Monitoring toxigenic Microcystis strains in the Missisquoi bay, Quebec, by PCR targeting multiple toxic gene loci

Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems

Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events can threaten local wildlife, public health, and the utilization of recreational waters. For the detection/quantification of cyanobacteria and cyanotoxins, both the United States Environmental Protection Agency (USEPA) and Health Canada increasingly indicate that molecular methods can be useful. However, each molecular detection method has specific advantages and limitations for monitoring HABs in recreational water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, and machine learning/artificial intelligence, can be integrated with standard/conventional methods to overcome the limitations associated with traditional cyanobacterial detection methodology. We examine advances in cyanobacterial cell lysis methodology and conventional/modern molecular detection methods, including imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, and machine learning/AI-based prediction models. This review focuses specifically on methodologies likely to be employed for recreational water ecosystems, especially in the Great Lakes region of North America.

Cyanotoxin-encoding genes as powerful predictors of cyanotoxin production during harmful cyanobacterial blooms in an inland freshwater lake: Evaluating a novel early-warning system

Freshwater harmful cyanobacterial blooms (HCBs) potentially produce excessive cyanotoxins, mainly microcystins (MCs), significantly threatening aquatic ecosystems and public health. Accurately predicting HCBs is thus essential to developing effective HCB mitigation and prevention strategies. We previously developed a novel early-warning system that uses cyanotoxin-encoding genes to predict cyanotoxin production in Harsha Lake, Ohio, USA, in 2015. In this study, we evaluated the efficacy of the early-warning system in forecasting the 2016 HCB in the same lake. We also examined potential HCB drivers and cyanobacterial community composition. Our results revealed that the cyanobacterial community was stable at the phylum level but changed dynamically at the genus level over time. Microcystis and Planktothrix were the major MC-producing genera that thrived in June and July and produced high concentrations of MCs (peak level 10.22 μg·L^-1). The abundances of the MC-encoding gene cluster mcy and its transcript levels significantly correlated with total MC concentrations (before the MC concentrations peaked) and accurately predicted MC production as revealed by logistic equations. When the Microcystis-specific gene mcyG reached approximately 1.5 × 10³ copies·mL^-1 or when its transcript level reached approximately 2.4 copies·mL^-1, total MC level exceeded 0.3 μg L^-1 (a health advisory limit) approximately one week later (weekly sampling scheme). This study suggested that cyanotoxin-encoding genes are promising predictors of MC production in inland freshwater lakes, such as Harsha Lake. The evaluated early-warning system can be a useful tool to assist lake managers in predicting, mitigating, and/or preventing HCBs.

Microbial community successions and their dynamic functions during harmful cyanobacterial blooms in a freshwater lake

The current study reports the community succession of different toxin and non-toxin producing cyanobacteria at different stages of cyanobacterial harmful algal blooms (CyanoHABs) and their connectivity with nitrogen and phosphorus cycles in a freshwater lake using an ecogenomics framework. Comprehensive high throughput DNA sequencing, water quality parameter measurements, and functional gene expressions over temporal and spatial scales were employed. Among the cyanobacterial community, the lake was initially dominated by Cyanobium during the months of May, June, and early July, and later primarily by Aphanizomenon and Dolichospermum depicting functional redundancy. Finally, Planktothrix appeared in late August and then the dominance switched to Planktothrix in September. Microcystis aeruginosa and Microcystis panniformis; two species responsible for cyanotoxin production, were also present in August and September, but in significantly smaller relative abundance. MC-LR (0.06-1.32 µg/L) and MC-RR (0.01-0.26 µg/L) were two major types of cyanotoxins detected. The presence of MC-LR and MC-RR were significantly correlated with the Microcystis-related genes (16SMic/mcyA/mcyG) and their expressions (r = 0.33 to 0.8, p < 0.05). The metabolic analyses further linked the presence of different cyanobacterial groups with distinct functions. The nitrogen metabolisms detected a relatively higher abundance of nitrite/nitrate reductase in early summer, indicating significant denitrification activity and the activation of N-fixation in the blooms dominated by Aphanizomenon/Dolichospermum (community richness) during nutrient-limited conditions. The phosphorus and carbohydrate metabolisms detected a trend to initiate a nutrient starvation alert and store nutrients from early summer, while utilizing the stored polyphosphate and carbohydrate (PPX and F6PPK) during the extreme ortho-P scarcity period, mostly in August or September. Specifically, the abundance of Aphanizomenon and Dolichospermum was positively correlated with the nitrogen-fixing nif gene and (p < 0.001) and the PPX enzyme for the stored polyphosphate utilization (r = 0.77, p < 0.001). Interestingly, the lake experienced a longer N-fixing period (2-3 months) before non-fixing cyanobacteria (Planktothrix) dominated the entire lake in late summer. The Provo Bay site, which is known to be nutrient-rich historically, had early episodes of filamentous cyanobacteria blooms compared to the rest of the lake.

