Publications by authors named "Timothy Paulitz"

48 Publications

Rhizosphere community selection reveals bacteria associated with reduced root disease.

Microbiome 2021 04 9;9(1):86. Epub 2021 Apr 9.

USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman, WA, 99164-6430, USA.

Background: Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities.

Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil.

Conclusions: Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity. Video Abstract.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40168-020-00997-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8035742PMC
April 2021

First Report of Crown Rot Caused by Fusarium redolens on Wheat in Kazakhstan.

Plant Dis 2021 Mar 29. Epub 2021 Mar 29.

CIMMYT Turkey, CIMMYT Uluslararası Buğday ve Mısır Geliştirme Merkezi, Şehit Cem Ersever Caddesi No : 9/11, Tarla Bitkileri Araştırma Enstitüsü Kampüsü içi, Ankara, Ankara, Turkey, 06170;

Fusarium crown rot, caused by several species within the genus, is a major constraint that results in significant losses in wheat production worldwide. In June 2019, diseased wheat plants with typical symptoms of crown rot, including discoloration on the first two or three internodes of the stem just above the soil line and stunted, dry rotted, and discolored roots were collected in several bread wheat fields during the maturity stage in Almaty, East Kazakhstan, and Karaganda Regions of Kazakhstan. For each field, approximately twenty tillers were randomly sampled. Symptomatic tissues were surface sterilized in 1% NaClO for 2 min, rinsed with sterile distilled water three times, air-dried in a laminar flow hood, and then transferred to Petri dishes containing one-fifth strength potato dextrose agar (PDA). After incubating in the dark at 23°C for 5 days, 79 single-spore isolates showing cultural and microscopic characteristics of Fusarium were obtained on PDA and Spezieller-Nährstoffarmer agar (SNA). Colonies were initially white but later produced a beige to pink diffusible pigment in PDA. Microconidia that formed on aerial monophialides were hyaline, 0 to 1 septum, oval- to kidney-shaped, and measured 4.3 to 10.3 × 1.9 to 3.4 µm (average 7.8 × 2.6 µm), whilst macroconidia were straight to slightly curved, 3 to 5 septate, and measured 18.7 to 38.8 × 2.9 to 6.6 µm (average 29.9 × 4.7 µm), with foot-shaped basal cells on SNA. Chlamydospores were present on PDA. Sequence analysis based on portions of translation elongation factor 1α (TEF1) and the nuclear ribosomal internal transcribed spacer region (ITS rDNA) loci with primers EF1/EF2 (O'Donnell et al. 1998) and ITS1/ITS4 (White et al. 1990) identified 29 of the 79 isolates as Fusarium redolens Wollenw. The sequences of the five representative isolates with 99.85% of similarity to those of F. redolens strains available in GenBank e.g., ITS (MT435063) and TEF1 (GU250584). The TEF1 (accession nos. MW403914-MW403918) and ITS rDNA (accession nos. MW397138-MW397142) sequences of the isolates were deposited in GenBank. The morphological features are consistent with the described features of F. redolens (Leslie and Summerell 2006). To confirm pathogenicity of the five isolates, five pre-germinated seeds of wheat cultivar Seri 82 were placed in a 9-cm-diameter pot filled with a sterile potting mix containing equal volumes of peat, vermiculite, and soil. An approximately 1-cm-diameter 7-day-old mycelial plug of each isolate was individually placed in contact with the seeds. Seeds were covered with the same potting mix, and then the pots were maintained for four weeks in a growth chamber at 23°C with a 12-h photoperiod. The experiment was conducted twice with three replicate 15-cm pots with 5 plants per pot. Controls were inoculated with sterile agar plugs using the same procedure. After four weeks, all the inoculated plants showed stunted growth with brown discoloration in most parts of the crown and roots, whereas no symptoms were observed in the control plants. The mean severity of the disease for each isolate was between 2.1 and 2.7 according to the scale of 1 to 5 described by Gebremariam et al. (2015). The pathogen was reisolated from crowns of diseased plants, but not from asymptomatic control tissues, and identified morphologically based on the methods described above, fulfilling Koch's postulates. Although several morphological features are shared by F. oxysporum and F. redolens, Baayen et al. (2001) showed that these species could be easily distinguished using molecular data. The pathogen was previously reported as F. redolens associated with crown rot of wheat in Turkey (Gebremariam et al. 2015) and Saskatchewan, Canada (Taheri et al. 2011). The presence of F. redolens causing crown rot is confirmed in the six wheat fields surveyed in Kazakhstan, for the first time. This pathogen may pose a risk for wheat production, and further studies needed to determine the impact on the crop in Kazakhstan.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-01-21-0015-PDNDOI Listing
March 2021

Plant-parasitic nematode associated with wheat in central, eastern, and south-eastern Kazakhstan.

Plant Dis 2021 Mar 23. Epub 2021 Mar 23.

CIMMYT Turkey, CIMMYT Uluslararası Buğday ve Mısır Geliştirme Merkezi, Şehit Cem Ersever Caddesi No : 9/11, Tarla Bitkileri Araştırma Enstitüsü Kampüsü içi, Ankara, Ankara, Turkey, 06170;

Kazakhstan is one of the biggest wheat producers, however, its wheat production is far below the average international wheat production standard due to biotic and abiotic stressors. Plant-parasitic nematodes are devastating for cereal production systems worldwide. A comprehensive survey was conducted in 2019 to identify plant-parasitic nematodes associated with wheat in different locations of central, eastern, and south-eastern Kazakhstan. The results revealed 33 root-lesion and 27 cyst nematode populations from the 77 localities sampled. These two genera occurred in separate or in mixed populations. The root-lesion populations were identified as Pratylenchus neglectus and P. thornei while all cyst nematodes were identified as Heterodera filipjevi. The identification of nematodes was firstly performed based on morphological and morphometric features and confirmed by BLAST and phylogenetic analyses based on the internal transcribed spacer and the D2-D3 expansion located in the 28S gene of ribosomal DNA for CCN and RLN populations, respectively. Pratylenchus neglectus and P. thornei populations from Kazakhstan showed a high similarity with the American, European, and Asian populations. Heterodera filipjevi populations formed a well-supported cluster with the corresponding populations from different countries and showed a slightly intraspecific polymorphism. Kazakhstan populations of H. filipjevi may have multiple introductions in Kazakhstan due to the divergence among them. The results of this study are of great importance for breeding programs and will enable awareness to extension advisors to develop measures to control these nematodes in cereal cropping areas in Kazakhstan.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-11-20-2424-SRDOI Listing
March 2021

Phytoparasitic nematodes of organic vegetables in the Argan Biosphere of Souss-Massa (Southern Morocco).

Environ Sci Pollut Res Int 2021 Feb 26. Epub 2021 Feb 26.

Laboratory of Biotechnology and Valorization of Natural Resources, Faculty of Sciences, Agadir, Ibn Zohr University, BP 8106, 80000, Agadir, Morocco.

