By Erin Hurley
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You’ve probably been hearing a lot about cyanobacteria. If not, maybe you recognize their former name: blue-green algae. Would you believe these photosynthetic bacteria have existed for 3.5 billion years? They are one of the most common organisms on Earth and an important natural resource for healthy ecosystems.
Cyanobacteria produce oxygen through photosynthesis and have been doing so for eons. They played a major role in creating Earth’s oxygen-rich atmosphere! They also convert nitrogen and phosphorus into forms usable by plants. They can be found in all kinds of terrestrial and aquatic environments including freshwater, brackish water, and saltwater alike. Even when you can’t see cyanobacteria, they’re all around.
It’s when you can see cyanobacteria that you know they’ve gotten out of control in a particular environment. Imagine you are at the lake or the ocean, and the water has a dense, paint-like coating accompanied by a strange smell. This discoloration and odor is caused by an overgrowth of cyanobacteria, referred to as a ‘cyanobacteria bloom’, which can be an environmental hazard. Cyanobacteria blooms appear as a blue-green color when combined with pollen, but they can also be various colors such as reddish-brown and sometimes even white.
“If you can see a microbe, there’s a lot!” said Amanda McQuaid. McQuaid is a State Specialist in Water Quality and Ecotoxicology for Cooperative Extension, Director of the Lakes Lay Monitoring Program, Professor of Limnology, and Joint Faculty in the Department of Biological Sciences at the University of New Hampshire (UNH). She also co-manages the Center for Freshwater Biology at UNH. McQuaid is passionate about researching and educating the public on cyanotoxins.
Cyanobacteria blooms—or harmful algal blooms (HABs)—can lead to ‘hypoxia’, a dangerously low oxygen level in the water, and to subsequent dead zones. This happens when cyanobacteria blooms cover the surface of the water and prevent sunlight from reaching other photosynthetic plants, resulting in species die-offs.
In addition, when cyanobacteria die, other bacteria decompose them and this process further exhausts the oxygen in the water that is needed by aquatic species to live. This worsens these dead zones in a negative feedback loop which has consequences that ripple out from aquatic species and ecosystems to fishing, recreational activities, and tourism. This entire process is referred to as ‘eutrophication.’
In marine ecosystems, eutrophication and HABs exacerbate the effects that climate change is already having on species such as corals and makes these corals more susceptible to bleaching. This can result in the death of entire reef ecosystems and impact other species, including humans, that rely on these ecosystems.
Cyanobacteria blooms can also be harmful for terrestrial species including humans, dogs, eagles, and elephants. There are many kinds of cyanobacteria, and some kinds are able to produce toxins. Ingesting water that is experiencing an overgrowth of toxic cyanobacteria can cause sickness, disease, or even death, which has been referred to as ‘cyanotoxin poisoning.’ Some people are also sensitive even to skin contact.
“There’s a lot of things to be concerned about without fresh water… because fresh water is life,” said McQuaid.
A common cause of cyanobacteria blooms in water bodies is nutrient enrichment due to runoff from nearby lawns or farms that have been sprayed with synthetic nitrogen and phosphorus fertilizers, pesticides, or herbicides. Biogeochemical flows, including phosphorus and nitrogen cycles, are classified by scientists as one of the nine planetary boundaries which are “critical global processes that regulate the stability and resilience of the Earth.”
However, when a planetary boundary is crossed, it can lead to “large-scale abrupt or irreversible environmental changes.” With industrial agriculture using synthetic nitrogen and phosphorus fertilizers and pesticides on a massive scale, the biogeochemical boundary has already been surpassed, which is contributing to our planet’s current state of instability.
Chocorua Lake Conservancy (CLC) has taken steps to reduce the risk of nutrient pollution, and therefore harmful cyanobacteria blooms, in the freshwater ecosystem the organization works to protect. In fact, the lake holds the second longest uninterrupted record of water quality monitoring in New Hampshire. But it took commitment to get there.
Back in 1981, when CLC joined the NH Lakes Lay Monitoring program led by the Center for Freshwater Biology at UNH, it was one of the first lakes to do so. For the last 44 years, at least ten samples have been taken annually from various lake locations and tested for eight water-quality indicators. In 1995, because CLC already had nearly a decade and a half of data, water quality monitoring volunteers were able to spot signs of decreasing water quality at Chocorua Lake. Specifically, there were higher amounts of algae due to increasing amounts of phosphorus.
So in 2001, CLC conducted the Berms and Swales Project in which they established a system for catching highway runoff before it reaches the lake. They won “Conservation Award of the Year” from the Carroll County Conservation District for this project and, a year after the system was implemented, water quality monitoring statistics determined that the amount of phosphorus reaching Chocorua Lake had decreased by a colossal 82 percent.
In 2024 and 2025, CLC led a shoreline restoration project to mitigate and prevent erosion, restore vegetation, improve aquatic and terrestrial habitat, and protect water quality. Earlier this year, in response to the increasing frequency of large rain events, a “rock garden” drainage system was also constructed to act as a barrier between road runoff and the lake.
Another interesting development is Environmental DNA, or eDNA, which has been applied in conservation management and biomonitoring efforts.
