Bacterial Community Dynamics Distinguish Poultry Compost from Dairy Compost and Non-Amended Soils Planted with Spinach

Deborah A Neher,Patricia D Millner,Thomas R Weicht,Marie A Limoges,Manan Sharma,Catherine Donnelly

doi:10.3390/microorganisms8101601

Deborah A Neher, Patricia D Millner + Show 4 more

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https://doi.org/10.3390/microorganisms8101601

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Abstract

The aim of this study was to determine whether and how poultry litter compost and dairy manure compost alter the microbial communities within field soils planted with spinach. In three successive years, separate experimental plots on two fields received randomly assigned compost treatments varying in animal origin: dairy manure (DMC), poultry litter (PLC), or neither (NoC). The composition and function of bacterial and fungal communities were characterized by the amplicon sequencing of marker genes and by the ecoenzyme activity, respectively. The temporal autocorrelation within and among years was adjusted by principal response curves (PRC) to analyze the effect of compost on community composition among treatments. Bacteria in the phylum Bacteriodetes, classes Flavobacteriia and Spingobacteriales (Fluviicola, Flavobacteriia, and Pedobacter), were two to four times more abundant in soils amended with PLC than DMC or NoC consistently among fields and years. Fungi in the phylum Ascomycota were relatively abundant, but their composition was field-specific and without treatment differences. The ecoenzyme data verify that the effects of PLC and DMC on soil communities are based on their microbial composition and not a response to the C source or nutrient content of the compost.

Highlights

In 2015, the use of manure-derived fertilizer occurred in 11.7% of U.S fruit and vegetable farms, a significant 2.6% increase from six years prior
Poultry Litter Compost (PLC) changed the bacterial communities in field soil more than dairy manure compost (DMC) (Figure 1)
The genera representing the γ-Proteobacteria varied by field, the PLC amendments accounted for a greater abundance compared to the DMC- or NoC-amended soils over time (Figure 1)

Summary

Introduction

In 2015, the use of manure-derived fertilizer occurred in 11.7% of U.S fruit and vegetable farms, a significant 2.6% increase from six years prior. Much of this increase is attributable to the growing popularity of composted manure, which increased in use by 6.2% in the same period [1]. The bacteria and fungi in the consortia have evolved defenses (against other microbes) that can be harnessed to target and suppress plant pathogens. Likewise, these saprophytic microbes in compost may suppress foodborne pathogens through nutrient competition, antibiosis, inhibition, and predation [8]. Composts can serve as a means to introduce heterotrophic microbes that could alter indigenous soil microbiomes through antibiotic production, siderophores to sequester nutrients, or the production of enzymes that degrade cell walls [6]

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