Secondary metabolite gene expression and interplay of bacterial functions in a tropical freshwater cyanobacterial bloom

Microbial diversity, genomics, and phage-host interactions of cyanobacterial harmful algal blooms

The occurrence of cyanobacterial harmful algal blooms (cyanoHABs) is related to their physical and chemical environment. However, less is known about their associated microbial interactions and processes. In this study, cyanoHABs were analyzed as a microbial ecosystem, using 1 year of 16S rRNA sequencing and 70 metagenomes collected during the bloom season from Lake Okeechobee (Florida, USA). Biogeographical patterns observed in microbial community composition and function reflected ecological zones distinct in their physical and chemical parameters that resulted in bloom "hotspots" near major lake inflows. Changes in relative abundances of taxa within multiple phyla followed increasing bloom severity. Functional pathways that correlated with increasing bloom severity encoded organic nitrogen and phosphorus utilization, storage of nutrients, exchange of genetic material, phage defense, and protection against oxidative stress, suggesting that microbial interactions may promote cyanoHAB resilience. Cyanobacterial communities were highly diverse, with picocyanobacteria ubiquitous and oftentimes most abundant, especially in the absence of blooms. The identification of novel bloom-forming cyanobacteria and genomic comparisons indicated a functionally diverse cyanobacterial community with differences in its capability to store nitrogen using cyanophycin and to defend against phage using CRISPR and restriction-modification systems. Considering blooms in the context of a microbial ecosystem and their interactions in nature, physiologies and interactions supporting the proliferation and stability of cyanoHABs are proposed, including a role for phage infection of picocyanobacteria. This study displayed the power of "-omics" to reveal important biological processes that could support the effective management and prediction of cyanoHABs.

IMPORTANCE

Cyanobacterial harmful algal blooms pose a significant threat to aquatic ecosystems and human health. Although physical and chemical conditions in aquatic systems that facilitate bloom development are well studied, there are fundamental gaps in the biological understanding of the microbial ecosystem that makes a cyanobacterial bloom. High-throughput sequencing was used to determine the drivers of cyanobacteria blooms in nature. Multiple functions and interactions important to consider in cyanobacterial bloom ecology were identified. The microbial biodiversity of blooms revealed microbial functions, genomic characteristics, and interactions between cyanobacterial populations that could be involved in bloom stability and more coherently define cyanobacteria blooms. Our results highlight the importance of considering cyanobacterial blooms as a microbial ecosystem to predict, prevent, and mitigate them.

Unveiling the trifecta of cyanobacterial quorum sensing: LuxI, LuxR and LuxS as the intricate machinery for harmful algal bloom formation in freshwater ecosystems

Harmful algal blooms (HABs) are causing significant disruptions in freshwater ecosystems, primarily due to the proliferation of cyanobacteria. These blooms have a widespread impact on various lakes globally, leading to profound environmental and health consequences. Cyanobacteria, with their ability to produce diverse toxins, pose a particular concern as they negatively affect the well-being of humans and animals, exacerbating the situation. Notably, cyanobacteria utilize quorum sensing (QS) as a complex communication mechanism that facilitates coordinated growth and toxin production. QS plays a critical role in regulating the dynamics of HABs. However, recent advances in control and mitigation strategies have shown promising results in effectively managing and reducing the occurrence of HABs. This comprehensive review explores the intricate aspects of cyanobacteria development in freshwater ecosystems, explicitly focusing on deciphering the signaling molecules associated with QS and their corresponding genes. Furthermore, a concise overview of diverse measures implemented to efficiently control and mitigate the spread of these bacteria will be provided, shedding light on the ongoing global efforts to address this urgent environmental issue. By deepening our understanding of the mechanisms driving cyanobacteria growth and developing targeted control strategies, we hope to safeguard freshwater ecosystems and protect the health of humans and animals from the detrimental impacts of HABs.

Plasmid-Borne Biosynthetic Gene Clusters within a Permanently Stratified Marine Water Column

Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmid-encoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpene-synthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are mainly antimicrobial agents, and hence, their uptake via plasmids may increase the competitive advantage of those host taxa that acquire them. The ecological and evolutionary significance of smBGCs carried by prokaryotes in oxygen-depleted water columns is yet to be fully elucidated.

Spatio-temporal connectivity of a toxic cyanobacterial community and its associated microbiome along a freshwater-marine continuum

Due to climate changes and eutrophication, blooms of predominantly toxic freshwater cyanobacteria are intensifying and are likely to colonize estuaries, thus impacting benthic organisms and shellfish farming representing a major ecological, health and economic risk. In the natural environment, Microcystis form large mucilaginous colonies that influence the development of both cyanobacterial and embedded bacterial communities. However, little is known about the fate of natural colonies of Microcystis by salinity increase. In this study, we monitored the fate of a Microcystis dominated bloom and its microbiome along a French freshwater-marine gradient at different phases of a bloom. We demonstrated changes in the cyanobacterial genotypic composition, in the production of specific metabolites (toxins and compatible solutes) and in the heterotrophic bacteria structure in response to the salinity increase. In particular M. aeruginosa and M. wesenbergii survived salinities up to 20. Based on microcystin gene abundance, the cyanobacteria became more toxic during their estuarine transfer but with no selection of specific microcystin variants. An increase in compatible solutes occurred along the continuum with extensive trehalose and betaine accumulations. Salinity structured most the heterotrophic bacteria community, with an increased in the richness and diversity along the continuum. A core microbiome in the mucilage-associated attached fraction was highly abundant suggesting a strong interaction between Microcystis and its microbiome and a likely protecting role of the mucilage against an osmotic shock. These results underline the need to better determine the interactions between the Microcystis colonies and their microbiome as a likely key to their widespread success and adaptation to various environmental conditions.

An Electrochemical Aptasensor for the Detection of Freshwater Cyanobacteria

Aphanizomenon is a genus of cyanobacteria that is filamentous and nitrogen-fixing and inhabits aquatic environments. This genus is known as one of the major producers of cyanotoxins that can affect water quality after the bloom period. In this study, an electrochemical aptasensor is demonstrated using a specific aptamer to detect Aphanizomenon sp. ULC602 for the rapid and sensitive detection of this bacterium. The principal operation of the generated aptasensor is based on the conformational change in the aptamer attached to the electrode surface in the presence of the target bacterium, resulting in a decrease in the current peak, which is measured by square-wave voltammetry (SWV). This aptasensor has a limit of detection (LOD) of OD750~0.3, with an extension to OD750~1.2 and a sensitivity of 456.8 μA·OD750-1·cm-2 without interference from other cyanobacteria. This is the first aptasensor studied that provides rapid detection to monitor the spread of this bacterium quickly in a targeted manner.

Transcription of biochemical defenses by the harmful brown tide pelagophyte, Aureococcus anophagefferens, in response to the protozoan grazer, Oxyrrhis marina

Aureococcus anophagefferens is a small marine pelagophyte that forms recurrent harmful brown tides blooms with adverse ecological and economic impacts. During blooms, A. anophagefferens experiences lower zooplankton grazing mortality than other phytoplankton potentially due to the synthesis of anti-predator compounds including extracellular polysaccharides. This study characterized the transcriptomic response of A. anophagefferens when exposed to the protozooplankton, Oxyrrhis marina, and assessed whether this response involved chemical cues. Transcriptomes were generated from A. anophagefferens populations grown at high (1×106 cells mL-1) and low (5×105 cells mL-1) cell densities incubated directly with O. marina or receiving only filtrate from co-cultures of A. anophagefferens and O. marina to evaluate the role of chemical cues. There were a greater number of genes differentially expressed in response to grazing in the lower concentration of A. anophagefferens compared to the high concentration treatment and in response to direct grazing compared to filtrate. KEGG pathway analysis revealed that direct grazer exposure led to a significant increase in transcripts of genes encoding secondary metabolite production (p < 0.001). There was broad transcriptional evidence indicating the induction of biosynthetic pathways for polyketides and sterols in response to zooplankton grazers, compounds associated with damage to marine organisms. In addition, exposure to O. marina elicited changes in the abundance of transcripts associated with carbohydrate metabolism that could support the formation of an extracellular polysaccharide matrix including genes related to glycoprotein synthesis and carbohydrate transport. Collectively, these findings support the hypothesis that A. anophagefferens can induce biochemical pathways that reduce grazing mortality and support blooms.

Characterization and seasonal variation in biofilms attached to leaves of submerged plant

The microorganisms and functional predictions of leaf biofilms on submerged plants (Vallisneria natans (Val)) and in water samples (surface water (S) and bottom water (B)) in different seasons were evaluated in this study. S and B groups had 3249 identical operational taxonomic units (OTUs) (50.03%), while the Val group only had 1201 (18.49%) unique OTUs. There was significant overlap between microbial communities of S and B groups in the same season, while Val group showed the greater diversity. The dominant microbial clades were Proteobacteria (18.2-47.3%), Cyanobacteria (3.74-39.3%), Actinobacteria (1.64-29.3%), Bacteroidetes (1.31-21.7%), and Firmicutes (1.10-15.72%). Furthermore, there was a significant relationship between total organic carbon and the distribution of microbial taxa (p = 0.047), and TN may have altered the status of Cyanobacteria by affecting its biological nitrogen fixation capacity and reproductive capacity. The correlation network analysis results showed that the whole system consisted of 249 positive correlations and 111 negative correlations, indicating strong interactions between microbial communities. Functional predictions indicated that microbial functions were related to seasonal variation. These findings would guide the use of submerged plants to improve the diversity and stability of wetland microbial communities.

The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: Two new metagenome-assembled genomes from the South American clade

Two Raphidiopsis (=Cylindrospermopsis) raciborskii metagenome-assembled genomes (MAGs) were recovered from two freshwater metagenomic datasets sampled in 2011 and 2012 in Pampulha Lake, a hypereutrophic, artificial, shallow reservoir, located in the city of Belo Horizonte (MG), Brazil. Since the late 1970s, the lake has undergone increasing eutrophication pressure, due to wastewater input, leading to the occurrence of frequent cyanobacterial blooms. The major difference observed between PAMP2011 and PAMP2012 MAGs was the lack of the saxitoxin gene cluster in PAMP2012, which also presented a smaller genome, while PAMP2011 presented the complete sxt cluster and all essential proteins and clusters. The pangenome analysis was performed with all Raphidiopsis/Cylindrospermopsis genomes available at NCBI to date, with the addition of PAMP2011 and PAMP2012 MAGs (All33 subset), but also without the South American strains (noSA subset), and only among the South American strains (SA10 and SA8 subsets). We observed a substantial increase in the core genome size for the 'noSA' subset, in comparison to 'All33' subset, and since the core genome reflects the closeness among the pangenome members, the results strongly suggest that the conservation level of the essential gene repertoire seems to be affected by the geographic origin of the strains being analyzed, supporting the existence of a distinct SA clade. The Raphidiopsis pangenome comprised a total of 7943 orthologous protein clusters, and the two new MAGs increased the pangenome size by 11%. The pangenome based phylogenetic relationships among the 33 analyzed genomes showed that the SA genomes clustered together with 99% bootstrap support, reinforcing the metabolic particularity of the Raphidiopsis South American clade, related to its saxitoxin producing unique ability, while also indicating a different evolutionary history due to its geographic isolation.

Expression of Microcystis Biosynthetic Gene Clusters in Natural Populations Suggests Temporally Dynamic Synthesis of Novel and Known Secondary Metabolites in Western Lake Erie

Microcystis spp. produce diverse secondary metabolites within freshwater cyanobacterial harmful algal blooms (cyanoHABs) around the world. In addition to the biosynthetic gene clusters (BGCs) encoding known compounds, Microcystis genomes harbor numerous BGCs of unknown function, indicating a poorly understood chemical repertoire. While recent studies show that Microcystis produces several metabolites in the lab and field, little work has focused on analyzing the abundance and expression of its broader suite of BGCs during cyanoHAB events. Here, we use metagenomic and metatranscriptomic approaches to track the relative abundance of Microcystis BGCs and their transcripts throughout the 2014 western Lake Erie cyanoHAB. The results indicate the presence of several transcriptionally active BGCs that are predicted to synthesize both known and novel secondary metabolites. The abundance and expression of these BGCs shifted throughout the bloom, with transcript abundance levels correlating with temperature, nitrate, and phosphorus concentrations and the abundance of co-occurring predatory and competitive eukaryotic microorganisms, suggesting the importance of both abiotic and biotic controls in regulating expression. This work highlights the need for understanding the chemical ecology and potential risks to human and environmental health posed by secondary metabolites that are produced but often unmonitored. It also indicates the prospects for identifying pharmaceutical-like molecules from cyanoHAB-derived BGCs. IMPORTANCE Microcystis spp. dominate cyanobacterial harmful algal blooms (cyanoHABs) worldwide and pose significant threats to water quality through the production of secondary metabolites, many of which are toxic. While the toxicity and biochemistry of microcystins and several other compounds have been studied, the broader suite of secondary metabolites produced by Microcystis remains poorly understood, leaving gaps in our understanding of their impacts on human and ecosystem health. We used community DNA and RNA sequences to track the diversity of genes encoding synthesis of secondary metabolites in natural Microcystis populations and assess patterns of transcription in western Lake Erie cyanoHABs. Our results reveal the presence of both known gene clusters that encode toxic secondary metabolites as well as novel ones that may encode cryptic compounds. This research highlights the need for targeted studies of the secondary metabolite diversity in western Lake Erie, a vital freshwater source to the United States and Canada.

Metabolites dynamics exacerbated by external nutrients inputs into a Ceratium hirundinella-dominated bloom in the Pengxi River, Three Gorges Reservoir, China

Secondary metabolites (toxins) production during harmful algal blooms (HABs) further increases the public health risks associated with water quality deterioration from anthropogenic eutrophication. In the present study, the dynamic pattern in the production of metabolites under different nutrient conditions in Ceratium-dominated spring HABs was investigated in Pengxi River, China. Results revealed five (5) important toxins all attributable to the Dinophyceae including azaspiracid 2&4, okadaic acid, tetrodotoxin, brevetoxin, and saxitoxin, each exhibiting certain levels of specificity to the ecosystem enrichments. In effect, while the production of azaspiracid 2 and okadaic acid was N-driven, azaspiracid 4 and tetrodotoxin were enhanced by Ca enrichment. The ambient HABs community structure shows absolute ecosystem dominance by a dinoflagellate, Ceratium hirundinella with relative abundance ((RA = 78.81%, p ˂ 0.05). However, P enrichment triggered a slight shift (p ≥ 0.05) in the HABs species structure within the cyanobacteria strictly represented by Chroococcus minor (RA = 26.60%) and Dolichospermum circinalis (RA = 23.91%) initiating possible emergency dominance. The effect of nutrient addition on biomass production as chlorophyll-a (Chl-a) confirmed a P-limited ecosystem juxtaposed by a secondary limitation by Ca. The significant stimulation on biomass as Chl-a from day 3 through day 4 by N and the multiple enrichments designated as NPFeCa was attributed to luxury consumption rather than limitation following N repletion thus delaying biomass accumulation. The study, therefore, offers useful insights into the dynamic pattern of toxins during spring HABs while it also provides comprehensive knowledge of the HABs impact predictions in the TGR.

Determinants of Total and Active Microbial Communities Associated with Cyanobacterial Aggregates in a Eutrophic Lake

Cyanobacterial aggregates (CAs) comprised of photosynthetic and phycospheric microorganisms are often the cause of cyanobacterial blooms in eutrophic freshwater lakes. Although phylogenetic diversity in CAs has been extensively studied, much less was understood about the activity status of microorganisms inside CAs and determinants of their activities. In this study, the 16S rRNA gene (rDNA)-based total communities within CAs in Lake Taihu of China were analyzed over a period of 6 months during the bloom season; the 16S rRNA-based active communities during daytime, nighttime, and under anoxic conditions were also profiled. Synchronous turnover of both cyanobacterial and phycospheric communities was observed, suggesting the presence of close interactions. The rRNA/rDNA ratio-based relative activities of individual taxa were predominantly determined by their rDNA-based relative abundances. In particular, high-abundance taxa demonstrated comparatively lower activities, whereas low-abundance taxa were generally more active. In comparison, hydrophysicochemical factors as well as diurnal and redox conditions showed much less impact on relative activities of microbial taxa within CAs. Nonetheless, total and active communities exhibited differences in community assembly processes, the former of which were almost exclusively controlled by homogeneous selection during daytime and under anoxia. Taken together, the results from this study provide novel insights into the relationships among microbial activities, community structure, and environmental conditions and highlight the importance of further exploring the regulatory mechanisms of microbial activities at the community level. IMPORTANCE Cyanobacterial aggregates are important mediators of biogeochemical cycles in eutrophic lakes during cyanobacterial blooms, yet regulators of microbial activities within them are not well understood. This study revealed rDNA-based abundances strongly affected the relative activities of microbial taxa within Microcystis aggregates, as well as trade-off effects between microbial abundances and activities. Environmental conditions further improved the levels of relative activities and affected community assembly mechanisms in phycospheric communities. The relationships among microbial activities, abundances, and environmental conditions improve our understanding of the regulatory mechanisms of microbial activities in cyanobacterial aggregates and also provide a novel clue for studying determinants of microbial activities in other ecosystems.

Evaluation of environmental factors and microbial community structure in an important drinking-water reservoir across seasons

The composition of microbial communities varies in water and sediments, and changes in environmental factors have major effects on microbiomes. Here, we characterized variations in microbial communities and physicochemical factors at two sites in a large subtropical drinking water reservoir in southern China. The microbiomes of all sites, including the diversity and abundance of microbial species, were determined via metagenomics, and the relationships between microbiomes and physicochemical factors were determined via redundancy analysis. The dominant species in sediment and water samples differed; Dinobryon sp. LO226KS and Dinobryon divergens were dominant in sediment samples, whereas Candidatus Fonsibacter ubiquis and Microcystis elabens were dominant in water. The diversity was also significantly different in microbial alpha diversity between water and sediment habitats (p < 0.01). The trophic level index (TLI) was the major factor affecting the microbial community in water samples; Mycolicibacterium litorale and Mycolicibacterium phlei were significantly positively related to TLI. Furthermore, we also studied the distribution of algal toxin-encoding genes and antibiotic-resistant genes (ARGs) in the reservoir. It found that water samples contained more phycotoxin genes, with the cylindrospermopsin gene cluster most abundant. We found three genera highly related to cylindrospermopsin and explored a new cyanobacteria Aphanocapsa montana that may produce cylindrospermopsin based on the correlation through network analysis. The multidrug resistance gene was the most abundant ARG, while the relationship between ARGs and bacteria in sediment samples was more complicated than in water. The results of this study enhance our understanding of the effects of environmental factors on microbiomes. In conclusion, research on the properties, including profiles of algal toxin-encoding genes and ARGs, and microbial communities can aid water quality monitoring and conservation.

Cyanobacterial Blooms Are Not a Result of Positive Selection by Freshwater Eutrophication

Long-standing cyanobacterial harmful algal blooms (CyanoHABs) are known to result from synergistic interaction between elevated nutrients and superior ecophysiology of cyanobacteria. However, it remains to be determined whether CyanoHABs are a result of positive selection by eutrophic waters. To address this, we conducted molecular evolutionary analyses on the genomes of 9 bloom-forming cyanobacteria, combined with pangenomics and metatranscriptomics. The results showed no positive selection by water eutrophication. Instead, all homologous genes in the species are under strong purifying selection based on the ratio of divergence at nonsynonymous and synonymous sites (dN/dS) and phylogeny. The dN/dS < 0.85 (median = 0.3) for all homologous genes are similar between the genes in the pathways driving CyanoHABs and housekeeping functions. Phylogenetic support for non-positive selection comes from the mixed clustering of strains: strains of the same species from diverse geographic origins form the same clusters, while strains from the same origins form different clusters. Further support lies in the codon adaptation index (CAI) and single nucleotide polymorphism (SNP). The CAI ranged from 0.42 to 0.9 (mean = 0.75), which indicates high-level codon usage bias; the pathways for CyanoHABs and housekeeping functions showed a similar CAI. Interestingly, CAI was negatively correlated with gene expression in 3 metatranscriptomes. The numbers of SNPs were concentrated around 5 to 50. As the SNP number increases, the gene expression level decreases. These negative correlations agree with the population-level dN/dS and phylogeny in supporting purifying selection in bloom-forming cyanobacteria. In summary, superior ecophysiology appears to be acquired prior to water eutrophication. IMPORTANCE CyanoHABs are global environmental hazards, and their mechanisms of action are being intensively investigated. On an ecological scale, CyanoHABs are consequences of synergistic interactions between biological functions and elevated nutrients in eutrophic waters. On an evolutionary scale, one important question is how bloom-forming cyanobacteria acquire these superior biological functions. There are several possibilities, including adaptive evolution and horizontal gene transfer. Here, we explored the possibility of positive selection. We reasoned that there are two possible periods for cyanobacteria to acquire these functions: before the onset of water eutrophication or during water eutrophication. Either way, there should be molecular signatures in protein sequences for positive selection. Interestingly, we found no positive selection by water eutrophication, but strong purifying selection instead on nearly all the genes, suggesting these superior functions aiding CyanoHABs are acquired prior to water eutrophication.

Seasonal changes driving shifts of aquatic rhizosphere microbial community structure and the functional properties

Ecological floating beds could enable roots to become suspended and this allowed submerged roots to harbour various types of microbes. But, there was a lack of systematic research on microbial community structure changes and the influencing mechanisms. In this study, the ecological floating beds were constructed using selected plants [Cyperus involucratus Rottboll (Cyp), Thalia dealbata Fraser (Tha) and Iris tectorum Maxim (Iri)] that was compared with a control group [static water (S)]. The results showed that the highest abundance and diversity of root microbial communities were found in autumn, with the dominant taxa being Proteobacteria, Actinobacteriota, Cyanobacteria, Chloroflexi, Firmicutes, Bacteroidota, and Acidobacteriota. The microbial communities of Tha and Cyp groups greatly overlapped, while the Iri and control groups exhibited distinctly diverse communities. The root microbial populations of the same plant also reflected a large change in different seasons. Conversely, photosynthetic autotrophs and specialized anaerobes were more inclined to thrive at higher temperatures and lower DO concentrations and then they gradually became the dominant species. Microbial co-occurrences of the Tha and control groups were complex and showed both cooperation and competition. In addition, TOC was an important environmental factor that shaped the microbial community structures and DO changed the microbial community by affecting the abundance of aerobic and anaerobic bacteria. Microorganisms showed potential for degradation and metabolism of non-food substances with low/no corresponding metabolic pathways.

Characterization of phosphorus sorption and microbial community in lake sediments during overwinter and recruitment periods of cyanobacteria

The release of endogenous phosphorus from lacustrine sediment is a key element of freshwater eutrophication. The microbes in sediments may affect phosphorus migration and transformation during the growth of cyanobacteria, which may lead to the release of phosphorus from sediments and contribute to water eutrophication. To study phosphorus sorption and the microbial community structure in the overlying water and the vertical depth of sediments, samples in Meiliang Bay were collected during the dormancy and resuscitation phases of cyanobacteria. The results showed that there were high total phosphorus (TP) concentrations in the overlying water and sediment, with maximum values reached 0.24 mg L^-1 and 1059 mg kg^-1, respectively. Fitting by modified Langmuir model indicated that the partitioning coefficients (K_P) was, from greatest to least: bottom sediment (maximum of 0.923 L g^-1) > middle sediment (0.571 L g^-1) > surface sediment (0.262 L g^-1). During the cyanobacteria resuscitation stage, the relative abundance of Proteobacteria (18.37%-33.56%), Chloroflexi (9.57%-17.76%), Cyanobacteria (0.38%-2.62%), and the Nitrospirota phylum Thermodesulfovibrionia (4.61%-10.14%) were higher than the dormant period of cyanobacteria, and bacteria with phosphorus-solubilizing (27.27%-52.01%) accounted for the majority. The redundancy analysis (RDA) found that the structure of the microbial communities in sediments was significant correlation with organic phosphorus (OP) (P = 0.002) during recruitment period of cyanobacteria, which would accelerate the conversion of OP into soluble inorganic phosphorus and then gets released from sediment to water. The most predominant phylum among phosphorus-solubilizing bacteria (PSB) is Proteobacteria, followed by Actinobacteriota, which were positively correlated with equilibrium phosphorus concentration (EPC₀) (P < 0.05) during the cyanobacterial resuscitation phase. The sediments from the cyanobacteria resuscitation phase had phosphorus release risk and highlighted the significant role of the bacterial community.