Agroecological productivity of the Arganeraie Biosphere Reserve of Morocco is limited by the wide spread and dynamics of plant parasitic nematodes (PPN). Ecological studies of nematode communities are required to develop effective biological management of these bioagressors as conventional control methods of PPN are inadequate and have persistent harmful effects. Fifty-nine organic vegetable soils in Souss-Massa were nematologically sampled, and assessment of taxonomic proliferation was made in relation to host species, geographical origin, and climatic and microclimatic factors. Twenty-four nematode genera were identified as obligate and facultative plant feeders. Taxonomic diversity increased from Chtouka to Taroudant and Tiznit provinces. Soil texture, organic matter, pH, nitrogen, zinc, magnesium, copper, altitude, and humidity and temperature were seen to effect driving roles in the abundance, distribution, and community structures of nematodes. The most prevalent taxa posing a high risk to organic agriculture of Souss Massa were needle nematodes (Longidorus spp.) and root-knot nematodes (Meloidogyne spp.). Edaphic and climatic variables effected nematode populations greatly. A combination of biological treatments and appropriate agroecological practices restricting important economic PPN growth and enhancing soil quality are required to achieve sustainable management in the area.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11356-021-12986-8DOI Listing
February 2021

Decline in Soil Microbial Abundance When Camelina Introduced Into a Monoculture Wheat System.

Front Microbiol 2020 19;11:571178. Epub 2020 Nov 19.

Wheat Health, Genetics, and Quality Research, USDA-Agricultural Research Service, Washington State University, Pullman, WA, United States.

Camelina [ (L.) Crantz] of the Brassicaceae family is a potential alternative and oilseed biofuel crop for wheat ( L.)-based cropping systems of the Inland Pacific Northwest (PNW) of the United States. We investigated the effect of this relatively new rotational crop on soil microbial communities. An 8-year cropping systems experiment was initiated in 2007 at Lind, WA, to compare a 3-year rotation of winter wheat (WW)-camelina (C)-fallow (F) to the typical 2-year WW-F rotation. All phases of both rotations (total = 20 plots) were present every year to allow valid statistical analysis and data interpretations. Monoculture WW-F is the dominant system practiced by the vast majority of farmers on 1.56 million ha of cropland in the PNW drylands that receive <300 mm average annual precipitation. Microbial abundance and community composition were determined using phospholipid fatty acid analysis (PLFA) from soil samples collected during 3 consecutive years beginning in 2010. The abundance of fungi, mycorrhizae, Gram positive and negative bacteria, and total microbial abundance all declined over the 3-year period in the WW-C-F rotation compared to the WW-F rotation. All microbial lipid biomarkers were significantly less in fallow compared to WW of the WW-C-F rotation. The 2-year WW-F rotation demonstrated few differences in microbial lipid abundance and community structure between the rotation phases. Microbial abundance declined and community structure shifted in the 3-year WW-C-F rotation likely due to the combination of a crop followed by a 13-month-long fallow. The results of this study suggest that camelina in combination with a fallow period may disrupt microbial communities that have become stable under historical WW-F monocropping. Such disturbances have the potential to affect soil processes that have been provided by wheat-adapted microbial communities. However, the disruption appears to be short-lived with the microbial abundance of WW in the WW-C-F rotation, returning to similar levels observed in the WW-F rotation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.571178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710528PMC
November 2020

Potential of Moroccan entomopathogenic nematodes for the control of the Mediterranean fruit fly Ceratitis capitata Wiedemann (Diptera: Tephritidae).

Sci Rep 2020 11 5;10(1):19204. Epub 2020 Nov 5.

International Maize and Wheat Improvement Center (CIMMYT), P.K. 39, Emek, Ankara, 06511, Turkey.

The Mediterranean fruit fly, Ceratitis capitata Wiedemann, is a deleterious pest worldwide affecting fruit production. The entomopathogenic nematodes (EPNs) are a potential biocontrol agent that could be effectively used to control this Mediterranean fruit fly. In this study, five EPN strains reported from different fields in Morocco were evaluated for their efficacy against C. capitata. In laboratory assays, Steinernema feltiae-SF-MOR9, S. feltiae-SF-MOR10 and Heterorhabditis bacteriophora-HB-MOR7 strains showed significantly higher infectivity and penetration rates when compared to the other strains. S. feltiae-SF-MOR9 caused the highest larval mortality rate (80%) at 50 infective juveniles (IJs) cm. However, additional results showed that both S. feltiae strains were significantly effective in controlling C. capitata larvae in apricot (Prunus armeniaca) fruits on soil surface with high mortality rate at 50 and 100 IJs cm. Different soil textures and moisture levels resulted in a significant variation in EPN strain virulence against C. capitata. Sandy clay loam soil in combination with 50 IJs cm of S. feltiae (SF-MOR9 or SF-MOR10) caused a higher mortality rate of C. capitata larvae. Furthermore, applying these EPN strains at 50-100 IJs cm in combination with 10-15% moisture level showed optimal results against C. capitata larvae. Therefore, those two Moroccan EPN strains could be used as promising eco-friendly biological agents against C. capitata.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-76170-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645415PMC
November 2020

Chickpea Seed Rot and Damping-Off Caused by Metalaxyl-Resistant and Its Management with Ethaboxam.

Plant Dis 2021 Apr 29:PDIS08201659RE. Epub 2021 Apr 29.

Washington State University, Pullman, WA 99164.

Metalaxyl and its isomer mefenoxam have been the primary fungicides used as seed treatments in managing Pythium seed rot and damping-off of chickpea (). However, outbreaks of seed rot and damping-off of metalaxyl-treated chickpea seeds were found in the dryland agriculture regions of southeastern Washington and northern Idaho. spp. isolated from rotten seeds and associated soils showed high levels of resistance to metalaxyl. Large proportions (31 to 91%) of isolates resistant to metalaxyl were detected in areas where severe chickpea damping-off occurred and were observed in commercial chickpea fields over several years. All metalaxyl-resistant (MR) isolates were identified as var. . The metalaxyl resistance trait measured by EC values was stable over 10 generations in the absence of metalaxyl, and no observable fitness costs were associated with metalaxyl resistance. Under controlled conditions, metalaxyl treatments failed to protect chickpea seeds from seed rot and damping-off after inoculation with MR isolates. In culture, ethaboxam inhibited mycelial growth of both MR and metalaxyl-sensitive isolates. Greenhouse and field tests showed that ethaboxam is effective in managing MR . Ethaboxam in combination with metalaxyl is commonly applied as seed treatments in commercial chickpea production.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-08-20-1659-REDOI Listing
April 2021

Population Dynamics of Wheat Root Pathogens Under Different Tillage Systems in Northeast Oregon.

Plant Dis 2020 Oct 4;104(10):2649-2657. Epub 2020 Aug 4.

Columbia Basin Agricultural Research Center, Oregon State University, Adams, OR 97810.

