β-Diversity and taxonomic composition.
The patterns of bacterial and fungal β-diversity were visualized with nonmetric multidimensional scaling (NMDS) plots and tested for significant differences using analysis of similarity (ANOSIM). Bacterial β-diversity varied significantly within the study year, with May and July harboring significantly different communities from those of September and October, regardless of chronosequence age (
P = 0.001, ANOSIM with 999 permutations) (
Fig. 2a and Table S1a). The differences between May and July or between September and October were not significant (
P = 0.437 to 0.846, ANOSIM with 999 permutations) (Table S1a). All pairwise comparisons of bacterial community structure among chronosequence ages were significantly different (
P = 0.001 to 0.037, ANOSIM with 999 permutations) (Table S1b). Interestingly, the overall pattern of β-diversity across the chronosequence was maintained in each of the two clusters (
Fig. 2a), with bacterial community structure becoming more similar to those of reference sites with increasing chronosequence age. The magnitude of the shift in bacterial β-diversity within a year was comparable to that observed across decades of succession, as evidenced by separation on the NMDS plot (
Fig. 2a) and average Bray-Curtis similarity values among samples (data not shown). In contrast, fungal communities from different chronosequence ages clustered more tightly, without any overlap across ages (
Fig. 2b), and communities in each age were significantly different from all other ages (
P = 0.001, ANOSIM with 999 permutations). In contrast, intra-annual variability across months in each chronosequence age was not significant (
P = 0.146 to 0.996, ANOSIM with 999 permutations) (Table S2). In addition, multivariate dispersion analysis showed that the dispersion of bacterial communities by month and chronosequence age was not significantly different (Welch's two-sample
t test,
t = 1.629,
P = 0.147), while for fungi, the dispersion of fungal communities in each age class was significantly lower (i.e., tighter clustering) than when tested by month (Welch's two-sample
t test,
t = 3.2691,
P = 0.023).
Patterns of β-diversity were also related to soil and environmental data collected by Avera et al. (
36) at each site. Changes in temperature, moisture, total microbial biomass (TMB), substrate-induced respiration (SIR), and NH
4+ levels were significantly correlated with bacterial community shifts (
P = 0.001 to 0.041) (Table S3). Moisture and NH
4+ levels were mainly correlated with the intra-annual bacterial community shifts, with higher moisture in May and July and higher NH
4+ in September and October (
Fig. 2a). In contrast, SIR was mainly correlated with bacterial community shifts that occurred with chronosequence age, with an increase along the chronosequence. For fungi, changes in temperature, moisture, TMB, SIR, and NO
3− levels were significantly correlated with community shifts (
P = 0.001 to 0.004) (Table S3). SIR, TMB, and temperature were most strongly correlated with fungal shifts in β-diversity (
Fig. 2b), with higher SIR and TMB and lower soil temperature associated with fungal communities from older chronosequence ages than from newer ones. It is important to remember, however, that associated environmental factors could also be autocorrelated, and additional experimentation would be required to determine which might be directly driving or resulting from changes in soil microbiota.
The dominant bacterial phyla and proteobacterial classes across all samples were
Acidobacteria and
Alphaproteobacteria, respectively, representing 21.5% and 18.0% of all sequences assigned to the domain
Bacteria (
Fig. 3a). Sampling month had significant influences on some taxa, with the relative abundances of
Bacteroidetes,
Deltaproteobacteria,
Gemmatimonadetes,
Betaproteobacteria, and
Gammaproteobacteria significantly higher in May and July and the relative abundances of
Chloroflexi and
Planctomycetes significantly higher in September and October (
P < 0.05, Tukey's HSD test) (
Fig. 3b and Table S4). Chronosequence age also had significant influence on some taxa (
P < 0.05, analysis of variance [ANOVA]) (
Fig. 3c and Table S4). The relative abundances of
Actinobacteria,
Chloroflexi, and
Gemmatimonadetes were significantly higher in the 5-year sites than other sites, while the relative abundances of
Nitrospirae,
Alphaproteobacteria, and
Verrucomicrobia were significantly higher in later chronosequence ages.
Nitrospirae were higher in the 30-year and unmined (UM) sites than in the 5-year and 11-year sites,
Alphaproteobacteria were higher in the UM sites than in other sites, and
Verrucomicrobia were higher in UM sites than in the 5-, 11-, and 21-year sites (
P < 0.05, Tukey's HSD test). A summary of the most abundant OTUs that changed significantly across the chronosequence ages is presented in Fig. S6A.
Ascomycota and Basidiomycota were the dominant fungal phyla at all sites, representing 46% and 30% of classified OTUs, respectively, but their relative abundances were not clearly related to chronosequence age or sampling month. The dominant classes across all samples were Agaricomycetes (phylum Basidiomycota; 28.7%) and Sordariomycetes (phylum Ascomycota; 20.0%) (
Fig. 3d). Sampling month had significant effects on some fungal classes (
P < 0.05, ANOVA) (
Fig. 3e and Table S4). Dothideomycetes was significantly different between July and October, and incertae sedis within Zygomycota was significantly different between May and September. Chronosequence ages had significant effects on more taxa, including Dothideomycetes, Eurotiomycetes, Leotiomycetes, Sordariomycetes, Rozellomycota, and incertae sedis within Zygomycota (
P < 0.05, ANOVA) (
Fig. 3f and Table S4). The relative abundances of Dothideomycetes and Sordariomycetes were significantly higher in the 5-year sites than in other sites, while the relative abundance of Agaricomycetes was significantly higher in the UM sites than in the 5-year sites. The relative abundance of incertae sedis in Zygomycota was significantly higher in the 30-year and UM sites than in the 5- and 11-year sites. All related
P values are shown in Table S4, and the most abundant fungal OTUs that changed significantly across the chronosequence ages are summarized in Fig. S6B.
