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SummaryPlants and mycorrhizal fungi form close mutualistic relationships that affect how resources flow between organisms and within ecosystems. Common mycorrhizal networks (CMNs) could facilitate preferential transfer of carbon and limiting nutrients but this preference remains difficult to predict. Do common mycorrhizal networks favor fungal growth at the expense of plant resource demands (a fungi-centric view), or are they passive channels through which plants regulate resource fluxes (a plant-centric view)? We used stable isotope tracers (13C and15N), plant traits, and fungal DNA, to quantify above- and belowground allocation and transfer of carbon and nitrogen between 18 plant species in restored prairie and introduced pasture systems in the Pacific Northwest, USA. We found that related plant species and connectivity with fungal communities did not predict resource flow. Instead, plant functional type and tissue stoichiometry were the most important predictors of interspecific resource transfer. Labeled “donor” plants assimilated isotopic tracers at similar rates; however, nitrogen was preferentially transferred to annual and forb “receiver” plants compared to perennial and grass receiver plants. This corresponded tissue stoichiometry differences. Our findings point to a simple mechanistic answer for long-standing questions regarding mutualism and transfer of resources between plants via mycorrhizal networks.

Arbuscular mycorrhizal (AM) symbioses between plants and fungi are essential to the functioning of terrestrial ecosystems through maintaining soil stability, controlling nutrient cycles (e.g. C, N, P and K), and influencing competitive dynamics in plant communities. Despite the importance of AM symbioses, the ecological coassembly patterns of AM fungi-plant partners are not well characterized across environmental gradients. Further, it is unclear whether fungi forming associations with several plants of the same or different species – forming common mycorrhizal networks (CMNs) – preferentially allocate limiting resources within natural plant communities at the local-scale. We used an experimental prairie-pasture grassland system in three sites along a latitudinal gradient ranging from cool/wet to warm/dry climates to investigate how environmental conditions, local plant diversity and drought shift AM fungal composition and plant-fungal coassembly patterns across spatial scales. We show that plant-AM fungal assembly patterns are hierarchically structured, with environmental variables driving differences in AM fungal communities at the largest spatial scale (across sites), and plant host identity and diversity governing AM assembly at the local scale (within plot). Bipartite interaction networks revealed evidence for preferential partner selection between plants and fungi, while there was no evidence for nested assembly of plant-fungal partners. At the plot-level, we applied stable isotopes (13C and15N) to illustrate CMN assembly and nutritional function. There was no significant correlation between increased resource transfer among plants in a plot that shared more AM fungal partners; however, we identified specific AM fungi that were indicator taxa for increased plant isotope enrichment. Further research integrating stable isotope probing of fungal DNA in plant roots is necessary to more clearly illustrate the form and function of CMNs in grasslands under different environmental and plant diversity conditions.

The projected increase in warming and drought severity (i.e., hotter and drier summers) in the U.S. Pacific Northwest (PNW) may negatively impact grassland plant composition and ecosystem function, with further implications for sustainable land management in the region. To test the vulnerability of Mediterranean grassland function to climate change, we quantified the response of grassland communities to multiannual warming (+2.5°C) and drought (−40% precipitation) by quantifying plant species diversity, legume cover, and biogeochemical controls on and patterns of soil asymbiotic nitrogen fixation (ANF). We hypothesized that the effects of warming on plant functional diversity would increase soil ANF inputs by decreasing legume cover and soil nitrogen availability. Given that asymbiotic N fixers can increase soil organic carbon (C) and nitrogen (N) availability under drought, we hypothesized that the effect of drought on grassland plant cover correlated with increased soil ANF. We surveyed the vegetation and collected composite soil samples from five co-located plots under control (ambient), drought and warming conditions during the fall and spring seasons. In control and drought plots, we quantified the moderator effect of plant composition by comparing low-diversity (unmanipulated plant composition) and high-diversity (manipulated composition) grassland plots. We used a point intercept technique to survey plot-level plant community composition and calculate Shannon’s diversity index and percent cover of legumes (members of Fabaceae according to the Integrated Taxonomic Information System). We measured ANF by incubating collected soils with N-labeled dinitrogen (15N2), and quantified total soil C, total and available N, available phosphorus (P) and iron (Fe) pools, pH, and soil water holding capacity. Plant species diversity decreased significantly with warming and along the drought severity gradient. ANF response to warming varied by season and site, with rates increasing along the drought severity gradient in the fall but decreasing in the spring. Total soil inorganic N was the strongest predictor of ANF response to warming in the spring but not in the fall. Soil ANF response to drought increased with drought intensity; while soil ANF increased nearly twofold in the southernmost (warm and dry) site, ANF decreased in the northernmost (cool and wet) site. ANF response to drought also varied depending on plant diversity, where low-diversity grasslands had more predictable response to drought than high-diversity grasslands. Soil P availability and pH were the most important variables explaining ANF variability across vegetation types and sites. Our study highlights the importance of using soil-plant-atmosphere interactions to assess grassland ecosystem resilience to drought and warming in the PNW.

Demographic studies measure drivers of plant fecundity including seed production and survival, but few address both abiotic and biotic drivers of germination such as variation in climate among sites, population density, maternal plants, seed type and fungal pathogen abundance. We examined germination and microbial communities of seeds of Danthonia californica, which are either chasmogamous (external, wind-pollinated) or cleistogamous (internal, self-fertilized) and Festuca roemeri, which are solely chasmogamous. Seed populations were sourced across environmental gradients. We tested germination and used high-throughput sequencing to characterize seed fungal community structure. For F. roemeri, maternal plants significantly influenced germination as did climate and pathogens; germination increased from wetter, cooler sites. For D. californica, the main drivers of germination were maternal plant, seed type and pathogens; on average, more chasmogamous seeds germinated. Fungal communities depended largely on seed type, with fewer fungi associated with cleistogamous seeds, but the communities also depended on site factors such as vapor pressure deficit, plant density and whether the seeds had germinated. Putative pathogens that were negatively correlated with germination were more abundant for both D. californica and F. roemeri chasmogamous seeds than D. californica cleistogamous seeds. In D. californica, cleistogamous and chasmogamous seeds contain vastly different fungal communities.

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6±9482.3μg CH4 m-2 d-1), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8±120.5μg CH4 m-2 d-1), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2±35.7μg CH4 m-2 d-1), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.

Soil microbes are essential to the continued productivity of sustainably-managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability, and coffee productivity have been demonstrated, but the effect of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, we surveyed the soil fungal and bacterial communities, as well as soil chemistry and canopy composition in a Nicaraguan coffee cooperative, across 19 individual farms. Using amplicon sequencing, we found that management (organic or conventional), stand age, and previous land use strongly affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, our results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e., an agricultural plot’s previous land use) and short-term press disturbance (i.e., farm age).One-sentence-summaryThe composition of soil fungal and bacteria communities in shade coffee plantations depend on the combination of the farm’s management type, its previous land use, and the coffee plants’ stand age, but are differently influenced by each.

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with changes to ecosystem processes, including substantial increases in soil methane (CH4) emission. The drivers of this change in CH4flux are not well understood. To address this knowledge gap, we measured soil CH4flux, environmental conditions, and belowground microbial community attributes across a land use change gradient (old growth primary forest, cattle pasture, and secondary forest regrowth) in two Amazon Basin regions. Primary forest soils exhibited CH4uptake at modest rates, while pasture soils exhibited CH4emission at high but variable rates. Secondary forest soils exhibited low rates of CH4uptake, suggesting that forest regrowth following pasture abandonment could reverse the CH4sink-to-source trend. While few environmental variables were significantly associated with CH4flux, we identified numerous microbial community attributes in the surface soil that explained substantial variation in CH4flux with land use change. Among the strongest predictors were the relative abundance and diversity of methanogens, which both increased in pasture relative to forests. We further identified individual taxa that were associated with CH4fluxes and which collectively explained ~50% of flux variance. These taxa included methanogens and methanotrophs, as well as taxa that may indirectly influence CH4flux through acetate production, iron reduction, and nitrogen transformations. Each land type had a unique subset of taxa associated with CH4fluxes, suggesting that land use change alters CH4cycling through shifts in microbial community composition. Taken together, our results suggest that changes in CH4flux from agricultural conversion could be driven by microbial responses to land use change in the surface soil, with both direct and indirect effects on CH4cycling. This demonstrates the central role of microorganisms in mediating ecosystem responses to land use change in the Amazon Basin.

