Open Notebook Series: Ocean Acidification

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As part of a monthly UnSeminar Series there will be a discussion June 27th 9:30 AM in the FTR 103 on Ocean Acidification.

The Open Notebook UnSeminar Series is focused on bringing together disparate research groups interested in sharing experiences, collaboration, and discussing issues related to large data sets, reproducibility, and science.

Everyone is welcome to attend. There will likely be a few slides, but primarily this is an informal discussion of what researchers are doing and how we might collaborate better. Please contact Emma Timmins-Schiffman if you have any questions.

Evidence for an amoeba-like infectious stage of Ichthyophonus sp. and description of a circulating blood stage: a probable mechanism for dispersal within the fish host.

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Evidence for an amoeba-like infectious stage of Ichthyophonus sp. and description of a circulating blood stage: a probable mechanism for dispersal within the fish host.

J Parasitol. 2013 Apr;99(2):235-40

Authors: Kocan R, LaPatra S, Hershberger P

Abstract
Small amoeboid cells, believed to be the infectious stage of Ichthyophonus sp., were observed in the bolus (stomach contents) and tunica propria (stomach wall) of Pacific staghorn sculpins and rainbow trout shortly after they ingested Ichthyophonus sp.-infected tissues. By 24-48 hr post-exposure (PE) the parasite morphed from the classically reported multinucleate thick walled schizonts to 2 distinct cell types, i.e., a larger multinucleate amoeboid cell surrounded by a narrow translucent zone and a smaller spherical cell surrounded by a “halo” and resembling a small schizont. Both cell types also appeared in the tunica propria, indicating that they had recently penetrated the columnar epithelium of the stomach. No Ichthyophonus sp. pseudo-hyphae (“germination tubes”) were observed in the bolus or penetrating the stomach wall. Simultaneously, Ichthyophonus sp. was isolated in vitro from aortic blood, which was consistently positive from 6 to 144 hr PE, then only intermittently for the next 4 wk. Small PAS-positive cells observed in blood cultures grew into colonies consisting of non-septate tubules (pseudo-hyphae) terminating in multinucleated knob-like apices similar to those seen in organ explant cultures. Organ explants were culture positive every day; however, typical Ichthyophonus sp. schizonts were not observed histologically until 20-25 days PE. From 20 to 60 days PE, schizont diameter increased from ≤ 25 μm to ≥ 82 μm. Based on the data presented herein, we are confident that we have resolved the life cycle of Ichthyophonus sp. within the piscivorous host.

PMID: 22924915 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/22924915?dopt=Abstract

Pesticides in Urban Streams and Prespawn Mortality of Pacific Coho Salmon.

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Pesticides in Urban Streams and Prespawn Mortality of Pacific Coho Salmon.

Arch Environ Contam Toxicol. 2013 Jun 7;

Authors: King KA, Grue CE, Grassley JM, Hearsey JW

Abstract
The listing of several runs of Pacific salmon as threatened or endangered and associated federal, state, and local efforts to restore/enhance salmon habitat in the Pacific Northwest make it imperative that the factors associated with these population declines are understood. Prespawn mortality (PSM) has been documented in coho salmon (Oncorhynchus kisutch) within urban streams in western Washington since the late 1990s and is characterized by a suite of neurological and respiratory symptoms with mortality occurring shortly thereafter. Mortality rates in returning adults have ranged between 17 and 100 %. The cause of PSM is not known, but the presence of pesticide residues within urban streams led to a hypothesis that PSM in coho salmon and pesticides in urban streams were linked. We exposed pairs of “green” (unripe) prespawn male and female coho salmon to a pesticide mixture (“cocktail”) reported in urban streams in western Washington State, USA. Longevity, ripening in female salmon, and brain acetylcholinesterase were not significantly affected by continuous exposure to the maximum reported concentrations of the pesticides. Fertilization, hatching success, and growth of fry were also not affected when green adults were exposed to these concentrations for 96 h. The absence of effects suggests it is unlikely that pesticides within stormwater are singularly responsible for PSM in coho salmon or that they impair the reproductive capability of exposed adults.

