Microbial succession from a subsequent secondary death event following mass mortality

Abstract

Background Each death event can be characterized by its associated microbes – a living community of bacteria composed of carcass, soil, and insect-introduced bacterial species – a necrobiome. With the possibility for close succession of these death events, it may be beneficial to characterize how the magnitude of an initial death event may impact the decomposition and necrobiomes of subsequent death events in close proximity. In this paper we hope to characterize the microbial communities associated with a proximate subsequent death event, and distinguish any changes within those communities based on the magnitude of an initial death event and the biomass of preexisting carcass (es) undergoing decomposition. For this experiment, 6 feral swine carcasses in containers were placed in the vicinity of preexisting and ongoing carcass decomposition at sites of three different scales of decomposing carcass biomass. Swab samples were collected from the skin and eye sockets of the container pigs and subjected to 16 s rRNA sequencing and OTU assignment. Results PERMANOVA analysis of the bacterial taxa showed that there was no significant difference in the bacterial communities based on initial mortality event biomass size, but we did see a change in the bacterial communities over time, and slight differences between the skin and ocular cavity communities. Even without soil input, necrobiome communities can change rapidly. Further characterization of the bacterial necrobiome included utilization of the Random Forest algorithm to identify the most important predictors for time of decomposition. Sample sets were also scanned for notable human and swine-associated pathogens. Conclusions The applications from this study are many, ranging from establishing the environmental impacts of mass mortality events to understanding the importance of scavenger, and scavenger microbial community input on decomposition.

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

“…The Kraken2 taxonomic profile of the microbial contigs identified by PyDamage identified as ancient (Fig. 7) is consistent with bacteria known to be members of the (Schnorr et al, 2016;Pasolli et al, 2019;Singh et al, 2017), as well as taxonomic groups known to be involved in initial decomposition, such as Clostridium (145 contigs) (Hyde et al, 2017;Harrison et al, 2020;Dash & Das, 2020). In addition, eukaryotic contigs were assigned to humans (18 contigs), and to the plant families Fabaceae (18 contigs) and Solanaceae (18 contigs), two families of economically important crops in the Americas that include beans, tomatoes, chile peppers, and tobacco.…”

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNAde novoassembly

“…The Kraken2 taxonomic profile of the microbial contigs identified by PyDamage identified as ancient (Figure 6) is consistent with bacteria known to be members of the human gut microbiome, including Prevotella (239 contigs), Treponema (166 contigs), Bacteroides (103 contigs), Lachnospiraceae (119 contigs) Blautia (36 contigs), Ruminococcus (25 contigs), Phocaeicola (18 contigs) and Romboutsia (16 contigs) (Schnorr et al, 2016;Pasolli et al, 2019;Singh et al, 2017), as well as taxonomic groups known to be involved in initial decomposition, such as Clostridium (145 contigs) (Hyde et al, 2017;Harrison et al, 2020;Dash and Das, 2020). In addition, eukaryotic contigs were assigned to humans (18 contigs), and to the plant families Fabaceae (18 contigs) and Solanaceae (18 contigs), two families of economically important crops in the Americas that include beans, tomatoes, chile peppers, and tobacco.…”

“…For other questions and where additional authentication criteria are available (such as taxonomic information or metagenomic bins), lower thresholds may be applied to reduce the number of false negatives due to insufficient coverage or contig length. (Hyde et al, 2017;Harrison et al, 2020;Dash and Das, 2020). DNA from bacteria that participated early in this process (shortly after death or defecation), will carry similar levels of damage as the endogenous DNA because they are of similar age.…”

“…These taxa are known to be important early decomposers in the necrobiome (Harrison et al, 2020), and the damage they carry suggests that they likely participated in the early degradation of the paleofeces before decomposition was arrested by the extreme aridity of the rockshelter.…”

“…Within the exogenous fraction, however, the DNA may span a range of ages. Nearly all ancient remains undergo some degree of degradation and decomposition, during which either endogenous (thanatomicrobiome) or exogenous (necrobiome) bacteria invade the remains and grow (Hyde et al, 2017; Harrison et al, 2020; Dash and Das, 2020). DNA from bacteria that participated early in this process (shortly after death or defecation), will carry similar levels of damage as the endogenous DNA because they are of similar age.…”