New image analysis tool to study biomass and morphotypes of three ...
New image analysis tool to study biomass and morphotypes of three ...
New image analysis tool to study biomass and morphotypes of three ...
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The following appendices accompany the article<br />
FEATURE ARTICLE<br />
<strong>New</strong> <strong>image</strong> <strong>analysis</strong> <strong><strong>to</strong>ol</strong> <strong>to</strong> <strong>study</strong> <strong>biomass</strong> <strong>and</strong> <strong>morphotypes</strong><br />
<strong>of</strong> <strong>three</strong> major bacterioplank<strong>to</strong>n groups in an alpine lake<br />
Thomas Posch 1, *, Josef Franzoi 2 , Martin Prader 2 , Michaela Maria Salcher 1<br />
1 Department <strong>of</strong> Limnology, Institute <strong>of</strong> Plant Biology, University <strong>of</strong> Zürich, Seestrasse 187, 8802 Kilchberg, Switzerl<strong>and</strong><br />
2 Institute <strong>of</strong> Ecology, University <strong>of</strong> Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria<br />
*Email: posch@limnol.uzh.ch<br />
Aquatic Microbial Ecology 54:113–126 (2009)
Appendix 1. Summary <strong>of</strong> recent (since the year 2002) studies reporting proportions (%) <strong>of</strong><br />
Bacteria on <strong>to</strong>tal DAPI stained particles in freshwater systems. Bacteria were either<br />
hybridized by the FISH or the CARD-FISH technique, using probes EUB338 or EUBI-III.<br />
For studies published before 2002 we refer <strong>to</strong> the review by Bouvier & del Giorgio (2003)<br />
System Habitat Type FISH CARD-<br />
FISH<br />
Applied<br />
probe<br />
Reference<br />
Achensee Surface L 64 EUBI-III Warnecke et al. 2005<br />
Delaware estuary River inflow E 62-76 EUB338 Yokokawa et al. 2004<br />
Dilution culture<br />
Surface – salinity E 45-80 EUB 338 Kirchman et al. 2003<br />
gradient<br />
Drachensee Surface L 82 EUBI-III Warnecke et al. 2005<br />
Geirneggsee Surface L 89 EUBI-III Warnecke et al. 2005<br />
Gossenköllesee Surface L 55-60 60-90 EUB338 Sekar et al. 2003<br />
Surface L 81 EUBI-III Warnecke et al. 2005<br />
Surface L 85-90 EUB338 Pérez & Sommaruga 2006<br />
Grosse Fuchskuhle<br />
NE basin<br />
Grosse Fuchskuhle<br />
SW basin<br />
Nutrient<br />
L 82-96 EUB338 Pérez & Sommaruga 2007<br />
enrichment<br />
Surface L 82-93 EUBI-III Allgaier & Grossart 2006<br />
Surface L 85-95 60-100 EUB338 Sekar et al. 2003<br />
Surface L 89-97 EUBI-III Allgaier & Grossart 2006<br />
Lake Aydat<br />
Free bacteria<br />
Attached bacteria<br />
L 57±15<br />
75±5<br />
EUB338 Lemarch<strong>and</strong> et al. 2006<br />
Lake Breiter Surface L 84-100 EUBI-III Allgaier & Grossart 2006<br />
Luzin<br />
Lake Cadagno Surface L 60-70 40-80 EUB338 Sekar et al. 2003<br />
Lake Čer<strong>to</strong>vo<br />
Surface<br />
Bot<strong>to</strong>m<br />
L 22-56<br />
0-34<br />
EUB338 Vrba et al. 2003<br />
Lake Constance Surface L 10-59 EUB338 Zwisler et al. 2003<br />
Lake Pavin<br />
Lake Plešné<br />
Lake Prášilské<br />
Lake Stechlin<br />
Free bacteria<br />
Attached bacteria<br />
Surface<br />
Bot<strong>to</strong>m<br />
Surface<br />
Bot<strong>to</strong>m<br />
Surface<br />
Bot<strong>to</strong>m<br />
L 49±12<br />
77±9<br />
L 17-59<br />
25-37<br />
L 17-61<br />
22-53<br />
L 35-98<br />
36-99<br />
EUB338 Lemarch<strong>and</strong> et al. 2006<br />
EUB338 Vrba et al. 2003<br />
EUB338 Vrba et al. 2003<br />
EUBI-III Allgaier & Grossart 2006<br />
Lake Tiefwaren Surface L 77-100 EUBI-III Allgaier & Grossart 2006<br />
Mackenzie River Surface L 52-64 EUB338 Garneau et al. 2006<br />
Mittlerer<br />
Plenderlesee<br />
Surface L 95 EUBI-III Warnecke et al. 2005
Appendix 1 (continued)<br />
North Pine Dam<br />
(Drinking water<br />
reservoir)<br />
Oberer<br />
Plenderlesee<br />
Surface<br />
Bot<strong>to</strong>m<br />
L 11-21<br />
21-23<br />
41-54<br />
52-57<br />
EUB338 Nielsen et al. 2006<br />
Surface L 86 EUBI-III Warnecke et al. 2005<br />
Orlik reservoir Surface L 35-60 EUB338 Mašín et al. 2003<br />
Piburger See Surface L 40-50 40-80 EUB338 Sekar et al. 2003<br />
Manipulated size L 39-89 EUBI-III Salcher et al. 2007<br />
fractions<br />
Surface L 63-75 EUBI-III Salcher et al. 2007<br />
Surface L 63 EUBI-III Warnecke et al. 2005<br />
Římov reservoir Surface L 56-83 EUB338 Mašín et al. 2003<br />
Manipulated size L 50-85 EUB338 Šimek et al. 2003<br />
fractions<br />
Manipulated size<br />
fractions<br />
L 55-85 EUB338 Horňák et al. 2005<br />
Manipulated size L 62-89 EUB338 Horňák et al. 2006<br />
fractions<br />
Manipulated size L 45-70 EUB338 Weinbauer et al. 2007<br />
fractions<br />
Manipulated size L 65-78 EUBI-III Horňák et al. 2008<br />
fractions<br />
Surface L 56-86 EUB338 Šimek et al. 2008<br />
Rotfelssee Surface L 91 EUBI-III Warnecke et al. 2005<br />
Sau reservoir Manipulated size L 43-76 EUB338 Gasol et al. 2002<br />
fractions<br />
Seebensee Surface L 76 EUBI-III Warnecke et al. 2005<br />
Schwarzsee ob Surface L 91 EUBI-III Warnecke et al. 2005<br />
Sölden<br />
5 high mountain Surface L 52-67 EUB338 Wu et al. 2006<br />
lakes (Tibetan<br />
Plateau)<br />
Ranges L 0-95 35-100<br />
Groundwater G 6-21 59-75 EUB338 Wilharitz et al. 2007<br />
Groundwater<br />
G 9-25 62-82 EUBI-III Wilhartitz et al. 2007<br />
spring<br />
Eutrophic pond L 75 25* EUB338 Schönhuber et al. 1997<br />
Freshwater<br />
R 56 EUB338 Stevens et al. 2007<br />
drainage channel<br />
Warnow (lowl<strong>and</strong> Surface R 14-63 EUB338 Freese et al. 2006<br />
river)<br />
Mahoning River Bi<strong>of</strong>ilm R 16->100 EUB338 Olapade & Leff 2004<br />
Stream Benthic detritus R 27-47 32-41 EUB338 Fazi et al. 2005<br />
Ranges G, R 6-100 25-82<br />
* : no cell permeabilization, E = estuary (freshwater part), G = groundwater, L = lake, R = river
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APPENDIX 2. Screenshots <strong>of</strong> the <strong>image</strong> <strong>analysis</strong> procedure for the detection <strong>of</strong> DAPI stained bacterial<br />
<strong>morphotypes</strong>. The following <strong>morphotypes</strong> are visible: (A) large rods (elongation >2.3), 2 misclassified vibrioid<br />
cells are marked by circles; (B) vibrio-shaped cells; (C) large cocci; (D) small rods; (E) small cocci; (F)<br />
summary picture <strong>to</strong> control the effectiveness <strong>of</strong> the detection process