PMID: 23744049 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23744049?dopt=Abstract

Ecological response and physical stability of habitat enhancements along an urban armored shoreline

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Ecological response and physical stability of habitat enhancements along an urban armored shoreline

Jason D. Tofta, Corresponding author contact information, E-mail the corresponding author,
Andrea S. Ogstonb,
Sarah M. Heerhartza,
Jeffery R. Cordella,
Emilie E. Flemerb

http://dx.doi.org/10.1016/j.ecoleng.2013.04.022

Highlights

  • Shoreline enhancements seek to restore upon armored conditions.
  • In our study the two enhancements were a habitat bench and pocket beach.
  • Juvenile Chinook salmon and larval fishes used the habitat bench and pocket beach.
  • Aquatic invertebrates and terrestrial insects showed positive responses.
  • Physical components of the habitat bench and pocket beach were relatively stable.

Abstract
Shoreline armoring is prevalent worldwide and has resulted in substantial habitat alteration in heavily urbanized areas. The biological and physical processes associated with these shorelines have in many cases been compromised, which has led to a recent focus on how to design and implement projects to restore some of the lost or impaired functions, termed enhancement. We describe a multi-year effort testing whether an enhanced site has improved conditions in Seattle, WA, USA, along urban marine shorelines of Puget Sound. The Olympic Sculpture Park opened in January 2007 and included construction of two shallow-water features: a low-terrace habitat bench placed in front of an existing seawall, and a constructed pocket beach that replaced existing riprap. Riparian vegetation was also planted in the uplands replacing impervious surfaces and manicured lawn. We measured the functions of these sites by sampling both before and after enhancements (2005, 2007, and 2009), and comparing to adjacent armored shorelines. Although we are limited in our ability to make generalizations beyond this specific site due to only having one replicate of each shoreline type, the unique aspects of this urban enhancement make it useful as a case study that can apply to other urban systems. Fishes that are dependent on shallow water habitat were a main focus of sampling, specifically outmigrating juvenile salmon (Oncorhynchus spp.) and larvae of other species. Terrestrial and aquatic invertebrates were also assessed, both as a metric for habitat quality and as a determinant of available prey resources for juvenile salmon. Physical features of the created habitats were monitored in post-enhancement years to measure their stability. Results showed that shoreline enhancements increased densities of larval fishes and juvenile salmon and measurements of juvenile salmon feeding behavior dependent on the year, and provided habitat for invertebrate assemblages that were different from armored shorelines and had high taxa richness. Physical resilience depended on both natural processes and human activities, demonstrating the need to incorporate anthropogenic use into the management of urban shorelines.
Keywords

http://www.sciencedirect.com/science/article/pii/S0925857413001407

Hybridization between genetically modified Atlantic salmon and wild brown trout reveals novel ecological interactions

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Story picked up by outlets including BBC, CBC, Guardian, Telegraph, CBC radio.

Hybridization between genetically modified Atlantic salmon and wild brown trout reveals novel ecological interactions

  1. Krista B. Oke
  2. Peter A. H. Westley,
  3. Darek T. R. Moreau
  4. Ian A. Fleming

Abstract

Interspecific hybridization is a route for transgenes from genetically modified (GM) animals to invade wild populations, yet the ecological effects and potential risks that may emerge from such hybridization are unknown. Through experimental crosses, we demonstrate transmission of a growth hormone transgene via hybridization between a candidate for commercial aquaculture production, GM Atlantic salmon (Salmo salar) and closely related wild brown trout (Salmo trutta). Transgenic hybrids were viable and grew more rapidly than transgenic salmon and other non-transgenic crosses in hatchery-like conditions. In stream mesocosms designed to more closely emulate natural conditions, transgenic hybrids appeared to express competitive dominance and suppressed the growth of transgenic and non-transgenic (wild-type) salmon by 82 and 54 per cent, respectively. To the best of our knowledge, this is the first demonstration of environmental impacts of hybridization between a GM animal and a closely related species. These results provide empirical evidence of the first steps towards introgression of foreign transgenes into the genomes of new species and contribute to the growing evidence that transgenic animals have complex and context-specific interactions with wild populations. We suggest that interspecific hybridization be explicitly considered when assessing the environmental consequences should transgenic animals escape to nature.

