Master of Science / Department of Agronomy / Nathan O. Nelson / Phosphorus (P) loss from non-point agricultural sources has been identified as a main contributor to degraded surface water quality throughout the United States. Excessive P inputs to surface waters can lead to eutrophication, increased water treatment costs, and negative health impacts. Therefore, agricultural best management practices (BMP) that promote water quality, through minimizing P loss, must be identified. Studies outlined in this thesis aim to determine the impacts of cover crops and P fertilizer placement on P loss in surface runoff and nutrient cycling in a no-till corn (Zea mays)-soybean (Glycine max) rotation and provide insight into how cover crop species selection and termination method affects potential P loss from crop tissue. The first study examined combined effects of cover crop and P fertilizer placement on total P, dissolved reactive P (DRP) and sediment losses in surface runoff from natural precipitation events. This large-scale field study was conducted near Manhattan, Kansas, at the Kansas Agricultural Watershed (KAW) Field Laboratory during the 2016 and 2017 cropping years. Two levels of cover crop [no cover crop (NC) and cover crop (CC)] and three levels of P fertilizer management [no P (CN), fall broadcast P (FB), and spring injected P (SI)] were used. Flow-weighted composite water samples were collected from precipitation events generating greater than 2.0 mm of surface runoff. Results from this study found the CC treatment increased DRP losses compared to NC in both cropping years; however, CC reduced sediment loss by over 50% compared to NC. Application of P fertilizer increased DRP losses compared CN in both cropping years, although SI resulted in lower quantities of DRP loss compared to FB. In addition, this study found that CC reduced biomass and yield of corn compared to NC and therefore decreased nutrient uptake, removal, and deposition during the 2017 cropping year. However, no negative impacts of CC on biomass or yield were observed during the 2015 (corn) and 2016 (soybean) cropping years. Application of P fertilizer increased the concentration of Melich-3 P and total P in the top 0-5 cm of soil compared to CN; however, no differences between P fertilizer management practice were observed for concentrations of Melich-3 P at 5-15 cm. A greenhouse-based study determined the impacts of cover crop species (brassica, grass, and legume), termination method (clipping, freezing, and herbicide), and time after termination (1, 7, and 14 days after termination) on total P and water-extractable P (WEP) release from cover crop biomass. Freezing increased WEP concentration of crop tissue by more than 140% compared to clipping and herbicide. Additionally, at 7 and 14 days after termination, both concentration of WEP and fraction of WEP compared total P increased compared to 1 DAT. Findings from these studies suggest the use of cover crops may unintentionally result in greater DRP losses in surface runoff. However, addition of a cover crop can dramatically reduce erosion losses. In addition, cover crop species selection can directly impact the quantity of P being taken up and released by crop tissue. Understanding the impact of crop species selection may help create new BMPs which aim to reduce P loss.

Field experiments were conducted to evaluate cover crop interseeding time and species effect on sugarbeet production during 2018 and 2019 growing seasons. Cover crops were first interseeded in June and second interseeding was done in late June or early July. Four cover crops species, Austrian pea (Pisum sativum L.), winter rye (Secale cereale L.), winter camelina [Camelina sativa (L.) Crantz], and brown mustard (Brassica juncea L.), were examined. First interseeding resulted in significantly higher cover crop biomass than second interseeding. In 2018, the highest recoverable sugar yield was observed with pea (13.9 Mg ha-1) and camelina (6.6 Mg ha-1) first-interseeded, at Ada and Downer, MN, respectively. In 2019, camelina (11.2 Mg ha-1) at Ada, MN, and pea (12.4 Mg ha-1) at Prosper, ND both second-interseeded, had the highest recoverable sugar yield. Cover crops had no negative impacts on sugarbeet, but the selection of species and planting time are critical.

