Pseudomonas aeruginosa isolated from marine environments in Tokyo Bay

The Iron Metalloproteome of Pseudomonas aeruginosa Under Oxic and Anoxic Conditions

Pseudomonas aeruginosa is a major contributor to human infections and is widely distributed in the environment. Its ability for growth under aerobic and anaerobic conditions provides adaptability to environmental changes and in confronting immune responses. We applied native 2-dimensional metalloproteomics to P. aeruginosa to examine how use of iron within the metallome responds to oxic and anoxic conditions. Analyses revealed four iron peaks comprised of metalloproteins with synergistic functions, including: 1) respiratory and metabolic enzymes, 2) oxidative stress response enzymes, 3) DNA synthesis and nitrogen assimilation enzymes, and 4) denitrification enzymes and related copper enzymes. Fe peaks were larger under anoxic conditions, consistent with increased iron demand due to anaerobic metabolism and with the denitrification peak absent under oxic conditions. Three ferritins co-eluted with the first and third iron peaks, localizing iron storage with these functions. Several enzymes were more abundant at low oxygen, including alkylhydroperoxide reductase C that deactivates organic radicals produced by denitrification, all three classes of ribonucleotide reductases (including monomers and oligomer forms), ferritin (increasing in ratio relative to bacterioferritin), and denitrification enzymes. Superoxide dismutase and homogentisate 1,2-dioxygenase were more abundant at high oxygen. Several Fe peaks contained iron metalloproteins that co-eluted earlier than their predicted size, implying additional protein-protein interactions and suggestive of cellular organization that contributes to iron prioritization in Pseudomonas with its large genome and flexible metabolism. This study characterized the iron metalloproteome of one of the more complex prokaryotic microorganisms, attributing enhanced iron use under anaerobic denitrifying metabolism to its specific metalloprotein constituents.

Investigation of the presence and persistence of bacteria in seawater and oysters from an aquaculture farm in Rehoboth Bay, Delaware

The filter-feeding nature of oysters, anthropogenic activities, and increasing agriculture in Delaware compromise the microbial safety of Eastern oysters from local aquaculture farms. From July to October 2023, we evaluated the presence and persistence of eight bacteria in seawater and oysters produced from off-bottom and bottom cultures at Sally Cove, an aquaculture farm within Rehoboth Bay in Delaware. A control site within Sally Cove, which was without oyster cultures, was also included in the study. Seawater temperature, salinity, pH, and dissolved oxygen were measured in situ during sampling. Molecular confirmation with PCR and qPCR showed that Vibrio parahaemolyticus, Shiga-toxin-producing Escherichia coli, Salmonella enterica, Staphylococcus aureus, Pseudomonas aeruginosa, and Clostridium spp. were present and persisted in seawater and oyster samples from both cultures at Sally Cove and in off-bottom and bottom seawater samples from the control site throughout the study. Shigella spp. and Listeria monocytogenes were consistently found in seawater and oyster samples from July to September. However, Shigella spp. was only detected in samples from the bottom cultures, whereas L. monocytogenes was undetectable in all samples from both cultures in October. The observed temperature, salinity, pH, and dissolved oxygen levels across the study period were in the range of 15.30-29.67°C, 29.33-31.87 ppt, 7.25-7.95, and 3.79-8.10 mg/L, respectively, and comparable with the conditions suitable for the growth and survival of these bacteria. These findings suggest that consuming raw oysters from Sally Cove poses contamination risks from several bacteria, especially in the summer months.IMPORTANCEAlthough studies have evaluated bacterial contamination in seawater and oysters within the Delaware Inland Bays and nearby areas, the focus has primarily been on Vibrio species. However, other bacteria have been found in seawater and seafood at various locations and could potentially occur in oysters produced from aquaculture farms within the Delaware Inland Bays. Sally Cove is an oyster aquaculture farm that produces Eastern oysters (Crassostrea virginica) for consumption in Delaware using both off-bottom and bottom culturing methods. The risk of bacterial contamination from consuming raw oysters from this farm is unknown. This paper shows the presence and persistence of several bacteria, including those associated with waste, in seawater and oysters at the farm. The findings can inform consumers about the contamination risks from consuming raw oysters produced at the farm.

Estimating taxonomic and functional structure along a tropical estuary: linking metabolic traits and aspects of ecosystem functioning

Microbial life forms are among the most ubiquitous on Earth, yet many remain understudied in Caribbean estuaries. We report on the prokaryote community composition of the Urabá Estuary in the Colombian Caribbean using 16S rRNA gene-transcript sequencing. We also assessed potential functional diversity through 38 metabolic traits inferred from 16S rRNA gene data. Water samples were collected from six sampling stations at two depths with contrasting light-penetration conditions along an approximately 100 km transect in the Gulf of Urabá in December 2019. Non-metric multidimensional scaling analysis grouped the samples into two distinct clusters along the transect and between depths. The primary variables influencing the prokaryote community composition were the sampling station, depth, salinity, and dissolved oxygen levels. Twenty percent of genera (i.e., 58 out 285) account for 95% of the differences between groups along the transect and among depths. All of the 38 metabolic traits studied showed some significant relationship with the tested environmental variables, especially salinity and except with temperature. Another non-metric multidimensional scaling analysis, based on community-weighted mean of traits, also grouped the samples in two clusters along the transect and over depth. Biodiversity facets, such as richness, evenness, and redundancy, indicated that environmental variations-stemming from river discharges-introduce an imbalance in functional diversity between surface prokaryote communities closer to the estuary's head and bottom communities closer to the ocean. Our research broadens the use of 16S rRNA gene transcripts beyond mere taxonomic assignments, furthering the field of trait-based prokaryote community ecology in transitional aquatic ecosystems.IMPORTANCEThe resilience of a dynamic ecosystem is directly tied to the ability of its microbes to navigate environmental gradients. This study delves into the changes in prokaryote community composition and functional diversity within the Urabá Estuary (Colombian Caribbean) for the first time. We integrate data from 16S rRNA gene transcripts (taxonomic and functional) with environmental variability to gain an understanding of this under-researched ecosystem using a multi-faceted macroecological framework. We found that significant shifts in prokaryote composition and in primary changes in functional diversity were influenced by physical-chemical fluctuations across the estuary's environmental gradient. Furthermore, we identified a potential disparity in functional diversity. Near-surface communities closer to the estuary's head exhibited differences compared to deeper communities situated farther away. Our research serves as a roadmap for posing new inquiries about the potential functional diversity of prokaryote communities in highly dynamic ecosystems, pushing forward the domain of multi-trait-based prokaryote community ecology.

Pseudomonas aeruginosa Isolates from Water Samples of the Gulf of Mexico Show Similar Virulence Properties but Different Antibiotic Susceptibility Profiles than Clinical Isolates

Pseudomonas aeruginosa is an opportunistic pathogen found in a wide variety of environments, including soil, water, and habitats associated with animals, humans, and plants. From a One Health perspective, which recognizes the interconnectedness of human, animal, and environmental health, it is important to study the virulence characteristics and antibiotic susceptibility of environmental bacteria. In this study, we compared the virulence properties and the antibiotic resistance profiles of seven isolates collected from the Gulf of Mexico with those of seven clinical strains of P. aeruginosa. Our results indicate that the marine and clinical isolates tested exhibit similar virulence properties; they expressed different virulence factors and were able to kill Galleria mellonella larvae, an animal model commonly used to analyze the pathogenicity of many bacteria, including P. aeruginosa. In contrast, the clinical strains showed higher antibiotic resistance than the marine isolates. Consistently, the clinical strains exhibited a higher prevalence of class 1 integron, an indicator of anthropogenic impact, compared with the marine isolates. Thus, our results indicate that the P. aeruginosa marine strains analyzed in this study, isolated from the Gulf of Mexico, have similar virulence properties, but lower antibiotic resistance, than those from hospitals.

