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Abstract Background Plastics are an indispensable part of our daily life. However, mismanagement at their end-of-life results in severe environmental consequences. The microbial conversion of these polymers into new value-added products offers a promising alternative. In this study, we engineered the soil-bacterium Comamonas testosteroni KF-1, a natural degrader of terephthalic acid, for the conversion of the latter to the high-value product 2-pyrone-4,6-dicarboxylic acid. Results In order to convert terephthalic acid to 2-pyrone-4,6-dicarboxylic acid, we deleted the native PDC hydrolase and observed only a limited amount of product formation. To test whether this was the result of an inhibition of terephthalic acid uptake by the carbon source for growth (i.e. glycolic acid), the consumption of both carbon sources was monitored in the wild-type strain. Both carbon sources were consumed at the same time, indicating that catabolite repression was not the case. Next, we investigated if the activity of pathway enzymes remained the same in the wild-type and mutant strain. Here again, no statistical differences could be observed. Finally, we hypothesized that the presence of a pmdK variant in the degradation operon could be responsible for the observed phenotype and created a double deletion mutant strain. This newly created strain accumulated PDC to a larger extent and again consumed both carbon sources. The double deletion strain was then used in a bioreactor experiment, leading to the accumulation of 6.5 g/L of product in 24 h with an overall productivity of 0.27 g/L/h. Conclusions This study shows the production of the chemical building block 2-pyrone-4,6-dicarboxylic acid from terephthalic acid through an engineered C. testosteroni KF-1 strain. It was observed that both a deletion of the native PDC hydrolase as well as a pmdK variant is needed to achieve high conversion yields. A product titer of 6.5 g/L in 24 h with an overall productivity of 0.27 g/L/h was achieved.

The etiopathogenesis of diverticular disease is unknown. To compare the fecal and mucosa-associated microbiota between participants with and without diverticulosis and participants who later developed diverticulitis versus those that did not from a population-based study. The PopCol study, conducted in Stockholm, Sweden, invited a random sample of 3556 adults to participate, of which 745 underwent colonoscopy. Overall, 130 participants (17.5%) had diverticulosis. 16S rRNA gene sequencing was conducted on available sigmoid biopsy samples from 529 and fecal samples from 251 individuals. We identified individuals who subsequently developed acute diverticulitis up to 13 years after sample collection. In a case-control design matching for gender, age (+/−5 years), smoking and antibiotic exposure, we compared taxonomic composition, richness and diversity of the microbiota between participants with or without diverticulosis, and between participants who later developed acute diverticulitis versus those who did not. No differences in microbiota richness or diversity were observed between participants with or without diverticulosis, nor for those who developed diverticulitis compared with those who did not. No bacterial taxa were significantly different between participants with diverticulosis compared with those without diverticulosis. Individuals who later developed acute diverticulitis (2.8%) had a higher abundance of genus Comamonas than those who did not (p =.027). In a population-based cohort study the only significant difference was that those who later develop diverticulitis had more abundance of genus Comamonas. The significance of Comamonas is unclear, suggesting a limited role for the gut microbiota in the etiopathogenesis of diverticular disease. [ABSTRACT FROM AUTHOR]

Sodium tripolyphosphate (STPP) là chất phụ gia được sử dụng rộng rãi trong chế biến thủy sản. Nồng độ phosphate cao trong nước thải chế biến thủy sản nếu không được xử lý sẽ gây phú dưỡng hóa dẫn đến tảo nở hoa từ đó làm ô nhiễm nguồn nước và ảnh hưởng đến sức khỏe cộng đồng. Mục tiêu của nghiên cứu là phân lập và tuyển chọn các dòng vi khuẩn trong nước thải chế biến thủy sản có khả năng hấp thu và hóa hướng động theo STPP. Từ các mẫu nước được thu ở hệ thống xử lý nước thải của công ty chế biến thủy sản tại tỉnh Sóc Trăng, 27 dòng vi khuẩn có khả năng hấp thu STPP đã được phân lập, trong đó, 11 dòng vi khuẩn gồm PAE1.1, PAE1.2, PAE1.4, PAE1.6, PAE1.7, PAN1.1, PAN1.12, PAN1.5, POU1.2, POU1.3 và POU1.4 có khả năng tạo sinh khối cao và hấp thu trên 50% STPP ở nồng độ 200 ppm sau 24 giờ nuôi cấy. Ba dòng vi khuẩn POU1.3, POU1.4 và PAN1.12 có khả năng hấp thu cao và hóa hướng động theo STPP được định danh lần lượt là Acinetobacter sp. POU1.3, Acinetobacter sp. POU1.4 và Comamonas sp. PAN1.12 dựa vào kết quả phân tích và so sánh trình tự gen 16S-rRNA.

Background: Plastics are an indispensable part of our daily life. However, mismanagement at their end-of-life results in severe environmental consequences. The microbial conversion of these polymers into new value-added products offers a promising alternative. In this study, we engineered the soil-bacterium Comamonas testosteroni KF-1, a natural degrader of terephthalic acid, for the conversion of the latter to the high-value product 2-pyrone-4,6-dicarboxylic acid. Results: In order to convert terephthalic acid to 2-pyrone-4,6-dicarboxylic acid, we deleted the native PDC hydrolase and observed only a limited amount of product formation. To test whether this was the result of an inhibition of terephthalic acid uptake by the carbon source for growth (i.e. glycolic acid), the consumption of both carbon sources was monitored in the wild-type strain. Both carbon sources were consumed at the same time, indicating that catabolite repression was not the case. Next, we investigated if the activity of pathway enzymes remained the same in the wild-type and mutant strain. Here again, no statistical differences could be observed. Finally, we hypothesized that the presence of a pmdK variant in the degradation operon could be responsible for the observed phenotype and created a double deletion mutant strain. This newly created strain accumulated PDC to a larger extent and again consumed both carbon sources. The double deletion strain was then used in a bioreactor experiment, leading to the accumulation of 6.5 g/L of product in 24 h with an overall productivity of 0.27 g/L/h. Conclusions: This study shows the production of the chemical building block 2-pyrone-4,6-dicarboxylic acid from terephthalic acid through an engineered C. testosteroni KF-1 strain. It was observed that both a deletion of the native PDC hydrolase as well as a pmdK variant is needed to achieve high conversion yields. A product titer of 6.5 g/L in 24 h with an overall productivity of 0.27 g/L/h was achieved. [ABSTRACT FROM AUTHOR]

Acute appendicitis is the leading cause of urgent surgery. Recently, there have been several case reports linking Comamonas, a globally distributed environmental bacterial species, to appendicitis. The patients described below were admitted through the emergency room of a second-level hospital unit in Guayaquil city, presenting symptoms consistent with acute abdomen and initially diagnosed with acute appendicitis prior to surgical intervention. In all cases, surgical or pediatric surgical services collected microbiological samples for further analysis, and the results are detailed below.

Polyethylene terephthalate (PET) is a prevalent synthetic polymer that is known to contaminate marine and terrestrial environments. Currently, only a limited number of PET-active microorganisms and enzymes (PETases) are known. This is in part linked to the lack of highly sensitive function-based screening assays for PET-active enzymes. Here, we report on the construction of a fluorescent biosensor based on Comamonas thiooxidans strain S23. C. thiooxidans S23 transports and metabolizes TPA, one of the main breakdown products of PET, using a specific tripartite tricarboxylate transporter (TTT) and various mono- and dioxygenases encoded in its genome in a conserved operon ranging from tphC-tphA1. TphR, an IclR-type transcriptional regulator is found upstream of the tphC-tphA1 cluster where TPA induces transcription of tphC-tphA1 up to 88-fold in exponentially growing cells. In the present study, we show that the C. thiooxidans S23 wild-type strain, carrying the sfGFP gene fused to the tphC promoter, senses TPA at concentrations as low as 10 mM. Moreover, a deletion mutant lacking the catabolic genes involved in TPA degradation thphA2-A1 (ΔtphA2A3BA1) is up to 10,000-fold more sensitive and detects TPA concentrations in the nanomolar range. This is, to our knowledge, the most sensitive reporter strain for TPA and we demonstrate that it can be used for the detection of enzymatic PET breakdown products. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the relationship among pollutant removal performance, microbial community structure and potential gene function of immobilized microorganisms in coking wastewater (CWW) treatment process. The results showed that the immobilized biomass containing strain Comamonas sp. ZF-3 displayed greater resistance to CWW and higher COD, NH4+-N removal efficiency (92%, 60%) than free cells (48%, 7%), meanwhile, the results from GC-MS proved main organic pollutants in CWW including phenolic compounds, heterocyclic compounds and polycyclic aromatic hydrocarbons were basically removed by immobilized microorganisms. During 123 days of degradation experiment, high-throughput 16S rRNA gene sequencing analysis of immobilized carriers showed more stable and diverse microbial community, which was consistent with simultaneous removal of COD and NH4+-N observed in carrier experiment. Among them, Comamonas sp. ZF-3 continuously remained at the highest proportion (23.25%) in immobilized carrier, while Nitrosomonas (1.47%) and Nitrospira (1.90%) were simultaneously detected. Moreover, microbial community of immobilized carriers showed higher relative abundance of potential function in membrane transport and xenobiotics biodegradation and metabolism, which may indirectly displayed biodegradation activity of immobilized functional microorganisms. This work illustrated the survival status and potential gene function of immobilized microorganisms, and provided basis for practical application of immobilized carriers in CWW treatment., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Comamonas spp. are non-fermenting Gram-negative bacilli. They were first discovered in 1894, and since then, twenty-four species have been characterized. The natural habitat of these bacteria is soil, wastewater/sludge, fresh water such as ponds and rivers, and the animal intestinal microbiome. They were also isolated from industrial settings, such as activated sludge and polluted soil, and from the hospital environment and clinical samples, such as urine, pus, blood, feces, and kidney. Comamonas spp. are associated with environmental bioremediation and are considered an important environmental bacterium rather than a human pathogen. However, in the 1980s, they became a concern when several human infections associated with these species were reported. Here, the Comamonas genus was examined in terms of its members, identification techniques, and pathogenicity. Seventy-seven infection cases associated with these microorganisms that have been discussed in the literature were identified and investigated in this project. All relevant information regarding year of infection, country of origin, patient information such as age, sex, underlying medical conditions if any, type of infection caused by the Comamonas species, antibiotic susceptibility testing, treatment, and outcomes for the patient were extracted from case reports. The findings suggest that even though Comamonas spp. are thought of as being of low virulence, they have caused harmful health conditions in many healthy individuals and even death in patients with underlying conditions. Antimicrobial treatment of infections associated with these species, in general, was not very difficult; however, it can become an issue in the future because some strains are already resistant to different classes of antibiotics. Therefore, these pathogens should be considered of such importance that they should be included in the hospital screening programs. [ABSTRACT FROM AUTHOR]

Comamonas spp. are Gram-negative bacteria that catabolize a wide range of organic and inorganic substrates. Comamonas spp. are abundant in aquatic and soil environments, including wastewater, and can cause opportunistic infections in humans. Because of their potential in wastewater bioaugmentation and bioremediation strategies, the identification of Comamonas species harboring genes encoding carbapenemases and other clinically important antibiotic resistance genes warrant further investigation. Here, we present an analysis of 39 whole-genome sequences comprising three Comamonas species from aquatic environments in South Australia that were recovered on media supplemented with carbapenems. The analysis includes a detailed description of 33 Comamonas denitrificans isolates, some of which carried chromosomally acquired blaGES-5, blaOXA, and aminoglycoside resistance (aadA) genes located on putative genomic islands (GIs). All blaGES-5- and blaOXA-containing GIs appear to be unique to this Australian collection of C. denitrificans. Notably, most open reading frames (ORFs) within the GIs, including all antimicrobial resistance (AMR) genes, had adjacent attC sites, indicating that these ORFs are mobile gene cassettes. One C. denitrificans isolate carried an IncP-1 plasmid with genes involved in xenobiotic degradation and response to oxidative stress. Our assessment of the sequences highlights the very distant nature of C. denitrificans to the other Comamonas species and its apparent disposition to acquire antimicrobial resistance genes on putative genomic islands. [ABSTRACT FROM AUTHOR]

ABSTRACT Gluconeogenic carbon metabolism is not well understood, especially within the context of flux partitioning between energy generation and biomass production, despite the importance of gluconeogenic carbon substrates in natural and engineered carbon processing. Here, using multiple omics approaches, we elucidate the metabolic mechanisms that facilitate gluconeogenic fast-growth phenotypes in Pseudomonas putida and Comamonas testosteroni, two Proteobacteria species with distinct metabolic networks. In contrast to the genetic constraint of C. testosteroni, which lacks the enzymes required for both sugar uptake and a complete oxidative pentose phosphate (PP) pathway, sugar metabolism in P. putida is known to generate surplus NADPH by relying on the oxidative PP pathway within its characteristic cyclic connection between the Entner-Doudoroff (ED) and Embden-Meyerhoff-Parnas (EMP) pathways. Remarkably, similar to the genome-based metabolic decoupling in C. testosteroni, our 13C-fluxomics reveals an inactive oxidative PP pathway and disconnected EMP and ED pathways in P. putida during gluconeogenic feeding, thus requiring transhydrogenase reactions to supply NADPH for anabolism in both species by leveraging the high tricarboxylic acid cycle flux during gluconeogenic growth. Furthermore, metabolomics and proteomics analyses of both species during gluconeogenic feeding, relative to glycolytic feeding, demonstrate a 5-fold depletion in phosphorylated metabolites and the absence of or up to a 17-fold decrease in proteins of the PP and ED pathways. Such metabolic remodeling, which is reportedly lacking in Escherichia coli exhibiting a gluconeogenic slow-growth phenotype, may serve to minimize futile carbon cycling while favoring the gluconeogenic metabolic regime in relevant proteobacterial species. IMPORTANCE Glycolytic metabolism of sugars is extensively studied in the Proteobacteria, but gluconeogenic carbon sources (e.g., organic acids, amino acids, aromatics) that feed into the tricarboxylic acid (TCA) cycle are widely reported to produce a fast-growth phenotype, particularly in species with biotechnological relevance. Much remains unknown about the importance of glycolysis-associated pathways in the metabolism of gluconeogenic carbon substrates. Here, we demonstrate that two distinct proteobacterial species, through genetic constraints or metabolic regulation at specific metabolic nodes, bypass the oxidative PP pathway during gluconeogenic growth and avoid unnecessary carbon fluxes by depleting protein investment into connected glycolysis pathways. Both species can leverage instead the high TCA cycle flux during gluconeogenic feeding to meet NADPH demand. Importantly, lack of a complete oxidative pentose phosphate pathway is a widespread metabolic trait in Proteobacteria with a gluconeogenic carbon preference, thus highlighting the important relevance of our findings toward elucidating the metabolic architecture in these bacteria.

Comamonas spp. are non-fermenting Gram-negative bacilli. They were first discovered in 1894, and since then, twenty-four species have been characterized. The natural habitat of these bacteria is soil, wastewater/sludge, fresh water such as ponds and rivers, and the animal intestinal microbiome. They were also isolated from industrial settings, such as activated sludge and polluted soil, and from the hospital environment and clinical samples, such as urine, pus, blood, feces, and kidney. Comamonas spp. are associated with environmental bioremediation and are considered an important environmental bacterium rather than a human pathogen. However, in the 1980s, they became a concern when several human infections associated with these species were reported. Here, the Comamonas genus was examined in terms of its members, identification techniques, and pathogenicity. Seventy-seven infection cases associated with these microorganisms that have been discussed in the literature were identified and investigated in this project. All relevant information regarding year of infection, country of origin, patient information such as age, sex, underlying medical conditions if any, type of infection caused by the Comamonas species, antibiotic susceptibility testing, treatment, and outcomes for the patient were extracted from case reports. The findings suggest that even though Comamonas spp. are thought of as being of low virulence, they have caused harmful health conditions in many healthy individuals and even death in patients with underlying conditions. Antimicrobial treatment of infections associated with these species, in general, was not very difficult; however, it can become an issue in the future because some strains are already resistant to different classes of antibiotics. Therefore, these pathogens should be considered of such importance that they should be included in the hospital screening programs.

Worldwide, humanity is facing a major environmental crisis with the disposal of heavy metal contaminated waste. The current study describes, for the first time, the interactions between gram-negative Comamonas aquatica and filamentous fungus Fusarium solani in removing heavy metal toxicity as an eco-friendly system. When combined, C. aquatica and F. solani grew well in a co-culture setup without showing any antagonistic indications. Monoculture versus co-culture setups were used to determine the metal tolerance concentration (MTC). Based on the metal tolerance concentration (MTC) values, cells of C. aquatica were able to tolerate 4, 5, 6, and 7 mM of Cr, Zn, Cu, and Ni, respectively. Moreover, C. aquatica withstood up to 6 mM of Pb. Although F. solani exhibited sensitivity to high concentrations of heavy metals in monoculture, the MTC of F. solani increased considerably in a co-culture setup. The results presented here revealed that F. solani facilitated the dispersion of C. aquatica and heightened bioavailability, whereas C. aquatica reduced the toxicity of heavy metals and promoted the growth of F. solani. Transmission electron microscopy (TEM) displayed different mechanisms for heavy metal removal by C. aquatica. Biosorption was evident for Cr and Pb, while transformation was recorded for Ni and Zn. Also, C. aquatica was able to reduce and accumulate Cu in cells. [ABSTRACT FROM AUTHOR]

BACKGROUND Quinoline is an ubiquitous pollutant widely spread in the environment, which can be eliminated efficiently by microbial degradation. In this study, two quinoline‐degrading Comamonas sp. strains Z1 and Z3 were isolated from activated sludge, and the degradation characteristics and genome annotation were investigated in detail. RESULTS: Strain Z1 exhibited a superior capacity for quinoline degradation, which could completely degrade 50–300 mg L−1 quinoline within 8–24 h, whereas strain Z3 required 14–36 h to remove 50–200 mg L−1 quinoline. The suitable pHs for strains Z1 and Z3 were 8.0 and 7.0, respectively, and metal ions such as Mn2+, Ni2+, Cu2+, Co2+ and Hg2+ could greatly inhibit bacterial growth and quinoline degradation. Intermediates of 2‐hydroxyquinoline, 2,8‐dihydroxyquinoline, 8‐hydroxycoumarin, 2,3‐dihydroxyphenylpropionic acids and 2‐hydroxy‐6‐oxonona‐2,4‐diene‐1,9‐dioate were detected by liquid chromatography coupled to Q‐Exactive high‐resolution mass spectrometry. Thus, the biodegradation of quinoline by Comamonas sp. strains possibly proceeded via the 8‐hydroxycoumarin pathway. Genomic sequencing of strains Z1 and Z3 revealed a similar pattern, and a large number of functional genes were predicted to participate in degradation of aromatics. The key genes responsible for quinoline degradation also were identified, such as qor, mhp and bph. Furthermore, quinoline 2‐oxidoreductase (Qor) from strains Z1 and Z3 displayed 47.74%–61.17% similarities with previously reported Qor, which catalyzed the first step of quinoline degradation, and the maximal specific activity in cell‐free extracts of strains Z1 and Z3 was 0.264 and 0.062 U mg protein−1, respectively. CONCLUSION: This study should provide efficient microbial resources and useful genomic information for quinoline bioremediation. © 2020 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Widespread application of chloronitrobenzenes as feedstocks for the production of industrial chemicals and pharmaceuticals has resulted in extensive environmental contamination with these toxic compounds, where they pose significant risks to the health of humans and wildlife. While biotreatment in general is an attractive solution for remediation, its effectiveness is limited with chloronitrobenzenes due to the small number of strains that can effectively mineralize these compounds and their ability to degrade only select isomers. To address this need, we created engineered strains with a novel degradation pathway that reduces the total number of steps required to convert chloronitrobenzenes into compounds of central metabolism. We examined the ability of 2-nitrotoluene 2,3-dioxygenase from Acidovorax sp. strain JS42, nitrobenzene 1,2-dioxygenase (NBDO) from Comamonas sp. strain JS765, as well as active-site mutants of NBDO to generate chlorocatechols from chloronitrobenzenes, and identified the most efficient enzymes. Introduction of the wild-type NBDO and the F293Q variant into Ralstonia sp. strain JS705, a strain carrying the modified ortho pathway for chlorocatechol metabolism, resulted in bacterial strains that were able to sustainably grow on all three chloronitrobenzene isomers without addition of co-substrates or co-inducers. These first-generation engineered strains demonstrate the utility of nitroarene dioxygenases in expanding the metabolic capabilities of bacteria and provide new options for improved biotreatment of chloronitrobenzene-contaminated sites.

The terrestrial deep subsurface is host to significant and diverse microbial populations. However, these microbial populations remain poorly characterized, partially due to the inherent difficulty of sampling, in situ studies, and isolating of the in situ microbes. Motivated by the ability of microbes to gain energy from redox reactions at mineral interfaces, we here present in situ electrochemical colonization (ISEC) reactor as a method to directly study microbial electron transfer activity and to enable the capture and isolation of electrochemically active microbes. We installed a potentiostatically controlled ISEC reactor containing four working electrodes 1,500 m below the surface at the Sanford Underground Research Facility (SURF). The working electrodes were poised at different redox potentials to mimic energy-yielding mineral reducing and oxidizing reactions predicted to occur at this site. We present a 16S rRNA analysis of the in situ electrode-associated microbial communities, revealing the dominance of novel bacterial lineages under cathodic conditions. We also demonstrate that the in situ electrodes can be further used for downstream electrochemical laboratory enrichment and isolation of novel strains. Using this workflow, we isolated Bacillus, Anaerospora, Comamonas, Cupriavidus, and Azonexus strains from the electrode-attached biomass. Finally, the extracellular electron transfer (EET) activity of Comamonas strain (isolated at −0.19 V vs. SHE and designated WE1-1D1) and Bacillus strain (isolated at +0.53 V vs. SHE and designated WE4-1A1-BC) from and to a poised electrode, respectively, were confirmed in electrochemical reactors. Our study highlights the utility of in situ electrodes and electrochemical enrichment workflows to shed light on microbial activity in the deep terrestrial subsurface.

Under more intensified cropping conditions agriculture will face increasing incidences of soil-borne plant pests and pathogens, leading to increasingly higher yield losses world-wide. Soil-borne disease complexes, in particular, are especially difficult to control. In order to better understand soil-borne Meloidogyne-based disease complexes, we studied the volatile-based control mechanism of associated bacteria as well as the rhizospheric microbiome on Ugandan tomato plants presenting different levels of root-galling damage, using a multiphasic approach. The experimental design was based on representative samplings of healthy and infected tomato plants from two field locations in Uganda, to establish species collections and DNA libraries. Root galling symptoms on tomato resulted from a multispecies infection of root-knot nematodes (Meloidogyne spp.). Results revealed that 16.5% of the bacterial strain collection produced nematicidal volatile organic compounds (nVOC) active against Meloidogyne. Using SPME GC-MS, diverse VOC were identified, including sulfuric compounds, alkenes and one pyrazine. Around 28% of the bacterial strains were also antagonistic toward at least one fungal pathogen of the disease complex. However, antagonistic interactions appear highly specific. Nematicidal antagonists included Pseudomonas, Comamonas, and Variovorax and fungicidal antagonists belonged to Bacillus, which interestingly, were primarily recovered from healthy roots, while nematode antagonists were prominent in the rhizosphere and roots of diseased roots. In summary, all antagonists comprised up to 6.4% of the tomato root microbiota. In general, the microbiota of healthy and diseased root endospheres differed significantly in alpha and quantitative beta diversity indices. Bacteria-derived volatiles appear to provide a remarkable, yet wholly unexploited, potential to control Meloidogyne-based soil-borne disease complexes. The highly specific observed antagonism indicates that a combination of volatiles or VOC-producing bacteria are necessary to counter the range of pathogens involved in such complexes.

ABSTRACT Complex chemosensory systems control multiple biological functions in bacteria, such as chemotaxis, gene regulation, and cell cycle progression. Many species contain more than one chemosensory system per genome, but little is known about their potential interplay. In this study, we reveal cross talk between two chemosensory pathways that modulate chemotaxis and biofilm formation in Comamonas testosteroni. We demonstrate that some chemoreceptors that govern chemotaxis also contribute to biofilm formation and these chemoreceptors can physically interact with components of both pathways. Finally, we show that the chemotaxis histidine kinase CheA can phosphorylate not only its cognate response regulator CheY2 but also one of the response regulators from the pathway mediating biofilm formation, FlmD. The phosphoryl group transfer from CheA to CheY2 is much faster than that from CheA to FlmD, which is consistent with chemotaxis being a fast response and biofilm formation being a much slower developmental process. We propose that cross talk between chemosensory pathways may play a role in coordination of complex behaviors in bacteria. IMPORTANCE In many bacteria, two or more homologous chemosensory pathways control several cellular functions, such as motility and gene regulation, in response to changes in the cell’s microenvironment. Cross talk between signal transduction systems is poorly understood; while generally it is considered to be undesired, in some instances it might be beneficial for coregulation of complex behaviors. We demonstrate that several receptors from the pathway controlling motility can physically interact with downstream components of the pathway controlling biofilm formation. We further show that a kinase from the pathway controlling motility can also phosphorylate a response regulator from the pathway controlling biofilm formation. We propose that cross talk between two chemosensory pathways might be involved in coordination of two types of cell behavior—chemotaxis and biofilm formation.

Rationale: Comamonas kerstersii mainly causes intra-abdominal infections with favorable outcomes due to high antibiotic susceptibility. We report the first case of pneumonia caused by C Kerstersii, which promoted patient death, and a second urinary tract infection by C Kerstersii with extensive drug resistance., Patient Concerns: A 46-year-old male (Case 1) with craniocerebral injury underwent emergency decompressive craniectomy, but his condition deteriorated further and presented with discontinuous fever, small moist rales on both lungs, and respiratory failure. Retrospective average nucleotide identity (ANI) analysis of the genomic sequence of the sputum isolate identified it as C Kerstersii 12322-1, antimicrobial susceptibility testing (AST) revealed that it was sensitive to 18 of 21 tested antibiotics.An 82-year-old male (Case 2) with hypertrophic prostate experienced gradual obstruction during urination, and a urine test revealed WBC ++. Retrospective ANI analysis of the urine isolate identified it as C Kerstersii 121606, which was resistant to 18 of 21 tested antibiotics., Diagnoses: Case 1 was diagnosed empirically as pneumonia caused by C Kerstersii strain 12322-1 secondary to craniocerebral injury and confirmed by retrospective ANI analysis; case 2 was diagnosed empirically as urinary infection secondary to prostate hyperplasia caused by C Kerstersii strain 121606 confirmed by the retrospective ANI analysis., Interventions: Case 1 was administered cefoxitin, cefodizime, imipenem-cilastatin sodium, and underwent comprehensive salvage management. Case 2 was administered doxycycline alone., Outcomes: Case 1 died partially because of untimely identification of the responsible bacteria-12322-1. Case 2 was cured even 121606 exhibited an extensive drug resistance feature., Lessons: Except for intra-abdominal infections with good prognosis, we verified that C Kerstersii could also cause extra-abdominal infections, such as the first pneumonia case and urinary infection. It could promote patient death; actual infections were underestimated due to identification difficulties, posing a health threat due to the presence of extensive drug resistance., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2024 the Author(s). Published by Wolters Kluwer Health, Inc.)

Five strains of two novel species were isolated from the wastewater treatment systems of a pharmaceutical factory located in Zhejiang province, PR China. Strains ZM22 T and Y6 were identified as belonging to a potential novel species of the genus Comamonas , whereas strains ZM23 T , ZM24 and ZM25 were identified as belonging to a novel species of the genus Pseudomonas . These strains were characterized by polyphasic approaches including 16S rRNA gene analysis, multi-locus sequence analysis, average nucleotide identity (ANI), in silico DNA-DNA hybridization ( is DDH), physiological and biochemical tests, as well as chemotaxonomic analysis. Genome-based phylogenetic analysis further confirmed that strains ZM22 T and Y6 form a distinct clade closely related to Comamonas testosteroni ATCC 11996 T and Comamonas thiooxydans DSM 17888 T . Strains ZM23 T , ZM24 and ZM25 were grouped as a separate clade closely related to Pseudomonas nitroreducens DSM 14399 T and Pseudomonas nicosulfuronedens LAM1902 T . The orthoANI and is DDH results indicated that strains ZM22 T and Y6 belong to the same species. In addition, genomic DNA fingerprinting demonstrated that these strains do not originate from a single clone. The same results were observed for strains ZM23 T , ZM24 and ZM25. Strains ZM22 T and Y6 were resistant to multiple antibiotics, whereas strains ZM23 T , ZM24 and ZM25 were able to degrade an emerging pollutant, triclosan. The phylogenetic, physiological and biochemical characteristics, as well as chemotaxonomy, allowed these strains to be distinguished from their genus, and we therefore propose the names Comamonas resistens sp. nov. (type strain ZM22=MCCC 1K08496 T =KCTC 82561 T ) and Pseudomonas triclosanedens sp. nov. (type strain ZM23 T =MCCC 1K08497 T =JCM 36056 T ), respectively.

Two novel indole acetic acid-producing strains, 5MLIR T and D4N7, were isolated from Indosasa shibataeoides in Yongzhou, Hunan province, and Phyllostachys edulis in Hangzhou, Zhejiang province, respectively. Based on their 16S rRNA sequences, strains 5MLIR T and D4N7 were closely related to Comamonas antarcticus 16-35-5 T (98.4 % sequence similarity), and the results of 92-core gene phylogenetic trees showed that strains 5MLIR T and D4N7 formed a phylogenetic lineage within the clade comprising Comamonas species. The complete genome size of strain 5MLIR T was 4.49 Mb including two plasmids, and the DNA G+C content was 66.5 mol%. The draft genome of strain D4N7 was 4.26 Mb with 66.7 mol% G+C content. The average nucleotide identity and digital DNA-DNA hybridization values among strain 5MLIR T and species in the genus Comamonas were all below the species delineation threshold. The colonies of strain 5MLIR T and D4N7 were circular with regular margins, convex, pale yellow and 1.0-2.0 mm in diameter when incubated at 30 °C for 3 days. Strains 5MLIR T and D4N7 grew optimally at 30 °C, pH 7.0 and 1.0 % NaCl. The respiratory isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Polyphasic analyses indicated that strains 5MLIR T and D4N7 could be distinguished from related validly named Comamonas species and represent a novel species of the genus Comamonas , for which the name Comamonas endophytica sp. nov. is proposed. The type strain is 5MLIR T (=ACCC 62069 T =GDMCC 1.2958 T =JCM 35331 T ).

Under more intensified cropping conditions agriculture will face increasing incidences of soil-borne plant pests and pathogens, leading to increasingly higher yield losses world-wide. Soil-borne disease complexes, in particular, are especially difficult to control. In order to better understand soil-borne Meloidogyne -based disease complexes, we studied the volatile-based control mechanism of associated bacteria as well as the rhizospheric microbiome on Ugandan tomato plants presenting different levels of root-galling damage, using a multiphasic approach. The experimental design was based on representative samplings of healthy and infected tomato plants from two field locations in Uganda, to establish species collections and DNA libraries. Root galling symptoms on tomato resulted from a multispecies infection of root-knot nematodes (Meloidogyne spp.). Results revealed that 16.5% of the bacterial strain collection produced nematicidal volatile organic compounds (nVOC) active against Meloidogyne. Using SPME GC-MS, diverse VOC were identified, including sulfuric compounds, alkenes and one pyrazine. Around 28% of the bacterial strains were also antagonistic toward at least one fungal pathogen of the disease complex. However, antagonistic interactions appear highly specific. Nematicidal antagonists included Pseudomonas , Comamonas , and Variovorax and fungicidal antagonists belonged to Bacillus , which interestingly, were primarily recovered from healthy roots, while nematode antagonists were prominent in the rhizosphere and roots of diseased roots. In summary, all antagonists comprised up to 6.4% of the tomato root microbiota. In general, the microbiota of healthy and diseased root endospheres differed significantly in alpha and quantitative beta diversity indices. Bacteria-derived volatiles appear to provide a remarkable, yet wholly unexploited, potential to control Meloidogyne -based soil-borne disease complexes. The highly specific observed antagonism indicates that a combination of volatiles or VOC-producing bacteria are necessary to counter the range of pathogens involved in such complexes. [ABSTRACT FROM AUTHOR]

Industrialization often causes polycyclic aromatic hydrocarbon (PAH) and heavy metal contamination of soil and water. In this study, we isolated a bacterium from bottom mud water around a park of Kawasaki Port, Japan, that degrades the 5‐ring PAH dibenz[a,h]anthracene (DBA). The strain, Comamonas sp. 3ah48, degraded 29% of DBA (30 μg ml−1) in 7 days, and the degradation level increased drastically, to 59%, by the addition of glutamate to the medium. The strain also degraded 40, 14, 15 and 19% of pyrene (Pyr), benzo[b]fluoranthene (BbF), benzo[k]fluoranthene (BkF) and benzo[g,h,i]perylene (BghiP) respectively. Benzo[a]pyrene (BaP) was degraded only when glutamate was added to the medium. Strain 3ah48 retained its degradation levels in the presence of 2 mmol l−1 Co2+, Zn2+ or Cr2+, at almost the same level as that without metal, and increased the DBA degradation level to 57% in the presence of 2 mmol l−1 Cu2+, suggesting the possibility of the presence of laccase. Significance and Impact of the Study: Sixteen polycyclic aromatic hydrocarbons (PAHs) are listed as priority pollutants by the United States Environmental Protection Agency (USEPA). Information about the biodegradation of one of those PAHs, dibenz[a,h]anthracene (DBA), is limited. The present study focuses on DBA degradation by Comamonas sp. 3ah48 strain isolated around Kawasaki Port, Japan. Comamonas sp. 3ah48, cultured with the addition of glutamate to the medium, was found to increase the degradation level of DBA and to degrade DBA even in the presence of high concentrations of heavy metals. [ABSTRACT FROM AUTHOR]

Understanding the dynamics of biofilm development in response to chemical cues and signals is required toward the development of controllable biofilm‐mediated bioprocesses. In this study, we report a new biofilm growth system that integrates a microfluidic gradient mixer with a biofilm growth chamber. The biofilm growth system allows biofilms to grow under defined solute gradients and enables nondestructive monitoring of the biofilm development dynamics in response to the defined gradients. The solute gradients generated in the system were simulated and then validated experimentally. We then demonstrated the applicability of the biofilm growth system in studying biofilm development under defined solute gradients. Specifically, we examined biofilm development of Shewanella oneidensis and Comamonas testosteroni under a defined calcium and nitrate gradient, respectively. Using two C. testosteroni strains (WDL7 and I2), we further demonstrated the applicability of our biofilm growth system to study the development of coculture biofilms under a defined solute gradient. Our results show that the biofilm growth system we have developed here can be a promising tool to reveal the dynamics of biofilm development in response to chemical cues and signals as well as the interorganism interactions in coculture biofilms. In this study, we report a new biofilm growth system that integrates a microfluidic gradient mixer with a biofilm growth chamber and demonstrate its applicability to study the development of biofilms under defined solute gradients. [ABSTRACT FROM AUTHOR]

Comamonas is often reported to be one of the major members of microbial communities in various natural and engineered environments. Versatile catabolic capabilities of Comamonas have been studied extensively in the last decade. In contrast, little is known about the ecological roles and adaptation of Comamonas to different environments as well as the virulence of potentially pathogenic Comamonas strains. In this study, we provide genomic insights into the potential ecological roles and virulence of Comamonas by analysing the entire gene set (pangenome) and the genes present in all genomes (core genome) using 34 genomes of 11 different Comamonas species. The analyses revealed that the metabolic pathways enabling Comamonas to acquire energy from various nutrient sources are well conserved. Genes for denitrification and ammonification are abundant in Comamonas, suggesting that Comamonas plays an important role in the nitrogen biogeochemical cycle. They also encode sophisticated redox sensory systems and diverse c-di-GMP controlling systems, allowing them to be able to effectively adjust their biofilm lifestyle to changing environments. The virulence factors in Comamonas were found to be highly species-specific. The conserved strategies used by potentially pathogenic Comamonas for surface adherence, motility control, nutrient acquisition and stress tolerance were also revealed.

ABSTRACT Steroids are abundant growth substrates for bacteria in natural, engineered, and host-associated environments. This study analyzed the distribution of the aerobic 9,10-seco steroid degradation pathway in 346 publically available metagenomes from diverse environments. Our results show that steroid-degrading bacteria are globally distributed and prevalent in particular environments, such as wastewater treatment plants, soil, plant rhizospheres, and the marine environment, including marine sponges. Genomic signature-based sequence binning recovered 45 metagenome-assembled genomes containing a majority of 9,10-seco pathway genes. Only Actinobacteria and Proteobacteria were identified as steroid degraders, but we identified several alpha- and gammaproteobacterial lineages not previously known to degrade steroids. Actino- and proteobacterial steroid degraders coexisted in wastewater, while soil and rhizosphere samples contained mostly actinobacterial ones. Actinobacterial steroid degraders were found in deep ocean samples, while mostly alpha- and gammaproteobacterial ones were found in other marine samples, including sponges. Isolation of steroid-degrading bacteria from sponges confirmed their presence. Phylogenetic analysis of key steroid degradation proteins suggested their biochemical novelty in genomes from sponges and other environments. This study shows that the ecological significance as well as taxonomic and biochemical diversity of bacterial steroid degradation has so far been largely underestimated, especially in the marine environment. IMPORTANCE Microbial steroid degradation is a critical process for biomass decomposition in natural environments, for removal of important pollutants during wastewater treatment, and for pathogenesis of bacteria associated with tuberculosis and other bacteria. To date, microbial steroid degradation was mainly studied in a few model organisms, while the ecological significance of steroid degradation remained largely unexplored. This study provides the first analysis of aerobic steroid degradation in diverse natural, engineered, and host-associated environments via bioinformatic analysis of an extensive metagenome data set. We found that steroid-degrading bacteria are globally distributed and prevalent in wastewater treatment plants, soil, plant rhizospheres, and the marine environment, especially in marine sponges. We show that the ecological significance as well as the taxonomic and biochemical diversity of bacterial steroid degradation has been largely underestimated. This study greatly expands our ecological and evolutionary understanding of microbial steroid degradation.

Two bacterial isolates were recovered from wetland sediments from Tims Branch, a heavy metal contaminated wetland located at the Savannah River Site. Draft genomes of the two recovered isolates, Rhodoblastus strain 17X3 and Comamonas strain 17RB, were generated from Illumina MiSeq sequencing data., Competing Interests: The authors declare no conflict of interest.

The biodegradation pathway of 3-aminobenzoate has been documented, but little is known about the sequence and biochemical properties of the proteins involved. In the present study, a 10,083-bp DNA fragment involved in 3-aminobenzoate degradation was identified in 3-aminobenzoate-degrading Comamonas sp. strain QT12. The mabA gene, whose encoded protein shares 39% amino acid sequence identity with 3-hydroxybenzoate 6-hydroxylase of Polaromonas naphthalenivorans CJ2, was identified on this DNA fragment, and the mabA-disrupted mutant was unable to grow on and convert 3-aminobenzoate. MabA was heterologously expressed in Escherichia coli and purified to homogeneity as an approximately ~ 48-kDa His-tagged protein. It was characterized as 3-aminobenzoate 6-hydroxylase capable of catalyzing the conversion of 3-aminobenzoate to 5-aminosalicylate, incorporating one oxygen atom from dioxygen into the product. It contains a non-covalent but tightly bound FAD as the prosthetic group and NADH as an external electron donor. 5-Aminosalicylate was produced with equimolar consumption of NADH. The apparent Km and kcat values of the purified enzyme for 3-aminobenzoate were 158.51 ± 4.74 μM and 6.49 ± 0.17 s−1, respectively, and those for NADH were 189.85 ± 55.70 μM and 7.41 ± 1.39 s−1, respectively. The results suggest that mabA is essential for 3-aminobenzoate degradation in strain QT12, and that 3-aminobenzoate is the primary and physiological substrate of MabA. [ABSTRACT FROM AUTHOR]

Discarded PE-based products pose a social and environmental threat because of their recalcitrance to degradation, a consequence of the unique set of PE’s physicochemical properties. In this study we isolated nine novel PE-degrading bacteria from plastic debris found in soil of the savanna-like Brazilian Cerrado. These bacterial strains from the genera Comamonas , Delftia , and Stenotrophomonas showed metabolic activity and cellular viability after a 90-day incubation with PE as the sole carbon source. ATR/FTIR indicated that biodegraded PE undergone oxidation, vinylene formation, chain scission, among other chemical changes. Considerable nanoroughness shifts and vast damages to the micrometric surface were confirmed by AFM and SEM. Further, phase imaging revealed a 46.7% decrease in the viscous area of biodegraded PE whereas Raman spectroscopy confirmed a loss in its crystalline content, suggesting the assimilation of smaller fragments. Intriguingly, biodegraded PE chemical fingerprint suggests that these strains use novel biochemical strategies in the biodegradation process. Our results indicate that these microbes are capable of degrading unpretreated PE of very high molecular weight (191,000 g mol −1 ) and survive for long periods under this condition, suggesting not only practical applications in waste management and environmental decontamination, but also future directions to understand the unraveled metabolism of synthetic polymers. [ABSTRACT FROM AUTHOR]

Ideonella sakaiensis is the bacterium that can survive by degrading polyethylene terephthalate (PET) plastic, and terephthalic acid (TPA) binding protein (IsTBP) is an essential periplasmic protein for uptake of TPA into the cytosol for complete degradation of PET. Here, we demonstrated that IsTBP has remarkably high specificity for TPA among 33 monophenolic compounds and two 1,6-dicarboxylic acids tested. Structural comparisons with 6-carboxylic acid binding protein (RpAdpC) and TBP from Comamonas sp. E6 (CsTphC) revealed the key structural features that contribute to high TPA specificity and affinity of IsTBP. We also elucidated the molecular mechanism underlying the conformational change upon TPA binding. In addition, we developed the IsTBP variant with enhanced TPA sensitivity, which can be expanded for the use of TBP as a biosensor for PET degradation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)