Genomic-based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America.

Genomic-based epidemiology can provide insight into the origins and spread of herbicide resistance mechanisms in weeds. We used kochia (Bassia scoparia) populations resistant to the herbicide glyphosate from across western North America to test the alternative hypotheses that (i) a single EPSPS gene duplication event occurred initially in the Central Great Plains and then subsequently spread to all other geographical areas now exhibiting glyphosate-resistant kochia populations or that (ii) gene duplication occurred multiple times in independent events in a case of parallel evolution. We used qPCR markers previously developed for measuring the structure of the EPSPS tandem duplication to investigate whether all glyphosate-resistant individuals had the same EPSPS repeat structure. We also investigated population structure using simple sequence repeat markers to determine the relatedness of kochia populations from across the Central Great Plains, Northern Plains and the Pacific Northwest. We found that the original EPSPS duplication genotype was predominant in the Central Great Plains where glyphosate resistance was first reported. We identified two additional EPSPS duplication genotypes, one having geographical associations with the Northern Plains and the other with the Pacific Northwest. The EPSPS duplication genotype from the Pacific Northwest seems likely to represent a second, independent evolutionary origin of a resistance allele. We found evidence of gene flow across populations and a general lack of population structure. The results support at least two independent evolutionary origins of glyphosate resistance in kochia, followed by substantial and mostly geographically localized gene flow to spread the resistance alleles into diverse genetic backgrounds.

Plastic response to early shade avoidance cues has season-long effect on Beta vulgaris growth and development.

Early-emerging weeds are known to negatively affect crop growth but the mechanisms by which weeds reduce crop yield are not fully understood. In a 4-year study, we evaluated the effect of duration of weed-reflected light on sugar beet (Beta vulgaris L.) growth and development. The study included an early-season weed removal series and a late-season weed addition series of treatments arranged in a randomized complete block, and the study design minimized direct resource competition. If weeds were present from emergence until the two true-leaf sugar beet stage, sugar beet leaf area was reduced 22%, leaf biomass reduced 25%, and root biomass reduced 32% compared to sugar beet grown season-long without surrounding weeds. Leaf area, leaf biomass, and root biomass was similar whether weeds were removed at the two true-leaf stage (approximately 330 GDD after planting) or allowed to remain until sugar beet harvest (approximately 1,240 GDD after planting). Adding weeds at the two true-leaf stage and leaving them until harvest (~1,240 GDD) reduced sugar beet leaf and root biomass by 18% and 23%, respectively. This work suggests sugar beet responds early and near-irreversibly to weed presence and has implications for crop management genetic improvement.

Seed Predation of Interseeded Cover Crops and Resulting Impacts on Ground Beetles.

Interseeding cover crops into standing grains can promote both agronomic and environmental benefits within agroecosystems. Producers must decide which cover crops are the best fit for their goals, and whether diverse cover crop mixtures provide benefits that are worth the increased seed cost. Broadcast seeding is an accessible strategy to try interseeding but can lead to patchy establishment; it is unknown how much seed loss is due to seed predators. In a two-year study, six cover crop species-planted as either single species or mixtures-were interseeded into standing corn. We evaluated seed predation at the time of seeding, agronomic impact through cover crop, and weedy biomass at the end of the season, and conservation impact through activity-density of ground beetles (Coleoptera: Carabidae). Cover crop seeds were vulnerable to seed predation, primarily by vertebrate seed predators, and seed loss varied across cover crop species. Cover crop biomass did not differ according to cover crop diversity and weedy biomass was not affected by cover crop presence or species. Cover crop diversity effects on carabid activity-density were inconsistent: carabids were higher in diverse mixtures in 1 year of the study, but only predicted by vegetative cover, not by cover crop, in the second year. Interseeding cover crops into corn has potential benefits for ground beetles, although the value of mixtures must be further explored.

How to use statistics to claim antagonism and synergism from binary mixture experiments.

