Subalpine Grass Microbiomes, Fungi, and Climate Interactions

Local RMBL work added a key insight: fungal partners can shape where their host plants live. In subalpine meadows, the Epichloë endophyte of marsh bluegrass (Poa leptocoma) was shown to narrow the plant's germination niche toward wetter, streamside microsites, effectively differentiating it from its endophyte-free relative nodding bluegrass (Poa reflexa) (Kazenel et al., 2015). Complementary experiments confirmed that endophyte symbiosis improved host performance under flooded conditions (Adams et al., 2017), establishing that microscopic partners can have macroscopic consequences for plant distributions.

Key findings

A central lesson from Gunnison Basin research is that elevation is a poor stand-in for warming. After 23 years of experimental heating at RMBL, fungal colonization, diversity, and composition all responded to warming, but in ways that did not match patterns seen across natural elevation gradients (Kazenel et al., 2019). Leaf-dwelling fungi proved consistently more sensitive than root-dwelling fungi, a result echoed in a recent multi-site synthesis showing that warming reduced septate fungal colonization by roughly 90% in leaves but only 35% in roots (Edwards et al., 2025). Host plant identity often matters more than climate: across nine grass species sampled along replicated elevation gradients, plant species and plant size predicted foliar fungal communities far better than temperature did (Kivlin et al., 2019).

Warming also reshapes the broader plant–microbe–herbivore network. Over two decades of experimental warming, sedge frequency rose while grass frequency declined (Rudgers et al., 2014), and herbivore attack became 13% more likely and 29% more damaging in heated plots, especially following wetter weather (Lynn et al., 2023). Soil biota play a parallel role at range edges: when low-elevation soil microbes were transplanted upslope in greenhouse and field tests, alpine grasses actually grew 21–40% larger than in their resident soils, suggesting that novel microbes arriving with climate change may sometimes release plants from carbon-demanding partners (Lynn et al., 2019). Mammalian herbivores, by contrast, constrain plants: excluding gophers and ungulates increased alpine plant biomass and projected population growth most strongly at the low-elevation edges of species' ranges, identifying herbivory as a key driver of where alpine plants can persist (Lynn et al., 2021). Pocket gopher disturbance itself peaks at mid-elevation (~3,150 m) where temperatures, forb cover, and plant diversity are highest, suggesting that gopher-driven soil turnover may intensify as climate warms (Lynn et al., 2018).

Finally, foundational community-level work has shown that phylogenetic relatedness predicts herbivore damage in Rocky Mountain plant communities, with closely related neighbors sharing more enemies (Ness et al., 2011), and that dominance by particular grasses such as Festuca need not suppress subordinate diversity — abiotic variation in soil nitrogen and temperature often matters more (LaPlante & Souza, 2018).

Current frontier

Early work in the 1990s and 2000s established that fungal symbionts existed and varied across mountains; studies from 2010 to 2019 — the bulk of the publication record here — pinned down how host identity, elevation, and warming each shape these partnerships. Research since 2020 has shifted toward longer-term, multi-site, and mechanistic questions. The most recent results from the RMBL warming experiment show that after nearly three decades of heating, plant–fungal coupling itself is decoupling: shrubs have increased 150% while forbs and grasses each declined about 28%, AMF and septate root colonization fell 17–20%, and saprophytic (decomposer) fungi rose 10% — a shift toward a more conservative, woody-dominated ecosystem (Souza et al., 2026). Comparable multi-site work demonstrates that warming weakens the chemical conversation between fungi and their host plants, breaking down correlations between endophyte communities and plant metabolism (Edwards et al., 2025).

New methods are accelerating these insights. DNA metabarcoding now allows researchers to identify thousands of fungal taxa from a single leaf or root, while soil inoculum transplants and elevational fungal transplant experiments move partners across the landscape to test causation directly. Recent invasion ecology work is extending the framework to non-native plants, showing that yellow toadflax (Linaria vulgaris) leaves measurable soil legacy effects that may facilitate reinvasion in Colorado but not in Illinois (Novak et al., 2025). A broader conceptual push asks how to predict which organisms can keep up with anthropogenic change at all, identifying five barriers — from quantifying environmental change to mapping heritable trait variation — that mountain systems are well-positioned to address (Gabor et al., 2021).

