Relatedness of Macrophomina phaseolina isolates from tallgrass prairie, maize, soybean and sorghum

Confronting stresses affecting olive cultivation from the holobiont perspective

The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.

Molecular interactions between the soilborne pathogenic fungus Macrophomina phaseolina and its host plants

Mentioned for the first time in an article 1971, the occurrence of the term "Macrophomina phaseolina" has experienced a steep increase in the scientific literature over the past 15 years. Concurrently, incidences of M. phaseolina-caused crop diseases have been getting more frequent. The high levels of diversity and plasticity observed for M. phasolina genomes along with a rich equipment of plant cell wall degrading enzymes, secondary metabolites and putative virulence effectors as well as the unusual longevity of microsclerotia, their asexual reproduction structures, make this pathogen very difficult to control and crop protection against it very challenging. During the past years several studies have emerged reporting on host defense measures against M. phaseolina, as well as mechanisms of pathogenicity employed by this fungal pathogen. While most of these studies have been performed in crop systems, such as soybean or sesame, recently interactions of M. phaseolina with the model plant Arabidopsis thaliana have been described. Collectively, results from various studies are hinting at a complex infection cycle of M. phaseolina, which exhibits an early biotrophic phase and switches to necrotrophy at later time points during the infection process. Consequently, responses of the hosts are complex and seem coordinated by multiple defense-associated phytohormones. However, at this point no robust and strong host defense mechanism against M. phaseolina has been described.

Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia

Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.

Evaluating the Role of Exogenously Applied Ascorbic Acid in Rescuing Soybean Plant Health in The Presence of Pathogen-Induced Oxidative Stress

Charcoal rot, caused by the soilborne hemibiotrophic fungus Macrophomina phaseolina, is a prevalent and economically significant plant disease. It is hypothesized that M. phaseolina induces oxidative stress-mediated senescence in plants. Infection by M. phaseolina results in the host’s accumulation of reactive oxygen species (ROS) that contribute toward basal defense. However, the production of ROS could also lead to cellular damage and senescence in host tissue. This study aimed to determine if ascorbic acid, a ROS scavenging molecule, could quench M. phaseolina-induced hydrogen peroxide (H₂O₂) generation in a soybean-M. phaseolina pathosystem. In vitro sensitivity tests showed that M. phaseolina isolates were sensitive to L-ascorbic acid (LAA) at concentrations of 10.5 to 14.3 mM based on IC₅₀ (half-maximal inhibitory concentration) data. In planta cut-stem assays demonstrated that pre-treatment with 10 mM of either LAA (reduced form) or DHAA (dehydroascorbic acid; oxidized form) significantly decreased lesion length compared to the non-pretreated control and post-treatments with both ascorbic acid forms after M. phaseolina inoculation. Further, H₂O₂ quantification from ascorbic acid-pretreated tissue followed by M. phaseolina inoculation showed significantly less accumulation of H₂O₂ than the inoculated control or the mock-inoculated control. This result demonstrated that M. phaseolina not only induced H₂O₂ after host infection but also increased ROS-mediated senescence. This study shows the potential of ascorbic acid, an effective ROS scavenger, to limit ROS-mediated senescence associated with M. phaseolina infection.

Phenotypic Variability and Genetic Diversity of the Pathogenic Fungus Macrophomina phaseolina from Several Hosts and Host Specialization in Strawberry

Macrophomina phaseolina, is a pathogenic soil-borne fungus that affects more than 500 plant species, causing various types of disease to several crops, among which is the crown and root rot disease in strawberry. Its wide variability has been characterized reiteratively in the literature, but little is known about its virulence mechanisms. Morphological, physiological, genetic and phytopathogenic parameters were evaluated among 32 isolates of Macrophomina from different hosts occurring in Argentina and Spain. Colony characteristics, average size of microsclerotia, chlorate phenotype and mycelial growth at different temperatures (5º-40 °C), and pH (3.0-8.0) were recorded. The morphological and physiological traits were heterogeneous and did not show any association with the genetic structure nor with their pathogenicity. Most of the isolates (71.9%) exhibited chlorate-sensitive phenotype. The optimal growth temperature range was between 25 °C and 35 °C, and the optimal pH varied between 4.0 and 6.0. The genetic structure analyzed with four DNA markers (EF-1α, ITS, CAL and TUB) showed little diversity among isolates of M. phaseolina, with no clear association with the country of origin, but a significant association with the host. Based on their phylogenetic affinity, one isolate was reclassified as M. pseudophaseolina and another one as M. tecta. It is the first report of M. pseudophaseolina causing charcoal rot on beans, in Argentina, and the first report of M. tecta outside Australia. Pathogenicity tests on strawberry plants revealed marked host specialization, being the isolates obtained from strawberry more virulent than those from other hosts.

