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Data for Impacts of Legacy and Contemporary Nitrogen Inputs on N2O and CO2 Emissions in Miscanthus and Maize Cultivated Soils
Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteu s ( M × g ) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M × g and maize were grown. A 150-day soil incubation experiment was conducted using soils from a long-term M × g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in M × g soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient-rich soils, also increased with higher legacy fertilization rates in M × g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops.
Algae Biofilm Produced from Anaerobic Digester Wastewater Demonstrated as Biofertilizer for Dwarf Wheat
Aims: To correlate yield of dwarf wheat fertilized with algae biofilm produced using anaerobic digester effluent (digestate) from a municipal water resource recovery facility as nutrient source and compare with yield using non-algae biofilm based fertilizers and a negative control. Study Design: Greenhouse testing for measurement of biomass yields and statistical analysis of wheat yield data results. Place and Duration of Study: Department of Biological Engineering Algae Processing and Products Facility greenhouse between March and June, 2024. Methodology: Yield of a dwarf cultivar of red spring wheat was measured as a function of four treatments including three fertilizers and a negative control: (1) algae biofilm cultivated on anaerobic digester effluent, (2) positive control of Osmocote commercial slow release fertilizer, (3) anaerobic digester biosolids, and (4) negative control with no fertilizer addition. Results: Average yield values (gm) for the four treatments were: (1) 1.25, (2) 0.99, (3) 0.72, and (4) 0.52, respectively. Algae biofilm fertilizer performed significantly better than Osmocote with P = .002, anaerobic digester biosolids with P = .05, and no fertilizer addition with P = .05. Struvite, a slow release fertilizer, was observed to be associated with the algae biofilm as a precipitate of the high concentrations of nutrients within the anaerobic digester water. Struvite (MgNH4PO46H2O) releases plant available nitrogen and phosphorus over time and is biologically precipitated due to the increase in solution pH as a result of photosynthesis by the algae biofilm. Conclusion: Algae biofilm cultivated on anaerobic digester wastewater can serve as a biofertilizer for recycling nutrients within the biosphere for sustainable nutrient management.
Impacts of Legacy and Contemporary Nitrogen Inputs on N 2 O and CO 2 Emissions in Miscanthus and Maize Cultivated Soils
ABSTRACT Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteus (M×g) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N 2 O) and carbon dioxide (CO 2 ) emissions, as well as key N cycling genes in soils where M×g and maize were grown. A 150‐day soil incubation experiment was conducted using soils from a long‐term M×g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha −1 year −1 ) and a contemporary amendment (60 mg N kg −1 ) with negative control (0 mg N kg −1 ). We observed significant increases in cumulative N 2 O emissions in Mxg soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amo A gene abundance, which plays a significant role in nitrification in nutrient‐rich soils, also increased with higher legacy fertilization rates in M×g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N 2 O emissions, but cumulative CO 2 emissions and amo A gene abundance significantly increased. The abundances of nor B genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N 2 O emissions, particularly for perennial bioenergy crops.
Agricultural Management Legacy Effects on Switchgrass Growth and Soil Carbon Gains
Switchgrass ( Panicum virgatum L.) is a native North American grass currently considered a high-potential bioenergy feedstock crop. However, previous reports questioned its effectiveness in generating soil organic carbon (SOC) gains, with resultant uncertainty regarding the monoculture switchgrass's impact on the environmental sustainability of bioenergy agriculture. We hypothesize that the inconsistencies in past SOC accrual results might be due, in part, to differences in prior land management among the systems subsequently planted to switchgrass. To test this hypothesis, we measured SOC and other soil properties, root biomass, and switchgrass growth in an experimental site with a 30-year history of contrasting tillage and N-fertilization treatments, 7 years after switchgrass establishment. We determined switchgrass' monthly gross primary production (GPP) for six consecutive years and conducted deep soil sampling. Nitrogen fertilization expectedly stimulated switchgrass growth; however, a tendency for better plant growth was also observed under unfertilized settings in the former no-till soil. In topsoil, SOC significantly increased from 2007 to 2023 in fertilized treatments of both tillage histories, with the greatest increase observed in fertilized no-till. Fertilized no-till also had the highest particulate organic matter content in the topsoil, with no differences among the treatments observed in deeper soil layers. However, regardless of fertilization, the tillage history had a strong effect on stratification with depth of SOC, total N, and microbial biomass C. Results suggested that historic and ongoing N fertilization had a substantial impact on switchgrass growth and soil characteristics, while tillage legacy had a much weaker, but still discernible, effect.
germs-lab/PAPER_miscanthus_soil_response
Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteus (M×g) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M×g and maize were grown. A 150-day soil incubation experiment was conducted using soils from a long-term M×g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in Mxg soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient-rich soils, also increased with higher legacy fertilization rates in M×g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops.
Connecting Nitrogen Transformations Mediated by the Rhizosphere Microbiome to Perennial Cropping System Productivity in Marginal Lands
The demand for energy from biofuel production is increasing, prompting concerns about the environmental impact and long-term sustainability of bioenergy cropping systems. These cropping systems will make up much of our future landscapes, and threaten to take the place of food cropping systems. Many life cycle analyses of bioenergy sustainability focus on carbon accrual and budgets, since they want to maximize carbon accrual while producing alternative fuel. Less attention has been given to nitrogen (N) dynamics in these systems. N is the most commonly limiting nutrient for plants, but applying nitrogen fertilizer- as we do for most cropping systems – is harmful to the environment, energetically costly, and produces greenhouse gases. In other words, adding nitrogen by fertilizer bioenergy systems could add to the very problems (climate change) it is trying to address. This is especially true for the areas that are proposed for bioenergy systems: marginal lands. These more degraded lands do not complete with food crops, but do have limited nitrogen. If we are to use these marginal lands for bioenergy, we need to understand the mechanisms regulating nutrient acquisition, and identify ways that bioenergy crops can get nitrogen in sustainable ways. Nutrient acquisition in the soil is performed by microbes in the root zone, or rhizosphere. Microbes can either mineralize nitrogen in the soil (from organic forms) or fix nitrogen from the air, in a process called nitrogen fixation. The goal of our project was thus to understand how the rhizosphere microbiome provides nutrients to bioenergy crops on marginal lands. We focus especially on the process of nitrogen fixation, since it has potential to get “fertilizer for free” that has much less environmental harm. We investigated this goal using sites from the DOE Great Lakes Bioenergy Research Center (GLBRC) in the upper Midwest, and associated lab and ‘omics methods. We group our findings into three major areas. First, we showed that nitrogen fixation, the conversion of N2 gas from the air to ammonium that is usable by plants, is performed in bioenergy soils, and benefits switchgrass crops. While more well-studied in leguminous plants, free-living nitrogen fixation can occur in some systems, and represents a potential opportunity to gain ‘free’ sustainable nitrogen source. We identified the nitrogen fixing bacteria that were most active in providing switchgrass with N, and showed that the drivers of nitrogen fixation occurred at a microscale; it is not well-predicted by bulk variables like soil moisture or plant phenology. Second, we showed that nitrogen fixation is not suppressed by long-term fertilizer. We expected that plentiful nitrogen would reduce the symbiotic relationship between nitrogen fixers and plants, and ‘downregulate’ fixation. We did not find evidence for this, either after long-term fertilizer in the field, or short-term fertilizer in the greenhouse. Finally, we identified the root exudates, carbon compounds that are emitted from the root, that best stimulate nitrogen fixation. We found that carbohydrates were better at stimulating fixation than organic acids. We expected these exudates to be emitted from the plant in periods of high N demand, but we found they are emitted when N is plentiful. This suggests that the stimulation of N fixation by plants is a passive process. Overall, we show that nitrogen fixation has potential to support bioenergy cropping system, and future management could develop ways to maximize it. However, this may not be best achieved via the plant – we found very little evidence of a ‘transactional’ system by which plants are controlling when and where nitrogen fixation is stimulated. It will be better to understand how management practices like planting and fertilizer application affect the microscale soil dynamics, which will determine nitrogen fixation rates.
Data for Propagation Method and Planting Density Influence Canopy Developmental Transition and Biomass Productivity in Miscanthus × giganteus
Understanding how establishment practices influence the mechanisms underlying Miscanthus × giganteus (miscanthus) productivity and canopy development is critical for optimizing management. Data was collected during the juvenile (2011–2013) and mature (2024) phases of a long-term field experiment established in Urbana, Illinois, to evaluate the effects of propagation method (plug propagation [PP] and rhizome propagation [RP]), planting density (1.0, 0.75, and 0.25 plants m⁻²), and nitrogen application (0 and 67 kg N ha⁻¹) on end-of-season biomass yield, tiller mass, tiller density, and tiller height. Linear regression models identified the dominant predictors of yield across stand ages and management regimes. Planting density, nitrogen (N) application, and propagation method significantly influenced early yield and canopy development. During the juvenile phase, biomass yield was driven by tiller density due to canopy expansion; in the mature phase, yield became driven by tiller mass. The PP plots produced higher tiller density than the RP plots, resulting in faster canopy closure and higher juvenile-phase yields. Rhizome-propagated (RP) plots produced lower tiller density, but individual tillers were 3.3–6.4 g tiller−1 heavier than PP tillers. After the canopy reached equilibrium, the PP and RP yields were similar because greater RP tiller mass compensated for its lower tiller density. Higher planting density resulted in greater yield and tiller density during the second year (2012), but this effect was absent from the third year (2013) onward. In the juvenile phase, N fertilization enhanced yield by 1.6–3.4 Mg ha−1. Initiating fertilization in 2013 on unfertilized plots produced biomass similar to that in fertilized plots, suggesting yield recovery in the mature phase. These findings revealed that establishment strategies, including propagation method and planting density, influence juvenile miscanthus canopy development and productivity, transitioning from tiller-density- to mass-dominated yields, but not mature phase productivity.
Diverse PFAS produce unique transcriptomic changes linked to developmental toxicity in zebrafish
Per- and polyfluoroalkyl substances (PFAS) are a widespread and persistent class of contaminants posing significant environmental and human health concerns. Comprehensive understanding of the modes of action underlying toxicity among structurally diverse PFAS is mostly lacking. To address this need, we recently reported on our application of developing zebrafish to evaluate a large library of PFAS for developmental toxicity. In the present study, we prioritized 15 bioactive PFAS that induced significant morphological effects and performed RNA-sequencing to characterize early transcriptional responses at a single timepoint (48 h post fertilization) after early developmental exposures (8 h post fertilization). Internal concentrations of 5 of the 15 PFAS were measured from pooled whole fish samples across multiple timepoints between 24–120 h post fertilization, and additional temporal transcriptomics at several timepoints (48–96 h post fertilization) were conducted for Nafion byproduct 2. A broad range of differentially expressed gene counts were identified across the PFAS exposures. Most PFAS that elicited robust transcriptomic changes affected biological processes of the brain and nervous system development. While PFAS disrupted unique processes, we also found that similarities in some functional head groups of PFAS were associated with the disruption in expression of similar gene sets. Body burdens after early developmental exposures to select sulfonic acid PFAS, including Nafion byproduct 2, increased from the 24–96 h post fertilization sampling timepoints and were greater than those of sulfonamide PFAS of similar chain lengths. In parallel, the Nafion byproduct 2-induced transcriptional responses increased between 48 and 96 h post fertilization. PFAS characteristics based on toxicity, transcriptomic effects, and modes of action will contribute to further prioritization of PFAS structures for testing and informed hazard assessment.
Depth-dependent links between microbial taxa and nitrous oxide emissions in a long-term cotton cropping system employing soil health practices
Long-term management practices can shape soil microbial communities in ways that influence nitrogen (N) dynamics and nitrous oxide (N 2 O) emissions. We leverage a 41-year continuous cotton cropping experiment with contrasting tillage, cover cropping, and N fertilization regimes to investigate how these long-term strategies influence soil microbial communities and their associations with N 2 O fluxes during the cotton growing season. Using 16S rRNA gene metabarcoding, we assessed microbial composition in surface and subsurface soils and evaluated its relationship with temporal N 2 O emissions. Among the management practices, N fertilization – a known driver of N 2 O emissions – had the strongest effect on microbial community composition and was linked to a greater number of taxa correlated to N 2 O emissions, particularly in surface soils. Soil pH emerged as a key variable influencing microbial structure across depth and was negatively associated with both N 2 O emissions and microbial composition in the surface layers of fertilized soils. In total, 57 archaeal/bacterial taxa were correlated with N 2 O fluxes, but only seven were shared across depths, suggesting distinct microbial contributors in surface and subsurface soils. Several of these taxa have been previously reported to be associated with N and C cycling processes such as nitrate respiration or carbon turnover, indicating functional context to their correlation with N 2 O fluxes. Temporal shifts in the abundance of key taxa aligned with seasonal peaks in N 2 O emissions, notably in early and late August, and were most pronounced under conventional tillage, hairy vetch cover cropping, and N fertilization. While 16S-based associations cannot confirm functional gene presence or activity, these findings demonstrate that long-term fertilization and associated soil acidification are dominant drivers of microbial shifts linked to N 2 O emissions and highlight the importance of accounting for depth-specific and seasonal microbial dynamics when evaluating management impacts on greenhouse gas emissions.
Phosphorus budgets of intensively managed row crops at a long–term agroecosystem research site in the upper US Midwest
Phosphorus (P) budgets for cropping systems provide insights for keeping soil P at optimal levels for crops while avoiding excess inputs. We quantified 12 years of P inputs (fertilizer and atmospheric deposition) and outputs (harvest and leaching losses) for replicated maize (Zea mays L.)—soybean (Glycine max L.)—wheat (Triticum aestivum) crop rotations under conventional, no-till, reduced input, and biologically based (organic without compost or manure) management systems at the Kellogg Biological Station LTAR site in southwest Michigan. Conventional, no-till, and reduced input systems were fertilized between 13 and 50 kg P ha –1 depending on year. Soil test phosphorus (STP) was measured at 0- to 25-cm depth every autumn. Leached P was measured as dissolved P in the soil solution sampled beneath the rooting depth and combined with modeled percolation. Fertilization and harvest were the predominant P fluxes in the fertilized systems, whereas only harvest dominated P flux in the unfertilized organic system. Leaching losses were minor terms in the budgets, but leachate concentrations were nevertheless close to the range of concern for downstream eutrophication. Over the 12-year study period, the organic system exhibited a negative P balance (–82.0 kg P ha –1 ), coinciding with suboptimal STP levels, suggesting a need for P supplementation. In contrast, the fertilized systems showed positive P balances (mean: 70.1 kg P ha –1 ) with STP levels well above agronomic optima. Results underscore the importance of tailored P management strategies to sustain crop productivity while mitigating environmental impacts.
Microbially mediated nitrification improves modeled temperate forest responses to declining nitrogen deposition
As nitrogen deposition declines across the US, uncertainty remains in whether temperate forests will continue to sequester carbon. This uncertainty is amplified by ecosystem models that inaccurately capture the microbial mechanisms that drive soil carbon sequestration and nitrogen loss. Further, even soil process models that represent decomposer microbes and better capture soil carbon retention under nitrogen deposition broadly underrepresent microbial nitrogen transformations. To address this limitation, we leveraged three decades of biogeochemical cycling data from a whole-watershed nitrogen fertilization experiment to incorporate microbially-driven nitrification in the FUN-CORPSE (Fixation and Uptake of Nitrogen-Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment) model. Our objectives include: 1) Reproducing key ecosystem responses to fertilization, 2) Integrating microbially-explicit nitrification in FUN-CORPSE, and 3) Assessing modeled soil C and N under projected N deposition shifts. FUN-CORPSE accurately represented soil C and streamwater N losses under ambient N deposition and captured how fertilization induced a 25 % decline in plant C cost of N acquisition, reducing decomposition and increasing soil C. Furthermore, with microbially-explicit nitrification, FUN-CORPSE captured the 100 % increase in nitrification rates and the 50 % increase in streamwater nitrate loss under N fertilization. Specifically, incorporating microbial nitrification improved modeled streamwater N leaching from R 2 = 0.01 to R 2 = 0.57. Under declining N deposition, FUN-CORPSE simulates that N losses recover more quickly than soil C pools. However, the predicted return of soil C to pre-fertilized levels suggests that additional C sequestered due to N deposition may be vulnerable to loss over the next century.
