Inducible defenses: continuous reaction norms or threshold traits?

Phenotypically plastic traits can be expressed as continuous reaction norms or as threshold traits, but little is known about the selective conditions that favor one over the other. We study this question using a model of prey defenses in which prey can induce any level of defense conditional on cues that are informative of local predator density. The model incorporates a trade-off between defense expression and fecundity and feedback between the defense level of prey and predator attack rates. Both continuous reaction norms and threshold traits can emerge as evolutionarily stable solutions of defense induction, and we show that the shape of the trade-off curve plays a key role in determining the outcome. Threshold traits are favored when selection is disruptive. Ecological conditions that favor defense dimorphisms in the absence of cues will favor threshold traits in the presence of slightly informative cues. We caution that continuous reaction norms and threshold traits may result in similar patterns of defense expression at the population level, and we discuss potential pitfalls of inferring reaction norm type from observational data.     

Hair-loss epizootic in moose (Alces alces) associated with massive deer ked (Lipoptena cervi) infestation

Deer keds (Lipoptena cervi) are blood-sucking flies in the family Hippoboscidae; moose (Alces alces) are their main host in Scandinavia. There are no detailed reports of the negative impacts of deer keds on moose. In 2006 and 2007, hunters in southeastern Norway and midwestern Sweden found several moose cadavers with severe alopecia; numerous moose had extensive hair loss. Between February 2006 and June 2007, materials from 23 moose were submitted for laboratory examination and large numbers of deer keds were found in the coat of most animals. The body condition of the moose varied but was poor in animals with severe alopecia. The findings of enormous numbers of deer keds in the coat of the majority of the affected animals and a consistent histologic image (acute to chronic, multifocal to coalescing, eosinophilic to lymphocytic dermatitis), concurrent with the absence of any other lesions, trace element deficiencies, or dermal infections which are known to cause alopecia, suggest that the hair-loss epizootic was linked to massive infestations with deer keds. The emergence of this hair-loss syndrome implies that the dynamics between parasite and host have been disrupted by a currently unknown environmental or ecological factor. A high moose density, combined with extraordinarily mild weather June 2006-June 2007 and a particularly long period with the absence of night-frost in autumn of 2006, may have been ideal for deer ked development, survival, and optimal host acquisition.     

Flower: extracting information from pyrosequencing data

The SFF file format produced by Roche's 454 sequencing technology is a compact, binary format that contains the flow values that are used for base and quality calling of the reads. Applications, e.g. in metagenomics, often depend on accurate sequence information, and access to flow values is important to estimate the probability of errors. Unfortunately, the programs supplied by Roche for accessing this information are not publicly available. Flower is a program that can extract the information contained in SFF files, and convert it to various textual output formats. AVAILABILITY: Flower is freely available under the General Public License.     

Biomarkers in natural fish populations indicate adverse biological effects of offshore oil production

Background

Despite the growing awareness of the necessity of a sustainable development, the global economy continues to depend largely on the consumption of non-renewable energy resources. One such energy resource is fossil oil extracted from the seabed at offshore oil platforms. This type of oil production causes continuous environmental pollution from drilling waste, discharge of large amounts of produced water, and accidental spills.

Methods and principal findings

Samples from natural populations of haddock (Melanogrammus aeglefinus) and Atlantic cod (Gadus morhua) in two North Sea areas with extensive oil production were investigated. Exposure to and uptake of polycyclic aromatic hydrocarbons (PAHs) were demonstrated, and biomarker analyses revealed adverse biological effects, including induction of biotransformation enzymes, oxidative stress, altered fatty acid composition, and genotoxicity. Genotoxicity was reflected by a hepatic DNA adduct pattern typical for exposure to a mixture of PAHs. Control material was collected from a North Sea area without oil production and from remote Icelandic waters. The difference between the two control areas indicates significant background pollution in the North Sea.

Conclusion

It is most remarkable to obtain biomarker responses in natural fish populations in the open sea that are similar to the biomarker responses in fish from highly polluted areas close to a point source. Risk assessment of various threats to the marine fish populations in the North Sea, such as overfishing, global warming, and eutrophication, should also take into account the ecologically relevant impact of offshore oil production.     

Diel vertical migration of Arctic zooplankton during the polar night

High-latitude environments show extreme seasonal variation in physical and biological variables. The classic paradigm of Arctic marine ecosystems holds that most biological processes slow down or cease during the polar night. One key process that is generally assumed to cease during winter is diel vertical migration (DVM) of zooplankton. DVM constitutes the largest synchronized movement of biomass on the planet, and is of paramount importance for marine ecosystem function and carbon cycling. Here we present acoustic data that demonstrate a synchronized DVM behaviour of zooplankton that continues throughout the Arctic winter, in both open and ice-covered waters. We argue that even during the polar night, DVM is regulated by diel variations in solar and lunar illumination, which are at intensities far below the threshold of human perception. We also demonstrate that winter DVM is stronger in open waters compared with ice-covered waters. This suggests that the biologically mediated vertical flux of carbon will increase if there is a continued retreat of the Arctic winter sea ice cover.     

