4 DISCUSSION
Recent studies indicated that
changes of soil microbial communities as a result of various
agricultural management practices contribute to plant performance (Zhou
et al., 2014; Gao et al., 2019). Organic farming (Reganold & Wachter,
2016), no-tillage (Ashworth et al.,
2017), and rotation (Liu et al., 2019) have attracted the most
scientific attention in the field of microbial research, while
natural fallow practice has not been
investigated in detail to this regard. Importantly,
natural
fallow practice is widely used worldwide because of labor shortage and
areas unsuitable for mechanic agriculture. Therefore, the present study
investigated the microbial mechanisms underlying the different response
of N. tabacum plants to changes of soil microbiomes induced by
natural fallow and continuous N. tabacum cropping practices.
Clearly, different environmental conditions impose different selection
forces on plants (Anderson, 2016; Jansson & Hofmockel, 2020), while
biomass accumulation and allocation strategies may vary over time and
across environments (Poorter et al., 2012). First, the effects of
microorganisms on N.
tabacum fitness were investigated by reassembling soil microbial
communities. The results indicated that
changes
of soil microbiomes significantly decreased the total biomass
accumulation, changed biomass allocation patterns, and altered the
investment strategies in N. tabacum leaves grown in FS. However,
no similar changes were observed in plants grown in CCS (Figures 1a and
b). This suggests that soil microorganisms influence plant performance
related to the abiotic soil context
(Lozano et al., 2017; Mapelli et al., 2018). The LMA level is a key
trait to assess plant growth and an important indicator for plant
strategies (Poorter et al., 2009). In the present study, LMA levels
showed a plastic response to environmental differences and plants grown
in FS preferred to invest more in leaves and acquired a high leaf
density during the process of microbial community reassembly (Figure
1c). In general, herbaceous or woody plants with a slower relative
growth ratio (RGR) have a higher LMA level (Poorter et al., 2009). Thus,
this implies that N. tabacum growth may suffer more from negative
feedback of the reassembling soil microbial communities in response to
natural fallow practice than in response to continuous cropping
practice. In summary, these results suggested that soil microorganisms
of FS play a more important role in determining N. tabacumfitness than those of CCS. Considering that, in practice, continuousN. tabacum cropping does not exceed three years, the damage from
the changes of soil microbiomes to N. tabacum growth may be
exaggerated at least within the short length of continuous cropping.
Soil microorganisms regulate many ecosystem processes and play key roles
in nutrient cycling (Bender et al., 2016). However, the community
structure and function also appear to be readily influenced by
agricultural management practices. For example, bacterial network
properties under continuous N. tabacum cropping are more
sensitive to soil variables (Chen et al., 2018), while the abundances of
several beneficial fungal species increased in a continuous soybean
cropping practice (Liu et al., 2019). The present study identified no
significant difference of microbial community richness under both
management practices. However, bacterial and fungal community richness
was higher for bulk soil in F_NS than in F_S, while no significant
differences were found between C_NS and C_S. This suggests that the
abiotic context of FS exerts stronger effects on the reassembly of soil
microbiomes (de Vries et al., 2012; Erlandson et al., 2018).
Furthermore, the taxonomy of microbial diversity indicated differences
related to the management practice (Figures 2 and S3). For example,
although Proteobacteria, Actinobacteria, and Bacteroidetes dominated
both sample types, Firmicutes showed a relatively higher abundance in
CCS than in FS. Previous studies indicated that Firmicutes was closely
related to organic management (Hartman et al., 2018) and functioned in
response to receiving manure fertilizer (Hartmann et al., 2014). Hence,
this implies that relatively lower abundance of Firmicutes OTUs in FS
may result in a low nutrient utilization efficiency on the bacterial
level. This indirectly influenced N. tabacum growth, and finally
decreased biomass accumulation. Moreover, PCoA showed marked differences
among fungal communities of bulk soil; however, there was no significant
difference in the rhizosphere of fungal communities (Figure 3). This
indicates that the rhizosphere serves as a carbon-rich niche for the
establishment of microbial communities while bulk soil is rapidly
depleted of carbon and other nutrients by heterotrophic microbes (Sasse
et al., 2018). Thus, this further suggests that similar colonization and
coexistence conditions for fungi may exist in rhizosphere of N.
tabacum plants both under continuous cropping and natural fallow
practice. The results of the present study are consistent with a
previous study, showing that species richness was less variable in the
responses to different cropping systems than species composition
(Hartman et al., 2018).
