Indirect partitioning of soil respiration in a series of evergreen forest ecosystems

A simple estimation of heterotrophic respiration can be obtained analytically as the y-intercept of the linear regression between soil-surface CO₂ efflux and root biomass. In the present study, a development of this indirect methodology is presented by taking into consideration both the temporal variation and the spatial heterogeneity of heterotrophic respiration. For this purpose, soil CO₂ efflux, soil carbon content and main stand characteristics were estimated in seven evergreen forest ecosystems along an elevation gradient ranging from 250 to 1740 m. For each site and for each sampling date the measured soil CO₂ efflux (R _S) was predicted with the model R _S = a × S _C + b × R _D ± ε, where S _C is soil carbon content per unit area to a depth of 30 cm and R _D is the root density of the 2–5 mm root class. Regressions with statistically significant a and b coefficients allowed the indirect separation of the two components of soil CO₂ efflux. Considering that the different sampling dates were characterized by different soil temperature, it was possible to investigate the temporal and thermal dependency of autotrophic and heterotrophic respiration. It was estimated that annual autotrophic respiration accounts for 16–58% of total soil CO₂ efflux in the seven different evergreen ecosystems. In addition, our observations show a decrease of annual autotrophic respiration at increasing availability of soil nitrogen. Section Editor: A. Hodge     

First record of Pliensbachian (Lower Jurassic) amber and associated palynoflora from the Monti Lessini (northern Italy)

The fossil record of amber dates back to the Palaeozoic, but it is only since the Mesozoic that amber became relatively common, probably because of the spreading of resin-producing plants. In Italy, the oldest ambers come from the Middle and Upper Triassic of the Dolomites. Cretaceous ambers come from some Albian sites in the Dolomites and from the Coniacian–Santonian of Vernasso, Julian Prealps, northern Italy. Until now, no Jurassic sites with amber have been reported in Italy, and this “Jurassic gap” seems generalized, since there are only a few Jurassic ambers described all over the world. Here, we report the first finding of Lower Jurassic (Pliensbachian) amber from the Bellori locality (Grezzana, Verona Province, Northern Italy). The amber was found in two clayey-coal levels containing plant remains and cuticles, with subordinate bivalves, foraminifera and ostracods. Palynomorphs of the amber levels are dominated by levigate and ornamented spores (ferns) and Circumpolles (conifers). Foraminiferal linings and algal cysts are also present. The freshwater alga Pseudoschizaea is reported for the first time from the Lower Jurassic. The amber shows different kinds of preservation, some peculiar features probably connected with the plant structure, and colours ranging from light yellow to blackish red. Moreover, it includes millimetre-sized wood structures (“mummified wood”) and gas bubbles. Fourier-transform–Infrared, thermogravimetric and differential thermogravimetric analyses were carried out and resulted in a clear characterization of this amber with respect to all others known so far. These data, together with sedimentological observations and fossil content analysis, suggest a coastal palaeoenvironment under rather wet conditions, comparable with the present-day Everglades, with the addition of a monsoonal climate as in the modern southern Asia.     

Reproduction and condition of the scallop Adamussium colbecki (Smith 1902), the sea-urchin Sterechinus neumayeri (Meissner 1900) and the sea-star Odontaster validus Koehler 1911 at Terra Nova Bay (Ross Sea): different strategies related to inter-annual variations in food availability

Soft-bottom zoobenthic communities at Terra Nova Bay down to 100 m depth are mainly characterised by the presence of three species, generally occurring together and reaching high values of density: the scallop Adamussium colbecki (Smith 1902), the echinoid Sterechinus neumayeri (Meissner 1900) and the asteroid Odontaster validus Koehler 1911. These three species have a planktotrophic larval behaviour, but differ in terms of extent of gametogenic cycle and in feeding behaviour. The aim of this work is to give a first account of their reproductive conditions at Terra Nova Bay, comparing two following summer seasons, characterised by quite different ice-coverage and, consequently, food availability in the water column. The comparative analysis of the data evidences strong inter-annual differences in the scallop, a suspension-feeding species. In contrast, no significant changes were found in the two echinoderms, suggesting that a 2-year oogenic cycle, coupled with the opportunistic feeding behaviour, allow successful management of inter-annual shortcomings in food supply. On a latitudinal perspective, the comparison between data from McMurdo Sound and Terra Nova Bay shows small (for the echinoderms) or greater (for the scallop) geographical shifts in spawning occurrence.     

