Generation of RAPD-PCR primers for the identification of isolates of Glomus mosseae, an arbuscular mycorrhizal fungus

Molecular Variability in North Indian Isolates of Cylindrocladium quinquieseptatum Causing Eucalyptus Leaf and Seedling Blight

Cylindrocladium quinqueseptatum has been considered as the most destructive pathogen of Eucalyptus nurseries and plantations in north India. Genetic resistance has not been determined against this disease in Eucalyptus and genetic diversity among the fungal population in northern India is not known. Seventy three isolates from infected leaves and twigs of Eucalyptus were collected from different northern Indian state and analyzed through RAPD-PCR for screening genetic diversity. The UPGMA cluster analysis score of 284 loci permitted identification of 11 population lines and an outlier. This molecular variability prevalent among the north Indian population of the pathogen can used in identifying Cylindrocladium leaf and seedling blight resistant Eucalyptus germplasm.

Temporal temperature gradient gel electrophoresis (TTGE) as a tool for the characterization of arbuscular mycorrhizal fungi

The aim of this study was to assess the feasibility of using temporal temperature gradient electrophoresis (TTGE) of PCR-amplified 18S rDNA fragments of different Glomus species for their detection and characterization. Screening of Glomus clarum, Glomus constrictum, Glomus coronatum, Glomus intraradices, Glomus mosseae and Glomus viscosum by PCR-TGGE revealed that the NS31-AM1 region of the 18S rRNA gene contained insufficient variation to discriminate between them. In contrast, TTGE analysis of the NS31-Glo1 region, which was obtained by nested PCR of the NS31-AM1 amplicon, showed that each species was characterized by a specific TTGE fingerprint. However, isolates of the same species could not be distinguished. The nested PCR-TTGE approach developed allowed identification of the Glomus species colonising the roots of different plant species.

Rapid determination of fungal colonization and arbuscule formation in roots of Medicago truncatula using real-time (RT) PCR

The quantifications of root colonization and symbiotic activity in the arbuscular mycorrhizal (AM) association of Medicago truncatula and Glomus intraradices were performed by quantitative polymerase chain reaction (real-time PCR). A strong correlation between fungal colonization of the root system and the amounts of fungal rDNA and rRNA were shown. In contrast, the transcript levels of the AM-specific phosphate transporter 4 from M. truncatula (MtPT4) correlate with arbuscule formation rather than with fungal colonization. These results suggest (i) that real-time PCR assay is a rapid, useful, and accurate method for the determination of arbuscular mycorrhizal features, (ii) that the amount of fungal rDNA or rRNA is a good parameter to estimate fungal colonization, and (iii) that it is necessary to evaluate the amount of other transcripts-like the MtPT4 transcript-to obtain additional information about the symbiotic state of the colonized root system.

Prospects and limitations for mycorrhizas in biocontrol of root pathogens

More than 80 disease biocontrol products are on the market worldwide, but none of these contain mycor rhizal fungi. This is despite ample evidence that both arbuscular mycorrhizal fungi and ectomycorrhizal fungi can control a number of plant diseases. A procedure for successful development of disease biocontrol agents in general is used as a background to examine the potential for achieving commercial mycorrhizal biocontrol agents. This includes (i) selection and screening; (ii) characterization involving identification, studies of modes of action and ecophysiology, as well as inoculum production, formulation, application and shelf life; (iii) registration. The last stage is problematic for mycorrhizal fungi, as currently they can be sold as plant growth promoters without any form of costly registration, even though in some instances they may actually function to some extent through biocontrol activity. The significance of this approach is discussed, and some possible ways of enhancing biocontrol by mycorrhizas are considered.Key words: arbuscular mycorrhizas, ectomycorrhizas, biological disease control, soilborne pathogens, modes of action, ecology.

Rapid and reliable DNA extraction techniques from trypan-blue-stained mycorrhizal roots: comparison of two methods

Two improved DNA extraction techniques from trypan-blue-stained root fragments were developed and compared for rapid and reliable analyses. In Method A, 1 cm trypan-blue-stained mycorrhizal root fragments were individually isolated, crushed by bead beating, and purified with Chelex-100 (Bio-Rad). In Method B, DNA extraction was carried out using an UltraClean microbial DNA isolation kit (MoBio Laboratories). DNA was extracted from the mycorrhizal roots of four plant species, quantified by UV absorbance, and PCR-amplified with primers specific to arbuscular mycorrhizal fungi. Although PCR inhibitors might still exist when using Method A, appropriate dilution and employment of nested-PCR overcame this problem. Method B removed PCR inhibitors, but sometimes, depending on the mycorrhizal colonization within the root fragments, it also required nested PCR. In conclusion, both methods enabled us to handle many samples in a short time. Method B provided greater reliability and Method A provided better cost performance. Both techniques can be useful for PCR-based applications to identify species and estimate species composition after measuring mycorrhizal colonization rate with trypan blue staining.

Morphology and molecular diversity of arbuscular mycorrhizal fungi in wild and cultivated yew (Taxus baccata)

Taxus baccata L. roots collected from two sites in southern Germany were heavily colonized by arbuscular mycorrhizal fungi (AMF). The colonization pattern was of the Paris type. The diversity of the colonizing AMF species was investigated using polymerase chain reaction based molecular techniques. The internal transcribed spacer (ITS) region of the DNA from AMF within the roots was amplified using Glomeromycota-specific primers and then cloned and sequenced. Phylogenetic analysis using a data set of 5.8S rDNA sequences from a wide range of glomeralean taxa as well as data sets of partial ITS2 sequences from glomeralean subgroups indicated root colonization by four sequence types of Glomus and one sequence type of Archaeospora. These sequence types are distinct from any previously published sequences and differed between the two study sites.Key words: arbuscular mycorrhiza, Paris-type AM, molecular diversity, ribosomal internal transcribed spacers, Taxus baccata.

DNA extraction method for PCR in mycorrhizal fungi

AIMS

To develop a simple and rapid DNA extraction protocol for PCR in mycorrhizal fungi.

METHODS AND RESULTS

The protocol combines the application of rapid freezing and boiling cycles and passage of the extracts through DNA purification columns. PCR amplifiable DNA was obtained from a number of endo- and ecto-mycorrhizal fungi using minute quantities of spores and mycelium, respectively.

CONCLUSION

DNA extracted following the method, was used to successfully amplify regions of interest from high as well as low copy number genes. The amplicons were suitable for further downstream applications such as sequencing and PCR-RFLPs.

SIGNIFICANCE AND IMPACT OF THE STUDY

The protocol described is simple, short and facilitates rapid isolation of PCR amplifiable genomic DNA from a large number of fungal isolates in a single day. The method requires only minute quantities of starting material and is suitable for mycorrhizal fungi as well as a range of other fungi.

Taxon-specific oligonucleotide primers for detection of two ancient endomycorrhizal fungi, Glomus occultum and Glomus brasilianum

A unique oligonucleotide pair, GOCC56:GOCC427, was designed that correctly primed specific amplification of a approximately 370-bp sequence spanning the ITS and 5.8S rDNA regions of Glomus occultum and Glomus brasilianum. In addition, this primer pair successfully detected G. occultum and G. brasilianum DNA in nested PCR using a primary PCR product amplified from highly diluted extracts of colonized corn (Zea mays) roots using modified ITS1:ITS4 primers. A second primer pair, GBRAS86:GBRAS388, primed specific amplification of a approximately 200-bp sequence spanning the ITS and 5.8S rDNA regions present only in G. brasilianum and Glomus strain GR582. Combined use of both primer pairs provides the means to detect and differentiate two ancient endomycorrhizal species, G. occultum and G. brasilianum, undetectable by standard root staining procedures. Sequence analysis showed that the purported G. occultum strain GR582 is likely a strain of G. brasilianum.

The arbuscular mycorrhizal symbiosis: a molecular review of the fungal dimension

Mycorrhizal associations vary widely in structure and function, but the most common interaction is the arbuscular mycorrhizal (AM) symbiosis. This interaction is formed between the roots of over 80% of all terrestrial plant species and Zygomycete fungi from the Order Glomales. These fungi are termed AM fungi and are obligate symbionts which form endomycorrhizal symbioses. This symbiosis confers benefits directly to the host plant's growth and development through the acquisition of P and other mineral nutrients from the soil by the fungus. In addition, they may also enhance the plant's resistance to biotic and abiotic stresses. These beneficial effects of the AM symbiosis occur as a result of a complex molecular dialogue between the two symbiotic partners. Identifying the molecules involved in the dialogue is a prerequisite for a greater understanding of the symbiosis. Ongoing research attempts to understand the underlying dialogue and concomitant molecular changes occurring in the plant and the fungus during the establishment of a functioning AM symbiosis. This paper focuses on the molecular approaches being used to study AM fungal genes being expressed in the symbiotic and asymbiotic stages of its lifecycle. In addition, the importance of studying these fungi, in relation to understanding plant processes, is discussed briefly.

