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This study combines geospatial data and a classification scheme that uses landform elements to derive landform complexes that codify the collection of soils data at variable scale within a single field site. Our experiment was initiated in 2018 on three, 1.6 ha self-contained watersheds representing a southern tall grass prairie (STGP), a system of continuous winter wheat (Triticum aestivum) tilled via offset disking and chisel plow (WWCT), and a minimally disturbed winter wheat system that was periodically planted to a warm season forage, typically sorghum-sudangrass (Sorghum bicolor L.) (WWMT) from 1978 to 2018. A class I soil survey was conducted in 2018 by grid sampling the landscape of all watershed systems at the site. The survey indicated four distinct catena were present across all watersheds, which enabled us to utilize a split block design. This statistical approach allowed for testing of interactions among management practices, landscape position, and soil depth to obtain means and standard errors for different edaphic properties. Using a hydraulic probe, 144 random soil cores were collected to a 30 cm depth at each of the four 4.6 m by 3.8 m replicated blocks per landscape position (tread, riser, and toe) within the three watersheds. Cores were further divided into three depths (0 to 5, 5 to 15, and 15 to 30 cm). Baseline analyses included Mehlich-3, soil sulfate (SO4) and DTPA-sorbitol extractions, soil texture, bulk density, pH, total soil organic carbon (TSOC) and total soil nitrogen (TSN), particulate organic matter (POM), and nonhydrolysable C (RCAH), the resistant fraction of soil organic C. The majority of edaphic properties associated with soil classification varied with landscape position and depth. These included clay content, base saturation (calcium [Ca], magnesium [Mg], and potassium [K]), pH, and sulfur in the form of sulfate (SO4-S) and phosphorus (P). Carbon and N fractions varied with land use, conservation practices, and/or depth. The establishment of replicate sampling stations that account for and limit the spatial variability of edaphic properties within defined landform complexes enables researchers to more accurately quantify the effects of conservation practices and land management.

Scientific concepts and measurements that relate soil and water resources are lacking in several areas, limiting our development of a framework or nexus to assess soil-watershed health. Current research designs rely on land management practices as a proxy for soil condition. Yet, conservation practices are often studied in isolation of each other, and adoption may be driven by state and federal farm programs that can incentivize a given management practice without accounting for current, novel farmer driven adoption of conservation systems. Despite the value of conservation management, its ability to predict soil health is often limited if based solely on land management because chemical, physical and biological processes vary across time, discipline, and terrain. Similarly, connections between soil health and water quality are constrained due to several "grand challenges" that include dissimilar scales and the number of metrics required to correlate soil and water systems. Equally important is soil sampling within the critical flow path(s) that determines sediment/contaminant loading. In some instances, most of the sediment/contaminant loading during a portion or entire year results from channel and bank erosion and not overland flow that may not be within conservation management hectares. Additional challenges include legacy effects of prior land management, climate variability, and varying turnover rates of soil and water systems. This special section aims to frame research issues that inspire new approaches and collaborations for tackling the challenge of leveraging soil health to strengthen water management across plot, field, and watershed scales, using models, statistics, and other novel methodologies. This article is protected by copyright. All rights reserved.

Potential carbon mineralization (Cmin) is a commonly used indicator of soil health, with greater Cmin values interpreted as healthier soil. While Cmin values are typically greater in agricultural soils managed with minimal physical disturbance, the mechanisms driving the increases remain poorly understood. This study assessed bacterial and archaeal community structure and potential microbial drivers of Cmin in soils maintained under various degrees of physical disturbance. Potential carbon mineralization, 16S rRNA sequences, and soil characterization data were collected as part of the North American Project to Evaluate Soil Health Measurements (NAPESHM). Results showed that type of cropping system, intensity of physical disturbance, and soil pH influenced microbial sensitivity to physical disturbance. Furthermore, 28% of amplicon sequence variants (ASVs), which were important in modeling Cmin, were enriched under soils managed with minimal physical disturbance. Sequences identified as enriched under minimal disturbance and important for modeling Cmin, were linked to organisms which could produce extracellular polymeric substances and contained metabolic strategies suited for tolerating environmental stressors. Understanding how physical disturbance shapes microbial communities across climates and inherent soil properties and drives changes in Cmin provides the context necessary to evaluate management impacts on standardized measures of soil microbial activity. Foundation for Food and Agricultural Research [523926]; Samuel Roberts Noble Foundation; General Mills Published version Foundation for Food and Agricultural Research (grant ID 523926), General Mills, and The Samuel Roberts Noble Foundation.

The USDA-ARS Grazinglands Research Laboratory (GRL) operates four research watersheds at three spatial scales representing a gamut of topographic, physiographic, vegetative, or agricultural conditions characteristic of the Southern Great Plains (SGP). The mission of GRL is to address “agricultural sustainability, climate change, ecosystem services, and conservation of natural resources at the watershed or landscape scale”— a primary objective of the USDA-ARS Conservation Effects Assessment Project (CEAP) and the Long-Term Agro-Ecosystem Research (LTAR) network. Assessment of the impacts of conservation practices in agricultural watersheds requires long-term research sites of varying size due to differences in scales required to codify and evaluate the collection of water and soil data. The two larger (> 600 km2) watersheds provide primarily observational data collected for use in hydrologic modeling and large-scale investigations. Modeling is used to quantify benefits of conservation and best management practices to meet selected environmental endpoints. The Little Washita River (LWREW) and Fort Cobb Reservoir (FCREW) experimental watersheds are located in southwestern Oklahoma, USA, and have been part of the GRL research catchment portfolio since 1961 and 2004, respectively. The two smaller catchment areas are located on the grounds of the GRL in Central Oklahoma and are a collection of eight plot-scale watersheds, The Water Research and Erosion Units (WRE) and ten farm-scale watersheds the Grazinglands Research agroEcosystems and the ENvironment (GREEN) Farm that allow replicated manipulative and/or process-based investigations. The WRE, established in 1976, consists of eight contiguous 1.6 ha sized plots. The GREEN Farm comprises 162 ha. Both catchments contain alternative agricultural systems that are evaluated for intensification, sustainability, resiliency, minimization of environmental impact, and profitability in anticipation of climate shifts and extremes. Measurements collected across the four watersheds includes but are not limited to components of water balance, soil erosion, runoff, water quality, nutrient and water use efficiency and soil health.

