Phylogenomic Analysis of Secondary Metabolism in the Toxic Cyanobacterial Genera Anabaena, Dolichospermum and Aphanizomenon

Metagenomics reveals spatial variation in cyanobacterial composition, function, and biosynthetic potential in the Winam Gulf, Lake Victoria, Kenya

The Winam Gulf in the Kenyan region of Lake Victoria experiences prolific, year-round cyanobacterial harmful algal blooms (cyanoHABs) which pose threats to human, livestock, and ecosystem health. To our knowledge, there is limited molecular research on the gulf's cyanoHABs, and thus, the strategies employed for survival and proliferation by toxigenic cyanobacteria in this region remain largely unexplored. Here, we used metagenomics to analyze the Winam Gulf's cyanobacterial composition, function, and biosynthetic potential. Dolichospermum was the dominant bloom-forming cyanobacterium, co-occurring with Microcystis at most sites. Microcystis and Planktothrix were more abundant in shallow and turbid sites. Metagenome-assembled genomes (MAGs) of Dolichospermum harbored nitrogen fixation genes, suggesting diazotrophy as a potential mechanism supporting the proliferation of Dolichospermum in the nitrogen-limited gulf. Over 300 biosynthetic gene clusters (BGCs) putatively encoding the synthesis of toxins and other secondary metabolites were identified across the gulf, even at sites where there were no visible cyanoHAB events. Almost all BGCs identified had no known synthesis product, indicating a diverse and novel biosynthetic repertoire capable of synthesizing harmful or potentially therapeutic metabolites. Microcystis MAGs contained mcy genes encoding the synthesis of hepatotoxic microcystins which are a concern for drinking water safety. These findings illustrate the spatial variation of bloom-forming cyanobacteria in the Winam Gulf and their available strategies to dominate different ecological niches. This study underscores the need for further use of genomic techniques to elucidate the dynamics and mitigate the potentially harmful effects of cyanoHABs and their associated toxins on human, environmental, and economic health.

Microcystin-LR in drinking water: An emerging role of mitochondrial-induced epigenetic modifications and possible mitigation strategies

Algal blooms are a serious menace to freshwater bodies all over the world. These blooms typically comprise cyanobacterial outgrowths that produce a heptapeptide toxin, Microcystin-LR (MC-LR). Chronic MC-LR exposure impairs mitochondrial-nuclear crosstalk, ROS generation, activation of DNA damage repair pathways, apoptosis, and calcium homeostasis by interfering with PC/MAPK/RTK/PI3K signaling. The discovery of the toxin's biosynthesis pathways paved the way for the development of molecular techniques for the early detection of microcystin. Phosphatase inhibition-based bioassays, high-performance liquid chromatography, and enzyme-linked immunosorbent tests have recently been employed to identify MC-LR in aquatic ecosystems. Biosensors are an exciting alternative for effective on-site analysis and field-based characterization. Here, we present a synthesis of evidence supporting MC-LR as a mitotoxicant, examine various detection methods, and propose a novel theory for the relevance of MC-LR-induced breakdown of mitochondrial machinery and its myriad biological ramifications in human health and disease.

Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase

The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits. Novel regulatory subunits, biotin lipoyl attachment domain-containing proteins (BADC) and carboxyltransferase interactors (CTI) (both three-gene families in Arabidopsis) represent new effectors specific to plants and certain algal species. The evolutionary history of these genes in autotrophic eukaryotes remains elusive, making it an ongoing area of research. Analyses of potential protein-protein and co-occurrence interactions, informed by gene network patterns using the STRING database, in Arabidopsis thaliana and Chlamydomonas reinhardtii unveil intricate gene associations with ACCase, suggesting a complex interplay between FA synthesis and other cellular processes. Among both species, a higher number of co-expressed genes was identified in Arabidopsis, indicating a wider potential regulatory network of ACCase in plants. This review investigates the extent to which these genes arose in autotrophic eukaryotes and provides insights into their evolutionary trajectory. This article is part of the theme issue 'The evolution of plant metabolism'.

Phylogenetic and molecular characteristics of two Aphanizomenon strains from the Curonian Lagoon, Southeastern Baltic Sea and their biological activities

Polyphasic approach has become a generally accepted method for the classification of cyanobacteria. In this study, we present a detailed characterisation of two strains, KUCC C1 and KUCC C2, isolated from the Curonian Lagoon and classified to the Aphanizomenon genus. Despite phylogenetic similarity, the strains differ with respect to morphology, ultrastructure characteristics, and the metabolite profile. In the KUCC C1 extract, three unknown peptides and eight anabaenopeptins were detected, while KUCC C2 produced one unknown peptide and one aeruginosin. In both strains, a total of eleven pigments were detected. The production of myxoxantophyll, chlorophyll-a, chlorophylide-a, and zeaxanthin was higher in KUCC C2 than in KUCC C1. Extracts from both strains of Aphanizomenon also had different effects in antibacterial, anticancer and enzyme inhibition assays. Comprehensive analyses of Aphanizomenon strains performed in this study showed significant diversity between the isolates from the same bloom sample. These differences should be considered when exploring the ecological significance and biotechnological potential of a given population.

