Molecular analysis of bacterial microbiota associated with oysters (Crassostrea gigas and Crassostrea corteziensis) in different growth phases at two cultivation sites

Microbiota Dysbiosis in Mytilus chilensis Is Induced by Hypoxia, Leading to Molecular and Functional Consequences

Bivalve microbiota play a vital role in host health, supporting nutrient processing, immunity, and disease resistance. However, the increasing hypoxia in Chilean coastal waters, caused by climate change and eutrophication, threatens to disrupt this microbial balance, potentially promoting pathogens and impairing essential functions. Mytilus chilensis is vulnerable to hypoxia-reoxygenation cycles, yet the effects on its microbiota remain poorly understood. This study investigates the impact of hypoxia on the structure and functional potential of the microbial communities residing in the gills and digestive glands of M. chilensis. Employing full-length 16S rRNA gene sequencing, we explored hypoxia's effects on microbial diversity and functional capacity. Our results revealed significant alterations in the microbial composition, with a shift towards facultative anaerobes thriving in low oxygen environments. Notably, there was a decrease in dominant bacterial taxa such as Rhodobacterales, while opportunistic pathogens such as Vibrio and Aeromonas exhibited increased abundance. Functional analysis indicated a decline in critical microbial functions associated with nutrient metabolism and immune support, potentially jeopardizing the health and survival of the host. This study sheds light on the intricate interactions between host-associated microbiota and environmental stressors, underlining the importance of managing the microbiota in the face of climate change and aquaculture practices.

The core microbiome of cultured Pacific oyster spat is affected by age but not mortality

The Pacific oyster is the most widely cultured shellfish worldwide, but production has been affected by mortality events, including in hatcheries that supply the seed for growers. Several pathogens cause disease in oysters, but in many cases, mortality events cannot be attributed to a single agent and appear to be multifactorial, involving environmental variables and microbial interactions. As an organism's microbiome can provide resilience against pathogens and environmental stressors, we investigated the microbiomes in cohorts of freshly settled oyster spat, some of which experienced notable mortality. Deep sequencing of 16S rRNA gene fragments did not show a significant difference among the microbiomes of cohorts experiencing different mortality levels, but revealed a characteristic core microbiome comprising 74 taxa. Irrespective of mortality, the relative abundance of taxa in the core microbiomes changed significantly as the spat aged, yet remained distinct from the microbial community in the surrounding water. The core microbiome was dominated by bacteria in the families Rhodobacteraceae, Nitrosomonadaceae, Flavobacteriaceae, Pirellulaeceae, and Saprospiraceae. Within these families, 14 taxa designated as the "Hard-Core Microbiome" were indicative of changes in the core microbiome as the spat aged. The variability in diversity and richness of the core taxa decreased with age, implying niche occupation. As well, there was exchange of microbes with surrounding water during development of the core microbiome. The shift in the core microbiome demonstrates the dynamic nature of the microbiome as oyster spat age.IMPORTANCEThe Pacific oyster (Magallana gigas, also known as Crassostrea gigas) is the most widely cultivated shellfish and is important to the economy of many coastal communities. However, high mortality of spat during the first few days following metamorphosis can affect the seed supply to oyster growers. Here, we show that the microbiome composition of recently settled oyster spat experiencing low or high mortality was not significantly different. Instead, development of the core microbiome was associated with spat aging and was partially driven by dispersal through the water. These findings imply the importance of early-stage rearing conditions for spat microbiome development in aquaculture facilities. Furthermore, shellfish growers could gain information about the developmental state of the oyster spat microbiome by assessing key taxa. Additionally, the study provides a baseline microbiome for future hypothesis testing and potential probiotic applications on developing spat.

Persistent tissue-specific resident microbiota in oysters across a broad geographical range

Marine animals often harbour complex microbial communities that influence their physiology. However, strong evidence for resident microbiomes in marine bivalves is lacking, despite their contribution to estuarine habitats and coastal economies. We investigated whether marine bivalves harbour stable, resident microorganisms in specific tissues or if their microbiomes primarily consist of transient members reflecting the environmental microbial pool. Conducting a latitudinal study of wild eastern oysters (Crassostrea virginica) along the East Coast of the United States, we aimed to identify resident microorganisms that persist across a wide geographical range. Our results revealed that microbial communities in seawater and sediment samples followed latitudinal diversity patterns driven by geographic location. In contrast, oyster-associated microbiomes were distinct from their surrounding environments and exhibited tissue-specific compositions. Notably, oyster microbiomes showed greater similarity within the same tissue type across different geographic locations than among different tissue types within the same location. This indicates the presence of tissue-specific resident microbes that persist across large geographical ranges. We identified a persistent set of resident microbiome members for each tissue type, with key microbial members consistent across all locations. These findings underscore the oyster host's role in selecting its microbiome and highlight the importance of tissue-specific microbial communities in understanding bivalve-associated microbiomes.

Environmental and Sublethal Concentrations of Polystyrene Nanoplastics Induced Antioxidant System, Transcriptomic Responses, and Disturbed Gut Microbiota in Oyster Magallana Hongkongensis

Nanoplastics (NPs) are emerging contaminants having persistent nature, diverse ecological impacts, and potential food safety risks. Here, we examined the ecotoxicity of 80 nm polystyrene nanoplastics (PS-NPs) at environmentally relevant concentrations (ERCs, 10 and 100 μg/L), and sublethal concentrations (SLCs, 500 and 2500 μg/L) in Magallana hongkongensis. Results showed that SLCs significantly (p < 0.05) increased superoxide dismutase (SOD), catalase (CAT), and alkaline phosphatase (AKP) activities and altered tnfα, cat, gst, sod, and se-gpx genetic expressions. Further, PS-NP exposure at both levels reduced beneficial bacteria and increased potentially pathogenic bacteria in the gut. In transcriptomic analysis, 5118 and 4180 differentially expressed genes (DEGs) were identified at ERCs, while 5665 and 4817 DEGs were found at SLCs, respectively. Upregulated DEGs enriched lysosomes, ABC transporters, and apoptosis pathways, while downregulated DEGs enriched ribosomal pathways. Overall, ERCs significantly altered gut microbiota and transcriptomic responses, while SLCs, in addition, also impacted the antioxidant and immune systems.

Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster reefs

Oyster reefs are invaluable ecosystems that provide a wide array of critical ecosystem services, including water filtration, coastal protection, and habitat provision for various marine species. However, these essential habitats face escalating threats from climate change and anthropogenic stressors. To combat these challenges, numerous oyster restoration initiatives have been undertaken, representing a global effort to preserve and restore these vital ecosystems. A significant, yet poorly understood, component of oyster reefs is the microbial communities. These communities account for a substantial proportion of marine reefs and are pivotal in driving key biogeochemical processes. Particularly, the environmental microbiome plays a crucial role in supporting the health and resilience of oyster populations. In our study, we sought to shed light on the microbiome within oyster reef ecosystems by characterizing the abundance, and diversity of microorganisms in the soil, biofilm, and oysters in 4 sites using a combinatorial approach to identify differentially abundant microbes by sample type and by sampling location. Our investigation revealed distinct microbial taxa in oysters, sediment and biofilm. The maximum Shannon Index indicated a slightly increased diversity in Heron's Head (5.47), followed by Brickyard park (5.35), Dunphy Park (5.17) and Point Pinole (4.85). This is likely to be driven by significantly higher oyster mortality observed at Point Pinole during routine monitoring and restoration efforts. Interestingly Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with the biofilm. Yet we have limited understanding of their beneficial and/or detrimental implications to oyster growth and survival. By unraveling the intricate relationships in microbial composition across an oyster reef, our study contributes to advancing the knowledge needed to support effective oyster reef conservation and restoration efforts.

Paralytic shellfish toxins producing dinoflagellates cause dysbacteriosis in scallop gut microbial biofilms

Filter-feeding bivalves could accumulate paralytic shellfish toxins (PSTs) produced by harmful dinoflagellates through diet. Despite that bivalves are resistant to these neurotoxins due to possessing PST-resistant sodium channel, exposure to PSTs-producing dinoflagellates impair bivalve survival. We hypothesized that ingesting PSTs-producing dinoflagellates may influence the gut microbiota, and then the health of bivalves. To test this idea, we compared the gut microbiota of the scallop Patinopecten yessoensis, after feeding with PST-producing or non-toxic dinoflagellates. Exposure to PSTs-producing dinoflagellates resulted in a decline of gut microbial diversity and a disturbance of community structure, accompanied by a significant increase in the abundance and richness of pathogenic bacteria, represented by Vibrio. Moreover, network analysis demonstrated extensive positive correlations between pathogenic bacteria abundances and PSTs concentrations in the digestive glands of the scallops. Furthermore, isolation of a dominant Vibrio strain and its genomic analysis revealed a variety of virulence factors, including the tolC outer membrane exporter, which were expressed in the gut microbiota. Finally, the infection experiment demonstrated scallop mortality caused by the isolated Vibrio strain; further, the pathogenicity of this Vibrio strain was attenuated by a mutation in the tolC gene. Together, these findings demonstrated that the PSTs may affect gut microbiota via direct and taxa-specific interactions with opportunistic pathogens, which proliferate after transition from seawater to the gut environment. The present study has revealed novel mechanisms towards deciphering the puzzles in environmental disturbances-caused death of an important aquaculture species.

Microbiome profile of the Antarctic clam Laternula elliptica

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.

Assessing the microbiota of the snail intermediate host of trematodes, Galba truncatula

BACKGROUND

The microbiome is known to play key roles in health and disease, including host susceptibility to parasite infections. The freshwater snail Galba truncatula is the intermediate host for many trematode species, including the liver and rumen flukes Fasciola hepatica and Calicophoron daubneyi, respectively. The snail-parasite system has previously been investigated. However, the specific interaction between the snail-associated microbiota and intra-snail developmental stages of trematodes has yet to be explored.

METHODS

Galba truncatula snails were collected from farms in Northern Ireland and trematode infection was diagnosed using PCR. High-throughput sequencing analysis of the bacterial 16S ribosomal DNA V3-V4 hypervariable regions was subsequently applied to characterise the microbiota of both uninfected and infected snails.

RESULTS

We first showed that the snail harboured microbiota that was distinct for its environment. The microbiota of infected snails was found to differ significantly from that of uninfected snails. In particular, the bacterial genera Mycoplasma and Methylotenera were significantly more abundant in infected snails, while genera Sphingomonas and Nocardioides were predominantly associated with uninfected snails.

CONCLUSION

These findings pave the way to future studies on the functional roles of bacteria in host-parasite relationships.

Diversities and Shifts of Microbial Communities Associated with Farmed Oysters (Crassostrea gigas) and Their Surrounding Environments in Laoshan Bay Marine Ranching, China

Pacific oysters (Crassostrea gigas) are widely cultured in Chinese marine ranching with high economic value. However, mass death of farmed oysters has occurred frequently in recent years because of diseases and environmental disturbance (e.g., high temperatures). In order to analyze the potential relationships between microorganisms and the death of farmed oysters, we compared the dynamics of bacterial and protist communities in oysters at different growth phases using high-throughput sequencing. The results showed that the microbial communities in farmed oysters significantly changed and were markedly different from microbes in natural oysters and the surrounding environments. The number of biomarker taxa among farmed oysters and their surrounding environments decreased gradually with the growth of oysters. During the mass death of farmed oysters, the microbial communities' abundance of ecological function genes changed, and the correlations among microorganisms disappeared. These results enrich our understanding of the dynamics of microbial communities in farmed oysters at different growth phases, illustrating the characteristics of interactions among microorganisms during the mass death of farmed oysters. Our study is beneficial to promote the healthy aquaculture of oysters.

Changes in Bacterial Communities of Kumamoto Oyster Larvae During Their Early Development and Following Vibrio Infection Resulting in a Mass Mortality Event

Vibrio and Ostreid herpesvirus 1 are responsible for mass mortalities of oyster larvae in hatcheries. Relevant works have focused on their relationships with the disease when larval mortality occurs. On the contrary, little is known about how the resident microbiota in oyster larvae responds to Vibrio-infected disease causing mortality as the disease progressed, whereas this knowledge is fundamental to unveil the etiology of the disease. Here, we analyzed the temporal succession of the microbiome of Kumamoto oyster (Crassostrea sikamea) larvae during their early development, accompanied by a Vibrio-caused mortality event that occurred at the post D-stage of larval development in a shellfish hatchery in Ningbo, China, on June 2020. The main causative agent of larval mortality was attributable to Vibrio infection, which was confirmed by linearly increased Vibrio abundance over disease progression. Larval bacterial communities dramatically changed over host development and disease progression, as highlighted by reduced α-diversity and less diverse core taxa when the disease occurred. Null model and phylogenetic-based mean nearest taxon distance analyses showed that the relative importance of deterministic processes governing larval bacterial assembly initially increased over host development, whereas this dominance was depleted over disease progression. Furthermore, we screened the disease-discriminatory taxa with a significant change in their relative abundances, which could be indicative of disease progression. In addition, network analysis revealed that disease occurrence remodeled the co-occurrence patterns and niche characteristics of larval microbiota. Our findings demonstrate that the dysbiosis of resident bacterial communities and the shift of microecological mechanisms in the larval microbiome may contribute to mortality during oyster early development.