Plant growth-promoting rhizobacteria (PGPR) have beneficial effects on the host plant that include acquisition of nutrients such as iron (Fe). In this study, the impact of varying concentrations of nanoscale zero-valent iron (NZVI, 1, 2 and 5 g L−1) on a PGPR, Pseudomonas fluorescens' viability, growth and production of siderophores was investigated. Microscale zero-valent iron (MZVI) particles were also included in this study to determine and compare the effects of particle size on Fe acquisition and use by Pseudomonas fluorescens. Siderophores chelate insoluble forms of Fe that are then rendered bioavailable to P. fluorescens as well as some plants. This research indicates that the Fe species derived from lower concentrations of NZVI additions (1 g L−1) are bioavailable and can be utilized as a nutrient by P. fluorescens without the bacteria producing siderophores, an energy intensive process. Also, NZVI application as a fertilizer has promise for better utilization of Fe by plants. P. fluorescens colony forming units (log10 CFU mL−1) growth in cultures containing 1 g L−1 NZVI were significantly higher exceeded (14 units) than those grown without NZVI additions (13 units). The majority of P. fluorescens cells treated with 2 and 5 g L−1 were nonviable and produced limited colony forming units (4 units). The effects of NZVI on siderophore production by P. fluorescens were assessed using chrome azurol S (CAS) plates and real time quantitative reverse transcription PCR (qRT-PCR). Further, expression of genes involved in Fe utilization [putative pvdS (PFL 4190) and a bacterioferritin-associated ferredoxin gene (PFL 4858)] were targeted using real time quantitative reverse transcription PCR (qRT-PCR). Expression of both genes was below detection limits in cultures exposed to NZVI but measurable in MZVI and control treatments, again indicating potential ease in uptake of Fe by P. fluorescens from NZVI. Transmission electron microscopy (TEM) revealed the presence of NZVI particles on the exterior and interior of cells; energy dispersive X-ray spectroscopy (EDS) verified that the material was derived from NZVI and that Fe concentrations were higher in the interior of cells exposed to 1 g L−1 NZVI compared to the control. The research findings from this study indicate that NZVI has the potential to accumulate in plant growth-promoting rhizobacteria and affect the growth of organisms in environments like the rhizobiome which may affect plant growth positively. This research opens up opportunities for future studies to determine the effects of Fe and other nutrients and micronutrients derived from nanomaterials, particularly in oligotrophic systems.

Organic agroecological systems “produce goods using methods that preserve the environment” but can be a substantial source of greenhouse gases (GHG) if not managed properly. The objective of this experiment was to monitor nitrogen (N) and carbon (C) transformations in soils resulting from N additions, water filled pore space (WFPS) and prior tillage management during a simulated freeze-thaw. Incubated soils were taken from two USDA certified organic five-year small grain rotations with mixed legume cover crops that varied only in tillage, conventional (CT) vs. no-tillage (NT) for 3 yr prior to sampling. Soils incubated for 149 d were left unamended or amended with 15N labelled urea or sugar beet residue and maintained at 40, 60 and 80% WFPS. Non-metric multidimensional scaling (NMS) verified that soils amended with beet vs urea clustered separately in ordination space. A two way PerMANOVA analysis confirmed a significant interaction between WFPS and N amendment (p = 0.0002). Prior tillage management, N treatment and WFPS had a significant effect on GHG emission from soils. At 40% WFPS, soil previously in NT amended with beet residues emitted more nitrous oxide (N2O) and carbon dioxide (CO2) relative to soil previously in CT. At 60% WFPS, soil previously in CT amended with beet residues emitted greater N2O and less CO2 relative to soil previously in NT. Our research indicates that climate, carbon stocks and duration of prior tillage management determined the potential of no-till to reduce GHG emissions during a simulated freeze-thaw. Growers should note that as much as 4.51% of nitrates (NO3−) in residues can be lost as N2O at an average soil temperature of 10 °C.

This research aided in determining the impacts on rumen microbial ecology when supplemental forages and feedstuffs were added for 48 h after an initial 24-h in vitro rumen fermentation of orchardgrass (Dactylis glomerata L.) hay. Short-term shifts in bovine rumen community structure (bacteria, archea, protozoa, and fungi) resulting from each separate forage and feedstuff addition were measured using unique operational taxonomic units (OTU)s contained in terminal-restriction fragment length polymorphism (T-RFLP) profiles. The Tukey Vacuum Cleaner Analysis (TVCA) model of bacteria accounted for 66.3% of the treatment variance and OTUs clustered into 3 distinct groupings. The model developed for TVCA analysis of archaea accounted for 76.6% of the treatment variance and OTUs clustered into 2 distinct groupings. The TVCA treatment variance of protozoa accounted for 75.8% and OTUs clustered into 3 distinct groupings. Additions of various forages and feedstuffs did not result in shifts in fungal community structure in the short-term experiment. Our results demonstrate that the rumen ecology using initial T-RFLP profiles in vitro of bacteria, archaea, and protozoa and a TVCA analysis can identify pattern groupings of forages and feedstuffs. Groupings of forages and feedstuffs can help refine supplementation for improved nutritional management of ruminants.

