Empirical and theoretical bacterial diversity in four Arizona soils

Abstract

Understanding patterns of biodiversity in microbial communities is severely constrained by the difficulty of adequately sampling these complex systems. We illustrate the problem with empirical data from small surveys (200-member 16S rRNA gene clone libraries) of four bacterial soil communities from two locations in Arizona. Among the four surveys, nearly 500 species-level groups ( Dunbar et al., Appl. Environ. Microbiol. 65:662-1669, 1999) and 21 bacterial divisions were documented, including four new candidate divisions provisionally designated SC1, SC2, SC3, and SC4. We devised a simple approach to constructing theoretical null models of bacterial species abundance. These null models provide, for the first time, detailed descriptions of soil bacterial community structure that can be used to guide experimental design. Models based on a lognormal distribution were consistent with the observed sizes of the four communities and the richness of the clone surveys. Predictions from the models showed that the species richness of small surveys from complex communities is reproducible, whereas the species composition is not. By using the models, we can now estimate the required survey scale to document specified fractions of community diversity. For example, documentation of half the species in each model community would require surveys of 16,284 to 44,000 individuals. However, quantitative comparisons of half the species in two communities would require surveys at least 10-fold larger for each community.

FIG. 1.

Relative abundance of bacterial divisions found in 16S rRNA gene clone libraries four Arizona soils. Absence of a visible bar indicates that no representative clones were found in the library.

FIG. 2.

Division-level sampling curves. Curves were calculated by rarefaction (13, 30). Data from the Yellowstone hot spring were obtained from reference .

FIG. 3.

Ranked abundance plot of division diversity. For each environmental sample, the divisions documented in clone libraries were ranked in order of decreasing abundance. Curves shown in the plot are best-fit power functions. The spread of data points was examined visually for evidence of a lognormal distribution.

FIG. 4.

Comparison of theoretical lognormal models with observed data from four Arizona soils. Fifteen model communities were constructed by using three different values for R_max (10, 11, and 12) and five different values for S_T (2,000, 4,000, 6,000, 8,000, and 10,000 species). Data from 12 of the models are shown in the figure. The solid square and diamond represent observed data from Sunset Crater and Cosnino interspace soils, respectively. The semifilled square and diamond represent observed data from Sunset Crater and Cosnino rhizosphere soils, respectively. The plotted symbols for the Arizona communities would be positioned artificially high (by 5 to 20%) if the surveys contained PCR artifacts.

FIG. 5.

Theoretical lognormal model series most consistent with observed data from four Arizona soils. (A) Lognormal species rank abundance plots. Each curve shows the population size of each species (ranked in order of decreasing abundance) from the theoretical community. The sum of population sizes for all the species in a community is the calculated community size, N_T. The inset panel illustrates the normal distribution achieved by plotting species population sizes on a geometric scale, log₂. The first interval (the −11 octave) contains a single species represented by one individual (1 cell [g of soil]⁻¹). The second octave contains species represented by two or three individuals, etc. (B) Cumulative biomass distribution for species from lognormal models shown in panel A. The species are ranked in order of decreasing abundance.

FIG. 6.

Sampling curves for lognormal model communities. (A) Species richness sampling curves. The curves were calculated by rarefaction. The number at the apex of each curve shows the percentage of the total number of species, S_T, from each community expected in a sample size of 50,000 individuals. The triangles indicate the sample size required to document half the species richness of each model community. (B) Species composition sampling curves based on a 95% confidence interval. Each curve shows the sample size required for confident sampling of a specified set of species (each set includes the given species number on the x axis and all the preceding species on the x axis). Species are ranked in order of decreasing population size. Sampling curves from model communities that differ 2.5-fold in species number (R_max11 curves) and 8-fold in community size (R_max10 and R_max12 curves) are shown.