Use of qPCR and RT-qPCR for monitoring variations of microcystin producers and as an early warning system to predict toxin production in an Ohio inland lake

Public concern over cyanobacterial blooms has increased due to their higher frequency of occurrence and their potential ecological and health impacts. Detection of microcystin (MC) producers (MCPs) using qPCR and RT-qPCR allows for the rapid identification of blooms by combining specificity and sensitivity with a relatively high throughput capability. Investigation of MCP population composition (correlation, dominance), toxin gene expression, and relationship to MC concentration was conducted using a panel of qPCR assays targeting mcyA, E and G on weekly and daily water samples collected from an Ohio inland reservoir lake. Further, these data were used to develop early warning thresholds for prediction of MC concentrations exceeding the US EPA Health Advisory cutoff value (>0.3 μg L-1) using receiver operating characteristic curves and tobit regression. MCP Microcystis genomic copy number made up approximately 35% of the total Microcystis spp. and was the dominant toxic subpopulation of MCPs. The expressed MCPs were 0.2% of the extant genomic copy numbers, while toxic Microcystis had higher expressed proportion (0.5%) than that of toxic Planktothrix (0.04%). Microcystis toxin genes increased in June and July but decreased in August and September along with similar trends of cell replication. Quantities of both RT-qPCR and qPCR followed the same trend and were highly correlated with MC-ADDA, while RT-qPCR not only reflected the active toxin genes or toxic species, but also indicated the beginning and ending of toxin production. A one-week early warning of MC exceedance over the EPA Health Advisory was based on signaling of qPCR and RT-qPCR using receiver operating characteristic curves. This study illustrates the potential use of qPCR or RT-qPCR as an early warning system of extant and MC producing potentials during a toxic algal bloom, with predictive powers of 50%-60% and 30%-40% (p < 0.001), respectively, and false positive rates of about 70% for both LC-MS/MS or ELISA.

An Optical Biosensor-Based Quantification of the Microcystin Synthetase A Gene: Early Warning of Toxic Cyanobacterial Blooming

The monitoring and control of toxic cyanobacterial strains, which can produce microcystins, is critical to protect human and ecological health. We herein reported an optical-biosensor-based quantification of the microcystin synthetase A (mcyA) gene so as to discriminate microcystin-producing strains from nonproducing strains. In this assay, the mcyA-specific ssDNA probes were designed in silico with an on-line tool and then synthesized to be covalently immobilized on an optical-fiber surface. Production of fluorescently modified target DNA fragment amplicons was accomplished through the use of Cy5-tagged deoxycytidine triphosphates (dCTPs) in the polymerase chain reaction (PCR) method, which resulted in copies with internally labeled multiple sites per DNA molecule and delivered great sensitivity. With a facile surface-based hybridization process, the PCR amplicons were captured on the optical-fiber surface and were induced by an evanescent-wave field into fluorescence emission. Under the optimum conditions, the detection limit was found to be 10 pM (S/N ratio = 3) and equaled 10³ gene copies/mL. The assay was triumphantly demonstrated for PCR amplicons of mcyA detection and showed satisfactory stability and reproducibility. Moreover, the sensing system exhibited excellent selectivity with quantitative spike recoveries from 87 to 102% for M. aeruginosa species in the mixed samples. There results confirmed that the method would serve as an accurate, cost-effective, and rapid technique for in-field testing of toxic Microcystis sp. in water, giving early information for water quality monitoring against microcystin-producing cyanobacteria.

