Multilevel community assembly of the tadpole gut microbiome

Abstract

<jats:title>Abstract</jats:title><jats:p>The assembly of local communities is likely to reflect the effects of local environmental factors associated with filters that act at larger spatial scales. Dissecting these multiscale effects remains a timely challenge that is particularly important for host-associated microbiomes. We investigated the relative roles of local selection (due to host species identity) and regional effects (due to water body identity) on the community structure of bacteria in the gut of tadpoles from three biogeographic areas and used graph theory and metanetwork approaches to explore and illustrate the distribution of bacteria across different ponds. The pond of origin, which represents a regional species pool of bacteria, was in general more important in shaping the gut microbiome of tadpoles than host species identity. The resulting metanetworks are modular and indicate relatively few species of bacteria occurring in more than one pond. Thus, each pond represents a relatively distinct species pool of bacteria available for community assembly of the tadpole microbiomes. Our findings indicate that microbiome community assembly in amphibian larvae, as in many other communities, is a multiscale process with important regional effects that constrain how local (i.e. host-dependent) filters act to influence microbiome community composition.</jats:p>

Skin and gut microbiomes of tadpoles vary differently with host and water environment: a short-term experiment using 16S metabarcoding

“…Contrary to the skin, gut communities of the two species exhibited similar diversity levels but shared few OTUs evidencing again the host effect even if under the same diet. Previous studies have also found significant host-effects on gut bacteria and proposed different gut physiologies and diet as most likely explanations 9,10,14 . The strong host-specificity of microbiomes makes it a challenge to generalize conclusions about the effects of habitat alterations like the one studied here, but on the other hand increase the need for experimentation in a wide range of species.…”

“…Both skin and gut bacteria communities are affected by biotic and abiotic environmental factors as well as host characteristics 2 . For example, amphibian skin-associated bacteria have been observed to vary according to host identity (e.g., species, ecology, behavior), habitat (e.g., water parameters, soil use, human presence), and climate conditions (e.g., temperature, humidity) [5][6][7] ; gut microbes are often highly associated with dietary preferences, gut mucosal structure, and water source 5,[8][9][10] .…”

Experimental depletion of gut microbiota diversity reduces host thermal tolerance and fitness under heat stress in a vertebrate ectotherm

“…The affected phyla included those such as Dependentiae, Plantomycetes, WPS-2, and Verrucomicrobia, which are common to aquatic and soil habitats 48–51 , and were also highly abundant in tadpole guts colonized with natural pond water, but were absent or present at very low abundances in depleted tadpoles (Supplementary Table 2). Because green frog tadpoles develop externally to the mother and lack parental care, it is likely a high proportion of their symbiotic microbes come from transmission of environmental microbes 52 , and therefore, depleting these communities results in a depleted gut microbiome.…”

Stabilization and optimization of host-microbe-environment interactions as a potential reason for the behavior of natal philopatry

“…For example, some animal species predominantly acquire host-associated microbial communities from the environment each new generation, such as stinkbugs [82] and bioluminescent squid [83]. Studies in tadpoles [84] and several fish species [85,86] demonstrate that the gut microbiota largely reflects those microbes present in their surrounding environments. In nest-building species, such as birds, the characteristics and environmental microbiome of nesting material can influence the composition of their offspring's microbiome [87,88].…”