Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass and reference genome properties

Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships, in comparison to taxonomic marker gene based approaches (metabarcoding). However, little is known about the factors that influence metagenomics data from eukaryotic communities, such as differences among organism groups, properties of reference genomes and genome assemblies. We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades and potworms. We shotgun-sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes. We recovered 90% of the species, and observed relatively high false positive detection rates. We found strong differences in reads assigned to different taxa, with some groups consistently attracting more hits than others. Biomass could be predicted from read counts after considering taxon-specific differences. Larger genomes more complete assemblies consistently attracted more reads than genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. Properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We provide a roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing, and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.

Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass and reference genome properties

Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes and genome assemblies. We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades and potworms. We shotgun-sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes. We recovered 90% of the species, and observed relatively high false positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g. springtails) consistently attracting more hits than others (e.g. enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We provide a roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing, and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.

Soil invertebrates of coniferous forests along a gradient of air pollution (Komi Republic)

The role of soil invertebrates in the cycle of substances, soil-forming processes and the provision of ecosystem services is undeniable. Therefore, soil invertebrates are valuable in bioindication studies. Comprehensive research of soil invertebrates in the production area of Mondi Syktyvkar JSC as the largest pulp and paper enterprise in the European part of Russia was initiated in 2003. A huge amount of data about composition, abundance and structure of soil macro- and mesofauna along an impact gradient was accumulated during the period from 2003 to 2019 years. These data can be used to study local biodiversity, monitor the state of soil invertebrate communities and assess the impact of the pulp and paper industry on the environment. Datasets here presented include information from a monitoring programme for soil invertebrates that inhabit coniferous forests in the production area of Mondi Syktyvkar JSC (Komi Republic). The assemblages' structure of macrofauna, collembolans and nematodes are described. Information on the number of individuals of springtail species, nematodes genera and macrofauna taxa is given. A total of 11146 sampling events of macrofauna, 6673 sampling events of Collembola, and 2592 sampling events of Nematoda are recorded along a gradient of air pollution from pulp and paper industry emissions.

Temporal Changes in the Function of Bacterial Assemblages Associated With Decomposing Earthworms

Soil invertebrate corpse decomposition is an ecologically significant, yet poorly understood, process affecting nutrient biogeochemical cycling in terrestrial ecosystems. Here, we attempted to answer how the substrate chemistry and microbial community change during soil invertebrate (earthworm) decomposition and what roles microbes play in this process. Specifically, the dead earthworms (Amynthas corticis) were buried in two soils where the earthworms inhabited, or not, until more than 50% of the earthworm mass was lost. For both soils, earthworms decomposed faster during the early stage (between 0 and 3 days), as reflected by the higher rate of decomposition and increased accumulation of dissolved organic matter (DOM). This decomposition pattern was paralleled by bacterial community dynamics, where bacterial richness and diversity were significantly higher during early decomposition (p < 0.05) with the relative abundances of many genera decreasing as decomposition progressed. The succession of the bacterial community composition was significantly correlated with time-course changes in DOM composition (p < 0.05). Particularly, more functional groups (e.g., microbes associated with carbon, nitrogen, and sulfur cycling) were identified to be linked with the change of a specific DOM type during the early decomposition phase. By exploring the ecologically important process of soil invertebrate decomposition and its associated bacterial communities, this study provides evidence, e.g., a statistically significant positive correlation between bacterial community and DOM compositions, which supports the widely recognized yet less-tested microbial community structure–function relationship hypothesis in invertebrate decomposition.

Impact of Nesting Socotra Cormorants on Terrestrial Invertebrate Communities

Seabirds and some inland waterbirds nest in densely aggregated colonies. Nesting activities for a duration of months could lead to large quantities of guano deposition that affects the soil chemistry, flora and fauna. We assessed the effects of nesting Socotra Cormorants on soil invertebrates on Siniya Island, United Arab Emirates. Artificial substrate traps were set in nesting and non-nesting areas to sample invertebrates both before and after nesting had occurred. Diversity of soil invertebrate taxa decreased significantly in nesting areas compared to non-nesting areas after the commencement of nesting. This indicated that nesting activities had a negative effect on diversity. Among selected taxa, isopods and spiders decreased significantly in response to nesting activities. In contrast, ants were likely affected by habitat while beetles did not change significantly in response to nesting activities, suggesting that their numbers probably fluctuated in relation to seasonality. Ticks increased significantly but only in non-nesting areas. Thus, the impact of nesting varied between taxa depending on life history and seasonality. Our observations reflect the dynamic nature of invertebrate abundance that is affected by seasonality and the hyper-abundance of nesting seabirds.