Erosion and sedimentation pose serious threats to soil and water quality worldwide, including in the U.S. southern Great Plains. To better understand these processes in agricultural landscapes, eight 1.6-ha watersheds were established and instrumented in 1976 at the USDA-ARS Grazinglands Research Laboratory, ∼50 km west of Oklahoma City near El Reno, OK, to measure precipitation and surface runoff quantity and quality. Prior to construction, all watersheds were in native grass, primarily big bluestem (Andropogon gerardii Vitman.), little bluestem [Schizachyrium scoparium (Michx.) Nash], and Indiangrass [Sorghastrum nutans (L.) Nash]; afterwards, four of the eight watersheds were cropped initially into winter wheat (Triticum aestivum L.) (two conventionally tilled and two minimally or no-till). Although there have been many peer-reviewed papers from the Water Resources and Erosion (WRE) watersheds, none included all the datasets collected during the period 1977-1999. The objectives of this paper were (a) to present and discuss all archived historical data, including methods of collection and analysis, (b) to provide summary analyses of the variability in each dataset, and (c) to provide details about how to access these datasets. These datasets are valuable resources to improve modeling in relation to land use and management changes, climate variability, and other environmental factors and may be useful in developing strategies to mitigate environmental impacts of agricultural systems. They are available at https://doi.org/10.15482/USDA.ADC/1518421.

The fertility and soil health of organic agroecosystems are determined in part by the size and turnover rate of soil carbon (C) and nitrogen (N) pools. Our research contrasts the effects of best management practices (BMP) (reduction in soil disturbance, addition of organic amendments) on C and N cycling in soils from two field sites representing five organic agroecosystems. Total soil organic C (SOC), a standard measure of soil health, contains equal amounts of biologically and non-biologically active C that is not associated with release of mineral N. A three-pool first-order model can be used to estimate the size and turnover rates of C pools but requires data from a long-term incubation. Our research highlights the use of two rapid C fractions, hydrolysable and permanganate (0.02 M) oxidizable C, to assess shifts in biologically active C. Adoption of BMP in organic management systems reduced the partitioning of C to the active pool while augmenting the slow pool C. These pools are associated with potentially mineralizable N supplied by residues, amendments and soil organic matter affecting the concentration and release of mineral N to crops. Our data show that minimizing disturbance (no tillage, pasture) and mixed compost additions have the potential to reduce carbon dioxide emissions while enhancing slow pool C and or its turnover, a reservoir of nutrients available to the soil biota. Use of these rapid, sensitive indicators of biological C activity will aid growers in determining whether a BMP fosters nutrient loss or retention prior to shifts in total SOC.

This paper reports studies to elucidate the potential relationships between porosity and surface functionality of biochar and soil water retention characteristics. The biochars studied were produced from pine wood (PW), hybrid poplar wood (HP), and pine bark (PB) at temperatures of 350°C and 600°C. The resulting materials were then oxidized under air at 250°C to generate oxygenated functional groups on the surface. All biochar were thoroughly characterized (surface and bulk properties) and their hydrological properties measured in blends with Quincy sand. We prepared 39 microcosms for this study to examine the effect of biochar functionalities and porosity on the hydro-physical properties of Quincy sand. Each biochar was thoroughly mixed with the soil at 20gkg-1. The field capacity, wilting point, and total available soil moisture of the bio-char/Quincy sand mixtures were measured for both dry and wet ranges. The soil water potentials and soil water contents were fitted using the model of van Genuchten. Our results indicated that the amount of oxygenated functional groups on the surface of biochars clearly differentiated the biochars in terms of hydrophilicity, with the oxidized biochars being superior, followed by the low-temperature biochars, while the high temperature biochars possessed lowest hydrophilicity. As a result, oxidized biochars exhibited better wettability compared to unoxidized biochars, regardless their feedstock source. Significant correlation occurred between the total acidic functional groups on biochar surface and water contents at different matric potentials. Over a wide range of soil water potentials, oxidized biochar-soil mixtures held more water than the unoxidized biochar-soil mixtures except in the region between -0.1 and -5kPa of ψ, which is near saturation. Soil water contents at different matric potentials were significantly inter-correlated (P

Diverse crop rotations, cover crops and the possibility of integrating livestock make organic systems potentially more sustainable than other agroecosystems. Lower reactive nitrogen (N) in organic systems minimizes the potential for N losses. However, addition of organic manures and residues containing mineralizable N and carbon (C) have the potential to enhance nitrous oxide (N 2 O) emissions. We conducted a 39 d laboratory incubation to assess key microbiological drivers controlling nitrification and denitrification in long-term organic agroecosystems during simulated freeze-thaw cycles. Soils were collected from two annual organic vegetable systems receiving 1) mixed-compost, or 2) broiler litter and 3) an organic perennial pasture system cropped to vegetables every third year. Soil microcosms amended with 15 N labelled sugar beet residue or unamended were maintained at 40, 60 and 80% of water filled pore space (WFPS). Significant N 2 O was emitted (4287–6138 μg kg −1 soil) via denitrification from amended soil microcosms at 3 °C and 80% WFPS. Archaeal (AOA) and bacterial (AOB) nitrifier amoA gene copies were affected by temperature and reactive N species during freeze-thaws. Long-term organic vegetable cropping systems receiving mixed-compost additions had the potential to accumulate C and immobilize excess reactive soil N (particularly nitrates) thereby improving soil health and reducing N 2 O emissions.

This paper reports the effects of pyrolysis temperature on biochar to oxidation by air. Eighteen biochars were produced from the pyrolysis of Douglas fir wood (DFW), Douglas fir bark (DFB), and hybrid poplar wood (HP) at six temperatures (623, 673, 723, 773, 823 and 873 K) in a lab scale spoon reactor. The oxidation step for all biochars produced was conducted at 523 K in the presence of air in a spoon reactor. The elemental and proximate analyses of all the oxidized and un-oxidized chars suggest that the carbonaceous materials produced at low temperature are more susceptible to oxidation than those produced at high temperature. A number of surface properties of resultant biochars were examined to better understand how pyrolysis temperatures and feedstock sources relate to the development of surface characteristics. The removal of volatiles during the pyrolysis step resulted in the gradual creation of microporosity detectable by CO 2 adsorption but which was difficult to detect with N 2 adsorption, suggesting that the chars contain micropores mostly less than 1 nm in entrance dimension. In some cases, the surface area decreased after being oxidized likely due to the blockage of micropores by oxygen-containing functional groups. The surface composition determined by XPS and Boehm titration confirms that greater quantities of carbonyl and carboxyl groups are formed on biochars produced at low temperature. The formation of these oxygenated functional groups contributes to add negative charges on the surface and consequently the pH at the point of zero charge increases for un-oxidized biochars.

