Study of the influence of tributyrin-supplemented diets on the gut bacterial communities of rainbow trout (Oncorhynchus mykiss).

Dietary supplementation with triglyceride tributyrin (TBT), a butyrate precursor, has been associated with beneficial effects on fish health and improvements in the ability of carnivorous fish to tolerate higher levels of plant-based protein. In this study, we aimed to investigate the effects of a plant-based diet supplemented with TBT on the structural diversity and putative function of the digesta-associated bacterial communities of rainbow trout (Oncorhynchus mykiss). In addition to this, we also assessed the response of fish gut digestive enzyme activities and chyme metabolic profile in response to TBT supplementation. Our results indicated that TBT had no significant effects on the overall fish gut bacterial communities, digestive enzyme activities or metabolic profile when compared with non-supplemented controls. However, a more in-depth analysis into the most abundant taxa showed that diets at the highest TBT concentrations (0.2% and 0.4%) selectively inhibited members of the Enterobacterales order and reduced the relative abundance of a bacterial population related to Klebsiella pneumoniae, a potential fish pathogen. Furthermore, the predicted functional analysis of the bacterial communities indicated that increased levels of TBT were associated with depleted KEGG pathways related to pathogenesis. The specific effects of TBT on gut bacterial communities observed here are intriguing and encourage further studies to investigate the potential of this triglyceride to promote pathogen suppression in the fish gut environment, namely in the context of aquaculture.

A Study of Sponge Symbionts from Different Light Habitats.

The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.

In vitro study of the modulatory effects of heat-killed bacterial biomass on aquaculture bacterioplankton communities.

Recent studies have shown that the addition of non-viable microbial biomass or their components (postbiotics) to fish feed can modulate the gut microbiome and positively influence fish health in aquaculture systems. However, no information was hitherto available on the use of non-viable microbial biomass to manipulate aquaculture bacterioplankton communities. To fill this gap, here we used an in vitro model to assess the effects of heat-killed biomasses of an antagonistic strain Pseudoalteromonas rubra SubTr2 and a non-antagonist strain Escherichia coli DH5α on bacterioplankton communities of a recirculating aquaculture system (RAS). Our results showed that these biomasses can have generalist and species-specific effects on aquaculture bacterioplankton structure and function. In addition, they enriched the abundance of bacterial predators, reduced bacterial load and potentially influenced nutrient cycling and pathogen development in aquaculture water. Despite its preliminary nature, for the first time, this study showed that heat-killed microbial biomass has potential application as an in situ modulator of bacterioplankton in aquaculture systems.

Effect of glycerol feed-supplementation on seabass metabolism and gut microbiota.

Dietary glycerol supplementation in aquaculture feed is seen as an alternative and inexpensive way to fuel fish metabolism, attenuate metabolic utilization of dietary proteins and, subsequently, reduce nitrogen excretion. In this study, we evaluated the impact of dietary glycerol supplementation on nitrogen excretion of European seabass (Dicentrarchus labrax) and its effects on metabolite profile and bacterial community composition of gut digesta. These effects were evaluated in a 60-day trial with fish fed diets supplemented with 2.5% or 5% (w/w) refined glycerol and without glycerol supplementation. Nuclear magnetic resonance spectroscopy and high-throughput 16S rRNA gene sequencing were used to characterize the effects of glycerol supplementation on digesta metabolite and bacterial community composition of 6-h postprandial fish. Our results showed that ammonia excretion was not altered by dietary glycerol supplementation, and the highest glycerol dosage was associated with significant increases in amino acids and a decrease of ergogenic creatine in digesta metabolome. Concomitantly, significant decreases in putative amino acid degradation pathways were detected in the predicted metagenome analysis, suggesting a metabolic shift. Taxon-specific analysis revealed significant increases in abundance of some specific genera (e.g., Burkholderia and Vibrio) and bacterial diversity. Overall, our results indicate glycerol supplementation may decrease amino acid catabolism without adversely affecting fish gut bacterial communities.Key points• Glycerol can be an inexpensive and energetic alternative in fish feed formulations.• Glycerol did not affect nitrogen excretion and gut bacteriome composition.• Glycerol reduced uptake of amino acids and increased uptake of ergogenic creatine.• Glycerol reduced putative amino acid degradation pathways in predicted metagenome.

Microcosm evaluation of the impact of oil contamination and chemical dispersant addition on bacterial communities and sediment remediation of an estuarine port environment.

AIM: To evaluate the interactive effects of oil contamination and chemical dispersant application on bacterial composition and sediment remediation of an estuarine port environment. METHODS AND RESULTS: A multifactorial controlled microcosm experiment was set up using sediment cores retrieved from an estuarine port area located at Ria de Aveiro lagoon (Aveiro, Portugal). An oil spill with and without chemical dispersant addition was simulated. Sediment oil hydrocarbon concentrations and benthic bacterial community structure were evaluated by GC-MS and 16S rRNA high-throughput sequencing respectively. Although initially (first 10 days) chemical dispersion of oil enhanced the concentrations of the heavier polycyclic aromatic hydrocarbons and of the C22 -C30 alkane group, with time (21 days), no significant differences in hydrocarbon concentrations were detected among treatments. Moreover, no significant changes were detected in the structure of sediment bacterial communities, which mainly consisted of operational taxonomic units related to hydrocarbon-contaminated marine environments. We hypothesize that the environmental background of the sampling site preconditioned the communities' response to additional contamination. CONCLUSION: This experimental microcosm study showed that the chemical dispersion of oil did not influence sediment remediation or bacterial community composition. SIGNIFICANCE AND IMPACT OF THE STUDY: Our study showed that chemical dispersion of oil may not improve the remediation of port sediments. Further studies are needed to investigate the impact of chemical dispersants in combination with bioremediation strategies on the process of sediment remediation in port areas.

Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe-pollutant interactions in a remote environment.

Recalcitrant polycyclic aromatic hydrocarbons (PAHs) released into seawater end up in the deep sea sediments (DSSs). However, their fate here is often oversimplified by theoretical models. Biodegradation of PAHs in DSSs, is assumed to be similar to biodegradation in surface habitats, despite high hydrostatic pressures and low temperatures that should significantly limit PAH biodegradation. Bacteria residing in the DSSs (related mainly to α- and γ-Proteobacteria) have been shown to or predicted to possess distinct genes, enzymes and metabolic pathways, indicating an adaptation of these bacterial communities to the psychro-peizophilic conditions of the DSSs. This work summarizes some of the most recent research on DSS hydrocarbonoclastic populations and mechanisms of PAH degradation and discusses the challenges posed by future high CO2 and UV climate scenarios on biodegradation of PAHs in DSSs.