Diversity of fungi in organic soils under a moorland – Scots pine (Pinus sylvestris L.) gradient

Abstract

The conservation and regeneration of native Scots pine (Pinus sylvestris L.) woodlands is being actively encouraged by conservation agencies in the UK because of their high biodiversity value. In the present study, the consequences of regeneration on terrestrial fungal communities was determined in three parallel transects running from open moorland, through an intermediate zone showing seedling colonization, into a mature Scots pine forest at Abernethy Forest, Cairngorm, Scotland. Soil cores were taken at 18 m intervals along each 180 m transect, and the diversity of the soil fungal community was investigated by DGGE and sequence analysis of ITS fragments PCR-amplified from DNA extracted from soil. Analysis of DGGE profiles generated for two of the three transects indicates a clear shift in the community from the moorland region of the transects to the forest region. Whereas a few bands were present at all sampling points across the transects, the majority of bands were unique to either the moorland or forest samples. FASTA database searches of ITS sequence data generated from excised DGGE bands revealed the closest species match for each band. In some cases, the similarity of ITS sequences to database sequences was poor, but the remaining sequences were most closely related to ITS sequences of both mycorrhizal and non-mycorrhizal fungi. The data are discussed in relation to the effect of native pine woodland expansion on the soil fungal community.

Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters

“…Recently, substantial advances have been made in our understanding of the fungal community ecology in natural environments through the application of molecular techniques, including clone library construction (Borneman and Hartin, 2000), automated rRNA intergenic space analysis (Ranjard et al, 2001), terminal restriction fragment length polymorphism (Lord et al, 2002) and denaturing gradient gel electrophoresis (DGGE) (May et al, 2001;Smit et al, 2003). DGGE coupled with clone library construction has been shown to be an efficient molecular approach to study fungal communities in diverse terrestrial environments (May et al, 2001;Anderson et al, 2003;Smit et al, 2003;Anderson and Cairney, 2004;Arenz et al, 2006;Artz et al, 2007;Wang et al, 2008b). However, none of these molecular methods has been used to explore mycoplankton (that is, planktonic aquatic fungi) communities.…”

Spatial and temporal diversity of wood decomposer communities in different forest stands, determined by ITS rDNA targeted TGGE

“…The number of visible bands after electrophoresis was lower than in the case of ITS. In addition Anderson et al [2] noted that the ITS1F and ITS2 primers gave the sharpest and most consistent electrophoresis profiles in their fungal diversity study in organic soils. The primer pair efficiently amplified both asco-and basidiomycetes species in the present study as well as in Gardes and Bruns' study [9].…”

Characterization of Ectomycorrhizal species through molecular biology tools and morphotyping

“…The oligonucleotide primers amplify regions of the ribosomal DNA (rDNA), especially the ITS regions, for ECM fungi (Anderson et al, 2003). There are no specific oligonucleotide primers for ECM fungi, as the ectomycorrhizae are formed by a diverse range of fungi belonging to different phyla, families and genera of which other non-mycorrhizal species are also part (Siqueira et al, 2010).…”

“…DNA sequences with different base compositions denature at different positions in polyacrylamide gels containing a linear (DGGE) or temperature (TGGE) denaturing gradient on the basis of guanine (G) and cytosine (C) contents (Anderson, 2006) . DGGE/TGGE have been widely used in studies on microbial communities, because they are fast and visual methods to investigate communities of soil fungi, especially when the objective is to investigate changes or alterations in community composition (Anderson et al, 2003). DGGE has been used to evaluate the diversity of fungi in forest soils with ECM fungi mycelia (Pennanen et al, 2001;Anderson et al, 2003;Smit et al, 2003;Landeweert et al, 2005).…”