Contribution and pathways of diazotroph-derived nitrogen to zooplankton during the VAHINE mesocosm experiment in the oligotrophic New Caledonia lagoon

In oligotrophic tropical and subtropical oceans, where strong stratification can limit the replenishment of surface nitrate, dinitrogen (N-2) fixation by diazotrophs can represent a significant source of nitrogen (N) for primary production. The VAHINE (VAriability of vertical and tropHIc transfer of fixed N-2 in the south-wEst Pacific) experiment was designed to examine the fate of diazotroph-derived nitrogen (DDN) in such ecosystems. In austral summer 2013, three large ( similar to aEuro parts per thousand aEuro-50aEuro-m(3)) in situ mesocosms were deployed for 23 days in the New Caledonia lagoon, an ecosystem that typifies the low-nutrient, low-chlorophyll environment, to stimulate diazotroph production. The zooplankton component of the study aimed to measure the incorporation of DDN into zooplankton biomass, and assess the role of direct diazotroph grazing by zooplankton as a DDN uptake pathway. Inside the mesocosms, the diatom-diazotroph association (DDA) het-1 predominated during days 5-15 while the unicellular diazotrophic cyanobacteria UCYN-C predominated during days 15-23. A Trichodesmium bloom was observed in the lagoon (outside the mesocosms) towards the end of the experiment. The zooplankton community was dominated by copepods (63aEuro-% of total abundance) for the duration of the experiment. Using two-source N isotope mixing models we estimated a mean similar to aEuro parts per thousand aEuro-28aEuro-% contribution of DDN to zooplankton nitrogen biomass at the start of the experiment, indicating that the natural summer peak of N-2 fixation in the lagoon was already contributing significantly to the zooplankton. Stimulation of N-2 fixation in the mesocosms corresponded with a generally low-level enhancement of DDN contribution to zooplankton nitrogen biomass, but with a peak of similar to aEuro parts per thousand aEuro-73aEuro-% in mesocosm 1 following the UCYN-C bloom. qPCR analysis targeting four of the common diazotroph groups present in the mesocosms (Trichodesmium, het-1, het-2, UCYN-C) demonstrated that all four were ingested by copepod grazers, and that their abundance in copepod stomachs generally corresponded with their in situ abundance. N-15(2) labelled grazing experiments therefore provided evidence for direct ingestion and assimilation of UCYN-C-derived N by the zooplankton, but not for het-1 and Trichodesmium, supporting an important role of secondary pathways of DDN to the zooplankton for the latter groups, i.e. DDN contributions to the dissolved N pool and uptake by nondiazotrophs. This study appears to provide the first evidence of direct UCYN-C grazing by zooplankton, and indicates that UCYN-C-derived N contributes significantly to the zooplankton food web in the New Caledonia lagoon through a combination of direct grazing and secondary pathways

Systematic Review and Meta-Analysis Toward Synthesis of Thresholds of Ocean Acidification Impacts on Calcifying Pteropods and Interactions With Warming

Interpreting the vulnerability of pelagic calcifiers to ocean acidification (OA) is enhanced by an understanding of their critical thresholds and how these thresholds are modified by other climate change stressors (e.g., warming). To address this need, we undertook a three-part data synthesis for pteropods, one of the calcifying zooplankton group. We conducted the first meta-analysis and threshold analysis of literature characterizing pteropod responses to OA and warming by synthetizing dataset comprising of 2,097 datapoints. Meta-analysis revealed the extent to which responses among studies conducted on differing life stages and disparate geographies could be integrated into a common analysis. The results demonstrated reduced calcification, growth, development, and survival to OA with increased magnitude of sensitivity in the early life stages, under prolonged duration, and with the concurrent exposure of OA and warming, but not species-specific sensitivity. Second, breakpoint analyses identified OA thresholds for several endpoints: dissolution (mild and severe), calcification, egg development, shell growth, and survival. Finally, consensus by a panel of pteropod experts was used to verify thresholds and assign confidence scores for five endpoints with a sufficient signal: noise ratio to develop life-stage specific, duration-dependent thresholds. The range of aragonite saturation state from 1.5–0.9 provides a risk range from early warning to lethal impacts, thus providing a rigorous basis for vulnerability assessments to guide climate change management responses, including an evaluation of the efficacy of local pollution management. In addition, meta-analyses with OA, and warming shows increased vulnerability in two pteropod processes, i.e., shell dissolution and survival, and thus pointing toward increased threshold sensitivity under combined stressor effect

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps

Sea-ice habitat minimizes grazing impact and predation risk for larval Antarctic krill

Survival of larval Antarctic krill (Euphausia superba) during winter is largely dependent upon the presence of sea ice as it provides an important source of food and shelter. We hypothesized that sea ice provides additional benefits because it hosts fewer competitors and provides reduced predation risk for krill larvae than the water column. To test our hypothesis, zooplankton were sampled in the Weddell-Scotia Confluence Zone at the ice-water interface (0–2 m) and in the water column (0–500 m) during August–October 2013. Grazing by mesozooplankton, expressed as a percentage of the phytoplankton standing stock, was higher in the water column (1.97 ± 1.84%) than at the ice-water interface (0.08 ± 0.09%), due to a high abundance of pelagic copepods. Predation risk by carnivorous macrozooplankton, expressed as a percentage of the mesozooplankton standing stock, was significantly lower at the ice-water interface (0.83 ± 0.57%; main predators amphipods, siphonophores and ctenophores) than in the water column (4.72 ± 5.85%; main predators chaetognaths and medusae). These results emphasize the important role of sea ice as a suitable winter habitat for larval krill with fewer competitors and lower predation risk. These benefits should be taken into account when considering the response of Antarctic krill to projected declines in sea ice. Whether reduced sea-ice algal production may be compensated for by increased water column production remains unclear, but the shelter provided by sea ice would be significantly reduced or disappear, thus increasing the predation risk on krill larvae