Genomic and metabolic versatility of Pseudomonas aeruginosa contributes to its inter-kingdom transmission and survival

Pseudomonas aeruginosa is one of the most versatile bacteria with renowned pathogenicity and extensive drug resistance. The diverse habitats of this bacterium include fresh, saline and drainage waters, soil, moist surfaces, taps, showerheads, pipelines, medical implants, nematodes, insects, plants, animals, birds and humans. The arsenal of virulence factors produced by P. aeruginosa includes pyocyanin, rhamnolipids, siderophores, lytic enzymes, toxins and polysaccharides. All these virulent elements coupled with intrinsic, adaptive and acquired antibiotic resistance facilitate persistent colonization and lethal infections in different hosts. To date, treating pulmonary diseases remains complicated due to the chronic secondary infections triggered by hospital-acquired P. aeruginosa. On the contrary, this bacterium can improve plant growth by suppressing phytopathogens and insects. Notably, P. aeruginosa is one of the very few bacteria capable of trans-kingdom transmission and infection. Transfer of P. aeruginosa strains from plant materials to hospital wards, animals to humans, and humans to their pets occurs relatively often. Recently, we have identified that plant-associated P. aeruginosa strains could be pathologically similar to clinical isolates. In this review, we have highlighted the genomic and metabolic factors that facilitate the dominance of P. aeruginosa across different biological kingdoms and the varying roles of this bacterium in plant and human health.

Four Novel Caudoviricetes Bacteriophages Isolated from Baltic Sea Water Infect Colonizers of Aurelia aurita

The moon jellyfish Aurelia aurita is associated with a highly diverse microbiota changing with provenance, tissue, and life stage. While the crucial relevance of bacteria to host fitness is well known, bacteriophages have often been neglected. Here, we aimed to isolate virulent phages targeting bacteria that are part of the A. aurita-associated microbiota. Four phages (Staphylococcus phage BSwM KMM1, Citrobacter phages BSwM KMM2-BSwM KMM4) were isolated from the Baltic Sea water column and characterized. Phages KMM2/3/4 infected representatives of Citrobacter, Shigella, and Escherichia (Enterobacteriaceae), whereas KMM1 infected Gram-positive Staphylococcus spp. All phages showed an up to 99% adsorption to host cells within 5 min, short latent periods (around 30 min), large burst sizes (mean of 128 pfu/cell), and high efficiency of plating (EOP > 0.5), demonstrating decent virulence, efficiency, and infectivity. Transmission electron microscopy and viral genome analysis revealed that all phages are novel species and belong to the class of Caudoviricetes harboring a tail and linear double-stranded DNA (formerly known as Siphovirus-like (KMM3) and Myovirus-like (KMM1/2/4) bacteriophages) with genome sizes between 50 and 138 kbp. In the future, these isolates will allow manipulation of the A. aurita-associated microbiota and provide new insights into phage impact on the multicellular host.

Genetic and environmental determinants of surface adaptations in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a well-studied Gram-negative opportunistic bacterium that thrives in markedly varied environments. It is a nutritionally versatile microbe that can colonize a host as well as exist in the environment. Unicellular, planktonic cells of P. aeruginosa can come together to perform a coordinated swarming movement or turn into a sessile, surface-adhered population called biofilm. These collective behaviours produce strikingly different outcomes. While swarming motility rapidly disseminates the bacterial population, biofilm collectively protects the population from environmental stresses such as heat, drought, toxic chemicals, grazing by predators, and attack by host immune cells and antibiotics. The ubiquitous nature of P. aeruginosa is likely to be supported by the timely transition between planktonic, swarming and biofilm lifestyles. The social behaviours of this bacteria viz biofilm and swarm modes are controlled by signals from quorum-sensing networks, LasI-LasR, RhlI-RhlR and PQS-MvfR, and several other sensory kinases and response regulators. A combination of environmental and genetic cues regulates the transition of the P. aeruginosa population to specific states. The current review is aimed at discussing key factors that promote physiologically distinct transitioning of the P. aeruginosa population.

Degradation potential of alkanes by diverse oil-degrading bacteria from deep-sea sediments of Haima cold seep areas, South China Sea

Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. Parvibaculum, Erythrobacter, Acinetobacter, Alcanivorax, Pseudomonas, Marinobacter, Halomonas, and Idiomarina were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to Acinetobacter, Alcanivorax, Kangiella, Limimaricola, Marinobacter, Flavobacterium, and Paracoccus, whose degradation rates were higher in crude oil (70.3–78.0%) than that in diesel oil (62.7–66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, Kangiella aquimarina F7, Acinetobacter venetianus F1, Limimaricola variabilis F8, Marinobacter nauticus J5, Flavobacterium sediminis N3, and Paracoccus sediminilitoris N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.

Fluid dynamics and cell‐bound Psl polysaccharide allows microplastic capture, aggregation and subsequent sedimentation by Pseudomonas aeruginosa in water

Decades after incorporating plastics into consumer markets, research shows that these polymers have spread worldwide. Fragmentation of large debris leads to smaller particles, collectively called microplastics (MPs), which have become ubiquitous in aquatic environments. A fundamental aspect of understanding the implications of MP contamination on ecosystems is resolving the complex interactions of these artificial substrates with microbial cells. Using polystyrene microparticles as model polymers, we conducted an exploratory study where these interactions are quantitatively analyzed using an in vitro system consisting of single‐bacterial species capturing and aggregating MPs in water. Here we show that the production of Psl exopolysaccharide by Pseudomonas aeruginosa (PA) does not alter MPs colloidal stability but plays a key role in microspheres adhesion to the cell surface. Further aggregation of MPs by PA cells depends on bacterial mobility and the presence of sufficient flow to prevent rapid sedimentation of early MP‐PA assembles. Surprisingly, cells in MP‐PA aggregates are not in a sessile state despite the production of Psl, enhancing the motility of the aggregates by an order of magnitude relative to passive diffusion. The generated data could inform the creation of predictive models that accurately describe the dynamics and influence of bacterial growth on plastics debris.

