Comamonadaceae
Betaproteobacteria
RNA, Ribosomal, 16S
DNA, Ribosomal
Sequence Analysis, DNA
Molecular Sequence Data
Electricity generation by direct oxidation of glucose in mediatorless microbial fuel cells. (1/138)
Abundant energy, stored primarily in the form of carbohydrates, can be found in waste biomass from agricultural, municipal and industrial sources as well as in dedicated energy crops, such as corn and other grains. Potential strategies for deriving useful forms of energy from carbohydrates include production of ethanol and conversion to hydrogen, but these approaches face technical and economic hurdles. An alternative strategy is direct conversion of sugars to electrical power. Existing transition metal-catalyzed fuel cells cannot be used to generate electric power from carbohydrates. Alternatively, biofuel cells in which whole cells or isolated redox enzymes catalyze the oxidation of the sugar have been developed, but their applicability has been limited by several factors, including (i) the need to add electron-shuttling compounds that mediate electron transfer from the cell to the anode, (ii) incomplete oxidation of the sugars and (iii) lack of long-term stability of the fuel cells. Here we report on a novel microorganism, Rhodoferax ferrireducens, that can oxidize glucose to CO(2) and quantitatively transfer electrons to graphite electrodes without the need for an electron-shuttling mediator. Growth is supported by energy derived from the electron transfer process itself and results in stable, long-term power production. (+info)Caenibacterium thermophilum gen. nov., sp. nov., isolated from a thermophilic aerobic digester of municipal sludge. (2/138)
A bacterial strain, N2-680(T) (=DSM 15264(T)=LMG 21760(T)), isolated from a thermophilic aerobic digester of municipal sludge, was characterized with respect to its morphology, physiology and taxonomy. Phenotypically, the isolate was a Gram-negative rod with a polar flagellum, catalase- and oxidase-positive, containing cytoplasmic inclusions of poly-beta-hydroxybutyrate and had an optimal growth temperature of about 47 degrees C. Strain N2-680(T) was unable to reduce nitrate and could use organic acids, amino acids and carbohydrates as single carbon sources. Chemotaxonomic analysis revealed that ubiquinone 8 was the major respiratory quinone of this organism and that phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. At 50 degrees C, the major components in fatty acid methyl ester analysis were C(16 : 0) and cyclo-C(17 : 0). The highest 16S rDNA sequence identity of isolate N2-680(T) was to Leptothrix mobilis and Ideonella dechloratans (95.7 %) and to Rubrivivax gelatinosus and Aquabacterium commune (95.6 %). 16S rDNA sequence similarities to species of two related thermophilic genera, Caldimonas manganoxidans and Tepidimonas ignava, were lower (93.6 and 94.7 %). On the basis of phylogenetic analyses and physiological and chemotaxonomic characteristics, it is proposed that isolate N2-680(T) represents a new genus and species, for which the name Caenibacterium thermophilum gen. nov., sp. nov. is proposed. (+info)QUANTITATIVE STUDIES OF THE EFFECT OF ORGANIC SUBSTRATES AND 2,4-DINITROPHENOL ON HETEROTROPHIC CARBON DIOXIDE FIXATION IN HYDROGENOMONAS FACILIS. (3/138)
McFadden, Bruce A. (Washington State University, Pullman), and H. Robert Homann. Quantitative studies of the effect of organic substrates and 2,4-dinitrophenol on heterotrophic carbon dioxide fixation in Hydrogenomonas facilis. J. Bacteriol. 86:971-977. 1963.-Whole cells of Hydrogenomonas facilis under heterotrophic conditions fixed levels of C(14)O(2) which depended upon the nature of the carbon source being oxidized. It was established that oxidative rates varied as a function of p(CO2). Therefore, all studies were conducted in the presence of 1.5 mole% CO(2) in the gas phase. With glucose-grown cells supplied with glucose as substrate, the heterotrophic fixation was curtailed 98% by the addition of 8.3 x 10(-4)m 2,4-dinitrophenol (DNP). A coupling between reductive fixation of CO(2) and heterotrophic oxidation of substrate is consistent with the observed effect of DNP. The efficiency of coupling of fixation with oxidation was studied for acetate, d-glucose, l-glutamate, d,l-lactate, d-ribose, and succinate as substrates. Kinetic studies showed that the