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"Bacteria Evolution."
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Kin : how we came to know our microbe relatives
By unlocking the evolutionary information contained in cells, biologists have been able to construct the Tree of Life and show that its three main stems are dominated by microbes. Plants and animals constitute a small upper branch in one stem. Soon we may know how life began over 3.5 billion years ago. John Ingraham tells this story of discovery.-- Provided by publisher
Book
Microwave and Millimeter-Wave Remote Sensing for Security Applications
Microwave and millimeter-wave remote sensing techniques are fast becoming a necessity in many aspects of security as detection and classification of objects or intruders becomes more difficult. This groundbreaking resource offers you expert guidance in this burgeoning area. It provides you with a thorough treatment of the principles of microwave and millimeter-wave remote sensing for security applications, as well as practical coverage of the design of radiometer, radar, and imaging systems. You learn how to design active and passive sensors for intruder detection, concealed object detection, and human activity classification. This detailed book presents the fundamental concepts practitioners need to understand, including electromagnetic wave propagation in free space and in media, antenna theory, and the principles of receiver design. You find in-depth discussions on the interactions of electromagnetic waves with human tissues, the atmosphere and various building and clothing materials. This timely volume explores recently developed detection techniques, such as micro-Doppler radar signatures and correlation radiometry. The book is supported with over 200 illustrations and 1,135 equations.
eBook
Life's engines : how microbes made Earth habitable
\"For almost four billion years, microbes had the primordial oceans all to themselves. The stewards of Earth, these organisms transformed the chemistry of our planet to make it habitable for plants, animals, and us. Life's Engines takes readers deep into the microscopic world to explore how these marvelous creatures made life on Earth possible--and how human life today would cease to exist without them. Paul Falkowski looks \"under the hood\" of microbes to find the engines of life, the actual working parts that do the biochemical heavy lifting for every living organism on Earth. With insight and humor, he explains how these miniature engines are built--and how they have been appropriated by and assembled like Lego sets within every creature that walks, swims, or flies. Falkowski shows how evolution works to maintain this core machinery of life, and how we and other animals are veritable conglomerations of microbes. A vibrantly entertaining book about the microbes that support our very existence, Life's Engines will inspire wonder about these elegantly complex nanomachines that have driven life since its origin. It also issues a timely warning about the dangers of tinkering with that machinery to make it more \"efficient\" at meeting the ever-growing demands of humans in the coming century.\"--Jacket.
Book
Evolution of primary producers in the sea
This text reference examines how photosynthesis evolved on Earth and how phytoplankton evolved through time - ultimately to permit the evolution of complex life, including human beings. The first of its kind, this book provides thorough coverage of key topics, with contributions by leading experts in biophysics, evolutionary biology, micropaleontology, marine ecology, and biogeochemistry.This exciting new book is of interest not only to students and researchers in marine science, but also to evolutionary biologists and ecologists interested in understanding the origins and diversification of life. Primary Producers of the Sea offers these students and researchers an understanding of the molecular evolution, phylogeny, fossil record, and environmental processes that collectively permits us to comprehend the rise of phytoplankton and their impact on Earth's ecology and biogeochemistry. It is certain to become the first and best word on this exhilarating topic. * Discusses the evolution of phytoplankton in the world's oceans as the first living organisms and the first and basic producers in the earths food chain* Includes the latest developments in the evolution and ecology of marine phytoplankton specifically with additional information on marine ecosystems and biogeochemical cycles* The only book to consider of the evolution of phytoplankton and its role in molecular evolution, biogeochemistry, paleontology, and oceanographic aspects * Written at a level suitable for related reading use in courses on the Evolution of the Biosphere, Ecological and Biological oceanography and marine biology, and Biodiversity
eBook
Living Trees: High-Quality Reproducible and Reusable Construction of Bacterial Phylogenetic Trees
An ideal bacterial phylogenetic tree accurately retraces evolutionary history and accurately incorporates mutational, recombination and other events on the appropriate branches. Current strain-level bacterial phylogenetic analysis based on large numbers of genomes lacks reliability and resolution, and is hard to be replicated, confirmed and reused, because of the highly divergent nature of microbial genomes. We present SNPs and Recombination Events Tree (SaRTree), a pipeline using six “living trees” modules that addresses problems arising from the high numbers and variable quality of bacterial genome sequences. It provides for reuse of the tree and offers a major step toward global standardization of phylogenetic analysis by generating deposit files including all steps involved in phylogenetic inference. The tree itself is a “living tree” that can be extended by addition of more sequences, or the deposit can be used to vary the programs or parameters used, to assess the effect of such changes. This approach will allow phylogeny papers to meet the traditional responsibility of providing data and analysis that can be repeated and critically evaluated by others. We used the Acinetobacter baumannii global clone I to illustrate use of SaRTree to optimize tree resolution. An Escherichia coli tree was built from 351 sequences selected from 11,162 genome sequences, with the others added back onto well-defined branches, to show how this facility can greatly improve the outcomes from genome sequencing. SaRTree is designed for prokaryote strain-level analysis but could be adapted for other usage.
