Ectomycorrhizal access to organic nitrogen mediates CO2 fertilization response in a dominant temperate tree

Climate mismatches with ectomycorrhizal fungi contribute to migration lag in North American tree range shifts

Climate change will likely shift plant and microbial distributions, creating geographic mismatches between plant hosts and essential microbial symbionts (e.g., ectomycorrhizal fungi, EMF). The loss of historical interactions, or the gain of novel associations, can have important consequences for biodiversity, ecosystem processes, and plant migration potential, yet few analyses exist that measure where mycorrhizal symbioses could be lost or gained across landscapes. Here, we examine climate change impacts on tree-EMF codistributions at the continent scale. We built species distribution models for 400 EMF species and 50 tree species, integrating fungal sequencing data from North American forest ecosystems with tree species occurrence records and long-term forest inventory data. Our results show the following: 1) tree and EMF climate suitability to shift toward higher latitudes; 2) climate shifts increase the size of shared tree-EMF habitat overall, but 35% of tree-EMF pairs are at risk of declining habitat overlap; 3) climate mismatches between trees and EMF are projected to be greater at northern vs. southern boundaries; and 4) tree migration lag is correlated with lower richness of climatically suitable EMF partners. This work represents a concentrated effort to quantify the spatial extent and location of tree-EMF climate envelope mismatches. Our findings also support a biotic mechanism partially explaining the failure of northward tree species migrations with climate change: reduced diversity of co-occurring and climate-compatible EMF symbionts at higher latitudes. We highlight the conservation implications for identifying areas where tree and EMF responses to climate change may be highly divergent.

Responses of vascular plant fine roots and associated microbial communities to whole-ecosystem warming and elevated CO2 in northern peatlands

Warming and elevated CO2 (eCO2) are expected to facilitate vascular plant encroachment in peatlands. The rhizosphere, where microbial activity is fueled by root turnover and exudates, plays a crucial role in biogeochemical cycling, and will likely at least partially dictate the response of the belowground carbon cycle to climate changes. We leveraged the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, to explore the effects of a whole-ecosystem warming gradient (+0°C to 9°C) and eCO2 on vascular plant fine roots and their associated microbes. We combined trait-based approaches with the profiling of fungal and prokaryote communities in plant roots and rhizospheres, through amplicon sequencing. Warming promoted self-reliance for resource uptake in trees and shrubs, while saprophytic fungi and putative chemoorganoheterotrophic bacteria utilizing plant-derived carbon substrates were favored in the root zone. Conversely, eCO2 promoted associations between trees and ectomycorrhizal fungi. Trees mostly associated with short-distance exploration-type fungi that preferentially use labile soil N. Additionally, eCO2 decreased the relative abundance of saprotrophs in tree roots. Our results indicate that plant fine-root trait variation is a crucial mechanism through which vascular plants in peatlands respond to climate change via their influence on microbial communities that regulate biogeochemical cycles.

Herbarium specimens reveal that mycorrhizal type does not mediate declining temperate tree nitrogen status over a century of environmental change

Rising atmospheric carbon dioxide concentrations (CO2) and atmospheric nitrogen (N) deposition have contrasting effects on ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) symbioses, potentially mediating forest responses to environmental change. In this study, we evaluated the cumulative effects of historical environmental change on N concentrations and δ15N values in AM plants, EM plants, EM fungi, and saprotrophic fungi using herbarium specimens collected in Minnesota, USA from 1871 to 2016. To better understand mycorrhizal mediation of foliar δ15N, we also analyzed a subset of previously published foliar δ15N values from across the United States to parse the effects of N deposition and CO2 rise. Over the last century in Minnesota, N concentrations declined among all groups except saprotrophic fungi. δ15N also declined among all groups of plants and fungi; however, foliar δ15N declined less in EM plants than in AM plants. In the analysis of previously published foliar δ15N values, this slope difference between EM and AM plants was better explained by nitrogen deposition than by CO2 rise. Mycorrhizal type did not explain trajectories of plant N concentrations. Instead, plants and EM fungi exhibited similar declines in N concentrations, consistent with declining forest N status despite moderate levels of N deposition.