Occurrence of Macrophomina phaseolina in Israel: Challenges for Disease Management and Crop Germplasm Enhancement

Macrophomina phaseolina is a soil-borne fungal pathogen infecting many important crop plants. The fungus, which can survive on crop debris for a long period of time, causes charcoal rot disease by secreting a diverse array of cell-wall degrading enzymes and toxins. M. phaseolina thrives during periods of high temperatures and arid conditions, as typically occur in Israel and other countries with a Mediterranean climate. Crop losses due to charcoal rot can be expected to increase and spread to other countries in a warming global climate. Management of this pathogen is challenging, requiring an array of approaches for the various crop hosts. Approaches that have had some success in Israel include grafting of melons and watermelons on resistant squash rootstocks and soil application of fungicide to reduce disease incidence in melons, fumigation and alterations in planting date and mulching of strawberries, and alteration in irrigation regime of cotton. Elsewhere, these approaches, as well as soil amendments and addition of organisms that are antagonistic to M. phaseolina, have had success in some crop situations. Management through host resistance would be the most sustainable approach, but it requires identifying a resistant germplasm for each crop and introgressing the resistance into the leading cultivars. Resistance to charcoal rot is under complex genetic control in most crops, posing a great challenge for its introgression into elite germplasm. Moreover, fast, reliable methods of screening for resistance would have to be developed for each crop. The toothpick-inoculation method used by us holds great promise for selecting resistant germplasm for melons and possibly for sesame, but other methodologies have to be devised for each individual crop.

A novel Arabidopsis pathosystem reveals cooperation of multiple hormonal response-pathways in host resistance against the global crop destroyer Macrophomina phaseolina

Dubbed as a "global destroyer of crops", the soil-borne fungus Macrophomina phaseolina (Mp) infects more than 500 plant species including many economically important cash crops. Host defenses against infection by this pathogen are poorly understood. We established interactions between Mp and Arabidopsis thaliana (Arabidopsis) as a model system to quantitatively assess host factors affecting the outcome of Mp infections. Using agar plate-based infection assays with different Arabidopsis genotypes, we found signaling mechanisms dependent on the plant hormones ethylene, jasmonic acid and salicylic acid to control host defense against this pathogen. By profiling host transcripts in Mp-infected roots of the wild-type Arabidopsis accession Col-0 and ein2/jar1, an ethylene/jasmonic acid-signaling deficient mutant that exhibits enhanced susceptibility to this pathogen, we identified hundreds of genes potentially contributing to a diverse array of defense responses, which seem coordinated by complex interplay between multiple hormonal response-pathways. Our results establish Mp/Arabidopsis interactions as a useful model pathosystem, allowing for application of the vast genomics-related resources of this versatile model plant to the systematic investigation of previously understudied host defenses against a major crop plant pathogen.

Soybean-Macrophomina phaseolina-Specific Interactions and Identification of a Novel Source of Resistance

Charcoal rot, caused by the fungus Macrophomina phaseolina, is an economically important disease of soybean (Glycine max) worldwide. Objectives of the present research were to (i) study the genetic and pathogenic diversity in a collection of M. phaseolina isolates from Argentina and Paraguay and (ii) develop an improved in vitro phenotyping method to evaluate disease response of soybean genotypes to M. phaseolina isolates. Cluster analysis showed no clear association among simple sequence repeat profiles, year of collection, pathogenicity, and geographical origin of the isolates from Argentina and Paraguay. Subsequently, the response of four soybean genotypes against seven M. phaseolina isolates was evaluated in the field and the results were confirmed using the in vitro assay developed. This assay, which is based on root disease development on soybean seedlings, allowed the detection of a differential level of aggressiveness among the isolates on four soybean genotypes. The results suggest the existence of specific interactions among soybean genotypes and M. phaseolina isolates. In addition, cultivar Munasqa RR showed a superior response against M. phaseolina compared with DT 97-4290 (moderately resistant), thus becoming a novel source of resistance to charcoal rot.

