Diversity and Abundance of Ice Nucleating Strains of Pseudomonas syringae in a Freshwater Lake in Virginia, USA

Diversity and ice nucleation activity of Pseudomonas syringae in drone-based water samples from eight lakes in Austria

Bacteria from the Pseudomonas syringae complex (comprised of at least 15 recognized species and more than 60 different pathovars of P. syringae sensu stricto) have been cultured from clouds, rain, snow, streams, rivers, and lakes. Some strains of P. syringae express an ice nucleation protein (hereafter referred to as ice+) that catalyzes the heterogeneous freezing of water. Though P. syringae has been sampled intensively from freshwater sources in the U.S. and France, little is known about the genetic diversity and ice nucleation activity of P. syringae in other parts of the world. We investigated the haplotype diversity and ice nucleation activity at -8 °C (ice+) of strains of P. syringae from water samples collected with drones in eight freshwater lakes in Austria. A phylogenetic analysis of citrate synthase (cts) sequences from 271 strains of bacteria isolated from a semi-selective medium for Pseudomonas revealed that 69% (188/271) belonged to the P. syringae complex and represented 32 haplotypes in phylogroups 1, 2, 7, 9, 10, 13, 14 and 15. Strains within the P. syringae complex were identified in all eight lakes, and seven lakes contained ice+ strains. Partial 16S rDNA sequences were analyzed from a total of 492 pure cultures of bacteria isolated from non-selective medium. Nearly half (43.5%; 214/492) were associated with the genus Pseudomonas. Five of the lakes (ALT, GRU, GOS, GOL, and WOR) were all distinguished by high levels of Pseudomanas (p ≤ 0.001). HIN, the highest elevation lake, had the highest percentage of ice+ strains. Our work highlights the potential for uncovering new haplotypes of P. syringae in aquatic habitats, and the use of robotic technologies to sample and characterize microbial life in remote settings.

Comparative bacteriome and antibiotic resistome analysis of water and sediment of the Ganga River of India

A comparative analysis between water and sediment can provide better information to understand the dynamics of the inhabitant microbiome and their respective antibiotic resistance genes of a river. Therefore, the present investigation was carried to explore the limited information available on bacterial microbiome and their predictive antibiotic resistance genes (ARGs) from water and sediment of the Ganga River. The study utilized the NGS-based sequences previously submitted under the accession number (PRJNA847424 and PRJNA892876). Overall analysis revealed that twenty phyla and fifty-four genera were shared between the water and sediment of the Ganga River. Of them, nine phyla and nineteen genera were observed as significantly different (p-value < 0.05). Where the majority of the genera were associated with the sediment samples over the water that identify the sediment samples as more diverse for species richness. Similarly, seventy-six ARGs were shared between water and sediment samples. Of the ten abundant antibiotic resistance pathways, seven were relatively abundant in sediment samples as compared to the water. Vancomycin resistance genes were significantly more abundant among sediment samples, whereas β-lactam resistance genes were equally distributed in water and sediment samples. The network analysis further revealed that five genera (Flavobacterium, Pseudomonas, Acinetobacter, Candidatus_divison CL5003, and Candidatus_division SWB02) showed a significantly positive correlation with six antibiotic resistance pathways (β-lactam, vancomycin, multidrug resistance, tetracycline, aminoglycoside, and macrolide resistance pathways). The study comes out with several findings where sediment may be considered as a more atrocious habitat for evolving the resistance mechanisms against threatful antibiotics over the water samples of the Ganga River.

