Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis?

Abstract

Molecular genetic approaches applied to environmental DNA have great potential for biodiversity research and ecosystem monitoring. A metagenome contains genetic information from all organisms captured in an environmental sample. It has been primarily used to study bacteria and archaea, but promising reports focusing on metazoan diversity are emerging. However, methodological uncertainties remain, and studies are required to validate the power and the limitations of such an approach when applied to macro-eukaryotes. Here, we analyzed water sample metagenomes to estimate zooplankton diversity in 22 freshwater lakes across Eastern Canada. We tested the coherence of data based on

Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?

“…This encouraging finding suggests that most of the eRNA captured is in a protected state (e.g., cellular, vesicular, or in stable molecular complexes) while free RNA forms, prone to degradation, are very short lived and potentially undetectable. Our recovery of extra-organismal eRNA reads (0.51%) was similar to metagenomic studies of natural aquatic ecosystems that found between 0.27% and 1.25% of environmental DNA (eDNA) reads to be likely of extra-organismal origin [47][48][49][50].…”

“…We similarly were able to recover Daphnia eRNA in all samples, and had an average of 0.51% of all eRNA reads mapping to the D. pulex reference genome (Table S2). Our recovery of extra-organismal eRNA reads was similar to metagenomic studies of natural aquatic ecosystems that found between 0.27% and 1.25% of environmental DNA (eDNA) reads to be likely of extraorganismal origin (Cowart et al, 2018;Monchamp et al, 2022;Stat et al, 2017;Székely et al, 2021). We pre-processed our libraries with rRNA depletion, but could have potentially increased our recovery of Daphnia eRNA reads by targeting eukaryotic RNA through poly(A) enrichment.…”

Tracking aquatic animals with sediment DNA records

“…From a sedDNA extract, shotgun sequencing can provide an ecosystem-wide perspective (e.g., from bacteria and archaea to fish and mammals; Table 2). However, without any manipulation, the metazoan signal contained within the output of reads from a single environmental sample is rather small (i.e., less than 1% of assigned reads; Monchamp et al 2022). Nonetheless, comparisons of classical zooplankton taxonomy analyses with metagenomic data based on eDNA extracted from water samples at the same sites, yielded results that were moderately congruent (Monchamp et al 2022).…”

“…However, without any manipulation, the metazoan signal contained within the output of reads from a single environmental sample is rather small (i.e., less than 1% of assigned reads; Monchamp et al 2022). Nonetheless, comparisons of classical zooplankton taxonomy analyses with metagenomic data based on eDNA extracted from water samples at the same sites, yielded results that were moderately congruent (Monchamp et al 2022). Furthermore, shotgun sequencing can be applied to study Daphnia resting eggs where this analytical platform can provide insight into the differentiation of populations among time points, and identify presence of functional genes and viral pathogens (Hewson et al 2013;Cordellier et al 2021;O'Grady et al 2022).…”

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India

“…They may be shed through skin, saliva, gametes, excreta, or corpus remains. Whole-genome shotgun sequencing (WGS based on next-generation sequencing (NGS is used to create a metagenome from eDNA which is taken straight from the environment, revealing complete genetic information of all the organisms present in that particular environment in a single stretch [87,64]. In situations where collecting whole organisms is difficult or not feasible, or in case of cryptic, endangered, hidden, invasive species, unculturable bacterial species, the fast-expanding study of eDNA has proved a boon to identifying species and conducting genetic analyses for conserving, managing, and research through metagenomics.…”