Biology subjects

Yang, W. H.

Publications and source records attributed to Yang, W. H..

10 recordsLinked to original sources

bioRxiv2026

Drought Dominates Engineered Lipid Sink Effects on Sorghum Physiology and Carbon Allocation

Determining the environmental limits that govern how engineered metabolic traits control whole-plant carbon (C) allocation is essential for developing climate-resilient bioenergy systems. Oil-enhanced sorghum offers a promising strategy to boost aboveground energy density, yet its system-wide effects on root C investment and soil C delivery, particularly under drought, are largely uncharacterized. Here, we provide the first comprehensive assessment of these interactions using whole-plant 13CO2 continuous labeling, depth-specific sampling of roots and rhizosphere soil, and coordinated measurements of photosynthesis, stomatal anatomy, tissue nitrogen, and root non-structural carbohydrates (NSCs). Under well-watered conditions, oil enhancement produced distinct aboveground physiological changes, including slightly longer stomata, lower stomatal density, significantly higher leaf nitrogen concentration and biomass, and greater leaf 13C enrichment. Importantly, these aboveground changes did not translate into detectable shifts in the allocation of recent photosynthate to belowground pools. In contrast, drought acted as a dominant regulatory factor, reorganizing C flow across both genotypes by suppressing photosynthesis and leaf water status, increasing root nitrogen and NSC reserves, and significantly promoting the retention of recent assimilates in shallow root systems. Depth-specific 13C patterns showed that drought reduced new C incorporation into deep roots while increasing 13C enrichment in deep rhizosphere soil, suggesting that drought altered the balance between C investment in root growth and rhizodeposit C inputs at depth. Ultimately, soil moisture availability was an overriding determinant of belowground C partitioning and vertical C delivery, superseding the influence of the engineered lipid sink. These findings provide new mechanistic insight into the environmental constraints on C flow in an engineered bioenergy crop and identify moisture-driven limitations as the primary bottleneck for translating synthetic metabolic innovations into robust, ecosystem-level C outcomes.

ecology↗

bioRxiv2024

Functional traits of ectomycorrhizal trees influence their effects on surrounding soil organic matter properties

Ectomycorrhizal (EM) effects on forest ecosystem carbon (C) and nitrogen (N) cycling are highly variable, which may be due to underappreciated functional differences among EM-associating trees. We hypothesize that differences in functional traits among EM tree genera will correspond to differences in soil organic matter (SOM) dynamics. We explored how differences among three genera of angiosperm EM trees (Quercus, Carya, and Tilia) in functional traits associated with leaf litter quality, resource use and allocation patterns, and microbiome assembly related to overall soil biogeochemical properties. In support of our hypothesis, we found consistent differences among EM tree genera in function traits. Quercus trees had lower litter quality, lower {delta}13C in SOM, higher {delta}15N in leaf tissues, greater oxidative extracellular enzyme activities, and higher EM fungal diversity than Tilia trees, while Carya trees were often intermediary. These functional traits corresponded to overall SOM C and N dynamics and soil fungal and bacterial community composition. Our findings suggest that trait variation among EM-associating tree species should be an important consideration in assessing plant-soil relationships such that EM trees cannot be categorized as a unified functional guild.

ecology↗

bioRxiv2024

Spatial variability of agricultural soil carbon dioxide and nitrous oxide fluxes: characterization and recommendations from spatially high-resolution, multi-year dataset

Mitigating agricultural soil greenhouse gas (GHG) emissions can contribute to meeting the global climate goals. High spatial and temporal resolution, large-scale, and multi-year data are necessary to characterize and predict spatial patterns of soil GHG fluxes to establish well-informed mitigation strategies, but not many of such datasets are currently available. To address this gap in data we collected two years of high spatial resolution (7.4 sampling points ha-1 over 2.0 to 5.4 ha area) in-season soil carbon dioxide (CO2) and nitrous oxide (N2O) fluxes from three commercial sites in central Illinois, one conventionally managed continuous corn and two under conservation practices in corn-soybean rotations typical of the region. At the field-scale, the spatial variability of CO2 was comparable across sites, years, and management practices, but N2O was on average 77% more spatially variable in the conventionally managed site. Analysis of N2O hotspots revealed that although they represent a similar proportion of the sampling areas across sites (conventional: 12%; conservation: 13%), hotspot contribution to field-wide emission was greater in the conventional site than in the conservation sites (conventional: 51%; conservation: 34%). Also, the spatial patterns, especially hotspot locations, of both gases were inter-annually inconsistent, with hotspots rarely occurring in the same location. Overall, our result indicated that traditional field-scale monitoring with gas chambers may not be the optimal approach to detect GHG hotspots in row crop systems, due to the unpredictable spatial heterogeneity of management practices. Still, our sensitivity analysis on the dataset demonstrated that sampling at a spatial resolution of 1.6 and 5.6 points ha-1 can provide reliable (< 25% error) estimates of field-scale soil CO2 and N2O fluxes, respectively.

biochemistry↗

bioRxiv2023

Distinct mechanisms drive plant-nitrifier interactions in topsoil and subsoil

Plants can influence soil microbes through resource acquisition and interference competition, with consequences for ecosystem function such as nitrification. However, how plants alter soil conditions to influence nitrifiers and nitrification rates remains poorly understood, especially in the subsoil. Here, coupling the 15N isotopic pool dilution technique, high throughput sequencing and in situ soil O2 monitoring, we investigated how a deep-rooted perennial grass, miscanthus, versus an adjacent shallow-rooted turfgrass reference shapes nitrifier assembly and function along 1 meter soil profiles. In topsoil, the suppression of ammonia (NH3) oxidizing archaea (AOA) and gross nitrification rates in miscanthus relative to the reference likely resulted from nitrifiers being outcompeted by plant roots and heterotrophic bacteria for ammonium (NH4+). The stronger tripartite competition under miscanthus may have been caused in part by the lower soil organic matter (SOM) content, which supported lower gross nitrogen (N) mineralization, the major soil process that produces NH4+. In contrast, below 10 cm soil depth, significantly greater gross nitrification rates were observed in miscanthus compared to the reference. This was likely driven by the significantly lower oxygen (O2) in miscanthus than reference subsoil, which selected against aerobic heterotrophic bacteria but in favor of AOA. Overall, we found that plants can regulate AOA community structure and function through different mechanisms in topsoil and subsoil, with suppression of nitrification in topsoil and enhancement of nitrification in subsoil.

ecology↗

bioRxiv2023

A new conceptual framework explaining spatial variation in soil nitrous oxide emissions

Soil emissions of nitrous oxide (N2O), a potent greenhouse gas, contribute substantially to global warming from agriculture. Spatial variation in N2O emissions within agricultural fields leads to high uncertainty in the benefits of climate-smart agricultural practices. Here, we present a new conceptual framework explaining spatial variation in soil N2O emissions developed from high spatial resolution automated measurements of soil N2O emissions together with measurements of gross N2O fluxes and soil physicochemical properties in two separately managed maize fields in central Illinois, USA. We found that sub-field locations with consistently low N2O emissions had distinct biogeochemical properties compared to locations where high emissions occurred episodically, leading to spatial variation in which factors control N2O production rates. In the consistent N2O cold spots, soil nitrate (NO3-) and dissolved organic carbon (DOC) constrained N2O production irrespective of changes in soil moisture. In contrast, in the episodic N2O hot spots which had higher soil NO3- and DOC availability, N2O production was stimulated by increases in soil moisture. These findings form the cannon model which conceptualizes how sub-field scale variation in soil NO3- and DOC determines where increases in soil moisture can trigger high soil N2O emissions within agricultural fields.

ecology↗

bioRxiv2023

Particulate organic matter drives spatial variation in denitrification potential at the field scale

High spatiotemporal variability in soil nitrous oxide (N2O) fluxes challenges quantification and prediction of emissions to evaluate the climate change mitigation outcomes of sustainable agricultural practices. Triggers for large, short-lived N2O emission pulses, such as rainfall and fertilization, alter soil oxygen (O2) and nitrate (NO3-) availability to favor N2O production via denitrification. However, the organic C (OC) needed to fuel denitrification may exhibit subfield variation that constrains the potential for high denitrification rates to occur, leading to spatial variation in N2O hot moments. We tested the hypothesis that the particulate organic matter (POM) fraction of soil organic matter controls subfield variation in denitrification potential by regulating availability of dissolved organic C (DOC), the form of OC used by denitrifiers. Among 20 soil samples collected across a maize field in central Illinois, USA, we found that potential denitrification rate was best predicted by POM C concentration (R2 = 0.35). Using multiple linear regression analysis that included other soil properties as explanatory variables, we found that POM C fraction of bulk soil (mg POM C g-1 SOC) was the most important predictor based on regression coefficient size (P < 0.01). Our results, which provide support for our hypothesis, suggest that consideration of the link between C and N cycling may be a key to predicting spatiotemporal variation in soil N2O emissions when denitrification is the dominant N2O source process.

ecology↗

bioRxiv2022

In Silico Evaluation of Plant Nitrification Suppression Effects on Agroecosystem Nitrogen Loss

AO_SCPLOWBSTRACTC_SCPLOWNitrification regulates potential for nitrogen (N) loss from ecosystems because it converts ammonium to nitrate, which is susceptible to leaching and gaseous emissions. Crops can suppress the microbes that perform nitrification by exuding nitrification-inhibiting compounds from their roots and taking up available ammonium, the substrate for nitrification. However, the effect of nitrification suppression on agroecosystem N losses remains poorly characterized, and a lack of temporal synchrony between nitrification, N losses, and nitrification suppression by plants could limit the effect of nitrification suppression. We used the DayCent-CABBI model to evaluate the effectiveness of the suppression of nitrification by sorghum to reduce N2O emissions and nitrate leaching in an energy sorghum/soybean rotation at the Energy Farm in Urbana-Champaign, IL. We simulated nitrification suppression at the measured levels (measNS) and at the maximum measured level applied to the entire growing season (maxNS), and we also explored ways to better utilize nitrification suppression by altering the timing of UAN fertilizer applications. Model experiments showed that most nitrification occurred immediately after fertilizer was applied, whereas nitrification suppression begins to ramp up more than a month after planting. On an annual basis, measNS experiments showed a 1-2% reduction in annual N2O emissions relative to no nitrification suppression (noNS), and maxNS experiments showed a 4-9% reduction in annual N2O emissions relative to noNS. Both nitrification suppression levels showed < 1% reduction in nitrate leaching. Altering the timing of fertilizer applications to better synchronize nitrification suppression with high soil ammonium levels had mixed effects on annual N2O emissions and nitrate leaching and sometimes resulted in increased N losses. The timing of simulated N2O emissions shifted with the timing of fertilization, and N2O emissions from denitrification increased when N2O emissions from nitrification decreased. Increasing N retention during the non-growing season may be more effective and growing-season nitrification suppression for reducing annual N losses in the rainfed Midwest, particularly for NO3- leaching in the early spring. Optimizing the timing of nitrification suppression alongside off-season N retention strategies would best improve the N sustainability of agroecosystems.

ecology↗

bioRxiv2020

Invasive garlic mustard demonstrates stronger relationships with pathotrophic than mycorrhizal fungi

The invasive forest plant garlic mustard (Alliaria petiolata) has been shown to alter soil microbial communities in the northeastern part of its invaded range in the United States, and this disruption of soil communities may contribute to its invasion success. However, garlic mustard allelochemistry can vary with invasion age, and it is not clear whether garlic mustards impacts on soil microbes are consistent over its invaded range. Here, we compare the composition and diversity of soil fungal, bacterial, and archaeal communities among garlic mustard present, absent, and removed treatments in replicated blocks across five forests in the midwestern United States with relatively young garlic mustard invasions (approximately 17-26 years old, with consistent management). We collected samples in May and August, corresponding to garlic mustard active and senescent life history stages. While soil fungal and bacterial/ archaeal communities (based on ITS2 region and 16S rRNA gene DNA sequencing, respectively) differed significantly between different blocks/ forests and over time, we found no significant effect of garlic mustard treatment on soil microbial community composition or the relative abundance of mycorrhizal, saprotrophic, or pathogenic fungal guilds. The lack of garlic mustard impacts on the soil microbial community in recently invaded central Illinois forests suggests that these well-documented impacts in the northeastern United States and in older invasions cannot necessarily be generalized across all environmental contexts.

ecology↗

bioRxiv2019

Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the U.S. to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.\n\nImportanceSoil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the U.S., we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored distinct communities compared to the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising amount of novel microbes with unique adaptations to oligotrophic subsurface conditions.

microbiology↗

bioRxiv2018

Comparing DNA, RNA and protein levels for measuring microbial activity in nitrogen-amended soils

Multi-omic techniques can offer a comprehensive overview of microbial communities at the gene, transcript and protein levels. However, to what extent these levels reflect in situ process rates is less clear, especially in highly complex habitats such as soils. Here we performed microcosm incubations using soil from a site with a history of agricultural management. Microcosms, amended with isotopically labelled ammonium and urea to simulate a fertilization event, showed nitrification (up to 4.1 {+/-} 0.87 {micro}g N-NO3- g-1 dry soil d-1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+[->]NH2OH[->]NO2-[->]NO3-) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria (AOB) Nitrosomonas and Nitrosospira. In contrast, ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox) nitrifiers showed stable gene expression during incubations but were generally more abundant (DNA level) than their Betaproteobacteria AOB counterparts. A strong relationship between nitrification activity and (mostly) betaproteobacterial ammonia monooxygenase (amoA; NH4+[->]NH2OH) and nitrite oxidoreductase (nxrA; NO2-[->]NO3-) transcript abundances revealed that mRNA levels quantitatively reflected measured activity and were generally more sensitive than the DNA level in the microcosm incubations. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing complex microbial communities and provide the molecular means to assess nitrification processes in soils.\n\nIMPORTANCEEven though the use of omic approaches has expanded our knowledge of the diversity of microbial communities in natural and engineered systems, it is less clear how well the use of whole community DNA-, RNA- or protein-based approaches reflect microbial activities. To this end, we directly compared the different levels of molecular information (i.e., DNA, RNA or proteins) in order to assess which level best correlated with isotope-based measurements of nitrification activity in agricultural soils after fertilization. This work reveals the strengths as well as the associated limitations of metagenomic, metatranscriptomic, and metaproteomic approaches in serving as reliable proxies for examining microbial activities in highly diverse environments like soils.

microbiology↗