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Cloud droplet number concentration (Nd) is crucial for understanding aerosol–cloud interactions (ACI) and associated radiative effects. We present evaluations of four ground-based Nd retrievals based on comprehensive datasets from the Atmospheric Radiation Measurement (ARM) Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) field campaign. The Nd retrieval methods use ARM ENA observatory ground-based remote sensing observations from a micropulse lidar, Raman lidar, cloud radar, and the ARM NDROP (Droplet Number Concentration) value-added product (VAP), all of which also retrieve cloud effective radius (re). The retrievals are compared against aircraft measurements from the fast cloud droplet probe (FCDP) and the cloud and aerosol spectrometer (CAS) obtained from low-level marine boundary layer clouds on 12 flight days during summer and winter seasons. Additionally, the in situ measurements are used to validate the assumptions and characterizations used in the retrieval algorithms. Statistical comparisons of the probability distribution function (PDF) of the Nd and cloud re retrievals with aircraft measurements demonstrate that these retrievals align well with in situ measurements for overcast clouds, but they may substantially differ for broken clouds or clouds with low liquid water path (LWP). The retrievals are applied to 4 years of ground-based remote sensing measurements of overcast marine boundary layer clouds at the ARM ENA observatory to find that Nd (re) values exhibit seasonal variations, with higher (lower) values during the summer season and lower (higher) values during the winter season. The ensemble of various retrievals using different measurements and retrieval algorithms such as those in this paper can help to quantify Nd retrieval uncertainties and identify reliable Nd retrieval scenarios. Of the retrieval methods, we recommend using the micropulse lidar-based method. This method has good agreement with in situ measurements, less sensitivity to issues arising from precipitation and low cloud LWP and/or optical depth, and broad applicability by functioning for both daytime and nighttime conditions.

IntroductionBovine respiratory disease (BRD) is one of the most important animal health problems in the beef industry. While bacterial culture and antimicrobial susceptibility testing have been used for diagnostic testing, the common practice of examining one isolate per species does not fully reflect the bacterial population in the sample. In contrast, a recent study with metagenomic sequencing of nasal swabs from feedlot cattle is promising in terms of bacterial pathogen identification and detection of antimicrobial resistance genes (ARGs). However, the sensitivity of metagenomic sequencing was impeded by the high proportion of host biomass in the nasal swab samples.MethodsThis pilot study employed a non-selective bacterial enrichment step before nucleic acid extraction to increase the relative proportion of bacterial DNA for sequencing.ResultsNon-selective bacterial enrichment increased the proportion of bacteria relative to host sequence data, allowing increased detection of BRD pathogens compared with unenriched samples. This process also allowed for enhanced detection of ARGs with species-level resolution, including detection of ARGs for bacterial species of interest that were not targeted for culture and susceptibility testing. The long-read sequencing approach enabled ARG detection on individual bacterial reads without the need for assembly. Metagenomics following non-selective bacterial enrichment resulted in substantial agreement for four of six comparisons with culture for respiratory bacteria and substantial or better correlation with qPCR. Comparison between isolate susceptibility results and detection of ARGs was best for macrolide ARGs in Mannheimia haemolytica reads but was also substantial for sulfonamide ARGs within M. haemolytica and Pasteurella multocida reads and tetracycline ARGs in Histophilus somni reads.DiscussionBy increasing the proportion of bacterial DNA relative to host DNA through non-selective enrichment, we demonstrated a corresponding increase in the proportion of sequencing data identifying BRD-associated pathogens and ARGs in deep nasopharyngeal swabs from feedlot cattle using long-read metagenomic sequencing. This method shows promise as a detection strategy for BRD pathogens and ARGs and strikes a balance between processing time, input costs, and generation of on-target data. This approach could serve as a valuable tool to inform antimicrobial management for BRD and support antimicrobial stewardship.

The detection of the early growth of drizzle particles in marine stratocumulus clouds is important for studying the transition from cloud water to rainwater. Radar reflectivity is commonly used to detect drizzle; however, its utility is limited to larger drizzle particles. Alternatively, radar Doppler spectrum skewness has proven to be a more sensitive quantity for the detection of drizzle embryos. Here, a machine learning (ML)-based technique that uses radar reflectivity and skewness for detecting small drizzle particles is presented. Aircraft in situ measurements are used to develop and validate the ML algorithm. The drizzle detection algorithm is applied to three Atmospheric Radiation Measurement (ARM) observational campaigns to investigate the drizzle occurrence in marine boundary layer clouds. It is found that drizzle is far more ubiquitous than previously thought; the traditional radar-reflectivity-based approach significantly underestimates the drizzle occurrence, especially in thin clouds with liquid water paths lower than 50 g m−2. Furthermore, the drizzle occurrence in marine boundary layer clouds differs among the three ARM campaigns, indicating that the drizzle formation, which is controlled by the microphysical process, is regime dependent. A complete understanding of the drizzle distribution climatology in marine stratocumulus clouds calls for more observational campaigns and continuing investigations.

Detection of liquid-containing cloud layers in thick mixed-phase clouds or multi-layer cloud situations from ground-based remote-sensing instruments still poses observational challenges, yet improvements are crucial since the existence of multi-layer liquid layers in mixed-phase cloud situations influences cloud radiative effects, cloud lifetime, and precipitation formation processes. Hydrometeor target classifications such as from Cloudnet that require a lidar signal for the classification of liquid are limited to the maximum height of lidar signal penetration and thus often lead to underestimations of liquid-containing cloud layers. Here we evaluate the Cloudnet liquid detection against the approach of Luke et al. (2010) which extracts morphological features in cloud-penetrating cloud radar Doppler spectra measurements in an artificial neural network (ANN) approach to classify liquid beyond full lidar signal attenuation based on the simulation of the two lidar parameters particle backscatter coefficient and particle depolarization ratio. We show that the ANN of Luke et al. (2010) which was trained under Arctic conditions can successfully be applied to observations at the mid-latitudes obtained during the 7-week-long ACCEPT field experiment in Cabauw, the Netherlands, in 2014. In a sensitivity study covering the whole duration of the ACCEPT campaign, different liquid-detection thresholds for ANN-predicted lidar variables are applied and evaluated against the Cloudnet target classification. Independent validation of the liquid mask from the standard Cloudnet target classification against the ANN-based technique is realized by comparisons to observations of microwave radiometer liquid-water path, ceilometer liquid-layer base altitude, and radiosonde relative humidity. In addition, a case-study comparison against the cloud feature mask detected by the space-borne lidar aboard the CALIPSO satellite is presented. Three conclusions were drawn from the investigation. First, it was found that the threshold selection criteria of liquid-related lidar backscatter and depolarization alone control the liquid detection considerably. Second, all threshold values used in the ANN framework were found to outperform the Cloudnet target classification for deep or multi-layer cloud situations where the lidar signal is fully attenuated within low liquid layers and the cloud radar is able to detect the microphysical fingerprint of liquid in higher cloud layers. Third, if lidar data are available, Cloudnet is at least as good as the ANN. The times when Cloudnet outperforms the ANN in liquid detections are often associated with situations where cloud dynamics smear the imprint of cloud microphysics on the radar Doppler spectra.

In many types of clouds, multiple hydrometeor populations can be present at the same time and height. Studying the evolution of these different hydrometeors in a time–height perspective can give valuable information on cloud particle composition and microphysical growth processes. However, as a prerequisite, the number of different hydrometeor types in a certain cloud volume needs to be quantified. This can be accomplished using cloud radar Doppler velocity spectra from profiling cloud radars if the different hydrometeor types have sufficiently different terminal fall velocities to produce individual Doppler spectrum peaks. Here we present a newly developed supervised machine learning radar Doppler spectra peak-finding algorithm (named PEAKO). In this approach, three adjustable parameters (spectrum smoothing span, prominence threshold, and minimum peak width at half-height) are varied to obtain the set of parameters which yields the best agreement of user-classified and machine-marked peaks. The algorithm was developed for Ka-band ARM zenith-pointing radar (KAZR) observations obtained in thick snowfall systems during the Atmospheric Radiation Measurement Program (ARM) mobile facility AMF2 deployment at Hyytiälä, Finland, during the Biogenic Aerosols – Effects on Clouds and Climate (BAECC) field campaign. The performance of PEAKO is evaluated by comparing its results to existing Doppler peak-finding algorithms. The new algorithm consistently identifies Doppler spectra peaks and outperforms other algorithms by reducing noise and increasing temporal and height consistency in detected features. In the future, the PEAKO algorithm will be adapted to other cloud radars and other types of clouds consisting of multiple hydrometeors in the same cloud volume.

