Nature should be the model for microbial sciences.

Abstract

Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 1028 cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.