Biomonitoring in Southeastern New England

Managing freshwater streams by studying the biological community

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The ArcGIS StoryMap has multiple sections that can be quickly accessed by using the navigation bar on the top of the page! Any words highlighted orange are defined in the Glossary. Highlighted words and phrases are links to external web pages.


Introduction

The Southeast New England region includes the coastal areas in Massachusetts and Rhode Island that are the watersheds of southern Cape Cod, Narragansett Bay, Buzzards Bay, Martha’s Vineyard, and Nantucket.

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EPA Southeastern New England Program Area

Freshwater streams flow through this region to the coast, providing important habitat for aquatic wildlife, and supporting a variety of uses to humans such as recreation (i.e., swimming, boating, fishing), education, spiritual ceremonies, and drinking water. Increasing development and human disturbance puts more pressure on freshwater stream ecosystems through the addition of pesticides, fertilizers, road salts, and other pollutants. These contaminants often enter streams during rainfall events where contaminants are carried from human-impacted land (i.e., city streets, suburban development, golf courses, or agricultural fields). Elevated levels of contaminants can cause unsightly algal blooms, make streams inhospitable for certain animals, or result in toxic water and fish. Development, by way of changing stream shapes and flow levels, can also result in the disappearance of certain habitats (e.g., loose cobble and riffles) and the animals which rely on those habitats.

Low-gradient streams and urban stressors. Top left: low-gradient stream; top right: bridge and development on river; bottom: wastewater treatment facility. Photo credits: Tetra Tech.

Organization logos of all collaborators.

To make informed decisions in the management, planning, and regulation of freshwater streams in the Southeast New England region, it is imperative to recognize the biological degradation of these ecosystems so that human disturbances can be mitigated. That is why,  NEIWPCC  and the Southeastern New England Program ( SNEP ) collaborated with  Tetra Tech , the Massachusetts Department of Environmental Protection ( MassDEP ), and the Rhode Island Department of Environmental Management ( RIDEM ) to develop a suite of tools that can be used to assess stream health by examining the aquatic community of those streams. This ArcGIS StoryMap describes the purpose of managing freshwater streams, how studying the biological community (i.e., biomonitoring) achieves this goal, and the tools developed to assess results.

Sampling in southeastern New England low-gradient streams. Photo credits: Tetra Tech.


Purpose

Under the United States Clean Water Act ( CWA ), state environmental agencies are tasked with monitoring and assessing streams and rivers. Currently, MassDEP and RIDEM collect water chemistry data and sample biological communities to assess the natural integrity of streams. Physical and chemical measures of ecosystem integrity include dissolved oxygen, water temperature, and the concentration of various toxicants (i.e., industrial chemicals) and salts. The biological component of ecosystem integrity, termed biological integrity, is defined below.

Biological Integrity --- The ability of an aquatic ecosystem to support and maintain a balanced, adaptive community of organisms having a species composition, diversity, and functional organization comparable to that of natural habitats within a region.

The community of organisms in question can depend on the purpose of the project but is often either fish, benthic macroinvertebrates, or algae. Macroinvertebrates (aquatic insects and other small stream-dwelling organisms) are often used for this purpose because they are found in all streams (except under extremely degraded conditions) and are relatively easy to collect. Measurements of physical, chemical, and biological integrity are compared against water quality standards that have been developed to ensure support of designated water body uses (e.g., clean drinking water, contact recreation, aquatic life).

Low-gradient, slow-moving stream in the SNEP region. Photo credits: Tetra Tech.

Along the coast of southeastern New England, non-tidal, low-gradient, slow-moving streams that either lack or have infrequent riffle habitat are fairly prevalent. Yet, until recently, stream assessment efforts in New England have not focused on these types of systems.

This project, referred to as the SNEP Low-gradient IBI development project, resulted in an assessment tool, called an Index of Biotic Integrity (IBI), developed specifically for low-gradient streams. Below, we describe the general concept of assessing the biological integrity of streams by monitoring aquatic organisms (using macroinvertebrates as an example) and then discuss the development of a macroinvertebrate IBI for low-gradient streams of the Southeast New England region.


What is biomonitoring?

