Below the Surface: Many Habitats Means Many Species

Habitat is the place where your needs are met: shelter is found and food is abundant. Not all species have the same needs, so variety truly is the spice of life.

The stream features we described in our last column—undercut banks, submerged wood structures, pools, and riffles—all create habitat for fish and other aquatic species. These habitats can be quite small and unique—such as a microhabitat of algae-covered rocks—or large and more generalized—such as a cold-water stream. When certain habitat is lost, certain species will cease to thrive. Let’s look at some of the habitat types we described in our last column and discover the species that inhabit them.

Stream bottoms with a mix of rock sizes and little mud and sand provide open nooks and crannies in which
fish can hide. Can you spot the American eel peeking out from beneath a rock? Photo: Sally Harold.

The streambed is a critically important habitat. The substrate (bottom) type will help to determine which species will thrive there. Due to glaciation and the scraping of ice sheets across the landscape, northern streams tend to have rocky bottoms made up of bedrock and boulders. (South of the reach of those glaciers, such as in the Carolinas, stream bottoms are composed of mud and silt.) Substrates in the Connecticut River watershed tributaries have a mixture of all grain sizes from silt to boulders and bedrock. The distribution of that substrate determines what lives where.

A wide diversity of aquatic insects start their life underwater as nymphs. During their life cycle they rise to the surface and take flight. Midges, for example, need soft mud and silt, often with embedded organic material, and low water velocity. They can tolerate polluted water with low dissolved oxygen.

Blackflies, another example, require unpolluted, well-oxygenated, flowing water. The northern part of our watershed has an abundance of such streams, and spring paddlers often suffer from blackfly bites! Blackfly, stonefly, and other nymphs cling to the sides of rocks to feed and hide from predators. They are the prime food source for most fish. Fish pluck them off rocks and eat them as they naturally drift downstream and when they emerge at the surface to fly away as mating adults.

A substrate with interstitial spaces between rocks is important to many species in our watershed, and luckily our rocky streams where there are no dams provide an abundance of these spaces. If interstitial spaces are filled with silt and sand, nymphs have nowhere to feed and hide and the food source for fish is reduced.

During the winter and low flow events, fish and mussels tuck in among the rocks, sometimes burrowing into the loose substrate. In sandy streams, where there are not a lot of rocks for shelter, some fish species may seek out pockets of partially decomposed leaves that accumulate in quiet corners of pools. Eels use a variety of substrates and may actually burrow into the sand.

Water velocity is another key component of stream habitat. A fish’s body morphology (shape) will influence the habitat it uses. Some species (like trout) are streamlined and shaped to let the fast water slip around them. They will be fine in riffles where the stream velocity is high. Other fish are bulky and laterally flattened (like a bluegill) and get buffeted by fast, turbulent flows. Like a worker carrying a sheet of plywood in strong winds, the bluegill does not do well in strong currents. It prefers (and was designed for) lakes and ponds. When washed out of those calmer water bodies into a stream, it will seek slower moving water in pools and eddies.

Even among the species that are adapted to flowing streams, there are morphological differences that determine habitat preferences. Consider the differences between brook trout and (juvenile) Atlantic salmon, and between blacknose dace and longnose dace. All four species live in flowing streams but have morphological features that allow them to adapt to the very specific habitats they prefer. Brook trout and blacknose dace are found in pools and along quiet stream edges. They may be able to migrate up through swifter flowing water, but that is not where they would routinely reside.

Atlantic salmon and longnose dace, on the other hand, seek faster currents, which allows them to utilize feeding habitat not available to the other two species. That they thrive there is in part due to their more streamlined bodies, swimming ability, and much larger pectoral fins (see accompanying photos). They use their pectoral fins like the wing flaps on an airplane—when they tilt the front of the fins downward, their bodies are forced downward holding them against the streambed.

Top: Blacknose dace (left) and brook trout (right) have smaller pectoral fins (those immediately behind the head), reflecting their preference for slower water. Bottom: longnose dace (left) and Atlantic salmon (right) belong to the same family as the fish above but have much larger pectoral fins to help adapt to fast flowing water.

In streams with loose, silt-free gravel and cobble bottoms, the irregular streambed surface creates reduced water velocity in the layer of water (the inch or so) immediately above the streambed, and these species can access that microhabitat. As a young salmon grows, it becomes stronger and more adept at living in heavy rapids, allowing it to intercept drifting food before it reaches the trout in the pool downstream.

For similar reasons, aquatic insect nymphs are often very flat, allowing them to hug the surface of rocks as they crawl around feeding. This also allows them to take advantage of the lower water velocity right at the surface of these submerged rocks.

Water temperature and quality also affect the species in a stream. Brook trout will only thrive in cool, clean water. Brown bullhead will thrive in warmer water and can tolerate some pollution.

As we discussed in the last column, some habitats are less stable in a stream and may be short-lived. This is not necessarily a bad thing. As habitat changes, it introduces opportunities for other species. High stream banks, for example, can be undercut when high water velocities scour away soil and rocks at or a bit above the typical water surface elevation. The gravel and cobbles that wash out of the bank during the undercutting process replenish rocks in the stream, which constantly conveys rocks and sand seaward.

The undercut bank can create a cave-like overhang that can serve as habitat for many species. Fish use this shady and cool habitat during bright warm days as a refuge from high water velocities. The overhang can provide protection from overhead predators, such as kingfishers. However, undercut banks can be a mixed blessing because they may also attract other predators such as turtles, mink, and otter.

When a stream bank is severely undercut, it may collapse into the stream, bringing with it trees and brush that were growing along the stream bank. This is an important source of wood in the stream. Or, when a tree growing on a stream bank falls due to lightning, snow, wind, or simply disease, that tree may get carried downstream until it gets hung up or it may span the stream completely. All components of these downed trees—the canopy, the rootwad, the stem—provide important habitat for fish, turtles, and mammals. Small macroinvertebrates munch on the wood and the biofilm that grows on it. Some species use the accumulations of instream wood and the microhabitats it creates to hide from predators. Predators, though, will come look for the hiders.

Often, when an undercut bank collapses, that detached clump of soil is washed away, leaving an exposed stream bank that continues to erode. These exposed sand and gravel stream banks are an important place for kingfishers and bank swallows to excavate their cave-like nests.

The diversity of habitat elements supports a diversity of species. The important takeaway is that when we straighten channels, remove instream wood, stabilize stream banks with rip-rap, or remove shoreline tree canopy, we reduce species diversity.

Steve Gephard is a fish biologist retired from the CTDEEP with a long association with the Connecticut River. Sally Harold has worked on dam removal and fish passage projects for over 20 years, including as Director of River Restoration and Fish Passage for the Connecticut Chapter of The Nature Conservancy. Steve and Sally collaborate on dam removals and fishway projects through RiverWork, LLC, and can be reached at Riverworkllc@gmail.com.