(a) (b) (c) (d) (e)

 Fig. 1. Images of dinoflagellates that have been identified as Amphidinium operculatum. But there are ~150 other described species in the genus; are all these the same species? Barcoding should help to resolve such uncertainties. (a) Illustration for the type description of A. operculatum Claparède & Lachmann 1859; (b) graphic image (http://microscope.mbl.edu); (c) light micrograph of CCMP strain 123 (http://microscope.mbl.edu); (d) light micrograph of CCAP strain 1102/06 (Edmund Nash); (e) non-motile cell (Mona Hoppenrath & Shauna Murray). Sorting out what we mean by a problem for such groups has, however, been somewhat side- Barcoding is a benchmarking process. type locality (Norway). If all the A. culture-based cross-referencing. Such stepped; first, by use of the ‘candidatus’ label for taxa that On their own, barcodes cannot confer operculatum strains match by barcoding, an advance will re-invigorate and have yet to be cultured (and hence don’t fully comply with the new species status, nor evaluate phylo- that will be reassuring. If they don’t, potentially revolutionize the study of species, and bringing order to higher current ICSP Code); and second, by a range of de-replication genetic relationships. Nevertheless, some further work – with more detailed protists, whilst greatly enhancing the procedures, including ribotyping (using 16S and 18S rRNA when used with an appropriate bio- characterization – will be necessary, value of relevant culture collections. level groupings, are important tag sequences) and whole-cell fingerprinting (e.g. based informatics database, relatively short since it is not obvious which strain on mass spectrometry). Although ribotyping isn’t generally DNA sequences (a few hundred base should retain the A. operculatum name Phil Williamson activities for microbial taxonomists. known as barcoding – the shorthand term for the molecular pairs) offer rapid and effective identifi- and be declared the epitype, as the School of Environmental Sciences, sequencing identification framework for higher plants and cation with good species separation new standard for future reference. The University of East Anglia, Norwich animals (www.barcodinglife.org) – it is basically the same (unambiguous outcomes for >90 % of original (1859) type illustration of A. NR4 7TJ (e [email protected]) But Phil Williamson and his thing: characterization using a short and species-specific case studies to date). Costs are current- operculatum is shown in Fig. 1, together DNA sequence from a standard position in the genome. ly $3 per DNA extract, with the anal- with some other images of organisms Robert A. Andersen colleagues argue that the real priorities ysis process taking a couple of hours. currently considered to be that species. Provasoli-Guillard National Center Protist issues The aim is to achieve at least an order of for Culture of Marine Phytoplankton, are more prosaic, yet pragmatic: For protists (used broadly, not implying monophyly), at magnitude reduction in costs and time International co-operation Bigelow Laboratory for Ocean least 200,000 species have been formally described, based within a decade, so that bio-barcode A co-ordinated, international approach Sciences, West Boothbay Harbor, ‘what exactly is out there?’ and ‘what on phenotypic features, and several thousand representative analysers can be routinely used in every to protist barcoding led by culture ME 04575, USA (e randersen@ strains are maintained in culture. But the evolutionary history science laboratory and school, and collections, and assisted by other mole- bigelow.org) of protists is extremely complex, and while phylum-level taken on every field-collection trip. cular and non-molecular approaches, features should we use to routinely identities are reasonably clear, relationships between taxa are For animals, the COI (cytochrome will have other desirable outcomes. In Frithjof C. Küpper far from straightforward. Other major problems include the c oxidase I) locality is the preferred particular, barcodes will provide a robust NERC Culture Collection for Algae distinguish organisms of different near-impossibility of long-term culture of many parasitic, and gene region, while the suitability of a quality control of what is kept in culture, and Protozoa, Scottish Association highly host-specific, groups (yet these are arguably of greatest chloroplast gene is currently being whilst avoiding unnecessary replication. for Marine Science, Oban PA37 1QA kinds?’ economic importance); a lack of congruence of ICBN and investigated for plants. For protists, the This is important since collections pro- (e [email protected]) Why every protist needs a barcode odern systematics isn’t stamp-collecting. ICZN protocols in the protist realm (14 % of generic names Canadian Barcode of Life Network will vide the reference for species identity; Further reading Even for microbial taxa of relatively limit- for plants have also been used for non-plants); and a lack of initially compare COI data for around they also serve as patent depositories Hebert, P.D.N. & Gregory, T.R. (2005). ed known diversity, no-one expects to consensus on suprafamilial systematics (despite claims to the 1,000 DNA extracts (for ~100 species, (under the Budapest Treaty of 1977) and Syst Biol 54, 852–859. encounter the complete set. Efficient contrary in the November 2006 issue of Microbiology Today). ~10 strains of each). If that target does provide model organisms for physio- Jørgensen, M.F., Murray, S. & identification systems are, however, Furthermore, most original descriptions for protist species are not give good separation, other markers logical and biochemical studies. Mis- Daugbjerg, N. (2004). J Phycol 40, essential to link biodiversity and eco- based on light microscopy and ink drawings, not only making will be tested; alternatives anyway will labelling of cultures due to human error 351–365. Msystem services, to help achieve effective disease control and species identification for some groups an inherently subjective be necessary for protists lacking mito- can occur, even in extremely well- Patterson, D.J. (1999). Am Nat 154 to exploit biotechnological resources. All these applications and specialist occupation, but also potentially hiding major chondria suitable for rRNA analyses. managed collections. Without a routine suppl., S96–S124. require unambiguous and standardized naming frameworks, genetic diversity. genetic identity check, such mistakes Pedrós-Alió, C. (2006). Trends Microbiol anchoring the name to a real specimen or culture. That Testing the system are likely to be perpetuated. 14, 257–263. standard framework is currently provided by the International The barcoding solution Having several, independently collect- Sogin, M.L., Morrison, H.G., Huber, Codes for Botanical and Zoological Nomenclature, and the To help resolve many of the contradictions and uncertainties ed isolates of what is considered to In conclusion J.A., Welch D.M., Huse, S.M., Neal, be the same species is clearly of great International Committee on Systematics of Prokaryotes in protist taxonomy, genetic barcoding is the way forward, Gene sequencing approaches to taxono- P.R., Arrietta, J.M. & Herndl, G.J. (ICBN, ICZN and ICSP). Unfortunately, there are serious starting with material, particularly type strains, in inter- value to launch (and test) a protist my are not without critics, who have (2006). Proc Natl Acad Sci U S A 103, mismatches between the operational requirements of these nationally recognized culture collections. Such an approach barcoding initiative. For example, there expressed concern that principles are 12115–12120. Codes and microbial reality. At the current rate of progress, was unanimously agreed by 40 protist experts from 12 are currently at least eight strains of being sacrificed for the sake of expedi- it will take more than 600 years to properly describe the countries (Australia, Canada, Denmark, France, Germany, the marine dinoflagellate considered ency. But barcoding is intended to com- ~10 million ‘known unknowns’, and potentially an order of Japan, Malaysia, Netherlands, Norway, Russia, UK and USA) to be Amphidinium operculatum (and plement, not replace, traditional meth- magnitude higher for ‘unknown unknowns’. at a workshop last November in Portland, Maine, funded by many other strains of ‘Amphidinium ods for understanding and classifying For prokaryotes (bacteria and archaea), diversity issues are the Sloan Foundation and co-organized by the Culture Center sp.’) in seven culture collections in five whole organisms. For protists, the emph- particularly acute. In a single litre of seawater, there can be for Marine Phytoplankton (hosted by Bigelow Laboratory for countries. This material has been collect- asis is on facilitating identification, con- three times more prokaryotic operational taxonomic units Ocean Science) and the NERC Culture Collection of Algae ed from many locations, including the firming in hours what otherwise might than the global total of ~6,000 recognized species. The naming and Protozoa (Scottish Association for Marine Science). south-west Pacific, but none from the take many months of paper-based or

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