Impact of melatonin on the hydrogen peroxide treatment efficacy in Microcystis aeruginosa: Cell growth, oxidative stress response, and gene transcription

A study was conducted to determine how melatonin (MLT), a growth regulator, affects Microcystis aeruginosa cell behaviour and how MLT exposed cells respond to hydrogen peroxide (H₂O₂) treatment. MLT promotes the growth, chl-a content, Fv/Fm values, and microcystins (MCs) production of M. aeruginosa at low concentrations of 1-2.5 μmol/L but suppresses the growth at high concentrations (5-10 μmol/L). The cellular and genetic responses of MLT pre-treated cells to H₂O₂ treatment were examined further. Further research found that the cells pre-treated with MLT were susceptible to a range of growth-promoting, inhibiting and lethal effects when exposed to higher levels of H₂O₂. A dose-dependent pattern was observed under conditions of 0.05-0.2 mmol/L H₂O₂ with 0.5-2.5 μmol/L MLT concentrations to different degrees. High doses of H₂O₂ (0.2 and 0.3 mmol/L) typically lead to cell lysis and release of MCs in 5.0 and 10 μmol/L MLT pre-treated cells. A decrease in SOD/CAT activities and an increase in MDA levels validated the growth reduction. Furthermore, higher cell lysis and release of intracellular MCs were observed when H₂O₂ was increased for 5-10 μmol/L MLT pre-treated cells. This led to a higher accumulation of extracellular MCs. The results provide insight into how MLT influences H₂O₂ damage and assist in identifying situations where H₂O₂ treatment of cyanobacterial blooms is most appropriate.

The role of attached bacteria in the formation of Microcystis colony in Chentaizi River

To further understand the role of attached bacteria in the formation of Microcystis colonies, we conducted a field investigation in Chentaizi River in Tianjin, China, which frequently suffers Microcystis blooms in summer. The results showed the average cell density of Microcystis was 2.31 × 10⁷ cell/L from July 19 to July 27, 2021. Free-living and attached bacteria communities shared similar phylum diversity, but the abundance changed obviously. The colony size of Microcystis and attached bacterial number in the colony showed an increasing trend during the whole sampling period. There was a significant positive correlation between Microcystis colonial size and attached bacterial density (P < 0.01), indicating attached bacteria could contribute the colony formation of Microcystis. The genus composition in attached bacterial community varied in colonies of different sizes. The relative abundance of Acinetobacter, Cloacibacterium, Sphingobacterium, and Ralstonia in >90 μm colonies were significantly higher than those in 8-20 μm and 20-90 μm colonies (P < 0.05). These genera might have positive effects on the colony formation of Microcystis during sampling.

Development of a Potentially New Algaecide for Controlling Harmful Cyanobacteria Blooms Which is Ecologically Safe and Selective

Harmful cyanobacterial blooms (HCBs) caused by Microcystis aeruginosa are of great concern as they negatively affect the aquatic environment and human health. Chemical methods could rapidly eradicate HCBs and have been used for many decades. However, many chemical reagents are not recommended to eliminate HCBs in the long term, given the possible destructive and toxic effects of the chemicals employed on non-target aquatic organisms. We developed a new algaecide, 2-((1,3,4-thiadiazol-2-yl)thio)-N-(4-chlorophenyl) acetamide (Q2), to control harmful cyanobacteria while being environmentally friendly and selective. In our study, Q2 effectively inhibited cyanobacterial growth, especially of M. aeruginosa, but did not affect eukaryotic algae in test concentrations. A critical mechanism was revealed by transcriptome and metagenomic results showing that Q2 affects multiple cellular targets of cyanobacteria for HCB control, including the destruction of organelles, damage in the photosynthesis center, as well as inhibition of gas vesicle growth, and these changes can be highly relevant to the decrease of quorum-sensing functional KEGG pathways. Furthermore, Q2 did not affect the microbial composition and could recover the disrupted aquatic functional pathways in a short period. This is different from the impact on ecosystem functioning of the traditionally used harmful algaecide diuron. All these results verified that Q2 could be friendly to the aquatic environment, providing a new directional choice in managing HCBs in the future.

Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence

Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H₂O₂. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.

Factors Driving Microbial Community Dynamics and Potential Health Effects of Bacterial Pathogen on Landscape Lakes with Reclaimed Water Replenishment in Beijing, PR China

Assessing the bacteria pathogens in the lakes with reclaimed water as major influents are important for public health. This study investigated microbial communities of five landscape lakes replenished by reclaimed water, then analyzed driven factors and identified health effects of bacterial pathogens. 16S rRNA gene sequence analysis demonstrated that Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, and Verrucomicrobia were the most dominant phyla in five landscape lakes. The microbial community diversities were higher in June and July than that in other months. Temperature, total nitrogen and phosphorus were the main drivers of the dominant microbial from the Redundancy analysis (RDA) results. Various potential bacterial pathogens were identified, including Pseudomonas, GKS98_freshwater_group, Sporosarcina, Pseudochrobactrum, Streptomyces and Bacillus, etc, some of which are easily infectious to human. The microbial network analysis showed that some potential pathogens were nodes that had significant health effects. The work provides a basis for understanding the microbial community dynamics and safety issues for health effects in landscape lakes replenished by reclaimed water.

Phycocyanin-rich Synechococcus dominates the blooms in a tropical estuary lake

Cyanobacterial blooms challenge the safe water supply in estuary reservoirs. Yet, data are limited for the variation of phytoplankton dynamics during an algal bloom event at refined scales, which is essential for interpreting the formation and cessation of blooms. The present study investigated the biweekly abundances and dynamics of pico- and nano-phytoplankton in a tropical estuary lake following a prolonged bloom event. Flow cytometry analysis resolved eight phenotypically distinct groups of phytoplankton assigned to nano-eukaryotes (nano-EU), pico/nano-eukaryotes (PicoNano-EU), cryptophyte-like cells (CRPTO), Microcystis-like cells (MIC), pico-eukaryotes (Pico-EU) and three groups of Synechococcus-like cells. Total phytoplankton abundance ranged widely from 2.4 × 104 to 2.8 × 106 cells cm-3. The phytoplankton community was dominated by Synechococcus-like cells with high phycocyanin content (SYN-PC). Temporal dynamics of the phytoplankton community was phytoplankton- and site-specific. Peak values were observed for SYN-PC, SYN-PE2 (Synechococcus-like cells with low levels of phycoerythrin) and Pico-EU, while the temporal dynamics of other groups were less pronounced. Redundancy analysis (RDA) showed the importance of turbidity as an abiotic factor in the formation of the current SYN-PC induced blooms, and Spearman correlation analysis suggested a competitive relationship between SYN-PC and Pico-EU.

Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen

Elevated seawater temperatures have contributed to the rise of coral disease mediated by bacterial pathogens, such as the globally distributed Vibrio coralliilyticus, which utilizes coral mucus as a chemical cue to locate stressed corals. However, the physiological events in the pathogens that follow their entry into the coral host environment remain unknown. Here, we present simultaneous measurements of the behavioral and transcriptional responses of V. coralliilyticus BAA-450 incubated in coral mucus. Video microscopy revealed a strong and rapid chemokinetic behavioral response by the pathogen, characterized by a two-fold increase in average swimming speed within 6 min of coral mucus exposure. RNA sequencing showed that this bacterial behavior was accompanied by an equally rapid differential expression of 53% of the genes in the V. coralliilyticus genome. Specifically, transcript abundance 10 min after mucus exposure showed upregulation of genes involved in quorum sensing, biofilm formation, and nutrient metabolism, and downregulation of flagella synthesis and chemotaxis genes. After 60 min, we observed upregulation of genes associated with virulence, including zinc metalloproteases responsible for causing coral tissue damage and algal symbiont photoinactivation, and secretion systems that may export toxins. Together, our results suggest that V. coralliilyticus employs a suite of behavioral and transcriptional responses to rapidly shift into a distinct infection mode within minutes of exposure to the coral microenvironment.

Co-occurring microorganisms regulate the succession of cyanobacterial harmful algal blooms

Cyanobacterial harmful algal blooms (CyanoHABs) have been found to transmit from N2 fixer-dominated to non-N2 fixer-dominated in many freshwater environments when the supply of N decreases. To elucidate the mechanisms underlying such "counter-intuitive" CyanoHAB species succession, metatranscriptomes (biotic data) and water quality-related variables (abiotic data) were analyzed weekly during a bloom season in Harsha Lake, a multipurpose lake that serves as a drinking water source and recreational ground. Our results showed that CyanoHABs in Harsha Lake started with N2-fixing Anabaena in June (ANA stage) when N was high, and transitioned to non-N2-fixing Microcystis- and Planktothrix-dominated in July (MIC-PLA stage) when N became limited (low TN/TP). Meanwhile, the concentrations of cyanotoxins, i.e., microcystins were significantly higher in the MIC-PLA stage. Water quality results revealed that N species (i.e., TN, TN/TP) and water temperature were significantly correlated with cyanobacterial biomass. Expression levels of several C- and N-processing-related cyanobacterial genes were highly predictive of the biomass of their species. More importantly, the biomasses of Microcystis and Planktothrix were also significantly associated with expressions of microbial genes (mostly from heterotrophic bacteria) related to processing organic substrates (alkaline phosphatase, peptidase, carbohydrate-active enzymes) and cyanophage genes. Collectively, our results suggest that besides environmental conditions and inherent traits of specific cyanobacterial species, the development and succession of CyanoHABs are regulated by co-occurring microorganisms. Specifically, the co-occurring microorganisms can alleviate the nutrient limitation of cyanobacteria by remineralizing organic compounds.

Cyanobacterial bloom induces structural and functional succession of microbial communities in eutrophic lake sediments

Cyanobacterial blooms have considerable effects on lacustrine microbial communities. The current study explored the temporal pattern of sedimentary archaea and bacteria during cyanobacterial bloom in a eutrophic lake. With the sampling period divided into bloom phase, interval phase and end phase according to the variation of physicochemical parameters, the structures and functions of both kingdoms presented a significant difference among phases. Bloom phases could be characterized with the lowest diversity and up-regulated functions in biodegradation of cyanobacterial metabolites driven by bacteria. Archaeal community showed an increased metabolic function during interval phases, including active methanogenesis sensitive to carbon input. The highest diversity and an enrichment of hub genera in microbial network were both observed in end phase, allowing for closer cooperation among groups involved in cyanobacteria-derived organic matter transformation. Although the archaeal community was less variable or diverse than bacteria, methanogenic functions dramatically fluctuated with cyanobacterial dynamics. And microbial groups related to methane cycling played an important role in microbial network. The results provided new insights into temporal dynamics of lacustrine microbial communities and microbial co-occurrence, and highlighted the significant ecological role of methane cycling-related microbes in lake sediments under the influence of cyanobacterial blooms.

Microbial sulfur metabolism and environmental implications

Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.

Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions?

Specific interactions have been highlighted between cyanobacteria and chemotrophic bacteria within the cyanosphere, suggesting that nutrients recycling could be optimized by cyanobacteria/bacteria exchanges. In order to determine the respective metabolic roles of the cyanobacterial and bacterial consortia (microbiome), a day-night metatranscriptomic analysis was performed on Dolichospermum sp. (N₂ -fixer) and Microcystis sp. (non N₂ -fixer) natural blooms occurring successively within a French peri-urban lake. The taxonomical and functional analysis of the metatranscriptoms have highlighted specific association of bacteria within the cyanosphere, driven by the cyanobacteria identity, without strongly modifying the functional composition of the microbiomes, suggesting functional redundancy within the cyanosphere. Moreover, the functional composition of these active communities was driven by the living mode. During the two successive bloom events, it appeared that NH₄ ⁺ (newly fixed and/or allochthonous) was preferentially transformed into amino acids for the both the microbiome and the cyanobacteria, while phosphate metabolism was enhanced, suggesting that due to a high cellular growth, P limitation might take place within the cyanosphere consortium.

Hormones induce the metabolic growth and cytotoxin production of Microcystis aeruginosa under terpinolene stress

Several organic compounds released into the aquatic environment have a detrimental impact on humans and other organisms. There is a lack of knowledge about natural hormones and herbicides on non-target organisms, including cyanobacteria. In this study, the response of Microcystis aeruginosa to four phytohormones, indole-3-acetic acid (IAA; 10^-5), zeatin (ZT; 10^-5), abscisic acid (ABA; 10^-7), and brassinolide (BRL; 10^-9 mol/L), exposed to terpinolene (TPN; (0.44, 0.88, 1.17, or 1.62 mmol/L) at the cellular and genetic levels were investigated. The results showed that TPN could inhibit the growth and photosynthetic activities and stimulate microcystins (MCs) of M. aeruginosa at various levels through the co-occurrence of oxidative stress, antioxidant defense activities, and an imbalance of the antioxidative system. Hormones played critical roles in the growth promotion and photosynthetic activity by enhancing the antioxidant defense mechanisms and MCs production of M. aeruginosa under TPN stress in both hormone and TPN dose-dependent manner. The growth performance and photosynthetic activities of M. aeruginosa were significant with IAA (p < 0.01) and BSL (p < 0.05) compared to ZT and ABA, as TPN concentrations increased. Hormones stimulated the MCs production significantly BSL (p < 0.05) at various levels and protected the cells against TPN-induced oxidative stress and expression of mcyB and mcyD genes involve in MCs synthesis. Our results indicated that hormone contamination in eutrophic lakes might increase the risk of Microcystis aeruginosa bloom and microcystin production with the TPN association.

Competitive interactions as a mechanism for chemical diversity maintenance in Nodularia spumigena

Nodularia spumigena is a bloom-forming diazotrophic cyanobacterium inhabiting brackish waters worldwide. This species produces non-ribosomal peptides (NRPs), including the hepatotoxin nodularin, often referred to as cyanotoxin. Several known classes of NRPs have various biological activities, although their modes of action are poorly understood. In the Baltic N. spumigena, there is a high NRP chemodiversity among strains, allowing their grouping in specific chemotypes and subgroups. Therefore, it is relevant to ask whether the NRP production is affected by intraspecific interactions between the co-existing strains. Using a novel approach that combines culture technique and liquid chromatography-tandem mass spectrometry for the NRP analysis, we examined N. spumigena strains under mono- and co-culture conditions. The test strains were selected to represent N. spumigena belonging to the same or different chemotype subgroups. In this setup, we observed physiological and metabolic responses in the test strains grown without cell contact. The changes in NRP levels to co-culture conditions were conserved within a chemotype subgroup but different between the subgroups. Our results suggest that intraspecific interactions may promote a chemical diversity in N. spumigena population, with higher NRP production compared to a single-strain population. Studying allelochemical signalling in this cyanobacterium is crucial for understanding toxicity mechanisms and plankton community interactions in the Baltic Sea and other aquatic systems experiencing regular blooms.

