Analysis of partial Glomales SSU rRNA gene sequences: implications for primer design and phylogeny

Schüβler, Arthur; Gehrig, Hans; Schwarzott, Daniel; Walker, Chris

doi:10.1017/s0953756200003725

Cited by 127 publications

(71 citation statements)

References 48 publications

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“…The fact that the isolated Leptosphaeria sp. contained sequences very closely matching those of T1 and T3 (9,20) makes it very likely that the previously reported sequences T1 and T3 also came from a fungus in the Leptosphaeria genus living inside healthy S. castanea spores rather than as contaminants on the surface of the spores as previously suggested (24). The further observation of fungal hyphae inside S. castanea spores with a morphology similar to that of the isolated Leptosphaeria sp.…”

supporting

confidence: 79%

“…The question therefore arises as to what is the true origin of these sequences. Other researchers have suggested that these sequences are the result of fungal contaminants on the AMF spore wall (24). Three possibilities were suggested by Redecker et al (20): (i) that these sequences were from contaminating fungi on the surface of the AMF spores, (ii) that they were sequences from ascomycetes which were living inside S. castanea spores, and (iii) that they originated from the S. castanea genome.…”

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confidence: 99%

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Identification and Isolation of Two Ascomycete Fungi from Spores of the Arbuscular Mycorrhizal Fungus Scutellospora castanea

Hijri

Redecker

Petetot

et al. 2002

Appl Environ Microbiol

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Two filamentous fungi with different phenotypes were isolated from crushed healthy spores or perforated dead spores of the arbuscular mycorrhizal fungus (AMF) Scutellospora castanea. Based on comparative sequence analysis of 5.8S ribosomal DNA and internal transcribed spacer fragments, one isolate, obtained from perforated dead spores only, was assigned to the genus Nectria, and the second, obtained from both healthy and dead spores, was assigned to Leptosphaeria, a genus that also contains pathogens of plants in the Brassicaceae. PCR and randomly amplified polymorphic DNA-PCR analyses, however, did not indicate similarities between pathogens and the isolate. The presence of the two isolates in both healthy spores and perforated dead spores of S. castanea was finally confirmed by transmission electron microscopy by using distinctive characteristics of the isolates and S. castanea. The role of this fungus in S. castanea spores remains unclear, but the results serve as a strong warning that sequences obtained from apparently healthy AMF spores cannot be presumed to be of glomalean origin and that this could present problems for studies on AMF genes.The order Glomales (class Zygomycota) comprises arbuscular mycorrhizal fungi (AMF) that are able to form mutualistic symbioses with roots of approximately 60% of all plant species (25). AMF are important for plants because they assist plants in absorbing nutrients, especially phosphate (14), and have a protective role against plant-pathogenic fungi (10, 17). It has also been shown that the diversity of AMF is an important determinant of plant diversity and productivity (26,27,28). AMF are obligate biotrophs. Their hyphae are coenocytic, and asexual spores form on the termini of hyphae (8). These spores contain hundreds to thousands of nuclei per spore (1,11,29). In the species Scutellospora castanea, one spore contains approximately 800 nuclei (11). The spores are the only form by which individual species can be identified on the basis of morphological characteristics (33).Because of the symbiotic function of AMF, there is great interest in identifying AMF genes that are involved in the establishment and functioning of the symbiosis. However, at present, very few genes other than rRNA genes have been studied in these fungi. Several studies have shown that genetic diversity of the internal transcribed spacer (ITS) exists among and within single spores (9,16,22). Six different ITS1-5.8S-ITS2 types (T1 to T6) from S. castanea were reported (8). The 5.8S sequences published by Hijri et al. (9) were subsequently used in a phylogenetic analysis of Glomales and other fungi (20). This analysis showed that the highly divergent sequences T1, T3, T5, and T6 clustered within the ascomycetes (with Phoma-Leptosphaeria as the closest relatives to T1 and T3). Other studies have also reported sequences of rRNA genes obtained from glomalean spores that clustered in the ascomycetes in phylogenetic analyses (4,12,18). The question therefore arises as to what is the true origin of these s...

