Science-based Trials of Rowcrops Integrated with Prairie Strips (STRIPS) can improve water quality and reduce antimicrobial resistance genes (ARGs) from manured field runoff. Prior studies showed significant reductions in ARG abundances with prairie strips, but no enrichment was detected in surface soil layers, prompting further investigation into transport pathways. We hypothesized that ARGs may move vertically through strip soils. In an 8-week soil column experiment, we characterized the vertical transport of manure-amendment ARGs in prairie strip soils and leachate, comparing columns amended with anaerobically digested swine manure (ADM) and undigested swine manure (UDM) to a mineral-based control (mineral solution amendment [MIN]). In amendment manures, the ARG concentrations in ADM and UDM were similar, and ADM had increased antibiotic residual concentrations. ADM and UDM amendments resulted in elevated ARG abundances in soil and leachate compared to MIN. After manure amendment, ARGs were transported up to 52.5 cm from the soil surface after rainfall events. Tetracycline resistance genes were persistently detected in amended subsurface soils, with tetM detectable until week 8 in both ADM and UDM amended soils, and tetO persisting to week 3 in ADM and week 8 in UDM amended soils. Generally, ADM amendments had lower ARG persistence than UDM, highlighting different transport dynamics depending on manure treatment. Most manure-derived ARGs appeared to be retained or degraded within the strip soil profiles, with only 9.6 and 6.1 percent of UDM and ADM amendment ARGs recovered, respectively. Our results support that prairie strips can mitigate ARGs from manured field stormwater runoff and that ARGs are transported vertically through the soils and mostly retained at surface depths.

Swine manure management systems (MMSs) are critical for nutrient cycling. Common swine MMS storage types in the United States are deep pits, anaerobic lagoons, and slurry storages. This study presents a synthesis of literature documenting nutrient and carbon (C) partitioning via a material mass balance approach for four manure treatment technologies: acidification (ACID; n = 4 papers), aeration (AER; n = 16), solid-liquid separation (SLS; n = 11), and anaerobic digestion (AD; n = 23) that can be used in-line with one or more of these common storage types. Mass balance data were primarily extracted for nitrogen (N), phosphorus (P), and C (AD only) from lab and pilot-scale studies, with nutrient flows normalized to influent characteristics. The ACID papers suggested significant reductions in gaseous losses with ACID; however, the effluent concentration and available mass/volume and gas data together did not document realistic N partitioning. Among SLS systems, urine-feces segregation and filtration retained the most and least amount of solids in the solid fraction, respectively. AD converts organic matter into biogas; for most mesophilic digesters, 56%-66% of the C remained in the effluent; the mass retained in the sludge is underreported. In AER studies, the partitioning of N into different N gases depended on the amount of AER. As pass-through technologies, AD and SLS are easier to incorporate in lagoon and slurry storage systems. ACID and AER can be physically incorporated in common MMSs; however, treatment could hinder anaerobic lagoon function. Understanding nutrient partitioning will benefit from concurrent monitoring of multiple nutrients in the liquid, solid, and/or gas streams.

The low adoption of annual cover crops in the United States Corn Belt has motivated research into novel cover cropping systems that mitigate the degrading of water quality due to soil and nutrient loss without compromising corn (Zea mays L.) yield. This 3-year field study compared a Kentucky bluegrass (Poa pratensis L.) as a perennial groundcover (PGC), two interseeded annual cover crop systems (standard and wide-row), and a no-cover control for their effects on corn yield and subsurface drainage water quality. Each plot was monitored weekly for subsurface drainage flow and nutrient losses using a randomized complete block design with three replicates. The study occurred during a period of below-average precipitation, which caused strong year-to-year and seasonal variations in treatment performance. Treatment effects were most evident in the study's wettest year, when increased rainfall following a dry season caused a summer nitrate flush. During this high-leaching summer period, all cover crop systems reduced nitrate concentrations compared to the control. When averaged across the entire study, the high-biomass wide-row interseeded system reduced flow-weighted NO3-N concentrations by 22% but reduced grain yield 20%. In contrast, the PGC system reduced NO3-N by 20% with no associated grain yield loss. These findings highlight a critical yield trade-off for wide-row annual cover cropping systems and suggest that perennial systems like Kentucky bluegrass PGC are a promising strategy for mitigating early summer nitrate losses.