Metabarcoding profiling of microbial diversity associated with trout fish farming

Earthy and musty off-flavors are routinely observed in farmed trout worldwide. The microbial association to the production of those off-flavors was previously reported. The current manuscript aimed to catalog the microbial enrichment (eukaryotes and prokaryotes) in semi-intensive aquaculture freshwater sources that might influence the trout aquaculture quality production. The 16S rRNA and ITS metabarcoding analyses were applied on the inflow- and pond-water samples from trout farms previously recorded a malodor fish products and located alongside Moosach and Sempt Rivers in Bavaria province, Germany. The results showed that more than 99% of the detected prokaryotic OTUs (Operational Taxonomic Unit identification) were bacteria as of ~ 75.57% were Proteobacteria, and ~ 14.4% were Bacteroidetes. Meanwhile, 118 out of 233 of the eukaryotic OTUs were known species. Of these, ~ 45% were plant pathogens, and ~ 28% were mushroom/yeasts. Based on the comparative analysis between inflow- and pond-water samples, several pro- and eukaryotic microorganisms that affect the trout aquaculture water quality and industry have been detected, including the malodor-producing microorganisms, e.g., Cyanobacteria and Actinobacteria, along with fish infectious microorganisms, e.g., Chilodonella cyprinid, Metschnikowia bicuspidate. Additionally, the effect of the human- and industrial-related activities around the sampling area on the microbiota of the investigated farms were highlighted.

Current Knowledge on Microviridin from Cyanobacteria

Cyanobacteria are a rich source of secondary metabolites with a vast biotechnological potential. These compounds have intrigued the scientific community due their uniqueness and diversity, which is guaranteed by a rich enzymatic apparatus. The ribosomally synthesized and post-translationally modified peptides (RiPPs) are among the most promising metabolite groups derived from cyanobacteria. They are interested in numerous biological and ecological processes, many of which are entirely unknown. Microviridins are among the most recognized class of ribosomal peptides formed by cyanobacteria. These oligopeptides are potent inhibitors of protease; thus, they can be used for drug development and the control of mosquitoes. They also play a key ecological role in the defense of cyanobacteria against microcrustaceans. The purpose of this review is to systematically identify the key characteristics of microviridins, including its chemical structure and biosynthesis, as well as its biotechnological and ecological significance.

Tracing the active genetic diversity of Microcystis and Microcystis phage through a temporal survey of Taihu

Harmful algal blooms are commonly thought to be dominated by a single genus, but they are not homogenous communities. Current approaches, both molecular and culture-based, often overlook fine-scale variations in community composition that can influence bloom dynamics. We combined homology-based searches (BLASTX) and phylogenetics to distinguish and quantify Microcystis host and phage members across a summer season during a 2014 Microcystis- dominated bloom that occurred in Lake Tai (Taihu), China. We found 47 different genotypes of the Microcystis-specific DNA-dependent RNA polymerase (rpoB), which included several morphospecies. Microcystis flos-aquae and Microcystis wesenbergii accounted for ~86% of total Microcystis transcripts, while the more commonly studied Microcystis aeruginosa only accounted for ~7%. Microcystis genotypes were classified into three temporal groups according to their expression patterns across the course of the bloom: early, constant and late. All Microcystis morphospecies were present in each group, indicating that expression patterns were likely dictated by competition driven by environmental factors, not phylogeny. We identified three primary Microcystis-infecting phages based on the viral terminase, including a novel Siphoviridae phage that may be capable of lysogeny. Within our dataset, Myoviridae phages consistent with those infecting Microcystis in a lytic manner were positively correlated to the early host genotypes, while the Siphoviridae phages were positively correlated to the late host genotypes, when the Myoviridae phages express putative genetic markers for lysogeny. The expression of genes in the microcystin-encoding mcy cassette was estimated using mcyA, which revealed 24 Microcystis-specific genotypes that were negatively correlated to the early host genotypes. Of all environmental factors measured, pH best described the temporal shift in the Microcystis community genotypic composition, promoting hypotheses regarding carbon concentration mechanisms and oxidative stress. Our work expounds on the complexity of HAB events, using a well-studied dataset to highlight the need for increased resolution of community dynamics.

Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies

Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of indicator species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.

Imaging mass spectrometry of interspecies metabolic exchange revealed the allelopathic interaction between Microcystis aeruginosa and its antagonist

The frequent outbreaks of cyanobacterial blooms which caused serious societal and economic loss have become a worldwide problem. Interactions between toxic cyanobacteria and heterotrophic bacteria competitors play a pivotal role in the formation of toxic cyanobacterial bloom, but the underlying mechanisms of interactions between them await further research. The antagonist activity of Pseudomonas grimontii (P.grimontii) was confirmed by reduction in chlorophyll a concentration of Microcystis aeruginosa (M. aeruginosa) in an infected culture for a 7d period. The initial concentration of P.grimontii affected the M. aeruginosa activity significantly. When the 10% (V/V) concentration of P.grimontii A01 and P.grimontii A14 cultures were infected, the reduction of M. aeruginosa reached to 91.81% and 78.25% after 7 days, respectively. While a 0.1% (v/v) concentration of P.grimontii A01 and P.grimontii A14 cultures were infected, the M. aeruginosa increased 31.13% and 16.67% occurred, respectively. The content of reactive oxygen species (ROS) and malondialdehyde (MDA) increased with increasing of P.grimontii fermentation liquid, indicating the M. aeruginosa underwent oxidative stress. Using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry (IMS) profiling of co-cultures of M. aeruginosa and its antagonist P.grimontii, we revealed novel interspecies allelopathic interactions and compete molecule. We showed the spatial secondary metabolites may mediate the interactions in which P.grimontii inhibits growth of M. aeruginosa. Additionally, we revealed how M. aeruginosa feedback to the P.grimontii, which stimulates secondary metabolites such as [D-Asp3]-microcystin-LR released by M. aeruginosa. IMS method highlights the significance of allelopathic interactions between a widely distributed toxic cyanobacteria and its bacteria competitors.

Antioxidant responses in cyanobacterium Microcystis aeruginosa caused by two commonly used UV filters, benzophenone-1 and benzophenone-3, at environmentally relevant concentrations

Benzophenone-type ultraviolet filters (BPs) have recently been recognized as emerging organic contaminants. In the present study, the cyanobacterium Microcystis aeruginosa was exposed to environmentally relevant levels (0.01-1000 μg L^-1) of benzophenone-1 (BP-1) and benzophenone-3 (BP-3) for seven days. A battery of tested endpoints associated with photosynthetic pigments and oxidative stress was employed for a better understanding of the mode of action. The tested cyanobacterium could uptake the two BPs (27.4-54.9%) from culture media. The two BPs were able to inhibit the production of chlorophyll a (chl-a) and promote the accumulation of carotenoids, leading to unaffected chl-a autofluorescence. Slightly increased malondialdehyde (MDA) contents suggested that BP-1 and BP-3 caused moderate oxidative stress. BP-1 stimulated the activities of superoxide dismutase (SOD), glutathione reductase (GR) and glutathione S-transferase (GST) in M. aeruginosa while BP-3 increased the activities of SOD, GST, and glutathione (GSH), showing a concentration- and time-dependent relationship. The activities of other biomarkers, such as catalase (CAT) and glutathione peroxidase (GPx) fluctuated depending on exposure time and concentration. The overall results suggested that the two BPs can trigger moderate oxidative stress in M. aeruginosa and the tested cyanobacterium was capable of alleviating stress by different mechanisms.

