Vertebrate decomposition is accelerated by soil microbes

Abstract

Carrion decomposition is an ecologically important natural phenomenon influenced by a complex set of factors, including temperature, moisture, and the activity of microorganisms, invertebrates, and scavengers. The role of soil microbes as decomposers in this process is essential but not well understood and represents a knowledge gap in carrion ecology. To better define the role and sources of microbes in carrion decomposition, lab-reared mice were decomposed on either (i) soil with an intact microbial community or (ii) soil that was sterilized. We characterized the microbial community (16S rRNA gene for bacteria and archaea, and the 18S rRNA gene for fungi and microbial eukaryotes) for three body sites along with the underlying soil (i.e., gravesoils) at time intervals coinciding with visible changes in carrion morphology. Our results indicate that mice placed on soil with intact microbial communities reach advanced stages of decomposition 2 to 3 times faster than those placed on sterile soil. Microbial communities associated with skin and gravesoils of carrion in stages of active and advanced decay were significantly different between soil types (sterile versus untreated), suggesting that substrates on which carrion decompose may partially determine the microbial decomposer community. However, the source of the decomposer community (soil- versus carcass-associated microbes) was not clear in our data set, suggesting that greater sequencing depth needs to be employed to identify the origin of the decomposer communities in carrion decomposition. Overall, our data show that soil microbial communities have a significant impact on the rate at which carrion decomposes and have important implications for understanding carrion ecology.

FIG 1

Experimental setup. Each mouse carcass was placed on either sterile or untreated soil in a polypropylene container “grave” with air holes to prevent anaerobic conditions. Tupperware containers were grouped by treatment (sterilized soil versus untreated soil) in secondary filter-top polycarbonate cages.

FIG 2

Effects of sterilization treatment on soils. Shown is the relative abundance of microbial eukaryotic (18S) late-stage decomposition soils (A), bacterial (16S) taxa in day 0 soils (B), and bacterial taxa in late-stage decomposition soils (C). Each stacked bar shows the relative abundance of eukaryotes or bacteria in a single sample. Microbial eukaryotic DNA was not detected in day 0 soils after sterilization treatment. For 18S, taxa are shaded by phylum: Fungi, red/pink; Excavata, green; Nematoda, yellow; Alveolata, blue; Stramenopiles, purple. Other low-abundance taxa are represented as gray.

FIG 3

(A) Average pH values are shown for untreated (dark circles) and sterilization-treated (open circles) soil for each sampling event (in days since time zero) with standard error bars, for which n = 5. (B and C) Megysei visual keys and points for the skin of the head (orange circles) and the skin of the torso (blue triangles) on sterile (B) and untreated (C) soil. Fresh, 1 point; discoloration, 2 points; bloat-purging, 3 points; purging-bloat, 4 points; sagging flesh, 5 points; sinking flesh, 6 points; caving flesh, 7 points; mummification, 8 points. Purging of the torso (3 points) preceded that of the head (4 points). The general state of carcass decomposition is indicated by the horizontal lines to separate fresh, active, and advanced decay. These data suggest that rupture occurred sometime before 9 days in the untreated experimental group and before 20 days in the sterilization-treated soil experimental group.

FIG 4

(A) Relative abundance of microbial eukaryotic taxa is shown at the highest level of taxonomic resolution for each sample site and each treatment (sterile versus untreated soil substrate). Each stacked bar shows the relative abundance of eukaryotes or bacteria in a single sample. Taxa are shaded by phylum: Fungi, red/pink; Excavata, green; Nematoda, yellow; Alveolata, blue; Stramenopiles, purple. Other low-abundance taxa are represented as gray. (B) Relative abundance of host-associated, late-stage decomposition bacterial communities with taxa abundance shown at the phylum level. Each bar in the figure represent the relative abundance of a given taxa for a single sample.

FIG 5

(A) PCoA plot based on unweighted UniFrac distances of microbial eukaryotic communities sampled during late-stage decomposition showing sterile treated soil (pink) versus untreated soil (blue). (B) PCoA plot based on unweighted UniFrac distances of microbial bacterial communities sampled during late-stage decomposition showing sterile treated soil (pink) versus untreated soil (blue).

FIG 6

Bayesian source tracking analysis. Each rectangle is composed of 100 columns representing the mixture of sources estimated in one of 100 Gibbs sampling draws (23). (A) “Leave-one-out” source predictions for day 0 source communities. The distinctness of source communities was tested by leaving each source sample out and estimating its source community. Sources were highly distinct, with a small proportion of misassignments between fecal and cecum communities, which is not surprising given that fecal material passes through the cecum. (B) Bayesian source tracking results of late-stage decomposition bacterial communities using source communities shown in panel A. In cases in which proportions of the late-stage decomposition bacterial community were not accurately represented by a day 0 source, it was assigned to an “unknown community” (shown in gray).