Fig 1.
Decreased abundances of mycorrhizal fungi and Gram-negative bacteria during RS-EX treatment as determined by phospholipid fatty acid (PLFA) analyses of soil samples.
PLFA analyses of A. untreated control soil samples and B. of soil during RS-EX exposure were performed by GC-MS measurements. Marker fatty acids for different taxonomic groups are listed in S2 Table. Data show means ± SD (n = 3). Significant differences between RS-EX treated and control samples are indicated by asterisks (t-test; *, p<0.05; **, p<0.005). 32 d recovery, 28 d of RS-EX treatment followed by 32 d without treatment. Arrows indicate increased or decreased amounts of bacterial or fungal PLFAs after RS-EX application.
Fig 2.
Accumulation of phosphatidic acid indicates decomposition of microbial soil organisms during RS-EX treatment.
Alterations in phospholipid composition of A. control and B. RS-EX treated soils as determined by Q-TOF mass spectrometry. Bars in panels A and B represent means ± SD (n = 3). Significant differences to control are indicated by asterisks (**, p ≤ 0.05). PA, phosphatidic acid; PC, phosphatidylcholine; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PI, phosphatidylinositol. Red arrows indicate increased or decreased amounts of bacterial or fungal phospholipids after RS-EX application.
Fig 3.
Alterations in bacterial and fungal community structures during RS-EX treatment revealed by alterations in phosphatidylethanolamine (PE) molecular species composition.
Changes in PE molecular species in A. control and B. RS-EX treated soil samples were measured by Q-TOF mass spectrometry. Markers for bacteria (Bact) and fungi are indicated. Means ± SD are shown (n = 3). Asterisks indicate significant differences to control (t-test; *, p < 0.05; **, p < 0.005). Fatty acids of molecular species are indicated in S2 Table. Arrows indicate increased or decreased amounts of bacterial or fungal molecular species of PE after RS-EX application.
Fig 4.
Changes in microbial enzyme activities during RS-EX treatment of soils.
The activities for A. esterases/lipases, B. phospholipases A and C. proteases are shown for control (grey bars) and RS-EX treated (black bars) soil extracts. Data show mean ± SD (n = 3). Significant differences of the control or RS-EX treated measurements at the different days to the control samples at 7 d are indicated (t test; *, p<0.05; **, p<0.005).
Fig 5.
Changes in archaeal and bacterial diversity during RS-EX treatment.
The bacterial and archaeal diversity of A. control (average of 0–28 d), and B. RS-EX treated soil (average of 0–28 d) is shown. Relative OTU abundances derived from the numbers of 16S RNA reads are indicated by the sizes of filled circles. Open circles indicate higher-order taxa (circle sizes not in scale). Extinction of OTUs is depicted by crosses. Arch, Archaea; Bact, Bacteria; Acido, Acidobacteria; Actino, Actinobacteria; Arma, Armatimonadetes; Can Div, Candidate Division; Chlo, Chloroflexi; Bactes, Bacteriodetes; Fir, Firmicutes; Gem, Gemmatimonadetes; Nit, Nitrospirae; Pla, Planctomycetes; Ver, Verrucomicrobia; Tha, Thaumarchaeota. Other taxa are listed in S3 Table.
Fig 6.
Changes in abundance of soil α, β, γ, δ Proteobacteria (Prot).
The figure shows the relative abundances of A. control samples (averages of 0 d—28 d) and B. of RS-EX treated soils (averages of 0 d -28 d). The sizes of the filled circles indicate abundances of soil bacterial OTUs derived from 16S rRNA gene sequencing. Open circles depict higher-order taxa (circle sizes not in scale). Crosses indicate extinction of OTUs. The abundances of Acinetobacter (Acineto) and Thermomonas (Ther) dramatically increased after RS-EX treatment. Taxa are listed in S3 Table.
Table 1.
Taxonomic classification of cultivable bacteria and fungi.
Fig 7.
Changes in the community composition of basidiomycota and zygomycota.
Basidiomycota (Basi) and Zygomycota (Zyg) OTU abundances derived from internal transcribed spacer (ITS) region sequencing in A. control soil samples and B. during RS-EX exposure (7, 14, 21, 28 d). Filled circle sizes indicate average OTU abundances. Highly abundant taxa are depicted by circle sections, and abundances given in %. Open circles indicate higher-order taxa (circle sizes not in scale). Extinction of OTUs is depicted by crosses. Trich, Trichosporon; Mor, Mortierella. Other taxa are listed in S4 Table.
Fig 8.
Breakdown of ascomycota diversity during RS-EX exposure.
Changes in Ascomycota (Asco) OTU abundances derived from internal transcribed spacer (ITS) region sequencing in soil samples of A. controls and B. during RS-EX exposure (7, 14, 21, 28 d). Average OTU abundances are indicated by the sizes of filled circles. Highly abundant taxa are depicted by circle sections, and abundances given in %. Open circles indicate higher-order taxa (circle sizes not in scale). Extinction of OTUs is depicted by crosses. Davi und, Davidiellaceae unclassified; Ha, Haematonectria; Pseuda, Pseudaleuria; Sor, Sordariomycetes; Sta, Staphylotrichum. Other taxa are listed in S4 Table.
Fig 9.
Increase in Arabidopsis growth after inoculation with cultivable bacteria from RS-EX treated soils.
A. Three-week-old Arabidopsis Col-0 seedlings growing on soil were inoculated with 10 mL of a bacteria suspension (OD600 = 0.05) and photos of the rosettes taken 3 weeks later. Control plants were inoculated with water. Numbers in brackets depict strain number. B. Fresh weights (FW) of Arabidopsis rosettes. Bacillus megaterium (48), Aminobacter aminovorans (49) and Bacillus cereus (59) exert the strongest growth promoting effect. Bars (means ± SD; n = 4). Numbers above bars indicate % change to control. Asterisks indicate significant differences to the control (**, p<0.01).