Martin Liermann

Genetic Diversity of Clinical and Environmental Vibrio parahaemolyticus Strains from the Pacific Northwest

ABSTRACT Since 1997, cases of Vibrio parahaemolyticus-related gastroenteritis from the consumption of raw oysters harvested in Washington State have been higher than historical levels. These cases have shown little or no correlation with concentrations of potentially pathogenic V. parahaemolyticus (positive for the thermostable direct hemolysin gene, tdh) in oysters, although significant concentrations of tdh + V. parahaemolyticus strains were isolated from shellfish-growing areas in the Pacific Northwest (PNW). We compared clinical and environmental strains isolated from the PNW to those from other geographic regions within the United States and Asia for the presence of virulence-associated genes, including the thermostable direct hemolysin (tdh), the thermostable-related hemolysin (trh), urease (ureR), the pandemic group specific markers orf8 and toxRS, and genes encoding both type 3 secretion systems (T3SS1 and T3SS2). The majority of clinical strains from the PNW were positive for tdh, trh, and ureR genes, while a significant proportion of environmental isolates were tdh + but trh negative. Hierarchical clustering grouped the majority of these clinical isolates into a cluster distinct from that including the pandemic strain RIMD2210633, clinical isolates from other geographical regions, and tdh +, trh-negative environmental isolates from the PNW. We detected T3SS2-related genes (T3SS2β) in environmental strains that were tdh and trh negative. The presence of significant concentrations of tdh +, trh-negative environmental strains in the PNW that have not been responsible for illness and T3SS2β in tdh- and trh-negative strains emphasizes the diversity in this species and the need to identify additional virulence markers for this bacterium to improve risk assessment tools for the detection of this pathogen.

The Influences of Body Size, Habitat Quality, and Competition on the Movement and Survival of Juvenile Coho Salmon during the Early Stages of Stream Recolonization

Abstract Understanding the factors influencing the success of juvenile Pacific salmon Oncorhynchus spp. in newly colonized habitats is essential to their recovery in large areas across the West Coast of the United States and Canada. We studied biotic and abiotic factors associated with survival during the early stages of colonization and population establishment of juvenile coho salmon O. kisutch in Rock Creek, a tributary of the upper Cedar River in the Lake Washington basin of Puget Sound, Washington. The stream was occupied by resident fishes (e.g., rainbow trout O. mykiss, cutthroat trout O. clarkii, speckled dace Rhinichthys osculus, and several sculpins Cottus spp.), but adult coho salmon and other anadromous fishes had been excluded by a dam from 1901 until fish ladder installation in 2003. We defined logistic regression models and used an information-theoretic approach to predict apparent survival with various combinations of individual fish condition, location competition, and local habitat quali...

Stock-Specific Size and Timing at Ocean Entry of Columbia River Juvenile Chinook Salmon and Steelhead: Implications for Early Ocean Growth

Abstract Juvenile salmon transitioning from freshwater to marine environments experience high variation in growth and survival, yet the specific causes of this variation are poorly understood. Size at and timing of ocean entry may contribute to this variation because they influence both the availability of prey and vulnerability to predators. To explore this issue, we used stock assignments based on genetic stock identification and internal tags to document the stock-specific size and timing of juvenile hatchery and presumed wild Columbia River Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss at ocean entry during 2007–2011. We found that juvenile salmon and steelhead had consistent stock-specific capture dates, with lower-river stocks typically having earlier timing than those originating farther upstream. Mean size also varied among stocks and was related to hatchery practices. Hatchery yearling Chinook Salmon and steelhead were consistently larger than wild fish from the same stocks, although timing in the estuary was similar. In contrast, hatchery subyearling Chinook Salmon were of similar size to wild fish but entered the ocean up to a month earlier. We evaluated the potential importance of these traits on early marine growth by estimating stock-specific growth rates for Chinook Salmon caught in estuarine and ocean habitats. Growth rates were related to relative ocean entry timing, with lower growth rates for stocks that had only recently arrived in marine waters. Our results demonstrate that stocks within a single basin can differ in their size and timing of ocean entry, life history traits that contribute to early marine growth and potentially to the survival of juvenile salmon. Our results also highlight the necessity of considering stock-specific variation in life history traits to understand salmon ecology and survival across the entire life cycle.

Using a Stream Network Census of Fish and Habitat to Assess Models of Juvenile Salmonid Distribution

Abstract We censused juvenile salmonids and stream habitat over two consecutive summers to test the ability of habitat models to explain the distribution of juvenile Coho Salmon Oncorhynchus kisutch, young-of-the-year (age-0) steelhead O. mykiss, and steelhead parr (age ≥1) within a network consisting of several different-sized streams. Our network-scale habitat models explained 27, 11, and 19% of the variation in density of juvenile Coho Salmon, age-0 steelhead, and steelhead parr, respectively, but strong levels of spatial autocorrelation were typically present in the residuals. Explanatory power of base habitat models increased and spatial autocorrelation decreased with the sequential inclusion of variables accounting for the effects of stream size, year, stream, reach location, and a tertiary interaction term. Stream-scale models were highly variable. Fish–habitat associations were rarely linear and ranged from negative to positive; the variable accounting for location of the habitat within a stream w...

More Sites or More Years? Optimal Study Design for Monitoring Fish Response to Watershed Restoration

Abstract Every year in the Pacific Northwest, hundreds of stream restoration projects are implemented at great expense in the hope that they will increase salmonid abundance. Our understanding of how salmonids interact with their freshwater habitat has steadily improved, but we are still a long way from being able to reliably predict population-level effects of individual projects. To determine whether these projects are in fact increasing salmonid abundance, we will need to implement restoration at the watershed scale, monitor the populations after the freshwater portion of their life history is completed, and replicate the experiment across multiple watersheds to produce results that can be generalized. Although there has been some progress in this direction, it has largely consisted of independent efforts at a relatively small scale. In this paper, we use smolt counts of coho salmon Oncorhynchus kisutch from streams in western Washington and Oregon, along with approximate restoration and monitoring cos...

Environmental influences on the seasonal distribution of Vibrio parahaemolyticus in the Pacific Northwest of the USA.

Populations of Vibrio parahaemolyticus in the environment can be influenced by numerous factors. We assessed the correlation of total (tl+) and potentially virulent (tdh+) V. parahaemolyticus in water with three harmful algal bloom (HAB) genera (Pseudo-nitzschia, Alexandrium and Dinophysis), the abundance of diatoms and dinoflagellates, chlorophyll-a and temperature, salinity and macronutrients at five sites in Washington State from 2008-2009. The variability in V. parahaemolyticus density was explained predominantly by strong seasonal trends where maximum densities occurred in June, 2 months prior to the highest seasonal water temperature. In spite of large geographic differences in temperature, salinity and nutrients, there was little evidence of corresponding differences in V. parahaemolyticus density. In addition, there was no evident relationship between V. parahaemolyticus and indices of HAB genera, perhaps due to a lack of significant HAB events during the sampling period. The only nutrient significantly associated with V. parahaemolyticus density after accounting for the seasonal trend was silicate. This negative relationship may be caused by a shift in cell wall structure for some diatom species to a chitinous substrate preferred by V. parahaemolyticus. Results from our study differ from those in other regions corroborating previous findings that environmental factors that trigger vibrio and HAB events may differ depending on geographic locations. Therefore caution should be used when applying results from one region to another.

Using Redd Attributes, Fry Density, and Otolith Microchemistry to Distinguish the Presence of Steelhead and Rainbow Trout in the Elwha River Dam Removal Project

AbstractThe removal of impassable dams can affect stream fish communities in many ways, including allowing previously separated anadromous and resident life history types to intermingle. Recolonization of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) into areas that were previously occupied solely by resident conspecifics presents a challenge for monitoring because (1) staging or spawning adults may be difficult to directly observe; and (2) the offspring of the two life history forms are indistinguishable during early life. We evaluated the utility of using redd attributes, fry (age-0) size, and fry density to distinguish the presence of steelhead and Rainbow Trout in the Elwha River, Washington. Redd area and substrate size differed between forms: steelhead redds were significantly larger and had a greater median substrate particle size than Rainbow Trout redds. Fry density was significantly higher in steelhead spawning reaches than in Rainbow Trout reaches during both survey years (2010 and 2...

Relocation and Recolonization of Coho Salmon in Two Tributaries to the Elwha River: Implications for Management and Monitoring

AbstractIn 2012 the lower of two Elwha River dams was breached, restoring access of anadromous salmonids to the middle Elwha River (between the two dams), including two distinct tributaries, Indian Creek and Little River. While comparable in size, Indian Creek is considerably less steep than Little River (mean slope of 1.0% versus 3.5%, respectively) and has a warmer stream temperature regime due to its source, Lake Sutherland. During and after breaching, Coho Salmon Oncorhynchus kisutch were relocated to these tributaries from lower Elwha River hatcheries (below the dams) to determine if individuals from a hatchery-dominated population would successfully spawn and seed the systems with juveniles and to assess differences in recolonization between the streams. Transplantation led to immediate spawning, which resulted in levels of smolt out-migrants per stream kilometer comparable with other established Coho Salmon populations in the Pacific Northwest. During the first 2 years of the relocation, redd densi...

Distribution, Density, and Size of Migratory and Fluvial Sculpins in Relation to Barriers in Puget Sound Lowland Streams

AbstractWe examined the effects of potential barriers on populations of migratory sculpins (Coastrange Sculpin Cottus aleuticus and Prickly Sculpin C. asper) and fluvial sculpins (Riffle Sculpin C. gulosus, Shorthead Sculpin C. confusus, and Torrent Sculpin C. rhotheus). Barriers can alter sculpin distribution because migratory sculpins have pelagic larvae that drift downstream to calm waters and juveniles and adults migrate upstream. We compared sculpin populations upstream and downstream of a barrier in 19 lowland streams in the Puget Sound region, Washington. Within each stream, we examined the farthest downstream barrier that would be most likely to impact the upstream movements of migratory sculpins. All study streams had populations of migratory sculpins in stream reaches downstream of the barrier. In 8 of the 19 streams with a barrier, at least one species of fluvial sculpin was also present. We also documented the relative distribution of migratory sculpins and fluvial sculpins in one reference st...

Diel Shifts in Microhabitat Selection of Steelhead and Coho Salmon Fry

AbstractDiel shifts in habitat selection of newly emerged steelhead Oncorhynchus mykiss and Coho Salmon O. kisutch fry were investigated in three northern California coastal watersheds. Steelhead and Coho Salmon fry occupied shallow water near stream margins during both day and night; however, the proportion of fry within 0.5 m of the stream margin increased from 6% during the day to 44% at night. Similarly, the proportion of fry in 10 cm of water or less increased from 26% during the day to 76% at night. Reductions in depth and distance to stream margins were significant at all sites, suggesting that these behaviors are common attributes for steelhead and Coho Salmon fry in this region. These results also suggest that newly emerged fry are potentially vulnerable to becoming stranded due to reductions in stream stage and water surface area, particularly at night. Although our observations were undertaken to better understand the risks to salmonids from vineyard water use for frost protection, the results ...