Diversity of soil Archaea in boreal forest before, and after clear-cutting and prescribed burning
Genetic diversity of forest soil Archaea was measured by extraction of total DNA from forest soil samples followed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), Southern blot hybridization and phylogenetic analysis of archaeal 16S rDNA. Soil samples from boreal forest treated with two regeneration practices were studied: clear-cutting (A) and clear-cutting followed by prescribed burning (B) 2 years later. The samples collected 1 year after the prescribed burning included a control soil (C) from an untreated standing forest. The PCR products from the three different soil samples were cloned and analyzed by RFLP. Soil samples A, B and C gave eight, nine and six different restriction profiles, respectively. New electrophoreses were run with clones of different digestion patterns, followed by Southern blotting and DNA hybridization with two different Crenarchaeota-specific oligonucleotide probes. Selected clones were sequenced and phylogenetically characterized. It was discovered that the clones from soils A and B are similar and differ from the clones isolated from the control soil C. Both the RFLP-hybridization study of the clones and phylogenetic analysis of selected sequences from all three types of soil supported the division of the new Crenarchaeota into two subgroups. It is shown that the RFLP-hybridization technique can be successfully used for preliminary evaluation of clone diversity in the rDNA library.