Urbanization led to the abundance of Gram-negative, chemo-organo-heterotrophs, and antibiotic resistance genes in the downstream regions of the Ganga River water of India

The present investigation assesses the bacterial microbiome and antibiotic resistance genes (ARGs) of the river Ganga from Uttarakhand (upstream region; US group) and Uttar Pradesh (downstream region; DS group) regions using a 16S rRNA amplicon-based metagenomic approach. Gram-negative, aerobic, and chemo-organotrophic bacteria made up the majority of the bacterial genera during the overall analysis. Physicochemical analysis revealed a higher concentration of nitrate and phosphate in the downstream sites of the Ganga River. The prevalence of Gemmatimonas, Flavobacterium, Arenimonas, and Verrucomicrobia in the water of the DS region indicates a high organic load. Pseudomonas and Flavobacterium emerged as the most prevalent genera among the 35 significantly different shared genera (p-value < 0.05) in the US and DS regions, respectively. Overall antibiotic resistance analysis of the samples showed the dominance of β-lactam resistance (33.92%) followed by CAMP (cationic antimicrobial peptide) resistance (27.75%), and multidrug resistance (19.17%), vancomycin resistance (17.84%), and tetracycline resistance (0.77%). While comparing, the DS group exhibited a higher abundance of ARGs over the US group, where the CAMP resistance and β-lactam ARGs were dominant in the respective regions. The correlation (p-value < 0.05) analysis showed that most bacteria exhibit a significant correlation with tetracycline resistance followed by the phenicol antibiotic. The present findings draw attention to the need for regulated disposal of multiform human-derived wastes into the Ganga River to reduce the irrepressible ARGs dissemination.

Next-Generation High-Throughput Sequencing to Evaluate Bacterial Communities in Freshwater Ecosystem in Hydroelectric Reservoirs

The quality of aquatic ecosystems is a major public health concern. The assessment and management of a freshwater system and the ecological monitoring of microorganisms that are present in it can provide indicators of the environment and water quality to protect human and animal health. with bacteria is. It is a major challenge to monitor the microbiological bacterial contamination status of surface water associated with anthropogenic activities within rivers and freshwater reservoirs. Understanding the composition of aquatic microbial communities can be beneficial for the early detection of pathogens, improving our knowledge of their ecological niches, and characterizing the assemblages of microbiota responsible for the degradation of contaminants and microbial substrates. The present study aimed to characterize the bacterial microbiota of water samples collected alongside the Madeira River and its small tributaries in rural areas near the Santo Antonio Energia hydroelectric power plant (SAE) reservoir in the municipality of Porto Velho, Rondonia state, Western Brazil. An Illumina 16s rRNA metagenomic approach was employed and the physicochemical characteristics of the water sample were assessed. We hypothesized that both water metagenomics and physicochemical parameters would vary across sampling sites. The most abundant genera found in the study were Acinetobacter, Deinococcus, and Pseudomonas. PERMANOVA and ANCOM analysis revealed that collection points sampled at the G4 location presented a significantly different microbiome compared to any other group, with the Chlamidomonadaceae family and Enhydrobacter genus being significantly more abundant. Our findings support the use of metagenomics to assess water quality standards for the protection of human and animal health in this microgeographic region.

The influence of Pseudomonas syringae on water freezing and ice melting

Pseudomonas syringae is a widely spread plant pathogen known to have ice-nucleating proteins that serve as crystallization sites promoting ice growth at near-zero temperatures. Three temperatures that characterize water freezing and ice melting are (i) the freezing point of water, (ii) the temperature of coexistence of ice and water, and (iii) the melting point of ice. Here we show the influence of different concentrations of P. syringae on these three parameters. P. syringae appears to affect both the freezing point of water and the temperature of the coexistence of ice and water. Additionally, we propose a research technique for studying the freezing/melting process that is simple and requires no complex equipment.

Pseudomonas viridiflava: An internal outsider of the Pseudomonas syringae species complex

Pseudomonas viridiflava is a gram-negative pseudomonad that is phylogenetically placed within the Pseudomonas syringae species complex. P. viridiflava has a wide host range and causes a variety of symptoms in different plant parts, including stems, leaves, and blossoms. Outside of its role as a pathogen, P. viridiflava also exists as an endophyte, epiphyte, and saprophyte. Increased reports of P. viridiflava causing disease on new hosts in recent years coincide with increased research on its genetic variability, virulence, phylogenetics, and phenotypes. There is high variation in its core genome, virulence factors, and phenotypic characteristics. The main virulence factors of this pathogen include the enzyme pectate lyase and virulence genes encoded within one or two pathogenicity islands. The delineation of P. viridiflava in the P. syringae complex has been investigated using several molecular approaches. P. viridiflava comprises its own species, within the complex. While seemingly an outsider to the complex as a whole due to differences in the core genome and virulence genes, low average nucleotide identity to other of P. syringae complex members, and some phenotypic traits, it remains as part of the complex. Defining phylogenetic, phenotypic, and genomic characteristics of P. viridiflava in comparison to other P. syringae members is important to understanding this pathogen and for the development of disease resistance and management practices.

TAXONOMY

Kingdom Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Family Pseudomonadaceae; Genus Pseudomonas; Species Pseudomonas syringae species complex, Genomospecies 6, Phylogroup 7 and 8.

MICROBIOLOGICAL PROPERTIES

Gram-negative, fluorescent, aerobic, motile, rod-shaped, oxidase negative, arginine dihydrolase negative, levan production negative (or positive), potato rot positive (or negative), tobacco hypersensitivity positive.

GENOME

There are two complete genomes, five chromosome-level genomes, and 1,540 genomes composed of multiple scaffolds of P. viridiflava available in the National Center for Biotechnology Information Genome database. The median total length of these assemblies is 5,975,050 bp, the median number of protein coding genes is 5,208, and the median G + C content is 59.3%.

DISEASE SYMPTOMS

P. viridiflava causes a variety of disease symptoms, including spots, streaks, necrosis, rots, and more in above- and below-ground plant parts on at least 50 hosts.

EPIDEMIOLOGY

There have been several significant disease outbreaks on field and horticultural crops caused by P. viridiflava since the turn of the century. P. viridiflava has been reported as a pathogen, epiphyte, endophyte, and saprophyte. This species has been isolated from a variety of environmental sources, including asymptomatic wild plants, snow, epilithic biofilms, and icepacks.

Seasonal ice nucleation activity of water samples from alpine rivers and lakes in Obergurgl, Austria

Heterogeneous ice nucleation plays an important role in many environmental processes such as ice cloud formation, freezing of water bodies or biological freeze protection in the cryosphere. New information is needed about the seasonal availability, nature, and activity of ice nucleating particles (INPs) in alpine environments. These INPs trigger the phase transition from liquid water to solid ice at elevated subzero temperatures. We collected water samples from a series of alpine rivers and lakes (two valleys and their rivers, an artificial pond, and a natural lake system) in Obergurgl, Austria in June 2016, July 2016, November 2016, and May 2017. Each alpine river and lake was sampled multiple times across different seasons, depending on site access during different times of the year. Water samples were filtered through a 0.22 μm membrane filter to separate microbial INPs from the water, and both fractions were analyzed for ice nucleation activity (INA) by an emulsion freezing method. Microorganisms were cultured from the filters, and the cultures then analyzed for INA. Portions of the filtered samples were concentrated by lyophilization to observe potential enhancement of INA. Two sediment samples were taken as reference points for inorganic INPs. Sub-micron INPs were observed in all of the alpine water sources studied, and a seasonal shift to a higher fraction of microbial ice nucleators cultured on selective media was observed during the winter collections. Particles larger than 0.22 μm showed INA, and microbes were cultured from this fraction. Results from 60 samples gave evidence of a seasonal change in INA, presence of submicrometer INPs, and show the abundance of culturable microorganisms, with late spring and early summer showing the most active biological INPs. With additional future research on this topic ski resorts could make use of such knowledge of geographical and seasonal trends of microbial INPs in freshwater habitats in order to improve the production of artificial snow.

Increasing Freshwater Salinity Impacts Aerosolized Bacteria

Increases in the salt concentration of freshwater result in detrimental impacts on water quality and ecosystem biodiversity. Biodiversity effects include freshwater microbiota, as increasing salinity can induce shifts in the structure of native freshwater bacterial communities, which could disturb their role in mediating basal ecosystem services. Moreover, salinity affects the wave breaking and bubble-bursting mechanisms via which water-to-air dispersal of bacteria occurs. Given this dual effect of freshwater salinity on waterborne bacterial communities and their aerosolization mechanism, further effects on aerosolized bacterial diversity and abundance are anticipated. Cumulative salt additions in the freshwater-euhaline continuum (0-35 g/kg) were administered to a freshwater sample aerosolized inside a breaking wave analogue tank. Waterborne and corresponding airborne bacteria were sampled at each salinity treatment and later analyzed for diversity and abundance. Results demonstrated that the airborne bacterial community was significantly different (PERMANOVA; F_1,22 = 155.1, r² = 0.38, p < 0.001) from the waterborne community. The relative aerosolization factor (r-AF), defined as the air-to-water relative abundance ratio, revealed that different bacterial families exhibited either an enhanced (r-AF ≫ 1), neutral (r-AF ∼ 1), or diminished (r-AF ≪ 1) transfer to the aerosol phase throughout the salinization gradient. Going from freshwater to euhaline conditions, aerosolized bacterial abundance exhibited a nonmonotonic response with a maximum peak at lower oligohaline conditions (0.5-1 g/kg), a decline at higher oligohaline conditions (5 g/kg), and a moderate increase at polyhaline-euhaline conditions (15-35 g/kg). Our results demonstrate that increases in freshwater salinity are likely to influence the abundance and diversity of aerosolized bacteria. These shifts in aerosolized bacterial communities might have broader implications on public health by increasing exposure to airborne pathogens via inhalation. Impacts on regional climate, related to changes in biological ice-nucleating particles (INPs) emission from freshwater, are also expected.

Overview of biological ice nucleating particles in the atmosphere

Biological particles in the Earth's atmosphere are a distinctive category of ice nucleating particles (INPs) due to their capability of facilitating ice crystal formation in clouds at relatively warm temperatures. Field observations and model simulations have shown that biological INPs affect cloud and precipitation formation and regulate regional or even global climate, although there are considerable uncertainties in modeling and large gaps between observed and model simulated contribution of biological particles to atmospheric INPs. This paper overviews the latest researches about biological INPs in the atmosphere. Firstly, we describe the primary ice nucleation mechanisms, and measurements and model simulations of atmospheric biological INPs. Secondly, we summarize the ice nucleating properties of biological INPs from diverse sources such as soils or dust, vegetation (e.g., leaves and pollen grains), sea spray, and fresh waters, and controlling factors of biological INPs in the atmosphere. Then we review the abundance and distribution of atmospheric biological INPs in diverse ecosystems. Finally, we discuss the open questions in further studies on atmospheric biological INPs, including the requirements for developing novel detection techniques and simulation models, as well as the comprehensive investigation of characteristics and influencing factors of atmospheric biological INPs.

Diversity of metals and metal-interactive bacterial populations in different types of Arctic snow and frost flowers: Implications on snow freeze-melt processes in a changing climate

Arctic snow has been shown to be a reactive interface for key physical, chemical, and microbiological processes, affecting the Arctic's oxidation, biodiversity, radiation, and climate. To explore the potential links between snow-borne metal contaminants and metal-interactive bacteria, to freezing/melting processes, we performed concurrent chemical characterization, genomic, and morphological analysis of five different Arctic snowpack (accumulated, blowing, fresh falling, surface hoar, and wind pack snow) and frost flower in Utqiaġvik (Barrow), Alaska, using Montreal urban snow as reference. Several complementary analytical techniques, including triple quad ICP-MS/MS along with various chromatography techniques, thermal ionization mass spectrometer (TIMS), high-resolution transition electron microscopy with electron dispersive X-ray spectroscopy (HR-TEM/EDS), and next generation sequencing (NGS), were deployed. Distinct metal composition and bacterial distribution among samples were observed. The concentration of 27 different transition, post-transition, rare, and radioactive metals were determined in molten snow and frost flower, as well as filtered samples. The range of three highest detected metal concentrations among samples were: Hg (3.294-134.485 μg/L), Fe (0.719-34.469 μg/L), and Sr (1.676-19,297.000 μg/L). NGS analysis led to the identification of metal interacting bacteria in all types of snow and frost flowers in the Arctic (blowing snow (1239), surface hoar snow (2243), windpack (2431), frost flowers (1440)), and Montreal urban snow (5498)) with specific bacterial genera such as: Acinetobacter, Arcenicella, Azospirillum (surface hoar snow), Arthrobacter, Paenibacillus (blowing snow), and Cycloclasticus, OM182 clade (frost flower). Several types of bacteria with confirmed or associated ice nucleation activity were observed in different types of snow, and frost flower including Pseudomonas genera (e.g., Pseudomonas fluorescens), Flavobacterium, Corynebacterium, and Pseudoxanthomonas. The implications of the above findings to snow-air interactions including nanoparticles, namely during melting and freezing cycles, and to probe the impact of various natural and anthropogenic activities are herein discussed.