Aquatic ecosystems are composed of physical, chemical, and biological components. Even though physical and chemical measures of water quality are useful to help identify sources of water contamination, they only indirectly measure the condition of aquatic ecosystems because they do not directly measure the aquatic life uses that the CWA is intended to support. Also, they only serve as a “snapshot” of ecosystem integrity because chemical concentrations can vary highly day-to-day due to the amount of rainfall, timing of discharges, and season.

Biological monitoring can often detect water quality problems that water chemistry analyses miss or underestimate.

Aquatic organisms (e.g., macroinvertebrates, fish, and algae) must cope with chemical, physical, and biological influences in their habitat over the course of their entire aquatic lifecycle, which in some cases can be multiple years. Because of this, biological communities integrate human-caused stressors over time. Biological monitoring can often detect water quality problems that water chemistry analyses miss or underestimate.

Field staff sample the biology and chemistry of streams to assess stream integrity and identify water quality problems. Photo credits: Tetra Tech.

State agencies and watershed monitoring groups use the structure of biological communities to evaluate stream integrity. The number and types of organisms present in a stream reflect the quality of their surroundings, so comparing biological samples to samples from minimally-disturbed, natural streams makes it possible to evaluate the biological integrity of the stream on a relative scale. The components of biomonitoring are as follows:

The organisms: macroinvertebrates

Many different biological communities can be sampled to evaluate biological integrity including algae, fish, and benthic macroinvertebrates. Macroinvertebrates make good biological indicators because:

  1. During their aquatic life stages, they are much less mobile than fish and so are less able to avoid the effects of pollutants
  2. They are prevalent in streams (i.e., may be in streams that lack fish)
  3. Different species have a wide range of pollution tolerance
  4. They can be consistently collected and analyzed

Photo Credits: Tom Danielson, Maine DEP

For example, compare the two macroinvertebrate communities. The left image is a sample from a polluted stream, whereas, the right image is from a nearly natural stream. Can you tell the difference?

The natural stream community is more diverse while the polluted community is dominated by only a few species. This is the essence of biomonitoring! How samples are evaluated by scientists is described in the following sections.

Photo Credits: Tom Danielson, Maine DEP

Find out more about using algae and fish in biomonitoring programs here:

Photo credits: Tetra Tech

Stream Gradient

State agencies have biomonitoring programs for a variety of waterbodies including streams, rivers, lakes, and wetlands. As mentioned above, the focus of this project was to develop assessment tools for low-gradient streams in Southeastern New England. Streams can be described in two categories based on their slope: high-gradient and low-gradient.

High-gradient streams are characterized as having steep slopes, rapid water movement, and abundant riffle habitats, whereas, low-gradient streams can be described by low slopes, slow water movement, and few or no riffle habitats.

These types of streams differ in the composition of biological communities, and thus, the response of stream organisms to stress will also vary.

Photo credits: Tetra Tech.

Site Selection

Biomonitoring relies on the comparison of stream conditions in test sites to conditions in natural, pollutant-free streams – termed “Reference Streams”. We expect that streams that are relatively undisturbed by human development and free of pollution would contain biological communities that are natural to the stream type and region. So, by comparing the biological community of a given stream to a reference stream, we can evaluate biological integrity along a gradient from “natural” to “severely degraded”.

State agencies often have a rotating schedule for sampling watersheds in their region over several years. Stream sites are either purposely targeted for sampling (due to their known intensities of human-caused stresses) or are randomly selected (for unbiased assessments – ideal for statistical analyses). To minimize variation due to seasonal differences, biological sampling occurs during a predefined time of year. The time is often summer when water levels are typically at the lowest of the year and levels of stress to aquatic organisms are presumed to be highest. In the SNEP low-gradient project the sampling period was from July 1-September 30.

Photo credits: Tetra Tech.

Sampling Methods

At each stream site, field staff collect macroinvertebrate and chemistry samples and assess the surrounding habitats.

Macroinvertebrate samples are collected in nets as a composite of jabs, sweeps, or kicks of the net through multiple habitats in the stream reach. Habitat types vary and may included submerged wood, submerged vegetation, undercut banks, overhanging vegetation, and hard substrate. The samples are brought back to a lab so that the macroinvertebrates can be identified and counted.

