Comparative analysis of three next-generation sequencing techniques to measure nosZ gene abundance in Missouri claypan soils.

Quantitative next-generation sequencing techniques have been critical in gaining a better understanding of microbial ecosystems. In soils, denitrifying microorganisms are responsible for dinitrogen (N2) production. The nosZ gene codes for nitrous oxide reductase, the enzyme facilitating the reduction of nitrous oxide (N2O) to N2. The objectives of this research were to: 1) understand how soil depth influences RNA concentration and nosZ gene abundance; 2) assess the spatial dependence of nosZ gene abundance in two claypan soil fields; and 3) compare and evaluate multiple RNA-based sequencing methods for quantifying nosZ gene abundance in soils in relation to dinitrogen (N2) production. Research sites consisted of two intensively studied claypan soil fields in Central Missouri, USA. Soil cores were collected from two landscape transects across both fields and analyzed for extractable soil RNA at two depths (0-15 cm and 15-30 cm). Measurements of nosZ gene abundance were obtained using real-time quantitative polymerase chain reaction (RT-qPCR), droplet digital polymerase chain reaction (ddPCR), and nanostring sequencing (NS). In both fields, soil RNA concentrations were significantly greater at 0-15 cm depth compared to 15-30 cm. These data indicated low overall soil microbial activity below 15 cm. Due to low quantities of extractable soil RNA in the subsoil, nosZ gene abundance was only determined in the 0-15 cm depth. Sequencing method comparisons of average nosZ gene abundance showed that NS results were constrained to a narrow range and were 10-20-fold lower than ddPCR and RT-qPCR at each landscape position within each field. Droplet digital PCR appears to be the most promising method, as it reflected changes in N2 production across landscape position.

Urea Nitrapyrin Placement Effects on Soil Nitrous Oxide Emissions in Claypan Soil.

Corn ( L.) production in poorly drained claypan soils in the US Midwest is a challenge due to low soil permeability, which may result in wetter soil conditions and relatively large amounts of soil NO emissions early in the growing season. The objectives of this study were to determine the effects of urea fertilizer placement with and without nitrapyrin (NI) on daily and cumulative soil NO emissions, and yield-scaled NO emissions in 2016 and 2017. Treatments included urea deep banded to a 20-cm depth (DB), urea deep banded to 20 cm plus NI (DB+NI), urea incorporated after a surface broadcast application to ∼8-cm depth (IA), urea broadcast on the soil surface (SA), and a nonfertilized control (NTC). Fertilizer was applied at 202 kg N ha. Surface soil NO efflux rates were generally lower (<50 g NO-N ha d) during the first 3 wk after N fertilization and latter parts of the growing seasons. When averaged across the 2016 and 2017 growing seasons, all fertilized treatments had significantly greater (2.33-5.60 kg NO-N ha, < 0.05) cumulative soil NO emissions than NTC. The DB+NI treatment had 54 and 55% lower cumulative soil NO emissions than IA and SA, respectively. In 2017, DB+NI had similar soil yield-scaled NO emissions to NTC. Percentage grain yield increase over NTC was highest for DB and DB+NI. Grain yield in 2016 was 14 to 18% higher for DB and DB+NI than SA. Results suggest that DB+NI is an effective management strategy for reducing cumulative soil NO emissions and increasing grain yields over the growing season.

Reducing phosphorus loss in tile water with managed drainage in a claypan soil.

Installing subsurface tile drain systems in poorly drained claypan soils to improve corn ( L.) yields could potentially increase environmental phosphorus (P) loss through the tile drainage system. The objectives of the study were to quantify the average concentration and loss of ortho-P in tile drain water from a claypan soil and to determine whether managed subsurface drainage (MD) could reduce ortho-P loss in tile water compared with free subsurface drainage (FD). Flow-weighted ortho-P concentration in the tile water was significantly lower with MD (0.09 mg L) compared with that of FD (0.15 mg L). Ortho-P loss in the tile water of this study was reduced with MD (36 g ha) by 80% compared with FD (180 g ha). Contrary to previous research, reduced ortho-P loss observed over the 4-yr study was not solely due to the reduced amount of water drained annually (63%) with MD compared with FD. During the spring period, when flow was similar between MD and FD, the concentration of ortho-P in the tile water generally was lower with MD compared with FD, which resulted in significantly less ortho-P loss with MD. We speculate that MD's ability to conserve water during the dry summer months increased corn's uptake of water and P, which reduced the amount of P available for leaching loss in the subsequent springs.