MOLECULAR AND CELLULAR ASPECTS OF THE ARBUSCULAR MYCORRHIZAL SYMBIOSIS

Arbuscular mycorrhizae are symbiotic associations formed between a wide range of plant species including angiosperms, gymnosperms, pteridophytes, and some bryophytes, and a limited range of fungi belonging to a single order, the Glomales. The symbiosis develops in the plant roots where the fungus colonizes the apoplast and cells of the cortex to access carbon supplied by the plant. The fungal contribution to the symbiosis is complex, but a major aspect includes the transfer of mineral nutrients, particularly phosphate from the soil to the plant. Development of this highly compatible association requires the coordinate molecular and cellular differentiation of both symbionts to form specialized interfaces over which bi-directional nutrient transfer occurs. Recent insights into the molecular events underlying these aspects of the symbiosis are discussed.

Intrasporal variability of ribosomal sequences in the endomycorrhizal fungus Gigaspora margarita

The sequence variability of the ribosomal internal transcribed spacer (ITS) region, which comprises the 5.8 gene and the flanking regions ITS1 and ITS2, was investigated in the arbuscular mycorrhizal fungus Gigaspora margarita. DNA analysis of a multispore preparation and three single spores led to the identification of 11 slightly different sequences (three variants within a single spore), indicating substantial intersporal and intrasporal genetic variability (up to 9% sequence divergence). The sequence variations inside a single spore may be higher than that observed between spores. Even so, primers designed on the ITS1 and ITS2 regions identified Gi. margarita isolates and detected the endophyte during colonization.

Characterization of root colonization profiles by a microcosm community of arbuscular mycorrhizal fungi using 25S rDNA-targeted nested PCR

The aim of the present work was to study colonization patterns in roots by different arbuscular mycorrhizal fungi developing from a mixed community in soil. As different fungi cannot be distinguished with certainty in planta on the basis of fungal structures, taxon-discriminating molecular probes were developed. The 5' end of the large ribosomal subunit containing the variable domains D1 and D2 was amplified by PCR from Glomus mosseae (BEG12), G. intraradices (LPA8), Gigaspora rosea (BEG9) and Scutellospora castanea (BEG1) using newly designed eukaryote-specific primers. Sequences of the amplification products showed high interspecies variability and PCR taxon-discriminating primers were designed to distinguish between each of these four fungi. A nested PCR, using universal eukaryotic primers for the first amplification and taxon-discriminating primers for the second, was performed on individual trypan blue-stained mycorrhizal root fragments of onion and leek, and root colonization by four fungi inoculated together in a microcosm experiment was estimated. More than one fungus was detected in the majority of root fragments and all four fungi frequently co-existed within the same root fragment. Root colonization by G. mosseae and G. intraradices was similar from individual mixed inoculum, whilst the frequency of S. castanea and Gig. rosea increased in the presence of the two Glomus species, suggesting that synergistic interactions may exist between some arbuscular mycorrhizal fungi.

Primers for polymerase chain reaction to detect genomic DNA of Toxocara canis and T. cati

Primers for polymerase chain reaction to amplify genomic DNA of both Toxocara canis and T. cati were constructed by adapting cloning and sequencing random amplified polymorphic DNA. The primers are expected to detect eggs and/or larvae of T. canis and T. cati, both of which are known to cause toxocariasis in humans.

Characterization of a highly repeated DNA sequence (SC1) from the arbuscular mycorrhizal fungus Scutellospora castanea and its detection in planta

A highly repeated DNA sequence from the genome of an arbuscular mycorrhizal fungus has been isolated and characterized. This 1,202-bp sequence (SC1) represents about 0.24% of the Scutellospora castanea genome, estimated to be 1 pg by flow cytometry. The sequence was shown to be a Scutellospora-specific probe in Southern blots and dot blot hybridizations. After complete sequencing of SC1, PCR primers were generated and used to amplify a 907-bp fragment from spores of S. castanea or from colonized Allium porrum roots. No amplification products were obtained with DNA from either spores or mycorrhizal root of other species of arbuscular mycorrhizal fungi. These primers were sufficiently specific for unequivocal detection of S. castanea in planta.