Design and evaluation of novel primers for the detection of genes encoding diverse enzymes of methylotrophy and autotrophy.

The phylogenetic significance of the diversity of key enzymes of methylotrophic and autotrophic metabolism is discussed. Primers for these key enzymes were designed using gene sequences encoding methanol dehydrogenase (mxaF; using subsets from database sequences for 22 Bacteria), hydroxypyruvate reductase (hpr; 36 sequences), methylamine dehydrogenase (mauA; 12 sequences), methanesulfonate monooxygenase (msmA; four sequences), and the ccbL and cbbM genes of ribulose bisphosphate carboxylase (26 and 23 sequences). These were effective in amplifying the correct gene products for the target genes in reference organisms and in test organisms not previously shown to contain the genes, as well as in some methylotrophic Proteobacteria isolated from the human mouth.

Facultative methylotrophs from the human oral cavity and methylotrophy in strains of Gordonia, Leifsonia, and Microbacterium.

We show that bacteria with methylotrophic potential are ubiquitous in the human mouth microbiota. Numerous strains of Actinobacteria (Brevibacterium, Gordonia, Leifsonia, Microbacterium, Micrococcus, Rhodococcus) and Proteobacteria (Achromobacter, Klebsiella, Methylobacterium, Pseudomonas, Ralstonia) were isolated, and one strain of each of the eleven genera was studied in detail. These strains expressed enzymes associated with methylotrophic metabolism (methanol, methylamine, and formate dehydrogenases), and the assimilation of one-carbon compounds by the serine pathway (hydroxypyruvate reductase).

Purification and characterization of dimethylsulfide monooxygenase from Hyphomicrobium sulfonivorans.

Dimethylsulfide (DMS) is a volatile organosulfur compound which has been implicated in the biogeochemical cycling of sulfur and in climate control. Microbial degradation is a major sink for DMS. DMS metabolism in some bacteria involves its oxidation by a DMS monooxygenase in the first step of the degradation pathway; however, this enzyme has remained uncharacterized until now.

Further evidence to justify reassignment of Mycoplasma mycoides subspecies mycoides Large Colony type to Mycoplasma mycoides subspecies capri.

Analysis, using the polymerase chain reaction (PCR), restriction enzyme endonuclease analysis (REA), protein profile patterns, random amplification of polymorphic DNA (RAPD) fingerprinting, 16S rRNA gene sequencing and antisera growth inhibition tests, of 22 strains of Mycoplasma mycoides subsp. mycoides Large Colony type (MmmLC) and eight strains of M. mycoides subsp.

Kinetics of substrate oxidation and hydrogen peroxide production by Mycoplasma mycoides subsp. mycoides Large Colony (LC) type and Mycoplasma mycoides subsp. capri.

Mycoplasma mycoides subsp. mycoides Large Colony (LC) type is a pathogen of goats causing contagious agalactia and respiratory disease, found on all continents where small ruminants are kept. It shares close genetic characteristics with M.

Novel methylotrophic bacteria isolated from the River Thames (London, UK).

Enrichment and elective culture for methylotrophs from sediment of the River Thames in central London yielded a diversity of pure cultures representing several genera of Gram-negative and Gram-positive bacteria, which were mainly of organisms not generally regarded as typically methylotrophic. Substrates leading to successful isolations included methanol, monomethylamine, dimethylamine, trimethylamine, methanesulfonate and dimethylsulfone. Several isolates were studied in detail and shown by their biochemical and morphological properties and 16S rRNA gene sequencing to be Sphingomonas melonis strain ET35, Mycobacterium fluoranthenivorans strain DSQ3, Rhodococcus erythropolis strain DSQ4, Brevibacterium casei strain MSQ5, Klebsiella oxytoca strains MMA/F and MMA/1, Pseudomonas mendocina strain TSQ4, and Flavobacterium sp.

Proposal that the strains of the Mycoplasma ovine/caprine serogroup 11 be reclassified as Mycoplasma bovigenitalium.

This proposal is our response to the recommendation of the International Committee on Systematics of Prokaryotes (Subcommittee on the taxonomy of Mollicutes) that we 'write a proposal to classify Mycoplasma bovigenitalium and ovine/caprine serogroup 11 as a single species'. Physiological and phylogenetic comparisons between 27 strains of M. bovigenitalium and Mycoplasma serogroup 11 showed that (i) growth and patterns of organic acid substrate use completely overlapped among strains; (ii) all had lipase and phosphatase activities; (iii) the strains were indistinguishable in their SDS-PAGE whole-cell protein profiles, which differed from five other species; (iv) strains were indistinguishable in immunoblotting of cell proteins and cross-reactivity in ELISA, but differed from other Mycoplasma species; (v) DNA-DNA hybridization did not distinguish between the two groups, and (vi) comparison of 16S and 23S rRNA gene sequences of ten strains of Mycoplasma serogroup 11 and six strains of M.

Reassessment of the phylogenetic relationships of Thiomonas cuprina.

The published sequence of the 16S rRNA gene of Thiomonas cuprina strain Hö5 (=DSM 5495T) (GenBank accession no. U67162) was found to be erroneous. The 16S rRNA genes from the type strain held by the DSMZ since 1990 (DSM 5495T=NBRC 102145T) and strain Hö5 maintained frozen in the Universität Regensburg for 23 years (=NBRC 102094) were sequenced and found to be identical, but to show no significant similarity to the U67162 sequence.

Confirmation of Thiomonas delicata (formerly Thiobacillus delicatus) as a distinct species of the genus Thiomonas Moreira and Amils 1997 with comments on some species currently assigned to the genus.

The transfer of Thiobacillus delicatus to the genus Thiomonas as a distinct species, Thiomonas delicata (type strain NBRC 14566T), is confirmed by its morphological and physiological properties, DNA-DNA hybridization and the grouping of its 16S rRNA gene sequence with those of other species of the genus. An emended formal description of Thiomonas delicata is given. The status of Thiomonas cuprina DSM 5495T as a member of the genus is reconsidered.

Redefining Paracoccus denitrificans and Paracoccus pantotrophus and the case for a reassessment of the strains held by international culture collections.

An outline of the current taxonomic diversity of the genus Paracoccus is presented. A definitive summary is given of the valid type strains of Paracoccus denitrificans and Paracoccus pantotrophus and of culture collection strains that can be assigned to these species. The case is established for a critical reassessment of the P.

The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans.

The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T.

A rapid chromogenic microtitre assay of arginine aminopeptidase activity in Mycoplasma strains.

Arginine-utilizing strains of Mycoplasma can be screened by assay of their arginine aminopeptidase activity. A standardized chromogenic method is described that enables enzyme detection in small volumes of cell suspension in less than 3 h. Cell suspensions (10 microl) in 96-well microtitre plates are incubated at 37 degrees C, pH 8.

Halothiobacillus neapolitanus strain OSWA isolated from "The Old Sulphur Well" at Harrogate (Yorkshire, England).

The "Old Sulphur Well" has a subterranean input of water containing 5.5mM total sulfide, which would be inhibitory to the growth of most bacteria. The obligately chemolithoautotrophic Halothiobacillus neapolitanus is a sulfur bacterium known to tolerate and metabolize high sulfide concentrations, and we report the isolation of H.

Molecular detection and isolation from antarctica of methylotrophic bacteria able to grow with methylated sulfur compounds.

This study is the first demonstration that a diverse facultatively methylotrophic microbiota exists in some Antarctic locations. PCR amplification of genes diagnostic for methylotrophs was carried out with bacterial DNA isolated from 14 soil and sediment samples from ten locations on Signy Island, South Orkney Islands, Antarctica. Genes encoding the mxaF of methanol dehydrogenase, the fdxA for Afipia ferredoxin, the msmA of methanesulfonate monooxygenase, and the 16S rRNA gene of Methylobacterium were detected in all samples tested.

Isolation and molecular detection of methylotrophic bacteria occurring in the human mouth.

Diverse methylotrophic bacteria were isolated from the tongue, and supra- and subgingival plaque in the mouths of volunteers and patients with periodontitis. One-carbon compounds such as dimethylsulfide in the mouth are likely to be used as growth substrates for these organisms. Methylotrophic strains of Bacillus, Brevibacterium casei, Hyphomicrobium sulfonivorans, Methylobacterium, Micrococcus luteus and Variovorax paradoxus were characterized physiologically and by their 16S rRNA gene sequences.

Isolation and properties of methanesulfonate-degrading Afipia felis from Antarctica and comparison with other strains of A. felis.

Three novel strains of methylotrophic Afipia felis were isolated from several locations on Signy Island, Antarctica, and a fourth from estuary sediment from the River Douro, Portugal. They were identified as strains of the alpha-2 proteobacterium A. felis by 16S rRNA gene sequence analysis.

A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy?

We assess the use to which bioinformatics in the form of bacterial genome sequences, functional gene probes and the protein sequence databases can be applied to hypotheses about obligate autotrophy in eubacteria. Obligate methanotrophy and obligate autotrophy among the chemo- and photo-lithotrophic bacteria lack satisfactory explanation a century or more after their discovery. Various causes of these phenomena have been suggested, which we review in the light of the information currently available.

Molecular detection and isolation of facultatively methylotrophic bacteria, including Methylobacterium podarium sp. nov., from the human foot microflora.

This is the first study to demonstrate that diverse methylotrophic bacteria occur in the human foot microflora. Polymerase chain reaction (PCR) amplification of DNA from the soles and toe clefts of feet of five subjects indicated Methylobacterium strains to be present in all cases. Polymerase chain reaction amplification also showed the gene for the alpha-subunit of methanol dehydrogenase (mxaF) to be present in all samples.

Enzymes of dimethylsulfone metabolism and the phylogenetic characterization of the facultative methylotrophs Arthrobacter sulfonivorans sp. nov., Arthrobacter methylotrophus sp. nov., and Hyphomicrobium sulfonivorans sp. nov.

Novel methylotrophic Arthrobacter and Hyphomicrobium species are described. Constitutive membrane-associated dimethylsulfone- and dimethylsulfoxide-reductases were found in Arthrobacter methylotrophus strain TGA and Hyphomicrobium sulfonivorans strain S1. Enzyme activities increased during growth with dimethylsulfone or dimethylsulfoxide, respectively, and different ratios of activity with different growth substrates indicated that they are separate enzymes.

Duplicate copies of genes encoding methanesulfonate monooxygenase in Marinosulfonomonas methylotropha strain TR3 and detection of methanesulfonate utilizers in the environment.

Marinosulfonomonas methylotropha strain TR3 is a marine methylotroph that uses methanesulfonic acid (MSA) as a sole carbon and energy source. The genes from M. methylotropha strain TR3 encoding methanesulfonate monooxygenase, the enzyme responsible for the initial oxidation of MSA to formaldehyde and sulfite, were cloned and sequenced.