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Microbial Genomics Sep 2023comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of...
comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of substantial debate. Therefore, our aim here was to investigate the distribution and evolution of photosynthesis in using comparative genomics and representative genomes from closely related taxa in the families and . We identified photosynthesis gene clusters (PGCs) in 25 genomes belonging to three different lineages, notably the so-called Photosynthetic, and supergroups. Also, two different PGC architectures were observed. One of these, PGC1, was present in genomes from the Photosynthetic supergroup and in three genomes from a species in the supergroup. The second cluster, PGC2, was also present in some strains from the supergroup, as well as in those from the supergroup. PGC2 was largely syntenic to the cluster found in and . Bayesian ancestral state reconstruction unambiguously showed that the ancestor of lacked a PGC and that it was acquired horizontally by various lineages. Maximum-likelihood phylogenetic analyses of individual photosynthesis genes also suggested multiple acquisitions through horizontal gene transfer, followed by vertical inheritance and gene losses within the different lineages. Overall, our findings add to the existing body of knowledge on ’s evolution and provide a meaningful basis from which to explore how these PGCs and the photosynthesis itself impact the physiology and ecology of these bacteria.
Topics: Bradyrhizobium; Photosynthesis
PubMed: 37676703
DOI: 10.1099/mgen.0.001105 -
International Journal of Systematic and... Oct 2020A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31, was...
A Gram-stain-negative, non-motile, coccus-shaped, catalase- and oxidase-positive, facultatively anaerobic and pink-pigmented bacterium, designated strain CQN31, was isolated from sediment of Changqiaohai Lake, Yunnan Province, China. Growth occurred at 4-45 °C (optimum, 37 °C), at pH 6.5-9.5 (optimum, pH 8.0) and with 0-1 % (w/v) NaCl (optimum, 0 %). C 7/C 6 and C were the predominant fatty acids. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidyldimethylethanolamine (PME) and one unidentified aminolipid (AL) were the major polar lipids. The G+C content of the genomic DNA was 71.5 %. 16S rRNA gene sequence comparisons indicated that strain CQN31 shared 96.8 % similarity with JCM 19527 and 95.9 % with EM0302. Digital DNA-DNA hybridization values between strain CQN31 and DSM 19981, DSM 14916 and NCTC 13291 were 21.0, 19.4 and 19.8 %, respectively. Average amino acid identity and average nucleotide identity values between strain CQN31 and DSM 19981, DSM 14916 and NCTC 13291 were 73.7, 63.4 and 61.9 %, and 79.2, 77.1 and 77.5%, respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain CQN31 as a representative of a novel species in the genus , for which the name sp. nov. is proposed. The type strain is CQN31 (=KCTC 62447=MCCC 1H00309).
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Geologic Sediments; Lakes; Methylobacteriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 32886590
DOI: 10.1099/ijsem.0.004436 -
International Journal of Systematic and... Oct 2019Two Gram-stain-negative, catalase- and oxidase-positive, non-spore-forming, aerobic, motile, flagellated, and coccus-shaped strains (Z23 and Z24) were isolated from...
Two Gram-stain-negative, catalase- and oxidase-positive, non-spore-forming, aerobic, motile, flagellated, and coccus-shaped strains (Z23 and Z24) were isolated from faeces of Tibetan antelopes () on the Qinghai-Tibet Plateau, PR China. Results of the morphological, biochemical, and phylogenetic studies indicated that they were similar to each other, but distinct from existing species of the genus . The proposed type strain, Z23, had 97.8, 97.1 and 96.8 % 16S rRNA similarity to DSM 14915, JCM 31878 and KACC 16529. Results from further phylogenetic analyses based on the 16S rRNA gene and 857 core genes indicated that the two strains were members of , but clearly separated from the currently recognized species. Strains Z23 had 43.8 %, 25.0 % DNA-DNA relatedness and 91.2, 81.3 % ANI values with DSM 14915 and KACC 16529. The genomic DNA G+C content of strain Z23 was 68.6 mol%. The major cellular fatty acids of strain Z23 were Cω7 and/or Cω6 and Ccyclo 8. The cell-wall sugars included glucose, rhamnose and ribose. Q-10 was the sole respiratory quinone, and spermidine was the major polyamine component. Polar lipids present in strain Z23 were phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, three aminolipids, two phospholipids and two unidentified lipids. Based on the distinct differences from other species judged from the genotypic and phenotypic data, a novel species represented by Z23 and Z24, sp. nov., is proposed. The type strain is Z23 (=CGMCC 1.16540=DSM 106207).
Topics: Animals; Antelopes; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Feces; Methylobacteriaceae; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone
PubMed: 31145678
DOI: 10.1099/ijsem.0.003479 -
Biotechnology Journal Jun 2020Methanol as a chemical feedstock is becoming increasingly important as it is derived from natural gas and is a feasible end-product for captured carbon dioxide.... (Review)
Review
Methanol as a chemical feedstock is becoming increasingly important as it is derived from natural gas and is a feasible end-product for captured carbon dioxide. Biological conversion of methanol through natural and synthetic methylotrophs increases the chemical repertoire and is an important direction for one carbon (C1) based chemical economy. Advances in the metabolic engineering and synthetic biology enable development of microbial cell factories for converting methanol into various platform chemicals. In this review, the current status of methanol utilizing microbial factory development is summarized. Also the development of synthetic methylotrophy and methanol-augmented bioproductions is discussed.
Topics: Amino Acids; Biological Products; Carbon Dioxide; Metabolic Engineering; Metabolic Networks and Pathways; Methanol; Methylobacterium extorquens; Saccharomycetales; Synthetic Biology
PubMed: 32281750
DOI: 10.1002/biot.201900356 -
International Journal of Systematic and... Mar 2023A strictly aerobic bacteriochlorophyll -containing alphaproteobacterium, designated strain S08, was isolated from a biofilm sampled at Tama River in Japan. The...
A strictly aerobic bacteriochlorophyll -containing alphaproteobacterium, designated strain S08, was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds and showed absorption maxima at 798 and 866 nm in the near-infrared region, typical for the presence of bacteriochlorophyll . The new bacterial isolate is Gram-negative, oxidase-negative and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S08 was closely related to species in the genus . The closest phylogenetic relative of strain S08 was TH-G33 (98.2 % sequence similarity). The major cellular fatty acids were C, C 2-OH and summed feature 8 (C 7/C 6). The predominant respiratory quinone was ubiquinone-9. The major polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an aminolipid. The G+C content of the genomic DNA was 70.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain S08 and the related type strains were all far lower than the cut-off value for the delineation of species. The results of polyphasic comparisons showed that strain S08 was clearly distinguishable from other members of the genus . Therefore, we propose a new species in the genus , namely, sp. nov. The type strain is S08 (=DSM 111902=NBRC 112025).
Topics: Fatty Acids; Rivers; Bacteriochlorophyll A; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Base Composition; Bacterial Typing Techniques; Sequence Analysis, DNA; Ubiquinone; Methylobacteriaceae; Biofilms; Phospholipids
PubMed: 37009860
DOI: 10.1099/ijsem.0.005810 -
IDCases 2023rarely causes infection in humans. We report that a patient with underlying rheumatoid arthritis and diabetes developed wrist septic arthritis and osteomyelitis due to...
rarely causes infection in humans. We report that a patient with underlying rheumatoid arthritis and diabetes developed wrist septic arthritis and osteomyelitis due to after steroid joint injection. After antibiotic and surgical treatment, the condition of the patient improved. We reviewed previously reported cases of soft tissue, joint and bone infection related to to understand the characteristics of joint and bone infection of .
PubMed: 37234729
DOI: 10.1016/j.idcr.2023.e01792 -
Journal of Pediatric Hematology/oncology Jul 2020Roseomonas gilardii is a Gram-negative coccobacillus identified in immunocompromised pediatric patients. A 5-year-old male with a history of HbSβ thalassemia status... (Review)
Review
Roseomonas gilardii is a Gram-negative coccobacillus identified in immunocompromised pediatric patients. A 5-year-old male with a history of HbSβ thalassemia status postsurgical splenectomy presented to the emergency department with fever. Blood cultures grew R. gilardii at 63 hours, but the patient had been discharged home at 48 hours. The patient was readmitted for repeat cultures and initiated on meropenem for 10 days as Roseomonas spp. are often resistant to third generation cephalosporins. R. gilardii is a rare cause of bacteremia in immunocompromised patients. Clinicians should consider Roseomonas in slow growing Gram-negative rod bacteremias, and consider meropenem as empiric coverage.
Topics: Bacteremia; Child, Preschool; Gram-Negative Bacterial Infections; Humans; Male; Methylobacteriaceae; Prognosis; Thalassemia
PubMed: 30951022
DOI: 10.1097/MPH.0000000000001476 -
International Journal of Microbiology 2022Hydrocarbon-derived pollutants are becoming one of the most concerning ecological issues. Thus, there is a need to investigate and develop innovative, low-cost,...
Hydrocarbon-derived pollutants are becoming one of the most concerning ecological issues. Thus, there is a need to investigate and develop innovative, low-cost, eco-friendly, and fast techniques to reduce and/or eliminate pollutants using biological agents. The study was conducted to isolate, characterize, and identify potential diesel-degrading bacteria. Samples were collected from flower farms, lakeshores, old aged garages, asphalt, and bitumen soils and spread on selective medium (Bushnell Haas mineral salt agar) containing diesel as the growth substrate. The isolates were characterized based on their growth patterns using optical density measurement, biochemical tests, and gravimetric analysis and identified using the Biolog database and 16S rRNA gene sequencing techniques. Subsequently, six diesel degraders were identified and belong to , , , , , and . Among these, based on gravimetric analysis, the three potent isolates AAUW23, AAUG11, and AAUG36 achieved 84%, 83.4%, and 83% diesel degradation efficiency, respectively, in 15 days. Consequently, the partial 16S rRNA gene sequences revealed that the two most potent bacterial strains (AAUW23 and AAUG11) were , while AAUG36 was . This study demonstrated that bacterial species isolated from hydrocarbon-contaminated and/or uncontaminated environments could be optimized to be used as potential bioremediation agents for diesel removal.
