Data from: Abiotic legacies mediate plant-soil feedback during early vegetation succession on rare earth element mine tailings
Data files
Dec 14, 2023 version files 1.24 MB
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DataUpload_zhu_JAE_202312.zip
1.23 MB
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README.md
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Abstract
An increasing number of studies have shown how feedback interactions between plants and soil can influence primary and secondary succession. However, very little is known about the patterns and mechanisms of such plant-soil feedbacks on stressed mine tailings ecosystem, which can be severely contaminated by a range of toxic elements.
In a two-phase plant-soil feedback experiment based on the rare earth element (REE) mine tailing soil, we investigated biotic (changes in bacterial and fungal community) and abiotic legacies (changes in chemical properties) of three pioneer grass species, and examined feedback effects of three grasses, two legumes and two woody plants with different root traits.
Positive plant-soil feedback was found in Miscanthus sinensis, Paspalum thunbergii and Tephrosia candida, and neutral feedback was observed in other four plants. These effects corresponded with an increase of nutrients and total organic carbon, as well as a decrease of acidity and extractable aluminum and REEs. There were less signs of biotic changes in the conditioned tailings.
The correlation analysis suggested a relationship between responses to soil legacies and root traits, as well as root economics spectrum. On the mine tailings, acquisitive species with higher specific root length appeared to have greater potential for positive feedback.
Synthesis and application: Our study shows that early succession on contaminated REE mine tailings may lead to more positive plant-soil feedback than predicted based on results of non-contaminated soils, mainly due to the alleviation of abiotic stress in tailings. Therefore, the improvement of specific abiotic soil stress and the trait-based selection of acquisitive plants should be preferentially considered to promote the primary restoration of degraded land.
README: Abiotic legacies mediate plant-soil feedback during early vegetation succession on rare earth element mine tailings
These datasets are derived from a two-phase plant-soil feedback experiment based on the rare earth element (REE) mine tailing. We investigated biotic (changes in bacterial and fungal community) and abiotic legacies (changes in chemical properties) of three pioneer grass species, and examined feedback effects to three grasses, two legumes and two woody plants with different root traits. More details about the study please find in the paper of Zhu et al (the same name as this dataset) or contact the corresponding author.
Dataset DOI link: https://doi.org/10.5061/dryad.ht76hdrnm
Description of the data and file structure
File list:
- (1) SoilAbioticData\Soil_Abiotic_Properties.csv
- (2) SoilBioticData\Bacterial_feature_table.txt
- (3) SoilBioticData\Bacterial_taxonomy.tsv
- (4) SoilBioticData\Fungal_feature_table.txt
- (5) SoilBioticData\Fungal_taxonomy.tsv
- (6) PlantTraitData\Plant_Info.csv
- (7) PlantTraitData\Plant-soil_Feedback.csv
- (8) PlantTraitData\Root_Functional_Traits.csv
Additional related data collected that was not included in the current data package:
- The raw sequences of the soil bacterial and fungal communities have been deposited in the Genome Sequence Archive in the publicly accessible Beijing Institute of Genomics Data Centre, Chinese Academy of Sciences, under accession number PRJCA009170 (http://bigd.big.ac.cn/gsa).
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DATA-SPECIFIC INFORMATION FOR: (1) SoilAbioticData\Soil_Abiotic_Properties.csv
1. Number of variables: 18
2. Number of cases/rows: 20
3. Variable List:
- sample ID: soil identities, 4 Treatments (5 replicates for each) in conditioning phase.
- pH_water: soil pH, analysed at a ratio of 1:2.5 (soil: deionized water, w/v).
- CaCl2_Al: soil extractable aluminum content, extracted by 0.01 M CaCl2 solution.
- CaCl2_K: soil extractable potassium content, extracted by 0.01 M CaCl2 solution.
- CaCl2_Mg: soil extractable potassium content, extracted by 0.01 M CaCl2 solution.
- CaCl2_Mn: soil extractable potassium content, extracted by 0.01 M CaCl2 solution.
- CaCl2_Na: soil extractable potassium content, extracted by 0.01 M CaCl2 solution.
- CaCl2_P: soil extractable potassium content, extracted by 0.01 M CaCl2 solution.
- CaCl2_S: soil extractable potassium content, extracted by 0.01 M CaCl2 solution.
- CaCl2_REEs: soil extractable potassium content, extracted by 0.01 M CaCl2 solution.
- Total_C: total carbon content.
- Total_N: total nitrogen content.
- Total_Organic_C: total organic carbon content.
- CN_ratio: the ratio of carbon:nitrogen content.
- Total_P: total content of phosphorus.
- Available_N: available nitrogen content.
- Available_P: available phosphorus content.
- Available_K: available potassium content.
4. Missing data codes: None
5. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: (2) SoilBioticData\Bacterial_feature_table.txt
1. Number of variables: 21
2. Number of cases/rows: 17322
3. Variable List:
- #ASV ID: amplicon sequence variants of bacterial community, clustered by high-quality reads.
- column 2~21: soil identities, 4 Treatments (5 replicates for each) in conditioning phase.