Microcystins are present in water treatment plant residuals and are impacted by extraction and quantification methodology

Microcystins (MCs), a toxin produced by some species of the photosynthetic autotrophic cyanobacteria, are the most studied and monitored cyanotoxin in water. Water treatment plant (WTP) residuals are the byproduct of water treatment consisting of solids removed from WTP processes and have been shown to contain cyanobacterial cells. However, the presence of MCs in WTP residuals has not been systematically demonstrated. Samples from four different WTPs across the United States were used to quantify MCs in residuals while assessing extraction and quantification methods adapted from water samples for solid matrices. MCs were present in 100% of samples. MC-LA was the most prevalent variant in these samples (70.05% of MCs quantified by UPLC-PDA). Natural degradation observed in a WTP storage lagoon was also investigated to determine the impact of physical, chemical, and biological processes on MC concentrations in high-biomass residuals. This study demonstrates that residuals of various characteristics across the United States contain MCs, and no one method was found to maximize results consistently across all samples. Cyanotoxins accumulating in WTP residuals are a growing concern. Implications of this work can help regulations and future studies of potential reuse applications and understanding of potential ecological significance of MCs accumulating in WTP residuals.

Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes

Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.

Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps

Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on a population of Dolichospermum lemmermannii collected during a surface bloom in Lake Garda in the summer of 2020. Using a phylogenomic approach, the almost complete metagenome-assembled genome obtained from the analysis allowed to clarify the taxonomic position of the species within the genus Dolichospermum and contributed to frame the taxonomy of this genus within the ADA group (Anabaena/Dolichospermum/Aphanizomenon). In addition to common functional traits represented in the central metabolism of photosynthetic cyanobacteria, the genome annotation uncovered some distinctive and adaptive traits that helped define the factors that promote and maintain bloom-forming heterocytous nitrogen-fixing Nostocales in oligotrophic lakes. In addition, genetic clusters were identified that potentially encode several secondary metabolites that were previously unknown in the populations evolving in the southern Alpine Lake district. These included geosmin, anabaenopetins, and other bioactive compounds. The results expanded the knowledge of the distinctive competitive traits that drive algal blooms and provided guidance for more targeted analyses of cyanobacterial metabolites with implications for human health and water resource use.

Distribution of toxigenic cyanobacteria in Alpine lakes and rivers as revealed by molecular screening

The increasing frequency of cyanobacteria blooms in waterbodies caused by ecosystem eutrophication could endanger human health. This risk can be mitigated by effective monitoring incorporating molecular methods. To date, most molecular studies on toxigenic cyanobacteria have been limited to microcystins (MCs), disregarding other cyanotoxins, to freshwater planktic habitats while ignoring benthic habitats, and to limited geographic areas (usually one or a few specific waterbodies). In this study, we used PCR-based methods including PCR product sequencing and chemical-analytical methods (LC-MS/MS) to screen many plankton (n = 123) and biofilm samples (n = 113) originating from 29 Alpine lakes and 18 rivers for their cyanotoxin production potential. Both mcyE (indicating MC synthesis) and anaC (indicating anatoxin (ATX) synthesis) gene fragments were able to qualitatively predict MC or ATX occurrence. The abundance of mcyE gene fragments was significantly related to MC concentrations in plankton samples (R2 = 0.61). mcyE gene fragments indicative of MC synthesis were most abundant in planktic samples (65 %) and were assigned to the genera Planktothrix and Microcystis. However, mcyE rarely occurred in biofilms of lakes and rivers, i.e., 4 % and 5 %, respectively, and were assigned to Microcystis, Planktothrix, and Nostoc. In contrast, anaC gene fragments occurred frequently in planktic samples (14 % assigned to Tychonema, Phormidium (Microcoleus), and Oscillatoria), but also in biofilms of lakes (49 %) and rivers (18 %) and were assigned to the genera Phormidium, Oscillatoria, and Nostocales. The cyrJ gene fragment indicating cylindrospermopsin synthesis occurred only once in plankton (assigned to Dolichospermum), while saxitoxin synthesis potential was not detected. For plankton samples, monomictic and less eutrophic conditions were positively related to mcyE/MC occurrence frequency, while oligomictic conditions were related to anaC/ATX frequency. The anaC/ATX frequency in biofilm was related to the lake habitats generally showing higher biodiversity as revealed from metabarcoding in a parallel study.

