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.