Manure is an impending source of carbon (C), sulfur (S) and water (H2O). Consequently, microbial populations utilize these constituents to produce methane (CH4), carbon dioxide (CO2), greenhouse gases (GHGs), and hydrogen sulfide (H2S). Application of nanoparticles (NPs) to stored manure is an emerging GHG mitigation technique. In this study, two NPs: nano zinc oxide (nZnO) and nano silver (nAg) were tested in swine manure stored under anaerobic conditions to determine their effectiveness in mitigating gaseous emissions and total gas production. The biological sources of gas production, i.e., microbial populations were characterized via Quantitative Polymerase Chain Reaction (qPCR) analysis. Additionally, pH, redox, and VFAs were determined using standard methods. Each treatment of the experiment was replicated three times and NPs were applied at a dose of 3 g/L of manure. Also, headspace gas from all treatment replicates were analyzed for CH4 and CO2 gas concentrations using an SRI-8610 Gas Chromatograph and H2S concentrations were measured using a Jerome 631X meter. Nanoparticles tested in this study reduced the cumulative gas volume by 16%–79% compared to the control. Among the NPs tested, only nZnO consistently reduced GHG concentrations by 37%–97%. Reductions in H2S concentrations ranged from 87% to 97%. Gaseous reductions were likely due to decreases in the activity and numbers of specific gas producing methanogenic archaea and sulfate reducing bacterial (SRB) species.

Modified protocols were adapted for PCR and culture based methods for the analysis of Pseudomonas fluorescens cells exposed to nanoscale zero-valent iron (NZVI) and iron (Fe) in bacterial growth nutrient media was determined by a modified atomic absorption spectrometric (AAS) analysis method. We adapted sets of microarray primers used to quantify gene expression of pvdS and a bacterioferritin-associated ferredoxin gene for use in real-time quantitative reverse transcription (qRT-PCR) analysis. pvdS is one of a cluster of genes regulating the synthesis of the siderophore pyoverdine that was also measured using chrome azrul S (CAS) plates. • The current protocol provides a detailed qRT-PCR method for quantifying genes involved in the acquisition and utilization of Fe in P. fluorescens cells exposed to NZVI. • The qRT-PCR results were independently corroborated with 2 culture based methods, growth curves and chrome azurol S (CAS) plate. • The modified AAS method was used to measure Fe in Tryptic Soy Broth (TSB) medium where sodium (Na) causes inference in iron measurement. Method name: Real-time quantitative reverse transcription (qRT-PCR) analysis, Keywords: qRT-PCR, Azrul S (CAS), Atomic absorption, Pyoverdine, Ferredoxin

Eighteen biochar samples were produced from the pyrolysis of Douglas fir wood (DFW), Douglas fir bark (DFB), and hybrid poplar wood (HP) at six temperatures (623, 673, 723, 773, 823 and 873 K) in a lab scale spoon reactor. Changes in the bulk composition of the biochar produced were examined by elemental and proximate analyses. The mass fraction of volatiles, oxygen and the ratios of oxygen to carbon (O/C) and hydrogen to carbon (H/C) decreased linearly with pyrolysis temperature. Surface properties of all the biochars produced (SEM morphology, CO 2 and N 2 adsorption, XPS analysis, Boehm titration, cation exchange capacity (CEC) and ζ-potential) were also studied. The removal of volatiles resulted in the gradual creation of microporosity detectable by CO 2 adsorption but which was difficult to detect with N 2 adsorption, suggesting that the chars contain micropores mostly less than 1 nm in entrance dimension. The XPS and Boehm titration confirmed that most oxygenated surface functional groups (presence of carbonyl, carboxyl and hydroxyl groups) are gradually removed as pyrolysis temperature increases. The changes in surface charge were studied by ζ-potential measurements and were found to vary directly with the content of oxygenated functional groups. Properties that depend on both surface area and the surface oxygenated functional groups, such as the cation exchange capacity, showed a more complex behavior. The composition of the ash and associated properties such as pH and electric conductivity (EC) were also measured. The total alkaline content increases with pyrolysis temperature leading to higher pHs and ECs.

Sodic soil remediation is an expensive, lengthy process during which producers need tools to demonstrate that sodium (Na+) remediation practices are improving soil health. The objective of this study was to determine if soil biological indicators can provide a short term assessment of the effectiveness of chemical management strategies used to remediate northern Great Plains sodium affected soils. This randomized complete block split-plot research experiment was conducted in a grassland which was converted to annual row crops. The soil at the site was an Exline (fine, smectitic, frigid Leptic Natrudolls). The experiment contained two drainage treatments (tile drained and no-drainage) and four chemical amendments (4.5 Mg ha−1 of gypsum, 9.1 Mg ha−1 of gypsum, 9.1 Mg ha−1 spent sugar beet lime, and a no amendment control). Base-line soil samples for biological assessment were collected in the fall of 2012 after tile drainage was installed. The sodium adsorption ratio (SAR) ranged from 0.4 to 16.7 with a range of electrical conductivity (EC) of 0.4–0.8 dS m−1. Gypsum and lime amendments were applied in 2013. Soil samples were collected for assessing soil health before and after application of amendments and throughout the growing season. This study utilizes a novel application of successional vector trajectories to compare shifts in measured soil health parameters associated with land use change and remediation of sodicity. Soil samples were analyzed for percent total soil carbon (C), nitrifier and denitrifier gene copies, soil enzyme assays (nitrate reductase, ammonia monooxegenase, urease, β glucosidase, alkaline phosphatase, arylsulfatase and fluorescein diacetate hydrolysis), EC, pH, SAR, and soil texture. Gene copies and enzyme activities were successfully used to differentiate between land uses and amendment applications. Ammonia oxidizing bacterial gene copies were higher where cropland was amended with gypsum. Successional vectors verified a significant shift in soil health due to land use change and amendment application. Gypsum applications reduced SAR, but increased soil EC. This work demonstrates that soil enzyme activities and gene copy numbers can be used to detect improvements in soil health.

