Sloan Foundation Workshop to ResolveMicroorganism Taxonomic and Culture

Collection Problems Arising from the New Barcoding Initiatives

Robert A. AndersenCCMP

Bigelow Laboratory for Ocean Sciences

Frithjof KüpperCCAP

Dunstaffnage Marine Laboratory, SAMS

Introductory Remarks

1. Do we envision DNA sequences playing a role in species identifications?

2. Do we see a need to establish a link between classical species descriptions and DNA sequences?

AmphidiniumOriginal Description

• Claparède, É. and Lachmann, J. 1859. Études sur les Infusoires et les Rhizopodes. Inst. Natl. Genevois 6(1): 410-411

• Type locality: Bergen Fjord, Norway

• CCAP Strains • CCAP 1102/4 Amphidinium sp., Kirby Creek, Hamford Water, Essex, England• CCAP 1102/5 Amphidinium sp., Scarborough, Yorkshire, England • CCMP Strains • CCMP119 Amphidinium operculatum, Knight Key, Florida USA, 8-10 µm x 14-53 µm• CCMP122 Amphidinium operculatum, collection site unknown, 5-12 µm x 9-16 µm• CCMP123 Amphidinium operculatum, Florida Keys, Tea Table Channel, Florida USA, 13-17 µm x 19-30 µm• CCMP1344 Amphidinium operculatum, Knight Key, Florida USA, 10-12 µm x 18-24 µ• CSIRO Strains • CS-109 Amphidinium sp., Coral Sea, Australia, • CS-259 Amphidinium sp., Kirrimine Beach, Queensland, Australia• CS-383 Amphidinium sp., Bicheno, Tasmania, Australia• CS-787/01 Amphidinium sp., Rock pool Wedge Bay, Tasmania, Australia• CS-787/02 Amphidinium sp., Rock pool Wedge Bay, Tasmania, Australia• MBIC Strains • MBIC10794 Amphidinium sp., Sesoko, Okinawa, Japan • MBIC11135 Amphidinium sp., Kin Bay, Okinawa, Japan • NEPCC Strains

• NEPCC670 Amphidinium operculatum, Japan, 31°22'N 113°55'W (Note: originally from CCMP124; this strain is now identified as Amphidinium carterae from Gulf of California, Mexico by CCMP]

• NEPCC799 Amphidinium operculatum, Knight Key, Florida USA• NIES Strains • NIES1368 Amphidinium operculatum, Suzu / Ishikawa, Japan • PLY Strains • PLY587 Amphidinium operculatum• PLY450 Amphidinium sp.• PLY440 Amphidinium sp.

• No type or authentic culture, and none is from the type locality.

• For the sake of argument, let us assume that the barcode sequences are different among the strains. Which strain (and barcode) will be chosen to represent the name Amphidinium operculatum?

• a. Do we choose the one closest to the type locality?

• b. Do we choose the one with the most publications?

• c. Do we choose the first one that was barcoded?

• d. Do we allow the barcoders to randomly select a strain?

• e. Do we choose the strain most closely resembling the type description?

• f. Do we ignore all of these cultures, return to the type locality and search for the organism again?

valid spp. total # spp. ink, EM etc. Biological Culture DNA

Aphelidea 11 8 NA 1 3

Apicomplexa 4296 4,541,500 375 4005 100

Apusomonadida 11 20 10 NA 1 1

Bicosoecida 47 100 10 NA 3 4

Cercomonadida 72 150 59 NA 6 13

Chlorarachniophyta 9 2 1 4 0

Choanoflagellida 161 200 140 NA 13 22

Chrysophyceae 700 2000 675 25 5 0

Ciliates 9000 8000 1500 99 99

Conjugating green algae 7000 21,000 6000 1000

Cryptomonas 126 111 1 14 14 14 epitypes

Diatoms 10,000 100,000 9988 12 12

Dinoflagellates 2000 3500 1970 30

Euglenids 1400 1700 1300 60 15 12

Foraminifera 4000 4000 0 0 10 private cultures

Haptophyta 300 750 290 10 30 0 Edvardsen/Probert

Labyrinthulomycota 50 500 40 20 10 12

Oomycetes 2000 500 250 250 0

Phaeophyceae 1800 2000 70 in culture

Phaeothamniophyceae 28 100 20 8 0 0

Pinguiophyceae 5 15 1 4 4 0

Schizocaldiophyceae 1 1 1 1 1

Synurophyceae 287 175 287 0 0 0

Thaumatomonadida 34 50 31 NA 2 3

subtotal 43338 29818 296

percent with type DNA 0.68%

percent with authentic culture

1.15%

Workshop Guidelines??

1. Be visionary

2. Try not to focus on today’s problems

3. Find broad solutions

Acknowledgements

• Alfred P. Sloan Foundation - Jesse Ausubel

• Canadian Barcode of Life Network - Paul Hebert and many others

• CBoL - David Schindel

• GenBank - EMBL - Scott Federhen and Guy Cochrane