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Metadatabase view - dataset: MIcrobial DIversity CHIP

General information

dataset entry ID:
SF_5
name of the dataset:
full name of the dataset:
MIcrobial DIversity CHIP
dataset short name:
MIDI-CHIP
type of dataset (more information):
species distribution data
data type:
point data/observation data
short description of the dataset/summary:
In order to be protected, biodiversity must be evaluated. For cyanobacteria, the traditional morphological measures of biodiversity are unsatisfactory.

We utilize molecular markers (like SSU rRNA) to define taxa on the basis of phylogeny. In freshwater ecosystems huge populations of cyanobacteria can occur. These blooms may release toxins that make the water poisonous. A second part of the study is to compare the temporal dynamics of biodiversity in both natural and disturbed lakes. This comparative analysis requires the use of ecological indexes to summarise the diversity of the samples and allow inferences about the ecosystem to be made.

Further information:
https://cordis.europa.eu/result/rcn/32069_en.html

Molecular dataset:
http://hdl.handle.net/2268/228148

keywords according to GCMD:
topic:
Biosphere, Biological Classification, Terrestrial Hydrosphere
ISO topic category according to ISO 19115:
Environment, Health, Inland Waters
INSPIRE keywords according to GEMET:
Species distribution
own science keywords:
cyanobacteria, microcystins, bloom, toxin, molecular
related project:
Design and testing of dna microarrays to monitor microbial diversity with adequate biodiversity indexes, using cyanobacteria in freshwater as a model system
funding:
EVK2-CT-1999-00026

Technical and administrative specifications

data format:
Access
operating system:
all Windows systems
English
current access level:
web (public)
http://hdl.handle.net/2268/228149
currently available through GBIF:
no
exchange planned:
no
data in data repository:
yes
specify repository:
http://hdl.handle.net/2268/228149
Do you plan to publish the data on the Freshwater Biodiversity Data Portal:
no
update level:
completed
type:
scientific paper
language:
English
contact details:
metadata contact person:
first, last name:
Yannick
 
Lara
phone:
003243663387
email:
ylara@ulg.ac.be
institution:
University of Liège
address:
Quartier Agora B6a
postal code, city:
4000
 
Liège
country
Belgium
technical contact person:
Yannick
 
Lara
003243663387
ylara@ulg.ac.be
scientific contact person:
first, last name:
Yannick
 
Lara
phone:
003243663387
email:
ylara@ulg.ac.be

Intellectual property rights and citation

dataset creator (data compiler):
contact name:
Yannick Lara
contact email:
ylara@uliege.be
contact institution:
University of Liège
data contributors to/owners of this dataset:
multiple
number:
10
data contributor/owner 1
contact name:
Annick Wilmotte
contact email:
awilmotte@ulg.ac.be
contact institute:
University of Liège
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

data contributor/owner 2
contact name:
Kaarina SIvonen
contact email:
Kaarina.Sivonen@helsinki.fi
contact institute:
University of Helsinki
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

data contributor/owner 3
contact name:
Gianluca De Bellis
contact email:
gianluca.debellis@itb.cnr.it
contact institute:
CNR-ITB
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

data contributor/owner 4
contact name:
Pirjo Kuuppo
contact email:
pirjo.kuuppo@ymparisto.fi
contact institute:
Finnish Environment Institute
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

data contributor/owner 5
contact name:
Stefano Ventura
contact email:
stefano.ventura@ise.cnr.it
contact institute:
CNR-ISE
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

data contributor/owner 6
contact name:
Beatrice Montanari
contact email:
b.montanari@unica-spa.it
contact institute:
Hera S.p.A.
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

data contributor/owner 7
contact name:
Peter Henderson
contact email:
peter@irchouse.demon.co.uk
contact institute:
PISCES Conservation Ltd
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

data contributor/owner 8
contact name:
Lucien Hoffmann
contact email:
hoffmann@crpgl.lu
contact institute:
CRP-Gabriel Lippmann
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

data contributor/owner 9
contact name:
Jiri Komarek
contact email:
Komarek@butbn.cas.cz
contact institute:
University of South Bohemia
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

data contributor/owner 10
contact name:
Zalewski Maciej
contact email:
mzal@biol.uni.lodz.pl
contact institute:
University of Lodz
criteria for using this part of the dataset:
The dataset is publicly available (data portal, data archive) and can be used without restrictions, but dataset creator/data contributors must be informed prior to publication. Data must be acknowledged and cited correctly.

