New approaches for isolation of previously uncultivated oral bacteria.

A significant number of microorganisms from the human oral cavity remain uncultivated. This is a major impediment to the study of human health since some of the uncultivated species may be involved in a variety of systemic diseases. We used a range of innovations previously developed to cultivate microorganisms from the human oral cavity, focusing on anaerobic species. These innovations include (i) in vivo cultivation to specifically enrich for species actively growing in the oral cavity (the "minitrap" method), (ii) single-cell long-term cultivation to minimize the effect of fast-growing microorganisms, and (iii) modifications of conventional enrichment techniques, using media that did not contain sugar, including glucose. To enable cultivation of obligate anaerobes, we maintained strict anaerobic conditions in most of our cultivation experiments. We report that, on a per cell basis, the most successful recovery was achieved using minitrap enrichment (11%), followed by single-cell cultivation (3%) and conventional plating (1%). Taxonomically, the richest collection was obtained using the single-cell cultivation method, followed by minitrap and conventional enrichment, comprising representatives of 13, 9, and 4 genera, respectively. Interestingly, no single species was isolated by all three methods, indicating method complementarity. An important result is the isolation and maintenance in pure culture of 10 strains previously only known by their molecular signatures, as well as representatives of what are likely to be three new microbial genera. We conclude that the ensemble of new methods we introduced will likely help close the gap between cultivated and uncultivated species from the human oral cavity.

Cellulose- and xylan-degrading thermophilic anaerobic bacteria from biocompost.

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S rRNA and glycosyl hydrolase family 48 (GH48) gene sequences revealed that two xylan-utilizing isolates were related to a Clostridium clariflavum strain and represent a distinct novel branch within the GH48 family. Both isolates possessed high cellulase and xylanase activity induced independently by either cellulose or xylan. Enzymatic activity decayed after growth cessation, with more-rapid disappearance of cellulase activity than of xylanase activity. A mixture of xylan and cellulose was utilized simultaneously, with a significant synergistic effect observed as a reduction of lag phase in cellulose degradation.

Biodegradation kinetics of the nitramine explosive CL-20 in soil and microbial cultures.

The cyclic nitramine explosive CL-20 (C(6)H(6)N(12)O(12), 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12 -hexaazaisowurtzitane) is a relatively new energetic compound which could be a persistent organic pollutant. To follow its biodegradation dynamics, CL-20 was added to soil alone or together with organic co-substrates and N-source and incubated under oxic and anoxic conditions. Without co-substrates, the CL-20 degradation was detectable only under anoxic conditions. The highest degradation rate was found under aerobic conditions and with the addition of co-substrates, succinate and pyruvate being more efficient than acetate, glucose, starch or yeast extract. When added to intact soil, CL-20 degradation was not affected by the N content, but in soil serially diluted with N-free succinate-mineral medium, the process became N-limited. About 40% of randomly selected bacterial colonies grown on succinate agar medium were able to decompose CL-20. Based on 16S rDNA gene sequence and cell morphology, they were affiliated to Pseudomonas, Rhodococcus, Ochrobactrum, Mycobacterium and Ralstonia. In the pure culture of Pseudomonas sp. MS-P grown on the succinate-mineral N(+) medium, the degradation kinetics were first order with the same apparent kinetic constant throughout growth and decline phases of the batch culture. The observed kinetics agreed with the model that supposes co-metabolic transformation of CL-20 uncoupled from cell growth, which can be carried out by several constitutive cellular enzymes with wide substrate specificity.

[Effect of culture conditions on growth and adhesion of Bacillus licheniformis]. / Rost and adgeziia Bacillus licheniformis v zavisimosti ot uslovii kul'tivirovaniia.

Adhesion to glass of actively growing cells of the thermophilic Bacillus licheniformis, isolated from the Medyaginskaya test borehole (Yaroslavl' oblast), was studied. The reversible adhesion (RA) manifests itself in a decline of cell density (short of cell lysis) in the liquid culture over the first 20-40 min of growth followed by normal exponential growth. The RA is minimal under favorable growth conditions but increases when cells are transferred to a new medium, especially one with a pH, temperature, salinity, or concentration of Ca2+ ions nonoptimal for the given species. Under unfavorable growth conditions, the adhesion becomes irreversible. The obtained data suggest that RA represents an adaptation mechanism important for population survival.

[Thermophilic bacterium Geobacillus uralicus growth is a function of temperature and pH: a synthetic chemostat model-based kinetic analysis ]. / Rost termofil'noi bakterii Geobacillus uralicus v zavisimosti ot temperatury i pH: kineticheskii analiz s ispol'zovaniem SKHM.

The synthetic chemostat model (SCM), originally developed to describe nonstationary growth under widely varying concentrations of the limiting substrate, was modified to account for the effects of nontrophic factors such as temperature and pH. The bacterium Geobacillus uralicus, isolated from an ultradeep well, was grown at temperatures ranging from 40 to 75 degrees C and at pH varying from 5 to 9. The biomass kinetics was reasonably well described by the SCM, including the phase of growth deceleration observed in the first hours after a change in the cultivation temperature. In an early stage of batch growth in a neutral or alkalescent medium, bacterial cells showed reversible attachment to the glass surface of the fermentation vessel. The temperature dependence of the maximum specific growth rate (micron) was fitted using the equation micron = Aexp(lambda T)/[1 + expB[1-C/(T + 273)]], where A, lambda, B, and C are constants. The maximum specific growth rate of 2.7 h-1 (generation time, 15.4 min) was attained on a complex nutrient medium (peptone and yeast extract) at 66.5 degrees C and pH 7.5. On a synthetic mineral medium with glucose, the specific growth rate declined to 1.2 h-1 and the optimal temperature for growth decreased to 62.3 degrees C.

[Growth and adhesion of Pseudomonas fluorescens in a batch culture: a kinetic analysis of the action of extracellular antiadhesins]. / Rost i adgeziia Pseudomonas fluorescens v periodicheskoi kul'ture: kineticheskii analiz deistviia vnekletochnykh antiadgezinov.

The work varifies 6 hypothetical models simulating the growth, respiration, and adhesion of cells to the walls of the cultivation flask. All the models postulate the synthesis of antiadhesins (AAs), i.e., extracellular metabolites decreasing the degree of cell adhesion. The models have the following distinguishing features: (model 1) the blocking of sorption centers on the glass walls by antiadhesins (the competitive inhibition of adhesion); (model 2) the noncompetitive inhibition of adhesion; (model 3) the accelerated release of bound cells; (model 4) a combination of models 1 and 3; (model 5) a combination of models 1 and 3 with a delay; (model 6) a combined action of two AAs, one of which, AA1, inhibits cell adhesion, and the other, AA2 (its synthesis is induced when the concentration of AA1 reaches a threshold level), stimulates the detachment of bound cells. Model 6 fits the relevant experimental data best. The delay effect is relatively small. The sigmoid character of the curve showing cell adhesion as a function of the antiadhesin concentration implies the existence of a strong cooperative effect in the adhesion inhibition. The models proposed satisfactorily simulate the growth, respiration, and adhesion of cells and AA synthesis in a batch bacterial culture grown either in a fresh nutrient medium or in the medium supplemented with the filtrate of a mature culture of the same species.

[Extracellular protease as a reversible adhesion regulator in Pseudomonas fluorescens]. / Vnekletochnaia proteaza kak reguliator obratimoi adgezii Pseudomonas fluorescens.

The investigation of growth dynamics and protein content in a batch Pseudomonas fluorescens culture grown in a synthetic medium with glucose as the sole source of carbon and energy showed that cells reversibly adhere to the walls of the cultivation flask during the first 2-3 h of growth. Over this time period, the total protein content of free and bound cells increased exponentially at a rate of 0.25 h-1, the fraction of proteins in cells being almost the same (60-70%). The protein content in the medium increased from 3 to 50 mg/l, reaching about 30% of the total protein of the culture. The addition of the exponential culture liquid filtrate to the medium together with the inoculum led to the complete inhibition of cell adhesion and a drastic activation of proteolysis, with a concurrent release of more than 80% of cellular proteins into the medium. After 3-5 h of growth, the concentration of extracellular proteins decreased to the control level. Exogenously added proteinase K inhibited cell adhesion, the effect being more pronounced for R-type than for S-type cells. The hypothesis is discussed that the short-term reversible adhesion of cells is regulated with the involvement of a mixture of hydrocarbons, which inactivate the functional activity of bacterial adhesins, and proteases, which digest these adhesins.

[Geobacillus uralicus, a new species of thermophilic bacteria]. / Geobacillus uralicus--novyi vid termofil'nykh bakterii.

The K2T strain of thermophilic spore-forming bacteria was isolated from a biofilm on the surface of a corroded pipeline in an extremely deep well (4680 m, 40-72 degrees C) in the Ural. The cells are rod-shaped, motile, gram-variable. They grow on a complex medium with tryptone and yeast extract and on a synthetic medium with glucose and mineral salts without additional growth factors. The cells use a wide range of organic substances as carbon and energy sources. They exhibit a respiratory metabolism but are also capable of anaerobic growth on a nitrate-containing medium and of fermentation. Growth occurs within the 40-75 degrees C temperature range (with an optimum of 65 degrees C) and at pH 5-9. The minimum generation time (15 min) was observed at pH 7.5. Ammonium salts and nitrates are used as nitrogen sources. The G + C content of the DNA is 54.5 mol%. From the morphological, physiological, and biochemical properties and the nucleotide sequence of the 16S rRNA gene, it was concluded that the isolate K2T represents a new species of the genus Geobacillus, Geobacillus uralicus.

[Nonlinearity in the growth of bacterial colonies: conditions and causes]. / Nelineinost' rosta bakterial'nykh kolonii: usloviia proiavleniia i prichiny.

The universally recognized kinetic model of colony growth, introduced by Pirt, predicts a linear increase of colony size. The linearity follows from the assumption that the colony expands through the growth of only such cells that are located immediately behind the moving colony front, in the so-called peripheral zone of constant width and density. In this work, Pirt's model was tested on two bacteria--Alcaligenes sp. and Pseudomonas fluorescens--having markedly distinct cultural properties and grown on agarized medium with pyruvate. The colony size dynamics was followed for different densities of the inoculum, ranging from a single cell to a microdroplet of bacterial suspension (10(5)-10(6) cells), and for different depths of the agar layer, determining the amount of available substrate. A linear growth mode was observed only with P. fluorescens and only in the case of growth from a microdroplet. When originating from a single cell, colonies of both organisms displayed nonlinear growth with a distinct peak of Kr (the rate of colony radius increase) occurring after 2-3 days of growth. The growth of P. fluorescens colonies showed virtually no dependence on the depth of the agarized medium, whereas the rate of colony size increase of Alcaligenes sp. turned out to be directly related to the medium layer thickness. The departure from linearity is consistently explained by a new kinetic chart stipulating a possible contribution to the colony growth not only of peripheral cells but also (much more distinct in Alcaligenes) of cells at the colony center. The colony growth dynamics is determined not only by the concentration of the limiting substrate but also by the amount of autoinhibitor, the synthesis of which is governed by age of cells. The distinctions of growth from a single cell and microdroplet could also originate as a result of dissociation into the R- and S-forms and competition between the corresponding subpopulations for oxygen and the common substrate.

[Saturated C21-C33 hydrocarbons are involved in the self-regulation of Pseudomonas fluorescens adhesion to a glass surface]. / Nasychshennye C21-C33 uglevodorody -- avtoreguliatory adgezii Pseudomonas fluorescens na stekle.

One of the two putative groups of antiadhesions was identified in Pseudomonas fluorescens by the method of gas chromatography-mass spectrometry. A mixture of high-molecular unbranched hydrocarbons (HC) with a chain length from 21 to 33 carbon atoms reduced cell adhesion to a glass surface. These HC accumulated in the culture liquid to a total concentration of 10-15 micrograms/l; the concentrations of individual HC ranged from 0.1 to 3.0 micrograms/l. After the addition of individual HC to the bacterial culture, the number of cells attached to the glass surface decreased. This decrease in cell adhesion was due to the enhanced aggregation of the bacterial cells, which promoted mechanical (hydrodynamic) cell detachment from the surface.

[Yeast biodiversity in hydromorphic soils with reference to grass-Sphagnum swamp in Western Siberia and the hammocky tundra region( Barrow, Alaska)]. / Bioraznoobrazie drozzhei v gidromorfnykh pochvakh na primere traviano-sfagnovogo bolota (zapadnaia Sibir') i kochkarnoi tundry (Barrow, Aliaska).

The microbiological analysis of 78 samples taken from a boreal bog in Western Siberia and from a tundra wetland soil in Alaska showed the presence of 23 yeast species belonging to the genera Bullera, Candida, Cryptococcus, Debaryomyces, Hanseniaspora, Metschnikowia, Mrakia, Pichia, Rhodotorula, Saccharomyces, Sporobolomyces, Torulaspora, and Trichosporon. Peat samples from the boreal bog were dominated by eurytopic anamorphic basidiomycetous species, such as Rhodotorula mucilaginosa and Sporobolomyces roseus, and by the ascomycetous yeasts Candida spp. and Debaryomyces hansenii. These samples also contained two rare ascomycetous species (Candida paludigena and Schizoblastosporion starkeyi-henricii), which so far have been found only in taiga wetland soils. The wetland Alaskan soil was dominated by one yeast species (Cryptococcus gilvescens), which is a typical inhabitant of tundra soils. Therefore, geographic factors may serve for a more reliable prediction of yeast diversity in soils than the physicochemical or ecotopic parameters of these soils.

Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.

A new genus, Methylocella, and a new species, Methylocella palustris, are proposed for three strains of methane-oxidizing bacteria isolated from acidic Sphagnum peat bogs. These bacteria are aerobic, Gram-negative, colourless, non-motile, straight and curved rods that utilize the serine pathway for carbon assimilation, multiply by normal cell division and contain intracellular poly-beta-hydroxybutyrate granules (one at each pole). These strains use methane and methanol as sole sources of carbon and energy and are moderately acidophilic organisms with growth between pH 4.5 and pH 7.0, the optimum being at pH 5.0-5.5. The temperature range for growth is 10-28 degrees C with the optimum at 15-20 degrees C. The intracytoplasmic membrane system is different from those of type I and II methanotrophs. Cells contain an extensive periplasmic space and a vesicular membrane system connected to the cytoplasmic membrane. The strains grew only on media with a low salt content (0.2-0.5 g l(-1)). All three strains were found to possess soluble methane monooxygenase and are able to fix atmospheric nitrogen via an oxygen-sensitive nitrogenase. No products were observed in a PCR with particulate methane monooxygenase-targeted primers; hybridization with a pmoA probe was also negative. The major phospholipid fatty acids are 18:1 acids. The G+C content of the DNA is 61.2 mol%. The three strains share identical 16S rRNA gene sequences and represent a novel lineage of methane-oxidizing bacteria within the alpha-subclass of the class Proteobacteria and are only moderately related to type II methanotrophs of the Methylocystis-Methylosinus group. The three strains are most closely related to the acidophilic heterotrophic bacterium Beijerinckia indica subsp. indica (96.5% 16S rDNA sequence similarity). Collectively, these strains comprise a new species and genus Methylocella palustris gen. nov., sp. nov.; strain KT (= ATCC 700799T) is the type strain.

[Extracellular factors of adaptation of Pneudomonas fluorescens batch cultures to adverse conditions]. / Vnekletochnye faktory adaptatsii k neblagopriiatnym usloviiam sredy v periodicheskoi kul'ture Pseudomonas fluorescens.

The culture liquid filtrate of an exponential-phase Pseudomonas fluorescens batch culture added to another P. fluorescens culture at the moment of inoculation was found (1) to prevent or diminish cell adsorption of the flask walls; (2) to enhance the intensity of cell respiration; (3) to shorten the period of adaptation of LB-grown cells to growth in glucose-containing mineral M9 medium; (4) to stimulate bacterial growth at supraoptimum temperature (36 degrees C) and pH values (4.8 and 9.2); and (5) to decrease the death rate of bacteria at the supraoptimum growth temperature. These results were interpreted as indicating that P. fluorescens cultures produce two types of regulatory exometabolites similar to those revealed earlier in Escherichia coli and Bacillus subtilis cultures: the direct-action adaptogenic factor XI capable of increasing bacterial resistance to unfavorable growth conditions (temperature and pH) and factor promoting adaptation to new media. Both factors are presumably low-molecular-weight hydrophilic nonprotein compounds.

Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands.

Acidic northern wetlands are an important source of methane, one of the gases that contributes to global warming. Methane oxidation in the surface of these acidic wetlands can reduce the methane flux to the atmosphere up to 90 percent. Here the isolation of three methanotrophic microorganisms from three boreal forest sites is reported. They are moderately acidophilic organisms and have a soluble methane monooxygenase. In contrast to the known groups of methanotrophs, 16S ribosomal DNA sequence analysis shows that they are affiliated with the acidophilic heterotrophic bacterium Beijerinckia indica subsp. indica.

[Simplified model of increase in colony diameter during growth of unicellular microorganisms and its use in evaluating the effect of biocides on microbial cells]. / Uproshchennaia model' rosta diametra kolonii odnokletochnykh mikroorganizmov i ee ispol'zovanie dlia otsenki vozdeistviia biotsidov na mikrobnye kletki.

A simplified model of increase in colony diameter is proposed. The model uses the size of single cells and several measurements of colony diameter during linear growth for calculating with good approximation the growth curve for the culture from the moment of inoculation. The parameter mu(m)', which is approximately 10% lower than the maximum specific growth rate of the colony biomass, could be also calculated. The effect of copper sulfate on the colony growth of Pseudomonas sp. G-1 was studied using the model. A high concentration of Cu2+ ions was found to result in decreases in the value of mu(m)', colony diameter, and the rate of increase in the colony diameter.

Acidophilic methanotrophic communities from Sphagnum peat bogs.

Highly enriched methanotrophic communities (> 25 serial transfers) were obtained from acidic ombrotrophic peat bogs from four boreal forest sites. The enrichment strategy involved using media conditions that were associated with the highest rates of methane uptake by the original peat samples, namely, the use of diluted mineral medium of low buffering capacity, moderate incubation temperature (20 degrees C), and pH values of 3 to 6. Enriched communities contained a mixture of rod-shaped bacteria arranged in aggregates with a minor contribution of Hyphomicrobium-like cells. The growth stoichiometry of isolates was characteristic of methanotrophic bacteria (CH4/O2/CO2 = 1:1.1:0.59), with an average apparent yield of 0.41 +/- 0.03 g of biomass C/g of CH4-C. DNA from each enrichment yielded a PCR product of the expected size with primers for both mmoX and mmoY genes of soluble methane monooxygenase. Two types of sequences were obtained for PCR-amplified fragments of mmoX. One of them exhibited high identity to the mmoX protein of the Methylocystis-Methylosinus group, whereas the other showed an equal level of divergence from both the Methylosinus-Methylocystis group and Methylococcus capsulatus (Bath) and formed a distinct branch. The pH optimum for growth and for CH4 uptake was 4.5 to 5.5, which is very similar to that for the optimum CH4 uptake observed in the original peat samples. These methanotrophs are moderate acidophiles rather than acidotolerant organisms, since their growth rate and methane uptake were much lower at neutral pH. The growth of the methanotrophic community was enhanced by using media with a very low salt content (20 to 200 mg/liter), more typical of their natural environment. All four enriched communities grew on N-free medium.

[Growth and substrate utilization by bacterial lawn on the agar surface: experiment and one-dimensional distributed model]. / Rost i potreblenie substrata bakterial'nym gazonom na poverkhnosti agara: éksperiment i odnomernaia raspredelennaia model'.

Cell mass dynamics of the lawns formed by Pseudomonas fluorescens and Alcaligenes sp. and the distribution profiles of the residual substrate in the agar layer were monitored. After one or two days of culturing, the concentration of pyruvate in the top agar layer adjacent to the lawn dropped below the level of detection, and, from this moment, the substrate was supplied to the lawn by diffusion from underlying agar layers. Diffusion of pyruvate in noninoculated bilayered agar was found to follow Fick's equation with the diffusion coefficient of 0.042 cm2/h. A distributed mathematical model adequately describing the growth of bacterial lawn was developed based on the diffusion equation and the Monod-Herbert kinetic model. Notable distinctions between the two cultures studied were revealed: pseudomonads had higher growth and death rates than Alcaligenes sp. and exhibited a greater affinity for the substrate.

[Biotransformation of nitrogen-containing compounds in the process of the continuous final purification of effluents from swine-breeding farms by immobilized cells]. / Biotransformatsiia azotsoderzhashchikh soedinenii v protsesse neprepyvnoi doochistki stokov svinokompleksov immobilizovannymi kletkami.

After their two-step purification in aeration tanks, effluents from a swine-breeding farm were subjected to final purification in a flow bioreactor with immobilized cells derived from activated sludge. The dynamics of nitrogen compounds were studied at the reactor inlet and outlet at three flow rates. The use of a simple mathematical model of the nitrogen balance allowed the rates of nitrogen assimilation-mineralization two nitrification stages, and nitrogen fixation-denitrification to be estimated. The first stage of nitrification was found to proceed intensely and produce high nitrite concentrations (up to 100 mg N/l, accounting for about half of the total N at the inlet). The second nitrification stage was inhibited, and nitrate was only produced after 3-4 weeks of continuous operation. The strategy of the final purification of effluents from nitrogen compounds is discussed on the basis of the known regulatory mechanisms of microbial activities in activated sludge.

[Growth and spore formation of Bacillus subtilis in periodic and dialysis cultured: experiment and modeling]. / Rost i sporobrazovanie Bacillus subtilis v periodicheskoi i dializnoi kul'turakh: éksperiment i modelirovanie.

The transition of bacilli to maintenance state in dialysis culture was revealed. The maintenance state is characterized by the lack of growth and spore formation. The experimental results are satisfactorily described by a modification of the synthetic chemostat model. As a results of model realization it was supposed that maintenance state of bacilli was connected with synthesis of autoinhibitor and initiation of spore formation.