Microbial community structure in a host-parasite system: the case of Prussian carp and its parasitic crustaceans.

AIMS: The aim of the study was to investigate the skin microbiota of Prussian carp infested by ectoparasites from the genera Argulus and Lernaea. METHODS AND RESULTS: Associated microbiota of skin of Prussian carp and ectoparasites were investigated by sequencing of the V3, V4 hypervariable regions of 16S rRNA using Illumina MiSeq sequencing platform. CONCLUSIONS: According to the Spearman rank correlation test, the increasing load of ulcerations of the skin of Prussian carp was weakly negatively correlated with reduction in the abundance of the following taxa: Acrobacter, bacteria C39 (Rhodocyclaceae), Rheinheimera, Comamonadaceae, Helicobacteraceae and Vogesella. In this study, the microbiota of ectoparasites from the genera Lernaea and Argulus were characterized for the first time. The microbiota associated with L. cyprinacea was significantly different from microbial communities of intact skin mucosa of both infested and uninfested fish and skin ulcers (ADONIS, P ≤ 0·05). The microbiota associated with parasitic crustaceans L. cyprinacea were dominated by unclassified bacteria from Comamonadaceae, Aeromonadaceae families and Vogesella. The dominant microbiota of A. foliaceus were represented by Flavobacterium, Corynebacterium and unclassified Comamonadaceae. SIGNIFICANCE AND IMPACT OF THE STUDY: Results from these studies indicate that ectoparasites have the potential to alter skin microbiota, which can play a possible role in the transmission of secondary bacterial infections in fish, caused by pathogenic bacteria.

Feeding habits shape infection levels by plerocercoids of the tapeworm Triaenophorus crassus in muscle of a sympatric pair of whitefish in an oligotrophic lake.

Lake Teletskoye (West Siberia, Russia) is inhabited by a sympatric pair of whitefish, with each member of the pair being characterized by different feeding habits. Coregonus lavaretus pidschian (Gmelin, 1789) is a large 'benthivorous' form, while C. l. pravdinellus (Dulkeit, 1949) is a small 'planktivorous' form. Fish were collected from the end of August to the middle of September in 2017 and 2019-2020 in the north part of Lake Teletskoye. For the 'benthivorous' form the prevalence, intensity and abundance of T. crassus ranged from 22.4% to 51.9%, 1.9-2.8 and 0.4-1.3, respectively, whereas the same indices for the 'planktivorous' form ranged from 94.7% to 97.5%, 4.2-4.8 and 4.0-4.7, respectively. The level of prevalence of infection and abundance of T. crassus in muscle was relatively stable among studied years for both forms. The level of prevalence was higher in the years 2019 and 2020 than in 2017 for the 'benthivorous' form, whereas for the 'planktivorous' form this index did not change during the studied years. For the first time, a partial sequencing of the cox1 gene (593 bp) for T. crassus was sequenced. All 15 plerocercoids of T. crassus were represented by four haplotypes.

The gut microbiota of Cystidicola farionis parasitizing the swim bladder of the nosed charr morph Salvelinus malma complex in Lake Kronotskoe (Kamchatka, Russia).

Using the approach of sequencing the V3-V4 region of the 16S rRNA gene, we have analyzed the bacterial diversity associated with the gut and "body" (other parts of nematode after dissection: cuticle, epidermis and longitudinal muscles, etc) of Cystidicola farionis parasitizing the swim bladder of different morphotypes of the nosed charr. Comparisons of the gut microbiota of nematodes with their "body" has revealed that the associated microbiota are closely related to each other. Taxonomic analysis indicated that the relative abundances of the dominant nematode-associated bacteria varied with individual fish. The common dominant microbiota of the gut and "body" of nematodes were represented by Aeromonas, Pseudomonas, Shewanella, and Yersinia, while the associated microbiota of the swim bladder of the nosed charr was dominated by Acinetobacter, Cetobacterium, Pajaroellobacter, Paracoccus, Pseudomonas, Shewanella. By comparing the associated microbiota of nematode parasitizing the different morphotypes of the nosed charr the difference in richness estimates (number of OTU's and Chao1) were revealed between the N1g and N2 morphs.

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish.

