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At least 19 recordsLinked to original sources
PubMed2004

Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the 'Alphaproteobacteria' and description of Angulomicrobium amanitiforme sp. nov.

The unusually shaped bacteria of the genera Stella, Labrys and Angulomicrobium have been described based on their cell morphology and biochemistry. However, their phylogenetic relationships remain unresolved. An earlier study that was based on 5S rRNA gene sequences placed the genus Stella within the 'Alphaproteobacteria'. In the present report, polar lipids and 16S rRNA genes of the type strains of the two species in the genus Stella, Stella humosa DSM 5900(T) and Stella vacuolata DSM 5901(T), are studied, as well as the type strains of the monospecific genera Labrys (Labrys monachus VKM B-1479(T)) and Angulomicrobium (Angulomicrobium tetraedrale DSM 5895(T)). It was found that the genus Stella belongs to the order Rhodospirillales in the family Rhodospirillaceae, and not to the Acetobacteraceae. Whilst the position of the genus Angulomicrobium in the family Hyphomicrobiaceae was confirmed, the genus Labrys could not be placed into any known family, but was adjacent to the family 'Beijerinckiaceae'. In addition, data were obtained for strain VKM B-1336, which was shown not to belong to the genus Angulomicrobium, and strain NCIMB 1785(T) (=DSM 15561(T)), for which the name Angulomicrobium amanitiforme sp. nov. is proposed.

Acetobacteraceae↗
PubMed2005

Community-level analysis: key genes of aerobic methane oxidation.

Aerobic methane-oxidizing bacteria (methanotrophs) are a diverse group of bacteria that are currently represented by 13 recognized genera. They play a major role in the global methane cycle and are widespread in nature with representatives found in soils, freshwater, seawater, freshwater and marine sediments, peat bogs and at extremes of temperature, salinity, and pH. There has been an interest in methanotrophs for their potential in bioremediation processes. Methanotroph diversity and ecology are often studied using the "functional" genes pmoA, mmoX, and mxaF, encoding subunits of the particulate methane monooxygenase, soluble methane monooxygenase, and the methanol dehydrogenase, respectively. This chapter describes methods used to detect and analyze these functional genes.

Alcohol Oxidoreductases↗
PubMed2003

Beijerinckia derxii releases plant growth regulators and amino acids in synthetic media independent of nitrogenase activity.

AIMS: This study aims at evaluating the ability of Beijerinckia derxii, a free-living nitrogen (N)-fixing bacterium frequently isolated from tropical soils, to release certain plant growth regulators [indoleacetic acid (IAA), ethylene, polyamines] and amino acids into the growth medium. METHODS AND RESULTS: The production of those substances was compared using both cultures in which nitrogenase was active (N-free medium) and cultures in which nitrogenase was repressed (combined-N cultures). Those cultures were grown under agitation and in absence of agitation. Total IAA production was higher in agitated, N-free cultures but specific production was greater in combined-N cultures under agitation. Putrescine and spermidine were detected under all conditions tested. Ethylene was produced in both N-free and combined-N cultures. A greatest diversity of amino acids was released in N-free cultures. CONCLUSIONS: There was no inhibition of the production of the analysed substances under conditions where nitrogenase was inactive. SIGNIFICANCE AND IMPACT OF THE STUDY: Beijerinckia derxii is potentially a producer of plant-active substances; its presence in the natural environment suggests that this bacterium may contribute to the development of other living organisms.

Amino Acids↗
PubMed2003

During stationary phase, Beijerinckia derxii shows nitrogenase activity concomitant with the release and accumulation of nitrogenated substances.

Beijerinckia derxii, a free-living nitrogen-fixing bacterium, maintained an increasing nitrogenase specific activity during the stationary growth phase. To verify the destination of the nitrogen fixed during this phase, intra and extracellular nitrogenated contents were analyzed. Organic nitrogen and amino acids were detected in the supernatant of the cultures. An increase in intracellular content of both nitrogen and protein occurred. Cytoplasmic granules indicated the presence of arginine. The ability of a non-diazotrophic bacterium (E. coli) to use B. derxii proteins as a source of nitrogen was observed concomitantly with E. coli growth. There is a suggestion that B. derxii contributes to the environment by both releasing nitrogenated substances and accumulating substances capable of being consumed after its death.

Beijerinckiaceae↗
PubMed2004

Survival of Beijerinckia sp. microencapsulated in carbohydrates by spray-drying.

The encapsulation of Beijerinckia sp. cell suspension in different wall materials using the spray drying technique was performed. Mat dextrin, dehydrated glucose syrups, gum acacia and modified starch materials were tested. Cell viability assays were carried out before and after drying and during storage of the products. The surface area and characteristics of the encapsulated powders were examined using BET adsorption of N(2) and scanning electron microscopy, respectively. The residual moisture content and water activity of the powders were also determined. The best results were obtained with the dehydrated glucose syrup, which resulted in products with the greatest per cent survival during the drying process and subsequent storage period. The products obtained with the dehydrated glucose syrup showed more uniform microcapsule surfaces at lower A(w) values and residual moisture content.

Beijerinckiaceae↗
PubMed2003

Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol.

Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped, methane-oxidizing bacteria were isolated from an acidic forest cambisol near Marburg, Germany, and were designated as strains BL2(T) and A1. These bacteria were morphologically and phenotypically similar to Methylocella palustris K(T). The cells possess a highly specific bipolar appearance. They lack the intracytoplasmic membranes common to all methane-oxidizing bacteria except Methylocella, but contain a vesicular membrane system connected to the cytoplasmic membrane. A soluble methane monooxygenase was present, but no particulate methane monooxygenase could be detected. These bacteria utilize the serine pathway for carbon assimilation. Strains BL2(T) and A1 are moderately acidophilic, mesophilic organisms capable of growth at pH values between 4.5 and 7 (with an optimum at pH 5.5) and at temperatures between 4 and 30 degrees C. Compared with Methylocella palustris K(T), these strains have greater tolerance of cold temperatures, dissolved salts and methanol. On the basis of 16S rRNA gene sequence identity, of species with validly published names, strain BL2(T) is most closely related to Methylocella palustris K(T) (97.3 % identity), Beijerinckia indica subsp. indica ATCC 9039(T) (97.1 %) and Methylocapsa acidiphila B2(T) (96.2 %). The DNA G+C content is 60 mol% and the major phospholipid fatty acid is 18 : 1omega7. Strain BL2(T) showed only 21-22 % DNA-DNA hybridization with Methylocella palustris K(T). The data therefore suggest that strains BL2(T) and A1 represent a novel species of Methylocella; the name Methylocella silvestris sp. nov. is proposed, with strain BL2(T) (=DSM 15510(T)=NCIMB 13906(T)) as the type strain.

Beijerinckiaceae↗
PubMed2004

NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria.

The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB). This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus BEIJERINCKIA: To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined. For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB. The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent. The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features. First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group. From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching. Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98.5 and 96.6 %, respectively) than would be expected from their 16S rRNA-based relationships. Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure with regard to nitrogen acquisition. This interpretation is corroborated by the observation that, in contrast to most other diazotrophs, M. acidiphila B2 and Beijerinckia spp. are capable of active growth on nitrogen-free media under fully aerobic conditions.

Bacterial Proteins↗
PubMed2005

Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2.

The molecular regulation of methane oxidation in the first fully authenticated facultative methanotroph Methylocella silvestris BL2 was assessed during growth on methane and acetate. Problems of poor growth of Methylocella spp. in small-scale batch culture were overcome by growth in fermentor culture. The genes encoding soluble methane monooxygenase were cloned and sequenced, which revealed that the structural genes for soluble methane monooxygenase, mmoXYBZDC, were adjacent to two genes, mmoR and mmoG, encoding a sigma54 transcriptional activator and a putative GroEL-like chaperone, located downstream (3') of mmoC. Transcriptional analysis revealed that the genes were all cotranscribed from a sigma54-dependent promoter located upstream (5') of mmo X. The transcriptional start site was mapped. Transcriptional analysis of soluble methane monooxygenase genes and expression studies on fermentor grown cultures showed that acetate repressed transcription of sMMO in M. silvestris BL2. The possibility of the presence of a particulate, membrane-bound methane monooxygenase enzyme in M. silvestris BL2 and the copper-mediated regulation of soluble methane monooxygenase was investigated. Both were shown to be absent. A promoter probe vector was constructed and used to assay transcription of the promoter of the soluble methane monoxygenase genes of M. silvestris BL2 grown under various conditions and with different substrates. These data represent the first insights into the molecular physiology of a facultative methanotroph.

Beijerinckiaceae↗
PubMed2007

Microscopical investigation of poly(3-hydroxybutyrate) granule formation in Azotobacter vinelandii.

