High proportions of bacteria are culturable across major biomes

Abstract

The paradigm that only 1% of microbes are culturable has had a profound impact on our understanding of microbial ecology and is still a major motivation for mostly using molecular tools to characterize microbial communities. However, this point is often expressed vaguely, suggesting that some scientists have different interpretations of the paradigm. In addition, there have been substantial advances in cultivation techniques suggesting that this paradigm may no longer be correct. To quantify bacterial culturability across six major biomes, I found that the median 16S rRNA similarity of bacteria to known cultured relatives was 97.3 ± 2.3% (s.d.). Furthermore, 52.0 ± 24% of sequences and 34.9 ± 23% of taxa (defined as >97% similar) had a closely related cultured relative. Thus, many cells and taxa across environments are culturable with known techniques, suggesting that the 1% paradigm is no longer correct.

Fig. 1

16S rRNA sequence similarity between community members and known isolates. a The median similarity between amplicon sequences and known isolates as a test of the ‘1% culturability paradigm’, H1. b The median similarity between representative amplicon sequences and known isolates as a test of H2. The error bars represent one standard error. c Box plot of proportion of sequences with a close relative in culture across biomes. d Proportion taxa with a close relative in culture as distributed across biomes. A taxon as well as a close cultured relative are here defined as 16S rRNA sequences sharing >97% similarity and binned using MOTHUR using the opticlust algorithm [9]. For the box plots, the gray line is the median, the box is the 25–75 percentile, and the errorbar is the 2.5–97.5 percentile of observations. See Table S1 for sample list

Fig. 2

Similarity between community members and known isolates as a function sequence threshold to define ‘closely-related’. a Proportion of sequences (H1) with cultured relatives across definitions of ‘closely-related’. b Proportion taxa (H2) with cultured relatives across definitions of ‘closely-related’. For the box-plot, the gray line is the median, the box is the 25–75 percentile, and the errorbar is the 2.5–97.5 percentile of observations (n = 40). Here, taxa and closely-related are both defined using a range of sequence similarities