Pseudomonas Diversity Within Urban Freshwaters

Freshwater lakes are home to bacterial communities with 1000s of interdependent species. Numerous high-throughput 16S rRNA gene sequence surveys have provided insight into the microbial taxa found within these waters. Prior surveys of Lake Michigan waters have identified bacterial species common to freshwater lakes as well as species likely introduced from the urban environment. We cultured bacterial isolates from samples taken from the Chicago nearshore waters of Lake Michigan in an effort to look more closely at the genetic diversity of species found there within. The most abundant genus detected was Pseudomonas, whose presence in freshwaters is often attributed to storm water or runoff. Whole genome sequencing was conducted for 15 Lake Michigan Pseudomonas strains, representative of eight species and three isolates that could not be resolved with named species. These genomes were examined specifically for genes encoding functionality which may be advantageous in their urban environment. Antibiotic resistance, amidst other known virulence factors and defense mechanisms, were identified in the genome annotations and verified in the lab. We also tested the Lake Michigan Pseudomonas strains for siderophore production and resistance to the heavy metals mercury and copper. As the study presented here shows, a variety of pseudomonads have inhabited the urban coastal waters of Lake Michigan.

Microorganisms Collected from the Surface of Freshwater Lakes Using a Drone Water Sampling System (DOWSE)

New tools and technology are needed to study microorganisms in freshwater environments. Little is known about spatial distribution and ice nucleation activity (INA) of microorganisms in freshwater lakes. We developed a system to collect water samples from the surface of lakes using a 3D-printed sampling device tethered to a drone (DOWSE, DrOne Water Sampling SystEm). The DOWSE was used to collect surface water samples at different distances from the shore (1, 25, and 50 m) at eight different freshwater lakes in Austria in June 2018. Water samples were filtered, and microorganisms were cultured on two different media types, TSA (a general growth medium) and KBC (a medium semi-selective for bacteria in the genus Pseudomonas). Mean concentrations (colony forming units per mL, or CFU/mL) of bacteria cultured on TSA ranged from 19,800 (Wörthersee) to 210,500 (Gosaulacke) CFU/mL, and mean concentrations of bacteria cultured on KBC ranged from 2590 (Ossiachersee) to 11,000 (Vorderer Gosausee) CFU/mL. There was no significant difference in sampling distance from the shore for concentrations of microbes cultured on TSA (p = 0.28). A wireless bathymetry sensor was tethered to the drone to map temperature and depth across the sampling domain of each of the lakes. At the 50 m distance from the shore, temperature ranged from 17 (Hinterer Gosausee, and Gosaulacke) to 26 °C (Wörthersee), and depth ranged from 2.8 (Gosaulacke) to 11.1 m (Grundlsee). Contour maps of concentrations of culturable bacteria across the drone sampling domain revealed areas of high concentrations (hot spots) in some of the lakes. The percentage of ice-nucleation active (ice+) bacteria cultured on KBC ranged from 0% (0/64) (Wörthersee) to 58% (42/72) (Vorderer Gosausee), with a mean of 28% (153/544) for the entire sample set. Future work aims to elucidate the structure and function of entire microbial assemblages within and among the Austrian lakes.

