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MSphere Feb 2019We examined the genomic adaptations of prevalent bacterial taxa in a highly nutrient- and ion-depleted freshwater environment located in the secondary cooling water...
We examined the genomic adaptations of prevalent bacterial taxa in a highly nutrient- and ion-depleted freshwater environment located in the secondary cooling water system of a nuclear research reactor. Using genome-centric metagenomics, we found that none of the prevalent bacterial taxa were related to typical freshwater bacterial lineages. We also did not identify strong signatures of genome streamlining, which has been shown to be one of the ecoevolutionary forces shaping the genome characteristics of bacterial taxa in nutrient-depleted environments. Instead, focusing on the dominant taxon, a novel sp. which we propose to name , we detected extensive positive selection on genes involved in phosphorus and carbon scavenging pathways. These genes were involved in the high-affinity phosphate uptake and storage into polyphosphate granules, metabolism of nitrogen-rich organic matter, and carbon/energy storage into polyhydroxyalkanoate. In parallel, comparative genomics revealed a high number of paralogs and an accessory genome significantly enriched in environmental sensing pathways (i.e., chemotaxis and motility), suggesting extensive gene expansions in The type strain of (LMG 30558) displayed optimal growth kinetics and productivity at low nutrient concentrations, as well as substantial cell size plasticity. Our findings with LMG 30558 demonstrate that positive selection and gene expansions may represent successful adaptive strategies to oligotrophic environments that preserve high growth rates and cellular productivity. By combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this system. In addition, microscopic and flow cytometric analysis of the first freshwater representative of this population ( LMG 30558) demonstrated phenotypic plasticity, possibly due to the metabolic versatility granted by its larger genome, to be a strategy to cope with nutrient limitation. Our study clearly demonstrates the need for the use of a broad set of genomic tools combined with culture-based physiological characterization assays to investigate and validate genomic adaptations.
Topics: Adaptation, Physiological; Carbon; Comamonadaceae; DNA, Bacterial; Fresh Water; Genome, Bacterial; Genomics; Metagenomics; Nuclear Reactors; Phosphorus; Phylogeny; Selection, Genetic
PubMed: 30728279
DOI: 10.1128/mSphereDirect.00011-19 -
Biocontrol Science 2012Bacteria capable of degrading 4-nonylphenol (NP) were isolated and identified, and their ability to degrade NP was determined. The screening of microorganisms in river...
Bacteria capable of degrading 4-nonylphenol (NP) were isolated and identified, and their ability to degrade NP was determined. The screening of microorganisms in river water and soil led to a collection of 23 strains of bacteria and five strains of fungi. Two strains of bacteria, identified as Pseudomonas sp. and Acidovorax sp., possessed great ability for degrading NP. The NP degradation rate of Pseudomonas sp. did not change with the NP concentration (50-100mg/L) . In contrast, the NP degradation rate of Acidovorax sp. increased with increasing NP concentration. Acidovorax sp. possessed the greatest NP degradation activity at 35°C. No NP degradation activity was observed for Pseudomonas sp. at temperatures higher than 30°C. Even when non-NP carbon sources such as glucose or sucrose were added, the NP degradation rates for both bacteria did not decrease. In addition, the estrogenic activity of NP decreased depending on the amount of NP residues determined by the yeast two-hybrid system.
Topics: Biodegradation, Environmental; Comamonadaceae; Estrogens; Phenols; Pseudomonas; Rivers; Soil Microbiology
PubMed: 23007106
DOI: 10.4265/bio.17.143 -
International Journal of Molecular... Aug 2022Bacterial fruit blotch (BFB) caused by (Ac) is a devastating watermelon disease that severely impacts the global watermelon industry. Like other Gram-negative bacteria,...
Bacterial fruit blotch (BFB) caused by (Ac) is a devastating watermelon disease that severely impacts the global watermelon industry. Like other Gram-negative bacteria, the type three secretion system (T3SS) is the main pathogenicity factor of . The T3SS apparatus gene codes for the Hrp pilus and serves as a conduit to secret effector proteins into host cells. In this study, we found that the deletion of in results in the loss of pathogenicity on hosts and the hypersensitive response on non-hosts. In addition, the mutant showed a reduction in in vitro growth, colonization, swimming and twitching motility, and displayed increases in biofilm formation ability compared to the wild type. However, when HrpE was transiently expressed in hosts, the defense responses, including reactive oxygen species bursts, callose deposition, and expression of defense-related genes, were activated. Thus, the growth in HrpE-pretreated hosts was suppressed. These results indicated that HrpE is essential for virulence but can also be used by hosts to help resist . Our findings provide a better understanding of the T3SS pathogenesis in , thus providing a molecular basis for biopesticide development, and facilitating the effective control of BFB.
Topics: Citrullus; Comamonadaceae; Immunity; Virulence
PubMed: 36012409
DOI: 10.3390/ijms23169144 -
PloS One 2018Serological methods are relatively convenient and simple for the detection of pathogens for front-line workers. On-site visualization of the test results plays a pivotal...
Serological methods are relatively convenient and simple for the detection of pathogens for front-line workers. On-site visualization of the test results plays a pivotal role in the process. However, an efficient, universal labeling agent for antibodies is needed for the development of efficient serological detection tools. In this study, a Bamboo mosaic virus (BaMV)-based viral vector was employed to express recombinant proteins, collectively designated GfED, consisting of Staphylococcus aureus Protein A domain ED (SpaED) fused to either the N- or C-terminal of an improved green florescent protein (GFP) with or without the coat protein (CP) of BaMV, efficiently in Chenopodium quinoa. The GfED in crude leaf extracts could specifically attach to IgG molecules of rabbits and mice, effectively labeling IgG with GFP, emitting green light at 506 nm when excited at 450 nm using simple, handheld equipment. To demonstrate the applicability of GfED in serological assays, we have developed a fluorescent dot blot assay for the rapid detection of Acidovorax citrulli (Ac), a bacterial pathogen of cucurbits, and BaMV, a viral pathogen of bamboos. By using the crude extracts of inoculated C. quinoa leaves expressing GfED as an IgG-labeling agent, the pathogens were easily and quickly detected through uncomplicated operations using simple equipment, with results observable by the naked eye. Examination using fluorescent microscopy and transmission electron microscopy revealed that the GfED subunits may assemble into virus-like particles, which were further involved in the formation of aggregates of GfED-antibody-antigen complexes with the potential for fluorescence signal enhancement. The results suggested that plant-expressed GfED may serve as a promising alternative of IgG-labeling agent for current serological assays.
Topics: Blotting, Western; Chenopodium; Comamonadaceae; Fluorescent Antibody Technique; Genetic Vectors; Microscopy, Electron, Transmission; Microscopy, Fluorescence; Plant Leaves; Plant Proteins; Plants; Polymerase Chain Reaction; Potexvirus
PubMed: 29408944
DOI: 10.1371/journal.pone.0192455 -
Journal of Microbiology and... Sep 2015The aim of this study was to develop a SYBR Green-based real-time PCR assay for the rapid, specific, and sensitive detection of Acidovorax avenae subsp. citrulli, which...
The aim of this study was to develop a SYBR Green-based real-time PCR assay for the rapid, specific, and sensitive detection of Acidovorax avenae subsp. citrulli, which causes bacterial fruit blotch (BFB), a serious disease of cucurbit plants. The molecular and serological methods currently available for the detection of this pathogen are insufficiently sensitive and specific. Thus, a novel SYBR Green-based real-time PCR assay targeting the YD-repeat protein gene of A. avenae subsp. citrulli was developed. The specificity of the primer set was evaluated using DNA purified from 6 isolates of A. avenae subsp. citrulli, 7 other Acidovorax species, and 22 of non-targeted strains, including pathogens and non-pathogens. The AC158F/R primer set amplified a single band of the expected size from genomic DNA obtained from the A. avenae subsp. citrulli strains but not from the genomic DNA of other Acidovorax species, including that of other bacterial genera. Using this assay, it was possible to detect at least one genomeequivalents of the cloned amplified target DNA using 5 × 10(0) fg/μl of purified genomic DNA per reaction or using a calibrated cell suspension, with 6.5 colony-forming units per reaction being employed. In addition, this assay is a highly sensitive and reliable method for identifying and quantifying the target pathogen in infected samples that does not require DNA extraction. Therefore, we suggest that this approach is suitable for the rapid and efficient diagnosis of A. avenae subsp. citrulli contaminations of seed lots and plants.
Topics: Bacterial Proteins; Bacteriological Techniques; Benzothiazoles; Comamonadaceae; Diamines; Organic Chemicals; Plant Diseases; Quinolines; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; Staining and Labeling; Time Factors
PubMed: 25951847
DOI: 10.4014/jmb.1502.02029 -
Microbiology (Reading, England) Nov 2017Genus Comamonas is a group of bacteria that are able to degrade a variety of environmental waste. Comamonas aquatica CJG (C. aquatica) in this genus is able to absorb...