. Impermeable covers have been one of the most popular choices for implementing manure anaerobic digestion to renewable natural gas projects; however, limited studies have evaluated how economies of scale affect the profitability of impermeable cover projects. We assessed dairy farms ranging from 100 to 5,000 head and swine farms ranging from 1,200 to 35,000 head to determine the herd size necessary for economically viable projects. System construction costs were estimated using literature values, with potential revenue streams estimated using average market prices. Estimated breakeven farm sizes for ten-year project lives were 1,000 dairy cows if the manure storage was emptied once annually, 1,400 dairy cows if the manure storage was emptied twice annually, and 11,000 wean-finish pigs using lagoon manure storage. Wean-finish pigs initially using a deep pit manure storage required more than 27,000 pigs to financially breakeven within ten years. While there are roughly 7,600 swine farms and 170 dairy farms in Iowa, only 79 individual farms in Iowa qualify as economically feasible renewable natural gas projects due to typical farm sizes and manure management systems prevalent in the Midwestern United States. RNG projects on these 79 farms could reduce manure management CO2e emissions by 1,138,000 MG annually. Future work must explore and develop strategies for renewable natural gas systems on farms with less than 1,000 cows or 10,000 pigs.

Outbreaks of infectious diseases involving depopulation of animals require on-farm practices to stage carcasses when final disposal methods are unavailable. The current study assessed various materials and techniques for containing carcasses to minimize leachate and biological substances. The tested materials included tarps, soil, corn stover (CS), and lime, while the methods involved covers, chemical additives, barriers, and containment. Treatments included the following: 1) control, carcasses in a pile; 2) carcasses wrapped in tarp material; 3) carcasses covered with tarp material; 4) carcasses covered by soil; 5) carcasses placed on CS base with tarp cover; 6) carcasses on CS base with CS covering; and 7) carcasses on CS base with a lime covering. Each treatment was run in triplicate using three carcasses per replicate. Temperatures, headspace gas, and leachate from carcasses were collected over a 91-day holding period. Pairwise comparisons of means were made when treatments were significantly different. Carcasses lost significant amounts of their liquid contents in the first 27 days. Leachate contents were initially filled with organic material and potassium that significantly declined with time, while Fe, Zn, and Cu concentrations increased significantly over time. Covers did not reduce leachate volume, but soil covers significantly reduced substances in the leachate. Corn stover barriers significantly reduced both leachate volume and substances in the leachate. Containing carcasses in tarp material was the most effective method for holding leachate and preventing its loss to the environment. This research demonstrates that growers should focus on sealing carcass containers and constructing barriers to limit surface contamination during depopulation events.

Swine manure is typically applied to agricultural land at agronomic rates, providing essential nutrients to crops and enhancing soil fertility. While providing nutrients, manure can also introduce pathogens and other contaminants, including antibiotic residues and antibiotic-resistant bacteria (ARB) and genes (ARGs), into the environment with subsequent threats of transfer to humans through the food chain. There are various manure management strategies that may be considered before land application to potentially mitigate the risks of antimicrobial resistance exposure. In a laboratory manure slurry incubation study, the effectiveness of five different manure treatment practices was evaluated. These practices included aeration, anaerobic digestion (AD), heat, liming, and solid-liquid separation (SLS), and were assessed for their ability to reduce antibiotics, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs). This study focused primarily on the impacts on tetracycline (TET), TET-resistant populations, and TET-resistant genes. Additionally, we evaluated the impacts of manure treatments on macrolide (MAC) resistance. We compared the effects of manure treatment on phenotypic resistance of TET, the concentration of TET and MAC residues, and copies of several TET- and MAC-resistant genes. For TET-resistant ARB, our results indicate that AD and liming are the most effective among all treatments. Liming was able to rapidly reduce TET-resistant ARB. Comparing ARGs and antibiotic residuals, we found AD to be the most effective treatment in reducing TET-resistant genes (tetO, tetM, and ermB) and total TET and MAC residues. This research provides valuable insights that can be used to recommend best management practices to farmers and policymakers to reduce dissemination of antimicrobial resistance through environmental pathways.

Achieving high yields in the large-scale agricultural systems that dominate the US landscape requires critical machine-enabled field operations to be executed in narrow windows of time. Novel cropping systems hold great promise to increase ecosystem services from these large-scale systems, but researchers and end-users need effective methods of representing the timing requirements of such systems. This gap prompted our exploration of approaches to visualize the timing of critical machine-enabled field operations. We refer to the resulting graphic as a field operations visualizer (FOV). We iterated multiple versions of the FOV through a user-centered process involving extensive stakeholder feedback. The resulting FOV version offers a straightforward method of visualizing operation sequences and identifying potential conflicts. Survey results suggest that the FOV provides significant operational insights to users about the timing challenges (or benefits) of novel cropping systems. The FOV may therefore be useful in guiding efforts to improve novel cropping systems and to thereby ultimately increase their deployment to deliver ecosystem services.

Swine manure is an alternative to synthetic fertilizers for providing crop nutrients. However, transportation costs, nutrient leakage, and gaseous emissions associated with using swine manure as fertilizer limit its agronomic benefits and cause environmental issues. In this study, we report the efficacy of nutrients (P as ortho-P and N as NH4+) recovery scheme from swine manure by batch equilibration and column leaching studies using different combinations of two biochars (untreated control biochar; control-BC and iron-modified biochar; iron-BC) and one zeolite with SiO2/Al2O3 = 30:1. Batch study employed different adsorbents (control biochar, followed by iron-BC, and zeolite) to obtain maximum adsorption (98.3% and 35.4%) and optimum desorption (66% and 18%) of P and N from the manure solution (1:5).A series of sand-matrix columns using the best combination of control-BC, iron-BC, and zeolite recovered 13,800mgkg-1 of P and 4,000mgkg-1 of N from manure solution after tenth cycles of leaching events. XRD and SEM-EDS analyses revealed the association of P with N and Mg, suggesting the adsorption of nutrients mostly through co-adsorption with manure colloids and precipitation as struvite. A series of soil-matrix column studies and a corn seed germination test were conducted to test the nutrient leaching/crop fertilization efficiencies using the recovered adsorbents. Inclusively, results showed that a proper combination of biochar and zeolite could effectively recover and concentrate nutrients from swine manure to develop crop fertilizer for easy transport and use in sustainable agriculture.

Pit recharge systems (PRS) control odor by managing organic solids in swine manure. However, there needs to be more understanding of PRS's effect on the microbiome composition and its impact on odor formation. A study was conducted to understand how recharge intervals used in PRS impact manure microbiome and odor formation. Bioreactors dynamically loaded simulated recharge intervals of 14, 10, and 4 days by diluting swine manure with lagoon effluent at varying ratios. Treatment ratios tested included 10:0 (control), 7:3 (typical Korean PRS), 5:5 (enhanced PRS #1), and 2:8 (enhanced PRS #2). Manure microbial membership, chemical concentrations, and odorant concentrations were used to identify the interactions between microbiota, manure, and odor. The initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent, respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9% or increased by 17.6%, respectively, with each unit dilution. Microbial community composition was controlled by both treatment (i.e., manure dilution ratio and barn source material) and environmental factors (i.e., solids and pH). Microbiome composition was correlated with manure odor formation profiles, but this effect was inseparable from environmental factors, which explained over 75% of the variance in odor profiles. Consequently, monitoring solids and pH in recharge waters will significantly impact odor control in PRS.