We review statistical approaches applicable for the analysis of data from binary mixture experiments, which are commonly used in pesticide science for evaluating antagonistic or synergistic effects. Specifically, two different situations are reviewed, one where every pesticide is only available at a single dose level and a mixture simply combines these doses, and one where the pesticides and their mixture are used at increasing doses. The former corresponds to using factorial designs whereas the latter corresponds to fixed-ratio designs. We consider dose addition and independent action as references for lack of antagonistic and synergistic effects. Data from factorial designs should be analyzed using two-way analysis of variance models whereas data from fixed-ratio designs should be analyzed using non-linear dose-response analysis. In most cases, independent action seems the more natural choice for factorial designs. In contrast, dose addition is more appropriate for fixed-ratio designs although dose addition is not equally compatible with all types of dose-response data. Fixed-ratio designs should be preferred as they allow validation of the assumed dose-response relationship and, consequently, provide much stronger claims about antagonistic and synergistic effects than factorial designs. Finally, it should be noted that, in any case, simple ways of summarizing pesticide mixture effects may come at the price of more or less restrictive modeling assumptions. © 2021 Society of Chemical Industry.

Long-term trends in the intensity and relative toxicity of herbicide use.

Herbicide use is among the most criticized aspects of modern farming, especially as it relates to genetically engineered (GE) crops. Many previous analyses have used flawed metrics to evaluate herbicide intensity and toxicity trends. Here, I show that herbicide use intensity increased over the last 25 years in maize, cotton, rice and wheat. Although GE crops have been previously implicated in increasing herbicide use, herbicide increases were more rapid in non-GE crops. Even as herbicide use increased, chronic toxicity associated with herbicide use decreased in two out of six crops, while acute toxicity decreased in four out of six crops. In the final year for which data were available (2014 or 2015), glyphosate accounted for 26% of maize, 43% of soybean and 45% of cotton herbicide applications. However, due to relatively low chronic toxicity, glyphosate contributed only 0.1, 0.3 and 3.5% of the chronic toxicity hazard in those crops, respectively.

EPSPS Gene Copy Number and Whole-Plant Glyphosate Resistance Level in Kochia scoparia.

Glyphosate-resistant (GR) Kochia scoparia has evolved in dryland chemical fallow systems throughout North America and the mechanism of resistance involves 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene duplication. Agricultural fields in four states were surveyed for K. scoparia in 2013 and tested for glyphosate-resistance level and EPSPS gene copy number. Glyphosate resistance was confirmed in K. scoparia populations collected from sugarbeet fields in Colorado, Wyoming, and Nebraska, and Montana. Glyphosate resistance was also confirmed in K. scoparia accessions collected from wheat-fallow fields in Montana. All GR samples had increased EPSPS gene copy number, with median population values up to 11 from sugarbeet fields and up to 13 in Montana wheat-fallow fields. The results indicate that glyphosate susceptibility can be accurately diagnosed using EPSPS gene copy number.

Correction: Commercial Crop Yields Reveal Strengths and Weaknesses for Organic Agriculture in the United States.

[This corrects the article DOI: 10.1371/journal.pone.0161673.].

Commercial Crop Yields Reveal Strengths and Weaknesses for Organic Agriculture in the United States.

Land area devoted to organic agriculture has increased steadily over the last 20 years in the United States, and elsewhere around the world. A primary criticism of organic agriculture is lower yield compared to non-organic systems. Previous analyses documenting the yield deficiency in organic production have relied mostly on data generated under experimental conditions, but these studies do not necessarily reflect the full range of innovation or practical limitations that are part of commercial agriculture. The analysis we present here offers a new perspective, based on organic yield data collected from over 10,000 organic farmers representing nearly 800,000 hectares of organic farmland. We used publicly available data from the United States Department of Agriculture to estimate yield differences between organic and conventional production methods for the 2014 production year. Similar to previous work, organic crop yields in our analysis were lower than conventional crop yields for most crops. Averaged across all crops, organic yield averaged 67% of conventional yield [corrected]. However, several crops had no significant difference in yields between organic and conventional production, and organic yields surpassed conventional yields for some hay crops. The organic to conventional yield ratio varied widely among crops, and in some cases, among locations within a crop. For soybean (Glycine max) and potato (Solanum tuberosum), organic yield was more similar to conventional yield in states where conventional yield was greatest. The opposite trend was observed for barley (Hordeum vulgare), wheat (Triticum aestevum), and hay crops, however, suggesting the geographical yield potential has an inconsistent effect on the organic yield gap.

