Population Differences and Host Species Predict Variation in the Diversity of Host-Associated Microbes in Hydra

Abstract

Most animals co-exist with diverse host-associated microbial organisms that often form complex communities varying between individuals, habitats, species and higher taxonomic levels. Factors driving variation in the diversity of host-associated microbes are complex and still poorly understood. Here, we describe the bacterial composition of field-collected Hydra, a freshwater cnidarian that forms stable associations with microbial species in the laboratory and displays complex interactions with components of the microbiota. We sampled Hydra polyps from 21 Central European water bodies and identified bacterial taxa through 16S rRNA sequencing. We asked whether diversity and taxonomic composition of host-associated bacteria depends on sampling location, habitat type, host species or host reproductive mode (sexual vs. asexual). Bacterial diversity was most strongly explained by sampling location, suggesting that the source environment plays an important role in the assembly of bacterial communities associated with Hydra polyps. We also found significant differences between host species in their bacterial composition that partly mirrored variations observed in lab strains. Furthermore, we detected a minor effect of host reproductive mode on bacterial diversity. Overall, our results suggest that extrinsic (habitat identity) factors predict the diversity of host-associated bacterial communities more strongly than intrinsic (species identity) factors, however, only a combination of both factors determines microbiota composition in Hydra.

Spontaneously occurring tumors in different wild-derived strains of hydra

“…Since the French and Hungarian laboratories have exchanged hydra strains in the past, we cannot exclude the hypothesis of a previous contamination with these Chlamydia strains before this study. Interestingly, there is no evidence of this bacterium in the natural microbiome of hydras sampled directly in the wild 28 , which can indicate either that these bacteria are rare or variably detectable. In addition, it is also possible that these bacteria became more abundant after few generations in the lab 21 .…”

The archaeome in metaorganism research, with a focus on marine models and their bacteria–archaea interactions

“…The H. vulgaris bacterial community consists of the genera Rhodoferax and Legionella with less than 20% of other genera. Curvibacter which are often present at relative abundances >70% in H. vulgaris ( Franzenburg et al, 2013 ; Taubenheim et al, 2022 ) were not observed here. This may potentially be linked to the primer sets used in the studies.…”

Resource availability modulates the effect of body size on reproductive development

“…and microbiota composition has strong effects on Hydra physiology (reviewed in: Taubenheim et al, 2022). This is all the more likely because we here detected a substantial drop in the survival rate of strain C2/7 relative to our previous study (Ngo et al, 2021).…”

“…Genetic differences among our strains are likely to be low (Miklós et al, 2021), and the laboratory conditions under which they were maintained were identical. However, they might differ in the composition of their associated microbiota (something that we currently do not know), and microbiota composition has strong effects on Hydra physiology (reviewed in: Taubenheim et al, 2022). This is all the more likely because we here detected a substantial drop in the survival rate of strain C2/7 relative to our previous study (Ngo et al, 2021).…”