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Agronomy
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Soil Microbial and Nematode Communities: Diversity, Function, and Responses to...
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Soil Microbial and Nematode Communities: Diversity, Function, and Responses to Agronomic Practices

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Farming Sustainability".

Deadline for manuscript submissions: 25 December 2026 | Viewed by 4461

Editors

Dr. Nikolaos Monokrousos

E-Mail Website
Guest Editor
Laboratory of Soil Ecology, International Hellenic University, 57001 Thessaloniki, Greece
Interests: soil microbial ecology; soil nematodes; soil enzymes; plant–soil microbe interactions
Special Issues, Collections and Topics in MDPI journals
Dr. Andrea Čerevková

E-Mail Website
Guest Editor
Laboratory of Plant Nematology, Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
Interests: morphological identification and taxonomic classification of free-living and plant parasitic nematodes; geographical distribution of soil nematodes in different types of agroecosystems and natural ecosystems
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soil microorganisms and nematodes play central roles in ecosystem functioning by regulating nutrient cycling, influencing plant–soil interactions, and contributing to organic matter turnover. Their communities are highly responsive to agronomic practices, which can either enhance or degrade soil biodiversity and function.

This Special Issue focuses on how management strategies such as organic and mineral fertilization, crop rotation, irrigation regimes, and biological amendments influence the composition, diversity, and ecological roles of soil microbial and nematode assemblages. Emphasis is placed on studies that explore community dynamics, trophic structure, microbe–nematode interactions, and contributions to soil food web stability.

We welcome submissions that apply field or greenhouse experiments, molecular tools, functional indices, or ecological modeling approaches. Manuscripts that integrate biological data with indicators of soil quality or resilience are particularly encouraged. The aim is to compile studies that improve our understanding of belowground biodiversity under managed conditions and contribute to the development of sustainable agricultural systems.

Dr. Nikolaos Monokrousos
Dr. Andrea Čerevková
Guest Editors

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 submissions that pass pre-check are 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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access semimonthly 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 2600 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 biodiversity
  • organic amendments
  • soil health indicators
  • microbe–nematode interactions
  • co-occurrence networks
  • plant–microbe interactions

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Published Papers (3 papers)

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Research

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16 pages, 5132 KB  
Article
Seasonal Drivers Exert Stronger Effects on Mesofauna Communities than Agricultural Management in Two Contrasting Arable Soils
by Ana Kiš, Goran Palijan, Olga Jovanović Glavaš, Tamara Đerđ, Danijel Jug, Irena Jug, Branimir Hackenberger Kutuzović and Davorka Hackenberger Kutuzović
Agronomy 2026, 16(14), 1316; https://doi.org/10.3390/agronomy16141316 - 10 Jul 2026
Viewed by 492
Abstract
Soil mesofauna play important roles in soil food webs, organic matter decomposition, and nutrient cycling. We quantified mesofauna responses to tillage, liming, fertilisation, and Geo2 biostimulant application at two Croatian experimental sites differing in soil type and land-use history: a long-term arable Stagnosol [...] Read more.
Soil mesofauna play important roles in soil food webs, organic matter decomposition, and nutrient cycling. We quantified mesofauna responses to tillage, liming, fertilisation, and Geo2 biostimulant application at two Croatian experimental sites differing in soil type and land-use history: a long-term arable Stagnosol in Čačinci and a recently converted Gleysol in Križevci. Mesofauna were sampled in spring and autumn 2023 and analysed using generalised linear mixed-effects models (GLMMs). Seasonal dynamics exerted the strongest influence on mesofauna communities, with Collembola and Acari abundances approximately sixfold and sevenfold higher, respectively, in spring than in autumn. A significant Season × Location interaction for total Acari and Oribatida indicated a stronger spring increase at Križevci. Liming increased Mesostigmata (+94%) and total Acari (+33%), while recommended fertilisation increased Entomobryomorpha (+78%) and total Collembola (+46%). In contrast, tillage treatments did not significantly affect the abundance of Acari, Collembola, or their major subgroups. The Collembola:Acari ratio remained relatively stable (0.56–0.93), suggesting parallel responses of dominant taxa. Overall, site-specific conditions and seasonal variation exerted stronger effects on soil mesofauna communities than the tested management practices, emphasising the importance of local environmental factors and land-use history in shaping mesofauna community dynamics in agricultural soils. Full article
(This article belongs to the Special Issue Soil Microbial and Nematode Communities: Diversity, Function, and Responses to Agronomic Practices)
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11 pages, 427 KB  
Article
Host Suitability of Winter Cover Crops for Meloidogyne enterolobii
by Churamani Khanal, Sagar GC, Homan Regmi and David Harshman
Agronomy 2026, 16(12), 1171; https://doi.org/10.3390/agronomy16121171 - 16 Jun 2026
Viewed by 329
Abstract
The guava root-knot nematode (Meloidogyne enterolobii) is a highly aggressive species of root-knot nematode that is not manageable with currently existing nematode management methods. This study was conducted to evaluate the suppressive ability of winter cover crops against M. enterolobii. [...] Read more.
The guava root-knot nematode (Meloidogyne enterolobii) is a highly aggressive species of root-knot nematode that is not manageable with currently existing nematode management methods. This study was conducted to evaluate the suppressive ability of winter cover crops against M. enterolobii. Eleven winter cover crops (rye, wheat, barley, triticale, oat, Austrian winter pea, crimson clover, balansa clover, hairy vetch, purple top turnip, and daikon radish) were evaluated against M. enterolobii in a growth room environment. Root-knot nematode-susceptible tomato (Solanum lycopersicum cv. Rutgers) was used as a control. Nematode reproduction on cover crops ranged from 1 to 501,373 eggs/g root, with oat supporting the least nematode reproduction and crimson clover supporting the greatest nematode reproduction. The crops significantly suppressing egg production on roots and second-stage juveniles in the soil relative to the control were oat, winter pea, wheat, barley, rye, and triticale. Hairy vetch, purple turnip, daikon radish, and crimson clover were good hosts, while balansa clover, wheat, winter pea, barley, rye, triticale and oat were poor or non-hosts, with the latter four crops producing substantial biomasses. Employment of these cover crops that suppress or do not support M. enterolobii reproduction while adding substantial biomass to the soil may lead to sustainable nematode management. Full article
(This article belongs to the Special Issue Soil Microbial and Nematode Communities: Diversity, Function, and Responses to Agronomic Practices)
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Review

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32 pages, 946 KB  
Review
Humic Substances and Plant Growth-Promoting Rhizobacteria (PGPR) as Biostimulants Against Plant-Parasitic Nematodes: Mechanisms, Synergistic Effects, and Applications
by Mehdi Beheshti, Lenka Demková and Lenka Bobuľská
Agronomy 2026, 16(11), 1029; https://doi.org/10.3390/agronomy16111029 - 22 May 2026
Viewed by 403
Abstract
Plant-parasitic nematodes (PPNs) rank among the most economically destructive soilborne pathogens worldwide, causing annual crop losses estimated at USD 125–175 billion. Traditional management of plant parasitic nematodes has depended significantly on synthetic nematicides; however, increasing regulatory constraints, environmental pollution, and the rise of [...] Read more.
Plant-parasitic nematodes (PPNs) rank among the most economically destructive soilborne pathogens worldwide, causing annual crop losses estimated at USD 125–175 billion. Traditional management of plant parasitic nematodes has depended significantly on synthetic nematicides; however, increasing regulatory constraints, environmental pollution, and the rise of resistant nematode populations have generated an urgent need for sustainable alternatives. Humic substances (HS), comprising humic acids, fulvic acids, and humins derived primarily from leonardite and lignite, represent biologically active components of soil organic matter. Their different functional groups, like carboxylic, phenolic, and carbonyl groups, have direct nematicidal and nematostatic effects by stopping eggs from hatching, slowing down juvenile development, and lowering infectivity. They also indirectly improve soil structure, nutrient bioavailability, and the composition of the rhizosphere microbiome. Plant growth-promoting rhizobacteria (PGPR), particularly Bacillus spp. and Pseudomonas spp., suppress PPN populations through antibiotic biosynthesis, cuticle-degrading hydrolytic enzymes, nematostatic volatile organic compounds, and elicitation of induced systemic resistance (ISR). This review methodically analyzes the individual and synergistic processes by which HS and PGPR inhibit PPNs and enhance plant growth. Humic compounds strongly promote PGPR rhizosphere colonization, augmenting microbial metabolic activity and bioinoculant stability, hence producing combinatorial suppressive effects unattainable by either input independently. The combined HS-PGPR approach is reliable and environmentally sustainable for comprehensive nematode control, requiring multidisciplinary research to achieve global sustainable agriculture. Full article
(This article belongs to the Special Issue Soil Microbial and Nematode Communities: Diversity, Function, and Responses to Agronomic Practices)
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