The present study quantifies the transport of Escherichia coli pathogenic O157:H7 and nonpathogenic K12 strains in water-saturated Quincy sand (QS) columns amended with oxidized (OX) or unoxidized (UO) pine wood (PW) or pine bark (PB) biochar produced at either 350 or 600 °C. Our results showed that (1) the addition of oxidized biochar into QS columns enhanced the transport of E. coli O157:H7 by 3.1 fold compared to the unoxidized counterparts, likely because of an increase in the repulsive forces due to their higher negative charge densities. (2) The retention of E. coli O157:H7 was 3.3 fold higher than that of E. coli K12 in all biochar-amended sand columns. (3) Increased application rates of unoxidized PW600 biochar from 0 to 20 wt % led to a reduction in the transport of E. coli O157:H7 and K12 from 98 to 10% and from 95 to 70%, respectively. Our data showed that mixing sand with PW350-UO at a 20 wt % application rate almost completely retained the pathogenic E. coli in the subsurface, suggesting that utilizing sand mixed with biochar can act as a promising biofilter capable of protecting natural aquafers from pathogens.

This research compared the accuracy of laboratory reference measurements of soil C and N fractions with soil reflectance spectra acquired using a portable field spectroradiometer with an illuminating contact probe. Soil samples were taken from eight, 1.6 ha watersheds, located in El Reno, Oklahoma on native warm season grasslands and agronomic managements with landform complexes serving as replicates within and among treatments. Soil samples were taken from 0&ndash, 30-cm. Measurements included total soil organic carbon (TSOC), total soil nitrogen (TSN), residual C of acid hydrolysis (RCAH), and particulate organic matter C (POMC) and N (POMN). Soil reflectance in the 350 to 2500 nm region was correlated with individual laboratory measurements. Each reference dataset was divided into model development data (70%) and model validation data (30%). Calibrated models were applied to validation datasets. Statistical analysis revealed that prediction efficiencies of soil reflectance models were highly quantitative. Coefficients of determination (R2) were near 1 (&ge, 0.90) and ratios of predicted values to the measured standard deviation (RPD) were &gt, 2, indicative of good predictive models. The field spectroradiometer enabled us to parameterize soil spatial variability and soil reflectance measurements, reducing the resources required to acquire edaphic measurements.

Biosolids have the potential to improve degraded soils in grain-fallow rotations. Our objectives were to determine if repeated biosolids applications in wheat ( L.)-fallow could supply adequate but not excessive N for grain production and increase soil C without creating a high risk of P loss. A replicated on-farm experiment was established in 1994 in central Washington, comparing anaerobically digested biosolids with anhydrous NH and a zero-N control. Biosolids were applied at 5, 7, and 9 Mg ha every fourth year through 2010 and incorporated 10 cm deep, while anhydrous NH plots received 56 kg ha N every second year. Grain yield and protein were determined. Soil chemical, biological, and bulk density analyses were made in 2012. Medium and high biosolids rates significantly increased grain yield (3.63 vs. 3.13 Mg ha) and protein (103 vs. 85 g kg) compared with anhydrous NH averaged across all crops. The medium biosolids rate had significantly lower bulk density (1.05 vs. 1.22 g kg) and greater total C (0-10-cm depth) (16.9 vs. 9.4 g kg), mineralizable N (156 vs. 52 mg kg), and extractable P (114 vs. 16 mg kg) than anhydrous NH. The P index site vulnerability increased from low for anhydrous NH to medium for the biosolids treatments. Soil NO-N was nearly always

Repeated applications of biosolids provide long-term benefits by increasing soil organic matter and N supply but can cause excess accumulation of P. Our objective was to determine the residual effects of repeated surface applications of biosolids on N availability and fate, tall fescue ( Schreb.) response, soil C, and P. A field experiment was started in 1993 to compare two biosolids products, each applied at three rates (6.7, 13.4, and 20.1 Mg ha yr), with synthetic N fertilizer (0 and 403 kg N ha yr as ammonium nitrate). Treatments were surface applied for 10 yr, followed by a 9-yr residual period where all plots received a reduced rate of inorganic N (202 kg N ha yr). Annual measurements included forage yield, N uptake, and soil nitrate N. Soil samples collected in 2002 and 2011 were analyzed for total C and N and Bray-1 P. Cumulative apparent N recoveries in harvested grass (1993-2010) were 51% for biosolids N and 72% for ammonium nitrate. Net fall soil nitrate N summed for the period 1993-2002 ranged from

Hydrogen sulfide (H2S) and greenhouse gases' emission from livestock production facilities are of concern to human welfare and the environment. Application of nanoparticles (NPs) has emerged as a potential option for minimizing these gaseous emissions. Application of bare NPs, however, could have an adverse effect on plants, soil, human health, and the environment. To minimize NPs' exposure to the environment by recovering them, NPs were entrapped in polymeric beads for treating livestock manure. The objectives of the research were to understand the mechanism of gaseous reduction in swine manure treated for 33 days with zinc oxide nanoparticles (nZnO) or nZnO-entrapped alginate (alginate-nZnO) beads by different characterization techniques. Headspace gases from treated manure flasks were collected in 2-6-day intervals during the experimental period and were analyzed for methane (CH4), carbon dioxide (CO2), and H2S concentrations. The microbial analysis of manure was carried out using bacterial plate counts and Real-Time Polymerase Chain Reaction methods. Morphology and chemical composition of alginate-nZnO beads were analyzed by Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS), and X-ray Photoelectron Spectroscopy (XPS). Alginate-nZnO beads or bare nZnO proved to be an effective NP in reducing H2S (up to 99%), CH4 (49-72%), and CO2 (46-62%) from manure stored under anaerobic conditions and these reductions are likely due to the microbial inhibitory effect from nZnO, as well as chemical conversion. Both SEM-EDS and XPS analysis confirmed the presence of zinc sulfide (ZnS) in the beads, which is likely formed by reacting nZnO with H2S.