Open questions

Several major puzzles remain. First, why do warming and elevation produce such different fungal responses, and which environmental cues — soil moisture, snowmelt timing, host phenology — actually drive symbiont composition? Second, when novel low-elevation microbes arrive at higher sites, will they help, hurt, or simply replace resident partners, and over what timescales? Third, how durable are the symbiotic disruptions documented under decades of warming — do plant–fungal networks reassemble, or does ecosystem function shift permanently toward a more conservative, woody state as Souza and colleagues suggest? Fourth, how do herbivores, pathogens, and fungal mutualists jointly set range limits, especially as upslope-moving mammals encounter alpine plants for the first time? Finally, the community needs trait- and genome-based frameworks that can predict which grass species and which fungal lineages have the capacity to track a rapidly changing Gunnison Basin — and which will be left behind.

References

Adams, A.E., Besozzi, E.M., Shahrokhi, G. (2017). Does a foliar endophyte improve plant fitness under flooding? Plant Ecology. →

Edwards, J., et al. (2025). Warming disrupts plant–fungal endophyte symbiosis more severely in leaves than roots. Global Change Biology. →

Gabor, C.R., et al. (2021). Understanding Organismal Capacity to Respond to Anthropogenic Change: Barriers and Solutions. Integrative and Comparative Biology. →

Kazenel, M.R., et al. (2015). A mutualistic endophyte alters the niche dimensions of its host plant. AoB Plants. →

Kazenel, M.R., Kivlin, S.N., Taylor, D.L., Lynn, J.S., Rudgers, J.A. (2019). Altitudinal gradients fail to predict fungal symbiont responses to warming. Ecology. →

Kivlin, S.N., Emery, S.M., Rudgers, J.A. (2013). Fungal symbionts alter plant responses to global change. American Journal of Botany. →

Kivlin, S.N., et al. (2017). Biogeography of plant-associated fungal symbionts in mountain ecosystems: A meta-analysis. Diversity and Distributions. →

Kivlin, S.N., et al. (2019). Plant Identity Influences Foliar Fungal Symbionts More Than Elevation in the Colorado Rocky Mountains. Microbial Ecology. →

LaPlante, E., Souza, L. (2018). Plant dominance in a subalpine montane meadow: biotic vs. abiotic controls of subordinate diversity within and across sites. PeerJ. →

Lynn, J.S., Canfield, S., Conover, R.R. (2019). Soil microbes that may accompany climate warming increase alpine plant production. Oecologia. →

Lynn, J.S., et al. (2018). Pocket gopher (Thomomys talpoides) soil disturbance peaks at mid-elevation and is associated with air temperature, forb cover, and plant diversity. Arctic, Antarctic, and Alpine Research. →

Lynn, J.S., et al. (2023). Herbivory damage but not plant disease under experimental warming is dependent on weather for three subalpine grass species. Journal of Animal Ecology. →

Lynn, J.S., Klanderud, K., Telford, R.J. (2021). Mammalian herbivores restrict the altitudinal range limits of alpine plants. Ecology Letters. →

Ness, J.H., Rollinson, E.J., Whitney, K.D. (2011). Phylogenetic distance can predict susceptibility to attack by natural enemies. Oikos. →

Novak, S., et al. (2025). Legacy effects and arbuscular mycorrhizal fungi of Linaria vulgaris invasion in Colorado and Illinois, USA. Invasive Plant Science and Management. →

Souza, L., et al. (2026). Experimental warming decouples plant-fungal symbiont interactions and leads to a more conservative ecosystem. PNAS. →

Mammalian herbivores restrict the altitudinal range limits of alpine plants

Data for 'Weak latitudinal gradients in insect herbivory for dominant rangeland grasses of North America'