Soil extracellular DNA fragments show variable degradation rates among sequences and environmental conditions
- Yunnan Key Laboratory of Soil Erosion Prevention and Green Development, Institute of International Rivers and Ecosecurity, Yunnan University, China
- State Key Laboratory for Vegetation Structure, Function and Construction (VegLab), Ministry of Education Key Laboratory for Ecosecurity of Southwest China, Yunnan University, China
- College of Life Sciences, University of Chinese Academy of Sciences, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, China
- School of Life Sciences, Yunnan University, China
Figures
Figure 1 with 3 supplements
The overall degradation rates of soil extracellular 16S rRNA gene amplicon fragments and their influential factors.
(a) The GAPDH F-tagged 16S rRNA gene amplicon fragment abundance at different incubation time points. (b, c) The degradation rate constants of soil extracellular 16S rRNA gene amplicon fragments across the study sites and different ecosystem types. (d) The factors influencing extracellular 16S rRNA gene degradation rates. (e) The influencing factors for the overall degradation rates of soil extracellular 16S rRNA gene amplicon fragments revealed by structural equation modeling. Orange and green lines indicate positive and negative relationships, respectively. Solid and dashed lines indicate significant and non-significant relationships, respectively. Path coefficients are denoted by numbers adjacent to the arrows, with arrow width reflecting their strength. (f) The influence of soil moisture on the degradation rates of soil microbial eDNA. Significance levels are indicated as follows: *p < 0.05, **p < 0.01, and ***p < 0.001. Moisture: soil moisture content; Abundance: prokaryotic abundance; NMDS1: the scores at the first axis of the NMDS ordination of prokaryotic community profiles; MAP: mean annual precipitation; Richness: soil prokaryotic richness; NMDS2: the scores at the second axis of the NMDS ordination of prokaryotic community profile; TK: soil total potassium contents; MAT: mean annual temperature; AP: soil available phosphorus content; TN: soil total nitrogen contents; and TOC: soil total organic carbon content.
Figure 1—figure supplement 1
Factors affecting the degradation rates of soil extracellular 16S rRNA gene amplicon fragments.
(a–f) The relationships between the overall degradation rates of soil extracellular 16S rRNA gene amplicon fragments and environmental factors; (g) the relationships among the sequence-specific degradation rates, contents, and the influencing intensity of extracellular 16S rRNA gene amplicon fragments.
The eDNA means the copies of extracellular 16S rRNA gene amplicon fragments. The T/I represents the ratios between the relative abundance of each prokaryotic ASVs based on the total DNA extraction to that based on intracellular DNA extraction, and it is used to indicate the influencing intensity of extracellular 16S rRNA gene amplicon fragments on the relative abundance of prokaryotic taxa. Moisture: soil moisture content; MAP: mean annual precipitation; and NMDS1: the scores at the first axis of the NMDS ordination of prokaryotic community profile.
Figure 1—figure supplement 2
The map of the sampling sites.
Figure 1—figure supplement 3
The experimental design.
Figure 2 with 2 supplements
The sequence-specific degradation rates of soil exogenous extracellular 16S rRNA gene amplicon fragments.
(a) Soil GAPDH F-tagged 16S rRNA gene richness. (b) The nonmetric multidimensional scaling (NMDS) ordination of the community profiles based on GAPDH F-tagged 16S rRNA gene amplicon fragments at different incubation time points. (c) The number of GAPDH F-tagged 16S rRNA gene ASVs within different degradation rate ranges.
Figure 2—figure supplement 1
Soil prokaryotic community composition based on GAPDH F-tagged 16S rRNA gene amplicon fragments at different incubation time points.
Figure 2—figure supplement 2
The relationships between community profile similarities based on the GAPDH F-tagged 16S rRNA gene amplicon fragments and the intervals of incubation time.
The similarities were calculated between the community profiles at time 0 and the other time points.
Figure 3 with 2 supplements
The difference in sequence-specific degradation rates of soil extracellular 16S rRNA gene amplicon fragments and their influencing factors.
