Beth K. Gugino

Farmer-oriented assessment of soil quality using field, laboratory, and VNIR spectroscopy methods

Soil quality and health are terms describing similar concepts, but the latter appeals to farmers and crop consultants as part of a holistic approach to soil management. We regard soil health as the integration and optimization of the physical, biological and chemical aspects of soils for improved productivity in an economic and sustainable manner. This paper describes the process used for the selection of soil quality/health indicators that comprise the new Cornell Soil Health Test. Over 1,500 samples collected from controlled research experiments and commercial farms were initially analyzed for 39 potential soil quality indicators. Four physical and four biological indicators were selected based on sensitivity to management, relevance to functional soil processes, ease and cost of sampling, and cost of analysis. Seven chemical indicators were also selected as they are part of the standard soil nutrient test. Soil health test reports were developed to allow for an overall assessment, as well as the identification of specific soil constraints. The new soil health test is being offered on a for-fee basis starting in 2007. In addition, visible near infrared reflectance spectroscopy was evaluated as a possible tool for low-cost soil health assessment. From preliminary analyses, the methodology shows promise for some but not all of the soil quality indicators. In conclusion, an inexpensive soil health test was developed for integrative assessment of the physical, biological, and chemical aspects of soils, thereby facilitating better soil management.

The 2009 late blight pandemic in the eastern United States - causes and results

The tomato late blight pandemic of 2009 made late blight into a household term in much of the eastern United States. Many home gardeners and many organic producers lost most if not all of their tomato crop, and their experiences were reported in the mainstream press. Some CSAs (Community Supported Agriculture) could not provide tomatoes to their members. In response, many questions emerged: How did it happen? What was unusual about this event compared to previous late blight epidemics? What is the current situation in 2012 and what can be done? Its easiest to answer these questions, and to understand the recent epidemics of late blight, if one knows a bit of the history of the disease and the biology of the causal agent, Phytophthora infestans.

Use of an integrative soil health test for evaluation of soil management impacts.

Understanding the response of soil quality indicators to changes in management practices is essential for sustainable land management. Soil quality indicators were measured for 2 years under established experiments with varying management histories and durations at four locations in New York State. The Willsboro (clay loam) and Aurora (silt loam) experiments were established in 1992, comparing no-till (NT) to plow-till (PT) management under corn ( Zea mays L.)–soybean ( Glycine max L.) rotation. The Chazy (silt loam) trial was established in 1973 as a factorial experiment comparing NT versus PT and the crop harvesting method (corn silage versus corn grain). The Geneva (silt loam) experiment was established in 2003 with vegetable rotations with and without intervening soil building crops, each under three tillage methods (NT, PT and zone-till (ZT)) and three cover cropping systems (none, rye and vetch). Physical indicators measured were wet aggregate stability (WAS), available water capacity (AWC) and surface hardness (SH) and subsurface hardness (SSH). Soil biological indicators included organic matter (OM), active carbon (AC), potentially mineralizable nitrogen (PMN) and root disease potential (RDP). Chemical indicators included pH, P, K, Mg, Fe, Mn and Zn. Results from the Willsboro and Aurora sites showed significant tillage effects for several indicators including WAS, AWC, OM, AC, pH, P, K, Mg, Fe and Mn. Generally, the NT treatment had better indicator values than the PT treatments. At the Chazy site, WAS, AWC, OM, AC, pH, K and Mg showed significant differences for tillage and/or harvest method, also with NT showing better indicator values compared to PT and corn grain better than corn silage. Aggregate stability was on average 2.5 times higher in NT compared to PT treatments at Willsboro, Aurora and Chazy sites. OM was also 1.2, 1.1 and 1.5 times higher in NT compared to PT treatments at Willsboro, Aurora and Chazy sites, respectively. At the Geneva site WAS, SH, AC, PMN, pH, P, K and Zn showed significant tillage effects. The cover crop effect was only significant for SH and PMN measurements. Indicators that gave consistent performance across locations included WAS, OM and AC, while PMN and RDP were site and management dependent. The composite soil health index (CSHI) significantly differentiated between contrasting management practices. The CSHI for the Willsboro site was 71% for NT and 59% for PT, while at the Aurora site it was 61% for NT and 48% for PT after 15 years of tillage treatments.

Discriminatory simplex and multiplex PCR for four species of the genus Sclerotinia.

