Compost is commonly used as an organic amendment in cropping systems such as vineyards, and has been shown to be beneficial to carbon (C) sequestration and soil health. As perennial crops, grapevines have a larger potential for C sequestration than most crops. Yet, there is a lack of understanding regarding the relationship between compost application rate, the magnitude of C sequestration, and its environmental tradeoff in the form of greenhouse gas (GHG) emissions. In the study, we investigated the effects of compost application rate on soil C sequestration, GHG emissions, crop growth, and overall soil health after two annual compost treatments at J. Lohr Vineyards and Wines, Paso Robles, CA. Compost was broadcasted to the entire plot area between harvest and the first precipitation in fall at the rate of 0 (control), 2, 4, and 6 tons/acre/year. Soil C sequestration, cumulative carbon dioxide (CO2) and nitrous oxide (N2O) emissions and soil physical properties were assessed at two functional locations (tractor row and vine row) and three depth increments (0-15, 15-30, and 30-60 cm). Cover crop biomass was determined in spring before mowing, while clusters per vine, cluster weight and yield were determined each year at harvest. Although compost application did not significantly affect total soil C stocks, significant increases in early indicators of C sequestration such as permanganate oxidizable carbon (POXC), aggregate distribution, and aggregate C content in large macroaggregates without increasing C mineralization suggests that C input from compost increased C stabilization in soil. Cumulative GHG emissions were not significantly affected by compost application. Both CO2 and N2O emissions were higher in the vine row than the tractor row in the dry season, but the trend for CO2 emissions was the opposite in the wet seasons. Seasonal patterns of GHG emissions were likely due to differences in plant activity and irrigation between functional locations. The lower bulk density in topsoil than subsoil, and the higher water holding capacity and aggregate stability in tractor row topsoil than in the vine row demonstrates how high C content improves soil physical properties. Cover crop growth and grape yield components were unaffected by compost application. Based on our results, early signs of C sequestration and improvements on overall soil health can be achieved in a coarse-texture vineyard in the Central Coast region after annually applying compost at a rate between 2 and 6 tons/acre for two years, without increasing GHG emissions or affecting grape yield. Further investigation is recommended to study the potential synergistic effects between compost application and cover cropping in vineyards if both practices are implemented at the same time.

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The microbial life in the soil is essential for providing a functioning habitat for plants to grow. A literature study was conducted to investigate the knowledge and science behind soil biology. The purpose of this study was to define what is soil health and how it is influenced by the soil microbial communities. The literature study concluded that the ability of soil biology to benefit plants includes a variety of aspects. Nutrient availability, soil structure and pest resistance are all greatly influenced by soil microbes.  To practically examine these theories, an experiment was conducted where Brandywine tomatoes where grown in three different scenarios. A commercial potting soil, Hasselfors ekojord, was used as substrate in all groups. In the control group (C) the plants were grown only in the substrate. In the second group (R), the seeds where treated with a microbial inoculum and then planted in the substrate. In the third group (RE), the same treatment as in R was done to the seeds and here, compost extract were also added to the RE group. The plants were grown in separate pots in a greenhouse and the growth rate was observed and documented as well as the total harvest. In the end of the growing season a chemical and biological analysis was done to the soil as well as a sap analysis on the leaves. The plant growth where similar among the groups although R and RE showed slightly higher growth rates in the later stages of the growing season. The harvested fruit was highest in C but not significantly. The microbial contents were high in all soils though more fungi communities in the RE and bacterial communities in C. The chemical analysis showed high nitrate concentrations in the leaves in C. In R and especially RE the nitrate conversion into amino acids and proteins where higher wish indicates that these groups are more resilient to pests like aphids. / Det mikrobiella livet i jorden är avgörande för att skapa en fungerande livsmiljö för växter. En litteraturstudie genomfördes för att undersöka nuvarande kunskap och vetenskap bakom markbiologi. Syftet med denna studie var att definiera markhälsa och hur den påverkas av det mikrobiella livet i jorden. Slutsatsen från denna litteraturstudie var att jordbiologins förmåga att gynna växter innefattar en rad olika aspekter. Näringstillgänglighet, markstruktur och skadedjursbeständighet påverkas starkt av jordmikrober.  För att praktiskt granska dessa teorier genomfördes ett experiment där Brandywine-tomater odlades i tre olika scenarier. En kommersiell plantjord, Hasselfors ekojord, användes som huvudsubstrat i alla grupper. I kontrollgruppen (C) odlades växterna endast i substratet. I den andra gruppen (R) behandlades frön med en mikrobiell ympning innan de såddes i substratet.I den tredje gruppen (RE) utfördes samma fröbehandling som i R och kompostextrakt tillsattes också till RE-gruppen. Växterna odlades i separata krukor i ett växthus och tillväxthastigheten observerades och dokumenterades liksom den totala skörden. I slutet av växtsäsongen gjordes en kemisk och biologisk analys av jorden samt en savanalys på bladen. Tillväxten var likartad bland grupperna även om R och RE visade något högre tillväxttakt i de senare stadierna av växtsäsongen. Skördad frukt per planta var högst i C, dock intesignifikant. Den mikrobiella koncentrationen var hög i alla jordar men mer svamporienterat i RE och bakterieorienterat i C. Den kemiska analysen visade högt nitratinnehåll i bladen i C. I R och särskilt i RE var nitratomvandlingen till aminosyror och proteiner högre vilket indikerar att dessa grupper är mer motståndskraftiga mot skadedjur så som bladlöss.

Economic and environmental concerns surrounding nitrogen (N) have motivated efforts to improve estimates of plant available N in soil in order to improve crop N management decisions. Cover crops have been recognized as an effective tool for protecting soil and enhancing soil function including N cycling. This recognition has increased the adoption of cover cropping in the United States. Despite this growing popularity, there is lack of consistent response of cover crop on soil health and only a few experiments have examined how cover crop impacts nitrogen (N) management in corn. Therefore, the objectives of this study were to: a) quantify the impacts of cover crops on various soil health indicators like permanganate oxidizable carbon (POXC), CO2 burst, autoclaved-citrate extractable (ACE)-soil protein, b) investigate the relationship between soil health indicators, soil nitrate (NO3-N) and ammonium (NH4-N), corn N requirement and corn yield, and c) study the decomposition and N release of different cover crops. In a comparison of cover crop treatments, there was a trend of increasing permanganate oxidizable carbon (POXC) and CO2 burst with cover crop compared to no-cover crop control in the short term (1 year). Additionally, CO2 burst values were significantly increased for a long-term site with cover crops compared to the control in both 2021 and 2022. A long-term cover crop study at 25 sites showed a weak relationship of CO2 burst, POXC, soil protein and NO3-N with agronomic optimum N rate (AONR), with r values ranging from 0.00 to 0.48, suggesting these indicators may not be reliable predictors of N available in soil and corn yield. However, there was significant relationship between NO3-N at N sidedress time and relative yield (r = 0.65) at these long-term sites. In short-term cover crop study (Chapter 1), Presidedress nitrate test (PSNT) nitrate concentration was >15 mg kg-1 at 5 sites and in long term cover crop study (Chapter 2), 15 sites had nitrate concentration > 15 mg kg-1 indicating potential of N sidedressing reduction when compared to current pre-sidedress N test (PSNT) N recommendation in Virginia, which is currently only recommended for sites receiving manure or biosolids. A cover crop decomposition study at Kentland showed that hairy vetch had a faster decomposition rate (k = 0.0377 g g-1 d-1) than rye and vetch mix (k = 0.0292 g g-1 d-1) or cereal rye (0.0227 g g-1 d-1) with 0 N fertilizer and released more N than cereal rye and rye and vetch mix. The difference in C: N ratio (hairy vetch (9-11:1), cereal rye (31-46:1), rye and vetch mix (19-20:1)) may have affected decomposition rate and N release of cover crops. Hairy vetch released significant amounts of N within a month of incubation, with 103 kg N ha-1 in 2021 and 57 kg N ha-1 in 2022. Overall, this study showed that cover crops did not have a consistent or significant effect on soil health indicators in short term. However, cover crops improved CO2 burst at long term cover crop site compared to no-cover, control. Future studies should focus on understanding best methods of predicting N available to subsequent crop and conduct cover crop decomposition studies across the state with different cover crop species and their mixture. / Doctor of Philosophy / Increasing food production and fertilizer application especially nitrogen has degraded the soils capacity to provide nutrient to crops. Cover crops are crops planted after harvesting main crops like corn, soybean and cotton to protect soil from erosion and improve the soil's nutrient supply capacity. Planting cover crops in fall rather than leaving soil bare can be a best management practice to improve the soils and reduce the nitrogen loss to water bodies. The purpose of this study was to measure soil properties that shows how healthy the soil is, find the relation of soil properties with corn N requirement and corn yield, and estimate decomposition rate and nitrogen release after cover crop termination. Results showed that one year of cover crop versus no-cover crop had no effect on active carbon (permanganate oxidizable carbon, POXC), microbial respiration (CO2 burst). However, long term cover cropping increased CO2 burst. In long term cover cropping fields, nitrate concentration measured before N sidedress time (also called presidedress nitrate test, PSNT) was increased at 15 sites indicating these sites could reduce their N sidedressing. Cover crop decomposition study showed that decomposition and nitrogen release from hairy vetch was faster than cereal rye, and cereal rye and vetch mixture. Overall, planting cover crop showed did not improve in short term but planting cover crop for long term have potential to reduce the amount of nitrogen fertilizer need for corn, especially when legume cover crops are use.

Encouraging greater implementation of conservation agriculture practices such as reduced tillage and cover crops may require better understanding of the effect of these practices on soil health. The overall objective of this study was to quantify soil health dynamics due to conservation agriculture practices and address methodological gaps in terms of measuring soil health parameters. We developed five sites across the state of Virginia; each site had replicated plots with combinations of reduced tillage versus disk tillage and wintertime cover crops versus no cover crops as experimental treatments. Soil and plant samples were collected 1-2 times per year for 3 years, and were analyzed for 30 soil health parameters. The parameters were first evaluated to determine if any consistently detected treatment differences. We then quantified the temporal dynamics of the eight most responsive soil health parameters, while considering influences of soil water content at time of tillage, cover crop biomass, and previous land management history. Of the analyzed parameters, only 2-4 mm aggregate stability and magnesium showed high responsiveness and consistency in identifying tillage and cover crop effects. None of the parameters detected treatment differences in all sites or at all times, yet samples collected after high biomass cover crops or after tillage in wet conditions tended to show significant treatment differences for multiple indicators. The previous history of management in each site may have affected trends in aggregate stability, but did not appear to influence other indicators. As soil aggregate stability was found to be the most important soil health parameter, our third study developed an improved method for measuring soil aggregate stability. This new method, Integrated Aggregate Stability (IAS), interprets aggregate stability using a laser diffraction machine. Overall, IAS showed higher correlation with the wet sieving method (R2 = 0.49 to 0.59) than widely used median aggregate size (d50) (R2 = 0.09 to 0.27). IAS can also quantify stability of macro- and micro-sized aggregates, which d50 cannot. When comparing between IAS and wet sieving, IAS requires considerably less time and sample amounts. Our fourth study focused on creating an inexpensive yet accurate tool for measuring soil respiration, as microbial assessments based on respiration rates have great potential for detecting rapid changes in soil health. Using an Arduino-based infrared gas analyzer (IRGA) sensor, we developed the Soil Microbial Activity Assessment Contraption (SMAAC) for less than $150. Our results show that SMAAC provided consistent readings with a commercial IRGA unit when tested using three different configurations. Altogether, the research presented in this dissertation identifies important soil health parameters and quantifies their temporal and between-site dynamics. Using this narrower set of indicators can help producers and practitioners save resources when conducting measurements to assess soil health effects of agricultural practices. Further, this work also provides improved measurement techniques for useful soil health parameters like aggregate stability and soil respiration. These findings and innovations should help to encourage greater adoption of agricultural management practices that build and preserve soil health. / Doctor of Philosophy / If we want to make sure that ample and safe food is available to future generations, then it is time that we produce food without damaging the soil. Many widely used soil management techniques like tillage and leaving the field bare can harm the soil and decrease productivity in the long run. One potential technique to produce food while protecting the soil and environment is conservation agriculture, which can include reduced tillage and cover cropping. Reduced tillage is a technique in which we grow food without majorly disturbing the soil, while cover crops are planted when cash crops are not in the field in order to