A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event

Migratory Shorebird Gut Microbes are not Associated with Bivalve Prey in Monsoon Tropical Australia

Migratory animals can carry symbionts over long distances. While well-studied for parasite and pathogen transmission, less is known about use of this route by other symbiotic taxa, particularly those non-pathogenic. Here we ask the question of whether gut bacteria can be spread between continents by long-distance bird migration, although gut microbiomes in birds may not be as stable or persistent as those of non-volant animals. We used amplicon sequencing of both bacterial 16S rRNA gene and Vibrio-centric hsp60 gene to determine whether the faecal bacteria of migratory great knots (Calidris tenuirostris) also occur in their main food source in Northern Australia or in nearby sand, comparing samples before and after the birds' long-distance migration. Our data suggest that there is little connectivity among the bacterial microbiomes, except in the bivalve prey. Our results are consistent with previous studies finding that bird faecal microbiomes were not host-specific and contrast with those showing an influence of diet on bird faecal bacteria. We also found little connectivity among Vibrio spp. However, although faecal sample sizes were small, the dominance of different individual Vibrio spp. suggests that they may have been well-established in knot guts and thus capable of moving with them on migration. We suggest that the physiological impacts of a long-distance migration may have caused shifts in the phyla comprising great knot faecal communities.

Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster

16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen (Vibrio parahaemolyticus) contamination and/or V. parahaemolyticus-specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treated-groups even when the bacterial composition was compared at the possible lowest-rank taxa, family/genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.

Acclimation in intertidal animals reduces potential pathogen load and increases survival following a heatwave

Intertidal animals can experience intense heat during a heatwave, leading to mortality. The causes of death for intertidal animals following heatwaves have often been attributed to a breakdown in physiological processes. This, however, contrasts with research in other animals where heatwave mortality is attributed to existing or opportunistic diseases. We acclimated intertidal oysters to four treatment levels, including an antibiotic treatment, and then exposed all treatments to a 50°C heatwave for 2 h, replicating what can be experienced on Australian shorelines. We found that both acclimation and antibiotics increased survival and reduced the presence of potential pathogens. Non-acclimated oysters had a significant shift in their microbiome, with increasing abundances of bacteria from the Vibrio genera, including known potential pathogens. Our results demonstrate that bacterial infection plays a pivotal role in post-heatwave mortality. We anticipate these findings to inform the management of aquaculture and intertidal habitats as climate change intensifies.

Elevated estuary water temperature drives fish gut dysbiosis and increased loads of pathogenic vibrionaceae

Marine water temperatures are increasing globally, with eastern Australian estuaries warming faster than predicted. There is growing evidence that this rapid warming of coastal waters is increasing the abundance and virulence of pathogenic members of the Vibrionaceae, posing a significant health risk to both humans and aquatic organisms. Fish disease, notably outbreaks of emerging pathogens in response to environmental perturbations such as heatwaves, have been recognised in aquaculture settings. Considerably less is known about how rising sea surface temperatures will impact the microbiology of wild fish populations, particularly those within estuarine systems that are more vulnerable to warming. We used a combination of Vibrio-specific quantitative PCR and amplicon sequencing of the 16S rRNA and hsp60 genes to examine seawater and fish (Pelates sexlineatus) gut microbial communities across a quasi-natural experimental system, where thermal pollution from coal-fired power stations creates a temperature gradient of up to 6 °C, compatible with future predicted temperature increases. At the warmest site, fish hindgut microbial communities were in a state of dysbiosis characterised by shifts in beta diversity and a proliferation (71.5% relative abundance) of the potential fish pathogen Photobacterium damselae subsp. damselae. Comparable patterns were not identified in the surrounding seawater, indicating opportunistic proliferation within estuarine fish guts under thermal stress. A subsequent evaluation of predicted future warming-related risk due to pathogenic Vibrionaceae in temperate estuarine fish demonstrated that warming is likely to drive opportunistic pathogen increases in the upper latitudinal range of this estuarine fish, potentially impacting adaptations to future warming. These findings represent a breakthrough in our understanding of the dynamics of emerging pathogens in populations of wild aquatic organisms within environments likely to experience rapid warming under future climate change.

Crassostrea gigas oysters from a non-intensive farming area naturally harbor potentially pathogenic vibrio strains

Farming intensification and climate change are inevitably linked to pathogen emergence in aquaculture. In this context, infectious diseases associated with vibrios span all developmental stages of the Pacific Oyster Crassostrea gigas. Moreover, virulence factors associated with pathogenicity spread among the vibrio community through horizontal gene transfer as part of the natural eco-evolutive dynamic of this group. Therefore, risk factors associated with the emergence of pathogens should be assessed before the appearance of mass mortalities in developing rearing areas. In this context, we characterized the vibrios community associated with oysters cultured in a non-intensive area free of massive mortalities located at Tongoy bay, Chile, through a culture-dependent approach. We taxonomically affiliated our isolates at the species level through the partial sequencing of the heat shock protein 60 gene and estimated their virulence potential through experimental infection of juvenile C. gigas. The vibrio community belonged almost entirely to the Splendidus clade, with Vibrio lentus being the most abundant species. The virulence potential of selected isolates was highly contrasted with oyster survival ranging between 100 and 30 %. Moreover, different vibrio species affected oyster survival at different rates, for instance V. splendidus TO2_12 produced most mortalities just 24 h after injection, while the V. lentus the most virulent strain TO6_11 produced sustained mortalities reaching 30 % of survival at day 4 after injection. Production of enzymes associated with pathogenicity was detected and hemolytic activity was positive for 50 % of the virulent strains and negative for 90 % of non-virulent strains, representing the phenotype that better relates to the virulence status of strains. Overall, results highlight that virulence is a trait present in the absence of disease expression, and therefore the monitoring of potentially pathogenic groups such as vibrios is essential to anticipate and manage oyster disease emergence in both established and under-development rearing areas.

Phylogenomic diversity of Vibrio species and other Gammaproteobacteria isolated from Pacific oysters (Crassostrea gigas) during a summer mortality outbreak

The Pacific oyster (PO), Crassostrea gigas, is an important commercial marine species but periodically experiences large stock losses due to disease events known as summer mortality. Summer mortality has been linked to environmental perturbations and numerous viral and bacterial agents, indicating this disease is multifactorial in nature. In 2013 and 2014, several summer mortality events occurred within the Port Stephens estuary (NSW, Australia). Extensive culture and molecular-based investigations were undertaken and several potentially pathogenic Vibrio species were identified. To improve species identification and genomically characterise isolates obtained from this outbreak, whole-genome sequencing (WGS) and subsequent genomic analyses were performed on 48 bacterial isolates, as well as a further nine isolates from other summer mortality studies using the same batch of juveniles. Average nucleotide identity (ANI) identified most isolates to the species level and included members of the Photobacterium, Pseudoalteromonas, Shewanella and Vibrio genera, with Vibrio species making up more than two-thirds of all species identified. Construction of a phylogenomic tree, ANI analysis, and pan-genome analysis of the 57 isolates represents the most comprehensive culture-based phylogenomic survey of Vibrios during a PO summer mortality event in Australian waters and revealed large genomic diversity in many of the identified species. Our analysis revealed limited and inconsistent associations between isolate species and their geographical origins, or host health status. Together with ANI and pan-genome results, these inconsistencies suggest that to determine the role that microbes may have in Pacific oyster summer mortality events, isolate identification must be at the taxonomic level of strain. Our WGS data (specifically, the accessory genomes) differentiated bacterial strains, and coupled with associated metadata, highlight the possibility of predicting a strain's environmental niche and level of pathogenicity.

Life history of oysters influences Vibrio parahaemolyticus accumulation in Pacific oysters (Crassostrea gigas)

Vibrio parahaemolyticus infection in humans is associated with raw oyster consumption. Evaluation of V. parahaemolyticus presence in oysters is of most interest because of the economic and public health issues that it represents. To explore V. parahaemolyticus accumulation and depuration in adult Crassostrea gigas, we developed a GFP-tagged V. parahaemolyticus strain (IFVp201-gfp⁺ ), as well as a rapid and efficient quantification method in C. gigas oysters haemolymph by flow cytometry. Impact of the life history of C. gigas on accumulation and depuration of V. parahaemolyticus IFVp201 was subsequently investigated. We found that naive oysters, i.e. grown in controlled facilities with UV treated seawater, accumulated significantly more IFVp201 than environmental oysters, i.e. grown in intertidal environment. We hypothesized that environmental oysters could have been immune primed, thus could limit V. parahaemolyticus accumulation. Meanwhile, both naive and environmental oysters had similar depuration rates.

cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae

The cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of "universal" PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.

An Integrative, Multiparametric Approach for the Comprehensive Assessment of Microbial Quality and Pollution in Aquaculture Systems

As the aquaculture sector significantly expanded worldwide in the past decades, the concept of sustainable aquaculture has developed with the challenge of not only maximizing benefits but also minimizing the negative impacts on the environment assuring, at the same time, food security. In this framework, monitoring and improving the microbiological water quality and animal health are a central topic. In the present study, we evaluated the seawater microbiological quality in a mariculture system located in a Mediterranean coastal area (Northern Ionian Sea, Italy). We furnished, for the first time, a microbial inventory based on conventional culture-based methods, integrated with the 16S rRNA gene metabarcoding approach for vibrios identification and diversity analyses, and further implemented with microbial metabolic profiling data obtained from the Biolog EcoPlate system. Microbiological pollution indicators, vibrios diversity, and microbial metabolism were determined in two different times of the year (July and December). All microbial parameters measured in July were markedly increased compared to those measured in December. The presence of potentially pathogenic vibrios is discussed concerning the risk of fish disease and human infections. Thus, the microbial inventory here proposed might represent a new multiparametric approach for the suitable surveillance of the microbial quality in a mariculture system. Consequently, it could be useful for ensuring the safety of both the reared species and the consumers in the light of sustainable, eco-friendly aquaculture management.

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.

Occurrence and dynamics of potentially pathogenic vibrios in the wet-dry tropics of northern Australia

Bacteria from the Vibrio genus are a ubiquitous component of coastal and estuarine ecosystems with several pathogenic Vibrio species displaying preferences for warm tropical waters. We studied the spatial and temporal abundance of three key human potential pathogens V. parahaemolyticus, V. cholerae and V. vulnificus in northern tropical Australia, over the wet and dry seasons, to identify environmental parameters influencing their abundance. Quantitative PCR (qPCR) analysis revealed that V. parahaemolyticus occurred more frequently and in higher abundance than V. cholerae and V. vulnificus across all locations examined. All three species were more abundant during the wet season, with V. parahaemolyticus abundance correlated to temperature and conductivity, whereas nutrient concentrations and turbidity best explained V. vulnificus abundance. In addition to these targeted qPCR analyses, we assessed the composition and dynamics of the entire Vibrio community using hsp60 amplicon sequencing. Using this approach, 42 Vibrio species were identified, including a number of other pathogenic species such as V. alginolyticus, V. mimicus and V. fluvialis. The Vibrio community was more diverse in the wet season, with temperature and dissolved oxygen as the key factors governing community composition. Seasonal differences were primarily driven by a greater abundance of V. parahaemolyticus and V. vulnificus during the wet season, while spatial differences were driven by different abundances of V. harveyi, V. campbellii, V. cholerae and V. navarrensis. When we related the abundance of Vibrio to other bacterial taxa, defined using 16S rRNA gene amplicon sequencing, V. parahaemolyticus was negatively correlated to several taxa, including members of the Rickettsiales and Saccharimonadales, while V. vulnificus was negatively correlated to Rhobacteriaceae and Cyanobiaceae. In contrast, V. alginolyticus, V. harveyi and V. mediterranei were all positively correlated to Cyanobacteria. These observations highlight the dynamic nature of Vibrio communities and expands current understanding of the processes governing the occurrence of potentially pathogenic Vibrio spp. in tropical coastal ecosystems.

Application of Quantitative-PCR to Monitor Netpen Sites in British Columbia (Canada) for Tenacibaculum Species

Tenacibaculum are frequently detected from fish with tenacibaculosis at aquaculture sites; however, information on the ecology of these bacteria is sparse. Quantitative-PCR assays were used to detect T. maritimum and T. dicentrarchi at commercial Atlantic salmon (Salmo salar) netpen sites throughout several tenacibaculosis outbreaks. T. dicentrarchi and T. maritimum were identified in live fish, dead fish, other organisms associated with netpens, water samples and on inanimate substrates, which indicates a ubiquitous distribution around stocked netpen sites. Before an outbreak, T. dicentrarchi was found throughout the environment and from fish, and T. maritimum was infrequently identified. During an outbreak, increases in the bacterial load in were recorded and no differences were recorded after an outbreak supporting the observed recrudescence of mouthrot. More bacteria were recorded in the summer months, with more mortality events and antibiotic treatments, indicating that seasonality may influence tenacibaculosis; however, outbreaks occurred in both seasons. Relationships were identified between fish mortalities and antimicrobial use to water quality parameters (temperature, salinity, dissolved oxygen) (p < 0.05), but with low R² values (<0.25), other variables are also involved. Furthermore, Tenacibaculum species appear to have a ubiquitous spatial and temporal distribution around stocked netpen sites, and with the potential to induce disease in Atlantic salmon, continued research is needed.

