The Leeuwenhoek Lecture, 1979 Experiments in microbial evolution: new enzymes, new metabolic activities

1980 ◽  
Vol 207 (1169) ◽  
pp. 385-404 ◽  
Keyword(s):  
Biological Evolution ◽  
Gene Mutations ◽  
Enzyme Synthesis ◽  
Microbial Evolution ◽  
Gene Duplications ◽  
Evolutionary Potential ◽  
Catabolic Pathways ◽  
Bacterial Populations ◽  
Catabolic Genes ◽  
Metabolic Activities

Biological evolution has resulted in a richness and diversity of species. Among microorganisms this is most evident in the wealth and diversity of biochemical transformations. Evidence for evolutionary relationships may be obtained from comparative studies, but with microorganisms it is also possible to follow evolution in action. Microbial populations adapt rapidly to changes in the environment and the evolution of new metabolic activities can be observed in laboratory experiments. The enzymes of many catabolic pathways are synthesized in response to the presence of inducing substrates. New catabolic activities may be acquired by mutations in regulatory genes resulting in alterations in the specificity of induction, or in enzyme synthesis in the absence of inducer. Mutations in structural genes may give rise to enzymes with altered substrate specificities. In bacteria, catabolic genes may be carried on plasmids and the exchange of plasmids among bacterial populations increases the evolutionary potential. Experiments in microbial evolution have produced strains with novel catabolic activities involving regulatory or structural gene mutations, gene duplications and plasmid exchange. Enzymes studied in this way include amidase, ribitol dehydrogenase, evolved (β-galactosidase, and enzymes of the catabolic pathways for pentoses and pentitols and haloaromatic compounds.

Selection, adaptation, and bacterial operons

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 265-271 ◽  
Author(s):  
Barry G. Hall
Keyword(s):  
Structural Gene ◽  
Point Mutations ◽  
Gene Mutations ◽  
Adaptive Mutation ◽  
Evolutionary Potential ◽  
Adaptive Mutations ◽  
Metabolic Functions ◽  
Metabolic Capability ◽  
Regulatory Mutations ◽  
Selection For

Bacteria are especially useful as systems to study the molecular basis of adaptive evolution. Selection for novel metabolic capabilities has allowed us to study the evolutionary potential of organisms and has shown that there are three major "strategies" for the evolution of new metabolic functions. (i) Regulatory mutations may allow a gene to be expressed under unusual conditions. If the product ofthat gene is already active toward a novel resource, then a regulatory mutation alone may confer a new metabolic capability. (ii) Structural gene mutations may alter the catalytic properties of enzymes so that they can act on novel substrates. These structural gene mutations may dramatically improve catalytic capabilities, and in some cases they can confer entirely new capabilities upon enzymes. In most cases both regulatory and structural gene mutations are required for the effective evolution of new metabolic functions. (iii) Operons that are normally silent, or cryptic, may be activated by either point mutations or by the action of mobile genetic elements. When activated, these operons can provide entirely new pathways for the metabolism of novel resources. Selection can also play a role in modulating the probability that a particular adaptive mutation will occur. In this paper I present evidence that a specific adaptive mutation, reversion of the metB1 mutation, occurs 60 to 80 times more frequently during prolonged selection on plates under conditions where the members of the population are not growing than it does in growing cells under nonselective conditions. This selective condition, methionine starvation, does not increase the frequency of other mutations unrelated to methionine biosynthesis. Thus, contrary to our present notions, selection can act not only to reveal preexisting mutations but to modulate the frequency with which adaptive mutations occur.Key words: mutation rates, molecular evolution, adaptive mutations, cryptic genes.

scholarly journals Spatial resource heterogeneity creates local hotspots of evolutionary potential

2017 ◽  
Author(s):  
Emily Dolson ◽  
Charles Ofria
Keyword(s):  
Explanatory Power ◽  
Biological Evolution ◽  
Biological Data ◽  
Heterogeneous Environments ◽  
Digital Evolution ◽  
Resource Heterogeneity ◽  
Evolutionary Potential ◽  
Local Conditions ◽  
Local Diversity ◽  
Novel Traits

AbstractDo local conditions influence evolution’s ability to produce new traits? Biological data demonstrate that evolutionary processes can be profoundly influenced by local conditions. However, the evolution of novel traits has not been addressed in this context, owing in part to the challenges of performing the necessary experiments with natural organisms. We conduct in silico experiments with the Avida Digital Evolution Platform to address this question. We created eight different spatially heterogeneous environments and ran 100 replicates in each. Within each environment, we examined the distribution of locations where nine different focal traits first evolved. Using spatial statistics methods, we identified regions within each environment that had significantly elevated probabilities of containing the first organism with a given trait (i.e. hotspots of evolutionary potential). Having demonstrated the presence of many such hotspots, we explored three potential mechanisms that could drive the formation of these patterns: proximity of specific resources, variation in local diversity, and variation in the sequence of locations the members of an evolutionary lineage occupy. Resource proximity and local diversity appear to have minimal explanatory power. Lineage paths through space, however, show some promising preliminary trends. If we can understand the processes that create evolutionary hotspots, we will be able to craft environments that are more effective at evolving targeted traits. This capability would be useful both to evolutionary computation, and to efforts to guide biological evolution.

