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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Arbuscular mycorrhizal fungal response to fire and urbanization in the Great Smoky Mountains National Park

Wildfires are increasing in frequency and intensity as drier and warmer climates increase plant detrital fuel loads. At the same time, increases in urbanization position 9% of fire-prone land within the United States at the wildland–urban interface. While rarely studied, the compounded effects of urbanization and wildfires may have unknown synergistically negative effects on ecosystems. Previous studies at the wildland–urban interface often focus on aboveground plant communities, but belowground ecosystems may also be affected by this double disturbance. In particular, it is unclear how much fire and urbanization independently or interactively affect nutritional symbioses such as those between arbuscular mycorrhizal (AM) fungi and the majority of terrestrial plants. In November 2016, extreme drought conditions and long-term fire suppression combined to create a wildfire within the Great Smoky Mountains National Park and the neighboring exurban city of Gatlinburg, TN. To understand how the double disturbance of urbanization and fire affected AM fungal communities, we collected fine roots from the 5 dominant understory species in September 2018 at each of 18 sites spanning 3 burn severities in both exurban and natural sites. Despite large variation in burn severity, plant species identity had the largest influence on AM fungi. AM fungal colonization, richness, and composition all varied most among plant species. Fire and urbanization did influence some AM fungal metrics; colonization was lower in burned sites and composition was more variable among exurban locations. There were no interactions among burn severity and urbanization on AM fungi. Our results point to the large influence of plant species identity structuring this obligate nutritional symbiosis regardless of disturbance regime. Therefore, the majority of AM fungal taxa may be buffered from fire-induced ecosystem changes if plant community composition largely remains intact, plant species life history traits allow for AM fungal persistence after fire disturbance, and/or nearby undisturbed habitat can act as an inoculum source for recolonization following fires. Thus, it is critical to maintain natural, undisturbed habitats interspersed within the wildland–urban interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Chronic drought differentially alters the belowground microbiome of drought tolerant and drought susceptible genotypes of Populus trichocarpa

Populus trichocarpa is an ecologically important tree species and economically important biofeedstock. Belowground, P. trichocarpa interacts with diverse microorganisms in the rhizosphere and root endosphere. These plant-microbial interactions can bolster a variety of plant processes, ranging from pathogen suppression to drought tolerance, yet we know little about the impact of chronic drought stress on P. trichocarpa’s belowground microbiomes. To investigate the interactive effect of chronic drought on belowground microbial communities across genetically different P. trichocarpa hosts, we assessed archaeal/bacterial and fungal communities within the root endosphere, rhizosphere, and surrounding bulk soil of selected genotypes in a long-term drought experiment in Boardman, OR, USA. We sequenced the 16S rRNA and ITS2 gene region on samples collected from 16 distinct P. trichocarpa genotypes in plots with full or reduced irrigation. Eight of these genotypes have been previously identified as drought tolerant while the other eight genotypes were drought susceptible. While reduced irrigation influenced the composition of every archaeal/bacterial microbiome compartment, fungal communities were only affected in the rhizosphere and bulk soil compartments. Drought-tolerant bacteria, such as Actinobacteria, were differentially abundant in reduced irrigation across all belowground microbiomes. Host drought-tolerance influenced plant-associated microbiome compartments but had little impact on the bulk soil compartment. Drought-tolerant trees were enriched for potential growth-promoting microorganisms in the root endosphere and rhizosphere, including Sphingomonas bacteria and ectomycorrhizal fungi. Overall, associations of growth-promoting microbes in drought resistant P. trichocarpa genotypes can be leveraged to improve biofeedstock productivity in regions prone to periodic drought.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Plant Hosts Modify Belowground Microbial Community Response to Extreme Drought

Drought stress negatively impacts microbial activity, yet the magnitude of stress responses is likely dependent on a diversity of belowground interactions. Populus trichocarpa individuals and no-plant bulk soils were exposed to extended drought (~0.03% gravimetric water content [GWC] after 12 days), rewet, and a 12-day “recovery” period to determine the effects of plant presence in mediating soil microbiome stability to water stress. Plant metabolomic analyses indicated that drought exposure increased host investment in C and N metabolic pathways (amino acids, fatty acids, phenolic glycosides) regardless of recovery. Several metabolites positively correlated with root-associated microbial alpha-diversity, but not those of soil communities. Soil bacterial community composition shifted with P. trichocarpa presence and with drought relative to irrigated controls, whereas soil fungal composition shifted only with plant presence. However, root fungal communities strongly shifted with drought, whereas root bacterial communities changed to a lesser degree. The proportion of bacterial water-stress opportunistic operational taxonomic units (OTUs) (enriched counts in drought) was high (~11%) at the end of drying phases and maintained after rewet and recovery phases in bulk soils, but it declined over time in soils with plants present. For root fungi, opportunistic OTUs were high at the end of recovery in drought treatments (~17% abundance), although relatively not responsive in soils, particularly planted soils (<0.5% abundance for sensitive or opportunistic). These data indicate that plants modulate soil and root-associated microbial drought responses via tight plant-microbe linkages during extreme drought scenarios, but trajectories after extreme drought vary with plant habitat and microbial functional groups.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fungal and bacterial growth variation due to drought and nitrogen addition experimental treatments. Loma Ridge Experimental Project. 2010-2012

Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities. This data package includes ten csv files (five data files and their corresponding data dictionaries) and one file-level metadata excel file. Data files contains information about which plots were exposed to treatments related to drought and nitrogen, information about litter bags reciprocal transplants manipulation for water input and nitrogen, detail information about water addition, precipitation records, and litter variables collected. Data dictionary files include detail explanation for each column in the data files. The file-level metadata file describes each file mentioned above. All the analyses were done using the R software.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Environmental harshness mediates the relationship between aboveground and belowground communities in Antarctica

Linkages between aboveground and belowground communities are a key but globally under-researched component of responses to environmental change. Given the logistical complications to studying these relationships, much of our knowledge derives from laboratory experiments and localized field studies which have so far yielded inconsistent results. Because environmental factors may alter relationships between above- and belowground communities, there is a need for broad-scale field studies testing these interactions. The Antarctic Peninsula provides an ideal test setting, given the relatively simple communities both above- and belowground. The Peninsula is also experiencing rapid environmental changes, including alterations in species diversity and distribution both above- and belowground. Thus, an improved understanding of the broad-scale consequences of altered environments and vegetation communities for the soil microbiome is of high priority. To determine the nature and strength of the relationship between in situ plant and soil communities across a broad spatial scale and range of environmental conditions, we sampled soil communities at 9 locations (spanning 60–72°S along the Scotia Arc and Antarctic Peninsula) beneath the major aboveground habitats (moss, grass, lichen, algae and bare soil). We measured a comprehensive suite of soil physicochemical properties, microbial (bacterial and fungal) diversity and composition, and invertebrate abundance and community composition to determine the relationships between plant and soil communities. Furthermore, our results suggest that, with increased environmental severity, plant cover types become more important for influencing the physicochemical soil environment, and therefore the soil microbial communities. Although we found site-specific relationships, broad-scale patterns reveal significant differences among bare soils and vegetated soils, particularly soils beneath grass and moss. This suggests that expansion of vegetation communities under current climate warming projections will be accompanied by shifts in the soil microbiome, with important implications for the ecosystem functioning with which they are associated.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition

Abstract Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8–1.0 °C for 10 years and then 1.5–2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fungal community structure and function shifts with atmospheric nitrogen deposition

Fungal decomposition of soil organic matter depends on soil nitrogen (N) availability. This ecosystem process is being jeopardized by changes in N inputs that have resulted from a tripling of atmospheric N deposition in the last century. Soil fungi are impacted by atmospheric N deposition due to higher N availability, as soils are acidified, or as micronutrients become increasingly limiting. Fungal communities that persist with chronic N deposition may be enriched with traits that enable them to tolerate environmental stress, which may trade-off with traits enabling organic matter decomposition. We hypothesized that fungal communities would respond to N deposition by shifting community composition and functional gene abundances toward those that tolerate stress but are weak decomposers. We sampled soils at seven eastern US hardwood forests where ambient N deposition varied from 3.2 to 12.6 kg N ha -1 year -1 , five of which also have experimental plots where atmospheric N deposition was simulated through fertilizer application treatments (25–50 kg N ha -1 year -1 ). Fungal community and functional responses to fertilizer varied across the ambient N deposition gradient. Fungal biomass and richness increased with simulated N deposition at sites with low ambient deposition and decreased at sites with high ambient deposition. Fungal functional genes involved in hydrolysis of organic matter increased with ambient N deposition while genes involved in oxidation of organic matter decreased. One of four genes involved in generalized abiotic stress tolerance increased with ambient N deposition. In summary, we found that the divergent response to simulated N deposition depended on ambient N deposition levels. Fungal biomass, richness, and oxidative enzyme potential were reduced by N deposition where ambient N deposition was high suggesting fungal communities were pushed beyond an environmental stress threshold. Fungal community structure and function responses to N enrichment depended on ambient N deposition at a regional scale.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Investigating Bacterial-Fungal Interactions using Fungal Highway Columns in Diverse Environments and Substrates

Bacterial-fungal interactions (BFIs) play an integral role in shaping microbial community composition, biogeochemical functions, spatial dynamics, and microbial dispersal. Mycelial networks created by filamentous fungi or other filamentous microorganisms (e.g., Oomycetes) act as 'fungal highways' that can be utilized by bacteria for transport throughout heterogeneous environments, greatly facilitating their mobility and granting them access to regions that may be challenging or impossible to reach on their own (e.g., due to air pockets within the soil). Several devices and experimental protocols have been created to study these fungal highways, including fungal highway columns. The fungal highway column designed by our group can be used for a variety of in situ or in vitro applications, as well as with diverse environmental and host-associated sample types. Herein, we describe the methods for performing experiments with these columns, including designing, printing, sterilizing, and preparing the devices. The options for analyzing data obtained from the use of these devices are also discussed here, and troubleshooting advice regarding potential pitfalls associated with experiments using fungal highway columns is offered. These devices can be used to gain a more comprehensive understanding of the diversity, mechanisms, and dynamics of fungal highway BFIs to provide valuable insights into the structural and functional dynamics within complex environments (e.g., soils) and across diverse habitats in which bacteria and fungi co-exist.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microbial communities and biogeochemical functioning across peatlands in the Athabasca Oil Sands region of Canada: Implications for reclamation and management

Abstract Peatlands play an important role in global biogeochemical cycles and are essential for multiple ecosystem functions. Understanding the environmental drivers of microbial functioning and community structure can provide insights to enable effective and evidence‐based management. However, it remains largely unknown how microbial diversity contributes to the functioning of belowground processes. Addressing this gap in knowledge will provide a better understanding of microbial‐mediated processes in peatlands that are undergoing restoration or reclamation. This study assessed the changes in microbial community diversity and structure as well as soil function by measuring microbial respiration on a range of substrates from three natural fen types found in the Athabasca Oil Sands region of Alberta, Canada (a poor fen, a hypersaline fen, and a tree‐rich fen) and a nearby constructed fen undergoing reclamation following open pit mining. Overall, substrate induced respiration was significantly higher in the constructed fen. Alpha diversity of fungi and prokaryotes was highest in the tree‐rich fen, and the composition of microbial communities was significantly different between fens. Both fungal and prokaryotic communities were strongly related to pore water pH and temperature, with plant richness also contributing to the shape of fungal communities. In summary, microbial community structure reflects the underlying differences in soil condition across different fens but plays essential roles in the ecological functions of soil. These findings provide a new outlook for the management of peatlands undergoing post‐mining reclamation. Future research on peatland reclamation should consider the dynamic interaction between communities and ecosystem functionality, for which this study forms a useful baseline.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A Single Application of Compost Can Leave Lasting Impacts on Soil Microbial Community Structure and Alter Cross-Domain Interaction Networks

Our current understanding suggests that nutrient management strategies applied to agricultural soils over multiple years are required to cause major and stable shifts in soil microbial communities. However, some studies suggest that agricultural soils can benefit even from sporadic, single additions of organic matter. Here we investigate how single additions of high-quality organic matter can cause significant shifts in microbial soil communities over multiple cropping cycles. We grew radishes in a tropical Oxisol soil for six crop cycles after a single application of a high-nitrogen compost or urea. At planting and before biomass harvest, we sampled soils influenced by the radish rhizosphere and sequenced bacterial and archaeal 16S and fungal ITS rDNA marker genes. We measured microbial richness and diversity, community composition and structure, and constructed correlation networks to predict cross-domain microbial interactions. We found that a single application of compost, compared to urea or control, resulted in a persistent improved plant biomass response and led to sustained changes in the soil microbial community throughout the duration of the 227-day study. Compost altered the structure of both the fungal and prokaryotic microbial communities, introduced new microorganisms that persisted in the resident soil system, and altered soil microbial correlation network structure and hub taxa. In contrast, fertilization with urea did not significantly alter the structure of soil microbial communities compared to the control but reduced network complexity and altered hub taxa. This study highlights the significant impacts that high-quality organic matter fertilization can exert on agricultural soil microbiomes and adds to the growing body of knowledge on using organic fertilizers as a way to steer the soil microbiome toward a healthier soil.