efficiency of coupling (expressed as disintegrations per minute of C(14) per microliter of O(2)) was initially time-variable for all substrates; however, it approached a constant value after 30 to 45 min for acetate, glutamate, lactate, and succinate. The initial variation of the ratio with time was due primarily to C(14)O(2) uptake, which was nonlinear with time. Control studies in the absence of exogenous substrate indicated that CO(2) fixation may also be linked to oxidation of endogenous stores accumulated during heterotrophic growth. d-Ribose appears to be the most promising substrate for short-term fixation studies owing to the rapid incorporation of C(14) and the unusually low endogenous fixation rate by cells grown on ribose. Calculations reveal that, after isotopic equilibrium has occurred, the amount of CO(2) utilized during glucose oxidation is almost 50% of O(2) uptake during the same interval. Even during succinate oxidation, which was shown to be coupled much less effectively with CO(2) fixation, the CO(2) utilized during the same interval is 8% of O(2) uptake. (+info)UTILIZATION OF AROMATIC AMINO ACIDS BY HYDROGENOMONAS FACILIS. (4/138)
DeCicco, B. T. (Rutgers, The State University, New Brunswick, N.J.), and W. W. Umbreit. Utilization of aromatic amino acids by Hydrogenomonas facilis. J. Bacteriol. 88:1590-1594. 1964.-An auxotrophic mutant of Hydrogenomonas facilis was isolated which requires tryptophan, phenylalanine, and p-aminobenzoic acid (PABA) for growth. With glucose as the main carbon and energy source, the quantitative requirements for tryptophan and PABA were at normal microgram levels, but the requirement for phenylalanine was very large and approached substrate concentrations. The large phenylalanine requirement is due to a rapid oxidation and degradation of phenylalanine by the mutant. The utilization of both phenylalanine and glucose is adaptive, and the presence of phenylalanine partially inhibits the induction of the glucose-utilizing system. Wild-type H. facilis can utilize either phenylalanine or tyrosine for growth. Tracer studies indicated that during growth on phenylalanine, the aromatic ring is opened and degraded. Wild-type cells grown on either phenylalanine or tyrosine can oxidize phenylalanine, tyrosine, or phenylpyruvate without a lag. Another inducible pathway enables H. facilis to utilize either quinate or 3,4-dihydroxybenzoate for growth, and sequential adaptation studies revealed that quinate is converted to 3,4-dihydroxybenzoate during its degradation. Mutants may be obtained which can also utilize 2,5-dihydroxybenzoate for growth. (+info)CHARACTERIZATION OF POLY-BETA-HYDROXYBUTYRATE EXTRACTED FROM DIFFERENT BACTERIA. (5/138)
Lundgren, D. G. (Syracuse University, Syracuse, N.Y.), R. Alper, C. Schnaitman and R. H. Marchessault. Characterization of poly-beta-hydroxybutyrate extracted from different bacteria. J. Bacteriol. 89:245-251. 1965.-Poly-beta-hydroxybutyrate (PHB) from different bacterial genera was studied with regard to its crystal structure, infrared absorption, intrinsic viscosity, and electron microscopy. All PHB samples precipitated from dilute chloroform solution gave identical X-ray diffractograms confirming uniformity of crystal structure, and uniformity of molecular structure, based on the similarity of the recorded infrared spectra, was also established. Crystal morphology was also similar, showing the reported "lath" shape structure for purified polymer from Bacillus cereus. Intrinsic viscosity ranged from 0.04 to 11.5 depending upon the polymer treatment; polymer molecular weights, based upon viscometry, could be estimated to range from 1,000 to 250,000. It is concluded that the same basic molecule is involved in all PHB present in the bacterial kindgom. (+info)CHARACTERISTICS AND INTERMEDIATES OF SHORT-TERM C-14-O-2 INCORPORATION DURING RIBOSE OXIDATION BY HYDROGENOMONAS FACILIS. (6/138)
