Biodiversity Data Journal :
Data Paper (Biosciences)
|
Corresponding author:
Academic editor: Nicolas Bailly
Received: 29 Jan 2016 | Accepted: 01 Apr 2016 | Published: 06 Apr 2016
© 2016 Spyros Gkelis, Manthos Panou
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Gkelis S, Panou M (2016) Capturing biodiversity: linking a cyanobacteria culture collection to the “scratchpads” virtual research environment enhances biodiversity knowledge. Biodiversity Data Journal 4: e7965. https://doi.org/10.3897/BDJ.4.e7965
|
|
Currently, cyanobacterial diversity is examined using a polyphasic approach by assessing morphological and molecular data (
An online database on cyanobacteria has been created, namely the Cyanobacteria culture collection (CCC) (http://cyanobacteria.myspecies.info/) using as case studies cyanobacterial 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
Biodiversity is the study of the variety of life at all possible levels of the biological organisation (from genes to ecosystems) and scales of observation (from local to global). Therefore, studies of biodiversity are predicated on the capacity to bring together information from across a diverse spectrum of scientific fields (
Cyanobacteria are a large and morphologically very diverse group of photosynthetic prokaryotes, which occur almost in every illuminated habitat, and quantitatively are among the most important organisms on Earth (
Biodiversity research is at a pivotal point with research projects generating data at an ever increasing rate. Structuring, aggregating, linking and processing these data in a meaningful way is a major challenge (
In this paper, we present “Cyanobacteria culture collection” a database on cyanobacteria hosting, for the first time, information such as morphology/morphometry, biogeography, phylogeny, microphotographs, distribution maps, toxicology, and biochemical traits of cyanobacteria strains isolated from freshwaters of Greece. All those data are structured managed, and presented online and are publicly available through Scratchpads (
The purpose of this database is to make available data associated with cyanobacteria in Greece. The database features information about different traits (morphological, morphometric, biochemical) for cyanobacteria strains. The dataset represents a long-term and ongoing survey that aims to be useful in future investigations of cyanobacteria diversity, phylogeny, ecology, new metabolites discovery.
This dataset is primarily developed to sum our ongoing effort on exploring the biodiversity (morphological, genetic, metabolite) of photosynthetic organisms. Thus, the strains comprising the dataset are from freshwaters of Greece isolated during the past 15 years. However, marine cyanobacteria strains isolated from the Aegean Sea and thermophilic strains isolated from thermal springs (unpublished data) are soon to be included.
The strains were isolated during the years 1999-2015 from 12 different freshwater lakes and reservoirs (Table
Strain |
Origin (Lake or Reservoir) |
Collection date |
Chroococcus minutus AUTH 0599 |
Mikri Prespa |
5/8/1999 |
Microcystis flos-aquae AUTH 0410 |
Pamvotis |
21/8/2010 |
Microcystis aeruginosa AUTH 0610 |
Kastoria |
24/8/2010 |
Microcystis sp. AUTH 0710 |
Kastoria |
24/8/2010 |
Microcystis flos-aquae AUTH 1410 |
Pamvotis |
1/11/2010 |
Microcystis flos-aquae AUTH 1510 |
Pamvotis |
1/11/2010 |
Microcystis sp. AUTH 1610 |
Pamvotis |
1/11/2010 |
Microcystis sp. AUTH 1710 |
Pamvotis |
1/11/2010 |
Microcystis viridis AUTH 1810 |
Pamvotis |
1/11/2010 |
Microcystis sp. AUTH 2010 |
Pamvotis |
1/11/2010 |
Microcystis sp. AUTH 2110 |
Pamvotis |
1/11/2010 |
Microcystis sp. AUTH 2310 |
Pamvotis |
1/11/2010 |
Microcystis flos-aquae AUTH 2410 |
Pamvotis |
1/11/2010 |
Synechococcus sp. AUTH 0499 |
Cheimaditis |
5/8/1999 |
Synechococcus sp. AUTH 3010 |
Pamvotis |
1/11/2010 |
Limnothrix redekei AUTH 0310 |
Doirani |
21/8/2010 |
Jaaginema sp. AUTH 0110 |
Volvi |
21/8/2010 |
Jaaginema sp. AUTH 0210 |
Doirani |
21/8/2010 |
Jaaginema sp. AUTH 2210 |
Kerkini |
21/8/2010 |
Pseudanabaena sp. AUTH 0104 |
Pikrolimni |
27/9/2004 |
Anabaena cf. oscillarioides AUTH 0199 |
Paralimni |
19/7/1999 |
Anabaena sp. AUTH 0299 |
Paralimni |
19/7/1999 |
Anabaena cf. cylindrica AUTH 0699 |
Amvrakia |
19/8/1999 |
Anabaena sp. AUTH 0799 |
Kerkini |
26/8/1999 |
Anabaena sp. AUTH 0899 |
Kerkini |
26/8/1999 |
Anabaena sp. AUTH 2510 |
Doirani |
21/8/2010 |
Anabaena sp. AUTH 2610 |
Doirani |
21/8/2010 |
Anabaena sp. AUTH 2710 |
Doirani |
21/8/2010 |
Calothrix sp. AUTH 0399 |
Pamvotis |
22/7/1999 |
Limnothrix redekei AUTH 0114 |
Karla |
11/09/2013 |
Limnothrix redekei AUTH 0214 |
Karla |
11/09/2013 |
Limnothrix redekei AUTH 0314 |
Karla |
11/09/2013 |
Anabaenopsis elenkinii AUTH 0414 |
Karla |
11/09/2013 |
Planktothrix agarhii AUTH 0514 |
Karla |
11/09/2013 |
Pseudanabaena limnetica AUTH 0614 |
Karla |
11/09/2013 |
Pseudanabaena mucicola AUTH 0714 |
Karla |
11/09/2013 |
Microcystis AUTH 0814 |
Karla |
11/09/2013 |
Microcystis AUTH 0914 |
Karla |
11/09/2013 |
Microcystis AUTH 1014 |
Karla |
11/09/2013 |
Synechococcus AUTH 1114 |
Karla |
11/09/2013 |
Radiocystis AUTH 1214 |
Karla |
11/09/2013 |
Sphaerospermopsis aphanizomenoides AUTH 1314 |
Kalamaki |
22/11/2013 |
Cylindrospermopsis raciborskii AUTH 1414 |
Kalamaki |
22/11/2013 |
Limnothrix redekei AUTH 1514 |
Kalamaki |
22/11/2013 |
Anabaena/Dolichospermum AUTH 1614 |
Kalamaki |
21/02/2014 |
Anabaena/Dolichospermum AUTH 1714 |
Kalamaki |
21/02/2014 |
Hapalosiphon sp. AUTH 0115 |
Trichonida |
08/01/2015 |
The isolates are deposited in Aristotle University of Thessaloniki (AUTH) microalgae collection (Department of Botany, School of Biology). A Zeiss Axio imager z2 (Carl Zeiss, Germany) microscope using bright field and differential interference contrast (EC Plan-Neofluar 5x/0,16,EC Plan-Neofluar 10x/0.3, Plan- Apochromat 20x/0.8, Plan-Neofluar 40x/0.75 DIC, Plan- Neofluar 63x/1.25 Oil DIC, Plan-Neofluar 100x/1.30 Oil DIC) was used to assess morphological and morphometric characters. Microphotographs used in the database were taken with an Axio Cam MRc5 digital camera (Carl Zeiss, Germany). The strains were identified to the species or genus level according to
All taxa in the database were isolated from several Greek freshwater bodies. However, the database is constantly being expanded, so strains from other locations across Greece will be present in the database in the near future.
38°27'N and 41°11'N Latitude; 20°51'E and 23°21'E Longitude.
At present, the database contains 49 strains, representing 22 taxa, 16 genera and seven families (Chroococcaceae, Microcystaceae, Hapalosiphonaceae, Nostocaceae, Rivulariaceae, Phormidiaceae, Pseudanabaenaceae, Synechococcaceae), belonging to four orders in Cyanobacteria class: Chroococcales, Nostocales, Oscillatoriales and Synechococcales. A total of 18 taxa belong to Chroococcales, 15 to Nostocales, 12 to Oscillatoriales and four taxa the Synechococcales (Table
Preview of the “Cyanobacteria culture collection” database collection. The Taxonomy system is presented as part of the "Cyanobacteria" tab; an overview of the strain Chococcus minutus AUTH 0599 is shown as an example.
Rank | Scientific Name |
---|---|
species | Chroococcus minutus |
species | Microcystis flos-aquae |
species | Microcystis aeruginosa |
genus | Synechococcus |
species | Limnothrix redekei |
genus | Jaaginema |
genus | Pseudanabaena |
genus | Anabaena |
genus | Dolichospermum |
genus | Calothrix |
species | Planktothrix agardhii |
species | Pseudanabaena limnetica |
genus | Radiocystis |
species | Sphaerospermopsis aphanizomenoides |
species | Cylindrospermopsis raciborskii |
genus | Hapalosiphon |
species | Cuspidothrix elenkinii |
Information for each strain are given in different tabs after choosing a particular strain. Some strains were characterised based on their morphological features and 16S rRNA gene sequences (
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Column label | Column description |
---|---|
Basis of record | Living specimen or preserved sample |
Catalogue number | The number of each strain in the culture collection |
Collection code | The code of each strain in the culture collection |
Institution code | The institution's code for the collection |
Taxonomic name | Taxonomic name of each strain |
Date collected | Sample collection date |
GenBank number(s) | The number(s) for strains' sequences, where available |
Location | The waterbody where each strain was isolated from |
Date identified | The date each strain was identified |
Part of this work was supported by Aristotle University Research Committee Program “Enhancing Young Investigators-Lecturers: CYaNobacteria diversity Assessment throUgh sTrain pHylogenetic analyses) [CYN-AUTH]” (Contract No 87903) to SG. We thank E. Panteris for valuable help with microscopy, D. Koureas for support and ideas on biodiversity informatics tools, and V. Gerovasileiou for his support. Part of microphotographs and database build are Konstantina Siampouli’s final-year project supervised by SG. The authors would like to aknowledge COST Action ES1105 "CYANOCOST-Cyanobacterial blooms and toxins in water resources: Occurence, impacts and management" and COST Action ES1408 "EUALGAE – European Network for algal bio-products" for networking. We thank all students who helped in the maintenance of the culture collection during the course of this work.
SG conceived and designed the database and prepared the manuscript; MP built the database and contributed in manuscript preparation.