3.5 Species co-occurrence patterns
The co-occurrence network consisted of 3,705 associations among 1,100 OTUs (Table 2 and Fig. 5). The high power-law coefficient (R2 = 0.994) and modularity value (0.759) of the co-occurrence network indicated that the organization of the ecological network was not randomly connected and had modular structure (Table 2). The topological properties, such as average clustering coefficient and average path length in the empirical network were higher than those in the respective Erdös-Rényi random networks. Meanwhile, the small-world coefficient (46.136 ± 6.809) of the co-occurrence network was much greater than 1, suggesting that the co-occurrence network had a ‘small-world’ property.
Within the co-occurrence network, we identified 108, 616 and 376 OTUs for abundant, intermediate and rare taxa, respectively (Fig. 5a). There were 660 associations between abundant and intermediate taxa, and 674 links between rare and intermediate taxa. However, only 133 edges connected abundant and rare taxa. These results indicated that rare taxa frequently interacted more with intermediate taxa and themselves than with abundant taxa. In addition, both the degree and betweenness centrality values of abundant taxa were significantly higher than those of rare taxa (Fig. 5b).
The co-occurrence network was clearly divided into 8 major modules (Fig. 5c). Many of these modules were comprised of a group of OTUs that were phylogenetically close and belonged to the same clade (Fig. 5d). For example, modules 2 and 8 were predominated by OTUs belonging to Firmicutes and Actinobacteria, respectively. Moreover, the results of incidences of observed (O) and random (R) co-occurrence between all pairwise OTUs indicated that OTUs within the same phylum, including Verrucomicrobia, Firmicutes, Chloroflexi, Bacteroidetes, Actinobacteria, and Acidobacteria, tended to co-occur more often than expected by chance (with O/R ratios > 2.0, Table S4).
There were 28 module hubs and 10 connectors in the co-occurrence network (Fig. S6). According to the definition of keystone taxa as described in the Materials and Methods section, these module hubs and connectors can be regarded as keystone taxa. Of the 28 module hubs, 9 belonged to abundant taxa and 4 belonged to rare taxa, which were mainly affiliated with the phyla Acidobacteria, Bacteroidetes, Chloroflexi, Proteobacteria, and Verrucomicrobia (Table S5). 8 of the 10 connectors belonged to the intermediate taxa. The only connector from the abundant taxa belonged to Proteobacteria and the only connector from the rare taxa was affliated to Actinobacteria.