No-till or direct seeding can be described as seeding directly into the crop stubble from the previous season without use of tillage. A reduction in tillage can result in many benefits, including increased soil organic matter, increased water holding capacity, and reduced fuel costs. However, the effect of no-till and reduced tillage on crop root disease profiles is poorly understood. To study the effect of tillage on disease dynamics, soil samples were collected from commercial wheat fields representing a wide range of tillage strategies in fall 2016 and fall 2017. Because precipitation might affect soilborne diseases, wheat fields located across a diverse gradient of precipitation zones of the dryland Pacific Northwest were selected. spp., spp., and spp. were quantified from soil samples using soil dilution plating and quantitative PCR (qPCR) assays. Results of dilution plating showed that the colony counts of , , and at the genus level were negatively associated with tillage. However, the same patterns were not observed when specific causal agents of , , and that are known to be pathogenic on wheat were quantified with qPCR. Furthermore, precipitation affected the population density of some fungal pathogens (, , and AG 8). Within the scope of inference of this study, results of this study indicate that the benefits of adopting reduced tillage likely outweigh potential risk for increased root disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-03-19-0621-REDOI Listing
October 2020

An endophyte of (esparto or needle grass) from Tunisia is a novel species in the species complex.

Mycologia 2020 Jul-Aug;112(4):792-807. Epub 2020 Jun 18.

Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service , US Department of Agriculture, Peoria, Illinois 61604-3999.

Here, we report on the morphological, molecular, and chemical characterization of a novel species recovered from the roots and rhizosphere of (halfa, esparto, or needle grass) in central Tunisia. Formally described here as , this species is a member of the species complex but differs from the other two species within the complex, and , by its endophytic association with and its genealogical exclusivity based on multilocus phylogenetic analyses. To assess their sexual reproductive mode, a polymerase chain reaction (PCR) assay was designed and used to screen the three strains of , 51 of , and 14 of for mating type () idiomorph. Genetic architecture of the locus in the former two species suggests that if they reproduce sexually, it is via obligate outcrossing. By comparison, results of the PCR assay indicated that 13/14 of the strains possessed and idiomorphs and thus might be self-fertile or homothallic. However, when the strains were selfed, 11 failed to produce perithecia and one only produced several small abortive perithecia. Cirrhi with ascospores, however, were only produced by 8/28 and 4/84 of the variable size perithecia, respectively, of NRRL 29888 and 29890. The potential for the three clade species to produce mycotoxins, pigments, and phytohormones was assessed by screening whole genome sequence data and by analyzing extracts on cracked maize kernel cultures via liquid chromatography-mass spectrometry.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2020.1767493DOI Listing
June 2020

Identity and Pathogenicity of Fungi Associated with Crown and Root Rot of Dryland Winter Wheat in Azerbaijan.

Plant Dis 2020 Aug 26;104(8):2149-2157. Epub 2020 May 26.

International Maize and Wheat Improvement Centre (CIMMYT) P.O. Box. 39 Emek, Ankara, Turkey.

A comprehensive survey was performed to assess fungal populations associated with crown and root rot of wheat throughout the main wheat-growing areas of Azerbaijan. Samples were taken from 76 fields; 630 fungal strains were isolated, identified, and evaluated for pathogenicity. The identification was conducted with morphological and molecular tools such as species-specific PCR and DNA sequencing of the internal transcribed spacer (ITS) and -α (-α) loci. The fungus found in the greatest number of fields (44) was with 192 isolates, followed by . Other spp. isolates were identified: , , , , , , , and . , , , , and spp. isolates were also identified, associated with underground parts of wheat. Phylogenetic analyses based on ITS and -α sequences of the isolates showed that the isolates belonging to the same species were clearly separated in the dendrogram. Pathogenicity assays revealed that , , and were most aggressive; , , , , , and isolates were moderately aggressive; , , and were weakly aggressive; and others were nonpathogenic. The result of this study exhibited the existence of a wide range of species associated with crown and root rot of wheat in Azerbaijan. Additionally, this is the first report of , , , , and as pathogens on wheat in Azerbaijan. Azerbaijan is the second country after Algeria in which was detected.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-08-19-1799-REDOI Listing
August 2020

Core Rhizosphere Microbiomes of Dryland Wheat Are Influenced by Location and Land Use History.

Appl Environ Microbiol 2020 02 18;86(5). Epub 2020 Feb 18.

USDA-ARS Wheat Health, Genetics, and Quality Unit, Pullman, Washington, USA.

The Inland Pacific Northwest is one of the most productive dryland wheat production areas in the United States. We explored the bacterial and fungal communities associated with wheat in a controlled greenhouse experiment using soils from multiple locations to identify core taxa consistently associated with wheat roots and how land use history influences wheat-associated communities. Further, we examined microbial co-occurrence networks from wheat rhizospheres to identify candidate hub taxa. Location of origin and land use history (long-term no-till versus noncropped Conservation Reserve Program [CRP]) of soils were the strongest drivers of bacterial and fungal communities. Wheat rhizospheres were especially enriched in many bacterial families, while only a few fungal taxa were enriched in the rhizosphere. There was a core set of bacteria and fungi that was found in >95% of rhizosphere or bulk soil samples, including members of , , , , and Core fungal taxa in the rhizosphere included Nectriaceae, , , , and Overall, there were fewer core fungal taxa, and the rhizosphere effect was not as pronounced as with bacteria. Cross-domain co-occurrence networks were used to identify hub taxa in the wheat rhizosphere, which included bacterial and fungal taxa (e.g., , , , and ). Our results suggest that there is a relatively small group of core rhizosphere bacteria that were highly abundant on wheat roots regardless of soil origin and land use history. These core communities may play important roles in nutrient uptake, suppressing fungal pathogens, and other plant health functions. Plant-associated microbiomes are critical for plant health and other important agroecosystem processes. We assessed the bacterial and fungal microbiomes of wheat grown in soils from across a dryland wheat cropping systems in eastern Washington to identify the core microbiome on wheat roots that is consistent across soils from different locations and land use histories. Moreover, cross-domain co-occurrence network analysis identified core and hub taxa that may play important roles in microbial community assembly. Candidate core and hub taxa provide a starting point for targeting microbiome components likely to be critical to plant health and for constructing synthetic microbial communities for further experimentation. This work is one of the first examples of identifying a core microbiome on a major field crop grown across hundreds of square kilometers over a wide range of biogeographical zones.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.02135-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7028972PMC
February 2020

A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees.

Nat Commun 2019 10 22;10(1):4802. Epub 2019 Oct 22.

Department of Plant Medicine and Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.

Microbes can establish mutualistic interactions with plants and insects. Here we track the movement of an endophytic strain of Streptomyces bacteria throughout a managed strawberry ecosystem. We show that a Streptomyces isolate found in the rhizosphere and on flowers protects both the plant and pollinating honeybees from pathogens (phytopathogenic fungus Botrytis cinerea and pathogenic bacteria, respectively). The pollinators can transfer the Streptomyces bacteria among flowers and plants, and Streptomyces can move into the plant vascular bundle from the flowers and from the rhizosphere. Our results present a tripartite mutualism between Streptomyces, plant and pollinator partners.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-12785-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6805876PMC
October 2019

Soil Microbial Biomass and Fungi Reduced With Canola Introduced Into Long-Term Monoculture Wheat Rotations.

