Microbial community development and unseen diversity recovery in inoculated sterile soil

Soil is considered as one of the most biodiverse environments on Earth; yet, the taxonomy, occurrence, and role of its different microbial populations are largely unknown. Here, two sterilized soils (from England and Italy) were inoculated with a subsample of their initial microbial communities and/or those from the other soil to study their microbial community evolution. This approach compared two driving factors (original community and soil physico-chemical characteristics) for microbial community definition. After 2 months of incubation and based on metagenomic datasets, the two inoculated communities (from an English grassland and an Italian forest) possessed similar functional and taxonomical structures when inoculated in the same sterile soil. For example, the newly colonized Italian soil was dominated by Actinobacteria related organisms (>66 % of the detected community) with a functional distribution independent of the inoculated soil origin. In addition, some of the organisms that dominated the different inoculated communities after 2 months were similar for a given sterile soil whether they came from the English grassland or the Italian forest, and they had not been detected in the original microbial community from either soil. Thus, similar microorganisms with low representation from the two distinct communities emerged in each sterilized soil, thus increasing the microbial diversity recovered from the microbial community of the donor soil. So far, these observations support the idea that different temperate soil microbial communities have different evenness due to environmental physico-chemical variations, yet have similar community composition (richness), and thus develop similarly when colonizing the same habitat.     

A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield

The HIV envelope (Env) protein gp120 is protected from antibody recognition by a dense glycan shield. However, several of the recently identified PGT broadly neutralizing antibodies appear to interact directly with the HIV glycan coat. Crystal structures of antigen-binding fragments (Fabs) PGT 127 and 128 with Man(9) at 1.65 and 1.29 angstrom resolution, respectively, and glycan binding data delineate a specific high mannose-binding site. Fab PGT 128 complexed with a fully glycosylated gp120 outer domain at 3.25 angstroms reveals that the antibody penetrates the glycan shield and recognizes two conserved glycans as well as a short β-strand segment of the gp120 V3 loop, accounting for its high binding affinity and broad specificity. Furthermore, our data suggest that the high neutralization potency of PGT 127 and 128 immunoglobulin Gs may be mediated by cross-linking Env trimers on the viral surface.     

A supershear transition mechanism for cracks

Seismic data indicate that fault ruptures follow complicated paths with variable velocity because of inhomogeneities in initial stress or fracture energy. We report a phenomenon unique to three-dimensional cracks: Locally stronger fault sections, rather than slowing ruptures, drive them forward at velocities exceeding the shear wave speed. This supershear mechanism differentiates barrier and asperity models of fault heterogeneity, which previously have been regarded as indistinguishable. High strength barriers concentrate energy, producing potentially destructive pulses of strong ground motion.     

A sensitive real-time PCR assay for the detection of the two Melampsora medusae formae speciales on infected poplar leaves

Melampsora medusae is a quarantine fungus in the European Union (EU) that causes a damaging leaf rust disease on poplars. Two formae speciales of the pathogen can be distinguished, M. medusae f. sp. deltoidae and M. medusae f. sp. tremuloidae, but the EU plant health directive 2000/29/EC currently in force does not make the distinction between them. EU countries must have the ability to detect and identify rapidly the introduction of these quarantine fungi and to conduct extensive surveys in case of outbreaks. Efficient detection tools are thus needed. In this study, a sensitive real-time PCR assay was developed to detect the presence of M. medusae in poplar leaf samples. A unique primer/hydrolysis probe combination targeting both formae speciales was designed using species-specific polymorphisms observed within the internal transcribed spacer region. An additional primer/hydrolysis probe combination was designed from a region of the 28S rDNA that is highly conserved in the genus Melampsora and used in a separate real-time PCR assay in order to check the quality of the DNA extracted from Melampsora urediniospores. The test developed demonstrated a high sensitivity since it enables the reproducible detection of two M. medusae urediniospore in a mixture of 2 mg of urediniospores (ca 800 000 urediniospores) of other Melampsora species. This new real-time PCR tool should be useful for laboratories in charge of official analyses since it has many advantages over the techniques currently used to monitor this quarantine pathogen in Europe.     

