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1.
Front Microbiol ; 13: 908981, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36118206

RESUMO

Synthetic microbial communities (SynComs) could potentially enhance some functions of the plant microbiome and emerge as a promising inoculant for improving crop performance. Here, we characterized a collection of bacteria, previously isolated from the wheat rhizosphere, for their antifungal activity against soilborne fungal pathogens. Ten SynComs with different compositions from 14 bacterial strains were created. Seven SynComs protected wheat from Rhizoctonia solani AG8 infection, although SynComs were not more effective than single strains in reducing wheat root rot disease. Further, the mechanisms of interaction of the tested bacteria with each other and plants were explored. We found that nine bacteria and nine SynComs impacted the root growth of Arabidopsis. Nine bacteria and four SynComs significantly inhibited the growth of AG8 by producing volatiles. The cell-free supernatants from six bacteria inhibited the growth of AG8. Together, this study provided the potential for improving crop resilience by creating SynComs.

2.
Plant Dis ; 106(2): 357-359, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-34340566

RESUMO

In this Short Communication we describe the occurrence of mummy berry associated with huckleberry (Vaccinium membranaceum) caused by Monilinia spp. in Oregon. To our knowledge, this is the first report of a Monilinia spp. associated with mummy berry of huckleberry in Oregon. Sequence data from our specimens reveal the closest identity was Monilinia vaccinii-corymbosi, a pathogen of commercial blueberry (Vaccinium corymbosum). This may be a new species of Monilinia, not previously reported on huckleberry, and further investigation is needed. Of specific importance, the huckleberry holds cultural importance as a sacred First Food of the Confederated Tribes of the Umatilla Indian Reservation and other Pacific Northwest tribes. Although plant pathogen management in natural landscapes presents unique challenges, we will work with tribal authorities to determine whether cultural management techniques may mitigate yield loss due to Monilinia spp.


Assuntos
Huckleberry (Planta) , Vaccinium , Frutas , Oregon
3.
Front Microbiol ; 12: 576763, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34093451

RESUMO

Liming is an effective agricultural practice and is broadly used to ameliorate soil acidification in agricultural ecosystems. Our understanding of the impacts of lime application on the soil fungal community is scarce. In this study, we explored the responses of fungal communities to liming at two locations with decreasing soil pH in Oregon in the Pacific Northwest using high-throughput sequencing (Illumina MiSeq). Our results revealed that the location and liming did not significantly affect soil fungal diversity and richness, and the impact of soil depth on fungal diversity varied among locations. In contrast, location and soil depth had a strong effect on the structure and composition of soil fungal communities, whereas the impact of liming was much smaller, and location- and depth-dependent. Interestingly, families Lasiosphaeriaceae, Piskurozymaceae, and Sordariaceae predominated in the surface soil (0-7.5 cm) and were positively correlated with soil OM and aluminum, and negatively correlated with pH. The family Kickxellaceae which predominated in deeper soil (15-22.5 cm), had an opposite response to soil OM. Furthermore, some taxa in Ascomycota, such as Hypocreales, Peziza and Penicillium, were increased by liming at one of the locations (Moro). In conclusion, these findings suggest that fungal community structure and composition rather than fungal diversity responded to location, soil depth and liming. Compared to liming, location and depth had a stronger effect on the soil fungal community, but some specific fungal taxa shifted with lime application.

4.
Microbiome ; 9(1): 86, 2021 04 09.
Artigo em Inglês | MEDLINE | ID: mdl-33836842

RESUMO

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.


Assuntos
Rizosfera , Microbiologia do Solo , Bactérias/genética , Basidiomycota , Raízes de Plantas , RNA Ribossômico 16S/genética , Rhizoctonia
5.
Plant Dis ; 104(10): 2649-2657, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32749926

RESUMO

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. Fusarium spp., Pythium spp., and Rhizoctonia 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 Fusarium, Pythium, and Rhizoctonia at the genus level were negatively associated with tillage. However, the same patterns were not observed when specific causal agents of Fusarium, Pythium, and Rhizoctonia that are known to be pathogenic on wheat were quantified with qPCR. Furthermore, precipitation affected the population density of some fungal pathogens (F. culmorum, P. ultimum, and R. solani 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.


