Chicken Manure and Mushroom Residues Affect Soil Bacterial Community Structure but Not the Bacterial Resistome When Applied at the Same Rate of Nitrogen for 3 Years.

Frontiers in Microbiology
Shuang PengXiangui Lin

Abstract

Animal manure is a reservoir of antibiotic resistance genes (ARGs), and direct application of the manure will lead to spread of ARGs in farmland. Here, we explored the impacts of chicken manure and heat-treated chicken manure on the patterns of soil resistome after 3 years' application, with mushroom residues set as the plant-derived organic manure treatment. A total of 262 ARG subtypes were detected in chicken manure using high-throughput qPCR, and heat treatment can effectively remove 50 types of ARGs. Although ARG subtypes and abundance were both higher in chicken manure, there was no significant difference in the ARG profiles and total ARG abundance among three manure-treated soils. Soil bacteria community compositions were significantly different among manure-treated soils, but they were not significantly correlated with soil ARG profiles. Fast expectation-maximization microbial source tracking (FEAST) was used for quantifying the contributions of the potential sources to microbial taxa and ARGs in manure-fertilized soil. Results revealed that only 0.2% of the chicken manure-derived bacterial communities survived in soil, and intrinsic ARGs were the largest contributor of soil ARGs (95.8-99.7%); ARGs from chicken manure on...Continue Reading

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Software Mentioned

PERMANONA
vegan
Procrustes
FEAST
R package edgeR
Cutadapt
ggplot2
ANOSIM
SourceTracker
R

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