Livestock in the state of Iowa, United States (US) produce over 50 × 106 Mg of wet-basis manure yearly. Biogas production from manure’s anaerobic digestion (AD) can reduce greenhouse gas emissions, control odors, and provide renewable energy. Despite these benefits, AD is rarely deployed at swine farms in Iowa. In this work, we explore the economics of AD systems in Iowa to evaluate reasons for low deployment and explore the production cost impacts of biogas cleaning and injection into the natural gas grid, amending manure with biomass, and centralizing digesters across multiple farms. This work presents a static, spreadsheet-based technoeconomic model that embodies literature-based estimates of key system technical parameters, costs, and transportation fuel incentives and permits the examination of various scenarios. Key findings include that under the model assumptions, distributed, farm-scale digesters are not competitive with average natural gas prices in Iowa. A centralized production scenario can be competitive, provided that programs such as the low-carbon fuel standard (LCFS) and the renewable fuel standard (RFS) have sufficiently high credit values.

Swine manure is a potential source of plant-available ortho-phosphate (ortho-P) and ammonium (NH4+). However, transport and application issues restrict its widespread use in agriculture and cause water quality degradation. This study investigates the potential of biochar (BC) produced from corn stover (control-BC) and FeSO4 pre-treated corn stover (Fe-BC) and zeolite to recover ortho-P and NH4+ from liquid swine manure. Chemisorption increased ortho-P sorption from manure onto Fe-BC (29,831 mg kg(-1)) relative to control-BC (19,000 mg kg(-1)). During Mehlich III (M-III) desorption study, manure-treated Fe-BC and control-BC released 34% and 80% of adsorbed ortho-P, respectively. Increasing the BC loading rate from 5 g/L to 25 g/L in manure significantly dropped the M-III P desorption (<10%) for the Fe-BC but not for the control-BC. Sorption of manure NH4+ on Fe -BC, control-BC, and zeolite occurred by I) specific adsorption on surfaces and within pores, II) co-adsorption of NH4+ with manure colloids, and III) precipitation as N-mineral (struvite). The NH3 volatilization and KCl desorption studies revealed that NH4+ sorption/desorption from manure to BC cannot be explained by simple ion exchange or volatilization loss. The BC-zeolite combination increased the NH4+ recovery from manure (28-38%) relative to BC's without zeolite addition. SEM-EDS and XRD analyses revealed the association of P with both Mg and Fe and the presence of struvite (NH4MgPO4 center dot 6H(2)O) in batch and centrifuge studies. Our results suggest that low-cost BC and zeolite can recover ortho-P and NH4+ from liquid swine manure, which may facilitate its easy transport and widespread application in agriculture.

A growing global meat demand requires a decrease in the environmental impacts of meat production. Cultured meat (CM) can potentially address multiple challenges facing animal agriculture, including those related to animal welfare and environmental impacts, but existing cost analyses suggest it is hard for CM to match the relatively low costs of conventionally produced meat. This study analyzes literature reports to contextualize CM’s protein and calorie use efficiencies, comparing CM to animal meat products’ feed conversion ratios, areal productivities, and nitrogen management. Our analyses show that CM has greater protein and energy areal productivities than conventional meat products, and that waste nitrogen from spent media is critical to CM surpassing the nitrogen use efficiency of meat produced in swine and broiler land-applied manure systems. The CM nutrient management costs, arising from wastewater treatment and land application, are estimated to be more expensive than in conventional meat production. Overall, this study demonstrates that nitrogen management will be a key aspect of sustainability in CM production, as it is in conventional meat systems.

Antimicrobial resistance (AMR) can develop in deep-pit swine manure storage when bacteria are selectively pressured by unmetabolized antibiotics. Subsequent manure application on row crops is then a source of AMR into soil and downstream runoff water. Therefore, understanding the patterns of diverse antibiotic resistance genes (ARGs) in manure among different farms is important for both interpreting the results of the detection of these genes from previous studies and for the use of these genes as bioindicators of manure borne antibiotic resistance in the environment. Previous studies of manure-associated ARGs are based on limited samples of manures. To better understand the distribution of ARGs between manures, we characterized manures from 48 geographically independent swine farms across Iowa. The objectives of this study were to characterize the distribution of ARGs among these manures and to evaluate what factors in manure management may influence the presence of ARGs in manures. Our analysis included quantification of two commonly found ARGs in swine manure, ermB and tetM. Additionally, we characterized a broader suite of 31 ARGs which allowed for simultaneous assays of the presence or absence of multiple genes. We found the company integrator had a significant effect on both ermB (P=0.0007) and tetM gene concentrations (P=0.0425). Our broad analysis on ARG profiles found that the tet(36) gene was broadly present in swine manures, followed by the detection of tetT, tetM, erm(35), ermF, ermB, str, aadD, and intl3 in samples from 14 farms. Finally, we provide a comparison of methods to detect ARGs in manures, specifically comparing conventional and high-throughput qPCR and discuss their role in ARG environmental monitoring efforts. Results of this study provide insight into commonalities of ARG presence in manure holding pits and provide supporting evidence that company integrator decisions may impact ARG concentrations.

