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At least 307 records · Page 17Linked to original sources
PubMed2001

Long term adaptation of a microbial population to a permanent metabolic constraint: overcoming thymineless death by experimental evolution of Escherichia coli.

BACKGROUND: To maintain populations of microbial cells under controlled conditions of growth and environment for an indefinite duration is a prerequisite for experimentally evolving natural isolates of wild-type species or recombinant strains. This goal is beyond the scope of current continuous culture apparatus because these devices positively select mutants that evade dilution, primarily through attachment to vessel surfaces, resulting in persistent sub-populations of uncontrollable size and growth rate. RESULTS: To overcome this drawback, a device with two growth chambers periodically undergoing transient phases of sterilization was designed. The robustness of this device was assessed by propagating an E. coli strain under permanent thymine starvation for over 880 days, i.e. metabolic conditions notoriously known to lead to cell death and clogging of cultivation vessels. Ten thousand generations were required to obtain a descendant lineage that could resist thymine starvation and had recovered wild-type growth rate. CONCLUSIONS: This approach provides a technological framework for the diversification and improvement of microbial strains by long-term adaptation to inescapable metabolic constraints. An E. coli strain that is totally resistant to thymineless death was selected.

Adaptation, Physiological↗
PubMed2006

The co-evolution of host cationic antimicrobial peptides and microbial resistance.

Endogenous cationic antimicrobial peptides (CAMPs) are among the most ancient and efficient components of host defence. It is somewhat of an enigma that bacteria have not developed highly effective CAMP-resistance mechanisms, such as those that inhibit many therapeutic antibiotics. Here, we propose that CAMPs and CAMP-resistance mechanisms have co-evolved, leading to a transient host-pathogen balance that has shaped the existing CAMP repertoire. Elucidating the underlying principles of this process could help in the development of more sustainable antibiotics.

Animals↗
PubMed2000

Measurement of heat evolution and correlation with oxygen consumption during microbial growth. Reprinted from Biotechnology and Bioengineering, Vol. XI, Issue 3, Pages 269-281 (1968).

A procedure for measuring the rate of heat production from a fermentation has been developed. The method is based on measuring the rate of temperature rise of the fermentation broth resulting from metabolism, when the temperature controller is turned off. The heat accumulation measured in this manner is then corrected for heat losses and gains. A sensitive thermistor is used to follow the temperature rise with time. This procedure is shown to be as accurate as previous methods but much simpler in execution. Using this technique, the rate of heat production during metabolism was found to correlate with the rate of oxygen consumption. Experiments were performed using bacteria (E. coli and B. subtilis), a yeast (C. intermedia), and a mold (A. niger). The substrates investigated included glucose, molasses, and soy bean meal. The proportionality constant for the correlation is independent of the growth rate, slightly dependent on the substrate, and possibly dependent on the type of organism growth. This correlation has considerable potential for predicting heat evolution from the metabolism of microorganisms on simple or complex substrates and providing quantitative parameters necessary for heat removal calculations.

Aspergillus niger↗
PubMed2007

Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution.

New questions about microbial ecology and diversity combined with significant improvement in the resolving power of molecular tools have helped the reemergence of the field of prokaryotic biogeography. Here, we show that biogeography may constitute a cornerstone approach to study diversity patterns at different taxonomic levels in the prokaryotic world. Fundamental processes leading to the formation of biogeographic patterns are examined in an evolutionary and ecological context. Based on different evolutionary scenarios, biogeographic patterns are thus posited to consist of dramatic range expansion or regression events that would be the results of evolutionary and ecological forces at play at the genotype level. The deterministic or random nature of those underlying processes is, however, questioned in light of recent surveys. Such scenarios led us to predict the existence of particular genes whose presence or polymorphism would be associated with cosmopolitan taxa. Furthermore, several conceptual and methodological pitfalls that could hamper future developments of the field are identified, and future approaches and new lines of investigation are suggested.

Archaea↗
PubMed2006

Effects of soil storage on the microbial community and degradation of metsulfuron-methyl.

The effect storage had on the microbial biomass in two soils (Trevino and Fargo) was compared to the effect storage had on each soil's capacity to degrade metsulfuron-methyl. Soils were collected from the field and used fresh (<3 weeks old) or stored at 20 and 4 degrees C for 3 or 6 months. The phospholipid fatty acid content of the soils was used to monitor changes in the microbial biomass during storage and incubation in a flow-through apparatus. In both soils, [phenyl-U-14C]metsulfuron-methyl was used to monitor changes in the route and rate of degradation along with 14CO2 evolution (mineralization). Total microbial biomasses in both soils were significantly reduced for soils incubated in the flow-through apparatus, whereas only the Trevino soil's microbial biomass was significantly reduced as a result of storage. The microbial communities of both soils were significantly different as a result of storage as shown by discriminant analysis. In both soils, degradation rate, pathway of degradation, and mineralization of metsulfuron-methyl were significantly affected by storage compared to fresh soil. The half-life of metsulfuron-methyl increased significantly (P < 0.05) in the Trevino soil from 45 days (fresh) to 63 days (stored soil), whereas in the Fargo soil half-lives increased significantly (P < 0.05) from 23 days (fresh) to 29 days (soils stored for 6 months). In both soils, mineralization of [14C]metsulfuron-methyl was significantly (P < 0.05) higher in fresh soils compared to stored soils. The degradation pathways of metsulfuron-methyl changed with storage as evidenced by the loss of formation of one biologically derived metabolite (degradate) in stored soils compared to fresh soils.

Arylsulfonates↗
PubMed2002

Microbial population genomics and ecology.

The origins of biological complexity in microbial ecosystems are encoded within the collective genomes of the community. Cultivation-independent genomic studies provide direct access to the genomes of naturally occurring microbes, cultivated or not. Genome-enabled approaches are now significantly advancing current knowledge of genome content, diversity, population biology and evolution in natural microbial populations.

Ecology↗
PubMed2004

Infectious diseases in the 21st century: old challenges and new opportunities.

Infectious diseases are the confrontation of two worlds, the microbial world and the world of human physiology. Although these two worlds are as a whole governed by the same laws of nature, they show substantial differences: the microbiological world is 1000 times older, and was initiated by the development of the archaea, the 'living organisms of the extreme': its biomass and its diversity are immense - two to three billion species or 60% of the total biomass of the planet. The number of pathogens that adapted to man, however, is extremely limited - barely 1000. Thus, over billions of years, an evolution of the microbial world took place from 'early life', characterized by chemosynthesis, to the 'modern pathogens', and entailed a dramatic 'concentration' of life conditions and an adaptation towards a narrow range of requirements - those allowing survival in the human body. Within the last two centuries, these two slowly evolving systems, microbial life and human life, were profoundly modified in an unprecedented manner by a third player, human civilization, with its global impact on the environment through physical, chemical, societal, and climatic determinants. An appreciation of the evolution of infectious diseases in the 21st century and of the development of new diagnostic and therapeutic strategies therefore requires a full understanding of these three domains: human physiology, microbiology, and the environment. This review will put major emphasis on the environmental role of civilization on infectious diseases before considering new opportunities to combat them through novel and creative solutions.

Civilization↗
PubMed2003

Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation.

Genomic markers for anaerobic microbial processes in marine sediments-sulfate reduction, methanogenesis, and anaerobic methane oxidation-reveal the structure of sulfate-reducing, methanogenic, and methane-oxidizing microbial communities (including uncultured members); they allow inferences about the evolution of these ancient microbial pathways; and they open genomic windows into extreme microbial habitats, such as deep subsurface sediments and hydrothermal vents, that are analogs for the early Earth and for extraterrestrial microbiota.

Bacteria, Anaerobic↗
PubMed2002

Crystal structure of microbial transglutaminase from Streptoverticillium mobaraense.

The crystal structure of a microbial transglutaminase from Streptoverticillium mobaraense has been determined at 2.4 A resolution. The protein folds into a plate-like shape, and has one deep cleft at the edge of the molecule. Its overall structure is completely different from that of the factor XIII-like transglutaminase, which possesses a cysteine protease-like catalytic triad. The catalytic residue, Cys(64), exists at the bottom of the cleft. Asp(255) resides at the position nearest to Cys(64) and is also adjacent to His(274). Interestingly, Cys(64), Asp(255), and His(274) superimpose well on the catalytic triad "Cys-His-Asp" of the factor XIII-like transglutaminase, in this order. The secondary structure frameworks around these residues are also similar to each other. These results imply that both transglutaminases are related by convergent evolution; however, the microbial transglutaminase has developed a novel catalytic mechanism specialized for the cross-linking reaction. The structure accounts well for the catalytic mechanism, in which Asp(255) is considered to be enzymatically essential, as well as for the causes of the higher reaction rate, the broader substrate specificity, and the lower deamidation activity of this enzyme.

Amino Acid Sequence↗
PubMed1998

Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces.

We examined the distributions of short tandemly repeated DNAs (microsatellites) in nine complete microbial genomes (Saccharomyces cerevisiae, Archaeoglobus fulgidus, Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Methanococcus jannaschii, Mycoplasma pneumoniae, M. genitalium, and Synechocystis PCC6803.) These repeats contribute differently to the global features of these genomes, and we explore the evolutionary implications of these differences by empirical examination of length polymorphisms at 20 long triplet-repeats repeats in S. cerevisiae, and by comparison of observed and expected repeat distributions. All of a sample of 20 microsatellites found in S. cerevisiae are highly polymorphic in length, suggesting that mutation pressure overcomes overall selection for small genome size that will tend to shorten or eliminate unnecessary DNA. By comparison, prokaryotes have fewer long repeats than expected, except for a few statistically improbable repeats that appear to function in gene regulation. Finally, we find that in all these genomes there is an excess of repeats shorter than those traditionally considered to be microsatellites. This finding suggests that even in prokaryotes these repeats are being generated by mutational pressures. These results have important potential implications for understanding genome stability and evolution in these microbial species.

Bacteria↗
PubMed2000

The evolutionary physiology of animal flight: paleobiological and present perspectives.

Recent geophysical analyses suggest the presence of a late Paleozoic oxygen pulse beginning in the late Devonian and continuing through to the late Carboniferous. During this period, plant terrestrialization and global carbon deposition resulted in a dramatic increase in atmospheric oxygen levels, ultimately yielding concentrations potentially as high as 35% relative to the contemporary value of 21%. Such hyperoxia of the late Paleozoic atmosphere may have physiologically facilitated the initial evolution of insect flight metabolism. Widespread gigantism in late Paleozoic insects and other arthropods is also consistent with enhanced oxygen flux within diffusion-limited tracheal systems. Because total atmospheric pressure increases with increased oxygen partial pressure, concurrently hyperdense conditions would have augmented aerodynamic force production in early forms of flying insects. By the late Permian, evolution of decompositional microbial and fungal communities, together with disequilibrium in rates of carbon deposition, gradually reduced oxygen concentrations to values possibly as low as 15%. The disappearance of giant insects by the end of the Permian is consistent with extinction of these taxa for reasons of asphyxiation on a geological time scale. As with winged insects, the multiple historical origins of vertebrate flight in the late Jurassic and Cretaceous correlate temporally with periods of elevated atmospheric oxygen. Much discussion of flight performance in Archaeopteryx assumes a contemporary atmospheric composition. Elevated oxygen levels in the mid- to late Mesozoic would, however, have facilitated aerodynamic force production and enhanced muscle power output for ancestral birds, as well as for precursors to bats and pterosaurs.

Animals↗
PubMed2005

Microbial monitoring of the influence of the stabilization degree of sludge when applied to soil.

The aim of this study was to establish the degree of stabilization of sludge and its influence on the evolution of total aerobic micro-organisms and those of faecal origin when the sludge is applied to soil. Two different sludges were used, from a food industry (D) and from an urban treatment plant, (E). Both sludges were stabilized aerobically in laboratory conditions. The stabilization process was monitored by following the evolution of pathogenic micro-organisms and the content of total solids and volatile matter in suspension, while on the other hand the microbial evolution of the samples of soil plus sludge and control soil (S) were monitored over an incubation period of 80 days. After 20 or 40 days of incubation, in both sludge treatments the populations of pathogenic micro-organisms of faecal origin were below detectable limits, regardless of the degree of stabilization of the sludge. Soil without sludge treatment did not show pathogenic micro-organisms.

Bacteria↗
PubMed1997

Strategies for whole microbial genome sequencing and analysis.

The introduction of methods for automated DNA sequence analysis nearly a decade ago, together with more recent advances in the field of bioinformatics, have revolutionized biology and medicine and have ushered in a new era of genomic science, the study of genes and genomes. These new technologies have had an impact on many areas of research, including the association between genes and disease, in DNA-based diagnostics, and in the sequencing of genomes from human and other model organisms. The demonstration in 1995, that automated DNA sequencing methods could be used to decipher the entire genome sequence of a free-living organism, Haemophilus influenzae, was a milestone in both the genomics and microbial fields [1]. Since the first report of the complete sequence of H. influenzae, these methodologies have been adopted by laboratories around the world. The complete genomic sequence of five eubacterial species [1-5], one archaea [6], and the eukaryote, Saccharomyces cerevisiae [7], have been reported in the last 18 months. At the beginning of 1997 more than a dozen microbial genome projects are at or near completion, with many others in progress. It is likely that in the next few years we will see the complete sequence of perhaps as many as 30-40 microbial genomes. In this article, we will review methods for whole genome sequencing and analysis and examine how this information can be exploited to better understand microbial physiology and evolution.

Base Sequence↗
PubMed2004

Influence of the application of sewage sludge on the degradation of pesticides in the soil.

A study was made of the influence of the application of sewage sludge on the degradation of pesticides in the soil. Two kinds of sludge were used, with different characteristics, one from an urban treatment plant and one from a food processing plant. Three organophosphorus insecticides, fenitrothion, diazinon and dimethoate, were studied. The relative importance was determined of the chemical and biological degradation processes, which involved experiments on soil and sterile soil samples. A comparative study was also made of the degradation of pesticide residues and the evolution of the microbial population. The application of sludge seems to have a complex effect on the degradation of pesticides, determined by the bioavailability and biodegradability of their active ingredient. The biodegradation of pesticide residues brings about alterations in the microorganism population of the soil.

Biodegradation, Environmental↗
PubMed2005

Some lessons from Rickettsia genomics.

Sequencing of the Rickettsia conorii genome and its comparison with its closest sequenced pathogenic relative, i.e., Rickettsia prowazekii, provided powerful insights into the evolution of these microbial pathogens. However, advances in our knowledge of rickettsial diseases are still hindered by the difficulty of working with strict intracellular bacteria and their hosts. Information gained from comparing the genomes of closely related organisms will shed new light on proteins susceptible to be targeted in specific diagnostic assays, by new antimicrobial drugs, and that could be employed in the generation of future rickettsial vaccines. In this review we present a detailed comparison of the metabolic pathways of these bacteria as well as the polymorphisms of their membrane proteins, transporters and putative virulence factors. Environmental adaptation of Rickettsia is also discussed.

Amino Acid Sequence↗
PubMed2025

The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.

The human intestinal microbiota is a dynamic ecosystem shaped by extensive horizontal gene transfer, particularly in individuals from industrialized populations. In this review, we discuss recent advances in our understanding of how mobile genetic elements (MGEs) contribute to microbial ecology and evolution in this diverse community, focusing on MGEs carrying fitness-conferring genes. Bacteroidales species can colonize individuals for decades and serve as major hubs for MGE exchange. Most MGEs are highly variable across individuals and geographies. Occasionally, conserved MGEs can spread across geography and lifestyles. Functional characterizations of MGEs reveal their roles in antibiotic resistance, interbacterial antagonism, biofilm formation, immune evasion, and nutrient acquisition, among others. Substantive progress in our understanding of MGEs in the gut microbiome offers promising avenues for therapeutic microbiome interventions. However, major challenges remain in functional prediction, host-MGE linkage, and experimental characterization.

Humans↗