Long-term aerosol and cloud database from correlative EARLINET-CALIPSO observations

The European Aerosol Research Lidar Network, EARLINET, performs correlative observations during CALIPSO overpasses based on a sophisticated measurement strategy since June 2006. Within a dedicated activity supported by the European Space Agency (ESA), sixteen EARLINET stations contributed about 1500 measurements during an intensive observational period from May 2008 to October 2009. From these measurements, we establish a long-term aerosol and cloud database of correlative EARLINET-CALIPSO observations. This database shall provide a basis for homogenizing long-term space-borne observations conducted with different lidar instruments operating at different wavelengths on various platforms over the next decade(s). The database is also used to study the quality and representativeness of satellite lidar cross sections along an orbit against long-term lidar network observations on a continental scale.Postprint (published version

EARLINET instrument intercomparison campaigns: overview on strategy and results

This paper introduces the recent European Aerosol Research Lidar Network (EARLINET) quality-assurance efforts at instrument level. Within two dedicated campaigns and five single-site intercomparison activities, 21 EARLINET systems from 18 EARLINET stations were intercompared between 2009 and 2013. A comprehensive strategy for campaign setup and data evaluation has been established. Eleven systems from nine EARLINET stations participated in the EARLINET Lidar Intercomparison 2009 (EARLI09). In this campaign, three reference systems were qualified which served as traveling standards thereafter. EARLINET systems from nine other stations have been compared against these reference systems since 2009. We present and discuss comparisons at signal and at product level from all campaigns for more than 100 individual measurement channels at the wavelengths of 355, 387, 532, and 607¿nm. It is shown that in most cases, a very good agreement of the compared systems with the respective reference is obtained. Mean signal deviations in predefined height ranges are typically below ±2¿%. Particle backscatter and extinction coefficients agree within ±2¿¿×¿¿10-4¿km-1¿sr-1 and ±¿0.01¿km-1, respectively, in most cases. For systems or channels that showed larger discrepancies, an in-depth analysis of deficiencies was performed and technical solutions and upgrades were proposed and realized. The intercomparisons have reinforced confidence in the EARLINET data quality and allowed us to draw conclusions on necessary system improvements for some instruments and to identify major challenges that need to be tackled in the future.Peer ReviewedPostprint (published version

Response of wheat plants under post-anthesis stress induced by defoliation: II. Contribution of peduncle morpho-anatomical traits and carbon reserves to grain yield

Assimilated carbon during vegetative and early reproductive growth in wheat is temporarily stored in stem internodes and leaf sheaths (LSs), and can later be remobilized and transported to developing grain. The present study was undertaken to determine the effect of several peduncle (the uppermost internode) morpho-anatomical and biochemical traits on grain weight, and to assess the contribution of the peduncle water-soluble carbohydrate (WSC) reserves shortly after anthesis to its variation. In 2-year field trials, 61 wheat genotypes were used (27 F-4:5 families, 17 parents used for the crosses and the 17 current best standards), comparing intact control plants (CP) with plants that were defoliated (DP) by cutting off all leaf blades 10 days after anthesis. Estimated contributions of peduncle (culm (C) and flag LS) assimilate reserves to grain weight/spike were from 006 to 031 and from 011 to 045 in CP and DP plants, respectively. In both CP and DP plants, a higher contribution was from the LS than from the C. High peduncle reserve mobilization efficiency, a longer exposed part of the peduncle and larger C storage capacity (through higher parenchyma and/or lower lignified area) were of specific benefit for maintaining grain weight in defoliated plants. F-4:5 families had higher transport capacity in the peduncle, but without any improvement in WSC-related traits compared with the best standards

Long-term aerosol and cloud database from correlative EARLINET-CALIPSO observations

The European Aerosol Research Lidar Network, EARLINET, performs correlative observations during CALIPSO overpasses based on a sophisticated measurement strategy since June 2006. Within a dedicated activity supported by the European Space Agency (ESA), sixteen EARLINET stations contributed about 1500 measurements during an intensive observational period from May 2008 to October 2009. From these measurements, we establish a long-term aerosol and cloud database of correlative EARLINET-CALIPSO observations. This database shall provide a basis for homogenizing long-term space-borne observations conducted with different lidar instruments operating at different wavelengths on various platforms over the next decade(s). The database is also used to study the quality and representativeness of satellite lidar cross sections along an orbit against long-term lidar network observations on a continental scale

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities

Long-term aerosol and cloud database from correlative EARLINET-CALIPSO observations

The European Aerosol Research Lidar Network, EARLINET, performs correlative observations during CALIPSO overpasses based on a sophisticated measurement strategy since June 2006. Within a dedicated activity supported by the European Space Agency (ESA), sixteen EARLINET stations contributed about 1500 measurements during an intensive observational period from May 2008 to October 2009. From these measurements, we establish a long-term aerosol and cloud database of correlative EARLINET-CALIPSO observations. This database shall provide a basis for homogenizing long-term space-borne observations conducted with different lidar instruments operating at different wavelengths on various platforms over the next decade(s). The database is also used to study the quality and representativeness of satellite lidar cross sections along an orbit against long-term lidar network observations on a continental scale

EARLINET instrument intercomparison campaigns: overview on strategy and results

This paper introduces the recent European Aerosol Research Lidar Network (EARLINET) quality-assurance efforts at instrument level. Within two dedicated campaigns and five single-site intercomparison activities, 21 EARLINET systems from 18 EARLINET stations were intercompared between 2009 and 2013. A comprehensive strategy for campaign setup and data evaluation has been established. Eleven systems from nine EARLINET stations participated in the EARLINET Lidar Intercomparison 2009 (EARLI09). In this campaign, three reference systems were qualified which served as traveling standards thereafter. EARLINET systems from nine other stations have been compared against these reference systems since 2009. We present and discuss comparisons at signal and at product level from all campaigns for more than 100 individual measurement channels at the wavelengths of 355, 387, 532, and 607¿nm. It is shown that in most cases, a very good agreement of the compared systems with the respective reference is obtained. Mean signal deviations in predefined height ranges are typically below ±2¿%. Particle backscatter and extinction coefficients agree within ±2¿¿×¿¿10-4¿km-1¿sr-1 and ±¿0.01¿km-1, respectively, in most cases. For systems or channels that showed larger discrepancies, an in-depth analysis of deficiencies was performed and technical solutions and upgrades were proposed and realized. The intercomparisons have reinforced confidence in the EARLINET data quality and allowed us to draw conclusions on necessary system improvements for some instruments and to identify major challenges that need to be tackled in the future.Peer Reviewe

A global metagenomic map of urban microbiomes and antimicrobial resistance.

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections