Computational protocol: Effects of combined application of nitrogen fertilizer and biochar on the nitrification and ammonia oxidizers in an intensive vegetable soil

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Protocol publication

[…] To identify the main T-RFs, the AOB and AOA clone libraries from the control soil were constructed with the same primers used in the qPCR analysis. Following manufacturer’s instructions, clones were generated by a TOPO® TA Cloning kit (Invitrogen, Carlsbad, CA). And the T-RFLPs were transformed into numerical data using ABI 3730 × L DNA analyzer (Applied Biosystems). Phylogenetic analyses were conducted with MEGA software (Tamura et al. ). The sequences were performed using the BLAST program in the GenBank database. Nucleotide sequences of amoA genes for the clone libraries in this study have deposited in GenBank under the accession numbers MF616026–MF616122. [...] Correlation, variance analyses (ANOVA) and the multiple stepwise linear regression were performed by IBM SPSS Statistics version 21.0. Principal component analysis (PCA) were performed using R studio with VEGAN package. All figures were generated using OriginPro 8.5. […]

Pipeline specifications

Software tools MEGA, SPSS
Applications Miscellaneous, Phylogenetics
Chemicals Ammonia, Nitrogen