Toxic cyanobacterial bloom triggers in missisquoi bay, lake champlain, as determined by next-generation sequencing and quantitative PCR

Missisquoi Bay (MB) is a temperate eutrophic freshwater lake that frequently experiences toxic Microcystis-dominated cyanobacterial blooms. Non-point sources are responsible for the high concentrations of phosphorus and nitrogen in the bay. This study combined data from environmental parameters, E. coli counts, high-throughput sequencing of 16S rRNA gene amplicons, quantitative PCR (16S rRNA and mcyD genes) and toxin analyses to identify the main bloom-promoting factors. In 2009, nutrient concentrations correlated with E. coli counts, abundance of total cyanobacterial cells, Microcystis 16S rRNA and mcyD genes and intracellular microcystin. Total and dissolved phosphorus also correlated significantly with rainfall. The major cyanobacterial taxa were members of the orders Chroococcales and Nostocales. The genus Microcystis was the main mcyD-carrier and main microcystin producer. Our results suggested that increasing nutrient concentrations and total nitrogen:total phosphorus (TN:TP) ratios approaching 11:1, coupled with an increase in temperature, promoted Microcystis-dominated toxic blooms. Although the importance of nutrient ratios and absolute concentrations on cyanobacterial and Microcystis dynamics have been documented in other laboratories, an optimum TN:TP ratio for Microcystis dominance has not been previously observed in situ. This observation provides further support that nutrient ratios are an important determinant of species composition in natural phytoplankton assemblages.

Comparison of cyanobacterial microcystin synthetase (mcy) E gene transcript levels, mcy E gene copies, and biomass as indicators of microcystin risk under laboratory and field conditions

Increased incidences of mixed assemblages of microcystin-producing and nonproducing cyanobacterial strains in freshwater bodies necessitate development of reliable proxies for cyanotoxin risk assessment. Detection of microcystin biosynthetic genes in water blooms of cyanobacteria is generally indicative of the presence of potentially toxic cyanobacterial strains. Although much effort has been devoted toward elucidating the microcystin biosynthesis mechanisms in many cyanobacteria genera, little is known about the impacts of co-occurring cyanobacteria on cellular growth, mcy gene expression, or mcy gene copy distribution. The present study utilized conventional microscopy, qPCR assays, and enzyme-linked immunosorbent assay to study how competition between microcystin-producing Microcystis aeruginosa CPCC 299 and Planktothrix agardhii NIVA-CYA 126 impacts mcyE gene expression, mcyE gene copies, and microcystin concentration under controlled laboratory conditions. Furthermore, analyses of environmental water samples from the Missisquoi Bay, Quebec, enabled us to determine how the various potential toxigenic cyanobacterial biomass proxies correlated with cellular microcystin concentrations in a freshwater lake. Results from our laboratory study indicated significant downregulation of mcyE gene expression in mixed cultures of M. aeruginosa plus P. agardhii on most sampling days in agreement with depressed growth recorded in the mixed cultures, suggesting that interaction between the two species probably resulted in suppressed growth and mcyE gene expression in the mixed cultures. Furthermore, although mcyE gene copies and McyE transcripts were detected in all laboratory and field samples with measureable microcystin levels, only mcyE gene copies showed significant positive correlations (R(2) > 0.7) with microcystin concentrations, while McyE transcript levels did not. These results suggest that mcyE gene copies are better indicators of potential risks from microcystins than McyE transcript levels or conventional biomass proxies, especially in water bodies comprising mixed assemblages of toxic and nontoxic cyanobacteria.