Water quality measurements taken at each site include water temperature, pH, conductivity, dissolved oxygen, and transparency. Simultaneously, the in-stream and surrounding habitat are assessed and include an evaluation of land use, the shape of the stream and whether it has been altered, the amount of woody debris (great habitat for organisms), and more.

Photo credits: Tetra Tech

Biomonitoring summary

Biomonitoring is best used for detecting impacts to aquatic ecosystems and for assessing their relative severity compared to expectations for comparable natural systems. Once an impact is detected, additional information on water chemistry or toxicity can be used to identify the source and implement a restoration strategy. Following restoration, biomonitoring can evaluate the effectiveness of such work.

Some advantages of using biomonitoring to assess results include:

  • Biological communities reflect overall ecosystem integrity
  • Biological communities provide an integrative response to stressors over time
  • Where criteria for specific stressors do not exist, biological communities may be the only practical way to evaluate stream resource conditions

What is an IBI?

A wide variety of indicators are used to monitor and assess streams, but among the most useful are those that integrate and reflect the impacts to aquatic systems. Macroinvertebrates living in streams experience an entire spectrum of environmental conditions including stressors caused by human activities. They provide a direct, comprehensive perspective on water quality, and lend themselves well to tools such as the Index of Biotic Integrity (IBI).

You can think of an Index of Biotic Integrity (IBI) as a type of medical questionnaire for streams.

An IBI is a measurement tool that is composed of multiple metrics that each describe a unique aspect of the biological community to assess overall stream integrity. You can compare an IBI to a type of questionnaire. For example, imagine a medical questionnaire in which questions target multiple aspects of your lifestyle to assess your overall health. Now that’s a bit of an oversimplification of the level of effort to develop such a tool, yet, the concept is quite similar. Metrics are combined to provide an overall IBI score which is an indication of stream quality. 

The process of summarizing macroinvertebrate samples using metrics and IBI scores to assess streams under the Clean Water Act (CWA). Photo credits: Ben Block, Tetra Tech and Tom Danielson, Maine DEP

Indices of Biological Integrity can help scientists:

  • Measure the health of aquatic organisms and the suitability of their environment
  • Identify types of stressors that are damaging streams (e.g., sediment, salts, toxicants)
  • Develop management approaches to protect or restore streams
  • Evaluate the effectiveness of protection and restoration efforts

In the SNEP low-gradient project, an IBI was developed for use in southeastern New England low-gradient streams. Various components of the project are described below.

Sample Collection

Macroinvertebrate samples were collected at stream sites by MassDEP and Tetra Tech field crews throughout Massachusetts and Rhode Island. The Southeastern New England Program (SNEP) has a focus on watersheds that drain to the south of Rhode Island and eastern Massachusetts, as shown by the highlighted boundary. MassDEP also provided samples from low-gradient streams throughout Massachusetts to bolster the amount of data to use in the project.

Click on a site to explore its information and photos! Perhaps you can find a stream near your home!

Map developed by: Ben Block, Tetra Tech

Taxa identification and association with traits

Macroinvertebrate samples were sent to macroinvertebrate taxonomists at  Cole Ecological, Inc. , a certified taxonomist, who identified and counted every organism in each sample, often to the species level.

Each taxon was associated with representative traits that are the basis for building metrics of an Index of Biotic Integrity (IBI). Traits for macroinvertebrates are like traits for humans (e.g., height, eye color, favorite food, etc.). Below are the groups of traits considered for each taxon:

  • Functional feeding group – refers to the way a taxon consumes food
  • Tolerance – relative sensitivity to pollution/disturbance
  • Life cycle (voltinism) – the number of generations a taxon typically has in one year
  • Habit – how a taxon moves or maintains position in its environment
  • Thermal preference – how cool or warm a taxon prefers its environment

Photo credits: Tom Danielson, Maine DEP

Disturbance Designation

A vital part of IBI development is to identify and differentiate between poor-quality sites (i.e., stressed sites – poor stream integrity) from high-quality sites (i.e., reference sites – excellent stream integrity).