Sclerotinia sclerotiorum (Lib.) de Bary, S. minor Jagger, S. trifoliorum Eriks, and S. homoeocarpa F.T. Benn are the most relevant plant pathogenic species within the genus Sclerotinia because of their large range of economically important hosts, including tomato, peanut, alfalfa, and turfgrass, among others. Species identification based on morphological characteristics is challenging and time demanding, especially when one crop hosts multiple species. The objective of this study was to design specific primers compatible with multiplexing, for rapid, sensitive and accurate detection and discrimination among four Sclerotinia species. Specific primers were designed for the aspartyl protease gene of S. sclerotiorum, the calmodulin gene of S. trifoliorum, the elongation factor-1 alpha gene of S. homoeocarpa, and the laccase 2 gene of S. minor. The specificity and sensitivity of each primer set was tested individually and in multiplex against isolates of each species and validated using genomic DNA from infected plants. Each primer set consistently amplified DNA of its target gene only. DNA fragments of different sizes were amplified: a 264 bp PCR product for S. minor, a 218 bp product for S. homoeocarpa, a 171 bp product for S. sclerotiorum, and a 97 bp product for S. trifoliorum. These primer sets can be used individually or in multiplex for identification of Sclerotinia spp. in pure culture or from infected plants. The multiplex assay had a lower sensitivity limit than the simplex assays (0.0001 pg/μL DNA of each species). The multiplex assay developed is an accurate and rapid tool to differentiate between the most relevant plant pathogenic Sclerotinia species in a single PCR reaction.

Highly diverse endophytic and soil Fusarium oxysporum populations associated with field-grown tomato plants

ABSTRACT The diversity and genetic differentiation of populations of Fusarium oxysporum associated with tomato fields, both endophytes obtained from tomato plants and isolates obtained from soil surrounding the sampled plants, were investigated. A total of 609 isolates of F. oxysporum were obtained, 295 isolates from a total of 32 asymptomatic tomato plants in two fields and 314 isolates from eight soil cores sampled from the area surrounding the plants. Included in this total were 112 isolates from the stems of all 32 plants, a niche that has not been previously included in F. oxysporum population genetics studies. Isolates were characterized using the DNA sequence of the translation elongation factor 1α gene. A diverse population of 26 sequence types was found, although two sequence types represented nearly two-thirds of the isolates studied. The sequence types were placed in different phylogenetic clades within F. oxysporum, and endophytic isolates were not monophyletic. Multiple sequence types were found in all plants, with an average of 4.2 per plant. The population compositions differed between the two fields but not between soil samples within each field. A certain degree of differentiation was observed between populations associated with different tomato cultivars, suggesting that the host genotype may affect the composition of plant-associated F. oxysporum populations. No clear patterns of genetic differentiation were observed between endophyte populations and soil populations, suggesting a lack of specialization of endophytic isolates.

An ephemeral sexual population of Phytophthora infestans in the Northeastern United States and Canada.

Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013, 20 rare and diverse genotypes of P. infestans were detected in a region that centered around central New York State. The ratio of A1 to A2 mating types among these genotypes was close to the 50∶50 ratio expected for sexual recombination. These genotypes were diverse at the glucose-6-phosphate isomerase locus, differed in their microsatellite profiles, showed different banding patterns in a restriction fragment length polymorphism assay using a moderately repetitive and highly polymorphic probe (RG57), were polymorphic for four different nuclear genes and differed in their sensitivity to the systemic fungicide mefenoxam. The null hypothesis of linkage equilibrium was not rejected, which suggests the population could be sexual. These new genotypes were monomorphic in their mitochondrial haplotype that was the same as US-22. Through parentage exclusion testing using microsatellite data and sequences of four nuclear genes, recent dominant lineages US-8, US-11, US-23, and US-24 were excluded as possible parents for these genotypes. Further analyses indicated that US-22 could not be eliminated as a possible parent for 14 of the 20 genotypes. We conclude that US-22 could be a parent of some, but not all, of the new genotypes found in 2010 and 2011. There were at least two other parents for this population and the genotypic characteristics of the other parents were identified.

Developing Standard Protocols for Soil Quality Monitoring and Assessment

Africa’s agricultural viability and food security depend heavily on its soil quality. However, while approaches to measuring air and water quality are widely established, standardized, publicly-available soil quality assessment protocols are largely non-existent. This chapter describes the process we have used in selecting and developing a set of inexpensive, agronomically meaningful, low-infrastructure-requiring indicators of soil quality (SQ), which make up the Cornell Soil Health Test (CSHT). In 2006, the CSHT was made available to the public in New York State (NYS), United States, similar to the widely available soil nutrient tests. Case studies show the CSHT’s success at measuring constraints in agronomically essential soil processes and differences between management practices in NYS. It thus helps farmers to specifically target management practices to alleviate quantified constraints. Such indicators have the potential to be developed into standardized soil quality tests for use by African agricultural non-governmental and government organizations and larger commercial farmers to better understand agricultural problems related to soil constraints and to develop management solutions. Low cost and infrastructure requirements make these tests excellent tools for numerous low-budget extension and NGO-based experiments established in collaboration with local small farmers, as well as to quantify the status and trends of soil degradation at regional and national scales.

