Brief Summary of Minutes of Annual Meeting

Multi-State Project Meeting S-1053

Minutes and notes from the Annual Meeting

December 4th, 2015

Time: 9 am- 4 pm CST

Location: Noble Research Center – Oklahoma State University, Stillwater, OK

Member attendees:

Fulya Baysal-Gurel                Tennessee State University

Carla Garzon                          Oklahoma State University

Franz Lichtner                       Colorado State University (representing Kirk Broders)

Craig Rothrock                      University of Arkansas

Luisa Santamaria                  Oregon State University

Harald Scherm,                      University of Georgia (Administrative Advisor)

Invited and student attendees:

George Abawi                                    Cornell University

Maria Soledad Benitez          USDA-ARS  Brookings, South Dakota

Nathan Walker                      Oklahoma State University

Stephen Marek                      Oklahoma State University

Fernanda Proaño-Cuenca    Oklahoma State University

Andres Espindola                  Oklahoma State University

Luisa Santamaria (Chair) provided a brief overview of her applied research projects on root rot diseases in ornamentals caused by Phytophthora plurivora and Pythium. Also presented her current extension and outreach programs in and effort to educate the workforce at the nursery industry in Oregon using technology and hybrid classes.

Harald Scherm, the Administrative Adviser for S-1053, reported on a few national issues of interest. He mentioned the chartering of the public-private Foundation for Food and Agriculture Research which emerged out of the 2014 Farm Bill. Once matching private funds are secured, the Foundation will have $200 million to invest in research in two priority areas, 1) More productive, sustainable agriculture, and 2) Better health through food. The former priority area may be of particular interest to the group since it includes a sub-theme titled "Transforming soil health."

Scherm also mentioned the discussions that are currently ongoing at the national level regarding USDA's new Open Access implementation plan, which will have important implications for making both publications and the digital data that led to the conclusions in these papers available in publicly accessible and curated data bases. The details of how, where, and in what format these data should be deposited, and who pays for long-term duration, is still being worked out at this time.

With regard to NIFA funding programs, Scherm reported that the Center of Excellence provision will be carried forward into the FY16 RFAs, although the language may change based on review panel feedback during the previous funding cycle. If multiple members of S-1053 participated in a grant proposal, it should be relatively straightforward to make the case for a Center of Excellence.

Carla Garzon and her students provided information regarding their current research on characterization and identification of Pythium and Globisporangium species present in ornamental greenhouses from Long Island, NY in 2014 and the draft genome of Sclerotinia minor.

Fulya Baysal-Gurel provided information regarding current research on soil- borne diseases of woody ornamentals in nursery production systems in Tennessee. 

Craig Rothrock provided information on Rhizoctonia and spatial soilborne disease pattern research in Arkansas.

Franz Lichtner on behalf of Kirk Broders provided an overview of work related to soil microbial community change over time and space relative to plant variety mixtures.

Further discussions:

Possibility of meeting at the 2016 APS Annual Meeting in Tampa, Florida as a group to enhance collaboration and interaction in the group. Harald Scherm, Carla Garzon and Fulya Baysal-Gurel will be sending out e-mail in March to determine the meeting details.

Possibility of pre-application for USDA-NIFA SCRI Research and Extension Planning Project in December 2016.  Fulya Baysal-Gurel will be sending out request to set up conference call in June 2016.

Business meeting:

Location for the next meeting was discussed and the meeting will be held in Tennessee (Nashville or McMinnville). The next chair (Craig Rothrock) and the new secretary (Fulya Baysal-Gurel) will be informing the group members regarding meeting date and location.

Fulya Baysal-Gurel was elected as the new secretary of the group for 2016.

1. Evaluate the population genetic diversity of soilborne pathogens and antagonistic microorganisms in different growing systems and regions using traditional and metagenomic approaches.

