A. S. Rozanov

Biosphere Origin and Evolution

Problems of Biosphere Evolution and Origin of Life.- On Important Stages of Geosphere and Biosphere Evolution.- Microbial Biosphere.- Prebiological Stages of Evolution and RNA World on the Earth and in the Space.- Astrocatalysis Hypothesis for Origin of Life Problem.- Comets, Carbonaceous Meteorites, and the Origin of the Biosphere.- Hierarchical Scale-Free Representation of Biological Realm-Its Origin and Evolution.- The Prebiotic Phase of the Origin of Life as Seen by a Physical Chemist.- Prebiotic Carbohydrates and Their Derivates.- Theoretical and Computer Modeling of Evolution of Autocatalytic Systems in a Flow Reactor.- RNA World: First Steps Towards Functional Molecules.- Trans Hammerhead Ribozyme: Ligation vs. Cleavage.- Paradoxical Bistate Status of a Prebiotic Microsystem: Universal Predecessor of Life.- Archaen-Proterozoic Ecosystems: Their Interaction and Contemporary Analogous.- The Ancient Anoxic Biosphere Was Not As We Know It.- Evolutionary Aspects of Geochemical Activity of Microbial Mats in Lakes and Hydrotherms of Baikal Rift Zone.- On the concept for the Organization of the Modern Biosphere in the Terrestrial Subsurface.- Biomineralization and Evolution. Coevolution of Mineral and Biological Worlds.- Visualization of the Silicon Biomineralization in Cyanobacteria, Sponges and Diatoms.- Transformational Changes in Argillaceous Minerals due to Cyanobacteria.- Coevolution of Geological and Biological Events in Phanerozoe.- Ecological Revolution Through Ordovician Biosphere (495 to 435 Ma ages): Start of the Coherent Life Evolution.- Ecosystems and Molecular Genetic Factors of Organism Evolution.- Evolution by Gene Duplications: from the Origin of the Genetic Code to the Human Genome.- Evolution of the Translation Termination System in Eukaryotes.- The Hedgehog Signaling Cascade System: Evolution and Functional Dynamics.- Approaches to the Resolution of Contradictions Between Phylogenetic Systems Based on Paleontological and Molecular Data.- Chromosomes and Speciation.- Biotic Turnover in Superorganism Systems: Several Principles of Establishment and Sustenance (Theoretical Analysis, Debatable Issues).- Chromosomes and Continents.- Biosphere and Human Being.- Genetic Landscape of the Central Asia and Volga-Ural Region.- Problems of Reconstruction of Paleoenvironment and Conditions of the Habitability of the Ancient Man by the Example of Northwestern Altai.- The Settling of the Ancient Man by the Example of North-Western Altai.- Evolutionary History of Wheats-the Main Cereal of Mankind.

Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia)

BackgroundGeothermal areas are of great interest for the study of microbial communities. The results of such investigations can be used in a variety of fields (ecology, microbiology, medicine) to answer fundamental questions, as well as those with practical benefits. Uzon caldera is located in the Uzon-Geyser depression that is situated in the centre of the Karym-Semyachin region of the East Kamchatka graben-synclinorium. The microbial communities of Zavarzin spring are well studied; however, its benthic microbial mat has not been previously described.ResultsPyrosequencing of the V3 region of the 16S rRNA gene was used to study the benthic microbial community of the Zavarzin thermal spring (Uzon Caldera, Kamchatka). The community is dominated by bacteria (>95% of all sequences), including thermophilic, chemoorganotrophic Caldiserica (33.0%) and Dictyoglomi (24.8%). The benthic community and the previously examined planktonic community of Zavarzin spring have qualitatively similar, but quantitatively different, compositions.ConclusionsIn this study, we performed a metagenomic analysis of the benthic microbial mat of Zavarzin spring. We compared this benthic community to microbial communities found in the water and of an integral probe consisting of water and bottom sediments. Various phylogenetic groups of microorganisms, including potentially new ones, represent the full-fledged trophic system of Zavarzin. A thorough geochemical study of the spring was performed.

Identification of Bacillus strains by MALDI TOF MS using geometric approach.

Microorganism identification by MALDI TOF mass-spectrometry is based on the comparison of the mass spectrum of the studied organism with those of reference strains. It is a rapid and reliable method. However, commercial databases and programs are mostly designed for identification of clinically important strains and can be used only for particular mass spectrometer models. The need for open platforms and reference databases is obvious. In this study we describe a geometric approach for microorganism identification by mass spectra and demonstrate its capabilities by analyzing 24 strains belonging to the Bacillus pumilus group. This method is based on representing mass spectra as points on a multidimensional space, which allows us to use geometric distances to compare the spectra. Delimitation of microorganisms performed by geometric approach correlates well with the results of molecular phylogenetic analysis and clustering using Biotyper 3.1. All three methods used allowed us to reliably divide the strains into two groups corresponding to closely related species, Bacillus pumilus and Bacillus altitudinis. The method developed by us will be implemented in a Web interface designed for using open reference databases for microorganism identification. The data is available at http://www.bionet.nsc.ru/mbl/database/database.html.

Geobacillus icigianus sp. nov., a thermophilic bacterium isolated from a hot spring.

A Gram-reaction-positive, motile, thermophilic spore-forming strain, G1w1(T), was isolated from a hot spring of the Valley of Geysers, Kamchatka (Russia). Based on data from the present polyphasic taxonomic study, including phylogenetic analysis of 16S rRNA and spo0A gene sequences, the strain is considered to represent a novel species of the genus Geobacillus, for which the name Geobacillus icigianus sp. nov. is proposed. The type strain is G1w1(T) ( = VKM B-2853(T) = DSM 28325(T)).

Adaptive capabilities of microorganisms of salt lakes of the Altai Region under conditions of early Mars

Adaptive capacity of bacteria and archaea from salt lakes of the Altai Region are discussed. It is established that halophilic archaea (genus Halorubrum) and halotolerant bacteria (genus Halomonas) grow in a wide range of pH and mineralization (in the presence of Cl−, SO42−, ClO4−, Mg2+) and survive at low temperatures with a minor decrease in viability.

Theoretical and practical issues of hydrocarbon biological oxidation by microorganisms

This study is focused on the theoretical issues of biological oxidation of oil hydrocarbons varying from alkanes to polycyclic aromatic hydrocarbons. The biochemical mechanisms of the decomposition of the oil components are shown, as well as the review of data represented in the conventional data bases. The results of the microbial community studies, inhabiting the natural oil seeps of the Uzon caldera, are described in detail. It is the first study of the ecophysiological characteristics of oil-degrading microorganisms isolated from the thermal oil seeps of the caldera.

Bioinformatics analysis of the genome of Geobacillus stearothermophilus 22 Strain isolated from the Garga hot spring, Baikal Region

A new strain, Geobacillus stearothermophilus 22, was isolated from the Garga hot spring in the Bargusin Valley, Baikal Region, Russia. The morphology and biochemistry of the strain were analyzed, and full genome sequencing was conducted. The sequence was subjected to bioinformatics analysis. The nucleotide sequences (contigs) of the strain were found to be similar to the genome of the thermophilic strain G. kaustophilus Y412MC52. The proteome of the new strain was analyzed. Enzymes that belong to hemicellulases (endoxylanase, beta-xylosidase, and arabinofuranosidase) and the endocellulase enzyme were detected.

An Integrated Study to Analyze Salt Lake Microbial Community Structure (Novosibirsk Oblast, Russia)

Salt Lake is one of the lakes in the system,consisting of a huge amount of salt and bitter-salty lakes in Novosibirsk Oblast and Altai Krai.These lakes are unique and highly unstable systems where the parameters of geochemical

Recombinant strains of Saccharomyces cerevisiae for ethanol production from plant biomass

Saccharomyces cerevisiae is the most convenient organism widely used for ethanol production from sugars in industry thanks to the high rates of growth and ethanol fermentation and biosynthesis under unaerobic conditions, as well as its tolerance to a high ethanol concentration and low pH level. Lignocellulosic biomass is considered to be the most advantageous source of sugars. The sugar which can be obtained from it is the combination of hexoses and pentoses. However, the S. cerevisiae strains in current use are poorly adapted to the fermentation of pentasaccharides, which make it imperative to optimize the metabolic processes in the currently available bioethanol producers for pentasaccharides utilization. This work reviews the approaches which were currently developed to address this issue using recombinant strains of S. cerevisiae.

Current state of genetic and metabolic engineering of the genus Geobacillus aimed at production of ethanol and organic acids

Thermophilic bacteria are being extensively used in biotechnology. Species of the genus Geobacillus rank among the most prospective thermophiles. The current methods of genetic and metabolic engineering of these microorganisms are considered in the article. Examples of their use in various branches of biotechnology are presented.