Pseudomonas Research Articles

Bioprospecting secondary metabolites with antimicrobial properties from soil bacteria in high-temperature ecosystems

BackgroundThe ongoing emergence and spread of drug-resistant pathogens necessitate urgent solutions. Natural products from bacterial sources are recognized as a promising source of antibiotics. This study aimed to isolate and characterize soil microorganisms from extremely hot environments and to screen their secondary metabolites for antibacterial activity.MethodsBacterial isolates were identified using standard culture techniques. Primary and secondary screenings for antimicrobial activity were conducted using the Modified Kirby-Bauer antibiotic susceptibility test against five bacterial species. Based on the efficacy of antimicrobial activity against these target pathogens, the isolate Pseudomonas sp. strain ASTU00105 was selected for further characterization through whole genomic sequencing. Secondary metabolites were analyzed using GC–MS, and antioxidant activities were also evaluated.ResultsA total of 76 isolates were identified, and their secondary metabolites were tested against Escherichia coli, Salmonella typhi, Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, and Candida albicans. Seventeen isolates (22.37%) exhibited antimicrobial activity. Isolate ASTU00105 exhibited the highest activity against all the test organisms and was selected for further analysis. Whole-genome sequencing using the Nanopore MinION sequencer revealed that strain ASTU00105 belonged to the genus Pseudomonas with the highest similarity (95.97%) to Pseudomonas stutzeri, and designated as Pseudomonas sp. strain ASTU00105. Upon Average Nucleotide Identity (ANI) analysis, the strain exhibited 87.81% sequence similarity with genes of the closest type strain, suggesting its novelty and distinctiveness within the Pseudomonas genus. The genomic analysis of the isolated strain revealed 6 biosynthetic gene cluster (BGC) genes dispersed throughout the entire genome, which are implicated in the synthesis of antimicrobial secondary metabolites. The major chemical compounds detected in the EtAc extracts as detected by gas chromatography-mass spectrometry (GC–MS) were phenol, 2,5-bis (1,1-dimethylethyl) (36.6%), followed by 1,2-Benzenedicarboxylic acid, diethyl ester (12.22%), Eicosane (9.71%), Dibutyl phthalate (3.93%), and 1-Dodecanol (2.34%).In conclusionPseudomonas sp. strain ASTU00105 exhibited the greatest potential for producing secondary metabolites with significant antimicrobial activity.

Promising strains of phosphate-mobilizing rhizobacteria resistant to glyphosate and nickel

A search was carried out for phosphate-soluble rhizobacteria capable of growing in the presence of different concentrations of the herbicide glyphosate and nickel heavy metal ions (Ni2+). Using the Muromtsev medium, the phosphate-mobilizing activity was determined only in 3 out of 20 strains of Rhizobium spp. – with a low solubilization index (IS). On the contrary, all strains of Pseudomonas sp. showed a positive result, and the highest IS was in Pseudomonas sp. OBA 2.4.1 and GOR 4.17. The highest growth activity under stressful conditions was shown by 4 strains of Pseudomonas spp.: OBA 2.4.1, OBA 2.9, 4.17 and STA 3, their growth was noticeably inhibited with an increase in the concentration of glyphosate in the medium to 10.0 mg/ml. The growth activity of Rhizobium spp. strains was characterized as average. When growing on a medium with NiCl2, Pseudomonas strains sp. 65 HM and 67 HM grew to a concentration of 9 mM NiCl2 in the medium, at a concentration of 11 mM, strain 67 HM gave growth in the form of single colonies. These strains were isolated from soil samples taken from sites contaminated with chemical effluents. It is possible that nickel chlorides were already present in such soil in high concentrations exceeding the norm, that is why these strains had such high resistance to nickel ions. Thus, Rhizobium sp. strains did not have the most active PGPR properties, but different strains of Pseudomonas sp. showed high resistance to glyphosate and nickel chloride. Thus, Pseudomonas sp. they demostrated their high ability to adapt to stressful conditions. It is such PGPR bacteria (Plant Growth Promoting Rhizo bacteria) that can be considered as biological agents to increase the efficiency of bioremediation of agricultural soils.

Study of Endophytic Bacteria in Pearl Millet [Pennisetum glaucum (L.) R. Br.] Roots

Aims: The current investigation aims to isolate and identify the root endophytic bacteria from Pearl millet (Pennisetum glaucum) variety MSH-1970, as well as evaluate the qualities that promote plant growth. Study Design: The study involves isolating endophytic bacteria, performing biochemical and molecular characterization, and evaluating their ability to stimulate plant development through biochemical tests. Place and Duration of Study: Departmentof Bioscience and Biotechnology, Banasthali Vidyapith, Tonk, Niwai, Rajasthan, 2022–2023. Methodology: Pearl millet MSH-1970 was planted in pots in the greenhouse of the Department of Bioscience and Biotechnology and endophytic bacterial strains were isolated. The isolates' morphological features were recorded using Bergey's Manual of Systemic Bacteriology, and biochemical testing was done. 16s rRNA gene PCR was used to do molecular characterization of the potential endophyte, and the PCR product was sequenced. Ammonia production, phosphate solubilization, and HCN production were used to identify the properties that promote plant development. Results: The initial culture of endophytic bacteria isolated from the pearl millet variety MSH-1970 yielded 14 colonies on Nutrient agar medium. One of the colonies, BVCA-16 could solubilize phosphate, and generate hydrogen cyanide, and ammonia. Using 16f-16r and 63f-1244r primers, a molecular analysis of BVCA16 revealed 99.92% similarity with Pseudomonas sp. AUS22.The sequence was submitted to Genebank NCBI as Pseudomonas sp. strain BVCA-16, accession number OR350932. Conclusion: In the Pearl millet variety MSH-1970, the endophytic bacteria Pseudomonas sp. strain BVCA-16 was identified and it showed potential to promote plant growth.

Exploring IAA biosynthesis and plant growth promotion mechanism for tomato root endophytes with incomplete IAA synthesis pathways

Exploring indoleacetic acid (IAA) biosynthesis pathways of plant growth promoting bacteria and their ability to synthesize IAA is crucial for understanding the promotion mechanism and for developing more efficient microbial fertilizer. In this study, 118 bacterial endophytic strains were isolated from tomato root and 68 isolates were identified as members of Bacillus and Pseudomonas genus. After screening abilities to synthesize IAA in vitro and promote plant growth for these identified Bacillus and Pseudomonas strains, 7 endophytic strains Bacillus sp. Y_21, B. paramycoides Y_29, B. albus Y_96, B. cereus Y_121, P. plecoglossicida Y_157, Bacillus sp. Y_165 and B. aryabhattai Y_170 strains showed a significant promotion role on wheat root or leaf, including 4 endophytic strains with the potential ability to utilize intermediate metabolites, such as tryptamine and indole acetamide, to produce IAA. Genomic sequencing analysis for selected representative plant growth promoting endophytes showed that IAA-producing bacteria B. cereus mr31 and P. putida Y_166 separately harbored a complete indoleacetamide (IAM) and complete tryptamine (TAM) pathway; whereas, Bacillus sp. Y_165 and B. aryabhattai Y_170, two strains producing IAA not using tryptophan but with indole-3-acetamide, had an incomplete IAM pathway. Fermentation experiments of three genome-sequenced strains using wheat or tomato root extracts as substrate, and combining with UHPLC–MS/MS analysis for wheat root extracts, demonstrated that Bacillus sp. Y_165 strain might produce IAA by using the plant-derived indole-3-acetamide. Our study first demonstrated a novel potential mechanism for the plant growth promoting endophytes to biosynthesize IAA using plant-derived intermediates. This additional mechanism has deepened our understanding of how bacterial endophytes promote plant health and resilience, offering valuable insights about how plants regulate IAA homeostasis within their internal tissues in association with bacterial endophytes.Graphical

Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization.

