Invasive Fish Program

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Students Engaging the Environment: A Student and Scientist Collaboration to Assess Aquatic Invasive Species (supported by the USDA National Institute of Food and Agriculture HATCH project 2014-15-242).

In response to teacher feedback, we have modified the Invasive Fish monitoring kit format to enhance classroom participation and speed up the collection process. Documentation on the website has also been modified to reflect the changes, so please read accompanying materials carefully.

Teachers may request materials for sampling up to 3 DIFFERENT SITES at one time. We will now provide 3 separate filtration set-ups per site (including a separate pump, flask, and funnel for each location) to allow the three locations within a site to be processed by different students at the same time. Since there are 3 sets of equipment, we will include materials for 3 controls and 3 samples (one control and one sample for each location). There will now be 6 filters per site, 3 of which will be controls which pass through the filter relatively easily, so filtration should proceed more quickly.

Please note that it is possible to collect water and process it within 18 – 24 hours in the classroom, if the water is kept on ice or in the refrigerator (NOT the freezer) until processing, and if care is taken to insure no cross-contamination in the classroom. Each site should be processed on a separate table or desk to minimize cross-contamination.

Please do not request multiple kits for use at the same site. Our resources are limited and we need to cover as many different sites across the state as possible. If you want to engage multiple classes in the activity but have access to only 1 waterway, we can supply extra filters and collection tubes so that multiple classes can resample the same site using one set of equipment. It is important to return the FIRST set of filters to Cornell for processing. The other sets can be used for teaching purposes and to allow multiple classes to take part in the exercise, but will not be analyzed. The data obtained from the first collection will be representative of the site tested, and can be shared with all of the participating students. Contact us directly for more details.

You can check out the maps of schools and teachers who have contributed to our project so far. Clicking on the brown teardrop shape on the map will bring up information about the school and teacher involved in that site. You can also display all of the schools involved by clicking on the “all items” icon under schools. Clicking on the round symbols (color coded for positive or negative results) will bring up individual schools, date of collection, and GPS coordinates.


Introduction

What are invasive species?

Why are invasive fish species a problem?

What fish species does this program monitor?

How is the monitoring carried out?

How is the eDNA collected?

How is qPCR used to monitor for the presence of eDNA from invasive species?

What happens to the data collected?


Introduction

Aquatic Invasive Species (AIS) pose a serious threat to the ecosystems around the world. The distribution of species can change rapidly, and early detection of an invasive species is a critical first step in monitoring spread and managing responses. We use a student-oriented citizen scientist approach to monitor for the presence of invasive fish species throughout New York.

  • Teachers and students play a critical role in monitoring the spread of invasive fish species using materials and protocols supplied by this program. Students collect environmental DNA (eDNA) from water samples from nearby lakes, streams, or ponds, using GPS coordinates to identify each site surveyed.
  •  eDNA samples are sent to Cornell University for analysis using a process known as quantitative PCR (qPCR). Although aquatic invasive species are often difficult to detect, current qPCR technology shows great promise for detecting the presence of even very low numbers of a wide range of species by monitoring for the presence of specific kinds of eDNA.
  •  The information generated by the qPCR analysis is incorporated into an invasive fish species database identifying locations that yield a positive test for any of the species being monitored. The results from the water samples submitted are also returned to the teachers and students for classroom analysis and discussion.

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What are invasive species?

For centuries human activities have helped spread plants and animals around the world, intentionally or unintentionally expanding the range of many organisms beyond their original locations. Species (a group of similar animals, plants, or other living things that share common characteristics and can interbreed and produce young) living in an area where they are naturally and historically found are often called “native” species. Native species have adapted to their local habitats through a continuing interaction between their inherited characteristics and their environment. For thousands of years, natural barriers determined where organisms lived and helped defined their habitat, creating dynamic, natural ecosystems. Within their natural ecosystems, native organisms develop unique balanced relationships with both their physical environments and with the other organisms around them. As human activities have expanded, things have changed.

The ability to move people and products around the globe has been the basis of some of mankind’s greatest achievements, but increased mobility has also greatly increased the transfer of all types of organisms to new environments where they were not previously found. Species introduced into an area where they did not previously live are called “non-native” species, sometimes also known as exotic, nuisance, or non-indigenous species. Often, species introduced into a new wild environment will be unable to establish a viable population and will disappear with no ill effects. However, sometimes newly introduced species will thrive, outcompeting native species and destroying fragile ecosystems. Non-native species that damage the environment or disrupt existing ecosystems, or that result in economic loss or endanger human health, are generally referred to as “invasive” species. Many types of organisms, from plants to animals to microbes can be invasive. Invasive species can be introduced from other countries or from other parts of the same country.
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Why are invasive fish species a problem?

Invasive fish species are a growing problem nationwide, especially in coastal regions and in the Great Lakes and surrounding areas. Invasive fish species can cause serious environmental problems and cause significant economic losses, often rapidly disrupting the fragile balance of natural ecosystems, and threatening the diversity and abundance of native aquatic species. The resulting loss of native fish can lead to important economic consequences, affecting a wide range of commercial, agricultural, aquacultural, and recreational activities. Globally, the introduction and spread of non-native species around the world has been described as a major threat to a stable natural environment and to global species biodiversity.

The introduction of invasive fish species is of particular concern because of the ease and frequency of waterway contamination by non-native fish. Aquatic species are often introduced into new areas as a result of the dumping of large amounts of ballast water (the water that is pumped into huge tanks to stabilize unloaded ships, and discharged at the next port of call, along with any surviving organisms) by large ships. Around the world, millions of tons of ballast water are exchanged daily, transporting within it aquatic species from microscopic plankton to fish. On a smaller scale, commercial activities such as aquaculture and the aquarium trade in exotic fish species can sometimes lead to the accidental or purposeful release of fish species into areas where they have never been found before. Even well-intentioned plans to introduce non-native species to control biological problems have backfired and resulted in serious damage by invasive species. For example, the introduction of grass carp to control the spread of unwanted aquatic plants has lead to the destruction of native plant species in inland lakes, resulting in tremendous damage to lake ecology and ecosystems at all levels. Recreational boaters and fishermen can also contribute to the problem by transporting fish (even baitfish) between rivers and lakes, resulting in cross-contamination of previously unaffected waters. Owners of household aquaria can potentially contaminate a waterway simply by dumping the contents of their home aquarium into a lake or stream. While nuisance species are most commonly first introduced into navigable waters, recreational users can easily spread them to pristine rivers, streams, lakes, ponds, and reservoirs.
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What fish species does this program monitor?

This project monitors for the presence of the following three invasive fish species, all of which pose a potential threat to New York waters.
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Sea Lamprey (Petromyzon marinus)

lamprey mouth

Boca de lamprea, liicensed under CC BY-SA 3.0 via Wikimedia Commons

Sea lamprey are native to the Atlantic Ocean but were introduced into the Great Lakes in the 1800s through a series of manmade locks and shipping canals. By the late 1940s all of the Great Lakes contained large populations of sea lamprey that caused serious damage to lake trout and other important fish species. For part of its life cycle, the sea lamprey feeds on the blood of host fish. Sea lamprey have a large sucking disc for a mouth, filled with sharp teeth and a file like tongue. They use the sucking disc and teeth to attach to prey fish, and rasp through the scales and skin to feed on blood and other body fluids, often resulting in the death of the prey. The lamprey attack is so destructive that only about 1 out of 7 fish will survive an attack. During its life, which can last from an average of 6 to as long as 20 years, a single lamprey can kill large numbers of native lake and rainbow trout, whitefish, chubs, walleye, and catfish. The economic effect of this invasive species has been enormous. For example, before the spread of the sea lamprey invasion, the United States and Canada harvested about 15 million pounds of lake trout from the upper Great Lakes each year. By the 1960s the total lake trout catch had dropped to only about 300,000 pounds. In Lake Michigan alone the catch dropped from 5.5 million pounds in 1946 to 402 pounds in 1953 (data from the Great Lakes Fishery Commission). Today there is an ongoing sea lamprey control program that is helping to reduce sea lamprey populations in many areas, but vigilant monitoring is still a key factor in controlling this highly destructive invasive species.
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Asian Carp (Several species of carp are collectively known in the United States as Asian carp)

