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1 GUIDE to the NOMENCLATURE and FORMAL TAXONOMIC TREATMENT of OXYPHOTOTROPH PRO

1 GUIDE to the NOMENCLATURE and FORMAL TAXONOMIC TREATMENT of OXYPHOTOTROPH PROKARYOTES (Cyanoprokaryotes) PROPOSAL 2 The proposal of this „Cyano-Guide“ was initiated in the frame of the 8th IAC Symposium in Kastanienbaum, Switzerland, in 1979 (the main theme of this symposium was „Cyanophyta vs. cyanobacteria, principles and problems in taxonomic treatment of natural populations vs. axenic cultures“), and the 9th IAC Symposium in Kastanienbaum and Dübendorf in 1983 (main theme: „Recommendations for a unified approach to the taxonomy of cyanophytes“). Because the proposal of special nomenclatoric rules for cyanophytes/ cyanobacteria seemed to be not acceptable in that time, the preparation of a „Cyano-Guide“ respecting nomenclatoric prescriptions of both, Botanical and Bacteriological Codes, was recommended. The main part of the present Guide was prepared in the period 1983-1990, and from that time not published. However, the urgent need of principles of the nomenclatoric treatment of cyanobacteria increases with intense development of cyanobacterial research in last years, and therefore we send for discussion this proposal (with several recent corrections) as a first step to solve the theory of cyanobacterial nomenclature. The main premises are respected: (i) the rules must be acceptable for both, ecologically and experimentally (bacteriologically) oriented scientists; (ii) the binomial nomenclature can not be avoided (latin names can not be eliminated). Please, read also our „Foreword“ and „Preamble“, where our approach to this difficult problem is more explained. We shall be thankful for all comments, critical remarks and proposals. Jiří Komárek Stjepko Golubić 3 CONTENTS Contents ...........................................………………………………………………………......... Foreword ........................………………..…………………………………….............................. Preamble ...........................................…...……………………………………………….……..... Chapter 1. General Considerations ...…....................………………………………….……….... Section 1. Principles ..................….....……………………………………………..…........... Section 2. Organization .....…………………………………….………..............….............. Chapter 2. Comments to Rules and Recommendations ......……………..…………………....... Section 3. Definitions .............………………….……………………………...................... Section 4. Ranks of Taxa .....................…………………………………………….............. Section 5. Naming of Taxa and Strains ...........………………………………….……......... Section 6. Typification, Starting Points, Priority ......………………………………………. Section 7. Orthography of Names and Epithets ..... ....……………… ....………………..... Section 8. Citation of Authors and Additive Abbreviations. ....……………… ....………... Section 9. Valid publications ........................…………...………………………………...... Section 10. Retention, Choice and Rejection of Names ........………………...…………….. Chapter 3. Conservations ........................... ....……………… ....………………………............ Section 11. Handling with Approved Lists of Conserved Names ....……………………….. Appendix 1. Approved List of Conserved Generic Names ....………………...... Appendix 2. Approved List of Conserved Specific Epithets ....………………... Appendix 3. List of Synonyms and Important Rejected Names ……… ....…………… Appendix 4. List of Type and Reference Strains....................………………………. Appendix 5. List of Collections with Type Strains .... ....……………….... Appendix 6. Abbreviations of Names of Common Authors .... ....………………. Appendix 7. Recommended Journals for Publication of New Taxa ................................... Appendix 8. Schemes of Latin Diagnoses .................... Register ....................................................... 4 The used abbreviations: ICBN = International Code of Botanical Nomenclature ICNB = International Code of Nomenclature of Bacteria Art. = Article of this Guide art. (in connection with ICBN or ICNB) = article in concerning Code Cyano-Guide = this "Guide to the nomenclature treatment of oxyphototroph Prokaryotes". 5 FOREWORD The progress in the Cyanophyte/Cyanobacterial (Cyanoprokaryote) research led to the enormous increase of our knowledge of this group of oxyphototroph microorganisms in last decades. Their bacterial cell structure was recognized in detail and the plant ecological and biochemical properties (presence of chlorophyll a and phycobilins, presence of photosystem II, etc.) were intensely studied. Moreover the group of Prochlorophytes (Chloroprokaryotes) with analogous prokaryotic cell structure and ecological function, but with chlorophylls a and b and without phyco- bilins was discovered, and appeared closely related to Cyanobacteria. The "Cyanophytes" were traditionally classified as "Blue-green Algae", with respect to their morphological diversity and size corresponding to other microalgae, as well as to their function in natural biotopes. Therefore, they were for a long period in the field of interest of botanists (phycologists) and ecologists, and treated as microscopic plant organisms. The detailed cytological and biochemical studies performed by bacteriologists with the use of pure culture strains and of biochemical and el-microscopic procedures, led to the proposal to change the common name of these organisms ("Cyanobacteria" instead of "Cyanophyceae"), and to the opinion, that they should be classified as bacteria and nomenclatorically ruled by the Code of Nomenclature of Bacteria. The introduction of important model strains into the laboratory practice supported this approach. However, this proposal could not be commonly accepted by scientists in spite of the clear prokaryotic character of cells. The populations of cyanoprokaryotes grow in various niches of the biosphere and play an important role in different biotopes belonging to the important oxyphototrophic producers, and the field ecologists are in actual need of orientation in their phenotype system. The possibility to keep a restricted number of known Cyanoprokaryota species in cultured strains in characteristical morphotypes, and the difficulties in culturing of a row of ecologically extreme ecotypes, complicate the simple application of the International Code of Nomenclature of Bacteria (ICBN). However, the International Code of Botanical Nomenclature (ICBN) adopted mainly for vascular plants (or, at least, for eucaryotic plant organisms), is not quite convenient for Cyanoprokaryote as well. From this situation and from the endeavour to come to any compromise of the bacteriological and botanical approaches, several proposals leading to the compatible nomenclatoric procedures using the both bacteriological and botanical Codes were published. The important steps in this endeavour are the compromising proposals of FRIEDMANN et BOROWITZKA (Taxon 31, p. 673-683, 1982) and, recently, the corresponding chapters in the both editions of Bergey’s Manual of Systematic Bacteriology (Vol. 3, CASTENHOLZ et al. 1989, p. 1712-1714; CASTENHOLZ et al. 2001, p. 1710-1806), from which the majority of proposed principles should be accepted in the nomenclature treatment of Cyanophyta/Cyanobacteria. There exist now two Codes of Nomenclature (ICNB and ICBN), which are applicable for oxyphototroph prokaryotes, however, none without obstacles. This Guide to the Nomenclature Treatment of Oxyphototroph Prokaryotes (Cyano-Guide) was elaborated during last years, respecting prescriptions of both Codes, and discussed in several taxonomic sessions of cyanobacteriologists in the frame of the IAC-symposia from 1988 (International Association for Cyanophyte/Cyanobacterial Research) and the grant EU MIDI-CHIP. In particular, we are indebted for valuable comments to: Konstantinos Anagnostidis (Athens), Christopher Boutte (Liège), Richard W. Castenholz (Eugene, Oregon), Pierre Compère (Meise), Lucien Hoffmann (Luxembourg), Jeffrey R. Johansen (Cleveland), John W.G. Lund (Ambleside), Aharon Oren (Haifa), Pirjo Rajaniemi (Helsinki), Kaarina Sivonen (Helsinki), Stefano 6 Ventura (Bologna), Annick Wilmotte (Liège). There was decided to coincide the text with mentioned proposals of FRIEDMANN et BOROWITZKA 1982, CASTENHOLZ et WATERBURY 1989 and CASTENHOLZ 2001, as much as possible. We tried to prepare the Guide, therefore, in a form respecting the modern knowledge about this group, all applicable prescriptions of both mentioned Codes and to keep it opened to the possible useful changes. We accept the opinion, that the nomenclature is conventional and must help to taxonomists, ecologists and experimental scientists in the orientation in the system, and not to complicate their work. More- over, the unification of the opinions of "bacteriologist" and "botanists" as much as possible, is quite indisputable. This Guide is not yet accepted as a "Code", but the principle "pacta sunt servanda" is valid in any nature human community and we hope, that it will be corrected, adapted and accepted by all, who like to work with the fascinating oxyphototroph prokaryotes, cyanophytes, cyanobacteria or prochlorophytes. In Třeboň and Boston, January 1st, 1990. Jiří Komárek, Třeboň Stjepko Golubić, Boston 7 PREAMBLE The algal vs. bacterial characters of oxygenic photosynthetic prokaryotes, i.e., cyanoprokaryotes (Cyanoprokaryota, Cyanophyceae, Cyanobacteria, blue-green algae) and chloroprokaryotes (Chloroprokaryota, Prochlorophyceae, Prochlorales) have been intensely studied particularly from 1960 and discussed in the past decades. The prokaryotic nature, bacterial type of cell structure of these organisms, or the fact that they carry out oxygenic (plant type) photosynthesis possessing chlorophyll a are, of course, not disputable, however, differences in taxonomic and nomenclatorial approaches and practices, that originated from different scientific traditions, remain unsettled. The arguments put forward by representatives of different approaches to taxonomy of Cyanoprokaryota are formidable, but the willingness to resolve the problem by consensus, and thus prevent a creation of at least two separate treatments with separate nomenclatural jurisdiction, remains to be equally strong. Protagonists of both school of thought, one phycological with ecological concerns, and the other bacteriological in tradition and concerned with pure cultures and experimental approaches have been meeting and collaborating. The possibilities to arrive to a unified approach to taxonomy of Cyanoprokaryota and Chloroprokaryota has been evaluated. Among other problems, it has been stated that the elimination of the traditional binomial nomenclature referring to genera and species of Cyanoprokaryota as they are encountered in nature in favor of a taxonomy based on pure cultures alone is unacceptable, because of the difficulties in culturing of many, sometimes ecologically extremely important species, and because of difficulties to establish the identities of those taxa which are present in pure cultures as to the natural taxa of their origin. The International Code of Nomenclature of Bacteria (ICNB) did satisfy all the requirements identified by taxonomists active in ecological settings of Cyanoprokaryota. On the other hand, the International Code of Botanical Nomenclature (ICBN), which was largely adapted from practices developed for and applied to "higher plants" has been criticized by both phycologically (ecologically) and uploads/S4/ cyano-guide.pdf