Auxotrophs of soil bacteria

The great plate count anomaly is a perplexing mystery in modern biology. This phenomenon describes the observation that most microorganisms cannot be cultivated under laboratory conditions. One explanation is obligate metabolic interactions among community members. However, an empirical test of this hypothesis is pending. Here we address this issue by systematically analysing 27 soil microbial communities. By screening 6,931 bacterial isolates, we find up to 50% of community members could not produce all growth-essential metabolites, which commonly included multiple amino acids simultaneously (i.e. 73%). Genomic analysis of 62 sequenced strains suggested that accumulation of insertion sequences and specific gene loss is associated with the observed auxotrophies. Finally, both metabolic models, computational analysis, and cocultivation experiments evidenced that other genotypes can complement the metabolic needs of a given auxotroph, thus facilitating its growth. Therefore, our results demonstrate that in nature, bacteria mainly exist within multicellular metabolic networks, thus explaining their unculturability.