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.