Search

Charcoal rot, caused by the soilborne fungus Macrophomina phaseolina (Mp) poses a serious threat to soybean health and harvests at a global scale. Mp exhibits varying distribution patterns across fields, which complicates our ability to predict disease occurrences and outbreaks. Therefore, determining the spatial distribution of Mp abundance and its relation with soil physicochemical properties would help to inform precision management decisions for mitigating charcoal rot. To achieve this, Mp colony forming units (CFU) and edaphic properties were evaluated in 297 soybean fields located in the main soybean growing regions across 7 Departments of Paraguay. A pattern of decreasing CFU density was observed from the south-eastern to the western part of the country. While several edaphic factors are positively correlated with Mp CFU, pH showed a significant negative correlation with CFU. Both spatial and non-spatial model suggest that cation exchange capacity, percentage of clay, and pH could be potential predictors of Mp CFU abundance. Including spatial dependence of edaphic factors improved the prediction of Mp CFU more effectively than classical statistical models. We demonstrated that the occurrence of Mp shows a significant spatial clustering pattern as indicated by Moran's I. Our findings will help growers and policy-makers make informed decisions for managing Mp by improving our ability to predict which agricultural fields and soils are at greatest risk for charcoal rot.

Heterodera glycines , the soybean cyst nematode (SCN), and fungal pathogen Macrophomina phaseolina are economically important soybean pathogens that may coinfest fields. Resistance remains the most effective management tactic for SCN, and the rhg1-b resistance allele derived from plant introduction 88788 is most commonly deployed in the northern United States. The concomitant effects of SCN and M. phaseolina on soybean performance, as well as the effect of the rhg1-b allele in two different genetic backgrounds, were evaluated in three environments (during 2013 to 2015) and a greenhouse bioassay. Within two soybean populations, half of the lines had the rhg1-b allele, and the other half had the susceptible allele in the backgrounds of the cultivars IA3023 and LD00-3309. Significant interactions between soybean rhg1-b allele and M. phaseolina -infested plots were observed in 2014. In all experiments, initial SCN populations (Pi) and M. phaseolina in roots were associated with reduced soybean yield. SCN reproduction factor (RF = final population/Pi) was affected by SCN Pi, rhg1-b , and genetic background. A background-by-genotype interaction on yield was observed only in 2015, with a stronger rhg1-b effect in the LD00-3309 background, which suggested that the susceptible parent 'IA3023' is tolerant to SCN. SCN female index from greenhouse experiments was compared with field RF, and Lin's concordance and Pearson's correlation coefficients decreased with increasing field SCN Pi in soil. In this study, both SCN and M. phaseolina reduced soybean yield asymptomatically, and the impact of SCN rhg1-b resistance was dependent on SCN virulence but also population density.

The effects of sampling depth and crop growth stage on the population density of lesion nematodes were investigated in three commercial fields in Wayne and Fulton Counties, Ohio, during the 2016 and 2017 growing seasons. Soil samples were collected at five growth stages by removing 15 soil cores to a depth of 70 cm from each of 25 plots per field-year. Cores were divided into seven 10-cm sections, and nematodes were extracted from the soil and root fractions of each of them. Pratylenchus crenatus and P. thornei were detected in approximately 84 and 78% of the samples collected in Wayne and Fulton Counties, respectively. Depth significantly affected total population density of both species as well as densities in the soil and root factions in all field-years, but the effects of growth stage and its interaction with depth varied with field-year. In most cases, mean population densities were higher from 10 to 40 cm soil depth than at the reference 40 to 50 cm depth and lower from 50 to 70 cm. There were quadratic relationships between population density (on the log link scale) and depth, with the highest peaks in estimated predicted densities generally occurring between 20 and 40 cm, depending on crop growth stage and growing conditions. These findings suggest that the standard practice of sampling between growth stages V3 and V6 to a depth of 45 to 50 cm and using the entire core for extraction and enumeration could lead to underestimation of population densities of P. crenatus and P. thornei .

