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At least 883 records · Page 49Linked to original sources
PubMed2004

High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis of base-specific cleavage products is an efficient, highly accurate tool for the detection of single base sequence variations. We describe the first application of this comparative sequencing strategy for automated high-throughput mutation detection in microbial genomes. The method was applied to identify DNA sequence changes that occurred in Escherichia coli K-12 MG1655 during laboratory adaptive evolution to new optimal growth phenotypes. Experiments were based on a genome-scale in silico model of E. coli metabolism and growth. This model computes several phenotypic functions and predicts optimal growth rates. To identify mutations underlying a 40-d adaptive laboratory evolution on glycerol, we resequenced 4.4% of the E. coli-K12 MG1655 genome in several clones picked at the end of the evolutionary process. The 1.54-Mb screen was completed in 13.5 h. This resequencing study is the largest reported by MALDI-TOF mass spectrometry to date. Ten mutations in 40 clones and three deviations from the reference sequence were detected. Mutations were predominantly found within the glycerol kinase gene. Functional characterization of the most prominent mutation shows its metabolic impact on the process of adaptive evolution. All sequence changes were independently confirmed by genotyping and Sanger-sequencing. We demonstrate that comparative sequencing by base-specific cleavage and MALDI-TOF mass spectrometry is an automated, fast, and highly accurate alternative to capillary sequencing.

Adaptation, Biological↗
PubMed1999

Effect of high pressure homogenization on microbial and chemico-physical characteristics of goat cheeses.

The objective of this work was to compare goat cheeses obtained from milk previously subjected to high pressure homogenization (1000 bar) with those produced from untreated milk and milk subjected to sanitization (61 degrees C; 20 min) or to pasteurization (72 degrees C; 15 s). The pressure homogenization treatment had both direct and indirect effects on cheese characteristics and their evolution during ripening. The direct effects were principally linked to the change in water-binding capacity of proteins as shown also by the lower whey separation. The indirect effects involved the microbial growth or activity and, particularly, modifications of the population of the lactic acid bacteria that occurred naturally and their evolution as well as a more precocious yeast and mold growth with a consequent rapid rise in pH. Although the treatment proved to enhance both proteolytic and lipolytic activities according to Fourier transform infrared analysis, which was used to obtain a rapid description of the biochemical modification, the cheeses homogenized under high pressure showed relevant qualitative differences only in the zone corresponding to amide I and amide II signals of proteins. The activation of these enzymatic activities observed in the homogenized cheeses could be either an indirect effect of the shift of the microbial population or a consequence of a different exposure of the macromolecules to the enzymatic activity. Scanning electron microscopy analyses of goat cheeses revealed that cheeses homogenized under high pressure had a more homogeneous microstructure than did the others.

Animals↗
PubMed2001

Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton.

Phylogenetic information from ribosomal RNA genes directly amplified from the environment changed our view of the biosphere, revealing an extraordinary diversity of previously undetected prokaryotic lineages. Using ribosomal RNA genes from marine picoplankton, several new groups of bacteria and archaea have been identified, some of which are abundant. Little is known, however, about the diversity of the smallest planktonic eukaryotes, and available information in general concerns the phytoplankton of the euphotic region. Here we recover eukaryotes in the size fraction 0.2-5 microm from the aphotic zone (250-3,000 m deep) in the Antarctic polar front. The most diverse and relatively abundant were two new groups of alveolate sequences, related to dinoflagellates that are found at all studied depths. These may be important components of the microbial community in the deep ocean. Their phylogenetic position suggests a radiation early in the evolution of alveolates.

Animals↗
PubMed2026

Biosynthesis and heterologous production of the α-agarofuran scaffold of Celangulin V from Celastrus angulatus.

Celangulin V is a widely used biopesticide derived from Celastrus angulatus, and features antifeedant and insecticidal properties as a dihydro-β-agarofuran (DHβAF) sesquiterpenoid. Its biosynthesis remains largely unexplored. Here, we assemble a chromosome-level and haplotype-resolved reference genome of C. angulatus, with each haplotype assembled into 23 pseudochromosomes and achieving scaffold N50 of 14.31 and 14.01 Mb, respectively. This high-quality genome reveals that a recent β whole-genome triplication (β-WGT) event occurred ~34.3 million years ago, and that the expansion of sesquiterpene synthases and cytochrome P450s from the CYP71BE family results from whole-genome duplication (WGD) event and tandem duplication, respectively. We identify CaTPS16 as a γ-eudesmol synthase, and show that CYP71BE416 further catalyzes the γ-eudesmol to tetrahydrofuran ring α-agarofuran for Celangulin V biosynthesis. We further achieve the de novo synthesis of α-agarofuran in Saccharomyces cerevisiae through combined coexpression of these genes. This study has significantly increases the available genomic resources of the Celastraceae family, improves our understanding of the biosynthetic origins and evolution of the tetrahydrofuran ring in DHβAF sesquiterpenoids, and enables its heterologous bioproduction in microbial chassis.

Celastrus↗
PubMed2025

Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series.

MOTIVATION: The lineage dynamics and history of cells in a population reflect the interplay of evolutionary forces they experience, including mutation, drift, and selection. When the population is polyclonal, lineage dynamics also manifest the extent of clonal competition among co-existing mutational variants. If the population exists in a community of other species, the lineage dynamics could also reflect the population's ecological interaction with the rest of the community. Recent advances in high-resolution lineage tracking via DNA barcoding, coupled with next-generation sequencing of bacteria, yeast, and mammalian cells, allow for precise quantification of clonal dynamics in these organisms. RESULTS: In this work, we introduce Doblin, an R suite for identifying dominant barcode lineages based on high-resolution lineage tracking data. We first benchmarked Doblin's accuracy using lineage data from evolutionary simulations, showing that it recovers the clones' identity and relative fitness in the simulation. Next, we applied Doblin to analyze clonal dynamics in laboratory evolutions of Escherichia coli populations undergoing antibiotic treatment and in colonization experiments of the gut microbial community. Doblin's versatility allows it to be applied to lineage time-series data across different experimental setups. AVAILABILITY AND IMPLEMENTATION: Doblin is available on CRAN (https://CRAN.R-project.org/package=doblin) and Github (https://github.com/dagagf/doblin).

DNA Barcoding, Taxonomic↗
PubMed1985

[Survival of Azospirillum in the rhizosphere of Festuca arundinacea].

In two experiments Festuca seeds (4 or 20 seeds/pot in first or second experiment respectively) were inoculated with Azospirillum strains (sp 7, mutant streptomycin resistant and G strain) in controlled laboratory conditions. Two illumination regimes were employed (197 and 274 microE. m-2.s-1, respectively). sp 7 cell number was determined during both experiments. The total number of diazotrophic bacteria was also determined on different dates. In both experiments the control pots received the same number of autoclaving bacteria. The results suggested that: (i) sp 7 number decreased in both experiments to 4 - 5% from initial number in 22 and 23 day after inoculation. This suggests that the plant density and illumination range employed did not affect the inoculum survival; (ii) the evolution of the number of different native diazotrophics strains, along the experiment, showed that this microbial number decrease in inoculated and control pots was related to the initial number.

Poaceae↗
PubMed1977

Influence of salts on the microbial activity in arid and simi-humid soils.

The influence of salt mixtures consisting of Ca (H2PO4)2, trace elements, CaSO4, CaCO3, Na2CO3, NaCl, and K2SO4 in different combinations on the nitrifying power, evolution of carbon dioxide, and the total number of bacteria was studied in arid soils (sandy and alluvial) and semi-humid ones (chernozem and rendzina). Salt mixtures comprising either monocalcium phosphate or sodium chloride showed highly inhibiting action on the studied microbial activities in sandy, alluvial, and chernozem soils, while monocalcium phosphate stimulated the heterotrophs of rendzina. Trace elements favoured the autotrophs of the caly soils. The other different salt mixtures acted according to the salt combination and nature of the microbial activity.

Bacteria↗
PubMed1998

Evolution of competitive fitness in experimental populations of E. coli: what makes one genotype a better competitor than another?

An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of Escherichia coli and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. Here, we review experiments to identify the phenotypic bases of improved competitive fitness in twelve E. coli populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate. After 10,000 generations, the average fitness of the derived genotypes had increased by approximately 50% relative to the ancestor, based on competition experiments using marked strains in the same environment. The growth kinetics of the ancestral and derived genotypes showed that the latter have a shorter lag phase upon transfer into fresh medium and a higher maximum growth rate. Competition experiments were also performed in environments where other substrates were substituted for glucose. The derived genotypes are generally more fit in competition for those substrates that use the same mechanism of transport as glucose, which suggests that enhanced transport was an important target of natural selection in the evolutionary environment. All of the derived genotypes produce much larger cells than does the ancestor, even when both types are forced to grow at the same rate. Some but not all, of the derived genotypes also have greatly elevated mutation rates. Efforts are now underway to identify the genetic changes that underlie those phenotypic changes, especially substrate specificity and elevated mutation rate for which there are good candidate loci. Identification and subsequent manipulation of these genes may provide new insights into the reproducibility of adaptive evolution, the importance of co-adapted gene complexes, and the extent to which distinct phenotypes (e.g., substrate specificity and cell size) are affected by the same mutations.

Adaptation, Physiological↗
PubMed2006

Cell evolution and Earth history: stasis and revolution.

This synthesis has three main parts. The first discusses the overall tree of life and nature of the last common ancestor (cenancestor). I emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. Second, I map the tree onto the fossil record and discuss dates of key events and their biogeochemical impact. Finally, I present a broad synthesis, discussing evidence for a three-phase history of life. The first phase began perhaps ca 3.5 Gyr ago, when the origin of cells and anoxic photosynthesis generated the arguably most primitive prokaryote phylum, Chlorobacteria (= Chloroflexi), the first negibacteria with cells bounded by two acyl ester phospholipid membranes. After this 'chlorobacterial age' of benthic anaerobic evolution protected from UV radiation by mineral grains, two momentous quantum evolutionary episodes of cellular innovation and microbial radiation dramatically transformed the Earth's surface: the glycobacterial revolution initiated an oxygenic 'age of cyanobacteria' and, as the ozone layer grew, the rise of plankton; immensely later, probably as recently as ca 0.9 Gyr ago, the neomuran revolution ushered in the 'age of eukaryotes', Archaebacteria (arguably the youngest bacterial phylum), and morphological complexity. Diversification of glycobacteria ca 2.8 Gyr ago, predominantly inhabiting stratified benthic mats, I suggest caused serial depletion of 13C by ribulose 1,5-bis-phosphate caboxylase/oxygenase (Rubisco) to yield ultralight late Archaean organic carbon formerly attributed to methanogenesis plus methanotrophy. The late origin of archaebacterial methanogenesis ca 720 Myr ago perhaps triggered snowball Earth episodes by slight global warming increasing weathering and reducing CO2 levels, to yield runaway cooling; the origin of anaerobic methane oxidation ca 570 Myr ago reduced methane flux at source, stabilizing Phanerozoic climates. I argue that the major cellular innovations exhibit a pattern of quantum evolution followed by very rapid radiation and then substantial stasis, as described by Simpson. They yielded organisms that are a mosaic of extremely conservative and radically novel features, as characterized by De Beer's phrase 'mosaic evolution'. Evolution is not evenly paced and there are no real molecular clocks.

Archaea↗
PubMed2001

A new look at microbial leaching patterns on sulfide minerals.

Leaching patterns on sulfide minerals were investigated by high-resolution scanning electron microscopy (SEM). Our goal was to evaluate the relative contributions of inorganic surface reactions and reactions localized by attached cells to surface morphology evolution. Experiments utilized pyrite (FeS(2)), marcasite (FeS(2)) and arsenopyrite (FeAsS), and two iron-oxidizing prokaryotes in order to determine the importance of cell type, crystal structure, and mineral dissolution rate in microbially induced pit formation. Pyrite surfaces were reacted with the iron-oxidizing bacterium Acidithiobacillus ferrooxidans (at 25 degrees C), the iron-oxidizing archaeon 'Ferroplasma acidarmanus' (at 37 degrees C), and abiotically in the presence of Fe(3+) ions. In all three experiments, discrete bacillus-sized (1-2 µm) and -shaped (elliptical) pits developed on pyrite surfaces within 1 week of reaction. Results show that attaching cells are not necessary for pit formation on pyrite. Marcasite and arsenopyrite surfaces were reacted with A. ferrooxidans (at 25 degrees C) and 'F. acidarmanus' (at 37 degrees C). Cell-sized and cell-shaped dissolution pits were not observed on marcasite or arsenopyrite at any point during reaction with A. ferrooxidans, or on marcasite surfaces reacted with 'F. acidarmanus'. However, individual 'F. acidarmanus' cells were found within individual shallow (<0.5 µm deep) pits. The size and shape (round rather than elliptical) of the pits conformed closely to the shape of F. acidarmanus (cells) pits on arsenopyrite. We infer these pits to be cell-induced. We attribute the formation of pits readily detectable (by SEM) to the higher reactivity of arsenopyrite compared to pyrite and marcasite under the conditions the experiment was conducted. These pits contributed little to the overall surface topographical evolution, and most likely did not significantly increase surface area during reaction. Our results suggest that overall sulfide mineral dissolution may be dominated by surface reactions with Fe(3+) rather than by reactions at the cell-mineral interface.

Journal Article↗
PubMed2006

Microbial availability and size fractionation of dissolved organic carbon after drought in an intermittent stream: biogeochemical link across the stream-riparian interface.

The evolution of dissolved organic carbon (DOC) molecular-weight fractions, DOC biodegradability (BDOC), DOC origin [fluorescence index (FI)], and enzyme activities between the stream waters (main and ephemeral channel) and ground waters (riparian and hillslope) were analyzed during the transition from drought to precipitation in a forested Mediterranean stream. After the first rains, DOC content in stream water reached its maximum value (10-18 mg L(-1)), being explained by the leaching of deciduous leaves accumulated on the stream bed during drought. During this period, the largest molecules (>10 kDa), were the most biodegradable, as indicated by high BDOC values measured during storm events and high enzymatic activities (especially for leucine-aminopeptidase). DOC >100 kDa was strongly immobilized (78%) at the stream-riparian interface, whereas the smallest molecules (<1 kDa) were highly mobile and accumulated in ground waters, indicating their greater recalcitrance. Differential enzymatic patterns between compartments showed a fast utilization of polysaccharides in the flowing water but a major protein utilization in the ground water. The results of the FI indicated a more terrestrial origin of the larger molecules in the flowing water, also suggesting that transformation of material occurs through the stream-riparian interface. Microbial immobilization and fast utilization of the most biodegradable fraction at the stream-riparian interface is suggested as a relevant DOC retention mechanism just after initial recharging of the ground water compartment. Large and rapid DOC inputs entering the intermittent river system during the transition from drought to precipitation provide available N and C sources for the heterotrophs. Heterotrophs efficiently utilize these resources that were in limited supply during the period of drought. Such changes in C cycling may highlight possible changes in organic matter dynamics under the prediction of extended drying periods in aquatic ecosystems.

Bacteria↗
PubMed1975

Influence of salts on the microbial activities in arid and semi-humid soils.

The influence of salt mixtures consisting of Ca(H2PO4)2, trace elements, CaSO4, CaCO3, Na2CO3, NaCl and K2SO4 in different combinations on the nitrifying power, evolution of carbon dioxide and the total number of bacteria was studied in arid soils (sandy and alluvial) and semi-humid ones (chernozem and rendzina). Salt mixtures comprising of either mono-calcium phosphate or sodium chloride showed highly inhibiting action on the studied microbial activities in sandy, alluvial and chernozem soils, whilst mono-calcium phosphate stimulated the heterotrophs of rendzina. Trace elements stimulated the autotrophs of the clay soils. The other different salts mixtures acted according to the salt combination and nature of the microbial activity.

Bacteria↗
PubMed2006

Antimicrobial drugs that target human--not microbial--genotypes or phenotypes: a paradigm change in human evolutionary response to pathogen selection pressure.

Conventional antimicrobial drugs that target microbial life processes impose a selection pressure on pathogens and attenuate pathogen imposed selection pressure on human hosts. The simultaneous increase and decrease that result in pathogen and human host evolvability/adaptability, respectively, distorts the natural Darwinian evolutionary process. Such drugs may create an aberrant Darwinian genotype in human hosts that is ill prepared to resist emerging virulent pathogenic strains in the event of a decrease in host ontogenic potential. In contrast, antimicrobial drugs that target host human genes exert a selective pressure both on the human genome (without population decimation) as well as on pathogenic microbes. Such drugs maintain the evolvability/adaptability of the host in tandem with that of the pathogens in the context of Darwinian evolution. Such drugs retain the capacity of the human host to evolve genotypes that may confer resistance to future pathogenic microbial strains, to assimilate prokaryotic endosymbionts and to increase the probability of survival in the event of a decrease in host ontogenic potential.

Anti-Infective Agents↗
PubMed2005

Parallel genotypic adaptation: when evolution repeats itself.

Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together.

Adaptation, Biological↗