ACTINOMYCETE TAXONOMY

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1 SOCIETY FOR INDUSTRIAL MICROBIOLOGY ACTINOMYCETE TAXONOMY (Procedures for Studying Aerobic Actinomycetes with Emphasis on the Streptomycetes) Edited by A. Dietz Research Laboratories, The Upjohn Company Kalamazoo, Michigan and D.W. Thayer Department of Biological Sciences, Texas Tech University Lubbock, Texas universitatsbibuothsk \ NANNO'^? INFOPf/.A'f lonsijiyuothek ) SIM SPECIAL PUBLICATION NUMBER 6 Copyright 1980 Society for Industrial Microbiology - "All Rights Reserved"

2 TABLE OF CONTENTS Introduction 1 Procedures for studying and characterizing actinomycetes with emphasis on the streptomycetes. Part I. An industrial laboratory approach 2 Part II. A government laboratory approach 152 Part III. A university laboratory approach (emphasis on generic characterization) Numerical taxonomy and DNA homology 292 Microscopy 328 Nomenclature ; 345 Glossary 358 Index 375 Author «375 Media 38 iv

3 PART I. An Industrial Laboratory Approach A. DIETZ (Research Laboratories, The Upjohn Company) Actinomycetes - what are they? 3 Why did we have a workshop on actinomycetes? 4 Why emphasize streptomycetes? 5 Obj ectives of the workshop 6 Significant characterization information 10 Slides (Listing of cultures photographed for inclusion with text) 13 Procedures for obtaining significant characterization information for actinomycetes 18 Other procedures 22 Media for actinomycete characterization studies 26 Development of taxonomic concepts 32 Keys for actinomycete genus and species determination 34 TUC KEYS 1. Generic key A. Dietz Streptomycete key (based on Ektachrome or Ektacolor) A. Dietz Development of a computer key for actinomycetes R. E. Barnes Key for identification of actinomycetes with emphasis on the genus Streptomyaes...R. E. Barnes, A. Dietz, G. P. Li 56 USEFUL KEYS (listed chronologically) I. GENERIC KEYS 141 II. SPECIES KEYS 141 Useful references to actinomycetes (listed chronologically) I. General 144 II. Specific Genera 147 Literature Cited 149 Copyright The Upjohn Company "All Rights Reserved" 2

4 PART II. A Government Laboratory Appoach I T. G. Pridham and A. J. Lyons (NRRC, USDA) I. Isolation II. Purification III. Counting IV. Media for Isolation, Counting, Maintenance, Preservation, and Characterization of Aerobic Aatinomyoetales 166 V. Strain Acquisition 177 A. Handling 177 B. Records 179 VI. Strain Preservation 179 A. Lyophile Process 179 B. Soil Culture 187 VII. Characterization of Strains for Generic Identification 192 VIII. Identity to Genus of Aatinomyeetales Containing LL-Diaminopimelic Acid 192 IX. Key to Genera of Aatinomyeetales Containing LL-Diaminopimelic Acid 192 X. Characterization of Strains for Identification 194 XI. Identification of Strains of Streptomyces and Streptoverticillia with Key 204 XII. Addendum - Identification of "Unknown" by Workshop Participants 211 XIII. Legends of Figures 214 XIV. Figures XV. Literature

5 PART III. A University Laboratory Approach Mary P. and Hubert A. Lechevalier (Rutgers) Introduction 227 Cell Composition 228 Methods Used in Whole Cell Analysis 229 Methods Used in Cell Wall Analysis of Actinomycetes 234 Glycolylation of Muramic Acid 238 Separation of Actinomycetes into Genera Based on Morphology and Cell Wall Composition 239 Mycolic Acids 239 Phospholipids 245 Respiratory Quinones 256 Classification Based on Morphology and Chemical Characteristics 258 Appendix of Reagents 261 Literature Cited 262 Tables Table 1. Major Critical Constituents of Cell Walls of Actinomycetes 266 Table 2. Cell Wall Types and Whole-Cell Sugar Patterns of Aerobic Actinomycetes Containing meso-diaminopimelic Acid 267 Table 3. Presence of Major Amounts of Glycolic Acid in Actinomycetes 268 Table 4. Summary of the Properties of Fermentative Actinomycetes 269 Table 5. Genera of Aatinomyeetales with a Type I Cell Wall 270 Table 6. Genera of Aatinomyeetales with a Type II Cell Wall 271 Table 7. Genera of Aatinomyeetales with a Type III Cell Wall 272 Table 8. Genera of Aatinomyoetales with a Type IV Cell Wall' 273 Table 9. Phospholipid Patterns of Aerobic Actinomycetes

6 Table 10. Phospholipid Fatty Acid Types 275 Table 11. Menaquinone Composition of Aatinomyoetales 276 Table 12. Chemotaxonomic Summary of the Aatinomyoetales 278 Legends of Figures 281 Figures 284

7 NUMERICAL TAXONOMY AND DNA HOMOLOGY. W. H. Trejo (The Squibb Institute for Medical Research) Abstract 293 NUMERICAL TAXONOMY 29 4 Introduction 294 Common Pitfalls in Numerical Taxonomy Studies 296 Guide for Numerical Taxonomy Study 300 Application of Numerical Taxonomy to Special Problems in Classification 310 Computer Assisted Identification 312 DNA HOMOLOGY 313 Procedure for the Isolation of DNA from Streptomycetes 313 Procedure for DNA Homology by Free Reassociation. 313 Tables Table 1. Unit Characters Useful for Streptomycete Taxonomy 304 Table 2. Some Comments on Techniques Employed in DNA Reassociation Studies 314 Table 3. Homology Relationships Among Strains of Stveptomyces 321 Figures Figure 1. Cluster Diagram of Groups 309 Figure 2. Semi-matrix of a Hypothetical Cluster 311 Literature Cited

8 MICROSCOPY J. A. Brown (w. C. McCrone Associates, Inc.) ^SS. Abstract 328 Introduction 328 Optical Microscopy (OM or LM) 328 Transmission Electron Microscopy (TEM) 329 Scanning Electron Microscopy (SEM) 330 Operational Principles of the SEM 330 Sample Preparation for the SEM 332 Micrographic Interpretation 334 SEM Observations 336 Conclusions 337 Literature Cited 337 Figures 338 I 1 ")-!

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