Terrestrial Origin for Abundant Riverine Nanoscale Ice-Nucleating Particles

Ice-nucleating particles (INPs) associated with fresh waters are a neglected, but integral component of the water cycle. Abundant INPs were identified from surface waters of both the Maumee River and Lake Erie with ice nucleus spectra spanning a temperature range from -3 to -15 °C. The majority of river INPs were submicron in size and attributed to biogenic macromolecules, inferred from the denaturation of ice-nucleation activity by heat. In a watershed dominated by row-crop agriculture, higher concentrations of INPs were found in river samples compared to lake samples. Further, ice-nucleating temperatures differed between river and lake samples, which indicated different populations of INPs. Seasonal analysis of INPs that were active at warmer temperatures (≥-10 °C; INP_-10) showed their concentration to correlate with river discharge, suggesting a watershed origin of these INPs. A terrestrial origin for INPs in the Maumee River was further supported by a correspondence between the ice-nucleation signatures of river INPs and INPs derived from the soil fungus Mortierella alpina. Aerosols derived from turbulence features in the river carry INP_-10, although their potential influence on regional weather is unclear. INP_-10 contained within aerosols generated from a weir spanning the river, ranged in concentration from 1 to 11 INP m^-3, which represented a fold-change of 3.2 over average INP_-10 concentrations sampled from aerosols at control locations.

Wind-driven spume droplet production and the transport of Pseudomonas syringae from aquatic environments

Natural aquatic environments such as oceans, lakes, and rivers are home to a tremendous diversity of microorganisms. Some may cross the air-water interface within droplets and become airborne, with the potential to impact the Earth’s radiation budget, precipitation processes, and spread of disease. Larger droplets are likely to return to the water or adjacent land, but smaller droplets may be suspended in the atmosphere for transport over long distances. Here, we report on a series of controlled laboratory experiments to quantify wind-driven droplet production from a freshwater source for low wind speeds. The rate of droplet production increased quadratically with wind speed above a critical value (10-m equivalent 5.7 m/s) where droplet production initiated. Droplet diameter and ejection speeds were fit by a gamma distribution. The droplet mass flux and momentum flux increased with wind speed. Two mechanisms of droplet production, bubble bursting and fragmentation, yielded different distributions for diameter, speed, and angle. At a wind speed of about 3.5 m/s, aqueous suspensions of the ice-nucleating bacterium Pseudomonas syringae were collected at rates of 283 cells m⁻² s⁻¹ at 5 cm above the water surface, and at 14 cells m⁻² s⁻¹ at 10 cm above the water surface. At a wind speed of about 4.0 m/s, aqueous suspensions of P. syringae were collected at rates of 509 cells m⁻² s⁻¹ at 5 cm above the water surface, and at 81 cells m⁻² s⁻¹ at 10 cm above the water surface. The potential for microbial flux into the atmosphere from aquatic environments was calculated using known concentrations of bacteria in natural freshwater systems. Up to 3.1 × 10⁴ cells m⁻² s⁻¹ of water surface were estimated to leave the water in potentially suspended droplets (diameters <100 µm). Understanding the sources and mechanisms for bacteria to aerosolize from freshwater aquatic sources may aid in designing management strategies for pathogenic bacteria, and could shed light on how bacteria are involved in mesoscale atmospheric processes.

Coordinated Sampling of Microorganisms Over Freshwater and Saltwater Environments Using an Unmanned Surface Vehicle (USV) and a Small Unmanned Aircraft System (sUAS)