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confidence: 79%

mentioning

confidence: 99%

Identification and Isolation of Two Ascomycete Fungi from Spores of the Arbuscular Mycorrhizal Fungus Scutellospora castanea

Hijri

Redecker

Petetot

et al. 2002

Appl Environ Microbiol

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“…So far, to our knowledge there have been no studies combining molecular genetic variation with variation in quantitative genetic traits (QGTs) in an AMF field population. This lack of data is surprising, given that a remarkably high amount of genetic variability exists in an AMF species and within individual spores (6)(7)(8)(9)(10). AMF are coenocytic, with many nuclei coexisting in a common cytoplasm, and one species of AMF has recently been shown to be multigenomic, harboring genetically different nuclei (11).…”

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confidence: 99%

High genetic variability and low local diversity in a population of arbuscular mycorrhizal fungi

Koch

Kuhn²,

Fontanillas³

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

185

260

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Arbuscular mycorrhizal fungi (AMF) are ecologically important root symbionts of most terrestrial plants. Ecological studies of AMF have concentrated on differences between species; largely assuming little variability within AMF species. Although AMF are clonal, they have evolved to contain a surprisingly high within-species genetic variability, and genetically different nuclei can coexist within individual spores. These traits could potentially lead to within-population genetic variation, causing differences in physiology and symbiotic function in AMF populations, a consequence that has been largely neglected. We found highly significant genetic and phenotypic variation among isolates of a population of Glomus intraradices but relatively low total observed genetic diversity. Because we maintained the isolated population in a constant environment, phenotypic variation can be considered as variation in quantitative genetic traits. In view of the large genetic differences among isolates by randomly sampling two individual spores, <50% of the total observed population genetic diversity is represented. Adding an isolate from a distant population did not increase total observed genetic diversity. Genetic variation exceeded variation in quantitative genetic traits, indicating that selection acted on the population to retain similar traits, which might be because of the multigenomic nature of AMF, where considerable genetic redundancy could buffer the effects of changes in the genetic content of phenotypic traits. These results have direct implications for ecological research and for studying AMF genes, improving commercial AMF inoculum, and understanding evolutionary mechanisms in multigenomic organisms.

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“…Nevertheless, an advantage for the use of primer pair AM1/NS31 is the relatively large amounts of DNA sequence information derived from this primer pair available. A subsequent study (Zhang et al, 2010) was aimed the variable V3-V4 region of the 18S rDNA of AMF gene, by using nested PCR in three steps: (1) first round PCR, using primers GeoA2 and Geo11 (Schwarzott and Schüssler, 2001); (2) second round, using primers above-mentioned AM1/ NS31-GC; and (3) third round using NS31-GC/Glol. In that study, the AMF community from rhizosphere of two shrubs species was investigated and the species richness ranged from 17 to 25 AMF species.…”

Section: Wwwintechopencommentioning

confidence: 99%

Advances in Molecular Diversity of Arbuscular Mycorrhizal Fungi (Phylum Glomeromycota) in Forest Ecosystems

Patreze¹,

Moreira²,

Tsai³

2012

Forest Ecosystems - More Than Just Trees

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Analysis of partial Glomales SSU rRNA gene sequences: implications for primer design and phylogeny

Cited by 127 publications

References 48 publications

Identification and Isolation of Two Ascomycete Fungi from Spores of the Arbuscular Mycorrhizal Fungus Scutellospora castanea

Identification and Isolation of Two Ascomycete Fungi from Spores of the Arbuscular Mycorrhizal Fungus Scutellospora castanea

High genetic variability and low local diversity in a population of arbuscular mycorrhizal fungi

Advances in Molecular Diversity of Arbuscular Mycorrhizal Fungi (Phylum Glomeromycota) in Forest Ecosystems

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