Harnessing the potential: advances in cyanobacterial natural product research and biotechnology

Covering: 2000 to 2023Cyanobacteria produce a variety of bioactive natural products that can pose a threat to humans and animals as environmental toxins, but also have potential for or inspire pharmaceutical use. As oxygenic phototrophs, cyanobacteria furthermore hold great promise for sustainable biotechnology. Yet, the necessary tools for exploiting their biotechnological potential have so far been established only for a few model strains of cyanobacteria, while large untapped biosynthetic resources are hidden in slow-growing cyanobacterial genera that are difficult to access by genetic techniques. In recent years, several approaches have been developed to circumvent the bottlenecks in cyanobacterial natural product research. Here, we summarize current progress that has been made in unlocking or characterizing cryptic metabolic pathways using integrated omics techniques, orphan gene cluster activation, use of genetic approaches in original producers, heterologous expression and chemo-enzymatic techniques. We are mainly highlighting genomic mining concepts and strategies towards high-titer production of cyanobacterial natural products from the last 10 years and discuss the need for further research developments in this field.

Intensification of harmful cyanobacterial blooms in a eutrophic, temperate lake caused by nitrogen, temperature, and CO2

Warmer temperatures can significantly increase the intensity of cyanobacterial harmful algal blooms (CHABs) in eutrophic freshwater ecosystems. However, few studies have examined the effects of CO2 enrichment in tandem with elevated temperature and/or nutrients on cyanobacterial taxa in freshwater ecosystems. Here, we observed changes in the biomass of cyanobacteria, nutrients, pH, and carbonate chemistry over a two-year period in a shallow, eutrophic freshwater lake and performed experiments to examine the effects and co-effects of CO2, temperature, and nutrient enrichment on cyanobacterial and N2-fixing (diazotrophic) communities assessed via high throughput sequencing of the 16S rRNA and nifH genes, respectively. During both years, there were significant CHABs (50-500 μg cyanobacterial chlorophyll-a L-1) and lake CO2 levels were undersaturated (≤300 μatm pCO2). NH4+ significantly increased the net growth rates of cyanobacteria as well as the biomass of the diazotrophic cyanobacterial order Nostocales under elevated and ambient CO2 conditions. In a fall experiment, the N2 fixation rates of Nostocales were significantly higher when populations were enriched with CO2 and P, relative to CO2-enriched populations that were not amended with P. During a summer experiment, N2 fixation rates increased significantly under N and CO2 - enriched conditions relative to N-enriched and ambient CO2 conditions. Nostocales dominated the diazotrophic communities of both experiments, achieving the highest relative abundance under CO2-enriched conditions when N was added in the first experiment and when CO2 and temperature were elevated in the second experiment, when N2 fixation rates also increased significantly. Collectively, this study indicates that N promotes cyanobacterial blooms including those formed by Dolichospermum and that the biomass and N2 fixation rates of diazotrophic cyanobacterial taxa may benefit from enhanced CO2 levels in eutrophic lakes.

Effects of the catastrophic 2020 Yangtze River seasonal floods on microcystins and environmental conditions in Three Gorges Reservoir Area, China

Introduction

During July and August 2020, Three Gorges Reservoir Area (TGRA) suffered from catastrophic seasonal floods. Floods changed environmental conditions and caused increase in concentration of microcystins (MCs) which is a common and potent cyanotoxin. However, the effects and seasonal variations of MCs, cyanobacteria, and environmental conditions in TGRA after the 2020 Yangtze River extreme seasonal floods remain largely unclear, and relevant studies are lacking in the literature.

Methods

A total of 12 representative sampling sites were selected to perform concentration measurement of relevant water quality objectives and MCs in the representative area of the TGRA. The sampling period was from July 2020 to October 2021, which included the flood period. Organic membrane filters were used to perform the DNA extraction and analyses of the 16S rRNA microbiome sequencing data.

Results

Results showed the seasonal floods result in significant increases in the mean values of microcystin-RR (MCRR), microcystin-YR (MCYR), and microcystin-LR (MCLR) concentration and some water quality objectives (i.e., turbidity) in the hinterland of TGRA compared with that in non-flood periods (p < 0.05). The mean values of some water quality objectives (i.e., total nitrogen (TN), total phosphorus (TP), total dissolved phosphorus (TDP), and turbidity), MC concentration (i.e., MCRR, MCYR, and MCLR), and cyanobacteria abundance (i.e., Cyanobium_PCC-6307 and Planktothrix_NIVA-CYA_15) displayed clear tendency of increasing in summer and autumn and decreasing in winter and spring in the hinterland of TGRA.

Discussions

The results suggest that seasonal floods lead to changes in MC concentration and environmental conditions in the hinterland of TGRA. Moreover, the increase in temperature leads to changes in water quality objectives, which may cause water eutrophication. In turn, water eutrophication results in the increase in cyanobacteria abundance and MC concentration. In particular, the increased MC concentration may further contribute to adverse effects on human health.