Canopy Uptake of 15NH3 by Four Temperate Tree Species and the Interaction with Leaf Properties

Tree canopies are believed to act as a sink of atmospheric ammonia (NH₃). However, few studies have compared the uptake efficiency of different tree species. This study assessed the uptake of ¹⁵N-labelled NH₃ at 5, 20, 50 and 100?ppb_v by leaves and twigs of potted silver birch, European beech, pedunculate oak and Scots pine saplings in June, August and September 2008. Additionally, foliar uptake of ¹³C-labelled carbon dioxide (¹³CO₂) and leaf stomatal characteristics were determined per species and treatment date and the relation with ¹⁵NH₃ uptake and estimated stomatal ¹⁵NH₃ uptake were assessed. Both ¹⁵NH₃ and ¹³CO₂ uptake were affected by tree species and treatment date, but only ¹⁵NH₃ uptake was influenced by the applied NH₃ concentration. Depending on the treatment date, ¹⁵NH₃ uptake by leaves and twigs was highest at 5 (September), 20 (June) or 50 (August) ppb_v. Birch, beech and oak leaves showed the highest uptake in August, while for pine needles this was in June and, except at 5?ppb_v in June, the ¹⁵NH₃ uptake was always higher for the deciduous species than for pine. For all species except beech ¹³CO₂ uptake was highest in August and on every treatment date the ¹³CO₂ uptake by leaves of deciduous species was significantly higher than by pine needles. Leaf characteristics and ¹³CO₂ uptake did not provide a strong explanation for the observed differences in ¹⁵NH₃ uptake. This study shows that on the short-term a high interspecific variability exists in NH₃ uptake, which depends on the time in the growing season.     

A comparative review of fisheries management experiences in the European Union and in other countries worldwide: Iceland,Australia, and New Zealand

This study compares the details and performance of fisheries management between the EU and a selection of other countries worldwide: Iceland, New Zealand, and Australia, which are considered in many respects to be among the most advanced in the world in fisheries management. Fisheries management in the EU, Iceland, Australia, and New Zealand has developed following different paths, despite being based on similar instruments and principles. Iceland, Australia, and New Zealand have been at the forefront of developing management practices such as stakeholder involvement, legally binding management targets (Australia, New Zealand), individual transferable quotas, and discard bans (Iceland, New Zealand). The EU has since the beginning of the 21st century taken significant steps to better involve stakeholders and establish quantitative targets through management plans, and a landing obligation is gradually being implemented from 2015 onward. The management of domestic fisheries resources in Australia, New Zealand, and Iceland has, overall, performed better than in the EU, in terms of conservation and economic efficiency. It should, however, be stressed that, compared to Australia, New Zealand, and Iceland, (i) initial over‐capacity was more of an issue in the EU when management measures became legally binding and also that (ii) EU has been progressive in developing common enforcement standards, on stocks shared by sovereign nations. The situation of EU fisheries has substantially improved over the period 2004–2013 in the northeast Atlantic, with fishery status getting close to that in the other jurisdictions, but the lack of recovery for Mediterranean fish stocks remains a concern.     

Phosphorus use efficiency of improved faba bean (Vicia faba) varieties in low‐input agro‐ecosystems

The use of phosphorus (P)‐efficient legumes is a prerequisite for sustainable intensification of low‐input agro‐ecosystems. A study was undertaken in a farmer's field in the tropical highlands of Ethiopia to assess the agronomic performance, P acquisition efficiency (PAE), and P utilization efficiency (PUE) of six improved faba bean varieties (Vicia faba L. var. CS‐20DK, Degaga, Gebelcho, Moti, Obse, Walki) without and with P application. Varieties showed significant variations in PUE, but P application had no significant effect on PUE. Variety Moti demonstrated highest PUE of 272 kg grain kg^?1 P, which was 1.6‐fold higher than the lowest PUE (164 kg grain kg^?1 P) of Gebelcho. PUE was significantly and positively correlated with grain yield (r = 0.542) and negatively correlated with shoot PAE (r = –0.541), indicating that PUE is important for grain yield. The results demonstrate that variations in grain and biomass yield of faba beans were largely due to differences in PUE and not due to PAE. Therefore, we argue that genetic resources of faba bean varieties showing optimal agronomic performance and high PUE in low‐input agro‐ecosystems should be better explored. Introduction of such varieties in low‐input cereal‐based cropping systems could improve and enhance P use efficiency at the system level.     

Effects of groundcover management on soil properties, tree physiology, foliar chemistry and growth in a newly established Fraser fir (Abies fraseri [Pursh] Poir) plantation in Michigan, United States of America

Incorporating cover crops into Christmas tree plantations may potentially improve soil fertility, tree growth and quality and be an alternative to commercial nitrogen (N) fertilizers. However, cover crops may compete with the trees for water and other nutrients than N. This study was carried out to assess whether soil fertility, tree survival and growth could be improved by incorporating leguminous and non-leguminous cover crops into the Fraser fir (Abies fraseri) production system. Dutch white clover (Trifolium pratense), alfalfa (Medicago sativa) and perennial ryegrass (Lolium perenne) were grown in a newly established Fraser fir plantation using two cover crop management practices; no banding (NB) by growing each cover crop throughout the entire plot and banding (B) by creating a 61 cm-wide bare zone centered on the tree rows. A conventionally-managed system (CONV) was used as a control. The cover crop aboveground biomass and N content were assessed. Soil available N (NO₃ ⁻ and NH₄ ⁺) and N mineralization were measured at 0–15, 15–30 and 30–45 cm soil depths. Tree survival, growth, photochemical efficiency of photosystem II (F_v/F_m), branch water potential (Ψ_w) and foliar nutrients were also evaluated. Biomass production was as high as 13.9, 10.2 and 5.9 Mg DM ha⁻¹ year⁻¹ for clover, alfalfa and ryegrass, respectively. Cover cropping increased soil available N by 1.5- and 2.2-fold relative the CONV in the top soil layer in 2007 and 2008, respectively. Tree seedling survival and growth in the B and CONV systems were similar. In contrast, NB treatments resulted in poor seedling survival and growth relative to the B and CONV plots. Plant Ψ_w and F_v/F_m decreased significantly for A. fraseri seedlings on the NB treatments relative to their counterparts on the B and CONV plots. However, cover cropping had marginal effects on foliar nutrients. Cover cropping with banding can be an efficient strategy for maintaining productivity in Fraser fir Christmas plantations.     

Model performance of tree height-diameter relationships in the central Congo Basin

Key message

Tree heights in the central Congo Basin are overestimated using best-available height-diameter models. These errors are propagated into the estimation of aboveground biomass and canopy height, causing significant bias when used for calibration of remote sensing products in this region.

Context

Tree height-diameter models are important components of estimating aboveground biomass (AGB) and calibrating remote sensing products in tropical forests.

Aims

For a data-poor area of the central Congo Basin, we quantified height-diameter model performance of local, regional and pan-tropical models for their use in estimating AGB and canopy height.

Methods

At three old-growth forest sites, we assessed the bias introduced in height estimation by regional and pan-tropical height-diameter models. We developed an optimal local model with site-level randomizations accounted for by using a mixed-effects modeling approach. We quantified the error propagation of modeled heights for estimating AGB and canopy height.

Results

Regional and pan-tropical height-diameter models produced a significant overestimation in tree height, propagating into significant overestimations of AGB and Lorey’s height. The pan-tropical model accounting for climatic drivers performed better than the regional models. We present a local height-diameter model which produced nonsignificant errors for AGB and canopy height estimations at our study area.

Conclusion

The application of general models at our study area introduced bias in tree height estimations and the derived stand-level variables. Improved delimitation of regions in tropical Africa with similar forest structure is needed to produce models fit for calibrating remote sensing products.

     

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.