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      No rest for resting spores: Can predators mitigate clubroot disease?

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          Abstract

          The clubroot pathogen Plasmodiophora brassicae is a major and growing problem for the cultivation of Brassica crops. As conventional control disease management methods are ineffective or prohibited due to their ecological impact, and crop resistance is frequently broken, biological control of the pathogen has become a key focus for the development of sustainable agricultural systems. Here we provide a perspective review on the unexplored impact of soil microbiome predators, and their potential use as biocontrol agents, using clubroot disease as an example. We highlight several pathways by which microbiome predators can reduce clubroot in soils, including directly through predation and indirectly by inducing a clubroot‐suppressive microbiome. We further discuss how some microbiome predators might, in contrast, benefit clubroot disease spread through mechanisms such as phoresy toward hosts. We highlight that gaps in knowledge need to be filled that hinder wider application of microbiome predators against P. brassicae alone, and in combination with known biocontrol agents.

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          The global burden of pathogens and pests on major food crops

          Crop pathogens and pests reduce the yield and quality of agricultural production. They cause substantial economic losses and reduce food security at household, national and global levels. Quantitative, standardized information on crop losses is difficult to compile and compare across crops, agroecosystems and regions. Here, we report on an expert-based assessment of crop health, and provide numerical estimates of yield losses on an individual pathogen and pest basis for five major crops globally and in food security hotspots. Our results document losses associated with 137 pathogens and pests associated with wheat, rice, maize, potato and soybean worldwide. Our yield loss (range) estimates at a global level and per hotspot for wheat (21.5% (10.1-28.1%)), rice (30.0% (24.6-40.9%)), maize (22.5% (19.5-41.1%)), potato (17.2% (8.1-21.0%)) and soybean (21.4% (11.0-32.4%)) suggest that the highest losses are associated with food-deficit regions with fast-growing populations, and frequently with emerging or re-emerging pests and diseases. Our assessment highlights differences in impacts among crop pathogens and pests and among food security hotspots. This analysis contributes critical information to prioritize crop health management to improve the sustainability of agroecosystems in delivering services to societies.
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            Understanding and exploiting plant beneficial microbes.

            After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.
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              The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model

              Background Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm’s natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics. Results Nematodes sampled directly from their native habitats carry a species-rich bacterial community, dominated by Proteobacteria such as Enterobacteriaceae and members of the genera Pseudomonas, Stenotrophomonas, Ochrobactrum, and Sphingomonas. The C. elegans microbiome is distinct from that of the worm’s natural environment and the congeneric species C. remanei. Exposure to a derived experimental microbiome revealed that bacterial composition is influenced by host developmental stage and genotype. These experiments also showed that the microbes enhance host fitness under standard and also stressful conditions (e.g., high temperature and either low or high osmolarity). Taking advantage of the nematode’s transparency, we further demonstrate that several Proteobacteria are able to enter the C. elegans gut and that an Ochrobactrum isolate even seems to be able to persist in the intestines under stressful conditions. Moreover, three Pseudomonas isolates produce an anti-fungal effect in vitro which we show can contribute to the worm’s defense against fungal pathogens in vivo. Conclusion This first systematic analysis of the nematode’s native microbiome reveals a species-rich bacterial community to be associated with C. elegans, which is likely of central importance for our understanding of the worm’s biology. The information acquired and the microbial isolates now available for experimental work establishes C. elegans as a tractable model for the in-depth dissection of host-microbiome interactions. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0258-1) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Journal
                Journal of Sustainable Agriculture and Environment
                J of Sust Agri & Env
                Wiley
                2767-035X
                2767-035X
                June 2023
                April 26 2023
                June 2023
                : 2
                : 2
                : 131-139
                Affiliations
                [1 ] Teagasc, Department of Environment Soils and Landuse Wexford Ireland
                [2 ] Department of Plant Science, Laboratory of Nematology Wageningen University & Research Wageningen The Netherlands
                Article
                10.1002/sae2.12042
                dd6a08e4-a3b5-44d2-8ae2-78436286709d
                © 2023

                http://creativecommons.org/licenses/by/4.0/

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