Seasonal Variations in the Gut Fungal Communities of Hooded Crane (Grus monacha) at Wintering and Stopover Sites in China

The “gut fungal microbiome” maintains the immune system, homeostasis, and various physiological functions of an organism. Different factors shape and affect gut fungal diversity and community composition, such as environment, habitat type, food resources, and seasons during migration. Wild birds amid migration are exposed to different habitats with different environments, available food resources, and seasons, which may substantially impact their gut fungal community composition and diversity. The hooded crane (Grus monacha) is a known migratory bird that migrates over long distances and is exposed to varied habitats with different environments and food types. We investigated the differences in gut fungal diversity and community composition between wintering and stopover sites amid three migratory seasons. We deduced the gut fungal pathogenic diversity and community composition during winter, fall, and spring by using high throughput sequencing (Illumina Mi-seq), and the internal transcribed region 2 (ITS2) was examined. Samples were collected from Shengjin Lake in the winter and Lindian during the fall and spring. The dominant fungal phyla found across the three seasons were Ascomycota, Basidiomycota, Zygomycota, and Rozellomycota. The gut fungal alpha diversity showed significant shifts during winter at the wintering site compared with the fall and spring seasons at the stopover site. The fungal community composition exhibited a significant change across the three seasons (ANOSIM p = 0.001). The results also demonstrated that the diversity and relative abundance of potential pathogens also showed divergence in winter compared to fall and spring. This study provides the basis for understanding the discrepancy in gut fungal diversity and community composition during migratory seasons at both wintering and stopover grounds. It also suggests that conservation measures should be applied to the conservation of hooded cranes and other wild birds, as the risk of cross-infection increases during seasonal migration.

Effects of Food Changes on Intestinal Bacterial Diversity of Wintering Hooded Cranes (Grus monacha)

As food is recognised as an important factor affecting the intestinal microbiota, seasonal changes in diet can influence the community composition. The hooded crane (Grus monacha) is an endangered migratory waterbird species, with some of the population wintering in the sallow lakes in the middle and lower Yangtze River floodplain. Their food resources have changed seasonally, with a reduction resulting from wetland degradation. To cope with seasonal changes in food availability, hooded cranes must constantly adjust their foraging strategies to survive. We studied the effect of changes in diet on the intestinal bacterial diversity of hooded cranes at Shengjin Lake, using faecal microanalysis and high-throughput sequencing. The results show that the main foods of hooded cranes were Polygonum criopolitanum, Oryza sativa, and Carex spp., which were significantly related to the composition of the intestinal bacterial community. In addition, foods available from the similar habitats were more similar, and the corresponding hooded crane intestinal bacteria were also more similar. The relative abundance of Lactobacillus acidipiscis in January and March was significantly higher than in November. Our research shows that the intestinal bacteria of hooded cranes actively adapt to diet changes to overcome the negative impact of the reduction in food resources, which is vital to the survival of hooded cranes.

Is Intestinal Bacterial Diversity Enhanced by Trans-Species Spread in the Mixed-Species Flock of Hooded Crane (Grus monacha) and Bean Goose (Anser fabalis) Wintering in the Lower and Middle Yangtze River Floodplain?

Diversity of gut microbes is influenced by many aspects, including the host internal factors and even direct or indirect contact with other birds, which is particularly important for mixed-species wintering waterbird flocks. In this study, Illumina high-throughput sequencing was used to analyze the intestinal bacteria of the hooded crane and bean goose whose niches overlap at Shengjin Lake. We tested whether contact time enhances the trans-species spread of gut bacteria. Results indicate alpha-diversity and microbial composition displayed significant separation between the two hosts in every wintering period, although the number of bacteria types shared increased with increasing contact time. For the same species, with the lengthening of contact time, alpha-diversity and the number of operational taxonomic units (OTUs) in the host intestine augmented, and the common OTUs and structural similarity of microflora in the middle and late periods were more than in the early and middle periods. In addition, we found a very high proportion of shared pathogens. Our results indicate that, although intestinal microflora of different species were separated, direct or indirect contact in the mixed-species flock caused the spread of gut bacteria trans-species, indicating that more attention should be paid to intestinal pathogens in wild birds.

Dramatic shifts in intestinal fungal community between wintering Hooded Crane and Domestic Goose

Background The intestinal microbiota play remarkable roles in maintaining the health of their hosts. Recent studies focused on gut bacterial diversity in birds and poultry, with little information about the ecological functions of their gut fungal community. Methods The high-throughput sequencing was applied to compare intestinal fungal community structure between Hooded Crane (Grus monacha) and Domestic Goose (Anser anser domesticus), and infer the potential pathogens of each species at Shengjin Lake of China. Results Intestinal fungal alpha diversity was higher in Hooded Crane than Greylag Goose (Anser anser). Gut fungal community composition showed dramatic shifts between the two species. Hooded Cranes mainly eat Vallisneria natans and Potamogeton malaianus, while artificial hurl food (i.e., paddy) was the main food resource for Domestic Geese, suggesting that the variations in fungal community might be induced by different diets between the two hosts. Two enriched genera (i.e., Acremonium and Rhodotorula) which could increase host’s digestion were detected in guts of Hooded Cranes. In addition, there were 42 pathogenic amplicon sequence variants (ASVs), 17% of which shared in Hooded Crane and Greylag Goose. The Hooded Crane had higher gut fungal pathogenic diversity and abundance relative to Greylag Goose. Conclusions The study demonstrated that divergence in intestinal fungal community structure might be induced by different diets between wintering Hooded Crane and Domestic Goose. Hooded Crane might rely more on their gut fungal taxa to acquire nutrients from indigestible food resources. Our study also implied that more research should focus on intestinal pathogens in wild birds and domestic poultry, as they might increase risk of disease in other animals, even human beings. The degree of cross infection in pathogens among wild birds and sympatric poultry should be clearly verified in future study.