Heisey, Steven↗
DOE OSTI2020

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation

The hemlock woolly adelgid ( Adelges tsugae , HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii , that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.

16S rRNA↗
DOE OSTI2023

Climate change–induced stress disrupts ectomycorrhizal interaction networks at the boreal–temperate ecotone

The interaction networks formed by ectomycorrhizal fungi (EMF) and their tree hosts, which are important to both forest recruitment and ecosystem carbon and nutrient retention, may be particularly susceptible to climate change at the boreal–temperate forest ecotone where environmental conditions are changing rapidly. Here, we quantified the compositional and functional trait responses of EMF communities and their interaction networks with two boreal ( Pinus banksiana and Betula papyrifera ) and two temperate ( Pinus strobus and Quercus macrocarpa ) hosts to a factorial combination of experimentally elevated temperatures and reduced rainfall in a long-term open-air field experiment. The study was conducted at the B4WarmED (Boreal Forest Warming at an Ecotone in Danger) experiment in Minnesota, USA, where infrared lamps and buried heating cables elevate temperatures (ambient, +3.1 °C) and rain-out shelters reduce growing season precipitation (ambient, ~30% reduction). EMF communities were characterized and interaction networks inferred from metabarcoding of fungal-colonized root tips. Warming and rainfall reduction significantly altered EMF community composition, leading to an increase in the relative abundance of EMF with contact-short distance exploration types. These compositional changes, which likely limited the capacity for mycelial connections between trees, corresponded with shifts from highly redundant EMF interaction networks under ambient conditions to less redundant (more specialized) networks. Further, the observed changes in EMF communities and interaction networks were correlated with changes in soil moisture and host photosynthesis. Collectively, these results indicate that the projected changes in climate will likely lead to significant shifts in the traits, structure, and integrity of EMF communities as well as their interaction networks in forest ecosystems at the boreal–temperate ecotone.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Heavy and wet: The consequences of violating assumptions of measuring soil microbial growth efficiency using the 18O water method

Soils store more carbon than the biosphere and atmosphere combined, and the efficiency to which soil microorganisms allocate carbon to growth rather than respiration is increasingly considered a proxy for the soil capacity to store carbon. This carbon use efficiency (CUE) is measured via different methods, and more recently, the 18O-H2O method has been embraced as a significant improvement for measuring CUE of soil microbial communities. Based on extrapolating 18O incorporation into DNA to new biomass, this measurement makes various implicit assumptions about the microbial community at hand. Here we conducted a literature review to evaluate how viable these assumptions are and then developed a mathematical model to test how violating them affects estimates of the growth component of CUE in soil. We applied this model to previously collected data from two kinds of soil microbial communities. By changing one parameter at a time, we confirmed our previous observation that CUE was reduced by fungal removal. Our results also show that depending on the microbial community composition, there can be substantial discrepancies between estimated and true microbial growth. Of the numerous implicit assumptions that might be violated, not accounting for the contribution of sources of oxygen other than extracellular water to DNA leads to a consistent underestimation of CUE. We present a framework that allows researchers to evaluate how their experimental conditions may influence their 18O-H2O-based CUE measurements and suggest the parameters that need further constraining to more accurately quantify growth and CUE.

Environmental Sciences & Ecology↗
DOE OSTI2022

The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin Valley

Abstract Dispersal is a key force in the assembly of fungal communities and the air is the dominant route of dispersal for most fungi. Understanding the dynamics of airborne fungi is important for determining their source and for helping to prevent fungal disease. This understanding is important in the San Joaquin Valley of California, which is home to 4.2 million people and where the airborne fungus Coccidioides is responsible for the most important fungal disease of otherwise healthy humans, coccidioidomycosis. The San Joaquin Valley is the most productive agricultural region in the United States, with the principal crops grown therein susceptible to fungal pathogens. Here, we characterize the fungal community in soil and air on undeveloped and agricultural land in the San Joaquin Valley using metabarcoding of the internal transcribed spacer 2 variable region of fungal rDNA. Using 1,002 individual samples, we report one of the most extensive studies of fungi sampled simultaneously from air and soil using modern sequencing techniques. We find that the air mycobiome in the San Joaquin Valley is distinct from the soil mycobiome, and that the assemblages of airborne fungi from sites as far apart as 160 km are far more similar to one another than to the fungal communities in nearby soils. Additionally, we present evidence that airborne fungi in the San Joaquin Valley are subject to dispersal limitation and cyclical intra‐annual patterns of community composition. Our findings are broadly applicable to understanding the dispersal of airborne fungi and the taxonomic structure of airborne fungal assemblages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Climate, soil mineralogy and mycorrhizal fungi influence soil organic matter fractions in eastern US temperate forests

