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To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

The variability of branch-level hydraulic properties was assessed across 12 Scots pine populations covering a wide range of environmental conditions, including some of the southernmost populations of the species. The aims were to relate this variability to differences in climate, and to study the potential tradeoffs between traits. Traits measured included wood density, radial growth, xylem anatomy, sapwood- and leaf-specific hydraulic conductivity (K(S) and K(L)), vulnerability to embolism, leaf-to-sapwood area ratio (A(L) : A(S)), needle carbon isotope discrimination (delta 13C) and nitrogen content, and specific leaf area. Between-population variability was high for most of the hydraulic traits studied, but it was directly associated with climate dryness (defined as a combination of atmospheric moisture demand and availability) only for A(L) : A(S), K(L) and delta 13C. Shoot radial growth and A(L) : A(S) declined with stand development, which is consistent with a strategy to avoid exceedingly low water potentials as tree size increases. In addition, we did not find evidence at the intraspecific level of some associations between hydraulic traits that have been commonly reported across species. The adjustment of Scots pine's hydraulic system to local climatic conditions occurred primarily through modifications of A(L) : A(S) and direct stomatal control, whereas intraspecific variation in vulnerability to embolism and leaf physiology appears to be limited.

The current Coronavirus (COVID-19) pandemic has impacted and changed lives on a global scale since its emergence and spread from China in late 2019. It has caused millions of infections, and thousands of deaths worldwide. However, the control of this pandemic still remains unachievable in many African countries including Egypt and Nigeria, despite the application of some strict preventive and control measures. Therefore, this study assessed the knowledge, attitude, and perceptions of Egyptians and Nigerians towards the COVID-19 pandemic. This study was designed as a cross-sectional community-based questionnaire survey in both countries. Participants' demography, knowledge, attitude, and perceptions towards the COVID-19 outbreak were obtained using a convenience sampling technique. Data collected were subjected to descriptive statistics and logistic regression analysis. A total of 1437 respondents were included in this preliminary report. The mean knowledge score was 14.7±2.3. The majority of the respondents (61.6%) had a satisfactory knowledge of the disease. Age (18-39 years), education (College/bachelors), and background of respondents were factors influencing knowledge levels. The attitude of most respondents (68.9%) towards instituted preventive measures was satisfactory with an average attitude score of 6.9 ± 1.2. The majority of the respondents (96%) practiced self-isolation and socialdistancing but only 36% follow all health recommendations. The perception of most respondents (62.1%) on the global efforts at controlling the virus and preventing further spread was satisfactory with an average score of 10.9 ± 2.7. Only 22% of the respondents were satisfied with their country's handling of the pandemic. An apprehensive understanding of the current status in Africa through studies like KAP is crucial to avoid Africa being the next epicenter of the pandemic. For the populace to follow standard infection prevention and control

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, N e , increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of N e over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes.

To preserve natural ecosystems and their biodiversity, there is a need to anticipate future ecosystem changes through better understanding of underlying drivers and assembly processes determining community composition. Assembly processes can be understood as a set of filters acting at different spatio-temporal scales that jointly define the structure and composition of communities. Here, we explore the underlying assembly processes shaping marine fish species distribution and composition, using the heavily exploited North Sea. Our aims are to study 1) the relative importance of the different assembly processes shaping marine fish communities, 2) the key environmental drivers determining species distributions and composition, and to 3) quantify the role of traits in determining species niches and responses to the environment. Specifically, we fit a joint species distribution model (JSDM) using 31 years of standardized scientific bottom trawl survey data for 67 fish species. We use a set of environmental variables and species' traits representing morphology, life history, reproduction and diet, while also accounting for phylogenetic relationships of species. Environmental variables, primarily related to temperature, explained over one third of the variance in species occurrence, while spatial effects explained half of the variability across species. This shows that environmental filtering and spatially-structured processes are the main drivers shaping the community assembly. Furthermore, among the total variance of individual species occurrences, 12.5% could be explained by traits, which improve the mechanistic understanding on species responses to environmental change. Hence, model predictions from JSDMs accounting for traits, environmental niches and potential interactions among multiple species can provide relevant simulations and forecasts with the potential to inform spatial management and conservation efforts aiming to preserve biodiversity and its associated services vital for human well-being.

Cavitation resistance is a key parameter to understand tree drought tolerance but little is known about the mechanisms of air entry into xylem conduits. For conifers three mechanisms have been proposed: (1) a rupture of pit margo microfibrils, (2) a displacement of the pit torus from its normal sealing position over the pit aperture, and (3) a rupture of an air-water menisci in a pore of the pit margo. In this article, we report experimental results on three coniferous species suggesting additional mechanisms. First, when xylem segments were injected with a fluid at a pressure sufficient to aspirate pit tori and well above the pressure for cavitation induction we failed to detect the increase in sample conductance that should have been caused by torus displacement from blocking the pit aperture or by membrane rupture. Second, by injecting xylem samples with different surfactant solutions, we found a linear relation between sample vulnerability to cavitation and fluid surface tension. This suggests that cavitation in conifers could also be provoked by the capillary failure of an air-water meniscus in coherence with the prediction of Young-Laplace's equation. Within the bordered pit membrane, the exact position of this capillary seeding is unknown. The possible Achilles' heel could be the seal between tori and pit walls or holes in the torus. The mechanism of water-stress-induced cavitation in conifers could then be relatively similar to the one currently proposed for angiosperms.

1. Plants exhibit a wide variety in traits at different organizational levels. Intraspecific and interspecific studies have potential to demonstrate functional relationships and trade-offs amongst traits, with potential consequences for growth. However, the distinction between the correlative and functional nature of trait covariation presents a challenge because traits interact in complex ways. 2. We present an intraspecific study on Scots pine branches and use functional multi-trait concepts to organize and understand trait interactions and their impacts on growth. Branch-level traits were assessed for 97 branches from 12 Scots pine sites across Europe. 3. To test alternative hypotheses on cause-effect relationships between anatomical traits, hydraulic traits and branch growth, we measured for each branch: the tracheid hydraulic diameter, double cell wall thickness, cell lumen span area, wood density, cavitation vulnerability, wood-specific hydraulic conductivity, the leaf area to sapwood area ratio and branch growth. We used mixed linear effect models and path models to show how anatomical traits determine hydraulic traits and, in turn, how those traits influence growth. 4. Tracheid hydraulic diameter was the best predictor of cavitation vulnerability (R₂ = 0-09 explained by path model) and specific conductivity (R₂ = 0-19) amongst anatomical traits. Leaf area to sapwood area ratio had the strongest direct effect on branch growth (R₂ = 0-19) and was positively associated with the tracheid hydraulic diameter (R₂ = 0-22). A number of bivariate correlations between traits could be explained by these functional relationships amongst traits. 5. The plasticity in tracheid hydraulic diameter (10.0-15.1 um) and leaf area to sapwood area ratio (600-6051 cm₂ cm⁻₂) and the maintenance of a minimum leaf water potential (between -2 and -2.5 MPa) appear to drive the anatomical and hydraulic traits of Scots pine across Europe. These properties are major drivers of the functional trait network underlying the growth variation amongst pine branches and thus possibly contribute to the ecological success of pines at a local and continental scale.

Recent evidence of ion-mediated changes in pit membrane porosity suggests that plants may modulate the hydraulic conductance of their xylem conduits. Under the current paradigm, membrane porosity also determines conduit vulnerability to water stress-induced cavitation. Therefore, the hypothesis of an ion-mediated regulation of xylem vulnerability to cavitation in trees was tested. Segments of five Angiosperm and two Gymnosperm species were infiltrated with ultra-pure deionized water as a reference fluid or with a 50 mM KCl solution. KCl had a strong impact on segment conductance with either a positive or a negative effect across species. When 1 mM CaCl2 was added to the reference solution, the effect of KCl was minimized for most species. By contrast, segment vulnerability to cavitation was only slightly influenced by the presence of KCl in the solution. From this it was concluded that the mechanisms controlling pit membrane permeability to water flow and its resistance to the penetration of air bubbles are largely uncoupled, which suggests that the hypothesis of a porous structure of pit membranes should be revisited.