"How to properly implement section 7.2 and 7.6 for a microbiological lab?"
You question relates to the Selection, verification and validation of methods (clause 7.2 section 7.2.1 and 7.2.2) as well as evaluation of measurement uncertainty (clause 7.6).
Selection of a method and its validation involves ensuring you are using the correct method for the purpose. Microbiological laboratory activities can be diverse, beyond enumeration of microbes, so can involve standard or non-standard methods and diverse techniques and equipment. The validation experiments must demonstrate that the method is suitable to detect and identify one or more analyte in all the matrices of interest (e.g. water, foodstuff), using the required instruments or techniques. Typically if a rapid test is used, this would have to be verified for suitable performance against a gold-standard test for the purpose. If the kit is commercially available and validated, then you would need to show you can achieve a suitable performance in terms of the relevant validation parameters. Microbiological validation parameters generally include specificity, sensitivity, accuracy, trueness, precision, reproducibility, and ruggedness.
Regarding measurement uncertainty you need to 1) identify the contributions and 2) evaluate. It depends highly on the method - principles or experience of the performance of the method. For example, consider any condition that by your experience or principle of the method, has a contribution to variability. Sources of uncertainty typically come from sampling, storage, sample preperation (homogenization / extraction), weighing, pipetting, dilutions and of course the quantitation of colonies – either by counting manually, automatically or semiautomated methods to calculate the Most Probable Number (MPN). You would basically consider what trueness and replicate data you can acquire – for example replicates for laboratory control samples and reference cultures. Method validation data and ongoing quality control data can be used.
Commercial kits may report uncertainty limits for the main sources, then you do not need to do any further estimation, just control the system
I suggest you contact your accreditation body and or regulatory bodies (e.g FDA) for their policies and guidelines on microbiology laboratory method validations and evaluation of measurement uncertainty. Also look at other industry guidelines (perhaps references from the accreditation body guidelines) to provide more detail. There are also ISO standards, for example ISO 19036:2019 Microbiology of the food chain - Estimation of measurement uncertainty for quantitative determinations.
For more information regarding the method validation and measurement uncertainty, see the ISO 17025 toolkit document templates: