title: Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities.
abstract: Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants. Residual contaminants were precipitated by adding 0.6mL of 0.5M CaCl2. Four cell lysis methods were applied to test their compatibility with the pretreatment (prewashing+Ca2+flocculation) and to ultimately identify the optimal cell lysis method for analyzing fungal communities in forest soils. The results showed that pretreatment with TNP+Triton X-100+skim milk (100mM Tris, 100mM Na4P2O7, 1% polyvinylpyrrolidone, 100mM NaCl, 0.05% Triton X-100, 4% skim milk, pH 10.0) removed most soil humic contaminants. When the pretreatment was combined with Ca2+flocculation, the purity of all soil DNA samples was further improved. DNA samples obtained by the fast glass bead-beating method (MethodFGB) had the highest purity. The resulting DNA was successfully used, without further purification steps, as a template for polymerase chain reaction targeting fungal internal transcribed spacer regions. The results obtained by terminal restriction fragment length polymorphism analysis indicated that the MethodFGBrevealed greater fungal diversity and more distinctive community structure compared with the other methods tested. Our study provides a protocol for fungal cell lysis in soil, which is fast, convenient, and effective for analyzing fungal communities in forest soils.
authors.affiliation: Northwest A&F University, College of Forestry, Yangling, China; Guangxi University, Forestry College, Nanning, Guangxi 530004, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Cheng
authors.affiliation: Northwest A&F University, College of Forestry, Yangling, China; Northwest A&F University, Qinling National Forest Ecosystem Research Station, Yangling, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Hou
authors.affiliation: Purdue University, Hardwood Tree Improvement & Regeneration Center, Northern Research Station, West Lafayette, USA.
authors.forename: Keith
authors.initials: K
authors.lastname: Woeste
authors.affiliation: Northwest A&F University, College of Forestry, Yangling, China.
authors.forename: Zhengchun
authors.initials: Z
authors.lastname: Shang
authors.affiliation: Shangluo University, Department of Biological and Medical Engineering, Shangluo, China.
authors.forename: Xiaobang
authors.initials: X
authors.lastname: Peng
authors.affiliation: Northwest University,College of Life Science, Xi'an, Shaanxi 710069, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhao
authors.affiliation: Northwest A&F University, College of Forestry, Yangling, China; Northwest A&F University, Qinling National Forest Ecosystem Research Station, Yangling, China. Electronic address: sxzhang@nwsuaf.edu.cn.
authors.forename: Shuoxin
authors.initials: S
authors.lastname: Zhang
mesh_terms: D002122:Calcium Chloride; D004269:DNA, Bacterial; D004271:DNA, Fungal; D065928:Forests; D005658:Fungi / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D064307:Microbiota; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D004271:DNA, Fungal; D012987:Soil; D002122:Calcium Chloride
keywords: Cell lysis; DNA extraction method; DNA purity; Fungal community; Terminal restriction fragment length polymorphism