Front Microbiol 2019 11;10:1488. Epub 2019 Jul 11.

Wheat Health, Genetics, and Quality Research Unit, USDA-Agricultural Research Service, Washington State University, Pullman, WA, United States.

With increasing canola ( L.) acreage in the Inland Pacific Northwest of the USA, we investigated the effect of this relatively new rotational crop on soil microbial communities and the performance of subsequent wheat ( L.) crops. In a 6-year on-farm canola-wheat rotation study conducted near Davenport, WA, grain yields of spring wheat (SW) following winter canola (WC) were reduced an average of 17% compared to SW yields following winter wheat (WW). Using soil samples collected and analyzed every year from that study, the objective of this research was to determine the differences and similarities in the soil microbial communities associated with WC and WW, and if those differences were associated with SW yield response. Microbial biomass and community composition were determined using phospholipid fatty acid analysis (PLFA). The WC-associated microbial community contained significantly less fungi, mycorrhizae, and total microbial biomass than WW. Additionally, reduced fungal and mycorrhizal abundance in SW following WC suggests that the canola rotation effect can persist. A biocidal secondary metabolite of canola, isothiocyanate, may be a potential mechanism mediating the decline in soil microbial biomass. These results demonstrate the relationship between soil microbial community composition and crop productivity. Our data suggest that WC can have significant effects on soil microbial communities that ultimately drive microbially mediated soil processes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2019.01488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637790PMC
July 2019

Mining the Drilosphere: Bacterial Communities and Denitrifier Abundance in a No-Till Wheat Cropping System.

Front Microbiol 2019 26;10:1339. Epub 2019 Jun 26.

Wheat Health, Genetics and Quality Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, WA, United States.

Earthworms play important roles in no-till cropping systems by redistributing crop residue to lower soil horizons, providing macropores for root growth, increasing water infiltration, enhancing soil quality and organic matter, and stimulating nitrogen cycling. The soil impacted by earthworm activity, including burrows, casts, and middens, is termed the drilosphere. The objective of this study was to determine the effect of earthworms on soil microbial community composition in the drilosphere at different landscape slope positions. Soil cores (50 cm depth) were extracted from three landscape locations (top, middle, and bottom slope positions) on a sloping aspect of a no-till wheat farm. Soil was sampled at the bottom of the soil core from inside multiple earthworm () channels (drilosphere) and from adjacent bulk soil. Bacterial communities were characterized for 16S rRNA gene diversity using high-throughput sequencing and functional denitrifier gene abundance (, and ) by quantitative PCR. Bacterial communities were structured primarily by the landscape slope position of the soil core followed by source (bulk versus drilosphere soil), with a significant interaction between core position and source. The families AKIW874, Chitinophagaceae, and Comamonadaceae and the genera , and were more abundant in the drilosphere compared to the bulk soil. Most of the individual bacterial taxa enriched in the drilosphere versus bulk soil were members of Actinobacteria, including Micrococcales, Gaiellaceae, Solirubrobacterales, and . In general, the greatest differences in communities were observed in comparisons of the top and bottom slope positions in which the bottom slope communities had significantly greater richness, diversity, and denitrifier abundance than the top slope position. Populations of denitrifiers (i.e., ratio of + to 16S rRNA) were more abundant in earthworm-impacted soils and there was a significant impact of on soil community composition which was observed only in the top landscape position. There were significant correlations between the abundance of and and taxa within Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, suggesting a broad diversity of denitrifying bacteria. Earthworms influence the soil microbial communities, but the impact depends on the slope location in a variable landscape, which likely reflects different soil characteristics.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2019.01339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611406PMC
June 2019

Distribution of Cereal Cyst Nematodes ( and ) in Eastern Washington State.

Plant Dis 2019 Sep 12;103(9):2171-2178. Epub 2019 Jul 12.

USDA-ARS, Wheat Health, Genetics and Quality Research Unit, United States Department of Agriculture, Pullman, WA 99164-6420, U.S.A.

Cereal cyst nematodes (CCN; and ), cause substantial worldwide yield loss in small grain cereals such as wheat, barley, and oat. was first detected in the United States in western Oregon in 1974 and had spread to northeast Oregon by the mid-1980s. Although was detected in eastern Washington in 1984, extensive infestations were not recognized until 2010. , first detected in Oregon in 2008, was found in eastern Washington in 2014. To gain more information about the distribution of these two species, an extensive survey was undertaken in eastern Washington, and methods were developed to distinguish species using DNA sequencing of single cysts. In this study, we surveyed 356 wheat and barley fields in eastern Washington from 2007 to 2017. CCN from the infested locations were identified to species level by sequencing the ribosomal internal transcribed spacers (ITS) and/or 28S ribosomal RNA (rRNA) genes. The sequences were compared in the GenBank database in the National Center for Biotechnology Information (NCBI) to identify species. The results show that is primarily confined to southern Whitman County, WA; and has a wider distribution across the higher precipitation annual cropping area of eastern Whitman County. Knowledge of species identification is critical for deployment of host resistance as an effective means of management, since resistance genes for one species of CCN may not be effective against the other.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-10-18-1881-SRDOI Listing
September 2019

Biosolids and Tillage Practices Influence Soil Bacterial Communities in Dryland Wheat.

Microb Ecol 2019 Oct 22;78(3):737-752. Epub 2019 Feb 22.

Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA.

Class B biosolids are used in dryland wheat (Triticum aestivum L.) production in eastern Washington as a source of nutrients and to increase soil organic matter, but little is known about their effects on bacterial communities and potential for harboring human pathogens. Moreover, conservation tillage is promoted to reduce erosion and soil degradation. We explored the impacts of biosolids or synthetic fertilizer in combination with traditional (conventional) or conservation tillage on soil bacterial communities. Bacterial communities were characterized from fresh biosolids, biosolid aggregates embedded in soil, and soil after a second application of biosolids using high-throughput amplicon sequencing. Biosolid application significantly affected bacterial communities, even 4 years after their application. Bacteria in the families Clostridiaceae, Norcardiaceae, Anaerolinaceae, Dietziaceae, and Planococcaceae were more abundant in fresh biosolids, biosolid aggregates, and soils treated with biosolids than in synthetically fertilized soils. Taxa identified as Turcibacter, Dietzia, Clostridiaceae, and Anaerolineaceae were highly abundant in biosolid aggregates in the soil and likely originated from the biosolids. In contrast, Oxalobacteriaceae, Streptomyceteaceae, Janthinobacterium, Pseudomonas, Kribbella, and Bacillus were rare in the fresh biosolids, but relatively abundant in biosolid aggregates in the soil, and probably originated from the soil to colonize the substrate. However, tillage had relatively minor effects on bacterial communities, with only a small number of taxa differing in relative abundance between traditional and conventional tillage. Although biosolid-associated bacteria persisted in soil, potentially pathogenic taxa were extremely rare and no toxin genes for key groups (Salmonella, Clostridium) were detectable, suggesting that although fecal contamination was apparent via indicator taxa, pathogen populations had declined to low levels. Thus, biosolid amendments had profound effects on soil bacterial communities both by introducing gut- or digester-derived bacteria and by enriching potentially beneficial indigenous soil populations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00248-019-01339-1DOI Listing
October 2019

Fungal community composition and diversity vary with soil depth and landscape position in a no-till wheat-based cropping system.