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.IMPORTANCEHorizontal gene transfer (HGT) is a key process in microbial evolution, but the factors limiting HGT are poorly understood. Aside from the rather unique scenario of antibiotic resistance, the evolutionary benefits of pathway acquisition are still unclear. To experimentally test the effects of pathway acquisition, we transferred a pathway for catabolism of a plant-derived aromatic compound between soil bacteria isolated from the roots of poplar trees and determined the resulting phenotypic and fitness effects. We found that pathway acquisition allowed bacteria to grow using the plant-derived compound in the laboratory, but that this new phenotype did not provide an advantage when the bacteria were reinoculated onto plant roots. These results suggest that the benefits of pathway acquisition may be small when measured under ecologically-relevant conditions. From an engineering perspective, efforts to alter microbial community composition in situ by manipulating catabolic pathways or nutrient availability will be challenging when gaining access to a new niche does not provide a benefit.

Characterization and identification of Pseudomonas sp. AW4, an arsenic-resistant and plant growth-promoting bacteria isolated from the soybean (Glycine max L.) rhizosphere.

Pseudomonas sp. AW4 is a highly arsenic (As) resistant bacterium with plant growth promoting properties, originally isolated from the soybean (Glycine max L.) rhizosphere. In order to safely use this isolate in diverse bioformulations, its characterization needs to be completed and a reliable identification must be provided. In the present work, we analyzed the morpho-physiological, biochemical and genomic characteristics of Pseudomonas sp. AW4. Identification of the isolate varied according to the parameters analyzed, mainly biochemical and physiological tests or individual genes and phylogenetic analyses. In this regard, we performed massive sequencing of its genome, in order to consistently complete its characterization and identification. Pseudomonas sp. AW4 formed a monophyletic clade with P. urmiensis SWRI10, presenting 3.08% of unique genes against this reference isolate. More than 70% of AW4 genes were also shared with P. oryziphila strain 1257 NZ and with P. reidholzensis strain CCOS 865. The search for genes related to As resistance evidenced the presence of the operon arsHRBC. Taken together, results of the present work allow identification of this bacterium as Pseudomonas urmiensis AW4 and open up a number of opportunities to study this strain and understand the mechanisms of arsenic resistance and plant growth promotion.

New Bacteriophage Pseudomonas Phage Ka1 from a Trivia of Lake Baikal

New Bacteriophage Pseudomonas Phage Ka1 from a Trivia of Lake Baikal

Pseudomonas boreofloridensis sp. nov., and Pseudomonas citrulli sp. nov., isolated from watermelon in Florida.

Three fluorescent bacterial strains, K1, K13 and K18, were obtained from watermelon (Citrullus lanatus) foliage symptomatic of bacterial leaf spot of cucurbits in Florida. The strains underwent phenotypic characterization, including LOPAT (levan production, oxidase activity, pectolytic activity on potato, arginine dihydrolase production and hypersensitive response (HR) on both tobacco and tomato) and pathogenicity testing on watermelon and squash seedlings. Whole-genome sequencing of the isolates was performed, and multi-locus sequence analysis (MLSA) utilizing housekeeping genes gltA, rpoD, gapA and gyrB placed the isolates into two distinct clades within the Pseudomonas genus. Average nucleotide identity based on blast (ANIb) was used to compare the isolates to Pseudomonas reference genomes. Using ANIb, the closest relatives to the novel strains were identified as Pseudomonas wayambapalatensis (K1 : 82.58%; K13 : 83.77%) and Pseudomonas kilonensis (K18 : 87.16%), although ANIb values were below the 95% threshold for species delineation. DNA-DNA hybridization (genome-genome distance calculation method), comparison to the online Type Genome Server, Biolog biochemical profiling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were also unable to identify the isolates as any known species of Pseudomonas. Based on the combination of genetic and phenotypic data, we conclude that these isolates represent two novel Pseudomonas species, for which we propose the names Pseudomonas boreofloridensis sp. nov. (K1, K13T, NCPPB 4759=LMG 33364) and Pseudomonas citrulli sp. nov. (K18T, NCPPB 4761=LMG 33365). The specific epithet boreofloridensis was chosen for the geographic location of isolation (northern Florida), while citrulli designates the host of origin (C. lanatus).

A Comprehensive Genome Mining Analysis of Biosynthetic Gene Clusters in Pseudomonas sp. SXM-1

Very resistant pathogenic microorganisms have been reported to current antibiotics in the last decade. Therefore, there is a great need to understand not only resistance metabolism but also secondary metabolites of pathogenic microorganisms. Genome mining tools have so far been improved to understand secondary metabolites from biosynthetic gene clusters. Microorganisms predicted for their genomes and secondary metabolites using these tools are widely employed in pharmaceutical and industrial studies. Pseudomonas spp. are widely used in recombinant DNA technology to produce commercial products. Bioinformatics-based in silico tools significantly contribute to the discovery of new bioactive compounds for pharmacy and medicine. This study aims to conduct a comprehensive gene cluster analysis of the Pseudomonas sp. SXM-1 strain isolated from the coastal seawater of Xiamen Bay using antiSMASH (7.0.1). The accession number of Pseudomonas sp. SXM-1 strain was retrieved from NCBI. 14 regions were found, including non-ribosomal peptides metallophores (NRP-metallophore), nonribosomal peptide-synthetase (NRPS), NRPS-like, ribosomally synthesized and post-translationally modified peptide-like (RiPP-like), betalactone, nonribosomal peptide-synthetase (NRPS), ectoine and N-acetylglutaminylglutamine amide (NAGGN). Analysis of all 14 regions revealed secondary metabolites with potential applications in diverse fields. Microbiologists are strongly advised to conduct wet-lab experiments to validate the secondary metabolites discussed in this study.

Isolation of halotolerant Pseudomonas sp. KW-2 for the effective degradation p-arsanilic acid and immobilization its released inorganic arsenic

p-arsanilic acid (p-ASA) contamination in highly saline environments has received increasing attention; however, p-ASA removal by salt-tolerant Mn(II)-oxidizing bacteria (MnOB) has not yet been reported. In this study, a salt-tolerant Mn(II)-oxidizing bacterium, Pseudomonas sp. KW-2, was isolated, and its capacity to efficiently oxidize Mn(II), form biogenic Mn oxides (BMO) and remove p-ASA was evaluated. Batch experiments indicated that KW-2 had good Mn(II) oxidation capacity (BMO~100μM) when the salinity of the medium ranged from 15.00g/L to 55.00g/L. Strain KW-2 exhibited strong p-ASA removal efficiency (80.38%) via in situ-formed BMO when the initial concentration of p-ASA was 5.00mg/L. p-ASA removal by strain KW-2 was driven primarily by the oxidation of BMO (84.45%), and the released inorganic arsenic major entered the crystal structure of the BMO precipitates. This study provides a feasible method for the bioremediation of p-ASA in high-salt environments.

The paradoxical effects of beneficial bacteria on Solanum lycopersicum under Cd stress.

This study investigated the complex interactions between a novel consortium and tomato seedlings under cadmium (Cd) stress. The consortium consists of two bacteria, Pseudomonas sp. HS4 and Paenarthrobacter sp. AS8, both with proven plant growth-promoting (PGP) properties, isolated from Cd hyperaccumulators. Our research highlights the paradoxical effects of these bacteria, revealing their dual role in reducing Cd uptake while simultaneously inducing oxidative stress in plants. Hydroponic experiments showed that the consortium reduced Cd accumulation in tomato shoots by 52% compared to uninoculated controls. However, this reduction was accompanied by decreased plant biomass and increased oxidative stress, with malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) levels up to 80% and 160% higher, respectively, in inoculated plants. Root H₂O₂ production increased by 38% under 50 μM Cd without a corresponding rise in catalase (CAT) activity. Despite Cd exposure, the consortium promoted chlorophyll and carotenoid synthesis, restoring pigment levels to those of unstressed controls. Gene expression analysis revealed a complex impact on stress responses, with inoculation suppressing Sl1 gene expression in roots and upregulating the oxidative stress-related GR-1 gene in shoots. These findings highlight the complex and multifaceted relationship between beneficial bacteria and plant fitness under heavy metal stress, with significant implications for sustainable agriculture. The study raises new questions regarding the broader physiological and ecological impacts of applying hyperaccumulator-associated bacteria in crop management, emphasizing the necessity for deeper mechanistic insights into these interactions to fully harness their potential in improving crop resilience and productivity.

Exploring the Plant Growth-Promotion Properties of Rhizospheric and Endophytic Bacteria Associated with Robinia pseudoacacia L. in Serpentine Soil.

