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Abstract In aquatic ecosystems, both phytoplankton and bacteria play pivotal roles. Based on 16S rRNA gene sequencing, considerable research focused on phytoplankton colony attached and free-living bacteria has revealed the close relationship between them, and indicated that the entire bacterial community mediates crucial biogeochemical processes in aquatic ecosystems. However, our understanding of their distribution patterns and response to environmental factors remains poor. Besides, picocyanobacteria, which were omitted from attached bacteria analysis, were reported to be important in cyanobacterial blooms. To explore the spatiotemporal variation of the entire bacterial community with their driving environmental factors and detect the relationships among them, we collected 61 water samples spanning one year and the entire Lake Taihu regions for surveying the entire bacterial community. Our results indicated: 1) seasonal variation of the bacterial community composition was stronger than spatial variation due to the clearly seasonal variation of Microcystis , Synechococcus (pico-cyanobacteria) and other bacteria (Actinomycetales , Pirellulaceae and Sphingobacteriaceae); 2) the spatial distribution of the bacterial community showed that different phyla were dominant in different regions; 3) the bacterial co-occurrence networks varied seasonally and were dominated by Microcystis, ACK-M1, Chthoniobacteraceae, Synechococcus, Pirellulaceae and Pelagibacteraceae ; 4) phytoplankton density, chlorophyll a , water temperature and total nitrogen were the major factors that drove the spatiotemporal variation of bacterial community composition. This study revealed the seasonal succession and spatial distribution of the entire bacterial community in Lake Taihu, providing new insights into the relationship between water bloom-forming cyanobacterial species and other bacteria, and their response to environmental factors in eutrophic freshwater ecosystem. Graphical abstract Unlabelled Image Highlights • Analyzed the seasonal and spatial dynamics of the entire bacterial community composition involved in cyanobacterial blooms • Found strong seasonal but weak spatial succession in bacterial community composition due to the cyanobacterial variation • Explored the relationships among Microcystis , Synechococcus (pico-cyanobacteria) and their related bacteria • Determined the main factors that drove the spatiotemporal variation of bacterial community composition [ABSTRACT FROM AUTHOR]

• Analyzed the taxonomic and functional dynamics of microbial community to algal blooms. • Constructed 161 high-quality metagenome-assembled genomes by binning analysis. • Cyanobacterial strains showed diverse energy pathways, transporters and prokaryotic defense systems. • Nitrogen and phosphorus influence the microbial structure by affecting co-pathways. Freshwater lakes are threatened by harmful cyanobacterial blooms, whose basic unit is Cyanobacterial Aggregate (CA). CA-attached bacteria play a significant role through different blooming stages with substantial variation of their taxonomic structure. However, little is known about their functional variations and functional links with cyanobacteria due to the lack of reference genomes. In this longitudinal study, we collected 16 CA samples from Lake Taihu, one of China's largest freshwater lakes, from April 2015 to February 2016, and sequenced their V4 region of 16S rRNA genes, full metagenomes (MG), and metatranscriptomes (MT). The analysis of these data revealed the dynamics of microbial taxonomic and functional structure in CAs, influenced by both external environmental factors and internal metabolism. 55 OTUs, 456 genes, and 37 transcripts showed significantly differential abundance across the early, middle, and late blooming stages (ANOVA test, P < 0.05). Total nitrogen and total phosphorus were proved to be the most important environmental drivers of microbial taxonomic and functional variations in CAs (Mantel's r > 0.25, P < 0.05). We constructed 161 high-quality metagenome-assembled genomes (MAGs), out of which 22 were cyanobacterial strains with diverse energy pathways, transporters and prokaryotic defense systems. Based on these MAGs, we constructed a cyanobacteria-bacteria co-nitrogen-pathway and a cyanobacteria-bacteria co-phosphorus-pathway, by which we demonstrated how nitrogen and phosphorus influence the dynamics of the microbial structure to a certain extent by affecting these co-pathways. Overall, these results characterized the taxonomic, functional, and transcriptional variations of microbes in CAs through different blooming stages. Genome assembly and metabolic analysis of cyanobacteria and their attached bacteria suggested that the material exchange and signal transduction do, indeed, exist among them. Our understanding of the underlying molecular pathways for cyanobacterial blooms could lead to the control of blooms by interventional strategies to disrupt critical microbes' expression. [Display omitted] [ABSTRACT FROM AUTHOR]

