Ancient biomolecules from deep ice cores reveal a forested southern Greenland

It is difficult to obtain fossil data from the 10% of Earth's terrestrial surface that is covered by thick glaciers and ice sheets, and hence, knowledge of the paleoenvironments of these regions has remained limited. We show that DNA and amino acids from buried organisms can be recovered from the basal sections of deep ice cores, enabling reconstructions of past flora and fauna. We show that high-altitude southern Greenland, currently lying below more than 2 kilometers of ice, was inhabited by a diverse array of conifer trees and insects within the past million years. The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections.     

Weak northern and strong tropical land carbon uptake from vertical profiles of atmospheric CO2

Measurements of midday vertical atmospheric CO2 distributions reveal annual-mean vertical CO2 gradients that are inconsistent with atmospheric models that estimate a large transfer of terrestrial carbon from tropical to northern latitudes. The three models that most closely reproduce the observed annual-mean vertical CO2 gradients estimate weaker northern uptake of -1.5 petagrams of carbon per year (Pg C year(-1)) and weaker tropical emission of +0.1 Pg C year(-1) compared with previous consensus estimates of -2.4 and +1.8 Pg C year(-1), respectively. This suggests that northern terrestrial uptake of industrial CO2 emissions plays a smaller role than previously thought and that, after subtracting land-use emissions, tropical ecosystems may currently be strong sinks for CO2.     

Structural basis of transcription: separation of RNA from DNA by RNA polymerase II

The structure of an RNA polymerase II-transcribing complex has been determined in the posttranslocation state, with a vacancy at the growing end of the RNA-DNA hybrid helix. At the opposite end of the hybrid helix, the RNA separates from the template DNA. This separation of nucleic acid strands is brought about by interaction with a set of proteins loops in a strand/loop network. Formation of the network must occur in the transition from abortive initiation to promoter escape.     

Opaline sediments of the southeastern coastal plain and horizon a: biogenic origin

Scanning electron microscope techniques show that Eocene opaline claystones (fuller's earth and buhrstone) of the Atlantic and Gulf Coastal Plain, deposits long considered volcanic in origin, are actually highly altered diatomites formed as transgressive facies in normal marine continental shelf environmnents. These findings are in agreement with a biogenic origin for time-equivalent horizon A and A deep-sea cherts of the North Atlantic and Caribbean.     

Phytoalexins from the Vitaceae: biosynthesis, phytoalexin gene expression in transgenic plants, antifungal activity, and metabolism

Resistance of plants to infection by phytopathogenic microorganisms is the result of multiple defense reactions comprising both constitutive and inducible barriers. In grapevine, the most frequently observed and best characterized defense mechanisms are the accumulation of phytoalexins and the synthesis of PR-proteins. Particular attention has been given here to stilbene phytoalexins produced by Vitaceae, specifically, their pathway of biosynthesis (including stilbene phytoalexin gene transfer experiments to other plants) and their biological activity together with fungal metabolism.     

Efficient profile-likelihood confidence intervals for capture-recapture models

In a capture-recapture analysis, uncertainty in the parameter estimates is usually expressed by presenting classical Wald-type confidence intervals. This approach involves (1) the assumption that the maximum likelihood estimates are asymptotically normal and (2) numerical computation of the variance-covariance matrix of these estimates. When the sample size is small or when the estimates are on the boundary of their domain, a Wald confidence interval often performs badly. A natural alternative is to use profile-likelihood confidence intervals. In general, these intervals require a greater amount of computation. We propose a new implementation of this approach that is efficient, both in reducing the amount of computation and in coping with boundary estimates. We also show how profile-likelihood confidence intervals can be adjusted for overdispersion. Simulations were used to check whether nominal coverage levels were attained, and allowed us to compare this approach with the classical Wald procedure. We illustrate this work by considering a multi-state model for a sooty shearwater (Puffinus griseus) population.     

