Temporal dynamics of bacterial communities in soil and leachate water after swine manure application

Authors: RIEKE, ELIZABETH - Iowa State University; SOUPIR, MICHELLE - Iowa State University; Moorman, Thomas; YANG, FAN - Iowa State University; HOWE, ADINA - Iowa State University

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2018
Publication Date: 12/21/2018
Citation: Rieke, E.L., Soupir, M.L., Moorman, T.B., Yang, F., Howe, A. 2018. Temporal dynamics of bacterial communities in soil and leachate water after swine manure application. Frontiers in Microbiology. 9(3197). https://doi.org/10.3389/fmicb.2018.03197.
DOI: https://doi.org/10.3389/fmicb.2018.03197

Interpretive Summary: Application of swine manure to agricultural land allows recycling of plant nutrients, but excess nitrate, phosphorus, and fecal bacteria may degrade water quality especially where fields have artificial subsurface drainage. However, relatively 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. DNA 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. Tillage accounted for only a small fraction of the variability in bacterial communities. 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 Actinomyecetales 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. 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. Knowledge of which bacteria increase after manure application may allow better interpretation of plant responses to manure application. This research will be useful to scientists seeking to understand and manipulate the soil microbiome.

Technical Abstract: Application of swine manure to agricultural land allows recycling of plant nutrients, but excess nitrate, phosphorus, and fecal bacteria may degrade water quality especially where fields have artificial subsurface drainage. However, relatively 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. Tillage accounted for only a small fraction of the variability in bacterial communities. 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 Actinomyecetales 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 manure communities. 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.