Patterns of Sediment Fungal Community Dependent on Farming Practices in Aquaculture Ponds

Dry and wet seasonal variations of the sediment fungal community composition in the semi-arid region of the Dali River, Northwest China

Microbial communities play an important role in water quality regulation and biogeochemical cycling in freshwater ecosystems. However, there has been a lack of research on the seasonal variation of sediment microorganisms in the sediments of small river basins in typical semi-arid region. In this study, high-throughput DNA sequencing was used to investigate the fungal community and its influencing factors in the sediment of the Dali River in the dry and wet seasons. The results showed that there were obvious seasonal differences in fungal alpha diversity. The diversity and richness of fungi in the dry season were greater than that in the wet season, but the evenness of fungi in the dry season was lower than that in the wet season. In addition, Ascomycota and Basidiomycota were the most important phyla in the Dali River fungal community, but their distributions showed clear seasonal differences. In the dry season, the relative abundance of Ascomycota and Basidiomycota were 12.34-46.42% and 17.59-27.20%, respectively. In the wet season, the relative abundances of these two phyla were 24.33-36.56% and 5.75-12.26%, respectively. PICRUSt2 was used to predict the metabolic function of fungal community in the sediment, and it was found that at the first level, the proportion of biosynthesis in the dry season was higher than that in the wet season. The ecological network structure showed that the fungal community in the wet season was more complex and stable than that in the dry season. The characteristic fungi in the dry season sediment were chytrid fungi in the family Rhizophydiaceae and the order Rhizophydiales, whereas those in the wet season sediment were in the orders Eurotiales and Saccharomycetales. Canonical correspondence analysis (CCA) showed that the physicochemical properties of water and sediment together explained a greater proportion of the dry-season fungal community changes than of the wet-season changes. In the dry season, temperature and ammonia nitrogen in the water were the main factors affecting the change of fungal community, whereas in the wet season, total nitrogen concentration of the water, electrical conductivity, total organic carbon and available phosphorus of the sediment, pH, and temperature were the main factors affecting the changes in fungal community composition. The results of this study enhanced our understanding of microbial communities in semi-arid river ecosystems, and highlight the importance of the management and protection in river ecosystems.

Effects of Different Sources of Culture Substrate on the Growth and Immune Performance of the Red Swamp Crayfish (Procambarus clarkii)

The substrate in the aquatic environment plays a crucial role in nutrient deposition and recovery for the growth of aquatic organisms. In order to optimize the culture medium of Procambarus Clarkii, culture media from different sources were selected in this study to explore their effects on the growth and immune performance of red swamp crayfish. The results showed that the weight gain rate (WGR), body length growth rate (BLGR) and specific growth rate (SGR) in group I2 were the highest, followed by group I1 and group I3. The WGR and SGR of crayfish in the I1 and I2 groups were significantly higher than those in the I3 group (p < 0.05). The activities of acid phosphatase (ACP), alkaline phosphatase (AKP) and superoxide dismutase (SOD) were the highest in group I2, followed by group I3, and the lowest in group I1. The expression trends in growth-related genes, nuclear hormone receptor (E75), molt-inhibiting hormone (MIH) and chitinase genes were similar, and the expression levels in the I2 group were higher than those in the I1 and I3 groups. It was noted that the expression levels of E75 and MIH genes in the I2 group were significantly higher than those in the I3 group (p < 0.05). α diversity analysis of 16S rRNA data showed that there was no statistically significant difference in the abundance of intestinal flora among the three culture substrate groups. The β diversity in the Xitangni group, crayfish Tangni group and Shuitangni group was significantly different. These changes in microbiota suggest that using different substrates to culture crayfish leads to differences in gut microbiota diversity. To sum up, the growth in crayfish and immune performance influenced by the culture substrate condition and aquatic breeding sediment substrates, rather than crab pool and paddy field pond sediment substrates, showed a better effect.

A new species of Dictyochaeta (Sordariomycetes, Chaetosphaeriales, Chaetosphaeriaceae) from freshwater habitats in China

Background

Freshwater fungi refer to the fungi that depend on the freshwater habitats for the whole life cycle or part of their life cycle. In this context, a new aquatic hyphomycete was isolated from decaying wood in a freshwater habitat in Jiangxi Province, China.

New information

Dictyochaetajiangxiensis sp. nov., a new aquatic hyphomycete, is characterised by its unbranched, septate, base-fertile conidiophores with multisepta and single phialide at the apex, brown, sterile seta, monophialidic, subcylindrical conidiogenous cells narrowing below the funnel-shaped collarette, hyaline, unicellular, thin-walled, smooth, guttulate, falcate to subclavate conidia narrowly rounded at both ends with hair-like appendages. Phylogenetically, the new species Dictyochaetajiangxiensis clustered together with Dictyochaetabrevis MFLU 19-0216 in a well-supported clade, but formed a separate branch. In order to better define the taxonomic status of the new species, a phylogenetic tree of most closely-related taxa in Chaetosphaeriaceae was established, based on multi-locus sequences (ITS and LSU). The novel species is described and illustrated. Newly-generated molecular data of Dictyochaetajiangxiensis is also provided.

