Biology subjects

Bowman, J. P.

Publications and source records attributed to Bowman, J. P..

5 recordsLinked to original sources

bioRxiv2024

Heat stress impacts the gut microbiome of Atlantic salmon by promoting growth of Vibrionaceae and is associated with extensive cast production

Atlantic salmon (Salmo salar) when exposed to heat stress have reduced voluntary feeding and exhibit changes in digesta consistency. This study was performed to determine what bacterial species occur and the overall bacterial abundance in the gut microbiome in heat stressed Atlantic salmon. For this Atlantic salmon in seawater tanks at 15{degrees}C were fed for 2 to 4 weeks. Tank temperatures were increased to 19{degrees}C until voluntary feeding abated at which point tank temperatures were cooled to 15{degrees}C for 4 weeks. At the end of each temperature phase the fish were stripped of feces and microbiome profiles were determined using 16S rRNA V1-V3 metabarcoding. The tank experiment was repeated three times in successive years. Vibrionaceae comprised most reads after the warm phase completed. The prominent levels of Vibrionaceae were accompanied by a large predominance of cast (sloughed intestinal mucosa) containing fecal samples. qPCR estimated Vibrionaceae cell populations increased 1.9-3.4 log units/g after the warm phase but and slightly decreased by 0.3-1.1 log units/g after the 15{degrees}C recovery phase. The results indicated heat stress induced inappetence corresponds to increased cast production accompanied by predominance of Vibrionaceae. Vibrionaceae colonizing the Atlantic salmon gut should be the focus of studies on the microbiology of thermally induced inappetence and dysbiosis in Atlantic salmon. Key ContributionThe experiments confirm that thermal stress increased cast production in Atlantic salmon. The increase in cast production coincides with increased predominance of Vibrionaceae. Though the growth of Vibrionaceae in the gut of salmon is not associated with acute disease it may represent a dysbiosis effect. The results suggest extended summers in regions where sea surface temperatures are at the tolerance limits require increased husbandry management of farmed fish. In addition, more studies are needed to determine if novel approaches can limit overgrowth of Vibrionaceae.

microbiology↗

bioRxiv2024

Characterization of bacteria colonizing the mucosal layer of the gastrointestinal tract of Atlantic salmon farmed in a warm water region

Atlantic salmon (Salmo salar) farmed in seawater in Tasmania (lutruwita) can experience temperatures close to their thermotolerance limit during summer. Gut microbiome data from eight successive annual surveys and a specific survey of GI tract mucosa and digesta bacterial cross-sectional distributions indicated members of the genus Aliivibrio, Vibrio, and an unclassified Mycoplasmoidaceae are the main colonizers of the gut mucosal layer in Tasmanian farmed salmon. Peak abundance levels are reached after 7-8 months, corresponding to the late summer, following the transfer of hatchery smolt to seawater farms. Salmon Aliivibrio isolates comprise three novel non-bioluminescent species distinct from species found in the northern hemisphere growing regions. Along with other Aliivibrio species these species share many genes required for host colonization and biofilm formation and also include species and strain-level dependent features. Two of the novel Aliivibrio species surprisingly possessed genes for cytolethal distending toxin while the more predominant species lacked any known virulence genes. The overall observations suggest a small number of species actively colonize the mucosal layer of Atlantic salmon farmed in Tasmania and that this process is strongly influenced by the environmental temperature.

microbiology↗

bioRxiv2022

Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture

Finfish aquaculture is one of the fastest-growing primary industries globally and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. However, little is known about the effect of the aquaculture in the bacterioplankton community. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Our results revealed natural stratification in bacterioplankton strongly associated to NOx, conductivity, salinity, temperature and PO4. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment.

microbiology↗

bioRxiv2022

The importance of environmental parameters and mixing zone in shaping estuarine microbial communities along a freshwater-marine gradient.

Microbial communities are important elements in the marine environment, contributing to nutrient cycling and biogeochemical processes. Estuaries comprise environments exhibiting characteristics from freshwater to marine, leading to distinct microbial communities across this environmental gradient. Here, we examine the spatial dynamics of microbial communities in Macquarie Harbour, an estuarine system on the West coast of Tasmania, Australia. Water was sampled along the estuary to explore the structure and composition of the microbial communities using 16S/18S rRNA gene amplicon sequencing. Multivariate analyses showed environmental variables and community compositions varying along a longitudinal (river to adjacent ocean) gradient at the surface. In the harbour, differences in the microbial community were observed between surface (0-1 m) and intermediate depths (4.5-11 m depth). The results of differential abundance, network and Partial Least Square analyses suggest that Macquarie Harbour is a mixing zone, where the distributions of archaeal, bacterial and eukaryotic communities are influenced by oceanic and riverine inputs. Coupled with the natural characteristics of the Harbour, the heterotrophic component of this microbial communities inhabiting the surface and intermediate waters may play important roles in the nutrient cycle in the studied area. These results provide critical insights into the Macquarie Harbour environment and the importance of understanding the role of microbial communities for similar systems elsewhere.

microbiology↗

bioRxiv2019

Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota

Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, and commercial fishing through wild stock enhancements, and aquaculture production. Flow through (FT) hatcheries require more water than Recirculating-Aquaculture-Systems (RAS) which enable up to 99% of water to be recycled thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of the built environment of a hatchery from three Atl salmon hatcheries (RAS n=2, FT n=1). Six juvenile fish were sampled from tanks in each of the hatcheries for a total of 60 fish across 10 tanks. Water and tank side biofilm samples were collected from each of the tanks along with three salmon body sites (gill, skin, and digesta) to assess mucosal microbiota using 16S rRNA sequencing. The water and tank biofilm had more microbial richness than fish mucus while skin and digesta from RAS fish had 2x the richness of FT fish. Body sites each had unique microbial communities (P<0.001) and were influenced by the various hatchery systems (P<0.001) with RAS systems more similar. Water and especially tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin and digesta communities were more similar to the origin tank biofilm vs. all other experimental tanks suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome with the skin microbiome as an important intermediate.\n\nIMPORTANCEAtlantic salmon, Salmo salar, is the most farmed marine fish worldwide with an annual production of 2,248 million metric tonnes in 2016. Salmon hatcheries are increasingly changing from flow through towards RAS design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies on hatcheries have focused either on the fish mucosal microbiota or the built environment microbiota, but have not combined the two to understand interactions. Our study evaluates how water and tank biofilm microbiota influences fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and furthermore how this can influence the fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for a beneficial phenotype.

microbiology↗