In addition, individuals were isolated in pure cultures to identify, study properties, test for secondary metabolites, and determine the genetic composition ( /science/pure-culture). With extensive progress in selectivity profiles, diagnostic properties, chromogenic reactions, pre- and selective enrichment power, culture media were the main tools to estimate viable counts, enrich, select and differentiate groups of bacteria. The well-known solid culture media consisting of meat extract, peptones and agar, were developed by the 1890s. Introducing their pioneer work on the germ-disease theory, both Louis Pasteur and Robert Koch, and their associates, were able to present their nutrient broth “Bouillon, Nährflüssigkeit” and solid culture media, together with single colony isolation and pure cultures studies. Since the discovery of microorganisms, in vitro cultivation and isolation of bacteria in pure cultures has represented one of the major pillars in developing the science of microbiology.
The birth and development of in vitro cultivation and pure culture studies The clear message to fellow plant microbiologists is to apply plant-tailored culturomic techniques that might open up novel procedures to obtain not-yet-cultured organisms and extend the known plant microbiota repertoire to unprecedented levels. As well, the great success of culturomics of the human microbiota is considered with the main objective of encouraging microbiologists to continue minimizing the gap between the microbial richness in nature and the number of species in culture, for the benefit of both basic and applied microbiology. Here, the progress in culturing procedures for plant microbiota depending on plant-based culture media, and their proficiency in obtaining single prokaryotic isolates of novel and rapidly increasing candidate phyla are reviewed. Despite the comprehensive knowledge which already was gained using metagenomic and metatranscriptomic methods, there still exists a big gap in understanding in vivo microbial gene functioning in planta, since many differentially expressed genes or gene families are not yet annotated. Sequencing, assembling, and annotation of pure microbial strain genomes provide higher quality data compared to environmental metagenome analyses, and can substantially improve gene and protein database information. Improving cultivability of a wider range of bacterial and archaeal community members, living natively in natural environments and within plants, is a prerequisite to better understanding plant-microbiota interactions and their functions in such very complex systems.
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