Surveying soil faunal communities using a direct molecular approach |
| |
Authors: | Heather C. Hamilton Kyle Wickings Noah Fierer |
| |
Affiliation: | a Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA b Odum School of Ecology, University of Georgia, Athens, GA 30602, USA c School of Forestry and Environmental Studies, Yale University, New Haven, CT 06511, USA d Department of Ecology and Evolutionary Biology, University of Colorado, Campus Box 334, Boulder, CO 80309-0216, USA |
| |
Abstract: | Soil faunal communities are often phylogenetically diverse and the accurate assessment of the taxonomic structure of these communities is both time-consuming and requires a high level of taxonomic expertise. Here we describe a DNA sequence-based methodology for characterizing soil micro- and mesofaunal communities that is similar to the molecular approaches commonly used to survey soil microbial diversity. The technique involves the direct extraction of faunal DNA from soil, PCR amplification of the extracted DNA with metazoan-specific primers, followed by the construction of clone libraries and direct sequencing of individual PCR products. We used this technique to characterize micro- and mesofaunal community composition from six individual soils representing two land-use types. The technique captured the more abundant faunal groups in the soils (nematodes, Collembola, Acari, tardigrades, enchytraeids) and provided sufficient taxonomic resolution to describe the overall structure of the communities. We compared the results obtained using this molecular approach to results obtained using a traditional, microscopy-based approach and found that the results were broadly similar. However, since biases are inherent in both methods it remains unclear which method provides a more accurate assessment of soil faunal community composition. Although this molecular approach has some distinct disadvantages over the more widely-used direct extraction methods, one advantage is that the taxonomic identification it can provide will be more accurate and consistent across research groups, facilitating effective comparisons of mesofaunal surveys. |
| |
Keywords: | Soil fauna 18S rRNA genes Small-subunit rRNA genes Soil metazoa Nematodes Collembola Acari |
本文献已被 ScienceDirect 等数据库收录! |
|