Challenges of modeling ocean basin ecosystems

With increasing pressure for a more ecological approach to marine fisheries and environmental management, there is a growing need to understand and predict changes in marine ecosystems. Biogeochemical and physical oceanographic models are well developed, but extending these further up the food web to include zooplankton and fish is a major challenge. The difficulty arises because organisms at higher trophic levels are longer lived, with important variability in abundance and distribution at basin and decadal scales. Those organisms at higher trophic levels also have complex life histories compared to microbes, further complicating their coupling to lower trophic levels and the physical system. We discuss a strategy that builds on recent advances in modeling and observations and suggest a way forward that includes approaches to coupling across trophic levels and the inclusion of uncertainty.     

The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.     

Biochemical composition and kinetics of C and N mineralization of animal wastes: a typological approach

Forty-seven different animal wastes were characterized using chemical and organic matter fractionation methods (water extraction and Van Soest method) and 224-day incubation studies to assess their decomposition in soil. Simple correlation and multiple factor analysis were performed to establish relationships between the composition of these wastes and C and N mineralization. Carbon and N contents ranged from 101 to 469 mg C kg⁻¹ dry matter (d.m.) and from 4 to 39 mg N kg⁻¹ d.m. Soluble C and N represented less than 9% of organic C and 1.5% of total N at 20°C, respectively. The C fractions soluble at 100°C or in neutral detergent were larger and represented 14 and 32% of the organic C, respectively. The hemicellulose-like (HEM) and cellulose-like (CEL) fractions contained about 16.5 and 6% of the organic N, respectively. The C distribution in the lignin-like (LIG) and CEL fractions was comparable, but the former contained more N. Carbon mineralization varied from 5 to 62% of the organic C added during the 224-day incubation; 70% of the wastes induced net N mineralization at the end of incubation (from 3 to 51% of organic N). Other wastes induced net soil inorganic N immobilization, from −1 to −31% of the organic N added. Most highly significant correlations were established between the C mineralization and the C present in the water-soluble fraction at 20°C, and the HEM and LIG fractions. Relationships between N mineralization and biochemical characteristics were weak, except with the soluble Van Soest fraction, and highly significant correlations were observed between N mineralization rates calculated at 224 days of incubation and the organic N content or C/N ratio of wastes. Finally, an objective hierarchical classification based on composition criteria and C and N mineralization led to the definition of six different classes of wastes. It permitted differentiation between four composted wastes and intrinsically different wastes (i.e., cattle manures, pig manures, and poultry manures) which could not be objectively regrouped. It also placed some very different types of waste (solid phase from pig slurry separation, pig manures, and composted pig mixtures) in the same class.     

Abiotic degradation of lignified cell walls by carbonate and copper salt

This study reports on the destructuration of Wheat straw and Spruce wood cell walls after maceration in potassium carbonate or sodium hydroxide at pH = 10 in the presence of copper acetate. The alkaline treatments had a predominant impact on the wheat straw cell wall components over copper acetate. Either K-carbonate or Na-hydroxide extracted from wheat straw a particular lignin fraction rich in condensed C-C linkages, leading to the unmasking of new ether-linked sub-structures in the cell wall. This unmasking was increased in the presence of copper salt but only in the nonextracted Wheat straw sample incubated in carbonate and not in the corresponding extractive-free sample. This difference was related to the leaching of compounds from the nonextracted cell wall, which could sustain oxidative activity of copper by hindering its precipitation into inactive hydroxide and/or carbonate species. In Spruce wood samples, copper salt was the principal factor impacting on the lignin structure over alkali alone. Its effect was, however, only detected at the level of C-C linked dimers. These results confirmed that unmasking of lignin sub-structures also occurred in Spruce wood, but probably through mechanisms different from that evidenced in Wheat straw.     

Possible role of plant phenolics in the production of trichothecenes by Fusarium graminearum strains on different fractions of maize kernels

Four trichothecene-producing strains of Fusarium graminearum were grown on three maize grain fractions, whole grain, degermed grain, and the germ, to determine the effect of natural substrates on mycotoxin production. Monitoring the ergosterol content after 25 days of incubation indicated that fungal growth on all grain fractions was comparable. Trichothecene (TCT) production was highest on degermed grain, less on whole grain, and very low or nondetectable on the germ; similar results were found with four different strains. It was concluded that inhibitor(s) of TCT biosynthesis were present in maize germ. The presence of phenolic compounds was investigated in the different fractions. The hydroxamate 4-acetylbenzoxazolin-2-one (4-ABOA), a known inhibitor of mycotoxin production, was found in the degermed and whole grain fractions but not in the germ. Therefore, the TCT inhibition observed on the maize germ fraction used in our study is clearly not linked to 4-ABOA. Other soluble phenolic compounds were found at a much higher concentration in the germ than in the two other fractions. The inhibition property of the soluble ester-bound extracts was tested in liquid culture. A possible role for these compounds is discussed.     

The origin of the A genome donor of wheats (Triticum: Poaceae) – a perspective based on the sequence variation of the 5S DNA gene units

In a prior study on the haplomes of wheat using the 5S rRNA gene we assigned the long A1 and short A1 unit classes to the A haplome in the diploid T. monococcum. The short A1 unit class is absent in the tetraploids T. turgidum and T. timopheevii and in the hexaploid T. aestivum, although present in the hexaploid T. zhukovskyi. Both T. turgidum and T. aestivum contained a different 5S DNA unit class labeled the short A2.The purpose of this paper was to study the short A2 units in the two diploid species to shed light on the theory that the A haplome donor of T. turgidum and T. aestivum was T. urartu. Fifty eight clones were obtained from 12 accessions, sequenced and analyzed. As expected T. baeoticum, which is often classified as a subspecies of T. monococcum, contained the long A1 and the short A1 5S DNA units. Unexpectedly, T. urartu had the long A1 and the short G1 unit classes instead and other units not found so far in Triticum. These findings support the hypothesis that the donor of the A genome in T. zhukovskyi was T. monococcum, as identified by the short A1 units. However, the short A1 units are absent in T. timopheevii, also a carrier of the A genome. The short G1 units found in T. urartu also identify it as a possible donor of the G genome to T. timopheevii. The short G1 units were also found in T. aestivum in our prior study. The long G1 unit class was not found in T. urartu but reported from T. timopheevii and T. zhukovskyi. The implications of these and related findings on the evolution of wheats are discussed.     

Relative contribution of phytates, fibers, and tannins to low iron and zinc in vitro solubility in pearl millet (Pennisetum glaucum) flour and grain fractions

In vitro digestions were performed on pearl millet flours with decreased phytate contents and on two dephytinized or nondephytinized pearl millet grain fractions, a decorticated fraction, and a bran fraction with low and high fiber and tannin contents, respectively. Insoluble residues of these digestions were then incubated with buffer or enzymatic solutions (xylanases and/or phytases), and the quantities of indigestible iron and zinc released by these different treatments were determined. In decorticated pearl millet grain, iron was chelated by phytates and by insoluble fibers, whereas zinc was almost exclusively chelated by phytates. In the bran of pearl millet grain, a high proportion of iron was chelated by iron-binding phenolic compounds, while the rest of iron as well as the majority of zinc were chelated in complexes between phytates and fibers. The low effect of phytase action on iron and zinc solubility of bran of pearl millet grain shows that, in the case of high fiber and tannin contents, the chelating effect of these compounds was higher than that of phytates.     

Exposure Patterns and Long Term Sequelae on Adults and Children in Two Canadian Indigenous Communities Exposed to Methylmercury

Health Canada has been collecting data on Inuit and First Nations' methylmercury (MeHg) levels for 25 years. A national overview has been completed and more focussed analyses have now been initiated. This paper deals with two interdependent analytical components: 1) a longitudinal overview of the two most extensively sampled communities in Canada: Grassy Narrows and Whitedog, the residents of which were exposed to ‘point source’ mercury pollution in the 1970's; 2) fetal and post-natal exposure to mercury in these two communities including an outline of the First Nation MeHg child development pilot project in the two communities. A retrospective analysis of Grassy Narrows and Whitedog shows a decreasing MeHg trend in both communities. In Grassy Narrows the average individual annual peak methylmercury level in blood has decreased significantly, from 23.80 ppb (range 1.50–322.90) in 1976 to 7.5 ppb (1.7–46.7) in 1995 (r=-0.65, p<0.001). In Whitedog the average peak has also decreased significantly, from 12.87 ppb (1.50–172.00) in 1976 to 6.1 ppb (1.7–33.3) in 1995 (r=-0.59, p<0.005). However, behind these positive trends is the reality of two communities still suffering the effects of disrupted lifestyles and socio-cultural damage. A number of cord blood samples, maternal blood samples, and samples from women of child-bearing age from these communities have been in the “risk” group (according to the 1990 WHO guidelines). We are therefore now assessing the long term effects of fetal exposure in the communities. Standard clinical examinations in the past failed to prove abnormalities attributable to methylmercury but did not include subtle neuropsychological development tests. Many of the fetally exposed children are now in secondary school. Therefore, we have initiated a pilot project to assess long term effects of methylmercury exposure on the neuropsychological development of these children whose fetal exposure we know. The pilot child development project which was initiated in 1995 in Grassy Narrows and Whitedog, with community support, includes four main components: i) a school records review, looking at attendance, marks, and atypical behaviour; ii) teachers' questionnaires, targeting child behaviour; iii) an in-depth neuropsychological test battery focussing on subtle factors, such as memory, attention, executive functions, perceptual functions and sensory / motor development; and iv) hair sampling, providing current MeHg levels to correlate with results from the previous sampling and findings from the first three components. An overview of progress is given.