Journal Article
It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements
Articles on CRISPR commonly open with some variant of the phrase “these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements.” There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical–computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.
Journal Article
Hot Spots of Site-Specific Integration into the Sinorhizobium meliloti Chromosome
The diversity of phage-related sequences (PRSs) and their site-specific integration into the genomes of nonpathogenic, agriculturally valuable, nitrogen-fixing root nodule bacteria, such as Sinorhizobium meliloti, were evaluated in this study. A total of 314 PRSs, ranging in size from 3.24 kb to 88.98 kb, were identified in the genomes of 27 S. meliloti strains. The amount of genetic information foreign to S. meliloti accumulated in all identified PRSs was 6.30 Mb. However, more than 53% of this information was contained in prophages (Phs) and genomic islands (GIs) integrated into genes encoding tRNAs (tRNA genes) located on the chromosomes of the rhizobial strains studied. It was found that phiLM21-like Phs were predominantly abundant in the genomes of S. meliloti strains of distant geographical origin, whereas RR1-A- and 16-3-like Phs were much less common. In addition, GIs predominantly contained fragments of phages infecting bacteria of distant taxa, while rhizobiophage-like sequences were unique. A site-specific integration analysis revealed that not all tRNA genes in S. meliloti are integration sites, but among those in which integration occurred, there were “hot spots” of integration into which either Phs or GIs were predominantly inserted. For the first time, it is shown that at these integration “hot spots”, not only is the homology of attP and attB strictly preserved, but integrases in PRSs similar to those of phages infecting the Proteobacteria genera Azospirillum or Pseudomonas are also present. The data presented greatly expand the understanding of the fate of phage-related sequences in host bacterial genomes and also raise new questions about the role of phages in bacterial–phage coevolution.
Journal Article
Genome rearrangements and phylogeny reconstruction in Yersinia pestis
Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis . Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.
Journal Article
Yeast–bacteria competition induced new metabolic traits through large-scale genomic rearrangements in Lachancea kluyveri
Large-scale chromosomal rearrangements are an important source of evolutionary novelty that may have reshaped the genomes of existing yeast species. They dramatically alter genome organization and gene expression fueling a phenotypic leap in response to environmental constraints. Although the emergence of such signatures of genetic diversity is thought to be associated with human exploitation of yeasts, less is known about the driving forces operating in natural habitats. Here we hypothesize that an ecological battlefield characteristic of every autumn when fruits ripen accounts for the genomic innovations in natural populations. We described a long-term cross-kingdom competition experiment between Lachancea kluyveri and five species of bacteria. Now, we report how we further subjected the same yeast to a sixth species of bacteria, Pseudomonas fluorescens, resulting in the appearance of a fixed and stably inherited large-scale genomic rearrangement in two out of three parallel evolution lines. The 'extra-banded' karyotype, characterized by a higher fitness and an elevated fermentative capacity, conferred the emergence of new metabolic traits in most carbon sources and osmolytes. We tracked down the event to a duplication and translocation event involving a 261-kb segment. Such an experimental setup described here is an attractive method for developing industrial strains without genetic engineering strategies.
Journal Article
Mechanisms of stationary-phase mutagenesis in bacteria: mutational processes in pseudomonads
In a growth-restricting environment, mutants arise that are able to take over bacterial populations by a process known as adaptive mutation or stationary-phase mutation. This process is best studied in Escherichia coli. The genus Pseudomonas represents one of the largest groups of bacteria able to colonize multiple habitats and to adapt rapidly to new environments. The majority of bacteria including pseudomonads contain a different set of DNA polymerases and DNA repair enzymes than those identified in E. coli. The aim of this review is to provide an overview of the results of studies of mutagenic processes in pseudomonads and to discuss these results in the light of the mechanisms of stationary-phase mutagenesis discovered in E. coli.
Journal Article