Pseudomonas phenolilytica sp. nov., a novel phenol-degrading bacterium

Integrated use of electrochemical anaerobic reactors and genomic based modeling for characterizing methanogenic activity in microbial communities exposed to BTEX contamination

In soil polluted with benzene, toluene, ethylbenzene, and xylenes (BTEX), oxygen is rapidly depleted by aerobic respiration, creating a redox gradient across the plume. Under anaerobic conditions, BTEX biodegradation is then coupled with fermentation and methanogenesis. This study aimed to characterize this multi-step process, focusing on the interactions and functional roles of key microbial groups involved. A reactor system, comprising an Anaerobic Bioreactor (AB) and two Microbial Electrolysis Cell (MEC) chambers, designed to represent different spatial zones along the redox gradient, operated for 160 days with intermittent exposure to BTEX. The functional differentiation of each chamber was reflected by the gas emission profiles: 50%, 12% and 84% methane in the AB, anode and cathode chambers, respectively. The taxonomic profiling, assessed using 16S amplicon sequencing, led to the identification chamber-characteristic taxonomic groups. To translate the taxonomic shift into a functional shift, community dynamics was transformed into a simulative platform based on genome scale metabolic models constructed for 21 species that capture both key functionalities and taxonomies. Representatives include BTEX degraders, fermenters, iron reducers acetoclastic and hydrogenotrophic methanogens. Functionality was inferred according to the identification of the functional gene bamA as a biomarker for anaerobic BTEX degradation, taxonomy and literature support. Comparison of the predicted performances of the reactor-specific communities confirmed that the simulation successfully captured the experimentally recorded functional variation. Variations in the predicted exchange profiles between chambers capture reported and novel competitive and cooperative interactions between methanogens and non-methanogens. Examples include the exchange profiles of hypoxanthine (HYXN) and acetate between fermenters and methanogens, suggesting mechanisms underlying the supportive/repressive effect of taxonomic divergence on methanogenesis. Hence, the platform represents a pioneering attempt to capture the full spectrum of community activity in methanogenic hydrocarbon biodegradation while supporting the future design of optimization strategies.

Phenotypic and Genomic Characterization of Pseudomonas wuhanensis sp. nov., a Novel Species with Promising Features as a Potential Plant Growth-Promoting and Biocontrol Agent

Plant growth-promoting rhizobacterial strain FP607T was isolated from the rhizosphere of beets in Wuhan, China. Strain FP607T exhibited significant antagonism toward several phytopathogenic bacteria, indicating that FP607T may produce antimicrobial metabolites and has a stronger biocontrol efficacy against plant pathogens. Growth-promoting tests showed that FP607T produced indole-3-acetic acid (IAA), NH3, and ferritin. The genome sequence of strain FP607T was 6,590,972 bp long with 59.0% G + C content. The optimum temperature range was 25-30 °C, and the optimum pH was 7. The cells of strain FP607T were Gram-negative, short, and rod-shaped, with polar flagella. The colonies on the King's B (KB) agar plates were light yellow, smooth, and circular, with regular edges. A phylogenetic analysis of the 16S rRNA sequence and a multilocus sequence analysis (MLSA) showed that strain FP607T was most closely related to the type of strain Pseudomonas farris SWRI79T. Based on a polyphasic taxonomic approach, strain FP607T was identified as a novel species within the genus Pseudomonas, for which the name Pseudomonas wuhanensis sp. nov. was proposed. The type of strain used was FP607T (JCM 35688, CGMCC 27743, and ACCC 62446).

Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera

Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.

Genomic and phenotypic analysis of a novel clinical isolate of Corynebacterium pyruviciproducens

BACKGROUND

Corynebacterium pyruviciproducens is a recently described species of Corynebacterium. There are few reports on the microbiological characteristics of the new species, and there is a lack of reports on the genomic analysis of the species.

RESULTS

This study involved a clinical isolate from the pus of a hospital patient with sebaceous gland abscesses. The clinically isolated strain was identified as C. pyruviciproducens strain WYJY-01. In this study, referring to Koch's postulates, we observed the pathological changes of animal models infected by intraperitoneal injection and subcutaneous injection of pure culture of the strain WYJY-01. Furthermore, the strain WYJY-01 was isolated and cultured again from animal models' subcutaneous abscess drainage fluid. Subsequently, the genomics of the strain WYJY-01 was analyzed. By comparing various gene databases, this study predicted the core secondary metabolite gene cluster of the strain WYJY-01, virulence factor genes carried by prophage, pathogenicity islands, and resistance islands. In addition, the genomes of C. pyruviciproducens strain WYJY-01, ATCC BAA-1742 T, and UMB0763 were analyzed by comparative genomics, and the differential genes of strain WYJY-01 were compared, and their functions were analyzed.

CONCLUSION

The findings showed that the strain WYJY-01 had pathogenicity, supplementing the phenotype characteristics of C. pyruviciproducens. Meanwhile, this research revealed the possible molecular mechanism of the pathogenicity of the strain WYJY-01 at the gene level through whole genome sequence analysis, providing a molecular basis for further research.

The aggregated biofilm dominated by Delftia tsuruhatensis enhances the removal efficiency of 2,4-dichlorophenol in a bioelectrochemical system

Bioelectrochemical system is a prospective strategy in organic-contaminated groundwater treatment, while few studies clearly distinguish the mechanisms of adsorption or biodegradation in this process, especially when dense biofilm is formed. This study employed a single chamber microbial electrolysis cell (MEC) with two three-dimensional electrodes for removing a typical organic contaminant, 2,4-dichlorophenol (DCP) from groundwater, which inoculated with anaerobic bacteria derived from sewage treatment plant. Compared with the single biodegradation system without electrodes, the three-dimensional electrodes with a high surface enabled an increase of alpha diversity of the microbial community (increased by 52.6% in Shannon index), and provided adaptive ecological niche for more bacteria. The application of weak voltage (0.6 V) furtherly optimized the microbial community structure, and promoted the aggregation of microorganisms with the formation of dense biofilm. Desorption experiment proved that the contaminants were removed from the groundwater mainly via adsorption by the biofilm rather than biodegradation, and compared with the reactor without electricity, the bioelectrochemical system increased the adsorption capacity from 50.0% to 74.5%. The aggregated bacteria on the surface of electrodes were mainly dominated by Delftia tsuruhatensis (85.0%), which could secrete extracellular polymers and has a high adsorption capacity (0.30 mg/g electrode material) for the contaminants. We found that a bioelectrochemical system with a three-dimensional electrode could stimulate the formation of dense biofilm and remove the organic contaminants as well as their possible more toxic degradation intermediates via adsorption. This study provides important guidance for applying bioelectrochemical system in groundwater or wastewater treatment.

Pseudomonas citri sp. nov., a potential novel plant growth promoting bacterium isolated from rhizosphere soil of citrus

A novel potential plant growth promoting bacterium, designated OPS13-3^T, was isolated from rhizosphere soil of citrus in Aotou Town of Guangzhou, Guangdong Province, PR China. It showed high ability to dissolve insoluble inorganic phosphate and organic phosphorus and to produce 3-indoleacetic acid (IAA) and siderophore. Cells of the novel strain were Gram-stain-negative, rod-shaped, aerobic and motile with polar flagellum. It shared the highest 16S rRNA gene similarity with Pseudomonas mucoides CCUG 74874^T (98.7%) and P. bijieensis LMG 31948^T (98.7%). Phylogenetic analyses based the 16S rRNA gene and genome sequences revealed that strain OPS13-3^T belonged to the genus Pseudomonas, and was most closely related to P. mediterranea ICMP 14184^T and P. corrugate ICMP 5819^T. The average nucleotide identity (ANI) and DNA-DNA hybridization (dDDH) values between the novel strain and closely relatives with high 16S rRNA gene similarities were 80.8‒87.5% and 24.7‒34.6%, respectively, which were much below the threshold values for species delimitation. The major fatty acids included C_16:0, C_10:0 3-OH and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c). It took ubiquinone 9 as the predominant respiratory quinone and the polar lipids contained phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), three unidentified phospholipids, an unidentified aminophospholipid and an unidentified lipid. Based on the phylogenetic, phenotypic and chemotaxonomic analyses and genome comparison, strain OPS13-3^T should be considered as a novel species of the genus Pseudomonas, for which the name Pseudomonas citri sp. nov. is proposed (type strain OPS13-3^T = GDMCC 1.3118^T = JCM 35385^T).

Characterization and Biodegradation of Phenol by Pseudomonas aeruginosa and Klebsiella variicola Strains Isolated from Sewage Sludge and Their Effect on Soybean Seeds Germination

Phenols are very soluble in water; as a result, they can pollute a massive volume of fresh water, wastewater, groundwater, oceans, and soil, negatively affecting plant germination and animal and human health. For the detoxification and bioremediation of phenol in wastewater, phenol biodegradation using novel bacteria isolated from sewage sludge was investigated. Twenty samples from sewage sludge (SS) were collected, and bacteria in SS contents were cultured in the mineral salt agar (MSA) containing phenol (500 mg/L). Twenty colonies (S1 up to S20) were recovered from all the tested SS samples. The characteristics of three bacterial properties, 16S rDNA sequencing, similarities, GenBank accession number, and phylogenetic analysis showed that strains S3, S10, and S18 were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Klebsiella variicola, respectively. P. aeruginosa, K. pneumoniae, and K. variicola were able to degrade 1000 mg/L phenol in the mineral salt medium. The bacterial strains from sewage sludge were efficient in removing 71.70 and 74.67% of phenol at 1000 mg/L within three days and could tolerate high phenol concentrations (2000 mg/L). The findings showed that P. aeruginosa, K. pneumoniae, and K. variicola could potentially treat phenolic water. All soybean and faba bean seeds were germinated after being treated with 250, 500, 750, and 1000 mg/L phenol in a mineral salt medium inoculated with these strains. The highest maximum phenol removal and detoxification rates were P. aeruginosa and K. variicola. These strains may help decompose and detoxify phenol from industrial wastewater with high phenol levels and bioremediating phenol-contaminated soils.