Comparative genomics of plant-asssociated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoir

Assessment of NAAPS-RA performance in Maritime Southeast Asia during CAMP2Ex

Monitoring and modeling aerosol particle life cycle in Southeast Asia (SEA) is challenged by high cloud cover, complex meteorology, and the wide range of aerosol species, sources, and transformations found throughout the region. Satellite observations are limited, and there are few in situ observations of aerosol extinction profiles, aerosol properties, and environmental conditions. Therefore, accurate aerosol model outputs are crucial for the region. This work evaluates the Navy Aerosol Analysis and Prediction System Reanalysis (NAAPS-RA) aerosol optical thickness (AOT) and light extinction products using airborne aerosol and meteorological measurements from the Cloud, Aerosol, and Monsoon Processes Philippines Experiment (CAMP2Ex) conducted in 2019 during the SEA southwest monsoon biomass burning season. Modeled AOTs and extinction coefficients are compared to those retrieved with a high spectral resolution lidar (HSRL-2). Agreement between simulated and retrieved AOT (R2Combining double low line 0.78, relative bias Combining double low line-5 %, normalized root mean square error (NRMSE) Combining double low line 48 %) and aerosol extinction coefficients (R2Combining double low line 0.80, 0.81, and 0.42; relative bias Combining double low line 3 %, -6 %, and -7 %; NRMSE Combining double low line 47 %, 53 %, and 118 % for altitudes between 40-500, 500-1500, and >1500 m, respectively) is quite good considering the challenging environment and few opportunities for assimilations of AOT from satellites during the campaign. Modeled relative humidities (RHs) are negatively biased at all altitudes (absolute bias Combining double low line-5 %, -8 %, and -3 % for altitudes 1500 m, respectively), motivating interest in the role of RH errors in AOT and extinction simulations. Interestingly, NAAPS-RA AOT and extinction agreement with the HSRL-2 does not change significantly (i.e., NRMSE values do not all decrease) when RHs from dropsondes are substituted into the model, yet biases all move in a positive direction. Further exploration suggests changes in modeled extinction are more sensitive to the actual magnitude of both the extinction coefficients and the dropsonde RHs being substituted into the model as opposed to the absolute differences between simulated and measured RHs. Finally, four case studies examine how model errors in RH and the hygroscopic growth parameter, γ, affect simulations of extinction in the mixed layer (ML). We find NAAPS-RA overestimates the hygroscopicity of (i) smoke particles from biomass burning in the Maritime Continent (MC) and (ii) anthropogenic emissions transported from East Asia. This work mainly provides insight into the relationship between errors in modeled RH and simulations of AOT and extinction in a humid and tropical environment influenced by a myriad of meteorological conditions and particle types. These results can be interpreted and addressed by the modeling community as part of the effort to better understand, quantify, and forecast atmospheric conditions in SEA. Copyright © 2022 Eva-Lou Edwards et al.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Aircraft Observations of Turbulence in Cloudy and Cloud-Free Boundary Layers Over the Western North Atlantic Ocean From ACTIVATE and Implications for the Earth System Model Evaluation and Development

This study examines boundary layer turbulence derived from high temporal resolution meteorological measurements from 40 research flights over the western North Atlantic Ocean during the 2020 deployments of ACTIVATE. Frequency distributions of various turbulent quantities reveal stronger turbulence during the winter deployment than in summer and for cloud-topped than in cloud-free boundary layers during the summer deployment. Maximum turbulence kinetic energy (TKE) is most often within cloud from observations in winter and summer, whereas it is mostly below cloud in both seasons by a global model turbulence parameterization. Bivariate frequency distributions are consistent with the bivariate Gaussian probability distribution functions assumed for the closure of higher-order turbulence/shallow convection parameterizations used by some global models. Turbulence simulated by the Community Atmosphere Model version 6 and the Energy Exascale Earth System Model Atmosphere Model version 2 using such parameterizations is not as strong as observed, with more TKE going into vertical wind perturbations rather than into zonal wind perturbations as observed, suggesting that the treatment of turbulence in Earth system models still needs to be further improved. © 2022. American Geophysical Union. All Rights Reserved.6 month embargo; first published: 15 September 2022This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Airborne HSRL-2 measurements of elevated aerosol depolarization associated with non-spherical sea salt

Airborne NASA Langley Research Center (LaRC) High Spectral Resolution Lidar-2 (HSRL-2) measurements acquired during the recent NASA Earth Venture Suborbital-3 (EVS-3) Aerosol Cloud Meteorology Interactions over the Western Atlantic Experiment (ACTIVATE) revealed elevated particulate linear depolarization associated with aerosols within the marine boundary layer. These observations were acquired off the east coast of the United States during both winter and summer 2020 and 2021 when the HSRL-2 was deployed on the NASA LaRC King Air aircraft. During 20 of 63 total flight days, particularly on days with cold air outbreaks, linear particulate depolarization at 532 nm exceeded 0.15–0.20 within the lowest several hundred meters of the atmosphere, indicating that these particles were non-spherical. Higher values of linear depolarization typically were measured at 355 nm and lower values were measured at 1,064 nm. Several lines of evidence suggest that these non-spherical particles were sea salt including aerosol extinction/backscatter ratio (“lidar ratio”) values of 20–25 sr measured at both 355 and 532 nm by the HSRL-2, higher values of particulate depolarization measured at low (< 60%) relative humidity, coincident airborne in situ size and composition measurements, and aerosol transport simulations. The elevated aerosol depolarization values were not correlated with wind speed but were correlated with salt mass fraction and effective radius of the aerosol when the relative humidity was below 60%. HSRL-2 measured median particulate extinction values of about 20 Mm−1 at 532 nm associated with these non-spherical sea salt particles and found that the aerosol optical depth (AOD) contributed by these particles remained small (0.03–0.04) but represented on average about 30%–40% of the total column AOD. Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) spaceborne lidar aerosol measurements during several cold air outbreaks and CALIOP retrievals of column aerosol lidar ratio using column AOD constraints suggest that CALIOP operational aerosol algorithms can misclassify these aerosols as dusty marine rather than marine aerosols. Such misclassification leads to ∼40–50% overestimates in the assumed lidar ratio and in subsequent retrievals of aerosol optical depth and aerosol extinction. Copyright © 2023 Ferrare, Hair, Hostetler, Shingler, Burton, Fenn, Clayton, Scarino, Harper, Seaman, Cook, Crosbie, Winstead, Ziemba, Thornhill, Robinson, Moore, Vaughan, Sorooshian, Schlosser, Liu, Zhang, Diskin, DiGangi, Nowak, Choi, Zuidema and Chellappan.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]