Bacteria play key roles in the ecology of both aquatic and terrestrial ecosystems; however, little is known about their diversity and biogeography, especially in the rare microbial biosphere of inland freshwater ecosystems. Here we investigated aspects of the community ecology and geographical distribution of abundant and rare bacterioplankton using high-throughput sequencing and examined the relative influence of local environmental variables and regional (spatial) factors on their geographical distribution patterns in 42 lakes and reservoirs across China. Our results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance-decay relationship. This suggests that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa. However, we identified some differences between the abundant and rare groups as both groups of bacteria showed a significant positive relationship between sites occupancy and abundance, but the abundant bacteria exhibited a weaker distance-decay relationship than the rare bacteria. Our results implied that rare subcommunities were mostly governed by local environmental variables, whereas the abundant subcommunities were mainly affected by regional factors. In addition, both local and regional variables that were significantly related to the spatial variation of abundant bacterial community composition were different to those of rare ones, suggesting that abundant and rare bacteria may have discrepant ecological niches and may play different roles in natural ecosystems.

All investigated reservoirs were eutrophicated based on the comprehensive TSI values; thus, our results provided an early warning of water degradation in Fujian reservoirs. Furthermore, the trophic state plays an important role in shaping community structure and in determining species diversity of algae. Therefore, long-term and regular monitoring of Euglenophyta, Cyanophyta, TN, TP and chlorophyll a in reservoirs is urgently needed to further understand the future trend of eutrophication and to develop a watershed-based strategy to manage the Cyanophyta bloom hazards.

Microbes are key components of aquatic ecosystems and play crucial roles in global biogeochemical cycles. However, the spatiotemporal dynamics of planktonic microbial community composition in riverine ecosystems are still poorly understood. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified 16S and 18S rRNA gene fragments and multivariate statistical methods to explore the spatiotemporal patterns and driving factors of planktonic bacterial and microbial eukaryotic communities in the subtropical Jiulong River, southeast China. Both bacterial and microbial eukaryotic communities varied significantly in time and were spatially structured according to upper stream, middle-lower stream and estuary. Among all the environmental factors measured, water temperature, conductivity, PO4-P and TN/TP were best related to the spatiotemporal distribution of bacterial community, while water temperature, conductivity, NOx-N and transparency were closest related to the variation of eukaryotic community. Variation partitioning, based on partial RDA, revealed that environmental factors played the most important roles in structuring the microbial assemblages by explaining 11.3% of bacterial variation and 17.5% of eukaryotic variation. However, pure spatial factors (6.5% for bacteria and 9.6% for eukaryotes) and temporal factors (3.3% for bacteria and 5.5% for eukaryotes) also explained some variation in microbial distribution, thus inherent spatial and temporal variation of microbial assemblages should be considered when assessing the impact of environmental factors on microbial communities.

Microorganisms play pivotal roles within aquatic ecosystems, affecting their structure, functioning and services. However, little is known about the effects of water stratification and mixing on the aquatic microbial community dynamics in subtropical reservoirs. In this study, we explored vertical and seasonal patterns of microbial diversity in the Dongzhen Reservoir (southeast China). Quantitative PCR, quantitative RT-PCR, and 454 pyrosequencing were used for an in-depth characterization of the bacterial community across time (every three months for one year) and space (five different water depths). Our results indicated that thermal and oxygen stratification shaped the phylogenetic composition of microbial communities in the reservoir. There were significant differences in physical, chemical and microbiological parameters between epilimnion and hypolimnion (P < 0.05). The RNA: DNA ratios were significantly lower in epilimnion and metalimnion but rapidly increased in hypolimnion (P < 0.05), suggesting that microorganisms were more active at low temperatures, low dissolved oxygen concentrations and high TN/TP ratios. Redundancy analysis and pathway analysis revealed a complex interplay of various environmental and biological factors by explaining the spatiotemporal variations in bacterial communities. Adaptive reservoir management strategies should consider carefully the effects of water stratification and mixing, together with the distribution patterns of aquatic microorganisms.

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Although it is widely recognized that cyanobacterial blooms have substantial influence on the plankton community in general, their correlations with the whole community of eukaryotic plankton at longer time scales remain largely unknown. Here, we investigated the temporal dynamics of eukaryotic plankton communities in two subtropical reservoirs over a 6-year period (2010–2015) following one cyanobacterial biomass cycle—the cyanobacterial bloom (middle 2010), cyanobacteria decrease (late 2010–early 2011), non-bloom (2011–2014), cyanobacteria increase, and second bloom (late 2014–2015). The eukaryotic community succession that strongly correlated with this cyanobacterial biomass cycle was divided into four periods, and each period had distinct characteristics in cyanobacterial biomass and environments in both reservoirs. Integrated co-occurrence networks of eukaryotic plankton based on the whole study period revealed that the cyanobacterial biomass had remarkably high network centralities, and the eukaryotic OTUs that had stronger correlations with the cyanobacterial biomass exhibited higher centralities. The integrated networks were also modularly responded to different eukaryotic succession periods, and therefore correlated with the cyanobacterial biomass cycle. Moreover, sub-networks based on the different eukaryotic succession periods indicated that the eukaryotic co-occurrence patterns were not constant but varied largely associating with the cyanobacterial biomass. Based on these long-term observations, our results reveal that the cyanobacterial biomass cycle created distinct niches between persistent bloom, non-bloom, decrease and increase of cyanobacteria, and therefore associated with distinct eukaryotic plankton patterns. Our results have important implications for understanding how complex aquatic plankton communities respond to cyanobacterial blooms under the changing environments.

Reservoirs are an important source of water supply in many densely populated areas in southeast China. Phytoplankton plays an important role in maintaining the structure and function of these reservoir ecosystems. Understanding of seasonal succession in phytoplankton communities and its driving factors is essential for effective water quality management in drinking-water reservoirs. In this study, water samples were collected monthly at the surface layers of riverine, transitional, and lacustrine zones from May 2010 to April 2011 in Tingxi Reservoir, southeast China. The phytoplankton showed distinct seasonal shifts in community structure at both taxonomic and functional levels. Cyanophyta was the dominant group in summer, especially species of Raphidiopsis in May and Aphanizomenon in June, and cyanobacterial dominance was promoted by both warmer conditions and excessive nutrients loading. Cyanophyta was gradually replaced by Cryptophyta (e.g., Chroomonas caudata) in abundance and by Bacillariophyta (Fragilaria sp. or Synedra sp. and Melosira sp.) in biomass with decreasing temperature. It appeared that seasonal shifts in phytoplankton composition were closely related to climate, nutrient status, and hydrology in this reservoir. Our partial RDA results clearly showed that water temperature and nutrients (TN and TP) were the most critical factors driving phytoplankton community shift in the abundance and biomass data, respectively. Further, with the global warming, cyanobacterial blooms may increase in distribution, duration, and intensity. In our study, the abundance and biomass of cyanobacteria had significant and positive correlations with temperature and phosphorus. Therefore, a stricter limit on nutrient input should be a priority in watershed management to protect drinking water from the effects of cyanobacterial blooms, especially in high-temperature period.