Biological aerosols (bioaerosols) are ubiquitous in terrestrial and aquatic environments and may influence cloud formation and precipitation processes. Little is known about the aerosolization and transport of bioaerosols from aquatic environments. We designed and deployed a bioaerosol-sampling system onboard an unmanned surface vehicle (USV; a remotely operated boat) to collect microbes and monitor particle sizes in the atmosphere above a salt pond in Falmouth, MA, United States and a freshwater lake in Dublin, VA, United States. The bioaerosol-sampling system included a series of 3D-printed impingers, two different optical particle counters, and a weather station. A small unmanned aircraft system (sUAS; a remotely operated airplane) was used in a coordinated effort with the USV to collect microorganisms on agar media 50 m above the surface of the water. Samples from the USV and sUAS were cultured on selective media to estimate concentrations of culturable microorganisms (bacteria and fungi). Concentrations of microbes from the sUAS ranged from 6 to 9 CFU/m³ over saltwater, and 12 to 16 CFU/m³ over freshwater (over 10-min sampling intervals) at 50 m above ground level (AGL). Concentrations from the USV ranged from 0 (LOD) to 42,411 CFU/m³ over saltwater, and 0 (LOD) to 56,809 CFU/m³ over freshwater (over 30-min sampling intervals) in air near the water surface. Particle concentrations recorded onboard the USV ranged from 0 (LOD) to 288 μg/m³ for PM1, 1 to 290 μg/m³ for PM2.5, and 1 to 290 μg/m³ for PM10. A general trend of increasing concentration with an increase in particle size was recorded by each sensor. Through laboratory testing, the collection efficiency of the 3D-printed impingers was determined to be 75% for 1 μm beads and 99% for 3 μm beads. Additional laboratory tests were conducted to determine the accuracy of the miniaturized optical particle counters used onboard the USV. Future work aims to understand the distribution of bioaerosols above aquatic environments and their potential association with cloud formation and precipitation processes.

Remote collection of microorganisms at two depths in a freshwater lake using an unmanned surface vehicle (USV)

Microorganisms are ubiquitous in freshwater aquatic environments, but little is known about their abundance, diversity, and transport. We designed and deployed a remote-operated water-sampling system onboard an unmanned surface vehicle (USV, a remote-controlled boat) to collect and characterize microbes in a freshwater lake in Virginia, USA. The USV collected water samples simultaneously at 5 and 50 cm below the surface of the water at three separate locations over three days in October, 2016. These samples were plated on a non-selective medium (TSA) and on a medium selective for the genus Pseudomonas (KBC) to estimate concentrations of culturable bacteria in the lake. Mean concentrations ranged from 134 to 407 CFU/mL for microbes cultured on TSA, and from 2 to 8 CFU/mL for microbes cultured on KBC. There was a significant difference in the concentration of microbes cultured on KBC across three sampling locations in the lake (P = 0.027), suggesting an uneven distribution of Pseudomonas across the locations sampled. There was also a significant difference in concentrations of microbes cultured on TSA across the three sampling days (P = 0.038), demonstrating daily fluctuations in concentrations of culturable bacteria. There was no significant difference in concentrations of microbes cultured on TSA (P = 0.707) and KBC (P = 0.641) across the two depths sampled, suggesting microorganisms were well-mixed between 5 and 50 cm below the surface of the water. About 1 percent (7/720) of the colonies recovered across all four sampling missions were ice nucleation active (ice+) at temperatures warmer than −10 °C. Our work extends traditional manned observations of aquatic environments to unmanned systems, and highlights the potential for USVs to understand the distribution and diversity of microbes within and above freshwater aquatic environments.

Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes

Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0–3.0 μm × 0.5–1 μm, motile and unable to form spores, it grows aerobically and cells show one single flagellum. Several genetic indices, the phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus and, the similarity of the 16S rDNA sequence was 100% with P. extremaustralis strain CT14–3^T. The draft genome of P. extremaustralis strain USBA-GBX-515 consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665 genes were predicted and of those, 5544 were protein coding genes and 121 were RNA genes. The distribution of genes into COG functional categories showed that most genes were classified in the category of amino acid transport and metabolism (10.5%) followed by transcription (8.4%) and signal transduction mechanisms (7.3%). We performed experimental analyses of the lipolytic activity and results showed activity mainly on short chain fatty acids. The genome analysis demonstrated the existence of two genes, lip515A and est515A, related to a triacylglycerol lipase and carboxylesterase, respectively. Ammonification genes were also observed, mainly nitrate reductase genes. Genes related with synthesis of poly-hydroxyalkanoates (PHAs), especially poly-hydroxybutyrates (PHBs), were detected. The phaABC and phbABC operons also appeared complete in the genome. P. extremaustralis strain USBA-GBX-515 conserves the same gene organization of the type strain CT14–3^T. We also thoroughly analyzed the potential for production of secondary metabolites finding close to 400 genes in 32 biosynthetic gene clusters involved in their production.