Root exudate composition reflects drought severity gradient in blue grama (Bouteloua gracilis)

Plant survival during environmental stress greatly affects ecosystem carbon (C) cycling, and plant–microbe interactions are central to plant stress survival. The release of C-rich root exudates is a key mechanism plants use to manage their microbiome, attracting beneficial microbes and/or suppressing harmful microbes to help plants withstand environmental stress. However, a critical knowledge gap is how plants alter root exudate concentration and composition under varying stress levels. In a greenhouse study, we imposed three drought treatments (control, mild, severe) on blue grama (Bouteloua gracilis Kunth Lag. Ex Griffiths), and measured plant physiology and root exudate concentration and composition using GC–MS, NMR, and FTICR. With increasing drought severity, root exudate total C and organic C increased concurrently with declining predawn leaf water potential and photosynthesis. Root exudate composition mirrored the physiological gradient of drought severity treatments. Specific compounds that are known to alter plant drought responses and the rhizosphere microbiome mirrored the drought severity-induced root exudate compositional gradient. Despite reducing C uptake, these plants actively invested C to root exudates with increasing drought severity. Patterns of plant physiology and root exudate concentration and composition co-varied along a gradient of drought severity.

Microbial Communities Influence Soil Dissolved Organic Carbon Concentration by Altering Metabolite Composition

Rapid microbial growth in the early phase of plant litter decomposition is viewed as an important component of soil organic matter (SOM) formation. However, the microbial taxa and chemical substrates that correlate with carbon storage are not well resolved. The complexity of microbial communities and diverse substrate chemistries that occur in natural soils make it difficult to identify links between community membership and decomposition processes in the soil environment. To identify potential relationships between microbes, soil organic matter, and their impact on carbon storage, we used sand microcosms to control for external environmental factors such as changes in temperature and moisture as well as the variability in available carbon that exist in soil cores. Using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) on microcosm samples from early phase litter decomposition, we found that protein- and tannin-like compounds exhibited the strongest correlation to dissolved organic carbon (DOC) concentration. Proteins correlated positively with DOC concentration, while tannins correlated negatively with DOC. Through random forest, neural network, and indicator species analyses, we identified 42 bacterial and 9 fungal taxa associated with DOC concentration. The majority of bacterial taxa (26 out of 42 taxa) belonged to the phylum Proteobacteria while all fungal taxa belonged to the phylum Ascomycota. Additionally, we identified significant connections between microorganisms and protein-like compounds and found that most taxa (12/14) correlated negatively with proteins indicating that microbial consumption of proteins is likely a significant driver of DOC concentration. This research links DOC concentration with microbial production and/or decomposition of specific metabolites to improve our understanding of microbial metabolism and carbon persistence.

Ectomycorrhizal and Dark Septate Fungal Associations of Pinyon Pine Are Differentially Affected by Experimental Drought and Warming

Changing climates can cause shifts in temperature and precipitation, resulting in warming and drought in some regions. Although each of these factors has been shown to detrimentally affect forest ecosystems worldwide, information on the impacts of the combined effects of warming and drought is lacking. Forest trees rely on mutualistic root-associated fungi that contribute significantly to plant health and protection against climate stresses. We used a six-year, ecosystem-scale temperature and precipitation manipulation experiment targeted to simulate the climate in 2100 in the Southwestern United States to quantify the effects of drought, warming and combined drought and warming on the root colonization (abundance), species composition and diversity of ectomycorrhizal fungi (EMF), and dark septate fungal endophytes in a widespread woodland tree, pinyon pine (Pinus edulis E.). Our results show that pinyon shoot growth after 6 years of these treatments was reduced more by drought than warming. The combined drought and warming treatment reduced the abundance and diversity of EMF more than either treatment alone. Individual ectomycorrhizal fungal taxa, including the drought tolerant Cenococcum geophilum, were present in all treatments but the combined drought and warming treatment. The combined drought and warming treatment also reduced the abundance of dark septate endophytes (DSE), but did not affect their diversity or species composition. The current year shoot growth of the trees correlated positively with ectomycorrhizal fungal diversity, highlighting the importance of diversity in mutualistic relationships to plant growth. Our results suggest that EMF may be more important than DSE to aboveground growth in P. edulis, but also more susceptible to the negative effects of combined climate stressors.

Differences in substrate use linked to divergent carbon flow during litter decomposition

Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

Effects of Soil Microbes on Functional Traits of Loblolly Pine (Pinus taeda) Seedling Families From Contrasting Climates

Examining factors that influence seedling establishment is essential for predicting the impacts of climate change on tree species' distributions. Seedlings originating from contrasting climates differentially express functional traits related to water and nutrient uptake and drought resistance that reflect their climate of origin and influence their responses to drought. Soil microbes may improve seedling establishment because they can enhance water and nutrient uptake and drought resistance. However, the relative influence of soil microbes on the expression of these functional traits between seedling families or populations from contrasting climates is unknown. To determine if soil microbes may differentially alter functional traits to enhance water and nutrient uptake and drought resistance between dry and wet families, seeds of loblolly pine families from the driest and wettest ends of its geographic range (dry, wet) were planted in sterilized sand (controls) or in sterilized sand inoculated with a soil microbial community (inoculated). Functional traits related to seedling establishment (germination), water and nutrient uptake and C allocation (root:shoot biomass ratio, root exudate concentration, leaf C:N, leaf N isotope composition (δ¹⁵N)), and drought resistance (turgor loss point, leaf carbon isotope composition (δ¹³C)) were measured. Then, plants were exposed to a drought treatment and possible shifts in photosynthetic performance were monitored using chlorophyll fluorescence. Inoculated plants exhibited significantly greater germination than controls regardless of family. The inoculation treatment significantly increased root:shoot biomass ratio in the wet family but not in the dry family, suggesting soil microbes alter functional traits that improve water and nutrient uptake more so in a family originating from a wetter climate than in a family originating from a drier climate. Microbial effects on photosynthetic performance during drought also differed between families, as photosynthetic performance of the dry inoculated group declined fastest. Regardless of treatment, the dry family exhibited a greater root:shoot biomass ratio, root exudate concentration, and leaf δ¹⁵N than the wet family. This indicates that the dry family allocated more resources belowground than the wet and the two family may have used different sources of plant available N, which may be related to their contrasting climates of origin and influence their drought resistance. Examination of variation in impacts of soil microbes on seedling physiology improves efforts to enhance seedling establishment and beneficial plant-microbe interactions under climate change.

Investigating old-growth ponderosa pine physiology using tree-rings, δ13 C, δ18 O, and a process-based model

In dealing with predicted changes in environmental conditions outside those experienced today, forest managers and researchers rely on process-based models to inform physiological processes and predict future forest growth responses. The carbon and oxygen isotope ratios of tree-ring cellulose (δ13 Ccell , δ18 Ocell ) reveal long-term, integrated physiological responses to environmental conditions. We incorporated a submodel of δ18 Ocell into the widely used Physiological Principles in Predicting Growth (3-PG) model for the first time, to complement a recently added δ13 Ccell submodel. We parameterized the model using previously reported stand characteristics and long-term trajectories of tree-ring growth, δ13 Ccell , and δ18 Ocell collected from the Metolius AmeriFlux site in central Oregon (upland trees). We then applied the parameterized model to a nearby set of riparian trees to investigate the physiological drivers of differences in observed basal area increment (BAI) and δ13 Ccell trajectories between upland and riparian trees. The model showed that greater available soil water and maximum canopy conductance likely explain the greater observed BAI and lower δ13 Ccell of riparian trees. Unexpectedly, both observed and simulated δ18 Ocell trajectories did not differ between the upland and riparian trees, likely due to similar δ18 O of source water isotope composition. The δ18 Ocell submodel with a Peclet effect improved model estimates of δ18 Ocell because its calculation utilizes 3-PG growth and allocation processes. Because simulated stand-level transpiration (E) is used in the δ18 O submodel, aspects of leaf-level anatomy such as the effective path length for transport of water from the xylem to the sites of evaporation could be estimated.

Fire deficits have increased drought sensitivity in dry conifer forests: Fire frequency and tree-ring carbon isotope evidence from Central Oregon

A century of fire suppression across the Western United States has led to more crowded forests and increased competition for resources. Studies of forest thinning or stand conditions after mortality events have provided indirect evidence for how competition can promote drought stress and predispose forests to severe fire and/or bark beetle outbreaks. Here, we demonstrate linkages between fire deficits and increasing drought stress through analyses of annually resolved tree-ring growth, fire scars, and carbon isotope discrimination (Δ¹³ C) across a dry mixed-conifer forest landscape. Fire deficits across the study area have increased the sensitivity of leaf gas exchange to drought stress over the past >100 years. Since 1910, stand basal area in these forests has more than doubled and fire-return intervals have increased from 25 to 140 years. Meanwhile, the portion of interannual variation in tree-ring Δ¹³ C explained by the Palmer Drought Severity Index has more than doubled in ca. 300-500-year-old Pinus ponderosa as well as in fire-intolerant, ca. 90-190-year-old Abies grandis. Drought stress has increased in stands with a basal area of ≥25 m² /ha in 1910, as indicated by negative temporal Δ¹³ C trends, whereas stands with basal area ≤25 m² /ha in 1910, due to frequent or intense wildfire activity in decades beforehand, were initially buffered from increased drought stress and have benefited more from rising ambient carbon dioxide concentrations, [CO₂ ], as demonstrated by positive temporal Δ¹³ C trends. Furthermore, the average Δ¹³ C response across all P. ponderosa since 1830 indicates that photosynthetic assimilation rates and stomatal conductance have been reduced by ~10% and ~20%, respectively, compared to expected trends due to increasing [CO₂ ]. Although disturbance legacies contribute to local-scale intensity of drought stress, fire deficits have reduced drought resistance of mixed-conifer forests and made them more susceptible to challenges by pests and pathogens and other disturbances.

Plant-microbe interactions before drought influence plant physiological responses to subsequent severe drought

We examined the effect of soil microbial communities on plant physiological responses to drought. Bouteloua gracilis seeds were planted in sterilized sand with (inoculated) and without (controls) soil microbial communities. After substantial growth, drought was imposed by completely withholding water. Before soil moisture declined to zero, inoculated plants germinated faster, were significantly taller, and maintained greater soil moisture than controls. The greater soil moisture of the inoculated plants allowed greater photosynthesis but also induced lower tissue drought tolerance (as indicated by turgor loss point) compared to controls. The inoculated plants were more susceptible to severe drought compared to control plants as indicated by significantly lower mean stomatal conductance, as well as marginally significantly greater mean wilting score, for the entire severe drought period after soil moisture declined to zero. Inoculated plants exhibited enhanced growth and photosynthesis and dampened drought stress over short timescales, but also increased susceptibility to drought over long timescales. This work demonstrates (1) an unexpected insight that microbes can have positive initial effects on plant performance, but negative impacts on plant performance during severe drought, and (2) that microbially altered effects on plant function during well-watered and moderate drought conditions can influence plant function under subsequent severe drought.