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International Journal of Systematic and... Jan 2024A Gram-stain-negative strain, designated as D2M1 was isolated from xylene-degrading enrichment culture and characterized using a polyphasic approach to determine its...
A Gram-stain-negative strain, designated as D2M1 was isolated from xylene-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain D2M1 belongs to the genus , with the highest 16S rRNA gene similarity to DSM 64 (99.93 %), followed by DSM 23535 (98.77 %) and MTCC 12652 (98.76 %). The draft genome sequence of strain D2M1 is 5.49 Mb long, and the G+C content of the genome is 64.2 mol%. Orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain D2M1 and its closest relatives were below the threshold values for species demarcation confirming that strain D2M1 is distinctly separated from its closest relatives. The whole genome analysis of the strain revealed a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete -cleavage pathway including an I.2.C-type catechol 2,3-dioxygenase (C23O) gene. The strain was able to degrade benzene and ethylbenzene as sole sources of carbon and energy under aerobic and microaerobic conditions. Cells were facultatively aerobic rods and motile with a single polar flagellum. The predominant fatty acids (>10 % of the total) of strain D2M1 were summed feature 3 (C 7/C 6), C and summed feature 8 (C 7/C 6). The major ubiquinone of strain D2M1 was Q8, while the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on polyphasic data, it is concluded that strain D2M1 represents a novel species of the genus , for which the name of sp. nov. is proposed. The type strain of the species is strain D2M1 (=DSM 115238=NCAIM B.02679).
Topics: Xylenes; RNA, Ribosomal, 16S; Base Composition; Fatty Acids; Phylogeny; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Hydrocarbons, Aromatic; Bacteria
PubMed: 38180316
DOI: 10.1099/ijsem.0.006219 -
Frontiers in Cellular and Infection... 2022Periodontitis and rheumatoid arthritis (RA) are two widespread chronic inflammatory diseases with a previously suggested association. The objective of the current study...
OBJECTIVES
Periodontitis and rheumatoid arthritis (RA) are two widespread chronic inflammatory diseases with a previously suggested association. The objective of the current study was to compare the oral microbial composition and host´s inflammatory mediator profile of saliva samples obtained from subjects with periodontitis, with and without RA, as well as to predict biomarkers, of bacterial pathogens and/or inflammatory mediators, for classification of samples associated with periodontitis and RA.
METHODS
Salivary samples were obtained from 53 patients with periodontitis and RA and 48 non-RA with chronic periodontitis. The microbial composition was identified using 16S rRNA gene sequencing and compared across periodontitis patients with and without RA. Levels of inflammatory mediators were determined using a multiplex bead assay, compared between the groups and correlated to the microbial profile. The achieved data was analysed using PCoA, DESeq2 and two machine learning algorithms, OPLS-DA and sPLS-DA.
RESULTS
Differential abundance DESeq2 analyses showed that the four most highly enriched (log2 FC >20) amplicon sequence variants (ASVs) in the non-RA periodontitis group included sp., sp., sp., and sp. whereas sp., sp., sp., and were the most highly enriched ASVs (log2 FC >20) in the RA group. OPLS-DA with log2 FC analyses demonstrated that the top ASVs with the highest importance included sp. having a positive correlation with non-RA group, and seven ASVs belonging to , sp., , , spp. and with a positive correlation with RA group. Among the detected inflammatory mediators in saliva samples, TWEAK/TNFSF12, IL-35, IFN-α2, pentraxin-3, gp130/sIL6Rb, sIL-6Ra, IL-19 and sTNF-R1 were found to be significantly increased in patients with periodontitis and RA compared to non-RA group with periodontitis. Moreover, correlations between ASVs and inflammatory mediators using sPLS-DA analysis revealed that TWEAK/TNFSF12, pentraxin-3 and IL-19 were positively correlated with the ASVs sp., , sp., and sp.
CONCLUSION
Our results suggest that the combination of microbes and host inflammatory mediators could be more efficient to be used as a predictable biomarker associated with periodontitis and RA, as compared to microbes and inflammatory mediators alone.
Topics: Arthritis, Rheumatoid; Chronic Periodontitis; Humans; Inflammation Mediators; Microbiota; RNA, Ribosomal, 16S
PubMed: 35360114
DOI: 10.3389/fcimb.2022.841139 -
Analytical and Bioanalytical Chemistry Jan 2022Human activities have greatly increased the input of reactive nitrogen species into the environment and disturbed the balance of the global N cycle. This imbalance may...
Human activities have greatly increased the input of reactive nitrogen species into the environment and disturbed the balance of the global N cycle. This imbalance may be offset by bacterial denitrification, an important process in maintaining the ecological balance of nitrogen. However, our understanding of the activity of mixotrophic denitrifying bacteria is not complete, as most research has focused on heterotrophic denitrification. The aim of this study was to investigate substrate preferences for two mixotrophic denitrifying bacterial strains, Acidovorax delafieldii and Hydrogenophaga taeniospiralis, under heterotrophic, autotrophic or mixotrophic conditions. This complex analysis was achieved by simultaneous identification and quantification of H, O, CO, N, N and NO in course of the denitrification process with help of cavity-enhanced Raman spectroscopic (CERS) multi-gas analysis. To disentangle electron donor preferences for both bacterial strains, microcosm-based incubation experiments under varying substrate conditions were conducted. We found that Acidovorax delafieldii preferentially performed heterotrophic denitrification in the mixotrophic sub-experiments, while Hydrogenophaga taeniospiralis preferred autotrophic denitrification in the mixotrophic incubation. These observations were supported by stoichiometric calculations. The results demonstrate the prowess of advanced Raman multi-gas analysis to study substrate use and electron donor preferences in denitrification, based on the comprehensive quantification of complex microbial gas exchange processes.
Topics: Bacteria; Bioreactors; Denitrification; Electrons; Humans; Nitrates; Nitrogen; Spectrum Analysis, Raman
PubMed: 34297136
DOI: 10.1007/s00216-021-03541-y -
Biotechnology Reports (Amsterdam,... Dec 2019In this study, after evaluating the degradation activity of enriched cultures from four crude oil-contaminated soils in mineral salt medium, the most efficient ones were...
In this study, after evaluating the degradation activity of enriched cultures from four crude oil-contaminated soils in mineral salt medium, the most efficient ones were selected for further studies. The chemical analysis of cell-free extract containing phenanthrene by HPLC suggested the superior enriched culture was able to degrade 87.66% of phenanthrene at the concentration of 40 mg L-1 within 10 days. This experiment was done under optimal conditions (37 °C, 10% salinity, and pH around 7 to 7.5). The 16S rRNA sequencing of isolates from this superior enriched culture indicated the highest similarity to (Q-SH3), (Q-SH12), and (Q-SH14). After biodegradation of phenanthrene in liquid medium, the extracts were analyzed to measure barley and alfalfa germination. Results showed a lower level of toxicity to the seeds, hence this enriched culture could be used for bioremediation of saline environments contaminated by phenanthrene and other similar compounds.
PubMed: 31763200
DOI: 10.1016/j.btre.2019.e00388 -
Astrobiology Nov 2019Urine is a major waste product of human metabolism and contains essential macro- and micronutrients to produce edible microorganisms and crops. Its biological conversion...
Media Optimization, Strain Compatibility, and Low-Shear Modeled Microgravity Exposure of Synthetic Microbial Communities for Urine Nitrification in Regenerative Life-Support Systems.
Urine is a major waste product of human metabolism and contains essential macro- and micronutrients to produce edible microorganisms and crops. Its biological conversion into a stable form can be obtained through urea hydrolysis, subsequent nitrification, and organics removal, to recover a nitrate-enriched stream, free of oxygen demand. In this study, the utilization of a microbial community for urine nitrification was optimized with the focus for space application. To assess the role of selected parameters that can impact ureolysis in urine, the activity of six ureolytic heterotrophs ( and ) was tested at different salinities, urea, and amino acid concentrations. The interaction of the ureolytic heterotrophs with a nitrifying consortium ( ATCC 19718 and ATCC 25931) was also tested. Lastly, microgravity was simulated in a clinostat utilizing hardware for in-flight experiments with active microbial cultures. The results indicate salt inhibition of the ureolysis at 30 mS cm, while amino acid nitrogen inhibits ureolysis in a strain-dependent manner. The combination of the nitrifiers with and resulted in a complete halt of the urea hydrolysis process, while in the case of incomplete nitrification was observed, and nitrite was not oxidized further to nitrate. Nitrate production was confirmed in all the other communities; however, the other heterotrophic strains most likely induced oxygen competition in the test setup, and nitrite accumulation was observed. Samples exposed to low-shear modeled microgravity through clinorotation behaved similarly to the static controls. Overall, nitrate production from urea was successfully demonstrated with synthetic microbial communities under terrestrial and simulated space gravity conditions, corroborating the application of this process in space.
