Community richness of amphibian skin bacteria correlates with bioclimate at the global scale

Abstract

Animal-associated microbiomes are integral to host health, yet key biotic and abiotic factors that shape host-associated microbial communities at the global scale remain poorly understood. We investigated global patterns in amphibian skin bacterial communities, incorporating samples from 2,349 individuals representing 205 amphibian species across a broad biogeographic range. We analyzed how biotic and abiotic factors correlate with skin microbial communities using multiple statistical approaches. Global amphibian skin bacterial richness was consistently correlated with temperature-associated factors. We found more diverse skin microbiomes in environments with colder winters and less stable thermal conditions, compared to environments with warm winters and less annual temperature variation. We used bioinformatically predicted bacterial growth rates, dormancy genes, and antibiotic synthesis genes, as well as inferred bacterial thermal growth optima to propose mechanistic hypotheses that may explain the observed patterns. We conclude that temporal and spatial characteristics of the host's macro-environment mediate microbial diversity.

Host-associated microbiomes are predicted by immune system complexity and climate

“…Similarly, a recent study of amphibian skin microbiomes found higher diversity on hosts in environments with colder winters and less stable thermal conditions (i.e., temperate regions [5];). Thus, increasing climatic variability appears to promote coexistence and diversity of external microbiomes, perhaps through ecological succession or dormancy mechanisms [5].…”

“…Similarly, a recent study of amphibian skin microbiomes found higher diversity on hosts in environments with colder winters and less stable thermal conditions (i.e., temperate regions [5];). Thus, increasing climatic variability appears to promote coexistence and diversity of external microbiomes, perhaps through ecological succession or dormancy mechanisms [5]. Nottingham et al [69] found that both plant diversity and soil microbiome diversity follow temperature (and elevation) gradients at a regional scale with more species under warmer conditions.…”

“…4, Additional file 1: Figure S3), and performed analyses of alpha and beta diversity metrics. Results of all analyses can be reproduced with the data included in Additional files 2, 3,4,5,6,7,8,9,10,11, and 12 (see the "Methods" section and Additional file 1 for a description of the data files provided), or re-analyzed in the future as bioinformatics techniques continue to improve.…”

“…skin surface microbiomes across 205 amphibian species found strong correlations with bioclimatic factors [5], while digestive microbiomes of mammals were influenced by diet and gut morphology, and indeed distinct from environmental microbiomes [6]. A substantial role of biotic interactions in shaping microbial communities was also obvious from a strong bacterial-fungal antagonism revealed by global patterns in topsoil and ocean microbiomes [7], a pattern also revealed on hosts [8][9][10][11].…”

Habitat suitability and distribution potential of Liberibacter species (“Candidatus Liberibacter asiaticus” and “Candidatus Liberibacter africanus”) associated with citrus greening disease

“…The hydrological regime, nutrient content, temperature conditions and biological interactions depend on the climate (Sabater et al, 2008). Bioclimatic conditions have also been shown to influence the abundance of the bacterial microbiome in amphibian microbiome (Kueneman et al, 2019). Thus, our approach seeks to provide an alternative method for surveillance purposes in addition to vector surveillance since non‐vector transmission (human‐mediated) is also a factor in the spread of the pathogen.…”