Environmental factors and host sex influence the skin microbiota structure of Hong Kong newt (Paramesotriton hongkongensis) in a coldspot of chytridiomycosis in subtropical East Asia

Abstract

Chytridiomycosis, an infectious skin disease caused by the chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans, poses a significant threat to amphibian biodiversity worldwide. Antifungal bacteria found on the skin of chytrid-resistant amphibians could potentially provide defense against chytridiomycosis and lower mortality rates among resistant individuals. The Hong Kong newt (Paramesotriton hongkongensis) is native to East Asia, a region suspected to be the origin of chytrids, and has exhibited asymptomatic infection, suggesting a long-term coexistence with the chytrids. Therefore, the skin microbiota of this resistant species warrant investigation, along with other factors that can affect the microbiota. Among the 149 newts sampled in their natural habitats in Hong Kong, China, putative antifungal bacteria were found in all individuals. There were 314 amplicon sequence variants distributed over 25 genera of putative antifungal bacteria; abundant ones included Acinetobacter, Flavobacterium, and Novosphingobium spp. The skin microbiota compositions were strongly influenced by the inter-site geographical distances. Despite inter-site differences, we identified some core skin microbes across sites that could be vital to P. hongkongensis. The dominant cores included the family Comamonadaceae, family Chitinophagaceae, and class Betaproteobacteria. Moreover, habitat elevation and host sex also exhibited significant effects on skin microbiota compositions. The antifungal bacteria found on these newts offer an important resource for conservation against chytridiomycosis, such as developing probiotic treatments for susceptible species.

Keywords: 16S amplicon sequencing; Batrachochytrium dendrobatidis; Batrachochytrium salamandrivorans; antifungal bacteria; host–pathogen–microbiota coevolution.

Figure 1

(a) Paramesotriton hongkongensis under water. Photo credit: Hon Shing Fung. (b) Map of Hong Kong showing New Territories, Lantau Island, and Hong Kong Island, with sampling sites indicated by colored spots. Elevation is represented by shades of gray. Stream system is shown by blue lines. Abbreviations of sampling sites: FSH, Fa Sam Hang; HC, Ho Chung; HT, Hok Tau; KP, Kowloon Peak; MLHH, Ma Lai Hau Hang; MTL, Mui Tsz Lam; PNS, Pak Ngau Shek; PFL, Pok Fu Lam; SLT, Sha Lo Tung; SP, Sunset Peak; TMS, Tai Mo Shan; TPK, Tai Po Kau; TT, Tai Tam; WLH, Wong Lung Hang; WKT, Wu Kau Tang.

Figure 2

Skin microbiota compositions of Paramesotriton hongkongensis by sampling sites. Relative read abundances of bacterial taxa of each skin swab sample are shown. All taxa are shown at the phylum level except that the three most abundant phyla, Proteobacteria, Bacteroidetes, and Verrucomicrobia, are reported at the class level. Color‐coded taxon in columns from left to right are presented in a top‐down manner in each bar. The most abundant taxon, the family Comamonadaceae (phylum: Proteobacteria; class: Betaproteobacteria), is specifically indicated. Bsal and Bd positive samples are marked by a red dot and a blue dot, respectively, above the corresponding bar. Refer to Fig. 1 for the abbreviations of sampling sites.

Figure 3

Alpha and gamma diversity of Paramesotriton hongkongensis skin microbiota from 15 sampling sites. (a) Alpha diversity—the mean effective number of amplicon sequence variants (ASVs) in an individual sample for each site and (b) gamma diversity—the total effective number of ASVs found in each site, when q ranges from 0 to 2 are shown.

Figure 4

Hierarchical clustering of Paramesotriton hongkongensis skin microbiota by sampling sites based on the Bray–Curtis dissimilarity. Clusters with at least five samples from the same site are highlighted by the site name. Refer to Fig. 1 for the abbreviations of sampling sites.

Figure 5

Effects of environmental and host factors on Paramesotriton hongkongensis skin microbiota. The (a) Bray–Curtis dissimilarity (P < 0.001, R ² = 0.21) and (b) Jaccard distance (P < 0.0001, R ² = 0.23) between the microbiota from different sites increased with the geographical distance between sites. (c) Microbiota composition (represented by principal coordinate axis 1 [PCo1] based on Bray–Curtis dissimilarity) varied with site elevation (P = 0.02). (d) The difference in microbiota composition between sexes (P < 0.01), shown as the differential residual distributions in the fitted model where sex was not included.