Self-diffusion in dense granular shear flows

Diffusivity is a key quantity in describing velocity fluctuations in granular materials. These fluctuations are the basis of many thermodynamic and hydrodynamic models which aim to provide a statistical description of granular systems. We present experimental results on diffusivity in dense, granular shear in a 2D Couette geometry. We find that self-diffusivities are proportional to the local shear rate with diffusivities along the mean flow approximately twice as large as those in the perpendicular direction. The magnitude of the diffusivity is D \approx \dot\gamma a^2 where a is the particle radius. However, the gradient in shear rate, coupling to the mean flow, and drag at the moving boundary lead to particle displacements that can appear sub- or super-diffusive. In particular, diffusion appears superdiffusive along the mean flow direction due to Taylor dispersion effects and subdiffusive along the perpendicular direction due to the gradient in shear rate. The anisotropic force network leads to an additional anisotropy in the diffusivity that is a property of dense systems with no obvious analog in rapid flows. Specifically, the diffusivity is supressed along the direction of the strong force network. A simple random walk simulation reproduces the key features of the data, such as the apparent superdiffusive and subdiffusive behavior arising from the mean flow, confirming the underlying diffusive motion. The additional anisotropy is not observed in the simulation since the strong force network is not included. Examples of correlated motion, such as transient vortices, and Levy flights are also observed. Although correlated motion creates velocity fields qualitatively different from Brownian motion and can introduce non-diffusive effects, on average the system appears simply diffusive.Comment: 13 pages, 20 figures (accepted to Phys. Rev. E

South African research in the Southern Ocean: New opportunities but serious challenges

South Africa has a long track record in Southern Ocean and Antarctic research and has recently invested considerable funds in acquiring new infrastructure for ongoing support of this research. This infrastructure includes a new base at Marion Island and a purpose-built ice capable research vessel, which greatly expand research opportunities. Despite this investment, South Africa's standing as a participant in this critical field is threatened by confusion, lack of funding, lack of consultation and lack of transparency. The research endeavour is presently bedevilled by political manoeuvring among groups with divergent interests that too often have little to do with science, while past and present contributors of research are excluded from discussions that aim to formulate research strategy. This state of affairs is detrimental to the country's aims of developing a leadership role in climate change and Antarctic research and squanders both financial and human capital

Multiple Routes of Pesticide Exposure for Honey Bees Living Near Agricultural Fields

Populations of honey bees and other pollinators have declined worldwide in recent years. A variety of stressors have been implicated as potential causes, including agricultural pesticides. Neonicotinoid insecticides, which are widely used and highly toxic to honey bees, have been found in previous analyses of honey bee pollen and comb material. However, the routes of exposure have remained largely undefined. We used LC/MS-MS to analyze samples of honey bees, pollen stored in the hive and several potential exposure routes associated with plantings of neonicotinoid treated maize. Our results demonstrate that bees are exposed to these compounds and several other agricultural pesticides in several ways throughout the foraging period. During spring, extremely high levels of clothianidin and thiamethoxam were found in planter exhaust material produced during the planting of treated maize seed. We also found neonicotinoids in the soil of each field we sampled, including unplanted fields. Plants visited by foraging bees (dandelions) growing near these fields were found to contain neonicotinoids as well. This indicates deposition of neonicotinoids on the flowers, uptake by the root system, or both. Dead bees collected near hive entrances during the spring sampling period were found to contain clothianidin as well, although whether exposure was oral (consuming pollen) or by contact (soil/planter dust) is unclear. We also detected the insecticide clothianidin in pollen collected by bees and stored in the hive. When maize plants in our field reached anthesis, maize pollen from treated seed was found to contain clothianidin and other pesticides; and honey bees in our study readily collected maize pollen. These findings clarify some of the mechanisms by which honey bees may be exposed to agricultural pesticides throughout the growing season. These results have implications for a wide range of large-scale annual cropping systems that utilize neonicotinoid seed treatments

Differentiating Salmonid Migratory Ecotypes Through Stable Isotope Analysis of Collagen: Archaeological and Ecological Applications

The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ13C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare

Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity.

Many genetic loci affect circulating lipid levels, but it remains unknown whether lifestyle factors, such as physical activity, modify these genetic effects. To identify lipid loci interacting with physical activity, we performed genome-wide analyses of circulating HDL cholesterol, LDL cholesterol, and triglyceride levels in up to 120,979 individuals of European, African, Asian, Hispanic, and Brazilian ancestry, with follow-up of suggestive associations in an additional 131,012 individuals. We find four loci, in/near CLASP1, LHX1, SNTA1, and CNTNAP2, that are associated with circulating lipid levels through interaction with physical activity; higher levels of physical activity enhance the HDL cholesterol-increasing effects of the CLASP1, LHX1, and SNTA1 loci and attenuate the LDL cholesterol-increasing effect of the CNTNAP2 locus. The CLASP1, LHX1, and SNTA1 regions harbor genes linked to muscle function and lipid metabolism. Our results elucidate the role of physical activity interactions in the genetic contribution to blood lipid levels