To our knowledge, this metagenomics study is the first of its kind to determine how cover crops and tillage management practices affect the soil microbiome in southern Illinois. Seven different cover crops were used over the course of two years from 2014 to 2015, and two different forms of tillage were used: Conventional Tillage (CT) and No-Tillage (NT). Four barcodes were used to generate libraries for the phylogenetic identification of fungi, bacteria, oomycetes, and fusaria: the ITS1, EF1a (Elongation Factor 1-a), and the V4 region of the 16s rRNA subunit. Targeted amplicon sequencing using 250 base pair Paired End (PE) reads yielded 14 x 106 base pair reads in total. Using these amplicons, we successfully unveiled the fungal and bacterial constituents of the studied field plots (database limitations considered) using the QIIME and NCBI Blast protocols. Specifically, this study had three goals 1) to determine if cover crops or tillage had a significant impact on the overall microbial diversity found in bulk soil samples taken from cover crop plots; 2) to determine if the incidence and abundance of individual bacterial or fungal taxa were affected by the cover crop or tillage treatment; 3) perform a bioinformatics methodology comparison for fungal identification using the ITS1 region between Qiime, and MEGAN protocols. Our results indicate many instances of cover crop or tillage interacting with one or more groupings of taxa. Significant whole community differences could be detected to the species (P=0.0335) and family (P=0.0001) taxonomic ranks of fungi using with the three most abundant families based on assigned reads being Mortierellaceae, Trichocomaceae, and Botryosphaeriaceae. Significant whole community interactions between tillage types and year at the level of phylum were observed between bacteria and archaea. Three main phyla constituting bacterial reads were Proteobacteria, Actinobacteria, and Acidobacteria. The primary driver in individual differences in bacterial populations appeared to be the year in which samples were taken either 2014 or 2015 (P=0.0001). This was attributed in part due to drastic fluctuations in weather from November 2014 to November 2015. Whole community differences and shifts could be observed based on cover crop down to the species level using both QIIME and NCBI BLAST protocols. The different dispersions and taxa found between cover crops imply that there is a relationship between certain organisms and the type of plant matter present. Tillage type, year, and cover crop were all found to have some degree of clustering based on reads taken from the four amplicons used. For comparison between NCBI and QIIME methodologies using the ITS1 region, the NCBI BLAST protocol provided the most overlap between taxa at the Order and Class taxonomic rankings. An upwards of 70% complementarity of taxa was found comparing the results after using the NCBI or the QIIME protocols. Whole community analysis using PERMANOVA revealed complementarity shifts based on treatment types when comparing both QIIME and NCBI protocols for taxonomic assignments visualized using PCoA plots. This comparison between the two methods for fungal community analysis using the ITS region, highlights the significant discrepancies as well as the complementarity of the two methodologies when analyzing fungal microbiomes.

In order to reduce nutrient losses and soil erosion in the United States Upper Midwest following soybean [Glycine max (L.) Merr.], cover crops can be intersown into standing soybean. The objective of this study was to determine the establishment of intersown cover crops and their impacts on a soybean-wheat (Triticum aestivum L.) rotation. Four cover crops, winter camelina [Camelina sativa (L.) Crantz], winter pea [Pisum sativum ssp. arvense (L.) Poir], winter rye (Secale cereale L.), and radish (Raphanus sativus L.), were directly sown into the ground at the R4 and R6 stages of soybean at two locations, Prosper and Fargo, ND in 2016-2018. Results indicated intersowing cover crops have no impact on soybean yield, can produce above ground biomass which ranged from 0.44 to 3.04 Mg ha-1, and show potential to mitigate soil nitrate losses in areas that grow soybean as a cash crop.

In the Midwest, it can be beneficial to interseed cover crops into corn (Zea mays L.) since there is a limited time for them to establish and grow after corn harvest. Research conducted in four environments in North Dakota quantified the impacts of planting method and time of planting when grown with or without corn competition on the establishment, and development of three cover crop species. Limited light intensity (less than 20%) under the corn canopy drastically reduced cover crop development. Soil water can also constrain cover crop establishment. Model simulations suggest soil water is more limiting for cover crop establishment in August compared with June or July. Interseeded cover crops had no effect on corn yield or the following soybean (Glycine max (L.) Merr.] crop due to minimal amounts of biomass produced.

