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.