Integrative taxonomic study of mononchid nematodes from riparian habitats in Bulgaria. I. Genera Mononchus Bastian, 1865 and Coomansus Jairajpuri & Khan, 1977 with the description of Mononchuspseudoaquaticus sp. nov. and a key to the species of Mononchus

The species diversity of the genera Mononchus Bastian, 1865 and Coomansus Jairajpuri & Khan, 1977 was assessed in a study of the mononchid nematodes from a wide range of riparian habitats in Bulgaria. Four species were identified based on morphological and morphometric data: Coomansusparvus (de Man, 1880), Mononchustruncatus Bastian, 1865, Mononchuspseudoaquaticus sp. nov., and Mononchus sp. The first three species were characterised both morphologically and molecularly (18S and 28S rRNA gene sequences) and the integration of these data and phylogenetic analyses provided support for their distinct species status. This paper provides detailed descriptions, morphometric data for multiple species populations, drawings and photomicrographs, and the first taxonomically verified sequences for C.parvus (n = 6), M.truncatus (sensu stricto) (n = 4) and M.pseudoaquaticus sp. nov. (n = 3). Comparative sequence and phylogenetic analyses suggested that the utility of the 18S rRNA gene for species delimitation is rather limited at least for some species complexes within the genus Mononchus. At the generic and suprageneric level, the 18S and 28S rDNA phylogenies both recovered the three genera represented by two or more species (Mononchus, Mylonchulus, and Parkellus) as monophyletic with strong support, the Mononchidae as paraphyletic, the Anatonchidae as monophyletic, and there was no support for a sister-group relationship between Mylonchulus and Mononchus. A key to the species of Mononchus is provided to facilitate the identification of the currently recognised 31 species.

The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.

Phylogenetic position of Ptychaphelenchus eucalypticola Hodda, 2009 within the Aphelenchoidoidea Skarbilovich, 1947 (Siddiqi, 1980) inferred from partial 18S and 28S rDNA gene sequences

At the time of description, the morphology of Ptychaphelenchus eucalypticola Hodda, 2009 indicated it could be assigned to either the Aphelenchoididae Skarbilovich, 1947 (Paramonov, 1953) or the Parasitaphelenchidae Ruehm, 1956 (Siddiqi, 1980) within the Aphelenchoidoidea Skarbilovich, 1947 (Siddiqi, 1980). Although P. eucalypticola was, tentatively, and remains assigned to the Aphelenchoididae, its relationships with other aphelenchoids have not been reassessed, and no molecular data were previously available for this species. We re-collected P. eucalypticola from its type host and locality, Eucalyptus macrorhyncha F. Muell. ex Benth., from Mount Ainslie, ACT, Australia. We performed Bayesian inference and maximum likelihood analyses of a concatenated 18S + 28S rDNA gene sequence dataset to determine the position of P. eucalypticola within the Aphelenchoidoidea, followed by 18S and 28S single-gene analyses to further assess relationships between this species and an expanded set of close relatives. All analyses indicated P. eucalypticola is correctly assigned to the Aphelenchoididae, in a clade comprising all species of Ficophagus Davies & Bartholomaeus, 2015 and some species presently assigned to Aphelenchoides Fisher, 1894, sister to Martininema Davies & Bartholomaeus, 2015 and additional species of Aphelenchoides. Our 18S single-gene analyses did not resolve the position of P. eucalypticola relative to Aphelenchoides and Ficophagus; however, our 28S single-gene analyses indicated a sister relationship between P. eucalypticola and Ficophagus. This sister relationship is plausible as the former species shares many characteristics with species of the latter genus; however, there are sufficient morphological differences to consider P. eucalypticola as representative of a distinct lineage within the Aphelenchoidoidea.

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 at different sequencing efforts. 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 over 95% 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. Results were similar among different sequencing efforts.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 show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief 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.

Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy

The use of bioindicator species is a widely applied approach to evaluate ecological conditions, and several indices have been designed for this purpose. To assess the impact of pollution, especially in sediments, a pollution-sensitive index based on nematodes, one of the most abundant and species-rich groups of metazoa, was developed. The NemaSPEAR[%] index in its original form relies on the morphological inspection of nematode species. The application of a morphologically based NemaSPEAR[%] at the genus-level was previously validated. The present study evaluated a NemaSPEAR[%] index based on metabarcoding of nematode communities and tested the potential of fragments from the 28S rDNA, 18S rDNA and cytochrome c oxidase subunit I (COI) genes. In general, molecular-based results tended to show a poorer condition than morphology-based results for the investigated sites. At the genus level, NemaSPEAR[%] values based on morphological data strongly correlated with those based on molecular data for both the 28S rDNA and the 18S rDNA gene fragments (R² = 0.86 and R² = 0.74, respectively). Within the dominant genera (>3%) identified by morphology, 68% were detected by at least one of the two ribosomal markers. At the species level, however, concordance was less pronounced, as there were several deviations of the molecular from the morphological data. These differences could mostly be attributed to shortcomings in the reference database used in the molecular-based assignments. Our pilot study shows that a molecularly based, genus-level NemaSPEAR[%] can be successfully applied to evaluate polluted sediment. Future studies need to validate this approach further, e.g. with bulk extractions of whole meiofaunal communities in order to circumvent time-consuming nematode isolation. Further database curation with abundant NemaSPEAR[%] species will also increase the applicability of this approach.

Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities

Biomonitoring approaches and investigations of many ecological questions require assessments of the biodiversity of a given habitat. Small organisms, ranging from protozoans to metazoans, are of great ecological importance and comprise a major share of the planet's biodiversity but they are extremely difficult to identify, due to their minute body sizes and indistinct structures. Thus, most biodiversity studies that include small organisms draw on several methods for species delimitation, ranging from traditional microscopy to molecular techniques. In this study, we compared the efficiency of these methods by analyzing a community of nematodes. Specifically, we evaluated the performances of traditional morphological identification, single-specimen barcoding (Sanger sequencing), and metabarcoding in the identification of 1500 nematodes from sediment samples. The molecular approaches were based on the analysis of the 28S ribosomal large and 18S small subunits (LSU and SSU). The morphological analysis resulted in the determination of 22 nematode species. Barcoding identified a comparable number of operational taxonomic units (OTUs) based on 28S rDNA (n = 20) and fewer OTUs based on 18S rDNA (n = 12). Metabarcoding identified a higher OTU number but fewer amplicon sequence variants (AVSs) (n = 48 OTUs, n = 17 ASVs for 28S rDNA, and n = 31 OTUs, n = 6 ASVs for 18S rDNA). Between the three approaches (morphology, barcoding, and metabarcoding), only three species (13.6%) were shared. This lack of taxonomic resolution hinders reliable community identifications to the species level. Further database curation will ensure the effective use of molecular species identification.

Soil nematode abundance and diversity from four vegetation types in Central Mexico

Soil nematode abundance and MOTU diversity were estimated from a geographically broad area of Mexico that included four out of seven recognised vegetation types. Vegetation types were assessed for abundance and diversity of nematode communities and inferred ecological relationships between them. Soils were sampled from tropical rainforest, tropical dry deciduous forest, temperate coniferous forest and xerophytic shrub during 2013, 2014 and 2015. Fourteen sampling sites withca10-20 samples per site from 11 localities spread across Central Mexico were assessed. Altitudes sampled ranged from 113 m a.s.l. (tropical coastal plain) to 2400 m a.s.l. (Trans-Mexican Volcanic Belt). Samples were drawn from conserved and cultivated plots from each sampling site covering an area of ⩾100 m2. A total of 13 263 individuals from 25 identified families of nematodes were collected. Family abundance and complementarity indices between sites revealed to some extent the affinities between vegetation types. Nevertheless, statistical analyses revealed no differences between nematode family abundances between sites, only between families across all sites. Molecular operational taxonomic units (MOTU) methods were employed as a framework to assess biodiversity. From these, 77 high-quality sequences for taxonomic barcoding were recovered and later identified with morphological traits. Only six sequences matched at a 98-99% level with those reported in GenBank. Sequences amounted to a total of 41 MOTU, where 100% of the MOTU from both conserved and disturbed tropical rainforest, tropical dry deciduous forest and xerophytic shrub exhibited a ⩾3% cut-off genetic identity, whilst temperate coniferous forest and disturbed temperate coniferous forest showed 73% and 70% respectively. In addition, 12.2% MOTU were shared among localities and 87.8% exhibited an apparently locality-limited distribution. The potential for a considerable diversity of nematodes, as revealed from a small sample of MOTU diversity, is discussed.