Development of a rapid PCR-Nucleic Acid Lateral Flow Immunoassay (PCR-NALFIA) based on rDNA IGS sequence analysis for the detection of Macrophomina phaseolina in soil

The 'Nucleic Acid Lateral Flow Immunoassay' (NALFIA) using a generic 'Lateral Flow Device' (LFD), combined with PCR employing labelled primers (PCR-NALFIA), enables to circumvent the use of electrophoresis, making the diagnostic procedure more rapid and easier. If the specific amplicon is present in the sample, a coloured band, with an intensity proportional to the amplicon concentration, will develop on the LFD strip in addition to the control band. Species-specific primers for M. phaseolina based on the rDNA intergenic spacer (IGS) were developed and their specificity was checked and confirmed using 20 isolates of M. phaseolina and other 16 non-target fungi. A DNA extraction protocol based on a bead-beating technique using silica beads, skimmed milk and PVP was also developed. The M. phaseolina specific primers MP102F/MP102R, 5' labelled with biotin and FITC respectively, were used in the PCR-NALFIA assay to identify the pathogen starting from mycelium or microsclerotia. Microsclerotia of M. phaseolina (1, 10, 100 and 200) were manipulated under a stereomicroscope and their DNA was extracted using microsclerotia alone or mixed with different types of soil. The resulting DNA, used for the PCR-NALFIA assay, provided positive results for all the samples tested. A semi-quantitative grey-scale reference card based on the PCR-NALFIA assay using intervals corresponding to microsclerotia soil number was developed. For this purpose, the normalized pixel grey volumes obtained after a densitometric analysis of the test line intensity generated by the LFD dipsticks were used.

Identification of charcoal rot resistance QTLs in sorghum using association and in silico analyses

Charcoal rot disease, a root and stem disease caused by the soil-borne fungus Macrophomina phaseolina (Tassi) Goid., is a major biotic stress that limits sorghum productivity worldwide. Charcoal rot resistance-related parameters, e.g., pre-emergence damping-off%, post-emergence damping-off%, charcoal rot disease severity, and plant survival rates, were measured in a structured sorghum population consisting of 107 landraces. Analysis of variance of charcoal rot resistance-related parameters revealed significant variations in the response to M. phaseolina infection within evaluated accessions. Continuous phenotypic variations for resistance-related parameters were observed indicating a quantitative inheritance of resistance. The population was genotyped using 181 simple sequence repeat (SSR) markers. Association analysis identified 13 markers significantly associated with quantitative trait genes (QTLs) conferring resistance to charcoal rot disease with an R² value ranging between 9.47 to 18.87%, nine of which are environment-specific loci. Several QTL-linked markers are significantly associated with more than one resistance-related parameter, suggesting that those QTLs might contain genes involved in the plant defense response. In silico analysis of four novel major QTLs identified 11 putative gene homologs that could be considered as candidate genes for resistance against charcoal rot disease. Cluster analysis using the genotypic data of 181 SSR markers from 107 sorghum accessions identified 12 main clusters. The results provide a basis for further functional characterization of charcoal rot disease resistance or defense genes in sorghum and for further dissection of their molecular mechanisms.

Molecular Identification and Genetic Characterization of Macrophomina phaseolina Strains Causing Pathogenicity on Sunflower and Chickpea

Macrophomina phaseolina is the most devastating pathogen which causes charcoal rot and root rot diseases in various economically important crops. Three strains M. phaseolina 1156, M. phaseolina 1160, and M. phaseolina PCMC/F1 were tested for their virulence on sunflower (Helianthus annuus L.) and chickpea (Cicer arietinum L.). The strains showed high virulence on both hosts with a disease score of 2 on chickpea and sunflower. The strains also increased the hydrogen per oxide (H2O2) content by 1.4- to 1.6-fold in root as well as shoot of chickpea and sunflower. A significant increase in antioxidant enzymes was observed in fungal infected plants which indicated prevalence of oxidative stress during pathogen propagation. The M. phaseolina strains also produced hydrolytic enzymes such as lipase, amylase, and protease with solubilization zone of 5-43 mm, 5-45 mm, and 12-35 mm, respectively. The M. phaseolina strains were identified by 18S rRNA and analyzed for genetic diversity by using random amplified polymorphic DNA (RAPD) markers. The findings based on RAPD markers and 18S rRNA sequence analysis clearly indicate genetic variation among the strains collected from different hosts. The genetically diverse strains were found to be pathogenic to sunflower and chickpea.

