Impacts of leachates from livestock carcass burial and manure heap sites on groundwater geochemistry and microbial community structure

<div><p>We investigated the impacts of leachates from a swine carcass burial site and a cow manure heap on the geochemical and microbiological properties of agricultural water samples, including leachate, groundwater from monitoring wells and background wells, and stream water. The leachate from the livestock burial site showed extremely high electrical conductivity, turbidity, and major ion concentrations, but low redox potential and dissolved oxygen levels. The groundwater in the monitoring wells adjacent to both sites showed severe contamination from the leachate, as indicated by the increases in EC, turbidity, Cl^-, and SO₄^2-. Bacteria from the phylum Firmicutes and Bacteriodetes and Archaea from the phylum Euryarchaeota were the major phyla in both the leachates and manure heap. However, the class- or genus-level components of these phyla differed markedly between the leachate and manure heap samples. The relative abundance of Firmicutes decreased from 35% to 0.3~13.9% in the monitoring wells and background wells at both sites. The Firmicutes in these wells was unlikely to have originated from the transportation of leachate to the surrounding environment because Firmicutes genera differed drastically between the leachate and monitoring wells. Meanwhile, sulfate-reducing bacteria (SRB) from the livestock carcass burial site were detected in the monitoring wells close to the leachate. This was likely because the release of carcass decomposition products, such as organic acids, to adjacent areas improved the suitability of the local environments for SRB, which were not abundant in the leachate. This study highlights the need to better understand microbial community dynamics along groundwater flow paths to evaluate bacterial transport in subsurface environments and provides new insights into the effective management of groundwater quality at both farm and regional scales.</p></div

Bacterial community composition at the phylum level (A) and genus level (B) of the samples collected from the livestock carcass burial site.

<p>Bacterial community composition at the phylum level (A) and genus level (B) of the samples collected from the livestock carcass burial site.</p

Study areas: livestock carcass burial site (A) and livestock manure heap site (B).

<p>The locations of the livestock burial sites, multi-level monitoring wells (IA and IB), and domestic groundwater wells (ID) are marked on the detailed map of the survey area. The locations of cow sheds, multi-level monitoring wells (YB and YC), the manure sampling point (YH), and the surface water stream runoff sampling point (YG) are marked on a detailed map of the survey area. The groundwater flow direction is represented by a blue arrow.</p

Archaeal community composition at the genus level of samples collected from the livestock carcass burial and livestock manure heap sites.

<p>The community composition data are not presented for samples with <20 sequences (i.e., ID, YB1, YC2, and YC3).</p

Bacterial community composition at the phylum level (A) and genus level (B) of the samples collected from the livestock manure heap site.

<p>Bacterial community composition at the phylum level (A) and genus level (B) of the samples collected from the livestock manure heap site.</p

Summary of the physical, chemical, and biological properties of the samples.

<p>Summary of the physical, chemical, and biological properties of the samples.</p

Non-metric multidimensional scaling (NMDS) plots of environmental variables and microbial community compositions at the phylum level in water samples collected from the livestock burial site (A) and both the livestock burial and manure heap sites (B).

<p>NMDS analysis within the vegan package of R software package based on dissimilarities calculated using the Bray–Curtis index of bacterial community composition for the relative abundance of each OTU in relation to the environmental variables. The direction and length of the vectors of water quality factors from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182579#pone.0182579.t001" target="_blank">Table 1</a> are computed by Bray–Curtis distances the "envfit()" function in the vegan package.</p

Principal coordinate analysis (PCoA) and UniFrac analysis of the bacterial communities associated with the leachate, groundwater, and feces samples.

<p>PCoA plots of the samples showing clustering by dissolved oxygen (A) and by distance from the carcass leachate (B). Unweighted pair group method with arithmetic mean (UPGMA) distance tree (C) of the MiSeq bacterial community structure. The percentages in parentheses for the PCoA indicate the proportion of variation explained by each ordination axis. The numbers on the nodes indicate the bootstrapping values for each node.</p