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Phytomicrobiome Research for Disease and Pathogen Management

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant–Soil Interactions".

Deadline for manuscript submissions: closed (30 October 2023) | Viewed by 27905

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Special Issue Editors

Dr. Wen Chen

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Guest Editor

1. Ottawa Research and Development Centre, AAFC, Ottawa, ON K1A 0C6, Canada
2. Department of Biology, University of Ottawa, Ottawa, ON, Canada
Interests: microbial ecology; bioinformatics; biovigilance; phytomicrobiome; sustainable agriculture
Special Issues, Collections and Topics in MDPI journals

Dr. Adeline Picot

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Guest Editor

Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Univ Brest, INRAE, F-29280 Plouzané, France
Interests: microbial ecology; plant fungal pathogens; mycotoxin; biocontrol

Special Issue Information

Dear Colleagues,

Plant health and productivity require a holistic view and an in-depth understanding of the diversity and functions of microorganisms associated with soil and plants, also known as phytomicrobiome, which include beneficial members that provide critical ecosystem services and pathogens threatening food safety and security. High-throughput omics tools, ranging from metabarcoding, metagenomics, metatranscriptomics, metaproteomics, to metabolomics, allow identify bioindicators (microorganisms, genes, and/or molecules) associated with ecosystem functioning, reveal synergisms and antagonisms among community members across kingdoms, and assess the impact of environmental (e.g. climate) and anthropological factors (e.g. agronomic practices). Such knowledge, coupled with culture-dependent and greenhouse/field experiments, also provides opportunities to develop innovative biocontrol approaches and assist in pathogen management for better plant and soil health.

This special issue of Plants looks forward to receiving contributions, either research papers or reviews, about the most recent significant insights dedicated to 1) phytomicrobiomes, their functions and dynamics in agroecosystems or forests, 2) the impact of environmental and anthropogenic factors, as well as 3) interactions among community members and, notably, towards phytopathogen communities (e.g. viruses, bacteria, fungi, oomycetes, protozoa, nematodes) or pests. Papers dedicated to the development of methods to harness beneficial phytomicrobiome as well as the assessment of their efficacy in improving plant and soil health are also welcome.

Dr. Wen Chen
Dr. Adeline Picot
Guest Editors

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. Plants 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 2700 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

biological control agent
biovigilance
climate change
high-throughput sequencing
high-throughput omics tools
microorganisms
plant pathogens
plant-microbe interaction
phytomicrobiome
soil suppressiveness
sustainable agriculture and forestry

Published Papers (9 papers)

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Research

Jump to: Review

12 pages, 1433 KiB

Open AccessArticle

ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data

by Clément Plessis, Thomas Jeanne, Antoine Dionne, Julien Vivancos, Arnaud Droit and Richard Hogue

Plants 2023, 12(21), 3678; https://doi.org/10.3390/plants12213678 - 25 Oct 2023

Viewed by 932

Abstract

The taxonomic assignment of sequences obtained by high throughput amplicon sequencing poses a limitation for various applications in the biomedical, environmental, and agricultural fields. Identifications are constrained by the length of the obtained sequences and the computational processes employed to efficiently assign taxonomy. Arriving at a consensus is often preferable to uncertain identification for ecological purposes. To address this issue, a new tool called “ASVmaker” has been developed to facilitate the creation of custom databases, thereby enhancing the precision of specific identifications. ASVmaker is specifically designed to generate reference databases for allocating amplicon sequencing data. It uses publicly available reference data and generates specific sequences derived from the primers used to create amplicon sequencing libraries. This versatile tool can complete taxonomic assignments performed with pre-trained classifiers from the SILVA and UNITE databases. Moreover, it enables the generation of comprehensive reference databases for specific genes in cases where no directly applicable database exists for taxonomic classification tools. Full article

(This article belongs to the Special Issue Phytomicrobiome Research for Disease and Pathogen Management)

