Response of forest soil euglyphid testate amoebae (Rhizaria: Cercozoa) to pig cadavers assessed by high-throughput sequencing

Abstract

Decomposing cadavers modify the soil environment, but the effect on soil organisms and especially on soil protists is still poorly documented. We conducted a 35-month experiment in a deciduous forest where soil samples were taken under pig cadavers, control plots and fake pigs (bags of similar volume as the pigs). We extracted total soil DNA, amplified the SSU ribosomal RNA (rRNA) gene V9 region and sequenced it by Illumina technology and analysed the data for euglyphid testate amoebae (Rhizaria: Euglyphida), a common group of protozoa known to respond to micro-environmental changes. We found 51 euglyphid operational taxonomic units (OTUs), 45 of which did not match any known sequence. Most OTUs decreased in abundance underneath cadavers between days 0 and 309, but some responded positively after a time lag. We sequenced the full-length SSU rRNA gene of two common OTUs that responded positively to cadavers; a phylogenetic analysis showed that they did not belong to any known euglyphid family. This study confirmed the existence of an unknown diversity of euglyphids and that they react to cadavers. Results suggest that metabarcoding of soil euglyphids could be used as a forensic tool to estimate the post-mortem interval (PMI) particularly for long-term (>2 months) PMI, for which no reliable tool exists.

Mycamoeba gemmipara nov. gen., nov. sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and its Unusual Life Cycle

“…DNA extraction, PCR of environmental DNA and sequencing of the V9 region of the 18S rRNA gene were performed as in (Seppey et al. ). The obtained reads were pretreated as in (de Vargas et al.…”

Taxonomic and functional traits responses of Sphagnum peatland testate amoebae to experimentally manipulated water table

“…In support for this view, in dry plots ventral aperture emerged as a significant trait at T6. Furthermore, community structure shifted towards the dominance of silica and agglutinate test composition, a common trait in mineral soils (Seppey et al, 2016;Szelecz et al, 2014;Tsyganov et al, 2012). On the contrary, in wet plots, where a compressed test does not represent a specific advantage, the proportion of species with a compressed test declined.…”

Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic

“…These ornamented and intricate structures provide valuable taxonomic information. Additionally, durable shells facilitate manipulation and identification for scientific areas that depend on counting individuals and species such as microbial community ecology, paleoenvironmental reconstruction, and even forensic science [6][7][8]. The presence of a hard part also increases possibilities of fossilization: examples of fossil shells range from Foraminifera, widely used as index fossils in the Phanerozoic, to the lesser known but older vase-shaped microfossils (VSMs) found as far back as the Tonian period in the Neoproterozoic (1,000-720 million years ago) [9].…”