MicroMPN: methods and software for high-throughput screening of microbe suppression in mixed populations

Screening assays are used to test if one or more microbes suppress a pathogen of interest. In the presence of more than one microbe, the screening method must be able to accurately distinguish viable pathogen cells from non-viable and non-target microbes in a sample. Current screening methods are time-consuming and require special reagents to detect viability in mixed microbial communities. Screening assays performed using soil or other complex matrices present additional challenges for screening. Here, we develop an experimental workflow based on the most probable number (MPN) assay for testing the ability of synthetic microbial communities to suppress a soil-borne pathogen. Our approach, fluorMPN, uses a fluorescently labeled pathogen and microplate format to enable high-throughput comparative screening. In parallel, we developed a command-line tool, MicroMPN, which significantly reduces the complexity of calculating MPN values from microplates. We compared the performance of the fluorMPN assay with spotting on agar and found that both methods produced strongly correlated counts of equal precision. The suppressive effect of synthetic communities on the pathogen was equally recoverable by both methods. The application of this workflow for discriminating which communities lead to pathogen reduction helps narrow down candidates for additional characterization. Together, the resources offered here are meant to facilitate and simplify the application of MPN-based assays for comparative screening projects.IMPORTANCEWe created a unified set of software and laboratory protocols for screening microbe libraries to assess the suppression of a pathogen in a mixed microbial community. Existing methods of fluorescent labeling were combined with the most probable number (MPN) assay in a microplate format to enumerate the reduction of a pathogenic soil microbe from complex soil matrices. This work provides a fluorescent expression vector available from Addgene, step-by-step laboratory protocols hosted by protocols.io, and MicroMPN, a command-line software for processing plate reader outputs. MicroMPN simplifies MPN estimation from 96- and 384-well microplates. The microplate screening assay is amenable to robotic automation with standard liquid handling robots, further reducing the hands-on processing time. This tool was designed to evaluate synthetic microbial communities for use as microbial inoculates or probiotics. The fluorMPN method is also useful for screening chemical and antimicrobial libraries for pathogen suppression in complex bacterial communities like soil.

Microbiome-Mediated Protection against Pathogens in Woody Plants

Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.

Implementing wood ants in biocontrol: Suppression of apple scab and reduced aphid tending

BACKGROUND

Ants can become efficient biocontrol agents in plantation crops as they prey on pest insects and may inhibit plant pathogens by excreting broad-spectrum antibiotics. However, ants also provide a disservice by augmenting attended honeydew producing homopterans. This disservice may be avoided by offering ants artificial sugar as an alternative to honeydew. Here we tested the effect of artificial sugar feeding on aphid abundance in an apple plot with wood ants (Formica polyctena, Förster), and tested the effect of ant presence on apple scab (Venturia inaequalis, Cooke) disease incidence.

RESULTS

Over a 2-year period, sugar feeding eliminated ant-attended aphid populations on the apple trees. Furthermore, scab symptoms on both leaves and apples were reduced considerably on ant trees compared to control trees without ants. The presence of ants on the trees reduced leaf scab infections by 34%, whereas spot numbers on fruits were reduced by between 53 and 81%, depending on apple variety. In addition, the spots were 56% smaller.

CONCLUSION

This shows that problems with wood ant-attended homopterans can be solved and that ants can control both insect pests and plant pathogens. We therefore propose wood ants as a new effective biocontrol agent suitable for implementation in apple orchards and possibly other plantation crops. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Plant growth-promoting microorganisms as biocontrol agents of plant diseases: Mechanisms, challenges and future perspectives

Plant diseases and pests are risk factors that threaten global food security. Excessive chemical pesticide applications are commonly used to reduce the effects of plant diseases caused by bacterial and fungal pathogens. A major concern, as we strive toward more sustainable agriculture, is to increase crop yields for the increasing population. Microbial biological control agents (MBCAs) have proved their efficacy to be a green strategy to manage plant diseases, stimulate plant growth and performance, and increase yield. Besides their role in growth enhancement, plant growth-promoting rhizobacteria/fungi (PGPR/PGPF) could suppress plant diseases by producing inhibitory chemicals and inducing immune responses in plants against phytopathogens. As biofertilizers and biopesticides, PGPR and PGPF are considered as feasible, attractive economic approach for sustainable agriculture; thus, resulting in a "win-win" situation. Several PGPR and PGPF strains have been identified as effective BCAs under environmentally controlled conditions. In general, any MBCA must overcome certain challenges before it can be registered or widely utilized to control diseases/pests. Successful MBCAs offer a practical solution to improve greenhouse crop performance with reduced fertilizer inputs and chemical pesticide applications. This current review aims to fill the gap in the current knowledge of plant growth-promoting microorganisms (PGPM), provide attention about the scientific basis for policy development, and recommend further research related to the applications of PGPM used for commercial purposes.