scholarly journals Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

2021 ◽  
Vol 9 ◽  
Author(s):  
Sandhya Mishra ◽  
Ziqiu Lin ◽  
Shimei Pang ◽  
Wenping Zhang ◽  
Pankaj Bhatt ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Complex Mixture ◽  
Nitrogen Sources ◽  
Degradation Process ◽  
Microbial Populations ◽  
Novel Proteins ◽  
Catabolic Genes ◽  
Xenobiotic Compounds ◽  
Metabolic Activities

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.

scholarly journals RHIZODEGRADATION OF PHENANTHRENE, ANTHRACENE AND PYRENE BY AUGMENTING BACILLUS CEREUS AND BACILLUS SUBTILIS STRAINS

2021 ◽  
Vol 9 (02) ◽  
pp. 89-96
Author(s):  
M. Poornachander Rao ◽  
◽  
Anitha Yerra ◽  
K. Satyaprasad ◽  
◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Bacillus Cereus ◽  
Contaminated Soils ◽  
Rhizosphere Soil ◽  
Culture Method ◽  
Experimental Period ◽  
Bacterial Strains ◽  
Bacterial Populations ◽  
Metabolic Activities ◽  
Pot Culture

Rhizodegradation is one of the best methods for the effective removal of dangerous polycyclic aromatic hydrocarbons pollutants from soil. This is operative due to the high persistent, non-bioavailability nature of PAHs and combined, sequential reactions of bacteria present in rhizosphere of plants. We have conducted pot-culture method to study the degradation of three PAHs compounds namely phenanthrene, anthracene and pyrene in artificially contaminated soils of rhizosphere and non-rhizosphere soil treatments of blackgram(Vignamungo L.) that augmented by two potential PAHs degraders namely Bacillus cereus CPOU13 and Bacillus subtilis SPC14 isolated from naturally contaminated soils for 90days. HPLC studies revealed that degradation percentages of the three PAHs in treatments were more where selected strains augmented to the soil treatments over the non-augmented soils. The rhizosphere treatments that have augmented strains recorded more degradation percentages of phenanthrene, anthracene and pyrene over the rhizosphere treatments that were non-augmented. Pyrene, a high molecular weight PAHs degraded maximum to 96.24% in rhizosphere soil treatment that is augmented with the strains while moderate degradation of pyrene recorded in non-autoclaved soil treatments that contain natural microbial communities. The study of counting of bacterial populations during the experimental period revealed that the populations of the selected and other natural bacteria were gradually increased from the first day, reached maximum by 60days and became almost consistent in 90days in all the treatments. It was also observed that the populations of bacteria were high in rhizosphere treatments compared to the non-rhizosphere soil treatments. With these results it has been predicted that degradation of PAHs in rhizosphere soil treatments is closely associated with the increasing PAHs degrading bacterial populations of selected bacterial strains that may consume more quantity of PAHs for their metabolic activities in rhizosphere soils. Key words: Rhizodegradation, PAHs, HPLC, pot culture.

Why the mechanisms of biological evolution are still not revealed?

2020 ◽  
Vol 2 (1) ◽  
pp. 1-8
Author(s):  
Abyt Ibraimov
Keyword(s):  
Natural Selection ◽  
Gene Duplication ◽  
Biological Evolution ◽  
Gene Mutations ◽  
Eukaryotic Genome ◽  
Biological Variability ◽  
Gene Recombination ◽  
Human Chromosomes ◽  
Main Obstacle

Since the days of Darwin, it is generally accepted that biological evolution rests on three pillars: variability, inheritance and selection. It is believed that main sources of variability, mechanisms of inheritance and forms of natural selection have been clarified. Nevertheless, for more than 150 years since the publication of “Origin of Species” no consensus as to the mechanisms of evolution emerged. It is highly likely that the main obstacle in elucidating the mechanisms of evolution is the incompleteness of our knowledge regarding the sources of biological variability. The following sources of variability are universally recognized: gene mutations, gene recombination during meiosis and gene duplication. However, the role of the non-genic part of the genome, which makes up the vast majority of DNA in eukaryotes, remains unclear. For example, in human chromosomes, about 98% of DNA is represented by non-coding nucleotide sequences (ncDNAs). Although no one excludes their possible role in evolution, nevertheless, studies aimed at elucidating the participation of the non-genic part of the genome in variability, inheritance and selection are extremely small. The possible role of ncDNAs in the origin of biological variability in the eukaryotic genome and their evolution is discussed.

scholarly journals Polyploidy and the Evolution of Complex Traits

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Lukasz Huminiecki ◽  
Gavin C. Conant
Keyword(s):  
Complex Traits ◽  
Genome Duplication ◽  
Single Gene ◽  
Whole Genome ◽  
Gene Duplications ◽  
Evolutionary Potential ◽  
Evolutionary Transitions ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Modern Evolutionary Theory

We explore how whole-genome duplications (WGDs) may have given rise to complex innovations in cellular networks, innovations that could not have evolved through sequential single-gene duplications. We focus on two classical WGD events, one in bakers’ yeast and the other at the base of vertebrates (i.e., two rounds of whole-genome duplication: 2R-WGD). Two complex adaptations are discussed in detail: aerobic ethanol fermentation in yeast and the rewiring of the vertebrate developmental regulatory network through the 2R-WGD. These two examples, derived from diverged branches on the eukaryotic tree, boldly underline the evolutionary potential of WGD in facilitating major evolutionary transitions. We close by arguing that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation

2020 ◽  
Author(s):  
Misagh Kordi ◽  
Soumya Kundu ◽  
Mukul S. Bansal
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Classification Accuracy ◽  
Software Package ◽  
Microbial Evolution ◽  
Homologous Gene ◽  
Gene Duplications ◽  
New Gene ◽  
Phylogenetic Reconciliation ◽  
The Impact

AbstractHorizontal gene transfer is one of the most important mechanisms for microbial evolution and adaptation. It is well known that horizontal gene transfer can be either additive or replacing depending on whether the transferred gene adds itself as a new gene in the recipient genome or replaces an existing homologous gene. Yet, all existing phylogenetic techniques for the inference of horizontal gene transfer assume either that all transfers are additive or that all transfers are replacing. This limitation not only affects the applicability and accuracy of these methods but also makes it difficult to distinguish between additive and replacing transfers.Here, we address this important problem by formalizing a phylogenetic reconciliation framework that simultaneously models both additive and replacing transfer events. Specifically, we (1) introduce the DTRL reconciliation framework that explicitly models both additive and replacing transfer events, along with gene duplications and losses, (2) prove that the underlying computational problem is NP-hard, (3) perform the first experimental study to assess the impact of replacing transfer events on the accuracy of the traditional DTL reconciliation model (which assumes that all transfers are additive) and demonstrate that traditional DTL reconciliation remains highly robust to the presence of replacing transfers, (4) propose a simple heuristic algorithm for DTRL reconciliation based on classifying transfer events inferred through DTL reconciliation as being replacing or additive, and (5) evaluate the classification accuracy of the heuristic under a range of evolutionary conditions. Thus, this work lays the methodological and algorithmic foundations for estimating DTRL reconciliations and distinguishing between additive and replacing transfers.An implementation of our heuristic for DTRL reconciliation is freely available open-source as part of the RANGER-DTL software package from https://compbio.engr.uconn.edu/software/ranger-dtl/.

The genetic basis of the spread of β-lactamase synthesis among plasmid-carrying bacteria

1980 ◽  
Vol 289 (1036) ◽  
pp. 349-359 ◽  
Keyword(s):  
Bacterial Population ◽  
Bacterial Species ◽  
Evolutionary Potential ◽  
Gram Positive ◽  
Bacterial Populations ◽  
Gram Negative ◽  
Evolutionary Relatedness ◽  
Independent Replication ◽  
New Hosts ◽  
The One

Despite the fact that β-lactamases from a range of bacterial species - Gram-positive and Gram-negative - show evolutionary relatedness, there is no set pattern to the genetic organization that underlies their synthesis and its regulation. Thus, for example, the enzymes of many Gram-positive species are extracellular and inducible, whereas their counterparts in Gram-negative bacteria are often produced constitutively into the periplasmic space of the cells concerned. Nor is the location of the β-lactamase genes always the same: in Escherichia coli and Staphylococcus aureus , for example, these are commonly plasmid-borne, whereas with other species the genes are chromosomal. Furthermore, the location may not be fixed: some strains of a species may, for example, have their β-lactamase genes on a plasmid, whereas others of the same species may carry the same genes as part of their chromosome. In many cases the highly flexible genetic arrangement that underlies β-lactamase synthesis derives from two main features: first, where plasmids are involved, their ability to be transferred to related species, and the fact that they can often replicate in their new hosts, ensure that the genes specifying a given type of β-lactamase may move from species to species. Thus one finds enzymes of the same type in many distinct strains and species. The second source of flexibility is that the gene concerned is often part of a transposon: a genetic element incapable of independent replication, but which can move from one bacterial replicon to another by a mechanism independent of normal generalized recombination. Thus, with many β-lactamases - as also with enzymes that inactivate other antibiotics - their genes may move from replicon to replicon within a given bacterial cell, and from cell to cell within a bacterial population. This, then, is an arrangement of much evolutionary potential: something which is operated upon by selection pressure to give rise to the resistant bacterial populations which cause so much trouble in our hospitals. In this context, moreover, one can even think of a third level of organization where plasmid-carrying bacteria move from one host to another by a process of cross-infection. Even though it is clear that some β-lactamase genes can spread rapidly in susceptible bacterial populations, there also exist mechanisms that limit the extent to which the spread of both plasmids and transposons occurs. For example, some strains are poor recipients for certain types of plasmid, and, at a lower level of organization, some plasmids are relatively immune to the transposition of β-lactamase transposons. Overall, therefore, as common with evolutionary systems, the performance of the system as it affects β-lactam resistance is dependent on a balance of positive and negative influences: transfer of plasmids and transposons, on the one hand, and immunity to such transfers on the other.

scholarly journals DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil

2020 ◽  
Author(s):  
Harry Lerner ◽  
Başak Öztürk ◽  
Anja B. Dohrmann ◽  
Joice Thomas ◽  
Kathleen Marchal ◽  
...  
Keyword(s):  
Agricultural Soils ◽  
Sequence Similarity ◽  
Stable Isotope Probing ◽  
Rrna Gene ◽  
Agricultural Field ◽  
Bacterial Populations ◽  
Catabolic Genes ◽  
Degrading Bacteria ◽  
History Of

AbstractThe frequent exposure of agricultural soils to pesticides often leads to microbial adaptation, including the development of dedicated microbial populations that utilize the pesticide compound as a carbon and energy source. Soil from an agricultural field in Halen (Belgium) with a history of linuron exposure has been studied for its linuron-degrading bacterial populations at two time points over the past decade and Variovorax was appointed as a key linuron degrader. Like most studies on pesticide degradation, these studies relied on isolates that were retrieved through bias-prone enrichment procedures and therefore might not represent the in situ active pesticide-degrading populations. In this study, we revisited the Halen field and applied, in addition to enrichment-based isolation, DNA stable isotope probing (DNA-SIP), to identify the in situ linuron degrading bacteria. DNA-SIP unambiguously linked Variovorax and its linuron catabolic genes to linuron dissipation, likely through synergistic cooperation between two species. Additionally, two linuron mineralizing Variovorax isolates were obtained with high 16S rRNA gene sequence similarity to strains isolated from the same field a decade earlier. The results confirm Variovorax as the in situ degrader of linuron in the studied agricultural field and corroborate the genus as key in the maintenance of a robust genetic memory regarding linuron degradation functionality in the examined field.

scholarly journals Microbiotic particles in water and soil, water-soil microbiota coalescences, and antimicrobial resistance

2021 ◽  
Author(s):  
Fernando Baquero ◽  
Teresa M. Coque ◽  
Natalia Guerra-Pinto ◽  
Juan-Carlos Galán ◽  
David Jiménez-Lalana ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Mass Movement ◽  
Soil Mass ◽  
Microbial Evolution ◽  
Anthropogenic Activity ◽  
Random Drift ◽  
Bacterial Populations ◽  
Antimicrobial Resistance Genes ◽  
Soil And Water

Bacterial organisms like surfaces. Water and soil contain a multiplicity of particulated material where bacterial populations and communities might attach. Microbiotic particles refers to any type of small particles (less than 2 mm) where bacteria (and other microbes) might attach, resulting in medium- long-term colonization. In this work, the interactions of bacterial organisms with microbiotic particles of the soil and water are reviewed. These particles include bacteria-bacteria aggregates, and aggregates with particles of fungi (particularly in the rhizosphere), protozoa, phytoplankton, zooplankton, biodetritus resulting from animal and vegetal decomposition, humus, mineral particles (clay, carbonates, silicates), and anthropogenic particles (including wastewater particles or microplastics). At they turn, these particles might interact and coalesce (as in the marine snow). Natural phenomena (from river flows to tides, tsunamis, currents, or heavy winds) and anthropogenic activity (such as agriculture, waste-water management, mining, soil-mass movement) favors interaction and merging between all these soil and water particles, and consequently coalescence of their bacterial-associated populations and communities, resulting in an enhancement of mixed-recombinant communities capable of genetic exchange, including antimicrobial resistance genes, particularly in antimicrobial-polluted environments. Particles also favor compartmentalization of bacterial populations favoring diversification and acquisition of mutational resistance by random drift. In general, microbial evolution is accelerated by the aggregation of microbiotic particles. We propose that the world spread of antimicrobial resistance might relate with the environmental dynamics of microbiotic particles, and discuss possible methods to reduce this problem influencing One Health and Planetary Health.

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