The 11 ribosome and chloroplast genes reveal the laws of various biological changes, interactions and synchronous aggregation in large shallow lakes

The mechanisms maintaining microbial community structure is strongly debated, referring to deterministic or stochastic process. How both prokaryotic and eukaryotic microbes in large shallow assemble and interact synchronously is crucial to understand bloom spread. Here we firstly employed comprehensive eleven ribosomal (nine of 18S, 28S, 16S) and chloroplast (two of rbcL) metabarcoding genes to unveil the synchronous activities of community assembly process, seasonal dynamics, distance-decay and co-occurring patterns for all of bacteriophankton (Bac), cyanobacteria (Cya), eukaryotic phytoplankton, zooplankton (Zoo) and fungi (Fun) between spring and summer in Tailake, with 116 samples for each season. The community composition and alpha diversity of all taxonomic groups varied between seasons. The bacteriophankton exhibited similar beta diversity between seasons whereas all other groups showed dinstinct patterns. While water temperature and NO3--N contributed to the diversity variation of all groups between seasons the envornmental factors slightly affect their variation among the lake regions. The cyanobacteria and zooplankton community similarity decreased with the increasing of geographic distance in summer whereas bacteriophankton, eukaryotic phytoplankton, zooplankton and fungi had no correlation between diversity similarity and distance. The diversity similarity of cyanobacteria and zooplankton was also positively correlated. The neutral model showed that the stochastic processes had influence in all groups in both seasons with more contribution to bacteriophankton community variation. All groups featured complex co-occurring patterns from each other and tended to be positive associated, with different patterns in both seasons. The Chlorophyta (Chlo), Bacillariophyta (Baci) and other eukaryotic phytoplankton exhibited no completely same seasonal dynamics and community assembly. Overall, our results indicated that the distance, dispersal capacity, environmental factors and biointeractions have different degree of affect for community assembly of various prokaryotic and eukaryotic microbes in large shallow lake between seasons. We also confirmed that different amplicon genes obtained different taxa assigenments, and different sample size featured different community dynamics evaluation. We strongly suggest researchers choose multiple gene markers and large samples size to get relatively accurate and powered conclusion for microbial community activities.