Root pathogen diversity and composition varies with climate in undisturbed grasslands, but less so in anthropogenically disturbed grasslands

Disease resistance gene count increases with rainfall in Silphium integrifolium

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n = 99) and PacBio long-read (n = 10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant's source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.

Soil Fungal Pathogens in Pinus pinaster Mature Reforestation: Silvicultural Treatments Effects

Soil fungal communities play a key role in multiple functions and ecosystem services within forest ecosystems. Today, forest ecosystems are subject to multiple environmental and anthropogenic disturbances (e.g., fire or forest management) that mainly lead to changes in vegetation as well as in plant-soil interactions. Soil pathogens play an important role in controlling plant diversity, ecosystem functions, and human and animal health. In this work we analyzed the response of soil plant pathogenic fungi to forest management in a Pinus pinaster reforestation. We started from an experimental design, in which forest thinning and gap cutting treatments were applied at different intensities and sizes, respectively. The fungal communities of plant pathogens in spring were described, and the effect of the silvicultural treatments was evaluated 5 years after their application, as were the possible relationships between soil plant pathogenic fungal communities and other environmental factors. Only a strong low thinning treatment (35% basal area) was able to generate homogeneous changes in soil pathogenic diversity. In the gaps, only the central position showed significant changes in the soil plant pathogenic fungi community.

National-scale investigation reveals the dominant role of phyllosphere fungal pathogens in sorghum yield loss

Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity.

Contrasting roles of fungal and oomycete pathogens in mediating nitrogen addition and winter grazing effects on biomass

Both bottom-up and top-down processes modulate plant communities. Fungal and oomycete pathogens are most common in global grasslands, and due to differences in their physiology, function, host range, and life cycles, they may differentially affect plants (in both intensity and direction). However, how fungal and oomycete pathogens regulate bottom-up and top-down effects on plant community biomass remains unclear. To this end, we conducted a 3-year field experiment in an alpine meadow incorporating mammalian herbivore exclosure, fungicide/oomyceticide application, and nitrogen addition treatments. We arranged 12 blocks with half randomly assigned to be mammalian herbivore exclosures (fenced to exclude grazing sheep), and the other half were fenced most of the year but not in winter (winter grazing control). Six 2.5 × 2.5 m square plots were established in each block, with each of the six plots assigned as control, nitrogen addition, fungicide application, oomyceticide application, nitrogen addition + fungicide application, and nitrogen addition + oomyceticide application. We found that fungicide application significantly increased plant community biomass (mainly Poaceae species) under nitrogen addition and promoted the bottom-up effect of nitrogen addition on plant community biomass by altering the community-weighted mean of plant height (via species turnover). Meanwhile, oomyceticide application significantly increased plant community biomass (mainly Poaceae species) when mammalian herbivores were excluded and weakened the top-down effect of winter grazing on plant community biomass by driving intraspecific variation in plant height. Our results highlight that fungal and oomycete pathogens play important (but differing) roles in mediating the effects of nutrient availability and higher trophic levels on plant community biomass. Mechanistically, we demonstrated that plant pathogen-related modulation of plant community biomass is achieved by alterations to plant height. Overall, this study combines both community and disease ecology to reveal complex interactions among higher trophic levels and their potential impacts on terrestrial ecosystem functioning under human disturbance.

The interaction of climate, plant, and soil factors drives putative soil fungal pathogen diversity and community structure in dry grasslands

Soil pathogens play important roles in shaping soil microbial diversity and controlling ecosystem functions. Though climate and local environmental factors and their influences on fungal pathogen communities have been examined separately, few studies explore the relative contributions of these factors. This is particularly crucial in eco-fragile regions, which are more sensitive to environmental changes. Herein we investigated the diversity and community structure of putative soil fungal pathogens in cold and dry grasslands on the Tibetan Plateau, using high-throughput sequencing. The results showed that steppe soils had the highest diversity of all pathogens and plant pathogens; contrastingly, meadow soils had the highest animal pathogen diversity. Structural equation modelling revealed that climate, plant, and soil had similar levels of influence on putative soil fungal pathogen diversity, with total effects ranging from 52% to 59% (all p < 0.001), with precipitation exhibiting a stronger direct effect than plant and soil factors. Putative soil fungal pathogen community structure gradually changed with desert, steppe, and meadow, and was primarily controlled by the interactions of climate, plant, and soil factors rather than by distinct factors individually. This finding contrasts with most studies of soil bacterial and fungal community structure, which generally report dominant roles of individual environmental factors.

Dilution of specialist pathogens drives productivity benefits from diversity in plant mixtures

Productivity benefits from diversity can arise when compatible pathogen hosts are buffered by unrelated neighbors, diluting pathogen impacts. However, the generality of pathogen dilution has been controversial and rarely tested within biodiversity manipulations. Here, we test whether soil pathogen dilution generates diversity- productivity relationships using a field biodiversity-manipulation experiment, greenhouse assays, and feedback modeling. We find that the accumulation of specialist pathogens in monocultures decreases host plant yields and that pathogen dilution predicts plant productivity gains derived from diversity. Pathogen specialization predicts the strength of the negative feedback between plant species in greenhouse assays. These feedbacks significantly predict the overyielding measured in the field the following year. This relationship strengthens when accounting for the expected dilution of pathogens in mixtures. Using a feedback model, we corroborate that pathogen dilution drives overyielding. Combined empirical and theoretical evidence indicate that specialist pathogen dilution generates overyielding and suggests that the risk of losing productivity benefits from diversity may be highest where environmental change decouples plant-microbe interactions.

Oomycete Soil Diversity Associated with Betula and Alnus in Forests and Urban Settings in the Nordic-Baltic Region

This study aimed to determine the differences and drivers of oomycete diversity and community composition in alder- and birch-dominated park and natural forest soils of the Fennoscandian and Baltic countries of Estonia, Finland, Lithuania, Norway, and Sweden. For this, we sequenced libraries of PCR products generated from the DNA of 111 soil samples collected across a climate gradient using oomycete-specific primers on a PacBio high-throughput sequencing platform. We found that oomycete communities are most affected by temperature seasonality, annual mean temperature, and mean temperature of the warmest quarter. Differences in composition were partly explained by the higher diversity of Saprolegniales in Sweden and Norway, as both total oomycete and Saprolegniales richness decreased significantly at higher longitudes, potentially indicating the preference of this group of oomycetes for a more temperate maritime climate. None of the evaluated climatic variables significantly affected the richness of Pythiales or Peronosporales. Interestingly, the relative abundance and richness of Pythiales was higher at urban sites compared to forest sites, whereas the opposite was true for Saprolegniales. Additionally, this is the first report of Phytophthora gallica and P. plurivora in Estonia. Our results indicate that the composition of oomycetes in soils is strongly influenced by climatic factors, and, therefore, changes in climate conditions associated with global warming may have the potential to significantly alter the distribution range of these microbes, which comprise many important pathogens of plants.

The influence of precipitation timing and amount on soil microbial community in a temperate desert ecosystem

Introduction

Global climate change may lead to changes in precipitation patterns. This may have a significant impact on the microbial communities present in the soil. However, the way these communities respond to seasonal variations in precipitation, particularly in the context of increased precipitation amounts, is not yet well understood.

Methods

To explore this issue, a five-year (2012-2016) field study was conducted at the northeast boundary of the Ulan Buh Desert, examining the effects of increased precipitation during different periods of the growing season on both bacterial and fungal communities. The study included five precipitation pattern treatments: a control group (C), as well as groups receiving 50 and 100% of the local mean annual precipitation amount (145 mm) during either the early growing season (E50 and E100) or the late growing season (L50 and L100). The taxonomic composition of the soil bacterial and fungal communities was analyzed using Illumina sequencing.