Faba bean (Vicia faba Roth) is grown worldwide as a protein source for food, used for animal feed, and is a common cover crop in Europe, but is underutilized in Midwest farming systems. Faba bean, field pea (Pisum sativum L.), and forage pea were evaluated for biomass and chemical composition when sown after wheat. Faba bean, forage pea, balansa clover (Trifolium michelanium Savi), red clover (T. pratense L.), and rye (Secale cereale L.) were evaluated similarly when intersown into maize. Cover crops after wheat had no significant biomass differences, averaging 1210 kg ha-1, enough to support 1.5 animal unit month (AUM) ha-1 for a 450 kg cow with calf. Rye yielded the greatest (374 kg ha-1) of the intercrops with faba bean averaging similarly and other intercrops averaging significantly less. Intercrops did not affect maize yield. Faba bean has similar potential as other commonly used cover crops in the Midwest.

Indiana University-Purdue University Indianapolis (IUPUI) / Nitrous oxide (N2O) is an atmospheric constituent that contributes to climate warming and stratospheric ozone depletion. A large fraction of the anthropogenic N2O emission originates from agricultural soils suggesting therefore a strong connection between N2O accumulation in the atmosphere and agricultural land management. During the last 2-3 decades, no-till (NT) farming and integration of cover crops into crop rotation represent two major developments in agriculture, but much remains to be learned about the impact of these management approaches on N2O emission and underlying biological soil factors. This dissertation focuses on the contribution of different components of the soil microflora to N2O production, and how different types of cover crops (legume vs grass) affect the soil microbial community composition, mineral N availability, and N2O emission in plowed (PT) and NT soils. To address these questions, several laboratory and greenhouse experiments were conducted. Results of these experiments documented soil microbial community responses to cover crop addition and could inform the selection of cover crops most suitable to soils under different tillage practices.

Early planting soybean (Glycine max L.) strategies across the mid-southern United States has complicated weed management in the form of post-harvest weed control. Research has investigated the use of cover crops to aid in management of weed populations during winter months, but conventional cover crops provides minimal weed management benefit immediately following cash crop harvest. Inter-seeding cover crop into crop canopies has potential to promote earlier cover crop establishment, thus creating higher potential for post-harvest weed management. However, factors such as inter-seeding timing, herbicide residue, as well as harvest aid applications must be considered. Therefore, studies were conducted in Mississippi in 2017, 2018, and 2019 to determine if cover crops inter-seeded through soybean could improve weed control used in conjunction with common management strategies in Mississippi production systems. Conclusions drawn from these studies indicate inter-seeded cover crops can be utilized in soybean production systems to improve weed management after harvest.

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Crop production, soil system, water quality, and economic impacts of four corn silage production systems were compared through a field study including 16 plots (4 replications of each treatment). Systems included a rye cover crop and application of liquid dairy manure in the spring and fall. The four management systems were: 1) traditional, 2) double-crop, 3) roll-down, and 4) undercut. In the fourth system, manure was applied below the soil surface during the undercutting process. In all other systems, manure was surface-applied. In the third system, the rye crop was flattened with a heavy roller after manure application. Simulated rainfall was applied within 48 h of manure application. Measured constituent concentrations in runoff were compared with water quality criteria. Costs and returns of all systems were compared. The undercut system reduced loadings of all nutrients, but increased total suspended solids (TSS) concentration as compared with all other systems. The mean volume of runoff from the undercut system was less than half that from any other system, which influenced all constituent loadings. Mean TSS concentration in runoff from the undercut system was over three times the mean of any other system. The roll-down system had no significant effect on water quality as compared to the traditional system. The undercut system was reasonably effective in keeping phosphate phosphorus levels below the criterion set for bathing water. None of the systems generally exceeded nitrate nitrogen concentration criteria. However, total phosphorus, orthophosphate, fecal coliform and e. coli criteria for drinking, bathing, shellfish harvest, and aesthetics were regularly exceeded by all of the systems. There were no differences among the treatments in effects on bacterial concentrations. The double-crop system produced significantly higher net returns than all other systems only if the value of the rye crop was $92.31/Mg or more. There were no significant differences in net returns of the traditional, roll-down, or undercut systems. / Ph. D.