Changes in the Microbial Community of the Mottled Skate (Beringraja pulchra) During Alkaline Fermentation

Beringraja pulchra, Cham-hong-eo in Korean, is a mottled skate which is belonging to the cartilaginous fish. Although this species is economically valuable in South Korea as an alkalinefermented food, there are few microbial studies on such fermentation. Here, we analyzed microbial changes and pH before, during, and after fermentation and examined the effect of inoculation by a skin microbiota mixture on the skate fermentation (control vs. treatment). To analyze microbial community, the V4 regions of bacterial 16S rRNA genes from the skates were amplified, sequenced and analyzed. During the skate fermentation, pH and total number of marine bacteria increased in both groups, while microbial diversity decreased after fermentation. Pseudomonas, which was predominant in the initial skate, declined by fermentation (Day 0: 11.39 ± 5.52%; Day 20: 0.61 ± 0.9%), while the abundance of Pseudoalteromonas increased dramatically (Day 0: 1.42 ± 0.41%; Day 20: 64.92 ± 24.15%). From our co-occurrence analysis, the Pseudoalteromonas was positively correlated with Aerococcaceae (r = 0.638) and Moraxella (r = 0.474), which also increased with fermentation, and negatively correlated with Pseudomonas (r = -0.847) during fermentation. There are no critically significant differences between control and treatment. These results revealed that the alkaline fermentation of skates dramatically changed the microbiota, but the initial inoculation by a skin microbiota mixture didn't show critical changes in the final microbial community. Our results extended understanding of microbial interactions and provided the new insights of microbial changes during alkaline fermentation.

Pseudomonas sivasensis sp. nov. isolated from farm fisheries in Turkey

A study of 91 isolates from fish farms in Turkey showed that isolates P7^T, P11, P24b, P29, P72, P73 and P158 belonged to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. The analysis of the sequences of the RNA polymerase sigma factor gene (rpoD) located these strains in the Pseudomonas fluorescens lineage of species within the P. fluorescens subgroup, close to the cluster composed of the species Pseudomonas grimontii, Pseudomonas marginalis and Pseudomonas panacis. Based on similarities in the 16S rRNA and rpoD gene sequences of three previously isolated strains from other origins (CCUG 57209, CCUG 62357 and W5.2-93) linked them to the same cluster. A polyphasic taxonomic approach including phenotypic characterization, fatty acid composition, and multilocus sequence analysis, together with whole-cell MALDI-TOF data, corroborated this assumption. The genome G+C mol% contents were 59.48 and 59.71, respectively. The average nucleotide indices based on BLAST analysis and the genome-to-genome distance calculation for the P7^T and CCUG 57209 strains with their closest relative, P. grimontii, were 88.16-88.29% and 38.10-38.20%, respectively. These data confirm that isolates P7^T, P11, P24b, P29, P72, P73, P158, CCUG 57209, CCUG 62357 and W5.2-93 represent a new species for which the name Pseudomonas sivasensis is proposed, with P7^T as a type strain (=CCUG 74260^T= and CECT30107^T).

Simple approach for the rapid estimation of BOD5 in food processing wastewater

A simple approach was developed for the rapid and accurate estimation of 5-day biochemical oxygen demand (BOD₅) in food processing wastewater. Immobilization of the natural microbial consortium that was collected from an aerobic compartment of a food processing wastewater treatment plant was simply performed by adhesion using a low-cost porous carrier. Pseudomonas aeruginosa, Bacillus cereus, and Streptomyces, whose salt-tolerance and ability to break down organic compounds have been widely reported, were found to be predominant. These microorganisms may cause an enhancement of the bioreactor response in the presence of sodium chloride. Consequently, a modified glucose-glutamic acid (GGA) calibration standard was proposed in which an appropriate amount of NaCl was added; this solution was found to be more effective in terms of accuracy and practicality than both conventional GGA and the synthetic wastewater recipe from the Organisation for Economic Cooperation and Development (OECD). The calibrated self-built packed-bed bioreactor exhibited good precision of 3% or less in predicting BOD₅ in influent, which is similar to the performance of the most common commercial biochemical oxygen demand (BOD) bioreactors. There was a statistical agreement between the results obtained from this rapid BOD biosensor and the conventional methods, even when testing treated wastewater samples.

Breakdown of Vibrio cholerae biofilm architecture induced by antibiotics disrupts community barrier function

Bacterial cells in nature are frequently exposed to changes in their chemical environment1,2. The response mechanisms of isolated cells to such stimuli have been investigated in great detail. By contrast, little is known about the emergent multicellular responses to environmental changes, such as antibiotic exposure3-7, which may hold the key to understanding the structure and functions of the most common type of bacterial communities: biofilms. Here, by monitoring all individual cells in Vibrio cholerae biofilms during exposure to antibiotics that are commonly administered for cholera infections, we found that translational inhibitors cause strong effects on cell size and shape, as well as biofilm architectural properties. We identified that single-cell-level responses result from the metabolic consequences of inhibition of protein synthesis and that the community-level responses result from an interplay of matrix composition, matrix dissociation and mechanical interactions between cells. We further observed that the antibiotic-induced changes in biofilm architecture have substantial effects on biofilm population dynamics and community assembly by enabling invasion of biofilms by bacteriophages and intruder cells of different species. These mechanistic causes and ecological consequences of biofilm exposure to antibiotics are an important step towards understanding collective bacterial responses to environmental changes, with implications for the effects of antimicrobial therapy on the ecological succession of biofilm communities.

Removal of Bacteria from Solids by Bubbles: Effect of Solid Wettability, Interaction Geometry, and Liquid-Vapor Interface Velocity

Air bubbles are a promising means of controlling fouling for a range of applications, particularly delaying fouling in marine environments. This work investigates the mechanism by which the collision of an air bubble with a solid removes adsorbed bacteria. A key feature of the work is that the numbers of bacteria were monitored via video microscopy throughout the collision; so, we were able to explore the mechanism of bacteria removal. When a bubble collides with a solid, an air-liquid interface crosses the solid twice, and we were able to distinguish the effects of the first and second air-liquid interfaces. The bacterium Pseudomonas aeruginosa was allowed to adhere to smooth poly(dimethylsiloxane) and then a collision with a bubble was investigated for one of three different approach geometries: perpendicular, parallel, and oscillating parallel to the solid surface. Other factors examined were the speed of the bubble, the duration of bacterial adhesion on the solid surface, and the wettability of the solid. Surface wettability was identified as the most significant factor. When the solid dewet, almost all bacteria were removed from hydrophobic surfaces upon the passage of the first air-liquid interface. In contrast, when a thin liquid film remained between the solid and the bubble (a hydrophilic solid), variable amounts of bacteria remained. Although almost all bacteria were initially removed from hydrophobic solids, many bacteria were redeposited on hydrophobic surfaces upon the passage of the second air-liquid interface, especially when the first and second air-liquid interfaces moved in opposite directions. As described previously, a lower velocity of the bubble allows more time for the thin liquid film to drain and improved removal efficiency on hydrophilic solids. A rougher solid (8 μm diameter hemispherical protrusions) decreased the detachment efficiency because bacteria and liquid were able to shelter in concavities.

