Influence of urbanization on the health of juvenile salmonids in Pacific Northwest perennial streams

Abstract

Increasing population and urbanization leads to stress in freshwater systems from a variety of anthropogenic influences including structural changes to habitat, temperature effects from increased runoff and reduced canopy cover, flow changes, and an increased presence of toxicants both from point- and non-point sources. Physical and chemical changes affect the biota within these urban streams at varying scales ranging from individual organisms to populations and communities creating complex interactions that present challenges for characterizing and monitoring the impact on species utilizing these freshwater habitats. Salmonids, specifically cutthroat trout (Oncorhynchus clarkii) and coho salmon (Oncorhynchus kisutch), extensively utilize small stream habitats influenced by this changing urban landscape. This study used a comprehensive fish health assessment concurrent with the U.S. Geological Survey’s Pacific Northwest Stream Quality Assessment in 2015. This study quantified impacts from disease in juvenile coho and cutthroat salmon, impacts to coho salmon growth within the context of environmental and ecological influences, and identified physiological responses in coho salmon from pollution. First, we used the previously established Geode fish health index to assess the extent that fish were diseased in these streams. Fish had elevated levels of disease in four moderately urbanized streams and had moderate disease levels in reference streams. Next, we used a bioenergetics growth modeling approach to assess the environmental factors affecting juvenile coho growth. For urban streams, we show mixed effects, whereby urban streams tended to be warmer, have earlier emergence dates and stronger early season growth. However, we also show that larger fish are under increased stress through lower growth efficiencies, especially later in the summer, when compared to fish from other streams. Finally, we related in stream contamination to physiological response in coho. We identified 52 stress genes of interest using next-generation sequencing (RNAseq) and designed a custom nanoString probe set for expression analysis using the nCounter platform. Multivariate methods were used to relate water and sediment contaminant concentrations to gene expression levels. Results indicate that elevated levels of PAHs, PCBs, and pesticides significantly correlated with increased expression of genes involved in detoxification of organic contaminants. This study presents the first time a probe-based multiplexed nanoString assay was successfully used to assess salmonids and provides an economical and comprehensive assessment tool to evaluate the exposure and physiological response of salmonids to in-stream contaminants. Together these assessments provide valuable monitoring tools to determine the relative impacts of disease, near-term environmental conditions, and contaminants to growth and physiological stress in salmonids.