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager's activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Heterodera glycines , the soybean cyst nematode, and Macrophomina phaseolina , causal agent of charcoal rot, are economically important soybean pathogens. The impact and effect of these pathogens on soybean yield in coinfested fields in the Midwest production region is not known. Both pathogens are soilborne, with spatially aggregated distribution and effects. Spatial regression analysis, therefore, is an appropriate method to account for the spatial dependency in either the dependent variable or regression error term from data produced in fields naturally infested with H. glycines and M. phaseolina . The objectives of this study were twofold: to evaluate the combined effect of H. glycines and M. phaseolina on soybean yield in naturally infested commercial fields with ordinary least squares and spatial regression models; and to evaluate, under environmentally controlled conditions, the combined effect of H. glycines and M. phaseolina through nematode reproduction and plant tissue fungal colonization. Six trials were conducted in fields naturally infested with H. glycines and M. phaseolina in Ohio. Systematic-grid sampling was used to determine the population densities of H. glycines and M. phaseolina , and soybean yield estimates. Though not used in any statistical analysis, M. phaseolina colony forming units from plant tissue, charcoal rot severity, and H. glycines type were also recorded and summarized. In two greenhouse experiments, treatments consisted of H. glycines alone, M. phaseolina alone, and coinfestation of soybean with both pathogens. Moran's I test indicated that the yield from five fields was spatially correlated ( P < 0.05) and aggregated. In these fields, to account for spatial dependence, spatial regression models were fitted to the data. Spatial regression analyses revealed a significant interaction effect between H. glycines and M. phaseolina on soybean yield for fields with high initial population densities of both pathogens. In the greenhouse experiments, H. glycines reproduction was significantly ( P < 0.05) reduced in the presence of M. phaseolina ; however, soybean tissue fungal colonization was not affected by the presence of H. glycines . The direct mechanisms by which H. glycines and M. phaseolina interact were not demonstrated in this study. Future studies must be conducted in the field and greenhouse to better understand this interaction effect.

Soil samples were collected from 425 corn fields in 28 Ohio counties between growth stages V3 and V6 during the 2013 and 2014 growing seasons. Ten morphological groups of plant-parasitic nematodes, namely spiral, lesion, lance, dagger, stunt, pin, ring, stubby-root, cyst, and "tylenchids" (several genera morphologically similar to members of the subfamily Tylenchinae [NCBI Taxonomy] including Cephelenchus, Filenchus, Malenchus, and Tylenchus) were identified. Eight species belonging to six of these groups were characterized. Spiral, tylenchids, lesion, pin, lance, stunt, and dagger nematodes were detected in 94, 96, 80, 57, 48, 48, and 37% of the fields, respectively, whereas the stubby-root, cyst, and ring nematodes were present in fewer than 14% of the samples. Averaged across fields, the spiral, tylenchids, and pin nematodes had the highest mean population densities. For all groups, incidence and population density varied among counties, and in some cases, among soil regions and cropping practices. Both population parameters were heterogeneous at multiple spatial scales, with the lowest heterogeneity among soil regions and the highest among fields within county and soil region. Estimated variances at the soil region level were not significantly different from zero for most of the nematodes evaluated. Stunt and lance were two of the most variable groups at all tested spatial scales. In general, the population densities were significantly more heterogeneous at the field level than at the county level. Findings from this study will be useful for developing sampling protocols and establishing on-farm trials to estimate losses and evaluate nematode management strategies.

Ten morphological groups of plant-parasitic nematodes (spiral, lesion, lance, dagger, stunt, pin, ring, stubby-root, cyst, and miscellaneous tylenchids) were detected in corn fields in Ohio, but the presence and population density of these groups varied among fields. Binary and ordinal logistic regression models were fitted to the data to estimate the odds of each group being present, and the lesion, lance, spiral, and pin nematode population densities being at moderate-high risk levels based on soil region, cropping sequence, tillage, and soil pH, silt content, and electrical conductivity. All covariates were associated with at least one nematode group, but soil region had the greatest and most consistent effect. Dagger and ring nematodes were more likely to be present in region 6 than in any of the other regions, whereas lance, stunt, pin, stubby-root, and spiral nematodes were more likely to be present in regions 1 to 5 than 6. Spiral, lance, and pin nematode population densities were more likely to be at moderate-high risk levels in regions 3 and 4 than in region 6. Fields under conservation tillage were two times more likely to have moderate-high risk lance nematode population densities than fields under conventional tillage. Similarly, pin nematode population densities were two times more likely to be at moderate-high risk levels in fields under rotation than in continuous corn. For every unit increase in soil pH, the odds of the spiral nematode population density being at moderate-high risk levels increased by 43%, but the odds of the lesion and pin nematode population densities being at the same risk level decreased by 63 and 29%, respectively. The predicted probability of lesion and lance population densities being at moderate-high risk levels decreased as the silt content of the soil increased. These finding will be useful for developing future nematode sampling protocols and for assessing the risk associated with nematodes in corn fields in Ohio.