Microbial Taxonomy Phylogeny And Biodiversity

The great diversity of microbial life is the remaining major reservoir of unknown biological diversity on earth. To understand this vast, but largely unperceived diversity with its untapped genetic, enzymatic and industrial potential, microbial systematics is undergoing a revolutionary change in its approach to describe novel taxa based on genomic/envirogenomic information. The characterization of an organism is no longer bounded by methodological barriers, and it is now possible to fully sequence the whole genome of a strain to study individual genes, or to examine the genetic information by using different techniques. In fact, application of genomics is helping not only to provide a better understanding of the boundaries of genera and higher levels of classification, but also to refine our definition of the species concept. In addition, increased understanding of phylogeny is allowing to predict the genetic potential of microorganisms for biotechnological applications and adaptation to environmental changes. The present Research Topic on “Microbial Taxonomy, Phylogeny and Biodiversity” compiles a collection of papers covering the use of genomic sequence data in microbial taxonomy and systematics, including evolutionary relatedness of microorganisms; application of comparative genomics in systematic studies; or metagenomic approaches for biodiversity studies. We hope that this eBook incentives and encourages researchers for future discussions on microbial taxonomy and phylogenetics.

Bacterial taxonomy as a specialized discipline is practised by a minority but the applications of taxonomy are important to most, if not all microbiologists. It is the implementation of taxonomic ideas and practises which gives rise to identification and typing systems, procedures for the analysis and characterization of biodiversity, hypotheses about the evolution of micro-organisms, and improved procedures for the isolation and implementation of bacteria in biotechnological processes. Without taxonomic theory providing a sound basis to these many facets of microbiology there would be severe problems faced by many scientists working with micro-organisms. Taxonomy comprises three sequential but independent processes; classification, nomenclature and identification. The first two stages are the prime concern of the specialist taxonomist but the third stage should result in identification schemes of value to all microbiologists. As the classification and identification of micro-organisms improves, largely due to the introduction of new technologies, so does its contribution to the subject as a whole. It therefore seemed timely to hold a conference in the autumn of 1993 devoted to microbial identification. Such a topic could not be addressed without some reference to the enabling discipline of classification, but the principal aims were to assess improvements in identification and typing and how these were benefiting microbiological topics ranging from ecological and biotechnological studies of extremophilic bacteria to the use of pyrolysis mass spectrometry in epidemiology. The meeting, which was held in Granada, Spain, was supported by FEMS (FEMS Symposium No.

This second edition of Modern Bacterial Taxonomy has been completely revised and expanded to include detailed coverage of molecular systematics including relevant aspects of nucleic acid sequences, the construction of phylogenetic trees, typing of bacteria by restriction fragment length polymorphisms, DNA hybridization probes and the use of the polymerase chain reaction in bacterial systematics.

Microbial Diversity in the Genomic Era, Second Edition presents techniques used for microbial taxonomy and phylogeny, along with their applications and respective strengths and challenges. Though many advanced techniques for the identification of unknown bacterium are available in the genomic era, a far fewer number of the total microbial species have been discovered and identified to date. With that in mind, this book incorporates recently developed biosystematics methods and approaches to assess microbial taxonomy, with suitable recommendations for where to apply them across the range of bacterial identification and infectious disease research. Here, international researchers in the field first provide a broad overview of microbial genomics research and microbiome directed medicine, followed by sections on molecular tools for microbial diversity research, extremophilic microbial diversity, functional microbial diversity across application areas, microbial diversity and infectious disease research, and future directions for research. Step-by-step methodologies are provided for key techniques, along with applied case studies breaking down recent research studies into the practical components, illuminating pathways for new studies across the field. This new edition has been fully updated to address advances in the field of microbiome directed medicine, and whole genome sequencing for studying microbial diversity, considering both recent technological advances and new applications areas, from extremophile studies to the latest approaches in human microbiome analysis. Instructs in techniques used for microbial taxonomy and phylogeny, with discussions of their applications and respective pros and cons Reviews the evolving field of microbial typing and the genomic technologies that enable comparative metagenomic analysis of complex microbial environments Covers microbiome directed translational research, as well as whole genome sequencing for studying microbial diversity, with newly added research protocols and case studies Reviews future applications in the field of microbiome directed medicine Features chapter contributions from global experts in the field

Every speck of dust, drop of water, and grain of soil and each part of every plant and animal contain their own worlds of microbes. Designed as a key text for upper-level undergraduates majoring in microbiology, genetics, or biology, Principles of Microbial Diversity provides a solid curriculum for students to explore the enormous range of biological diversity in the microbial world. Within these richly illustrated pages, author and professor James W. Brown provides a practical guide to microbial diversity from a phylogenetic perspective in which students learn to construct and interpret evolutionary trees from DNA sequences. He then offers a survey of the "tree of life" that establishes the necessary basic knowledge about the microbial world. Finally, the author draws the student's attention to the universe of microbial diversity with focused studies of the contributions that specific organisms make to the ecosystem. Principles of Microbial Diversity fills an empty niche in microbiology textbooks by providing an engaging, cutting-edge view of the "microbial zoo" that exists around us, covering bacteria, archaea, eukaryotes, and viruses.

This book discusses microbial diversity in various habitats and environments, its role in ecosystem maintenance, and its potential applications (e.g. biofertilizers, biocatalysts, antibiotics, other bioactive compounds, exopolysaccharides etc.). The respective chapters, all contributed by renowned experts, offer cutting-edge information in the fields of microbial ecology and biogeography. The book explains the reasons behind the occurrence of various biogeographies and highlights recent tools (e.g. metagenomics) that can aid in biogeography studies by providing information on nucleic acid sequence data, thereby directly identifying microorganisms in various habitats and environments. In turn, the book describes how human intervention results in depletion of biodiversity, and how numerous hotspots are now losing their endemic biodiversity, resulting in the loss of many ecologically important microorganisms. In closing, the book underscores the importance of microbial diversity for sustainable ecosystems.

Biodiversity of Microbial Life places the importance and novelty of the diversity of the microbial world in perspective with the biodiversity of plants and animals. Microbial diversity has driven the evolution of all life on Earth as well as the nutrient cycles, which are key to the operation of the biosphere. Microorganisms live in all ecosystems, even extreme environments not habitable to other organisms. Noted experts including Carl Woese, the originator of the Tree of Life, and Rita Colwell, who is now Director of the National Science Foundation, offer their unique perspectives on the extent and importance of microbial biodiversity. Special emphasis is placed on: * Evolution, speciation, and contrasts between microbial biodiversity and plant and animal biodiversity * Physiological and metabolic diversity of microorganisms * Biodiversity of microbial life in terrestrial and marine environments * Symbioses between microorganisms and plants, insects, and humans * Extreme environments populated exclusively or primarily by microorganisms including thermal vents and hot springs, polar sea ice environments, and subterranean ecosystems * Microorganisms and biotechnology Biodiversity of Microbial Life is an essential resource for all biologists interested in biodiversity.

This book is about phylogenetic diversity as an approach to reduce biodiversity losses in this period of mass extinction. Chapters in the first section deal with questions such as the way we value phylogenetic diversity among other criteria for biodiversity conservation; the choice of measures; the loss of phylogenetic diversity with extinction; the importance of organisms that are deeply branched in the tree of life, and the role of relict species. The second section is composed by contributions exploring methodological aspects, such as how to deal with abundance, sampling effort, or conflicting trees in analysis of phylogenetic diversity. The last section is devoted to applications, showing how phylogenetic diversity can be integrated in systematic conservation planning, in EDGE and HEDGE evaluations. This wide coverage makes the book a reference for academics, policy makers and stakeholders dealing with biodiversity conservation.