FEMS Microbiol Ecol 2018 07;94(7)

USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164, United States.

Soil edaphic characteristics are major drivers of fungal communities, but there is a lack of information on how communities vary with soil depth and landscape position in no-till cropping systems. Eastern Washington is dominated by dryland wheat grown on a highly variable landscape with steep, rolling hills. High-throughput sequencing of fungal ITS1 amplicons was used to characterize fungal communities across soil depth profiles (0 to 100 cm from the soil surface) among distinct landscape positions and aspects across a no-till wheat field. Fungal communities were highly stratified with soil depth, where deeper depths harbored distinct fungal taxa and more variable, less diverse fungal communities. Fungal communities from deep soils harbored a greater portion of taxa inferred to have pathotrophic or symbiotrophic in addition to saprotrophic lifestyles. Co-occurrence networks of fungal taxa became smaller and denser as soil depth increased. In contrast, differences between fungal communities from north-facing and south-facing slopes were relatively minor, suggesting that plant host, tillage, and fertilizer may be stronger drivers of fungal communities than landscape position.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/femsec/fiy098DOI Listing
July 2018

Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots.

Phytopathology 2018 May 21;108(5):582-594. Epub 2018 Mar 21.

First and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420.

The successional dynamics of root-colonizing microbes are hypothesized to be critical to displacing fungal pathogens that can proliferate after the use of some herbicides. Applications of glyphosate in particular, which compromises the plant defense system by interfering with the production of aromatic amino acids, are thought to promote a buildup of root pathogens and can result in a "greenbridge" between weeds or volunteers and crop hosts. By planting 2 to 3 weeks after spraying, growers can avoid most negative impacts of the greenbridge by allowing pathogen populations to decline, but with the added cost of delayed planting dates. However, the specific changes in microbial communities during this period of root death and the microbial taxa likely to be involved in displacing pathogens are poorly characterized. Using high-throughput sequencing, we characterized fungal and oomycete communities in roots after applications of herbicides with different modes of action (glyphosate or clethodim) and tracked their dynamics over 3 weeks in both naturally infested soil and soil inoculated with Rhizoctonia solani AG-8. We found that many unexpected taxa were present at high relative abundance (e.g., Pythium volutum and Myrmecridium species) in live and dying wheat roots and may play an under-recognized role in greenbridge dynamics. Moreover, communities were highly dynamic over time and had herbicide-specific successional patterns, but became relatively stable by 2 weeks after herbicide application. Network analysis of communities over time revealed patterns of interactions among taxa that were both common and unique to each herbicide treatment and identified two primary groups of taxa with many positive associations within-groups but negative associations between-groups, suggesting that these groups are antagonistic to one another in dying roots and may play a role in displacing pathogen populations during greenbridge dynamics.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-06-17-0212-RDOI Listing
May 2018

Location, Root Proximity, and Glyphosate-Use History Modulate the Effects of Glyphosate on Fungal Community Networks of Wheat.

Microb Ecol 2018 Jul 7;76(1):240-257. Epub 2017 Dec 7.

USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman, WA, 99164-6430, USA.

Glyphosate is the most-used herbicide worldwide and an essential tool for weed control in no-till cropping systems. However, concerns have been raised regarding the long-term effects of glyphosate on soil microbial communities. We examined the impact of repeated glyphosate application on bulk and rhizosphere soil fungal communities of wheat grown in four soils representative of the dryland wheat production region of Eastern Washington, USA. Further, using soils from paired fields, we contrasted the response of fungal communities that had a long history of glyphosate exposure and those that had no known exposure. Soil fungal communities were characterized after three cycles of wheat growth in the greenhouse followed by termination with glyphosate or manual clipping of plants. We found that cropping system, location, year, and root proximity were the primary drivers of fungal community compositions, and that glyphosate had only small impacts on fungal community composition or diversity. However, the taxa that responded to glyphosate applications differed between rhizosphere and bulk soil and between cropping systems. Further, a greater number of fungal OTUs responded to glyphosate in soils with a long history of glyphosate use. Finally, fungal co-occurrence patterns, but not co-occurrence network characteristics, differed substantially between glyphosate-treated and non-treated communities. Results suggest that most fungi influenced by glyphosate are saprophytes that likely feed on dying roots.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00248-017-1113-9DOI Listing
July 2018

Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems.

PLoS One 2017 12;12(9):e0184611. Epub 2017 Sep 12.

United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, Washington, United States of America.

In the dryland Pacific Northwest wheat cropping systems, no-till is becoming more prevalent as a way to reduce soil erosion and fuel inputs. Tillage can have a profound effect on microbial communities and soilborne fungal pathogens, such as Rhizoctonia. We compared the fungal communities in long-term no-till (NT) plots adjacent to conventionally tilled (CT) plots, over three years at two locations in Washington state and one location in Idaho, US. We used pyrosequencing of the fungal ITS gene and identified 422 OTUs after rarefication. Fungal richness was higher in NT compared to CT, in two of the locations. Humicola nigrescens, Cryptococcus terreus, Cadophora spp. Hydnodontaceae spp., and Exophiala spp. were more abundant in NT, while species of Glarea, Coniochaetales, Mycosphaerella tassiana, Cryptococcus bhutanensis, Chaetomium perlucidum, and Ulocladium chartarum were more abundant in CT in most locations. Other abundant groups that did not show any trends were Fusarium, Mortierella, Penicillium, Aspergillus, and Macroventuria. Plant pathogens such as Rhizoctonia (Ceratobasidiaceae) were not abundant enough to see tillage differences, but Microdochium bolleyi, a weak root pathogen, was more abundant in NT. Our results suggest that NT fungi are better adapted at utilizing intact, decaying roots as a food source and may exist as root endophytes. CT fungi can utilize mature plant residues that are turned into the soil with tillage as pioneer colonizers, and then produce large numbers of conidia. But a larger proportion of the fungal community is not affected by tillage and may be niche generalists.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184611PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5595340PMC
October 2017

Impacts of Repeated Glyphosate Use on Wheat-Associated Bacteria Are Small and Depend on Glyphosate Use History.

Appl Environ Microbiol 2017 Nov 31;83(22). Epub 2017 Oct 31.

USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Pullman, Washington, USA

Glyphosate is the most widely used herbicide worldwide and a critical tool for weed control in no-till cropping systems. However, there are concerns about the nontarget impacts of long-term glyphosate use on soil microbial communities. We investigated the impacts of repeated glyphosate treatments on bacterial communities in the soil and rhizosphere of wheat in soils with and without long-term history of glyphosate use. We cycled wheat in the greenhouse using soils from 4 paired fields under no-till (20+-year history of glyphosate) or no history of use. At each cycle, we terminated plants with glyphosate (2× the field rate) or by removing the crowns, and soil and rhizosphere bacterial communities were characterized. Location, cropping history, year, and proximity to the roots had much stronger effects on bacterial communities than did glyphosate, which only explained 2 to 5% of the variation. Less than 1% of all taxa were impacted by glyphosate, more in soils with a long history of use, and more increased than decreased in relative abundance. Glyphosate had minimal impacts on soil and rhizosphere bacteria of wheat, although dying roots after glyphosate application may provide a "greenbridge" favoring some copiotrophic taxa. Glyphosate (Roundup) is the most widely used herbicide in the world and the foundation of Roundup Ready soybeans, corn, and the no-till cropping system. However, there have been recent concerns about nontarget impacts of glyphosate on soil microbes. Using next-generation sequencing methods and glyphosate treatments of wheat plants, we described the bacterial communities in the soil and rhizosphere of wheat grown in Pacific Northwest soils across multiple years, different locations, and soils with different histories of glyphosate use. The effects of glyphosate were subtle and much less than those of drivers such as location and cropping systems. Only a small percentage of the bacterial groups were influenced by glyphosate, and most of those were stimulated, probably because of the dying roots. This study provides important information for the future of this important tool for no-till systems and the environmental benefits of reducing soil erosion and fossil fuel inputs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.01354-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5666137PMC
November 2017

An Improved Method for Establishing Accurate Water Potential Levels at Different Temperatures in Growth Media.

Front Microbiol 2017 11;8:1497. Epub 2017 Aug 11.

Wheat Health, Genetics, and Quality Research (USDA-ARS)Pullman, WA, United States.

NaCl, KCl, or PEG (polyethylene glycol)-amended potato dextrose broth (PDB), and potato dextrose agar (PDA) are essential for pure culture studies of water stress on fungi. Direct information on the actual water potential (WP) of this salt-amended PDB and PDA is lacking. Much fungal research in the past calculated WP of these salt-amended growth media by adding the WP of their constituents taken from individual salt dilution studies. But the WP of any complex solution will be modified by the level of synergism between its solutes. This study presents evidence of change in NaCl concentration due to synergism for attaining the same level of WP in NaCl solution, and NaCl amended PDB and PDA. The relation between WP and temperature and WP and salt concentration is also modified depending on the number of solutes in a growth medium. The WP of PEG-amended PDB increases with rising temperature, while that of NaCl/KCl amended PDB and PDA decreases with the increase of temperature. These results can be useful for doing pure culture studies on the biology and modeling the growth of air, water, and soil-borne fungi important in the food and agriculture industry and in terrestrial and aquatic ecosystems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2017.01497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5554502PMC
August 2017

Disease Suppressive Soils: New Insights from the Soil Microbiome.

Phytopathology 2017 Nov 20;107(11):1284-1297. Epub 2017 Sep 20.

First, third, and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Plant Pathology, University of Minnesota, St. Paul 55108.

Soils suppressive to soilborne pathogens have been identified worldwide for almost 60 years and attributed mainly to suppressive or antagonistic microorganisms. Rather than identifying, testing and applying potential biocontrol agents in an inundative fashion, research into suppressive soils has attempted to understand how indigenous microbiomes can reduce disease, even in the presence of the pathogen, susceptible host, and favorable environment. Recent advances in next-generation sequencing of microbiomes have provided new tools to reexamine and further characterize the nature of these soils. Two general types of suppression have been described: specific and general suppression, and theories have been developed around these two models. In this review, we will present three examples of currently-studied model systems with features representative of specific and general suppressiveness: suppression to take-all (Gaeumannomyces graminis var. tritici), Rhizoctonia bare patch of wheat (Rhizoctonia solani AG-8), and Streptomyces. To compare and contrast the two models of general versus specific suppression, we propose a number of hypotheses about the nature and ecology of microbial populations and communities of suppressive soils. We outline the potential and limitations of new molecular techniques that can provide novel ways of testing these hypotheses. Finally, we consider how this greater understanding of the phytobiome can facilitate sustainable disease management in agriculture by harnessing the potential of indigenous soil microbes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-03-17-0111-RVWDOI Listing
November 2017

Sensitivity of Rhizoctonia Isolates to Phenazine-1-Carboxylic Acid and Biological Control by Phenazine-Producing Pseudomonas spp.

Phytopathology 2017 06 4;107(6):692-703. Epub 2017 Apr 4.

First and second authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and fifth authors: United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430.

Rhizoctonia solani anastomosis groups (AG)-8 and AG-2-1 and R. oryzae are ubiquitous in cereal-based cropping systems of the Columbia Plateau of the Inland Pacific Northwest and commonly infect wheat. AG-8 and R. oryzae, causal agents of Rhizoctonia root rot and bare patch, are most commonly found in fields in the low-precipitation zone, whereas R. solani AG-2-1 is much less virulent on wheat and is distributed in fields throughout the low-, intermediate-, and high-precipitation zones. Fluorescent Pseudomonas spp. that produce the antibiotic phenazine-1-carboxylic acid (PCA) also are abundant in the rhizosphere of crops grown in the low-precipitation zone but their broader geographic distribution and effect on populations of Rhizoctonia is unknown. To address these questions, we surveyed the distribution of PCA producers (Phz) in 59 fields in cereal-based cropping systems throughout the Columbia Plateau. Phz Pseudomonas spp. were detected in 37 of 59 samples and comprised from 0 to 12.5% of the total culturable heterotrophic aerobic rhizosphere bacteria. The frequency with which individual plants were colonized by Phz pseudomonads ranged from 0 to 100%. High and moderate colonization frequencies of Phz pseudomonads were associated with roots from fields located in the driest areas whereas only moderate and low colonization frequencies were associated with crops where higher annual precipitation occurs. Thus, the geographic distribution of Phz pseudomonads overlaps closely with the distribution of R. solani AG-8 but not with that of R. oryzae or R. solani AG-2-1. Moreover, linear regression analysis demonstrated a highly significant inverse relationship between annual precipitation and the frequency of rhizospheres colonized by Phz pseudomonads. Phz pseudomonads representative of the four major indigenous species (P. aridus, P. cerealis, P. orientalis, and P. synxantha) suppressed Rhizoctonia root rot of wheat when applied as seed treatments. In vitro, mean 50% effective dose values for isolates of AG-8 and AG-2-1 from fields with high and low frequencies of phenazine producers did not differ significantly, nor was there a correlation between virulence of an isolate and sensitivity to PCA, resulting in rejection of the hypothesis that tolerance in Rhizoctonia spp. to PCA develops in nature upon exposure to Phz pseudomonads.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-07-16-0257-RDOI Listing
June 2017

Resistance to Multiple Soil-Borne Pathogens of the Pacific Northwest, USA Is Colocated in a Wheat Recombinant Inbred Line Population.

