Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing.

The sequencing platform and workflow strongly influence microbial community analyses through potential errors at each step. Effective diagnostics and experimental controls are needed to validate data and improve reproducibility. This cross-laboratory study evaluates sources of variability and error at three main steps of a standardized amplicon sequencing workflow (DNA extraction, polymerase chain reaction [PCR], and sequencing) using Oxford Nanopore MinION to analyze agricultural soils and a simple mock community. Variability in sequence results occurs at each step in the workflow with PCR errors and differences in library size greatly influencing diversity estimates. Common bioinformatic diagnostics and the mock community are ineffective at detecting PCR abnormalities. This work outlines several diagnostic checks and techniques to account for sequencing depth and ensure accuracy and reproducibility in soil community analyses. These diagnostics and the inclusion of a reference soil can help ensure data validity and facilitate the comparison of multiple sequencing runs within and between laboratories.

Milk Production, Body Weight, Body Condition Score, Activity, and Rumination of Organic Dairy Cattle Grazing Two Different Pasture Systems Incorporating Cool- and Warm-Season Forages.

Organic dairy cows were used to evaluate the effect of two organic pasture production systems (temperate grass species and warm-season annual grasses and cool-season annuals compared with temperate grasses only) across two grazing seasons (May to October of 2014 and 2015) on milk production, milk components (fat, protein, milk urea nitrogen (MUN), somatic cell score (SCS)), body weight, body condition score (BCS), and activity and rumination (min/day). Cows were assigned to two pasture systems across the grazing season at an organic research dairy in Morris, Minnesota. Pasture System 1 was cool-season perennials (CSP) and Pasture System 2 was a combination of System 1 and warm-season grasses and cool-season annuals. System 1 and System 2 cows had similar milk production (14.7 and 14.8 kg d-1), fat percentage (3.92% vs. 3.80%), protein percentage (3.21% vs. 3.17%), MUN (12.5 and 11.5 mg dL-1), and SCS (4.05 and 4.07), respectively. Cows in System 1 had greater daily rumination (530 min/day) compared to cows in System 2 (470 min/day). In summary, warm-season annual grasses may be incorporated into grazing systems for pastured dairy cattle.

Surface runoff and nutrient dynamics in cover crop-soybean systems in the Upper Midwest.

Relay-cropping of the novel oilseeds winter camelina (Camelina sativa L.) and pennycress (Thlaspi arvense L.) with short-season crops such as soybean [Glycine max (L.) Merr.] can provide economic and environmental incentives for adopting winter cover crop practices in the U.S. Upper Midwest. However, their ability to reduce nutrient loss in surface runoff is unknown. Accordingly, surface runoff and quality were evaluated during three seasonal phases (cover, intercrop, and soybean) over 2 yr in four cover crop-soybean treatments (pennycress, winter camelina, forage radish [Raphanus sativus L.], and winter rye [Secale cereale L.]) compared with no-till and chisel-till fallow treatments. Runoff was collected with Gerlach troughs and assessed for concentrations and loads of NO3 - -N, total mineral N, soluble reactive P (SRP), and total suspended solids (TSS). Cumulative runoff and nutrient loads were greater during the winter cover phase because of increased snow melt and freeze-thaw released nutrients from living vegetation. In contrast, cumulative TSS was greater during intercrop and soybean phases due to high-intensity rainfall events with an open soybean canopy. Average TSS loads during the intercrop phase were reduced by 75% in pennycress compared with fallow and radish treatments. During the soybean phase, average TSS, total mineral N, and SRP loads were generally elevated in cover crop treatments compared with no-till. Overwintering cover crops may contribute to mobility of nutrients solubilized from living or decomposing vegetation; however, this was balanced by their potential to reduce runoff and TSS during high-intensity spring rains.

Reduced Potential for Nitrogen Loss in Cover Crop-Soybean Relay Systems in a Cold Climate.