Assuntos
Rhizoctonia , Triticum , Noroeste dos Estados Unidos , Oregon , Dinâmica Populacional
6.
BMC Genomics ; 21(1): 247, 2020 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-32197579

RESUMO

BACKGROUND: The stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), threats world wheat production. Resistance to Pst is often overcome by pathogen virulence changes, but the mechanisms of variation are not clearly understood. To determine the role of mutation in Pst virulence changes, in previous studies 30 mutant isolates were developed from a least virulent isolate using ethyl methanesulfonate (EMS) mutagenesis and phenotyped for virulence changes. The progenitor isolate was sequenced, assembled and annotated for establishing a high-quality reference genome. In the present study, the 30 mutant isolates were sequenced and compared to the wide-type isolate to determine the genomic variation and identify candidates for avirulence (Avr) genes. RESULTS: The sequence reads of the 30 mutant isolates were mapped to the wild-type reference genome to identify genomic changes. After selecting EMS preferred mutations, 264,630 and 118,913 single nucleotide polymorphism (SNP) sites and 89,078 and 72,513 Indels (Insertion/deletion) were detected among the 30 mutant isolates compared to the primary scaffolds and haplotigs of the wild-type isolate, respectively. Deleterious variants including SNPs and Indels occurred in 1866 genes. Genome wide association analysis identified 754 genes associated with avirulence phenotypes. A total of 62 genes were found significantly associated to 16 avirulence genes after selection through six criteria for putative effectors and degree of association, including 48 genes encoding secreted proteins (SPs) and 14 non-SP genes but with high levels of association (P ≤ 0.001) to avirulence phenotypes. Eight of the SP genes were identified as avirulence-associated effectors with high-confidence as they met five or six criteria used to determine effectors. CONCLUSIONS: Genome sequence comparison of the mutant isolates with the progenitor isolate unraveled a large number of mutation sites along the genome and identified high-confidence effector genes as candidates for avirulence genes in Pst. Since the avirulence gene candidates were identified from associated SNPs and Indels caused by artificial mutagenesis, these avirulence gene candidates are valuable resources for elucidating the mechanisms of the pathogen pathogenicity, and will be studied to determine their functions in the interactions between the wheat host and the Pst pathogen.


Assuntos
Basidiomycota/patogenicidade , Mutação , Sequenciamento Completo do Genoma/métodos , Basidiomycota/genética , Basidiomycota/isolamento & purificação , Proteínas Fúngicas/genética , Sequenciamento de Nucleotídeos em Larga Escala , Mutação INDEL , Doenças das Plantas/microbiologia , Polimorfismo de Nucleotídeo Único , Triticum/microbiologia , Fatores de Virulência
7.
Appl Environ Microbiol ; 86(5)2020 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-31862727

RESUMO

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.


Assuntos
Agricultura/métodos , Microbiota , Rizosfera , Triticum/microbiologia , Geografia , Triticum/crescimento & desenvolvimento , Washington
8.
Phytopathology ; 109(9): 1509-1512, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31044663

RESUMO

Stripe rust caused by Puccinia striiformis is a disastrous disease of cereal crops and various grasses. To date, 14 stripe rust genomes are publicly available, including 13 P. striiformis f. sp. tritici and 1 P. striiformis f. sp. hordei. In this study, one isolate (11-281) of P. striiformis collected from wheatgrass (Agropyron cristatum), which is avirulent to most of standard differential genotypes of wheat and barley, was sequenced, assembled, and annotated. The sequences were assembled to a draft genome of 84.75 Mb, which is comparable with previously sequenced P. striiformis f. sp. tritici and P. striiformis f. sp. hordei isolates. The draft genome comprised 381 scaffolds and contained 1,829 predicted secreted proteins. The high-quality draft genome of the isolate is a valuable resource in shedding light on the evolution and pathogenicity of P. striiformis.


