Shalamar D. Armstrong

Manure Spills and Remediation Methods to Improve Water Quality

Within the last 2 decades the transition in livestock production technology and intensity has resulted in an increase in annual livestock production and a drastic decrease in the number of livestock operations. Consequently, the susceptibility of current livestock operations to experience manure spills is far greater relative to livestock farms 20 years ago, due to increased herd size per farm. Therefore, manure spills in agricultural communities have become a pervasive issue and have led to the catastrophic contributions of nutrients and pathogens to surface and groundwaters, human health issues, and large fish kills. Furthermore, the current remediation methods for manure spills that reach surface waters focus on mitigating contaminants in the water column and give no attention to the manure-exposed ditch sediments that remain in the fluvial system and continue to impair the water column. Therefore, this chapter addresses the causes, environmental impacts, and current and alternative remediation methods for manure spills in agricultural streams. Geographic data suggest that the location of animal-feeding operations and the occurrence of manure spills were highly correlated with the location of tile-drained agriculture fields. In addition, at least 14% of reported manure spills were separately attributed to the failure in waste storage equipment and over-application of manure in the states of Iowa and Ontario, Canada. Evaluations of the downstream impacts of manure spills have reported ammonia, total phosphorus, and total N concentrations that were at least 28 times the average upstream concentrations before the spill occurred. Studies have also determined that the current manure spill remediation method results in soluble phosphorus and nitrogen concentrations significantly greater than the Environmental Protection Agency total phosphorus nutrient critical limit, 24 h after the plume of the spill has passed. However, supplemental treatment of manure exposed sediments resulted in at least a 50% decrease in the soluble phosphorus concentrations which was in compliance with the phosphorus nutrient criteria.

In Field Measurements of Nitrogen Mineralization Following Fall Applications of N and the Termination of Winter Cover Crops

Little is known about the timing and quantity of nitrogen (N) mineralization from cover crop residue following cover crop termination. Therefore, the objective of this study was to examine the impact of cover crop species on the return of fall applied N to the soil in the spring following chemical and winter terminations. Fall N was applied (200 kg N ha−1) into a living stand of cereal rye, tillage radish, and control (no cover crop). After chemical termination in the spring, soil samples were collected weekly and were analyzed for inorganic N (NO3-N and NH4-N) to investigate mineralization over time. Cereal rye soil inorganic N concentrations were similar to that of the control in both the spring of 2012 and 2013. Fall N application into tillage radish, cereal rye, and control plots resulted in an average 91, 57, and 66% of the fall N application rate as inorganic N in the spring at the 0-20 cm depth, respectively. The inclusion of cover crops into conventional cropping systems stabilized N at the soil surface and has the potential to improve the efficiency of fall applied N.

Phosphorus and nitrogen loading depths in fluvial sediments following manure spill simulations

Armstrong, S. D., Smith, D. R., Owens, P. R., Joern, B. C., Leytem, A. B., Huang, C.H. and Adeola, L. 2011. Phosphorus and nitrogen loading depth in fluvial sediments following manure spill simulations. Can. J. Soil Sci. 91: 427-436. The depth of nitrogen (N) and phosphorus (P) loading in fluvial sediments following a manure spill has not been documented. Thus, the objectives of this study were: (i) to determine the depth of N and P enrichment as a result of a manure spill under base flow conditions using fluvarium techniques and (ii) to evaluate the impact of sediment particle size distribution on N and P enrichment depth. Manure spills were simulated using stream simulators and ditch sediments collected from agricultural drainage ditches. During the manure spill simulation, the P sorption capacity of all sediments exponentially decreased with time and the NH4-N sorption capacity remained constant with time. The P and NH4-N loading in all sediments were observed to the depth of 2 cm, but were most concentrated in the 0- to 1-cm depth ranging in concentrations from 3 to 12 mg P kg-1 and from 7.2 to 45 mg NH4-N kg-1. Data from this study give a basis for the advancement of manure spill remediation that will reduce the impairment of surface waters via the release of nutrients from enriched sediments following a manure spill.

ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis

The internally transcribed spacer (ITS) region between the small subunit ribosomal RNA gene and large subunit ribosomal RNA gene is a widely used phylogenetic marker for fungi and other taxa. The eukaryotic ITS contains the conserved 5.8S rRNA and is divided into the ITS1 and ITS2 hypervariable regions. These regions are variable in length and are amplified using primers complementary to the conserved regions of their flanking genes. Previous work has shown that removing the conserved regions results in more accurate taxonomic classification. An existing software program, ITSx, is capable of trimming FASTA sequences by matching hidden Markov model profiles to the ends of the conserved genes using the software suite HMMER. ITSxpress was developed to extend this technique from marker gene studies using Operational Taxonomic Units (OTU’s) to studies using exact sequence variants; a method used by the software packages Dada2, Deblur, QIIME 2, and Unoise. The sequence variant approach uses the quality scores of each read to identify sequences that are statistically likely to represent real sequences. ITSxpress enables this by processing FASTQ rather than FASTA files. The software also speeds up the trimming of reads by a factor of 14-23 times on a 4-core computer by temporarily clustering highly similar sequences that are common in amplicon data and utilizing optimized parameters for Hmmsearch. ITSxpress is available as a QIIME 2 plugin and a stand-alone application installable from the Python package index, Bioconda, and Github.

Re-Evaluation of Soil Nitrogen Sampling Strategy Effects on Statistical Power

ABSTRACT Soil sampling may be used as a decision-making tool for late-vegetative stage nitrogen (N) fertilizer applications in corn (Zea mays L.). Recommended sampling strategies following banded fertilizer applications commonly suggest taking cores from both on the fertilizer band (B) and off the band (O-B), however we hypothesized that soil nitrate concentrations (NO3−ppm) in the O-B were not influenced by N application rate. Analyzing samples from six experiments, we found there was a strong relationship between NO3−ppm and applied N rate in the B, but not the O-B position. Power analysis revealed that finding significant differences in applied N rates was only likely when sampling on the B and the difference in N rate was greater than 110 kg N ha−1. This demonstrates that soil N sampling is not sensitive to small differences in applied N, and that O-B soil cores may only dilute the ability to detect these differences. Abbreviations: B, on N fertilizer band; O-B, halfway between the corn row and the N fertilizer band; NO3−ppm, log-transformed nitrate-N concentration (ppm); NH4+ppm; ammonium-N concentration (ppm); D1, 0–30 cm depth; D2, 30–60 cm depth; C-220, contrast of N rates differing by 220 kg N ha−1; C-110, contrast of N rates differing by 110 kg N ha−1; C-55H, contrast of N rates differing by 55 kg N ha−1 at high N rates; C-55L, contrast of N rates differing by 55 kg N ha−1 at low N rates; A:N, ratio of non-transformed ammonium-N to nitrate-N concentrations; 0N, unfertilized treatment; CV, coefficient of variation; SE, standard error.