Hyperlocal Variation in Soil Iron and the Rhizosphere Bacterial Community Determines Dollar Spot Development in Amenity Turfgrass

Dollar spot, caused by the fungal pathogen Clarireedia spp., is an economically important foliar disease of amenity turfgrass in temperate climates worldwide. This disease often occurs in a highly variable manner, even on a local scale with relatively uniform environmental conditions. The objective of this study was to investigate mechanisms behind this local variation, focusing on contributions of the soil and rhizosphere microbiome. Turfgrass, rhizosphere, and bulk soil samples were collected from within a 256-m2 area of healthy turfgrass, transported to a controlled environment chamber, and inoculated with Clarireedia jacksonii Bacterial communities were profiled by targeting the 16S rRNA gene, and 16 different soil chemical properties were assessed. Despite their initial uniform appearance, the samples differentiated into highly susceptible and moderately susceptible groups following inoculation in the controlled environment chamber. The highly susceptible samples harbored a unique rhizosphere microbiome with suggestively lower relative abundance of putative antibiotic-producing bacterial taxa and higher predicted abundance of genes associated with xenobiotic biodegradation pathways. In addition, stepwise regression revealed that bulk soil iron content was the only significant soil characteristic that positively regressed with decreased dollar spot susceptibility during the peak disease development stage. These findings suggest that localized variation in soil iron induces the plant to select for a particular rhizosphere microbiome that alters the disease outcome. More broadly, further research in this area may indicate how plot-scale variability in soil properties can drive variable plant disease development through alterations in the rhizosphere microbiome.IMPORTANCE Dollar spot is the most economically important disease of amenity turfgrass, and more fungicides are applied targeting dollar spot than any other turfgrass disease. Dollar spot symptoms are small (3 to 5 cm), circular patches that develop in a highly variable manner within plot scale even under seemingly uniform conditions. The mechanism behind this variable development is unknown. This study observed that differences in dollar spot development over a 256-m2 area were associated with differences in bulk soil iron concentration and correlated with a particular rhizosphere microbiome. These findings provide interesting avenues for future research to further characterize the mechanisms behind the highly variable development of dollar spot, which may inform innovative control strategies. Additionally, these results suggest that small changes in soil properties can alter plant activity and hence the plant-associated microbial community, which has important implications for a broad array of agricultural and horticultural plant pathosystems.

Vector dynamics influence spatially imperfect genetic interventions against disease

Background and objectives

Genetic engineering and similar technologies offer promising new approaches to controlling human diseases by blocking transmission from vectors. However, in spatially structured populations, imperfect coverage of the vector will leave pockets in which the parasite may persist. Movement by humans may disrupt this local persistence and facilitate eradication when these pockets are small, spreading parasite reproduction outside unprotected areas and into areas that block its reproduction. Here, we consider the sensitivity of this process to biological details: do simple generalities emerge that may facilitate interventions?

Methodology

We develop formal mathematical models of this process similar to standard Ross–Macdonald models, but (i) specifying spatial structure of two patches, with vector transmission blocked in one patch but not in the other, (ii) allowing temporary human movement (travel instead of migration) and (iii) considering two different modes of mosquito biting.

Results

We find that there is no invariant effect of disrupting spatial structure with travel. For both biting models, travel out of the unprotected patch has different consequences than travel by visitors into the patch, but the effects are reversed between the two biting models.

Conclusions and implications

Overall, the effect of human travel on the maintenance of vector-borne diseases in structured habitats must be considered in light of the actual biology of mosquito abundances, biting dynamics and human movement patterns.

Lay summary: Genetic interventions against pathogens transmitted by insect vectors are promising methods of controlling infectious diseases. These interventions may be imperfect, leaving pockets where the parasite persists. How will human movement between protected and unprotected areas affect persistence? Mathematical models developed here show that the answer is ecology-dependent, depending on vector biting behavior.

Bacterial community richness shifts the balance between volatile organic compound-mediated microbe-pathogen and microbe-plant interactions

Even though bacteria are important in determining plant growth and health via volatile organic compounds (VOCs), it is unclear how these beneficial effects emerge in multi-species microbiomes. Here we studied this using a model plant-bacteria system, where we manipulated bacterial community richness and composition and determined the subsequent effects on VOC production and VOC-mediated pathogen suppression and plant growth-promotion. We assembled VOC-producing bacterial communities in different richness levels ranging from one to 12 strains using three soil-dwelling bacterial genera (Bacillus, Paenibacillus and Pseudomonas) and investigated how the composition and richness of bacterial community affect the production and functioning of VOCs. We found that VOC production correlated positively with pathogen suppression and plant growth promotion and that all bacteria produced a diverse set of VOCs. However, while pathogen suppression was maximized at intermediate community richness levels when the relative amount and the number of VOCs were the highest, plant growth promotion was maximized at low richness levels and was only affected by the relative amount of plant growth-promoting VOCs. The contrasting effects of richness could be explained by differences in the amount and number of produced VOCs and by opposing effects of community productivity and evenness on pathogen suppression and plant-growth promotion along the richness gradient. Together, these results suggest that the number of interacting bacterial species and the structure of the rhizosphere microbiome drive the balance between VOC-mediated microbe-pathogen and microbe-plant interactions potentially affecting plant disease outcomes in natural and agricultural ecosystems.

Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils

Disease suppressive soils offer effective protection to plants against infection by soil-borne pathogens, including fungi, oomycetes, bacteria, and nematodes. The specific disease suppression that operates in these soils is, in most cases, microbial in origin. Therefore, suppressive soils are considered as a rich resource for the discovery of beneficial microorganisms with novel antimicrobial and other plant protective traits. To date, several microbial genera have been proposed as key players in disease suppressiveness of soils, but the complexity of the microbial interactions as well as the underlying mechanisms and microbial traits remain elusive for most disease suppressive soils. Recent developments in next generation sequencing and other 'omics' technologies have provided new insights into the microbial ecology of disease suppressive soils and the identification of microbial consortia and traits involved in disease suppressiveness. Here, we review the results of recent 'omics'-based studies on the microbial basis of disease suppressive soils, with specific emphasis on the role of rhizosphere bacteria in this intriguing microbiological phenomenon.