Members of this multistate research project continue to provide new insight into the genetic diversity of a number of oomycete pathogens in a range of production systems. Oomycetes including Pythium and Phytophthora continue to cause significant damage on economically important vegetable, fruit, ornamental, and row crops in North America and around the world. New genetic resources and many new molecular markers were developed for the soilborne vegetable pathogen Phytophthora capsici. These include genomic DNA re-sequencing data for 18 P. capsici isolates recovered from locations worldwide and RNA sequencing data for 35 isolates of P. capsici at two time-points in the infection process of tomato (24 and 72 h). These resources provided the raw material to identify widely distributed and conserved polymorphic single nucleotide polymorphism (SNP) positions in the genome and to develop genotyping assays to assess genetic diversity in populations worldwide. Ongoing analyses of oomycetes baited from Tennessee streams and rivers (predominantly Phytophthora and Pythium) have identified species known to be pathogens of economically important nursery and forest plants.

Population genetic analyses have been completed for P. capsici in central and northern Mexico, indicating the populations are likely sexual and survive fallow or non-host periods as sexual oospores in the soil. In addition, novel SNP markers have been developed for the spinach downy mildew pathogen Peronospora effusa and were recently applied to populations from spinach production areas in Yuma, AZ and the Salinas Valley in CA.

Further research on oomycete pathogens has focused on assessing the genetic diversity of Phytopthora infestans inoculum in Andean soils. This work was presented in two B.S. Biotechnology Engineering dissertations written by two undergraduate students from the Universidad de las Fuerzas Armadas ESPE, who graduated in Summer 2013 in collaboration with researchers at Oklahoma State University (OSU). In related work at OSU, the multi-locus phylogenetic analysis of the Pythium irregulare complex was conducted confirming the species status of P. cryptoirregulare and P. vipa. Additionally, characterization of Pythium isolates from ornamental greenhouses in Long Island, NY in 2012 and 2013 by molecular barcoding (ITS) was completed. Current research is focused on the temporal analysis of these isolates, to understand seasonal changes in Pythium populations in ornamental operations.

Also at OSU, primers for PCR amplification of SSR markers for Phymatotrichopsis omnivora (cotton root rot) were developed. The genetic diversity and phylogenetic status of Fusarium proliferatum isolates from diverse continents and hosts was evaluated and confirmed to be monophyletic. SSR markers for characterization of F. proliferatum were validated and reported. A study on the genetic diversity of F. proliferatum in onions in Ecuador is in progress. A bioinformatics tool for detection and discrimination among Pythium spp. strains from metagenomic data from infected plant samples was developed and validated. Primers for multiplex PCR detection and discrimination of Ophiosphaerella spp. were designed and validated. A draft genome of Sclerotinia minor was assembled and is currently being annotated. E-probes for detection of expressed genes during the S. minor infection were generated and are being validated.

In related work taking place at Oregon State University, a new project funded by the Floriculture and Nursery Research Initiative (FNRI) to be developed in a collaborative agreement with the USDA-ARS Horticultural Crops Research Laboratory – Corvallis, will identify and characterize the most prevalent soilborne plant pathogens, including Phytophthora, Pythium, and Verticillium affecting commercial nursery production systems; develop novel and rapid assays to detect the most prevalent soilborne pathogens; and characterization of the roles of soil fungal communities in nutrient cycling and soil health.

Work in Minnesota has also focused on understanding the diversity of Pythium species present in crop soils using two different methods for collection of isolates. The two methods differed considerably in their efficiency. In one survey, Pythium species were obtained by baiting soil samples collected from 32 locations in Minnesota where stand establishment had been a problem. Only five species were identified in this survey. Pythium irregulare, Pythium recalcitrans, and Pythium ultimum were the predominant species. A related survey for Pythium species was conducted by isolating from symptomatic plants collected in the field. In this survey 30 Pythium species were isolated. The most common species found were Pythium ultimum, Pythium heterothallicum, Pythium sylvaticum, and Pythium oopapillum.. In both surveys Pythium species were identified and identity confirmed using both morphological and molecular techniques. These isolates are being screened for pathogenicity on corn and soybean.