The abundance of heterocystous blue-green algae in rice soils and inocula used for application in rice fields

Summary Algal populations were quantified (as colony-forming units [CFU] per square centimetre) in 102 samples of rice soils from the Philippines, India, Malaysia and Portugal, and in 22 samples of soil-based inocula from four countries. Heterocystous blue-green algae (BGA) were present in all samples. Nostoc was the dominant genus in most samples, followed by Anabaena and Calothrix. In soils, heterocystous BGA occurred at densities ranging from 1.0 × 10² to 8.0 × 10⁶ CFU/cm² (median 6.4 × 10⁴) and comprised, on average, 9% of the total CFU of algae. Their abundance was positively correlated with the pH and the available P content of the soils. In soil-based inocula, heterocystous BGA occurred at densities ranging from 4.6 × 10⁴ to 2.8 × 10⁷ CFU/g dw (dry weight), comprising only a moderate fraction (average 13%) of the total algae. In most soils, the density of indigenous N₂-fixing BGA was usually higher than that attained by applying recommended rates of soil-based inoculum. Whereas research on the practical utilization of BGA has been mostly directed towards inoculation with foreign strains, our results suggest that attention should also be given to agricultural practices that enhance the growth of indigenous strains already adapted to local environmental conditions.Maître de Recherches ORSTOM (France), Visiting Scientist at IRRI     

Alteration of soil microbial communities and water quality in restored wetlands

Land usage is a strong determinant of soil microbial community composition and activity, which in turn determine organic matter decomposition rates and decomposition products in soils. Microbial communities in permanently flooded wetlands, such as those created by wetland restoration on Sacramento-San Joaquin Delta islands in California, function under restricted aeration conditions that result in increasing anaerobiosis with depth. It was hypothesized that the change from agricultural management to permanently flooded wetland would alter microbial community composition, increase the amount and reactivity of dissolved organic carbon (DOC) compounds in Delta waters; and have a predominant impact on microbial communities as compared with the effects of other environmental factors including soil type and agricultural management. Based on phospholipid fatty acid (PLFA) analysis, active microbial communities of the restored wetlands were changed significantly from those of the agricultural fields, and wetland microbial communities varied widely with soil depth. The relative abundance of monounsaturated fatty acids decreased with increasing soil depth in both wetland and agricultural profiles, whereas branched fatty acids were relatively more abundant at all soil depths in wetlands as compared to agricultural fields. Decomposition conditions were linked to DOC quantity and quality using fatty acid functional groups to conclude that restricted aeration conditions found in the wetlands were strongly related to production of reactive carbon compounds. But current vegetation may have had an equally important role in determining DOC quality in restored wetlands. In a larger scale analysis, that included data from wetland and agricultural sites on Delta islands and data from two previous studies from the Sacramento Valley, an aeration gradient was defined as the predominant determinant of active microbial communities across soil types and land usage.     

Wandering spiders limit densities of a major microbi-detritivore in the forest-floor food web

In a long-term field experiment, densities of wandering spiders (i.e. species that do not build webs to capture prey) were reduced in order to determine whether or not a major group of microbi-detritivores, the Collembola (springtails), would increase in response to lowered spider predation. Thirty 4-m² fenced plots (15 spider-removal, 15 control plots) and 15 unfenced, undisturbed reference areas were established in a deciduous forest. Spiders were taken from the removal-treatment after being collected by periodic trapping with pitfall traps that contained no preservative, and by searching the litter surface. Judging from a comparison of the numbers captured during periodic censuses in spider-removal and control plots (one census period was two consecutive days of pitfall trapping), wandering spiders were rapidly reduced by ca. 50% and were maintained at levels lower than control plots for 1.3 years. The reduction in numbers was greatest for wolf spiders (Lycosidae; ≈90%). Of six families of Collembola abundant in the leaf litter during the experiment, one family, the Tomoceridae, exhibited a significant release from spider predation. Densities of tomocerids, which are the largest and most active springtails on the research site, gradually increased until they were consistently 2× higher in the spider-removal treatment than in either fenced control plots or unfenced, open reference areas.