G3 (Bethesda) 2017 04 3;7(4):1109-1116. Epub 2017 Apr 3.

Wheat Health, Genetics and Quality Research Unit, United States Department of Agriculture-Agricultural Research Service, Pullman, Washington 99164.

Soil-borne pathogens of the Pacific Northwest decrease yields in both spring and winter wheat. Pathogens of economic importance include , , , and AG8. Few options are available to growers to manage these pathogens and reduce yield loss, therefore the focus for breeding programs is on developing resistant wheat cultivars. A recombinant inbred line population, LouAu (MP-7, NSL 511036), was developed to identify quantitative trait loci (QTL) associated with resistance to and This same population was later suspected to be resistant to and AG8. This study confirms partial resistance to and AG8 is present in this population. Six major and 16 speculative QTL were identified across seven measured traits. Four of the six major QTL were found within the same genomic region of the 5A wheat chromosome suggesting shared gene(s) contribute to the resistance. These QTL will be useful in breeding programs looking to incorporate resistance to soil-borne pathogens in wheat cultivars.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1534/g3.116.038604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386859PMC
April 2017

Timing of Glyphosate Applications to Wheat Cover Crops to Reduce Onion Stunting Caused by Rhizoctonia solani.

Plant Dis 2016 Jul 7;100(7):1474-1481. Epub 2016 Mar 7.

Professor, Washington State University, Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon 98273.

Stunting caused by Rhizoctonia spp. is economically important in irrigated onion bulb crops in the semiarid Columbia Basin of Oregon and Washington, where cereal winter cover crops commonly are planted the previous fall to prevent wind erosion of soil. The cover crop is killed with herbicide application just before or shortly after onion seeding, so that the dead rows of cereal plants provide a physical barrier tall enough to protect onion seedlings against wind and sand blasting but not tall enough to shade onion seedlings. However, the cover crop also serves as a green bridge for Rhizoctonia spp. on cereal roots to colonize the onion roots, potentially resulting in severe stunting of onion seedlings. To determine the effect of timing of application of the herbicide glyphosate to reduce this green bridge effect and, subsequently, onion stunting, three herbicide application intervals preceding onion planting were evaluated in a grower's onion field in each of 2012 and 2014 in the Columbia Basin. The wheat cover crop was killed with a glyphosate application 27, 17, and 3 days before onion seeding in 2012 and 19, 10, and 3 days before seeding in 2014. As the interval between herbicide application and onion planting increased from 3 days to 19 and 27 days, the number of patches of stunted onion plants decreased by ≥55%, total area of stunted patches decreased by 54 to 63%, and patch severity index decreased by 59 to 65%. Similarly, the Rhizoctonia solani AG 8 DNA concentration in soil sampled from the dead cover crop rows declined as the interval between glyphosate application and onion seeding increased in the 2012 trial but not in the 2014 trial. R. solani AG 3 and AG 8 DNA concentrations in soil sampled from the cover crop rows were significantly positively correlated with the number of patches of stunted onion plants (r = 0.490 and 0.607 at P = 0.039 and 0.008, respectively), total area of stunted patches (r = 0.496 and 0.659 at P = 0.035 and 0.003, respectively), and patch severity index (r = 0.492 and 0.635 at P = 0.038 and 0.005, respectively) in the 2012 trial; however, these variables were only correlated significantly with R. solani AG 3 DNA concentration in the 2014 trial. Increasing the interval between herbicide application to the cover crop and onion planting provides a practical management tool for stunting in onion bulb crops.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-10-15-1234-REDOI Listing
July 2016

Pythium Species Associated with Damping-off of Pea in Certified Organic Fields in the Columbia Basin of Central Washington.

Plant Dis 2016 May 24;100(5):916-925. Epub 2016 Feb 24.

Washington State University Mount Vernon NWREC.

Organic vegetable production accounted for 19% of the total organic acreage in Washington State in 2013, with 1,700 ha of certified organic vegetable pea. However, production is challenged constantly with the threat of poor emergence after planting due to damping-off caused by Pythium spp. A survey of Pythium spp. in organic vegetable production areas of the semiarid Columbia Basin of central Washington was carried out in fall 2009 to identify species associated with damping-off during early spring planting. Of 305 isolates baited from soil sampled from 37 certified organic fields, 264 were identified to 16 Pythium spp. by sequencing the internal transcribed spacer region of ribosomal DNA. A soil DNA-CFU regression curve was developed using real-time quantitative polymerase chain reaction assays for each of the three predominant pathogenic species (Pythium abappressorium, the P. irregulare complex, and P. ultimum var. ultimum) found in soil sampled from the 37 fields. The P. irregulare complex, P. abappressorium, and P. ultimum var. ultimum were detected in 57, 78, and 100% of the fields sampled, respectively. A regression analysis was used to determine that P. ultimum var. ultimum ranged from 14 to 332 CFU/g of soil in the 37 fields, the P. irregulare complex ranged from 25 to 228 CFU/g of soil, and P. abappressorium DNA was below the quantifiable limit. In summary, P. ultimum var. ultimum was the most prevalent pathogenic Pythium sp. detected in certified organic fields in the semiarid Columbia Basin of central Washington but multiple Pythium spp. may be associated with damping-off in cool and wet, early spring planting conditions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-07-15-0774-REDOI Listing
May 2016

Molecular Characterization, Morphological Characteristics, Virulence, and Geographic Distribution of Rhizoctonia spp. in Washington State.

Phytopathology 2016 May 21;106(5):459-73. Epub 2016 Mar 21.

First and third authors: Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430; and second, fourth, and fifth authors: U.S. Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430.

Rhizoctonia root rot and bare patch, caused by Rhizoctonia solani anastomosis group (AG)-8 and R. oryzae, are chronic and important yield-limiting diseases of wheat and barley in the Inland Pacific Northwest (PNW) of the United States. Major gaps remain in our understanding of the epidemiology of these diseases, in part because multiple Rhizoctonia AGs and species can be isolated from the same cereal roots from the field, contributing to the challenge of identifying the causal agents correctly. In this study, a collection totaling 498 isolates of Rhizoctonia was assembled from surveys conducted from 2000 to 2009, 2010, and 2011 over a wide range of cereal production fields throughout Washington State in the PNW. To determine the identity of the isolates, PCR with AG- or species-specific primers and/or DNA sequence analysis of the internal transcribed spacers was performed. R. solani AG-2-1, AG-8, AG-10, AG-3, AG-4, and AG-11 comprised 157 (32%), 70 (14%), 21 (4%), 20 (4%), 1 (0.2%), and 1 (0.2%), respectively, of the total isolates. AG-I-like binucleate Rhizoctonia sp. comprised 44 (9%) of the total; and 53 (11%), 80 (16%), and 51 (10%) were identified as R. oryzae genotypes I, II, and III, respectively. Isolates of AG-2-1, the dominant Rhizoctonia, occurred in all six agronomic zones defined by annual precipitation and temperature within the region sampled. Isolates of AG-8 also were cosmopolitan in their distribution but the frequency of isolation varied among years, and they were most abundant in zones of low and moderate precipitation. R. oryzae was cosmopolitan, and collectively the three genotypes comprised 37% of the isolates. Only isolates of R. solani AG-8 and R. oryzae genotypes II and III (but not genotype I) caused symptoms typically associated with Rhizoctonia root rot and bare patch of wheat. Isolates of AG-2-1 caused only mild root rot and AG-I-like binucleate isolates and members of groups AG-3, AG-4, and AG-11 showed only slight or no discoloration of the roots. However, all isolates of AG-2-1 caused severe damping-off of canola, resulting in 100% mortality. Isolates of Rhizoctonia AG-8, AG-2-1, AG-10, AG-I-like binucleate Rhizoctonia, and R. oryzae genotypes I, II, and III could be distinguished by colony morphology on potato dextrose agar, by PCR with specific primers, or by the type and severity of disease on wheat and canola seedlings, and results of these approaches correlated completely. Based on cultured isolates, we also identified the geographic distribution of all of these Rhizoctonia isolates in cereal-based production systems throughout Washington State.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-09-15-0208-RDOI Listing
May 2016

Characterization and Pathogenicity of Rhizoctonia and Rhizoctonia-Like spp. From Pea Crops in the Columbia Basin of Oregon and Washington.

Plant Dis 2015 May;99(5):604-613

Professor, Washington State University Mount Vernon Northwestern Washington Research & Extension Center, Mount Vernon 98273.

Isolates of Rhizoctonia and Rhizoctonia-like spp. (n = 179) were baited selectively from soil and plant samples collected from irrigated pea crops in the semiarid Columbia Basin of Oregon and Washington from 2011 to 2013, and characterized to species, subspecies, and anastomosis groups (AG) based on sequences of the internal transcribed spacer region of ribosomal DNA. Rhizoctonia solani comprised 76% of all isolates, and included isolates of AG 4 (31% of all isolates), AG 2-1 (18%), AG 3 (10%), AG 8 (8%), AG 5 (5%), AG 10 (3%), and AG 9 (1%). The isolates of Ceratobasidium spp. (20%) comprised four AGs: AG K (11%), AG A (6%), AG I (2%), and AG I-like (1%). Waitea circinata isolates (4%) comprised two subspecies: W. circinata var. circinata (approximately 4%) and W. circinata var. zeae (<1%). Repeated pathogenicity tests of isolates of the 10 most frequently detected AGs and subspecies on 'Serge' pea at 15°C revealed that R. solani AG 2-1 caused the greatest reduction in pea emergence, followed by R. solani AG 4. R. solani AG 4 caused the most severe root rot, stunting, and reduction in pea seedling biomass, followed by isolates of AG 2-1. R. solani AG 8 did not affect emergence, plant height, and total biomass compared with noninoculated control plants; however, root rot caused by isolates of AG 8 was ranked the third most severe among isolates of the 10 Rhizoctonia subgroups, after that caused by isolates of AG 4 and AG 2-1. Isolates of other AGs and subspecies were either weakly virulent or nonpathogenic on pea. The most common AGs (AG 4 and AG 2-1) detected in pea fields in the Columbia Basin were also the most virulent. In a growers' pea crop grown for seed ('Prevail') planted 5 days after herbicide application and incorporation of a preceding winter wheat crop, severe stunting caused by Rhizoctonia spp. resulted in an average 75% yield loss within patches of stunted plants. In contrast, the yield of processing pea from a green pea crop of Serge did not differ significantly for plants sampled within versus outside patches of stunted plants; however, plants within patches were significantly more mature. In the Prevail seed crop, a greater frequency of R. solani AG 8 was detected than AG 2-1 or AG 4 from within patches of stunted plants, indicating that isolates of AG 8 may be associated with the root rot complex in some pea crops in the Columbia Basin.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-08-14-0803-REDOI Listing
May 2015

Stunted Patches in Onion Bulb Crops in Oregon and Washington: Etiology and Yield Loss.

Plant Dis 2015 May;99(5):648-658

Professor, Washington State University Mount Vernon NWREC, Mount Vernon 98273.

Onion stunting caused by Rhizoctonia spp. is an important soilborne disease on very sandy soils in the Columbia Basin of Oregon and Washington. From 2010 to 2013, 251 isolates of Rhizoctonia or Rhizoctonia-like spp. were obtained from soil and onion plant samples collected from inside and outside patches of stunted plants in 29 onion fields in the Columbia Basin. Sequence analysis of the internal transcribed spacer (ITS) region was used to identify the isolates, with 13 anastomosis groups (AGs) or subspecies detected. The most frequent was Waitea circinata var. circinata (25%), followed by Rhizoctonia solani AG 3 (17%), R. solani AG 4 (14%), Ceratobasidium sp. AG A (10%), R. solani AG 8 (7%), Ceratobasidium sp. AG K (6%), R. solani AG 2-1 (6%), W. circinata var. zeae (6%), R. solani AG 5 (4%), Ceratobasidium sp. AG G (2%), R. solani AG 11 (2%), and R. solani AG 1-1B and AG 10 (each <1%). However, the distribution of AGs and subspecies varied depending on whether soil or onion plants samples were collected within or adjacent to patches of stunted onion plants. In an attempt to predict the risk of onion stunting for a field prior to planting, DNA concentrations of AG 2-1, AG 3, AG 4, and AG 8 were quantified from bulk soil samples collected from each of nine growers' fields approximately 1 month before onion sowing in 2012. The preplant DNA concentrations did not show a significant association with the amount of stunting observed in the fields during the growing season. In contrast, the frequency of isolation and DNA concentration of R. solani AG 8 detected in soil samples collected during the growing season were greater from inside patches of stunted onion plants than from adjacent healthy areas of an onion crop sampled in 2012, but not for soil samples collected similarly from an onion crop in 2013. AG 2-1, AG 3, and AG 4 DNA concentrations did not differ significantly in soil sampled inside versus outside stunted patches in the fields sampled in 2012 and 2013. Relationships between the number of bulbs harvested or bulb weight versus severity of stunting were defined using correlation and regression analyses for six onion cultivars grown in seven fields surveyed in 2012 and 2013. Onion stunting reduced the average marketable bulb yield by 25 to 60% within stunted patches of the six cultivars. Stunting did not reduce onion plant stand but consistently reduced the size of bulbs, and yield reduction increased with increasing disease severity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-05-14-0441-REDOI Listing
May 2015