The Genomic Footprints of Urban Lakes. Detection of Cyanotoxins and Pathogens Using Environmental DNA

MORE THAN LANDSCAPE
At first glance, an urban lake can be perceived as a recreational space, composed of a body of water surrounded by flora and fauna. However, beyond appearance, intense biological activity takes place that contains crucial information about the health of the ecosystem and, in many cases, about the health of the human populations that interact with it. In recent years, scientific research has advanced in interpreting these hidden signals by analyzing genetic traces.

Lakes are fundamental elements of socioecosystems. They are emblematic landscapes in urban environments and function as recreational spaces, but they also provide ecosystem services that directly affect human well-being, such as climate regulation, flood mitigation, and the provision of habitat and support for biodiversity. However, the urbanization process has exerted numerous pressures on these water bodies, which manifest mainly in pollution through urban runoff (water stream from rain or ice-melting that runs over the surface of a given terrain or under it), excess nutrients and wastewater discharges, factors that promote eutrophication processes (an excess of nutrients that disrupts the balance of aquatic ecosystems) by which the ecological integrity is deteriorated and the composition of species present in these systems is modified.

One of the most relevant consequences of this deterioration is the proliferation of cyanobacteria capable of forming harmful algal blooms (CianoFANs) (Zamora-Barrios, Nandini & Sarma, 2023). Various environmental factors, such as temperature, solar radiation, water stagnation, and the nitrogen-phosphorus ratio (N:P), significantly influence the intensity and duration of these events (Villalobos, Suárez-Isla & García, 2025). Cyanobacteria are a group of photosynthetic microorganisms present in aquatic and terrestrial environments, which fulfill a fundamental ecological role by contributing to global primary production, oxygen generation and atmospheric nitrogen fixation, thus promoting nutrient cycling and ecosystem productivity.

CianoFANs in an urban lake.
 César Alejandro Zamora-Barrios

CYANOFANS IN URBAN LAKES
The most common genera of cyanobacteria in lakes, rivers, estuaries, and reservoirs are Microcystis, Planktothrix, Aphanizomenon, Anabaenopsis, Raphidiopsis, and Dolichospermum. It is estimated that more than half of the genera that cause these blooms include species capable of producing one or more cyanotoxins. These chemical compounds pose a significant risk to aquatic ecosystems and human health. Microcystins are among the most studied cyanotoxins and mainly affect the liver; they interfere with normal cellular processes, cause liver and kidney damage, and contribute to the development of tumors. Other toxins, such as anatoxins and saxitoxins, affect the nervous system by altering the transmission of signals between neurons and muscles, which can cause loss of coordination, paralysis, and respiratory failure. In addition, the production of BMAA, a non-protein amino acid linked to neurodegenerative diseases, as well as lipopolysaccharides (LPS), which are responsible for skin irritation, fever, and gastrointestinal conditions, has been documented (Huisman et al., 2018).

Algae Microcystis.
 NOAA Great Lakes Environmental Research Laboratory, 2013

Aphanizomenon.
 Natural Waterscapes

MONITORING CYANOBACTERIA
In several regions of the world, cyanobacteria populations are continuously monitored to prevent adverse effects associated with the toxins they produce. However, one of the main difficulties in monitoring this group is that, as they are microscopic organisms, their identification requires specialized equipment and a high level of experience to differentiate species. In addition, taxonomic identification of cyanobacteria is further complicated due to their morphological plasticity and to the high diversity of the group, so traditional microscopy-based methods often have limitations in distinguishing species accurately. Thus, genomic tools provide more accurate classification and monitoring (Bohmann et al., 2014).
 

Dolichospermum.
 Masa Zupancic, 2019

Planktothrix agardhii.
 FWC Research, 2011

INCORPORATING EDNA ANALYSIS INTO CYANOTOXIN SURVEILLANCE CAN IMPROVE EARLY WARNING CAPABILITIES BY IDENTIFYING THE PRESENCE OF TOXIN-PRODUCING CYANOBACTERIA BEFORE VISIBLE ALGAL BLOOMS DEVELOP OR TOXIN CONCENTRATIONS REACH DANGEROUS LEVELS

Genomic tools, particularly environmental DNA (eDNA) open new opportunities to monitor and diagnose biological threats in urban lakes (Amarasiri et al., 2021, Pawlowski et al., 2021). eDNA refers to genetic material released into the environment by organisms through cells, feces, secretions, or fragments of tissues and organs. In aquatic systems, this DNA is suspended or sedimented in the water, which allows the presence of organisms to be identified without the need to capture them directly.

