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Genotypic Analysis of Variability in Zygomycetes a Mini-Review

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Genotypic Analysis of Variability in Zygomycetes a Mini-Review Acta Biologica Hungarica 56 (3–4), pp. 345–357 (2005) GENOTYPIC ANALYSIS OF VARIABILITY IN ZYGOMYCETES A MINI-REVIEW M. TAKÓ* and Á. CSERNETICS Department of Microbiology, Faculty of Sciences, University of Szeged P.O. Box 533, H-6701 Szeged, Hungary (Received: February 21, 2005; accepted: March 11, 2005) Different types of molecular markers are available for use in evolutionary and population studies of microscopic fungi. These approaches have proved their merits and have been successfully applied to a wide range of fungal species belonging in the Ascomycetes and Basidiomycetes. Species in the class Zygomycetes have been rather neglected from this aspect. This review discusses the information avail- able from investigations of the genotypic variability in this group of fungi. Keywords: Genetic variability – molecular markers – Zygomycetes INTRODUCTION The fungal class Zygomycetes comprises about 900 species; some of them are very widespread and abundant in nature. Currently there is an increasing interest in the exploitation of the biotechnological potential of some zygomycetes; other represen- tatives of this group are known to be opportunistic pathogens of humans and animals. Certain other species are important as postharvest pathogens of agricultural products, or as spoilage microorganisms of certain foods. Molecular genotyping is of great potential for the provision of data for phylogenetic studies, taxonomic studies, diag- nostic applications (i.e. the recognition and determination of defined taxonomic enti- ties), epidemiology and population genetics and monitoring for biotechnologically exploitable strains. Nonetheless, most of these fungi have hence received only limit- ed attention to date. Among the scientific problems that are awaiting solution, species identification is notoriously difficult in certain taxa of the Zygomycetes. Identifications below the genus level have traditionally been based on morphological observations (and sometimes on the results of mating experiments). However, such approaches are essentially hampered by the lack of good morphological markers and the rather unique mating behaviour of these fungi. The establishment of different types of molecular markers provides a new possibility with which to handle these *Corresponding author; e-mail: [email protected] 0236-5383/$ 20.00 © 2005 Akadémiai Kiadó, Budapest 346 M. TAKÓ and Á. CSERNETICS questions [57, 59]. This review discusses the results and limitations of the molecular genotypic analysis in this fungal group. Isoenzyme analysis Isozyme analysis provides a well-established approach for the revelations of genetic variability in fungal populations. The protein polymorphisms detected reflect direct- ly on the genetic background of the fungi; this approach therefore offers a relatively neutral means of determining genetic variation. As numerous different isoenzymes can be detected, it makes isoenzyme analysis an extraordinary flexible approach [25]; the technique can be useful in resolutions at population, intraspecific and species levels. The characteristics determined by means of this method are generally accepted as beeing of independent genetic origin [21]. As concerns the various isozyme studies carried out with the Zygomycetes, the results obtained by Stout and Shaw [56] were rather controversial. They investigat- ed 28 isolates representing 20 Mucor species and found as much variation among M. racemosus isolates as among isolates representing different Mucor species. On the other hand, they did not observe any electrophoretic differences when 1 M. hiemalis and 1 M. mucedo strain were compared. Havens [16] carried out a similar survey in the section Hiemalis of the genus Mucor [50]: he coupled mating tests with isozyme analysis to reduce the possibility of misidentification. The strains investigated dis- played relatively high levels of polymorphism; the isozyme similarity and sexual compatibility exhibited a correlation coefficient of 0.61. When 30 isolates of 10 Mucor species were studied with the involvement of 13 different isoenzyme systems, the lowest degree of variation was found in the isoenzyme markers of M. plumbeus, a Mucor species with very characteristic morphological traits [71]. Mucor piriformis is an important postharvest pathogen of some fruits and vegeta- bles. Isozyme polymorphisms (tested with 6 enzyme activities) among 59 isolates of M. piriformis from pears and nectarines were low: 7 electrophoretic phenotypes were identified for all the enzymes. However, there was a correlation between the esterase, glucose-6-phosphate dehydrogenase and malate dehydrogenase banding patterns and the mating potency of the isolates