Guardian coverage: (note: the GM salmon are not crossed with Seal Eels, whatever those are!)

 

Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas).

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Characterization of genes involved in ceramide metabolism in the Pacific oyster (Crassostrea gigas).

BMC Res Notes. 2012;5:502

Authors: Timmins-Schiffman E, Roberts S

Abstract
BACKGROUND: The lipid signaling molecule, ceramide, is a key component of the vertebrate stress response, however, there is limited information concerning its role in invertebrate species. In order to identify genes involved in ceramide metabolism in bivalve molluscs, Pacific oyster genomic resources were examined for genes associated with ceramide metabolism and signaling.
RESULTS: Several genes were identified including full-length sequences characterized for serine palmitoyltransferase-1, 3-ketodihydrosphingosine reductase, acid ceramidase, and ceramide glucosyltransferase. Genes involved in ceramide synthesis and metabolism are conserved across taxa in both form and function. Expression analysis as assessed by quantitative PCR indicated all genes were expressed at high levels in gill tissue. The role of the ceramide pathway genes in the invertebrate stress response was also explored by measuring expression levels in adult oysters exposed to Vibrio vulnificus. Two genes demonstrated increased expression during the bacterial challenge: a gene involved in hydrolytic breakdown of ceramide (acid ceramidase) and a gene involved in de novo generation of ceramide (3-ketodihydrosphingosine reductase), suggesting a possible role of ceramide in the invertebrate stress and immune responses.
CONCLUSIONS: In silico and laboratory results support that Pacific oysters have the basic components of the ceramide metabolism pathway. These results also indicate that ceramide may have analogous functions in vertebrates and invertebrates. The gene expression pattern of acid ceramidase and 3-kethodihydrosphingosine reductase in response to bacterial exposure especially supports that ceramide and sphingolipid metabolism may be involved in the oyster’s stress and/or immune responses.

PMID: 22974230 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/22974230?dopt=Abstract

Can variation in prey density drive changes in predatory selection in natural systems? For salmon and brown bears, yes

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Curry J. Cunningham, Gregory T. Ruggerone, and Thomas P. Quinn

How does the availability of food affect the selectivity of the consumer? It has long been known that survival of prey can depend on their density, as predators become satiated or cannot catch them all. In addition, many studies have shown that predators are selective, tending to kill and consume some species or sizes of prey over others, but very few are examples of prey density driving patterns of selection by predators. Brown bears inhabiting coastal ecosystems of the Pacific Rim obtain much of their annual protein and fat supply by consuming the Pacific salmon that return annually to streams to spawn, and they tend to kill the larger salmon among those available to them. However, this is a world of feast and famine; the number of returning salmon can vary greatly from one year to the next.

Bear holding female sockeye salmon, removed from a Bristol Bay, Alaska stream during spawning. (Credit: Jason Ching, SAFS, University of Washington)

Utilizing 20 years of data including individual 41,240 salmon measurements from a small tributary of Bristol Bay, Alaska, scientists at the University of Washington have found that the strength of predatory selection by bears is inversely related to the density of their sockeye salmon prey. That is, contrary to the expectation that when the salmon are abundant the bears can choose the largest fish, the bears were more selective, tending to kill especially large fish, when salmon were scarce. This finding is especially interesting and important because these salmon populations are also exposed to a commercial fishery that is itself selective, tending to catch the large fish. The fishery has, therefore, both the direct form of selection and also intensifies size-selective predation by bears through the reduction in salmon density.

Read the full story in American Naturalist