Dual host-pathogen small RNA sequencing during wheat stem rust infection.

OBJECTIVES: RNA sequencing of two organisms in a symbiotic interaction can yield insights that are not found in samples from each organism alone. We present a sequencing dataset focusing on the small RNA fraction from wheat plants (Triticum aestivum) infected with the biotrophic pathogen wheat stem rust fungus (Puccinia graminis f.sp. tritici). Simultaneous small RNA sequencing of this agronomically important crop and its adversary can lead to a better understanding of the role of noncoding RNAs in both plant and fungal biology. DATA DESCRIPTION: Small RNA libraries were constructed from infected and mock-infected plant tissue and sequenced on the Ion Torrent platform. Quality control was performed to ensure sample and data integrity. Using this dataset, researchers can employ previously established methods to map subsets of reads exclusively to each organism's genome. Subsequent analyses can be undertaken to discover microRNAs, predict small RNA targets, and generate hypotheses for further laboratory experiments.

Small RNAs target native and cross-kingdom transcripts on both sides of the wheat stripe rust interaction.

The wheat stripe rust fungus (Puccinia striiformis f.sp. tritici) threatens global wheat production. Small RNAs (sRNAs) modulate plant defense induction, and RNA exchange between host and microbe causes cross-kingdom gene silencing, but few examples are known in rust fungi. This study combined sRNA, parallel analysis of RNA ends, and gene expression data to discover sRNA-target pairs on each side of the interaction. Specific wheat 24 nt sRNAs were suppressed, while particular 35 nt fragments were strongly induced upon infection. Wheat sRNAs cleaved fungal transcripts coding for a ribosomal protein and a glycosyl hydrolase effector. Fungal microRNA-like and phased 21 nt sRNAs originated from long inverted repeats near protein coding genes. Fungal sRNAs targeted native transcripts: transposons and kinases; and cross-kingdom transcripts: a wheat nucleotide-binding domain leucine-rich repeat receptor (NLR) and multiple defense-related transcription factor families. This work sheds light on host-microbe coevolution and delivers prospects for developing pathogen control biotechnology.

Rhizoctonia Resistance Is Negatively Correlated to Early Root Growth Rate in Synthetic Hexaploid Wheat Derivatives.

Resistance to the soilborne fungal pathogen Rhizoctonia solani AG-8 is desirable in adapted wheat and barley but remains an elusive trait for prebreeders and breeders. In a previous study, we observed that emergence and root growth was faster in the Rhizoctonia-susceptible 'Scarlet' than in its resistant counterpart, 'Scarlet-Rz1'. The objective of the current study was to quantify early root growth rate and total root length in resistant and susceptible synthetic hexaploid wheat lines, including parental lines and 22 recombinant inbred lines derived crosses between parental lines. In Petri dish assays, the susceptible lines displayed a faster rate of root growth during the first 40 h of root emergence compared with resistant lines. This growth differential was observed in 14-day and 48-h greenhouse assays, in which the total root length of susceptible parental lines was significantly (P < 0.05) greater than that of resistant parental lines. However, the resistant lines sustained less root loss compared with susceptible lines when R. solani AG-8 was present in the soil. Early root growth rate and total root length were not correlated to freezing tolerance in a set of wheat cultivars selected for cold tolerance. The findings indicated that early root growth was negatively correlated to R. solani AG-8 damage in resistant synthetic wheat lines developed for the Pacific Northwest, United States, and suggested that the dynamics of root emergence affect resistance to this soilborne pathogen.

Wheat Genotype-Specific Recruitment of Rhizosphere Bacterial Microbiota Under Controlled Environments.

Plants recruit beneficial microbial communities in the rhizosphere that are involved in a myriad of ecological services, such as improved soil quality, nutrient uptake, abiotic stress tolerance, and soil-borne disease suppression. Disease suppression caused by rhizosphere microbiomes has been important in managing soil-borne diseases in wheat. The low heritability of resistance in wheat to soil-borne diseases like Rhizoctonia root rot has made management of these diseases challenging, particularly in direct-seeded systems. Identification of wheat genotypes that recruit rhizosphere microbiomes that promote improved plant fitness and suppression of the pathogen could be an alternative approach to disease management through genetic improvement. Several growth chamber cycling experiments were conducted using six winter wheat genotypes (PI561725, PI561727, Eltan, Lewjain, Hill81, Madsen) to determine wheat genotypes that recruit suppressive microbiomes. At the end of the third cycle, suppression assays were done by inoculating R. solani into soils previously cultivated with specific wheat genotypes to test suppression of the pathogen by the microbiome. Microbiome composition was characterized by sequencing of 16S rDNA (V1-V3 region). Among the growth cycling lengths, 160-day growth cycles exhibited the most distinct rhizosphere microbiomes among the wheat genotypes. Suppression assays showed that rhizosphere microbiomes of different wheat genotypes resulted in significant differences in shoot length (value of p=0.018) and had an impact on the pathogenicity of R. solani, as observed in the reduced root disease scores (value of p=0.051). Furthermore, soils previously cultivated with the ALMT1 isogenic lines PI561725 and PI561727 exhibited better seedling vigor and reduced root disease. Microbiome analysis showed that Burkholderiales taxa, specifically Janthinobacterium, are differentially abundant in PI561727 and PI561725 cultivated soils and are associated with reduced root disease and better growth. This study demonstrates that specific wheat genotypes recruit different microbiomes in growth chamber conditions but the microbial community alterations were quite different from those previously observed in field plots, even though the same soils were used. Genotype selection or development appears to be a viable approach to controlling soil-borne diseases in a sustainable manner, and controlled environment assays can be used to see genetic differences but further work is needed to explain differences seen between growth chamber and field conditions.

