Principles of Microbial Diversity. James W. Brown

Once started, Ken April, Production Manager, and John Bell, Senior Production Editor, at the ASM Press made this book happen. Special thanks are also owed to the book’s interior and cover designer, Susan Brown Schmidler; Dianna Logan and Peggy Rupp at Dedicated Book Services, Clarinda, Iowa, who assembled this high-quality book from a collection of text files and images; Lindsay Williams, the diligent ASM Press Editorial and Rights Coordinator, who shepherded permissions; and the art renderer, Tom Webster of Lineworks, Inc., who created professional illustrations from what were, in some cases, little more than vague sketches.

      This text is based on a course I was hired (in part) to develop and teach in the Department of Microbiology at North Carolina State University. The success of this course is owed to those who recognized its importance before my arrival and encouraged and fostered its development afterwards—especially Leo Parks, Hosni Hassan, and Gerry Luginbuhl, but also the entire faculty of the department.

This book, and the phylogenetic perspective on which it is based, owes everything to Carl Woese, the intellectual father of modern microbiology. The course on which this text is based has its origin not just in Carl’s work generally but also very specifically in his fabulously important review article from 1987 (Woese CR. 1987. Bacterial evolution. Microbiol Rev 51:221–271). The importance and utility of the phylogenetic perspective have no better advocate than my postdoctoral mentor, Norm Pace, for whom no amount of thanks can suffice for his mentorship over the years.

      Enormous credit goes to those who captured the images of organisms used in this text. A picture is worth at least a thousand words. Photo credits are given with the images, but special thanks are warranted to a few who provided numerous images well beyond anything for which I had the right to ask: Michael Thomm and Reinhard Rachel, John Fuerst and Margaret Lindsay, and D. J. Patterson. A special thanks also goes to Howard Spero for allowing us to use his spectacular image of G. bulloides on the cover of this text.

      This book also owes its existence to another James W. Brown, my father, for his patient yet persistent encouragement, and to my mother, Phyllis Brown, who nurtured my scientific interests from the earliest possible age. Finally, and most importantly, I am forever grateful for the encouragement and patience of my wife, colleague, and collaborator, Melanie Lee-Brown.

       About the Author

FROM THE BEGINNING, Jim Brown had a keen interest in nature, including anything slow or unwary enough to be captured or observed in the woods, rivers, beach, or ocean that was always nearby. A single lecture on microbial diversity in a General Microbiology class while Jim was an undergraduate at Ball State University, and the announcement in that class of the discovery of an entirely new kind of living thing (the “archaebacteria”), sparked his lasting interest in microbiology. That led to undergraduate research examining Beggiatoa in a southern Indiana sulfur spring. He later earned his M.S. in Microbiology at Miami University and joined the MCD Biology Ph.D. program at The Ohio State University, where he worked on the molecular biology of methanogenic archaea with Professor John Reeve. He then moved to Indiana University for a postdoc in Professor Norm Pace’s lab, working on the comparative analysis of ribonuclease P RNA in Bacteria. Afterwards, Jim joined the Department of Microbiology at North Carolina State University (NCSU) and continued to work on RNase P in Archaea and the comparative analysis of RNA. Jim developed and teaches senior-level undergraduate lecture and lab courses in microbial diversity, which are the genesis of this textbook. Jim was awarded the NCSU and Alumni Outstanding Teacher awards in 2005 and the Alumni Association Distinguished Undergraduate Professor award in 2014. He has been a member of the ASM since Graduate School and is a long-time officer of the North Carolina branch of the ASM.

      In the well-known children’s story by Dr. Seuss, Horton the elephant discovers that a tiny speck of dust contains an entire world of creatures much too small for him to see.

      SECTION I

      Introduction to Microbial Diversity

      It turns out that every speck of dust, every drop of water, every grain of soil, and every part of every plant and animal around us contain their own worlds of microbial inhabitants (facing illustration).

      A very tiny fraction of these creatures can do us harm, causing misery, disease, and death, and these few creatures have given the microbial world a bad reputation. But the vast majority of microbes benefit us in essential ways that we fail to recognize. They created, and sustain, the world we live in. The famous paleontologist and evolutionary biologist Stephen J. Gould once wrote, “On any possible, reasonable, or fair criterion, bacteria are—and always have been—the dominant forms of life on Earth.”

      Welcome to Principles of Microbial Diversity. In this book we explore, a little bit, the enormous range of biological diversity in the microbial world.

      In the first section of the book, we establish a point of view from which to examine microbial diversity—call this the “phylogenetic perspective.” After some background material, this is primarily a problem-solving section, in which we learn how to construct and interpret evolutionary trees from DNA sequences. We finish up with a look at the universal “tree of life” constructed using this process.

      In the second section, we climb around in this “tree of life,” looking at some examples of microbes on the major branches of the tree—sort of a stroll through the microbial zoo. We extract some conceptual lessons from each group, but this section of the course is mostly about establishing a base of knowledge about the microbial world.

In the third and fourth sections, we learn about how microbiologists are beginning to explore the universe of microbial diversity “in the wild.” We do this directly from published research papers, starting with how new organisms are identified (usually without being cultivated) and progressing in steps to broad surveys of entire microbial communities and attempts to get a handle on how specific kinds of organisms contribute to the ecosystem. This is the conceptual and synthetic portion of the book.

      In the end, I hope you will have gained an appreciation for the “big picture” of the microbial world, an understanding of the power of the phylogenetic perspective, and a realization that the exploration of this world is just beginning, how this is being done, and the questions that drive this exploration.

      We live immersed in an infinite sea of the infinitesimal. Let’s have a look.

      1

      What Is Microbial Diversity?

       Facets of microbial diversity

      What is diversity? How exactly are organisms either similar to or different from each other? This seems like an easy question in the macroscopic world, but what about microbes?

       Morphological diversity

      Microbes are often divided by shape into rods, cocci, and spirals. Although these are the most common cell shapes, bacterial and archaeal cells also come in a wide range of other shapes: filaments (branched or unbranched), irregular, pleomorphic (different shapes under different conditions or even in the same culture), star-shaped, stalked, and many, many others. Haloquadratum is a flat, square organism, just like a bathroom tile (Fig. 1.1).

      Individual cells of whatever shape can be found in a variety of multicellular