In addition, this study highlighted the differences of context-specific
microbial clades between CCS and FS (Figures 4a and b; Tables 1 and 2).
Several bacterial groups, such as Firmicutes and Actinobacteria, only
showed significant enrichment in the bulk soil and rhizosphere of C_NS.
This suggested that these bacterial groups were associated with
receiving both manure fertilizer (Hartmann et al., 2014 and 2018) and
soil fertility (Mapelli et al., 2018). In parallel, several bacterial
groups were also found to be exclusively enriched in F_NS. For example,
previous studies implied that Sphingomonadales (including family
Sphingomonadaceae) has the ability to degrade a wide range of aromatic
compounds (Balkwill et al., 2006), cope with stress conditions, and
adapt to new habitats (Vaz-Moreira et al., 2011). Therefore, it has been
suggested that the relatively high abundance of Sphingomonadales found
in FS may be useful to improve N. tabacum growth environments.
Several key microbes involved in Xanthobacteraceae contribute to
nitrogen cycling (Zhu et al., 2018). The present study showed that
Xanthobacteraceae were significantly enriched in rhizosphere in F_NS,
suggesting that these microorganisms in the rhizosphere may play a key
role in helping N. tabacum plants to acquire nitrogen nutrition
when they grow in FS. In addition to bacterial clades, several fungal
clades, such as Rozellomycota, Eurotiomycetes, and Sordariomycetes, were
exclusively detected in the bulk soil in F_NS. This suggests that these
play distinct roles in the plant-soil feedback when N. tabacumplants are grown in FS. The fungal class Leotiomycetes (family
Myxotrichaceae and genus Oidiodendron ) was significantly enriched
in rhizosphere in C_NS. Myxotrichaceae is cellulolytic, and was implied
to play a significant role in the decomposition dynamics of litter (Rice
et al., 2006). Tremellomycetes and Dothideomycetes dominated the
rhizosphere in F_NS and may result in the difference between the
structural and functional differences from C_NS. Moreover, this study
also documented specific microbial clades in the reassembling soil
microbial communities (Figure 4c, Table S3). For example, the bacterial
family Rhodanobacteraceae, which belongs to the class of
Gammaproteobacteria, dominated the rhizosphere in F_S, and was implied
to have the capacity to degrade polycyclic aromatic hydrocarbons (Cazals
et al., 2019). Importantly, no fungal clade was significantly enriched
among the reassembled fungal communities. This again suggests that
similar colonization and coexistence conditions may exist for fungi in
the rhizosphere of N. tabacum . In conclusion, these differences
in composition suggest that not only plant performance (Sasse et al.,
2018), but also the specific differences in the abiotic context exert
distinct effects on the reassembly of the soil microbiome.
As far as we know, several common factors, including abiotic and biotic
factors, likely lead to the assembly of a core microbiome (Naylor et
al., 2017; Erlandson et al., 2018; Lundberg & Teixeira, 2018;
Perez-Jaramillo et al., 2019). In the present study, only 24.1%
bacterial OTUs and 13.2% fungal OTUs were identified as the core
microbiomes (Table S4), suggesting that most OTUs were specific and thatN. tabacum plants may have a strong strength of rhizosphere
effect. Previous studies suggested that the strength of the rhizosphere
effect is likely associated with the developmental stage of a plant
(Chaparro et al., 2013), root exudation (Zhalnina et al., 2018), host
genotype (Bulgarelli et al., 2015), and domestication (Edwards et al.,
2019). This study further compared the compositional differences between
bulk soil and rhizosphere and identified several context-specific
microbial species, especially those exclusively enriched in the
rhizosphere (Tables S5 and S6). This suggested that those species likely
elucidate the differences of rhizosphere bacterial and fungal
microbiomes between FS and CCS.
5 CONCLUSIONS
The findings of the present study imply that specific microbial
community assembly and especially a number of context-specific microbial
clades under different management practices (continuous cropping and
natural fallow) may lead to different growth and development inN. tabacum . In addition, a
set of positive changes of soil microbiomes induced by the natural
fallow practice could not completely enhance N. tabacum fitness,
while additional agricultural management practices such as targeted
microbial fertilizer application or rotation may compensate for the
shortcomings arising from a single measure.