Assuntos
Agropyron , Basidiomycota , Basidiomycota/genética , Hordeum/microbiologia , Doenças das Plantas/microbiologia , Triticum/microbiologia
9.
Environ Toxicol Chem ; 38(6): 1364-1371, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30790346

RESUMO

Soil contamination by chlorophenol compounds, such as 2,4,6-trichlorophenol (2,4,6-TCP), is of great concern because they are environmentally persistent, are difficult to degrade, and can lead to cancer. Thus, means of degrading these compounds in situ are desperately needed. Biochar was investigated as a material to sequester, reduce downward transport, and aid in soil 2,4,6-TCP degradation. In 2 column studies, wheat straw (Triticum aestivum L.)-derived biochar (pyrolyzed at 450 °C) application to soil (up to 5% by wt) improved soil water and soil organic carbon content. Biochar reduced 2,4,6-TCP downward transport, likely attributable to improved soil water mobility and retention, allowing 2,4,6-TCP to be more easily transported and sorbed to organic functional groups on biochar, leading to enhanced degradation. The 2,4,6-TCP was rapidly degraded into a combination of benzene derivatives and low-molecular weight organic compounds in the first 2 mo following biochar application. The present study provides evidence that biochars can be used to improve environmental quality by lessening the downward transport and enhancing the degradation of organochlorine compounds such as 2,4,6-TCP. Environ Toxicol Chem 2019;38:1364-1371. © 2019 SETAC.


Assuntos
Carvão Vegetal/farmacologia , Clorofenóis/química , Poluentes do Solo/química , Solo/química , Poluição Ambiental/análise , Espectroscopia de Infravermelho com Transformada de Fourier , Triticum
10.
New Phytol ; 222(3): 1561-1572, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30623449

RESUMO

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.


Assuntos
Basidiomycota/metabolismo , Proteínas Fúngicas/metabolismo , Plantas/imunologia , Plantas/microbiologia , Interferência de RNA , Alelos , Arabidopsis/microbiologia , Basidiomycota/genética , Morte Celular , Regulação Fúngica da Expressão Gênica , Proteínas de Fluorescência Verde/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Plantas Geneticamente Modificadas , RNA de Plantas/metabolismo , Tabaco/microbiologia , Transgenes
11.
BMC Genomics ; 19(1): 664, 2018 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-30208837

RESUMO

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.


Assuntos
Adaptação Fisiológica/genética , Basidiomycota/genética , Basidiomycota/fisiologia , Genômica , Interações Hospedeiro-Patógeno/genética , Doenças das Plantas/microbiologia , Evolução Molecular , Hordeum/microbiologia , Sequências Repetitivas de Ácido Nucleico/genética , Telômero/genética , Triticum/microbiologia
12.
Methods Mol Biol ; 1848: 139-150, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30182235

RESUMO

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.


Assuntos
Basidiomycota/fisiologia , Inativação Gênica , Interações Hospedeiro-Patógeno/genética , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Triticum/genética , Triticum/microbiologia , Vetores Genéticos/genética , Fenótipo , Doenças das Plantas/virologia , Interferência de RNA , Transdução Genética , Triticum/virologia
13.
Mol Plant Microbe Interact ; 31(11): 1117-1120, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-29792772

RESUMO

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.


Assuntos
Basidiomycota/genética , Genoma Fúngico/genética , Genômica , Hordeum/microbiologia , Doenças das Plantas/microbiologia , Triticum/microbiologia , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Fenótipo , Análise de Sequência de RNA
14.
Microb Ecol ; 76(1): 240-257, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29218372

RESUMO

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.


Assuntos
Redes Comunitárias , Glicina/análogos & derivados , Herbicidas/efeitos adversos , Micobioma/efeitos dos fármacos , Raízes de Plantas/microbiologia , Microbiologia do Solo , Triticum/microbiologia , Agricultura , Biodiversidade , DNA Fúngico/análise , Fungos/classificação , Fungos/efeitos dos fármacos , Fungos/genética , Glicina/efeitos adversos , Micobioma/genética , Rizosfera , Análise de Sequência de DNA , Solo/química , Washington
15.
Entropy (Basel) ; 20(12)2018 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-33266706

RESUMO

In 1923, Hadamard encountered a class of integrals with strong singularities when using a particular Green's function to solve the cylindrical wave equation. He ignored the infinite parts of such integrals after integrating by parts. Such an idea is very practical and useful in many physical models, e.g., the crack problems of both planar and three-dimensional elasticities. In this paper, we present the rectangular and trapezoidal formulas to approximate the Hadamard derivative by the idea of the finite part integral. Then, we apply the proposed numerical methods to the differential equation with the Hadamard derivative. Finally, several numerical examples are displayed to show the effectiveness of the basic idea and technique.