Asian carp were originally brought to the United States in the 1970s to help control algae growth on catfish farms and in wastewater treatment ponds. Two species of Asian carp were released from southern aquaculture facilities following flooding in the 1990s, and the invasion has been spreading north along the Mississippi ever since. In some areas of the Mississippi River, Asian carp have become the most abundant fish species, having already out-competed native fish. Asian carp have been identified in the canals connecting the Mississippi River to the Great Lakes. Unfortunately, Asian carp, which can grow up to four feet long and weigh more than 100 pounds, have no natural predators in their new environment. A single carp can eat up to 5 -10% of their body weight in plankton each day. By consuming nearly all of the available plankton, the primary food source for most of the native fish, the Asian carp can rapidly wipe out entire populations of native fish. In an effort to decrease the spread of Asian carp into new rivers and lakes, the U.S. Fish and Wildlife Service has placed several species of Asian carp to the federal list of injurious wildlife, making it illegal to transport live Asian carp, including viable eggs or hybrids of the species, across state lines except by special permit for zoological, education, medical, or scientific purposes.
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Round Goby (Neogobius melanostomus)

Round Goby were introduced into the Great Lakes through the ballast water from large cargo ships and were first identified here in 1990. Since their introduction, round Goby have caused significant ecological and economic problems. They have spread throughout the Mississippi River drainage area and into tributaries of the Great Lakes, including a sighting in one of the New York Finger Lakes (Cayuga Lake). Round Goby, which are bottom dwellers, compete very successfully with native bottom dwelling species like sculpins and darters for food, habitat, and spawning areas, and can cause substantial decreases in local populations of native fish. They also prey on small fish and eat the eggs and fry of larger native fish like lake trout.

The increased presence of round Goby has been shown to potentially impact the food chain supplying recreationally important fish like walleye and smallmouth bass. It has been noted that round Goby eat large amounts of zebra mussels, which in the short term may seem like an unexpected benefit. But, as with most environmental and ecological issues, it is important to look at the broad picture. Despite their large appetites, it is unlikely that round Goby will have a significant impact on zebra mussel populations. Equally important, the zebra mussels eaten by round Goby contain large amounts of various toxins that are found throughout the Great Lakes. Following intake of the zebra mussels, the toxins become concentrated in the Goby, which are in turn eaten by a variety of sport fish, including smallmouth and yellow bass, walleyes, yellow perch, and brown trout. This food chain can lead to high concentrations of dangerous toxins in sport fish that are eaten by humans, increasing health concerns related to consuming sport fish.
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How is the monitoring carried out?

A critical part of environmental monitoring is the widespread, accurate collection of water samples. The distribution of the invasive species can change very rapidly, and the presence and abundance of invasive species is often unknown in a particular area. Monitoring waterways for invasive fish species plays a key role in understanding the scope and extent of invasion, a critical first step in determining appropriate responses. Other than direct prevention, early detection and rapid response is the most cost effective method for dealing with invasive species. For many species, early detection can result in earlier and often less costly control. If new invasions can be detected before they become established, the chances of eliminating the problem are greatly increased, minimizing ecological and economic impacts and potentially resulting in significant savings in long-term control and management costs.

The collection of water samples is at the heart of this project. The engagement of citizen scientists has been important in monitoring both aquatic and terrestrial invasive species. As part of this project, students and teachers help track invasive sea lamprey, Asian carp, and round gobi throughout New York, which will greatly contribute to efforts to control the rapid spread of these destructive, costly pests.

There are a number of ways of monitoring a body of water for invasive fish, including visual sightings, catching or trapping, and, more recently, monitoring of species specific DNA from cells shed into the environment.  We use a very sensitive technology that monitors DNA found in environmental samples (environmental DNA  or eDNA). eDNA is genetic material that is found in environmental samples like water, soil, or air. eDNA can be either nuclear or mitochondrial DNA that is released into the environment as a result of the constant shedding of cells by all organisms into the environment. For example, fish cells can be shed into the water in multiple ways, including in mucous, feces, urine, or blood, or as flaked off skin cells. The cells shed into the environment all contain genetic material (DNA) that is unique to their species. When eDNA is collected, it is made up of DNA from all the different organisms present in the environment, including plants, animals, singled celled organism like protozoa, and bacteria.

Therefore, eDNA can be used to provide information about what organisms are or were recently present in a particular area.

When you isolate eDNA you don’t know what DNA is in the sample until you conduct a genetic analysis. For example, if you collect a bucket of water from a lake and collect DNA from that water, you potentially have eDNA from all of the organisms living in that lake. If that lake has fish in it, that eDNA will contain some fish DNA, along with many other DNAs from unknown sources. eDNA monitoring has been used in both fresh water and marine environments, and provides a highly efficient, sensitive, and cost-effective way to monitor for the presence of invasive species.
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How is the eDNA collected?

We provide a kit containing all of the materials needed to collect and filter multiple water samples from each site to be tested. The water sample is pumped through porous filters that will retain any cells shed by fish in the collection area. Although there is free eDNA in the environment, for this test we will actually be looking at DNA contained in cells released into the environment. That’s because the filters we are using will generally not trap free DNA molecules, but will retain intact cells. Since the half life of DNA (the amount of time required for the amount of measurable DNA to fall to half its value as measured at the beginning of the time period) from fish cells shed into the fresh water is at least 4-6 hours following shedding, the presence of a fish can potentially be detected even if it swam by several hours earlier. The filter paper containing cells from the water sample is placed into a vial containing a solution that protects the DNA from further breakdown and is sent back to Cornell University for DNA extraction and qPCR analysis. A detailed description of the collection technique is available for download.
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How is qPCR used to monitor for the presence of eDNA from invasive species?

To determine if the water collected contained DNA from any of the invasive species being monitored, total eDNA is extracted from the collection filter. A variation of the polymerase chain reaction (PCR) technique is used to determine if the eDNA sample contains DNA from any of the invasive fish species being tested for. The polymerase chain reaction (PCR) is a way to make thousands or even millions of copies of a small, highly specific region of DNA, starting with a very tiny amount of DNA. Generally the copies of DNA made are analyzed at the end of the reaction, usually by running them on an agarose gel. Using standard PCR methods, only the final product made during the PCR reaction can be analyzed. Quantiative PCR (qPCR) is a variation of the standard PCR technique that allows an analysis of the DNA copies being made in real time, as the reaction is actually going on. During the qPCR process, a fluorescent dye is incorporated into the newly made product. The DNA containing the dye can be measured on a special instrument that provides real time information about what DNA containing the dye is present in the reaction and how much.

One question commonly asked is “what does a qPCR test of eDNA actually tell us”. qPCR results are basically a single snapshot in time of the site sampled. The signal produced by the eDNA during the qPCR test relates to the presence or absence of a specific species, and the approximate density of that species at a the location tested at the time the sample was taken. The detection of eDNA from an invasive species does not provide information about the age or sex of individuals present at the time of sampling, and does not indicate whether the DNA came from a live organism or a recently dead one (for example a bait fish). Detection sensitivity is limited by how far away from the original source of the DNA the water was collected. The dispersal of eDNA in the environment is affected by factors like rapid water flow or wind. In addition, the rate at which eDNA breaks down is affected by environmental conditions like temperature and the local bacterial community. If the qPCR test signal does not give a positive signal, that may mean that the species being tested for is not present, or is there in such low abundance that the signal cannot be detected. A weak eDNA signal could represent a few cells from a non-resident fish that was transiently at the site tested and left behind some shed cells, or a fish that has recently died, or a fish that has just entered the site and has not yet deposited many cells in the water. A strong signal suggests the presence of a larger population of fish. Secondary testing of the same site later in time can help establish patterns of fish populations. Overall, qPCR is a very sensitive test that can be used to identify specific fish species even when they are present at very low numbers. For example, qPCR analysis of grass carp eDNA in a single water sample has picked up the presence of one grass carp in a 50 acre pond 10 feet deep under good conditions, although a lower sensitivity of one grass carp in a 2 acre pond has been seen when environmental conditions favor the rapid breakdown of shed cells.

qPCR machine and chart

The qPCR instrument and representative data collected on Asian carp eDNA.

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What happens to the data collected?

The information generated by the qPCR analysis is incorporated into an invasive fish species database identifying all locations tested, and indicating those sites that produced a positive test for any of the species being monitored. This information can help provide a clearer overview of the extent of invasion throughout New York, and will be very useful in framing potential responses to the problem. A map depicting all monitoring locations and the results obtained is publicly available. In addition, the qPCR results are returned to the teachers and students for classroom analysis and discussion.
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