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At least 127 records · Page 7Linked to original sources
PubMed1999

Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology.

A new microscopic method for simultaneously determining in situ the identities, activities, and specific substrate uptake profiles of individual bacterial cells within complex microbial communities was developed by combining fluorescent in situ hybridization (FISH) performed with rRNA-targeted oligonucleotide probes and microautoradiography. This method was evaluated by using defined artificial mixtures of Escherichia coli and Herpetosiphon aurantiacus under aerobic incubation conditions with added [3H]glucose. Subsequently, we were able to demonstrate the potential of this method by visualizing the uptake of organic and inorganic radiolabeled substrates ([14C]acetate, [14C]butyrate, [14C]bicarbonate, and 33Pi) in probe-defined populations from complex activated sludge microbial communities by using aerobic incubation conditions and anaerobic incubation conditions (with and without nitrate). For both defined cell mixtures and activated sludge, the method proved to be useful for simultaneous identification and analysis of the uptake of labeled substrates under the different experimental conditions used. Optimal results were obtained when fluorescently labeled oligonucleotides were applied prior to the microautoradiographic developing procedure. For single-cell resolution of FISH and microautoradiographic signals within activated sludge flocs, cryosectioned sample material was examined with a confocal laser scanning microscope. The combination of in situ rRNA hybridization techniques, cryosectioning, microautoradiography, and confocal laser scanning microscopy provides a unique opportunity for obtaining cultivation-independent insights into the structure and function of bacterial communities.

Aerobiosis↗
PubMed2000

Cyanobacterial-bacterial mat consortia: examining the functional unit of microbial survival and growth in extreme environments.

Cyanobacterial-bacterial consortial associations are taxonomically complex, metabolically interactive, self-sustaining prokaryotic communities representing pioneer and often the only biota inhabiting extreme aquatic and terrestrial environments. Laminated mats and aggregates exemplify such communities. The fossil record indicates that these associations represent the earliest extant inhabitants and modifiers (i.e. anoxic to oxic conditions) of the Earth's biosphere. Present-day consortia flourish in physically and chemically stressed environments, including nutrient-deplete, hypersaline, calcified, desiccated and high-irradiance ecosystems ranging from the tropics to polar regions. Consortial members exhibit extensive metabolic diversification, but have remained structurally simple. Structural simplicity, while advantageous in countering environmental extremes, presents a 'packaging problem' with regard to compartmentalizing potentially cross-inhibitory aerobic versus anaerobic growth processes. To circumvent these metabolic constraints, phototrophic cyanobacteria and microheterotrophs orient along microscale chemical (i.e. O2, pH, Eh) gradients to meet and optimize the biogeochemical processes (C, N, S cycling) essential for survival, growth and the maintenance of genetic diversity, needed to sustain life. Microscale ecophysiological, analytical, molecular (immunological and nucleic acid) techniques have helped to develop a mechanistic basis for understanding consortial growth and survival under extreme environmental conditions on Earth. Consortia are ideal model systems for developing a process-based understanding of the structural and functional requirements for life in extreme environments representative of the Earth's earliest biosphere and possibly other planets.

Adaptation, Physiological↗
PubMed1999

Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens.

In 1993, the WHO declared tuberculosis a global emergency on the basis that there are 8 million new cases per year. The complete genome of the strain H37Rv of the causative microorganism, Mycobacterium tuberculosis, comprising 3924 genes has been sequenced. We compared the proteomes of two non-virulent vaccine strains of M. bovis BCG (Chicago and Copenhagen) with two virulent strains of M. tuberculosis (H37Rv and Erdman) to identify protein candidates of value for the development of vaccines, diagnostics and therapeutics. The mycobacterial strains were analysed by two-dimensional electrophoresis (2-DE) combining non-equilibrium pH gradient electrophoresis (NEPHGE) with SDS-PAGE. Distinct and characteristic proteins were identified by mass spectrometry and introduced into a dynamic 2-DE database (http://www.mpiib-berlin.mpg.de/2D-PAGE). Silver-stained 2-DE patterns of mycobacterial cell proteins or culture supernatants contained 1800 or 800 spots, respectively, from which 263 were identified. Of these, 54 belong to the culture supernatant. Sixteen and 25 proteins differing in intensity or position between M. tuberculosis H37Rv and Erdman, and H37Rv and M. bovis BCG Chicago, respectively, were identified and categorized into protein classes. It is to be hoped that the availability of the mycobacterial proteome will facilitate the design of novel measures for prevention and therapy of one of the great health threats, tuberculosis.

Bacterial Proteins↗
PubMed2002

Functional analysis of microbial communities in aerobic-anaerobic sequencing batch reactors fed with different phosphorus/carbon (P/C) ratios.

Fluorescence in situ hybridization (FISH) was used to analyse the community composition of a sequencing batch reactor (SBR) operating with aerobic-anaerobic cycling and fed acetate as its sole carbon source. Phosphorus was removed from the SBR microbiologically. Marked shifts in the community structure occurred as the phosphorus/carbon (P/C) ratio in the feed was changed. When the P/C ratio was shifted from 1:10 to 1:50, FISH analysis showed that the percentage of beta-Proteobacteria fell from ca 77% of the total bacteria to ca 38%. This decrease in the beta-Proteobacteria coincided with a reduction in both the proportions of the beta-proteobacterial Rhodocyclus-related phosphorus-accumulating bacteria and the biomass phosphorus content. FISH/microautoradiography and FISH/poly beta-hydroxyalkanoate (PHA) staining showed that the Rhodocyclus-related bacteria assimilated acetate and synthesized PHAs anaerobically, and that they accumulated phosphorus aerobically. No Acinetobacter spp. could be detected in any of the communities, casting further doubt on their role in phosphorus-removing activated sludge systems. As the feed P/C ratio decreased there was a corresponding increase in the proportion of alpha-Proteobacteria and, to a smaller extent, in the proportion of gamma-Proteobacteria; both the alpha- and gamma-Proteobacteria consisted mostly of tetrad-forming cocci, fitting the description of the so-called 'G-bacteria' morphotype. The change in the proportions of Proteobacteria present paralleled increases in the biomass glycogen content. Both the alpha- and beta-proteobacterial 'G-bacterial' populations assimilated acetate and synthesized PHA anaerobically. The alpha-Proteobacteria are considered responsible for glycogen production in these SBR systems.

Bacteria, Aerobic↗
PubMed1992

Effect of microbial fermentation on functional specific gravity of small forage particles.

Two experiments were designed to determine the effect of gas production during in vitro digestion on functional specific gravity (FSG) of forage particles. In Exp. 1, FSG of ground alfalfa hay decreased from 1.123 to 1.049 between 3 and 9 h of incubation and increased thereafter to reach a plateau at 1.309 after 30 h of incubation. Gas production peaked at 6 h, but gas associated with particles increased until 9 h of incubation. Gas associated with solid residue was correlated to gas production (r = -.67) but also was influenced by gas holding capacity and rate of escape from the particles. In Exp. 2, measurements were performed on ground alfalfa hay, alfalfa silage, and bromegrass hay containing 42.6, 35, and 66.4% NDF, respectively. Gas production seemed to be related to the amount of readily available substrate. Although at 9 h of incubation more gas was produced by alfalfa silage (.235 mL.min-1.g of DM-1) than by bromegrass hay and alfalfa hay (.087 and .187 mL.min-1.g of DM-1, respectively), gas associated with particles was greater for alfalfa hay (.416 mL/g of DM) than for bromegrass hay and alfalfa silage (.256 and .281 mL/g of DM, respectively). The increase in FSG was more rapid for alfalfa silage than for the hays. After 27 h of digestion, gas associated with particles (milliliters per gram of DM) and FSG were .164, 1.226; .147, 1.235; and .001, 1.467 for bromegrass hay, alfalfa hay, and alfalfa silage, respectively. Gas produced during fermentation delayed the increase in specific gravity of forage particles.(ABSTRACT TRUNCATED AT 250 WORDS)

Animal Feed↗
PubMedDate not supplied

[Peculiarities of structure-function organization of microbial groups of soil contaminated by cement dust].

Long-term contamination of the forest soil by the cement dust leads to disturbances of stability of natural microbial groups, changes their quantitative and qualitative composition, results in substitution of some microbial associations by other ones. The intensive contamination of the soil by the effluents of cement integrated works, inhibits the intensity of nitrogen fixation processes and decay of the forest litter, development of micromycetes, results in the decrease of the length of mycelium and its biomass.

Bacteria↗
PubMed2003

Microbial and physiological characterization of weakly amylolytic but fast-growing lactic acid bacteria: a functional role in supporting microbial diversity in pozol, a Mexican fermented maize beverage.

Pozol is an acid beverage obtained from the natural fermentation of nixtamal (heat- and alkali-treated maize) dough. The concentration of mono- and disaccharides from maize is reduced during nixtamalization, so that starch is the main carbohydrate available for lactic acid fermentation. In order to provide some basis to understand the role of amylolytic lactic acid bacteria (ALAB) in this fermented food, their diversity and physiological characteristics were determined. Forty amylolytic strains were characterized by phenotypic and molecular taxonomic methods. Four different biotypes were distinguished via ribotyping; Streptococcus bovis strains were found to be predominant. Streptococcus macedonicus, Lactococcus lactis, and Enterococcus sulfureus strains were also identified. S. bovis strain 25124 showed extremely low amylase yield relative to biomass (139 U g [cell dry weight](-1)) and specific rate of amylase production (130.7 U g [cell dry weight](-1) h(-1)). In contrast, it showed a high specific growth rate (0.94 h(-1)) and an efficient energy conversion yield to bacterial cell biomass (0.31 g of biomass g of substrate(-1)). These would confer on the strain a competitive advantage and are the possible reasons for its dominance. Transient accumulation of maltooligosaccharides during fermentation could presumably serve as energy sources for nonamylolytic species in pozol fermentation. This would explain the observed diversity and the dominance of nonamylolytic lactic acid bacteria at the end of fermentation. These results are the first step to understanding the importance of ALAB during pozol fermentation.

Beverages↗
PubMed2003

A(r)Ray of hope in analysis of the function and diversity of microbial communities.

The vast majority of microorganisms in the environment remain uncultured, and their existence is known only from sequences retrieved by PCR. As a consequence, our understanding of the ecological function of dominant microbial populations in the environment is limited. We will review microbial diversity studies and show that these may have moved from an extreme underestimation to a potentially severe overestimation of diversity. The latter results from a simple PCR-generated artifact: the cloning of heteroduplex molecules followed by Escherichia coli mismatch repair, which may generate an exponential increase in observed sequence diversity. However, simple modifications to current PCR amplification protocols minimize such artifactual sequences and may bring within our reach estimation of bacterial diversity in environmental samples. Such estimates may spur new culture-independent approaches based on genomic and microarray technology, allowing correlation of phylogenetic identity with the ecological function of unculturable organisms. In particular, we are developing a DNA microarray that enables identification of individual populations active in utilization of specific organic substrates. The array consists of 16S and 23S rDNA-targeted oligonucleotides and is hybridized to RNA extracted from samples incubated with (14)C-labeled organic substrates. Populations that metabolize the substrate can be identified by the radiolabel incorporated in their rRNA after only one to two cell doublings, ensuring realistic preservation of community structure. Thus, the microarray approach may provide a powerful means to link microbial community structure with in situ function of individual populations.

Bacterial Physiological Phenomena↗
PubMedDate not supplied

Microbial pathway prediction: a functional group approach.

We have developed a system to predict microbial catabolism, using the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) as a knowledge base. The present system, available on the Web (http://umbbd.ahc.umn.edu/predict/), can predict biodegradation of most of the major aliphatic and aromatic organic functional groups containing C, H, N, O, and halogens. It can duplicate at least one known biodegradation pathway for 60% of the compounds in a 84-member validation set; most pathways that did not completely duplicate known metabolism could plausibly occur in nature. Users are encouraged, and have begun, to submit additional biotransformation rules and comment on existing rules; the system will further develop under the direction of the scientific community.

Biodegradation, Environmental↗
PubMed1986

Ruminal evacuation's effect on microbial activity and ruminal function.

The influence of evacuating, mixing and returning ruminal contents on microbial populations, volatile fatty acid (VFA) concentrations and liquid flow rate was investigated with four ruminal-cannulated Hereford steers (247 kg avg wt). Ruminoreticular contents were sampled, then completely removed, mixed for 5 min and returned to the rumen. Subsequent samples were taken immediately, 1 h and 4 h later. Non-evacuated steers were sampled at identical time intervals either 1 d before or after evacuation. Averaged over time, there was no significant difference between evacuated and non-evacuated steers in total anaerobic, cellulolytic and facultative bacteria, protozoa, oxidation-reduction potential, VFA concentrations, and liquid flow rates. There were no treatment X time interactions and, except for holotrich protozoa and VFA, no differences from time of sampling. Ruminal evacuation does not appear disruptive to anaerobiosis or detrimental to ruminal microorganisms and digestive processes.

Animals↗
PubMed1987

Establishment of a biochemically active intestinal ecosystem in ex-germfree rats.

A time course study for the establishment of some biochemical microbial intestinal functions was undertaken in ex-germfree rats conventionalized, i.e., colonized with conventional flora, in three different ways: untreated (group 1); contact with visitor rats (group 2); inoculated with intestinal contents from conventional rats (group 3). The first two groups of rats were inoculated with the intestinal contents from conventional rats after being out of the germfree isolators for 4 weeks. The biochemical parameters studied were degradation of mucin, inactivation of tryptic activity, conversion of cholesterol to coprostanol and of bilirubin to urobilinogen, degradation of beta-aspartylglycine, and formation of short-chain fatty acids. The results showed that the way in which the microbes were introduced and the microbial biochemical functions themselves were of importance. In several cases, social contacts, i.e., contact with visitor rats, were just as effective for the functionally adequate establishment of microbial intestinal functions as was inoculation with intestinal contents from conventional rats. Some of the biochemical parameters studied were established after a few days, whereas the establishment of others was markedly delayed. When inoculated after 4 weeks, all rats in the first two groups were colonized with conventional flora within 1 week. The results indicate that the model system described is suitable when studying buildup mechanisms in intestinal ecosystem(s).

Animals↗
PubMed2026

Long-Term Warming Reduces Bacterial Diversity and Functional Potential in Temperate Forest Soil.

Soil microbes are key regulators of forest carbon cycling, yet how their diversity and functional potential respond to long-term warming remains poorly understood. Here, we report a five-year in situ warming experiment in a temperate forest, combining ten repeated measurements of microbial diversity and functional gene potential, as well as continuous monitoring of soil CO2 flux. We found that warming progressively reduced bacterial diversity and induced phylogenetically conserved community reorganization. Under warming, community composition shifted in a phylogenetically conserved manner. Warming generally reduced the abundance of microbial functional genes across most carbon-, nitrogen-, and phosphorus-cycling gene categories, except for genes associated with starch decomposition. Warming also altered the factors associated with soil CO2 flux: microbial diversity showed a stronger association with soil CO2 flux under long-term warming, whereas soil moisture was the dominant predictor in the control treatment. This warming-enhanced biodiversity control over soil CO2 flux was associated with shifts in microbial functional potential, particularly increases in starch-degrading genes and microbial biomass production potential. Together, our results suggest that warming can restructure microbial communities in ways that strengthen biodiversity-dependent regulation of soil carbon cycling, with implications for climate-carbon feedbacks.

Soil Microbiology↗