Long-term stability of the genome structure of the cyanobacterium, Dolichospermum in a deep German lake

Dolichospermum is a cyanobacterial genus commonly associated with toxic blooms in lakes and brackish water bodies worldwide, and is a long-term resident of Lake Stechlin, northeastern Germany. In recent decades, shifts in the phosphorus loading and phytoplankton species composition have seen increased biomass of Dolichospermum during summer blooms from 1998, peaking around 2005, and declining after 2020. Cyanobacteria are known to rapidly adapt to new environments, facilitated by genome adaptation. To investigate the changes in genomic features that may have occurred in Lake Stechlin Dolichospermum during this time of increased phosphorus loading and higher biomass, whole genome sequence analysis was performed on samples of ten akinetes isolated from ten, 1 cm segments of a sediment core, representing a ∼45-year period from 1970 to 2017. Comparison of these genomes with genomes of extant isolates revealed a clade of Dolichospermum that clustered with the ADA-6 genus complex, with remarkable genome stability, without gene gain or loss events in response to recent environmental changes. The genome characteristics indicate that this species is suited to a deep-chlorophyll maximum, including additional light-harvesting and phosphorus scavenging genes. Population SNP analysis revealed two sub-populations that shifted in dominance as the lake transitioned between oligotrophic and eutrophic conditions. Overall, the results show little change within the population, despite diversity between extant populations from different geographic locations and the in-lake changes in phosphorus concentrations.

Understanding the Risks of Diffusion of Cyanobacteria Toxins in Rivers, Lakes, and Potable Water

Blue-green algae, or cyanobacteria, may be prevalent in our rivers and tap water. These minuscule bacteria can grow swiftly and form blooms in warm, nutrient-rich water. Toxins produced by cyanobacteria can pollute rivers and streams and harm the liver and nervous system in humans. This review highlights the properties of 25 toxin types produced by 12 different cyanobacteria genera. The review also covered strategies for reducing and controlling cyanobacteria issues. These include using physical or chemical treatments, cutting back on fertilizer input, algal lawn scrubbers, and antagonistic microorganisms for biocontrol. Micro-, nano- and ultrafiltration techniques could be used for the removal of internal and extracellular cyanotoxins, in addition to powdered or granular activated carbon, ozonation, sedimentation, ultraviolet radiation, potassium permanganate, free chlorine, and pre-treatment oxidation techniques. The efficiency of treatment techniques for removing intracellular and extracellular cyanotoxins is also demonstrated. These approaches aim to lessen the risks of cyanobacterial blooms and associated toxins. Effective management of cyanobacteria in water systems depends on early detection and quick action. Cyanobacteria cells and their toxins can be detected using microscopy, molecular methods, chromatography, and spectroscopy. Understanding the causes of blooms and the many ways for their detection and elimination will help the management of this crucial environmental issue.

Discovery, Function, and Engineering of Graspetides

Graspetides are a class of RiPPs (ribosomally synthesized and post-translationally modified peptides) defined by the presence of ester or amide side chain-side chain linkages resulting in peptide macrocycles. The graspetide name comes from the ATP-grasp enzymes that install the side chain-side chain linkages. This review covers the early, activity-based isolation of the first graspetides, marinostatins and microviridins, as well as the key genomics-driven experiments that established graspetide as RiPPs. The mechanism and structure of graspetide-associated ATP-grasp enzymes is discussed. Genome mining methods to discover new graspetides as well as the analytical techniques used to determine the linkages in graspetides are described. Extant knowledge on the bioactivity of graspetides as protease inhibitors is reviewed. Further chemical modifications to graspetides as well graspetide engineering studies are also described. We conclude with several suggestions about future directions of graspetide research.

Cyanobacteria: A Promising Source of Antifungal Metabolites

Cyanobacteria are a rich source of secondary metabolites, and they have received a great deal of attention due to their applicability in different industrial sectors. Some of these substances are known for their notorious ability to inhibit fungal growth. Such metabolites are very chemically and biologically diverse. They can belong to different chemical classes, including peptides, fatty acids, alkaloids, polyketides, and macrolides. Moreover, they can also target different cell components. Filamentous cyanobacteria have been the main source of these compounds. This review aims to identify the key features of these antifungal agents, as well as the sources from which they are obtained, their major targets, and the environmental factors involved when they are being produced. For the preparation of this work, a total of 642 documents dating from 1980 to 2022 were consulted, including patents, original research, review articles, and theses.

Transcriptionally active nitrogen fixation and biosynthesis of diverse secondary metabolites by Dolichospermum and Aphanizomenon-like Cyanobacteria in western Lake Erie Microcystis blooms

Cyanobacterial harmful algal blooms (cyanoHABs) in the western basin of Lake Erie are dominated by microcystin producing Microcystis spp., but other cyanobacterial taxa that coexist in these communities may play important roles in production of toxins and shaping bloom dynamics and community function. In this study, we used metagenomic and metatranscriptomic data from the 2014 western Lake Erie cyanoHAB to explore the genetic diversity and biosynthetic potential of cyanobacteria belonging to the Anabaena, Dolichospermum, Aphanizomenon (ADA) clade. We reconstructed two near-complete metagenome-assembled genomes from two distinct ADA clade species, each containing biosynthetic gene clusters that encode novel and known secondary metabolites, including those with toxic and/or known taste and odor properties, that were transcriptionally active. However, neither ADA metagenome-assembled genome contained genes encoding guanitoxins, anatoxins, or saxitoxins, which are known to be produced by ADA. The ADA cyanobacteria accounted for most of the metagenomic and metatranscriptomic reads from nitrogen fixation genes, suggesting they were the dominant N-fixers at the times and stations sampled. Despite their relatively low abundance, our results highlight the possibility that ADA taxa could influence the water quality and ecology of Microcystis blooms, although the extent of these impacts remains to be quantified.

