Rapid PCR-based method for the direct analysis of fungal communities in complex environmental samples

Pennanen, Taina; Paavolainen, Laura; Hantula, Jarkko

doi:10.1016/s0038-0717(00)00198-x

Cited by 70 publications

(35 citation statements)

References 6 publications

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“…The primers used were designed to amplify the 18S rDNAs of all three major phyla of fungi, i.e., Basidiomycota, Ascomycota, and Zygomycota, and our cloning and sequencing results support this specificity. Furthermore, Vainio and Hantula (40) and Pennanen et al (30) reported that no amplification products were obtained from bacterial and plant DNAs or from oomycota, nematode, or protozoan DNA. DGGE analysis of 18S rDNA fragments amplified with NS1 and FR1 from DNA directly extracted from soil or root samples allowed us to monitor the shifts in the relative abundance of fungal populations during plant growth development.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

Gomes¹,

Fagbola²,

Costa

et al. 2003

Appl Environ Microbiol

245

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The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants.

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Section: Discussionmentioning

confidence: 99%

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

Gomes¹,

Fagbola²,

Costa

et al. 2003

Appl Environ Microbiol

245

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“…However, we must note that these OTUs were obtained using DGGE, which reveals only the dominant species (30) due to incomplete resolution of bands in the gel (33). Importantly, this study showed that certain fungal species in the shiro (e.g., Piloderma sp.…”

Section: Discussionmentioning

confidence: 88%

Tricholoma matsutake Dominates Diverse Microbial Communities in Different Forest Soils

Vaario¹,

Fritze²,

Spetz³

et al. 2011

Appl Environ Microbiol

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Fungal and actinobacterial communities were analyzed together with soil chemistry and enzyme activities in order to profile the microbial diversity associated with the economically important mushroom Tricholoma matsutake. Samples of mycelium-soil aggregation (shiro) were collected from three experimental sites where sporocarps naturally formed. PCR was used to confirm the presence and absence of matsutake in soil samples. PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting and direct sequencing were used to identify fungi and actinobacteria in the mineral and organic soil layers separately. Soil enzyme activities and hemicellulotic carbohydrates were analyzed in a productive experimental site. Soil chemistry was investigated in both organic and mineral soil layers at all three experimental sites. Matsutake dominated in the shiro but also coexisted with a high diversity of fungi and actinobacteria. Tomentollopsis sp. in the organic layer above the shiro and Piloderma sp. in the shiro correlated positively with the presence of T. matsutake in all experimental sites. A Thermomonosporaceae bacterium and Nocardia sp. correlated positively with the presence of T. matsutake, and Streptomyces sp. was a common cohabitant in the shiro, although these operational taxonomic units (OTUs) did not occur at all sites. Significantly higher enzyme activity levels were detected in shiro soil. These enzymes are involved in the mobilization of carbon from organic matter decomposition. Matsutake was not associated with a particular soil chemistry compared to that of nearby sites where the fungus does not occur. The presence of a significant hemicellulose pool and the enzymes to degrade it indicates the potential for obtaining carbon from the soil rather than tree roots.

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“…Separation is based on the melting behavior of fragments with different sequence composition under increasing gradients of denaturants or temperature. Since its introduction for the analysis of bacterial community structure (Muyzer et al, 1993), this method has been widely used in the characterization of soil bacterial (Kozdroj and Van Elsas, 2000) and fungal (Pennanen et al, 2001;Kowalchuk et al, 2006) as well as micro-fauna communities (Waite et al, 2003;Foucher et al, 2004) from various environments. Kowalchuk et al (2002) was the first to apply DGGE to assess AMF diversity in sand dune soil and root samples.…”

Section: Introductionmentioning

confidence: 99%

A DGGE-cloning method to characterize arbuscular mycorrhizal community structure in soil

Liang¹,

Drijber²,

Lee³

et al. 2008

Soil Biology and Biochemistry

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Rapid PCR-based method for the direct analysis of fungal communities in complex environmental samples

Cited by 70 publications

References 6 publications

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

Tricholoma matsutake Dominates Diverse Microbial Communities in Different Forest Soils

A DGGE-cloning method to characterize arbuscular mycorrhizal community structure in soil

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