Results

After 5 years, the bacterial community composition had significantly changed in all treatment groups, with soil bacteria proving to be more sensitive to changes in precipitation timing than to increased precipitation amounts within the desert ecosystem. Specifically, the alpha diversity of bacterial communities in the late growing season plots (L50 and L100) decreased significantly, while no significant changes were observed in the early growing season plots (E50 and E100). In contrast, fungal community composition remained relatively stable in response to changes in precipitation patterns. Predictions of bacterial community function suggested that the potential functional taxa in the bacterial community associated with the cycling of carbon and nitrogen were significantly altered in the late growing season (L50 and L100).

Discussion

These findings emphasize the importance of precipitation timing in regulating microbial communities and ecosystem functions in arid regions experiencing increased precipitation amounts.

Predatory protists play predominant roles in suppressing soil-borne fungal pathogens under organic fertilization regimes

Soil-borne fungal pathogens pose a major threat to global agricultural production and food security. Pathogen-suppressive bacteria and plant beneficial protists are important components of soil microbiomes and essential to plant health and performance, but it remains largely unknown regarding how agricultural management practices influence the relative importance of protists and bacteria in plant disease suppression. Here, we characterized soil microbiomes (including fungi, protists, and bacteria) in bulk and sorghum rhizosphere soils with various long-term inorganic and organic fertilization regimes, and linked the changes in fungal plant pathogens with the protistan and bacterial communities. We found that the relative abundances of fungal pathogens were significantly decreased by organic fertilization regimes, and there was a significant difference in the community composition of fungal pathogens between inorganic and organic fertilization regimes. Organic fertilization significantly enhanced predatory protists but reduced the proportions of protistan phototrophs. Co-occurrence network analysis revealed more intensive connections between fungal plant pathogens with protists, especially predatory protists, than with bacterial taxa, which was further supported by stronger associations between the community structure of fungal pathogens and predatory protists. We identified more protist consumer taxa than bacterial taxa as predictors of fungal plant pathogens, and structural equation modelling revealed a more important impact of protist consumers than bacteria on fungal pathogens. Altogether, we provide new evidence that the disease inhibitory effects of long-term organic fertilization regimes could be best explained by the potential predation pressure of protists. Our findings advance the mechanistic understanding of the role of predator-prey interactions in controlling fungal diseases, and have implications for novel biocontrol strategies to mitigate the consequences of fungal infections for plant performance.

Climate change and plant pathogens

Global food security is threatened by climate change, both directly through responses of crop physiology and productivity, and indirectly through responses of plant-associated microbiota, including plant pathogens. While the interactions between host plants, pathogens and environmental drivers can be complex, recent research is beginning to indicate certain overall patterns in how plant diseases will affect crop production in future. Here, we review the results of three methodological approaches: large-scale observational studies, process-based disease models and experimental comparisons of pathosystems under current and future conditions. We find that observational studies have tended to identify rising temperatures as the primary driver of disease impact. Process-based models suggest that rising temperatures will lead to latitudinal shifts in disease pressure, but drying conditions could mitigate disease risk. Experimental studies suggest that rising atmospheric CO₂ will exacerbate disease impacts. Plant diseases may therefore counteract any crop yield increases due to climate change.

Rare Taxa Drive the Response of Soil Fungal Guilds to Soil Salinization in the Taklamakan Desert