Topics: Ammonia; Bioreactors; Ecological Systems, Closed; Heterotrophic Processes; Humans; Hydrolysis; Microbiota; Nitrates; Nitrification; Oxidation-Reduction; Space Flight; Urea; Urine; Weightlessness
PubMed: 31657947
DOI: 10.1089/ast.2018.1981 -
Systematic and Applied Microbiology Nov 2019During long-term extra-terrestrial missions, food is limited and waste is generated. By recycling valuable nutrients from this waste via regenerative life support...
During long-term extra-terrestrial missions, food is limited and waste is generated. By recycling valuable nutrients from this waste via regenerative life support systems, food can be produced in space. Astronauts' urine can, for instance, be nitrified by micro-organisms into a liquid nitrate fertilizer for plant growth in space. Due to stringent conditions in space, microbial communities need to be be defined (gnotobiotic); therefore, synthetic rather than mixed microbial communities are preferred. For urine nitrification, synthetic communities face challenges, such as from salinity, ureolysis, and organics. In this study, a synthetic microbial community containing an AOB (Nitrosomonas europaea), NOB (Nitrobacter winogradskyi), and three ureolytic heterotrophs (Pseudomonas fluorescens, Acidovorax delafieldii, and Delftia acidovorans) was compiled and evaluated for these challenges. In reactor 1, salt adaptation of the ammonium-fed AOB and NOB co-culture was possible up to 45mScm, which resembled undiluted nitrified urine, while maintaining a 44±10mgNH-NLd removal rate. In reactor 2, the nitrifiers and ureolytic heterotrophs were fed with urine and achieved a 15±6mg NO-NLd production rate for 1% and 10% synthetic and fresh real urine, respectively. Batch activity tests with this community using fresh real urine even reached 29±3mgNLd. Organics removal in the reactor (69±15%) should be optimized to generate a nitrate fertilizer for future space applications.
Topics: Ammonia; Bioreactors; Comamonadaceae; Delftia acidovorans; Microbiota; Nitrification; Nitrites; Nitrobacter; Nitrosomonas europaea; Pseudomonas fluorescens; Urea; Urine; Waste Disposal, Fluid
PubMed: 31623889
DOI: 10.1016/j.syapm.2019.126021 -
International Journal of Systematic and... May 2018A Gram-stain-negative, rod-shaped, aerobic, straw yellow, motile strain, designated KNDSW-TSA6, belonging to the genus Acidovorax, was isolated from a water sample of...
A Gram-stain-negative, rod-shaped, aerobic, straw yellow, motile strain, designated KNDSW-TSA6, belonging to the genus Acidovorax, was isolated from a water sample of the river Ganges, downstream of the city of Kanpur, Uttar Pradesh, India. Cells were aerobic, non-endospore-forming and motile with single polar flagella. It differed from its phylogenetically related strains by phenotypic characteristics such as hydrolysis of urea, gelatin, casein and DNA, and the catalase reaction. The major fatty acids were C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C18 : 1ω7c/C18 : 1ω6c. Phylogenetic analysis based on 16S rRNA and housekeeping genes (gyrb, recA and rpoB gene sequences), confirmed its placement within the genus Acidovorax as a novel species. Strain KNDSW-TSA6 showed highest 16S rRNA sequence similarity to Acidovorax soli BL21 (98.9 %), Acidovorax delafieldii ATCC 17505 (98.8 %), Acidovorax temperans CCUG 11779 (98.2 %), Acidovorax caeni R-24608 (97.9 %) and Acidovorax radicis N35 (97.6 %). The digital DNA-DNA hybridization and average nucleotide identity values calculated from whole genome sequences between strain KNDSW-TSA6 and the two most closely related strains A. soli BL21 and A. delafieldii ATCC 17505 were below the threshold values of 70 and 95 % respectively. Thus, the data from the polyphasic taxonomic analysis clearly indicates that strain KNDSW-TSA6 represents a novel species, for which the name Acidovorax kalamii sp. nov. is proposed. The type strain is Acidovorax kalamii (=MTCC 12652=KCTC 52819=VTCC-B-910010).
Topics: Bacterial Typing Techniques; Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Genes, Bacterial; India; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Rivers; Sequence Analysis, DNA
PubMed: 29616893
DOI: 10.1099/ijsem.0.002736 -
Chemosphere May 2018The potential of simultaneous removal of nitrate and phosphate from wastewater by a single anaerobic Fe(II) oxidizing denitrifiers (the strain PXL1) was assessed using...
The potential of simultaneous removal of nitrate and phosphate from wastewater by a single anaerobic Fe(II) oxidizing denitrifiers (the strain PXL1) was assessed using siderite biofilters under different influent TOC concentrations and hydraulic retention times (HRTs) over a 160-day trial. Higher TOC concentrations promoted NO removal, while there was no significant influence on PO removal. Lowering down HRT from 10 h to 5 h did not significantly influence NO and PO removal. The NO removal performance and microbial community structure in the biofilters indicated that NO was reduced to N by both strain PXL1 and heterotrophic Acidovorax delafieldii. Iron content analysis of the used siderite along the biofilters showed that PO removal was improved by the bio-oxidation of Fe(II) in siderite to Fe(III) via the strain PXL1. The coexistence of the strain PXL1 and natural siderite in nitrate-contaminated aquifers provides a practical technology for in situ remediation of nutrient contaminated waterbodies.
Topics: Autotrophic Processes; Bioreactors; Denitrification; Ferric Compounds; Filtration; Groundwater; Nitrates; Phosphates; Wastewater; Water Purification
PubMed: 29433026
DOI: 10.1016/j.chemosphere.2018.02.014 -
Scientific Reports Sep 2017Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated...
Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated tropical sediment. Here, using culture-based, metagenomic and computational approaches, we describe the diversity of bacteria, genes and enzymes involved in AsIII and AsV transformation in freshwater sediment and in anaerobic AsIII- and AsV-enrichment cultures (ECs). The taxonomic profile reveals significant differences among the communities. Arcobacter, Dechloromonas, Sedimentibacter and Clostridium thermopalmarium were exclusively found in ECs, whereas Anaerobacillus was restricted to AsV-EC. Novel taxa that are both AsV-reducers and AsIII-oxidizers were identified: Dechloromonas, Acidovorax facilis, A. delafieldii, Aquabacterium, Shewanella, C. thermopalmarium and Macellibacteroides fermentans. Phylogenic discrepancies were revealed among the aioA, arsC and arrA genes and those of other species, indicating horizontal gene transfer. ArsC and AioA have sets of amino acids that can be used to assess their functional and structural integrity and familial subgroups. The positions required for AsV reduction are conserved, suggesting strong selective pressure for maintaining the functionality of ArsC. Altogether, these findings highlight the role of freshwater sediment bacteria in arsenic mobility, and the untapped diversity of dissimilatory arsenate-reducing and arsenate-resistant bacteria, which might contribute to arsenic toxicity in aquatic environments.
Topics: Anaerobiosis; Arsenic; Bacteria; Biotransformation; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Enzymes; Fresh Water; Genetic Variation; Geologic Sediments; Metabolic Networks and Pathways; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Water Pollutants, Chemical
PubMed: 28894204
DOI: 10.1038/s41598-017-11548-8 -
International Journal of Systematic and... Nov 2011Strain N35(T) was isolated from surface-sterilized wheat roots and is a Gram-negative, aerobic, motile straight rod. Strain N35(T) tested oxidase-positive and...
Strain N35(T) was isolated from surface-sterilized wheat roots and is a Gram-negative, aerobic, motile straight rod. Strain N35(T) tested oxidase-positive and catalase-negative and grew optimally at pH 7.0, 30 °C and in the absence of NaCl. 16S rRNA gene sequence analysis showed over 97 % sequence similarity to strains of the environmental species Acidovorax delafieldii, A. facilis, A. defluvii, A. temperans, A. caeni and A. soli, as well as Acidovorax valerianellae, A. anthurii and Simplicispira metamorpha. DNA-DNA hybridization between strain N35(T) and phylogenetically closely related type strains was 25.3-55.7 %, which clearly separates the strain from these closely related species. Additionally, phenotypic properties, such as substrate metabolism profiles as determined by a Biolog GN2 assay and cell-wall fatty acid profiles, particularly contents of the fatty acids C(16 : 0), C(16 : 1)ω7c/t, C(17 : 0), C(17 : 0) cyclo, C(18 : 0) cyclo and C(19 : 0) cyclo, facilitated the differentiation of the newly isolated strain N35(T) from its closest relatives. The isolate underwent phenotypic variation at high frequency in laboratory media. The DNA G+C content was 64.9 mol%. We propose that strain N35(T) is classified as a representative of a novel species within the genus Acidovorax, and suggest the name Acidovorax radicis sp. nov. The type strain is strain N35(T) ( = DSM 23535(T) = LMG 25767(T)).
Topics: Base Composition; Comamonadaceae; DNA, Bacterial; Fatty Acids; Molecular Sequence Data; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sodium Chloride; Soil Microbiology; Triticum
PubMed: 21131505
DOI: 10.1099/ijs.0.025296-0