Bioswales and other forms of green infrastructure can be effective means to reduce environmental stresses in urban ecosystems; however, few studies have evaluated the ecology of these systems, or the role that plant selection and microbial assembly play in their function. For the current study, we examined the relationship between plant transpiration rates for five commonly planted herbaceous species in three bioswales in New York City, as well as bioswale soil microbial composition and soil chemistry. Soils were sampled near individual plants, with distinction made between upper (bioswale inlet) and lower slopes (bioswale outlet). We found high variation in transpiration rates across species, and that Nepeta × faassenii was the highest conductor (13.65 mmol H2O m–2s–1), while Panicum virgatum was the lowest conductor (2.67 mmol H2O m–2s–1) (p < 0.001). There was significant variation in percent N of leaves and soil, which did not relate to the higher water conductance in bioswales. Significantly higher C, N, and water content on the high end of bioswale slopes suggest storm water run-off is mostly absorbed on the inlet side. Bacterial and fungal communities were significantly clustered by bioswale and by plant species within each bioswale implying there are micro-environmental controls on the soil microbial composition, and that plant composition matters for microbial assemblages within bioswales. Plants with higher transpiration rates were associated with greater fungal and bacterial diversity at the level of the bioswale and at scale of the individual plant, suggesting a possible link between plant physiological traits and soil microbial communities. These data suggest that the specific plant palette selected for planting bioswales can have deterministic effects on the surrounding microbial communities which may further influence functions such as transpiration and nutrient cycling. These results may have implications for bioswale management to improve urban water quality and reduce stress on sewage systems after storm events by revising plant species palette selection based on the functional consequences of plant-microbial associations in engineered green infrastructure.

The role that mycorrhizal fungal associations play in the assembly of long-lived tree communities is poorly understood, especially in tropical forests, which have the highest tree diversity of any ecosystem. The lowland tropical rain forests of Southeast Asia are characterized by high levels of species richness within the family Dipterocarpaceae, the entirety of which has been shown to form obligate ectomycorrhizal (ECM) fungal associations. Differences in ECM assembly between co-occurring species of dipterocarp have been suggested, but never tested in adult trees, as a mechanism for maintaining the coexistence of closely related tree species in this family. Testing this hypothesis has proven difficult because the assembly of both dipterocarps and their ECM associates co-varies with the same edaphic variables. In this study, we used high-throughput DNA sequencing of soils and Sanger sequencing of root tips to evaluate how ECM fungi were structured within and across a clay-sand soil nutrient ecotone in a mixed-dipterocarp rain forest in Malaysian Borneo. We compared assembly patterns of ECM fungi in bulk soil to ECM root tips collected from three ecologically distinct species of dipterocarp. This design allowed us to test whether ECM fungi are more strongly structured by soil type or host specificity. As with previous studies of ECM fungi on this plot, we observed that clay vs. sand soil type strongly structured both the bulk soil and root tip ECM fungal communities. However, we also observed significantly different ECM communities associated with two of the three dipterocarp species evaluated on this plot. These results suggest that ECM fungal assembly on these species is shaped by a combination of biotic and abiotic factors, and that the soil edaphic niche occupied by different dipterocarp species may be mediated by distinct ECM fungal assemblages.