Generalized Growth of Estuarine, Household and Clinical Isolates of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen of particular concern to immune-compromised people, such as cystic fibrosis patients and burn victims. These bacteria grow in built environments including hospitals and households, and in natural environments such as rivers and estuaries. However, there is conflicting evidence whether recent environments like the human lung and open ocean affect P. aeruginosa growth performance in alternate environments. We hypothesized that bacteria recently isolated from dissimilar habitats should grow differently in media containing artificial versus natural resources. To test this idea, we examined growth of P. aeruginosa isolates from three environments (estuary, household, and clinic) in three media types: minimal-glucose lab medium, and media prepared from sugar maple leaves or big bluestem grass. We used automated spectrophotometry to measure high-resolution growth curves for all isolate by media combinations, and studied two fitness parameters: growth rate and maximum population density. Results showed high variability in growth rate among isolates, both overall and in its dependence on assay media, but this variability was not associated with habitat of isolation. In contrast, total growth (change in absorbance over the experiment) differed overall among habitats of isolation, and there were media-specific differences in mean total growth among habitats of isolation, and in among-habitat variability in the media-specific response. This was driven primarily by greater total growth of estuary isolates when compared with those from other habitats of origin, and greater media-specific variability among household isolates than those from other habitats of origin. Taken together, these results suggest that for growth rate P. aeruginosa bacteria appear to be broad generalists without regard to current or recent habitat, whereas for total growth a signature of recent ecological history can be detected.

Prevalence and antibiotic resistance of Pseudomonas aeruginosa in water samples in central Italy and molecular characterization of oprD in imipenem resistant isolates

Scope

This study aimed to analyse the prevalence, antibiotic resistance and genetic relatedness of P. aeruginosa isolates obtained from potable and recreational water samples (n. 8,351) collected from different settings (swimming pools, n. 207; healthcare facilities, n 1,684; accommodation facilities, n. 1,518; municipal waterworks, n. 4,500; residential buildings, n. 235). Possible mechanisms underlying resistance to imipenem, with particular focus on those involving oprD-based uptake, were also explored.

Methods and results

Isolation and identification of Pseudomonas aeruginosa was performed according to the standardized procedure UNI EN ISO 16266:2008 followed by PCR confirmation. Antibiotic Susceptibility testing was conducted according to EUCAST standardized disk diffusion method. Genetic relatedness of strains was carried out by RAPD. The sequence of the oprD gene was analyzed by standard method. Fifty-three samples (0.63%) were positive for P. aeruginosa, of which 10/207 (4.83%) were from swimming pools. Five isolates (9.43%) were resistant to imipenem, one to Ticarcillin + Clavulanate, one to both Piperacillin and Ticarcillin + Clavulanate. The highest isolation rate of imipenem resistant P. aeruginosa was observed in swimming pool water. Identical RAPD profiles were found in isolates from the same location in the same year or even in different years.

Conclusions

Imipenem resistant strains were identified as carbapenemase-negative and resistance has been associated with inactivating mutations within the oprD gene, with a concomitant loss of porin. RAPD results proved that a water system can remain colonized by one strain for long periods and the contamination may be difficult to eradicate.

This study has revealed the presence of P. aeruginosa in different water samples, including resistant strains, especially in swimming pools, and confirmed the role of porins as a contributing factor in carbapenem resistance in Gram-negative bacteria.

Acute Hepatopancreatic Necrosis Disease-Causing Vibrio parahaemolyticus Strains Maintain an Antibacterial Type VI Secretion System with Versatile Effector Repertoires

Acute hepatopancreatic necrosis disease (AHPND) is a newly emerging shrimp disease that has severely damaged the global shrimp industry. AHPND is caused by toxic strains of Vibrio parahaemolyticus that have acquired a "selfish plasmid" encoding the deadly binary toxins PirA^vp/PirB^vp To better understand the repertoire of virulence factors in AHPND-causing V. parahaemolyticus, we conducted a comparative analysis using the genome sequences of the clinical strain RIMD2210633 and of environmental non-AHPND and toxic AHPND isolates of V. parahaemolyticus Interestingly, we found that all of the AHPND strains, but none of the non-AHPND strains, harbor the antibacterial type VI secretion system 1 (T6SS1), which we previously identified and characterized in the clinical isolate RIMD2210633. This finding suggests that the acquisition of this T6SS might confer to AHPND-causing V. parahaemolyticus a fitness advantage over competing bacteria and facilitate shrimp infection. Additionally, we found highly dynamic effector loci in the T6SS1 of AHPND-causing strains, leading to diverse effector repertoires. Our discovery provides novel insights into AHPND-causing pathogens and reveals a potential target for disease control.IMPORTANCE Acute hepatopancreatic necrosis disease (AHPND) is a serious disease that has caused severe damage and significant financial losses to the global shrimp industry. To better understand and prevent this shrimp disease, it is essential to thoroughly characterize its causative agent, Vibrio parahaemolyticus Although the plasmid-encoded binary toxins PirA^vp/PirB^vp have been shown to be the primary cause of AHPND, it remains unknown whether other virulent factors are commonly present in V. parahaemolyticus and might play important roles during shrimp infection. Here, we analyzed the genome sequences of clinical, non-AHPND, and AHPND strains to characterize their repertoires of key virulence determinants. Our studies reveal that an antibacterial type VI secretion system is associated with the AHPND strains and differentiates them from non-AHPND strains, similar to what was seen with the PirA/PirB toxins. We propose that T6SS1 provides a selective advantage during shrimp infections.

Bile salt receptor complex activates a pathogenic type III secretion system

Bile is an important component of the human gastrointestinal tract with an essential role in food absorption and antimicrobial activities. Enteric bacterial pathogens have developed strategies to sense bile as an environmental cue to regulate virulence genes during infection. We discovered that Vibrio parahaemolyticus VtrC, along with VtrA and VtrB, are required for activating the virulence type III secretion system 2 in response to bile salts. The VtrA/VtrC complex activates VtrB in the presence of bile salts. The crystal structure of the periplasmic domains of the VtrA/VtrC heterodimer reveals a β-barrel with a hydrophobic inner chamber. A co-crystal structure of VtrA/VtrC with bile salt, along with biophysical and mutational analysis, demonstrates that the hydrophobic chamber binds bile salts and activates the virulence network. As part of a family of conserved signaling receptors, VtrA/VtrC provides structural and functional insights into the evolutionarily conserved mechanism used by bacteria to sense their environment.

Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River Estuary, China

Viruses are the most abundant biological entities in the oceans, and encompass a significant reservoir of genetic diversity. However, little is known about their biodiversity in estuary environments, which represent a highly dynamic and potentially more diverse habitat. Here, we report a metagenomic analysis of the dsDNA viral community from the Jiulong River Estuary (JRE), China, and provide a comparative analysis with other closely related environments. The results showed that the majority of JRE virome did not show any significant similarity to the database. For the major viral group (Caudovirales) detected in the sample, Podoviridae (44.88%) were the most abundant family, followed by Siphoviridae (32.98%) and Myoviridae (17.32%). The two most abundant viruses identified in the virome were phages HTVC010P and HMO-2011, which infect bacteria belonging to marine SAR11 and SAR116 clades, respectively. Two contigs larger than 20 kb, which show similar overall genome architectures to Celeribacter phage P12053L and Thalosomonas phage BA3, respectively, were generated during assembly. Comparative analysis showed that the JRE virome was more similar to marine viromes than to freshwater viromes, and shared a relative coarse-grain genetic overlap (averaging 14.14% ± 1.68%) with other coastal viromes. Our study indicated that the diversity and community structure of the virioplankton found in JRE were mainly affected by marine waters, with less influence from freshwater discharge.