To identify the best and worst streams, GIS-based variables (e.g., agricultural land cover, urban land cover, road density, and proximity to specific high-disturbance sites such as mines or dams) were used to summarize what is happening upstream of a stream and how that may affect integrity. For example, a stream that flows through a heavily agricultural landscape is likely to have lower integrity than a stream that flows through a forested landscape. However, agriculture is just one type of stressor - many more are often measured to completely assess human-caused stressors.

Photo credits: Tetra Tech

Index Development

The first step in index development was to calculate metrics from the taxa traits mentioned earlier. The number of EPT taxa (taxa of the insect orders Ephemeroptera [Mayflies], Plecoptera [Stoneflies], and Trichoptera [Caddisflies]) is a classic metric that describes how many of these pollution-sensitive taxa are represented in a sample. Presumably, having more pollution-sensitive taxa would indicate that the stream lacks pollution and has natural characteristics. The assumption as to how many pollution-sensitive taxa (e.g., EPT taxa) should be within a sample is determined by examining the results of those streams previously designated as ‘reference sites’ as these are likely the most natural, pollutant-free streams.

Tetra Tech used an R program to calculate over 150 metrics! Photo credits: Ben Block, Tetra Tech.

Evaluation and selection of metrics were the next steps in index development and involved the testing of many more metrics than end up going into the final index. Over 150 metrics were calculated and evaluated! Performance was determined by how well a metric could distinguish between reference and stressed sites – the larger the difference, the better. Ideally, an index comprises only those metrics that discriminate well between reference and stressed sites.

The third step was to compile multiple metrics (usually 5-10) into an index. Although 150 metrics were initially calculated , the number was winnowed down to 20 discriminating metrics that represented multiple aspects of the macroinvertebrate community, would respond to a broad range of stressors, and were not redundant with each other. A computer program was used to create indices comprised of 1-10 metrics which resulted in approximately 103,000 alternative index combinations! MassDEP and RIDEM staff relied heavily on statistics and professional judgment to pick just one index from all those options. The final index was assessed by testing it against various measures of ecosystem disturbance (e.g., habitat scores, dissolved oxygen, etc.) to make sure that it was responsive.

IBI Summary

Ultimately, an Index of Biotic Integrity (IBI) was developed specifically for the low-gradient streams of southeastern New England.

Before moving on to how MassDEP, RIDEM, and other watershed scientists can use this new assessment tool, we thought a video summary of biomonitoring and IBIs would be useful. Below is a video, produced by the Minnesota Pollution Control Agency (MPCA) that exquisitely describes the purpose of biomonitoring to protect waterbodies and how IBIs are used.

Try and listen carefully and notice how their methods compare to those described for southeastern New England!

Biological monitoring with the Minnesota Pollution Control Agency. Video produced by the MPCA.


Implementation and Use

The SNEP low-gradient IBI improves the ability of resource managers in the Southeast New England region to identify degradation in biological condition and water quality in low-gradient streams. The IBI was calibrated using the Reference Condition approach, which bases biological expectations on nearly natural reference sites. If a site receives an IBI score that does not resemble reference scores, it indicates that there might be stressors influencing the biological condition at that site. An online app that calculates IBI scores is available through R Shiny – it’s called  SNEPtools . Shiny apps are interactive web applications that are linked to R software, which is an open-source programming language and software environment for statistical computing. 

In general, IBIs can be used by state agencies and watershed groups to:

  • Identify and protect waterbodies with exceptional biological conditions
  • Maintain good water quality to support multiple uses such as diverse wildlife, fishing, swimming, boating, spiritual ceremonies, and drinking water
  • Determine if streams are achieving environmental goals
  • Identify streams that do not achieve environmental goals and prioritize them for restoration
  • Evaluate and document the success of restoration and conservation initiatives
  • Improve permit and licensing decisions by understanding the biological community
  • Implement Clean Water Act (CWA) programs for environmental protection

Get Involved!

If you would like to get involved with biomonitoring and have an interest in your local waterbodies, check out some of the volunteer programs in the northeastern US:

If you do not reside in the northeastern US, we suggest you reach out to your state environmental agency, local  NOAA Sea Grant program , or local watershed organization. Otherwise, you’re welcome to contact  Ben Block  as he would love to help find a group near you!