Cooccurrence network analysis.
Cooccurrence networks were generated separately for bacteria and fungi at each chronosequence age, and topological properties were calculated to characterize changes over time. The numbers of nodes and edges in the bacterial networks typically increased with increasing chronosequence age, with the unmined reference network having the highest number of nodes and edges (
Table 1). Moreover, the average degree also increased from early chronosequence ages (5 and 11 years) to later chronosequence ages (21 and 30 years) (
Table 1 and
Fig. 4). The average degree of the unmined reference bacterial network (at 11.66) is about 1.5 times those at 21 and 30 years (average degrees, 7.53 and 7.16, respectively). The networks in fungal communities, however, were markedly different from those in bacterial communities (
Table 1 and
Fig. 5). The numbers of fungal nodes and edges both peak at 21 years (
Table 1), with the fungal networks at 5 years having the smallest number of nodes and edges and the lowest average degree. The average degree of the unmined reference network is larger than that at 5 years but smaller than those at 11 years and 21 years. Overall, the nodes, edges, and average degree of fungal networks typically peaked in the middle chronosequence ages.
Networks in consecutive chronosequence ages were compared to identify overlapping nodes and edges. On average, 76% of bacterial nodes and 8% of bacterial edges in an earlier age appeared in the next age, and overlaps of both bacterial nodes and edges are significantly higher than would be expected from random (Fisher's exact test for node, P = 0.001 to 0.004; permutation test for edge with 999 permutations, P = 0.001) (Table S5). In contrast, a mean of 27% of fungal nodes and 0.5% of fungal edges in an earlier age appeared in the next chronosequence age, and the numbers of overlapping fungal nodes and edges are not significantly greater than random (Fisher's exact test for node, P = 0.872 to 0.999; permutation test for edge with 999 permutations, P = 0.614 to 0.990) (Table S5).
Among the overlapping bacterial nodes, about 30% belong to the phylum Acidobacteria, which is higher than the relative abundance of Acidobacteria among all OTUs used for network analysis (22%). Bacteroidetes and Planctomycetes were also overrepresented in overlapping nodes compared to their percentages in all OTUs, at 14% and 10% compared to 10% and 6%, respectively. In contrast, taxa that were underrepresented in overlaps included Actinobacteria (5% of overlapping nodes versus 13% of OTUs) and Alphaproteobacteria (11% of overlapping nodes versus 16% of OTUs). Among the 352 overlapping bacterial edges, 223 edges (63%) involve Acidobacteria, and 146 of 352 edges (42%) are between two Acidobacteria nodes. More broadly, about 86% of overlapping edges involve Acidobacteria, Bacteroidetes, or Planctomycetes, even though the combined relative abundance of these 3 taxa is only 38% of the total OTUs used for network analysis. Nodes involved in the overlapping edges have significantly higher degrees and closeness centrality than average (P = 0.001 to 0.006, Welch's two-sample t test), but the relative abundances of OTUs represented by those nodes are not always significantly different from average (P = 0.001 to 0.683, Welch's two-sample t test) (Table S6). The overlapping fungal nodes mainly belong to Agaricomycetes, Sordariomycetes, and Dothideomycetes, with Agaricomycetes being overrepresented (15% of overlapping nodes versus 12% of OTUs). In contrast to bacteria, there were only 3 overlapping fungal edges among all possible pairs of consecutive chronosequence ages.
The bacterial and fungal networks show different patterns of cooccurrence, typically with higher numbers of nodes and edges in bacterial networks. The bacterial networks typically contained a much higher number of interactions dominated by one large connected component that consisted of more than 65% of all OTUs (
Fig. 4). In contrast, fungal networks consisted of much fewer interactions scattered across multiple small clusters (i.e., only a few OTUs) that were discrete and densely clustered (higher clustering coefficients) (
Fig. 5 and
Table 1). It is important to note that the relatively low intra-annual turnover rates of fungi may result in less-detectable cooccurrences. However, the stark differences between the two sets of networks, which were observed consistently even when the networks were reanalyzed with a range of alternative correlation cutoffs (Fig. S3), suggest that there are real and significant differences between these sets of interactions. We also constructed bacterium-fungus cooccurrence networks with the 500 most abundant bacterial OTUs and the 500 most abundant fungal OTUs. In these networks, there are more bacterial nodes and edges than fungal (Fig. S5 and Table S8), which is consistent with our observations in the separate networks. Also, the number of bacterium-bacterium edges increased with increasing chronosequence age, while the number of fungus-fungus edges peaks at 21 years; these findings are also consistent with the trends in the separate networks. The number of bacterium-fungus edges increased with increasing chronosequence age, but they comprised only 7% of all edges on average. Additional characteristics of bacterial and fungal networks, including scale-free indices, small world indices, and modularity, are summarized in Table S7 and Fig. S4.