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Microorganisms
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Interactions between the Rhizosphere Microbiome and Plant Parasitic Nematodes
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Interactions between the Rhizosphere Microbiome and Plant Parasitic Nematodes

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 25251

Special Issue Editors

Dr. Ferenc Tóth

E-Mail Website
Guest Editor
Department of Zoology and Animal Ecology, Faculty of Agricultural and Environmental Sciences, Hungarian University of Agriculture and Life Sciences (formerly: Szent István University), 2100 Gödöllő, Hungary
Interests: organic plant protection; beneficial arthropods; nematodes; mulching; composted municipal green waste
Dr. Pratik Pravin Doshi

E-Mail Website
Guest Editor
ImMuniPot® Research Group, 2100 Gödöllő, Hungary
Interests: biological control; plant pests; plant pathology; integrated pest management; sustainable agriculture
Ms. Franciska Tóthné Bogdányi

E-Mail Website
Assistant Guest Editor
ImMuniPot® Research Group, 2100 Gödöllő, Hungary
Interests: composted municipal green waste (MGW); mulching; soil suppressivity; beneficial microorganisms; potting media

Special Issue Information

Dear Colleagues,

The drive to find more natural, organic options to control plant parasitic nematodes (PPNs), particularly members of the Meloidogyne genus, has resulted in the exploration and testing of a wide variety of beneficial microorganisms belonging to different bacterial and fungal taxa. With a more complex approach, the last few decades have also witnessed the expansion of our knowledge about the soil microbiome. Some of the new findings suggest that microbial life, health, sustainability, and soil suppressivity affect the abundance of PPNs.

Induced resistance, nematode-antagonistic bacteria and fungi, their interactions, and the microbiome of infested and non-infested soils have been studied and identified. While many of these were found to be promising, more and more practice options are being tested for their potential against PPNs.

The range and variety of existing scientific results on the topic of the soil microbiome and PPNs are already broad and keep expanding, but a compilation is needed to understand the nature of the innate suppressivity of soils to enhance the soil microbiome and exploit the benefits of mulching.

We believe that a nematode infestation is always a problem at the system level and should be examined, researched, and treated accordingly.

Therefore, we are calling for original research articles and reviews that shed light on participants in synergistic or antagonistic interactions within the soil. This Special Issue welcomes studies that map unusual interactions between microorganisms and PPNs. Studies on the topics of induced, soil-borne resistance and novel methods for controlling PPNs will also be appreciated.

Dr. Ferenc Tóth
Dr. Pratik Pravin Doshi
Ms. Franciska Tóthné Bogdányi
Guest Editors

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Keywords

  • plant parasitic nematodes
  • beneficial nematodes
  • soil microbiome
  • soil suppressivity
  • antagonism
  • agrotechnical measures
  • decomposer organisms
  • compost microbiome
  • induced suppressivity
  • nematode parasitism

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Published Papers (6 papers)

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Research

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23 pages, 3645 KiB  
Article
Historical Differentiation and Recent Hybridization in Natural Populations of the Nematode-Trapping Fungus Arthrobotrys oligospora in China
by Duanyong Zhou, Jianping Xu, Jianyong Dong, Haixia Li, Da Wang, Juan Gu, Ke-Qin Zhang and Ying Zhang
Microorganisms 2021, 9(9), 1919; https://doi.org/10.3390/microorganisms9091919 - 9 Sep 2021
Cited by 4 | Viewed by 2595
Abstract
Maintaining the effects of nematode-trapping fungi (NTF) agents in order to control plant-parasitic nematodes (PPNs) in different ecological environments has been a major challenge in biological control applications. To achieve such an objective, it is important to understand how populations of the biocontrol [...] Read more.
Maintaining the effects of nematode-trapping fungi (NTF) agents in order to control plant-parasitic nematodes (PPNs) in different ecological environments has been a major challenge in biological control applications. To achieve such an objective, it is important to understand how populations of the biocontrol agent NTF are geographically and ecologically structured. A previous study reported evidence for ecological adaptation in the model NTF species Arthrobotrys oligospora. However, their large-scale geographic structure, patterns of gene flow, their potential phenotypic diversification, and host specialization remain largely unknown. In this study, we developed a new panel of 20 polymorphic short tandem repeat (STR) markers and analyzed 239 isolates of A. oligospora from 19 geographic populations in China. In addition, DNA sequences at six nuclear gene loci and strain mating types (MAT) were obtained for these strains. Our analyses suggest historical divergence within the A. oligospora population in China. The genetically differentiated populations also showed phenotypic differences that may be related to their ecological adaptations. Interestingly, our analyses identified evidence for recent dispersion and hybridization among the historically subdivided geographic populations in nature. Together, our results indicate a changing population structure of A. oligospora in China and that care must be taken in selecting the appropriate strains as biocontrol agents that can effectively reproduce in agriculture soil while maintaining their nematode-trapping ability. Full article
(This article belongs to the Special Issue Interactions between the Rhizosphere Microbiome and Plant Parasitic Nematodes)
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18 pages, 2186 KiB  
Article
Exploiting the Innate Potential of Sorghum/Sorghum–Sudangrass Cover Crops to Improve Soil Microbial Profile That Can Lead to Suppression of Plant-Parasitic Nematodes
by Roshan Paudel, Philip Waisen and Koon-Hui Wang
Microorganisms 2021, 9(9), 1831; https://doi.org/10.3390/microorganisms9091831 - 29 Aug 2021
Cited by 14 | Viewed by 3788
Abstract
Sorghum/sorghum–sudangrass hybrids (SSgH) have been used as a cover crop to improve soil health by adding soil organic matter, enhancing microbial activities, and suppressing soil-borne pathogens in various cropping systems. A series of SSgH were screened for (1) allelopathic suppression and (2) improvement [...] Read more.
Sorghum/sorghum–sudangrass hybrids (SSgH) have been used as a cover crop to improve soil health by adding soil organic matter, enhancing microbial activities, and suppressing soil-borne pathogens in various cropping systems. A series of SSgH were screened for (1) allelopathic suppression and (2) improvement of soil edaphic factors and soil microbial profile against plant-parasitic nematode (PPNs). The allelopathic potential of SSgH against PPNs is hypothesized to vary by variety and age. In two greenhouse bioassays, ‘NX-D-61′ sorghum and the ‘Latte’ SSgH amendment provided the most suppressive allelopathic effect against the female formation of Meloidogyne incognita on mustard green seedlings when using 1-, 2-, or 3-month-old SSgH tissue, though most varieties showed a decrease in allelopathic effect as SSgH mature. A field trial was conducted where seven SSgH varieties were grown for 2.5 months and terminated using a flail mower, and eggplant was planted in a no-till system. Multivariate analysis of measured parameters revealed that increase in soil moisture, microbial biomass, respiration rate, nematode enrichment index, and sorghum biomass were negatively related to the initial abundance of PPNs and the root-gall index at 5 months after planting eggplant in a no-till system. These results suggested that improvement of soil health by SSgH could lead to suppression of PPN infection. Full article
(This article belongs to the Special Issue Interactions between the Rhizosphere Microbiome and Plant Parasitic Nematodes)
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19 pages, 3718 KiB  
Article
Screening of Rhizosphere Bacteria and Nematode Populations Associated with Soybean Roots in the Mpumalanga Highveld of South Africa
by Gerhard Engelbrecht, Sarina Claassens, Charlotte M. S. Mienie and Hendrika Fourie
Microorganisms 2021, 9(9), 1813; https://doi.org/10.3390/microorganisms9091813 - 26 Aug 2021
Cited by 8 | Viewed by 3153
Abstract
Soybean is among South Africa’s top crops in terms of production figures. Over the past few years there has been increasingly more damage caused to local soybean by plant-parasitic nematode infections. The presence of Meloidogyne (root-knot nematodes) and Pratylenchus spp. (root lesion nematodes) [...] Read more.
Soybean is among South Africa’s top crops in terms of production figures. Over the past few years there has been increasingly more damage caused to local soybean by plant-parasitic nematode infections. The presence of Meloidogyne (root-knot nematodes) and Pratylenchus spp. (root lesion nematodes) in soybean fields can cripple the country’s production, however, little is known about the soil microbial communities associated with soybean in relation to different levels of Meloidogyne and Pratylenchus infestations, as well as the interaction(s) between them. Therefore, this study aimed to identify the nematode population assemblages and endemic rhizosphere bacteria associated with soybean using Next Generation Sequencing (NGS). The abundance of bacterial genera that were then identified as being significant using linear discriminant analysis (LDA) Effect Size (LEfSe) was compared to the abundance of the most prevalent plant-parasitic nematode genera found across all sampled sites, viz. Meloidogyne and Pratylenchus. While several bacterial genera were identified as significant using LEfSe, only two with increased abundance were associated with decreased abundance of Meloidogyne and Pratylenchus. However, six bacterial genera were associated with decreased Pratylenchus abundance. It is therefore possible that endemic bacterial strains can serve as an alternative method for reducing densities of plant-parasitic nematode genera and in this way reduce the damages caused to this economically important crop. Full article
(This article belongs to the Special Issue Interactions between the Rhizosphere Microbiome and Plant Parasitic Nematodes)
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14 pages, 1385 KiB  
Article
Selection of Bacterial Strains for Control of Root-Knot Disease Caused by Meloidogyne incognita
by Varvara D. Migunova, Natalia S. Tomashevich, Alena N. Konrat, Svetlana V. Lychagina, Valentina M. Dubyaga, Trifone D’Addabbo, Nicola Sasanelli and Anzhela M. Asaturova
Microorganisms 2021, 9(8), 1698; https://doi.org/10.3390/microorganisms9081698 - 10 Aug 2021
Cited by 16 | Viewed by 3898
Abstract
Root-knot disease caused by Meloidogyne incognita leads to significant crop yield losses that may be aggravated by the association with pathogenic fungi and bacteria. Biological agents can be effectively used against the complex disease of root-knot nematode and pathogenic fungi. In this study, [...] Read more.
Root-knot disease caused by Meloidogyne incognita leads to significant crop yield losses that may be aggravated by the association with pathogenic fungi and bacteria. Biological agents can be effectively used against the complex disease of root-knot nematode and pathogenic fungi. In this study, 35 bacterial strains were analyzed for their in vitro nematicidal, antagonistic and growth stimulation activities. Based on results from the in vitro assays, grow-box experiments on tomato and cucumber were carried out with the strain BZR 86 of Bacillus velezensis applied at different concentrations. Effects of B. velezensis BZR 86 on the development of root-knot disease were evaluated by recording root gall index, number of galls and number of eggs in egg masses. Application of B. velezensis BZR 86 noticeably decreased the development of root-knot disease on tomato and cucumber plants, as well as significantly increased growth and biomass of cucumber plants in accordance with bacterial concentration. This study seems to demonstrate that strain B. velezensis BZR 86 could be an additional tool for an environmentally safe control of root-knot disease on horticultural crops. Full article
(This article belongs to the Special Issue Interactions between the Rhizosphere Microbiome and Plant Parasitic Nematodes)
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18 pages, 3685 KiB  
Article
Plants Specifically Modulate the Microbiome of Root-Lesion Nematodes in the Rhizosphere, Affecting Their Fitness
by Ahmed Elhady, Olivera Topalović and Holger Heuer
Microorganisms 2021, 9(4), 679; https://doi.org/10.3390/microorganisms9040679 - 25 Mar 2021
Cited by 14 | Viewed by 4055
Abstract
Plant-parasitic nematodes are a major constraint on agricultural production. They significantly impede crop yield. To complete their parasitism, they need to locate, disguise, and interact with plant signals exuded in the rhizosphere of the host plant. A specific subset of the soil microbiome [...] Read more.
Plant-parasitic nematodes are a major constraint on agricultural production. They significantly impede crop yield. To complete their parasitism, they need to locate, disguise, and interact with plant signals exuded in the rhizosphere of the host plant. A specific subset of the soil microbiome can attach to the surface of nematodes in a specific manner. We hypothesized that host plants recruit species of microbes as helpers against attacking nematode species, and that these helpers differ among plant species. We investigated to what extend the attached microbial species are determined by plant species, their root exudates, and how these microbes affect nematodes. We conditioned the soil microbiome in the rhizosphere of different plant species, then employed culture-independent and culture-dependent methods to study microbial attachment to the cuticle of the phytonematode Pratylenchus penetrans. Community fingerprints of nematode-attached fungi and bacteria showed that the plant species govern the microbiome associated with the nematode cuticle. Bacteria isolated from the cuticle belonged to Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Sphingobacteria, and Firmicutes. The isolates Microbacterium sp. i.14, Lysobacter capsici i.17, and Alcaligenes sp. i.37 showed the highest attachment rates to the cuticle. The isolates Bacillus cereus i.24 and L. capsici i.17 significantly antagonized P. penetrans after attachment. Significantly more bacteria attached to P. penetrans in microbiome suspensions from bulk soil or oat rhizosphere compared to Ethiopian mustard rhizosphere. However, the latter caused a better suppression of the nematode. Conditioning the cuticle of P. penetrans with root exudates significantly decreased the number of Microbacterium sp. i.14 attaching to the cuticle, suggesting induced changes of the cuticle structure. These findings will lead to a more knowledge-driven exploitation of microbial antagonists of plant-parasitic nematodes for plant protection. Full article
(This article belongs to the Special Issue Interactions between the Rhizosphere Microbiome and Plant Parasitic Nematodes)
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Review

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39 pages, 1003 KiB  
Review
Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes—A Review
by Franciska Tóthné Bogdányi, Krisztina Boziné Pullai, Pratik Doshi, Eszter Erdős, Lilla Diána Gilián, Károly Lajos, Paola Leonetti, Péter István Nagy, Vitantonio Pantaleo, Renáta Petrikovszki, Bozena Sera, Anikó Seres, Barbara Simon and Ferenc Tóth
Microorganisms 2021, 9(10), 2130; https://doi.org/10.3390/microorganisms9102130 - 11 Oct 2021
Cited by 23 | Viewed by 6325
Abstract
The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched [...] Read more.
The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a “soil environment” that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs. Full article
(This article belongs to the Special Issue Interactions between the Rhizosphere Microbiome and Plant Parasitic Nematodes)
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