Rhamnolipids in perspective: gene regulatory pathways, metabolic engineering, production and technological forecasting

Rhamnolipids have emerged as a very promising class of biosurfactants in the last decades, exhibiting properties of great interest in several industrial applications, and have represented a suitable alternative to chemically-synthesized surfactants. This class of biosurfactants has been extensively studied in recent years, aiming at their large-scale production based on renewable resources, which still require high financial costs. Development of non-pathogenic, high-producing strains has been the focus of a number of studies involving heterologous microbial hosts as platforms. However, the intricate gene regulation network controlling rhamnolipid biosynthesis represents a challenge to metabolic engineering and remains to be further understood and explored. This article provides an overview of the biosynthetic pathways and the main gene regulatory factors involved in rhamnolipid production within Pseudomonas aeruginosa, the prototypal producing species. In addition, we provide a perspective view into the main strategies applied to metabolic engineering and biotechnological production.

Extracellular proteases are released by ciliates in defined seawater microcosms

The biodegradation of proteins in seawater requires various proteases which are commonly thought to be mainly derived from heterotrophic bacteria. We, however, found that protists showed a high protease activity and continuously produced trypsin-type enzymes. The free-living marine heterotrophic ciliate Paranophrys marina together with an associated bacterium was isolated and used for microcosm incubation with different concentrations of killed bacteria as food for 10 days. The results showed that the co-existence of the ciliate with its associated bacterium produced a significant protease activity in both cell-associated and cell-free fractions while that in the associated bacterium only microcosm was negligible. The protease profiles are different between cell-associated and cell-free fractions, and a trypsin-type enzyme hydrolyzing Boc-Val-Leu-Lys-MCA was detected throughout the period in the presence of ciliates. This suggests that ciliates release proteases into the surrounding environment which could play a role in protein digestion outside cells. It has been previously suggested that bacteria are the major transformers in seawater. We here present additional data which indicates that protists, or at least ciliates with their specific enzymes, are a potential player in organic matter degradation in water columns.

A comparative study of coastal and clinical isolates of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium having a versatile metabolic potential and great ecological and clinical significance. The geographical distribution of P. aeruginosahas revealed the existence of an unbiased genetic arrangement in terrestrial isolates. In contrast, there are very few reports about P. aeruginosa strains from marine environments. The present work was aimed at studying the distribution of P. aeruginosa in coastal waters along the Indian Peninsula and understanding the environmental influence on genotypic, metabolic and phenotypic characteristics by comparing marine and clinical isolates. Of the 785 marine isolates obtained on selective media, only 32 (~4.1%) were identified as P. aeruginosa, based on their fatty acid methyl ester profiles. A low Euclidian distance value (< 2.5) obtained from chemotaxonomic analysis suggested that all the environmental (coastal and marine) isolates originated from a single species. While UPGMA analyses of AP-PCR and phenotypic profiles separated the environmental and clinical isolates, fatty acid biotyping showed overlapping between most clinical and environmental isolates. Our study revealed the genetic diversity among different environmental isolates of P. aeruginosa. While biogeographical separation was not evident based solely on phenotypic and metabolic typing, genomic and metatranscriptomic studies are more likely to show differences between these isolates. Thus, newer and more insightful methods are required to understand the ecological distribution of this complex group of bacteria.

NrsZ: a novel, processed, nitrogen-dependent, small non-coding RNA that regulates Pseudomonas aeruginosa PAO1 virulence

The opportunistic pathogen Pseudomonas aeruginosa PAO1 has a remarkable capacity to adapt to various environments and to survive with limited nutrients. Here, we report the discovery and characterization of a novel small non-coding RNA: NrsZ (nitrogen-regulated sRNA). We show that under nitrogen limitation, NrsZ is induced by the NtrB/C two component system, an important regulator of nitrogen assimilation and P. aeruginosa's swarming motility, in concert with the alternative sigma factor RpoN. Furthermore, we demonstrate that NrsZ modulates P. aeruginosa motility by controlling the production of rhamnolipid surfactants, virulence factors notably needed for swarming motility. This regulation takes place through the post-transcriptional control of rhlA, a gene essential for rhamnolipids synthesis. Interestingly, we also observed that NrsZ is processed in three similar short modules, and that the first short module encompassing the first 60 nucleotides is sufficient for NrsZ regulatory functions.

Diversity among strains of Pseudomonas aeruginosa from manure and soil, evaluated by multiple locus variable number tandem repeat analysis and antibiotic resistance profiles

The results of a multiple locus variable number of tandem repeat (VNTR) analysis (MLVA)-based study designed to understand the genetic diversity of soil and manure-borne Pseudomonas aeruginosa isolates, and the relationship between these isolates and a set of clinical and environmental isolates, are hereby reported. Fifteen described VNTR markers were first selected, and 62 isolates recovered from agricultural and industrial soils in France and Burkina Faso, and from cattle and horse manure, along with 26 snake-related isolates and 17 environmental and clinical isolates from international collections, were genotyped. Following a comparison with previously published 9-marker MLVA schemes, an optimal 13-marker MLVA scheme (MLVA13-Lyon) was identified that was found to be the most efficient, as it showed high typability (90%) and high discriminatory power (0.987). A comparison of MLVA with PFGE for typing of the snake-related isolates confirmed the MLVA13-Lyon scheme to be a robust method for quickly discriminating and inferring genetic relatedness among environmental isolates. The 62 isolates displayed wide diversity, since 41 MLVA types (i.e. MTs) were observed, with 26 MTs clustered in 10 MLVA clonal complexes (MCs). Three and eight MCs were found among soil and manure isolates, respectively. Only one MC contained both soil and manure-borne isolates. No common MC was observed between soil and manure-borne isolates and the snake-related or environmental and clinical isolates. Antibiotic resistance profiles were performed to determine a potential link between resistance properties and the selective pressure that might be present in the various habitats. Except for four soil and manure isolates resistant to ticarcillin and ticarcillin/clavulanic acid and one isolate from a hydrocarbon-contaminated soil resistant to imipenem, all environmental isolates showed wild-type antibiotic profiles.

Vibrio parahaemolyticus type VI secretion system 1 is activated in marine conditions to target bacteria, and is differentially regulated from system 2

Vibrio parahaemolyticus is a marine bacterium that thrives in warm climates. It is a leading cause of gastroenteritis resulting from consumption of contaminated uncooked shellfish. This bacterium harbors two putative type VI secretion systems (T6SS). T6SSs are widespread protein secretion systems found in many Gram-negative bacteria, and are often tightly regulated. For many T6SSs studied to date, the conditions and cues, as well as the regulatory mechanisms that control T6SS activity are unknown. In this study, we characterized the environmental conditions and cues that activate both V. parahaemolyticus T6SSs, and identified regulatory mechanisms that control T6SS gene expression and activity. We monitored the expression and secretion of the signature T6SS secreted proteins Hcp1 and Hcp2, and found that both T6SSs are differentially regulated by quorum sensing and surface sensing. We also showed that T6SS1 and T6SS2 require different temperature and salinity conditions to be active. Interestingly, T6SS1, which is found predominantly in clinical isolates, was most active under warm marine-like conditions. Moreover, we found that T6SS1 has anti-bacterial activity under these conditions. In addition, we identified two transcription regulators in the T6SS1 gene cluster that regulate Hcp1 expression, but are not required for immunity against self-intoxication. Further examination of environmental isolates revealed a correlation between the presence of T6SS1 and virulence of V. parahaemolyticus against other bacteria, and we also showed that different V. parahaemolyticus isolates can outcompete each other. We propose that T6SS1 and T6SS2 play different roles in the V. parahaemolyticus lifestyles, and suggest a role for T6SS1 in enhancing environmental fitness of V. parahaemolyticus in marine environments when competing for a niche in the presence of other bacterial populations.