Salinity Responses of Benthic Microbial Communities in a Solar Saltern (Eilat, Israel)

The salinity responses of cyanobacteria, anoxygenic phototrophs, sulfate reducers, and methanogens from the laminated endoevaporitic community in the solar salterns of Eilat, Israel, were studied in situ with oxygen microelectrodes and in the laboratory in slurries. The optimum salinity for the sulfate reduction rate in sediment slurries was between 100 and 120‰, and sulfate reduction was strongly inhibited at an in situ salinity of 215‰. Nevertheless, sulfate reduction was an important respiratory process in the crust, and reoxidation of formed sulfide accounted for a major part of the oxygen budget. Methanogens were well adapted to the in situ salinity but contributed little to the anaerobic mineralization in the crust. In slurries with a salinity of 180‰ or less, methanogens were inhibited by increased activity of sulfate-reducing bacteria. Unicellular and filamentous cyanobacteria metabolized at near-optimum rates at the in situ salinity, whereas the optimum salinity for anoxygenic phototrophs was between 100 and 120‰.     

Removal of municipal solid waste COD and NH4–N by phyto-reduction: A laboratory–scale comparison of terrestrial and aquatic species at different organic loads

Laboratory scale tests on phytodepuration of raw and pre-treated leachate from municipal sanitary waste were carried out with four vegetable aquatic and terrestrial species at different organic loads. We used the terrestrial species Stenotaphrum secundatum and the free-floating aquatic species Lemna minor, Eichhornia crassipes and Myriophyllum verticellatum to purify leachate from municipal solid waste. The organic load characterized by COD varied from 2–30 g m⁻² day⁻¹. Blanks using tap water served as controls. Duration of the experiments varied from 9–90 days. Maximum concentrations in the experiments were 1600 mg l⁻¹ COD and 300 mg l⁻¹ NH₄–N for S. secundatum. Best results in terms of COD, BOD, and ammonia removal were obtained for raw leachate with COD=2 g m⁻² day⁻¹ in free water surface (FWS) wetlands, and with 2 and 5 g m⁻² day⁻¹ in subsurface flow (SSF) wetlands. Results show that for pretreated leachate (labeled c) low in BOD and NH₄–N, the aquatic species showed low removal and stress even at the lowest load of COD=2 g m⁻² day⁻¹. We cannot say if this is due to the pretreatment itself or the chemical or microbial composition of this leachate. The Stenotaphrum system operated well with this load of leachate c. For untreated leachate (type a and b) the removal and plant growing conditions seemed good at COD=2 g m⁻² day⁻¹. For S. secundatum a load of COD=5 g m⁻² day⁻¹ operated well. All loads above COD=5 g m⁻² day⁻¹ caused low removal and stress, and the green parts of the plants disappeared. Oxygen was, however, consumed throughout the experimental period. For pretreated leachate (type c), the removal of COD were low (−24 to 17%) but good for NH₄–N (52–91%). This leachate also experienced high ammonia removal from the beginning of the experiments, probably due to existing consortia of nitrifying bacteria in it. Statistical analysis shows that the S. secundatum and L. minor systems maintained higher oxygen levels than the M. verticellatum and E. crassipes systems, when operated with tap water. For Lemna minor, this may be due to a better capacity for transporting oxygen into the water. With leachate all S. secundatum systems have higher oxygen levels than the aquatic systems, basically because the water content of the soil has been kept well below saturation. S. secundatum shows a significantly lower removal of COD than did the aquatic systems at a loading of COD=2 g m⁻² day⁻¹ of raw leachate. There is no significant difference between the systems in the removal of NH₄–N at a loading of COD=2 g m⁻² day⁻¹ of both types of leachate. E. crassipes has a lower removal of NH₄–N than M. verticellatum and S. secundatum at a loading of 5 g m⁻² day⁻¹ of COD of both types of leachate. In our experiments, it appears that the amount of free ammonia explains the toxicity of the leachate to the plants. This, however, does not exclude other possible toxic factors.     

Fast sequence clustering using a suffix array algorithm

MOTIVATION: Efficient clustering is important for handling the large amount of available EST sequences. Most contemporary methods are based on some kind of all-against-all comparison, resulting in a quadratic time complexity. A different approach is needed to keep up with the rapid growth of EST data. RESULTS: A new, fast EST clustering algorithm is presented. Sub-quadratic time complexity is achieved by using an algorithm based on suffix arrays. A prototype implementation has been developed and run on a benchmark data set. The produced clusterings are validated by comparing them to clusterings produced by other methods, and the results are quite promising. AVAILABILITY: The source code for the prototype implementation is available under a GPL license from http://www.ii.uib.no/~ketil/bio/.