Kenyan Isolates of Puccinia graminis f. sp. tritici from 2008 to 2014: Virulence to SrTmp in the Ug99 Race Group and Implications for Breeding Programs

Frequent emergence of new variants in the Puccinia graminis f. sp. tritici Ug99 race group in Kenya has made pathogen survey a priority. We analyzed 140 isolates from 78 P. graminis f. sp. tritici samples collected in Kenya between 2008 and 2014 and identified six races, including three not detected prior to 2013. Genotypic analysis of 20 isolates from 2013 and 2014 collections showed that the new races TTHST, TTKTK, and TTKTT belong to the Ug99 race group. International advanced breeding lines were evaluated against an isolate of TTKTT (Sr31, Sr24, and SrTmp virulence) at the seedling stage. From 169 advanced lines from Kenya, 23% of lines with resistance to races TTKSK and TTKST were susceptible to TTKTT and, from two North American regional nurseries, 44 and 91% of resistant lines were susceptible. Three lines with combined resistance genes were developed to facilitate pathogen monitoring and race identification. These results indicate the increasing virulence and variability in the Kenyan P. graminis f. sp. tritici population and reveal vulnerabilities of elite germplasm to new races.

Response of Sweet Sorghum Lines to Stalk Pathogens Fusarium thapsinum and Macrophomina phaseolina

Sweet sorghum (Sorghum bicolor (L.) Moench) has potential for bioenergy. It is adapted to a variety of U.S. locations and the extracted juice can be directly fermented into ethanol. However, little research on fungal stalk rots, diseases that pose serious constraints for yield and quality of juice and biomass, has been reported. A greenhouse bioassay was designed to assess charcoal rot (Macrophomina phaseolina) and Fusarium stalk rot (Fusarium thapsinum) in plants at maturity, the developmental stage at which these diseases are manifested. Multiple plantings of a susceptible grain line, RTx430, were used as a control for variation in flowering times among sweet sorghum lines. Lesion length measurements in inoculated peduncles were used to quantify disease severity. Sweet sorghum lines 'Rio' and 'M81E' exhibited resistance to F. thapsinum and M. phaseolina, respectively; and, in contrast, 'Colman' sorghum exhibited susceptibility to both pathogens. Lesion development over time in Colman was monitored. These results will enhance molecular and biochemical analyses of responses to pathogens, and breeding stalk-rot-resistant sweet sorghum lines.

History, Epidemic Evolution, and Model Burn-In for a Network of Annual Invasion: Soybean Rust

Ecological history may be an important driver of epidemics and disease emergence. We evaluated the role of history and two related concepts, the evolution of epidemics and the burn-in period required for fitting a model to epidemic observations, for the U.S. soybean rust epidemic (caused by Phakopsora pachyrhizi). This disease allows evaluation of replicate epidemics because the pathogen reinvades the United States each year. We used a new maximum likelihood estimation approach for fitting the network model based on observed U.S. epidemics. We evaluated the model burn-in period by comparing model fit based on each combination of other years of observation. When the miss error rates were weighted by 0.9 and false alarm error rates by 0.1, the mean error rate did decline, for most years, as more years were used to construct models. Models based on observations in years closer in time to the season being estimated gave lower miss error rates for later epidemic years. The weighted mean error rate was lower in backcasting than in forecasting, reflecting how the epidemic had evolved. Ongoing epidemic evolution, and potential model failure, can occur because of changes in climate, host resistance and spatial patterns, or pathogen evolution.

Identifying highly connected counties compensates for resource limitations when evaluating national spread of an invasive pathogen

Surveying invasive species can be highly resource intensive, yet near-real-time evaluations of invasion progress are important resources for management planning. In the case of the soybean rust invasion of the United States, a linked monitoring, prediction, and communication network saved U.S. soybean growers approximately $200 M/yr. Modeling of future movement of the pathogen (Phakopsora pachyrhizi) was based on data about current disease locations from an extensive network of sentinel plots. We developed a dynamic network model for U.S. soybean rust epidemics, with counties as nodes and link weights a function of host hectarage and wind speed and direction. We used the network model to compare four strategies for selecting an optimal subset of sentinel plots, listed here in order of increasing performance: random selection, zonal selection (based on more heavily weighting regions nearer the south, where the pathogen overwinters), frequency-based selection (based on how frequently the county had been infected in the past), and frequency-based selection weighted by the node strength of the sentinel plot in the network model. When dynamic network properties such as node strength are characterized for invasive species, this information can be used to reduce the resources necessary to survey and predict invasion progress.

