Changes in the level of bacitracin synthesis in autolysin-resistant strains of Bacillus licheniformis

Production of bacitracin by Bac. licheniformis 1001 and its spontaneous autolysin resistant variants was studied. It was found that the antibiotic activity of some variants was 1.5--2 times higher than that of the initial strain. No differences in the activity of serine exoprotease in the initial strain and resistant variants were observed. The latter variants lost their resistance to autolysis in 2--3 subcultures on solid and liquid nutrient media. their antibiotic activity in these cases decreased to the control level. The study indicates that there is a phenomenologic relation between the autolytic and antibiotic activities of Bac. licheniformis. The nature of the relation is not known yet. Possibly, it is due to changes in the specific metabolic steps connected with regulation of bacitracin synthesis.     

Protected environments allow parallel evolution of a bacterial pathogen in a patient subjected to long-term antibiotic therapy

Long-term antibiotic treatment offers a rare opportunity to study the evolution of bacteria within the same individual. The appearance of new variants has been suggested to take place via the selection of enhanced resistance in compartments of the body in which the antibiotic concentration is low. Laboratory models of protected compartments have elegantly demonstrated their potential in selecting novel variants. However, comparable data from patients have been rare. In this study, extended antibiotic therapy in a single patient suffering from multiple infected liver cysts has provided the opportunity to observe and analyse the molecular evolution of antibiotic resistance. Each isolate has the same basic ompC gene sequence that is distinct from other Escherichia coli isolates, which suggests that they derive from the same founder population. However, the isolates differ in their auxotrophic markers, in the pI values of their dominant beta-lactamase activities and in the mutations in the promoter region of the ampC gene leading to increased expression of the AmpC enzyme. The data provide strong evidence for a single focal infection expanding via parallel pathways of evolution to give a range of antibiotic-resistant isolates. These data suggest that the infected cysts provide numerous protected environments that are the foci for the separate development of distinct variants.     

Comparative study of the effect of antibiotics and antiseptics on Staphylococcus aureus

The routinely used antibiotics and antiseptics were compared with the same staphylococcal isolates by MIC ranges, the mean MIC for the strains, proportion of the variants resistant to the drugs, distribution of the strains by the resistance spectra and the number increase rate for the resistant variants in natural populations within 5-10-year periods. It was concluded that when used locally the antiseptics had some advantages over the antibiotics especially with respect to hospital strains. The authors believe that in developing new drugs, ++re-estimation of the routinely used ones, choosing the optimal drug for a particular case it is more important to consider the heterogeneity of microbial populations, the frequency of resistant variants and activity of the mechanisms of their selection under hospital conditions.     

Spontaneous variability of antibiotic biosynthesis in relation to morphogenetic processes in Actinomyces chromogenes var. trienicus]

Available data on possible relationship between the antibiotic activity of actinomycetes and the level of their differentiation, especially with their spore-formation ability, present certain interest with respect to possible relationship between the synthesis of antibiotics and the formation of secondary structures. The study of spontaneous stable variants of Actinomyces chromogenes var. trienicus demonstrates that all sporogenous variants produce the same complex of antibiotics as does the original population. The loss of the ability to synthesize antibiotics is observed only in the phenotypically different dwarf variant (VI). The impaired differentiation (the loss of spore-formation ability) is accompanied by disturbances in the antibiotic synthesis: asporogenous variants are either inactive or produce only 1 antibiotic from the complex synthesized by the original population. Changes in the structure of spore chains do not probably correlate with qualitative and quantitative measurable changes in the antibiotic synthesis. The statistic evidence is suggestive of the fact that the variant with a more complex profile and topography of aerial mycelium displays a higher activity.     

Metabolic Flux and Fitness

Studies of Escherichia coli under competition for lactose in chemostat cultures have been used to determine the selective effects of variation in the level of the beta-galactoside permease and the beta-galactosidase enzyme. The results determine the adaptive topography of these gene products relative to growth in limiting lactose and enable predictions concerning the selective effects of genetic variants found in natural populations. In the terms of metabolic control theory, the beta-galactosidase enzyme at wild-type-induced levels has a small control coefficient with respect to fitness (C = 0.018), and hence genetic variants resulting in minor changes in enzyme activity have disproportionately small effects on fitness. However, the apparent control coefficient of the beta-galactoside permease at wild-type-induced levels is large (C = 0.551), and hence even minor changes in activity affect fitness. Therefore, we predict that genetic polymorphisms in the lacZ gene are subject to less effective selection in natural populations than are those in the lacY gene. The beta-galactoside permease is also less efficient than might be expected, and possible forces resulting in selection for an intermediate optimum level of permease activity are considered. The selective forces that maintain the lactose operon in a regulated state in natural populations are also discussed.     

Genetic variance of sexually selected traits in waxmoths: maintenance by genotype x environment interaction

When traits experience directional selection, such as that imposed by sexual selection, their genetic variance is expected to diminish. Nonetheless, theory and findings from sexual selection predict and demonstrate that male traits favored by female choice retain substantial amounts of additive genetic variance. We explored this dilemma through an ecological genetic approach and focused on the potential contributions of genotype x environment interaction (GEI) to maintenance of additive genetic variance for male signal characters in the lesser waxmoth, Achroia grisella (Lepidoptera: Pyralidae). We artificially selected genetic variants for two male signal characters, signal rate (SR) and peak amplitude (PA), that influence female attraction and then examined the phenotypic plasticity of these variants (high- and low-SR and high- and low-PA lines) under a range of environmental conditions expected in natural populations. Our split-family breeding experiments indicated that two signal characters, SR and PA, and several developmental characters in both high- and low-SR and high- and low-PA lines displayed considerable phenotypic plasticity among the environments tested. Moreover, strong GEIs leading to crossover between high- and low-SR lines were found for SR and developmental period. Therefore, neither high- nor low-SR genetic variants would achieve maximum attractiveness and fitness in every environment, and those variants producing unattractive signals with low SRs under normal conditions may remain in populations provided that gene flow across environments or generation overlap are sufficiently high. We speculate that the phenotypic plasticity for SR and developmental period is adaptive in A. grisella populations experiencing a range of temperature and density conditions. Females mating with attractive (high-SR) males may be assured of obtaining good genes because these males sire offspring that develop more rapidly and a crossover for developmental period may parallel that for SR. Such parallel crossovers may be expected wherever good-genes sexual selection mechanisms operate.     

Natural Selection and Functional Potentials of Human Noncoding Elements Revealed by Analysis of Next Generation Sequencing Data

Noncoding DNA sequences (NCS) have attracted much attention recently due to their functional potentials. Here we attempted to reveal the functional roles of noncoding sequences from the point of view of natural selection that typically indicates the functional potentials of certain genomic elements. We analyzed nearly 37 million single nucleotide polymorphisms (SNPs) of Phase I data of the 1000 Genomes Project. We estimated a series of key parameters of population genetics and molecular evolution to characterize sequence variations of the noncoding genome within and between populations, and identified the natural selection footprints in NCS in worldwide human populations. Our results showed that purifying selection is prevalent and there is substantial constraint of variations in NCS, while positive selectionis more likely to be specific to some particular genomic regions and regional populations. Intriguingly, we observed larger fraction of non-conserved NCS variants with lower derived allele frequency in the genome, indicating possible functional gain of non-conserved NCS. Notably, NCS elements are enriched for potentially functional markers such as eQTLs, TF motif, and DNase I footprints in the genome. More interestingly, some NCS variants associated with diseases such as Alzheimer''s disease, Type 1 diabetes, and immune-related bowel disorder (IBD) showed signatures of positive selection, although the majority of NCS variants, reported as risk alleles by genome-wide association studies, showed signatures of negative selection. Our analyses provided compelling evidence of natural selection forces on noncoding sequences in the human genome and advanced our understanding of their functional potentials that play important roles in disease etiology and human evolution.     

Genomic analysis of adaptive differentiation in Drosophila melanogaster

Drosophila melanogaster shows clinal variation along latitudinal transects on multiple continents for several phenotypes, allozyme variants, sequence variants, and chromosome inversions. Previous investigation suggests that many such clines are due to spatially varying selection rather than demographic history, but the genomic extent of such selection is unknown. To map differentiation throughout the genome, we hybridized DNA from temperate and subtropical populations to Affymetrix tiling arrays. The dense genomic sampling of variants and low level of linkage disequilibrium in D. melanogaster enabled identification of many small, differentiated regions. Many regions are differentiated in parallel in the United States and Australia, strongly supporting the idea that they are influenced by spatially varying selection. Genomic differentiation is distributed nonrandomly with respect to gene function, even in regions differentiated on only one continent, providing further evidence for the role of selection. These data provide candidate genes for phenotypes known to vary clinally and implicate interesting new processes in genotype-by-environment interactions, including chorion proteins, proteins regulating meiotic recombination and segregation, gustatory and olfactory receptors, and proteins affecting synaptic function and behavior. This portrait of differentiation provides a genomic perspective on adaptation and the maintenance of variation through spatially varying selection.     

Allozymes and fitness: Evolution of a problem

It was expected that studies of electrophoretic variability in natural populations would resolve longstanding controversies concerning the form of natural selection and its effect on genetic variance in fitness. Recent studies of fitness components for allozymes in E. coli and Drosophila, where genetic backgrounds have been rigidly controlled, and experiments designed to detect small selection coefficients, suggest that selection is much weaker than earlier investigations would indicate. However, perturbing the metabolic background associated with specific loci often allows functional differences to be amplified to an experimentally measurable level. Frequencies of null activity variants in natural populations indicate that the fitness consequences of reduced activity in heterozygoles are probably very small. These results are supported by recent theoretical considerations suggesting that the activity variation associated with electrophoretic variation will have little effect on overall flux in many pathways.     

The Genomic Basis of Rapid Adaptation to Antibiotic Combination Therapy in Pseudomonas aeruginosa

Combination therapy is a common antibiotic treatment strategy that aims at minimizing the risk of resistance evolution in several infectious diseases. Nonetheless, evidence supporting its efficacy against the nosocomial opportunistic pathogen Pseudomonas aeruginosa remains elusive. Identification of the possible evolutionary paths to resistance in multidrug environments can help to explain treatment outcome. For this purpose, we here performed whole-genome sequencing of 127 previously evolved populations of P. aeruginosa adapted to sublethal doses of distinct antibiotic combinations and corresponding single-drug treatments, and experimentally characterized several of the identified variants. We found that alterations in the regulation of efflux pumps are the most favored mechanism of resistance, regardless of the environment. Unexpectedly, we repeatedly identified intergenic variants in the adapted populations, often with no additional mutations and usually associated with genes involved in efflux pump expression, possibly indicating a regulatory function of the intergenic regions. The experimental analysis of these variants demonstrated that the intergenic changes caused similar increases in resistance against single and multidrug treatments as those seen for efflux regulatory gene mutants. Surprisingly, we could find no substantial fitness costs for a majority of these variants, most likely enhancing their competitiveness toward sensitive cells, even in antibiotic-free environments. We conclude that the regulation of efflux is a central target of antibiotic-mediated selection in P. aeruginosa and that, importantly, changes in intergenic regions may represent a usually neglected alternative process underlying bacterial resistance evolution, which clearly deserves further attention in the future.     

Selection of strains of Streptomyces griseus Kr., the producer of a streptothricin antibiotic grisin, using the method of protoplast fusion

The effect of protoplasting on antibiotic activity of the grisin-producing organism was shown. High frequency of Grn- mutants after strain VG307f protoplasting and no capacity in these mutants for reversion to the initial Grn+ phenotype were shown. The reversion frequency was less than 10(-8). Moreover, it was shown that all the Grn- mutants lost their stability (GrnR) to the effect of their own antibiotic. With respect to strain VG212 there was noted a significant increase in the number of both the minus and the plus variants after the protoplast formation and regeneration. Fusing of protoplasts of strains VG307f and VG212 belonging to the divergent lines in selection of S. griseus Kr. yielded the phage stable strain VG7849 with high levels of the antibiotic production and improved technological properties.     

Spontaneous variability ofStreptomyces glomeratus,a producer of the anthracycline antibiotics beromycins

Spontaneous variants of the beromycin-producing strainStreptomyces glomeratus 3980 were divided into five groups (A-E) according to increasing antibiotic activity. The most active variants (group E) differed from the other types and the wild strain by a suppressed ability to produce aerial mycelium and melanoid pigment and by an increased production of propionic acid. Strains with a 12-fold higher antibiotic production capacity (with respect to strain 3980) were obtained by selection of superior segregants from submerged cultures of the E type.     

Parallel adaptation to climate above the 35th parallel

Independent or parallel evolution of similar traits is key to understanding the genetics and limitations of adaptation. Adaptation from the same genetic changes in different populations defines parallel evolution. Such genetic changes can derive from standing ancestral variation or de novo mutations and excludes instances of adaptive introgression. In this issue of Molecular Ecology, Walden et al.(2020) investigate the scale of parallel climate adaptation from standing genetic variation between two North American Arabidopsis lyrata lineages, each formed by a distinct evolutionary history during the last glacial cycle. By identifying adaptive variants correlated with three ecologically significant climatic gradients, they show that instead of the same genetic variants or even genes, parallel evolution is only observed at the level of biological processes. The evolution of independent adaptive variants to climate in two genetically close lineages is explained by their different post‐glacial demographic histories. Separate glacial refugia and strong population bottlenecks were probably sufficient to change the landscape of shared allele frequencies, hindering the possibility of parallel evolution.     

Effective selection of transgenic papaya plants with the PMI/Man selection system

The selectable marker gene phospho-mannose isomerase (pmi), which encodes the enzyme phospho-mannose isomerase (PMI) to enable selection of transformed cell lines on media containing mannose (Man), was evaluated for genetic transformation of papaya (Carica papaya L.). We found that papaya embryogenic calli have little or no PMI activity and cannot utilize Man as a carbon source; however, when calli were transformed with a pmi gene, the PMI activity was greatly increased and they could utilize Man as efficiently as sucrose. Plants regenerated from selected callus lines also exhibited PMI activity but at a lower specific activity level. Our transformation efficiency with Man selection was higher than that reported using antibiotic selection or with a visual marker. For papaya, the PMI/Man selection system for producing transgenic plants is a highly efficient addition to previously published methods for selection and may facilitate the stacking of multiple transgenes of interest. Additionally, since the PMI/Man selection system does not involve antibiotic or herbicide resistance genes, its use might reduce environmental concerns about the potential flow of those genes into related plant populations.     

Spontaneous and induced variability inStreptomyces nogalater producing nogalamycin

Variability in the production of nogalamycin byStreptomyces nogalater var.nogalater was followed in untreated and mutagenized populations of the standard strainNRRL 3035 and its spontaneous variant K-18 using the method of agar blocks with subsequent tests under submerged conditions. In both strains the most active variants were obtained by natural selection without mutagenic treatment; in this way productivity increased by 108% after two selection steps. Treatment with UV-radiation did not yield variants with a highly increased activity. Gamma-radiation extended the variability but, at the same time, substantially increased the number of non-producing and low-producing isolates. Relatively high yields of (+)-variants were obtained after treatment with nitrous acid but their activity did not reach that observed in the most active spontaneous variants.     

Influence of antibiotic treatment and Wolbachia curing on sexual isolation among Drosophila melanogaster cage populations

Speciation depends on the establishment of reproductive isolation between populations of the same species. Whether assortative mating evolves as a by-product of adaptation is a major question relevant to the origin of species by reproductive isolation. The long-term selection populations used here were originally established 30 years ago from a single cage population (originating from a maternal one) and subsequently subjected to divergent selection for tolerance of toxins in food (heavy metals versus ethanol) to investigate this question. Those populations now differ in sexual isolation and Wolbachia infection status. Wolbachia are common and widespread bacteria infecting arthropods and nematodes. Attention has recently focused on their potential role in insect speciation, due to post-mating sperm-egg incompatibilities induced by the bacteria. In this paper we examine the potential effect of Wolbachia on the level of sexual isolation. By antibiotic curing, we show that removal of Wolbachia decreases levels of mate discrimination (sexual isolation index) between populations by about 50%. Backcrossing experiments confirm that this effect is due to infection status rather than to genetic changes in the populations resulting from antibiotic treatment. Antibiotic treatment has no effect on mate discrimination level between uninfected populations. Our findings suggest that the presence of Wolbachia (or another undetected bacterial associate) act as an additive factor contributing to the level of pre-mating isolation between these Drosophila melanogaster populations. Given the ubiquity of bacterial associates of insects, such effects could be relevant to some speciation events.     

Parallel Geographic Variation in Drosophila melanogaster

Drosophila melanogaster, an ancestrally African species, has recently spread throughout the world, associated with human activity. The species has served as the focus of many studies investigating local adaptation relating to latitudinal variation in non-African populations, especially those from the United States and Australia. These studies have documented the existence of shared, genetically determined phenotypic clines for several life history and morphological traits. However, there are no studies designed to formally address the degree of shared latitudinal differentiation at the genomic level. Here we present our comparative analysis of such differentiation. Not surprisingly, we find evidence of substantial, shared selection responses on the two continents, probably resulting from selection on standing ancestral variation. The polymorphic inversion In(3R)P has an important effect on this pattern, but considerable parallelism is also observed across the genome in regions not associated with inversion polymorphism. Interestingly, parallel latitudinal differentiation is observed even for variants that are not particularly strongly differentiated, which suggests that very large numbers of polymorphisms are targets of spatially varying selection in this species.     

Changes in the phase variant spectra in the populations of lactic acid bacteria under antibiotic treatment

Effect of the antibiotics kanamycin and ampicillin on the growth and phase variation of the populations of four strains of lactic acid bacteria (Lactobacillus sp. M76AT, L. casei MB, Enterococcus faecium M, and E. faecium M3185) was studied. The presence of antibiotics in the medium resulted in a dose-dependent decrease in viable cell numbers and in partial or complete substitution of the dominant S variant with the minor Sm and Sb variants. The variants differed in colony morphology, as well as in some physiological, biochemical, biotechnological, and probiotic characteristics. The Sm type variants of all strains exhibited the highest resistance to antibiotics. High production of exopolysaccharides was found in Sb variants of lactobacilli and in S variants of enterococci. The highest antibacterial activity was found in Sm variants of lactobacilli, especially in Lactobacillus sp. M76AT. The latter is biotechnologically the most promising strain, since all variants fermented milk yielding the products with uniformly pronounced functional and organoleptic properties. These patterns are of importance for the understanding of the mechanisms of antibiotic resistance and for selection of the variants with desired properties, as well as for quality control of the lactic acid bacteria starter cultures.     

ARE PARALLEL MORPHOLOGIES OF CAVE ORGANISMS THE RESULT OF SIMILAR SELECTION PRESSURES?

The amphipod Gammarus minus is present in both caves and springs, with cave populations showing elaborated (size and antennae) and reduced (eye) characters relative to spring populations. Earlier studies have shown that cave populations resulted from independent invasions of hydrologically isolated subterranean drainages and that there is genetic variation for both elaborated and reduced characters. In this study we tested the hypothesis that a similar pattern of selection on isolated cave populations is responsible for the parallel evolution of cave morphologies. We used variation in mating success and fecundity to test for the presence of directional selection on eye, antennal, and body size characters in a set of cave and spring populations during a series of seasonal cross-sectional samplings. We found significant directional selection for smaller eyes in caves and larger eyes in springs, which supports the hypothesis that selection is responsible for reduced eye size in cave populations. We also found selection for larger body and antennal size in cave populations, which is consistent with the hypothesis that parallel patterns of selection in caves are responsible for the elaboration of body and antennal size. However, we found selection for larger body and antennal size in spring populations that is not consistent with the observed divergence of spring and cave populations. We suggest that unmeasured components of viability selection could be more important in springs than in caves and may act against the selection for larger size found in spring populations.     

Genomic Architecture of Rapid Parallel Adaptation to Fresh Water in a Wild Fish

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. However, the genetic architecture underlying these adaptive changes is still poorly understood. Using population genomic approaches, we investigated the genomic architecture that underlies rapid parallel adaptation of Coilia nasus to fresh water by comparing four freshwater-resident populations with their ancestral anadromous population. Linkage disequilibrium network analysis and population genetic analyses revealed two putative large chromosome inversions on LG6 and LG22, which were enriched for outlier loci and exhibited parallel association with freshwater adaptation. Drastic frequency shifts and elevated genetic differentiation were observed for the two chromosome inversions among populations, suggesting that both inversions would undergo divergent selection between anadromous and resident ecotypes. Enrichment analysis of genes within chromosome inversions showed significant enrichment of genes involved in metabolic process, immunoregulation, growth, maturation, osmoregulation, and so forth, which probably underlay differences in morphology, physiology and behavior between the anadromous and freshwater-resident forms. The availability of beneficial standing genetic variation, large optimum shift between marine and freshwater habitats, and high efficiency of selection with large population size could lead to the observed rapid parallel adaptive genomic change. We propose that chromosomal inversions might have played an important role during the evolution of rapid parallel ecological divergence in the face of environmental heterogeneity in C. nasus. Our study provides insights into the genomic basis of rapid adaptation of complex traits in novel habitats and highlights the importance of structural genomic variants in analyses of ecological adaptation.