Ganoderma lucidum: Insights on host range, diagnosis, and management strategies

Forest ecosystems play an important role in upholding life on our planet. However, the onslaught of fungal pathogens like Ganoderma lucidum, poses a threat by decimating numerous tree species. G. lucidum identified as a root pathogen, causing root rot in numerous tree species of horticulture and forestry importance. The fungus initiates infection through basidiospores, which germinate and penetrate within roots and start to degrade lignocellulosic components of plant cells. Early-stage detection of G. lucidum, is challenging, while in advance stages, the wood undergoes softening and a loss of tensile strength, rendering the disease incurable. Hence, effective management of G. lucidum necessitates a pivotal role of disease diagnostic techniques, which are currently underutilized or inadequately accessible. Subsequent implementation of suitable control measures becomes imperative to thwart disease occurrence and mitigate its impact in early stages, thus preserving the vitality of forest ecosystems. This study provides comprehensive overview of G. lucidum, covering taxonomy, pathogenicity, disease cycle, diagnosis and effective control measures, which will be helpful in formulating effective diagnostic techniques for early management of root rot disease.

Diagnosis of Soybean Diseases Caused by Fungal and Oomycete Pathogens: Existing Methods and New Developments

Soybean (Glycine max) acreage is increasing dramatically, together with the use of soybean as a source of vegetable protein and oil. However, soybean production is affected by several diseases, especially diseases caused by fungal seed-borne pathogens. As infected seeds often appear symptomless, diagnosis by applying accurate detection techniques is essential to prevent propagation of pathogens. Seed incubation on culture media is the traditional method to detect such pathogens. This method is simple, but fungi have to develop axenically and expert mycologists are required for species identification. Even experts may not be able to provide reliable type level identification because of close similarities between species. Other pathogens are soil-borne. Here, traditional methods for detection and identification pose even greater problems. Recently, molecular methods, based on analyzing DNA, have been developed for sensitive and specific identification. Here, we provide an overview of available molecular assays to identify species of the genera Diaporthe, Sclerotinia, Colletotrichum, Fusarium, Cercospora, Septoria, Macrophomina, Phialophora, Rhizoctonia, Phakopsora, Phytophthora, and Pythium, causing soybean diseases. We also describe the basic steps in establishing PCR-based detection methods, and we discuss potentials and challenges in using such assays.

Development of PCR-based assays to diagnose the major fungal pathogens infecting pulse crops, potential for germplasm health certification and quarantine processing

Plant diseases cause serious economic losses of agriculture production worldwide. Rapid, accurate and reliable diagnostic methods are required to alleviate the detection of fungal plant pathogens to prevent their spread and achieve effective management. This study was aimed to develop fast, reliable and highly sensitive diagnostics to detect fungal plant pathogens for quarantine processing, safe exchange and conservation of germplasms of pulse crops. Multiplex and real time PCR assays were developed for detection of Rhizoctonia solani, Macrophomina phaseolina, Ascochyta rabiei, Alternaria alternata, A. tenuissima, Fusarium oxysporum f. sp. ciceris, Sclerotium (Athelia) rolfsii, Sclerotinia sclerotiorum, Pseudocercospora cruenta and Cercospora canescens causing various diseases in pulse crops. Twenty-two sets of primers from various genomic regions such as cytochrome oxidase subunit (COX 1), internal transcribed spacer region (ITS), translation elongation factor-1 alpha (TEF-1α), large subunit (LSU), small subunit (SSU) and β-tubulin as well as two SCAR primers from RAPD profile were designed. The developed markers proved to be species-specific and validated against other fungal plant pathogens associated with pulses for cross-reactivity. The markers proved highly sensitive during conventional and qPCR analysis. Duplex PCR assays for R. solani and M. phaseolina; C. canescens and P. cruenta; A. alternata and A. tenuissima; and a quadruplex PCR assay for A. rabiei, S. sclerotiorum, S. rolfsii and F. oxysporum f. sp. ciceris were developed and validated for simultaneous detection of these pathogens in a single reaction. The assays developed in the present study were able to detect and identify major fungal plant pathogens causing disease in pulse crops.