Genus Comamonas is a group of bacteria that are able to degrade a variety of environmental waste. Comamonas aquatica CJG (C. aquatica) in this genus is able to absorb low-density lipoprotein but not high-density lipoprotein of human serum. Using H and C NMR spectroscopy, we found that the O-polysaccharide (O-antigen) of this bacterium is comprised of a disaccharide repeat (O-unit) of d-glucose and 2-O-acetyl-l-rhamnose, which is shared by Serratia marcescens O6. The O-antigen gene cluster of C. aquatica, which is located between coaX and tnp4 genes, contains rhamnose synthesis genes, glycosyl and acetyl transferase genes, and ATP-binding cassette transporter genes, and therefore is consistent with the O-antigen structure determined here.
Topics: Bacterial Proteins; Carbohydrate Sequence; Carbon-13 Magnetic Resonance Spectroscopy; Comamonas; Disaccharides; Escherichia coli Proteins; Glucose; Multigene Family; O Antigens; Protein Structure, Secondary; Proton Magnetic Resonance Spectroscopy; Rhamnose
PubMed: 29034863
DOI: 10.1099/mic.0.000551 -
International Journal of Systematic and... Aug 2021Three highly alkaliphilic bacterial strains designated as A1, H1 and B1 were isolated from two highly alkaline springs at The Cedars, a terrestrial serpentinizing site....
Three highly alkaliphilic bacterial strains designated as A1, H1 and B1 were isolated from two highly alkaline springs at The Cedars, a terrestrial serpentinizing site. Cells from all strains were motile, Gram-negative and rod-shaped. Strains A1, H1 and B1 were mesophilic (optimum, 30 °C), highly alkaliphilic (optimum, pH 11) and facultatively autotrophic. Major cellular fatty acids were saturated and monounsaturated hexadecenoic and octadecanoic acids. The genome size of strains A1, H1 and B1 was 2 574 013, 2 475 906 and 2 623 236 bp, and the G+C content was 66.0, 66.2 and 66.1 mol%, respectively. Analysis of the 16S rRNA genes showed the highest similarity to the genera (95.1-96.4 %), (93.0-93.6 %) and (93.0-96.6 %) in the family . Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on core gene sequences revealed that the isolated strains diverged from the related species, forming a distinct branch. Average amino acid identity values of strains A1, H1 and B1 against the genomes of related members in this family were below 67 %, which is below the suggested threshold for genera boundaries. Average nucleotide identity by blast values and digital DNA-DNA hybridization among the three strains were below 92.0 and 46.6 % respectively, which are below the suggested thresholds for species boundaries. Based on phylogenetic, genomic and phenotypic characterization, we propose gen. nov., sp. nov. (type strain A1=NBRC 111848=DSM 103917), sp. nov. (type strain H1= NBRC 111849=DSM 103920) and sp. nov. (type strain B1=NBRC 111850=DSM 103919) belonging to the family . We have designated the type species for the genus because it is the dominant species in The Cedars springs.
Topics: Bacterial Typing Techniques; Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Water Microbiology
PubMed: 34379584
DOI: 10.1099/ijsem.0.004945 -
Scientific Reports Oct 2022A mab cluster associated with 3-aminobenzoic acid (3AB) degradation was identified in Comamonas sp. QT12. However, the cellular response of Comamonas sp. QT12 to...
A mab cluster associated with 3-aminobenzoic acid (3AB) degradation was identified in Comamonas sp. QT12. However, the cellular response of Comamonas sp. QT12 to 3-aminobenzoic acid remains unclear. In this study, label-free quantitative proteome analysis based on LC-MS/MS was used to study the protein expression difference of strain QT12 under the condition of using 3AB (3AB) and citric acid/ammonium chloride as substrates (3ABCon). A total of 2068 proteins were identified, of which 239 were significantly up-regulated in 3AB group, 124 were significantly down-regulated in 3AB group, 624 were expressed only in 3AB group, and 216 were expressed only in 3ABCon group in 3AB group. KEGG pathway analysis found that 83 pathways were up-regulated and 49 pathways were down-regulated, In GO analysis, 315 paths were up-regulated and 156 paths were down-regulated. There were 6 genes in the mab cluster that were only detected in the 3AB group.The mab cluster was found to be related to degradation of 3AB. By knockout, it was found that the growth rate of the mutant △orf7 and △orf9 were slowed down. HPLC results showed that the mutant △orf7 and △orf9 could still degrade 3AB, it was found that orf7, orf9 were not key genes about 3AB degradation and they could be replaced by other genes in strain QT12. These findings improve our understanding of the molecular mechanisms underlying the cellular response of 3AB degradation in Comamonas bacterium.
Topics: Comamonas; Proteomics; Proteome; Chromatography, Liquid; Ammonium Chloride; Tandem Mass Spectrometry; Citric Acid
PubMed: 36266292
DOI: 10.1038/s41598-022-17570-9 -
MBio Aug 2021sp. strain JS3051 utilizes 2,3-dichloronitrobenzene (23DCNB), a toxic anthropogenic compound, as the sole carbon, nitrogen, and energy source for growth, but the...
sp. strain JS3051 utilizes 2,3-dichloronitrobenzene (23DCNB), a toxic anthropogenic compound, as the sole carbon, nitrogen, and energy source for growth, but the metabolic pathway and its origins are unknown. Here, we establish that a gene cluster (), encoding a Nag-like dioxygenase, is responsible for the initial oxidation of the 23DCNB molecule. The 2,3-dichloronitrobenzene dioxygenase system (DcbAaAbAcAd) catalyzes conversion of 23DCNB to 3,4-dichlorocatechol (34DCC). Site-directed mutagenesis studies indicated that residue 204 of DcbAc is crucial for the substrate specificity of 23DCNB dioxygenase. The presence of glutamic acid at position 204 of 23DCNB dioxygenase is unique among Nag-like dioxygenases. Genetic, biochemical, and structural evidence indicate that the 23DCNB dioxygenase is more closely related to 2-nitrotoluene dioxygenase from sp. strain JS42 than to the 34DCNB dioxygenase from sp. strain JS3050, which was isolated from the same site as strain JS3051. A gene cluster () encoding the enzymes for 34DCC catabolism, homologous to a operon in Pseudomonas knackmussii strain B13, is also on the chromosome at a distance of 2.5 Mb from the genes. Heterologously expressed DccA catalyzed ring cleavage of 34DCC with high affinity and catalytic efficiency. This work not only establishes the molecular mechanism for 23DCNB mineralization, but also enhances the understanding of the recent evolution of the catabolic pathways for nitroarenes. Because anthropogenic nitroaromatic compounds have entered the biosphere relatively recently, exploration of the recently evolved catabolic pathways can provide clues for adaptive evolutionary mechanisms in bacteria. The concept that nitroarene dioxygenases shared a common ancestor with naphthalene dioxygenase is well established. But their phylogeny and how they evolved in response to novel nitroaromatic compounds are largely unknown. Elucidation of the molecular basis for 23DCNB degradation revealed that the catabolic pathways of two DCNB isomers in different isolates from the same site were derived from different recent origins. Integrating structural models of catalytic subunits and enzymatic activities data provided new insight about how recently modified enzymes were selected depending on the structure of new substrates. This study enhances understanding and prediction of adaptive evolution of catabolic pathways in bacteria in response to new chemicals.
Topics: Comamonadaceae; Genome, Bacterial; Metabolic Networks and Pathways; Multigene Family; Nitrobenzenes; Substrate Specificity
PubMed: 34425699
DOI: 10.1128/mBio.02231-21 -
Scientific Reports Aug 2017Aspartate family amino acids (AFAAs) have important commercial values due to their wide spectrum of applications. Most if not all AFAAs are produced under aerobic...
Aspartate family amino acids (AFAAs) have important commercial values due to their wide spectrum of applications. Most if not all AFAAs are produced under aerobic conditions which is energy-intensive. To establish a cost-effective anaerobic process for production of AFAAs, it holds great promise to develop a new pathway enabling the conversion of oxoloacetate into aspartate through direct amination which is catalyzed by aspartate dehydrogenase (AspDH). Compared with the well studied aspartate aminotransferase and aspartate ammonia-lyase, only a few AspDHs are characterized till date, and failure to reproduce the high activity of AspDH from Rastonia eutropha documented in the literature encouraged us to screen and characterize novel AspDHs from different origins. Interestingly, the AspDHs from Klebsiella pneumoniae 34618 (KpnAspDH) and Delftia sp. Cs1-4 (DelAspDH) showed successful soluble expression. KpnAspDH and DelAspDH containing C-terminal hexa-histidine tags were purified and characterized for their catalytic properties. Notably, in addition to its high reductive amination activity, DelAspDH exhibited considerable stability as compared to the other source of AspDHs. This work thus provides novel enzyme resource for engineering strains capable of producing AFAAs under anaerobic conditions.
Topics: Amination; Amino Acid Oxidoreductases; Anaerobiosis; Aspartic Acid; Bacterial Proteins; Delftia; Enzyme Stability; Industrial Microbiology; Kinetics; Klebsiella pneumoniae; Recombinant Proteins; Substrate Specificity
PubMed: 28801651
DOI: 10.1038/s41598-017-05522-7