Sensitivity and efficacy of boscalid, fluazinam, and thiophanate-methyl for white mold control in snap bean in New York

White mold (Sclerotinia sclerotiorum) of leguminous crops in New York is generally managed with preventive applications of fungicides. However, no research has been conducted during the last decade to assess the sensitivity of the S. sclerotiorum population to fungicides or compare their performance under field conditions. The sensitivity of S. sclerotiorum to boscalid, fluazinam, and thiophanate-methyl was assessed in 151 isolates from 15 fields across New York using an agar dilution method with discriminatory concentrations. In addition, the effective concentration at which mycelial growth is reduced by 50% (EC50) was estimated for one representative isolate from each field. The efficacy of commercial formulations of each fungicide on white mold incidence in plants and pods was also tested in two field trials (2015 and 2016). The EC50 values ranged from 0.068 to 0.219, 0.001 to 0.002, and 1.23 to 2.15 µg/ml for boscalid, fluazinam, and thiophanate-methyl, respectively. Evidence of resistance was not found using the discriminatory concentration tests. The mycelial growth inhibition relative to the control ranged from 56 to 83%, 66 to 84%, and 53 to 83% at discriminatory concentrations of boscalid (5 µg a.i./ml), fluazinam (0.05 µg a.i./ml), and thiophanate-methyl (5 µg a.i./ml), respectively. Fourteen isolates with mycelial growth inhibition lower than 60% at 5 µg/ml of thiophanate-methyl, did not exhibit point mutations within a partial sequence of the β-tubulin gene. In the field trials, fungicides effectively reduced white mold incidence on plants by 75% (2015) and 93% (2016) and on pods by 81% (2015) and 87% (2016), both relative to the nontreated plots. However, fungicide applications led to significant increases in pod yield, relative to the nontreated plots, only in 2015 when the incidence of white mold on plants and pods were higher (85 and 49.2%) than in 2016 (31.3 and 10.3%). Although fungicide resistance was not detected, and thus control failures reported by New York snap bean growers may be due to other factors, further monitoring of sensitivity within the S. sclerotiorum population is encouraged as well as the use of rational systems to base their judicious and economic use.

Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology

Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study were US-8 (n = 28), US-11 (n = 27), US-23 (n = 166), and US-24 (n = 36), with isolates originating from 23 of the United States and Ontario, Canada. The majority of isolates were collected between 2010 and 2014 (94%), with the remaining isolates collected from 1994 to 2009, and 2015. Between 3,774 and 5,070 single-nucleotide polymorphisms (SNPs) were identified within each lineage and were used to investigate relationships among individuals. K-means hierarchical clustering revealed three clusters within lineage US-23, with US-23 isolates clustering more by collection year than by geographic origin. K-means hierarchical clustering did not reveal significant clustering within the smaller US-8, US-11, and US-24 data sets. Neighbor-joining (NJ) trees were also constructed for each lineage. All four NJ trees revealed evidence for pathogen dispersal and overwintering within regions, as well as long-distance pathogen transport across regions. In the US-23 NJ tree, grouping by year was more prominent than grouping by region, which indicates the importance of long-distance pathogen transport as a source of initial late blight inoculum. Our results support previous studies that found significant genetic diversity within clonal lineages of P. infestans and show that GBS offers sufficiently high resolution to detect sub-structuring within clonal populations.

An IPM Program for Managing Fungal Leaf Blight Diseases of Carrot in New York

Fungal leaf blight diseases caused by Cercospora carotae and Alternaria dauci occur annually on processing carrot in New York, with growers applying up to eight fungicide sprays to manage these diseases. An integrated pest management (IPM) program involving the use of a 25% disease incidence threshold to prompt the first fungicide application and timing subsequent sprays by monitoring for increases in disease severity and weather forecasts in conjunction with a 10- to 14-day spray interval was evaluated in grower fields in 1997 and 1998. The IPM plots, compared with the grower plots, required two to six fewer fungicide applications but showed no yield reduction. From 1999 to 2004, the IPM program was validated and the effect of crop rotation and carrot cultivar susceptibility also were assessed. Carrot plants growing in fields with 2-year or longer crop rotation intervals reached the 25% disease incidence threshold later in the season and required fewer fungicide applications. The less-susceptible carrot cultivars also reached the 25% disease incidence threshold later, required fewer fungicide applications, and were less severely diseased than more susceptible cultivars. Validation of the IPM program in New York showed that both fungal leaf blights can be managed effectively using a 25% incidence threshold to prompt the first fungicide spray and making the subsequent fungicide applications based on increases in disease severity, weather forecasts, and a 10- to 14-day spray interval.