Latitudinal patterns of magnitude and interannual variability in net ecosystem exchange regulated by biological and environmental variables

Over the last two and half decades, strong evidence showed that the terrestrial ecosystems are acting as a net sink for atmospheric carbon. However the spatial and temporal patterns of variation in the sink are not well known. In this study, we examined latitudinal patterns of interannual variability (IAV) in net ecosystem exchange (NEE) of CO₂ based on 163 site-years of eddy covariance data, from 39 northern-hemisphere research sites located at latitudes ranging from ∼29°N to ∼64°N. We computed the standard deviation of annual NEE integrals at individual sites to represent absolute interannual variability (AIAV), and the corresponding coefficient of variation as a measure of relative interannual variability (RIAV). Our results showed decreased trends of annual NEE with increasing latitude for both deciduous broadleaf forests and evergreen needleleaf forests. Gross primary production (GPP) explained a significant proportion of the spatial variation of NEE across evergreen needleleaf forests, whereas, across deciduous broadleaf forests, it is ecosystem respiration (Re). In addition, AIAV in GPP and Re increased significantly with latitude in deciduous broadleaf forests, but AIAV in GPP decreased significantly with latitude in evergreen needleleaf forests. Furthermore, RIAV in NEE, GPP, and Re appeared to increase significantly with latitude in deciduous broadleaf forests, but not in evergreen needleleaf forests. Correlation analyses showed air temperature was the primary environmental factor that determined RIAV of NEE in deciduous broadleaf forest across the North American sites, and none of the chosen climatic factors could explain RIAV of NEE in evergreen needleleaf forests. Mean annual NEE significantly increased with latitude in grasslands. Precipitation was dominant environmental factor for the spatial variation of magnitude and IAV in GPP and Re in grasslands.     

Dissolved carbon leaching from soil is a crucial component of the net ecosystem carbon balance

Estimates of carbon leaching losses from different land use systems are few and their contribution to the net ecosystem carbon balance is uncertain. We investigated leaching of dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), and dissolved methane (CH₄), at forests, grasslands, and croplands across Europe. Biogenic contributions to DIC were estimated by means of its δ¹³C signature. Leaching of biogenic DIC was 8.3±4.9 g m^?2 yr^?1 for forests, 24.1±7.2 g m^?2 yr^?1 for grasslands, and 14.6±4.8 g m^?2 yr^?1 for croplands. DOC leaching equalled 3.5±1.3 g m^?2 yr^?1 for forests, 5.3±2.0 g m^?2 yr^?1 for grasslands, and 4.1±1.3 g m^?2 yr^?1 for croplands. The average flux of total biogenic carbon across land use systems was 19.4±4.0 g C m^?2 yr^?1. Production of DOC in topsoils was positively related to their C/N ratio and DOC retention in subsoils was inversely related to the ratio of organic carbon to iron plus aluminium (hydr)oxides. Partial pressures of CO₂ in soil air and soil pH determined DIC concentrations and fluxes, but soil solutions were often supersaturated with DIC relative to soil air CO₂. Leaching losses of biogenic carbon (DOC plus biogenic DIC) from grasslands equalled 5–98% (median: 22%) of net ecosystem exchange (NEE) plus carbon inputs with fertilization minus carbon removal with harvest. Carbon leaching increased the net losses from cropland soils by 24–105% (median: 25%). For the majority of forest sites, leaching hardly affected actual net ecosystem carbon balances because of the small solubility of CO₂ in acidic forest soil solutions and large NEE. Leaching of CH₄ proved to be insignificant compared with other fluxes of carbon. Overall, our results show that leaching losses are particularly important for the carbon balance of agricultural systems.     

Aggregated seed arrival alters plant diversity in grassland communities

Aims Species aggregation is commonly seen in plant communities and may increase diversity by causing intraspecific competition to exceed interspecific competition. One potential source of this spatial aggregation is seed dispersal but it is unclear to what extent aggregated seed distributions affect plant diversity in real communities. Using a field experiment, I tested whether uniform or aggregated seed arrival alters community structure and whether these effects vary with sowing density.Methods The experiment consisted of two spatial seeding treatments (uniform and aggregated) that were fully crossed with three seed density treatments. Sixty, 3 × 4-m plots were arrayed in a low-diversity grassland located in Kansas, USA. Each plot was divided into forty-eight, 0.5 × 0.5-m patches. For aggregated seeding treatments, each of the 15 species was sown into three randomly selected patches within the plot (3×15 = 45). To create a uniform species arrival but control for the seed addition method, all 15 species were sown into 45 individual patches (with three patches remaining unsown) within each plot. Seed mass for each species was held constant at the plot scale between uniform or aggregated treatments within a given level of the sowing density treatment. After two growing seasons, plant density was quantified for all sown species in 15 randomly selected patches from each plot.Important findings I found evidence for shifts in community structure in response to the different spatial seeding patterns. The evenness of added species was higher under aggregated than uniform sowing patterns. There was no detectable effect of aggregated seed sowing on species richness at 3.75 m 2 scale. However, when species richness was extrapolated to larger scales (11.25 m 2), aggregated sowing was predicted to have greater richness than uniform sowing. Effects of seed aggregation on community structure were apparent only at moderate to high sowing rates, yet the latter are within the range of measured seed dispersal in similar grasslands. Additionally, as sowing density increased, seed mass became an increasingly effective predictor of relative abundances for added species, but only under uniform sowing patterns supporting the idea that aggregated dispersal may buffer weaker (smaller seeded) species from competition during colonization. This is the first experiment to show that aggregated seed dispersal patterns can increase at least some components of plant diversity in undisturbed grasslands and suggests that previous seed dispersal experiments, which utilize uniform seed sowing, may underestimate the potential effect of dispersal on plant community structure.     

Colonization of novel White Sands habitat is associated with changes in lizard anti‐predator behaviour

Colonization of novel habitats is often associated with differences in ecological community composition. For small diurnal animals, differences in predator diversity and abundance can lead to behavioural shifts in the novel habitat. The eastern fence lizard Sceloporus undulatus (Bosc and Daudin, 1801) recently colonized the gypsum dunes of White Sands, a predator‐poor community relative to the predator‐rich community of the surrounding Chihuahuan dark‐soil habitat. We used field experiments to assess S. undulatus anti‐predator behaviour in white‐sand versus dark‐soil habitats, and used laboratory assays to determine whether behavioural differences could be mediated by hormonal regulation. Overall, we found that white‐sand lizards were less vigilant but more wary than their dark‐soil counterparts; it took them longer to detect a simulated predator, but once detected they were more likely to retreat from their perches than dark‐soil lizards. At the proximate level, differences in anti‐predator behaviour could not be explained by differences in plasma hormone levels (corticosterone and testosterone); we detected elevated corticosterone for lizards in our stress treatment relative to control treatment, but found no differences between habitats in baseline or acute corticosterone levels. At the evolutionary level, we suggest that differences in anti‐predator behaviour may be explained by differences across habitats in predation environment, habituation, and/or the cost of retreating. Our study implicates changes in predator community composition in mediating ecological divergence in behaviour. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 657–667.     

Validation of a DNA methylation reference panel for the estimation of nucleated cells types in cord blood

Cord blood is widely used as surrogate tissue in epigenome-wide association studies of prenatal conditions. Cell type composition variation across samples can be an important confounder of epigenome-wide association studies in blood that constitute a mixture of cells. We evaluated a newly developed cord blood reference panel to impute cell type composition from DNA methylation levels, including nucleated red blood cells (nRBCs). We estimated cell type composition from 154 unique cord blood samples with available DNA methylation data as well as direct measurements of nucleated cell types. We observed high correlations between the estimated and measured composition for nRBCs (r = 0.92, R² = 0.85), lymphocytes (r = 0.77, R² = 0.58), and granulocytes (r = 0.72, R² = 0.52), and a moderate correlation for monocytes (r = 0.51, R² = 0.25) as well as relatively low root mean square errors from the residuals ranging from 1.4 to 5.4%. These results validate the use of the cord blood reference panel and highlight its utility and limitations for epidemiological studies.     

In utero arsenic exposure and epigenome-wide associations in placenta,umbilical artery,and human umbilical vein endothelial cells

Exposure to arsenic early in life has been associated with increased risk of several chronic diseases and is believed to alter epigenetic programming in utero. In the present study, we evaluate the epigenome-wide association of arsenic exposure in utero and DNA methylation in placenta (n = 37), umbilical artery (n = 45) and human umbilical vein endothelial cells (HUVEC) (n = 52) in a birth cohort using the Infinium HumanMethylation450 BeadChip array. Unadjusted and cell mixture adjusted associations for each tissue were examined along with enrichment analyses relative to CpG island location and omnibus permutation tests of association among biological pathways. One CpG in artery (cg26587014) and 4 CpGs in placenta (cg12825509; cg20554753; cg23439277; cg21055948) reached a Bonferroni adjusted level of significance. Several CpGs were differentially methylated in artery and placenta when controlling the false discovery rate (q-value<0.05), but none in HUVEC. Enrichment of hypomethylated CpG islands was observed for artery while hypermethylation of open sea regions were present in placenta relative to prenatal arsenic exposure. The melanogenesis pathway was differentially methylated in artery (Max F P < 0.001), placenta (Max F P < 0.001), and HUVEC (Max F P = 0.02). Similarly, the insulin-signaling pathway was differentially methylated in artery (Max F P = 0.02), placenta (Max F P = 0.02), and HUVEC (Max F P = 0.02). Our results show that prenatal arsenic exposure can alter DNA methylation in artery and placenta but not in HUVEC. Further studies are needed to determine if these alterations in DNA methylation mediate the effect of prenatal arsenic exposure and health outcomes later in life.     

