rRNA operon copy number reflects ecological strategies of bacteria

Abstract

Although natural selection appears to favor the elimination of gene redundancy in prokaryotes, multiple copies of each rRNA-encoding gene are common on bacterial chromosomes. Despite this conspicuous deviation from single-copy genes, no phenotype has been consistently associated with rRNA gene copy number. We found that the number of rRNA genes correlates with the rate at which phylogenetically diverse bacteria respond to resource availability. Soil bacteria that formed colonies rapidly upon exposure to a nutritionally complex medium contained an average of 5.5 copies of the small subunit rRNA gene, whereas bacteria that responded slowly contained an average of 1.4 copies. In soil microcosms pulsed with the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), indigenous populations of 2,4-D-degrading bacteria with multiple rRNA genes ( = 5.4) became dominant, whereas populations with fewer rRNA genes ( = 2.7) were favored in unamended controls. These findings demonstrate phenotypic effects associated with rRNA gene copy number that are indicative of ecological strategies influencing the structure of natural microbial communities.

FIG. 1

Correlation between time of colony appearance and rRNA operon copy number. (A) Colony appearance curve for isolates from conventional-tilled agricultural soil in Michigan (▵) and from rice paddy soils in Japan (adapted from reference 16) (▴). Each point represents the arithmetic average of colonies observed on a minimum of three agar plates at that time interval. Bacteria from the time intervals designated I and IV (groups described in reference 16) were isolated and characterized for rRNA operon copy number. (B) Mean number of rRNA operons for bacterial isolates from group I (early colony formers) and group IV (late colony formers) are presented as rice paddy isolates (filled bars; n = 6 [early] or 7 [late]), conventional-tilled soil isolates (open bars; n = 5 [early] or 6 [late]). Error bars are 1 standard deviation above the sample mean. Statistical analyses of early- and late-appearing sample populations were performed using Student's t test, assuming unequal sample variances (α = 0.05, df = 10).

FIG. 2

Phylogenetic distribution of bacteria characterized for rRNA operon copy number. Filled boxes indicate soil isolates that appeared early, while open boxes indicate isolates that appeared late. Isolates from conventional-tilled soils in Michigan (designated by prefix “KBS”) and rice paddy soils in Japan (designated by prefix “HF” or “HS”) are included. Values to the right of species' names indicate the number of rRNA operon equivalents per chromosome. Major phylogenetic divisions are indicated on the far right with abbreviations as follows: C/F/B, Cytophaga/Flexibacter/Bacteroides; CYN, cyanobacteria; SPR, spirochetes; TRM, thermophiles. Strain designations and literature references for 16S rRNA sequences and rRNA operon copy numbers used for this analysis are available online at the Ribosomal RNA Operon Copy Number Database (http://rdp.cme.msu.edu/rrn).

FIG. 3

Relationship between genome size and rRNA operon copy number. Phylogenetic groups represented: Proteobacteria subgroups α (n = 8), β (n = 3), γ (n = 9), and ɛ (n = 4), Cytophaga/Flexibacter/Bacteroides (n = 7), cyanobacteria (n = 4), spirochetes (n = 4), high-G+C gram-positive bacteria (n = 7), low-G+C gram-positive bacteria (n = 16), and thermophiles (n = 3). A linear regression for all data points was calculated using the least-squares method (P < 0.01 that no relationship exists), upper and lower 95% confidence bounds are indicated by dotted lines. The data used are available online at the Ribosomal RNA Operon Copy Number Database (http://rdp.cme.msu.edu/rrn).

FIG. 4

Distribution of rRNA operon copy number among 2,4-D-degrading bacteria isolated from amended and unamended soil microcosms. Species are identified based on similarity of 16S rRNA restriction patterns. The height of each bar reflects the abundance of that species relative to all isolates from that microcosm of 247 (A), 263 (B), or 327 (C) isolates. Numbers above bars indicate the rRNA operon copy number for each species; the mean number of rRNA operons per isolate is indicated for each treatment. Different isolates of the same species exhibited similar rRNA operon copy numbers (data not shown). Each treatment represents data from three replicate microcosms.