“Environmental DNA is just DNA you harvest from the environment. Many of us who enjoy the outdoors clearly follow the ‘leave no trace’ mentality. We take only pictures, we leave only footprints, and that’s that. Despite your best efforts, you are actually, though, still leaving bits and pieces of you behind. Probably in skin cells, maybe some hair, and for those of you that are extremely unfortunate on the trails, maybe a little bit of blood,” said Jill Emerson, Staff Scientist at Green Mountain Conservation Group in Effingham, NH.
eDNA, when collected in a water sample and tested, can indicate whether a cyanobacteria bloom has the potential to be toxic.
Chocorua Lake is lucky that thanks to conservation-minded landowners all around the lake, most of the lakeshore is wooded and houses are set back at some distance. Lakefront homeowners at lakes with houses and lawns closer to the shore can help protect their lakes by establishing rock drainage systems or planting native vegetation along their shoreline to absorb runoff, prevent shoreline erosion, and cleanse the water. In addition, drainpipes or rain gardens can also help to prevent runoff from roofs and driveways from reaching the lake. Well-constructed septic systems and avoiding fertilizer, pesticide, and herbicide use near waterbodies are also key to bloom prevention.
NH Lakes’ LakeSmart Program is a “free, non-regulatory, and voluntary education and recognition program encouraging community members to adopt habits that protect lake water quality, wildlife habitat, and property values.”
The New Hampshire Department of Environmental Services (NHDES) encourages people to report a bloom if they see one or suspect one, and has created a Bloom Report Form to do so. They also listed some other recommendations if you do suspect a bloom, which include not swimming in or drinking the water, and keeping any pets or livestock from doing so as well.
The NHDES’s Healthy Swimming Mapper posts current fecal bacteria advisories, cyanobacteria warnings, and cyanobacteria watches every day.
Each of these resources are there to keep us informed, safe, and to help us do our part in protecting water bodies that are absolutely teeming with life within, on, and around them.
Erin Hurley is a recent graduate of St. Thomas University in New Brunswick, Canada, where she studied Journalism and Environmental Studies. She is passionate about environmental conservation and is a lake lover at heart, having grown up on Lake Winnipesaukee in Moultonborough.
Lake Water Quality: Cyanobacteria & eDNA Research
Time stamps:
Cyanobacteria: 00:00:00
eDNA Research: 15:06:00
Q&A and conversation re: both: 38:01:00
With a changing climate and changing weather patterns come particular risks to lake water. The good news is that we have the capacity both to monitor lakes for cyanobacteria blooms and invasive aquatic plants, and to take (or avoid!) specific actions to support water quality in our lakes and rivers. Come learn what others in your community are doing to protect water in this region, and what you can do!
Please join Chocorua Lake Conservancy (CLC), Cook Memorial Library (CML), and Green Mountain Conservation Group (GMCG) for a Climate & Community program: Lake Water Quality: Cyanobacteria & eDNA Research with Amanda McQuaid, Associate UNH Cooperative Extension State Specialist and Professor of Water Quality and Ecotoxicology, and the Director of UNHCE’s Lakes Lay Monitoring Program, and Jill Emerson, Staff Scientist for GMCG.
The program has two parts: First, an overview of what we look for when monitoring lake water quality, and what factors contribute to water that is safe for humans and other beings or pose risks to lake water; an explanation of cyanobacteria, a naturally occurring organism that can pose health risks when the conditions support it to grow in excess, or “bloom”; and what actions we can take to prevent this excessive growth. Second, an introduction to the use of eDNA testing in water monitoring. Environmental DNA (eDNA) refers to genetic material shed by organisms into their surroundings, such as water, soil, or air. This DNA comes from sources like skin cells, hair, feces, or mucous and can be collected and analyzed to detect the presence of species in a specific environment. eDNA is a powerful, non-invasive tool used in ecology, conservation, and biodiversity monitoring to study species distribution, track invasive species, or identify rare or elusive organisms without direct observation or capture.
Jillian Emerson earned her B.S. in Microbiology/Molecular Biology with a minor in Chemistry from Quinnipiac University in 2008. After her degree completion she spent 10 years working in academic research in the Department of Molecular and Systems Biology (formerly Genetics) at the Geisel School of Medicine at Dartmouth College. Most of her work was focused in the area of circadian rhythms using a model fungal organism, Neurospora crassa. In 2018, she earned her ASCP certification in molecular biology (MB, ASCP(CM)). She is currently the Staff Scientist for Green Mountain Conservation Group in Effingham, NH. Most importantly, she loves dogs.
Amanda McQuaid (PhD ‘19UNH, she/her) is a State Specialist in Water Quality and Ecotoxicology for Cooperative Extension, Director of the Lakes Lay Monitoring Program, (Extension Associate) Professor of Limnology, and Joint Faculty in the Department of Biological Sciences at the University of New Hampshire. Amanda also co-manages the Center for Freshwater Biology; a participatory science and research-based collaboration in support of freshwater research, toxic cyanobacteria and water quality of lakes. Amanda has focused her research on the bioaccumulation of toxins in the aquatic environment, specifically how cyanotoxins transfer through water, air and food webs.