DNA- and RNA-derived assessments of fungal community composition in soil amended with sewage sludge rich in cadmium, copper and zinc

Anderson, Ian C.; Parkin, Pamela I.; Campbell, Colin D.

doi:10.1016/j.soilbio.2008.05.015

Cited by 43 publications

(22 citation statements)

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“…2008) also referred that the combined approach of using DGGE and cloning / sequencing to examine differences in soil fungal communities was not proved a useful method primarily due to the similarities in DGGE profiles between different samples and the fact that the identification of many of the sequenced bands remained unresolved because of their relatively low match with reference database sequences. M-TRFLP method has the ability to analyse several groups of microbial taxa simultaneously (Singh et al, 2006) and has recently been used to investigate the effects of Zn and Cu rich sludge on various groups of soil microbial taxa (Anderson, Parkin, 2008;Macdonald et al, 2011). As it has been referred, the observed decrease in 16:1 ω5c in the zinc-amended soils may reflect a part of the arbuscular mycorrhizal fungi to elevated heavy metal concentrations (Kelly et al, 1999), however, there is also evidence that 16:1 ω5c can be found in some groups of bacteria (Olsson et al, 1997).…”

Section: Total Percentage Of Metal-resistant Entomopathogenic Fungimentioning

confidence: 99%

Effect of zinc and copper on cultivable populations of soil fungi with special reference to entomopathogenic fungi

Pečiulytė¹,

Dirginčiutė-Volodkienė²

2012

Ekologija

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The effect of copper and zinc on cultivable soil fungi populations was investigated in a laboratory experiment. Samples of four different soils (arable sandy soil and loam clay; forest sandy soil and forest peat) were collected from sites located in Vilnius district, Lithuania. Metals' effect was elaborated by addition of metal salts (CuSO 4 and ZnSO 4 ) at appropriate concentrations into the growth medium (Czapek's agar) and evaluating culmedium (Czapek's agar) and evaluating cultivable fungi abundance and species diversity changes. Zinc or copper salt was added to the medium after its sterilization; zinc concentration varied from 0.05 to 0.20 M (by 0.05 M concentration range) and copper concentration -from 0.5 to 3.0 mM (by 0.15 mM concentration range). At elevated metal salt concentrations, the abundance of cultivable fungi decreased with a marked elimination of some fungi species as compared with a control medium (without metal addition) fungi cultures. Irrespective of a fungi community structure in different type soils, Cu was a stronger inhibitor of soil fungi population abundance than Zn, however, both metals showed a comparable effect on the fungi species diversity. The most resistant fungi belonged to common insect pathogens (Beuveria bassiana, Metarhizium anisopliae, Lecanicillium lecanii and Isaria spp.), which dominated comprising up to 90% of all recovered from the soils isolates, due to the metal salt concentration.

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Section: Total Percentage Of Metal-resistant Entomopathogenic Fungimentioning

confidence: 99%

Effect of zinc and copper on cultivable populations of soil fungi with special reference to entomopathogenic fungi

Pečiulytė¹,

Dirginčiutė-Volodkienė²

2012

Ekologija

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“…Previous studies of Ingoldian fungi in Tai Po Kau forest by traditional cultivation methods revealed diverse taxa [9]. However, molecular methods have now become a standard approach in microbiology and have been widely exploited [3–8, 16, 19–23]. Environmental DNA-based analysis in the past has revealed fungal diversity in forest ecosystems; however, it must be noted that the DNA can persist for species which are metabolically inactive and functionally less important [21, 22].…”

Section: Introductionmentioning

confidence: 99%

Comparison of DNA and RNA, and Cultivation Approaches for the Recovery of Terrestrial and Aquatic Fungi from Environmental Samples

2012

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Estimates of fungal biodiversity from environmental samples are all subject to bias. Major issues are that the commonly adopted cultivation-based approaches are suitable for taxa which grow readily under laboratory conditions, while the DNA-based approaches provide more reliable estimates, but do not indicate whether taxa are metabolically active. In this study, we have evaluated these approaches to estimate the fungal diversity in soil and freshwater samples from a subtropical forest, and compared these to RNA-based culture-independent approach intended to indicate the metabolically active fungal assemblage. In both soil and freshwater samples, the dominant taxon recovered by all three approaches was the same (Anguillospora furtiva). This taxon was cultivable from all samples and comprised 85–86 % DNA libraries and 90–91 % RNA libraries. The remaining taxa were phylogenetically diverse and spanned the Ascomycota, Basidiomycota, and Fungi incertae sedis. Their recovery was not consistent among the three approaches used and suggests that less abundant members of the assemblage may be subjected to greater bias when diversity estimates employ a single approach.Electronic supplementary materialThe online version of this article (doi:10.1007/s00284-012-0256-7) contains supplementary material, which is available to authorized users.

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“…Moreover, no studies to date have targeted RNA to detect changes in AM fungal communities in relation to Bt cropping. Targeting RNA, in addition to DNA, is thought to provide a more comprehensive picture of community dynamics, as RNA has a faster turnover rate than DNA-based assays, which may also recover DNA from dead or inactive AM fungal cells or spores (e.g., reference 29); targeting RNA might therefore better capture changes in active fungal communities (3,23).…”

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confidence: 99%

Testing Potential Effects of Maize Expressing the Bacillus thuringiensis Cry1Ab Endotoxin (Bt Maize) on Mycorrhizal Fungal Communities via DNA- and RNA-Based Pyrosequencing and Molecular Fingerprinting

Verbruggen

Kuramae

Hillekens

et al. 2012

Appl Environ Microbiol

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eThe cultivation of genetically modified (GM) crops has increased significantly over the last decades. However, concerns have been raised that some GM traits may negatively affect beneficial soil biota, such as arbuscular mycorrhizal fungi (AMF), potentially leading to alterations in soil functioning. Here, we test two maize varieties expressing the Bacillus thuringiensis Cry1Ab endotoxin (Bt maize) for their effects on soil AM fungal communities. We target both fungal DNA and RNA, which is new for AM fungi, and we use two strategies as an inclusive and robust way of detecting community differences: (i) 454 pyrosequencing using general fungal rRNA gene-directed primers and (ii) terminal restriction fragment length polymorphism (T-RFLP) profiling using AM fungus-specific markers. Potential GM-induced effects were compared to the normal natural variation of AM fungal communities across 15 different agricultural fields. AM fungi were found to be abundant in the experiment, accounting for 8% and 21% of total recovered DNA-and RNA-derived fungal sequences, respectively, after 104 days of plant growth. RNA-and DNA-based sequence analyses yielded most of the same AM fungal lineages. Our research yielded three major conclusions. First, no consistent differences were detected between AM fungal communities associated with GM plants and non-GM plants. Second, temporal variation in AMF community composition (between two measured time points) was bigger than GM trait-induced variation. Third, natural variation of AMF communities across 15 agricultural fields in The Netherlands, as well as withinfield temporal variation, was much higher than GM-induced variation. In conclusion, we found no indication that Bt maize cultivation poses a risk for AMF.

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DNA- and RNA-derived assessments of fungal community composition in soil amended with sewage sludge rich in cadmium, copper and zinc

Cited by 43 publications

References 40 publications

Effect of zinc and copper on cultivable populations of soil fungi with special reference to entomopathogenic fungi

Effect of zinc and copper on cultivable populations of soil fungi with special reference to entomopathogenic fungi

Comparison of DNA and RNA, and Cultivation Approaches for the Recovery of Terrestrial and Aquatic Fungi from Environmental Samples

Testing Potential Effects of Maize Expressing the Bacillus thuringiensis Cry1Ab Endotoxin (Bt Maize) on Mycorrhizal Fungal Communities via DNA- and RNA-Based Pyrosequencing and Molecular Fingerprinting

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