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26 pages, 11541 KiB

Open AccessArticle

Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding

by Marie Belair, Flora Pensec, Jean-Luc Jany, Gaétan Le Floch and Adeline Picot

Plants 2023, 12(12), 2383; https://doi.org/10.3390/plants12122383 - 20 Jun 2023

Cited by 2 | Viewed by 1504

Abstract

Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen–one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms. Full article

(This article belongs to the Special Issue Phytomicrobiome Research for Disease and Pathogen Management)

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21 pages, 2333 KiB

Open AccessArticle

Long-Term Tillage and Crop Rotation Regimes Reshape Soil-Borne Oomycete Communities in Soybean, Corn, and Wheat Production Systems

by Alison Claire Gahagan, Yichao Shi, Devon Radford, Malcolm J. Morrison, Edward Gregorich, Stéphane Aris-Brosou and Wen Chen

Plants 2023, 12(12), 2338; https://doi.org/10.3390/plants12122338 - 15 Jun 2023

Cited by 2 | Viewed by 1592

Abstract

Soil-borne oomycetes include devastating plant pathogens that cause substantial losses in the agricultural sector. To better manage this important group of pathogens, it is critical to understand how they respond to common agricultural practices, such as tillage and crop rotation. Here, a long-term field experiment was established using a split-plot design with tillage as the main plot factor (conventional tillage (CT) vs. no till (NT), two levels) and rotation as the subplot factor (monocultures of soybean, corn, or wheat, and corn–soybean–wheat rotation, four levels). Post-harvest soil oomycete communities were characterized over three consecutive years (2016–2018) by metabarcoding the Internal Transcribed Spacer 1 (ITS1) region. The community contained 292 amplicon sequence variants (ASVs) and was dominated by Globisporangium spp. (85.1% in abundance, 203 ASV) and Pythium spp. (10.4%, 51 ASV). NT decreased diversity and community compositional structure heterogeneity, while crop rotation only affected the community structure under CT. The interaction effects of tillage and rotation on most oomycetes species accentuated the complexity of managing these pathogens. Soil and crop health represented by soybean seedling vitality was lowest in soils under CT cultivating soybean or corn, while the grain yield of the three crops responded differently to tillage and crop rotation regimes. Full article

(This article belongs to the Special Issue Phytomicrobiome Research for Disease and Pathogen Management)

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18 pages, 5656 KiB

Open AccessArticle

Triazoles and Strobilurin Mixture Affects Soil Microbial Community and Incidences of Wheat Diseases

by Anastasia V. Vasilchenko, Darya V. Poshvina, Mikhail V. Semenov, Vyacheslav N. Timofeev, Alexandr V. Iashnikov, Artyom A. Stepanov, Arina N. Pervushina and Alexey S. Vasilchenko

Plants 2023, 12(3), 660; https://doi.org/10.3390/plants12030660 - 2 Feb 2023

Cited by 5 | Viewed by 2253

Abstract

Pesticides are widely used in agriculture as a pest control strategy. Despite the benefits of pesticides on crop yields, the persistence of chemical residues in soil has an unintended impact on non-targeted microorganisms. In the present study, we evaluated the potential adverse effects of a mixture of fungicides (difenoconazole, epoxiconazole, and kresoxim-methyl) on soil fungal and bacterial communities, as well as the manifestation of wheat diseases. In the fungicide-treated soil, the Shannon indices of both fungal and bacterial communities decreased, whereas the Chao1 indices did not differ compared to the control soil. Among bacterial taxa, the relative abundances of Arthrobacter and Sphingomonas increased in fungicide-treated soil due to their ability to utilize fungicides and other toxic compounds. Rhizopus and plant-beneficial Chaetomium were the dominant fungal genera, with their prevalence increasing by 2–4 times in the fungicide-treated soil. The genus Fusarium, which includes phytopathogenic species, which are notably responsible for root rot, was the most abundant taxon in each of the two conditions but its relative abundance was two times lower in fungicide-treated soils, consistent with a lower level of disease incidence in plants. The prediction of metabolic pathways revealed that the soil bacterial community had a high potential for degrading various pollutants, and the soil fungal community was in a state of recovery after the application of quinone outside inhibitor (Q_oI) fungicides. Fungicide-treated soil was characterized by an increase in soil microbial carbon, compared with the control soil. Collectively, the obtained results suggest that the application of difenoconazole, epoxiconazole, and kresoxim-methyl is an effective approach for pest control that does not pose a hazard for the soil ecosystem in the short term. However, it is necessary to carry out additional sampling to take into account the spatio-temporal impact of this fungicide mixture on the functional properties of the soil. Full article

