Effects of Earthworms on the Microbiomes and Antibiotic Resistomes of Detritus Fauna and Phyllospheres

Abstract

Our understanding of the influences of animals on microbial communities and antibiotic resistance genes (ARGs) throughout the food web is limited, particularly in the soil ecosystem. We performed a microcosm experiment using the combination of 16S rRNA gene high-throughput sequencing and highthroughput qPCR to study the effects of earthworms on the microbiomes and resistomes of the phyllospheres and soil detritus fauna. A full factorial design was employed in this study, including two earthworm treatments (control and earthworm addition) and two soil treatments (control and manure amendment). Earthworms changed the bacterial composition of the soil detritus fauna and the phyllosphere by modifying the shared habitat. Earthworms also reduced the number and abundance of ARGs in the soil fauna and phyllosphere microbiomes by changing their microbial communities, suggesting that earthworms may be able to provide a sustainable and natural solution to address the ARG crisis in the soil ecosystem. This study provides a new understanding on the effects of soil animals on microbial communities, driving shifts in the resistome of other animals and the phyllosphere, by altering the shared soil habitat.

Trophic level drives the host microbiome of soil invertebrates at a continental scale

“…We observed that all unique microbial taxa belong to Verrucomicrobia were exclusively found in nematodes, all unique microbial taxa belong to Bacteroidetes were only determined in nematodes, oribatid mites, and predatory mites, most of unique microbial taxa belong to Actinobacteria and Tenericutes were exclusively observed in oribatid mites and predatory mites, and many unique microbial taxa belong to Proteobacteria were only detected in nematodes, potworms, oribatid mites, and predatory mites. Some of these abundant and unique bacterial taxa were also reported in previous studies [ 12 – 15 , 19 ]. A collection of unassigned taxa with no genome representatives were exclusively found in potworms, oribatid mites, and predatory mites, which were highlighted by red dots in Fig.…”

“…These animal extinctions might hide a deeper crisis, involving the potential loss of thousands of unique microbial species living within the microbiome of these soil fauna (Scenarios 1 and 2; Fig. S1 ), because recent studies have shown that diverse microbial communities inhabit soil fauna [ 12 – 15 ]. The impact of invertebrate extinctions would not be as severe for microorganisms if different soil invertebrates shared similar microbiomes (Scenario 3; Fig.…”

“…In addition, understanding the assembly of microbial communities is critical in microbial ecology [ 21 – 23 ]. Previous studies have showed that substantial microbial variation occurs among individuals in the soil fauna microbiome [ 12 , 14 , 15 ]. However, few studies consider how microbial communities are assembled in the wild soil fauna.…”

Core Microbiota Drive the Prevalence of Extracellular Antibiotic Resistome in the Water Compartments

“…DNA samples were first dispensed, then the mixtures of primers and fluorescence (in 384-well plates) using the Multisample Nanodispenser. The cycling conditions were set according to previous studies 22, 28, 29 and shown as follows: 10 min denaturation at 95°C, 40 cycles with 30 s amplification at 95°C and 30 s final extension at 60°C. The amplification efficiencies within 1.8 to 2.2 were considered as positive results.…”

“…The amplification efficiencies within 1.8 to 2.2 were considered as positive results. Threshold of 31 cycles (C t ) was set to be detection limit 29 . Three replicates were conducted for each sample.…”