16.
Appl Environ Microbiol ; 83(22)2017 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-28864656

RESUMO

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.


Assuntos
Bactérias/efeitos dos fármacos , Glicina/análogos & derivados , Herbicidas/farmacologia , Triticum/microbiologia , Agricultura , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Glicina/farmacologia , Raízes de Plantas/microbiologia , Microbiologia do Solo , Triticum/efeitos dos fármacos
17.
PLoS One ; 12(9): e0184611, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28898288

RESUMO

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.


Assuntos
Produção Agrícola/métodos , Fungos/patogenicidade , Microbiota , Triticum/microbiologia , Adaptação Fisiológica , Secas , Fungos/classificação , Fungos/isolamento & purificação , Interações Hospedeiro-Patógeno
18.
Front Plant Sci ; 8: 132, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28243246

RESUMO

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.

19.
G3 (Bethesda) ; 7(2): 361-376, 2017 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-27913634

RESUMO

Three members of the Puccinia genus, Pucciniatriticina (Pt), Pstriiformis f.sp. tritici (Pst), and Pgraminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS) of the HD and STE3 alleles reduced wheat host infection.


Assuntos
Basidiomycota/genética , Genoma Fúngico , Análise de Sequência de DNA , Triticum/microbiologia , Basidiomycota/patogenicidade , Genes Fúngicos Tipo Acasalamento/genética , Estágios do Ciclo de Vida/genética , Anotação de Sequência Molecular , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Polimorfismo de Nucleotídeo Único , Receptores de Feromônios/genética , Triticum/genética , Triticum/crescimento & desenvolvimento
20.
Phytopathology ; 107(1): 75-83, 2017 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-27503371

RESUMO

Fungi that cause cereal rust diseases (genus Puccinia) are important pathogens of wheat globally. Upon infection, the fungus secretes a number of effector proteins. Although a large repository of putative effectors has been predicted using bioinformatic pipelines, the lack of available high-throughput effector screening systems has limited functional studies on these proteins. In this study, we mined the available transcriptomes of Puccinia graminis and P. striiformis to look for potential effectors that suppress host hypersensitive response (HR). Twenty small (<300 amino acids), secreted proteins, with no predicted functions were selected for the HR suppression assay using Nicotiana benthamiana, in which each of the proteins were transiently expressed and evaluated for their ability to suppress HR caused by four cytotoxic effector-R gene combinations (Cp/Rx, ATR13/RPP13, Rpt2/RPS-2, and GPA/RBP-1) and one mutated R gene-Pto(Y207D). Nine out of twenty proteins, designated Shr1 to Shr9 (suppressors of hypersensitive response), were found to suppress HR in N. benthamiana. These effectors varied in the effector-R gene defenses they suppressed, indicating these pathogens can interfere with a variety of host defense pathways. In addition to HR suppression, effector Shr7 also suppressed PAMP-triggered immune response triggered by flg22. Finally, delivery of Shr7 through Pseudomonas fluorescens EtHAn suppressed nonspecific HR induced by Pseudomonas syringae DC3000 in wheat, confirming its activity in a homologous system. Overall, this study provides the first evidence for the presence of effectors in Puccinia species suppressing multiple plant defense responses.


Assuntos
Proteínas de Bactérias/metabolismo , Basidiomycota/genética , Interações Hospedeiro-Patógeno , Doenças das Plantas/imunologia , Imunidade Vegetal , Triticum/imunologia , Proteínas de Bactérias/genética , Basidiomycota/fisiologia , Morte Celular , Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes Supressores , Hipersensibilidade , Doenças das Plantas/microbiologia , Folhas de Planta/genética , Folhas de Planta/imunologia , Folhas de Planta/microbiologia , Plantas Geneticamente Modificadas , Pseudomonas fluorescens/genética , Pseudomonas fluorescens/fisiologia , Espécies Reativas de Oxigênio/metabolismo , Tabaco/genética , Tabaco/imunologia , Tabaco/microbiologia , Transcriptoma , Triticum/genética , Triticum/microbiologia
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