Homeostasis and catabolism of choline and glycine betaine: lessons from Pseudomonas aeruginosa

Most sequenced bacteria possess mechanisms to import choline and glycine betaine (GB) into the cytoplasm. The primary role of choline in bacteria appears to be as the precursor to GB, and GB is thought to primarily act as a potent osmoprotectant. Choline and GB may play accessory roles in shaping microbial communities, based on their limited availability and ability to enhance survival under stress conditions. Choline and GB enrichment near eukaryotes suggests a role in the chemical relationships between these two kingdoms, and some of these interactions have been experimentally demonstrated. While many bacteria can convert choline to GB for osmoprotection, a variety of soil- and water-dwelling bacteria have catabolic pathways for the multistep conversion of choline, via GB, to glycine and can thereby use choline and GB as sole sources of carbon and nitrogen. In these choline catabolizers, the GB intermediate represents a metabolic decision point to determine whether GB is catabolized or stored as an osmo- and stress protectant. This minireview focuses on this decision point in Pseudomonas aeruginosa, which aerobically catabolizes choline and can use GB as an osmoprotectant and a nutrient source. P. aeruginosa is an experimentally tractable and ecologically relevant model to study the regulatory pathways controlling choline and GB homeostasis in choline-catabolizing bacteria. The study of P. aeruginosa associations with eukaryotes and other bacteria also makes this a powerful model to study the impact of choline and GB, and their associated regulatory and catabolic pathways, on host-microbe and microbe-microbe relationships.

Interspecies interaction between Pseudomonas aeruginosa and other microorganisms

Microbes interact with each other in multicellular communities and this interaction enables certain microorganisms to survive in various environments. Pseudomonas aeruginosa is a highly adaptable bacterium that ubiquitously inhabits diverse environments including soil, marine habitats, plants and animals. Behind this adaptivity, P. aeruginosa has abilities not only to outcompete others but also to communicate with each other to develop a multispecies community. In this review, we focus on how P. aeruginosa interacts with other microorganisms. P. aeruginosa secretes antimicrobial chemicals to compete and signal molecules to cooperate with other organisms. In other cases, it directly conveys antimicrobial enzymes to other bacteria using the Type VI secretion system (T6SS) or membrane vesicles (MVs). Quorum sensing is a central regulatory system used to exert their ability including antimicrobial effects and cooperation with other microbes. At least three quorum sensing systems are found in P. aeruginosa, Las, Rhl and Pseudomonas quinolone signal (PQS) systems. These quorum-sensing systems control the synthesis of extracellular antimicrobial chemicals as well as interaction with other organisms via T6SS or MVs. In addition, we explain the potential of microbial interaction analysis using several micro devices, which would bring fresh sensitivity to the study of interspecies interaction between P. aeruginosa and other organisms.

Use of intestinal Pseudomonas aeruginosa in fish to detect the environmental pollutant benzo[a]pyrene

This study examined the potential of Pseudomonas aeruginosa abundance in the intestines of fish as an indicator of exposure to benzo[a]pyrene (BaP). P. aeruginosa populations were enumerated in juvenile African catfish (Clarias gariepinus) injected intramuscularly three days previous with 0, 10, 30, 40, 50 or 70mg/kg of BaP. Hepatic EROD and GST activities and biliary fluorescent aromatic compounds (FACs) 1-OH BaP, 3-OH BaP, 7,8-D BaP and BaP were quantified to investigate agreements between the new indicator and established fish biomarkers. The shape of bacterial population (logarithm of colony-forming unit) dose-response curve generally matched those of biliary FACs concentrations. Conversely, the EROD and GST dose-response curves were generally the mirror images of the bacterial population curve. Changes in intestinal P. aeruginosa population appear to be an indirect effect of BaP exposure because exposure to 0-100μg/ml BaP had no effect on P. aeruginosa populations grown on agar plates containing BaP. Using intestinal P. aeruginosa population of fish as a universal indicator of BaP pollution in aquatic environments is discussed.Conversely, the EROD and GST dose-response curves were generally the mirror images of the bacterial population curve.

BqsR/BqsS constitute a two-component system that senses extracellular Fe(II) in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitous gram-negative bacterium best known as the predominant opportunistic pathogen infecting the lungs of cystic fibrosis patients. In this context, it is thought to form biofilms, within which locally reducing and acidic conditions can develop that favor the stability of ferrous iron [Fe(II)]. Because iron is a signal that stimulates biofilm formation, we performed a microarray study to determine whether P. aeruginosa strain PA14 exhibits a specific transcriptional response to extracellular Fe(II). Among the genes that were most upregulated in response to Fe(II) were those encoding the two-component system BqsR/BqsS, previously identified for its role in P. aeruginosa strain PAO1 biofilm decay (13); here, we demonstrate its role in extracellular Fe(II) sensing. bqsS and bqsR form an operon together with two small upstream genes, bqsP and bqsQ, and one downstream gene, bqsT. BqsR/BqsS sense extracellular Fe(II) at physiologically relevant concentrations (>10 μM) and elicit a specific transcriptional response, including its autoregulation. The sensor distinguishes between Fe(II), Fe(III), and other dipositive cations [Ca(II), Cu(II), Mg(II), Mn(II), Zn(II)] under aerobic or anaerobic conditions. The gene that is most upregulated by BqsR/BqsS, as measured by quantitative reverse transcription-PCR (qRT-PCR), is PA14_04180, which is predicted to encode a periplasmic oligonucleotide/oligosaccharide-binding domain (OB-fold) protein. Coincident with phenazine production during batch culture growth, Fe(II) becomes the majority of the total iron pool and bqsS is upregulated. The existence of a two-component system that senses Fe(II) indicates that extracellular Fe(II) is an important environmental signal for P. aeruginosa.

Rapid and sensitive detection of Pseudomonas aeruginosa in chlorinated water and aerosols targeting gyrB gene using real-time PCR

AIMS

For the rapid detection of Pseudomonas aeruginosa from chlorinated water and aerosols, gyrB gene-based real-time PCR assay was developed and investigated.

METHODS AND RESULTS

Two novel primer sets (pa722F/746MGB/899R and pa722F/746MGB/788R) were designed using the most updated 611 Pseudomonas and 748 other bacterial gyrB genes for achieving high specificity. Their specificity showed 100% accuracy when tested with various strains including clinical isolates from cystic fibrosis patients. The assay was tested with Ps. aeruginosa-containing chlorinated water and aerosols to simulate the waterborne and airborne transmission routes (detection limit 3·3 × 10² CFU per PCR-2·3 × 10³ CFU per PCR). No chlorine interference in real-time PCR was observed at drinking water level (c. 1 mg l⁻¹), but high level of chorine (12 mg l⁻¹) interfered the assay, and thus neutralization was needed. Pseudomonas aeruginosa in aerosol was successfully detected after capturing with gelatin filters with minimum 2 min of sampling time when the initial concentration of 10⁴ CFU ml⁻¹ bacteria existed in the nebulizer.

