Genomovars 11 to 18 of Pseudomonas stutzeri, identified among isolates from soil and marine sediment

Genomic Insights into Stutzerimonas kunmingensis TFRC-KFRI-1 Isolated from Manila Clam (Ruditapes philippinarum): Functional and Phylogenetic Analysis

Stutzerimonas kunmingensis TFRC-KFRI-1, isolated from the gut of Manila Clam in the sediment of the West Sea of Korea, was investigated for its potential as a probiotic bacterium. This strain, belonging to the family Pseudomonadaceae, was previously classified as Pseudomonas kunmingensis but later reclassified to the genus Stutzerimonas, known for species with bioremediation and probiotic properties. To evaluate its genomic features and potential applications, we performed draft-genome sequencing and analysis. The genome of S. kunmingensis TFRC-KFRI-1 was assembled into a 4,756,396 bp sequence with a 62.8% GC content. Genomic analysis suggested potential genes for carbohydrate degradation and lactic acid production. The strain exhibited high average nucleotide identity (ANI) and 16S rRNA similarity with S. kunmingensis HL22-2T, further supporting its potential as a probiotic. This genome sequence provides valuable insights into the functional capabilities of S. kunmingensis TFRC-KFRI-1 and its potential applications in various industries, including aquaculture and food biotechnology. The genome sequence is available under GenBank accession number JBGJJB000000000.1, with related project information under BioProject PRJNA1147901 and Bio-Sample SAMN43173893.

Pangenomic landscapes shape performances of a synthetic genetic circuit across Stutzerimonas species

Engineering identical genetic circuits into different species typically results in large differences in performance due to the unique cellular environmental context of each host, a phenomenon known as the "chassis-effect" or "context-dependency". A better understanding of how genomic and physiological contexts underpin the chassis-effect will improve biodesign strategies across diverse microorganisms. Here, we combined a pangenomic-based gene expression analysis with quantitative measurements of performance from an engineered genetic inverter device to uncover how genome structure and function relate to the observed chassis-effect across six closely related Stutzerimonas hosts. Our results reveal that genome architecture underpins divergent responses between our chosen non-model bacterial hosts to the engineered device. Specifically, differential expression of the core genome, gene clusters shared between all hosts, was found to be the main source of significant concordance to the observed differential genetic device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes involved in denitrification and components of trans-membrane transporter proteins were among the most differentially expressed gene clusters between hosts in response to the genetic device. Our results show that the chassis-effect can be traced along differences among the most conserved genome-encoded functions and that these differences create a unique biodesign space among closely related species.IMPORTANCEContemporary synthetic biology endeavors often default to a handful of model organisms to host their engineered systems. Model organisms such as Escherichia coli serve as attractive hosts due to their tractability but do not necessarily provide the ideal environment to optimize performance. As more novel microbes are domesticated for use as biotechnology platforms, synthetic biologists are urged to explore the chassis-design space to optimize their systems and deliver on the promises of synthetic biology. The consequences of the chassis-effect will therefore only become more relevant as the field of biodesign grows. In our work, we demonstrate that the performance of a genetic device is highly dependent on the host environment it operates within, promoting the notion that the chassis can be considered a design variable to tune circuit function. Importantly, our results unveil that the chassis-effect can be traced along similarities in genome architecture, specifically the shared core genome. Our study advocates for the exploration of the chassis-design space and is a step forward to empowering synthetic biologists with knowledge for more efficient exploration of the chassis-design space to enable the next generation of broad-host-range synthetic biology.

Growth and genetic analysis of Pseudomonas BT1 in a high-thiourea environment reveals the mechanisms by which it restores the ability to remove ammonia nitrogen from wastewater

Thiourea is widely present in wastewater and can inhibit the nitrification process, inducing the collapse of the nitrification system in sewage treatment plants. Pseudomonas BT1 can restore the ammonia nitrogen removal ability of wastewater treatment processes in which the nitrification system due to thiourea. However, the genetic mechanisms for BT1 are still unclear. In this study, we reported the first genome assembly for Pseudomonas BT1, which has a genome size of 5,576,102 bp and 5,115 predicted genes. Complete C and S metabolic cycles were identified in its genome, and some intersecting intermediate products were found in these cycles. BT1 can grow well and remove ammonia nitrogen at different thiourea concentrations, but it showed a better removal ability in high-thiourea environments. The longest gene activity stage of BT1 was observed in the high-thiourea environments by RNA sequencing, and genes related to maintaining intracellular copper homeostasis were highly expressed during the S metabolism process, which may be the key to restoring the ammonia nitrogen removal ability. Enzymes detected during the N and S cycles showed that BT1 reacts with thiourea to produce hydrogen but not sulphate, suggesting that BT1 may have genes that are involved in thiourea hydrolysis. In conclusion, the high-quality assembly of BT1 provides a valuable resource for analyzing its biological process and molecular mechanisms for thiourea metabolism. BT1 shows great application potential for the removal of thiourea from sewage treatment plants.

Comparative genomics of Stutzerimonas balearica (Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds

Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.

Comparative Genomics of Pseudomonas stutzeri Complex: Taxonomic Assignments and Genetic Diversity

Pseudomonas stutzeri is a species complex with extremely broad phenotypic and genotypic diversity. However, very little is known about its diversity, taxonomy and phylogeny at the genomic scale. To address these issues, we systematically and comprehensively defined the taxonomy and nomenclature for this species complex and explored its genetic diversity using hundreds of sequenced genomes. By combining average nucleotide identity (ANI) evaluation and phylogenetic inference approaches, we identified 123 P. stutzeri complex genomes covering at least six well-defined species among all sequenced Pseudomonas genomes; of these, 25 genomes represented novel members of this species complex. ANI values of ≥∼95% and digital DNA-DNA hybridization (dDDH) values of ≥∼60% in combination with phylogenomic analysis consistently and robustly supported the division of these strains into 27 genomovars (most likely species to some extent), comprising 16 known and 11 unknown genomovars. We revealed that 12 strains had mistaken taxonomic assignments, while 16 strains without species names can be assigned to the species level within the species complex. We observed an open pan-genome of the P. stutzeri complex comprising 13,261 gene families, among which approximately 45% gene families do not match any sequence present in the COG database, and a large proportion of accessory genes. The genome contents experienced extensive genetic gain and loss events, which may be one of the major mechanisms driving diversification within this species complex. Surprisingly, we found that the ectoine biosynthesis gene cluster (ect) was present in all genomes of P. stutzeri species complex strains but distributed at very low frequency (43 out of 9548) in other Pseudomonas genomes, suggesting a possible origin of the ancestors of P. stutzeri species complex in high-osmolarity environments. Collectively, our study highlights the potential of using whole-genome sequences to re-evaluate the current definition of the P. stutzeri complex, shedding new light on its genomic diversity and evolutionary history.

Isolation, identification, and pathological effects of beach sand bacterial extract on human skin keratinocytes in vitro

Background

Beaches are recreational spots for people. However, beach sand contains harmful microbes that affect human health, and there are no established methods for either sampling and identifying beach-borne pathogens or managing the quality of beach sand.

Method

This study was conducted with the aim of improving human safety at beaches and augmenting the quality of the beach experience. Beach sand was used as a resource to isolate bacteria due to its distinctive features and the biodiversity of the beach sand biota. A selected bacterial isolate termed FSRS was identified as Pseudomonas stutzeri using 16S rRNA sequencing and phylogenetic analysis, and the sequence was deposited in the NCBI GenBank database under the accession number MF599548. The isolated P. stutzeri bacterium was cultured in Luria-Bertani growth medium, and a crude extract was prepared using ethyl acetate to examine the potential pathogenic effect of P. stutzeri on human skin. A human skin keratinocyte cell line (HaCaT) was used to assess cell adhesion, cell viability, and cell proliferation using a morphological analysis and a WST-1 assay.

Result

The crude P. stutzeri extract inhibited cell adhesion and decreased cell viability in HaCaT cells. We concluded that the crude extract of P. stutzeri FSRS had a strong pathological effect on human skin cells.

Discussion

Beach visitors frequently get skin infections, but the exact cause of the infections is yet to be determined. The beach sand bacterium P. stutzeri may, therefore, be responsible for some of the dermatological problems experienced by people visiting the beach.

Use of Amplification Fragment Length Polymorphism to Genotype Pseudomonas stutzeri Strains Following Exposure to Ultraviolet Light A

Changes in ultraviolet light radiation can act as a selective force on the genetic and physiological traits of a microbial community. Two strains of the common soil bacterium Pseudomonas stutzeri, isolated from aquifer cores and from human spinal fluid were exposed to ultraviolet light. Amplification length polymorphism analysis (AFLP) was used to genotype this bacterial species and evaluate the effect of UVA-exposure on genomic DNA extracted from 18 survival colonies of the two strains compared to unexposed controls. AFLP showed a high discriminatory power, confirming the existence of different genotypes within the species and presence of DNA polymorphisms in UVA-exposed colonies.

Effect of toluene on Pseudomonas stutzeri ST-9 morphology - plasmolysis, cell size, and formation of outer membrane vesicles

Isolated toluene-degrading Pseudomonas stutzeri ST-9 bacteria were grown in a minimal medium containing toluene (100 mg·L(-1)) (MMT) or glucose (MMG) as the sole carbon source, with specific growth rates of 0.019 h(-1) and 0.042 h(-1), respectively. Scanning (SEM) as well as transmission (TEM) electron microscope analyses showed that the bacterial cells grown to mid-log phase in the presence of toluene possess a plasmolysis space. TEM analysis revealed that bacterial cells that were grown in MMT were surrounded by an additional "material" with small vesicles in between. Membrane integrity was analyzed by leakage of 260 nm absorbing material and demonstrated only 7% and 8% leakage from cultures grown in MMT compared with MMG. X-ray microanalysis showed a 4.3-fold increase in Mg and a 3-fold increase in P in cells grown in MMT compared with cells grown in MMG. Fluorescence-activated cell sorting (FACS) analysis indicated that the permeability of the membrane to propidium iodide was 12.6% and 19.6% when the cultures were grown in MMG and MMT, respectively. The bacterial cell length increased by 8.5% ± 0.1% and 17% ± 2%, as measured using SEM images and FACS analysis, respectively. The results obtained in this research show that the presence of toluene led to morphology changes, such as plasmolysis, cell size, and formation of outer membrane vesicles. However, it does not cause significant damage to membrane integrity.

Nar is the dominant dissimilatory nitrate reductase under high pressure conditions in the deep-sea denitrifier Pseudomonas sp. MT-1

The deep-sea denitrifier Pseudomonas sp. MT-1 has two gene clusters encoding dissimilatory nitrate reductases, periplasmic nitrate reductase (Nap) and membrane-bound nitrate reductase (Nar). In order to investigate the physiological role of these enzymes, we constructed the disrupted mutants of napA, narG, and narK (encoding the catalytic subunits of Nap and Nar, as well as the nitrate transporter, respectively). The napA mutant showed almost the same growth rate as the wild-type under both atmospheric and high pressure of 30 MPa. On the other hand, the narG and narK mutants showed growth deficiencies under atmospheric pressure which were more pronounced at a pressure of 30 MPa. Thus, Nar was shown to be the dominant dissimilatory nitrate reductase in MT-1, especially under high pressure, whereas Nap can support the growth with denitrification to some extent. Further, nitrate reductase activity of the soluble and membrane fractions of MT-1 was measured under high pressure. Both activities were highly piezotolerant even under a pressure of 150 MPa. Therefore, the stability of nitrate reductases under high pressure is not a limiting step for the growth of MT-1 under these conditions. Although the reason why Nar rather than Nap is dominant and the physiological role of Nap in MT-1 are still unclear, we have demonstrated the mechanisms of the denitrification system in the environment of the deep-sea.

The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions

The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.