Development of a Multiplex High-Throughput Diagnostic Assay for the Detection of Strawberry Crown Rot Diseases Using High-Resolution Melting Analysis

Rapid and accurate disease diagnosis is a prerequisite for an effective disease management program in strawberry production. In Florida, Colletotrichum spp., Phytophthora spp., and Macrophomina phaseolina are the primary microorganisms causing strawberry crown rot. Even though the diseases can be caused by different pathogens, symptoms are indistinguishable and equally devastating. To inform strawberry growers in a timely fashion of diagnostic results for effective deployment of chemical control practices, we developed a multiplex high-resolution melting (HRM) assay to rapidly and accurately detect the abovementioned pathogens. The multiplex HRM assays using three predesigned primer pairs showed high specificity for individual species by generating specific melting peaks without cross-reaction between primers or with other common strawberry pathogens. The amplification limit of the assay was 1 pg of Colletotrichum and Phytophthora and 100 pg of M. phaseolina DNA per 10-μl reaction. However, the presence of different melting peaks was observed in mixed DNA samples and was concentration and target DNA dependent. A crude DNA extraction protocol was developed to allow high-throughput screening by minimizing the inhibitory effects. Moreover, we applied the HRM assay to 522 plant samples and found high correlations between conventional pathogen isolation and HRM and between singleplex and multiplex assays. Altogether, this multiplex HRM assay is specific, cost effective, and reliable for the timely detection of strawberry crown rot pathogens.

Macrophomina phaseolina : General Characteristics of Pathogenicity and Methods of Control

Macrophomina phaseolina is a generalist soil-borne fungus present all over the world. It cause diseases such as stem and root rot, charcoal rot and seedling blight. Under high temperatures and low soil moisture, this fungus can cause substantial yield losses in crops such as soybean, sorghum and groundnut. The wide host range and high persistence of M. phaseolina in soil as microsclerotia make disease control challenging. Therefore, understanding the basis of the pathogenicity mechanisms as well as its interactions with host plants is crucial for controlling the pathogen. In this work, we aim to describe the general characteristics and pathogenicity mechanisms of M. phaseolina, as well as the hosts defense response. We also review the current methods and most promising forecoming ones to reach a responsible control of the pathogen, with minimal impacts to the environment and natural resources.

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.

Macrophomina phaseolina: an overlooked cutaneous infection, seed rot disease in humans

Rare and emerging opportunistic fungal pathogens are a serious and growing concern for immunosuppressed patients. Macrophomina phaseolina, an important soilborne plant pathogen in tropical and subtropical soil, should be considered in this category. It may be evident as a localized cutaneous cellulitis or as an ocular keratitis. We describe a 42-year-old diabetic male originally from India in whom a soft tissue mass of the foot proved to be an M. phaseolina cellulitis and review the literature. To our knowledge, only four individuals have been documented with infections with this organism, three of whom were immunocompromised.

Development of Molecular Methods to Detect Macrophomina phaseolina from Strawberry Plants and Soil

Macrophomina phaseolina is a broad-host-range fungus that shows some degree of host preference on strawberry, and causes symptoms that include crown rot and root rot. Recently, this pathogen has affected strawberry production as fumigation practices have changed, leaving many growers in California and around the world in need of accurate, rapid diagnostic tools for M. phaseolina in soil and infected plants. This study uses next-generation sequencing and comparative genomics to identify a locus that is unique to isolates within a main genotype shared by a majority of isolates that infect strawberry. This locus was used to develop a quantitative single-tube nested TaqMan polymerase chain reaction assay which is able to quantify as little as 2 to 3 microsclerotia/g of soil with 100% genotype specificity. An isothermal assay using recombinase polymerase amplification was developed from the same locus and has been validated on over 200 infected strawberry plants with a diagnostic sensitivity of 93% and a diagnostic specificity of 99%. Together, this work demonstrates the value of using new approaches to identify loci for detection and provides valuable diagnostic tools that can be used to monitor soil and strawberry plant samples for M. phaseolina.

Transcriptional Changes in Mycorrhizal and Nonmycorrhizal Soybean Plants upon Infection with the Fungal Pathogen Macrophomina phaseolina