Efficacy and environmental fate of imazapyr from directed helicopter applications targeting Tamarix species infestations in Colorado.

BACKGROUND: Aerial imazapyr applications are the most common and cost-effective method for controlling invasive tamarisk, but few studies have investigated whether or how infestation and site characteristics influence control and non-target impacts. This study used vertical stands with filter papers, plus soil and tree canopy sampling, to investigate how tamarisk canopies affected retention of applied imazapyr, soil herbicide residues and tree mortality. RESULTS: Tamarisk canopies captured 71% of aerially applied imazapyr, resulting in significantly lower soil residues beneath the tree canopy. Although initial imazapyr soil residue levels outside the tree canopy were 4 times greater than those inside, soil degradation occurred 2.4 times faster outside the tamarisk canopy and resulted in lower herbicide residues. Tamarisk mortality within 3 years was 70%, but variability in control appeared to be affected by non-linear stand boundaries and tall site obstructions. These same factors also increased variability in the actual quantity of herbicide applied, exacerbating collateral impacts on desirable understory species. CONCLUSION: While aerial imazapyr applications are highly effective in controlling tamarisk, our study provides evidence for the importance of evaluating overall site suitability for this management strategy so the probability of unintended ecological effects can be minimized.

Quantitative Evaluation of the Environmental Impact Quotient (EIQ) for Comparing Herbicides.

Various indicators of pesticide environmental risk have been proposed, and one of the most widely known and used is the environmental impact quotient (EIQ). The EIQ has been criticized by others in the past, but it continues to be used regularly in the weed science literature. The EIQ is typically considered an improvement over simply comparing the amount of herbicides applied by weight. Herbicides are treated differently compared to other pesticide groups when calculating the EIQ, and therefore, it is important to understand how different risk factors affect the EIQ for herbicides. The purpose of this work was to evaluate the suitability of the EIQ as an environmental indicator for herbicides. Simulation analysis was conducted to quantify relative sensitivity of the EIQ to changes in risk factors, and actual herbicide EIQ values were used to quantify the impact of herbicide application rate on the EIQ Field Use Rating. Herbicide use rate was highly correlated with the EIQ Field Use Rating (Spearman's rho >0.96, P-value <0.001) for two herbicide datasets. Two important risk factors for herbicides, leaching and surface runoff potential, are included in the EIQ calculation but explain less than 1% of total variation in the EIQ. Plant surface half-life was the risk factor with the greatest relative influence on herbicide EIQ, explaining 26 to 28% of the total variation in EIQ for actual and simulated EIQ values, respectively. For herbicides, the plant surface half-life risk factor is assigned values without any supporting quantitative data, and can result in EIQ estimates that are contrary to quantitative risk estimates for some herbicides. In its current form, the EIQ is a poor measure of herbicide environmental impact.

Interplanting annual ryegrass, wheat, oat, and corn to mitigate iron deficiency in dry beans.

This study evaluated whether grass intercropping can be used to alleviate Fe deficiency chlorosis in dry beans (Phaseolus vulgaris L.) grown in high pH, calcareous soils with low organic matter. Field studies were conducted at the University of Wyoming Sustainable Agriculture Research and Extension Center in 2009 and 2010. Black- and navy beans were grown alone or intercropped with annual ryegrass (Lolium multiflorum Lam.), oat (Avena sativa L.), corn (Zea mays L.), or spring wheat (Triticum aestivum L.) in a two-factor factorial strip-plot randomized complete block design. All four grass species increased chlorophyll intensity in dry beans. However, grass species did not increase iron (Fe) concentration in dry bean tissues suggesting inefficient utilization of Fe present in the dry bean tissues. In 2009, nitrate-nitrogen (NO3-N) and manganese (Mn) concentration in bean tissue were greater in bean monoculture than in grass intercropped beans. Bean monoculture also had greater soil NO3-N concentrations than grass intercropped treatments. In 2009, grass intercrops reduced dry bean yield >25% compared to bean monoculture. Annual ryegrass was the least competitive of the four annual grass species. This suggests that competition from grasses for nutrients, water, or light may have outweighed benefits accruing from grass intercropping. Additional studies are required to determine the appropriate grass and dry bean densities, as well as the optimum time of grass removal.

Potential beneficial uses of coalbed natural gas (CBNG) water.

The CBNG well water is typically managed by discharging into nearby disposal ponds. The CBNG well water could potentially be very useful in the water-limited regions (e.g., arid and semi-arid), but beneficial uses may be hindered by water quality problems. Objectives of this research were to: (1) examine trend analysis of nine years of CBNG well water at discharge (outfall) points and in corresponding disposal ponds, (2) evaluate geochemical processes, (3) identify potential water quality issues, and (4) find potential beneficial uses. The CBNG well water at discharge points and in corresponding disposal ponds was measured on-site for pH and electrical conductivity (EC). These water samples were also analyzed in the laboratory for calcium (Ca), sodium (Na), magnesium (Mg), potassium (K), iron (Fe), aluminum (Al), copper (Cu), arsenic (As), selenium (Se), cadmium (Cd), and barium (Ba). Total dissolved solids (TDS) were calculated from EC measurements. The sodium adsorption ratio (SAR) was calculated from Na, Ca, and Mg concentrations. Trend analyses of outfalls and disposal ponds were conducted separately so that the differences in trends could be compared. Trends in CBNG well water at discharge points are not always the same as trends in CBNG disposal ponds: environmental and geochemical processes play an important role in the water quality of these well waters. Overall trend analyses suggest that CBNG well water at discharge points in all basins of the Powder River Basin meets beneficial use criteria, except for SAR and to some extent EC, for aquatic life, livestock and wildlife watering, and irrigation. The CBNG well water in disposal ponds across all basins meets criteria for all beneficial uses except for As, pH, SAR, and to some extent EC for irrigation, aquatic life, and livestock and wildlife watering.

Influence of glyphosate on Rhizoctonia and Fusarium root rot in sugar beet.

This study tests the effect of glyphosate application on disease severity in glyphosate-resistant sugar beet, and examines whether the increase in disease is fungal or plant mediated. In greenhouse studies of glyphosate-resistant sugar beet, increased disease severity was observed following glyphosate application and inoculation with certain isolates of Rhizoctonia solani Kuhn and Fusarium oxysporum Schlecht. f. sp. betae Snyd. & Hans. Significant increases in disease severity were noted for R. solani AG-2-2 isolate R-9 and moderately virulent F. oxysporum isolate FOB13 on both cultivars tested, regardless of the duration between glyphosate application and pathogen challenge, but not with highly virulent F. oxysporum isolate F-19 or an isolate of R. solani AG-4. The increase in disease does not appear to be fungal mediated, since in vitro studies showed no positive impact of glyphosate on fungal growth or overwintering structure production or germination for either pathogen. Studies of glyphosate impact on sugar beet physiology showed that shikimic acid accumulation is tissue specific and the rate of accumulation is greatly reduced in resistant cultivars when compared with a susceptible cultivar. The results indicate that precautions need to be taken when certain soil-borne diseases are present if weed management for sugar beet is to include post-emergence glyphosate treatments.