Network construction
The OTUs with relative abundance<0.01% were removed to reduce
the rare OTUs in dataset. Only the OTUs occurred in more than half of
the samples were screened for the co-occurrence networks. The
co-occurrence networks were constructed based on the Spearman
correlation matrix with “Hmisc” package (Harrell, 2008). The nodes of
the networks indicated the species and the edges between them implied
the correlation between the OTUs. The P values were controlling
symmetrically for the further multiple test via the false discovery rate
(FDR) procedure (Benjamini, Krieger, & Yekutieli, 2006). A cutoff wall
was set up based on the Spearman correlation values and P values. All
the cutoff of correlation coefficient were 0.9 via random matrix
theory-based method. The cutoff of the P values for fungi and bacteria
were determined as 0.001 (Luo, Zhong, Yang, Scheuermann, & Zhou, 2006).
To simplify the network for better visualization, only fungal and
bacterial OTUs over than 30 and archaeal OTUs over than 5 were employed.
The matrix containing the information of nodes and edges were visulized
into image by Gephi platform using the algorithm of Fruchterman Reingold
(Bastian, Heymann, & Jacomy, 2009).