Macrophomina phaseolina is a soil-borne fungal pathogen with a wide host range that causes charcoal rot in soybean [Glycine max (L.) Merr.]. Control of the disease is a challenge, due to the absence of genetic resistance and effective chemical control. Alternative or complementary measures are needed, such as the use of biological control agents, in an integrated approach. Several studies have demonstrated the role of arbuscular mycorrhizal fungi (AMF) in enhancing plant resistance or tolerance to biotic stresses, decreasing the symptoms and pressure caused by various pests and diseases, including M. phaseolina in soybean. However, the specific contribution of AMF in the regulation of the plant response to M. phaseolina remains unclear. Therefore, the objective of the present study was to investigate, under strict in-vitro culture conditions, the global transcriptional changes in roots of premycorrhized soybean plantlets challenged by M. phaseolina (+AMF+Mp) as compared with nonmycorrhizal soybean plantlets (-AMF+Mp). MapMan software was used to distinguish transcriptional changes, with special emphasis on those related to plant defense responses. Soybean genes identified as strongly upregulated during infection by the pathogen included pathogenesis-related proteins, disease-resistance proteins, transcription factors, and secondary metabolism-related genes, as well as those encoding for signaling hormones. Remarkably, the +AMF+Mp treatment displayed a lower number of upregulated genes as compared with the -AMF+Mp treatment. AMF seemed to counteract or balance costs upon M. phaseolina infection, which could be associated to a negative impact on biomass and seed production. These detailed insights in soybean-AMF interaction help us to understand the complex underlying mechanisms involved in AMF-mediated biocontrol and support the importance of preserving and stimulating the existing plant-AMF associates, via adequate agricultural practices, to optimize their agro-ecological potential.

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.

Use of electrical penetration graphs (EPG) and quantitative PCR to evaluate the relationship between feeding behaviour and Pandora neoaphidis infection levels in green peach aphid, Myzus persicae

A real-time qPCR method was developed, validated, and used to quantity the fungal pathogen, P. neoaphidis, within aphids at different times during infection; colonization rate fitted the Gompertz model well (R² = 0.9356). Feeding behaviour of P. neoaphidis-infected and uninfected M. persicae were investigated, for the first time, using DC-electrical penetration graphs (DC-EPG) that characterized the waveforms made during different aphid stylet probing periods corresponding to epidermis penetration, salivation and ingestion. In the 6 h following the 12-h incubation period (to achieve infection), there were significant differences in the number of events of Np (non-probing) and C (stylet pathway) between infected and uninfected aphids. However, the difference between total duration of Np and C were not significantly different between infected and uninfected aphids. There were no significant differences in the number of events or total duration of E1 (phloem salivation) or E2 (phloem ingestion) between infected and uninfected aphids. There were significant differences in mean number of events and total duration of the pd waveform (intracellular punctures) in infected and uninfected aphids. In the 16 h prior to death, the same differences in behaviour were observed but they were even more obvious. Furthermore, the total duration time of E2 was significantly greater in uninfected aphids than infected aphids, a change that had not been observed in the first 6 h observation period. In conclusion, qPCR quantification demonstrated 'molecular' colonization levels throughout infection, and EPG data analysis during the two periods (during early infection and then during late infection just prior to death) demonstrated the actual physical effects of fungal infection on feeding behaviour of M. persicae; this has the potential to decrease the aphid's capacity of transmission and dispersal. These studies increase our understanding of the interaction between P. neoaphidis and its host aphid.

Potential Inoculum Sources and Incidence of Strawberry Soilborne Pathogens in Spain

The decline and death of strawberry plants in Spanish fruit production fields have mainly been attributed to the soilborne pathogens Macrophomina phaseolina, Phytophthora cactorum, and Fusarium spp. Inoculum sources of M. phaseolina and P. cactorum, and the incidence all three genera, were investigated in nurseries and fruit production fields over three consecutive seasons. M. phaseolina inoculum sources consisted of fumigated preplant fruit production soils (50%) and fumigated nursery soils (47%), although the pathogen could not be detected in nursery mother and runner plants. P. cactorum inoculum sources included nursery (20%) and preplant fruit production (17%) fumigated soils, and nursery runner plants (up to 15%). In fruit production plants, the average incidence of M. phaseolina and P. cactorum were 4.2 and 3.7%, respectively. Fusarium spp. inoculum sources could not be accessed extensively due to the lack of effective quantitative real-time PCR assays. Limited testing of nursery plants showed that Fusarium oxysporum f. sp. fragariae (Fof) was absent. In field production plants and soil, F. solani was the main pathogenic Fusarium spp., with Fof only identified once in a fruit production plant. Ineffectively fumigated soils in nurseries and production fields, along with infected runner plants, can be inoculum sources of soilborne strawberry pathogens in Spain.

Relationship between microbial community dynamics and process performance during thermophilic sludge bioleaching

Heavy metals can be removed from the sludge using bioleaching technologies at thermophilic condition, thereby providing an option for biotreatment of wasted sludge generated from wastewater treatment. The purposes of this study were to establish a molecular biology technique, real-time PCR, for the detection and enumeration of the sulfur-oxidizing bacteria during the thermophilic sludge bioleaching. The 16S rRNA gene for real-time PCR quantification targeted the bioleaching bacteria: Sulfobacillus thermosulfidooxidans, Sulfobacillus acidophilus, and Acidithiobacillus caldus. The specificity and stringency for thermophilic sulfur-oxidizing bacteria were tested before the experiments of monitoring the bacterial community, bacterial number during the thermophilic sludge bioleaching and the future application on testing various environmental samples. The results showed that S. acidophilus was identified as the dominant sulfur-oxidizing bacteria, while A. caldus and S. thermosulfidooxidans occurred in relatively low numbers. The total number of the sulfur-oxidizing bacteria increased during the thermophilic bioleaching process. Meanwhile, the decrease of pH, production of sulfate, degradation of SS/VSS, and solubilization of heavy metal were found to correlate well with the population of thermophilic sulfur-oxidizing bacteria during the bioleaching process. The real-time PCR used in this study is a suitable method to monitor numbers of thermophilic sulfur-oxidizing bacteria during the bioleaching process.

Development of a method for detection and quantification of B. brongniartii and B. bassiana in soil

A culture independent method based on qPCR was developed for the detection and quantification of two fungal inoculants in soil. The aim was to adapt a genotyping approach based on SSR (Simple Sequence Repeat) marker to a discriminating tracing of two different species of bioinoculants in soil, after their in-field release. Two entomopathogenic fungi, Beauveria bassiana and B. brongniartii, were traced and quantified in soil samples obtained from field trials. These two fungal species were used as biological agents in Poland to control Melolontha melolontha (European cockchafer), whose larvae live in soil menacing horticultural crops. Specificity of SSR markers was verified using controls consisting of: i) soil samples containing fungal spores of B. bassiana and B. brongniartii in known dilutions; ii) the DNA of the fungal microorganisms; iii) soil samples singly inoculated with each fungus species. An initial evaluation of the protocol was performed with analyses of soil DNA and mycelial DNA. Further, the simultaneous detection and quantification of B. bassiana and B. brongniartii in soil was achieved in field samples after application of the bio-inoculants. The protocol can be considered as a relatively low cost solution for the detection, identification and traceability of fungal bio-inoculants in soil.

Effect of Soil Inoculum Density and Temperature on the Incidence of Cucumber Black Root Rot

The effects of the density of Phomopsis sclerotioides in soil and other environmental factors on black root rot of cucumber were investigated. Cucumber plants were grown in soil containing P. sclerotioides at 1, 10, 100, and 1000 CFU/g. Wilt incidence from 3 to 7 weeks after transplanting was strongly correlated with P. sclerotioides density in soil (P < 0.05). Root rot of squash rootstock occurred in soil with very low inoculum densities (0.1 CFU/g), and was strongly related to P. sclerotioides density (Y = -0.3x + 1.2, R² = 0.743, P < 0.05) at 8 weeks after transplanting. Cucumber plants showed wilt symptoms in soil containing 1 CFU/g. Wilt symptoms in cucumber plants occurred 4 to 7 days earlier in soil at 22°C than in soil at 27 or 17°C. Root rot development could be predicted from the density of P. sclerotioides in soil and soil temperature. However, further studies on the effects of other environmental factors are required to test the linear model in commercial fields. This information is essential for determining the threshold pathogen density at which most control techniques, particularly those other than soil disinfection, will be effective.

PCR-based specific techniques used for detecting the most important pathogens on strawberry: a systematic review

BACKGROUND

Strawberry diseases are a major limiting factor that severely impact plant agronomic performance. Regarding limitations of traditional techniques for detection of pathogens, researchers have developed specific DNA-based tests as sensitive and specific techniques. The aim of this review is to provide an overview of polymerase chain reaction (PCR)-based methods used for detection or quantification of the most widespread strawberry pathogens, such as Fusarium oxysporum f.sp. fragariae, Phytophthora fragariae, Colletotrichum acutatum, Verticillium dahliae, Botrytis cinerea, Macrophomina phaseolina, and Xanthomonas fragariae. An updated and detailed list of published PCR protocols is presented and discussed, aimed at facilitating access to information that could be particularly useful for diagnostic laboratories in order to develop a rapid, cost-effective, and reliable monitoring technique.

METHODS

The study design was a systematic review of PCR-based techniques used for detection and quantification of strawberry pathogens. Using appropriate subject headings, AGRICOLA, AGRIS, BASE, Biological Abstracts, CAB Abstracts, Google Scholar, Scopus, Web of Knowledge, and SpringerLink databases were searched from their inception up to April 2014. Two assessors independently reviewed the titles, abstracts, and full articles of all identified citations. Selected articles were included if one of the mentioned strawberry pathogens was investigated based on PCR methods, and a summary of pre-analytical requirements for PCR was provided.