AIMS: The aim of the present study was to investigate the composition of the intestinal microbiota during the acute stage of a bacterial infection to understand how dysbiosis of the gut may influence overall taxonomic hierarchy and diversity, and determine if there exists a bacterial taxon(s) that serve as markers for healthy or diseased rainbow trout (Oncorhynchus mykiss). METHODS AND RESULTS: From July to September 2015, 29 specimens of 3-year-old (an average weight from 240·9 ± 37·7 to 850·7 ± 70·1 g) rainbow trout O. mykiss were studied. Next-generation high-throughput sequencing of the 16S ribosomal RNA genes was applied to stomach and intestinal samples to compare the impact of infection status on the microbiota of rainbow trout O. mykiss (Walbaum) from the northwest part of Eurasia (Karelian region, Russia). The alpha diversity (Chao1, Simpson and Shannon index) of the microbial community of healthy rainbow trout was significantly higher than in unhealthy fish. The greatest contribution to the gut microbial composition of healthy fish was made by OTU's belonging to Bacillus, Serratia, Pseudomonas, Cetobacterium and Lactobacillus. Microbiota of unhealthy fish in most cases was represented by the genera Serratia, Bacillus and Pseudomonas. In microbiota of unhealthy fish there were also registered unique taxa such as bacteria from the family Mycoplasmataceae and Renibacterium. Analysis of similarities test revealed the significant dissimilarity between the microbiota of stomach and intestine (P ≤ 0·05). CONCLUSIONS: A substantial finding was the absence of differences between microbial communities of the stomach and intestine in the unhealthy groups if compared with healthy fish. SIGNIFICANCE AND IMPACT OF THE STUDY: These results demonstrated alterations of the gut microbiota of farmed rainbow trout, O. mykiss during co-infections and can be useful for the development of new strategies for disease control programs.

Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake.

AIMS: The aim of this work was to study the gut microbial diversity from eight species of wild fish with different feeding habits, digestive physiology (gastric vs agastric) and provide comparative structural analysis of the microbial communities within their environment (food items, water, sediments and macrophytes). METHODS AND RESULTS: The microbiota of fish gut and their prey items were studied using next generation high-throughput sequencing of the 16S ribosomal RNA genes. A scatter plot based on PCoA scores demonstrated the microbiota formed three groups: (i) stomach and intestinal mucosa (IM), (ii) stomach and intestinal content (IC), and (iii) prey and environment. Comparisons using ANOSIM showed significant differences among IC of omnivorous, zoobenthivorous, zooplanktivorous-piscivorous fishes (P ≤ 0·1). No significant difference was detected for mucosa from the same groups (P > 0·1). CONCLUSIONS: Neither the interspecies differences in fish diet nor their phylogenetic position had any effect on the microbiome of the IM, but diet did influence the composition of the microbiota of the IC. SIGNIFICANCE AND IMPACT OF THE STUDY: The data demonstrate that fish harboured specific groups of bacteria that do not completely reflect the microbiota of the environment or prey.

A comparative study on microbiota from the intestine of Prussian carp (Carassius gibelio) and their aquatic environmental compartments, using different molecular methods.

AIMS: The aim of this study was to evaluate, via various molecular methods, the possible correlations between microbial community structure of Prussian carp and the environmental compartments of their habitat. METHODS AND RESULTS: Microbial communities in the intestine and environmental compartments were studied using PCR-screening, cloning and next-generation high-throughput sequencing of the 16S ribosomal RNA genes. The 16S rDNA metagenomic sequencing showed higher bacterial diversity in comparison with clone libraries, while group-specific PCR showed positive detection of nine bacteria phyla. Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria and Actinobacteria were most abundant both in the intestine and habitat environments. The comparative analyses reveal that the bacterial community in the Prussian carp intestine is most similar to that identified from the chironomid. CONCLUSIONS: This study demonstrated some differences between molecular methods and showed advantages and limitations associated with them. These differences have the potential to reduce bias in results obtained from analysis of the community structure. The advantages of each molecular technique can be used for a better understanding of microbial diversity. The microbiota of Prussian carp intestine is most similar to those from the chironomids. SIGNIFICANCE AND IMPACT OF THE STUDY: We investigated the diversity of the intestinal microbiota in an economically important aquaculture species, the Prussian carp (Carassius gibelio). The results provide significant information to discuss possible functions of these bacteria for further understanding of Prussian carp health.

Feeding habits and ontogenic changes in digestive enzyme patterns in five freshwater teleosts.

Feeding habits and the activity of digestive enzymes (total alkaline proteases, α-amylase and lipase) from dace Leuciscus leuciscus, roach Rutilus rutilus, Prussian carp Carassius auratus gibelio, perch Perca fluviatilis and pikeperch Sander lucioperca fry were studied in the Malye Chany Lake-Kargat Estuary (western Siberia, Russia). The diet of fry from all studied species was mainly composed of chironomid larvae and zooplanktonic organisms (i.e. cladocera and copepoda), whereas carnivorous species such as P. fluviatilis and S. lucioperca also preyed on fry from other fishes while detritus and microalgae were also important in the diet of ommivorous species. When comparing diet similarity (Sørensen-Dice index, Q(S)) among fry at different stages of development, both omnivorous and carnivorous species showed a high level of similarity (0.67 < Q(S) < 0.89 and 0.73 < Q(S)< 0.89, respectively). Diet similarity values were in agreement with the overall digestive activity profile analysed by cluster analysis. Diet similarity suggested potential trophic competition when zooplanktonic and benthic prey began to decline towards autumn. The analysis of pancreatic digestive enzymes revealed a correlation among their activities and fry feeding habits with α-amylase:total proteases (A:P) values higher than 1 in omnivorous species and lower (A:P ≤ 1) in carnivorous species.