tench (Tinca tinca L.) is one of the most valued species of the Cyprinidae. this species is commercially important and has been intensively domesticated in recent years. to avoid excessive production losses, the health of farm fish must be maintained. Characterization of the tench gut microbiome can help achieve this goal, as the gastrointestinal microbiome plays an important role in host health. As part of this characterization, investigating the influence of the environment and season will help to understand the interrelationship between host and gut microbiota. therefore, our aim was to use high-throughput 16S rRNA gene amplicon sequencing to profile the gut microbiome of tench. We studied two populations in summer and autumn: wild tench living in a lake and tench living in a pond in a semi-intensive fish farm. We found that, in the gut microbiome of all fish, the most abundant phylum was Proteobacteria, followed by Firmicutes, Bacteroidetes and Actinobacteria. Together, these phyla constituted up to 90% of the microbial communities. the abundance of Candidatus Xiphinematobacter differed significantly between lake and pond fish in summer, but not in autumn. In pond tench, Methylobacterium abundance was significantly lower in summer than in autumn. Mean Shannon, Chao1 indices and observed OTU's indicated that microbial biodiversity was greater in the gut of lake fish than in that of pond fish. Betadiversity analysis showed significant divergence between groups with both weighted and unweighted UniFrac distance matrices. Principal coordinates analysis revealed that more of the variance in microbial diversity was attributable to environment than to season. Although some of the diversity in lake tench gut microbiota could be attributable to feeding preferences of individual fish, our results suggest that environment is the main factor in determining gut microbiome diversity in tench.

This study characterized the gastrointestinal microbiome of nine juvenile farmed pikeperch Sander lucioperca using a metagenomics approach based on bacterial 16S rRNA gene sequencing. Potential changes in the gut microbiota during 2 months of S. lucioperca juvenile life were investigated. Results revealed that gut microbiota was dominated by Proteobacteria (95-92%), while other phyla Firmicutes (1-1·5%) and Actinobacteria (0·9-1·5%) were less abundant. At the family level, fish-gut microbiota were dominated by Enterobacteriaceae, which constituted c. 83% of all DNA sequence reads. Such a situation was present in all of the examined fish except one, which showed a different proportion of particular microbial taxa than the other fish. In this fish, a higher relative abundance (%) of Fusobacteria (21·0%), Bacteroidetes (9·5%) and Firmicutes (7·5%) was observed. There were no significant differences in the gut microbiome structure at different stages of development in the examined fish. This may indicate that Proteobacteria inhabiting the gut microbiota at an early stage of life are a necessary component of the pikeperch microbiome that may support proper nutrition of the fish. The information obtained on the gut microbiome could be useful in determining juvenile S. lucioperca health and improving rearing conditions by welfare monitoring in aquaculture.

The diversity of beta-lactam antibiotic resistance genes, with particular emphasis on carbapenemase genes, during the treatment process at two wastewater treatment plants (WWTPs) with different levels of hospital wastewater inflow was investigated using high-throughput sequencing. An additional aspect of the study was to determine the taxonomic diversity of microorganisms in the studied samples. The obtained results suggest that bacteria of the Fusobacteriaceae family, not associated to date with this phenomenon, may be involved in the spread of antibiotic resistance in the environment. In samples from both wastewater treatment plants, the dominant beta-lactamase genes included blaOXA, blaGES, blaBEL, blaCfxA, and blaTEM. It is worth noting that the blaKPC and blaNDM genes were only found in untreated municipal wastewater with a higher hospital wastewater content. Moreover, an increase in the abundance of the blaIMP gene after the biological treatment stage in the studied treatment plants was found. In wastewater characterized by a higher proportion of hospital wastewater, 94 correlations were observed, while in wastewater with its lower proportion, 41 correlations were noted. Considering the above, the current research indicates that the inflow of hospital wastewater contributes to the spread of antibiotic resistance in the aquatic environment.

The increasing popularity of pike in angling and fish farming has created a need to increase pike production. However, intensive pike farming is subject to limitations due to diseases and pathogens. Sodium chloride (NaCl) could be a good alternative to chemotherapeutics, especially for protecting the fish against pathogens and parasites at early life stages. However, the impact of high salinity on the symbiotic bacteria inhabiting freshwater fish is still unclear. Therefore, our objective was to analyze the gut microbiome to find possible changes caused by salinity. In this study, the influence of 3‰ and 7‰ salinity on pike fry was investigated. High-throughput 16S rRNA gene amplicon sequencing was used to profile the gut microbiome of the fish. It was found that salinity had a statistically significant influence on pike fry mortality. Mortality was highest in the 7‰ salinity group and lowest in the 3‰ group. Microbiological analysis indicated that Proteobacteria and Actinobacteria predominated in the pike gut microbiome in all examined groups, followed by lower percentages of Bacteroidetes and Firmicutes. There were no statistically significant differences in the percent abundance of bacterial taxa between the control group and groups with a higher salinity. Our results suggest that salinity influences the gut microbiome structure in pike fry, and that 3‰ salinity may be a good solution for culturing pike at this stage in their development.

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A metagenomic approach was used to investigate how the microbial community composition changes when an anammox-based granular sludge reactor is seeded with nitritation-anammox biomass from a wastewater treatment plant. In the seed sample, the abundance of Candidatus Kuenenia stuttgartiensis was similar to Candidatus Jettenia caeni (12.63 vs. 11.68%). This biomass was typical in terms of microbial nitrogen conversion; both ammonia (Nitrosomonas sp.) and nitrite (Nitrospira sp.) oxidizing bacteria were detected. In the lab-scale reactor, Candidatus Kuenenia stuttgartiensis and Candidatus Jettenia caeni bacteria were also present in equal proportions (18.57 vs. 20.89%). On the contrary, Candidatus Nitrospira defluvii bacteria were highly abundant in this reactor, but no known ammonia-oxidizing bacteria were detected. In light of recent studies showing that Nitrospira sp. are capable of complete nitrification, the results presented here may well indicate that both stages of nitrification in the anammox-based granular sludge reactor were performed by this bacteria.Electronic supplementary materialThe online version of this article (10.1007/s13353-017-0418-1) contains supplementary material, which is available to authorized users.

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