Historical Land Management Alters New Soil Carbon Inputs by Annual and Perennial Bioenergy Crops
Bioenergy and bioproduct markets are expanding to meet demand for climate-friendly goods and services. Perennial biomass crops are particularly well suited for this goal because of their high yields, low input requirements, and potential to increase soil carbon (C). However, it is unclear how much C is allocated into belowground pools by perennial bioenergy crops and whether the belowground benefits vary with nitrogen (N) fertilizer inputs. Using in situ 13 C pulse-chase labeling, we tested whether the sterile perennial grass Miscanthus × giganteus (miscanthus) or annual maize transfers more photosynthetic C to belowground pools. The experiment took place at two sites in Central and Northwest (NW) Iowa with different management histories and two nitrogen (N) fertilizer rates (0 and 224 kg N ha −1 year −1 ) to determine if the fate of plant-derived soil C depends on soil fertility and crop type (perennial or annual). Maize allocated a greater percentage of total new 13 C to roots than miscanthus, but miscanthus had greater new 13 C in total and belowground plant biomass. We found strong interactions between site and most soil measurements—including new 13 C in mineral and particulate soil organic matter (SOM) pools—which appears to be driven by differences in historical fertilizer management. The NW Iowa site, with a history of manure inputs, had greater plant-available nutrients (phosphorus, potassium, and ammonium) in soils, and resulted in less 13 C from miscanthus in SOM pools compared to maize (approximately 64% less in POM and 70% less in MAOM). In more nutrient-limited soils (Central site), miscanthus transferred 4.5 times more 13 C than maize to the more stable mineral-associated SOM pool. Our results suggest that past management, including historical manure inputs that affect a site's soil fertility, can influence the net C benefits of bioenergy crops.
Mapping Nitrogen Pathways in Organic Manure through GCAM
As the world has become more and more globalized, a need for a comprehensive and extensive modelling system that maps out the vast majority of processes and items around the world and can display how interdependent they are. Furthermore, such a model should be able to predict future processes and values such that it can guide scientific thinking and policy. This is where the importance of GCAM becomes so apparent. GCAM, the Global Change Analysis Model, that incorporates many different fields and can predict such a wide variety of processes. As the model expands and encompasses more fields and goes into greater detail, there is a need for previously incorporated processes to be further fleshed out. My project is dedicated to creating the organic nitrogen fertilizer pathway, such that there are two nitrogen fertilizer pathways, synthetic and organic (manure). Previously, only synthetic fertilizer was included, with all organic fertilizer (manure) being omitted from the model. Developing the synthetic path is relatively easy, as the process for creating synthetic fertilizer is an industrial process that has been perfected over decades, and thus has a very precise input/output coefficient of nitrogen, but determining that same coefficient for organic manure is much harder, because, well, digestion is not an industrial process, especially considering the many different types of animals have different processes, and a good amount of the manure they produce won’t be applied to the soil. I obtained data from the UN’s FAO on manure nitrogen applied to soil, and filled in the gaps and created many different visualizations to help comprehend the data. These findings will foster a greater understanding of nitrogen flows, which is crucial to fields like industrial agriculture, polluting runoff, and nitrifying bacteria and archaea in the soil.
Historical land management alters new soil carbon inputs by annual and perennial bioenergy crops
Bioenergy and bioproduct markets are expanding to meet demand for climate friendly goods and services. Perennial biomass crops are particularly well suited for this goal because of their high yields, low input requirements, and potential to increase soil carbon (C). However, it is unclear how much C is allocated into belowground pools by perennial bioenergy crops and whether the belowground benefits vary with nitrogen (N) fertilizer inputs. Using in situ 13C pulse-chase labeling, we tested whether the sterile perennial grass Miscanthus × giganteus ( miscanthus ) or annual maize transfers more photosynthetic C to belowground pools. The experiment took place at two sites in Central and Northwest (NW) Iowa with different management histories and two nitrogen (N) fertilizer rates (0 and 224 kg N ha-1 yr-1) to determine if the fate of plant-derived soil C depends on soil fertility and crop type (perennial or annual). Maize allocated a greater percentage of total new 13C to roots than miscanthus, but miscanthus had greater new 13C in total and belowground plant biomass. We found strong interactions between site and most soil measurements – including new 13C in mineral and particulate soil organic matter (SOM) pools –which appear to be driven by differences in historical fertilizer management. The NW Iowa site, with a history of manure inputs, had greater plant-available nutrients (phosphorus, potassium, and ammonium) in soils, and resulted in less 13C from miscanthus in SOM pools compared to maize (approximately 64% less in POM and 70% less in MAOM). In more nutrient-limited soils (Central site), miscanthus transferred 4.5 times more 13C than maize to the more stable mineral-associated SOM pool. Our results suggest that past management, including historical manure inputs that affect a site’s soil fertility, can influence the net C benefits of bioenergy crops.
Cover crops and poultry litter impact on soil structural stability in dryland soybean production in southeastern United States
Abstract This study explored the efficacy of soil aggregate indices in quantifying soil structural development, utilizing 5‐year field experiment data from the Southeastern United States. The experiment utilized a split‐plot design with cover crops (native vegetation as control, cereal rye (Secale cerealeL.), winter wheat (Triticum aestivum), hairy vetch (Vicia villosa), and mustard (Brassica rapa) plus cereal rye as the main factor and fertilizer source (no fertilizer as control, inorganic fertilizer with phosphorus, potassium, and elemental sulfur, and poultry litter) as the secondary factor. Aggregate size fractions were determined using the wet‐sieving method, and aggregate stability index (ASI), mean weight diameter (MWD), geometric mean diameter (GMD), and fractal dimension (FD) were calculated to assess soil structural stability. Main effects results indicated that cereal rye (55.11%) and poultry litter (50.97%) exhibited the highest ASI values. The highest MWD, GMD, and FD were observed under mustard plus cereal rye (1.187 mm), cereal rye (0.462 mm), and hairy vetch (2.573), respectively. Principal component analysis revealed that cover crops significantly improved soil aggregate structure and stability, overcoming limitations of sole fertilization practices. Regression analysis suggested that ASI, MWD, and GWD positively correlated with soil organic carbon, whereas FD negatively correlated with MWD, GMD, and ASI. Principal component analysis exhibited that FD decreased with increasing soil organic carbon, ASI, MWD, and GMD, demonstrating that lower FD values indicate enhanced soil aggregation and structure. Assessed indices, FD included, effectively gauged soil structural stability. These metrics should be prioritized in managerial decisions to support soil productivity and health in agricultural systems.
Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning
Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.
Data for Genetic Variation in Zea mays Influences Microbial Nitrification and DeNitrification in Conventional Agroecosystems
Nitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N2O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. To capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds ( Z. mays ssp. mays ), ex-PVP hybrids ( Z. mays ssp. may s), and teosinte ( Z. mays ssp. mexicana and Z. mays ssp. parviglumis ). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. Here we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N2O fluxes, with teosinte plots producing less GHG than maize plots. Taken together, these results suggest that Zea genetic variation can lead to changes in N-cycling processes that result in N leaching and N2O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability.