Toward a Census of Bacteria in Soil

Abstract

For more than a century, microbiologists have sought to determine the species richness of bacteria in soil, but the extreme complexity and unknown structure of soil microbial communities have obscured the answer. We developed a statistical model that makes the problem of estimating richness statistically accessible by evaluating the characteristics of samples drawn from simulated communities with parametric community distributions. We identified simulated communities with rank-abundance distributions that followed a truncated lognormal distribution whose samples resembled the structure of 16S rRNA gene sequence collections made using Alaskan and Minnesotan soils. The simulated communities constructed based on the distribution of 16S rRNA gene sequences sampled from the Alaskan and Minnesotan soils had a richness of 5,000 and 2,000 operational taxonomic units (OTUs), respectively, where an OTU represents a collection of sequences not more than 3% distant from each other. To sample each of these OTUs in the Alaskan 16S rRNA gene library at least twice, 480,000 sequences would be required; however, to estimate the richness of the simulated communities using nonparametric richness estimators would require only 18,000 sequences. Quantifying the richness of complex environments such as soil is an important step in building an ecological framework. We have shown that generating sufficient sequence data to do so requires less sequencing effort than completely sequencing a bacterial genome. Soil is more than dirt. It is the source and sink of nutrients, wastes, pharmaceuticals, and energy required to make Earth supportive of life—it is Earth's most vital organ. Although we know a considerable amount about the physical structure and chemistry of soil, there is a glaring paucity of knowledge regarding the microbial component responsible for its many functions. Over the past 100 years, microbiologists have attempted to characterize the biodiversity of microbial life in soil, and many had reached the unsatisfying conclusion that bacteria may be too diverse to count. Schloss and Handelsman have developed statistical models that they apply to molecular data to predict that the richness of bacteria in 0.5-g soil samples from Alaska and Minnesota were 5,000 and 2,000 species, respectively. At the current level of sampling, approximately 20% of the bacteria appear to be endemic to both soils. The enumeration and description of these organisms points to the need and relative ease of characterizing bacterial communities to identify the organisms responsible for sustaining all of life.