The response of marine low cloud systems to changes in aerosol concentration represents one of the largest uncertainties in climate simulations. Major contributions to this uncertainty are derived from poor understanding of aerosol under natural conditions and the perturbation by anthropogenic emissions. The eastern North Atlantic (ENA) is a region of persistent but diverse marine boundary layer (MBL) clouds, whose albedo and precipitation are highly susceptible to perturbations in aerosol properties. In this study, we examine MBL aerosol properties, trace gas mixing ratios, and meteorological parameters measured at the Atmospheric Radiation Measurement Climate Research Facility's ENA site on Graciosa Island, Azores, Portugal, during a 3-year period from 2015 to 2017. Measurements impacted by local pollution on Graciosa Island and during occasional intense biomass burning and dust events are excluded from this study. Submicron aerosol size distribution typically consists of three modes: Aitken (At, diameter Dp<∼100 nm), accumulation (Ac, Dp within ∼100 to ∼300 nm), and larger accumulation (LA, Dp>∼300 nm) modes, with average number concentrations (denoted as NAt, NAc, and NLA below) of 330, 114, and 14 cm−3, respectively. NAt, NAc, and NLA show contrasting seasonal variations, suggesting different sources and removal processes. NLA is dominated by sea spray aerosol (SSA) and is higher in winter and lower in summer. This is due to the seasonal variations of SSA production, in-cloud coalescence scavenging, and dilution by entrained free troposphere (FT) air. In comparison, SSA typically contributes a relatively minor fraction to NAt (10 %) and NAc (21 %) on an annual basis. In addition to SSA, sources of Ac-mode particles include entrainment of FT aerosols and condensation growth of Aitken-mode particles inside the MBL, while in-cloud coalescence scavenging is the major sink of NAc. The observed seasonal variation of NAc, being higher in summer and lower in winter, generally agrees with the steady-state concentration estimated from major sources and sinks. NAt is mainly controlled by entrainment of FT aerosol, coagulation loss, and growth of Aitken-mode particles into the Ac-mode size range. Our calculation suggests that besides the direct contribution from entrained FT Ac-mode particles, growth of entrained FT Aitken-mode particles in the MBL also represent a substantial source of cloud condensation nuclei (CCN), with the highest contribution potentially reaching 60 % during summer. The growth of Aitken-mode particles to CCN size is an expected result of the condensation of sulfuric acid, a product from dimethyl sulfide oxidation, suggesting that ocean ecosystems may have a substantial influence on MBL CCN populations in the ENA.

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

Knowledge of cloud phase (liquid, ice, mixed, etc.) is necessary to describe the radiative impact of clouds and their lifetimes, but is a property that is difficult to simulate correctly in climate models. One step towards improving those simulations is to make observations of cloud phase with sufficient accuracy to help constrain model representations of cloud processes. In this study, we outline a methodology using a basic Bayesian classifier to estimate the probabilities of cloud-phase class from Atmospheric Radiation Measurement (ARM) vertically pointing active remote sensors. The advantage of this method over previous ones is that it provides uncertainty information on the phase classification. We also test the value of including higher moments of the cloud radar Doppler spectrum than are traditionally used operationally. Using training data of known phase from the Mixed-Phase Arctic Cloud Experiment (M-PACE) field campaign, we demonstrate a proof of concept for how the method can be used to train an algorithm that identifies ice, liquid, mixed phase, and snow. Over 95 % of data are identified correctly for pure ice and liquid cases used in this study. Mixed-phase and snow cases are more problematic to identify correctly. When lidar data are not available, including additional information from the Doppler spectrum provides substantial improvement to the algorithm. This is a first step towards an operational algorithm and can be expanded to include additional categories such as drizzle with additional training data.

Radar Doppler spectra measurements are exploited to study a riming event when precipitating ice from a seeder cloud sediment through a supercooled liquid water (SLW) layer. The focus is on the "golden sample" case study for this type of analysis based on observations collected during the deployment of the Atmospheric Radiation Measurement Program's (ARM) mobile facility AMF2 at Hyytiälä, Finland, during the Biogenic Aerosols – Effects on Clouds and Climate (BAECC) field campaign. The presented analysis of the height evolution of the radar Doppler spectra is a state-of-the-art retrieval with profiling cloud radars in SLW layers beyond the traditional use of spectral moments. Dynamical effects are considered by following the particle population evolution along slanted tracks that are caused by horizontal advection of the cloud under wind shear conditions. In the SLW layer, the identified liquid peak is used as an air motion tracer to correct the Doppler spectra for vertical air motion and the ice peak is used to study the radar profiles of rimed particles. A 1-D steady-state bin microphysical model is constrained using the SLW and air motion profiles and cloud top radar observations. The observed radar moment profiles of the rimed snow can be simulated reasonably well by the model, but not without making several assumptions about the ice particle concentration and the relative role of deposition and aggregation. This suggests that in situ observations of key ice properties are needed to complement the profiling radar observations before process-oriented studies can effectively evaluate ice microphysical parameterizations.