3. RESULTS
3.1 Variation in
multifunctionality
We first explored the vertical variation in multifunctionality in desert
ecosystems. Overall, the multifunctionality index did not exhibit a
significant difference between whole superficial soils (0-20 cm) and
deep soils (20-100 cm) (p > 0.05) and slightly
decreased as soil depth increased through the soil profiles (Fig. 1 a,
b). We also found that the multifunctionality index significantly
decreased along the desertification gradient (Fig. 1 c) but did not show
different changes with depth between the superficial and deep soils
(Fig. 1 d).
Three individual functional indexes (C, N, and P processes) were
evaluated (Figure S1). Overall, the C and N processes were higher at the
potential desertification (PD) sites but did not show different changes
between the moderate desertification (MD) and severe desertification
(SD) sites. However, the P process did not differ between the whole
superficial and deep layers along the desertification gradient. The C
process did not exhibit a significant difference between superficial
soil and deep soil at the MD and SD sites. The N process differed
between superficial soil and deep soil at only the SD sites. The C and N
processes typically decreased as the soil depth increased throughout the
entire profile.
3.2 Variation in soil
microbiomes
We acquired a total of 5490761, 7562145, and 5357782 high-quality
bacterial, fungal, and archaeal sequences (from the 125 samples), which
were classified into 4890, 7723, and 3246
operational taxonomic units (OTUs), respectively. Bacteria were mainly
composed of the phyla Actinobacteria (40.06%), Proteobacteria
(27.23%), Chloroflexi (8.26%), and Acidobacteria (7.89%). Fungi were
mainly composed of the phyla Ascomycota (69.70%), Basidiomycota
(9.85%), and Zygomycota (5.39%). Archaea were mainly composed of the
phyla Thaumarchaeota (81.34%) and Euryarchaeota (15.27%). Overall,
Acidobacteria, Chloroflexi, and Thaumarchaeota typically increased,
while Actinobacteria, Proteobacteria, and Euryarchaeota significantly
decreased during the process of desertification (Figure S2).
Regarding the soil profiles, distinct variation trends of the
microbiomes were observed along the desertification gradient. First,
Ascomycota, Basidiomycota, Euryarchaeota and Thaumarchaeota did not
differ between the superficial and deep layers at any desertification
stage. In contrast to Proteobacteria, Acidobacteria, Actinobacteria and
Chloroflexi in the superficial soils were much richer than those in the
deep soils (Figure S3). Second, Acidobacteria, Actinobacteria,
Chloroflexi, and Thaumarchaeota significantly decreased and
Proteobacteria significantly increased as soil depth increased (Figure
S4). The most abundant phyla of bacteria, fungi, and archaea showed
distinct variation trends as soil depth increased along the
desertification gradient (Figure S5). The significance of the primary
phyla composing the microbiomes was confirmed by a Kruskal-Wallis H test
and least-squares linear regression analysis.
The alpha-diversity levels of the soil microbiomes were all higher at
the PD and MD sites than at the SD sites, except for the Shannon index
for archaea (Fig. 2). As soil depth increased, bacterial, fungal and
archaeal diversity exhibited different fluctuating trends in the desert
ecosystems. The Shannon and phylogenetic diversity indexes of bacterial
diversity significantly decreased as soil depth
increased,
and the phylogenetic diversity index of fungi significantly decreased,
but the Shannon diversity index of archaea significantly increased as
soil depth increased. Vertical variation tendencies were determined by
least-squares linear regression models. In addition, distinct variation
tendencies for alpha diversity were detected during the desertification
process (Figure S6). The Shannon index of bacteria at the SD sites and
the phylogenetic diversity index of bacteria did not exhibit different
changes between superficial and deep soils. The alpha diversity of fungi
in superficial and deep soils did not exhibit different changes, except
at the PD sites. The alpha diversity of archaea in superficial and deep
soils did not exhibit different changes, except for the Shannon index at
the MD sites.
NMDS analysis suggested that soil microbiomes at different
desertification sites formed distinct clusters in ordination space (Fig.
3). The significant spatial variations in species composition were
further confirmed by ANOSIM and ADONIS tests (Table S3). These
variations were the highest for bacteria, followed by fungi and archaea,
suggesting that the bacterial communities were more likely to be
reshaped by desertification. We observed different changes in
microbiomes between superficial and deep soils (Fig. 3 and Table S4).
These changes were larger for bacteria and archaea than for fungi,
suggesting that the bacterial and archaeal communities had higher
feedbacks with soil depths. The significant variations in beta diversity
among different microbiomes were evaluated and identified (Fig. 3).
Fungi exhibited the highest beta diversity, suggesting a higher
community dispersion level. The vertical spatial variation (VDR) of
different microbiomes was compared among the desertification sites. We
further found that the VDR slopes of the soil microbiomes at the PD
sites were steeper than those at the MD and SD sites. The bacterial and
archaeal VDR slopes were significantly steeper than the fungal VDR
slopes, suggesting that desertification markedly enhanced the vertical
variation in bacterial and archaeal communities but had less effect on
the variation in fungal communities.
3.3 Links between the microbial community and
multifunctionality
The relationships between the microbial community and multifunctionality
in desert ecosystems were explored (Figs. 4 and 5). The dominant
bacterial and archaeal phyla were significantly (P <
0.01) related to multifunctionality, but the dominant fungal phyla did
not exhibit different relationships (P > 0.05) (Fig.
4). The soil microbial diversity of bacteria and fungi was positively
related to multifunctionality, while archaeal diversity showed the
reverse pattern (Fig. 5). Further analyses provided evidence that
dominant species (Acidobacteria and Chloroflexi) and the fungal
phylogenetic diversity index had significantly stronger and more
positive correlations with multifunctionality than did microbial
diversity (Shannon and phylogenetic diversity indexes). Furthermore, we
found significantly stronger and more positive correlations between
microbial diversity and individual functions (i.e., C, N, and P
processes), as well as between this diversity and combinations of
functions (i.e., C and N, N and P, C and P, and C, N, and P processes)
(Table S5). In particular, Acidobacteria, Chloroflexi and fungal
phylogenetic diversity were positively and strongly related to the
individual functions and combinations of functions.
3.4 Accounting for soil multifunctionality drivers in desert
ecosystems
Random forest modelling was adopted to determine and compare the most
important predictors of multifunctionality in desert ecosystems. We
found that Acidobacteria and fungal phylogenetic diversity were more
important than the other multifunctionality predictors (Fig. 6 a). The
predominant predictors of multifunctionality differed between
superficial and deep soils (Fig. 6 b, c). While the fungal phylogenetic
diversity index best predicted multifunctionality in superficial soils,
Acidobacteria
and Thaumarchaeota were instead pivotal in deep soils. Further, the
microbial species index was the predominant predictor of
multifunctionality (Fig. 6 d).
Our structural equation modelling (SEM) explained 65.0% of the variance
in multifunctionality at the desertification sites (Fig. 7). The
microbial species index appeared to have a distinctly stronger total
positive effect than the biodiversity index on multifunctionality (Fig.
7 and Figure S7). Depth and soil electrical conductivity (EC) had the
strongest total positive effects on multifunctionality, as indicated by
the standardized total effects from SEM.