Unraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. Here, we used high-throughput sequencing to examine the relative contribution of selective and neutral processes in the assembly of abundant and rare subcommunities from three subtropical bays of China. We found that abundant and rare bacterial taxa were distinctly different in diversity, despite the similar biogeographic patterns and strong distance-decay relationships, but the dispersal of rare bacterial taxa was more limited than that of abundant taxa. Furthermore, the environmental (selective processes) and spatial (neutral processes) factors seemed to govern the assembly and biogeography of abundant and rare bacterial subcommunities, although both factors explained only a small fraction of variation within the rare subcommunity. More importantly, variation partitioning (based on adjusted R2 in redundancy analysis) showed that spatial factors exhibited a slightly greater influence on both abundant and rare subcommunities compared to environmental selection; however, the abundant subcommunity had a much stronger response to spatial factors (17.3% of pure variance was explained) than that shown by the rare bacteria (3.5%). These results demonstrate that environmental selection and neutral processes explained the similar biogeographic patterns of abundant and rare subcommunities, but a large proportion of unexplained variation in the rare taxa (91.1%) implies that more complex assembly mechanisms may exist to shape the rare bacterial assemblages in the three subtropical bays.

Background Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity. Results Here, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics. Conclusions Our findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture.

Recent research has greatly expanded our understanding of microbial metacommunities in aquatic ecosystems. However, patterns at the mesoscale are still poorly understood. We present the first simultaneous analyses of the biogeography and co-occurrence patterns of generalists and specialists marine bacteria from three subtropical bays of China and test for signals of ecological processes (i.e., stochastic and deterministic processes) in biogeography and community assembly. Results showed that compared to specialists, bacterial generalists were less diverse, and were more widely dispersed in the three subtropical bays. Network analysis indicated that both habitat generalists and specialists showed non-random co-occurrence patterns, and specialists had a more complex co-occurrence pattern than generalists. Further, specialists co-occurrence network exhibited distinct robust structure compared to generalists, indicating that the both taxa showed different network stability. Our null models indicated that the generalists and specialists were primarily shaped by deterministic processes-such as variable selection. However, deterministic processes played a greater role in the community variation of specialists (84%) than generalists (56%). The study has broadened our understanding of generalists and specialists distribution in the bacterioplankton; further revealing the dominant roles of similar ecological mechanisms (deterministic processes) in shaping the community assembly. The differences in complex and stable co-occurrence pattern between generalists and specialists could be driven by deterministic processes. By considering the roles of species traits and ecological processes, we provide a deeper mechanistic understanding of bacterial biogeographical and coexistence patterns.