Associations between soil properties and Pythium groups on soybean roots were investigated in 83 commercial soybean fields in North Dakota. A data set containing 2877 isolates of Pythium which included 26 known spp. and 1 unknown spp. and 13 soil properties from each field were analyzed. A Pearson correlation analysis was performed with all soil properties to observe any significant correlation between properties. Hierarchical clustering, indicator spp., and multi-response permutation procedures were used to identify groups of Pythium. Logistic regression analysis using stepwise selection was employed to calculate probability models for presence of groups based on soil properties. Three major Pythium groups were identified and three soil properties were associated with these groups. Group 1, characterized by P. ultimum, was associated with zinc levels; as zinc increased, the probability of group 1 being present increased (α = 0.05). Pythium group 2, characterized by Pythium kashmirense and an unknown Pythium sp., was associated with cation exchange capacity (CEC) (α

Organic cropping systems that utilize winter grown cereal–legume cover crop mixtures can increase plant available nitrogen (N) to a subsequent cash crop, but the rate of N release is uncertain due to variations in residue composition and environmental conditions. A study was conducted to evaluate N availability from rye (Secale cereale L.)–hairy vetch (Vicia villosa Roth) cover crop mixtures and to measure the response of organically grown sweet corn (Zea mays L.) to N provided by cover crop mixtures. Nitrogen availability from pure rye, pure hairy vetch, and rye–vetch mixtures was estimated using laboratory incubation with controlled temperature and soil moisture. Sweet corn N response was determined in a 2-year field experiment in western Washington with three cover crop treatments as main plots (50:50 rye–vetch seed mixture planted mid September, planted early October, and none) and four feather meal N rates as subplots (0, 56, 112 and 168 kg available N ha−1). Pure hairy vetch and a 75% rye–25% hairy vetch biomass mixture (R75V25) released similar amounts of N over 70 days in the laboratory incubation. But, the initial release of N from the (R75V25) treatment was nearly 70% lower, which may result in N release that is better timed with crop uptake. Cover crops in the field were dominated by rye and contained 34–76 kg ha−1 total N with C:N ranging from 18 to 27. Although time of planting and management of cover crop quality improved N uptake in sweet corn, cover crops provided only supplemental plant available N in this system.

Methods linking environmental function and microbial community composition are limited by phylogenetic resolution and throughput time. Denaturing gradient gel electrophoresis (DGGE) allows for resolution of ammonia-oxidizing bacteria strains separated by as little as one base pair (bp) in 16S rRNA gene sequence but is low throughput. In contrast, microarrays are high throughput. We have designed a microarray platform to identify the majority of environmental strains of betaproteobacterial ammonia oxidizers using signature oligonucleotide sequences. Seventy-seven target sequences or single-nucleotide polymorphisms (SNP) were derived from 183 betaproteobacterial ammonia oxidizer 16S rRNA gene sequences representing the genera Nitrosospira and Nitrosomonas of the β sub-class of Proteobacteria and the cluster groups of strains within each genera identified using DNA homology values. These sequences were obtained from the National Center for Biotechnology Information database. Templates isolated from pure cultures of betaproteobacterial ammonia oxidizers and soil samples incubated with and without dairy slurry were amplified using primers CTO189f and CTO654r. Amplicons were analyzed via DGGE and microarray hybridization. Mixtures of pure culture strains of betaproteobacterial ammonia oxidizers were used to simulate environmental samples containing a known number of sequences and template concentrations. Our DNA oligonucleotide microarray demonstrated highly specific detection of individual betaproteobacterial ammonia oxidizer strains amplified from pure cultures, model communities, and soil samples and provided resolution of community composition comparable to that of DGGE. High-throughput analyses of betaproteobacterial ammonia oxidizer communities will further our knowledge of their ecology and link process level functions to management practices such as dairy slurry applications and specific strains of betaproteobacterial ammonia-oxidizing bacteria.

In Triticum aestivum L. (wheat), the root-colonizing bacterium Pseudomonas fluorescens strain Q8r1-96 produces the antifungal metabolite 2,4-diacetylphloroglucinol (DAPG), suppresses damage caused by soilborne root pathogens, and modulates multiple stress or defense pathways in wheat roots. To test the hypothesis that DAPG is an inducer of root defense responses, we compared the impact of wild type and a DAPG null mutant on the abundance of fifteen wheat root defense gene homologues in two wheat cultivars, Buchanan and Tara, using real-time PCR. We also sought to determine whether the type III secretion system (T3SS) of Q8r1-96 is important for root defense gene induction by using a T3SS deletion mutant of Q8r1-96. Transcripts encoding dihydroxyacetone reductase, monodehydroascorbate reductase, a hypersensitive response-induced protein, pathogenesis-related protein10a (PR-10a) and two glutathione- S -transferases were induced in a strain–dependent manner relative to no-bacterium controls within the 24-h interval of the study. Our findings indicated that neither DAPG nor the T3SS were key single factors in the expression of all the root defense homologues. However, gene expression was induced to a greater degree in cv. Buchanan compared to cv. Tara. Clusters of co-induced transcripts also differed with the host cultivar-bacterial strain combination. Cultivar dependence of molecular root defense responses to biocontrol P. fluorescens has implications for the utility of biocontrol pseudomonads in greenhouse and field crop production systems.

Animal wastes are commonly used in a sustainable manner to fertilize crops. However, manures contain numerous pathogenic bacteria that can impact animal and human health. Treatment of animal waste by anaerobic digestion has the potential to reduce pathogen loading to land. This study was conducted to determine the fate of bacteria applied in raw and anaerobically digested dairy slurries that were broadcast and subsurface applied in a field of forage grasses. Digested slurry had significantly fewer indicator bacteria, Escherichia coli and fecal coliform at time of application. Anaerobic digestion did not increase the survivability of indicator bacteria. Waste treatment and application method did not affect the rate of bacteria die-off. There were fewer E. coli and fecal coliform at the end of each trial in the soils that received digested slurry. Anaerobic digestion of dairy waste has the potential to reduce pathogenic bacteria loading to cropland.

Terminal restriction fragment length polymorphism (T-RFLP) can be used to assess how land use management changes the dominant members of bacterial communities. We compared T-RFLP profiles obtained via amplification with forward primers (27, 63F) each coupled with the fluorescently labeled reverse primer (1392R) and multiple restriction enzymes to determine the best combination for interrogating soil bacterial populations in an agricultural soil used for potato production. Both primer pairs provide nearly universal recognition of a 1,400-bp sequence of the bacterial domain in the V(1)-V(3) region of the 16S ribosomal RNA (rRNA) gene relative to known sequences. Labeling the reverse primer allowed for direct comparison of each forward primer and the terminal restriction fragments' relative migration units obtained with each primer pair and restriction enzyme. Redundancy analysis (RDA) and nested multivariate analysis of variance (MANOVA) were used to assess the effects of primer pair and choice of restriction enzyme on the measured relative migration units. Our research indicates that the 63F-1392R amplimer pair provides a more complete description with respect to the bacterial communities present in this potato (Solanum tuberosum L.)-barley (Hordeum vulgare L.) rotation over seeded to crimson clover (Trifolium praense L.). Domain-specific 16S rRNA gene primers are rigorously tested to determine their ability to amplify across a target region of the gene. Yet, variability within or between T-RFLP profiles can result from factors independent of the primer pair. Therefore, researchers should use RDA and MANOVA analyses to evaluate the effects that additional laboratory and environmental variables have on bacterial diversity.

Humic acid (HA) is an important soil component that can improve nutrient availability and impact other important chemical, biological, and physical properties of soils. We investigated the lability of phosphorus (P) in the mobile HA and calcium humate fractions of four rice soils as measured by orthophosphate-releasing enzymatic hydrolysis and UV irradiation. Enzymatic hydrolysis releases hydrolyzable organic P, and UV irradiation abiotically releases P by breaking down phosphate-HA complexes. Less than 25% of the P in these fractions was detected in the soluble orthophosphate form (detectable soluble Pi). Enzymatic incubation increased detectable soluble Pi to 60% of total P. Treatment by UV irradiation alone released an additional 5% to 20% of humic-bound P compared with the untreated fractions. However, treatment by both UV irradiation and enzymatic hydrolysis released 0% to 14% of humic-bound P more than the amount of organic P that was enzymatically released from nonirradiated samples. The smaller amounts of P that were released from some humic fractions by both UV irradiation and enzymatic hydrolysis than by UV irradiation alone indicated some overlap between UV-degradable organic P and enzymatically labile organic P. Generally, about one half to two thirds of humic P in these rice soils was labile. These data demonstrated that either assumption that no P in humic fractions was labile P or all P in humic fractions was labile is not true. The lability of humic-bound P should be experimentally evaluated as reported in this work.

Amino acids and amino sugars comprise the bulk of soil N, so information on their chemical forms and cycling patterns should enable better understanding of soil N cycling. In this study of soil samples that had received animal manure, we evaluated the capabilities of a recently developed analysis for soil amino compounds (19 amino acids, two amino sugars) that consists of methanesulfonic acid extraction, anion chromatography, and pulsed amperometry detection. Soil samples were taken from a 28-d laboratory incubation of nine soils from six soil orders in six U.S. states that were amended with dairy manure slurry at a rate to simulate 300 kg N ha −1 . Manuring resulted in enrichment of the soils by nearly all measured amino compounds but to varying degrees. These enriched levels were relatively stable against mineralization during the short-term incubation, with most compounds having decreased modestly in concentration (mean 11%) by the end of the incubation, in contrast to slight increases (mean 3%) for three compounds that are associated with microbial activity and were not overly abundant in the manure: ornithine, glucosamine, and galactosamine. Several measurements of the extracted amino compounds varied signifi cantly among the nine soils. Our results illustrated some shortcomings of this analytical approach, including instability of small peaks and the need for a second extraction mode to maximize extraction of certain amino compounds. We identifi ed 41 to 43% of the total soil N as amino compounds for all soils and treatments, which is comparable to results reported previously for the conventional analysis involving HCl extraction and cation chromatography. Compared with conventional analysis, this approach might more effi ciently extract basic amino acids and less effi ciently extract acidic amino acids. Overall we found this approach to be a useful analysis.

Tillage, cropping system, and cover crops have seasonal and long‐term effects on the nitrogen (N) cycle and total soil organic carbon (C), which in turn affects soil quality. This study evaluated the effects of crop, cover crop, and tillage practices on inorganic N levels and total soil N, the timing of inorganic N release from hairy vetch and soybean, and the capacity for C sequestration. Cropping systems included continuous corn (Zea mays L.) and stalk residue, continuous corn and hairy vetch (Vicia villosa Roth), continuous soybeans (Glycine max L.) plus residue, and two corn/soybean rotations in corn alternate years with hairy vetch and ammonium nitrate (0, 85, and 170 kg N ha−1). Subplot treatments were moldboard plow and no tillage. Legumes coupled with no tillage reduced the N fertilizer requirement of corn, increased plant‐available N, and augmented total soil C and N stores.