Cyanobacterial blooms represent a significant environmental problem, threatening aquatic ecosystems worldwide. Caused by the eutrophication of water bodies and global climate change, these blooms have altered freshwater ecosystems worldwide during recent decades. Although cyanobacterial blooms are typically caused by blue-green cyanobacteria, which derive their color from the phycocyanin pigment, other pigmented cyanobacterial blooms have been frequently observed in water bodies. These blooms pose a serious environmental threat to inland waters, endangering global public health and aquatic ecosystems. Therefore, comprehending the mechanism of color variation in cyanobacterial blooms is crucial for revealing the outbreak mechanism and implementing effective prevention and control measures. This study developed a human–machine interactive workflow for extracting cyanobacterial blooms and recognizing their colors based on the Forel-Ule index and Sentinel-2 MultiSpectral Instrument data. Using this workflow, the authors conducted spatiotemporal analysis and statistical analysis of bloom color for cyanobacterial blooms in four typical eutrophic lakes from 2019 to 2022. The findings indicated a declining trend in cyanobacterial blooms across the four studied lakes over the years, among which Hulun Lake experienced an annual increase in cyanobacterial blooms and emerged as the lake with the most severe outbreak of such blooms in 2022. The yellowing status of cyanobacterial blooms varied among the four lakes, with Taihu Lake and Dianchi Lake exhibiting a relatively high proportion of green-yellow and yellow cyanobacterial blooms, followed by Chaohu Lake, whereas Hulun Lake had the lowest occurrence. The workflow developed in this study was implemented in Google Earth Engine and provided an automated, integrated, and rapid monitoring solution for the long-term monitoring and color recognition of cyanobacterial blooms. [ABSTRACT FROM AUTHOR]

• Response to P deficiency is species specific among cyanobacteria and therefore P limitation should be determined on population level other than ecosystem level. • Microcystis acclimated and adapted to low P and replaced Dolichospermum who couldn't survive P deficiency. • To combat cyanobacterial bloom, target of P controlling is largely dependent on dominant species. Dolichospermum (formerly Anabaena) and Microcystis cause harmful cyanobacterial blooms in freshwater ecosystems worldwide. Input reduction of both nitrogen (N) and phosphorus (P) are commonly recognized as basic ways of controlling blooms, but little is known about the roles of nutrients and their using strategy among cyanobacteria in triggering the succession of diazotrophic to non-diazotrophic cyanobacteria. In this study, we investigated in situ responses of cyanobactria to ambient P status during the transition from Dolichospermum flos-aquae to Microcystis spp. in Lake Taihu and Lake Chaohu. While dominant in phytoplankton community, D. flos-aquae experienced P deficiency as evidenced by qualitative detection of extracellular phosphatase via enzyme labeled fluorescence (ELF). The percentage of ELF-labelled D. flos-aquae cells was 33% when it dominated the phytoplankton community, and was 78% when it co-dominated with Microcystis spp., indicating an increase in P deficiency. Meanwhile, no ELF-labelled Microcystis cells were observed while polyphosphate body (PPB) were present, suggesting that Microcystis spp. were not P deficient. Additionally, the percentages of Microcystis cells containing PPB showed an inverted "U-shaped" relationship with concentrations on soluble reactive phosphorus (SRP). To validate the field observation, a laboratory study of the monocultures of the dominant cyanobacteria was conducted. Extracellular alkaline phosphatase activity (APA) and PPB accumulation were regulated by P availability in monocultures of D. flos-aquae. Interestingly, no cell bound extracellular phosphatase was found on Microcystis aeruginasa even in the culture without P supply. Consistently, the expressions of phosphatase encoding gene phoX showed no differences among the treatments. The way in which PPB accumulation occurred in Microcystis spp. in response to P availability in the cultures was similar to that observed in the field, demonstrating a strategy of energy conservation over P accumulation. The competitive advantage of Microcystis spp. was displayed at low P concentrations: where it could rapidly uptake and store inorganic P, which also increased the P deficiency of the coexisting phytoplankton species. Responses of P-transport gene pstS confirmed this hypothesis. The physiological and molecular mechanisms mentioned above enable Microcystis to survive and proliferate in environment with low available P supply more efficiently. In conclusion, different cyanobacterial species have distinct ways of responding to P availability, suggesting that the control of cyanobacterial blooms by targeted nutrient reduction is largely dependent upon the dominant species. P reduction is more effective in controlling diazotrophic cyanobacteria than non-diazotrophic cyanobacteria. [ABSTRACT FROM AUTHOR]

