1991 ; Wommack et al. 1995 ) and then counting them by
using TEM, as described above. However, the high costs, the
long analysis time required and the diffi culty of this method
led to the development of alternative, faster and less expen-
sive methods based on the use of epifl uorescence micros-
copy (EM). With these methods, virus-like particles (VLPs)
can be observed and counted after they have been labeled
with fl uorochromes that specifi cally bind to nucleic acids.
The most common fl uorochromes were DAPI
(4’,6’-diamino-2-phenylindole) (Porter and Feig 1980 ),
YOPRO-1 {4-[3-methyl-2,3-dihydro-(benzo-1,3-oxazole)-
2-methylmethyledene]-1-(39-trimethyl ammoniumpropyl)-
quinilinium diioide} (Hennes and Suttle 1995 ), and SYBR
Green I (Noble and Fuhrman 1998 ).Fig. 14.2 Surface ( a ), deep water ( b ) and sediment ( c ) viruses are
apparently different in their morphology in Lake Pavin: overview of the
general morphotypes of viruses in the water column, including the char-
acteristic free-occurring pelagic forms [Myoviridae ( a , b ), Siphoviridae
( c ), Podoviridae ( d ) and untailed phages ( e )], which are dominant, pri-
marily in the mixolimnion ( a ), and additionnal and more atypical forms
which occurred in the deep waters ( b ) and sediments ( c ). Bar scale
100 nmFig. 14.3 Example of TEM-visibly infected bacterial cells in Lake Pavin. Bar scale 100 nm