Relationship between the keystone species and functional roles
All
keystone taxa in the bacterial co-occurrence networks belonging to the
rare species (Table S2), indicating that rare taxa play a critical role
in the maintenance of microbial community structure. And we found that
the positive interactions between rare species and non-rare species were
greater than negative interactions.
This interactions between species
can provide the function and stability of ecosystems, for example, the
rare Symbiodinium taxa can significantly improve in the stability
of host-symbiont communities in a changing environment (Ziegler,
Eguiluz, Duarte, & Voolstra, 2018). Besides, the cooperation among
these taxa also can contribution to the adaptability of microbial
communities in complex environments, because the interaction networks
can offer a buffer for resisting the environmental disturbance (Konopka,
Lindemann, & Fredrickson, 2015). On the other hand, recent article
reported that low-abundance taxa could function as keystone species in
the rhizosphere networks (Shi et al., 2016), the disappearance or change
of these keystone species can lead to the disintegration of modules and
networks, even sub-network (Guimera & Amaral, 2005). And rare
microorganisms maintain a huge functional gene library, which can
indirectly enhance the function of abundant microorganisms (Jousset et
al., 2017). Therefore, rare taxa are equal to or more important than the
abundant taxa in sustaining the stability of ecosystems. The microbial
communities have a rich diversity of species. Each species has its own
set of genes, cell composition, and metabolic reactions, and it is
constantly in complex interaction with the surrounding environment.
Based on the
correlations
between keystone species abundance and functional abundance (Fig. 6), we
found that Pseudomonas was negatively correlated with most
functions in spring, for example, Membrane Transport, Cellular Processes
and Signaling, Immune System, Metabolism of Terpenoids and Polyketides,
Xenobiotics Biodegradation and Metabolism, and Excretory System. The
keystone species in summer were related to Cardiovascular Diseases,
Nervous System, Cell Communication, Sensory System, and
Neurodegenerative Diseases. In autumn, Bosea andHyphomicrobium were grouped together, belonging to Rhizobiales,
and participate in many of the same functions, indicating that
microorganisms with similar species composition are also similar in
functional composition.
The interactions between OTUs within the phylum or high-level taxa (Fig.
S3) indicated that taxonomically closely associated bacteria were also
ecologically closely related, which in turn also reflected their
synergistic relationships or common niche preferences. Apart from the
co-occurrence patterns between intra-phylum, such non-random patterns
also occurred between different phylum or between different high-level
taxa. A typical example was that members of the phyla Proteobacteria
were significant correlations with Bacteroidetes, Planctomycetes, and
Actinobacteria.
Relationship between the
keystone species and environmental variables
The eukaryotic phytoplankton in the
freshwater ecosystem responds rapidly and strongly to environmental
disturbances and is considered to be the most important indicators
reflecting environmental changes and ecosystem status. Most of the
keystone species detected in the eukaryotic phytoplankton co-occurrence
patterns were affiliated to the rare taxa, and only a small proportion
belong to the abundant taxa (Table S3), indicating that rare taxa are
still crucial in the aquatic ecosystem. Therefore, we studied the
different and complex responses of these keystone species to
environmental changes (Fig. 7). We found that DOC, nitrate, and Chl a
were significantly negative related to Monodus .Monoraphidium showed significantly negative correlation with
phosphate. Scenedesmus was significantly negative related to
nitrate, whereas Amphora was positive correlation with nitrate.
As the abundant taxa, Scenedesmus showed a significant positive
relationship with DOC.
The
less relevant co-occurrence pattern between OTUs within the phylum was
observed (Fig. S4), which was consistent with previous observation of
taxa over-dispersion in plant or animal natural communities (such as
sedge community and mammalian community) (Ju, Xia, Guo, Wang, & Zhang,
2014). This not only confirmed that over-dispersion of phylogeny may be
a common feature of all biological communities from microorganisms to
macro plants and animals (Hornerdevine & Bohannan, 2006), but also
showed the important influence of negative interactions (such as
competition) on community assembly.