Highlights Carcass and room temperatures, as well as CO, CO 2 , O 2 , and NH 3 , were continuously monitored. NH 3 release was approximately half when carcass leachate was removed from the shallow pit. Gompertz and logistic models fit data well for daily carcass mass reduction and leachate production. Abstract. A catastrophic mortality event for swine would present numerous challenges with the management and disposal of infected carcasses. This study explored a new strategy for biosecure in-barn processing of swine carcasses as an alternative to traditional management and disposal approaches. A small-scale, mobile laboratory with two discovery rooms (DRs), replicating a swine finishing facility, was constructed to execute tests of in-barn disposal methods. Carcasses were desiccated by subjection to heat at a room air temperature of 43°C (110°F) for 16 days. Three carcasses (average = 82 kg, SE=1.27 kg) were elevated over individual leachate collection systems in DRA, thereby removing leachate from the room. Three carcasses in DRB were placed on concrete slats with cumulative leachate collection in the pit below. Environmental data were collected for DR, outdoor, and slat temperatures; and CO2, CO, O2, and NH3 gas concentrations. Carcasses were characterized by rectal and shoulder temperature monitoring and daily weighing of carcasses and leachate in DRA. The air exchange rate for this unventilated system was quantified based on wind and thermal-driven infiltration. Room environments were compared for thermal performance and gas levels. Carcass temperatures were compared, and data suggested no significant impact of flooring material on internal carcass temperature. Gompertz and logistic models were fit to leachate production data and carcass mass reduction data. Ammonia generation rates were found to have a peak production rate of 96.5 g AU-1 day-1 (15.8 g animal-1 day-1) in DRA and 120 g AU-1 day-1 (19.7 g animal-1 day-1) in DRB. Over the study, the generation of NH3 in DRB (360 g) was nearly twice that of DRA (182 g) due to leachate removal. Further quantification and qualification of in-barn management strategies will better define biosecure disposal approaches in the event of a catastrophic mortality event. Keywords: Ammonia, Catastrophic event, Disposal, Foreign animal disease, Mortality management, Pig.

Intestinal tuft cells have been shown to induce type 2 immune responses during viable parasite infections, but whether oral supplementation with a parasitic exudate is able to promote type 2 immune responses that have been shown to positively regulate obesogenic metabolic processes is yet unresolved. High-fat fed mice were gavaged with pseudocoelomic fluid (PCF) derived from the helminth Ascaris suum or saline thrice a week during weeks 5-9, followed by examination of intestinal tuft cell activity, immune, and metabolic parameters. Helminth PCF upregulated expression of distinct genes in small intestinal tuft cells, including genes involved in regulation of RUNX1 and organic cation transporters. Helminth PCF also enhanced levels of innate lymphoid cells in the ileum, and eosinophils in epididymal white adipose tissue (eWAT). Network analyses revealed two distinct immunometabolic cues affected by oral helminth PCF in high-fat fed mice: one coupling the small intestinal tuft cell responses to the fat-to-lean mass ratio and a second coupling eosinophils in eWAT to general regulation of body fat mass. Our findings point to specific mechanisms by which oral supplementation with helminth PCF may translate into systems-wide effects linking to reduced body and fat mass gain in mice during high-fat feeding.

The labile organic or bioreactive fraction in manureis the foodand energy source that microbes continuously utilize. Biochar (BC)addition to manure following its application to soil improves thetotal C retention in soil. However, the relation between the BC applicationrate and the bioreactive C stability in manure is poorly understood.This study performed a short aging of swine manure with differentloading rates of BC (0-25 wt %) and evaluated bioreactive Cstability of these manure-BC mixtures using thermal, chemical,and spectral analyses. Findings suggest that increasing BC additionto manure causes (a) 13-42% less thermal decomposition of totallabile C, (b) 65-96% reduction of labile C release in hot water,and (c) 22-69% decrease of respirational C loss as comparedto manure; thus overall, it alters the manure-BC mixture'sC quality. Interestingly, 1% BC addition decreased the manure-BCmixture's C stability indices (H/C-org and VM/FCmolar ratios) compared to higher BC addition. The C-mineralizationstudy revealed that the addition of BC to manure altered the measuredinorganic C fraction of the mixture, which was further supported byFourier-transform infrared and X-ray diffraction analyses. The C-13 solid-state nuclear magnetic resonance suggests an increasein the aromatic index and a decrease in the alkyl to O-alkyl ratioas the BC to manure ratio increased. Inclusively, our results indicatethat the manure-BC mixtures were substantially (P < 0.05) more stable than manure, and application of these mixturescan have a larger impact on the soil-C turnover when compared to manureapplication.

Swine growers seeking to lower costs and environmental impact have turned to alternative carbohydrate feed sources. A feeding trial was conducted to determine the effect carbohydrate sources have on manure composition and gas emissions. A total of 48 gilts averaging 138 kg BW were fed diets consisting of (a) low fiber (LF) grain, or (b) high fiber (HF) aro-industrial co-product (AICP). The LF diets included corn and soybean meal (CSBM) and barley soybean meal (BSBM). The HF AICP diets were CSBM based and supplemented with one of the following materials: beet pulp; corn distillers dried grains with solubles; soybean hulls; or wheat bran. Diets were fed for 42 d with an average daily feed intake of 2.71 kg d-1. Feces and urine were collected twice daily and added to manure storage containers in which manure slurries were monitored for gas emissions and chemical properties. Manures of animals fed HF diets had significantly (P < 0.05) more excretion of solids, C, N, and organic N, but less total S compared to pigs fed the LF diets. Animals feed HF diets had significantly (P < 0.05) higher levels of ammonia, sulfide, volatile fatty acids, and phenols in manure compared to pigs fed the LF diets. Manure of animals fed HF diets had 30% (P < 0.05) lower NH3 and 17% lower hydrogen sulfide emissions; however, fiber had no impact on odor emissions. Based on the partitioning of nutrients, animals fed HF fiber diets had increased manure retention for C and N but decreased levels of N gas emissions and manure S. There were little differences in manure and gas emissions for animals fed LF diets, but the source of HF AICP diets had a significant impact on manure composition and gas emissions.