improve or sustain the soil. Understanding the soil-related benefits of conservation agriculture practices is important to encourage farmers to adopt these practices. In this study we tested the effects on soils of reduced tillage and cover crop practices versus conventional tillage and bare soil practices, using five locations across Virginia. We also developed improved methods for measuring two informative soil parameters. We found that, when looking at all of our five sites, the stability of soil aggregates, the rate at which water enters soil, and the nutrients in surface soils were all affected by the type of management that the soils were subjected to. Reduced tillage increased stability of soil aggregates when compared with conventional till. This increased stability of aggregates indicators lower potential for surface water runoff, erosion, and flooding when we practice reduced tillage. Cover cropping also increased stability of soil aggregates, especially when the cover crops attained substantial above-ground mass. Soil nutrients (which are essential for plants to grow) were also overall higher in the surface soil layers under no-till. Since the stability of soil aggregates was found to be an important benefit of CA practices, we also perceived a need for a better method for measuring stability of these aggregates. In response, we developed a new index called Integrated Aggregate Stability (IAS). IAS was found to give similar results as established methods, but the time required to get IAS result is about 10 minutes, whereas the time required for established methods like wet sieving is around 2 days. IAS measurements are therefore both accurate and quick to perform. We also focused on developing an inexpensive tool for measuring soil respiration. Soil respiration-based measurements help us to understand the activity of microbes in the soil. These microbes are very important for soils to function. Our tool, Soil Microbial Activity Assessment Contraption (SMAAC), was very consistent with a currently used tool and shows high potential for future use. Altogether, we found that no-tillage and cover cropping can increase stability of soil aggregates even within 1-3 years of starting those practices. No-till can also increase nutrient concentrations in the top soil layer. The tools and innovations developed in this study have the potential to increase the ability of farmers to assess soil health and also encourage greater adoption of conservation agriculture practices.

Soil health-based agricultural management practices are widely promoted to improve soil structure, infiltration and reduce erosion. This study was conducted at two locations in North-Central Mississippi to evaluate the influence of different cover crop species and poultry litter on soil health that can impact crop production, climate change, and resilience. The results indicated that the cover crops showed a little effect on some soil health indicators compared to control treatment. However, in one location, rye, and a mixture of cover crops decreased bulk density and increased available water content and organic matter. The poultry litter had a positive effect on most soil physical and chemical health indicators. The cover crop species at Pontotoc decreased bulk density, increased field capacity, CEC, and total carbon. However, there was no significant effect of cover crops on most soil chemical health indicators, and soil responses may take more than five years for the changes to appear.

The research uses cameras mounted to a vehicle to capture geotagged images while conducting a transect survey. The images from two capture dates were manually classified into different classes of previous crop, tillage systems, residue cover, and cover crop utilization. The raw data was compared against the Indiana Cropland Transect Survey and the USDA-NASS Cropland Data Layer. The symmetric Kullback-Liebler divergence method was used to compared the distributions looking for similarities. <div><br></div><div>The manually classified data was then used to build satellite segmentation models using artificial neural networks , decision trees, k nearest neighbors, random forests, and support vector machine methods. The models were compared using overall accuracy, kappa coefficient, specificity, sensitivity, positive prediction value, and negative prediction value. The best model for each category of previous crop, tillage system, residue cover, and cover crop was used to segment a Sentenial-2 imagery downloaded from Copernicus Open Access hub. The results of the segment were compared by looking at the agreement at individual pixel locations from the segmented raster to the manually classified data and the Indiana Cropland Transect Survey. </div><div><br></div><div>Finally, all the images captured were used to being the development of a automated image classifier using nested convolutional neural networks (CNN). A small set of images was used to build the CNN. That model when then make prediction on new unclassified images. The predictions were manually checked. The check images were used to the to build the training and validation pools for the models. The first network divided the images into field or not field.</div><div>The second branch was field images divided in to images containing green growing plants of brown dead plants or residues. The final branch was determining the amount of surface cover left on a field. The results from each run of the training process were saved and used to assess model performance looking at accuracy and loss.</div>