Phosphorus and nitrogen sorption to soils in the presence of poultry litter-derived dissolved organic matter.

Two environmental aspects associated with land application of poultry litter that have not been comprehensively evaluated are (i) the competition of dissolved organic matter (DOM) and P for soil sorption sites, and (ii) the sorption of dissolved organic nitrogen (DON) relative to inorganic nitrogen species (e.g., NO(3)(-) and NH(4)(+)) and dissolved organic carbon (DOC). The competition between DOM and P for sorption sites has often been assumed to increase the amount of P available for plant growth; however, elevating DOM concentrations may also increase P available for transport to water resources. Batch sorption experiments were conducted to (i) evaluate soil properties governing P sorption to benchmark soils of Southwestern Missouri, (ii) elucidate the impact of poultry litter-derived DOM on P sorption, and (iii) investigate DON retention relative to inorganic N species and DOC. Soils were reacted for 24 h with inorganic P (0-60 mg L(-1)) in the presence and absence of DOM (145 mg C L(-1)) using a background electrolyte solution comparable to DOM extracts (I = 10.8 mmol L(-1); pH 7.7). Soil P sorption was positively correlated with metal oxide (r(2) = 0.70) and clay content (r(2) = 0.79) and negatively correlated with Bray-1 extractable P (r(2) = 0.79). Poultry litter-derived DOM had no significant negative impact on P sorption. Dissolved organic nitrogen was preferentially removed from solution relative to (NO(3)(-)-N + NO(2)(-)-N), NH(4)(+)-N, and DOC. This research indicates that poultry litter-derived DOM is not likely to enhance inorganic P transport which contradicts the assumption that DOM released from organic wastes increases plant-available P when organic amendments and fertilizer P are co-applied. Additionally, this work demonstrates the need to further evaluate the fate and transport of DON in agroecosystem soils receiving poultry litter applications.

Bacterial diversity in rhizospheres of nontransgenic and transgenic corn.

Bacterial diversity in transgenic and nontransgenic corn rhizospheres was determined. In greenhouse and field studies, metabolic profiling and molecular analysis of 16S rRNAs differentiated bacterial communities among soil textures but not between corn varieties. We conclude that bacteria in corn rhizospheres are affected more by soil texture than by cultivation of transgenic varieties.

Phosphorus loss and runoff characteristics in three adjacent agricultural watersheds with claypan soils.

Effects of precipitation, runoff, and management on total phosphorus (TP) loss from three adjacent, row-cropped watersheds in the claypan region of northeastern Missouri were examined from 1991 to 1997 to understand factors affecting P loss in watersheds dominated by claypan soils. Runoff samples from each individual runoff event were analyzed for TP and sediment concentration. The annual TP loss ranged from 0.29 to 3.59 kg ha(-1) with a mean of 1.36 kg ha(-1) across all the watersheds during the study period. Significantly higher loss of TP from the watersheds was observed during the fallow period. Multiple small runoff events or several large runoff events contributed to loss of TP from the watersheds. Total P loss in 1993, a year with above-normal precipitation, accounted for 30% of the total TP loss observed over seven years. The five largest runoff events out of a total of 66 events observed over seven years accounted for 27% of the TP loss. The five largest sediment losses were responsible for 24% of the TP loss over seven years. Runoff volume and sediment loss explained 64 to 73% and 47 to 58% of the variation in TP loss on watersheds during the study. Flow duration and maximum flow accounted for 49 and 66% of TP loss, respectively. The results of this study suggest that management practices that reduce runoff volume, flow duration, maximum flow, and sediment loss, and that maintain a suitable vegetative cover throughout the year could lower P loss in claypan soils.