Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA

Vainio, Eeva J.; Hantula, Jarkko

doi:10.1017/s0953756200002471

Cited by 534 publications

(300 citation statements)

References 38 publications

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“…Vainio and Hantula (2000) showed that DGGE detected more fungal species than the culturing method from environment samples. However, the major limitation to generalized studies of soil fungi by purely molecular methods is the lack of discrimination in the technique between living and dead material, or active and dormant organisms (Bridge and Spooner 2001).…”

Section: Discussionmentioning

confidence: 99%

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

et al. 2008

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Background, aim, and scope Fertilization is an important agricultural practice for increasing crop yields. In order to maintain the soil sustainability, it is important to monitor the effects of fertilizer applications on the shifts of soil microorganisms, which control the cycling of many nutrients in the soil. Here, culture-dependent and cultureindependent approaches were used to analyze the soil bacterial and fungal quantities and community structure under seven fertilization treatments, including Control, Manure, Return (harvested peanut straw was returned to the plot), and chemical fertilizers of NPK, NP, NK, and PK. The objective of this study was to examine the effects on soil microbial composition and diversity of long-term organic and chemical fertilizer regimes in a Chinese upland red soil. Materials and methods Soil samples were collected from a long-term experiment station at Yingtan (28°15′N, 116°55′E), Jiangxi Province of China. The soil samples (0-20 cm) from four individual plots per treatment were collected. The total numbers of culturable bacteria and fungi were determined as colony forming units (CFUs) and selected colonies were identified on agar plates by dilution plate methods. Moreover, soil DNAs were extracted and bacterial 16S rRNA genes and fungal 18S rRNA genes were polymerase chain reaction amplified, and then analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. Results The organic fertilizers, especially manure, induced the least culturable bacterial CFUs, but the highest bacterial diversity ascertained by DGGE banding patterns. Chemical fertilizers, on the other hand, had less effect on the bacterial composition and diversity, with the NK treatment having the lowest CFUs. For the fungal community, the manure treatment had the largest CFUs but much fewer DGGE bands, also with the NK treatment having the lowest CFUs. The conventional identification of representative bacterial and fungal genera showed that long-term fertilization treatments resulted in differences in soil microbial composition and diversity. In particular, 42.4% of the identified bacterial isolates were classified into members of Arthrobacter. For fungi, Aspergillus, Penicillium, and Mucor were the most prevalent three genera, which accounted for 46.6% of the total identified fungi. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Discussion It was evident that more representative fungal genera appeared in organic treatments than other treatments, indicating that culturable fungi were more sensitive to organic than to chemical fertilizers. A very notable finding was that fungal CFUs appeared maximal in organic manure treatments. This was quite different from the

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Section: Discussionmentioning

confidence: 99%

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

et al. 2008

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“…The DNA quality and quantity were checked on a 1.2% agarose gel stained with ethidium bromide and visualized by UV trans-illumination (Sambrook, Fritsch, & Maniatis, 1989). The PCR used the U968 (40 bp GC clamp) and L1401 universal eubacterial primers (Heuer & Smalla, 1997) and primers FR1 (58 bp BC-clamp) and FF390 (Vainio & Hantula, 2000) for amplification of fungal smallsubunit (SSU) rDNA. The amount and quality of the obtained PCR products were again checked as described before.…”

Section: Inoculation and Isolation Of The Pathogenmentioning

confidence: 99%

Biological Soil Disinfestation (BSD), a new control method for potato brown rot, caused by Ralstonia solanacearum race 3 biovar 2

et al. 2007

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The potential of Biological Soil Disinfestation (BSD) to control potato brown rot, caused by Ralstonia solanacearum race 3 biovar 2, was investigated. BSD involves the induction of anaerobic soil conditions by increasing microbial respiration through incorporation of fresh organic amendments (here: grass or potato haulms) and by reducing re-supply of oxygen by covering with airtight plastic sheets. Control treatments were left without cover and amendment, or amended without covering or covered only without amendment. The effect of BSD on survival of R. solanacearum was tested at three different scales: in 1-l glass mesocosms under laboratory conditions, in 1.2-m-diam microplots positioned in an outdoor quarantine field, and in a naturally infested commercial field. Within a few days, anaerobic conditions developed in the BSD-treated soils. In the mesocosm and microplot experiment, anaerobic conditions persisted till the end of the 4-week experimental period. In the field experiment, the period of anaerobiosis was shorter due to birds damaging the plastic cover. In all three experiments, BSD reduced soil populations of R. solanacearum significantly by 92.5% to >99.9% compared to the non-amended and uncovered control treatments. In the field experiment, BSD also resulted in a significant reduction of R. solanacearum survival in potato tubers buried at 15 or 35 cm and in the rapid decomposition of superficially buried potatoes remaining after harvesting, thus destroying an important inoculum reservoir of R. solanacearum. The treatments with grass amendment only or covering with only plastic did not result in anaerobic conditions and did not decrease R. solanacearum populations during the experimental period. PCR-DGGE analyses of 16S-rDNA from soil samples of the various treatments in the mesocosm and microplot experiments revealed that BSD hardly affected bacterial diversity but did result in clear shifts in the composition of the bacterial community. The possible implications of

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“…The diversity of soil-and rhizosphere-inhabiting fungi is much higher than previously thought (Vandenkoornhuyse et al, 2002;Gams, 2007). Molecular tools were developed to analyse the structure of terrestrial fungal communities (Kowalchuk, 1999;Vainio and Hantula, 2000;Anderson and Cairney, 2004;Berg et al, 2005), but little is known about their diversity, biogeography and ecology, especially in native ecosystems. Furthermore, microorganisms comprise much of the Earth's biodiversity, but our knowledge about their biodiversity scaling relationships relative to that of plants and animals is limited (Green and Bohannan, 2006).…”

mentioning

confidence: 99%

Fungal diversity in the rhizosphere of endemic plant species of Tenerife (Canary Islands): relationship to vegetation zones and environmental factors

et al. 2008

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Knowledge about fungal diversity scaling relationships relative to that of plants is important to understand ecosystem functioning. Tenerife Island, a natural laboratory to study terrestrial biodiversity, is represented by six different vegetation zones characterized by specific abiotic conditions and plant communities with a high proportion of endemic plants. Little is known about the biodiversity of associated fungi. To understand the relationship between plant and fungal communities, we analysed soil/rhizosphere fungi from all vegetation zones. From 12 sampling points dispersed on the whole island, molecular analysis of fungal communities was determined by single-strand conformation polymorphism (SSCP) analysis using universal and specific primers for Trichoderma. The highly diverse fungal communities were mainly characterized by ectomycorrhizaforming Basidiomycota and a high proportion of yet-unidentified species. Besides, Trichodermaspecific SSCP resulted in low diversity of mainly cosmopolitan species, for example Hypocrea lixii/ T. harzianum. The dominance of T. harzianum was confirmed by cultivation. All Trichoderma isolates show an extraordinarily high antagonistic potential towards different groups of plant pathogens, supporting the hypothesis of extensive colonization by highly competitive Trichoderma species from the continent. In contrast, biodiversity patterns of the whole fungal and plant communities follow the same ecological rules. Furthermore, a high statistical correlation between fungal communities and the main environmental factors, temperature and precipitation, was found.

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Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA

Cited by 534 publications

References 38 publications

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

Biological Soil Disinfestation (BSD), a new control method for potato brown rot, caused by Ralstonia solanacearum race 3 biovar 2

Fungal diversity in the rhizosphere of endemic plant species of Tenerife (Canary Islands): relationship to vegetation zones and environmental factors

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