Climate change driven effects on transport, fate and biogeochemistry of trace element contaminants in coastal marine ecosystems

Human activities and climate change substantially threaten coastal areas, impacting ecosystem functions, services, and human-wellbeing. Trace elements, from both natural and anthropogenic sources, can contaminate coastal regions, and at high concentrations may become toxic to marine biota. Climate change is likely to affect the sources, sinks and cycling of trace elements in coastal systems: for example, riverine runoff is set to increase as precipitation in the Arctic intensifies, and more frequent extreme floods are expected to activate previously deeply buried trace elements. Furthermore, changes in human activity under a warming climate, such as increased Arctic shipping and potential geoengineering projects such as ocean alkalinity enhancement, will likely introduce more trace elements to coastal ecosystems. Advancing our understanding of trace element cycling is at present limited by factors including lack of data coverage in the Global South, challenges in studying multi-stressor effects and ecosystem responses, lack of long-term data, and the difficulty in parametrizing robust models in coastal environments

Towards a quality-controlled and accessible Pitzer model for seawater and related systems

We elaborate the need for a quality-controlled chemical speciation model for seawater and related natural waters, work which forms the major focus of SCOR Working Group 145. Model development is based on Pitzer equations for the seawater electrolyte and trace components. These equations can be used to calculate activities of dissolved ions and molecules and, in combination with thermodynamic equilibrium constants, chemical speciation. The major tasks to be addressed are ensuring internal consistency of the Pitzer model parameters (expressing the interactions between pairs and triplets of species, which ultimately determines the calculated activities), assessing uncertainties, and identifying important data gaps that should be addressed by new measurements. It is recognised that natural organic matter plays an important role in many aquatic ecosystems, and options for including this material in a Pitzer-based model are discussed. The process of model development begins with the core components which include the seawater electrolyte and the weak acids controlling pH. This core model can then be expanded by incorporating additional chemical components, changing the standard seawater composition and/or broadening the range of temperature and pressure, without compromising its validity. Seven important areas of application are identified: open ocean acidification; micro-nutrient biogeochemistry and geochemical tracers; micro-nutrient behaviour in laboratory studies; water quality in coastal and estuarine waters; cycling of nutrients and trace metals in pore waters; chemical equilibria in hydrothermal systems; brines and salt lakes

Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio

<p>Abstract</p> <p>Background</p> <p>Obtaining transcripts of homologs of closely related organisms and retrieving the reconstructed exon-intron patterns of the genes is a very important process during the analysis of the evolution of a protein family and the comparative analysis of the exon-intron structure of a certain gene from different species. Due to the ever-increasing speed of genome sequencing, the gap to genome annotation is growing. Thus, tools for the correct prediction and reconstruction of genes in related organisms become more and more important. The tool Scipio, which can also be used via the graphical interface WebScipio, performs significant hit processing of the output of the Blat program to account for sequencing errors, missing sequence, and fragmented genome assemblies. However, Scipio has so far been limited to high sequence similarity and unable to reconstruct short exons.</p> <p>Results</p> <p>Scipio and WebScipio have fundamentally been extended to better reconstruct very short exons and intron splice sites and to be better suited for cross-species gene structure predictions. The Needleman-Wunsch algorithm has been implemented for the search for short parts of the query sequence that were not recognized by Blat. Those regions might either be short exons, divergent sequence at intron splice sites, or very divergent exons. We have shown the benefit and use of new parameters with several protein examples from completely different protein families in searches against species from several kingdoms of the eukaryotes. The performance of the new Scipio version has been tested in comparison with several similar tools.</p> <p>Conclusions</p> <p>With the new version of Scipio very short exons, terminal and internal, of even just one amino acid can correctly be reconstructed. Scipio is also able to correctly predict almost all genes in cross-species searches even if the ancestors of the species separated more than 100 Myr ago and if the protein sequence identity is below 80%. For our test cases Scipio outperforms all other software tested. WebScipio has been restructured and provides easy access to the genome assemblies of about 640 eukaryotic species. Scipio and WebScipio are freely accessible at <url>http://www.webscipio.org</url>.</p

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive <i>Helicoverpa</i> pest species

BACKGROUND: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. RESULTS: We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes. CONCLUSIONS: The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant

2017 Research & Innovation Day Program

A one day showcase of applied research, social innovation, scholarship projects and activities.https://first.fanshawec.ca/cri_cripublications/1004/thumbnail.jp

Metals impact into the Paranaguá Estuarine Complex (Brazil) during the exceptional flood of 2011

Abstract Particulate and dissolved metal concentrations were determined after the largest flood in the last 30 years on the east-west axis of the Paranaguá Estuarine Complex (PEC) and compared to the those of the dry period at two stations. Results confirmed that the flood greatly affected riverine outflows and the behavior of metals in the PEC. In particular, a sharp decrease in salinity was followed by extremely high SPM concentrations leading to a decrease in DO concentrations at both stations. For the dissolved phase, ANOSIM analysis showed a significant dissimilarity at each station between the sampled periods, whereas for the particulate phase this dissimilarity was found only for the samplings taken at the Antonina Station. KD values suggested dissolved Cu behavior was related to the presence of organic complexes and dissolved Mn had sediment resuspension of redox sediments and or/pore water injection as sources. Metal concentrations were lower than in polluted estuaries, though high enrichment factors found after the flood pointed to the influence of anthropogenic sources. In conclusion, the flood's influence was more evident at the Antonina Station, due to its location in the upper estuary, whereas in Paranaguá a high SPM content with low metal concentration was found, following the common pattern generally found in other marine systems subject to heavy rainfall events