Computational protocol: Chronic fertilization of 37 years alters the phylogenetic structure of soil arbuscular mycorrhizal fungi in Chinese Mollisols

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Protocol publication

[…] We used Mothur 1.32 (http://www.mothur.org/) to process the sequencing data as described by Schloss et al. (). Barcode sequences were used to assign raw data by samples and low quality sequences were trimmed and excluded to obtain valid tags. Then, operational taxonomic units (OTUs) were defined by clustering at the 97% similarity level using UPARSE (Edgar ). Taxonomy was assigned to fungal OTUs according to the NCBI nucleotide sequences database. According to Camenzind et al. () and Williams et al. (), the sequences out of Glomeromycota, as well as OTU singletons, were detected by manual BLASTing against the GenBank non-redundant nucleotide database and then removed. As a result, the sequences belonged to Glomeromycota phylum were obtained. The alpha diversity indices of AMF were calculated using Mothur (Schloss et al. ). A principal coordinate analysis (PCoA) on the basis of the weighted Fast UniFrac metric was carried out to examine the effect of inorganic and organic fertilizers on AMF community composition and to compare between-sample variations (Marsh et al. ). Redundancy analysis (RDA) was performed to visualize the effect of edaphic factors on AMF community structure using CANOCO 5.0 software.SPSS (V19, Chicago, IL, USA) was used for statistical analysis. The differences in soil chemical properties, alpha diversity indices (Chao1, PD whole tree, Shannon) and AMF community abundances among samples were analyzed using one-way analysis of variance. Tukey’s procedure was followed for paired comparisons of different treatments. In all tests, P < 0.05 was considered significant. […]

Pipeline specifications

Software tools mothur, UPARSE, Fast Unifrac
Application 16S rRNA-seq analysis
Diseases Pulmonary Fibrosis
Chemicals Phosphorus