The swift rise of omics-approaches allows for investigating microbial diversity and plant-microbe interactions across diverse ecological communities and spatio-temporal scales. The environment, ...however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating -omic approaches into their plant disease research. We review -omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multi-omics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.
Soil disinfection using high temperatures
steam is a promising approach to manage plant pathogens, pests, and weeds. Soil steaming is a viable option for growers who are moving away from dependence ...on chemical soil fumigants, especially in plant nursery or high tunnel environments. However, there are few studies that investigate how soil steaming causes substantial disturbance to the soil by killing both target pathogens and other soil biota. Steaming treatments also change the trajectory of the soil microbiome as it reassembles over time. Growers are interested in the health of soils after using steam-disinfection, especially if a virulent pathogen colonizes the soil and then flourishes in a situation where there are very few microbes to suppress its growth. Should recruitment of a virulent pathogen occur in the soil, this could have devasting effects on seed germination, seedling establishment and survival. Beneficial microbes are often used to prevent the colonization of plant pathogens, especially after a soil-steaming event. Here, we experimentally test how soil fungal communities assemble after steaming disinfection. We introduce to steam-treated soil
, an important fungal pathogen of soybean and
, a known beneficial fungus used for soilborne pathogen suppression. Results show that
significantly affects the relative abundance and diversity of the soil fungal microbiome, however,
does not mitigate the amount of
in the steam treated soil. Within the
microbial addition, the soil fungal communities were similar to the control (steaming only). This result suggests inoculating the soil with
does not drastically alter the assembly trajectory of the soil fungal microbiome. Other soil amendments such as a combination of
spp. or other genera could suppress
growth and shift soil microbiome composition and function post-steaming, however, more experimental research is needed.
Abstract
Pathogenic fungi are a leading cause of crop disease and primarily spread through microscopic, durable spores adapted differentially for both persistence and dispersal via soil, animals, ...water, and/or the atmosphere. Computational Earth system models and air pollution models have been used to simulate atmospheric spore transport for aerial-dispersal-adapted (airborne) rust diseases, but the importance of atmospheric spore transport for soil-dispersal-adapted (soilborne) diseases remains unknown. While a few existing simulation studies have focused on
intra
continental dispersion, transoceanic and
inter
continental atmospheric transport of soilborne spores entrained in agricultural dust aerosols is understudied and may contribute to disease spread. This study adapts the Community Atmosphere Model, the atmospheric component of the Community Earth System Model, to simulate the global transport of the plant pathogenic soilborne fungus
Fusarium oxysporum
(
F. oxy
). Our sensitivity study assesses the model’s accuracy in long-distance aerosol transport and the impact of deposition rate on simulated long-distance spore transport in Summer 2020 during a major dust transport event from Northern Sub-Saharan Africa to the Caribbean and southeastern United States (U.S.). We find that decreasing wet and dry deposition rates by an order of magnitude improves representation of long-distance, trans-Atlantic dust transport. Simulations also suggest that a small number of spores can survive trans-Atlantic transport to be deposited in agricultural zones. This number is dependent on source spore parameterization, which we improved through a literature search to yield a global map of
F. oxy
spore distribution in source agricultural soils. Using this map and aerosol transport modeling, we show how potentially viable spore numbers in the atmosphere decrease with distance traveled and offer a novel danger index for modeled viable spore deposition in agricultural zones. Our work finds that intercontinental transport of viable spores to cropland is greatest between Eurasia, North Africa, and Sub-Saharan Africa, suggesting that future observational studies should concentrate on these regions.
Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost ...destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States' economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection.
The ability to detect and quantify aerially dispersed plant pathogens is essential for developing effective disease control measures and epidemiological models that optimize the timing for control. ...There is an acute need for managing the downy mildew pathogens infecting cucurbits and hop incited by members of the genus
(
clade 1 and 2 isolates and
, respectively). A highly specific multiplex TaqMan quantitative polymerase chain reaction (PCR) assay targeting unique sequences in the pathogens' mitochondrial genomes was developed that enables detection of all three taxa in a single multiplexed amplification. An internal control included in the reaction evaluated whether results were influenced by PCR inhibitors that can make it through the DNA extraction process. Reliable quantification of inoculum as low as three sporangia in a sample was observed. The multiplexed assay was tested with DNA extracted from purified sporangia, infected plant tissue, and environmental samples collected on impaction spore traps samplers. The ability to accurately detect and simultaneously quantify all three pathogens in a single multiplexed amplification should improve management options for controlling the diseases they cause.
The frequency and intensity of extreme heat in the environment have increased in the last decade. Extreme heating events (EHE) have wide-ranging impacts on biological systems from the molecular to ...the community level. However, the impacts of EHE have been poorly studied in pathogen–host systems. Here, we explore how EHE affects the interaction among the insect hosts,
Osmia cornifrons
and
Osmia lignaria
, and a protozoan pathogen,
Crithidia mellificae
. We compared changes in the upper limit for locomotion of hosts (Ct
max
), thermal boldness (voluntary exposure to Extreme Temperature Zones – ETZ) between healthy and infected host exposed to EHE, and the effect of host Ct
max
on pathogen growth rate. Our results showed that 1-day EHE significantly reduced the upper limit for locomotion of hosts by an average of 4 °C in healthy and 7 °C in infected hosts. Further, EHE significantly reduced the protozoan pathogen growth rate. EHE also reduced the hosts’ voluntary exposure to (or transit across) extreme (hot or cold) temperature zones (ETZ). Our results show that EHE reduces both hosts’ heat tolerance and pathogen fitness, and shed light on the implications of EHE on host–pathogen dynamics under warmer world.
The abundance of airborne fungal spores in agricultural and urban settings increases with greater air temperature, relative humidity, or precipitation. The same meteorological factors that affect ...temporal patterns in spore abundance in managed environments also vary spatially across natural habitats in association with differences in vegetation structure. Here we investigated how temporal and spatial variation in aerial spore abundance is affected by abiotic (weather) and biotic (vegetation) factors as a foundation for predicting how fungi may respond to changes in weather and land-use patterns. We measured the phenology of airborne fungal spores across a mosaic of naturally occurring vegetation types at different time scales to describe (1) how spore abundance changes over time, (2) which local meteorological variables are good predictors for airborne spore density, and (3) whether spore abundance differs across vegetation types. Using an air volumetric vacuum sampler, we collected spore samples at 3-h intervals over a 120-h period in a mixed-evergreen forest and coastal prairie to measure diurnal, nocturnal, and total airborne spore abundance across vegetation types. Spore samples were also collected at weekly and monthly intervals in mixed-evergreen forest, redwood forest, and maritime chaparral vegetation types from 12 field sites across two years. We found greater airborne spore densities during the wetter winter months compared to the drier summer months. Mean total spore abundance in the mixed-evergreen forest was twice than in the coastal prairie, but there were no significant differences in total airborne spore abundance among mixed-evergreen forest, redwood forest, and maritime chaparral vegetation types. Weekly and monthly peaks in airborne spore abundance corresponded with rain events and peaks in soil moisture. Overall, temporal patterns in meteorological factors were much more important in determining airborne fungal spore abundance than the vegetation type. This suggests that overall patterns of fungal spore dynamics may be predictable across heterogeneous landscapes based on local weather patterns.
•Fungal spore abundance peaked during the wet season over natural vegetation.•Air temperature and relative humidity strongly correspond with spore density.•Meteorology versus vegetation drives spore density across spatio-temporal scales.
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