During 2014-2015 the Minnesota researchers sampled seedling and soil from 49 soybean production fields that yielded 30 Pythium species and four Phytopythium species. The species were identified using ITS and COX1 sequences. Pathogenicity was evaluated in an in-vitro assay at three temperatures. Seven of the 21 Pythium spp. were pathogenic on both soybean and corn, reducing root growth by 20% or more, while two Pythium and one Phytopythium spp. were pathogenic only on soybeans. This is the first report of P. recalcitrans as a pathogen of soybean and of Phytopythium spp. as a pathogen on either corn or soybean in Minnesota. P. ultimum and P. irregulare were the most pathogenic Pythium species on either soybeans or corn. P. conidiophorum, P. irregulare, P. intermedium, P. ultimum, and P. sylvaticum were pathogenic on soybean at the three temperatures. P. acrogynum, P. inflatum, P. sylvaticum, P. ultimum increased in pathogenicity with increasing temperature. On corn P.antheridium, P. conidiophorum, P. intermedium, P. irregulare, P. heterothallicum, P. minus, P. recalcitrans, P. sylvaticum, and P. ultimum were pathogenic at 15 and 20^oC. At 25^oC pathogenicity of P. heterothallicum, P. minus, P recalcitrans, P. schmitthenneri,P. torulosum increased further.

Research on sweetpotato tip/end rot is focused on defining and evaluating the pathogen(s) associated with this disease problem. In 2012 it was determined that reniform nematode, Rotylenchulus reniformis, levels were increasing in many fields from a general survey and was suspected that they might form a disease complex resulting in greater tip/end rot in Mississippi. Research was established in 2013 to evaluate those interactions with the most common pathogen isolated, Macrophomina phaseolina and reniform nematode using different populations in the field and in the greenhouse. In 2014 and 2015, field and greenhouse trials were established and new trials for 2015-2016 are currently ongoing to study M. phaseolina isolates separately from the nematodes and together. Data from 2014-2015 (year 1 of interaction study) have not been analyzed and will be discussed during the next annual report.

Also at Mississippi State University, research on soybean charcoal rot is ongoing with the specific objectives 1) Characterization of endophytic bacterial and fungal communities associated with the soybean-charcoal rot disease system using both culture-dependent and independent analyses; and 2) Investigation of the effects of inoculation of bacteria and/or fungi on disease development and soybean growth.

Four pairs of diseased and asymptomatic plants were collected from patches of plants affected by charcoal rot in a soybean field in Leflore County near Sidon, MS in 2013 and 2014 (completed really in 2015). Four additional asymptomatic plants (controls) were collected from areas of the same field both years where no symptoms of the disease were evident. Each plant was prepared for bacterial and fungal endophyte examination through a series of washing steps and longitudinal division of the plant. One half of the plant was processed for isolation of bacterial endophytes and the other half was used for isolation of fungal endophytes. Fungal endophytes were isolated from each plant part (root, stem, leaf) separately. Three sets of plates were prepared and incubated in the three different oxygen environments. Plates were incubated in the dark at 28^oC for 48 to 72 h, at which time emerged mycelium was subcultured onto sterile plates containing the appropriate medium and incubated in the same environment as the original isolation plate for 10 days. Plates were initially grouped by morphological similarities. Cultural identifications for the two years of isolations continued into 2015 to further distinguish the groupings prior to molecular determinations. The ITS region of grouped isolates were amplified using primers ITS1f and ITS4 and products sequenced. Approximately 70% of the isolate sequences had acceptable reads for NCBI Library Blast determinations thus far and the other 30% are currently being regrown and re-sequenced. Approximately 14 taxa were identified with the most common ones being Fusarium solani (complex) generally found on the healthy plants, two Alternaria species and Fusarium chlamydosporum common on diseased soybeans, whereas two species of Phoma  and two Trichoderma species had greatest frequencies on healthy plants.  Many of the other fungal species found are antagonistic or may be biological controls. Other species of Fusarium can vary in their ability to derive nutrition but, for example, Fusarium solani strains have been shown to be effective in biological control of root pathogens. Furthermore, Verticillium lecanii identified here can be antagonistic to insects and is being used commercially for their control, but the fungus has been reported to be a pathogen of other fungi. Cladosporium sphaerospermum present in plant tissues is known to produce compounds that increase plant growth. However, the fungus was found equally on diseased and healthy plants. Additionally, over 20 other fungi identified across tissue types were primarily considered plant pathogens. Among the most abundant fungus species identified using the NCBI database, six belonged to the Diaporthe spp. complex and five to Fusarium spp. with the most common taxon Fusarium solani.

In 2015, library preparations were conducted for Illumina MiSeq whole-community study. From all tissues evaluated using cultural isolates, a portion of the cultured pieces was saved at -80°C. Data analysis training was done in November and actual analysis using the Mothur program is currently ongoing. Since the same tissue pieces were used for culture study, an attempt will be made statistically to compare those data with whole-community results. These efforts will go into 2016 and will be reported during the annual reporting cycle of next year.

Research on Rhizoctonia spp. conducted in the southern U.S. has characterized the spatial distribution of Rhizoctonia spp. in fields undergoing rice and soybean rotation in Arkansas. Rhizoctonia aerial blight of soybean is a disease caused by Rhizoctonia solani AG1-IA. This pathogen also causes sheath blight of rice. Populations and disease assessments were characterized in producers’ fields on a spatial scale to represent the topography of the field intermittent of the rice levee positions. Directional distribution ellipses for distribution of R. solani AG1-IA using soil and plant samples indicated agreement with drainage. Across years, distribution of R. solani AG1-IA appears to be controlled by levee position. Where levees do not form logical areas of collection, the greatest concentration of inoculum appears to be in the lower elevations of the field. The spatial distribution of the early-season inoculum of R. solani AG1-IA reiterates the idea that inoculum in the form of sclerotia and hyphae associated with rice residue floating and collecting at lower points within the levees. Spatial assessments of incidence of aerial blight and the height up the soybean plant at GPS positions intermittent the levee system validated models, indicating the highest amount of disease was in the logical areas of collection (a combination of levee position and elevation). Because the disease occurred in a similar distribution as the inoculum, a predictive model using geographically weighted regression analysis is being constructed for fields with no prior disease assessment. In these fields, elevation data has been provided by USGS (LiDAR) and levee data provided by the grower. Using a quantitative determination of levee bends (m/m²), prediction based on random assignment of geospatially tagged points should allow for the use of handheld GPS devices to guide scouting to areas with the highest likelihood of inoculum collection and aerial blight development.

Spatial sampling of soybean plants further confirmed R. solani AG11 as the most populous Rhizoctonia spp. in fields undergoing rice and soybean rotations in northeast Arkansas, on 25 to 34% of soybean plants. However, a new site in southeast Arkansas found higher level of R. solani AG7 (12 to 16 % colonization of soybean) than AG11 (6 to 10%). AG1 was rarely or never recovered. Application of the fungicide azoxystrobin limited the increase in colonization of soybean plants by R. solani compared with points not sprayed at both sites. The research reinforces the idea that populations of R. solani in soil colonize crops within the field and are dominated by populations that are not considered pathogenic.

Because prior years’ work had determined that R. solani AG11 was associated with areas of greater plant stand, experiments are currently in progress to determine its role in the rice/ soybean system and the potential benefit colonization of soybean may provide. R. solani AG1-IA also was observed causing aerial blight of peanut in Arkansas. Currently, there is a renewed interest in peanut production in the state, and production practices include irrigation and various rotation schemes with soybean and less frequently rice. Thus, this may be an important disease of peanut in Arkansas.