(This article belongs to the Special Issue Phytomicrobiome Research for Disease and Pathogen Management)

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25 pages, 7129 KiB

Open AccessArticle

Environmental Filtering Drives Fungal Phyllosphere Community in Regional Agricultural Landscapes

by Annika Hoffmann, Alexandra-Raluca Posirca, Simon Lewin, Gernot Verch, Carmen Büttner and Marina E. H. Müller

Plants 2023, 12(3), 507; https://doi.org/10.3390/plants12030507 - 22 Jan 2023

Cited by 1 | Viewed by 1571

Abstract

To adapt to climate change, several agricultural strategies are currently being explored, including a shift in land use areas. Regional differences in microbiome composition and associated phytopathogens need to be considered. However, most empirical studies on differences in the crop microbiome focused on soil communities, with insufficient attention to the phyllosphere. In this study, we focused on wheat ears in three regions in northeastern Germany (Magdeburger Börde (MBB), Müncheberger Sander (MSA), Uckermärkisches Hügelland (UKH)) with different yield potentials, soil, and climatic conditions. To gain insight into the fungal community at different sites, we used a metabarcoding approach (ITS-NGS). Further, we examined the diversity and abundance of Fusarium and Alternaria using culture-dependent and culture-independent techniques. For each region, the prevalence of different orders rich in phytopathogenic fungi was determined: Sporidiobolales in MBB, Capnodiales and Pleosporales in MSA, and Hypocreales in UKH were identified as taxonomic biomarkers. Additionally, F. graminearum was found predominantly in UKH, whereas F. poae was more abundant in the other two regions. Environmental filters seem to be strong drivers of these differences, but we also discuss the possible effects of dispersal and interaction filters. Our results can guide shifting cultivation regions to be selected in the future concerning their phytopathogenic infection potential. Full article

(This article belongs to the Special Issue Phytomicrobiome Research for Disease and Pathogen Management)

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Review

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36 pages, 1502 KiB

Open AccessReview

Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review

by Wen Chen, Dixi Modi and Adeline Picot

Plants 2023, 12(14), 2736; https://doi.org/10.3390/plants12142736 - 23 Jul 2023

Cited by 8 | Viewed by 6730

Abstract

The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome. Full article

(This article belongs to the Special Issue Phytomicrobiome Research for Disease and Pathogen Management)

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25 pages, 1234 KiB

Open AccessReview

Artificial Intelligence: A Promising Tool in Exploring the Phytomicrobiome in Managing Disease and Promoting Plant Health

by Liang Zhao, Sean Walkowiak and Wannakuwattewaduge Gerard Dilantha Fernando

Plants 2023, 12(9), 1852; https://doi.org/10.3390/plants12091852 - 30 Apr 2023

Cited by 2 | Viewed by 3836

Abstract

There is increasing interest in harnessing the microbiome to improve cropping systems. With the availability of high—throughput and low—cost sequencing technologies, gathering microbiome data is becoming more routine. However, the analysis of microbiome data is challenged by the size and complexity of the data, and the incomplete nature of many microbiome databases. Further, to bring microbiome data value, it often needs to be analyzed in conjunction with other complex data that impact on crop health and disease management, such as plant genotype and environmental factors. Artificial intelligence (AI), boosted through deep learning (DL), has achieved significant breakthroughs and is a powerful tool for managing large complex datasets such as the interplay between the microbiome, crop plants, and their environment. In this review, we aim to provide readers with a brief introduction to AI techniques, and we introduce how AI has been applied to areas of microbiome sequencing taxonomy, the functional annotation for microbiome sequences, associating the microbiome community with host traits, designing synthetic communities, genomic selection, field phenotyping, and disease forecasting. At the end of this review, we proposed further efforts that are required to fully exploit the power of AI in studying phytomicrobiomes. Full article

(This article belongs to the Special Issue Phytomicrobiome Research for Disease and Pathogen Management)

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18 pages, 1994 KiB

Open AccessReview

Agroecological Management of the Grey Mould Fungus Botrytis cinerea by Plant Growth-Promoting Bacteria

by Ma. del Carmen Orozco-Mosqueda, Ajay Kumar, Ayomide Emmanuel Fadiji, Olubukola Oluranti Babalola, Gerardo Puopolo and Gustavo Santoyo

Plants 2023, 12(3), 637; https://doi.org/10.3390/plants12030637 - 1 Feb 2023

Cited by 9 | Viewed by 4544

Abstract

Botrytis cinerea is the causal agent of grey mould and one of the most important plant pathogens in the world because of the damage it causes to fruits and vegetables. Although the application of botrycides is one of the most common plant protection strategies used in the world, the application of plant-beneficial bacteria might replace botrycides facilitating agroecological production practices. Based on this, we reviewed the different stages of B. cinerea infection in plants and the biocontrol mechanisms exerted by plant-beneficial bacteria, including the well-known plant growth-promoting bacteria (PGPB). Some PGPB mechanisms to control grey mould disease include antibiosis, space occupation, nutrient uptake, ethylene modulation, and the induction of plant defence mechanisms. In addition, recent studies on the action of anti-Botrytis compounds produced by PGPB and how they damage the conidial and mycelial structures of the pathogen are reviewed. Likewise, the advantages of individual inoculations of PGPB versus those that require the joint action of antagonist agents (microbial consortia) are discussed. Finally, it should be emphasised that PGPB are an excellent option to prevent grey mould in different crops and their use should be expanded for environmentally friendly agricultural practices. Full article

(This article belongs to the Special Issue Phytomicrobiome Research for Disease and Pathogen Management)

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25 pages, 3644 KiB

Open AccessReview

Serendipita indica—A Review from Agricultural Point of View

by Sana Saleem, Agnieszka Sekara and Robert Pokluda

Plants 2022, 11(24), 3417; https://doi.org/10.3390/plants11243417 - 7 Dec 2022

Cited by 7 | Viewed by 3434

Abstract

Fulfilling the food demand of a fast-growing population is a global concern, resulting in increased dependence of the agricultural sector on various chemical formulations for enhancing crop production. This leads to an overuse of chemicals, which is not only harmful to human and animal health, but also to the environment and the global economy. Environmental safety and sustainable production are major responsibilities of the agricultural sector, which is inherently linked to the conservation of the biodiversity, the economy, and human and animal health. Scientists, therefore, across the globe are seeking to develop eco-friendly and cost-effective strategies to mitigate these issues by putting more emphasis on the use of beneficial microorganisms. Here, we review the literature on Serendipita indica, a beneficial endophytic fungus, to bring to the fore its properties of cultivation, the ability to enhance plant growth, improve the quality of produced crops, mitigate various plant stresses, as well as protect the environment. The major points in this review are as follows: (1) Although various plant growth promoting microorganisms are available, the distinguishing character of S. indica being axenically cultivable with a wide range of hosts makes it more interesting for research. (2) S. indica has numerous functions, ranging from promoting plant growth and quality to alleviating abiotic and biotic stresses, suggesting the use of this fungus as a biofertiliser. It also improves the soil quality by limiting the movement of heavy metals in the soil, thus, protecting the environment. (3) S. indica’s modes of action are due to interactions with phytohormones, metabolites, photosynthates, and gene regulation, in addition to enhancing nutrient and water absorption. (4) Combined application of S. indica and nanoparticles showed synergistic promotion in crop growth, but the beneficial effects of these interactions require further investigation. This review concluded that S. indica has a great potential to be used as a plant growth promoter or biofertiliser, ensuring sustainable crop production and a healthy environment. Full article

(This article belongs to the Special Issue Phytomicrobiome Research for Disease and Pathogen Management)

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