Grupo de Ecoloxía Animal (GEA), Universidad de Vigo, Ourense E-36310, España.
Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, United States.
FEMS Microbiol Ecol. 2022 Aug 23;98(9). doi: 10.1093/femsec/fiac093.
Host evolutionary history is a key factor shaping the earthworm cast microbiome, although its effect can be shadowed by the earthworm's diet. To untangle dietary from taxon effects, we raised nine earthworm species on a uniform diet of cow manure and compared cast microbiome across species while controlling for diet. Our results showed that, under controlled laboratory conditions, earthworm microbiomes are species-specific, more diverse than that of the controlled diet, and mainly comprised of native bacteria (i.e. not acquired from the diet). Furthermore, diet has a medium to large convergence effect on microbiome composition since earthworms shared 16%-74% of their bacterial amplicon sequence variants (ASV). The interspecies core microbiome included 10 ASVs, while their intraspecies core microbiomes were larger and varied in ASV richness (24%-48%) and sequence abundance across earthworm species. This specificity in core microbiomes and variable degree of similarity in bacterial composition suggest that phylosymbiosis could determine earthworm microbiome assembly. However, lack of congruence between the earthworm phylogeny and the microbiome dendrogram suggests that a consistent diet fed over several generations may have weakened potential phylosymbiotic effects. Thus, cast microbiome assembly in earthworms seem to be the result of an interplay among host phylogeny and diet.
宿主进化史是塑造蚯蚓粪微生物组的关键因素，尽管其影响可能会被蚯蚓的饮食所掩盖。为了理清饮食和分类群的影响，我们用牛粪饲养了 9 种蚯蚓，并在控制饮食的情况下比较了不同物种的蚯蚓粪微生物组。研究结果表明，在受控的实验室条件下，蚯蚓微生物组具有物种特异性，比受控饮食更为多样化，主要由本地细菌组成（即不是从饮食中获得的）。此外，由于蚯蚓共享 16%-74%的细菌扩增子序列变异（ASV），因此饮食对微生物组组成具有中到大的收敛效应。种间核心微生物组包括 10 个 ASV，而其种内核心微生物组的 ASV 丰富度（24%-48%）和序列丰度在蚯蚓物种间差异较大。核心微生物组的这种特异性和细菌组成的可变相似程度表明，系统共生可能决定了蚯蚓微生物组的组装。然而，蚯蚓系统发育与微生物组系统发育树之间缺乏一致性表明，连续几代喂食一致的饮食可能削弱了潜在的系统共生效应。因此，蚯蚓粪便微生物组的组装似乎是宿主系统发育和饮食相互作用的结果。