Genomovar assignment of Pseudomonas stutzeri populations inhabiting produced oil reservoirs

Oil reservoirs are specific habitats for the survival and growth of microorganisms in general. Pseudomonas stutzeri which is believed to be an exogenous organism inoculated into oil reservoirs during the process of oil production was detected frequently in samples from oil reservoirs. Very little is known, however, about the distribution and genetic structure of P. stutzeri in the special environment of oil reservoirs. In this study, we collected 59 P. stutzeri 16S rRNA gene sequences that were identified in 42 samples from 25 different oil reservoirs and we isolated 11 cultured strains from two representative oil reservoirs aiming to analyze the diversity and genomovar assignment of the species in oil reservoirs. High diversity of P. stutzeri was observed, which was exemplified in the detection of sequences assigned to four known genomovars 1, 2, 3, 20 and eight unknown genomic groups of P. stutzeri. The frequent detection and predominance of strains belonging to genomovar 1 in most of the oil reservoirs under study indicated an association of genomovars of P. stutzeri with the oil field environments.

Whole-cell MALDI-TOF mass spectrometry and multilocus sequence analysis in the discrimination of Pseudomonas stutzeri populations: three novel genomovars

Pseudomonas stutzeri is a widely distributed species with very high genetic diversity and metabolic capacities, occupying many diverse ecological niches. A collection of 229 P. stutzeri strains isolated from different habitats and geographical locations has been previously characterised phylogenetically by rpoD gene sequencing analysis and in the present study 172 of them phenotypically by whole-cell MALDI-TOF mass spectrometry. Fifty-five strains were further analysed by multilocus sequencing analysis to determine the phylogenetic population structure. Both methods showed coherence in strain grouping; 226 strains were allocated in the 18 genomovars known presently. The remaining three strains are proposed as references for three novel genomovars in the species. The correlation and usefulness of sequence-based phylogenetic analysis and whole-cell MALDI-TOF mass spectrometry, which are essential for autoecological studies in microbial ecology, is discussed for the differentiation of P. stutzeri populations.

Isolation of Pseudomonas stutzeri in wastewater of catfish fish-ponds in the Mekong Delta and its application for wastewater treatment

The aim of this study was to explore the potential for reducing soluble N load in fishpond wastewater using naturally occurring denitrifying bacteria. Twenty-seven isolates were selected from in wastewater (liquid/solid) of catfish-ponds located along the Tien river, in the Mekong Delta, Vietnam in SW-LB medium (artificial seawater Luria-Britani medium) supplemented with 10 mM NH4 and NO3 and twenty-five isolates were identified as Pseudomonas stutzeri based on similarity of PCR-16S rRNA using universal primers and specific primers. Four isolates were effective in lowering soluble N (NH4, NO2 and NO3) levels in fishpond water from 10 mg/L to negligible amounts after four days. Further experiments are underway to determine the fate of N lost from solution and the relative activity of ammonia oxidation, and nitrite and nitrate reduction by P. stutzeri isolates.

Molecular analysis of diversity within the genus Pseudomonas in the lungs of cystic fibrosis patients

The genus Pseudomonas contains species that can act as human pathogens and are important in many infections such as those occurring in the lungs of many cystic fibrosis (CF) patients. Current methodologies that rely on the cultivation of bacteria are too cumbersome and often lack sufficient discriminatory power to define the diversity of Pseudomonas spp. As a result, molecular-based approaches have many advantages when attempting to differentiate between species of this genus. This study assessed the ability of terminal restriction fragment length polymorphism (T-RFLP) profiling of the 16S-23S rRNA ITS1 gene region to differentiate species of the genus Pseudomonas. Before application to clinical samples, this approach was validated on a panel of 10 different Pseudomonas spp. T-RFLP profiling of the 16S-23S rRNA ITS1 gene region amplified from these strains differentiated all Pseudomonas spp. tested. The presence of Pseudomonas spp. in CF sputum was assessed through the detection of this ITS1 gene region as amplified from DNA extracted from 40 samples of CF sputum. The ITS1 gene region was detected in 75% of these samples, including 5 from which no Pseudomonas spp. had been identified using culture-based methods. In silico analysis showed that all sequences amplified had a high homology with the ITS1 region of Pseudomonas aeruginosa. T-RFLP gave data that were consistent with the band being generated from P. aeruginosa for each patient. No correlation between Pseudomonas diversity and severity of lung disease was observed in this group of CF patients. This study has however shown that molecular analysis of the ITS1 region is effective in resolving diversity within the genus Pseudomonas. The wider use of this application is discussed.

Effect of organic carbon on nitrification efficiency and community composition of nitrifying biofilms

The effects of organic carbon/inorganic nitrogen (C/N) ratio on the nitrification processes and the community shifts of nitrifying biofilms were investigated by kinetic comparison and denaturing gradient gel electrophoresis (DGGE) analysis. The results showed that the nitrification rate decreased with an increasing organic concentration. However, the effect became weak when the carbon concentration reached a sufficiently high level. Denitrification was detected after organic carbon was added. The 12 h ammonium removal rate ranged from 85% to 30% at C/N = 0.5, 1, 2, 4, 8, and 16, as compared to the control (C/N = 0). The loss of nitrogen after 24 h at C/N = 0.5, 1, 2, 4, 8, and 16 was 31%, 18%, 24%, 65%, 59%, and 62%, respectively. The sequence analysis of 16S rRNA gene fragments revealed that the dominant populations changed from nitrifying bacteria (Nitrosomonas europaea and Nitrobacter sp.) to denitrifying bacteria (Pseudomonas sp., Acidovorax sp. and Comamonas sp.) with an increasing C/N ratio. Although at high C/N ratio the denitrifying bacteria were the dominant populations, nitrifying bacteria grew simultaneously. Consequently, nitrification process coexisted with denitrification.

Molecular analysis of the nitrogen cycle in deep-sea microorganisms from the Nankai Trough: genes for nitrification and denitrification from deep-sea environmental DNA

Nitrification and denitrification are bacterial functions, which are important for the global nitrogen cycle. Thus, it is important to study the diversity and distribution of bacteria in the environment, which are involved in the nitrogen cycle on the earth. Ammonia monooxygenase encoded by the amoA gene and nitrite reductase encoded by nirK or nirS are essential enzymes for nitrificaton and denitrification, respectively. These genes can be used as markers for the identification of organisms in the nitrogen cycle. In this study, we identified amoA (42 clones) and nirS (98 clones) genes in parallel from samples recovered from the deep-sea of the Nankai Trough. Genes for nirK could not be amplified from these samples. The obtained amoA sequences were not so closely related to those of amoA genes from previously isolated environmental organisms and those of genes from environmental DNAs. On the other hand, the nirS genes sequenced showed some relationship to some extent with the latter genes. However, some of the newly sequenced genes formed clusters, which contained no previously identified genes on a phylogenetic tree. These are likely present in specific denitrifiers from the deep-sea. The results of this study further suggest that nitrifiers and denitrifiers live in the same area of the Nankai Trough and the nitrogen cycle exists even in the deep-sea.

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.

Genotype versus phenotype in the circumscription of bacterial species: the case of Pseudomonas stutzeri and Pseudomonas chloritidismutans

The phenotypic characteristic of strain AW-1(T) of Pseudomonas chloritidismutans that is most relevant from the taxonomic point of view appears to be the capacity of growth under anaerobic conditions using chlorate as electron acceptor. This property is not restricted to this species only within the genus Pseudomonas, since it is also present in strains of genomovars 1 or 5, and 3 of Pseudomonas stutzeri. P. chloritidismutans has been described as a non-denitrifying species, but the isolation of variants that are able to grow anaerobically in the presence of nitrate is possible after subcultivation under selective conditions. The subdivision of P. stutzeri into a number of species on the basis of these characteristics does not help to clarify the phylogenetic relationships among the members of an otherwise coherent group of strains, and the considerations presented in this communication support the reclassification of the new species name P. chloritidismutans, which in our opinion, should be considered as a Junior name of P. stutzeri. A multilocus sequence analysis, together with a phenotypic analysis of the anaerobic oxidative metabolism, gives new insights into the phylogeny and evolution of the species.