Whether interstitial space features were the main factors affecting sediment microbial community structures in Chaohu Lake

Sediments cover a majority of Earth's surface and are essential for global biogeochemical cycles. The effects of sediment physiochemical features on microbial community structures have attracted attention in recent years. However, the question of whether the interstitial space has significant effects on microbial community structures in submerged sediments remains unclear. In this study, based on identified OTUs (operational taxonomic units), correlation analysis, RDA analysis, and Permanova analysis were applied into investigating the effects of interstitial space volume, interstitial gas space, volumetric water content, sediment particle features (average size and evenness), and sediment depth on microbial community structures in different sedimentation areas of Chaohu Lake (Anhui Province, China). Our results indicated that sediment depth was the closest one to the main environmental gradient. The destruction effects of gas space on sediment structures can physically affect the similarity of the whole microbial community in all layers in river dominated sedimentation area (where methane emits actively). However, including gas space, none of the five interstitial space parameters were significant with accounting for the microbial community structures in a sediment layer. Thus, except for the happening of active physical destruction on sediment structures (for example, methane ebullition), sediment interstitial space parameters were ineffective for affecting microbial community structures in all sedimentation areas.

Improvement of aquaculture water quality by mixed Bacillus and its effects on microbial community structure

Microbial remediation, especially the application of probiotics, has recently gained popularity in improving water quality and maintaining aquatic animal health. The efficacy and mechanism of mixed Bacillus for improvement of water quality and its effects on aquatic microbial community structure remain unknown. To elucidate these issues, we applied two groups of mixed Bacillus (Bacillus megaterium and Bacillus subtilis (A0 + BS) and Bacillus megaterium and Bacillus coagulans (A0 + BC)) to the aquaculture system of Crucian carp. Our results showed that the improvement effect of mixed Bacillus A0 + BS on water quality was better than that of A0 + BC, and the NH₄⁺-N, NO₂^--N, NO₃^--N, and total phosphorus (TP) concentrations were reduced by 46.3%, 76.3%, 35.6%, and 80.3%, respectively. In addition, both groups of mixed Bacillus increased the diversity of the bacterial community and decreased the diversity of the fungal community. Microbial community analysis showed that mixed Bacillus A0 + BS increased the relative abundance of bacteria related with nitrogen and phosphorus removal, such as Proteobacteria, Actinobacteria, Comamonas, and Stenotrophomonas, but decreased the relative abundance of pathogenic bacteria (Acinetobacter and Pseudomonas) and fungi (Epicoccum and Fusarium). Redundancy analysis showed that NH₄⁺-N, NO₂^--N, and TP were the primary environmental factors affecting the microbial community in aquaculture water. PICRUST analysis indicated that all functional pathways in the A0 + BS group were richer than those in other groups. These results indicated that mixed Bacillus A0 + BS addition produced good results in reducing nitrogenous and phosphorus compounds and shaped a favorable microbial community structure to further improve water quality.

Sustainability of the rice-crayfish co-culture aquaculture model: microbiome profiles based on multi-kingdom analyses

While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e., bacteria, archaea, viruses, and eukaryotes) were performed using environmental (i.e., water and sediment) and animal gut (i.e., crayfish and crab gut) microbial samples from the RCFP and other aquaculture models, including the crab-crayfish co-culture, crayfish culture, and crab culture models, to evaluate the sustainability of the RCFP systematically. Results showed that RCFP samples are enriched with a distinct set of microbes, including Shewanella, Ferroplasma, Leishmania, and Siphoviridae, when compared with other aquaculture models. Additionally, most microbes in the RCFP samples, especially microbes from different kingdoms, were densely and positively connected, which indicates their robustness against environmental stress. Whereas microbes in different aquaculture models demonstrated moderate levels of horizontal gene transfer (HGT) across kingdoms, the RCFP showed relatively lower frequencies of HGT events, especially those involving antibiotic resistance genes. Finally, environmental factors, including pH, oxidation-reduction potential, temperature, and total nitrogen, contributed profoundly to shaping the microbial communities in these aquaculture models. Interestingly, compared with other models, the microbial communities of the RCFP model were less influenced by these environmental factors, which suggests that microbes in the latter have stronger ability to resist environmental stress. The findings collectively reflect the unique multi-kingdom microbial patterns of the RCFP model and suggest that this model is a sustainable model from the perspective of microbiome profiles.

Gut Microbial Alterations in Diarrheal Baer's Pochards (Aythya baeri)

The structure and composition of gut microbiota correlate with the occurrence and development of host health and disease. Diarrhea can cause alterations in gut microbiota in animals, and the changes in the gut microbial structure and composition may affect the development of diarrhea. However, there is a scarcity of information on the effects of diarrhea on gut fungal composition and structure, particularly in Baer's pochard (Aythya baeri). The current study was performed for high-throughput sequencing of the fungal-specific internal transcribed spacer 1 (ITS-1) to detect the differences of gut mycobiota in healthy and diarrheal Baer's pochard. Results showed that the gut mycobiota not only decreased significantly in diversity but also in structure and composition. Statistical analysis between two groups revealed a significant decrease in the abundance of phylum Rozellomycota, Zoopagomycota, Mortierellomycota, and Kickxellomycota in diarrheal Baer's pochard. At the genus levels, fungal relative abundance changed significantly in 95 genera, with 56 fungal genera, such as Wickerhamomyces, Alternaria, Penicillium, Cystofilobasidium, and Filobasidium, increasing significantly in the gut of the diarrheal Baer's pochard. In conclusion, the current study revealed the discrepancy in the gut fungal diversity and community composition between the healthy and diarrheal Baer's pochard, laying the basis for elucidating the relationship between diarrhea and the gut mycobiota in Baer's pochard.