The eDNA analysis process involves four main stages (figure 1):

Figure 2. General diagram of the environmental DNA framework application process.
 Modificado de Cruz-Cano et al., 2024

1. Sampling with protocols that prevent cross-contamination and ensure the integrity of the genetic material.
2. DNA extraction as it is generally done.
3. Amplification and sequencing using specialized techniques and massive sequencing platforms.
4. Bioinformatic analysis with taxonomic and functional identification.

These types of tools have clear advantages over traditional monitoring methods such as microscopy or culture, as they allow the detection of rare or difficult-to-observe organisms, offer greater sensitivity, reduce long-term sampling costs, and enable the early detection of toxic blooms before changes are visible.

Incorporating eDNA analysis into cyanotoxin surveillance can improve early warning capabilities by identifying the presence of toxin-producing cyanobacteria before visible algal blooms develop or toxin concentrations reach dangerous levels. This screening is crucial for timely public health interventions, adjustments in water treatment, and ecosystem management measures. In addition, eDNA methods can be applied in various aquatic environments, from freshwater lakes and reservoirs to estuaries and coastal areas, allowing for extensive spatial and temporal monitoring coverage (Garner et al., 2021).

THE ONE HEALTH COMPREHENSIVE APPROACH
Monitoring cyanobacteria is essential within the framework of the One Health approach, promoted by the World Health Organization, which recognizes the interdependence between human, animal, and environmental health, and allows understanding, identifying, and managing water quality in urban environments (figure 2). For this reason, the implementation of surveillance systems that integrate environmental, ecological, and health information becomes a priority (Manganelli, Testai & Codd, 2025).
 

Figure 3. Integration of cyanobacteria monitoring in urban lakes with the One Health approach.
 Elaboración propia

Building an effective surveillance mechanism will help detect harmful blooms early, prevent exposure to toxins, and manage ecosystems sustainably. The integration of environmental data, public health monitoring, and veterinary knowledge ensures a comprehensive risk assessment and mitigation strategies to protect all sectors affected by cyanobacteria proliferation.

The integration of eDNA-based surveillance into the One Health approach has the advantage of encouraging multisectoral collaboration to address complex health challenges. In addition, generating accurate data on the composition of the cyanobacterial community and the presence of toxin genes provides public health officials, veterinarians, scientists, and environmental managers with actionable information to coordinate responses to address these complex risks in social-ecological systems.

Among the applications of eDNA-generated information in various parts of the world is guiding water treatment plants to adjust filtration and disinfection processes, providing recommendations to limit human recreational exposure, and support wildlife conservation by identifying habitats at risk of toxic blooms, or the fact that agricultural sectors benefit by avoiding irrigation with contaminated water, protecting the health of crops and livestock. The incorporation of eDNA into cyanotoxin monitoring programs also provides relevant information to long-term ecological research as well as climate change studies by identifying changes in cyanobacteria populations and toxin dynamics over time. This information is vital for predicting the occurrence of blooms, understanding environmental factors, and evaluating the effectiveness of mitigation strategies.

THE LASTING SUCCESS OF THE IMPLEMENTATION OF EDNA-BASED MONITORING DEPENDS ON ENCOURAGING ACTIVE PARTICIPATION AT THE COMMUNITY AND EDUCATIONAL LEVELS

To harness the potential of eDNA in urban lake management, it is necessary to prioritize interdisciplinary approaches such as One Health that promote this technic as a key element of environmental and conservation monitoring. One of the pillars on which its success rests is the integration of state-of-the-art technological advances that increase the sensitivity, accuracy, and speed of CianoFANS’ detection. However, the technological approach alone cannot sustain this progress; it is essential to establish sound planning and ensure consistent financing schemes that support long-term monitoring programs.

 Elaboración propia

These programs form the basis for the continuous generation of high-quality data, essential for identifying temporal trends, detecting early signs of environmental stress, or the presence of invasive species, and designing adaptive management strategies in line with the changing dynamics of urban aquatic ecosystems.

Likewise, the lasting success of the implementation of eDNA-based monitoring depends on encouraging active participation at the community and educational levels. By involving the local community and academia, broader environmental awareness is promoted, deepens public understanding of ecological risks, and fosters a sense of collective responsibility and proactive management.

CianoFANs at urban lake.
 César Alejandro Zamora-Barrios

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