Microbial Community Composition in Soils Amended with Biomass-Derived Charcoal (Biochar) as Assessed by T-RFLP Fingerprinting of Genomic DNA.

Adding biochar to agricultural soils is being used increasingly as a means to improve soil fertility and sequester carbon (C). Yet, the effects of biochar on soil microbial communities in temperate areas are not well known. We investigated changes in soil microbial community composition by use of terminal restriction fragment length polymorphism (T-RFLP) PCR fingerprinting. Bulk and rhizosphere soils were sampled from an ongoing experiment in Aurora, NY, where soils were amended with 0, 3, 12, and 30 kg ha^-1 corn stover biochar. We compared three widely used DNA extraction protocols: M-1, modified from LaMontagne et al. (2002); M-II, MoBio Powersoil^TM DNA extraction kit (Cambio, Cambridge, UK); and M-III, MoBio UltraClean^TM Soil DNA extraction kit (Cambio), for their ability to extract genomic DNA from biochar-amended soils. DNA yield, purity, and ability to PCR amplify the 16S rRNA genes of bacteria and the ITS region of fungi were compared. The presence of biochar in soil significantly decreased DNA recovery efficiency of all three methods, with the recovery rate ranging from 1.6 - 6.1%. In the presence of biochar, M-I and M-II extracted more DNA than M-III. However, use of M-II and M-III yielded higher quality DNA and resulted in improved PCR amplification, regardless of the biochar amendment rate. The highest efficiency (yield plus purity) of DNA extraction was observed for M-II. Interactive Principal Component Analysis (IPCA) of T-RFLP fingerprint data suggested that the extraction method had no significant effect on the profiles generated, which were reproducible across multiple analyses. There were highly significant effects of biochar amendment rate and sampling location (bulk vs rhizosphere) on both bacterial and fungal community composition. Cloning and sequencing of PCR amplicons is being used to further dissect the dominant changes in community composition and assess their impact on diverse soil processes.