| changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. | during an experiment in two laboratory-scale enclosures filled with lake water (130 liters each) we noticed the almost-complete lysis of the cyanobacterial population. based on electron microscopic observations of viral particles inside cyanobacterial filaments and counts of virus-like particles, we concluded that a viral lysis of the filamentous cyanobacteria had taken place. denaturing gradient gel electrophoresis (dgge) of 16s ribosomal dna fragments qualitatively monitored the removal of the ... | 1999 | 9925618 |
| high-affinity methane oxidation by a soil enrichment culture containing a type ii methanotroph. | methanotrophic bacteria in an organic soil were enriched on gaseous mixing ratios of <275 parts per million of volume (ppmv) of methane (ch4). after 4 years of growth and periodic dilution (>10(20) times the initial soil inoculum), a mixed culture was obtained which displayed an apparent half-saturation constant [km(app)] for ch4 of 56 to 186 nm (40 to 132 ppmv). this value was the same as that measured in the soil itself and about 1 order of magnitude lower than reported values for pure culture ... | 1999 | 10049856 |
| quantification of hyphomicrobium populations in activated sludge from an industrial wastewater treatment system as determined by 16s rrna analysis. | the bacterial community structure of the activated sludge from a 25 million-gal-per-day industrial wastewater treatment plant was investigated using rrna analysis. 16s ribosomal dna (rdna) libraries were created from three sludge samples taken on different dates. partial rrna gene sequences were obtained for 46 rdna clones, and nearly complete 16s rrna sequences were obtained for 18 clones. seventeen of these clones were members of the beta subdivision, and their sequences showed high homology t ... | 2000 | 10698787 |
| quantitative molecular assay for fingerprinting microbial communities of wastewater and estrogen-degrading consortia. | a quantitative fingerprinting method, called the real-time terminal restriction fragment length polymorphism (real-time-t-rflp) assay, was developed for simultaneous determination of microbial diversity and abundance within a complex community. the real-time-t-rflp assay was developed by incorporating the quantitative feature of real-time pcr and the fingerprinting feature of t-rflp analysis. the assay was validated by using a model microbial community containing three pure strains, an escherich ... | 2005 | 15746346 |
| complex regulatory pathways coordinate cell-cycle progression and development in caulobacter crescentus. | caulobacter crescentus has become the predominant bacterial model system to study the regulation of cell-cycle progression. stage-specific processes such as chromosome replication and segregation, and cell division are coordinated with the development of four polar structures: the flagellum, pili, stalk, and holdfast. the production, activation, localization, and proteolysis of specific regulatory proteins at precise times during the cell cycle culminate in the ability of the cell to produce two ... | 2009 | 18929067 |
| {gamma}-glutamylmethylamide is an essential intermediate in the metabolism of methylamine by methylocella silvestris. | methylocella silvestris bl2, a facultative methane utilizer, can grow on monomethylamine (mma) as a sole carbon and nitrogen source. no activity of mma dehydrogenase was detectable. instead, this bacterium utilizes a methylated amino acid pathway (gamma-glutamylmethylamide [gma] and n-methylglutamate [nmg]) for mma metabolism. the activities of the two key enzymes in this pathway, gma synthetase and nmg dehydrogenase, were found when the bacterium was grown on mma. gma was detected by high-perfo ... | 2010 | 20472738 |
| nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. | genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (aoa) might play a major role in nitrification on earth. however, only one pure isolate of this group from a marine environment has so far been obtained, demonstrating archaeal ammonia oxidation coupled with autotrophic growth similar to the bacterial counterparts. here we describe th ... | 2011 | 21525411 |
| rhizosphere microbial community structure in relation to root location and plant iron nutritional status. | root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. to examine this question, we performed an experiment with barley (hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. plants were grown in an iron-limiting soil in root box microcosms. one-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter ... | 2000 | 10618246 |
| molecular detection of bacteria in plant tissues, using universal 16s ribosomal dna degenerated primers. | highly specific, sensitive and rapid tests are required for the detection and identification of covert bacterial contaminations in plant tissue cultures. current methods available for this purpose are tedious, time consuming, highly error prone, expensive, require advanced technical expertise and are sometimes ineffective. we report here the development of a sensitive polymerase chain reaction (pcr) based method for the rapid detection and identification of bacteria occurring in plant tissue cul ... | 2014 | 26019546 |
| the methanol dehydrogenase gene, mxaf, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments. | the mxaf gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the alpha-, beta- and gammaproteobacteria. it is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoa and mmox genes, which are absent in some methanotrophic proteobacterial genera. this study examined the potential for using the mxaf gene as a functional and phylogenetic marker for methanotrophs. mxaf and 16s r ... | 2013 | 23451130 |
| physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation. | ammonia-oxidizing archaea (aoa) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. here, we report the cultivation and characterization of two novel nitrosopumilus strains, originating from coastal surface waters of the northern adriatic sea. the combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentia ... | 2015 | 26528837 |
| physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation. | ammonia-oxidizing archaea (aoa) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. here, we report the cultivation and characterization of two novel nitrosopumilus strains, originating from coastal surface waters of the northern adriatic sea. the combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentia ... | 2015 | 26528837 |
| adhesins involved in attachment to abiotic surfaces by gram-negative bacteria. | during the first step of biofilm formation, initial attachment is dictated by physicochemical and electrostatic interactions between the surface and the bacterial envelope. depending on the nature of these interactions, attachment can be transient or permanent. to achieve irreversible attachment, bacterial cells have developed a series of surface adhesins promoting specific or nonspecific adhesion under various environmental conditions. this article reviews the recent advances in our understandi ... | 2015 | 26350310 |
| microbial communities on seafloor basalts at dorado outcrop reflect level of alteration and highlight global lithic clades. | areas of exposed basalt along mid-ocean ridges and at seafloor outcrops serve as conduits of fluid flux into and out of a subsurface ocean, and microbe-mineral interactions can influence alteration reactions at the rock-water interface. located on the eastern flank of the east pacific rise, dorado outcrop is a site of low-temperature (<20°c) hydrothermal venting and represents a new end-member in the current survey of seafloor basalt biomes. consistent with prior studies, a survey of 16s rrna ge ... | 2015 | 26779122 |
| microbial survey of a full-scale, biologically active filter for treatment of drinking water. | the microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. nitrosomonas, nitrospira, sphingomonadales, and rhizobiales dominated the clone libraries. the results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods. | 2012 | 22752177 |
| the expanding world of methylotrophic metabolism. | in the past few years, the field of methylotrophy has undergone a significant transformation in terms of discovery of novel types of methylotrophs, novel modes of methylotrophy, and novel metabolic pathways. this time has also been marked by the resolution of long-standing questions regarding methylotrophy and the challenge of long-standing dogmas. this chapter is not intended to provide a comprehensive review of metabolism of methylotrophic bacteria. instead we focus on significant recent disco ... | 2009 | 19514844 |
| microscale and molecular assessment of impacts of nickel, nutrients, and oxygen level on structure and function of river biofilm communities. | studies were carried out to assess the influence of nutrients, dissolved oxygen (do) concentration, and nickel (ni) on river biofilm development, structure, function, and community composition. biofilms were cultivated in rotating annular reactors with river water at a do concentration of 0.5 or 7.5 mg liter(-1), with or without a combination of carbon, nitrogen, and phosphorus (cnp) and with or without ni at 0.5 mg liter(-1). the effects of ni were apparent in the elimination of cyanobacterial ... | 2004 | 15240316 |
| modular evolution of the integrase domain in the ty3/gypsy class of ltr retrotransposons. | a phylogenetic analysis of the ty3/gypsy group of retrotransposons identified a conserved domain (gpy/f) present in the integrases of several members of this group as well as of certain vertebrate retroviruses. the analysis suggested an evolutionary scheme for the acquisition and loss of the gpy/f domain as well as the acquisition of a chromodomain module in the integrase encoded by this group of elements that may direct targeting specificity in the host genome. | 1999 | 10233986 |