Abstract
Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.
Highlights
Antimicrobial resistance (AMR) has been considered as one of the major challenges to global public health
Depending on the animal source, genes conferring tetracycline and aminoglycoside resistance have been shown to be highly prevalent in animal fecal matter, or manure (Fang et al, 2018; Han et al, 2018; Munk et al, 2018; Xie et al, 2018a), and Firmicutes, Bacteroidetes, and Proteobacteria are the predominant phyla in dairy manure (Lopatto et al, 2019; Wichmann et al, 2014)
Manure application resulted in the input of manure-derived bacteria that did not affect the overall community composition
Summary
Antimicrobial resistance (AMR) has been considered as one of the major challenges to global public health. The gene groups encoding antimicrobial resistance – defined as resistome – in manure and soils are clearly different (Noyes et al, 2016). Depending on the animal source, genes conferring tetracycline and aminoglycoside resistance have been shown to be highly prevalent in animal fecal matter, or manure (Fang et al, 2018; Han et al, 2018; Munk et al, 2018; Xie et al, 2018a), and Firmicutes, Bacteroidetes, and Proteobacteria are the predominant phyla in dairy manure (Lopatto et al, 2019; Wichmann et al, 2014). The bacteriome can be dominated by Acidobacteria, Actinobacteria, and Proteobacteria (Kaiser et al, 2016; Lopatto et al, 2019), but through manure fertilization, the community structure may change due to the input of nutrients (Pan et al, 2014), antimicrobial compound residues (Jechalke et al, 2014a), or manure-derived taxa
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