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‘Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects

Correspondence
G. Firrao
firrao{at}uniud.it

	ABSTRACT

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The trivial name ‘phytoplasma’ has been adopted to collectively name wall-less, non-helical prokaryotes that colonize plant phloem and insects, which were formerly known as mycoplasma-like organisms. Although phytoplasmas have not yet been cultivated in vitro, phylogenetic analyses based on various conserved genes have shown that they represent a distinct, monophyletic clade within the class Mollicutes. It is proposed here to accommodate phytoplasmas within the novel genus ‘Candidatus (Ca.) Phytoplasma’. Given the diversity within ‘Ca. Phytoplasma’, several subtaxa are needed to accommodate organisms that share <97·5 % similarity among their 16S rRNA gene sequences. This report describes the properties of ‘Ca. Phytoplasma’, a taxon that includes the species ‘Ca. Phytoplasma aurantifolia’ (the prokaryote associated with witches'-broom disease of small-fruited acid lime), ‘Ca. Phytoplasma australiense’ (associated with Australian grapevine yellows), ‘Ca. Phytoplasma fraxini’ (associated with ash yellows), ‘Ca. Phytoplasma japonicum’ (associated with Japanese hydrangea phyllody), ‘Ca. Phytoplasma brasiliense’ (associated with hibiscus witches'-broom in Brazil), ‘Ca. Phytoplasma castaneae’ (associated with chestnut witches'-broom in Korea), ‘Ca. Phytoplasma asteris' (associated with aster yellows), ‘Ca. Phytoplasma mali’ (associated with apple proliferation), ‘Ca. Phytoplasma phoenicium’ (associated with almond lethal disease), ‘Ca. Phytoplasma trifolii’ (associated with clover proliferation), ‘Ca. Phytoplasma cynodontis' (associated with Bermuda grass white leaf), ‘Ca. Phytoplasma ziziphi’ (associated with jujube witches'-broom), ‘Ca. Phytoplasma oryzae’ (associated with rice yellow dwarf) and six species-level taxa for which the Candidatus species designation has not yet been formally proposed (for the phytoplasmas associated with X-disease of peach, grapevine flavescence dorée, Central American coconut lethal yellows, Tanzanian lethal decline of coconut, Nigerian lethal decline of coconut and loofah witches'-broom, respectively). Additional species are needed to accommodate organisms that, despite their 16S rRNA gene sequence being >97·5 % similar to those of other ‘Ca. Phytoplasma’ species, are characterized by distinctive biological, phytopathological and genetic properties. These include ‘Ca. Phytoplasma pyri’ (associated with pear decline), ‘Ca. Phytoplasma prunorum’ (associated with European stone fruit yellows), ‘Ca. Phytoplasma spartii’ (associated with spartium witches'-broom), ‘Ca. Phytoplasma rhamni’ (associated with buckthorn witches'-broom), ‘Ca. Phytoplasma allocasuarinae’ (associated with allocasuarina yellows), ‘Ca. Phytoplasma ulmi’ (associated with elm yellows) and an additional taxon for the stolbur phytoplasma. Conversely, some organisms, despite their 16S rRNA gene sequence being <97·5 % similar to that of any other ‘Ca. Phytoplasma’ species, are not presently described as Candidatus species, due to their poor overall characterization.

Published online ahead of print on 13 February 2004 as DOI 10.1099/ijs.0.02854-0.

This paper is dedicated to the memory of Monique Garnier-Semancik, fine scientist and friend.

	INTRODUCTION

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Evidence that some plant diseases were associated with phloem colonization by prokaryotes that morphologically resembled mycoplasmas was first presented by Doi et al. (1967). Since then, several hundred plant syndromes have been associated with and thought to be caused by so-called ‘mycoplasma-like organisms' [reviewed by McCoy et al. (1989) and Seemüller et al. (1998)]. Due to their inability to grow in vitro, they were poorly characterized until the advent of molecular biology. Lately, rRNA gene sequencing has provided evidence that the non-spiroplasma, wall-less prokaryotes that colonize plant phloem and insects constitute a large, monophyletic group within the class Mollicutes (Lim & Sears, 1989; Kuske & Kirkpatrick, 1992; Sears & Kirkpatrick, 1994). Therefore, at the 9th Congress of the International Organization of Mycoplasmology in 1992, the Phytoplasma Working Team of the International Research Project for Comparative Mycoplasmology (IRPCM) adopted the trivial name ‘phytoplasma’ to identify prokaryotes that belong to this group and to represent its present composition (International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Mollicutes, 1993). Since then, several distinct taxa have been described as ‘Candidatus (Ca.) Phytoplasma aurantifolia’ (Zreik et al., 1995), ‘Ca. Phytoplasma australiense’ (Davis et al., 1997), ‘Ca. Phytoplasma australasia’ (White et al., 1998), ‘Ca. Phytoplasma fraxini’ (Griffiths et al., 1999), ‘Ca. Phytoplasma japonicum’ (Sawayanagi et al., 1999), ‘Ca. Phytoplasma brasiliense’ (Montano et al., 2001), ‘Ca. Phytoplasma castaneae’ (Jung et al., 2002), ‘Ca. Phytoplasma phoenicium’ (Verdin et al., 2003), ‘Ca. Phytoplasma ziziphi’ (Jung et al., 2003a), ‘Ca. Phytoplasma oryzae’ (Jung et al., 2003b) and ‘Ca. Phytoplasma ulmi’ (Lee et al., 2004b), but a general description of the comprehensive taxon ‘Ca. Phytoplasma’ itself has not yet been provided.

According to a recently adopted taxonomic rule (Murray & Schleifer, 1994; Murray & Stackebrandt, 1995), the properties of uncultured organisms should be recorded by a Candidatus designation. The scope of the present paper is to provide a formal description of the genus ‘Ca. Phytoplasma’ and to summarize its species composition.

	METHODS

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16S rRNA gene sequence analysis.
All GenBank records containing sequences that were defined, or could be referred to, as phytoplasma 16S rRNA genes were downloaded. Partial sequences that contained <1200 bp within the first 1400 positions at the 5' end of the 16S rRNA gene were discarded. Seventy of the 194 selected sequences were aligned manually by using the sequence editor SEQPUP (Gilbert, 1996). Using the profile alignment option of the program CLUSTAL_X (Thompson et al., 1997), the remaining 124 sequences were added to the manual alignment. Distances between sequences were calculated by using the method of Jukes & Cantor (1969) by the DNADIST program of the PHYLIP package (Felsenstein, 1995). The alignment was deposited in TreeBase (http://www.treebase.org/treebase/) under the accession no. S1048-1787. A dendrogram was constructed with the neighbour-joining method of Saitou & Nei (1987) with the CLUSTAL_X program (Thompson et al., 1997) and was used to assist group definition. Sequence signatures were determined with ALISCAN (De Marta & Firrao, 2003). A second alignment that contains only the sequences of reference strains for the ‘Ca. Phytoplasma’ species recognized in this work is available from TreeBase under the accession no. S1048-1788.

	RESULTS AND DISCUSSION

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Evidence for an unambiguously identifiable taxon to encompass all plant-pathogenic, non-helical Mollicutes has been provided by several independent phylogenetic analyses (Lim & Sears, 1989; Kuske & Kirkpatrick, 1992; Namba et al., 1993b; Gundersen et al., 1994; Kirkpatrick et al., 1994; Sears & Kirkpatrick, 1994; Seemüller et al., 1994, 1998, 2002; Smart et al., 1994; Toth et al., 1994; Tymon et al., 1998; Lee et al., 2000). Accordingly, phytoplasmas represent a clearly distinct, monophyletic cluster within the class Mollicutes.

Description of ‘Candidatus Phytoplasma’
‘Candidatus Phytoplasma’ (from phytos, Greek for plant and plasma, Greek for thing moulded) [(Mollicutes) NC; NA; O; NAS (GenBank accession no. M30790); oligonucleotide sequence of unique region of the 16S rRNA gene is CAAGAYBATKATGTKTAGCYGGDCT; P (Plant, phloem; Insect, salivary gland); M].

Morphology.
‘Ca. Phytoplasma’ cells are surrounded by a single-unit membrane, lack rigid cell walls and are pleomorphic in shape (Doi et al., 1967). When observed by transmission electron microscopy, they appear as rounded to filamentous, pleomorphic bodies with a mean diameter of 200–800 nm [reviewed by Kirkpatrick (1992) and Lee et al. (2000)].

Habitat.
Organisms that belong to the genus ‘Ca. Phytoplasma’ inhabit the phloem sieve elements (and, more rarely, also parenchymal cells) of vascular plants and the gut, haemolymph, salivary gland and other organs of sap-sucking insects. In insect hosts, they may cause premature mortality. In plant hosts, they may cause complex syndromes with specific symptoms, such as virescence, phyllody, sterility of flowers, proliferation of auxiliary or axillary shoots, abnormal elongation of internodes and many other, often less specific symptoms [reviewed by McCoy et al. (1989), Kirkpatrick (1992) and Lee et al. (2000)].

Antibiotic sensitivity.
Members of the genus ‘Ca. Phytoplasma’ are sensitive to antibiotics of the tetracycline group, but not to penicillin (Ishiie et al., 1967).

Base composition of DNA.
According to results from buoyant density centrifugation, the G+C content of ‘Ca. Phytoplasma’ DNA is 23–29 mol% (Kollar & Seemüller, 1989; Sears et al., 1989).

Chromosome size.
The size of ‘Ca. Phytoplasma’ chromosomes ranges from 530 kbp to 1350 bp, as estimated from mobility on PFGE (Neimark & Kirkpatrick, 1993; Marcone et al., 1999).

Codon usage.
Members of the genus ‘Ca. Phytoplasma’ use UGA as a stop codon and not as a tryptophan codon, as in several other mycoplasmas (Lim & Sears, 1991; Toth et al., 1994).

Sterols in cellular membrane.
‘Ca. Phytoplasma’ membranes are resistant to digitonin and sensitive to hypotonic salt solutions, and are therefore similar to those of non-sterol-requiring mollicutes (Lim et al., 1992).

rRNA.
Specific nucleotide signatures that are characteristic of ‘Ca. Phytoplasma’ are: A at position 242, T at position 286 and T at position 1247 (in the sequence with GenBank accession no. M30790). Oligonucleotides that have been shown to specifically target ‘Ca. Phytoplasma’ 16S rRNA genes in PCRs have been published (Deng & Hiruki, 1991; Ahrens & Seemüller, 1992; Firrao et al., 1993; Lee et al., 1993b; Namba et al., 1993a; Schneider et al., 1993; Padovan et al., 1995; Gundersen & Lee, 1996). All strains of ‘Ca. Phytoplasma’ that have been investigated so far have two rRNA operons (Schneider & Seemüller, 1994; Firrao et al., 1996b; Lauer & Seemüller, 2000; Padovan et al., 2000; Marcone & Seemüller, 2001) and, usually, a single tRNA^Ile in the spacer region between the 16S and 23S rRNA genes (Kuske & Kirkpatrick, 1992; Smart et al., 1996). Heterogeneity of the two operons is apparent in some phytoplasmas (Lee et al., 1993b; Firrao et al., 1996a; Liefting et al., 1996; Davis & Sinclair, 1998; Jomantiene et al., 2002).

Species belonging to ‘Ca. Phytoplasma’
A similarity matrix that included all 16S rRNA gene sequences of named phytoplasma strains that were deposited in public databases was constructed. Sequences were ordered in a dendrogram and groups of sequences that shared 97·5 % or more similarity among themselves and <97·5 % similarity with any other sequence were identified. One sequence from each group was selected as representative and the corresponding strain is described as a subtaxon within the ‘Ca. Phytoplasma’ taxon. According to Stackebrandt & Goebel (1994), ‘at sequence homology values below about 97·5 % [in the 16S rRNA gene], it is unlikely that two organisms have more than 60 to 70 % DNA similarity and hence that they are related at the species level’.

A congruent amount of results has already been produced in recent years, showing that phytoplasma strains that have <97·5 % similarity in their 16S rRNA gene sequence actually represent different organisms, on the basis of phylogenetic analysis based on 16S rRNA gene sequences (Namba et al., 1993b; Gundersen et al., 1994; Seemüller et al., 1994, 1998; Tymon et al., 1998; Lee et al., 2000), 16S–23S rRNA gene spacer sequences (Kirkpatrick et al., 1994), 23S rRNA gene sequences (Guo et al., 1998), ribosomal protein gene sequences (Jomantiene et al., 1998; Lee et al., 1998), transcription factor Tu gene (Schneider et al., 1997a), restriction analysis of the same genes (Schneider et al., 1993, 1997a, b; Vibio et al., 1996; Lee et al., 1998), RFLP of total DNA with chromosomal probes (Lee & Davis, 1988; Bertaccini et al., 1990; Harrison et al., 1991, 1992; Hibben et al., 1991; Kuske et al., 1991; Lee et al., 1991, 1992a, b, 1993a; Daire et al., 1992; Davis et al., 1992a, b; Ahrens et al., 1993; Mäurer et al., 1993; Chen et al., 1994; Griffiths et al., 1994; Davis & Sinclair, 1998) and biological properties, such as insect vector specificity (Tsai, 1979; Shiomi & Sugiura, 1984; Kirkpatrick, 1992).

However, there is evidence that some groups that are defined at 97·5 % or higher 16S rRNA gene sequence similarity include phytoplasma strains with very different biological (i.e. insect vector), phytopathological (i.e. host plant specificity and symptomatology) and molecular (i.e. chromosome size) characteristics. These strains need to be distinguished taxonomically. It has been highlighted in the past that in several taxonomic groups, organisms with highly similar or even identical 16S rRNA gene sequences may nevertheless share <70 % DNA similarity (as estimated by DNA–DNA reassociation studies) and therefore belong to different species (Fox et al., 1992; Stackebrandt & Goebel, 1994; Stackebrandt et al., 2002; Botti & Bertaccini, 2003). In the case of the phytoplasmas, there are also practical reasons of concern, as organisms that share high 16S rRNA gene sequence similarity may cause different plant diseases, subject to quarantine regulations. Therefore, in addition to the minimal set of species belonging to ‘Ca. Phytoplasma’ that are defined by 97·5 % 16S rRNA gene sequence similarity, more Candidatus species have been defined to distinguish between those organisms that proved to be significantly different on the basis of biological and genetic properties.

In order to prevent nomenclatural confusion that may arise from the description of poorly differentiated novel taxa, the Phytoplasma/Spiroplasma Working Team of the IRPCM (2000) suggested rules for the description of organisms as novel taxa within ‘Ca. Phytoplasma’, as follows.

(a) The ‘Ca. Phytoplasma’ species description should refer to a single, unique 16S rRNA gene sequence (>1200 bp). The strain from which this sequence was obtained should be named the ‘reference strain’ and not the ‘type strain’. Strains in which even minimal differences in the 16S rRNA gene sequence from the reference strain are detected do not ‘belong’ to the Candidatus species, but are ‘related’ to it.

(b) In general, a strain can be described as a novel ‘Ca. Phytoplasma’ species if its 16S rRNA gene sequence has <97·5 % similarity to that of any previously described ‘Ca. Phytoplasma’ species.

(c) There are, however, cases of phytoplasmas that share >97·5 % of their 16S rRNA gene sequence, but clearly represent ecologically separated populations and, therefore, may deserve description as separate species. For such cases, description of two different species is recommended only when all three of the following conditions apply:

(i) the two phytoplasmas are transmitted by different vectors;

(ii) the two phytoplasmas have a different natural plant host (or, at least, their behaviour is significantly different in the same plant host);

(iii) there is evidence of significant molecular diversity, achieved by either hybridization to cloned DNA probes, serological reaction or PCR-based assay.

(d) The rank of subspecies should not be used.