Winter cover crops might reduce nutrient loss to leaching in the Upper Midwest. New oilseed-bearing cash cover crops, such as winter camelina ( L.) and pennycress ( L.), may provide needed incentives. However, the abilities of these crops to sequester labile soil nutrients are unknown. To address this unknown, N in shoot biomass, plant-available N and P in soil, and NO-N and soluble reactive P in soil water collected from lysimeters placed at 30, 60, and 100 cm were measured in cover crop and fallow treatments established in spring wheat ( L.) stubble and followed through a cover crop-soybean [ (L.) Merr.] rotation. Five no-till cover treatments (forage radish [ L.], winter rye [ L.], field pennycress, and winter camelina) were compared with two fallow treatments (chisel till and no-till). Pennycress and winter camelina were harvested at maturity after relay sowing of soybean. Winter rye and radish sequestered more N in autumn shoot biomass, ranging from 26 to 38 kg N ha, but overwintering oilseeds matched or exceeded N uptake in spring, ranging 28 to 49 kg N ha before soybean planting. Nitrogen uptake was reflected by reductions in soil water NO-N during cover crop and intercropping phases for all cover treatments (mean = 4 mg L), compared with fallow treatments (mean = 31 mg L). Cash cover crops like pennycress and winter camelina provide both environmental and potential economic resources to growers. They are cash-generating crops able to sequester labile soil nutrients, which protects and promotes soil health from autumn through early summer.

Flowering dynamics and pollinator visitation of oilseed echium (Echium plantagineum).

Echium (Echium plantagineum L.) is an alternative oilseed crop in summer-wet temperate regions that provides floral resources to pollinators. Its seed oil is rich in omega-3 fatty acids, such as stearidonic acid, which is desired highly by the cosmetic industry. Seeds were sown in field plots over three years in western Minnesota in spring (early-sown) or early summer (late-sown), and flower abundance, pollinator visitation, and seed yields were studied. Initial flowering commenced 41 to 55 d after sowing, and anthesis duration (first flowering to harvest) was 34 to 70 d. Late sowing dates delayed anthesis, but increased the intensity of visitation by pollinators. Cumulative flower densities ranged from 1 to 4.5 billion ha-1. Flowers attracted numerous honey bees (Apis mellifera L.), as many as 35 per minute of observation, which represented about 50% of all insect visitors. Early-sown echium produced seed yields up to 750 kg ha-1, which were 2-29 times higher than those of late-sown echium. Early sowing of echium in Minnesota provides abundant floral resources for pollinators for up to two months and simultaneously produces seed yields whose profits rival those of corn (Zea mays L.).

Do mitigation strategies reduce global warming potential in the northern U.S. corn belt?

Agricultural management practices that enhance C sequestration, reduce greenhouse gas emission (nitrous oxide [N2O], methane [CH4], and carbon dioxide [CO2]), and promote productivity are needed to mitigate global warming without sacrificing food production. The objectives of the study were to compare productivity, greenhouse gas emission, and change in soil C over time and to assess whether global warming potential and global warming potential per unit biomass produced were reduced through combined mitigation strategies when implemented in the northern U.S. Corn Belt. The systems compared were (i) business as usual (BAU); (ii) maximum C sequestration (MAXC); and (iii) optimum greenhouse gas benefit (OGGB). Biomass production, greenhouse gas flux change in total and organic soil C, and global warming potential were compared among the three systems. Soil organic C accumulated only in the surface 0 to 5 cm. Three-year average emission of N2O and CH was similar among all management systems. When integrated from planting to planting, N2O emission was similar for MAXC and OGGB systems, although only MAXC was fertilized. Overall, the three systems had similar global warming potential based on 4-yr changes in soil organic C, but average rotation biomass was less in the OGGB systems. Global warming potential per dry crop yield was the least for the MAXC system and the most for OGGB system. This suggests management practices designed to reduce global warming potential can be achieved without a loss of productivity. For example, MAXC systems over time may provide sufficient soil C sequestration to offset associated greenhouse gas emission.

Agricultural opportunities to mitigate greenhouse gas emissions.

Agriculture is a source for three primary greenhouse gases (GHGs): CO(2), CH(4), and N(2)O. It can also be a sink for CO(2) through C sequestration into biomass products and soil organic matter. We summarized the literature on GHG emissions and C sequestration, providing a perspective on how agriculture can reduce its GHG burden and how it can help to mitigate GHG emissions through conservation measures. Impacts of agricultural practices and systems on GHG emission are reviewed and potential trade-offs among potential mitigation options are discussed. Conservation practices that help prevent soil erosion, may also sequester soil C and enhance CH(4) consumption. Managing N to match crop needs can reduce N(2)O emission and avoid adverse impacts on water quality. Manipulating animal diet and manure management can reduce CH(4) and N(2)O emission from animal agriculture. All segments of agriculture have management options that can reduce agriculture's environmental footprint.