Dynamics of the bacterial community in a channel catfish nursery pond with a cage-pond integration system

Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1-V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

Impact of Temperature, Nutrients and Heavy Metals on Bacterial Diversity and Ecosystem Functioning Studied by Freshwater Microcosms and High-Throughput DNA Sequencing

Microbial communities are fundamental components in freshwater, and community shifts in ecosystem structure are indicative of changing environmental conditions. This study aimed at investigating the influence of key environmental parameters on bacterial diversity and ecosystem functioning (i.e. organic matter breakdown) in laboratory freshwater microcosms. The effects of varying temperatures (5, 20 and 35 °C), nutrients (representing low, medium and high urbanization) and heavy metals Copper (Cu) and Zinc (Zn) on bacterial diversity and organic matter (OM) breakdown were studied by using leaf bags and capsules filled with polycaprolactonediol-2000 (PCP-2000), respectively. The leaf-associated bacterial diversity was determined by next-generation sequencing of SSU rRNA gene amplicons. The results showed that bacterial diversity increased at high temperature (35 °C) with more operational taxonomic units (OTUs) as compared to medium (20 °C) or low (5 °C) temperatures, whereas nutrient variation had fewer effects on the bacterial community structure. In contrast, the presence of heavy metals, especially high concentrations (100 μM) of Cu, reduced the number of OTUs in the leaf-associated bacterial community. The higher temperatures and nutrient levels accelerated PCP-2000 breakdown rate, but this was impeded by a high concentration (100 μM) of Cu in the short term, though no effect of Zn on breakdown rate was observed. The overall results indicate that temperature and variated heavy metals are among the key factors that affect bacterial diversity and ecosystem functioning in freshwater systems.