McFadden, B. A. (Washington State University, Pullman), and H. R. Homann. Characteristics and intermediates of short-term C(14)O(2) incorporation during ribose oxidation by Hydrogenomonas facilis. J. Bacteriol. 89:839-847. 1965.-Ribose-grown cells of Hydrogenomonas facilis, which had been suspended in growth medium and were oxidizing ribose, were exposed to HC(14)O(3) (-) of high specific activity. The uptake was proportional to cell mass. Short-term uptake (less than 2 min) was completely inhibited by 10(-3)m 2,4-dinitrophenol (DNP) or by <4 x 10(-6)mm-chlorocarbonyl cyanide phenylhydrazone, and to the extent of 42% by 5 x 10(-5)m DNP. The following observations were made in kinetic studies (8, 16, 35, 67, 96, and 181 sec) of fixation in the presence of ribose. Glutamate was extensively labeled in periods up to 3 min. It was one of the major early products, containing 30% of the label at 8 sec. The sugar phosphate fraction was not detectably labeled at 8 or 16 sec, but its C(14)-content increased rapidly to 27% at 35 sec and then slowly decreased. Label in phosphoglycerate, phosphoenolpyruvate, and alanine did not appear until 35 sec, and did not exceed about 7, 2, and 3%, respectively, of the total extracted radioactivity. Adenosine triphosphate and adenosine diphosphate were heavily labeled after fixation in a pilot study for 125 sec. Although considerable radioactivity incorporated during the pilot study was intractable by the extraction procedure employed, virtually no C(14) was found in the residue in poly-beta-hydroxybutyric acid. A large number of amino acids and organic acids and some organic phosphates were not detectably labeled in any of the experiments. Omission of ribose greatly diminished incorporation, particularly into glutamate. (+info)NICKEL-DEPENDENT CHEMOLITHOTROPHIC GROWTH OF TWO HYDROGENOMONAS STRAINS. (7/138)
Bartha, R. (University of Washington, Seattle), and E. J. Ordal. Nickel-dependent chemolithotrophic growth of two Hydrogenomonas strains. J. Bacteriol. 89:1015-1019. 1965.-The trace element requirements for growth of facultative chemolithotrophic Hydrogenomonas strains H1 and H16 were investigated under both autotrophic and heterotrophic conditions. The organisms were grown in a mineral medium, rendered deficient in trace elements by extraction with 8-hydroxyquinoline and chloroform, and, in some cases, by coprecipitation with copper. The organic substrates, succinate and fumarate, used for heterotrophic growth were treated in a similar fashion. Acetate and butyrate were purified by redistillation. It was found that iron alone was required for heterotrophic growth (optimal concentration, 1.5 x 10(-6)m Fe(+++)), but cells grown chemolithotrophically on molecular hydrogen required the addition of nickel. The yield of protein was proportional to the nickel added, reaching a maximum at 3 x 10(-7)m Ni(++). Manganese, cobalt, copper, and zinc, alone or in combination, failed to substitute for nickel in the experiments with Hydrogenomonas. Although nickel is required specifically for the chemolithotrophic growth of Hydrogenomonas, nickel deficiency did not affect: (i) the synthesis or activation of hydrogenase, (ii) the Knallgas reaction, (iii) the assimilation of CO(2) by resting cells, or the synthesis of the storage material poly-beta-hydroxybutyric acid. It is suggested that nickel participates in some reaction involved in CO(2) fixation by growing cells. (+info)Nutritional requirements for Hydrogenomonas eutropha. (8/138)
Repaske, Roy (National Institute of Allergy and Infectious Diseases, Bethesda, Md.). Nutritional requirements for Hydrogenomonas eutropha. J. Bacteriol. 83: 418-422. 1962.-A simple apparatus for the autotrophic cultivation of Hydrogenomonas eutropha in 100-ml shake cultures is described. Nitrogen, in the form of ammonium, nitrate, or urea, was used for growth; nitrite could not be utilized. Optimal growth occurred at pH 6.4 to 6.8 at 30 C. H. eutropha grew best in an atmosphere containing 15 to 25% oxygen and 10% carbon dioxide. Below these concentrations each of the gases was limiting. Growth was shown to be dependent on iron, and the rate of growth was a function of iron concentration and its state of oxidation. (+info)Comamonadaceae is a family of gram-negative, aerobic or facultatively anaerobic bacteria that are commonly found in various environments such as soil, water, and the rhizosphere of plants. The name Comamonadaceae comes from the type genus Comamonas. Members of this family are known to be metabolically versatile and can degrade a wide range of organic compounds, including aromatic compounds and polysaccharides. Some species in this family are also known to be opportunistic pathogens in humans, causing infections such as pneumonia, bacteremia, and meningitis.
Betaproteobacteria is a class of proteobacteria, a group of gram-negative bacteria. This class includes several genera of bacteria that are widely distributed in the environment, and can be found in soil, water, and various organisms including humans. Some members of Betaproteobacteria are important pathogens, causing diseases such as meningitis, pneumonia, and urinary tract infections. Other members of this class are capable of breaking down environmental pollutants, making them useful in bioremediation applications.
Sewage is not typically considered a medical term, but it does have relevance to public health and medicine. Sewage is the wastewater that is produced by households and industries, which contains a variety of contaminants including human waste, chemicals, and other pollutants. It can contain various pathogens such as bacteria, viruses, and parasites, which can cause diseases in humans if they come into contact with it or consume contaminated food or water. Therefore, the proper treatment and disposal of sewage is essential to prevent the spread of infectious diseases and protect public health.
Ribosomal RNA (rRNA) is a type of RNA that combines with proteins to form ribosomes, which are complex structures inside cells where protein synthesis occurs. The "16S" refers to the sedimentation coefficient of the rRNA molecule, which is a measure of its size and shape. In particular, 16S rRNA is a component of the smaller subunit of the prokaryotic ribosome (found in bacteria and archaea), and is often used as a molecular marker for identifying and classifying these organisms due to its relative stability and conservation among species. The sequence of 16S rRNA can be compared across different species to determine their evolutionary relationships and taxonomic positions.
Ribosomal DNA (rDNA) refers to the specific regions of DNA in a cell that contain the genes for ribosomal RNA (rRNA). Ribosomes are complex structures composed of proteins and rRNA, which play a crucial role in protein synthesis by translating messenger RNA (mRNA) into proteins.
In humans, there are four types of rRNA molecules: 18S, 5.8S, 28S, and 5S. These rRNAs are encoded by multiple copies of rDNA genes that are organized in clusters on specific chromosomes. In humans, the majority of rDNA genes are located on the short arms of acrocentric chromosomes 13, 14, 15, 21, and 22.
Each cluster of rDNA genes contains both transcribed and non-transcribed spacer regions. The transcribed regions contain the genes for the four types of rRNA, while the non-transcribed spacers contain regulatory elements that control the transcription of the rRNA genes.
The number of rDNA copies varies between species and even within individuals of the same species. The copy number can also change during development and in response to environmental factors. Variations in rDNA copy number have been associated with various diseases, including cancer and neurological disorders.
Phylogeny is the evolutionary history and relationship among biological entities, such as species or genes, based on their shared characteristics. In other words, it refers to the branching pattern of evolution that shows how various organisms have descended from a common ancestor over time. Phylogenetic analysis involves constructing a tree-like diagram called a phylogenetic tree, which depicts the inferred evolutionary relationships among organisms or genes based on molecular sequence data or other types of characters. This information is crucial for understanding the diversity and distribution of life on Earth, as well as for studying the emergence and spread of diseases.