Nitrogen and phosphorus significantly alter growth, nitrogen fixation, anatoxin-a content, and the transcriptome of the bloom-forming cyanobacterium, Dolichospermum

While freshwater cyanobacteria are traditionally thought to be limited by the availability of phosphorus (P), fixed nitrogen (N) supply can promote the growth and/or toxin production of some genera. This study characterizes how growth on N2 (control), nitrate (NO3 -), ammonium (NH4 +), and urea as well as P limitation altered the growth, toxin production, N2 fixation, and gene expression of an anatoxin-a (ATX-A) - producing strain of Dolichospermum sp. 54. The transcriptomes of fixed N and P-limited cultures differed significantly from those of fixed N-deplete, P-replete (control) cultures, while the transcriptomes of P-replete cultures amended with either NH4 + or NO3 - were not significantly different relative to those of the control. Growth rates of Dolichospermum (sp. 54) were significantly higher when grown on fixed N relative to without fixed N; growth on NH4 + was also significantly greater than growth on NO3 -. NH4 + and urea significantly lowered N2 fixation and nifD gene transcript abundance relative to the control while cultures amended with NO3 - exhibited N2 fixation and nifD gene transcript abundance that was not different from the control. Cultures grown on NH4 + exhibited the lowest ATX-A content per cell and lower transcript abundance of genes associated ATX-A synthesis (ana), while the abundance of transcripts of several ana genes were highest under fixed N and P - limited conditions. The significant negative correlation between growth rate and cellular anatoxin quota as well as the significantly higher number of transcripts of ana genes in cultures deprived of fixed N and P relative to P-replete cultures amended with NH4 + suggests ATX-A was being actively synthesized under P limitation. Collectively, these findings indicate that management strategies that do not regulate fixed N loading will leave eutrophic water bodies vulnerable to more intense and toxic (due to increased biomass) blooms of Dolichospermum.

Early and late cyanobacterial bloomers in a shallow, eutrophic lake

Cyanobacterial blooms present challenges for water treatment, especially in regions like the Canadian prairies where poor water quality intensifies water treatment issues. Buoyant cyanobacteria that resist sedimentation present a challenge as water treatment operators attempt to balance pre-treatment and toxic disinfection by-products. Here, we used microscopy to identify and describe the succession of cyanobacterial species in Buffalo Pound Lake, a key drinking water supply. We used indicator species analysis to identify temporal grouping structures throughout two sampling seasons from May to October 2018 and 2019. Our findings highlight two key cyanobacterial bloom phases - a mid-summer diazotrophic bloom of Dolichospermum spp. and an autumn Planktothrix agardhii bloom. Dolichospermum crassa and Woronichinia compacta served as indicators of the mid-summer and autumn bloom phases, respectively. Different cyanobacterial metabolites were associated with the distinct bloom phases in both years: toxic microcystins were associated with the mid-summer Dolichospermum bloom and some newly monitored cyanopeptides (anabaenopeptin A and B) with the autumn Planktothrix bloom. Despite forming a significant proportion of the autumn phytoplankton biomass (>60%), the Planktothrix bloom had previously not been detected by sensor or laboratory-derived chlorophyll-a. Our results demonstrate the power of targeted taxonomic identification of key species as a tool for managers of bloom-prone systems. Moreover, we describe an autumn Planktothrix agardhii bloom that has the potential to disrupt water treatment due to its evasion of detection. Our findings highlight the importance of identifying this autumn bloom given the expectation that warmer temperatures and a longer ice-free season will become the norm.

Cyanopeptides restriction and degradation co-mediate microbiota assembly during a freshwater cyanobacterial harmful algal bloom (CyanoHAB)

Cyanobacterial harmful algal blooms (CyanoHABs) are globally intensifying and exacerbated by climate change and eutrophication. However, microbiota assembly mechanisms underlying CyanoHABs remain elusive. Especially, cyanopeptides, as a group of bioactive secondary metabolites of cyanobacteria, could affect microbiota assembly and ecosystem function. Here, the trajectory of cyanopeptides was followed and linked to microbiota during Microcystis-dominated CyanoHABs in Lake Taihu, China. The most abundant cyanopeptide classes detected included microginin, spumigin, microcystin, nodularin and cyanopeptolin with total MC-LR-equivalent concentrations between 0.23 and 2051.54 ppb, of which cyanotoxins beyond microcystins (e.g., cyanostatin B and nodularin_R) far exceeded reported organismal IC₅₀ and negatively correlated with microbiota diversity, exerting potential collective eco-toxicities stronger than microcystins alone. The microbial communities were differentiated by size fraction and sampling date throughout CyanoHABs, and surprisingly, their variances were better explained by cyanopeptides (19-38%) than nutrients (0-16%). Cyanopeptides restriction (e.g., inhibition) and degradation were first quantitatively verified as the deterministic drivers governing community assembly, with stochastic processes being associated with the interplay between cyanopeptide dynamics and lake microbiota. This study presents an emerging paradigm in which cyanopeptides restriction and degradation co-mediate lake water microbiota assembly, unveiling new insights into the ecotoxicological significance of CyanoHABs to freshwater ecosystems.

