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1. Biogeography of root‐associated fungi in foundation grasses of North American plains

   https://doi.org/10.1111/jbi.14260  

   Rudgers, Jennifer A. ; Fox, Sam ; Porras‐Alfaro, Andrea ; Herrera, Jose ; Reazin, Chris ; Kent, Dylan R. ; Souza, Lara ; Chung, YanYi Anny ; Jumpponen, Ari ( November 2021 , Journal of Biogeography)

   Roots and rhizospheres host diverse microbial communities that can influence the fitness, phenotypes, and environmental tolerances of plants. Documenting the biogeography of these microbiomes can detect the potential for a changing environment to disrupt host‐microbe interactions, particularly in cases where microbes buffer hosts against abiotic stressors. We evaluated whether root‐associated fungi had poleward declines in diversity, tested whether fungal communities in roots shifted near host plant range edges, and determined the relative importance of environmental and host predictors of root fungal community structure.

   North American plains grasslands.

   Foundation grasses –Andropogon gerardii, Bouteloua dactyloides, B. eriopoda, B. gracilis,andSchizachyrium scopariumand root fungi.

   At each of 24 sites representing three replicate 17°–latitudinal gradients, we collected roots from 12 individuals per species along five transects spaced 10 m apart (40 m × 40 m grid). We used next‐generation sequencing of ITS2, direct fungal culturing from roots, and microscopy to survey fungi associated with grass roots.

   Root‐associated fungi did not follow the poleward declines in diversity documented for many animals and plants. Instead, host plant identity had the largest influence on fungal community structure. Edaphic factors outranked climate or host plant traits as correlates of fungal community structure; however, the relative importance of environmental predictors differed among plant species. As sampling approached host species range edges, fungal composition converged in similarity among individual plants of each grass species.

   Environmental predictors of root‐associated fungi depended strongly on host plant species identity. Biogeographic patterns in fungal composition suggested a homogenizing influence of stressors at host plant range limits. Results predict that communities of non‐mycorrhizal, root‐associated fungi in the North American plains will be more sensitive to future changes in host plant ranges and edaphic factors than to the direct effects of climate.

    

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2. Root-associated fungal communities exposed to experimental drought

   https://doi.org/10.6073/pasta/f530f48c02d152590057d20febe47e31  

   Lagueux, Devon E ( January 2020 , Environmental Data Initiative)

   Plant-associated fungi can ameliorate abiotic stress in their hosts, and changes in these fungal communities can alter plant productivity, species interactions, community structure and ecosystem processes. We investigated the response of root-associated fungi to experimental drought (66% reduction in growing season precipitation) across six North American grassland ecosystem types to determine how extreme drought alters root-associated fungi, and understand what abiotic factors influence root fungal community composition across grassland ecosystems. Next generation sequencing of the fungal ITS2 region demonstrated that drought primarily re-ordered fungal species’ relative abundances within host plant species, with different fungal responses depending on host identity. Grass species that declined more under drought trended toward less community re-ordering of root fungi than species less sensitive to drought. Host identity and grassland ecosystem type defined the magnitude of drought effects on community composition, diversity, and root colonization, and the most important factor affecting fungal composition was plant species identity. 

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3. Grass species identity shapes communities of root and leaf fungi more than elevation

   https://doi.org/10.1038/s43705-022-00107-6  

   Kivlin, Stephanie N. ; Mann, Michael A. ; Lynn, Joshua S. ; Kazenel, Melanie R. ; Taylor, D. Lee ; Rudgers, Jennifer A. ( March 2022 , ISME Communications)

   Fungal symbionts can buffer plants from environmental extremes and may affect host capacities to acclimate, adapt, or redistribute under environmental change; however, the distributions of fungal symbionts along abiotic gradients are poorly described. Fungal mutualists should be the most beneficial in abiotically stressful environments, and the structure of networks of plant-fungal interactions likely shift along gradients, even when fungal community composition does not track environmental stress. We sampled 634 unique combinations of fungal endophytes and mycorrhizal fungi, grass species identities, and sampling locations from 66 sites across six replicate altitudinal gradients in the western Colorado Rocky Mountains. The diversity and composition of leaf endophytic, root endophytic, and arbuscular mycorrhizal (AM) fungal guilds and the overall abundance of fungal functional groups (pathogens, saprotrophs, mutualists) tracked grass host identity more closely than elevation. Network structures of root endophytes become more nested and less specialized at higher elevations, but network structures of other fungal guilds did not vary with elevation. Overall, grass species identity had overriding influence on the diversity and composition of above- and belowground fungal endophytes and AM fungi, despite large environmental variation. Therefore, in our system climate change may rarely directly affect fungal symbionts. Instead, fungal symbiont distributions will most likely track the range dynamics of host grasses.

    

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4. Regional biogeography versus intra-annual dynamics of the root and soil microbiome

   https://doi.org/10.1186/s40793-023-00504-x  

   Bell-Dereske, Lukas P. ; Benucci, Gian Maria Niccolò ; da Costa, Pedro Beschoren ; Bonito, Gregory ; Friesen, Maren L. ; Tiemann, Lisa K. ; Evans, Sarah E. ( June 2023 , Environmental Microbiome)

   Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil).

   To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community.

   Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.

    

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5. Plant Identity Influences Foliar Fungal Symbionts More Than Elevation in the Colorado Rocky Mountains

   https://doi.org/10.1007/s00248-019-01336-4  

   Kivlin, Stephanie N. ; Kazenel, Melanie R. ; Lynn, Joshua S. ; Lee Taylor, D. ; Rudgers, Jennifer A. ( February 2019 , Microbial Ecology)

   Despite colonizing nearly every plant on Earth, foliar fungal symbionts have received little attention in studies on the biogeography of host-associated microbes. Evidence from regional scale studies suggests that foliar fungal symbiont distributions are influenced both by plant hosts and environmental variation in climate and soil resources. However, previous surveys have focused on either one plant host across an environmental gradient or one gradient and multiple plant hosts, making it difficult to disentangle the influence of host identity from the influence of the environment on foliar endophyte communities. We used a culture-based approach to survey fungal symbiont composition in the leaves of nine C3 grass species along replicated elevation gradients in grasslands of the Colorado Rocky Mountains. In these ecosystems, the taxonomic richness and composition of foliar fungal symbionts were mostly structured by the taxonomic identity of the plant host rather than by variation in climate. Plant traits related to size (height and leaf length) were the best predictors of foliar fungal symbiont composition and diversity, and composition did not vary predictably with plant evolutionary history. The largest plants had the most diverse and distinctive fungal communities. These results suggest that across the ~ 300 m elevation range that we sampled, foliar fungal symbionts may indirectly experience climate change by tracking the shifting distributions of plant hosts rather than tracking climate directly. 

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