Microbial Identification in the Environment

Historically, bacterial identification has relied on phenotypic characteristics observed in pure culture, and phenotypic diagnostics remain a cornerstone of routine bacteriological monitoring, particularly in hygiene assessments. At the same time, classic environmental microbiology put a particular focus on bacteria in their respective biogeochemical roles as drivers of element cycles or biotransformation processes, whereas taxonomic identification of environmental microbes remained conditional to prior isolation. The need to differentiate bacterial genotypes directly in field samples probably emerged from the study of environmental pathogens but has gained widespread adoption with rRNA-based phylogenetics: Barcoding by next generation sequencing has revolutionized microbial community ecology, and fluorescence in situ hybridisation with rRNA-targeted probes allowed for environmental quantification of genotypically defined pro- and eukaryotic populations while preserving aspects of their phenotype. However, phylogenetic resolution based on rRNA genes often proved insufficient for the distinction of ecologically unique genotypes within microbiomes. Genome-resolved metagenomics offers higher taxonomic resolution and additionally also provides insights into the "physiological potential" of individual populations. While invaluable, this approache also introduces a 'caterpillar - butterfly' dilemma when inferring phenotypes from genomic data. In my presentation, I will explore strategies for achieving sufficient genotypic resolution in microbial identification while integrating ecophysiological insights essential for ecological interpretation.