Below are the first 10 and last 10 pages of uncorrected machine-read text (when available) of this chapter, followed by the top 30 algorithmically extracted key phrases from the chapter as a whole.
Intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text on the opening pages of each chapter. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.
Do not use for reproduction, copying, pasting, or reading; exclusively for search engines.
OCR for page 111
14. Academic Publications –Fred A. Rainey39 Louisiana State University As a bacterial taxonomist, today’s discussions have been somewhat surprising for me. I was under the impression that someone who publishes a paper about, say, a mouse with a new trait has to make the mouse accessible to everyone who might want to work on it, but this seems not to be the case. We bacterial taxonomists are a bit more civilized in that if we describe a bacterial species, we have to deposit it in two culture collections in two different countries in the world. This is mandated by the Bacteriological Code, which is overseen by the International Committee of Systematics of the Prokaryotes. When you submit a paper for publication describing a species, your paper cannot be published and your species name cannot be validly published unless you provide a certificate of deposit from the culture collections. Perhaps this is something that could be applied in other areas of biological science. Today, however, I am going to describe an academic publication, Bergey’s Manual of Systematic Bacteriology, which is the work of many bacterial taxonomists and which is published by Bergey’s Manual Trust. The trust is a nonprofit private organization whose role is to produce updated classification and descriptive information about the species of bacteria and archaea. All of this work is done by volunteers. There are no paid members. There are trustees, associates, and all of the authors who contribute the information. Our editorial office is currently at the Department of Microbiology at the University of Georgia. In addition to our main goal of providing up-to-date descriptive information on bacteria and archaea, we also provide an unofficial classification of the bacteria and the archaea using a phylogeny based on the 16S ribosomal RNA gene, which is the gene that is accepted as the hierarchical phylogeny in the prokaryotes. One of our aims has been to provide the scientific community with an inexpensive resource on bacterial taxonomy—books that are not as expensive as most academic publications, which would be accessible even to graduate students and maybe even, in the case of one of our publications, to undergraduates. We also promote bacterial and archaeal taxonomy through publications and scientific meetings. The trust was formed in 1936 as an outgrowth of the Society for Bacteriology, which is now the American Society for Microbiology. The founding trustees were David Bergey, Robert Breed, and Everitt Murray. I am not quite sure how the trust came to be named after Bergey. The trust signed a contract with the publisher Williams & Wilkins to publish Bergey’s Manual of Determinative Bacteriology, of which nine editions have been published so far. The activities of the trust are supported totally by royalties from these publications. The current trustees come not only from the United States but also from the United Kingdom, Germany, Belgium, and Korea, so it is truly an international organization. We have two current publications. One is the ninth edition of the Bergey’s Manual of Determinative Bacteriology, which was last published in 1994, so it is 39 Presentation slides available at: http://sites.nationalacademies.org/xpedio/idcplg?IdcService=GET_FILE&dDocName=PGA_053721&Rev isionSelectionMethod=Latest. 111
OCR for page 111
somewhat out of date. Interestingly enough, it is still in print and sells very well. It is only out of date in that it does not include information on new organisms that have been described since then. However, it has a lot of valuable information on the older organisms, including many of the organisms that people deal with in clinical situations, in industry, and especially in university teaching laboratories. In the last eight or nine years, we have been involved in producing a second edition of Bergey’s Manual of Systematic Bacteriology. This is a much more substantial publication, and this second edition will comprise five volumes. Volume 1 was published in 2001, Volume 2 was published in 2005, and Volume 3 was published last week. Volume 4 is in press and should be also published by early 2010. We hope to have Volume 5 completed in 2010 as well. This second edition is being published by Springer. It is an interesting publication deal because we do everything up to the point of the typesetting and then deal directly with the commercial typesetter, which prints it, and Springer distributes it. In short, it is not the typical academic book situation where the editor collects the manuscripts and sends them to the publisher, which takes it from there. This five-volume work has approximately 600 individual authors involved. The authors, who are from many countries around the world, are each experts in a particular taxonomic group. They assemble the information on each organism described in the literature and then write about it for the publication. This approach guarantees that the information comes directly from the experts, the people who have done the most work with the particular organisms and may be presumed know the most about it. It is quite an achievement to get all these people together to write for the publication. The book is aimed at a global audience of microbiologists and other professionals who work in such areas as the biodiversity of microorganisms and the animal and human health community, as well as at undergraduate and graduate students. The trust has a variety of other activities as well. We publish a taxonomic outline, as I mentioned before. It is available on our website (www.bergeys.org) and shows a total hierarchical structure from the high-level taxa down to the genus level for all of the bacteria and the archaea. We also give out a number of awards. The Bergey’s Award is given each year to a young to middle-aged scientist who has made a significant contribution to bacterial taxonomy. The Bergey’s Medal recognizes senior scientists who have had a lifetime commitment to the field of systematic bacteriology. And we promote the field of bacterial taxonomy by sponsoring sessions at meetings and having experts from various places participate. To give you an idea of what the five-volume Bergey’s Manual of Systematic Bacteriology has to offer, Volume 3 describes 240 genera and 1,346 species belonging to the phylum Firmicutes, which are also known as the low G+C Gram- positive bacteria. This includes a number of well known bacteria, such as Bacillus and Clostridium and Streptococcus species. More generally, the book describes many medically and industrially important organisms. I know that many people have been waiting for this book for quite some time. Each volume is organized with a taxonomic outline at the beginning, followed by descriptions of all taxa that fall within the part of the phylogenetic tree covered by that particular volume. We describe the upper-level taxa—the phylum, the classes, the orders, and the families—and then the lower-level taxa, the genera, species, and subspecies. In some cases there are serovars and pathovars described as well. 112
OCR for page 111
Volume 3 has 1,450 pages and is available on the Springer Web site for $249, which is a bargain for what you get in terms of the number of pages and the amount of information. It is a high-quality, hard copy book with glossy paper and many pictures, photomicrographs, and diagrams. Each of the chapters describes all the information available on a particular genus and on all of the species of that genus, and that information includes all of the phenotypic data as well as some genotypic data. The chapter will also describe how to differentiate each particular species from the other species of the genus as well as how to differentiate particular genera from related genera. As useful as all this is, however, we are still in the situation of publishing a book—a paper thing that is basically like a doorstop and is not something you can easily carry around with you. Nor is it easy to access if you are away from your desk or your bookshelves. So at some point we will need to move from paper to a digital format, but doing so will require us to deal with a variety of issues. First is the amount of material and information that we have. Each of our species descriptions has probably between 150 and 200 characters. We have 8,000 described prokaryote species, so that is a lot of characters. I know that this may not sound like a lot compared with the amount of genome data that is being accumulated, but in bacterial taxonomy terms it is a lot of characters. The second major problem is that we are dealing with a moving target. Every day there are papers being submitted describing new species. Each month when the International Journal of Systematic and Evolutionary Microbiology is published there are perhaps 10 additional genera and 20, 30, or 40 additional species in each new issue. Keeping this body of information updated is a major task. An author who writes about a particular genus may not be enthusiastic about updating the genus chapter just because one additional species has been added. However this updating is important in the context of comparative taxonomy. We need to come up with some workable way of updating the publication on a regular basis. Volume 1 was published in 2001, and there are now probably about 580 genera that were discovered too late to be included in the relevant volume. There are various options for dealing with this issue that we could go ahead with right now. We could, for example, have Web-based access to the information, either in the form of PDFs of the individual chapters or as Web pages in which everything could be searchable and fully linked. We have also considered having some sort of Wiki-type format in the future. It would not be as totally open that anyone could write about anything and change anything they wanted to, but rather the authors of those chapters could continually update their chapters, so that it would be a living document. We are also considering the question of how to get all this information about the characteristics of the organisms, which exists as chapters on the genera and the species, into a database format. This is something we probably have to move to in the future. Then there are also some issues associated who actually owns the data. Even though the volumes are published by Springer, Bergey’s Manual Trust owns the copyright on the printed books, but all of the factual data come initially from the primary literature. The original papers are all referenced in the volumes, but the information is being lifted from the primary literature by the authors of the chapters. Finally, we must determine how we will fund the updating and curating of all of these data in the future and how often we should be updating the data. We are quite 113
OCR for page 111
happy to have all of this be open access, but we will have to have some sort of funding to keep the activity moving along. 114