7-epi-cylindrospermopsin and microcystin producers among diverse Anabaena/Dolichospermum/Aphanizomenon CyanoHABs in Oregon, USA

Several genomes of Nostocales ADA clade members from the US Pacific Northwest were recently sequenced. Biosynthetic genes for microcystin, cylindrospermopsin or anatoxin-a were present in 7 of the 15 Dolichospermum/Anabaena strains and none of the 5 Aphanizomenon flos-aquae (AFA) strains. Toxin analyses (ELISA and LC-MS/MS) were conducted to quantitate and identify microcystin (MC) and cylindrospermopsin (CYN) congeners/analogs in samples dominated by Dolichospermum spp. of known genome sequence. MC-LR was the main congener produced by Dolichospermum spp. from Junipers Reservoir, Lake Billy Chinook and Odell Lake, while a congener provisionally identified as [Dha⁷]MC-HtyR was produced by a Dolichospermum sp. in Detroit Reservoir. A second Dolichospermum sp. from Detroit Reservoir was found to produce 7-epi-CYN, with 7-deoxy-CYN also present, but no CYN. The monitoring history of each of these lakes indicates the capacity for high levels of cyanotoxins during periods when Dolichospermum spp. are the dominant cyanobacteria. The diversity of ADA strains found in the US Pacific NW emphasizes the importance of these cyanobacteria as potentially toxic HAB formers in this temperate climatic region. Our results linking congener and genetic identity add data points that will help guide development of improved tools for predicting congener specificity from cyanotoxin gene sequences.

Characterization and Diversity of Microcystins Produced by Cyanobacteria from the Curonian Lagoon (SE Baltic Sea)

Microcystins (MCs) are the most widely distributed and structurally diverse cyanotoxins that can have significant health impacts on living organisms, including humans. The identification of MC variants and their quantification is very important for toxicological assessment. Within this study, we explored the diversity of MCs and their potential producers from the Curonian Lagoon. MC profiles were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, while the potential producers were detected based on the presence of genus-specific mcyE gene sequences. Among the numerous MCs detected, one new potential MC variant with m/z 1057 was partially characterized. Moreover, two other MCs with m/z 1075 and m/z 1068 might belong to new variants with serine (Ser), rarely detected in position one of the peptides. They might also represent MC-Y(OMe)R and MC-WR, respectively. However, the application of a low-resolution MS/MS system made the unambiguous identification of the MCs impossible. Based on this example, the problems of peptide structure identification are discussed in the work. Genetic analysis revealed that potential MCs producers include Dolichospermum/Anabaena, Microcystis spp., and Planktothrix agardhii. The diversity and temporal variations in MC profiles may indicate the presence of several chemotypes of cyanobacteria in the Curonian Lagoon.

Draft genome and description of Waterburya agarophytonicola gen. nov. sp. nov. (Pleurocapsales, Cyanobacteria): a seaweed symbiont

This work introduces Waterburya agarophytonicola Bonthond and Shalygin gen. nov., sp. nov, a baeocyte producing cyanobacterium that was isolated from the rhodophyte Agarophyton vermiculophyllum (Ohmi) Gurgel et al., an invasive seaweed that has spread across the northern hemisphere. The new species genome reveals a diverse repertoire of chemotaxis and adhesion related genes, including genes coding for type IV pili assembly proteins and a high number of genes coding for filamentous hemagglutinin family (FHA) proteins. Among a genetic basis for the synthesis of siderophores, carotenoids and numerous vitamins, W. agarophytonicola is potentially capable of producing cobalamin (vitamin B₁₂), for which A. vermiculophyllum is an auxotroph. With a taxonomic description of the genus and species and a draft genome, this study provides as a basis for future research, to uncover the nature of this geographically independent association between seaweed and cyanobiont.

