Special Issue "Soil Nematodes Research"

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Animal Diversity".

Deadline for manuscript submissions: 15 December 2020.

Special Issue Editor

Prof. Dr. Liliane Ruess
Website
Guest Editor
Humboldt-Universität zu Berlin, Institute of Biology, Ecology Group, Philippstraße 13, 10115 Berlin, Germany
Interests: free-living nematodes; soil ecology; nematodes as indicators; soil food webs; trophic biomarkers; fatty acids; stable isotopes; biodiversity; soil nutrient cycling; land use

Special Issue Information

Dear Colleagues,

Nematodes are the most abundant metazoa on earth, and their extraordinary high species number makes them third only to insects and mollusks in the animal kingdom. Their great density and trophic diversity across soil ecosystems highlights their functional role, e.g., in nutrient cycling or food web interactions. Nematode community analysis has developed into a powerful tool to broaden our understanding in taxonomic and functional diversity in soil, which is critically important for current ecosystem threads such as climate change or land use. Moreover, the relative magnitudes of the root, bacterial, and fungal soil energy channels are assessed by the trophic structure of the nematode fauna. Finally, metabolic footprints unify functional diversity and body-mass distribution of nematodes, providing metrics for ecosystem services. Compared with their key role in soils, the taxonomic and ecological expertise in this group of small roundworms is far less developed. This calls for connecting the various studies in soil nematode ecology, to make considerable progress in both basic and applied areas.

This Special Issue provides a platform to highlight new research and significant advances in the understanding of soil nematode diversity and function. This comprises, e.g., standardization of methods to assess nematode community structure as well as laboratory experiments aiming for a mechanistic understanding of species functions and community composition. Moreover, environmental surveys are invited determining the influence of functional composition and functional diversity on ecosystem processes by classic morphological as well as molecular or biochemical approaches. In the context of ecosystem services and soil health, biomass and metabolic activity of species are further meaningful measures. In a nutshell, all kind of studies are welcome considering nematodes as a key biological component in soil ecosystems.

Prof. Dr. Liliane Ruess
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Soil nematodes
  • Diversity
  • Functional role
  • Food webs
  • Grazing
  • Metabolic footprints
  • Soil energy and carbon pathways
  • Green and brown food chain
  • Ecosystem services
  • Soil health

Published Papers (2 papers)

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Research

Open AccessArticle
Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities
Diversity 2020, 12(10), 388; https://doi.org/10.3390/d12100388 - 09 Oct 2020
Abstract
While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the application of high throughput approaches to study the ecology of nematodes remains unresolved due to several issues, e.g., whether to include an initial nematode extraction step or not, the [...] Read more.
While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the application of high throughput approaches to study the ecology of nematodes remains unresolved due to several issues, e.g., whether to include an initial nematode extraction step or not, the lack of consensus on the best performing primer combination, and the absence of a curated nematode reference database. The objective of this method development study was to compare different primer sets to identify the most suitable primer set for the metabarcoding of nematodes without initial nematode extraction. We tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition of COI gene), SSU_04F/SSU_22R (18S rRNA, V1-V2 regions), and Nemf/18Sr2b (18S rRNA, V6-V8 regions) from earlier studies, as well as MMSF/MMSR (18S rRNA, V4-V5 regions), a newly developed primer set. We used DNA from 22 nematode taxa, 10 mock communities, 20 soil samples, 4 root samples, and one bulk soil. We amplified the target regions from the DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the Nemf/18Sr2b primer set was superior for detecting soil nematodes compared to the other primer sets based on our sequencing results and on the annotation of our sequence reads at the genus and species ranks. This primer set generated 74% reads of Nematoda origin in the soil samples. Additionally, this primer set did well with the mock communities, detecting all the included specimens. It also worked better in the root samples than the other primer set that was tested. Therefore, we suggest that the Nemf/18Sr2b primer set could be used to study rhizosphere soil and root associated nematodes, and this can be done without an initial nematode extraction step. Full article
(This article belongs to the Special Issue Soil Nematodes Research)
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Open AccessArticle
A Case Study of Nematode Communities’ Dynamics along Successional Paths in the Reclaimed Landfill
Diversity 2020, 12(7), 274; https://doi.org/10.3390/d12070274 - 09 Jul 2020
Abstract
We assessed the abundance and composition of nematode communities in soil under herbaceous vegetation in reclaimed landfill sites at different ages after closure (3, 10 and 14 years) compared to those in neighboring semi-natural grazed grasslands (reference sites). We further applied network analysis [...] Read more.
We assessed the abundance and composition of nematode communities in soil under herbaceous vegetation in reclaimed landfill sites at different ages after closure (3, 10 and 14 years) compared to those in neighboring semi-natural grazed grasslands (reference sites). We further applied network analysis based on the co-occurrence patterns of nematodes. Nematode abundance decreased between 3 and10 years of regeneration, but significantly increased from 10 to 14 years of regeneration. The number and identity of genera were comparable along the succession; however, there were dissimilarities in community composition during early- and mid-succession. The diversity, community composition and abundance at the sites after 14 years of regeneration converged with those at the reference sites. Moreover, changes during succession were not accompanied by the maturation of the soil food web, as demonstrated by Enrichment and Channel indices. In all the networks, centrality and modularity metrics differed significantly from those for random networks, whereas cohesion metrics showed no difference. All the networks exhibited Small-worldness indices higher than one, demonstrating that the networks of the interactions among genera at all the sites shared features that matched both random and non-random networks. The succession trajectory in reclaimed landfills was represented by a sequence of changes that differed in relation to the variable under consideration; network parameters tended to converge with those of a relatively resistant reference community, while the Enrichment and Channel indices did not. Additionally, the succession trajectory was not linear or steady; only the Channel index and Worldness index showed linear responses to succession time. However, across all the successional stages, the resource status remained basal or degraded while the nematode communities had an enhanced ability to cope with sudden changes. Full article
(This article belongs to the Special Issue Soil Nematodes Research)
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