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Diversity
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Soil Nematodes Research
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Soil Nematodes Research

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

Deadline for manuscript submissions: closed (15 December 2020) | Viewed by 25203

Special Issue Editor

Prof. Dr. Liliane Ruess

E-Mail 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

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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 2100 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

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Published Papers (4 papers)

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Research

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19 pages, 1002 KiB  
Article
Nematode Community-Based Soil Food Web Analysis of Ferralsol, Lithosol and Nitosol Soil Groups in Ghana, Kenya and Malawi Reveals Distinct Soil Health Degradations
by Haddish Melakeberhan, ZinThuZar Maung, Isaac Lartey, Senol Yildiz, Jenni Gronseth, Jiaguo Qi, George N. Karuku, John W. Kimenju, Charles Kwoseh and Thomas Adjei-Gyapong
Diversity 2021, 13(3), 101; https://doi.org/10.3390/d13030101 - 25 Feb 2021
Cited by 11 | Viewed by 2968
Abstract
Determining if the vast soil health degradations across the seven major soil groups (orders) of Sub-Saharan Africa (SSA) can be managed on the basis of a one-size-fits-all or location-specific approach is limited by a lack of soil group-based understanding of soil health degradations. [...] Read more.
Determining if the vast soil health degradations across the seven major soil groups (orders) of Sub-Saharan Africa (SSA) can be managed on the basis of a one-size-fits-all or location-specific approach is limited by a lack of soil group-based understanding of soil health degradations. We used the relationship between changes in nematode population dynamics relative to food and reproduction (enrichment, EI) and resistance to disturbance (structure, SI) indices to characterize the soil food web (SFW) and soil health conditions of Ferralsol, Lithosol and Nitosol soil groups in Ghana, Kenya and Malawi. We applied bivariate correlations of EI, SI, soil pH, soil organic carbon (SOC), and texture (sand, silt and clay) to identify integrated indicator parameters, and principal component analysis (PCA) to determine how all measured parameters, soil groups, and countries align. A total of 512 georeferenced soil samples from disturbed (agricultural) and undisturbed (natural vegetation) landscapes were analyzed. Nematode trophic group abundance was low and varied by soil group, landscape and country. The resource-limited and degraded SFW conditions separated by soil groups and by country. EI and SI correlation with SOC varied by landscape, soil group or country. PCA alignment showed separation of soil groups within and across countries. The study developed the first biophysicochemical proof-of-concept that the soil groups need to be treated separately when formulating scalable soil health management strategies in SSA. Full article
(This article belongs to the Special Issue Soil Nematodes Research)
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14 pages, 1737 KiB  
Article
Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities
by Md. Maniruzzaman Sikder, Mette Vestergård, Rumakanta Sapkota, Tina Kyndt and Mogens Nicolaisen
Diversity 2020, 12(10), 388; https://doi.org/10.3390/d12100388 - 9 Oct 2020
Cited by 22 | Viewed by 6864
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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16 pages, 1874 KiB  
Article
A Case Study of Nematode Communities’ Dynamics along Successional Paths in the Reclaimed Landfill
by George P. Stamou, Maria D. Argyropoulou, Ignacio Rodriguez-Polo, George Boutsis, Pantelitsa Kapagianni and Efimia M. Papatheodorou
Diversity 2020, 12(7), 274; https://doi.org/10.3390/d12070274 - 9 Jul 2020
Cited by 11 | Viewed by 2871
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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Review

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22 pages, 1194 KiB  
Review
Functional Diversity of Soil Nematodes in Relation to the Impact of Agriculture—A Review
by Stela Lazarova, Danny Coyne, Mayra G. Rodríguez, Belkis Peteira and Aurelio Ciancio
Diversity 2021, 13(2), 64; https://doi.org/10.3390/d13020064 - 4 Feb 2021
Cited by 44 | Viewed by 11449
Abstract
The analysis of the functional diversity of soil nematodes requires detailed knowledge on theoretical aspects of the biodiversity–ecosystem functioning relationship in natural and managed terrestrial ecosystems. Basic approaches applied are reviewed, focusing on the impact and value of soil nematode diversity in crop [...] Read more.
The analysis of the functional diversity of soil nematodes requires detailed knowledge on theoretical aspects of the biodiversity–ecosystem functioning relationship in natural and managed terrestrial ecosystems. Basic approaches applied are reviewed, focusing on the impact and value of soil nematode diversity in crop production and on the most consistent external drivers affecting their stability. The role of nematode trophic guilds in two intensively cultivated crops are examined in more detail, as representative of agriculture from tropical/subtropical (banana) and temperate (apple) climates. The multiple facets of nematode network analysis, for management of multitrophic interactions and restoration purposes, represent complex tasks that require the integration of different interdisciplinary expertise. Understanding the evolutionary basis of nematode diversity at the field level, and its response to current changes, will help to explain the observed community shifts. Integrating approaches based on evolutionary biology, population genetics and ecology can quantify the contribution of nematode fauna to fundamental soil functions. These include carbon transformation, nutrient cycling, pest control and disease transmission. In conclusion, different facets of nematode diversity such as trophic groups, life history traits, variability in body size and/or taxa identities in combination with DNA-based techniques are needed in order to disclose nematode–soil–ecosystem functioning relationships. Further experimental studies are required to define locally adapted and sustainable management practices, through ecosystem-based approaches and nature-based solutions. Full article
(This article belongs to the Special Issue Soil Nematodes Research)
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