Capturing biodiversity: linking a cyanobacteria culture collection to the “scratchpads” virtual research environment enhances biodiversity knowledge

Publication Type:Journal Article
Year of Publication:2016
Authors:Gkelis, S, Panou, M
Journal:Biodiversity Data Journal
Date Published:apr
Keywords:biodiversity informatics, cyanobacteria, database, morphology, phylogeny, Scratchpads, taxonomy


Currently, cyanobacterial diversity is examined using a polyphasic approach by assessing morphological and molecular data (Komárek 2015). However, the comparison of morphological and genetic data is sometimes hindered by the lack of cultures of several cyanobacterial morphospecies and inadequate morphological data of sequenced strains (Rajaniemi et al. 2005). Furthermore, in order to evaluate the phenotypic plasticity within defined taxa, the variability observed in cultures has to be compared to the range in natural variation (Komárek and Mareš 2012). Thus, new tools are needed to aggregate, link and process data in a meaningful way, in order to properly study and understand cyanodiversity.

New information
An online database on cyanobacteria has been created, namely the Cyanobacteria culture collection (CCC) ( using as case studies cyano- bacterial strains isolated from lakes of Greece, which are part of the AUTH culture collection (School of Biology, Aristotle University of Thessaloniki). The database hosts, for the first time, information and data such as morphology/morphometry, biogeography, phylogeny, microphotographs, distribution maps, toxicology and biochemical traits of the strains. All this data are structured managed, and presented online and are publicly accessible with a recently developed tool, namely “Scratchpads”, a taxon-centric virtual research environment allowing browsing the taxonomic classification and retrieving various kinds of relevant information for each taxon.

cyanobacteria, database, Scratchpads, taxonomy, morphology, phylogeny, biodiversity informatics

Taxonomic name: 
Chroococcus minutus TAU-MAC 0599 (Cyanobacteria), Microcystis flos- aquae TAU-MAC 0410 (Cyanobacteria), Microcystis aeruginosa TAU-MAC 0610 (Cyanobacteria), Microcystis sp. TAU-MAC 0710 (Cyanobacteria), Microcystis flos- aquae TAU-MAC 1410 (Cyanobacteria), Microcystis flos- aquae TAU-MAC 1510 (Cyanobacteria), Microcystis flos- aquae TAU-MAC 1610 (Cyanobacteria), Microcystis sp. TAU-MAC 1710 (Cyanobacteria), Microcystis viridis TAU-MAC 1810 (Cyanobacteria), Microcystis sp. TAU-MAC 2010 (Cyanobacteria), Microcystis flos- aquae TAU-MAC 2110 (Cyanobacteria), Microcystis sp. TAU-MAC 2310 (Cyanobacteria), Microcystis flos- aquae TAU-MAC 2410 (Cyanobacteria), Synechococcus sp. TAU-MAC 0499 (Cyanobacteria), Limnothrix redekei TAU-MAC 0310 (Cyanobacteria), Synechococcus sp. TAU-MAC 3010 (Cyanobacteria), Jaaginema sp. TAU-MAC 0110 (Cyanobacteria), Jaaginema sp. TAU-MAC 0210 (Cyanobacteria), Jaaginema sp. TAU-MAC 2210 (Cyanobacteria), Pseudanabaena sp. TAU-MAC 0104 (Cyanobacteria), Anabaena cf. oscillarioides TAU-MAC 0199 (Cyanobacteria), Anabaena sp. TAU-MAC 0299 (Cyanobacteria), Anabaena cf. cylindrica TAU-MAC 0699 (Cyanobacteria), Anabaena sp. TAU-MAC 0799 (Cyanobacteria), Anabaena sp. TAU-MAC 0899 (Cyanobacteria), Anabaena sp. TAU-MAC 2510 (Cyanobacteria), Anabaena sp. TAU-MAC 2610 (Cyanobacteria), Anabaena sp. TAU-MAC 2710 (Cyanobacteria), Calothrix sp. TAU-MAC 0399 (Cyanobacteria), Anabaena (Cyanobacteria), Calothrix (Cyanobacteria), Limnothrix (Cyanobacteria), Microcystis (Cyanobacteria), Cyanobacteria (Cyanobacteria)
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith