Implementing Green Infrastructure for the Spatial Planning of Peri-Urban Areas in Geneva, Switzerland

The concept of green infrastructure (GI) seeks to identify and prioritize areas of high ecological value for wildlife and people, to improve the integration of natural values in landscape planning decisions. In 2018, the canton of Geneva, Switzerland, established a roadmap for biodiversity conservation, which includes the operationalization of GI covering 30% of the territory by 2030. In this paper, we demonstrate a GI mapping framework in the canton of Geneva. Our approach is based on the combined assessment of three 'pillars', namely species' distribution, landscape structure and connectivity, and ecosystem services, to optimize the allocation of conservation actions using the spatial prioritization software, Zonation. The identified priority conservation areas closely overlap existing natural reserves. Including the three pillars in the landscape prioritization should also improve adhesion to the GI idea, without undermining the protection of threatened species. With regards to land use planning, public and private land parcels with high values for GI may require specific incentives to maintain their desirable characteristics, as they are more likely to be degraded than areas with more building restrictions. Visualizing priority conservation areas in a spatially explicit manner will support decision-makers in Geneva to optimally allocate limited resources for ecosystem preservation.Peer reviewe

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

Background Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome. Findings Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. Ab initio gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development, and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20-30% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed inPeer reviewe

Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing

BACKGROUND Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS). RESULTS We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently. CONCLUSION Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define

Quantifying the contributions of native and non-native trees to a city’s biodiversity and ecosystem services

Urban trees are appreciated for their intrinsic value and their contributions to human well-being. Here, we analysed a database of 115′686 non-forest trees (1’025 species) to quantify the present contributions of native and non-native trees to biodiversity (taxonomic richness) in the metropolitan area of Geneva, Switzerland. Non-native trees made up 90 % of species and 40 % of individuals. A subset of these individuals with more detailed phenotypic information (N = 50’718 trees; 527 species) was used to quantify five regulating ecosystem services (micro-particle capture, carbon sequestration, water interception, microclimatic cooling, and support for pollinators), three cultural ecosystem services (natural heritage, recreational, and aesthetic value) and two disservices (allergies and biological invasiveness). Non-native and native trees generated roughly identical regulating services, on a per-tree basis, as these are linked primarily to tree morphology rather than to tree-origin. Non-native trees generated cultural ecosystem services that were greater than native trees, on a per-tree basis, with the exception of the notion of “natural heritage”. For example, 79 % (163/207) of trees independently identified as “remarkable” by the canton of Geneva were non-native. Our results illustrate that non-native trees represent a significant source of biodiversity and ecosystem services both in absolute terms and on a per-tree basis. Given the empirical importance of non-native trees in many cities, and the likelihood that their importance will increase with future climate change, we suggest that non-native trees be considered in conservation assessments and strategic planning both for intrinsic reasons and for their contributions to human well-being

Established and potential predictors of blood loss during lung transplant surgery

Lung transplantation is an established therapeutic procedure for end stage lung diseases. Its success may be impaired by perioperative complications. Intraoperative blood loss and the resulting blood transfusion are among the most common complications. The various factors contributing to increased blood loss during lung transplantation are only scarcely investigated and not yet completely understood. This is in sharp contrast to other surgical fields, as in orthopedic surgery, liver transplantation and cardiac surgery the contributors to blood loss are well identified. This narrative review article aims to highlight the acknowledged factors influencing blood loss in lung transplantation (such as double vs. single lung transplant) and to discuss potential factors that may be of interest for further research or helpful to develop strategies targeting risk factors in order to minimize blood loss during lung transplantation and finally improve patient outcome

Earthworms as ecosystem engineers ::a review

The concept of ecosystem engineering has emerged decades ago and highlights the direct or indirect modulation of available resources by organisms through their biological activities. Ecosystem engineers create biogenic structures (aggregates, burrows) that may serve as habitats for other species than themselves. This chapter aims at overviewing the key role played by earthworms as ecosystem engineers through their bioturbation activities involving soil mixing as well as their influence on the decomposition and mineralization of litter by breaking down organic matter, and their influence on the gas and water exchange or nutrient transfer in the soil. Focus is made on the engineering processes and especially the formation of biogenic structures in relation to soil structure (burrows, casts) in the framework of soil function interactions, particularly in the drilosphere. Special attention is paid to soil aggregates’ fabric and new tools that may help to discriminate their origin. Finally, management and ecosystem engineer’s future challenges will be highlighted regarding soil ecosystem services in the context of ecosystem restoration

Earthworms, plants, and Soils

The importance of engineers is increasingly recognized in soil science because of their implication in most important pedological processes. Furthermore, they contribute to ecological functions provided by soils in both natural and human-modified environments. In this review, we focus on the role of two ecosystem engineers: (1) plants, their root system, and associated microorganisms and (2) earthworms. First, we explain why they are considered as major soil engineers, and which variables (texture, porosity, nutrient, and moisture dynamics) control their activities in space and time (hotspots and hot moments). Then, their roles in three processes of soil formation are reviewed, namely, rock and mineral weathering, soil structure (formation, stabilization, and disintegration), and bioturbation. For each of them, the involved mechanisms that occur at different spatial scales (from local to landscape) are presented. On one hand, tree uprooting plays a key role in rock weathering and soil profile bioturbation. In addition, living and dead roots also contribute to rock alteration and aggregation. On the other hand, earthworms are mainly involved in the formation of aggregates and burrows through their bioturbation activities and to a less extent in weathering processes. The long-term effects of such mechanisms on soil heterogeneity, soil development, and pathways of pedogenesis are discussed. Finally, we show how these two main ecosystem engineers contribute to provisioning and regulating services. Through their physical activities of burrowing and soil aggregation, earthworms and plants increase plant productivity, water infiltration, and climate warming mitigation. They act as catalysts and provide, transform, and translocate organic matter and nutrients throughout the soil profile. Finally, due to inter- and intraspecific interactions and/or symbiosis with microorganisms (arbuscular fungi, bacteria), they enhance soil fertility, decrease parasitic action, and bioremediate some pollutants. Future research is, however, still needed for a better understanding of the relationships between adequate soil management, agricultural practices, and soil biota in a perspective of relevant maintenance and durability of ecological services

Earthworms as ecosystem engineers : a review

The concept of ecosystem engineering has emerged decades ago and highlights the direct or indirect modulation of available resources by organisms through their biological activities. Ecosystem engineers create biogenic structures (aggregates, burrows) that may serve as habitats for other species than themselves. This chapter aims at overviewing the key role played by earthworms as ecosystem engineers through their bioturbation activities involving soil mixing as well as their influence on the decomposition and mineralization of litter by breaking down organic matter, and their influence on the gas and water exchange or nutrient transfer in the soil. Focus is made on the engineering processes and especially the formation of biogenic structures in relation to soil structure (burrows, casts) in the framework of soil function interactions, particularly in the drilosphere. Special attention is paid to soil aggregates’ fabric and new tools that may help to discriminate their origin. Finally, management and ecosystem engineer’s future challenges will be highlighted regarding soil ecosystem services in the context of ecosystem restoration

Composition and superposition of alluvial deposits drive macro-biological soil engineering and organic matter dynamics in floodplains

(IF 4.34 [2018]; Q1)International audienceSoil structure formation in alluvial soils is a fundamental process in near-natural floodplains. A stable soil structure is essential for many ecosystem services and helps to prevent river bank erosion. Plants and earthworms are successful soil engineering organisms that improve the soil structural stability through the incorporation of mineral and organic matter into soil aggregates. However, the heterogeneous succession of different textured mineral and buried organic matter layers could impede the development of a stable soil structure. Our study aims at improving the current understanding of soil structure formation and organic matter dynamics in near natural alluvial soils. We investigate the effects of soil engineering organisms, the composition, and the superimposition of different alluvial deposits on the structuration patterns, the aggregate stability, and organic matter dynamics in in vitro soil columns, representing sediment deposition processes in alluvial soils. Two successions of three different deposits, silt–buried litter–sand, and the inverse, were set up in mesocosms and allocated to four different treatments, i.e. plants, earthworms, plants + earthworms, and a control. X-ray computed tomography was used to identify structuration patterns generated by ecosystem engineers, i.e. plant root galleries and earthworm tunnels. Organic matter dynamics in macro-aggregates were investigated by Rock-Eval pyrolysis. Plant roots only extended in the top layers, whereas earthworms preferentially selected the buried litter and the silt layers. Soil structural stability measured via water stable aggregates (%WSA) increased in the presence of plants and in aggregates recovered from the buried litter layer. Organic matter dynamics were controlled by a complex interplay between the type of engineer, the composition (silt, sand, buried litter) and the succession of the deposits in the mesocosm. Our results indicate that the progress and efficiency of soil structure formation in alluvial soils strongly depends on the textural sequences of alluvial deposits