DNA Sequence Analysis is the systematic determination of the order of nucleotides in a DNA molecule. It is a critical component of modern molecular biology, genetics, and genetic engineering. The process involves determining the exact order of the four nucleotide bases - adenine (A), guanine (G), cytosine (C), and thymine (T) - in a DNA molecule or fragment. This information is used in various applications such as identifying gene mutations, studying evolutionary relationships, developing molecular markers for breeding, and diagnosing genetic diseases.
The process of DNA Sequence Analysis typically involves several steps, including DNA extraction, PCR amplification (if necessary), purification, sequencing reaction, and electrophoresis. The resulting data is then analyzed using specialized software to determine the exact sequence of nucleotides.
In recent years, high-throughput DNA sequencing technologies have revolutionized the field of genomics, enabling the rapid and cost-effective sequencing of entire genomes. This has led to an explosion of genomic data and new insights into the genetic basis of many diseases and traits.
Bacterial DNA refers to the genetic material found in bacteria. It is composed of a double-stranded helix containing four nucleotide bases - adenine (A), thymine (T), guanine (G), and cytosine (C) - that are linked together by phosphodiester bonds. The sequence of these bases in the DNA molecule carries the genetic information necessary for the growth, development, and reproduction of bacteria.
Bacterial DNA is circular in most bacterial species, although some have linear chromosomes. In addition to the main chromosome, many bacteria also contain small circular pieces of DNA called plasmids that can carry additional genes and provide resistance to antibiotics or other environmental stressors.
Unlike eukaryotic cells, which have their DNA enclosed within a nucleus, bacterial DNA is present in the cytoplasm of the cell, where it is in direct contact with the cell's metabolic machinery. This allows for rapid gene expression and regulation in response to changing environmental conditions.
Molecular sequence data refers to the specific arrangement of molecules, most commonly nucleotides in DNA or RNA, or amino acids in proteins, that make up a biological macromolecule. This data is generated through laboratory techniques such as sequencing, and provides information about the exact order of the constituent molecules. This data is crucial in various fields of biology, including genetics, evolution, and molecular biology, allowing for comparisons between different organisms, identification of genetic variations, and studies of gene function and regulation.
Comamonadaceae
Acidovorax delafieldii
Acidovorax anthurii
Extensimonas
Purple bacteria
Caenimonas
Acidovorax
Hydrogenophaga pseudoflava
Ideonella
Roseateles
Xenophilus (bacterium)
Caldimonas
Ottowia
Delftia deserti
Hydrogenophaga taeniospiralis
Giesbergeria
Diaphorobacter
Polaromonas
Acidovorax wohlfahrtii
Delftia acidovorans
Hydrogenophaga intermedia
Aquabacterium hongkongensis
Ideonella dechloratans
Macromonas bipunctata
Variovorax
Delftia
Acidovorax cattleyae
Rhodoferax
Rosalind Franklin
Thiomonas
Comamonadaceae - Wikipedia
Comamonadaceae maps - Encyclopedia of Life
SdhR: Comamonadaceae
LldR: Comamonadaceae
Delftia acidovorans
Frontiers | Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an...
12:42 am
Effect of life stage and pesticide exposure on the gut microbiota of Aedes albopictus and Culex pipiens L | Scientific Reports
Yucatán's underwater caves host diverse microbial communities
HOMD :: Taxon Info
Frontiers | Comparative analysis of scalp and gut microbiome in androgenetic alopecia: A Korean cross-sectional study
Name Taxonomy in SILVA v123
Small Things Considered: Happy Together… Life of the Bacterial Consortium Chlorochromatium aggregatum
Microbes and Environments
Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters | Microbiome |...
Bacterial community structure and denitrifier (nir-gene) abundance in soil water and groundwater beneath agricultural land in...
Fate of Escherichia coli in dialysis device exposed into sewage influent and activated sludge | Journal of Water and Health |...
Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence...
Bacterial endophytes from seeds of conifers with potential role in biocontrol: microbiome analysis - IOBC-WPRS
Pre GI: BLASTP Hits
Delftia - Wikispecies
Browse
Pre GI: Gene
MicrobiomePrescription
HOMD :: Order
Taxonomy of the genus Acidovorax Willems et al. 1990 emend. Willems et al. 1992
Bacteria2
- But one family of bacteria ( Comamonadaceae ) acted as a popular social butterfly - appearing at nearly two-thirds of the "cafeteria tables. (eurasiareview.com)
- For seeds it was found that diversity of endophytic bacteria in the composition of microbiome is low and is determined by four main families: Enterobacteriaceae, Pseudomonadaceae, Oxalobacteraceae and Comamonadaceae. (iobc-wprs.org)
Betaproteobacteria1
- The Comamonadaceae are a family of the Betaproteobacteria. (wikipedia.org)
Burkholderiaceae2
- The most abundant mosquito-associated bacterial OTUs were from the families Burkholderiaceae, Pseudomonadaceae, Comamonadaceae, and Xanthomonadaceae. (cdc.gov)
- Strains isolated from environmental sources such as soil, rhizosphere, sediment or sludge show a higher content of catabolic genes in their genomes compared with strains isolated from human, animal or plant hosts, but no significant difference is found among Alcaligenaceae, Burkholderiaceae and Comamonadaceae families, indicating that habitat is more of a determinant than phylogenetic origin in shaping aromatic catabolic versatility. (uai.cl)
Delftia2
- The central rod with a single polar flagellum is a β-proteobacter within family Comamonadaceae (genus level relatives include Variovorax, Rhodoferax , and Delftia ). (asmblog.org)
- Both Delftia and Comamonas belong to the family of the Comamonadaceae. (sciepub.com)
Genera1
- Members of the betaproteobacterial genera Curvibacter , Aquabacterium , and Polaromonas ( Comamonadaceae ) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. (biomedcentral.com)
Family2
- Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov.,comb. (wikipedia.org)
- family Comamonadaceae Willems et al. (namesforlife.com)
Aerobic1
- Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. (wustl.edu)
Water1
- the unclassified Comamonadaceae was dominant in water samples from waste tires, while Mycobacterium and Carnobacterium, dominated Ae. (illinois.edu)
Proteobacteria1
- Comparisons of bacterial abundances across all taxonomic levels showed differences for phylum Proteobacteria (p = 0.038) and family Comamonadaceae (p = 0.035). (nih.gov)
Xanthomonadaceae2
- Beta- (Comamonadaceae) and Gammaproteobacteria (Xanthomonadaceae) were also important MCPA-[13C] consumers in burrow walls only, indicating that earthworms favor betaproteobacterial MCPA degraders. (uni-bayreuth.de)
- Sphingomonadaceae dominated MCPA-[13C] consumers in bulk soil and burrow wall microcosms, while Beta- and Gammaproteobacteria (Burkholderiacea, Comamonadaceae, Oxalobacteraceae, and Xanthomonadaceae) dominated MCPA-[13C] consumers in microcosms of cast, indicating that the latter taxa are prone to respond to MCPA in cast. (uni-bayreuth.de)
Pseudomonadaceae1
- Almost all differentially expressed OTUs belonging to the families Weeksellaceae, S24-7, Comamonadaceae, Lachnospiraceae, Moraxellaceae and Pseudomonadaceae (39% of OTUs) were over expressed in WA animals. (nih.gov)
RRNA2
- Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov.,comb. (wikipedia.org)
- The dominance of phylotypes affiliated to Chlorobiaceae, Rhodocyclaceae and Comamonadaceae was revealed by 16S rRNA illumina sequencing in the control and the MFC anode, presumably associated with benzene degradation. (ufz.de)