Identifying the primary controls of particulate (POM) and mineral-associated organic matter (MAOM) content in soils is critical for determining future stocks of soil carbon (C) and nitrogen (N) across the globe. However, drivers of these soil organic matter fractions are likely to vary among ecosystems in response to climate, soil type and the composition of local biological communities. We tested how soil factors, climate and plant–fungal associations influenced the distribution and concentrations of C and N in MAOM and POM in seven temperate forests in the National Ecological Observatory Network (NEON) across the eastern United States. Samples of upper mineral horizon soil within each forest were collected in plots representing a gradient of dominant tree–mycorrhizal association, allowing us to test how plant and microbial communities influenced POM and MAOM across sites differing in climate and soil conditions. We found that concentrations of C and N in soil organic matter were primarily driven by soil mineralogy, but the relative abundance of MAOM versus POM C was strongly linked to plot-level mycorrhizal dominance. Furthermore, the effect of dominant tree mycorrhizal type on the distribution of N among POM and MAOM fractions was sensitive to local climate: in cooler sites, an increasing proportion of ectomycorrhizal-associated trees was associated with lower proportions of N in MAOM, but in warmer sites, we found the reverse. As an indicator of soil carbon age, we measured radiocarbon in the MAOM fraction but found that within and across sites, Δ 14 C was unrelated to mycorrhizal dominance, climate, or soil factors, suggesting that additional site-specific factors may be primary determinants of long-term SOM persistence. Our results indicate that while soil mineralogy primarily controls SOM C and N concentrations, the distribution of SOM among density fractions depends on the composition of vegetation and microbial communities, with these effects varying across sites with distinct climates. Here we also suggest that within biomes, the age of mineral-associated soil carbon is not clearly linked to the factors that control concentrations of MAOM C and N.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient

In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO43-). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO43- from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO₄³⁻ and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO₄³-. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.

arbuscular mycorrhizal fungi↗
DOE OSTI2023

Elevated temperature alters microbial communities, but not decomposition rates, during 3 years of in situ peat decomposition

ABSTRACT Peatlands are large carbon sinks with primary production outpacing decomposition of organic matter. Results from the S pruce and P eatland R esponses U nder C hanging E nvironments (SPRUCE) study show net losses of organic matter and increased greenhouse gas production from peatlands in response to whole-ecosystem warming. Here, we investigated how warming and elevated CO 2 impact peat microbial communities and peat soil decomposition rates and characterized microbial communities through amplicon sequencing and compositional changes across four depth increments. Microbial diversity and community composition were significantly impacted by soil depth, temperature, and CO 2 treatment. Bacterial/archaeal α-diversity increased significantly with increasing temperature, and fungal α-diversity was lower under elevated CO 2 treatments. Trans domain microbial networks showed higher complexity of microbial communities in decomposition ladder depths from the warmed enclosures, and the number of highly connected hub taxa within the networks was positively correlated with temperature. Methanogenic hubs were identified in the networks constructed from the warmest enclosures, indicating increased importance of methanogenesis in response to warming. Microbial community responses were not however reflected in measures of peat soil decomposition, as warming and elevated CO 2 had no significant short-term effects on soil mass loss or composition. Regardless of treatment, on average only 4.5% of the original soil mass was lost after 3 years and variation between replicates was high, potentially masking treatment effects. Previous results at the SPRUCE experiment have shown warming is accelerating organic-matter decomposition and CO 2 and CH 4 production, and our results suggest these changes may be driven by warming-induced shifts in microbial communities. IMPORTANCE Microbial community changes in response to climate change drivers have the potential to alter the trajectory of important ecosystem functions. In this paper, we show that while microbial communities in peatland systems responded to manipulations of temperature and CO 2 concentrations, these changes were not associated with similar responses in peat decomposition rates over 3 years. It is unclear however from our current studies whether this functional resiliency over 3 years will continue over the longer time scales relevant to peatland ecosystem functions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions

ABSTRACT Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context—propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)—is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering. IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).

59 BASIC BIOLOGICAL SCIENCES↗