• Cyanobacteria impacted plankton bio-diversity and resource use efficiency. • No clear relation between cyanobacteria and phytoplankton absolute abundances. • Cyanobacteria had opposite relation with phytoplankton and zooplankton bio-diversities. • Cyanobacteria increased total algae and cladocerans RUEs. • Cyanobacteria decreased phytoplankton and rotifers RUEs. Cyanobacterial blooms are global threats to freshwater ecosystem functioning, human health, and ecoservices. We assessed impacts of cyanobacterial bloom intensity on plankton ecosystem functioning using eukaryotic phytoplankton and zooplankton indicators and associated key physicochemical data collected from four seasons of two years at 24 evenly distributed sites in Lake Taihu that has year-around cyanobacterial blooms. Our analyses involved comparison of four site-groups with different bloom intensities and analyzing all sampling sites together using comparison, hierarchical partitioning analysis, generalized additive mixed model, and structural equation model. We found that cyanobacterial abundance positively associated with TP and temperature (negatively with TN:TP), while phytoplankton positively associated with TN. There was an inverse relation trend between relative abundances of phytoplankton and cyanobacteria, but there was no clear trend between absolute abundances of phytoplankton and cyanobacteria. Rotifers were most dominant when cyanobacteria were unabundant, while cladocerans presented higher abundance when cyanobacteria were in high abundance. Phytoplankton functional richness and species richness negatively and zooplankton functional richness and species richness positively associated with cyanobacterial bloom intensity. Cyanobacterial bloom intensity negatively associated with resource use efficiencies (RUEs) of phytoplankton and rotifers, and positively associated with RUE of cladocerans. Our analytical approach of integrating comparison of site-groups and analyzing all sites together uncovered how cyanobacterial bloom intensity shifted and altered physicochemical and biological conditions and plankton ecosystem functioning, and identified the mechanism and strength of the interactive linkages among physicochemical and biological indicators. Although our results may be different from oligotrophic lakes or reservoirs, our findings provide new insights in understanding the impacts of cyanobacterial bloom intensity on the dynamics of plankton communities and ecosystem functioning for polymictic eutrophic lakes, which may have broad application in enhancing the knowledge of this subject and provides the science base for managing polymictic eutrophic lake water quality and ecosystem functioning. [ABSTRACT FROM AUTHOR]

Cells of Microcystis are associated with heterotrophic bacteria and organized in colonies in natural environment, which are basic elements in the mass occurrence of cyanobacterial species. Analyzing these colonies by using metagenomics is helpful to understand species composition and relationship. Meanwhile, the difference in population abundance among Microcystis colonies could be used to recover genome bins from metagenome assemblies. Herein, we designed a pipeline to obtain high-quality genomes of mutualistic bacteria from single natural Microcystis colonies. Single colonies were lysed, and then amplified by using multiple displacement amplification to overcome the DNA quantity limit. A two-step assembly was performed after sequencing and scaffolds were grouped into putative bins based on their differential-coverage among species. We analyzed six natural colonies of three prevailing Microcystis species from Lake Taihu. Clustering results proved that colonies of the same species were similar in the microbial community composition. Eight putative population genome bins with wide bacterial diversity and different GC content were identified based on coverage difference among colonies. At the phylum level, proteobacteria was the most abundant besides cyanobacteria. Six of the population bins were further refined into nearly complete genomes (completeness > 90%). [ABSTRACT FROM AUTHOR]