Spatial and Temporal Diversity of Cyanometabolites in the Eutrophic Curonian Lagoon (SE Baltic Sea)

This work aims to determine the profiles of cyanopeptides and anatoxin synthetized by cyanobacteria in the Lithuanian part of the Curonian Lagoon (SE Baltic Sea) and to characterize their spatial and temporal patterns in this ecosystem. Cyanometabolites were analysed by a LC-MS/MS system and were coupled to a hybrid triple quadrupole/linear ion trap mass spectrometer. During the investigation period (2013–2017), 10 microcystins, nodularin, anatoxin-a, 16 anabaenopeptins, including 1 oscillamide, 12 aeruginosins, 1 aeruginosamide, 3 cyanopeptolins and 4 microginins were detected. The most frequently detected metabolites were found at all investigated sites. Demethylated microcystin variants and anabaenopeptins had the strongest relationship with Planktothrix agardhii, while non-demethylated microcystin variants and anatoxin had the strongest relationship with Microcystis spp. Low concentrations of some microcystins: [Asp3]MC-RR, MC-RR, MC-LR, as well as a few other cyanopeptides: AP-A and AEG-A were found during the cold period (December–March). Over the study period, Aphanizomenon, Planktothrix and Microcystis were the main dominant cyanobacteria species, while Planktothrix, Microcystis, and Dolichospermum were potentially producers of cyanopeptides and anatoxin detected in samples from the Curonian Lagoon.

Cyanobacterial Toxins and Peptides in Lake Vegoritis, Greece

Cyanotoxins (CTs) produced by cyanobacteria in surface freshwater are a major threat for public health and aquatic ecosystems. Cyanobacteria can also produce a wide variety of other understudied bioactive metabolites such as oligopeptides microginins (MGs), aeruginosins (AERs), aeruginosamides (AEGs) and anabaenopeptins (APs). This study reports on the co-occurrence of CTs and cyanopeptides (CPs) in Lake Vegoritis, Greece and presents their variant-specific profiles obtained during 3-years of monitoring (2018–2020). Fifteen CTs (cylindrospermopsin (CYN), anatoxin (ATX), nodularin (NOD), and 12 microcystins (MCs)) and ten CPs (3 APs, 4 MGs, 2 AERs and aeruginosamide (AEG A)) were targeted using an extended and validated LC-MS/MS protocol for the simultaneous determination of multi-class CTs and CPs. Results showed the presence of MCs (MC-LR, MC-RR, MC-YR, dmMC-LR, dmMC-RR, MC-HtyR, and MC-HilR) and CYN at concentrations of <1 μg/L, with MC-LR (79%) and CYN (71%) being the most frequently occurring. Anabaenopeptins B (AP B) and F (AP F) were detected in almost all samples and microginin T1 (MG T1) was the most abundant CP, reaching 47.0 μg/L. This is the first report of the co-occurrence of CTs and CPs in Lake Vegoritis, which is used for irrigation, fishing and recreational activities. The findings support the need for further investigations of the occurrence of CTs and the less studied cyanobacterial metabolites in lakes, to promote risk assessment with relevance to human exposure.

Cyanotoxin Screening in BACA Culture Collection: Identification of New Cylindrospermopsin Producing Cyanobacteria

Microcystins (MCs), Saxitoxins (STXs), and Cylindrospermopsins (CYNs) are some of the more well-known cyanotoxins. Taking into consideration the impacts of cyanotoxins, many studies have focused on the identification of unknown cyanotoxin(s)-producing strains. This study aimed to screen strains from the Azorean Bank of Algae and Cyanobacteria (BACA) for MCs, STX, and CYN production. A total of 157 strains were searched for mcy, sxt, and cyr producing genes by PCR, toxin identification by ESI-LC-MS/MS, and cyanotoxin-producing strains morphological identification and confirmation by 16S rRNA phylogenetic analysis. Cyanotoxin-producing genes were amplified in 13 strains and four were confirmed as toxin producers by ESI-LC-MS/MS. As expected Aphanizomenon gracile BACA0041 was confirmed as an STX producer, with amplification of genes sxtA, sxtG, sxtH, and sxtI, and Microcystis aeruginosa BACA0148 as an MC-LR producer, with amplification of genes mcyC, mcyD, mcyE, and mcyG. Two nostocalean strains, BACA0025 and BACA0031, were positive for both cyrB and cyrC genes and ESI-LC-MS/MS confirmed CYN production. Although these strains morphologically resemble Sphaerospermopsis, the 16S rRNA phylogenetic analysis reveals that they probably belong to a new genus.

Comparative genomics of the ADA clade within the Nostocales

The ADA clade of Nostocales cyanobacteria, a group that is prominent in current harmful algal bloom events, now includes over 40 genome sequences with the recent addition of sixteen novel sequenced genomes (Dreher et al., Harmful Algae, 2021). Fourteen genomes are complete (closed), enabling highly detailed assessments of gene content and genome architecture. ADA genomes contain 5 rRNA operons, genes expected to support a photoautotrophic and diazotrophic lifestyle, and a varied array of genes for the synthesis of bioactive secondary metabolites. Genes for the production of the taste-and-odor compound geosmin and the four major classes of cyanotoxins - anatoxin-a, cylindrospermopsin, microcystin and saxitoxin - are represented in members of the ADA clade. Notably, the gene array for the synthesis of cylindrospermopsin by Dolichospermum sp. DET69 was located on a plasmid, raising the possibility of facile horizontal transmission. However, genes supporting independent conjugative transfer of this plasmid are lacking. Further, analysis of genomic loci containing this and other cyanotoxin gene arrays shows evidence that these arrays have long-term stability and do not appear to be genomic islands easily capable of horizontal transmission to other cells. There is considerable diversity in the gene complements of individual ADA genomes, including the variable presence of physiologically important genes: genomes in three species-level subclades lack the gas vesicle genes that facilitate a planktonic lifestyle, and, surprisingly, the genome of Cuspidothrix issatschenkoi CHARLIE-1, a reported diazotroph, lacks the genes for nitrogen fixation. Notably, phylogenetically related genomes possess limited synteny, indicating a prominent role for chromosome rearrangements during ADA strain evolution. The genomes contain abundant insertion sequences and repetitive transposase genes, which could be the main drivers of genome rearrangement through active transposition and homologous recombination. No prophages were found, and no evidence of viral infection was observed in the bloom population samples from which the genomes discussed here were derived. Phages thus seem to have a limited influence on ADA evolution.