Root-lesion nematodes, Pratylenchus spp., are serious pathogens of potato plants worldwide. Several management practices can control Pratylenchus spp.; however, they all have shown some limitations. Therefore, environmentally-safe, low-cost, and effective control strategies are needed as possible alternative to currently used strategies. This thesis was designed to assess if liquid hog manure (LHM) holds such potential. The objectives of this thesis were to determine: (i) the prevalence and identity of species of Pratylenchus spp. in Manitoba potato fields, (ii) if short-chain volatile fatty acids (VFA) in LHM are the constituents responsible for the manure’s toxicity to Pratylenchus spp. using solution exposure experiments (iii) the effectiveness of LHM in killing Pratylenchus spp. in soil, and (iv) the impact of LHM on nematode communities. Pratylenchus spp. were detected in 39% of 31 potato fields surveyed in Manitoba with population densities ranging, for positive fields, from 45 to 631 nematodes kg-1 fresh soil. Morphometrics of female nematodes and molecular diagnosis (using species-specific PCR primers) showed that the species of Pratylenchus present in the potato fields to be P. neglectus. Potato, cv. Russet Burbank, showed to be a poor host to two populations of Pratylenchus spp. from Manitoba potato fields. Accordingly, P. neglectus does not seem to be a limitation to potato production in Manitoba; thus, P. penetrans, the most widely spread and damaging species to potato was used in the successive studies of assessing the use of LHM to control Pratylenchus spp. in potato fields. VFA (acetic, propionic, n-butyric, isobutyric, n-valeric, isovaleric, and n-caproic acids) accounted for the majority of the lethal effect of LHM to P. penetrans under acidic conditions. VFA in LHM killed Pratylenchus spp. in soil and acidification seemed to enhance its ability when VFA concentration in the manure is low. LHM did not act as a soil fumigant eliminating soil trophic interactions but increased bottom-up food web interactions. VFA in LHM persisted in the soil for four days with biological degradation being their mode of loss. In conclusion, LHM is potentially an effective and low-cost strategy to control Pratylenchus spp. and its efficacy can be improved by acidification. / October 2009

Root-lesion nematodes, Pratylenchus spp., are serious pathogens of potato plants worldwide. Several management practices can control Pratylenchus spp.; however, they all have shown some limitations. Therefore, environmentally-safe, low-cost, and effective control strategies are needed as possible alternative to currently used strategies. This thesis was designed to assess if liquid hog manure (LHM) holds such potential. The objectives of this thesis were to determine: (i) the prevalence and identity of species of Pratylenchus spp. in Manitoba potato fields, (ii) if short-chain volatile fatty acids (VFA) in LHM are the constituents responsible for the manure’s toxicity to Pratylenchus spp. using solution exposure experiments (iii) the effectiveness of LHM in killing Pratylenchus spp. in soil, and (iv) the impact of LHM on nematode communities. Pratylenchus spp. were detected in 39% of 31 potato fields surveyed in Manitoba with population densities ranging, for positive fields, from 45 to 631 nematodes kg-1 fresh soil. Morphometrics of female nematodes and molecular diagnosis (using species-specific PCR primers) showed that the species of Pratylenchus present in the potato fields to be P. neglectus. Potato, cv. Russet Burbank, showed to be a poor host to two populations of Pratylenchus spp. from Manitoba potato fields. Accordingly, P. neglectus does not seem to be a limitation to potato production in Manitoba; thus, P. penetrans, the most widely spread and damaging species to potato was used in the successive studies of assessing the use of LHM to control Pratylenchus spp. in potato fields. VFA (acetic, propionic, n-butyric, isobutyric, n-valeric, isovaleric, and n-caproic acids) accounted for the majority of the lethal effect of LHM to P. penetrans under acidic conditions. VFA in LHM killed Pratylenchus spp. in soil and acidification seemed to enhance its ability when VFA concentration in the manure is low. LHM did not act as a soil fumigant eliminating soil trophic interactions but increased bottom-up food web interactions. VFA in LHM persisted in the soil for four days with biological degradation being their mode of loss. In conclusion, LHM is potentially an effective and low-cost strategy to control Pratylenchus spp. and its efficacy can be improved by acidification.