اصول تنوع میکروبی (کتاب‌های ASM)

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. Cover 1 Contents 6 Preface 10 Acknowledgments 12 About the Author 14 SECTION I: Introduction to Microbial Diversity 17 1 What Is Microbial Diversity? 19 Facets of microbial diversity 19 The fundamental similarity of all living things 25 2 Context and Historical Baggage 29 The evolution of evolutionary thought 29 Taxonomy and phylogeny 35 The false eukaryote-prokaryote dichotomy 36 3 Phylogenetic Information 39 Deciding which organisms and sequences to use in the analysis 40 Obtaining the required sequence data 43 Assembling sequences in a multiple-sequence alignment 46 4 Constructing a Phylogenetic Tree 55 Tree construction: the neighbor-joining method 56 How to read a phylogenetic tree 65 Example analysis 71 5 Tree Construction Complexities 77 Substitution models 77 Treeing algorithms 81 Bootstrapping 83 6 Alternatives to Small-Subunit rRNA Analysis 87 SSU rRNA cannot be used to distinguish closely related organisms 87 Alternative sequences 88 Alternatives to sequence-based methods 92 7 The Tree of Life 99 Major lessons of the “Big Tree of Life” 99 Rooting the “Tree of Life” 102 The caveat of horizontal transfer 104 SECTION II: The Microbial Zoo 109 8 Primitive Thermophilic Bacteria 111 Phylum Aquificae (Aquifex and relatives) 112 Phylum Thermotogae (Thermotoga and relatives) 116 Other primitive thermophiles 118 Thermophilic ancestry of Bacteria 119 Life at high temperatures 119 9 Green Phototrophic Bacteria 125 Phylum Chloroflexi (green nonsulfur bacteria) 126 Phylum Chlorobi (green sulfur bacteria) 131 Phylum Cyanobacteria (blue-green algae) 134 Other green phototrophs 142 Bacterial photosynthesis 142 Carbon fixation 145 10 Proteobacteria 149 Phylum Proteobacteria (purple bacteria and relatives) 149 Class Alphaproteobacteria 151 Class Betaproteobacteria 157 Class Gammaproteobacteria 162 Class Deltaproteobacteria 168 Class Epsilonproteobacteria 172 The concept of “proteobacteria” 175 11 Gram-Positive Bacteria 179 What does being gram positive mean? 180 An alternative view of gram-positive bacteria 181 Phylum Firmicutes (low G+C gram-positive bacteria) 181 Phylum Actinobacteria (high G+C gram-positive bacteria) 190 Bacterial development 197 Bacterial multicellularity 198 12 Spirochetes and Bacteroids 201 Phylum Spirochaetae 202 Phylum Bacteroidetes (sphingobacteria or Bacteroides/Flavobacterium/Cytophaga group) 207 Bacterial motility 211 13 Deinococci, Chlamydiae, and Planctomycetes 217 Phylum Deinococcus-Thermus 218 Phylum Chlamydiae (Chlamydia and relatives) 223 Phylum Planctomycetes (Planctomyces and relatives) 227 Reductive evolution in parasites 233 14 Bacterial Phyla with Few or No Cultivated Species 235 How do we know about these organisms? 237 Phyla with few cultivated species 239 Phyla with no cultivated species 246 Phylogenetic groups at all levels are dominated by uncultivated sequences 248 How much of the microbial world do we know about? 248 15 Archaea 251 General properties of the Archaea 251 Phylum Crenarchaeota 254 Phylum Euryarchaeota 259 Phylum Korarchaeota 270 Phylum Nanoarchaeota 271 Archaea as . . . 272 16 Eukaryotes 275 General properties of the eukaryotes 276 Unikonta 278 Plantae 281 Chromalveolata 284 Rhizaria 288 Excavata 293 17 Viruses and Prions 299 Viruses 299 Prions 306 SECTION III: Microbial Populations 311 18 Identification of Uncultivated Organisms 313 19 Sequence-Based Microbial Surveys 321 20 Fluorescent In Situ Hybridization Surveys 337 Fluorescent in situ hybridization 337 Confocal laser scanning microscopy 338 21 Molecular Fingerprinting of Microbial Populations 343 Denaturing gradient gel electrophoresis 344 Terminal restriction fragment length polymorphism 347 22 Linking Phenotype and Phylotype 353 The genomic or metagenomic approach 354 The stable-isotope probing approach 357 SECTION IV: Conclusion: The Phylogenetic Perspective 365 23 Genomics, Comparative Genomics, and Metagenomics 367 Genomics 367 Comparative genomics 374 Metagenomics 377 24 Origins and Early Evolution 381 The timescale 381 Ancient microbial fossils 384 The last common ancestor 386 The RNA world hypothesis 387 The emergence of life 390 Index 395 A 395 B 396 C 396 D 397 E 397 F 398 G 398 H 399 I 399 J 399 K 399 L 399 M 400 N 400 O 400 P 401 R 402 S 402 T 403 U 404 V 404 W 404 Just Published! 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. Praise for Principles of Microbial Diversity “We desperately needed a book that climbs the big tree, branch by branch, written both for undergraduates and as a reference. Principles of Microbial Diversity is that book!” -Jo Handelsman, Howard Hughes Medical Institute Professor, Frederick Phineas Rose Professor, Department of Molecular, Cellular and Developmental Biology, Yale University “What an absolutely fabulous book! Jim Brown captures the excitement and transformative impact that microbial diversity has brought to the field of microbiology in a text appropriate for students. Principles of Microbial Diversity belongs on every microbiologist’s bookshelf.” -Hazel A. Barton, Associate Professor of Biology, Associate Professor of Geosciences, University of Akron James (Jim) W. Brown’s lasting interest in microbiology was sparked by a single lecture on microbial diversity in an undergraduate microbiology class at Ball State University and by the announcement in that class of the discovery of an entirely new kind of living thing, the "archaebacteria." He went on to earn his MS in Microbiology at Miami University and his PhD in the Molecular, Cellular, and Developmental Biology program at The Ohio State University. Jim developed and continues to teach senior-level undergraduate lecture and lab courses in microbial diversity at North Carolina State University (NCSU), which are the genesis of this textbook. He was awarded the NCSU Alumni Association Distinguished Undergraduate Professor award in 2014. For more on the book and information on requesting an examination copy please visit http://www.asmscience.org/instructors Interested in purchasing this title as an electronic publication? Click here for the electronic version on Vital Source! Click here for the electronic version on RedShelf! Paperback, 416 pages, full color throughout, illustrations, glossary, index. 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." What Is Microbial Diversity? -- Context And Historical Baggage -- Phylogenetic Information -- Constructing A Phylogenetic Tree -- Tree Construction Complexities -- Alternatives To Small-subunit Rrna Analysis -- The Tree Of Life -- Primitive Thermophilic Bacteria -- Green Phototrophic Bacteria -- Proteobacteria -- Gram-positive Bacteria -- Spirochetes And Bacteroids -- Deinococci, Chlamydiae, And Planctomycetes -- Bacterial Phyla With Few Or No Cultivated Species -- Archaea -- Eukaryotes -- Viruses And Prions -- Identification Of Uncultivated Organisms -- Sequence-based Microbial Surveys -- Fluorescent In Situ Hybridization Surveys -- Molecular Fingerprinting Of Microbial Populations -- Linking Phenotype And Phylotype -- Genomics, Comparative Genomics, And Metagenomics -- Origins And Early Evolution. James W. Brown, Department Of Biological Sciences, North Carolina State University, Raleigh, North Carolina. Includes Bibliographical References And Index.