Gut Microbiota and Transcriptomics Reveal the Effect of Human Norovirus Bioaccumulation on Oysters (Crassostrea gigas)

Human norovirus (HuNoV) is a major foodborne pathogen that causes acute viral gastroenteritis, and oysters are one of the main carriers of HuNoV transmission. While progress has been made toward understanding the pattern of oyster-bioaccumulated HuNoV, the response of oysters to HuNoV bioaccumulation, including changes in gene expression and gut microbiota, is unclear. In this study, histo-blood group antigen (HBGA)-like molecule expression and gene regulation features and the HuNoV-microbiome interactions of oysters during HuNoV bioaccumulation were characterized. With the prolongation of bioaccumulation time, the HuNoV content and expression of type A HBGA-like molecules in oysters increased and stabilized. HuNoV also altered the expression of immunity- and glycosphingolipid biosynthesis-related genes. Prolonged bioaccumulation of HuNoV can reduce the abundance and change the composition of the oyster gut microbiota. In particular, with the extension of bioaccumulation time, the abundance of Blautia, Agathobacter, Faecalibacterium, Terrisporobacter, Bifidobacterium, Lactobacillus, and Ruminococcus decreased, while the abundance of Vibrio and Alphaproteobacteria increased. This study provides potential candidates for identifying functional genes involved in the bioaccumulation of HuNoV in oysters. More importantly, it provides the first description of the changes in gut microbiota during HuNoV bioaccumulation in oysters. IMPORTANCE The role of the oyster gut microbiota in HuNoV bioaccumulation is poorly understood. This study revealed, for the first time, the changes in gut microbiota and gene expression of oysters with HuNoV bioaccumulation. This study enriches the understanding of the impact of HuNoV bioaccumulation on oysters and provides a new direction for the study of the molecular mechanism of HuNoV bioaccumulation in oysters.

Exploring the Dynamic of Bacterial Communities in Manila Clam (Ruditapes philippinarum) During Refrigerated Storage

Microorganism contamination is one of the most important factors affecting the spoilage and food safety of Manila clams. This study aimed to gain insights into bacterial composition and the dynamic change of bacterial communities on retailed Manila clam during refrigerated storage within the edible period. High-throughput sequencing was conducted to monitor the bacterial population with the prolongation of storage time of Day 0, Day 1, and Day 3. Result demonstrated that phyla of Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi composed the majority of bacterial communities during the whole observation process. Furthermore, the increase of Proteobacteria showed a positive correlation with the storage time, whereas Acidobacteriota and Chloroflexi continued to decline in storage. For genus annotation, none of genus obtained dominant population in storage. From Day 0 to Day 1, the genera of Streptomyces, Bradyrhizobium, and Mycobacterium significantly increased; meanwhile, 12 genera significantly decreased. Compared with samples at Day 0, a total of 15 genera significantly decreased with the reduced proportion ranging from 0.50 to 4.40% at Day 3. At the end of the storage, the genus Crossiella became the most redundant population. Both the richness and diversity decreased at the start of storage at Day 1, and then slightly increased at Day 3 was observed. Based on the result in this study, strategy targeting the increased bacteria could be tested to improve the consumption quality and safety of refrigerated clam.

Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound

The Olympia oyster (Ostrea lurida) of the Puget Sound suffered a dramatic population crash, but restoration efforts hope to revive this native species. One overlooked variable in the process of assessing ecosystem health is association of bacteria with marine organisms and the environments they occupy. Oyster microbiomes are known to differ significantly between species, tissue type, and the habitat in which they are found. The goals of this study were to determine the impact of field site and habitat on the oyster microbiome and to identify core oyster-associated bacteria in the Puget Sound. Olympia oysters from one parental family were deployed at four sites in the Puget Sound both inside and outside of eelgrass (Zostera marina) beds. Using 16S rRNA gene amplicon sequencing of the oyster gut, shell, and surrounding seawater and sediment, we demonstrate that gut-associated bacteria are distinct from the surrounding environment and vary by field site. Furthermore, regional differences in the gut microbiota are associated with the survival rates of oysters at each site after 2 months of field exposure. However, habitat type had no influence on microbiome diversity. Further work is needed to identify the specific bacterial dynamics that are associated with oyster physiology and survival rates.

IMPORTANCE This is the first exploration of the microbial colonizers of the Olympia oyster, a native oyster species to the West Coast, which is a focus of restoration efforts. The patterns of differential microbial colonization by location reveal microscale characteristics of potential restoration sites which are not typically considered. These microbial dynamics can provide a more holistic perspective on the factors that may influence oyster performance.

Determining the Composition of Resident and Transient Members of the Oyster Microbiome

To better understand how complex microbial communities become assembled on eukaryotic hosts, it is essential to disentangle the balance between stochastic and deterministic processes that drive their assembly. Deterministic processes can create consistent patterns of microbiome membership that result in persistent resident communities, while stochastic processes can result in random fluctuation of microbiome members that are transient with regard to their association to the host. We sampled oyster reefs from six different populations across the east coast of the United States. At each site we collected gill tissues for microbial community analysis and additionally collected and shipped live oysters to Northeastern University where they were held in a common garden experiment. We then examined the microbiome shifts in gill tissues weekly for 6 weeks using 16S rRNA gene amplicon sequencing. We found a strong population-specific signal in the microbial community composition of field-sampled oysters. Surprisingly, the oysters sampled during the common garden experiment maintained compositionally distinct gill-associated microbial communities that reflected their wild population of origin, even after rearing them in a common garden for several weeks. This indicates that oyster gill-associated microbiota are predominantly composed of resident microbes specific to host population, rather than being a reflection of their immediate biotic and abiotic surroundings. However, certain bacterial taxa tended to appear more frequently on individuals from different populations than on individuals from the same population, indicating that there is a small portion of the gill microbiome that is transient and is readily exchanged with the environmental pool of microbes. Regardless, the majority of gill-associated microbes were resident members that were specific to each oyster population, suggesting that there are strong deterministic factors that govern a large portion of the gill microbiome. A small portion of the microbial communities, however, was transient and moved among oyster populations, indicating that stochastic assembly also contributes to the oyster gill microbiome. Our results are relevant to the oyster aquaculture industry and oyster conservation efforts because resident members of the oyster microbiome may represent microbes that are important to oyster health and some of these key members vary depending on oyster population.

Recent advances in bivalve-microbiota interactions for disease prevention in aquaculture

In bivalves, no clear-cut functional role of microbiota has yet been identified, although many publications suggest that they could be involved in nutrition or immunity of their host. In the context of climate change, integrative approaches at the crossroads of disciplines have been developed to explore the environment-host-pathogen-microbiota system. Here, we attempt to synthesize work on (1) the current methodologies to analyse bivalve microbiota, (2) the comparison of microbiota between species, between host compartments and their surrounding habitat, (3) how the bivalve microbiota are governed by environmental factors and host genetics and (4) how host-associated microorganisms act as a buffer against pathogens and/or promote recovery, and could thereby play a role in the prevention of disease or mortalities.

Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues

Diseases of bivalves of aquacultural importance, including the valuable Australian silver-lipped pearl oyster (Pinctada maxima), have been increasing in frequency and severity. The bivalve microbiome is linked to health and disease dynamics, particularly in oysters, with putative pathogens within the Vibrio genus commonly implicated in oyster diseases. Previous studies have been biased toward the Pacific oyster because of its global dominance in oyster aquaculture, while much less is known about the microbiome of P. maxima. We sought to address this knowledge gap by characterizing the P. maxima bacterial community, and we hypothesized that bacterial community composition, and specifically the occurrence of Vibrio, will vary according to the sampled microenvironment. We also predicted that the inside shell swab bacterial composition could represent a source of microbial spillover biofilm into the solid pearl oyster tissues, thus providing a useful predictive sampling environment. We found that there was significant heterogeneity in bacterial composition between different pearl oyster tissues, which is consistent with patterns reported in other bivalve species and supports the hypothesis that each tissue type represents a unique microenvironment for bacterial colonization. We suggest that, based on the strong effect of tissue-type on the pearl oyster bacterial community, future studies should apply caution when attempting to compare microbial patterns from different locations, and when searching for disease agents. The lack of association with water at each farm also supported the unique nature of the microbial communities in oyster tissues. In contrast to the whole bacterial community, there was no significant difference in the Vibrio community among tissue types nor location. These results suggest that Vibrio species are shared among different pearl oyster tissues. In particular, the similarity between the haemolymph, inside shell and solid tissues, suggests that the haemolymph and inside shell environment is a source of microbial spillover into the oyster tissues, and a potentially useful tool for non-destructive routine disease testing and early warning surveillance. These data provide important foundational information for future studies identifying the factors that drive microbial assembly in a valuable aquaculture species.

Dietary Exposure of Pacific Oyster (Crassostrea gigas) Larvae to Compromised Microalgae Results in Impaired Fitness and Microbiome Shift

The Pacific oyster Crassostrea gigas is the world's most cultivated oyster and seed supply is heavily reliant on hatchery production where recurring mass mortality events are a major constraint. Outbreaks of bacterial infection via microalgal feed are frequently implicated in these mortalities. This study assessed the effects of feeding compromised microalgae to developing oyster larvae. Intentionally 'stressed' (high pH) or non-stressed microalgae were fed to 11 day-old oyster larvae at two feeding rations for 96 h, followed by a recovery period. Biological endpoints of larval performance were measured following the 96 h exposure and subsequent recovery. Bacterial communities associated with the microalgae feed, rearing seawater, and the oyster larvae, were characterized and correlated with effects on oyster fitness parameters. Feeding stressed algae to oyster larvae for 96 h increased the occurrence of deformities (>70% vs. 20% in control), reduced feeding and swimming ability, and slowed development. Following the recovery period, fewer larvae reached pediveliger stage (2.7% vs. 36% in control) and became spat (1.5% vs. 6.6% in control). The quantity of stressed algae supplied to oyster larvae also influenced overall larval performance, with high feeding rations generally causing greater impairment than low rations. Bacterial profiling using 16S rRNA showed that most bacterial families characterized in larval tissue were also present in larval rearing seawater and in the microalgae feed (98%). The rearing seawater showed the highest bacterial richness compared to the larval and the microalgal compartments, regardless of feeding regime. In larval tissue, bacterial richness was highest in stressed and high-feed treatments, and negatively correlated with larval fitness parameters. These results suggest significant dysbiosis induced by compromised feed and/or increased feed ration. Several bacterial genera (e.g., Halomonas, Marinomonas) were strongly associated with impaired larval performance while the presence of genera in larvae including Vibrio was closely associated with overfeeding. Our research demonstrated that metabarcoding can be effectively used to identify microbiota features associated with larval fitness.

Microbial Profiles of Retail Pacific Oysters (Crassostrea gigas) From Guangdong Province, China

Oysters are one of the main aquatic products sold in coastal areas worldwide and are popular among consumers because of their delicious taste and nutritional value. However, the microorganisms present in oysters may pose health risks to consumers. In this study, the microbial communities of Pacific oysters (Crassostrea gigas) collected from aquatic product markets in three cities (Guangzhou, Zhuhai, and Jiangmen) of Guangdong Province, China, where raw oysters are popular, were investigated. The plate counts of viable bacteria in oysters collected in the three cities were all approximately 2 log colony-forming units/g. High-throughput sequencing analysis of the V3–V4 region of the 16Sribosomal DNA gene showed a high level of microbial diversity in oysters, as evidenced by both alpha and beta diversity analysis. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla of the microorganisms present in these samples. A variety of pathogenic bacteria, including the fatal foodborne pathogen Vibrio vulnificus, were found, and Vibrio was the dominant genus. Additionally, the relationship between other microbial species and pathogenic microorganisms may be mostly symbiotic in oysters. These data provide insights into the microbial communities of retail oysters in the Guangdong region and indicate a considerable risk related to the consumption of raw oysters.

From Farm to Fingers: an Exploration of Probiotics for Oysters, from Production to Human Consumption

Oysters hold a unique place within the field of aquaculture as one of the only organisms that is regularly shipped live to be consumed whole and raw. The microbiota of oysters is capable of adapting to a wide range of environmental conditions within their dynamic estuarine environments; however, human aquaculture practices can challenge the resilience of this microbial community. Several discrete stages in oyster cultivation and market processing can cause disruption to the oyster microbiota, thus increasing the possibility of proliferation by pathogens and spoilage bacteria. These same pressure points offer the opportunity for the application of probiotics to help decrease disease occurrence in stocks, improve product yields, minimize the risk of shellfish poisoning, and increase product shelf life. This review provides a summary of the current knowledge on oyster microbiota, the impact of aquaculture upon this community, and the current status of oyster probiotic development. In response to this biotechnological gap, the authors highlight opportunities of highest potential impact within the aquaculture pipeline and propose a strategy for oyster-specific probiotic candidate development.

Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery

BACKGROUND

Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and host health, respectively. The introduction of pathogenic microbes that shift microbiome community structure can lead to illness and death. Understanding the dynamics of microbiomes across a diversity of environments and hosts will help us to better understand which taxa forecast survival and which forecast mortality events.

RESULTS

We characterized the bacterial community microbiome in the water of a commercial shellfish hatchery in Washington state, USA, where the hatchery has been plagued by recurring and unexplained larval mortality events. By applying the complementary methods of metagenomics and metaproteomics we were able to more fully characterize the bacterial taxa in the hatchery at high (pH 8.2) and low (pH 7.1) pH that were metabolically active versus present but not contributing metabolically. There were shifts in the taxonomy and functional profile of the microbiome between pH and over time. Based on detected metagenomic reads and metaproteomic peptide spectral matches, some taxa were more metabolically active than expected based on presence alone (Deltaproteobacteria, Alphaproteobacteria) and some were less metabolically active than expected (e.g., Betaproteobacteria, Cytophagia). There was little correlation between potential and realized metabolic function based on Gene Ontology analysis of detected genes and peptides.

CONCLUSION

The complementary methods of metagenomics and metaproteomics contribute to a more full characterization of bacterial taxa that are potentially active versus truly metabolically active and thus impact water quality and inter-trophic relationships.

Gut Microbial Composition and Diversity in Four Ophiuroid Species: Divergence Between Suspension Feeder and Scavenger and Their Symbiotic Microbes

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.

Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column

The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because of their immense metabolic and ecological potential. To obtain a comprehensive understanding on this aspect, we previously reported on the isolation and preliminary genomic characterization of three Pseudomonas species isolated from minced oyster tissue (P. alcaligenes strain OT69); oyster mantle fluid (P. stutzeri strain MF28) and the water collected from top of the oyster reef (P. aeruginosa strain WC55), respectively. In this comparative genomic analysis study conducted on these three targeted pseudomonads, native to the eastern oyster and its surrounding environment, provided further insights into their unique functional traits, conserved gene pools between the selected pseudomonads, as well as genes that render unique characteristics in context to metabolic traits recruited during their evolutionary history via horizontal gene transfer events as well as phage-mediated incorporation of genes. Moreover, the strains also supported extensively developed resistomes, which suggests that environmental microorganisms native to relatively pristine environments, such as Apalachicola Bay, Florida, have also recruited an arsenal of antibiotic resistant gene determinants, thus posing an emerging public health concern.

Amazonia Seasons Have an Influence in the Composition of Bacterial Gut Microbiota of Mangrove Oysters (Crassostrea gasar)

The mangrove oysters (Crassostrea gasar) are molluscs native to the Amazonia region and their exploration and farming has increased considerably in recent years. These animals are farmed on beds built in the rivers of the Amazonia estuaries and, therefore, the composition of their microbiome should be directly influenced by environmental conditions. Our work aimed to evaluate the changes in bacterial composition of oyster's microbiota at two different seasons (rainy and dry). For this purpose, we amplified and sequenced the V3-V4 regions of the 16S rRNA gene. Sequencing was performed on the Illumina MiSeq platform. According to the rarefaction curve, the sampling effort was sufficient to describe the bacterial diversity in the samples. Alpha-diversity indexes showed that the bacterial microbiota of oysters is richer during the rainy season. This richness is possibly associated with the diversity at lower taxonomic levels, since the relative abundance of bacterial phyla in the two seasons remained relatively constant. The main phyla found include Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Similar results were found for the species Crassostrea gigas, Crassostrea sikamea, and Crassostrea corteziensis. Beta-diversity analysis showed that the bacterial composition of oyster's gut microbiota was quite different in the two seasons. Our data demonstrate the close relationship between the environment and the microbiome of these molluscs, reinforcing the need for conservation and sustainable management of estuaries in the Amazonia.

Regional and oyster microenvironmental scale heterogeneity in the Pacific oyster bacterial community

Different organs of a host represent distinct microenvironments resulting in the establishment of multiple discrete bacterial communities within a host. These discrete bacterial communities can also vary according to geographical location. For the Pacific oyster, Crassostrea gigas, the factors governing bacterial diversity and abundance of different oyster microenvironments are poorly understood. In this study, the factors shaping bacterial abundance, diversity and composition associated with the C. gigas mantle, gill, adductor muscle and digestive gland were characterised using 16S (V3-V4) rRNA amplicon sequencing across six discrete estuaries. Both location and tissue-type, with tissue-type being the stronger determinant, were factors driving bacterial community composition. Bacterial communities from wave-dominated estuaries had similar compositions and higher bacterial abundance despite being geographically distant from one another, possibly indicating that functional estuarine morphology characteristics are a factor shaping the oyster bacterial community. Despite the bacterial community heterogeneity, examinations of the core bacterial community identified Spirochaetaceae bacteria as conserved across all sites and samples. Whereas members of the Vulcaniibacterium, Spirochaetaceae and Margulisbacteria, and Polynucleobacter were regionally conserved members of the digestive gland, gill and mantle bacterial communities, respectively. This indicates that baseline bacterial community profiles for specific locations are necessary when investigating bacterial communities in oyster health.

The marine intertidal zone shapes oyster and clam digestive bacterial microbiota

Digestive microbiota provide a wide range of beneficial effects on host physiology and are therefore likely to play a key role in marine intertidal bivalve ability to acclimatize to the intertidal zone. This study investigated the effect of intertidal levels on the digestive bacterial microbiota of oysters (Crassostrea gigas) and clams (Ruditapes philippinarum), two bivalves with different ecological niches. Based on 16S rRNA region sequencing, digestive glands, seawater and sediments harbored specific bacterial communities, dominated by operational taxonomic units assigned to the Mycoplasmatales,Desulfobacterales and Rhodobacterales orders, respectively. Field implantation modified digestive bacterial microbiota of both bivalve species according to their intertidal position. Rhodospirillales and Legionellales abundances increased in oysters and clams from the low intertidal level, respectively. After a 14-day depuration process, these effects were still observed, especially for clams, while digestive bacterial microbiota of oysters were subjected to more short-term environmental changes. Nevertheless, 3.5 months stay on an intertidal zone was enough to leave an environmental footprint on the digestive bacterial microbiota, suggesting the existence of autochthonous bivalve bacteria. When comparing clams from the three intertidal levels, 20% of the bacterial assemblage was shared among the levels and it was dominated by an operational taxonomic unit affiliated to the Mycoplasmataceae and Spirochaetaceae families.

