Kit-based, low-toxicity method for extracting and purifying fungal DNA from ectomycorrhizal roots

Resistance and recovery of soil microbial communities in the face of Alliaria petiolata invasions

Invaders can gain ecological advantages because of their evolutionary novelty, but little is known about how these novel advantages will change over time as the invader and invaded community evolve in response to each other. Invasive plants often gain such an advantage through alteration of soil microbial communities. In soil communities sampled from sites along a gradient of invasion history with Alliaria petiolata, microbial richness tended to decline, but the community's resistance to A. petiolata's effects generally increased with increasing history of invasion. However, sensitive microbial taxa appeared to recover in the two oldest sites, leading to an increase in richness, but consequent decrease in resistance. This may be because of evolutionary changes in the A. petiolata populations, which tend to reduce their investment to allelopathic compounds over time. These results show that, over time, microbial communities can develop resistance to an invasive plant but at the cost of lower richness. However, over longer time-scales evolution in the invasive species may allow for the recovery of soil microbial communities.

Nucleic Acid Isolation from Ecological Samples—Fungal Associations, Mycorrhizae

Mycorrhizal fungi are among the most common symbioses found in terrestrial ecosystems, both natural and managed. They are important for many reasons, but most notably because of their positive effects on plant growth, which are mediated by their uptake of nutrients from the soil and transport of these to the roots. Moreover, many edible fungi are mycorrhizal. The study of mycorrhizal fungi has been hampered by the inability to identify species and individuals in the soil. This has been greatly aided by DNA-based methods, which first require the extraction of DNA. Herein, I discuss some general concerns that must be considered when extracting and purifying DNA from ecological samples and offer specific methods for soil, mycorrhizal roots, and fruiting bodies. These methods are rapid, safe, effective, relatively inexpensive, and convenient because they are based on commercially available kits.

Rapid and reliable DNA extraction techniques from trypan-blue-stained mycorrhizal roots: comparison of two methods

Two improved DNA extraction techniques from trypan-blue-stained root fragments were developed and compared for rapid and reliable analyses. In Method A, 1 cm trypan-blue-stained mycorrhizal root fragments were individually isolated, crushed by bead beating, and purified with Chelex-100 (Bio-Rad). In Method B, DNA extraction was carried out using an UltraClean microbial DNA isolation kit (MoBio Laboratories). DNA was extracted from the mycorrhizal roots of four plant species, quantified by UV absorbance, and PCR-amplified with primers specific to arbuscular mycorrhizal fungi. Although PCR inhibitors might still exist when using Method A, appropriate dilution and employment of nested-PCR overcame this problem. Method B removed PCR inhibitors, but sometimes, depending on the mycorrhizal colonization within the root fragments, it also required nested PCR. In conclusion, both methods enabled us to handle many samples in a short time. Method B provided greater reliability and Method A provided better cost performance. Both techniques can be useful for PCR-based applications to identify species and estimate species composition after measuring mycorrhizal colonization rate with trypan blue staining.

Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis

•   Niche differentiation for different soil substrates has been proposed as a mechanism contributing to ectomycorrhizal fungal diversity. This hypothesis has been largely untestable because of a lack of techniques to study the in situ distribution of ectomycorrhizal hyphae. •   We developed a technique involving soil DNA extraction, PCR and terminal restriction fragment length polymorphism (T-RFLP) analysis for species identification to investigate the vertical distribution of fungal hyphae in four distinct layers of the forest floor (lower litter, F-layer, H-layer, and B-horizon) of a Pinus resinosa plantation. •   Fungal communities differed markedly among the four layers. Cluster analysis suggested six different patterns of resource utilization: litter-layer specialists, litter-layer generalists, F-layer, H-layer, and B-horizon species, and multilayer generalists. Known ectomycorrhizal species were found in all six clusters. •   This spatial partitioning observed among ectomycorrhizal fungi along a single, relatively simple substrate-resource gradient supports the niche differentiation hypothesis as an important mechanism contributing to ectomycorrhizal fungal diversity.