Rhizosphere community selection reveals bacteria associated with reduced root disease.

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.

Image-Based Phenotyping of Flowering Intensity in Cool-Season Crops.

The timing and duration of flowering are key agronomic traits that are often associated with the ability of a variety to escape abiotic stress such as heat and drought. Flowering information is valuable in both plant breeding and agricultural production management. Visual assessment, the standard protocol used for phenotyping flowering, is a low-throughput and subjective method. In this study, we evaluated multiple imaging sensors (RGB and multiple multispectral cameras), image resolution (proximal/remote sensing at 1.6 to 30 m above ground level/AGL), and image processing (standard and unsupervised learning) techniques in monitoring flowering intensity of four cool-season crops (canola, camelina, chickpea, and pea) to enhance the accuracy and efficiency in quantifying flowering traits. The features (flower area, percentage of flower area with respect to canopy area) extracted from proximal (1.6-2.2 m AGL) RGB and multispectral (with near infrared, green and blue band) image data were strongly correlated (r up to 0.89) with visual rating scores, especially in pea and canola. The features extracted from unmanned aerial vehicle integrated RGB image data (15-30 m AGL) could also accurately detect and quantify large flowers of winter canola (r up to 0.84), spring canola (r up to 0.72), and pea (r up to 0.72), but not camelina or chickpea flowers. When standard image processing using thresholds and unsupervised machine learning such as k-means clustering were utilized for flower detection and feature extraction, the results were comparable. In general, for applicability of imaging for flower detection, it is recommended that the image data resolution (i.e., ground sampling distance) is at least 2-3 times smaller than that of the flower size. Overall, this study demonstrates the feasibility of utilizing imaging for monitoring flowering intensity in multiple varieties of evaluated crops.

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

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 Bradyrhizobium, Sphingomonadaceae, Massilia, Variovorax, Oxalobacteraceae, and Caulobacteraceae Core fungal taxa in the rhizosphere included Nectriaceae, Ulocladium, Alternaria, Mortierella, and Microdochium 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., Sphingomonas, Massilia, Knufia, and Microdochium). 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.IMPORTANCE 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.

High-throughput Siderophore Screening from Environmental Samples: Plant Tissues, Bulk Soils, and Rhizosphere Soils.

Siderophores (low-molecular weight metal chelating compounds) are important in various ecological phenomenon ranging from iron (Fe) biogeochemical cycling in soils, to pathogen competition, plant growth promotion, and cross-kingdom signaling. Furthermore, siderophores are also of commercial interest in bioleaching and bioweathering of metal-bearing minerals and ores. A rapid, cost effective, and robust means of quantitatively assessing siderophore production in complex samples is key to identifying important aspects of the ecological ramifications of siderophore activity, including, novel siderophore producing microbes. The method presented here was developed to assess siderophore activity of in-tact microbiome communities, in environmental samples, such as soil or plant tissues. The samples were homogenized and diluted in a modified M9 medium (without Fe), and enrichment cultures were incubated for 3 days. Siderophore production was assessed in samples at 24, 48, and 72 hours (h) using a novel 96-well microplate CAS (Chrome azurol sulphonate)-Fe agar assay, an adaptation of the traditionally tedious and time-consuming colorimetric method of assessing siderophore activity, performed on individual cultivated microbial isolates. We applied our method to 4 different genotypes/Lines of wheat (Triticum aestivum L.), including Lewjain, Madsen, and PI561725, and PI561727 commonly grown in the inland Pacific Northwest. Siderophore production was clearly impacted by the genotype of wheat, and in the specific types of plant tissues observed. We successfully used our method to rapidly screen for the influence of plant genotype on siderophore production, a key function in terrestrial and aquatic ecosystems. We produced many technical replicates, yielding very reliable statistical differences in soils and within plant tissues. Importantly, the results show the proposed method can be used to rapidly examine siderophore production in complex samples with a high degree of reliability, in a manner that allows communities to be preserved for later work to identify taxa and functional genes.

A novel fungal effector from Puccinia graminis suppressing RNA silencing and plant defense responses.

Fungal plant pathogens, like rust-causing biotrophic fungi, secrete hundreds of effectors into plant cells to subvert host immunity and promote pathogenicity on their host plants by manipulating specific physiological processes or signal pathways, but the actual function has been demonstrated for very few of these proteins. Here, we show that the PgtSR1 effector proteins, encoded by two allelic genes (PgtSR1-a and PgtSR1-b), from the wheat stem rust pathogen Puccinia graminis f. sp. tritici (Pgt), suppress RNA silencing in plants and impede plant defenses by altering the abundance of small RNAs that serve as defense regulators. Expression of the PgtSR1s in plants revealed that the PgtSR1s promote susceptibility to multiple pathogens and partially suppress cell death triggered by multiple R proteins. Overall, our study provides the first evidence that the filamentous fungus P. graminis has evolved to produce fungal suppressors of RNA silencing and indicates that PgtSR1s suppress both basal defenses and effector triggered immunity.

Analysis of miRNAs in Two Wheat Cultivars Infected With Puccinia striiformis f. sp. tritici.

MicroRNAs are small RNAs that regulate gene expression in eukaryotes. In this study, we analyzed the small RNA profiles of two cultivars that exhibit different reactions to stripe rust infection: one susceptible, the other partially resistant. Using small RNA libraries prepared from the two wheat cultivars infected with stripe rust fungus (Puccinia striiformis f. sp. tritici), we identified 182 previously known miRNAs, 91 variants of known miRNAs, and 163 candidate novel wheat miRNAs. Known miRNA loci were usually copied in all three wheat sub-genomes, whereas novel miRNA loci were often specific to a single sub-genome. DESeq2 analysis of differentially expressed microRNAs revealed 23 miRNAs that exhibit cultivar-specific differences. TA078/miR399b showed cultivar-specific differential regulation in response to infection. Using different target prediction algorithms, 145 miRNAs were predicted to target wheat genes, while 69 miRNAs were predicted to target fungal genes. We also confirmed reciprocal expression of TA078/miR399b and tae-miR9664 and their target genes in different treatments, providing evidence for miRNA-mediated regulation during infection. Both known and novel miRNAs were predicted to target fungal genes, suggesting trans-kingdom regulation of gene expression. Overall, this study contributes to the current repository of wheat miRNAs and provides novel information on the yet-uncharacterized roles for miRNAs in the wheat-stripe rust pathosystem.

Host-Induced Gene Silencing (HIGS) for Elucidating Puccinia Gene Function in Wheat.

Biotrophic fungi (Puccinia spp.) cause devastating diseases of wheat and other cereal species globally. The function of large repertories of genes from Puccinia spp. still needs to be discovered to understand the infection process of these obligate parasites, eventually to protect plants from rust diseases. Functional analysis of targeted genes is challenging due to the inherent difficulties with culturing the fungus and transforming the host. RNA interference (RNAi) is a conserved gene regulation process in eukaryotes and known to be a powerful genetic tool in plant biotechnology. More recently, host-induced gene silencing (HIGS) has been developed to assess pathogen gene function in plants. HIGS is an RNAi-based process where double stranded RNA (dsRNA) homologous to a pathogen gene can be expressed in a plant to induce targeted silencing of the pathogen gene. Here we described a detailed HIGS protocol for functional analysis of rust genes from Puccinia species in cereals. As an example we describe an experiment silencing the tryptophan 2-monooxygenase gene (Pgt-IaaM) from Puccinia graminis f. sp. tritici (Pgt) that is involved in virulence to wheat.

Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei).