Occurrence, antibiotic-resistance and virulence of E. coli strains isolated from mangrove oysters (Crassostrea gasar) farmed in estuaries of Amazonia

Concentration of bacterial species indicative of fecal contamination in the gut of mangrove oysters (Crassostrea gasar) is a major concern for public health and food surveillance. Our work aimed to determine the occurrence, antibiotic-resistance, phylogenetic profile and virulence of Escherichia coli strains isolated from C. gasar farmed in four estuaries of Amazonia. Santo Antônio de Urindeua was the sampling point with the highest number of E. coli cells in oyster samples (10⁴ per 100 g of sample). Twenty-four isolates (52.2%) showed resistance to cephalotin and 18 to amoxicillin (39.1%). Eighteen clonal populations were determined by rep-PCR and were mainly affiliated to the pathogenic and commensal phylo-groups B1 and D. The presence of elt genes suggests that 10 of these clones belong to the Enterotoxigenic Escherichia coli pathotype. Plasmids, mostly of the F incompatibility group, were detected in the majority of the strains. All isolates were susceptible to last-resort antibiotics.

The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginica

Long-standing evidence supports the importance of maintaining healthy populations of microbiota for the survival, homeostasis, and complete development of marine mollusks. However, the long-term ecological effects of agricultural runoff on these populations remains largely unknown. Atrazine (6-Chloro-n-ethyl-n'-(1-methylethyl)-triazine-2,4-diamine), a prevalent herbicide in the United States, is often used along tributaries of the Chesapeake Bay where oyster breeding programs are concentrated. To investigate any potential effects atrazine maybe having on mollusk-prokaryote interactions, we used 16S rRNA gene amplicons to evaluate how microbial compositions shift in response to exposure of environmentally relevant concentrations of atrazine previously found within the Chesapeake Bay. The dominant bacterial genera found within all groups included those belonging to Pseudoalteromonas, Burkholderia, Bacteroides, Lactobacillis, Acetobacter, Allobaculum, Ruminococcus, and Nocardia. Our results support previously published findings of a possible core microbial community in Crassostrea virginica. We also report a novel finding: oysters exposed to atrazine concentrations as low as 3 µg/L saw a significant loss of a key mutualistic microbial species and a subsequent colonization of a pathogenic bacteria Nocardia. We conclude that exposure to atrazine in the Chesapeake Bay may be contributing to a significant shift in the microbiomes of juvenile oysters that reduces fitness and impedes natural and artificial repopulation of the oyster species within the Bay.

Metagenomic analysis of the bacterial microbiota associated with cultured oysters (Crassostrea sp.) in estuarine environments

In this work, we identified the bacterial microbiota associated with farmed oystersin estuarine regions of four states in the north eastern region of Brazil. During the drought and rainy seasons, for eight months, twenty oysters were sampled seasonally from seven different marine farms. In the laboratory, DNA extraction, amplification, and sequencing of the 16S rRNA gene were performed to establish the taxonomic units. We identified 106 genera of bacteria belonging to 103 families, 70 orders, 39 classes, and 21 phyla. Out of the total, 40 of the genera represented bacteria potentially pathogenic to humans; of these, nine are known to cause foodborne diseases and six are potentially pathogenic to oysters. The most prevalent genera were Mycoplasma, Propionigenium, Psychrilyobacter, and Arcobacter. The results indicate the need for more systematic monitoring of bacteria of the genus Mycoplasma in oyster farming operations in the Brazilian north eastern region. Currently, Mycoplasma is not one of the microorganisms analysed and monitored by order of Brazilian legislation during the oyster production and/or commercialization process, even though this genus was the most prevalent at all sampling points and presents pathogenic potential both for oysters and for consumers.

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

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 storage – which 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.

Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern

Planorbidae snails are the intermediate host for the trematode parasite of the Schistosoma genus, which is responsible for schistosomiasis, a disease that affects both humans and cattle. The microbiota for Schistosoma has already been described as having an effect on host/parasite interactions, specifically through immunological interactions. Here, we sought to characterize the microbiota composition of seven Planorbidae species and strains. Individual snail microbiota was determined using 16S ribosomal DNA amplicon sequencing. The bacterial composition was highly specific to the host strain with limited interindividual variation. In addition, it displayed complete congruence with host phylogeny, revealing a phylosymbiosis pattern. These results were confirmed in a common garden, suggesting that the host highly constrains microbial composition. This study presents the first comparison of bacterial communities between several intermediate snail hosts of Schistosoma parasites, paving the way for further studies on the understanding of this tripartite interaction.

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

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.

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.

Host-microbiota interactions shed light on mortality events in the striped venus clam Chamelea gallina

Mass mortalities due to disease outbreaks have recently affected a number of major taxa in marine ecosystems. Climate- and pollution-induced stress may compromise host immune defenses, increasing the risk of opportunistic diseases. Despite growing evidence that mass mortality events affecting marine species worldwide are strongly influenced by the interplay of numerous environmental factors, the reductionist approaches most frequently used to investigate these factors hindered the interpretation of these multifactorial pathologies. In this study, we propose a broader approach based on the combination of RNA-sequencing and 16S microbiota analyses to decipher the factors underlying mass mortality in the striped venus clam, Chamelea gallina, along the Adriatic coast. On one hand, gene expression profiling and functional analyses of microbial communities showed the over-expression of several genes and molecular pathways involved in xenobiotic metabolism, suggesting potential chemical contamination in mortality sites. On the other hand, the down-regulation of several genes involved in immune and stress response, and the over-representation of opportunistic pathogens such as Vibrio and Photobacterium spp. indicates that these microbial species may take advantage of compromised host immune pathways and defense mechanisms that are potentially affected by chemical exposure, resulting in periodic mortality events. We propose the application of our approach to interpret and anticipate the risks inherent in the combined effects of pollutants and microbes on marine animals in today's rapidly changing environment.

Influence of environment on the pathogenesis of Ostreid herpesvirus-1 (OsHV-1) infections in Pacific oysters (Crassostrea gigas) through differential microbiome responses

The oyster microbiome is thought to contribute to the pathogenesis of mass mortality disease in Pacific oysters, associated with OsHV-1. As filter-feeders, oysters host a microbiota that can be influenced by the estuarine environment. This may alter susceptibility to OsHV-1 infections, causing variable mortality. This study aimed at: (1) differences in the microbiome of Pacific oysters with a common origin but grown in geographically distinct estuaries; (2) evaluating changes occurring in the microbiota, especially in Vibrio, and (3) differential responses of the oyster microbiome, in response to an OsHV-1 infection. Pacific oysters sourced from a single hatchery but raised separately in Patonga Creek, Shoalhaven River and Clyde River of NSW, Australia, were used and challenged with OsHV-1. The initial microbiome composition was different in the three batches and changed further, post-injection (p < 0.05). The Patonga oysters with the highest mortality also had higher OsHV-1 and Vibrio quantities compared to the other two batches (p < 0.05). The higher initial bacterial diversity in Patonga oysters decreased in moribund oysters which was not observed in the other two batches (p < 0.05). The microbiome of survivors of OsHV-1 infection and negative control oysters of two batches, did not show any changes with the relevant pre-challenged microbiome. A strong correlation was observed between the OsHV-1 and Vibrio quantities in OsHV-1 infected oysters (r = 0.6; p < 0.001). In conclusion, the Pacific oyster microbiome differed in different batches despite a common hatchery origin. Different microbiomes responded differently with a differential outcome of OsHV-1 challenge. The higher Vibrio load in oysters with higher OsHV-1 content and higher mortality, suggests a role in Vibrio in the pathogenesis of this mortality disease. This study provided insights of the potential of different estuarine environments to shape the Pacific oyster microbiome and how different microbiomes are associated with different outcomes of OsHV-1 infection.

Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling

Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world’s most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster Pinctada margaritifera, a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from P. margaritifera individuals: the gill, gonad, byssus gland, haemolymph, mantle, adductor muscle, mucus, and gut. Richness of bacterial Operational Taxonomic Units (OTUs) and phylogenetic diversity differed between host tissues, with mucous layers displaying the highest richness and diversity. This multi-tissues approach permitted the identification of consistent microbial members, together constituting the core microbiome of P. margaritifera, including Alpha- and Gammaproteobacteria, Flavobacteriia, and Spirochaetes. We also found a high representation of Endozoicimonaceae symbionts, indicating that they may be of particular importance to oyster health, survival and homeostasis, as in many other coral reef animals. Our study demonstrates that the microbial communities and their associated predicted functional profiles are tissue specific. Inferred physiological functions were supported by current physiological data available for the associated bacterial taxa specific to each tissue. This work provides the first baseline of microbial community composition in P. margaritifera, providing a solid foundation for future research into this commercially important species and emphasises the important effects of tissue differentiation in structuring the oyster microbiome.

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

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.

Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary

Marine biogeographic boundaries act as barriers to dispersal for many animal species, thereby creating distinctive faunas on either side. However, how such boundaries affect the distributions of microbial taxa remains poorly known. To test whether biogeographic boundaries influence the diversity and composition of host-associated microbiota, we analysed the microbiomes of three species of common intertidal gastropods at two sites separated by the biogeographic boundary at Point Conception (PtC), CA, using 16S rRNA gene sequencing. Our results show that each host species shows microbiome compositional specificity, even across PtC, and that alpha diversity does not change significantly across this boundary for any of the gastropod hosts. However, for two of the host species, beta diversity differs significantly across PtC, indicating that there may be multiple levels of organization of the marine gastropod microbiome. Overall, our results suggest that while biogeographic boundaries do not constrain the distribution of a core set of microbes associated with each host species, they can play a role in structuring the transient portion of the microbiome.

Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease

Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or detrimental role in OsHV-1 μvar disease outbreaks.

Bacterial spoilage profiles in the gills of Pacific oysters (Crassostrea gigas) and Eastern oysters (C. virginica) during refrigerated storage

Microorganisms harbored in oyster gills are potentially related to the spoilage and safety of oyster during storage. In this study, the microbial activities and pH changes of the gills of the two species, Crassostrea gigas and C. virginica, harvested from three different sites were determined and sensory evaluation was conducted during refrigerated storage. The bacteria in gills with an initial aerobic plate count (APC) of 3.1-4.5 log CFU/g rose remarkably to 7.8-8.8 log CFU/g after 8-days of storage. The APC of Enterobacteriaceae increased from 2.5 to 3.6 log CFU/g to 4.5-4.8 log CFU/g, and that of lactic acid bacteria (LAB) fluctuated in the range of 1.4-3.0 log CFU/g during the whole storage period. The results of sensory analysis indicated that the oysters had 8-days of shelf-life and that the gill presented the fastest deterioration rate. The pH of all samples showed a decrease in the early stages followed by an increased after 4-days of storage. The dynamic changes in microbial profiles were depicted to characterize gill spoilage by Illumina Miseq sequencing to characterize gill spoilage. The results revealed that oysters harvested at different sites showed common bacterial profiles containing Arcobacter, Spirochaeta, Pseudoalteromonas, Marinomonas, Fusobacterium, Psychrobacter, Psychromonas, and Oceanisphaera when spoiled, especially, among which Psychrobacter and Psychromonas (psychrotrophic genus) were represented as the most important gill spoiled bacteria during refrigerated storage, and Arcobacter with pathogenic potential was the dominated bacteria in all spoiled oysters. The consumption quality and safety of refrigerated oysters could be greatly improved by targeted control of bacteria in oyster gills according to the results the present study provided.

Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event

The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013-2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1-V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.

Spoilage microbial community profiling by 16S rRNA amplicon sequencing of modified atmosphere packaged live mussels stored at 4oC

There is little information on the microbial communities associated with modified atmosphere (MA)-packaged live mussels. There is also a dearth of information on how pre-packaging depuration modifies the microbial communities and spoilage of live mussels. Amplicon sequencing was used to describe spoilage microbial succession in MA-packaged live mussels during storage at 4 °C. Proteobacteria, Cyanobacteria and Firmicutes were the three major phyla observed in the mussel meat and pouch water of undepurated and depurated mussels. Among these phyla, Cyanobacteria was more predominant on day 0 in mussel meat of undepurated and depurated mussels while Proteobacteria was predominant in commercially-depurated mussels. Synechococcus was apparently dominant on days 0-7 in the meat of undepurated mussels and days 0-10 in depurated mussels. Shewanella was dominant on day 0 in commercially-depurated mussels and dominant on day 15 in undepurated while Acidaminococcus was dominant in depurated mussels on day 15. Psychromonas was observed to be dominant in commercially-depurated mussels on day 7 and further shifted to Acinetobacter by day 10 and 15. In the pouch water, Acinetobacter was dominant throughout the storage days in undepurated mussels while Psychrobacter was predominant in both depurated and commercially-depurated mussels. This study demonstrated the impact of depuration on the microbiota and the spoilage mechanism of MA-packaged live mussels. Shewanella was easily removed through depuration. However, spoilage bacteria such as Acidaminococcus could not be easily removed although they are not important at the beginning but grew at the end. Pouch water contributed suitable biological medium for the growth of Acinetobacter and Psychrobacter and both enhanced the growth of spoilage bacteria such as Shewanella and Acidaminococcus.

Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates

While most Vibrionaceae are considered generalists that thrive on diverse substrates, including animal-derived material, we show that Vibrio breoganii has specialized for the consumption of marine macroalga-derived substrates. Genomic and physiological comparisons of V. breoganii with other Vibrionaceae isolates revealed the ability to degrade alginate, laminarin, and additional glycans present in algal cell walls. Moreover, the widely conserved ability to hydrolyze animal-derived polymers, including chitin and glycogen, was lost, along with the ability to efficiently grow on a variety of amino acids. Ecological data showing associations with particulate algal material but not zooplankton further support this shift in niche preference, and the loss of motility appears to reflect a sessile macroalga-associated lifestyle. Together, these findings indicate that algal polysaccharides have become a major source of carbon and energy in V. breoganii, and these ecophysiological adaptations may facilitate transient commensal associations with marine invertebrates that feed on algae.IMPORTANCE Vibrios are often considered animal specialists or generalists. Here, we show that Vibrio breoganii has undergone massive genomic changes to become specialized on algal carbohydrates. Accompanying genomic changes include massive gene import and loss. These vibrios may help us better understand how algal biomass is degraded in the environment and may serve as a blueprint on how to optimize the conversion of algae to biofuels.

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams

Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key, although still not fully understood, player that must be considered to assess the toxicity of environmental contaminants. Bacteria-dependent metabolism of xenobiotics may indeed modulate the host toxicity. Conversely, environmental variables (including pollution) may alter the microbial community and/or its metabolic activity leading to host physiological alterations that may contribute to their toxicity. Here, 16s rRNA gene amplicon sequencing has been applied to characterize the hepatopancreas microbiota composition of the Manila clam, Ruditapes philippinarum. The animals were collected in the Venice lagoon area, which is subject to different anthropogenic pressures, mainly represented by the industrial activities of Porto Marghera (PM). Seasonal and geographic differences in clam microbiotas were explored and linked to host response to chemical stress identified in a previous study at the transcriptome level, establishing potential interactions among hosts, microbes, and environmental parameters. The obtained results showed the recurrent presence of putatively detoxifying bacterial taxa in PM clams during winter and over-representation of several metabolic pathways involved in xenobiotic degradation, which suggested the potential for host-microbial synergistic detoxifying actions. Strong interaction between seasonal and chemically-induced responses was also observed, which partially obscured such potentially synergistic actions. Seasonal variables and exposure to toxicants were therefore shown to interact and substantially affect clam microbiota, which appeared to mirror host response to environmental variation. It is clear that understanding how animals respond to chemical stress cannot ignore a key component of such response, the microbiota.

Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach

The eastern oyster (Crassostrea virginica) is a foundation species providing significant ecosystem services. However, the roles of oyster microbiomes have not been integrated into any of the services, particularly nitrogen removal through denitrification. We investigated the composition and denitrification potential of oyster microbiomes with an approach that combined 16S rRNA gene analysis, metabolic inference, qPCR of the nitrous oxide reductase gene (nosZ), and N₂ flux measurements. Microbiomes of the oyster digestive gland, the oyster shell, and sediments adjacent to the oyster reef were examined based on next generation sequencing (NGS) of 16S rRNA gene amplicons. Denitrification potentials of the microbiomes were determined by metabolic inferences using a customized denitrification gene and genome database with the paprica (PAthway PRediction by phylogenetIC plAcement) bioinformatics pipeline. Denitrification genes examined included nitrite reductase (nirS and nirK) and nitrous oxide reductase (nosZ), which was further subdivided by genotype into clade I (nosZI) or clade II (nosZII). Continuous flow through experiments measuring N₂ fluxes were conducted with the oysters, shells, and sediments to compare denitrification activities. Paprica properly classified the composition of microbiomes, showing similar classification results from Silva, Greengenes and RDP databases. Microbiomes of the oyster digestive glands and shells were quite different from each other and from the sediments. The relative abundance of denitrifying bacteria inferred by paprica was higher in oysters and shells than in sediments suggesting that oysters act as hotspots for denitrification in the marine environment. Similarly, the inferred nosZI gene abundances were also higher in the oyster and shell microbiomes than in the sediment microbiome. Gene abundances for nosZI were verified with qPCR of nosZI genes, which showed a significant positive correlation (F_1,7 = 14.7, p = 6.0x10^-3, R² = 0.68). N₂ flux rates were significantly higher in the oyster (364.4 ± 23.5 μmol N-N₂ m^-2 h^-1) and oyster shell (355.3 ± 6.4 μmol N-N₂ m^-2 h^-1) compared to the sediment (270.5 ± 20.1 μmol N-N₂ m^-2 h^-1). Thus, bacteria carrying nosZI genes were found to be an important denitrifier, facilitating nitrogen removal in oyster reefs. In addition, this is the first study to validate the use of 16S gene based metabolic inference as a method for determining microbiome function, such as denitrification, by comparing inference results with qPCR gene quantification and rate measurements.

Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment

Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0.005), Chao1 diversity (p = 0.005), and Shannon diversity (p < 0.001), with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs) classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001) with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N)-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001)) increased with mussels, while NC10 (2.1-fold (p < 0.001)), ANME-2d (1.8-fold (p < 0.001)), and Candidatus Nitrososphaera (1.5-fold (p < 0.001)) decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.

Streptomyces effect on the bacterial microbiota associated to Crassostrea sikamea oyster

AIM

To determine the composition and diversity of the microbiota associated to Crassostrea sikamea treated during 30 days with Streptomyces strains N7 and RL8.

METHODS AND RESULTS

DNA was extracted from oysters followed by 16S rRNA gene amplification and pyrosequencing. The highest and lowest species diversity richness was observed in the initial and final control group, whereas Streptomyces-treated oysters exhibited intermediate values. Proteobacteria was the most abundant phylum (81·4-95·1%), followed by Bacteroidetes, Actinobacteria and Firmicutes. The genera Anderseniella, Oceanicola, Roseovarius, Ruegeria, Sulfitobacter, Granulosicoccus and Marinicella encompassed the core microbiota of all experimental groups. The genus Bacteriovorax was detected in all groups except in the final control and the depurated N7, whereas Vibrio remained undetected in all Streptomyces-treated groups. RL8 was the only group that harboured the genus Streptomyces in its microbiota. Principal component analysis showed that Streptomyces strains significantly changed oyster microbiota with respect to the initial and final control.

CONCLUSIONS

Crassostrea sikamea treated with Streptomyces showed high species diversity and a microbiota composition shift, characterized by keeping the predator genus Bacteriovorax and decreasing the pathogenic Vibrio.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first culture-independent study showing the effect of Streptomyces over the oyster microbiota. It also sheds light about the potential use of Streptomyces to improve mollusc health and safety for consumers after the depuration process.

Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales

Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics.