Abstract
Animals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms Eisenia andrei and E. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts, Microbacteriaceae, Verminephrobacter and Ca. Nephrothrix, which accounted for 88% and 66% of the sequences respectively. Verminephrobacter and Ca. Nephrothrix showed a high rate of sequence variation, suggesting that they could be biparentally acquired during mating. The other bacterial species inhabiting the cocoons came from the bedding, where they accounted for a small fraction of the diversity (27% and 7% of bacterial species for E. andrei and E. fetida bedding). Hence, earthworm cocoon microbiome includes a large fraction of the vertically-transmitted symbionts and a minor fraction, but more diverse, horizontally and non-randomly acquired from the environment. These data suggest that horizontally-transmitted bacteria to cocoons may play an important role in the adaptation of earthworms to new environments or diets.
Highlights
Animals and bacteria establish associations with different degrees of specificity, but most of their symbiotic relationships are established during the embryonic development of the animal hosts[1]
Bacterial communities in all samples were mainly comprised of amplicon sequence variants (ASVs) belonging to the phyla Proteobacteria, Bacteroidetes and Actinobacteria, which contributed to 93% of the sequences, which decreased to 89% when removing the contribution of the three vertical transmitted nephridial symbionts (Table 1)
Actinobacteria were more abundant in E. andrei than in E. fetida samples, there were only higher in bedding than cocoon samples in E. fetida (470%, Supplementary Figure 2)
Summary
Animals and bacteria establish associations with different degrees of specificity, but most of their symbiotic relationships are established during the embryonic development of the animal hosts[1]. Previous studies have showed that cocoons of the earthworm Eisenia fetida harbour bacterial populations initially comprising around 108–109 CFU ml−1 14,19. Eisenia fetida (Savigny, 1826) and Eisenia andrei Bouché, 1972 (Oligochaeta, Lumbricidae) are of great importance in vermicomposting, a potential source of protein for animal consumption, and as fishing bait[26] They are commonly used as animal models in ecotoxicology, physiology, biochemical, and genetic studies[26]. Eisenia andrei and E. fetida are a good model to study bacterial colonization of cocoons because they are sister taxa[27,28], inhabit organic rich substrates[29], and their activity generates species-specific microbial profiles in the environments where they live[30]. We assessed whether cocoon microbiotas consist of bacterial groups of vertically transmitted symbionts plus random environmental bacteria incorporated during cocoon formation or whether there is selective recruitment during cocoon colonization
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