(e) The reference strain should be made available to the scientific community from the authors of the Candidatus species description paper and it should be deposited (unless in vitro micropropagation proves impossible) in the micropropagated collection of Dr Assunta Bertaccini, DiSTA, Patologia Vegetale, Università di Bologna, Italy.

(f) Manuscripts that describe a novel ‘Ca. Phytoplasma’ species should preferably be submitted to the International Journal of Systematic and Evolutionary Microbiology (IJSEM).

(g) The abbreviation for Candidatus is Ca. (e.g. ‘Ca. Phytoplasma japonicum’ stands for ‘Candidatus Phytoplasma japonicum’).

It is recommended that future descriptions of ‘Ca. Phytoplasma’ species follow the above rules. In order to provide a standard reference for the calculation of 16S rRNA gene sequence similarities between potential novel isolates and currently described ‘Ca. Phytoplasma’ species, a reference sequence alignment is available from TreeBase under accession no. S1048-1788 (see Methods). For direct comparison and reference, strains that have been used to define each ‘Ca. Phytoplasma’ species can be obtained from the collection of A. Bertaccini (see address above). For phytoplasmas that cannot be maintained in in vitro propagation collections, reference DNA (total DNA extracted from an infected plant) should be obtained from the corresponding author of the species description papers.

Table 1 reports a list of taxa that belong to ‘Ca. Phytoplasma’, identified as described above, and a list of 16S rRNA gene sequences of related strains. The listed taxa either have already been described individually in past issues of IJSEM or are described in accompanying papers in this issue or in forthcoming papers; the reader is referred to the original papers for their detailed descriptions (Zreik et al., 1995; Davis et al., 1997; White et al., 1998; Griffiths et al., 1999; Sawayanagi et al., 1999; Montano et al., 2001; Jung et al., 2002, 2003a, b; Hiruki & Wang, 2004; Lee et al., 2004a, b; Marcone et al., 2004a, b; Seemüller & Schneider, 2004). The taxon ‘Ca. Phytoplasma australasia’ is not retained, as its 16S rRNA gene sequence is 99·5 % similar to that of ‘Ca. Phytoplasma aurantifolia’ and there is no evidence that conditions (i) and (iii) of rule (c) above are satisfied.

	ACKNOWLEDGEMENTS

 
The IRPCM Phytoplasma/Spiroplasma Working Team – Phytoplasma taxonomy group consists of: G. Firrao (head), Università di Udine, Italy; M. Andersen, HortResearch, Auckland, New Zealand; A. Bertaccini, Alma Mater Studiorum University of Bologna, Bologna, Italy; E. Boudon, INRA, Dijon, France; J. M. Bové, Université de Bordeaux 2 and INRA, I.B.V.M., Villenave d'Ornon, France; X. Daire, INRA, Dijon, France; R. E. Davis, ARS-USDA, Beltsville, MD, USA; J. Fletcher, Oklahoma State University, Stillwater, OK, USA; M. Garnier, INRA, Villenave d'Ornon, France; K. S. Gibb, Charles Darwin University, Darwin, Australia; D. E. Gundersen-Rindal, ARS-USDA, Beltsville, MD, USA; N. Harrison, University of Florida, Fort Lauderdale, FL, USA; C. Hiruki, University of Alberta, Edmonton, Canada; B. C. Kirkpatrick, University of California, Davis, CA, USA; P. Jones, Rothamsted Research, Harpenden, UK; C. R. Kuske, Los Alamos National Laboratory, Los Alamos, NM, USA; I.-M. Lee, ARS-USDA, Beltsville, MD, USA; L. Liefting, HortResearch, Auckland, New Zealand; C. Marcone, Università degli Studi della Basilicata, Potenza, Italy; S. Namba, University of Tokyo, Tokyo, Japan; B. Schneider, Biologische Bundesanstalt, Dossenheim, Germany; B. B. Sears, Michigan State University, East Lansing, MI, USA; E. Seemüller, Biologische Bundesanstalt, Dossenheim, Germany; C. D. Smart, Cornell University, Geneva, NY, USA; C. Streten, Charles Darwin University, Darwin, Australia; and K. Wang, University of Alberta, Edmonton, Canada.

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