Salinization poses great threats to soil fungal communities that would cause the losses of ecosystems services. Soil fungal communities are composed of different functional guilds such as saprotrophic, symbiotrophic, and pathotrophic fungi, and each guild includes many rare taxa and a few abundant taxa. Despite of low abundance, rare taxa may be crucial in determining the responses of entire soil fungal communities to salinization. However, it remains poorly understood how rare taxa mediate the impacts of soil salinization on soil fungal community structure. Here, we took advantage of a salinity gradient in a desert ecosystem ranging from 0.60 to 31.09 g kg^-1 that was created by a 12-year saline-water irrigation and assessed how the rare vs. abundant taxa of soil saprotrophic, symbiotrophic, and pathotrophic fungi respond to soil salinization through changes in the community biodiversity and composition. We found that the rare taxa of soil saprotrophic, symbiotrophic, and pathographic fungi were more sensitive to changes in soil salinity compared to the abundant taxa. In addition, the community composition of rare taxa of the saprotrophic and pathotrophic fungi not the symbiotrophic fungi was positively associated with soil salinity change. However, the symbiotrophic fungi showed greater variations in the species richness along the salinity gradient. These findings highlight the importance to differentiate rare taxa in predicting how the biodiversity and functional groups of soil fungal communities respond to soil salinization.

The Proportion of Soil-Borne Fungal Pathogens Increases with Elevated Organic Carbon in Agricultural Soils

Soil-borne fungal phytopathogens are important threats to soil and crop health. However, their community composition and environmental determinants remain unclear. Here, we explored the effects of agricultural fertilization regime (i.e., organic material application) on soil fungal phytopathogens, using data sets from a combination of field survey and long-term experiment. We found that soil organic carbon was the key factor that affected the diversity and relative abundance of fungal phytopathogens in agricultural soils. The dominant genera of phytopathogens including Monographella was also strongly associated with soil organic carbon. In addition, the elevated soil organic carbon enhanced the node proportion of phytopathogens and the positive interactions within the fungal community in the network. Results of the long-term experiment revealed that applications of crop straw and fresh livestock manure significantly increased the proportion of phytopathogens, which were associated with the elevated soil organic carbon. This work offers new insights into the occurrence and environmental factors of fungal phytopathogens in agricultural soils, which are fundamental to control their impacts on the soil and crop systems. IMPORTANCE Fungal phytopathogens are important threats to soil and crop health, but their community composition and environmental determinants remain unclear. We found that soil organic carbon is the key factor of the prevalence of fungal phytopathogens through a field survey, which is also supported by our long-term (6-year) experiment showing the applications of crop straw and fresh livestock manure significantly increased the proportion of fungal phytopathogens. These findings advance our understanding of the occurrence and environmental drivers of soil-borne fungal phytopathogens under agricultural fertilization regime and have important implications for the control of soil-borne pathogens.

Chasing Ghosts: Race, Racism, and the Future of Microbiome Research

In this article, we argue that a careful examination of human microbiome science's relationship with race and racism is necessary to foster equitable social and ecological relations in the field. We point to the origins and evolution of the problematic use of race in microbiome literature by demonstrating the increased usage of race both explicitly and implicitly in and beyond the human microbiome sciences. We demonstrate how these uses limit the future of rigorous and just microbiome research. We conclude with an outline of alternative actionable ways to build a more effective, antiracist microbiome science.

Precipitation increases the abundance of fungal plant pathogens in Eucalyptus phyllosphere

Understanding the current and future distributions of plant pathogens is critical to predict the plant performance and related economic benefits in the changing environment. Yet, little is known about the roles of environmental drivers in shaping the profiles of fungal plant pathogens in phyllosphere, an important habitat of microbiomes on Earth. Here, using a large-scale investigation of Eucalyptus phyllospheric microbiomes in Australia and the multiple linear regression model, we show that precipitation is the most important predictor of fungal taxonomic diversity and abundance. The abundance of fungal plant pathogens in phyllosphere exhibited a positive linear relationship with precipitation. With this empirical dataset, we constructed current and future atlases of phyllosphere plant pathogens to estimate their spatial distributions under different climate change scenarios. Our atlases indicate that the abundance of fungal plant pathogens would increase especially in the coastal regions with up to 100-fold increase compared with the current abundance. These findings advance our understanding of the distributions of fungal plant pathogens in phyllospheric microbiomes under the climate change, which can improve our ability to predict and mitigate their impacts on plant productivity and economic losses.