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

Fungal community composition predicts forest carbon storage at a continental scale

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

Warming influences carbon and nitrogen assimilation between a widespread Ericaceous shrub and root-associated fungi

High-latitude ecosystems are warming faster than other biomes and are often dominated by a ground layer of Ericaceous shrubs, which can respond positively to warming. The carbon-for-nitrogen (C-for-N) exchange between Ericaceous shrubs and root-associated fungi may underlie shrub responses to warming, but has been understudied. In a glasshouse setting, we examined the effects of warming on the C-for-N exchange between the Ericaceous shrub Empetrum nigrum ssp. hermaphroditum and its root-associated fungi. We applied different 13 C and 15 N isotope labels, including a simple organic N form (glycine) and a complex organic N form (moss litter) and quantified their assimilation into soil, plant biomass, and root fungal biomass pools. We found that warming lowered the amount of 13 C partitioned to root-associated fungi per unit of glycine 15 N assimilated by E. nigrum, but only in the short term. By contrast, warming increased the amount of 13 C partitioned to root-associated fungi per unit of moss 15 N assimilated by E. nigrum. Our study suggests that climate warming affects the short-term exchange of C and N between a widespread Ericaceous shrub and root-associated fungi. Furthermore, while most isotope tracing studies use labile N sources, we demonstrate that a ubiquitous recalcitrant N source may produce contrasting results.

Ectomycorrhizal trees rely on nitrogen resorption less than arbuscular mycorrhizal trees globally

Nitrogen (N) resorption is an important pathway of N conservation, contributing to an important proportion of plant N requirement. However, whether the ratio of N resorption to N requirement may be affected by environmental factors, mycorrhizal types or atmospheric CO2 concentration remains unclear. Here, we conducted a meta-analysis on the impacts of environmental factors and mycorrhizal types on this ratio. We found this ratio in ectomycorrhizal (EM) trees decreased with mean annual precipitation, mean annual temperature, soil total N content and atmospheric CO2 concentration and was significantly lower than that in arbuscular mycorrhizal (AM) trees. An in situ 15 N tracing experiment further confirmed that AM trees have a stronger reliance on N resorption than EM trees. Our study suggests that AM and EM trees potentially have different strategies for alleviation of progressive N limitation, highlighting the necessity of incorporating plant mycorrhizal types into Earth System Models.

Temporal dynamics of soil dissolved organic carbon in temperate forest managed by prescribed burning in Northeast China

Dissolved organic carbon (DOC) is an important function of soil organic carbon and sensitive to environmental disturbance. Few studies have explored the variations in soil DOC dynamics and effects on soil physicochemical properties following prescribed burnings. In this study, Pinus koraiensis plantation forests in Northeast China were selected and subjected to prescribed burning in early November 2018. Soil DOC and different soil physicochemical and biological properties in the 0-10 cm and 10-20 cm soil layers were sampled six times within two years after a prescribed burning. In this study, some soil physicochemical (SOC, TN, and ST) and microbial biomass properties (MBC) recovered within two years after a prescribed burning. Compared to the unburned control stands, the post-fire soil DOC concentrations in the upper and lower soil layers increased by 16% and 12%, respectively. Soil DOC concentrations varied with sampling time, and peaked one year after the prescribed burning. Our results showed that soil chemical properties (NH4+-N and pH) rather than biological properties (microbial biomass) were the main driving factors for changes in post-fire soil DOC concentrations. Current study provides an important reference for post-fire and seasonal soil C cycling in plantation forests of Northeast China.

Functional genomics gives new insights into the ectomycorrhizal degradation of chitin

Ectomycorrhizal (EcM) fungi play a crucial role in the mineral nitrogen (N) nutrition of their host trees. While it has been proposed that several EcM species also mobilize organic N, studies reporting the EcM ability to degrade N-containing polymers, such as chitin, remain scarce. Here, we assessed the capacity of a representative collection of 16 EcM species to acquire ¹⁵ N from ¹⁵ N-chitin. In addition, we combined genomics and transcriptomics to identify pathways involved in exogenous chitin degradation between these fungal strains. Boletus edulis, Imleria badia, Suillus luteus, and Hebeloma cylindrosporum efficiently mobilized N from exogenous chitin. EcM genomes primarily contained genes encoding for the direct hydrolysis of chitin. Further, we found a significant relationship between the capacity of EcM fungi to assimilate organic N from chitin and their genomic and transcriptomic potentials for chitin degradation. These findings demonstrate that certain EcM fungal species depolymerize chitin using hydrolytic mechanisms and that endochitinases, but not exochitinases, represent the enzymatic bottleneck of chitin degradation. Finally, this study shows that the degradation of exogenous chitin by EcM fungi might be a key functional trait of nutrient cycling in forests dominated by EcM fungi.

Advancing research on ectomycorrhizal fungal adaptation with landscape genomics

Ectomycorrhizal (ECM) fungi serve key functions in forest ecosystems by supplying water and nutrients to tree hosts, yet mutualistic plant-fungi interactions are jeopardised by environmental alterations. Here, we discuss the great potential and current limitations of landscape genomics in investigating signatures of local adaptation in natural populations of ECM fungi.

Forest tree growth is linked to mycorrhizal fungal composition and function across Europe

Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.

Deciphering Rhizosphere Microbiome Assembly of Castanea henryi in Plantation and Natural Forest

Based on the importance and sensitivity of microbial communities to changes in the forest ecosystem, soil microorganisms can be used to indicate the health of the forest system. The metagenome sequencing was used to analyze the changes of microbial communities between natural and plantation Castanea henryi forests for understanding the effect of forest types on soil microbial communities. Our result showed the soil microbial diversity and richness were higher in the natural forests than in the plantation. Proteobacteria, Actinobacteria, and Acidobacteria are the dominant categories in the C. henryi rhizosphere, and Proteobacteria and Actinobacteria were significantly enriched in the natural forest while Acidobacteria was significantly enriched in the plantation. Meanwhile, the functional gene diversity and the abundance of functions in the natural forest were higher than that of the plantation. Furthermore, we found that the microbial network in the natural forests had more complex than in the plantation. We also emphasized the low-abundance taxa may play an important role in the network structure. These results clearly showed that microbial communities, in response to different forest types, provide valuable information to manipulate microbiomes to improve soil conditions of plantation.

Ectomycorrhizal fungal decay traits along a soil nitrogen gradient

The extent to which ectomycorrhizal (ECM) fungi decay soil organic matter (SOM) has implications for accurately predicting forest ecosystem response to climate change. Investigating the distribution of gene traits associated with SOM decay among ectomycorrhizal fungal communities could improve understanding of SOM dynamics and plant nutrition. We hypothesized that soil inorganic nitrogen (N) availability structures the distribution of ECM fungal genes associated with SOM decay and, specifically, that ECM fungal communities occurring in inorganic N-poor soils have greater SOM decay potential. To test this hypothesis, we paired amplicon and shotgun metagenomic sequencing of 60 ECM fungal communities associating with Quercus rubra along a natural soil inorganic N gradient. Ectomycorrhizal fungal communities occurring in low inorganic N soils were enriched in gene families involved in the decay of lignin, cellulose, and chitin. Ectomycorrhizal fungal community composition was the strongest driver of shifts in metagenomic estimates of fungal decay potential. Our study simultaneously illuminates the identity of key ECM fungal taxa and gene families potentially involved in the decay of SOM, and we link rhizomorphic and medium-distance hyphal morphologies with enhanced SOM decay potential. Coupled shifts in ECM fungal community composition and community-level decay gene frequencies are consistent with outcomes of trait-mediated community assembly processes.

Decay by ectomycorrhizal fungi couples soil organic matter to nitrogen availability

Interactions between soil nitrogen (N) availability, fungal community composition, and soil organic matter (SOM) regulate soil carbon (C) dynamics in many forest ecosystems, but context dependency in these relationships has precluded general predictive theory. We found that ectomycorrhizal (ECM) fungi with peroxidases decreased with increasing inorganic N availability across a natural inorganic N gradient in northern temperate forests, whereas ligninolytic fungal saprotrophs exhibited no response. Lignin-derived SOM and soil C were negatively correlated with ECM fungi with peroxidases and were positively correlated with inorganic N availability, suggesting decay of lignin-derived SOM by these ECM fungi reduced soil C storage. The correlations we observed link SOM decay in temperate forests to tradeoffs in tree N nutrition and ECM composition, and we propose SOM varies along a single continuum across temperate and boreal ecosystems depending upon how tree allocation to functionally distinct ECM taxa and environmental stress covary with soil N availability.