In 2015, the Arkansas research group also evaluated other soilborne pathogens. Meloidogyne incognita and Rotylenchulus reniformis are economically important plant pathogenic nematode species in cotton production. Thielaviopsis basicola causes black root rot of cotton. For cool and wet soils, black root rot results in stunting and reduced vigor that can negatively impact yield. When either of these nematodes feed on cotton roots, black root rot can worsen. Evidence from 2001-2003, in a texturally diverse cotton field near Portland, AR, suggested that populations of M. incognita had the greatest effect on yield in soils with greater sand content. Additionally, exhaustive nematode assays indicated that R. reniformis was increasing in population and distribution in the field. Since that work, the field has continued to be planted in cotton until being planted in soybean in 2013. From the original 512 plots, nematode and T. basicola population densities were measured through 2013. Over the 10+ year period, the population and distribution of M. incognita decreased while that of R. reniformis increased. Thielaviopsis basicola populations and distributions were consistent. There was significantly aggregated distributions of all pathogens in all years except 2011, and trend surface models indicated Range values decreased for M. incognita but increased for R. reniformis prior to 2013. The analyses further indicated a significantly dispersed distribution and inverse relationship in 3 of 4 years and 2 of 4 years respectively confirming competition and displacement of M. incognita by R. reniformis. In all years, a significant negative correlation existed between T. basicola and percent sand fraction and a significant positive correlation between the fungus and percent silt and clay. Pathogen populations were not related to yield loss across soil textures. The greatest yield consequence occurred in the sandier areas of the field, indicating these three pathogens should be managed site-specifically by textural zone.

2. Examine the effect of traditional or newly developed management strategies (chemical, cultural, and biological), soil physicochemical properties, or introduced biological control agents on the microbial community and its ability to suppress soilborne pathogens.

In Iowa, work is being conducted on the importance of the soil microbial community in carbon cycling as plant residues are decomposed. The researchers studied the partitioning of carbon contained in corn residue during decomposition, affecting the sequestration of carbon in soil, into microbial biomass and carbon dioxide respiration. They found weak evidence that pH-stressed bacterial cells use more carbon for cell maintenance and produce less biomass in an incubation study.

Corn residue was collected from the field and characterized for carbon, nitrogen, and other elements. They isolated three bacilli (Bacillus pasteurii, B. circulans, and B. sphaericus). A Webster soil (Typic Endoaquolls) was sampled and analyzed for nutrients and moisture tension. The pH of the soil was adjusted from 6.5 to 7.5 and 5.5 to test the hypothesis that stressed cells (in this case pH-stressed) would use more carbon during residue decomposition for cell maintenance and less for new cell production. Corn residue was added and mixed into the test soil in Mason jar mesocosms and autoclaved. A known quantity of each Bacillus sp. was individually added and incubated at room temperature (20-25°C). B. pasteurii degraded the corn residue most rapidly, with the rate of decomposition being greater at pH 7.5 than 6.5 and 5.5. All other treatments followed a similar pattern having greater rates of decomposition at pH 7.5. Microbial biomass C for all treatments also followed a similar pattern and increased to a peak on day 21, where microbial biomass carbon (MBC -- the amount of the carbon in the residue that ends up in the living tissue of the soil) was significantly different. The lowest MBC values were observed at pH 5.5 with B. circulans, followed by B. sphaericus, and then B. pasteurii. The least amount of MBC was observed when the rate of CO₂ evolution was at its greatest. Our data provided weak evidence that stressed cells required more metabolized C for cell maintenance, but differences existed among the three isolates and an overall generalization could not be made.

The project has provided for the training of an M.S. student in soil microbiology and biochemistry. Furthermore, students in an undergraduate/graduate dual-listed course (Agron 485/585) helped evaluate the technique used to measure carbon dioxide evolutions. Additionally, one undergraduate student gained laboratory experiences during the summer of 2015.

Multiple members of the multistate research project continue to investigate better management strategies for the control of Pythium and the effect different chemical, biological and cultural management strategies have on Pythium community dynamics. In Oregon, an in vitro sensitivity test to determine fungicide resistance of three species of Pythium (P. irregulare, P. sylvaticum, and P. ultimum) was completed. A total of 119 Pythium isolates from forest nurseries in Oregon were tested for resistance to mefenoxam. Six different concentrations of the fungicide were evaluated. A paper with this data and additional results from evaluations with other fungicides was submitted for review in Plant Disease.