Bridging taxonomic and disciplinary divides in infectious disease

Pathogens traverse disciplinary and taxonomic boundaries, yet infectious disease research occurs in many separate disciplines including plant pathology, veterinary and human medicine, and ecological and evolutionary sciences. These disciplines have different traditions, goals, and terminology, creating gaps in communication. Bridging these disciplinary and taxonomic gaps promises novel insights and important synergistic advances in control of infectious disease. An approach integrated across the plant-animal divide would advance our understanding of disease by quantifying critical processes including transmission, community interactions, pathogen evolution, and complexity at multiple spatial and temporal scales. These advances require more substantial investment in basic disease research.

Genetic diversity and effect of temperature and pH on the growth of Macrophomina phaseolina isolates from sunflower fields in Hungary

The effects of temperature and pH on the growth of 45 Hungarian Macrophomina phaseolina isolates from different locations and hosts were compared on the basis of their genetic diversity. One Spanish and two Serbian isolates were also included in the experiment. The most favourable temperature regimes for the development of the isolates ranged between 25 and 35 °C. The optimal pH for the pathogen varied between 4.0 and 6.0, but growth was observed on potato dextrose agar even at pH values of 3.0, 7.0 and 8.0. RAPD analysis with 13 different primer pairs generated 148 unambiguous bands. RFLP analysis involving 8 different restriction endonucleases was performed on a 1550 bp fragment of the rDNA region containing internal transcribed spacers (ITS1, ITS2), the 5.8S rDNA and part of the 25S rDNA. The greatest genetic distance values were obtained for three isolates, two from Hungary and one from Spain, which had similar values, but were quite distinct from all the others. A strong positive correlation was observed between the genetic distances and the growth parameters measured at various temperatures, and between the geographical data and the growth data sets at different pH values, but the correlation was less strong in the latter case. While Hungarian M. phaseolina populations are thought to reproduce clonally, the present results indicate the coexistence of different haplotypes in this area, and besides the geographical dominance of a given haplotype it was found that a closer genetic relationship might exist between spatially distinct haplotypes.

Genomic and resistance gene homolog diversity of the dominant tallgrass prairie species across the U.S. Great Plains precipitation gradient

BACKGROUND

Environmental variables such as moisture availability are often important in determining species prevalence and intraspecific diversity. The population genetic structure of dominant plant species in response to a cline of these variables has rarely been addressed. We evaluated the spatial genetic structure and diversity of Andropogon gerardii populations across the U.S. Great Plains precipitation gradient, ranging from approximately 48 cm/year to 105 cm/year.

METHODOLOGY/PRINCIPAL FINDINGS

Genomic diversity was evaluated with AFLP markers and diversity of a disease resistance gene homolog was evaluated by PCR-amplification and digestion with restriction enzymes. We determined the degree of spatial genetic structure using Mantel tests. Genomic and resistance gene homolog diversity were evaluated across prairies using Shannon's index and by averaging haplotype dissimilarity. Trends in diversity across prairies were determined using linear regression of diversity on average precipitation for each prairie. We identified significant spatial genetic structure, with genomic similarity decreasing as a function of distance between samples. However, our data indicated that genome-wide diversity did not vary consistently across the precipitation gradient. In contrast, we found that disease resistance gene homolog diversity was positively correlated with precipitation.

SIGNIFICANCE

Prairie remnants differ in the genetic resources they maintain. Selection and evolution in this disease resistance homolog is environmentally dependent. Overall, we found that, though this environmental gradient may not predict genomic diversity, individual traits such as disease resistance genes may vary significantly.

Maladaptation in wild populations of the generalist plant pathogen Pseudomonas syringae

Multihost pathogens occur widely on both natural and agriculturally managed hosts. Despite the importance of such generalists, evolutionary studies of host-pathogen interactions have largely focused on tightly coupled interactions between species pairs. We characterized resistance in a collection of Arabidopsis thaliana hosts, including 24 accessions collected from the Midwest USA and 24 from around the world, and patterns of virulence in a collection of Pseudomonas syringae strains, including 24 strains collected from wild Midwest populations of A. thaliana (residents) and 18 from an array of cultivated species (nonresidents). All of the nonresident strains and half of the resident strains elicited a resistance response on one or more A. thaliana accessions. The resident strains that failed to elicit any resistance response possessed an alternative type III secretion system (T3SS) that is unable to deliver effectors into plant host cells; as a result, these seemingly nonpathogenic strains are incapable of engaging in gene for gene interactions with A. thaliana. The remaining resident strains triggered greater resistance compared to nonresident strains, consistent with maladaptation of the resident bacterial population. We weigh the plausibility of two explanations: general maladaptation of pathogen strains and a more novel hypothesis whereby community level epidemiological dynamics result in adaptive dynamics favoring ephemeral hosts like A. thaliana.