Serpentine soils are characterized as a unique environment with low nutrient availability and high heavy metal concentrations, often hostile to many plant species. Even though these unfavorable conditions hinder the growth of various plants, particular vegetation with different adaptive mechanisms thrives undisturbed. One of the main contributors to serpentine adaptation represents serpentine bacteria with plant growth-promoting properties that assemble delicate interactions with serpentine plants. Robinia pseudoacacia L. is an invasive but adaptive species with phytoremediation potential and demonstrates extraordinary success in this environment. To explore more in-depth the role of plant growth-promoting serpentine bacteria, we isolated them and tested their various plant growth-promoting traits both from the rhizosphere and roots of R. pseudoacacia. Based on the demonstrated plant growth-promoting traits such as siderophore production, phosphate solubilization, nitrogen fixation, indole-3-acetic acid production, and ACC deaminase production, we sequenced overall 25 isolates, 14 from the rhizosphere and 11 from the roots. Although more efficient in exhibiting plant growthpromoting traits, rhizospheric bacteria showed a low rate of diversity in comparison to endophytic bacteria. The majority of the isolates from the rhizosphere belong to Pseudomonas, while isolates from the roots exhibited higher diversity with genera Pseudomonas, Bacillus, Staphylococcus, Lysinibacillus and Brevibacterium/Peribacillus/Bacillus. The capacity of the described bacteria to produce siderophores, solubilize phosphate, and fix nitrogen highlights their central role in enhancing nutrient availability and facilitating R. pseudoacacia adaptation to serpentine soils. The findings highlight the potential significance of serpentine bacteria, particularly Pseudomonas, in contributing to the resilience and growth of R. pseudoacacia in serpentine environments.

Colonization of phthalate-degrading endophytic bacterial consortium altered bacterial community and enzyme activity in plants

Phthalates (PAEs) are widely distributed hazardous organic compounds that pose threats to ecosystems and human health. Endophytic bacteria can effectively eliminate PAEs contamination risk. However, limited information is available regarding the impact of endophytic bacterial colonization on bacterial communities within plants. In this study, the endophytic bacterial consortium EN was colonized in lettuce by seed soaking, root irrigation, leaf spraying, and combined spraying-irrigation, resulting in a marked improvement in plant growth. The findings revealed that consortium EN colonization through combined spraying-irrigation exhibited superior degradation capability with 40.54% PAEs removal from soil. Meanwhile, the residual PAEs in lettuce decreased by 94.05% compared with the uninoculated treatment. High-throughput sequencing analysis indicated that colonization of consortium EN altered the bacterial community in lettuce. Specifically, the relative abundance of the dominant genus Pseudomonas was significantly higher than that in the uninoculated control (P < 0.01). Additionally, colonization enhanced the activities of peroxidase and catalase in lettuce, thereby improving plant resistance. This work offers a theoretical foundation for comprehending the mechanism underlying the bioremediation of PAEs contamination by endophytic bacteria in soil-plant system.

Identification of stem melanosis of wheat (Pseudomonas cichorii) by real-time PCR

The phytopathogenic bacterium, Pseudomonas cichorii, affects a wide range of crops in filed and greenhouse production and causes wheat stem melanosis, which has been regulated by importers of Russian grain products. It is crucial to update the identification method based on real-time polymerase chain reaction (PCR) (PCR-RT). This method helps confirming P. cichorii in wheat samples. A 90 base pair long section of the hrcRST pathogenicity gene cluster was used as the target. Positive results were obtained for reference strains, confirmed by amplicon sequencing. Nucleotide sequences were then compared to the typical strain, DSM 50259. As a result of comparative DNA analysis, the sequences of the direct primer and probe were modified. The possibility of using a modification of 6FAM/BHQ1 dye/quencher available on the territory of the Russian Federation was demonstrated. The specificity of the new PCR-RT primer system PscF/PscHrc751R/PscP1 was assessed using 107 bacterial strains of the genus Pseudomonas, including P. cichorii, P. fuscovaginae, P. syringae, P. trivialis, P. viridiflava, P. chlororaphis, P. lutea and P. orientalis. The DNA of 4 strains (P. poae, P. graminis and 2 strains of P. fluorescens) showed a non-specific reaction at the 35–37 cycle threshold, with an accumulation that did not appear exponential. The analytical sensitivity of the test allows for the detection of P. cichorii at a concentration of 10^1 CFU/mL. The PCR-RV PscF/PscHrc751R/PscP1 test can be used as a screening tool for the detection of P. cichorii in plant products and for the characterization of pure bacterial cultures.

Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms.

The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier "Pseudomonas putida" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as "Pseudomonas putida" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.

Pseudomonas otitidis Bacteremia in a Patient with Cancer During the Palliative-care Phase: A Case Report.

Pseudomonas otitidis bacteremia is rare. We herein report a case of bacteremia caused by P. otitidis in a patient with advanced appendiceal cancer. A 79-year-old Japanese man developed infection when he was admitted to our hospital for palliative care. Blood culture revealed the presence of Pseudomonas spp. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to identify the organism accurately. The patient was treated with a two-week course of piperacillin/tazobactam, and the bacteremia was successfully controlled. Clinicians should be aware that P. otitidis can cause bacteremia, particularly in immunocompromised patients.

Increasing of Spring Wheat Plant Resistance to Copper Toxicity by Application of Plant Growth-Promoting Rhizobacteria on Metal-Contaminated Soil

Effects of plant growth-promoting rhizobacteria of the Pseudomonas genus application on growth of spring wheat plants was studied in pot experiment on agrogrey soil artificially contaminated with Cu in increased concentration. Increasing of plants resistance to metal toxicity by application of bacteria was found. Chemical composition of plants and uptake of Cu and biophilic elements N, P, K, Ca, Mg, Fe, Zn and Mn by shoots and roots were determined. Positive effect of bacteria on plant growth in contamination of soil with Cu is due to increase in nutrient uptake by plants from soil, concentration and accumulation of metal in roots that indicates protective response reaction of plants to soil contamination with Cu. Bacteria increased Cu uptake by plant shoots from contaminated soil – enhanced phytoextraction without changes in soil medium reaction.

Engineering a vanillate-producing strain of Pseudomonas sp. NGC7 corresponding to aromatic compounds derived from the continuous catalytic alkaline oxidation of sulfite lignin

IntroductionLignin is a promising resource for obtaining aromatic materials, however, its heterogeneous structure poses a challenge for effective utilization. One approach to produce homogeneous aromatic materials from lignin involves the application of microbial catabolism, which is gaining attention. This current study focused on constructing a catabolic pathway in Pseudomonas sp. NGC7 to produce vanillate (VA) from aromatic compounds derived from the chemical depolymerization of sulfite lignin.ResultsAlkaline oxidation of sulfite lignin was performed using a hydroxide nanorod copper foam [Cu(OH)2/CF]-equipped flow reactor. The flow reactor operated continuously for 50 h without clogging and it yielded a sulfite lignin stream containing acetovanillone (AV), vanillin (VN), and VA as the major aromatic monomers. The catabolic pathway of Pseudomonas sp. NGC7 was optimized to maximize VA production from aromatic monomers in the sulfite lignin stream derived from this oxidation process. Pseudomonas sp. NGC7 possesses four gene sets for vanillate O-demethylase, comprising the oxygenase component (vanA) and its oxidoreductase component (vanB). Among these, the vanA4B4 gene set was identified as the key contributor to VA catabolism. To facilitate the conversion of AV to VA, AV-converting enzyme genes from Sphingobium lignivorans SYK-6 were introduced. The ΔvanA4B4 strain, harboring these AV-converting genes, produced VA from the sulfite lignin stream with 91 mol%. Further disruption of vanA1B1, vanA2B2, vanA3B3, and a vanillin reductase gene, in addition to vanA4B4, and introduction of a 5-carboxyvanillate decarboxylase gene from S. lignivorans SYK-6 to utilize 5-carboxyvanillin and 5-carboxyvanillate from the sulfite lignin stream for VA production achieved a VA yield of 103 mol%.ConclusionDeveloping methods to overcome lignin heterogeneity is essential for its use as a raw material. Consolidating continuous alkaline oxidation of lignin in a Cu(OH)2/CF-packed flow reactor and biological funneling using an engineered catabolic pathway of Pseudomonas sp. NGC7 is a promising approach to produce VA for aromatic materials synthesis. NGC7 possesses a higher adaptability to various aromatic compounds generated from the alkaline oxidation of lignin and its natural ability to grow on p-hydroxyphenyl, guaiacyl, and syringyl compounds underscores its potential as a bacterial chassis for VA production from a wide range of lignin-derived aromatic compounds.Graphical

Microbial profile of biofilms formed inside recovered plastic bottles and contamination of food products therein conditioned: Case of Hibiscus sabdariffa L. beverage

Recovered plastic bottles are reused in Cameroon as food packaging for the conditioning of certain foods called “traditional” based on production processes and structures. However, the recycling process of these bottles does not ensure the complete removal of contaminants present in the bottles, particularly biofilms. In the present study, focus was made on the contamination of Hibiscus sabdariffa beverage by biofilms formed inside recovered plastic bottles. Recovered and ready-to-be-reused plastic bottles were sampled from traditional food producers. The presence of biofilms inside bottles was screened and the microbial profile of biofilms was assessed. H. sabdariffa beverages prepared under aseptic conditions were conditioned in recovered plastic bottles and stored for 35 days at 4°C. During storage, the microbiological and physicochemical quality of the beverages was followed each 7th day. Biofilms were found in all bottles analyzed and their microflora were made of microorganisms belonging to genera Salmonella, Shigella, Vibrio, Escherichia, Pseudomonas, Klebsiella, Staphylococcus and Candida, with the dominance of the genus Pseudomonas (37.10 %) and Pseudomonas aeruginosa (21.35 %) at the level of species. Amongst the 135 isolates screened, the greatest biofilm-forming abilities were recorded for E. coli P5 (0.62±0.02), Staphylococcus aureus P13 (0.67±0.05), Klebsiella pneumoniae P15 (0.66±0.03), and Vibrio cholerae P7 (0.67±0.01). The microbial loads of beverages stored at 4°C in recovered plastic bottles collected from the producers were all out of norm on day 7, thus suggesting a reduced shelf-life of up to 7 days. The presence of microorganisms in beverages conditioned in bottles cleaned in the lab while applying the good hygiene practices suggests that, although there was an improvement with significant reduction of biofilms and thus microbial contamination, further improvements of the cleaning process through response surface methodology are needed.

Effects of snake fungal disease (ophidiomycosis) on the skin microbiome across two major experimental scales.

Emerging infectious diseases are increasingly recognized as a significant threat to global biodiversity conservation. Elucidating the relationship between pathogens and the host microbiome could lead to novel approaches for mitigating disease impacts. Pathogens can alter the host microbiome by inducing dysbiosis, an ecological state characterized by a reduction in bacterial alpha diversity, an increase in pathobionts, or a shift in beta diversity. We used the snake fungal disease (SFD;ophidiomycosis), system to examine how an emerging pathogen may induce dysbiosis across two experimental scales. We used quantitative polymerase chain reaction, bacterial amplicon sequencing, and a deep learning neural network to characterize the skin microbiome of free-ranging snakes across a broad phylogenetic and spatial extent. Habitat suitability models were used to find variables associated with fungal presence on the landscape. We also conducted a laboratory study of northern watersnakes to examine temporal changes in the skin microbiome following inoculation with Ophidiomyces ophidiicola. Patterns characteristic of dysbiosis were found at both scales, as were nonlinear changes in alpha and alterations in beta diversity, although structural-level and dispersion changes differed between field and laboratory contexts. The neural network was far more accurate (99.8% positive predictive value [PPV]) in predicting disease state than other analytic techniques (36.4% PPV). The genus Pseudomonas was characteristic of disease-negative microbiomes, whereas, positive snakes were characterized by the pathobionts Chryseobacterium, Paracoccus, and Sphingobacterium. Geographic regions suitable for O. ophidiicola had high pathogen loads (>0.66 maximum sensitivity+specificity). We found that pathogen-induced dysbiosis of the microbiome followed predictable trends, that disease state could be classified with neural network analyses, and that habitat suitability models predicted habitat for the SFD pathogen.