During 2015, at Oregon State University – NWREC, efforts to establish guidelines for developing and implementing disease control strategies in managing Phytophthora root rot continues. We have an ongoing trial to determine effectiveness of varying concentrations of calcium amendments, in the form of gypsum, against inoculum of two soilborne pathogens, Phytophthora cinnamomi and P. plurivora. These two species are of most concern in terms of crop loss at nurseries (Parke et al., 2014). Evidence suggests that calcium amendments in plant growth substrates can be effective in controlling P. cinnamomi root rot of avocado (Messenger, et al. 2000). P. plurivora is a recently discovered species causing severe root rot on many plant hosts in European nurseries. Both pathogens have wide host ranges. However, growers do not know the economic risk associated with these pathogens in their nurseries, and there is little information about disease control treatments that are effective for managing these pathogens.

Pythium is an ecologically diverse group of microorganisms found in virtually all soils, but little is known about the effect of crop rotation on Pythium communities. To understand the effect of crop rotation on species diversity, researcher in Arkansas collected soil from plots following a long-term rotation study including rice, corn, soybean and wheat. Soil from each plot was placed in cups, wetted to saturation, planted with the soybean cultivar Hutcheson, and incubated at 25°C. After 3 days, seeds were collected and washed in running water and placed on 2% water agar to bait Pythium from soils. Molecular identification was performed by sequencing the ITS region and conducting a Blast analysis to a curated reference database. A total of 320 isolates were identified representing 12 species. Overall, the most frequently recovered species were P. spinosum, P. irregulare, P. pereocandrum and P. sylvaticum. In continuous rice production, P. spinosum was the most prevalent species isolated. In the soybean-wheat-rice and rice-wheat-soybean-wheat rotations, P. spinosum and P. irregulare were the most frequently recovered, while P. irregulare and P. sylvaticum were the most frequently recovered species in the soybean-rice and rice–soybean rotations. Pythium species composition reflected the frequency at which a susceptible host was planted in the rotation.

Sudden death syndrome of soybean (SDS) is caused by the fungus Fusarium virguliforme. The fungus infects and initially causes deterioration of the crown and upper taproot. As the plants enter the reproductive stages of development, foliar symptoms are often observed where reddish brown lesions form on the leaves and defoliation occurs after significant leaf damage. In 2014, a field near Dumas, AR and a field near Yancopin, AR were confirmed to have SDS. At R5, aerial imagery was obtained by flying a Cessna 172 with a Geovantage Geoscanner sensor package having a 4-band multispectral unit utilizing blue, green and red light wavelengths in the visible part of the spectrum and near-infrared (NIR) beyond the red visible light bands. The near infrared imagery was georeferenced and added as a layer in ArcGIS 10.2. Yield data was collected on a John Deere 9870 combine with a factory installed yield monitor and stored as a georeferenced file for the field near Yancopin. Soil EC was collected for both fields with a Veris 3150 soil EC mapping system on 12-ft centers and stored as a georeferenced file. The yield and soil EC data were added to the same .mxd as the NIR aerial imagery. A field boundary was digitized in ARCMap and 5000 random points assigned within the boundary using the random points tool in ArcToolbox. The NIR, yield, and soil EC were sampled at each random point using the spatial join tool in ArcToolbox. Data were then analyzed using Moran’s I to determine spatial autocorrelation and distribution and spatial regression to determine spatial dependence and relationships in GeoDa 1.6.6. In both fields, NIR revealed severe localized defoliation. Spatial regression analysis indicated a significant (P=0.05) relationship between soil texture and defoliation where the majority of the disease was correlated with soil EC readings in the 20-35 ds/m range. Yield data was only obtained and analyzed for one field, with yield correlating negatively to both soil texture and defoliation. The evidence suggests that SDS could be managed site-specifically. This method could be applied to determine the distributions of other soilborne diseases or potential interactions with SDS.

