Principles of Microbial Diversity

James W. Brown

• Publisher: ASM Press
• Year: 2014
• ISBN:
  9781683673415
• Edition: 1
• Topic: Sciences biologiques
• Subtopic: Génétique et génomique

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.

SECTION II
The Microbial Zoo

In this section, we take a stroll through the microbial world, as if it were a zoo or garden. No zoo contains all animals, but only representatives; a complete collection would overwhelm both visitor and keeper alike. Tus, we focus on the most prevalent and well understood groups of organisms, and we discuss only a small number of representatives from each. Most of these phylogenetic groups contain a wide range of organisms; there are something like 5,000 described species of Bacteria alone, and given any reasonable definition of “species” there must be many orders of magnitude more to be found in nature.

Section II is dominated by a discussion of various groups of Bacteria (chapters 8 to 14), followed by shorter discussion of the Archaea (chapter 15), Eukarya (chapter 16), and lastly viruses and prions (chapter 17). Because so many chapters in this section are about the various groups of Bacteria, an introduction to the relationships within this group might be helpful.

The Bacteria

The Bacteria can mostly be divided into 13 traditional groups (Kingdoms or Phyla, depending on your nomenclature), related by the tree shown in Fig. 1. Most of these branches of Bacteria, and certainly most of the branches with lots of known and abundant species, radiate from a single region of the tree, the “main radiation.” There are (perhaps) some earlier branches; these are minor groups with few species that are not generally abundant, and they are primitive organisms (short branch length) and mostly thermophilic.

Early, primitive, thermophilic branches:

Aquifex and relatives (including Thermocrinus, the pink filamentous mat former in Yellowstone hot springs)

Thermotoga and relatives

Green nonsulfur bacteria (including Chloroflexus, the golden mat former in Yellowstone hot springs)

Main radiation:

Deinococci (including Thermus)

Spirochetes: common in the environment and as animal symbionts

Green sulfur bacteria: green anaerobic sulfur-oxiding photosynthesizers, not familiar to most people

Cytophaga/Bacteroids/Flavobacteria: Bacteroides is an abundant gut organism in humans; the aerobes are common but unfamiliar

Planctomycetes: common but few are cultivated and so are little understood Chlamydiae (hopefully you know this one, but not too well): a small, closely related cluster of species

Firmicutes: the low-G+C gram-positive bacteria (now we have reached the hugely common groups—these are predominant in soil and include lots of pathogens and symbionts)

Actinobacteria: the high-G+C gram-positive bacteria (also abundant in soil and as pathogens and symbionts)

Cyanobacteria: the blue-green algae, which carry out oxygenic photosynthesis and power the biosphere today Proteobacteria: most gram-negative bacteria you would think of are members...