New image analysis tool to study biomass and morphotypes of three ...

The following appendices accompany the article
FEATURE ARTICLE
New image analysis tool to study biomass and morphotypes
of three major bacterioplankton groups in an alpine lake
Thomas Posch 1, *, Josef Franzoi 2 , Martin Prader 2 , Michaela Maria Salcher 1
1 Department of Limnology, Institute of Plant Biology, University of Zürich, Seestrasse 187, 8802 Kilchberg, Switzerland
2 Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
*Email: posch@limnol.uzh.ch
Aquatic Microbial Ecology 54:113–126 (2009)

Appendix 1. Summary of recent (since the year 2002) studies reporting proportions (%) of
Bacteria on total DAPI stained particles in freshwater systems. Bacteria were either
hybridized by the FISH or the CARD-FISH technique, using probes EUB338 or EUBI-III.
For studies published before 2002 we refer to the review by Bouvier & del Giorgio (2003)
System Habitat Type FISH CARD-
FISH
Applied
probe
Reference
Achensee Surface L 64 EUBI-III Warnecke et al. 2005
Delaware estuary River inflow E 62-76 EUB338 Yokokawa et al. 2004
Dilution culture
Surface – salinity E 45-80 EUB 338 Kirchman et al. 2003
gradient
Drachensee Surface L 82 EUBI-III Warnecke et al. 2005
Geirneggsee Surface L 89 EUBI-III Warnecke et al. 2005
Gossenköllesee Surface L 55-60 60-90 EUB338 Sekar et al. 2003
Surface L 81 EUBI-III Warnecke et al. 2005
Surface L 85-90 EUB338 Pérez & Sommaruga 2006
Grosse Fuchskuhle
NE basin
Grosse Fuchskuhle
SW basin
Nutrient
L 82-96 EUB338 Pérez & Sommaruga 2007
enrichment
Surface L 82-93 EUBI-III Allgaier & Grossart 2006
Surface L 85-95 60-100 EUB338 Sekar et al. 2003
Surface L 89-97 EUBI-III Allgaier & Grossart 2006
Lake Aydat
Free bacteria
Attached bacteria
L 57±15
75±5
EUB338 Lemarchand et al. 2006
Lake Breiter Surface L 84-100 EUBI-III Allgaier & Grossart 2006
Luzin
Lake Cadagno Surface L 60-70 40-80 EUB338 Sekar et al. 2003
Lake Čertovo
Surface
Bottom
L 22-56
0-34
EUB338 Vrba et al. 2003
Lake Constance Surface L 10-59 EUB338 Zwisler et al. 2003
Lake Pavin
Lake Plešné
Lake Prášilské
Lake Stechlin
Free bacteria
Attached bacteria
Surface
Bottom
Surface
Bottom
Surface
Bottom
L 49±12
77±9
L 17-59
25-37
L 17-61
22-53
L 35-98
36-99
EUB338 Lemarchand et al. 2006
EUB338 Vrba et al. 2003
EUB338 Vrba et al. 2003
EUBI-III Allgaier & Grossart 2006
Lake Tiefwaren Surface L 77-100 EUBI-III Allgaier & Grossart 2006
Mackenzie River Surface L 52-64 EUB338 Garneau et al. 2006
Mittlerer
Plenderlesee
Surface L 95 EUBI-III Warnecke et al. 2005

Appendix 1 (continued)
North Pine Dam
(Drinking water
reservoir)
Oberer
Plenderlesee
Surface
Bottom
L 11-21
21-23
41-54
52-57
EUB338 Nielsen et al. 2006
Surface L 86 EUBI-III Warnecke et al. 2005
Orlik reservoir Surface L 35-60 EUB338 Mašín et al. 2003
Piburger See Surface L 40-50 40-80 EUB338 Sekar et al. 2003
Manipulated size L 39-89 EUBI-III Salcher et al. 2007
fractions
Surface L 63-75 EUBI-III Salcher et al. 2007
Surface L 63 EUBI-III Warnecke et al. 2005
Římov reservoir Surface L 56-83 EUB338 Mašín et al. 2003
Manipulated size L 50-85 EUB338 Šimek et al. 2003
fractions
Manipulated size
fractions
L 55-85 EUB338 Horňák et al. 2005
Manipulated size L 62-89 EUB338 Horňák et al. 2006
fractions
Manipulated size L 45-70 EUB338 Weinbauer et al. 2007
fractions
Manipulated size L 65-78 EUBI-III Horňák et al. 2008
fractions
Surface L 56-86 EUB338 Šimek et al. 2008
Rotfelssee Surface L 91 EUBI-III Warnecke et al. 2005
Sau reservoir Manipulated size L 43-76 EUB338 Gasol et al. 2002
fractions
Seebensee Surface L 76 EUBI-III Warnecke et al. 2005
Schwarzsee ob Surface L 91 EUBI-III Warnecke et al. 2005
Sölden
5 high mountain Surface L 52-67 EUB338 Wu et al. 2006
lakes (Tibetan
Plateau)
Ranges L 0-95 35-100
Groundwater G 6-21 59-75 EUB338 Wilharitz et al. 2007
Groundwater
G 9-25 62-82 EUBI-III Wilhartitz et al. 2007
spring
Eutrophic pond L 75 25* EUB338 Schönhuber et al. 1997
Freshwater
R 56 EUB338 Stevens et al. 2007
drainage channel
Warnow (lowland Surface R 14-63 EUB338 Freese et al. 2006
river)
Mahoning River Biofilm R 16->100 EUB338 Olapade & Leff 2004
Stream Benthic detritus R 27-47 32-41 EUB338 Fazi et al. 2005
Ranges G, R 6-100 25-82
* : no cell permeabilization, E = estuary (freshwater part), G = groundwater, L = lake, R = river

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APPENDIX 2. Screenshots of the image analysis procedure for the detection of DAPI stained bacterial
morphotypes. The following morphotypes are visible: (A) large rods (elongation >2.3), 2 misclassified vibrioid
cells are marked by circles; (B) vibrio-shaped cells; (C) large cocci; (D) small rods; (E) small cocci; (F)
summary picture to control the effectiveness of the detection process