Brassica green manure soil amendments were investigated as a possible alternative to chemical management of soilborne diseases in ornamental landscape and bedding plants. The objective was to determine the importance of crop selection and application rate of brassica green manures for disease caused by Rhizoctonia solani on impatiens and petunia. Microplot experiments were conducted over 2 years using brassica green manure from Brassica juncea 'Fumus' and 'Bionute', and Brassica napus 'Jetton', at the application rates of 700, 1400, and 4200 g/m² fresh weight aboveground biomass. Microplots were artificially infested to evaluate disease on these ornamentals, with a second set of experiments using noninfested plots to examine effects of the green manure alone on plant growth. All brassica green manure crops reduced disease symptoms in both impatiens and petunias. Rate of brassica application was more important than brassica crop variety for use as a green manure. The highest rate of the brassica green manure decreased crown lesions by 21 and 24%, root discoloration by 9 and 7%, and R. solani isolation by 15 and 8% for impatiens and petunias, respectively, for 4200 g/m² compared with 700 g/m² rates of application. No phytotoxic effects were observed from the brassica green manures following a waiting period of 4 weeks between amending the soil and planting the ornamental crops.

At OSU in 2015, Fungicide hormesis was examined on Fusarium proliferatum using multiple modes of action. F. proliferatum radial growth in vitro was significantly and consistently stimulated by one contact fungicide. The effect of hormesis on fumonisin production was assessed and statistical analysis of the data is in progress.

Research at Mississippi State University has focused on understanding the genetics and biochemistry of soilborne and endophytic bacteria against plants pathogens. More than 800 bacterial isolates were obtained from soil and plant samples, and tested for antimicrobial activities using standard bioassay procedures. Approximately 80 isolates showed significant antifungal activities against Geotrichum candidum and more than 40 isolates exhibited significant antibiotic activities against Erwinia amylovora. These isolates were further purified and preserved at -80^oC. The isolates have been identified to be Bacillus spp., Pseudomonas spp., Burkholderia spp. and Streptomyces spp. using 16S rDNA sequence analysis. In a separate study, we investigated the genes associated with production of the antifungal compound occidiofungin produced by the soilborne bacterium Burkholderia contaminans strain M14. In collaboration with Dr. Jim Smith, we have characterized the functions of the ocfC and ocfN genes in antimicrobial activities.

The etiology of root rot caused by Fusarium solani is being investigated in Minnesota. The effects of F. solani on soybean plant germination and growth is influenced by fungal isolate, soybean cultivar, stage of plant development, soil temperature, and soil moisture. In general, soil inoculation with F. solani caused poor germination and reduced plant populations. However, plants that did germinate and flowered appeared to benefit from infection with greater root and aboveground growth and greater seed yield. Research was conducted into the effects of inoculation methods and inoculum substrates infested with F. solani or F. virguliforme on disease symptom expression and plant growth. Management of this root rot fungus should emphasize control of its harmful effects on plant populations during seed germination. When investigating the etiology of F. solani, spurious symptoms, particularly lesion-like root discoloration and poor root development, were observed when many infested inoculum substrates such as seed of sorghum, rye, barley, or oats are used to inoculate soil during screening experiments. Inoculation with uninfested seed resulted in poor root development and decreased plant growth when compared with either plants root-inoculated with infested substrates or with an uninoculated control. The effect is dependent on species of plant seed used (most severe effects were seen with red sorghum as a substrate) but is also determined by the soybean cultivar planted. These effects are particularly relevant for evaluation of soybean cultivars and evaluation of pathogenicity of fungal isolates and can cause misleading symptoms unrelated to the effect of the pathogen.

Sensitivity to azoxystrobin, ethaboxam, mefenoxam, pyraclostrobin, and trifloxystrobin of isolates of ten pathogenic Pythium species was tested in an in-vitro assay. Isolates of Pythium and Phytopythium species varied in sensitivity to the fungicides, but most were highly sensitive to mefenoxam and ethaboxam, with EC50 values <10^-2 of that observed for the strobilurin fungicides. Only P. acrogynum did not display any sensitivity to ethaboxam at rates of 0.0, 0.5 or 5 µg/ml. Treatment with 100 µg/ml decreased growth by only 24%. However, only one isolate of P. acrogynum was available for testing and it is unknown if these results are representative of the species. The results indicate that Pythium spp. in Minnesota soybean fields are diverse, vary in sensitivity to fungicides, and may be significant causes of seedling disease on soybean and corn.

