pThis volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment.p pChapters cover different organism types i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image iin situi interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful iMethods in Molecular Biologyi series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocol