Litter quality controls the earthworm microbiome in cropping fields

Agriculture is using litter inputs (such as straw) as an alternative to inorganic fertilization; however, little is known about how these inputs can alter the microbiome of our soils. Earthworms are major ecosystem engineers and play a critical role in decomposing litter in terrestrial ecosystems, assisted by their gut microbiomes. However, very little is known about how litter types and combinations, and their associated quality (labile vs recalcitrant), regulate the microbiome of earthworms. Here, we conducted a 42-day microcosm experiment to investigate the influence of two litter (straw) types, with contrasting recalcitrance, and its combination in driving the microbiome associated with different earthworm compartments, including soils, casts and guts. In each compartment, samples were collected every 14 days, and the microbiome was measured by16S rRNA amplicon sequencing. We found that the labile peanut straw initially decreased bacterial richness with this effect being diluted with time. Litter quality and earthworm compartment independently and significantly affect the resultant bacterial community composition (P ≤ 0.01). Litter inputs also resulted in unique microbiomes, which differ across compartments, including soils, casts and guts. Litter quality can result in contrasting soil and earthworms’ microbiomes in cropping fields, and these may act as indicators of management story with consequences for the conservation of soil microbiomes and fertility under litter fertilization.