CONCLUSIONS

A highly specific and rapid assay (2-3 h) was developed by targeting gyrB gene for the detection of Ps. aeruginosa in chlorinated water and aerosols, combined with optimized sample collection methods and sample processing, so the direct DNA extraction from either water or aerosol was possible while achieving the desired sensitivity of the method.

SIGNIFICANCE AND IMPACT OF THE STUDY

  The new assay can provide timely and accurate risk assessment to prevent Ps. aeruginosa exposure from water and aerosol, resulting in reduced disease burden, especially among immune-compromised and susceptible individuals. This approach can be easily utilized as a platform technology for the detection of other types of micro-organisms, especially for those that are transmitted via water and aerosol routes, such as Legionella pneumophila.

Lyngbyoic acid, a "tagged" fatty acid from a marine cyanobacterium, disrupts quorum sensing in Pseudomonas aeruginosa

Quorum sensing (QS) is a mechanism of bacterial gene regulation in response to increases in population density. Perhaps most studied are QS pathways mediated by acylhomoserine lactones (AHLs) in Gram-negative bacteria. Production of small molecule QS signals, their accumulation within a diffusion-limited environment and their binding to a LuxR-type receptor trigger QS-controlled gene regulatory cascades. In Pseudomonas aeruginosa, for example, binding of AHLs to their cognate receptors (LasR, RhlR) controls production of virulence factors, pigments, antibiotics and other behaviors important for its interactions with eukaryotic hosts and other bacteria. We have previously shown that marine cyanobacteria produce QS-inhibitory molecules, including 8-epi-malyngamide C (1), malyngamide C (2) and malyngolide (3). Here we isolated a new small cyclopropane-containing fatty acid, lyngbyoic acid (4), as a major metabolite of the marine cyanobacterium, Lyngbya cf. majuscula, collected at various sites in Florida. We screened 4 against four reporters based on different AHL receptors (LuxR, AhyR, TraR and LasR) and found that 4 most strongly affected LasR. We also show that 4 reduces pyocyanin and elastase (LasB) both on the protein and transcript level in wild-type P. aeruginosa, and that 4 directly inhibits LasB enzymatic activity. Conversely, dodecanoic acid (9) increased pyocyanin and LasB, demonstrating that the fused cyclopropane "tag" is functionally relevant and potentially confers resistance to β-oxidation. Global transcriptional effects of 4 in some ways replicate the gene expression changes of P. aeruginosa during chronic lung infections of cystic fibrosis patients, with reduced lasR signaling, increased biofilm and expression of the virulence locus HSI-I. Compound 4 may therefore prove to be a useful tool in the study of P. aeruginosa adaption during such chronic infections.

Differences of genetic diversity and antibiotics susceptibility of Pseudomonas aeruginosa isolated from hospital, river and coastal seawater

Pseudomonas aeruginosa is an opportunistic pathogen, and ubiquitously found in natural environments. However, details on difference between clinical and environmental isolates have not been reported enough. In this study, we defined existence of marine specific genogroup and different drug susceptibility among isolates from clinical, river and coastal seawaters. Pseudomonas aeruginosa were isolated by using cetrimide kanamycin nalidixic acid agar media and incubation at 42°C, which was specific selection method of this bacterium from the natural aquatic samples. Pulse field gel electrophoresis analysis showed that the levels of genetic variation within P. aeruginosa were different among environmental sites. Pulse field gel electrophoresis also showed a lower diversity within P. aeruginosa in the coastal waters; and coastal strains isolated different sampling points were positioned closely in the same cluster. Most of the aquatic isolates were sensitive to most of the drugs tested and 'intermediate' to panipenem on the contrast to the clinical isolates, suggesting that the clinical use of antibiotics affect significantly to the emergence of the drug-resistant P. aeruginosa.

Bioactive substances produced by marine isolates of Pseudomonas

Pseudomonas is a genus of non-fermentative gram-negative Gammaproteobacteria found both on land and in the water. Many terrestrial isolates of this genus have been studied extensively. While many produce bioactive substances, enzymes, and biosurfactants, other Pseudomonas isolates are used for biological control of plant diseases and bioremediation. In contrast, only a few marine isolates of this genus have been described that produce novel bioactive substances. The chemical structures of the bioactive substances from marine Pseudomonas are diverse, including pyroles, pseudopeptide pyrrolidinedione, phloroglucinol, phenazine, benzaldehyde, quinoline, quinolone, phenanthren, phthalate, andrimid, moiramides, zafrin and bushrin. Some of these bioactive compounds are antimicrobial agents, and dibutyl phthalate and di-(2-ethylhexyl) phthalate have been reported to be cathepsin B inhibitors. In addition to being heterogeneous in terms of their structures, the antibacterial substances produced by Pseudomonas also have diverse mechanisms of action: some affect the bacterial cell membrane, causing bacterial cell lysis, whereas others act as acetyl-CoA carboxylase and nitrous oxide synthesis inhibitors. Marine Pseudomonas spp. have been isolated from a wide range of marine environments and are a potential untapped source for medically relevant bioactive substances.

Multilocus sequence typing and phylogenetic analyses of Pseudomonas aeruginosa Isolates from the ocean

Recent isolation of Pseudomonas aeruginosa strains from the open ocean and subsequent pulsed-field gel electrophoresis analyses indicate that these strains have a unique genotype (N. H. Khan, Y. Ishii, N. Kimata-Kino, H. Esaki, T. Nishino, M. Nishimura, and K. Kogure, Microb. Ecol. 53:173-186, 2007). We hypothesized that ocean P. aeruginosa strains have a unique phylogenetic position relative to other strains. The objective of this study was to clarify the intraspecies phylogenetic relationship between marine strains and other strains from various geographical locations. Considering the advantages of using databases, multilocus sequence typing (MLST) was chosen for the typing and discrimination of ocean P. aeruginosa strains. Seven housekeeping genes (acsA, aroE, guaA, mutL, nuoD, ppsA, and trpE) were analyzed, and the results were compared with data on the MLST website. These genes were also used for phylogenetic analysis of P. aeruginosa. Rooted and unrooted phylogenetic trees were generated for each gene locus and the concatenated gene fragments. MLST data showed that all the ocean strains were new. Trees constructed for individual and concatenated genes revealed that ocean P. aeruginosa strains have clusters distinct from those of other P. aeruginosa strains. These clusters roughly reflected the geographical locations of the isolates. These data support our previous findings that P. aeruginosa strains are present in the ocean. It can be concluded that the ocean P. aeruginosa strains have diverged from other isolates and form a distinct cluster based on MLST and phylogenetic analyses of seven housekeeping genes.

Pseudomonas aeruginosa uses type III secretion system to kill biofilm-associated amoebae

Bacteria and protozoa coexist in a wide range of biofilm communities of natural, technical and medical importance. Generally, this interaction is characterized by the extensive grazing activity of protozoa on bacterial prey populations. We hypothesized that the close spatial coexistence in biofilms should allow opportunistic pathogenic bacteria to utilize their eukaryote-targeting arsenal to attack and exploit protozoan host cells. Studying cocultures of the environmental pathogen Pseudomonas aeruginosa and the amoeba Acanthamoeba castellanii, we found that P. aeruginosa rapidly colonized and killed biofilm-associated amoebae by a quorum-sensing independent mechanism. Analysis of the amoeba-induced transcriptome indicated the involvement of the P. aeruginosa type III secretion system (T3SS) in this interaction. A comparison of mutants with specific defects in the T3SS demonstrated the use of the secretion apparatus and the effectors ExoU, ExoS and ExoT in the killing process, of which ExoU had the greatest impact. T3SS-mediated virulence towards A. castellanii was found to be controlled by the global regulators RpoN and RpoS and through modulation of cAMP and alginate biosynthesis. Our findings suggest that conserved virulence pathways and specifically the T3SS play a central role in bacteria-protozoa interactions in biofilms and may be instrumental for the environmental persistence and evolution of opportunistic bacterial pathogens.

Biological treatment of tannery wastewater by using salt-tolerant bacterial strains

BACKGROUND

High salinity (1-10% w/v) of tannery wastewater makes it difficult to be treated by conventional biological treatment. Salt tolerant microbes can adapt to these saline conditions and degrade the organics in saline wastewater.

RESULTS

Four salt tolerant bacterial strains isolated from marine and tannery saline wastewater samples were identified as Pseudomonas aeruginosa, Bacillus flexus, Exiguobacterium homiense and Staphylococcus aureus. Growth factors of the identified strains were optimized. Tannery saline wastewater obtained from a Common Effluent Treatment Plant (CETP) near Chennai (southern India) was treated with pure and mixed consortia of four salt tolerant bacterial strains. Experiments with optimized conditions and varying salt content (between 2 and 10% (w/v) were conducted. Salt inhibition effects on COD removal rate were noted. Comparative analysis was made by treating the tannery saline wastewater with activated sludge obtained from CETP and with natural habitat microbes present in raw tannery saline wastewater.

CONCLUSION

Salt tolerant bacterial mixed consortia showed appreciable biodegradation at all saline concentrations (2%, 4%, 6%, 8% and 10% w/v) with 80% COD reduction in particular at 8% salinity level the consortia could be used as suitable working cultures for tannery saline wastewater treatment.

Improved reliability of Pseudomonas aeruginosa PCR detection by the use of the species-specific ecfX gene target

Reliability of the most widely used PCR screenings for the human opportunistic pathogen Pseudomonas aeruginosa was evaluated. Specificity analyses showed the gyrB, toxA, and 16S-23S rDNA internal transcribed spacer (ITS) but not the 16S rDNA, oprI, oprL, and fliC PCR screenings to discriminate P. aeruginosa cells from a collection of fifteen Pseudomonas species. Sensitivity analyses showed all these PCR except the toxA one to be reliable for 100% of the P. aeruginosa strains tested in this study. Specificity of the ITS and gyrB PCR screenings were further investigated on 9 soils and 29 freshwater DNA extracts of different origins, and on DNA extracted from 3 horse manures. The ITS PCR showed the highest efficacy on water and soil DNA extracts but only the gyrB one detected P. aeruginosa DNA in horse manure. DNA sequence analyses of ITS and gyrB PCR products revealed uncertainties and false positive results in these P. aeruginosa identification schemes. A novel PCR screening, targeting the ecfX gene, was thus developed. ecfX encodes an ECF (extracytoplasmic function) sigma factor which is restricted to P. aeruginosa, and might play a role in haem-uptake and virulence. Specificity and sensitivity analyses showed the ecfX PCR screening to be highly reliable, giving PCR products of the expected size for all P. aeruginosa strains tested and not amplifying DNA from any of the other Pseudomonas species tested. The ecfX PCR screening was validated on environmental DNA extracts. DNA sequence analyses of the ecfX PCR products confirmed their identity and allocation to P. aeruginosa. These investigations suggest a preferential colonization of water rather than soil environments by P. aeruginosa. Detection limits of P. aeruginosa in environmental samples were improved by the ecfX PCR screening.

Isolation of Pseudomonas aeruginosa from open ocean and comparison with freshwater, clinical, and animal isolates

Pseudomonas aeruginosa is an opportunistic pathogen responsible for morbidity and mortality in humans, animals, and plants. This bacterium has been regarded to be widely present in terrestrial and freshwater environments, but not in open ocean environments. Our purpose was to clarify its presence in open ocean, and their genotypic and physiological characteristics were compared with those of isolates from clinical, animal, and freshwater sources. Water samples were collected from freshwater, bays, and offshore environments in Japan. Sixty-two isolates, including 26 from the open ocean, were identified as P. aeruginosa by phenotypic characteristics and the BD Phoenix System. Pulsed-field gel electrophoresis (PFGE) was performed on all strains, together with 21 clinical and 8 animal strains. The results showed that open ocean strains are composed of a few genotypes, which are separated from other strains. Although some clinical isolates made a cluster, other strains tended to mix together. Different antibiotypes were observed among marine isolates that had similar PFGE and serotyping patterns. Some were multidrug-resistant. Laboratory-based microcosm study were carried out to see the responses of P. aeruginosa toward increased NaCl concentrations in deionized water (DW). Marine strains showed better survival with the increase, whereas river and clinical strains were suppressed by the increase. These findings illustrate the potential significance of open ocean as a possible reservoir of P. aeruginosa, and there may be clones unique to this environment. To our knowledge, this is the first report on the presence and characterization of P. aeruginosa in the open ocean.

Multilocus sequence typing breathes life into a microbial metagenome

Shot-gun sequencing of DNA isolated from the environment and the assembly of metagenomes from the resulting data has considerably advanced the study of microbial diversity. However, the subsequent matching of these hypothetical metagenomes to cultivable microorganisms is a limitation of such cultivation-independent methods of population analysis. Using a nucleotide sequence-based genetic typing method, multilocus sequence typing, we were able for the first time to match clonal cultivable isolates to a published and controversial bacterial metagenome, Burkholderia SAR-1, which derived from analysis of the Sargasso Sea. The matching cultivable isolates were all associated with infection and geographically widely distributed; taxonomic analysis demonstrated they were members of Burkholderia cepacia complex Group K. Comparison of the Burkholderia SAR-1 metagenome to closely related B. cepacia complex genomes indicated that it was greater than 98% intact in terms of conserved genes, and it also shared complete sequence identity with the cultivable isolates at random loci beyond the genes sampled by the multilocus sequence typing. Two features of the extant cultivable clones support the argument that the Burkholderia SAR-1 sequence may have been a contaminant in the original metagenomic survey: (i) their growth in conditions reflective of sea water was poor, suggesting the ocean was not their preferred habitat, and (ii) several of the matching isolates were epidemiologically linked to outbreaks of infection that resulted from contaminated medical devices or products, indicating an adaptive fitness of this bacterial strain towards contamination-associated environments. The ability to match identical cultivable strains of bacteria to a hypothetical metagenome is a unique feature of nucleotide sequence-based microbial typing methods; such matching would not have been possible with more traditional methods of genetic typing, such as those based on pattern matching of genomic restriction fragments or amplified DNA fragments. Overall, we have taken the first steps in moving the status of the Burkholderia SAR-1 metagenome from a hypothetical entity towards the basis for life of cultivable strains that may now be analysed in conjunction with the assembled metagenomic sequence data by the wider scientific community.

Biology of Pseudomonas stutzeri

Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.