2.5 Community assembly processes and habitat niche breadth
To evaluate the assembly processes of microbial communities at each sampling site, the standardized effect size measure of the mean nearest taxon distance (ses.MNTD) was calculated to estimate phylogenetic clustering degrees within each community using the ‘picante’ package in R (Purcell et al., 2007). Negative and positive ses.MNTD values denote shorter and longer nearest taxon distances within a community, respectively, than expected by chance, and the level of phylogenetic clustering or dispersion, respectively (Webb et al., 2002). We also explored differences in phylogenetic turnover between samples using the between-community version of the β-mean-nearest taxon distance (βMNTD) to investigate the underlying community assembly mechanisms (Stegen et al., 2013). Differences between observed βMNTD and the null expectation based on 999 randomization repeats are divided by the standard deviation (of the null expectation) to obtain the β-nearest taxon index (βNTI) (Stegen et al., 2013). βNTI values >+2 and <-2 indicated significantly greater or less phylogenetic turnover than expected by chance, respectively, as a result of the influence of deterministic selection (e.g., environmental filtering, biotic interactions, non-random diversification) in communities, while values between -2 and +2 indicated dominance of stochastic processes (e.g., weak selection, weak dispersal, and diversification) in community assembly (Stegen et al., 2012; Zhou & Ning, 2017).
Niche breadth was calculated using the Levin’s niche breadth index (B) equation (Pandit et al., 2009):
\(B_{j\ =\ }\frac{1}{\sum_{i=1}^{N}P_{\text{ij}}^{2}}\),
where \(B_{j}\) represents habitat niche breadth of OTU \(j\) in a metacommunity; \(N\) is the total number of communities in each metacommunity; \(P_{\text{ij}}\) is the proportion of OTU \(j\) in metacommunity \(i\). A high \(B\) indicates that the OTU occurs extensively and evenly along a wide range of locations, representing wide habitat niche breadth. The average \(B\)-values of all OTUs within each sampling community (\(B_{\text{com}}\)) were calculated and indicated habit niche breadth at the community level. To evaluate the niche breadth of each phylum within a metacommunity, the average Z-scores for OTUs within each phylum were calculated on a common scale based on standard deviation units (for all taxa within the community). A microbial group with a wider niche breadth is considered more metabolically flexible in the metacommunity than other microbial groups (Luan et al., 2020). Differences in average Z-score values for each phylum in communities in different stages of grassland degradation were explored to investigate variation in niche breadth at the phylum level across different levels of degradation.