Chapter 2 – Aquatic Communities Protocol

Principal Investigators: Dezene Huber, Mark Shrimpton, Daniel Erasmus, Brent Murray, Lisa Poirier, Allan Costello, Jeanne Robert


Rivers and streams are complex open-transport systems with physical properties that vary over time and space (Knighton 1984). Riparian zones at the boundary of the terrestrial and aquatic systems have dynamic physical properties that change in response to fluvial and non-fluvial disturbances (Gregory et al. 1991). Small headwater streams lack the energy to determine their own path, but stream morphology and the riparian zone is determined by roughness elements, valley gradient and hydrology. As streams become larger, the energy within the system is greater and capable of creating floodplains and modifying the landscape through which they flow (Knighton 1984; Church 1992). The same processes also affect morphology of the riparian zone. Small high-gradient streams have riparian zones composed of large and rough sediments, mostly of non-alluvial origin (Church 1992). Further downstream, riparian zones are predominantly composed of sediments deposited from the alluvial channel (Knighton 1984).

Riparian zones are important for ecosystem function as they provide important physical and biological features needed for productivity and aquatic biodiversity. Many species found in small streams depend on the energy that is provided by organic matter from the riparian zone, but also the habitat complexity that is created from physical inputs such as large woody debris. Larger river systems are less dependent on riparian inputs for productivity, but the riparian zone plays an important role in stabilizing fluvial processes in river systems. Construction of the 463-km long Pacific Trails Pipeline (PTP) will affect riparian areas where the right-of-way (RoW) runs adjacent to rivers and streams and where it crosses these aquatic systems. We, therefore, proposed to evaluate the potential effect of the PTP on the aquatic community function at sites where the pipeline crosses rivers and streams. Because of delays in pipeline construction beyond the UNBC BMAP, we focused on method development and baseline biodiversity assessment in order to predict best practices for ensuring aquatic ecosystem resilience during and after construction, when it occurs.

Baseline biodiversity in temperate streams includes the aquatic invertebrates and fish that are intimately associated with bottom substrates. Many benthic invertebrates depend on gravel and cobble of stream beds to provide spaces for attachment, protection, feeding, and the interstitial flow of water for oxygen consumption (Wood and Armitage 1997). There is also a link to vertebrate fauna as many invertebrate species that reside on coarse substrates are preferred prey for fish.

Environmental impact assessments on freshwater systems rely in large part on assessments of shifts in aquatic invertebrate populations and diversity. Benthic macroinvertebrates, in particular, are useful for assessing site-specific effects: they tend to stay in a small area, are relatively easy to identify to Family level or beyond, and species assemblages include multiple trophic levels and tolerances, permitting assessment of cumulative effects (Barbour et al. 1999). Aquatic invertebrates, particularly the immature stages of certain groups of insects, are also very responsive to changes in water quality such as levels of particulate matter or dissolved oxygen.

Traditional impact assessments make use of what is commonly referred to as "EPT" (i.e., Ephemeroptera [mayflies], Plecoptera [stoneflies], and Trichoptera [caddisflies]). These three groups are important members of stream ecosystems and food webs, but are also susceptible to a variety of environmental effects and disturbances. In some assessment methods, fly larvae (Diptera) are also included. Various count and ratio calculations of EPT and Diptera Families or species are considered to be accurate measures of overall stream health (Hilsenhoff 1988; Reif 2002). Much of the reason for relying on EPT ratios, beyond their known sensitivity to conditions, is the fact that traditional assessment methods have relied on highly trained personnel with taxonomical knowledge of various species groups combined with labor- and time-intensive work at a microscope. As such, detailed data collection on individual species is often not conducted, relying instead on gross counts and comparisons of large groups at the Family or Order taxonomic levels. Although this has proven adequate, recent advances in the use of environmental DNA (eDNA) combined with massive taxonomic DNA barcoding efforts (e.g., the Barcode of Life project, and the growth of species-specific DNA sequence databases have allowed us to develop genetic methods for stream biodiversity assessment.