Accurately characterizing phosphorus (P) forms is a prerequisite to developing effective remediation strategies to minimize the adverse environmental impact of agricultural expansion. Modified or unmodified Hedley sequential fractionation procedures have been widely used for characterizing P forms in soil, animal manure, and biosolids. Hydrochloric acid (HCl) fractions in these procedures have often been assumed to contain no organic P. As a result, many researchers for the last two decades have measured concentrations of inorganic P in HCl fractions without measuring organic P. In this study, we measured colorimetrically concentrations of inorganic P in untreated (control) HCl fractions after 3-phytase incubation or oxidative autoclaving of these fractions. Phosphorus concentrations in some samples were also determined by inductively coupled plasma optical emission spectroscopy. The increases in measured P concentrations, compared with the controls, were attributed to organic P in these fractions. Data for 15 soil and eight manure samples indicated that, although HCl fractions of some samples contained negligible amounts of organic P, others contained significant amounts of organic P. The concentrations of organic P were greater than inorganic P in one soil sample and two manure samples. We recommend that organic P in HCl fractions be measured experimentally to determine whether the HCl fraction contains inorganic and organic P. Identification of possible organic P species contained in HCl fractions of the Hedley sequential fractionation schemes would provide more accurate and comprehensive knowledge of the fates and interchanges of P forms in soil and animal manure under various environmental conditions.

The uniformity, low cost and ease of application associated with inorganic fertilizers have diminished the use of organic nutrient sources. Concern for food safety, the environment and the need to dispose of animal and municipal wastes have focused attention on organic sources of N such as animal-derived amendments, green manures, and crop rotations. Managing organic N sources to provide sufficient N for crop growth requires knowledge of C and N decomposition over several years, particularly where manure and compost are applied. We report a comparison of compost and chemical fertilizer, use of a corn–corn–soybean–wheat rotation compared to continuous corn and the use of cover crops. Nitrogen (150 d) and C incubations (317 d) were conducted to determine the effect of cropping system and nutrient management on: N mineralization potential (NMP), the mineralizable organic N pool (No), the mean residence time (MRT) of No, C mineralization (Cmin), and soil organic carbon (SOC) pool sizes and fluxes. Compost applications over 6 y increased the resistant pool of C by 30% and the slow pool of C by 10%. The compost treatment contained 14% greater soil organic C than the fertilizer management. Nitrogen was limiting on all compost treatments with the exception of first year corn following wheat fallow and clover cover crop. The clover cover crop and wheat-fallow increased inorganic N in both nutrient managements. We recommend that growers adjust their N fertilizer recommendation to reflect the quantity and timing of N mineralized from organic N sources and the N immobilization that can be associated with compost or other residue applications. Proper management of nutrients from compost, cover crops and rotations can maintain soil fertility and increase C sequestration.

Nitrification potential is the maximum capacity of a soil’s population of nitrifying bacteria to transform NH4+-N to NO3−-N. Time of season and the effect of several management practices on nitrification potentials were measured via an amended slurry method, shaken for 24 h at 25 °C. Management strategies that reduce potential nitrification rates without limiting plant N uptake may increase the ratio of plant biomass to plant N content (PB:N), the aboveground net primary production (ANPP) per unit of N in ANPP, and decrease the amount of NO3− available for leaching, and/or conversion to N2O. Sites were located in Hickory Corners, MI, USA, on Haplic Luvisols. Management practices included: substitution of compost for N fertilizer, use of a rotation in place of continuous maize and the addition of cover crops. A previously tilled, successional grassland was used as a contrast to agricultural managements. Where N fertilizer was applied, nitrification potential increased in late May and again in late August–October. The seasonal pattern was similar but less pronounced where compost was applied. Nitrification rates were 4.2 times greater than that of the successional site when N fertilizer was applied. Use of N fertilizer increased nitrification potentials 1.5 times above treatments where compost was applied during 1998 and 1999 in the 6th and 7th years of the rotation. In some instances, nitrification potentials could be correlated with in situ NO3−-N measurements. Average PB:Ns in the fertilizer management were greater or equivalent to the successional grassland site. Compost increased PB:N above that of N fertilizer. Utilization of compost decreased nitrification potentials, maintained yields, and increased PB:N. The crop N content was lower when compost was applied. Thus, grain and stover quality may be lowered and need to be monitored.

Management practices that influence the quantity of C inputs returned to the soil from cropping systems and compost applications alter subsequent biotic activity broadly, contribute to seasonal fluctuations in nutrient dynamics, and may increase C sequestration. The effects of crop rotations and compost applications on soil-C sequestration and decompostion, and the turnover time of C 4 -derived corn C were assessed via changes in the C content and 13 C values of particulate organic matter (POM) and total soil organic C (SOC). The majority of organic inputs entered the POM fraction, defined as the sand-sized soil separates remaining on a 53-μm sieve after removal of residues (>2 mm), dispersion in 5% sodium polyphosphate, and 12 h of shaking. Before the application of compost to soil, 85% of the C in the compost material was classified as POM. Measurements of POM-C in the soil were 45% higher and SOC was 16% greater where compost was applied in place of N fertilizer. Addition of compost to POM-C diminished the value of POM as an indicator of short-term changes in nutrient dynamics. However, POM-C remaining from compost applications made during the period 1993 to 1997 may be an indicator of enhanced macroaggregate stability: improved soil tilth and the retention of soil C and N. The turnover time of C 4 -derived C in the POM fraction was 11 years compared with 22 years in SOC. The presence of compost C did not affect the turnover time of corn-derived C. High cropping intensity and chisel plow management increased C sequestration relative to the preceding alfalfa management.