PubMed: 35096070
DOI: 10.1155/2022/5655767 -
Journal of Applied Microbiology Feb 2022Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while...
AIM
Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while growing on glucose and carbazole medium.
METHODS AND RESULTS
The bacterium R. cervicalis was isolated from a soil sample contaminated with crude petroleum oil. PCR amplification ascertained the existence of some hydrocarbon-degrading catabolic genes (alkB and PAH-RHDα, C12O, and C23O) in the bacterial genome. GC-MS and RP-HPLC analyses demonstrated 62% and 60% carbazole degradation, respectively, by R. cervicalis 144 h post-incubation at 37℃ and pH 6.5. Due to the paucity of protein databases, expressions of only 29 and 14 intracellular proteins were explicitly recognized and quantitated by mass spectrometry analysis when R. cervicalis was grown in carbazole and glucose medium, respectively. FTIR, NMR and HR-MS/MS analyses demonstrated the lipopeptide nature of the purified biosurfactant produced by R. cervicalis. The biosurfactant is also presumed to assist in the solubilization of carbazole.
CONCLUSION
The isolated R. cervicalis strain is a potential candidate for the bioremediation of carbazole in petroleum-oil-contaminated sites.
SIGNIFICANCE AND IMPACT OF THE STUDY
This is the first report of the promising R. cervicalis strain proficient in carbazole biodegradation.
Topics: Biodegradation, Environmental; Carbazoles; Lipopeptides; Methylobacteriaceae; Petroleum; Proteomics; Surface-Active Agents; Tandem Mass Spectrometry
PubMed: 34415661
DOI: 10.1111/jam.15258 -
Seminars in Cancer Biology Nov 2022The higher incidence of bladder cancer in men has long been attributed to environmental factors, including smoking. The fact that the sex ratio of bladder cancer remains... (Review)
Review
The higher incidence of bladder cancer in men has long been attributed to environmental factors, including smoking. The fact that the sex ratio of bladder cancer remains consistently weighted toward men despite the remarkable increase in the prevalence of smoking among women suggests that other risk factors influence the incidence rates of bladder cancer. These factors may include the urinary microbiota. In this study, we provide a review of recent literature regarding the association between bladder cancer and changes in the urinary microbiota, with a focus on the potential role of uropathogens in the microbiota and sex in bladder cancer. Four databases were systematically searched up to 31 March 2021 to identify human case-controlled studies that evaluated the relationship between urinary microbiota and bladder cancer. We combined bacterial taxa that were significantly higher or lower in the bladder cancer group in each study in the urine (voided and catheterized) and tissue samples. Findings from sixteen eligible studies were analyzed. The total sample size of the included studies was 708 participants, including 449 (63.4 %) bladder cancer patients and 259 (36.6 %) participants in the control group. When considering only the taxa that have been reported in at least two different studies, we observed that with regards to neoplastic tissues, no increased taxa were reported, while Lactobacillus (2/5 of the studies on tissue samples) was increased in nonneoplastic-tissue compared to neoplastic-tissues at the genus level. In catheterized urine, Veillonella (2/3 of the studies on catheterized urine) was increased in bladder cancer patients compared to the control groups at the genus level. In voided urine, Acinetobacter, Actinomyces, Aeromonas, Anaerococcus, Pseudomonas, and Tepidomonas were increased in the bladder cancer patients, while Lactobacillus, Roseomonas, Veillonella were increased in the control groups. Regarding gender, the genus Actinotignum was increased in female participants while Streptococcus was increased in male participants at the genus level. Regarding potential uropathogens in the urinary microbiota, Escherichia-Shigella provided conflicting results, with both showing higher and lower levels in the bladder cancer groups. However, the family Enterobacteriaceae was lower in the bladder cancer groups than in the control groups. In conclusion, there is no consensus on what taxa of the urinary microbiota are associated with bladder cancer according to the sample type. Findings on the potential role of uropathogens in the urinary microbiota in bladder cancer remain inconsistent. Due to the limited number of studies, further studies on urinary microbiota and bladder cancer are needed to address this issue. Given that all publications concerning the urinary microbiota and bladder cancer have been performed using 16S rRNA gene sequencing, we propose that polyphasic approaches, including culture-dependent techniques, may allow for a more comprehensive investigation of the urinary microbiota associated with bladder cancer.
Topics: Humans; Female; Male; Urinary Bladder Neoplasms; RNA, Ribosomal, 16S; Urinary Bladder; Microbiota; Bacteria
PubMed: 34979272
DOI: 10.1016/j.semcancer.2021.12.010