HighlightsVariability of manure N content on the day of application was a major contributor to plot-to-plot N rate variability.Using the average of previous years’ manure samples is a valid strategy to improve the accuracy of P application.Estimated economic losses from missing target manure N rates averaged $34.27 ha-1 year-1 ($13.87 ac-1 year-1).Improving N rate accuracy with real-time N sensing provided an estimated value of $7 to $44 ha-1 ($3 to $18 ac-1).Abstract. Liquid livestock manure application presents both opportunities for replacing commercial fertilizer and challenges to doing so accurately. This study demonstrated the challenges in achieving a target N application rate using liquid swine manure on eighteen 0.4 ha research plots at the Northeast Research and Demonstration Farm (NERF) near Nashua, Iowa. Differences between the nutrient analyses of manure from a pre-application sample and samples taken on the day of application, equipment adjustments, field conditions, and changing manure nutrient content during pit pumping contributed to variability in the actual N rate applied. The coefficient of variability (CV) of manure N during manure pumping ranged from 2.7 to 13.6, with an 8-year average of 6.5. A weighted-average CV for applied manure volume ranged from 1.5 to 4.7, with an 8-year average CV of 3.2, suggesting that plot-to-plot variability in manure volume was less of an issue for achieving the target N rate than was the variability of manure N on the day of application. A separate analysis of manure from six Iowa swine farms showed that using the average of the previous years’ manure samples improved accuracy for phosphorus at Farm 2, whereas using a single sample from the application year improved accuracy for potassium at Farm 5. Averaged across the six farms, using the average of the previous years’ manure samples resulted in less error for phosphorus than using a single sample from the application year. For nitrogen, there was no significant difference between the two approaches within or across farms (p < 0.1). The average economic loss from missing the target N rate in the NERF study was $34.27 ± $32.49 ha-1 year-1 ($13.87 ± $13.15 ac-1 year-1). The estimated economic value from using real-time nutrient sensing to improve N rate accuracy ranged from $7.56 to $32.03 ha-1 ($3.06 to $12.96 ac-1) in a corn-soybean rotation and from $10.38 to $44.41 ha-1 ($4.20 to $17.97 ac-1) in continuous corn. This study illustrates the need for new technologies for real-time manure nutrient sensing and on-the-go rate adjustment. The economic analysis can serve as a guide for manure applicators when evaluating the feasibility of manure nutrient-sensing systems. Keywords: Manure application, Manure management, Manure nutrient content, Manure nutrient sensing, Manure rate calibration.

Tape stripping is a non-invasive skin sampling technique, which has recently gained use for the study of the transcriptome of atopic dermatitis (AD), a common inflammatory skin disorder characterized by a defective epidermal barrier and perturbated immune response. Here, we performed BRB-seq—a low cost, multiplex-based, transcriptomic profiling technique—on tape-stripped skin from 30 AD patients and 30 healthy controls to evaluate the methods’ ability to assess the epidermal AD transcriptome. An AD signature consisting of 91 differentially expressed genes, specific for skin barrier and inflammatory response, was identified. The gene expression in the outermost layers, stratum corneum and stratum granulosum, of the skin showed highest correlation between tape-stripped skin and matched full-thickness punch biopsies. However, we observed that low and highly variable transcript counts, probably due to low RNA yield and RNA degradation in the tape-stripped skin samples, were a limiting factor for epidermal transcriptome profiling as compared to punch biopsies. We conclude that deep BRB-seq of tape-stripped skin is needed to counteract large between-sample RNA yield variation and highly zero-inflated data in order to apply this protocol for population-wide screening of the epidermal transcriptome in inflammatory skin diseases.

BACKGROUND Molecular skin profiling techniques, typically performed on skin samples taken by punch biopsy, have enhanced the understanding of the pathophysiology of atopic dermatitis (AD), thereby enabling the development of novel targeted therapeutics. However, punch biopsies are not always feasible or desirable, and novel minimally invasive methods such as skin tape stripping have been developed. AIM To develop, optimize and validate a novel tape stripping method guided by noninvasive in vivo skin imaging to sample atopic skin in children. METHODS Skin tape stripping-based procedures were compared and optimized using data from 30 healthy controls (HCs: 5 adults, 25 children) and 39 atopic children. Evaluations were guided by high-resolution photography, reflectance confocal microscopy, optical coherence tomography and transepidermal water loss measurements. We assessed and compared adverse events (AEs), the time needed to perform the sampling and the cDNA levels obtained from the tapes. RESULTS Tape stripping methods based on previously described protocols resulted in erosions in all participants and required a median time of 65 min to perform (range 60-70 min), but provided good cDNA yield. Shorter durations appeared less invasive but provided lower cDNA yield. The final optimized tape stripping protocol, using 11 tapes of 22 mm in diameter, each applied twice for 5 s with 90° rotation, did not produce significant AEs, was completed within a median time of 7 min (range 5-15 min) and provided good cDNA yield both in HCs and atopic children. CONCLUSION Our minimally invasive method is safe and reliable, and provides reproducible acquisition of cDNA in atopic children. In addition, it enables rapid sample collection, a crucial factor in clinical practice.