Hello Katarzyna. There are many ways to test the viability of bacteria when they are exposed to bactericidal substances. I am currently performing research on using a substance to treat bacteria in contaminated water. Finding the way to test the viability and counting the bacteria was one of the most difficult and tedious aspects. I am not familiar with filamentous bacteria, so you might have to read some research literature to figure out what techniques are commonly and accurately used to evaluate the viability of filamentous bacteria as well as what bactericidal substances were used. It's a lot of information, but I hope it helps. It definitely helped me. Good luck!

Flow Cytometry (Link: https://en.wikipedia.org/wiki/Flow_cytometry ) => Flow cytometry is very good in measuring quantifiable characteristics of bacterial cells. Here are some of the functions of it => "Cell Counting, Cell Sorting, Determining Cell Characteristics and Functions as a Response to Treatment, Detecting Microorganisms, Biomarker Detection, Protein Engineering Detection".

Fluorescence Microscopy (Link: https://www.news-medical.net/life-sciences/Using-Fluorescence-Microscopy-to-Study-Bacteria.aspx) => Fluorescence microscopy can also be used to study the viability of bacterial cells. Fluorescent dyes - such as propidium iodide and SYTO9 - can be used for this purpose. SYTO9 can permeate the membranes and thus can identify all the bacterial population, while propidium iodide is membrane-impermeable. Propidium iodide is used as a marker of degraded or comprised membranes, thus SYTO9 can be used to differentiate nonviable (dead) bacterial cells from live cells. Fluorescent microscopy is often used to visualize nuclei stained using DAPI (4′,6-diamidino-2-phenylindole). This is a DNA stain that appears blue under the microcope. The luminosity of the fluorescent signal from DAPI can increase almost 20-fold upon binding to the AT regions of double stranded DNA. The excitation wavelength of the stain is in the violet region of the spectrum (i.e. 405 nm). Although it is conventionally used to stain fixed cells, it can also be used to stain the nuclei of live cells when the concentration is increased. Once the nuclei are stained, they can be counted post-imaging using image processing software to count the number of cells present in a sample.

- Pour Plate Technique (Link: https://microbeonline.com/pour-plate-method-principle-procedure-uses-dis-advantages/) => Pour plate method is usually the method of choice for counting the number of colony-forming bacteria present in a liquid specimen.  In this method, fixed amount of inoculum (generally 1 ml) from a broth/sample is placed in the center of sterile Petri dish using a sterile pipette. Molten cooled agar (approx. 15mL) is then poured into the Petri dish containing the inoculum and mixed well.  After the solidification of the agar, the plate is inverted and incubated at 37°C for 24-48 hours. Microorganisms will grow both on the surface and within the medium. Colonies that grow within the medium generally are small in size and may be confluent; the few that grow on the agar surface are of the same size and appearance as those on a streak plate. Each (both large and small) colony is carefully counted (using magnifying colony counter if needed). Each colony represents a “colony forming unit” (CFU). The number of microorganisms present in the particular test sample is determined using the formula: CFU/mL= CFU * dilution factor * 1/aliquot. For accurate counts, the optimum count should be within the range of 30-300 colonies/plate. To insure a countable plate a series of dilutions should be plated.

- Streak Plate Technique (Link: https://microbeonline.com/streak-plate-method-principle-purpose-procedure-results/) => Streak plate technique is used for the isolation into pure culture of the organisms (mostly bacteria), from mixed population.  The inoculum is streaked over the agar surface in such a way that it  “thins out” the bacteria. Some individual bacterial cells are separated and well spaced from each other. As the original sample is diluted by streaking it over successive quadrants, the number of organisms decreases. Usually by the third or fourth quadrant only a few organisms are transferred which will give discrete colony forming units (CFUs). => Principles: The sample/inoculum is diluted by streaking it across the surface of the agar plate.  While streaking in successive areas of the plate, the inoculum is diluted to the point where there is only one bacterial cell deposited every few millimeters on the surface of the agar plate.  When these lone bacterial cells divide and give rise to thousands and thousands of new bacterial cells, an isolated colony is formed.   Pure cultures can be obtained by picking well isolated colonies and re-streaking these on fresh agar plates.

- Membrane Filtration (Link: https://microbeonline.com/membrane-filter-technique/) => Membrane filters have a known uniform porosity of predetermined size (generally 0.45 µm ) sufficiently small to trap microorganisms.Using the membrane filter technique, sample is passed through the membrane using a filter funnel and vacuum system. Any organisms in the sample are concentrated on the surface of the membrane.  The membrane, with its trapped bacteria, is then placed in a special plate containing a pad saturated with the appropriate medium. The passage of nutrients through the filter during incubation facilitates the growth of organisms in the form of colonies, on the upper surface of the membrane. Discrete colonies thus formed  can be easily transferred to confirmation media.  

Membrane filter technique is an effective, accepted technique for testing fluid samples for microbiological contamination. It involves less preparation than many traditional methods, and is one of a few methods that will allow the isolation and enumeration of microorganisms.  Membrane filters are used extensively in the laboratory and in industry to sterilize fluid materials.

Most Probable Number Technique (Link: https://microbeonline.com/probable-number-mpn-test-principle-procedure-results/ ) => Most Probable Number (MPN)  is a method used to estimate the concentration of viable microorganisms in a sample by means of  replicate liquid broth growth in ten-fold dilutions. It is commonly used in estimating microbial populations in soils, waters, agricultural products and is particularly useful with samples that contain particulate material that interferes with plate count enumeration methods. MPN is most commonly applied for quality testing of water i.e to ensure whether the water is safe or not in terms of bacteria present in it. A group of bacteria commonly referred as fecal coliforms act as  an indicator for fecal contamination of water. The presence of very few fecal coliform bacteria would indicate that a water probably contains no disease‑causing organisms, while the presence of large numbers of fecal coliform bacteria would indicate a very high probability that the water  could contain disease‑producing organisms making the water unsafe for consumption. => Principle: Water to be tested is diluted serially and inoculated in lactose broth, coliforms if  present in water utilize the lactose present in the medium to produce acid and gas.The presence of acid is indicated by color change of the medium and the presence of gas is detected as gas bubbles collected in the inverted durham tube present in the medium. The number of total coliforms is determined by counting the number of tubes giving positive reaction (i.e both color change and gas production) and comparing the pattern of positive results (the number of tubes showing growth at each dilution) with standard statistical tables.