Depuration processes affect the Vibrio community in the microbiota of the Manila clam, Ruditapes philippinarum

As filter-feeders, bivalve molluscs accumulate Vibrio into edible tissues. Consequently, an accurate assessment of depuration procedures and the characterization of the persistent Vibrio community in depurated shellfish represent a key issue to guarantee food safety in shellfish products. The present study investigated changes in the natural Vibrio community composition of the Ruditapes philippinarum microbiota with specific focus on human pathogenic species. For this purpose, the study proposed a MLSA-NGS approach (rRNA 16S, recA and pyrH) for the detection and identification of Vibrio species. Clam microbiota were analysed before and after depuration procedures performed in four depuration plants, using culture-dependent and independent approaches. Microbiological counts and NGS data revealed differences in terms of both contamination load and Vibrio community between depuration plants. The novel MLSA-NGS approach allowed for a clear definition of the Vibrio species specific to each depuration plant. Specifically, depurated clam microbiota showed presence of human pathogenic species. Ozone treatments and the density of clams in the depuration tank probably influenced the level of contamination and the Vibrio community composition. The composition of Vibrio community specific to each plant should be carefully evaluated during the risk assessment to guarantee a food-safe shellfish-product for the consumer.

Fitness costs associated with maternal immune priming in the oyster

Maternal immune priming is the transfer of immunity from mother to offspring, which may reduce the offspring's risk of disease from a pathogen that previously infected its mother. Maternal immune priming has been described in at least 25 invertebrate taxa, including Crassostrea gigas. Larvae of C. gigas have improved survival to Ostreid herpesvirus (OsHV-1) if their mothers are either infected with OsHV-1 or were injected with a virus mimic called poly(I:C). However, fitness costs associated with maternal immune priming in C. gigas are unknown. Here, we show C. gigas larvae produced from poly(I:C)-treated mothers are smaller, and have higher total bacteria and Vibrio loads compared to control larvae. These results suggest that the improved offspring survival of C. gigas to OsHV-1 due to maternal immune priming with poly(I:C) is potentially traded off with other important life history traits, such as larval growth rate and destabilisation of the microbiome.

Vibrio-bivalve interactions in health and disease

In the marine environment, bivalve mollusks constitute habitats for bacteria of the Vibrionaceae family. Vibrios belong to the microbiota of healthy oysters and mussels, which have the ability to concentrate bacteria in their tissues and body fluids, including the hemolymph. Remarkably, these important aquaculture species respond differently to infectious diseases. While oysters are the subject of recurrent mass mortalities at different life stages, mussels appear rather resistant to infections. Thus, Vibrio species are associated with the main diseases affecting the worldwide oyster production. Here, we review the current knowledge on Vibrio-bivalve interaction in oysters (Crassostrea sp.) and mussels (Mytilus sp.). We discuss the transient versus stable associations of vibrios with their bivalve hosts as well as technical issues limiting the monitoring of these bacteria in bivalve health and disease. Based on the current knowledge of oyster/mussel immunity and their interactions with Vibrio species pathogenic for oyster, we discuss how differences in immune effectors could contribute to the higher resistance of mussels to infections. Finally, we review the multiple strategies evolved by pathogenic vibrios to circumvent the potent immune defences of bivalves and how key virulence mechanisms could have been positively or negatively selected in the marine environment through interactions with predators.

Vibrio communities along a salinity gradient within a marine saltern hypersaline environment (Saline di Tarquinia, Italy)

Vibrio species are ubiquitous in a number of different aquatic environments and promptly adapting to environmental changes due to high genome plasticity. The presence of these bacteria in marine salterns, in relation to a salinity gradient has been not investigated yet. Moreover, it is not clear if these hypersaline environments could represent a reservoir for Vibrio spp. This work investigated, through a metagenetic approach, the distribution of Vibrio (over 2 years) in different ponds along the salinity gradient within the 'Saline di Tarquinia' salterns, considering also the adjacent coastal waters and an isolated brine storage basin (BSB). Vibrio occurrence was higher in the sea than in the ponds and BSB, where it usually represented a rare taxon (abundance <1%). In the sea, it showed abundances in-between 1%-2.6% in 8 months out of 24. Four OTUs were assigned to the Vibrio genus; except for one that was more abundant in BSB, the others were much higher in the sea. Redundancy analysis (RDA) suggested a different distribution of the OTUs in relation to water temperature and salinity. Vibrio was found, even with low abundances, at the highest salinities also, suggesting the salterns as a possible reservoir for the bacterium.