Complete genomes derived by directly sequencing freshwater bloom populations emphasize the significance of the genus level ADA clade within the Nostocales

The genome sequences of 16 Nostocales cyanobacteria have been determined. Most of them are complete or near-complete genome sequences derived by long-read metagenome sequencing of recent harmful algal blooms (HABs) in freshwater lakes without the potential bias of culture isolation. The genomes are all members of the recently recognized ADA clade (Driscoll et al., Harmful Algae, 77:93, 2018), which we argue represents a genus. We identify 10 putative species-level branches within the clade, on the basis of 91-gene phylogenomic and average nucleotide identity analyses. The assembled genomes each correspond to a single morphotype in the original sample, but distinct genomes from different HABs in some cases correspond to similar morphotypes. We present data indicating that the ADA clade is a highly significant component of current cyanobacterial HABs, including members assigned to the prevalent Dolichospermum and Aphanizomenon genera, as well as Cuspidothrix and Anabaena. In general, currently used genus and species names within the ADA clade are not monophyletic. We infer that the morphological characters routinely used in taxonomic assignments are not reliable for discriminating species within the ADA clade. Taxonomic revisions will be needed to create a genus with a single name (we recommend Anabaena) and to adopt species names that do not depend on morphological traits that lack sufficient discrimination and specificity, while recognizing the utility of some easily observable and distinct morphologies.

Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake's sediment

Hatching resting stages of ecologically important organisms such as Daphnia from lake sediments, referred to as resurrection ecology, is a powerful approach to assess changes in alleles and traits over time. However, the utility of the approach is constrained by a few obstacles, including low and/or biased hatching among genotypes. Here, we eliminated such bottlenecks by investigating DNA sequences isolated directly (i.e. without hatching) from resting eggs found in the sediments of Lake Constance spanning pre-, peri-, and post-eutrophication. While we expected genome-wide changes, we specifically expected changes in alleles related to pathways involved in mitigating effects of cyanobacterial toxins. We used pairwise F_ST-analyses to identify transcripts that showed strongest divergence among the four different populations and a clustering analysis to identify correlations between allele frequency shifts and changes in abiotic and biotic lake parameters. In a cluster that correlated with the increased abundance of cyanobacteria in Lake Constance we find genes that have been reported earlier to be differentially expressed in response to the cyanobacterial toxin microcystin and to microcystin-free cyanobacteria. We further reveal the enrichment of gene ontology terms that have been shown to be involved in microcystin-related responses in other organisms but not yet in Daphnia and as such are candidate loci for adaptation of natural Daphnia populations to increased cyanobacterial abundances. In conclusion this approach of investigating DNA extracted from Daphnia resting stages allowed to determine frequency changes of loci in a natural population over time.

Insight into Unprecedented Diversity of Cyanopeptides in Eutrophic Ponds Using an MS/MS Networking Approach

Man-made shallow fishponds in the Czech Republic have been facing high eutrophication since the 1950s. Anthropogenic eutrophication and feeding of fish have strongly affected the physicochemical properties of water and its aquatic community composition, leading to harmful algal bloom formation. In our current study, we characterized the phytoplankton community across three eutrophic ponds to assess the phytoplankton dynamics during the vegetation season. We microscopically identified and quantified 29 cyanobacterial taxa comprising non-toxigenic and toxigenic species. Further, a detailed cyanopeptides (CNPs) profiling was performed using molecular networking analysis of liquid chromatography-tandem mass spectrometry (LC-MS/MS) data coupled with a dereplication strategy. This MS networking approach, coupled with dereplication, on the online global natural product social networking (GNPS) web platform led us to putatively identify forty CNPs: fourteen anabaenopeptins, ten microcystins, five cyanopeptolins, six microginins, two cyanobactins, a dipeptide radiosumin, a cyclooctapeptide planktocyclin, and epidolastatin 12. We applied the binary logistic regression to estimate the CNPs producers by correlating the GNPS data with the species abundance. The usage of the GNPS web platform proved a valuable approach for the rapid and simultaneous detection of a large number of peptides and rapid risk assessments for harmful blooms.