RESULTS

A total of 259 titles and abstracts were reviewed, of which 22 full texts met all the inclusion criteria. Our systematic review identified ten different protocols for X. fragariae, eight for P. fragariae, four for B. cinerea, six for C. acutatum, three for V. dahlia, and only one for F. oxysporum. The accuracy and sensitivity of PCR diagnostic methods is the focus of most studies included in this review. However, a large proportion of errors in laboratories occur in the pre-analytical phase of the testing process. Due to heterogeneity, results could not be meta-analyzed.

CONCLUSIONS

From a systematic review of the currently available published literature, effective detection assays to detect the major strawberry pathogens have been developed. These assays can function as a basis for clinical labs, regulatory personnel, and other diagnosticians to adapt or implement for detection of these six important strawberry pathogens.

A real-time qPCR assay to quantify Ophiocordyceps sinensis biomass in Thitarodes larvae

Ophiocordyceps sinensis, an entomogenous fungus parasitic in the larvae of moths (Lepidoptera), is one of the most valuable medicinal fungi, and it only distributed naturally on the Tibetan Plateau. The parasitical amount of O. sinensis in various tissues of the host Thitarodes larvae has an important role in study the occurrence and developmental mechanisms of O. sinensis, but there no an effective method to detect the fungal anamorph. A real-time quantitative PCR (qPCR) system, including a pair of species-specific ITS primers and its related program, was developed for O. sinensis assay with high reliability and efficiency. A calibration curve was established and exhibited a very good linear correlation between the fungal biomass and the C T values (R (2)=0.999419) by the qPCR system. Based on this method, O. sinensis was detected rapidly in four tissues of its host caterpillars, and the results were shown as following: the maximum content of O. sinensis parasitized in the fat-body, and next came body-wall; both of them were much larger than that observed in the haemolymph and intestinal-wall. Taken together, these results show that qPCR assays may become useful tools for study on developmental mechanism of O. sinensis.

Cold-active hydrolases producing bacteria from two different sub-glacial Himalayan lakes

Microorganisms, native to the cold environments have successfully acclimatized their physiological, metabolic, and biological features, exhibiting uniqueness in their enzymes, proteins, and membrane structures. These cold-active enzymes have immense biotechnological potential. The diversity of culturable bacteria in two different water lakes (the sub-glacial freshwater and the brackish) of Himalayas was analyzed using SYBR green staining and cultural methods. A total of 140 bacteria were isolated and were grouped as psychrophiles, psychrotrophs, and psychrotolerant organisms, based on their optimal temperature for growth. The amplified ribosomal DNA restriction analysis using three restriction enzymes facilitated the grouping of these isolates into 96 genotypes at ≥85% polymorphism. Phylogenetic analysis using 16S rRNA gene sequences revealed that the bacterial strains from both lakes belonged to Firmicutes, Proteobacteria (α, β, and γ) or Actinobacteria. Screening of the germplasm for the activity of different cold-active hydrolases such as protease, amylase, xylanase, and cellulase, revealed that about 16 isolates were positive, and exhibiting a wide range of stability at various temperature and pH. Our results suggest that the distinctly different ecosystems of sub-glacial freshwater and brackish water lakes have diverse groups of bacteria, which can be an excellent source of extracellular hydrolases with a wide range of thermal stability.

Emerging phytopathogen Macrophomina phaseolina: biology, economic importance and current diagnostic trends

Macrophomina phaseolina (Tassi) Goid. is an important phytopathogenic fungus, infecting a large number of plant species and surviving for up to 15 years in the soil as a saprophyte. Although considerable research related to the biology and ecology of Macrophomina has been conducted, it continues to cause huge economic losses in many crops. Research is needed to improve the identification and characterization of genetic variability within their epidemiological and pathological niches. Better understanding of the variability within the pathogen population for traits that influence fitness and soil survival will certainly lead to improved management strategies for Macrophomina. In this context, the present review discusses various biological aspects and distribution of M. phaseolina throughout the world and their importance to different plant species. Accurate identification of the fungus has been aided with the use of nucleic acid-based molecular techniques. The development of PCR-based methods for identification and detection of M. phaseolina are highly sensitive and specific. Early diagnosis and accurate detection of pathogens is an essential step in plant disease management as well as quarantine. The progress in the development of various molecular tools used for the detection, identification and characterization of Macrophomina isolates were also discussed.