A protocol specialized for microbial DNA extraction from living poplar wood


  • Xiao Li YU Huazhong Agricultural University, College of Horticulture and Forestry Sciences/ Hubei Engineering Technology Research Center for Forestry Information, Wuhan 430070 (CN)
  • Xing Yi HU Hubei Academy of Forestry, Wuhan 430075 (CN)
  • Xiu Xiu WANG Huazhong Agricultural University, College of Horticulture and Forestry Sciences/ Hubei Engineering Technology Research Center for Forestry Information, Wuhan 430070 (CN)
  • Xin Ye ZHANG Hubei Academy of Forestry, Wuhan 430075 (CN)
  • Ke Bing DU Huazhong Agricultural University, College of Horticulture and Forestry Sciences/ Hubei Engineering Technology Research Center for Forestry Information, Wuhan 430070 (CN)




bacterial DNA, DNA quality, fungal DNA, Populus, wet heartwood


Microbial DNA extraction is a critical step in metagenomic research. High contents of chemical substances in wood tissues always cause low microbial DNA yield and quality. Up to date, almost no specialized methods involved in microbial DNA extraction from living wood were reported. In this study, an improved protocol (M1) concerning microbial DNA extraction from living poplar wood was developed. We compared microbial DNA yield and quality by M1 with those by other seven methods, including PowerSoil DNA isolation kit (M2), two soil microbial DNA extraction methods (M3 and M4), poplar genomic DNA extraction method from wood (M5), and microbial DNA extraction method from herb stems (M6), isolating bacteria (M7) and isolating fungus (M8). Results showed that M1 yielded much better quality and concentration of microbial DNA than the other methods (M2-M8) from both poplar wetwood and sapwood tissues. Following M1 protocol, 1 g of wetwood sample could yield 272.27 ng/ul (vol=50 ul) pure microbial DNA with the absorption ratios of 1.87 (A260/A230) and 1.66 (A260/A280). For 1 g of sapwood sample, these values were 361.83 ng/ul, 1.85 and 2.24, respectively. These DNA could be stably visualized by agarose gel electrophoresis and amplified by primer sets of bacteria (16S V3-V4, 16S-V4, 16S V4-V5) and fungus (ITS1, ITS2). While, the other seven methods only obtained less or contaminated microbial DNA, which could not be amplified stably by aforementioned primer sets. Our protocol provided an approach for microbial community study in living poplar wood in a more accurate way by molecular biology techniques.


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How to Cite

YU, X. L., HU, X. Y., WANG, X. X., ZHANG, X. Y., & DU, K. B. (2022). A protocol specialized for microbial DNA extraction from living poplar wood. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 50(4), 12822. https://doi.org/10.15835/nbha50312822



Research Articles
DOI: 10.15835/nbha50312822