Castro-Rocha, A., Shrestha, S., Lyon, B., Grimaldo-Pantoja, G., Juan Pedro Flores-Marges, José Valero-Galván, Marisela Aguirre-Ramírez, Pedro Osuna-Ávila, Nuria Gómez-Dorantes, Graciela Ávila-Quezada, José de Jesús Luna-Ruíz, Gerardo Rodríguez-Alvarado, Sylvia Patricia Fernández-Pavía and Kurt Lamour. 2016. An initial assessment of genetic diversity for Phytophthora capsici in northern and central Mexico. Mycological Progress 15:1-12.

Abd-Elmagid, A., Hunger, R., Garzon, C.D., Jub H, Payton M, and Melouk H. 2015. Effect of osmotic and matric potentials on Sclerotinia minor and Sclerotinia sclerotiorum virulence on peanut. Int. J. Phytopathol. 4:147-158.

Cochran, K. A., and Rothrock, C. S. 2015. Brassica green manure amendments for management of Rhizoctonia solani in two annual ornamental crops in the field. Hortscience 50:555–558.

Espíndola AS, Schneider W, Hoyt P, Marek SM, Garzon CD. 2015. A new approach for detecting fungal and oomycete plant pathogens in next generation sequencing metagenome data utilizing electronic probes. International Journal of Data Mining and Bioinformatics 12(2):115-128.

Greer, A. M., Spurlock, T. N., Coker, C. M. 2015. First report of Neocosmospora stem rot of soybean caused by Neocosmospora vasinfecta in Arkansas. Plant Dis. 99:554.

Liu, Y., Baird, S.M., Qiao, J., Du, Y., and Lu, S.E. 2015. SecG is required for antibiotic activities of Pseudomonas sp. YL23 against Erwinia amylovora and Dickeya chrysanthemi. Journal of Basic Microbiology 55(5):617-624.

Parke, J.L., Knaus, B.J., Fieland, V.J., Lewis, C., and N.J. Grunwald. 2014. Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management. Phytopathology 104(10):1052-1062.

Rothrock, C. S., Avanzato, M. V., and Rupe, J. C. 2015. Pythium seed rot, damping-off and root rot. Pages 76-79 in: Compendium of Soybean Diseases, 5th ed. G. L. Hartman, J. C. Rupe, E. J. Sikora, L.L. Domier, J. A. Davis, and K. L. Steffey, eds. APS Press, St. Paul.

Spurlock, T. N., Rothrock, C. S., Monfort, W. S. 2015. Evaluation of methods to quantify populations of Rhizoctonia in soil. Plant Dis. 99:836-841.

Spurlock, T. N., Kirkpatrick, T. L., Rothrock, C. S., Monfort, W. S. 2015. Displacement of Meloidogyne incognita by Rotylenchulus reniformis during a 10 year cotton monoculture   and implications for site-specific management. (Abstr.) Phytopathology 105:S2.10.

Wang, X.Q., Bi, T., Li, X., Zhang, L., and Lu, S.E. 2015. First report of corn whorl rot caused by Serratia marcescens in China. Journal of Phytopathology 163(11-12):1059-1063.

Wang, X.Q., Showmaker, K.C., Yu, X.Q., Bi, T., Hsu, C.Y., Baird, S.M., Peterson, D.G., Li, X.D., and Lu, S.E.. 2014. Draft genome sequence of Burkholderia pyrrocinia Lyc2, a biological control strain that can suppress multiple plant microbial pathogens. Genome Announcements 2(5):e00991-14. doi:10.1128/genomeA.00991-14.

Wilson, K. D., Rothrock, C. S., Spurlock, T. N. 2015. Spatial examination of soil factors on cotton seedling disease pressure. ACPA Research Conference 2015, Fayetteville, AR.

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