Additional Resources

For more information on biomonitoring and the development of indices of biotic integrity, we welcome you to peruse the following websites or contact any of the project partners. Below is a link to a technical StoryMap that describes the IBI development process in more detail. For additional detail and reading, you can download the full report (and data) from GitHub.

Contacts:

 Ben Block  - Aquatic Ecologist, Tetra Tech

 Maryann Dugan  - Environmental Analyst, NEIWPCC

 James Meek  - Environmental Analyst, MassDEP

 Katie DeGoosh  - Environmental Analyst, RI DEM


Glossary

Algae – A diverse group of aquatic organisms that are photosynthetic, are often prey for invertebrates, and are valuable indicators of water quality.

Algal blooms – blooms of algae, often associated with nutrient pollution, float on top of polluted waterbodies. Blooms often are made up of Cyanobacteria which can produce toxins that damage the human liver and nervous systems.

Aquatic wildlife – Any animals that live at least part of their lifecycle in fresh water.

Benthic macroinvertebrates - Benthic macroinvertebrates are insects and other animals without a backbone that live on the bottom of virtually all waterbodies. Although some of these animals spend their entire lives in the water, many of them grow up to be terrestrial insects that are familiar to most people. Common macroinvertebrates include insects (e.g., mayfly and dragonfly larvae), worms, leeches, clams, and snails.

Biological integrity - the ability of an aquatic ecosystem to support and maintain a balanced, adaptive community of organisms having a species composition, diversity, and functional organization comparable to that of natural habitats within a region.

Biomonitoring – the use of organisms to measure environmental impacts

Ecosystem – a biological community of organisms that interact with themselves and their environment.

Environmental stressors – any physical, chemical, or biological entity that can cause a harmful response.

GIS - geographic information system, a system for storing and manipulating geographical information on a computer.

Habitat – the environment where an organism normally lives and grows

Index of Biotic Integrity (IBI) – a scientific tool typically used to identify and classify water pollution problems by examining the composition of the biological community

Integrity – the ability of an aquatic ecosystem to maintain functionality and be comparable to natural habitats within a region.

Riffles - the shallower, faster moving sections of a stream.

Stream reach - A reach is a section of a stream along which similar hydrologic conditions exist, such as discharge, depth, area, and slope.

Taxonomy - The science of classifying organisms by a predetermined system. The most common system is that of Carl Linnaeus, which classifies organisms by kingdom, phylum, order, family, genus, and species, with kingdom being the broadest group and species the most specific.

Taxon - a taxonomic group of any rank, such as a species, family, or class.

Watersheds - A watershed is an area of land that drains all the streams and rainfall to a common outlet such as the outflow of a reservoir, mouth of a bay, or any point along a stream channel. Synonyms sometimes include “drainage basin” or “catchment”.

Credits

Photos were largely taken from Tetra Tech's internal photo library from various projects. Macroinvertebrate photos were provided and kindly shared for public use by Tom Danielson, Maine DEP. Collaborators on the low-gradient index development project and contributors to this StoryMap include staff from Tetra Tech, NEIWPCC, RI DEM, and MassDEP.

The Low-Gradient Coastal Index of Biotic Integrity (IBI) for Wadeable Waters in Southern New England project was supported by the Southeast New England Program (SNEP) Watershed Grants. SNEP Watershed Grants are funded by the U.S. Environmental Protection Agency (EPA) through a collaboration with Restore America's Estuaries (RAE) and awarded to the New England Interstate Water Pollution Control Commission [now NEIWPCC]. For more on SNEP Watershed Grants, see www.snepgrants.org.

Low-gradient, slow-moving stream in the SNEP region. Photo credits: Tetra Tech.

Field staff sample the biology and chemistry of streams to assess stream integrity and identify water quality problems. Photo credits: Tetra Tech.

The process of summarizing macroinvertebrate samples using metrics and IBI scores to assess streams under the Clean Water Act (CWA). Photo credits: Ben Block, Tetra Tech and Tom Danielson, Maine DEP

Tetra Tech used an R program to calculate over 150 metrics! Photo credits: Ben Block, Tetra Tech.

Low-gradient streams and urban stressors. Top left: low-gradient stream; top right: bridge and development on river; bottom: wastewater treatment facility. Photo credits: Tetra Tech.

Organization logos of all collaborators.