Diversity of Planctomycetes in soil in relation to soil history and environmental heterogeneity

Abstract

Members of the Planctomycetes, which were once thought to occur primarily in aquatic environments, have been discovered in soils on five continents, revealing that these Bacteria are a widespread and numerically abundant component of microbial communities in soil. We examined the diversity of Planctomycetes in soil samples obtained from experimental plots at an agricultural site in order to assess the extent of Planctomycetes diversity in soil, to determine whether management effects such as past land cover and compost addition affected the composition of the Planctomycetes community, and to determine whether the observations made could provide insight into the ecological distribution of these organisms. Analysis of Planctomycetes 16S rRNA gene sequences revealed a total of 312 +/- 35 unique phylotypes in the soil at the site examined. The majority of these Planctomycetes sequences were unique, and the sequences had phylogenetic affiliations that included all major lineages in the Planctomycetaceae, as well as several novel groups of deeply divergent Planctomycetes. Both soil management history and compost amendment had significant effects on the Planctomycetes diversity, and variations in soil organic matter, Ca2+ content, and pH were associated with variations in the Planctomycetes community composition. In addition, Planctomycetes richness increased in proportion to the area sampled and was correlated with the spatial heterogeneity of nitrate, which was associated with the soil management history at the orchard site examined. This report provides the first systematic assessment of the diversity of Planctomycetes in soil and also provides evidence that the diversity of this group increases with area as defined by the general power law description of the taxon-area relationship.

FIG. 1.

Rank abundance curves and summary statistics for Planctomycetes diversity with OTUs defined at 97% (A), 99% (B), and 100% (C) similarity of 16S rRNA gene sequences. Note that for the sake of clarity the scales on the y axes are not the same. S_ob, total number of OTUs observed; 1/D, reciprocal of the Simpson's index.

FIG. 2.

Neighbor-joining tree calculated from 535 nucleotide positions showing Planctomycetaceae 16S rRNA sequences described in this study. Sequences are indicated by symbols indicating their origins, as follows: ▪, old row with compost; •, old row control; □, grass lane with compost; ○, grass lane control. Other Planctomycetaceae sequences are included for reference; species or strain designations are indicated for cultivated isolates, while sequences from noncultivated organisms are indicated by their Ribosomal Database Project identification code numbers (beginning with S000). Pla., Planctomyces; Iso., Isosphaera. The scale bar indicates a 10% difference between nucleotide sequences. The arrow indicates a subgroup of the genus Pirellula as discussed in the text.

FIG. 3.

Phylogenetic tree showing the relationship of the deeply divergent Planctomycetes 16S rRNA gene sequences obtained in this study (boldface type) to other deeply divergent sequences in the Planctomycetes. The tree was calculated using 1,235 aligned nucleotide positions and maximum likelihood analysis. The numbers at nodes indicate bootstrap support; the numbers above the lines are values obtained from the maximum likelihood analysis, and the numbers below the lines were obtained from the parsimony analysis. The asterisks indicate that fewer than 50% of the trees supported a node. EC, environmental cluster. The scale bar indicates a 10% difference between nucleotide sequences.

FIG. 4.

Spatially explicit scaling of Planctomycetes diversity with respect to treatment (calculated with OTUs defined at a 99% 16S rRNA sequence similarity cutoff). (A) Average Chao1 estimates and standard deviations calculated for individual treatments (n = 4) (line 1), for all two-way treatment combinations (n = 6) (line 2), for all three-way treatment combinations (n = 4) (line 3), and for all treatments (n = 1) (line 4). (B) Log of Chao1 as a function of the log of area calculated for sequences sampled in a spatially explicit manner as described above (⧫) and for corresponding numbers of sequences selected at random from the collection of all sequences (▪).

FIG. 5.

Chao1 diversity estimates for Planctomycetes 16S rRNA sequences with OTUs defined at 99% similarity. (A) Chao1 curves for each of the four individual libraries. (B) Results when the libraries were pooled based on compost amendment or soil history.

FIG. 6.

Redundancy analysis plot of the differences in Planctomycetes community composition as assessed by PCR-DGGE of 16S rRNA genes based on treatment effects and the environmental variables pH, NO₃ N content (NO₃), organic matter content (SOM), and Ca²⁺ content (Ca⁺⁺). Each symbol represents a PCR-DGGE pattern for one replicate plot from one treatment. The treatments are indicated by symbols as follows: ▪, old row with compost; •, old row control; □, grass lane with compost; ○, grass lane control.

FIG. 7.

Relationship between the Chao1 estimate of diversity and the coefficients of variation (C.V.) for the NO₃ N content in the four treatments analyzed. The error bars indicate the standard deviations of the Chao1 estimates.