first of all, you should specify what eco-group of ciliates you are interested in. I'm familiar with Paolo's papers and it seems that they are mainly about ciliates in rivers bottom. But methods for lakes are not differ much. Nevertheless I think that priority in sub-sampling is of Prof. Jakov Tseeb (my teacher!) who realized such approach in 30-th (1937) of the last century in the Crimea peninsular. For this field investigations he was put into prison for 3 years by soviets as a spy of Germany !!! as some salt lkes were closly near the miltary object. Detailed citation you can find in my book
Book From energy budget of small hydrobionts to the flow of energ...
Between publication in English you can see my authorized publications of Chapters of the book published long time ago in Russian in Kiev:
for plankton - Chapter Protistoplankton of the reservoir and its role in production...
for benthos
Chapter Protisto-, microzoo - and mesozoobenthos, their bioproductio...
For periphytos approach somewhat differ esp for the aquatic vegetation
Article Epiphytic Ciliata of the Dnieper reservoirs.
As periphytic can be classified communities of ciliates on pebble and other macroobjects (for ciliates'' size!).
As well you should take into consideration verical distribution of ciliates
Article Free-living Planktonic Infusoria of the Dnieper-Bug Liman an...
I'm not alone in this investigations and should note that existing a lot of publication on lakes (esp on protistoplankton-cilioplankton) that are cited in my modest papers as well...
Do not hesitate to contact me for further attempts...