citation of this dataset:
author(s):
Lara, Y., Wilmotte, A., Boutte, C., Grubisic, S., Balthasart, P., De Bellis, G., Castiglioni, B., Rizzi, E., Frosini, A., Sivonen, K., Rajaniemi, P., Rantala, A., Kuuppo, P., Lepistö, L., Ventura, S., Mugnai, M.A., Turichia, S., Tedioli, G., Henderson, P., Seaby, R., Hoffmann, L., Willame, R., Komarek, J., Komárková, J., Hrouzek, P., Zalewski, M., Tarczynska, M., Mankiewicz, J., Zydorczyk, K. & Jurczak, T.
title and journal (name, number, pages):
MIcrobial DIversity CHIP database
citation of the metadata:
author(s):
Lara Y., Wilmotte A., Sivonen K., De Bellis G., Kuuppo P., Ventura S., Montarani B., Henderson P., Hoffmann L., Zalewski M. & Komárek J.
title and journal (name, number, pages):
Metadata compilation for the MIDI-CHIP dataset. Freshwater Metadata Journal 37: 1-8
year:
2018
doi (if applicable):
https://doi.org/10.15504/fmj.2018.37

dataset related references:
reference 1:
author(s):
Boutte, C., Mankiewicz-Boczek, J., Komarkova, J., Grubisic, S., Izydorczyk, K., Wautelet, F., Jurczak, T., Zalewski, M. & Wilmotte, A.
title:
Diversity of planktonic cyanobacteria and microcystin occurrence in Polish water bodies investigated using a polyphasic approach. Aquatic Microbial Ecology 51: 223–236.
year:
2008
reference 2:
author(s):
Boutte, C., Grubisic, S., Balthasart, P. & Wilmotte, A.
title:
Testing of primers for the study of cyanobacterial molecular diversity by DGGE. Journal of Microbiological Methods 65(3): 542-550.
year:
2006
reference 3:
author(s):
Boutte, C., Komarkova, J., Grubisic, S., Znachor, P., Bataille, A., Zapomelova, E., Gullukaya, A., Jezberova, J. & Wilmotte, A.
title:
A polyphasic approach to assess the cyanobacterial diversity of summer samples from Czech reservoirs. Algological Studies 117: 177-195.
year:
2005
reference 4:
author(s):
Castiglioni, B., Rizzi, E., Frosini, A., Sivonen, K., Rajaniemi, P., Rantala, A., Mugnai, M.A., Ventura, S., Wilmotte, A., Boutte, C., Grubisic, S., Balthasart, P., Consolandi, C., Bordoni, R., Mezzelani, A., Battaglia, C. & De Bellis, G.
title:
Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria. Applied and Environmental Microbiology 70(12): 7161-7172.
year:
2004
reference 5:
author(s):
Rajaniemi-Wacklin, P., Rantala, A., Mugnai, M.A., Turicchia, S. & Sivonen, K.
title:
Correspondence between phylogeny and morphology of Snowella spp. and Woronichinia naegeliana, cyanobacteria commonly occurring in lakes. Journal of Phycology 42: 226-232.
year:
2006
reference 6:
author(s):
Rantala, A., Fewer, D.P., Hisbergues, M., Rouhiainen, L., Vaitomaa, J., Börner, T. & Sivonen, K.
title:
Phylogenetic evidence for the early evolution of microcystin synthesis. Proceedings of the National Academy of Sciences of the United States of America 101: 568-573.
year:
2004
reference 7:
author(s):
Via-Ordorika, L., Fastner, J., Kurmayer, R., Hisbergues, M., Dittmann, E., Komarek, J., Erhard, M. & Chorus, I.
title:
Distribution of microcystin-producing and non-microcystin-producing Microcystis sp. in European freshwater bodies: detection of microcystins and microcystin genes in individual colonies. Systematic and Applied Microbiology 27: 592-602.
year:
2004
reference 8:
author(s):
Willame, R., Boutte, C., Grubisic, S., Balthasart, P., Wilmotte, A. & Hoffmann, L.
title:
Seasonal cyanobacterial dynamics in a mesoeutrophic reservoir: microscopic counts and DGGE (Denaturing Gradient Gel Electrophoresis). Algological Studies 129: 71-94.
year:
2009