DNA methylation arrays as surrogate measures of cell mixture distribution

ABSTRACT: BACKGROUND: There has been a long-standing need in biomedical research for a method that quantifies the normally mixed composition of leukocytes beyond what is possible by simple histological or flow cytometric assessments. The latter is restricted by the labile nature of protein epitopes, requirements for cell processing, and timely cell analysis. In a diverse array of diseases and following numerous immune-toxic exposures, leukocyte composition will critically inform the underlying immuno-biology to most chronic medical conditions. Emerging research demonstrates that DNA methylation is responsible for cellular differentiation, and when measured in whole peripheral blood, serves to distinguish cancer cases from controls. RESULTS: Here we present a method, similar to regression calibration, for inferring changes in the distribution of white blood cells between different subpopulations (e.g. cases and controls) using DNA methylation signatures, in combination with a previously obtained external validation set consisting of signatures from purified leukocyte samples. We validate the fundamental idea in a cell mixture reconstruction experiment, then demonstrate our method on DNA methylation data sets from several studies, including data from a Head and Neck Squamous Cell Carcinoma (HNSCC) study and an ovarian cancer study. Our method produces results consistent with prior biological findings, thereby validating the approach. CONCLUSIONS: Our method, in combination with an appropriate external validation set, promises new opportunities for large-scale immunological studies of both disease states and noxious exposures.     

Decreases in activation energy and substrate affinity in cold-adapted A4-lactate dehydrogenase: evidence from the Antarctic notothenioid fish Chaenocephalus aceratus

Enzyme function is strongly affected by temperature, and orthologs from species adapted to different thermal environments often show temperature compensation in kinetic properties. Antarctic notothenioid fishes live in a habitat of constant, extreme cold (-1.86 +/- 2 degrees C), and orthologs of the enzyme A4-lactate dehydrogenase (A4-LDH) in these species have adapted to this environment through higher catalytic rates, lower Arrhenius activation energies (Ea), and increases in the apparent Michaelis constant for the substrate pyruvate (Km(PYR)). Here, site-directed mutagenesis was used to determine which amino acid substitutions found in A4-LDH of the notothenioid Chaenocephalus aceratus, with respect to orthologs from warm-adapted teleosts, are responsible for these adaptive changes in enzyme function. Km(PYR) was measured in eight single and two double mutants, and Ea was tested in five single and two double mutants in the temperature range 0 degrees C-20 degrees C. Of the four mutants that had an effect on these parameters, two increased Ea but did not affect Km(PYR) (Gly224Ser, Ala310Pro), and two increased both Ea and Km(PYR) (Glu233Met, Gln317Val). The double mutants Glu233Met/Ala310Pro and Glu233Met/Gln317Val increased Km(PYR) and Ea to levels not significantly different from the A4-LDH of a warm temperate fish (Gillichthys mirabilis, habitat temperature 10 degrees C-35 degrees C). The four single mutants are associated with two alpha-helices that move during the catalytic cycle; those that affect Ea but not Km(PYR) are further from the active site than those that affect both parameters. These results provide evidence that (1) cold adaptation in A4-LDH involves changes in mobility of catalytically important molecular structures; (2) these changes may alter activation energy alone or activation energy and substrate affinity together; and (3) the extent to which these parameters are affected may depend on the location of the substitutions within the mobile alpha-helices, perhaps due to differences in proximity to the active site.     

Early Jurassic gastropods from England

Abstract: Twenty‐five gastropod taxa are reported from the Early Jurassic (Hettangian to Toarcian) of England. Of these, 14 are identified to species level, and the remaining 11 are treated in open nomenclature. One genus (Lensataphrus) and six species are introduced as new. The new species are Lensataphrus tatei, Lensataphrus tenuis, Tricarilda toddi, Cylindrobullina dorsetensis, Cylindrobullina ventricosa and Consobrinella greeni. The following new combinations are introduced: Cassianopsis hebertana (d’Orbigny, 1852) for Neritopsis hebertana; Cryptaulax abscisum (Terquem and Piette, 1868) for Cerithium abscisum; and Cylindrobullina avena (Terquem, 1855) for Striactaeonina avena. Most of the genera and some of the species are also known from Central Europe (Germany and France). Typical vetigastropod genera that are present in England and Central Europe are Colpomphalus, Costataphrus, Ooliticia, Eucycloscala and Eucycloidea. The caenogastropod genera Levipleura and Cryptaulax are present in both regions, as are the heterobranchs Tricarilda and Cylindrobullina. The heterobranch genus Consobrinella is reported from England for the first time. Gastropods seem to follow the diversity trends of other marine invertebrates during the Early Jurassic. They diversify until the Late Pliensbachian but decrease sharply in number around the Pliensbachian–Toarcian boundary. This may reflect both regional anoxia and a global mass extinction event in the Early Toarcian.