(a) The paired comparison of degradation rates among different ASVs. In the heatmap, each cell represents a pairwise comparison between two ASVs. Blue indicates that the degradation rate of the ASVs listed in the row (row ASVs) is significantly lower than that of the ASVs listed in the column (column ASVs); red indicates that the row ASVs have a significantly higher degradation rate than the column ASV. A positive t value indicates that the row ASVs degrade significantly faster than the column ASVs; a negative t value indicates the opposite. Significance levels are indicated as follows: *p < 0.05, **p < 0.01, and ***p < 0.001. (b) The relationships between the sequence-specific degradation rate profiles and environmental factors. NO3−-N: soil NO3−-N contents; NH4+-N: soil NH4+-N contents; TN: soil total N contents; TP: soil total P contents; TK: soil total K contents; TOC: soil total organic carbon content; MAT: mean annual temperature; and MAP: mean annual precipitation.
Figure 3—figure supplement 1
The relationships between the degradation rates of extracellular 16S rRNA gene amplicon fragments and the G+C content of DNA sequence.
Figure 3—figure supplement 2
The relationships between the degradation rates of extracellular 16S rRNA gene amplicon fragments of the dominant phyla (top 10) and different influencing factors.
MAT: mean annual temperature and MAP: mean annual precipitation.
Figure 4 with 1 supplement
The differences in the abundance, richness, Shannon, and community composition between total and PMA-treated soil prokaryotes.
(a) The abundance of total and PMA-treated soil prokaryotes. (b, c) The richness and Shannon index of total and PMA-treated soil prokaryotes. (d) The differences between the relative abundance of total and intracellular ASVs. The red points represent the prokaryotic taxa exhibiting statistically significant differences. (e) The nonmetric multidimensional scaling (NMDS) ordination of total and PMA-treated soil prokaryotes. Different colors represent samples from different sites. (f) The Bray–Curtis dissimilarity between total and PMA-treated soil prokaryotes.
Figure 4—figure supplement 1
The nonmetric multidimensional scaling (NMDS) ordination of total and PMA-treated soil prokaryotes in different ecosystems.
The different colors represent samples from different sites.
Figure 5
Effects of eDNA exclusion on soil prokaryotic community composition and its relationships with environmental factors.
(a) The taxa with significant differences between total and intact cell prokaryotic communities. P1: Thermoplasmatota; P2: Nitrospirota; P3: Fibrobacterota; P4: Entotheonellaeota; P5: Elusimicrobiota; P6: Armatimonadota; P7: Myxococcota; C1: Thermoplasmata; C2: Nitrospiria; C3: Vampirivibrionia; C4: Clostridia; C5: Bacilli; C6: Armatimonadia; C7: Chthonomonadetes; C8: Polyangia; C9: Blastocatellia; C10: Parcubacteria; C11: Bacteroidia; C12: Thermoleophilia; O1: Nitrospirales; O2: Abditibacteriales; O3: Clostridiales; O4: Bacillales; O5: Armatimonadales; O6: Pyrinomonadales; O7: Bryobacterales; O8: Chitinophagales; O9: Rubrobacterales; O10: Propionibacteriales; and O11: Corynebacteriales. (b) The relationships between soil prokaryotic community profiles and environmental factors. NO3−-N: soil NO3−-N contents; NH4+-N: soil NH4+-N contents; Moisture: soil moisture content; MAT: mean annual temperature; MAP: mean annual precipitation; TP: soil total P contents; TK: soil total K contents; and TOC: soil total organic carbon contents.
Figure 6
Schematic illustration of the experimental workflow for determining the overall and sequence-specific degradation rates of soil extracellular 16S rRNA gene amplicon fragments.
Additional files
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Supplementary file 1
Supplementary tables.
(A) The geographic and climate information of the sampling sites included in this study. (B) The soil properties of the sampling sites included and the amount of exogenous DNA added in this study.
- https://cdn.elifesciences.org/articles/110251/elife-110251-supp1-v1.docx
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MDAR checklist
- https://cdn.elifesciences.org/articles/110251/elife-110251-mdarchecklist1-v1.docx
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Soil extracellular DNA fragments show variable degradation rates among sequences and environmental conditions
eLife 15:RP110251.
https://doi.org/10.7554/eLife.110251.3