General data specifications

regional coverage of the dataset:
spatial extent of the dataset:
continental
continents:
Europe
countries:
Europe: Belgium, Czech Republic, Finland, France, Italy, Luxembourg, Poland
world climatic regions according to Köppen:
Group C: temperate/mesothermal climates
Group D: continental/microthermal climate
freshwater ecoregions of the world (FEOW) according to WWF:
 
Europe:
Central & Western Europe
European ecoregions according to Illies (WFD):
Italy, Corsica and Malta (ER3), Western Plains (ER13), Baltic Province (ER15), Fenno-Scandian Shield (ER22)
ecosystem type:
lakes/ponds
covered timeframe:
year from
2000
 
year to:
2004

Site specifications

coordinate system/grid data:
grid data available:
no
comments:
Note that there are no coordinate data available for the sites, only local names.
 
number of sites:
100 - 1000
exact number of sites:
197

Biological data

biological data origin:
from sampling
specify project:
MIDI-CHIP project
specify method:
organism group addressed:
other group(s): cyanobacteria
comments:
We only study the diversity of cyanobacteria.

Sample resolution

other group(s)

taxonomic resolution:
order, genus, species
percentage of species level data:
60
comments:
Anabaena compacta, Anabaena cf. affinis, Anabaena cf. circinalis macrospora, Anabaena cf. crassa, Anabaena cf. oscillarioides, Anabaena cf. spiroides, Anabaena circinalis, Anabaena compacta, Anabaena crassa, Anabaena flos-aquae, Anabaena lemmermannii, Anabaena mendotae, Anabaena mucosa, Anabaena planktonica, Anabaena sigmoidea, Anabaena solitaria, Anabaena spiroides, Anabaena vigueri, Anabaenopsis nadsonii, Anabaenopsis sp., Anabaena sp., Aphanizomenon aphanizomenoides, Aphanizomenon cf. flexuosum, Aphanizomenon flos-aquae, Aphanizomenon gracile, Aphanizomenon issatschenkoi, Aphanizomenon ovalisporum, Aphanizomenon sp., Aphanocapsa holsatica, Aphanocapsa incerta, Aphanocapsa sp., Aphanothace minutissima (cf.), Aphanothece brevis, Aphanothece microscopica, Aphanothece sp., Aphanothece stagnina, Calothrix sp., Chroococcales, Chroococcus sp., Cyanobacterium cf. plankticum, Cyanobium cf. plankticum, Cyanobium sp., Cyanodictyon imperfectum, Cyanosarcina sp., Cyanothece sp., Cylindrospermopsis raciborskii, Geitleribactron pertificum, Geitleribactron sp., Aphanocapsa, Geitlerinema sp., Geitlerinema spendida, Geitlerinema splendidum, Gloeotrichia sp., Komvophoron sp., Leptolyngbya sp.,Limnothrix planktonica, Lyngbya sp., Merismopedia sp.,Microcysitis viridis, Microcystis aeruginosa, Microcystis botrys, Microcystis flos-aquae, Microcystis ichtyoblabe,Microcystis sp., Microcystis viridis, Nostoc sp., Nostocales, Oscillatoria and Spirulina, Oscillatoria sp., Phormidium autumnale, Phormidium cf. autumnale, Phormidium sp., Planktolyngbya breviarticulata, Planktolyngbya sp., Planktothrix agardhii, Planktothrix sp., Planktotrix rubescens, Plectonema sp., Pleurocapsales, Pseudanabaena limnetica, Pseudanabaena mucicola, Pseudanabaena, woronichnia, Pseudoanabaena galeata, Pseudoanabaena sp., Snowella litoralis, Spirulina major, Synechocystis sp., Synechococcus cf. nidulans, Synechococcus sp.,Synechococcus sp. (Aphanocapsa holsatica?),Synechococcus/Cyanobium, Synechocystis sp.,Tolypothrix sp., Woronichinia naegeliana

taxonomic coding:
taxalist according to:
Komárek, J. & Anagnostidis, K. (1998)
reference(s):
Komárek, J. & Anagnostidis, K. (1998): Cyanoprokaryota 1. Teil: Chroococcales. - In: Ettl, H., Gärtner, G., Heynig, H. & Mollenhauer, D.(eds): Süsswasserflora von Mitteleuropa 19/1, Gustav Fischer, Jena-Stuttgart-Lübeck-Ulm, 548 pp.
sample specifications:

Other specifications

GIS layers, shape files related to the dataset:
no data available
availability of photos:
no
availability of maps:
no
quality control procedures:
Were any quality control procedures applied to your dataset?
no
Querytime: 0.12687 sec