A mammalian functional nitrate reductase that regulates nitrite and nitric oxide homeostasis

Inorganic nitrite (NO(2)(-)) is emerging as a regulator of physiological functions and tissue responses to ischemia, whereas the more stable nitrate anion (NO(3)(-)) is generally considered to be biologically inert. Bacteria express nitrate reductases that produce nitrite, but mammals lack these specific enzymes. Here we report on nitrate reductase activity in rodent and human tissues that results in formation of nitrite and nitric oxide (NO) and is attenuated by the xanthine oxidoreductase inhibitor allopurinol. Nitrate administration to normoxic rats resulted in elevated levels of circulating nitrite that were again attenuated by allopurinol. Similar effects of nitrate were seen in endothelial NO synthase-deficient and germ-free mice, thereby excluding vascular NO synthase activation and bacteria as the source of nitrite. Nitrate pretreatment attenuated the increase in systemic blood pressure caused by NO synthase inhibition and enhanced blood flow during post-ischemic reperfusion. Our findings suggest a role for mammalian nitrate reduction in regulation of nitrite and NO homeostasis.     

Codominant water control on global interannual variability and trends in land surface phenology and greenness

Identifying the relative importance of climatic and other environmental controls on the interannual variability and trends in global land surface phenology and greenness is challenging. Firstly, quantifications of land surface phenology and greenness dynamics are impaired by differences between satellite data sets and phenology detection methods. Secondly, dynamic global vegetation models (DGVMs) that can be used to diagnose controls still reveal structural limitations and contrasting sensitivities to environmental drivers. Thus, we assessed the performance of a new developed phenology module within the LPJmL (Lund–Potsdam–Jena managed Lands) DGVM with a comprehensive ensemble of three satellite data sets of vegetation greenness and ten phenology detection methods, thereby thoroughly accounting for observational uncertainties. The improved and tested model allows us quantifying the relative importance of environmental controls on interannual variability and trends of land surface phenology and greenness at regional and global scales. We found that start of growing season interannual variability and trends are in addition to cold temperature mainly controlled by incoming radiation and water availability in temperate and boreal forests. Warming‐induced prolongations of the growing season in high latitudes are dampened by a limited availability of light. For peak greenness, interannual variability and trends are dominantly controlled by water availability and land‐use and land‐cover change (LULCC) in all regions. Stronger greening trends in boreal forests of Siberia than in North America are associated with a stronger increase in water availability from melting permafrost soils. Our findings emphasize that in addition to cold temperatures, water availability is a codominant control for start of growing season and peak greenness trends at the global scale.     

COPD patients with chronic bronchitis and higher sputum eosinophil counts show increased type-2 and PDE4 gene expression in sputum

Chronic obstructive pulmonary disease (COPD) patients with higher eosinophil counts are associated with increased clinical response to phosphodiesterase-4-inhibitors (PDE4i). However, the underlying inflammatory mechanisms associated with this increased response is not yet elucidated. This post hoc analysis focused on sputum gene expression in patients with chronic bronchitis who underwent 32-day treatment with two doses of the inhaled PDE4i CHF6001 (tanimilast) or placebo on top of triple therapy. Biological characterization and treatment effects were assessed between patients with different sputum eosinophil levels (eosinophil^high ≥ 3%; eosinophil^low < 3%) at baseline (primary samples) or at the end of the treatment of the placebo arm (validation samples). Forty-one genes were differentially expressed in primary samples (p-adjusted for false discovery rate < 0.05); all up-regulated in eosinophil^high patients and functionally enriched for type-2 and PDE4 inflammatory processes. Eleven out of nineteen genes having immune system biological processes annotations including IL5RA, ALOX15, IL1RL1, CLC, GATA1 and PDE4D were replicated using validation samples. The expression of a number of these inflammatory mediators was reduced by tanimilast treatment, with greater effects observed in eosinophil^high patients. These findings suggest that type-2 and PDE4 overexpression in COPD patients with higher sputum eosinophil counts contribute to the differential clinical response to PDE4i observed in previous clinical trials.     

A fuzzy anomaly indicator for environmental monitoring at continental scale

Environmental status assessment and monitoring can be performed by the integration of multi-source datasets at continental and global scales. We propose a methodology for the development of a new anomaly indicator (AI) which can highlight the occurrence of anomalous conditions in a synthetic fashion by analysis of a set of spatial input data. Anomalous conditions are defined relative to long-term average assumed as normal or reference status of the vegetated land surface. The indicator is defined according to fuzzy set theory which is a powerful means of handling uncertain and imprecise knowledge of environmental systems. The indicator integrates, in an innovative way, the anomaly scores of a set of contributing factors extracted from the analysis of historical time series, mainly of Earth observations data. These time series are used to automatically derive the fuzzy membership functions that quantify the contribution of each factor to the final indicator. No reference data and expert knowledge are strictly required for the implementation of the AI although the methodology allows customization where this type of information is available. The method was tested over the African continent for the period 1996–2002; monthly AI values were derived with input datasets of vegetation phenology and rainfall estimates. The output AI continental maps bring new information by integrating multiple factors and they highlight patterns of anomalous conditions of the status of the environment. The analysis of the correlation with the El Niño Southern Oscillation (ENSO) shows that the AI is able to identify the effects of this phenomenon and its spatio-temporal dynamics. The 1997–1998 and 2000–2001 ENSO events are clearly highlighted by the highest AI values in specific regions of the continent. The indicator proposed is a valuable tool which can help guide in depth and detailed investigations of environmental conditions at local scale.     

BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

Affinity capture of DNA methylation combined with high-throughput sequencing strikes a good balance between the high cost of whole genome bisulfite sequencing and the low coverage of methylation arrays. We present BayMeth, an empirical Bayes approach that uses a fully methylated control sample to transform observed read counts into regional methylation levels. In our model, inefficient capture can readily be distinguished from low methylation levels. BayMeth improves on existing methods, allows explicit modeling of copy number variation, and offers computationally efficient analytical mean and variance estimators. BayMeth is available in the Repitools Bioconductor package.     

Complex adjustments of photosynthetic potentials and internal diffusion conductance to current and previous light availabilities and leaf age in Mediterranean evergreen species Quercus ilex

Mature non-senescent leaves of evergreen species become gradually shaded as new foliage develops and canopy expands, but the interactive effects of integrated light during leaf formation (Q(int)G), current light (Q(int)C) and leaf age on foliage photosynthetic competence are poorly understood. In Quercus ilex L., we measured the responses of leaf structural and physiological variables to Q(int)C and Q(int)G for four leaf age classes. Leaf aging resulted in increases in leaf dry mass per unit area (M(A)), and leaf dry to fresh mass ratio (D(F)) and decreases in N content per dry mass (N(M)). N content per area (N(A)) was independent of age, indicating that decreases in N(M) reflected dilution of leaf N because of accumulation of dry mass (NA = N(M) M(A)). M(A), D(F) and N(A) scaled positively with irradiance, whereas these age-specific correlations were stronger with leaf growth light than with current leaf light. Area-based maximum ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) carboxylase activity (V(cmax)A), capacity for photosynthetic electron transport (J(max)A) and the rate of non-photorespiratory respiration in light (R(d)A) were also positively associated with irradiance. Differently from leaf structural characteristics, for all data pooled, these relationships were stronger with current light with little differences among leaves of different age. Acclimation to current leaf light environment was achieved by light-dependent partitioning of N in rate-limiting proteins. Mass-based physiological activities decreased with increasing leaf age, reflecting dilution of leaf N and a larger fraction of non-photosynthetic N in older leaves. This resulted in age-dependent modification of leaf photosynthetic potentials versus N relationships. Internal diffusion conductance (g(m)) per unit area (g(m)A) increased curvilinearly with increasing irradiance for two youngest leaf age classes and was independent of light for older leaves. In contrast, g(m) per dry mass (g(m)M) was negatively associated with light in current-year leaves. Greater photosynthetic potentials and moderate changes in diffusion conductance resulted in greater internal diffusion limitations of photosynthesis in higher light. Both area- and mass-based g(m) decreased with increasing leaf age. The decrease in diffusion conductance was larger than changes in photosynthetic potentials, leading to larger CO2 drawdown from leaf internal air space to chloroplasts (delta(c)) in older leaves. The increases in diffusion limitations in older leaves and at higher light scaled with age- and light-dependent increases in MA and D(F). Overall, our study demonstrates a large potential of foliage photosynthetic acclimation to changes in leaf light environment, but also highlights enhanced structural diffusion limitations in older leaves that result from leaf structural acclimation to previous rather than to current light environment and accumulation of structural compounds with leaf age.