…”

Section: Discussionmentioning

confidence: 99%

Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima

et al. 2020

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Background: Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While the effect of environmental change on the composition of the coral microbiome has been heavily studied, we know very little about the composition and sensitivity of the microbiome associated with clams. Here, we explore the influence of increasing temperature on the microbial community (bacteria and dinoflagellates from the family Symbiodiniaceae) harbored by giant clams, maintained either in isolation or exposed to other reef species. We created artificial benthic assemblages using two coral species (Pocillopora damicornis and Acropora cytherea) and one giant clam species (Tridacna maxima) and studied the microbial community in the latter using metagenomics. Results: Our results led to three major conclusions. First, the health status of giant clams depended on the composition of the benthic species assemblages. Second, we discovered distinct microbiotypes in the studied T. maxima population, one of which was disproportionately dominated by Vibrionaceae and directly linked to clam mortality. Third, neither the increase in water temperature nor the composition of the benthic assemblage had a significant effect on the composition of the Symbiodiniaceae and bacterial communities of T. maxima. Conclusions: Altogether, our results suggest that at least three microbiotypes naturally exist in the studied clam populations, regardless of water temperature. These microbiotypes plausibly provide similar functions to the clam host via alternate molecular pathways as well as microbiotype-specific functions. This redundancy in functions among microbiotypes together with their specificities provides hope that giant clam populations can tolerate some levels of environmental variation such as increased temperature. Importantly, the composition of the benthic assemblage could make clams susceptible to infections by Vibrionaceae, especially when water temperature increases.

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Microbial Ecology of the Bivalvia, with an Emphasis on the Family Ostreidae

Cited by 67 publications

References 144 publications

Exploring the Potential of the Microbiome as a Marker of the Geographic Origin of Fresh Seafood

Exploring the Potential of the Microbiome as a Marker of the Geographic Origin of Fresh Seafood

The role of tissue type, sampling and nucleic acid purification methodology on the inferred composition of Pacific oyster ( Crassostrea gigas ) microbiome

Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima

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