Poly(3-hydroxybutyrate) (PHB) granule formation in Azotobacter vinelandii was investigated by laser scanning fluorescence microscopy after staining the cells with Nilered and Baclight. Cells that had been starved for a carbon source for > or =3 days were almost free of PHB granules. Formation of visible PHB granules started within 1-2 h after transfer of the cells to a medium permissive for PHB accumulation. Fluorescent PHB granules at the early stages of formation were exclusively found in the cell periphery of the 2-3 mum ovoid-shaped cells. After 3 h of PHB accumulation or later, PHB granules were also found to be detached from the cell periphery. Our results indicate that PHB granule formation apparently begins at the inner site of the cytoplasmic membrane. This finding is different from previous assumptions that PHB granule formation occurs randomly in the cytoplasm of PHB-accumulating bacteria.

Azotobacter vinelandii↗
PubMed2005

First genome data from uncultured upland soil cluster alpha methanotrophs provide further evidence for a close phylogenetic relationship to Methylocapsa acidiphila B2 and for high-affinity methanotrophy involving particulate methane monooxygenase.

Members of upland soil cluster alpha (USC alpha) are assumed to be methanotrophic bacteria (MB) adapted to the trace level of atmospheric methane. So far, these MB have eluded all cultivation attempts. While the 16S rRNA phylogeny of USC alpha members is still not known, phylogenies constructed for the active-site polypeptide (encoded by pmoA) of particulate methane monooxygenase (pMMO) placed USC alpha next to the alphaproteobacterial Methylocapsa acidiphila B2. To assess whether the pmoA tree reflects the evolutionary identity of USC alpha, a 42-kb genomic contig of a USC alpha representative was obtained from acidic forest soil by screening a metagenomic fosmid library of 250,000 clones using pmoA-targeted PCR. For comparison, a 101-kb genomic contig from M. acidiphila was analyzed, including the pmo operon. The following three lines of evidence confirmed a close phylogenetic relationship between USC alpha and M. acidiphila: (i) tetranucleotide frequency patterns of 5-kb genomic subfragments, (ii) annotation and comparative analysis of the genomic fragments against all completely sequenced genomes available in public domain databases, and (iii) three single gene phylogenies constructed using the deduced amino acid sequences of a putative prephenate dehydratase, a staphylococcal-like nuclease, and a putative zinc metalloprotease. A comparative analysis of the pmo operons of USC alpha and M. acidiphila corroborated previous reports that both the pmo operon structure and the predicted secondary structure of deduced pMMO are highly conserved among all MB.

Bacteria↗
PubMed2005

Methylotrophic autotrophy in Beijerinckia mobilis.

Representatives of the genus Beijerinckia are known as heterotrophic, dinitrogen-fixing bacteria which utilize a wide range of multicarbon compounds. Here we show that at least one of the currently known species of this genus, i.e., Beijerinckia mobilis, is also capable of methylotrophic metabolism coupled with the ribulose bisphosphate (RuBP) pathway of C1 assimilation. A complete suite of dehydrogenases commonly involved in the sequential oxidation of methanol via formaldehyde and formate to CO2 was detected in cell extracts of B. mobilis grown on CH3OH. Carbon dioxide produced by oxidation of methanol was further assimilated via the RuBP pathway as evidenced by reasonably high activities of phosphoribulokinase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Detection and partial sequence analysis of genes encoding the large subunits of methanol dehydrogenase (mxaF) and form I RubisCO (cbbL) provided genotypic evidence for methylotrophic autotrophy in B. mobilis.

Alcohol Oxidoreductases↗
PubMed2003

Activity and survival of spray-dried Beijerinckia sp. microencapsulated in different carbohydrates.

This study examined the possibility of preserving Beijerinckia cultures by encapsulation using a spray drier, for use in biotechnological processes in the production of biopolymers. An adequate choice of the wall (coating) material is one of the factors that will determine the degree of cell survival and the maintenance of fermentative activity in the encapsulated inoculum. Malt dextrin, dehydrated glucose syrups, modified starch, and acacia (gum arabic) were used as wall materials. The results showed that spray-dried Beijerinckia encapsulated in malt dextrin, stored for 2 mo, and inoculated into sterile must after rehydration presented the greatest stability with respect to fermentative activity, although the glucose-encapsulated cells showed the highest percentage of viability during spray drying and during the storage period.

Beijerinckiaceae↗