BACKGROUND: Plant fungal pathogens can rapidly evolve and adapt to new environmental conditions in response to sudden changes of host populations in agro-ecosystems. However, the genomic basis of their host adaptation, especially at the forma specialis level, remains unclear. RESULTS: We sequenced two isolates each representing Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), different formae speciales of the stripe rust fungus P. striiformis highly adapted to wheat and barley, respectively. The divergence of Pst and Psh, estimated to start 8.12 million years ago, has been driven by high nucleotide mutation rates. The high genomic variation within dikaryotic urediniospores of P. striiformis has provided raw genetic materials for genome evolution. No specific gene families have enriched in either isolate, but extensive gene loss events have occurred in both Pst and Psh after the divergence from their most recent common ancestor. A large number of isolate-specific genes were identified, with unique genomic features compared to the conserved genes, including 1) significantly shorter in length; 2) significantly less expressed; 3) significantly closer to transposable elements; and 4) redundant in pathways. The presence of specific genes in one isolate (or forma specialis) was resulted from the loss of the homologues in the other isolate (or forma specialis) by the replacements of transposable elements or losses of genomic fragments. In addition, different patterns and numbers of telomeric repeats were observed between the isolates. CONCLUSIONS: Host adaptation of P. striiformis at the forma specialis level is a complex pathogenic trait, involving not only virulence-related genes but also other genes. Gene loss, which might be adaptive and driven by transposable element activities, provides genomic basis for host adaptation of different formae speciales of P. striiformis.

Genome Sequence Resources for the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) and the Barley Stripe Rust Pathogen (Puccinia striiformis f. sp. hordei).

Puccinia striiformis f. sp. tritici causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei causes stripe rust on barley. Several P. striiformis f. sp. tritici genomes are available, but no P. striiformis f. sp. hordei genome is available. More genomes of P. striiformis f. sp. tritici and P. striiformis f. sp. hordei are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced P. striiformis f. sp. tritici isolate 93-210 and P. striiformis f. sp. hordei isolate 93TX-2, using PacBio and Illumina technologies and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interactions.

Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize.

Goss's wilt (GW) of maize is caused by the Gram-positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn) and has spread in recent years throughout the Great Plains, posing a threat to production. The genetic basis of plant resistance is unknown. Here, a simple method for quantifying disease symptoms was developed and used to select cohorts of highly resistant and highly susceptible lines known as extreme phenotypes (XP). Copy number variation (CNV) analyses using whole genome sequences of bulked XP revealed 141 genes containing CNV between the two XP groups. The CNV genes include the previously identified common rust resistant locus rp1. Multiple Rp1 accessions with distinct rp1 haplotypes in an otherwise susceptible accession exhibited hypersensitive responses upon inoculation. GW provides an excellent system for the genetic dissection of diseases caused by closely related subspecies of C. michiganesis. Further work will facilitate breeding strategies to control GW and provide needed insight into the resistance mechanism of important related diseases such as bacterial canker of tomato and bacterial ring rot of potato.

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

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.

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

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.IMPORTANCE 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.

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

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.

Foundational and Translational Research Opportunities to Improve Plant Health.

Reader Comments | Submit a Comment The white paper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on nonsustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture.

Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars.

Minimal tillage management of extensive crops like wheat can provide significant environmental services but can also lead to adverse interactions between soil borne microbes and the host. Little is known about the ability of the wheat cultivar to alter the microbial community from a long-term recruitment standpoint, and whether this recruitment is consistent across field sites. To address this, nine winter wheat cultivars were grown for two consecutive seasons on the same plots on two different farm sites and assessed for their ability to alter the rhizosphere bacterial communities in a minimal tillage system. Using deep amplicon sequencing of the V1-V3 region of the 16S rDNA, a total of 26,604 operational taxonomic units (OTUs) were found across these two sites. A core bacteriome consisting of 962 OTUs were found to exist in 95% of the wheat rhizosphere samples. Differences in the relative abundances for these wheat cultivars were observed. Of these differences, 24 of the OTUs were found to be significantly different by wheat cultivar and these differences occurred at both locations. Several of the cultivar-associated OTUs were found to correspond with strains that may provide beneficial services to the host plant. Network correlations demonstrated significant co-occurrences for different taxa and their respective OTUs, and in some cases, these interactions were determined by the wheat cultivar. Microbial abundances did not play a role in the number of correlations, and the majority of the co-occurrences were shown to be positively associated. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to determine potential functions associated with OTUs by association with rhizosphere members which have sequenced metagenomics data. Potentially beneficial pathways for nitrogen, sulfur, phosphorus, and malate metabolism, as well as antimicrobial compounds, were inferred from this analysis. Differences in these pathways and their associated functions were found to differ by wheat cultivar. In conclusion, our study suggests wheat cultivars are involved in shaping the rhizosphere by differentially altering the bacterial OTUs consistently across different sites, and these altered bacterial communities may provide beneficial services to the host.

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

Soil-borne pathogens of the Pacific Northwest decrease yields in both spring and winter wheat. Pathogens of economic importance include Fusarium culmorum, Pratylenchus neglectus, P. thornei, and Rhizoctonia solani 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 P. neglectus and P. thornei This same population was later suspected to be resistant to F. culmorum and R. solani AG8. This study confirms partial resistance to F. culmorum and R. solani 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.