from pears; those with mating abilities (plus and minus isolates) were clearly different from those without mating abilities (neutral isolates). The 30 isolates from nectarines proved to be very homogeneous genetical- ly; they did not reveal any polymorphisms [66]. Such a lack of isoenzyme polymor- phisms has also been observed in Gilbertella persicaria (originally described as Choanephora persicaria), which is known to be a storage-rot microorganism pri- marily of peaches: however, in this case no correlation was found between the isoen- zyme markers and the mating abilities [35, 39]. Homothallism is rather rare in the genus Mucor, where most of the known species are heterothallic. In a study, in which 10 strains of Mucor genevensis (a homothallic and dimorphic species), and representatives of 2 new homothallic species (Mucor meguroense and Mucor hachijyoensis) were investigated, substantial polymorphism Acta Biologica Hungarica 56, 2005 Genotypic analysis of variability in Zygomycetes 347 of the isoenzyme markers was detected in M. genevensis [62]. Though both the M. meguroense strain and the M. hachijyoensis strain revealed characteristic differences, they grouped closer to the homothallic M. genevensis than to the heterothallic M. pir- iformis and M. hiemalis strains. These results are interesting in comparison with a study on Rhizomucor isolates [73]. These thermophilic fungi are of interest both as aetiological agents of zygomycosis and for their biotechnological abilities. As con- cerns the 2 ubiquitous species of the genus, R. miehei has been found to be homothal- lic, while R. pusillus is mainly heterothallic [51]. In an isoenzyme study (coupled with carbon source assimilation tests), 18 R. miehei and R. pusillus isolates were assayed. While substantial polymorphism was found among the R. pusillus strains, the investigated R. miehei strains proved to be homogeneous; no difference was revealed with the 5 enzyme systems investigated. One explanation could be that this phenomenon is connected with the homothallic and (mainly) heterothallic natures of R. miehei and R. pusillus, respectively. However, in this case the background of the high variability observed in M. genevensis remains unresolved. The relatively low polymorphism observed in these works suggest that isozyme analysis is not the most appropriate method of choice when individual isolates are to be characterized, but it demonstrates the value of this approach for the detection intraspecific diversity within a species. Random amplified polymorphic DNA (RAPD) analysis Among the molecular approaches available, RAPD analysis has proved to be a rapid and sensitive method. This is the reason why this technique has been used efficient- ly for the genotypic analysis of the Zygomycetes for various purposes. A biological control study demands the ability to distinguish released pathogens from locally occurring isolates of the same species. Zoophthora radicans (Entomophthorales) is a pathogen of the potato leafhopper. RAPD analysis was applied to Z. radicans isolates to determine the spread of fungi released into the envi- ronment. Besides verifying the successful establishment of experimental release, RAPD analysis revealed clear relationships among isolates derived from the same host taxon [18]. Entomophaga grylli is a pathogen that displays host-specific variance to grasshop- per subfamilies. In the study by Bidochka et al. [4] 3 pathotypes of the E. grylli species complex were clearly differentiated by RAPD analysis (and two other mole- cular techniques). The pathotypes exhibited different amplification patterns: there was little or no interisolate variability in RAPD fragment patterns within each patho- type. RAPD analysis has been used to generate DNA fragments that are unique to iso- lates of 2 arbuscular mycorrhizal fungi: Glomus mosseae and Gigaspora margarita. Species-specific primer pairs have been established, allowing the subsequent specif- ic identification of these fungi [1]. Acta Biologica Hungarica 56, 2005 348 M. TAKÓ and Á. CSERNETICS The population structure of Basidiobolus (the number and distribution of the fun- gus in the soil and litter) was also studied via RAPD analysis. Isolates of Basidio- bolus and Conidiobolus (a related fungus) were obtained from different soil samples. RAPD analysis indicated that each Basidiobolus isolate is genetically unique; conse- quently, there is no evidence of clonal growth in soil. This study suggested that in some cases the intestines of reptiles and perhaps other animals may be a more sig- nificant reservoir than the soil for Basidiobolus [30]. Seven strains of the facultative mycoparasite Parasitella parasitica proved to be highly diverse when they were compared by RAPD analysis. This technique allowed their division into 2 groups, but they showed no morphological differences and the
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