Dredging mitigates cyanobacterial bloom in eutrophic Lake Nanhu: Shifts in associations between the bacterioplankton community and sediment biogeochemistry

Cyanobacterial blooms are a worldwide environmental problem, which is partly attributed to their access to excessive nitrogen (N) and phosphorus (P). Preventing the blooms by reducing N and P from internal inputs is viewed as a challenge. To evaluate the effects of dredging on cyanobacterial abundances and bacterioplankton communities, water and sediment samples were collected from eutrophic Lake Nanhu (Wuhan, China) before dredging (2017) and after dredging (2018). After dredging, significant decreases were observed for sediment nutrients (e.g., C, N, and P sources); C-, N-, P-, and S-cycling-related enzyme activity; N- and P-cycling-related gene abundance; microbial abundance; and dramatic changes were observed in the composition of the sediment microbial community. The release rates of nutrient including nitrogen, phosphorus, and organic matter decreased after dredging, and sediment biogeochemistry was closely correlated to nutrient release rates. Additionally, our observations and analyses indicated that the abundance and diversity of the bacterioplankton community decreased significantly, the composition and interaction of the bacterioplankton community dramatically changed, and the bacterioplankton community function (e.g., N, P-cycling-related enzymes and proteins) down regulated after dredging. Water and sediment physicochemical factors explained 72.28% variation in bacterioplankton community composition, and these physicochemical factors were significantly correlated with diversity, composition, and function of bacterioplankton community. Our findings emphasized that cyanobacterial blooms in freshwater ecosystems were closely correlated with noncyanobacterial bacterioplankton that were largely conserved at the phylum level, with Proteobacteria, Actinobacteria, and Bacteroidetes as the main taxa. To our knowledge, this is the first report clarifying the mechanism of cyanobacterial blooms mitigation by dredging, via changing the association between the bacterioplankton community and sediment biogeochemistry. Our findings are of significance and indicate that dredging is effective for mitigating cyanobacterial blooms.

The Complicated and Confusing Ecology of Microcystis Blooms

Blooms of the toxin-producing cyanobacterium Microcystis are increasing globally, leading to the loss of ecosystem services, threats to human health, as well as the deaths of pets and husbandry animals. While nutrient availability is a well-known driver of algal biomass, the factors controlling “who” is present in fresh waters are more complicated. Microcystis possesses multiple strategies to adapt to temperature, light, changes in nutrient chemistry, herbivory, and parasitism that provide a selective advantage over its competitors.

Blooms of the toxin-producing cyanobacterium Microcystis are increasing globally, leading to the loss of ecosystem services, threats to human health, as well as the deaths of pets and husbandry animals. While nutrient availability is a well-known driver of algal biomass, the factors controlling “who” is present in fresh waters are more complicated. Microcystis possesses multiple strategies to adapt to temperature, light, changes in nutrient chemistry, herbivory, and parasitism that provide a selective advantage over its competitors. Moreover, its ability to alter ecosystem pH provides it a further advantage that helps exclude many of its planktonic competitors. While decades of nutrient monitoring have provided us with the tools to predict the accumulation of phytoplankton biomass, here, we point to factors on the horizon that may inform us why Microcystis is presently the dominant bloom former in freshwaters around the world.

Increased algicidal activity of Aeromonas veronii in response to Microcystis aeruginosa: interspecies crosstalk and secondary metabolites synergism

Toxic Microcystis spp. blooms constitute a serious threat to water quality worldwide. Aeromonas veronii was isolated from Microcystis sp. colonies collected in Lake Kinneret. Spent Aeromonas media inhibits the growth of Microcystis aeruginosa MGK isolated from Lake Kinneret. The inhibition was much stronger when Aeromonas growth medium contained spent media from MGK suggesting that Aeromonas recognized its presence and produced secondary metabolites that inhibit Microcystis growth. Fractionations of the crude extract and analyses of the active fractions identified several secondary metabolites including lumichrome in Aeromonas media. Application of lumichrome at concentrations as low as 4 nM severely inhibited Microcystis growth. Inactivation of aviH in the lumichrome biosynthetic pathway altered the lumichrome level in Aeromonas and the extent of MGK growth inhibition. Conversely, the initial lag in Aeromonas growth was significantly longer when provided with Microcystis spent media but Aeromonas was able to resume normal growth. The longer was pre-exposure to Microcystis spent media the shorter was the lag phase in Aeromonas growth indicating the presence of, and acclimation to, secondary MGK metabolite(s) the nature of which was not revealed. Our study may help to control toxic Microcystis blooms taking advantage of chemical languages used in the interspecies communication.

Microbial community analysis and correlation with 2-methylisoborneol occurrence in landscape lakes of Beijing

The microbial community is an important factor influencing the health of the water ecosystem in landscape lakes; in particular, proliferation of some cyanobacteria could cause odor problems. Exploring the microbial community is important for water quality management. In this study, focusing on seven landscape lakes in Beijing, the microbial communities were investigated based on 16S rRNA gene amplicon sequencing, and typical odor-causing compounds and interfering factors were identified. The results showed that 2-methylisoborneol (MIB) was the major odor-causing compound responsible for the earthy/musty odor in landscape lakes. For algal communities, Chlorella and Diatoms were the main eukaryote algae in the water. The bacterial community was dominated by Proteobacteria at the phylum level, and then Cyanobacteria, Actinobacteria, and Firmicutes, etc., most of which were the major phyla of the heterotrophic bacterial population. The richness and diversity of bacteria in natural-water-source lakes were higher than those in reclaimed-water-source lakes. Synechococcus (Cyanobacteria) and GKS98 (Proteobacteria) in reclaimed-water-source lakes were higher than those in natural-water-source lakes, however, CL500-29 (Actinobacteria) in natural-water-source lakes was higher than that in reclaimed-water-source lakes. These bacteria also had significantly positive correlations with MIB. Cyanobacteria and Actinobacteria were the main MIB compound contributors to the variability of MIB in the landscape lakes in Beijing.

Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms

Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.

Physiological effects of nitrate, ammonium, and urea on the growth and microcystins contamination of Microcystis aeruginosa: Implication for nitrogen mitigation

The effects of three commonly bioavailable nitrogen (N) sources (nitrate, ammonium, and urea) on regulating the growth and microcystins (MCs) production of Microcystis aeruginosa (M. aeruginosa) at environmentally relevant concentrations were investigated from a physiological perspective. Changes in amino acid quotas as well as the transcripts of target genes associated with N metabolism (ntcA, pipX and glnB) and toxin formation (mcyA and mcyD) were determined. Results indicated that increases in nitrate and urea concentrations enhanced M. aeruginosa growth, but high ammonium concentration (7 mg-N/L) suppressed the growth. The total intracellular MCs (IMCs) content was well correlated (0.65, p < 0.001) to amino acids (the sum of methionine, leucine, serine, alanine, arginine, glutamic acid, and aspartic acid) associated with MCs production. Ammonium favors amino acid synthesis in M. aeruginosa, thus cells grown under high concentrations of ammonium (7 mg-N/L) had sufficient precursors for MCs production, which might lead to higher IMCs. Both high and low ammonium concentration resulted in high total extracellular MCs (EMCs) level in water, despite of their different mechanisms. These results indicated that mitigation of nitrogen in eutrophic waters should be very cautious of unexpected risks, as the reduction of ammonium may have the risk of stimulating M. aeruginosa growth or increasing EMCs levels.

Cooccurrence of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa

Viruses play important roles in regulating the abundance and composition of bacterial populations in aquatic ecosystems. The bloom-forming toxic cyanobacterium Microcystis aeruginosa is predicted to interact with diverse cyanoviruses, resulting in Microcystis population diversification. However, current knowledge of the genomes from these viruses and their infection programs is limited to those of Microcystis virus Ma-LMM01. Here, we performed a time series sampling at a small pond in Japan during a Microcystis bloom and then investigated the genomic information and transcriptional dynamics of Microcystis-interacting viruses using metagenomic and metatranscriptomic approaches. We identified 15 viral genomic fragments classified into three groups, groups I (including Ma-LMM01), II (high abundance and transcriptional activity), and III (new lineages). According to the phylogenetic distribution of Microcystis strains possessing spacers against each viral group, the group II-original viruses interacted with all three phylogenetically distinct Microcystis population types (phylotypes), whereas the groups I and III-original viruses interacted with only one or two phylotypes, indicating the cooccurrence of broad- (group II) and narrow (groups I and III)-host-range viruses in the bloom. These viral fragments showed the highest transcriptional levels during daytime regardless of their genomic differences. Interestingly, M. aeruginosa expressed antiviral defense genes in the environment, unlike what was seen with an Ma-LMM01 infection in a previous culture experiment. Given that broad-host-range viruses often induce antiviral responses within alternative hosts, our findings suggest that such antiviral responses might inhibit viral multiplication, mainly that of broad-host-range viruses like those in group II.IMPORTANCE The bloom-forming toxic cyanobacterium Microcystis aeruginosa is thought to have diversified its population through the interactions between host and viruses in antiviral defense systems. However, current knowledge of viral genomes and infection programs is limited to those of Microcystis virus Ma-LMM01, which was a narrow host range in which it can escape from the highly abundant host defense systems. Our metagenomic approaches unveiled the cooccurrence of narrow- and broad-host-range Microcystis viruses, which included fifteen viral genomic fragments from Microcystis blooms that were classified into three groups. Interestingly, Microcystis antiviral defense genes were expressed against viral infection in the environment, unlike what was seen in a culture experiment with Ma-LMM01. Given that viruses with a broad host range often induce antiviral responses within alternative hosts, our findings suggest that antiviral responses inhibit viral reproduction, especially that of broad-range viruses like those in group II. This paper augments our understanding of the interactions between M. aeruginosa and its viruses and fills an important knowledge gap.

Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States)

This study examined diel shifts in metabolic functions of Microcystis spp. during a 48-h Lagrangian survey of a toxin-producing cyanobacterial bloom in western Lake Erie in the aftermath of the 2014 Toledo Water Crisis. Transcripts mapped to the genomes of recently sequenced lower Great Lakes Microcystis isolates showed distinct patterns of gene expression between samples collected across day (10:00 h, 16:00 h) and night (22:00 h, 04:00 h). Daytime transcripts were enriched in functions related to Photosystem II (e.g., psbA), nitrogen and phosphate acquisition, cell division (ftsHZ), heat shock response (dnaK, groEL), and uptake of inorganic carbon (rbc, bicA). Genes transcribed during nighttime included those involved in phycobilisome protein synthesis and Photosystem I core subunits. Hierarchical clustering and principal component analysis (PCA) showed a tightly clustered group of nighttime expressed genes, whereas daytime transcripts were separated from each other over the 48-h duration. Lack of uniform clustering within the daytime transcripts suggested that the partitioning of gene expression in Microcystis is dependent on both circadian regulation and physicochemical changes within the environment.

Development of a new extraction method based on high-intensity ultra-sonication to study RNA regulation of the filamentous cyanobacteria Planktothrix

Efficient RNA extraction methods are needed to study transcript regulation. Such methods must lyse the cell without degrading the genetic material. For cyanobacteria this can be particularly challenging because of the presence of the cyanobacteria cell envelope. The great breath of cyanobacterial shape and size (unicellular, colonial, or filamentous multicellular) created a variety of cell lysis methods. However, there is still a lack of reliable techniques for nucleic acid extraction for several types of cyanobacteria.

Here we designed and tested 15 extraction methods using physical, thermic or chemical stress on the filamentous cyanobacteria Planktothrix agardhii. Techniques based on the use of beads, sonication, and heat shock appeared to be too soft to break the Planktothrix agardhii cell envelope, whereas techniques based on the use of detergents degraded the cell envelope but also the RNA. Two protocols allowed to successfully obtain good-quality RNA. The first protocol consisted to manually crush the frozen cell pellet with a pestle and the second was based on the use of high-intensity ultra-sonication. When comparing these two, the high-intensity ultra-sonication protocol was less laborious, faster and allowed to extract 3.5 times more RNA compared to the liquid nitrogen pestle protocol. The high-intensity ultra-sonication protocol was then tested on five Planktothrix strains, this protocol allowed to obtain >8.5 μg of RNA for approximatively 3.5 × 10⁸ cells. The extracted RNA were characterized by 260/280 and 260/230 ratio > to 2, indicating that the samples were devoid of contaminant, and RNA Quality Number > to 7, meaning that the integrity of RNA was preserved with this extraction method. In conclusion, the method we developed based on high-intensity ultra-sonication proved its efficacy in the extraction of Planktothrix RNA and could be helpful for other types of samples.

Microbial Metabolomics: A General Overview

In the biosciences, there has been growing interest in the elucidation of gene function. Consequently, metabolomics has garnered a lot of attention of late due to its provision of metabolic information pertaining to both function and phenotype. Furthermore, when metabolomics data is integrated with other "omics" data, precise characterization of metabolic activity can be achieved. This chapter briefly introduces a few important aspects of the metabolome, the challenges faced when acquiring metabolomic information and the steps that are necessary to overcoming them. This chapter also briefly covers current analytical technologies and some microbial metabolomic applications.

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change

Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environmental change is not well known. Metagenomes allow examination of genetic responses of the entire microbial community to environmental change. However, it is challenging to link metagenomes directly to biogeochemical process rates. Here, we investigate metagenomic responses in natural bacterioplankton communities to simulated environmental stressors in the Baltic Sea, including increased river water input, increased nutrient concentration, and reduced oxygen level. This allowed us to identify informative prokaryotic gene markers, responding to environmental perturbation. Our results demonstrate that metagenomic and metabolic changes in bacterial communities in response to environmental stressors are influenced both by the initial community composition and by the biogeochemical factors shaping the functional response. Furthermore, the different sources of dissolved organic matter (DOM) had the largest impact on metagenomic blueprint. Most prominently, changes in DOM loads influenced specific transporter types reflecting the substrate availability and DOC assimilation and consumption pathways. The results provide new knowledge for developing models of ecosystem structure and biogeochemical cycling in future climate change scenarios and advance our exploration of the potential use of marine microorganisms as markers for environmental conditions.

Influence of cyanobacteria, mixotrophic flagellates, and virioplankton size fraction on transcription of microcystin synthesis genes in the toxic cyanobacterium Microcystis aeruginosa

Toxic cyanobacteria such as Microcystis aeruginosa are a worldwide concern in freshwater reservoirs. Problems associated with their mass occurrence are predicted to increase in the future due to global warming. The hepatotoxic secondary metabolite microcystin is of particular concern in this context. This study aimed to determine whether co-occurring microorganisms influence the expression of microcystin biosynthesis genes. To this end, we performed cocultivation experiments and measured mcyB and mcyD transcripts in M. aeruginosa using RT-qPCR. We utilized representatives from three different plankton groups: the picocyanobacterium Synechococcus elongatus, the unicellular flagellate grazer Ochromonas danica, and virioplankton from two different lakes. The presence of S. elongatus significantly increased mcyB and mcyD transcription in M. aeruginosa. Cocultivation with the mixotrophic chrysophyte O. danica did not increase the transcription of mcyB and mcyD; in fact, mcyD transcripts decreased significantly. The virioplankton size fraction of environmental water samples induced a significant increase in mcyB and mcyD transcription when obtained from lakes with cyanobacterial blooms. Our results show that co-occurring microorganisms influence the expression of microcystin biosynthesis genes in M. aeruginosa.

Metaproteomics reveals major microbial players and their metabolic activities during the blooming period of a marine dinoflagellate Prorocentrum donghaiense

Interactions between bacteria and phytoplankton during bloom events are essential for both partners, which impacts their physiology, alters ambient chemistry and shapes ecosystem diversity. Here, we investigated the community structure and metabolic activities of free-living bacterioplankton in different blooming phases of a dinoflagellate Prorocentrum donghaiense using a metaproteomic approach. The Fibrobacteres-Chlorobi-Bacteroidetes group, Rhodobacteraceae, SAR11 and SAR86 clades contributed largely to the bacterial community in the middle-blooming phase while the Pseudoalteromonadaceae exclusively dominated in the late-blooming phase. Transporters and membrane proteins, especially TonB-dependent receptors were highly abundant in both blooming phases. Proteins involved in carbon metabolism, energy metabolism and stress response were frequently detected in the middle-blooming phase while proteins participating in proteolysis and central carbon metabolism were abundant in the late-blooming phase. Beta-glucosidase with putative algicidal capability was identified from the Pseudoalteromonadaceae only in the late-blooming phase, suggesting an active role of this group in lysing P. donghaiense cells. Our results indicated that diverse substrate utilization strategies and different capabilities for environmental adaptation among bacteria shaped their distinct niches in different bloom phases, and certain bacterial species from the Pseudoalteromonadaceae might be crucial for the termination of a dinoflagellate bloom.