Temporal Dynamics of Bacterial Communities in Soil and Leachate Water After Swine Manure Application.

Fan Yang,Elizabeth L Rieke,Thomas B Moorman,Michelle L Soupir,Adina C Howe

doi:10.3389/fmicb.2018.03197

Abstract

Application of swine manure to agricultural land allows recycling of plant nutrients, but excess nitrate, phosphorus and fecal bacteria impact surface and drainage water quality. While agronomic and water quality impacts are well studied, little is known about the impact of swine manure slurry on soil microbial communities. We applied swine manure to intact soil columns collected from plots maintained under chisel plow or no-till with corn and soybean rotation. Targeted 16S-rRNA gene sequencing was used to characterize and to identify shifts in bacterial communities in soil over 108 days after swine manure application. In addition, six simulated rainfalls were applied during this time. Drainage water from the columns and surface soil were sampled, and DNA was extracted and sequenced. Unique DNA sequences (OTU) associated with 12 orders of bacteria were responsible for the majority of OTUs stimulated by manure application. Proteobacteria were most prevalent, followed by Bacteroidetes, Firmicutes, Actinobacteria, and Spirochaetes. While the majority of the 12 orders decreased after day 59, relative abundances of genes associated with Rhizobiales and Actinomycetales in soil increased. Bacterial orders which were stimulated by manure application in soil had varied responses in drainage waters over the course of the experiment. We also identified a “manure-specific core” of five genera who comprised 13% of the manure community and were not significantly abundant in non-manured control soils. Of these five genera, Clostridium sensu stricto was the only genus which did not return to pre-manure relative abundance in soil by day 108. Our results show that enrichment responses after manure amendment could result from displacement of native soil bacteria by manure-borne bacteria during the application process or growth of native bacteria using manure-derived available nutrients.

Highlights

Rising demands for pork products in developing countries has led to increased production in the United States (Narrod et al, 2011)
In order to identify and track bacterial populations directly introduced into soil and drainage through manure application, we identified manure-derived operational taxonomic units (MDOs), which were considered a set of core bacteria specific to the swine manure and not abundant in soils
The enrichment of bacteria after manure amendments could be the direct result of manure amendment through the displacement of native soil bacteria by manure-borne bacteria or enrichment of native bacteria responding to manure available nutrients

Summary

Introduction

Rising demands for pork products in developing countries has led to increased production in the United States (Narrod et al, 2011). Because swine manure contains valuable nutrients, it is often applied to agricultural land as an alternative to inorganic fertilizer. Swine manure application has been observed to increase aggregate stability, bacterial diversity and soil microbial biomass and activity following application (Larkin et al, 2006; Hammesfahr et al, 2008, 2011; Zhang et al, 2012; Adesanya et al, 2016). The addition of organic nutrients through manure amendments introduces foreign microbial communities, which could be of concern to humans, e.g., fecal-borne pathogens, to surrounding soils (Ziemer et al, 2010; Gordoncillo et al, 2013; Haack et al, 2015; Givens et al, 2016). Manure-associated nutrients and microbial communities are transported to downstream waters (Sharpley and Withers, 1994; Hoang et al, 2013; Luby et al, 2016)

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