Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil

Abstract

Bacteria belonging to phylum Gemmatimonadetes comprise approximately 2% of soil bacterial communities. However, little is known of their ecology due to a lack of cultured representation. Here we present evidence from biogeographical analyses and seasonal quantification of Gemmatimonadetes in soils, which suggests an adaptation to low soil moisture.

Fig. 1.

Relative abundances of Gemmatimonadetes (as a proportion of total bacterial community) in soils and sediments reported in published 16S rRNA gene libraries. Studies are grouped by library size as follows: >5,000 sequences (pyrosequencing libraries) (black squares), 500 to 2000 (small pyrosequencing libraries and large clone libraries) (gray squares), and <500 sequences (clone libraries) (white squares). Studies referenced are as follows: Antarctic dry soils (6, 14), alpine hyper arid soils (9), hot desert (8, 39, 47), alpine tundra (37), Antarctic peninsula/coastal (6, 45), semiarid soils (1, 26, 32), prairies/grasslands (12, 41), pasture (22), crop agriculture (7, 22, 29, 41, 50), temperate forest (17, 22, 29, 30, 41), tropical forest (13), moist acidic tundra (5), and freshwater sediments (27, 48).

Fig. 2.

Neighbor-joining phylogenetic tree of 456 Gemmatimonadetes 16S rRNA gene sequences deposited in RDP (>1,200 bp in length). Fibrobacter succinogenes was used as an outgroup. Sequences are listed by GenBank accession number and colored according to the sample type as follows: arid soils and deserts (tan), forest soil (dark green), prairie and grassland soil (light green), agricultural crop soil (yellow), alpine and tundra soil (brown), rock surfaces (black), soil contaminated with organics and hydrocarbons (pink), soil contaminated with radioactive waste (red), wastewater and activated sludge (light blue), freshwater sediments and saturated soils (medium blue), and marine sediments (navy blue). The three major clade divisions are labeled G1, G2, and G3.

Fig. 3.

Principal components analysis of sequences of the phylum Gemmatimonadetes shown in Fig. 2 (n = 456) by environment type. Soil types are as follows: crop agriculture (SoilAg); alpine (SoilAlpine); arid and desert (SoilArid); grassland, prairie, and pasture (SoilGrass); and forest (SoilForest). Also included are soils contaminated with organics (SoilContamOrg) and radioactive wastes (SoilContamRadio), freshwater sediments and saturated soils (SedimentsFW), marine sediments (SedimentsMar), rock surfaces (Rock), and wastewater and activated sludge (WWAS). Significant clusters are circled.

Fig. 4.

Relative abundance of Gemmatimonadetes bacteria (clades G1 and G3) in five soil types at the Kellogg Biological Station over time. Quantities are expressed as a percentage of the total bacterial 16S rRNA genes. Land treatments include conventional agriculture (T1), organic agriculture (T4), early succession meadows (T7 and T8), and mid-succession forest (SF2) (see text for descriptions). Each point represents the mean and standard deviation of 3 replicate land plots.

Fig. 5.

Gemmatimonadetes 16S rRNA gene copies (expressed as a percentage of total bacterial 16S rRNA gene copies) related to percent soil moisture (A) and soil pH (B). Land treatments include conventional agriculture (T1), organic agriculture (T4), early succession meadows (T7 and T8), and mid-succession forest (SF2) (see text for descriptions).