4. Missing data codes: None
5. Specialized formats or other abbreviations used:
- (1) CK - control soil
- (2) M.s. - Miscanthus sinensis
- (3) P. t. - Paspalum thunbergii
- (4) D.s. - Digitaria sanguinalis
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DATA-SPECIFIC INFORMATION FOR: (3) SoilBioticData\Bacterial_taxonomy.tsv
1. Number of variables: 3
2. Number of cases/rows: 17322
3. Variable List:
- Feature ID: the same as "#ASV ID", amplicon sequence variants of bacterial community, clustered by high-quality reads.
- Taxon: taxonomy of each ASV.
- Confidence: confidence of taxonomy classfication.
4. Missing data codes: None
5. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: (4) SoilBioticData\Fungal_feature_table.txt
1. Number of variables: 21
2. Number of cases/rows: 2660
3. Variable List:
- #ASV ID: amplicon sequence variants of fungal community, clustered by high-quality reads.
- column 2~21: soil identities, 4 Treatments (5 replicates for each) in conditioning phase.
4. Missing data codes: None
5. Specialized formats or other abbreviations used:
- (1) CK - control soil
- (2) M.s. - Miscanthus sinensis
- (3) P. t. - Paspalum thunbergii
- (4) D.s. - Digitaria sanguinalis
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DATA-SPECIFIC INFORMATION FOR: (5) SoilBioticData\Fungal_taxonomy.tsv
1. Number of variables: 3
2. Number of cases/rows: 2660
3. Variable List:
- Feature ID: the same as "#ASV ID", amplicon sequence variants of fungal community, clustered by high-quality reads.
- Taxon: taxonomy of each ASV.
- Confidence: confidence of taxonomy classfication.
4. Missing data codes: None
5. Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: (6) PlantTraitData\Plant_Info.csv
1. Number of variables: 3
2. Number of cases/rows: 11
3. Variable List:
- Cultivating_Phase: the experimental phase, including "conditioning phase" and "feedback phase".
- Plant_Species: plant species (control pots were planting nothing) in both cultivating phase.
- Data_Processing_ID: the abbreviation ID for each treatment during data presenting and processing.
4. Missing data codes: None
5. Specialized formats or other abbreviations used: as it shown in the file.
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DATA-SPECIFIC INFORMATION FOR: (7) PlantTraitData\Plant-soil_Feedback.csv
1. Number of variables: 4
2. Number of cases/rows: 140 & 105
3. Variable List:
- Sample_ID_1: sample ID of plant samples in feedback phase.
- Aver_total_biomass(g): Averaged individual biomass (including roots and shoots) of plant samples in feedback phase.
- Sample_ID_2: sample ID of plant samples in feedback phase (for PSF calculating result).
- PSF_value: Plant-soil feedback value (The feedback effect was calculated as the difference in biomass (BM) of a focal plant a grown on plant A conditioned and control soils divided by the maximum biomass of the focal plant a on either plant A conditioned or control soils: PSFA-a = (BMA-a – BMcontrol-a) / max(BMA-a, BMcontrol-a)).
4. Missing data codes: None
5. Specialized formats or other abbreviations used: as it shown in the file (6).
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DATA-SPECIFIC INFORMATION FOR: (8) PlantTraitData\Root_Functional_Traits.csv
1. Number of variables: 13
2. Number of cases/rows: 140
3. Variable List:
- Sample ID: sample ID of plant samples in feedback phase.
- Shoot_Biomass(g): averaged individual shoot biomass of plant samples in feedback phase.
- Root_Biomass(g): averaged individual root biomass of plant samples in feedback phase.
- Root_Length(cm): total root length of plant samples in feedback phase.
- Root_Volume(cm3): total root volume of plant samples in feedback phase.
- Average_Diameter(mm): average root diameter of plant samples in feedback phase.
- Root_Carbon_Content(mg/g): root carbon content of plant samples in feedback phase.
- Root_Nitrogen_Content(mg/g): root nitrogen content of plant samples in feedback phase.
- CN_Ratio: The ratio of root carbon to nitrogen content of plant samples in feedback phase.
- Specific_Root_Length(cm/g): The root length divided by root mass of plant samples in feedback phase.
- Root_Tissue_Density(g/cm3): The ratio of root mass to the volume of plant samples in feedback phase.
- Fine_Root_Diameter(mm): The diameter of fine roots (diameter < 2mm) of plant samples in feedback phase.
- Root_Shoot_Ratio: The ratio of root mass to shoot mass of plant samples in feedback phase.
4. Missing data codes: None
5. Specialized formats or other abbreviations used: as it shown in the file (6).
Sharing/Access information
Data was derived from the following source:
Zhu, S.-C., Liu, W.-S., Chen, Z.-W., Liu, X.-R., Zheng, H.-X., Chen, B.-Y., Zhi, X.-Y., Chao, Y., Qiu, R.-L., Chu, C.-j., Liu, C., Morel, J.L., van der Ent, A. & Tang, Y.-T. Abiotic legacies mediate plant-soil feedback during early vegetation succession on Rare Earth Element mine tailings. Journal of Applied Ecology.
Methods
In a two-phase plant-soil feedback experiment based on the rare earth element (REE) mine tailing soil, we investigated biotic (changes in bacterial and fungal community) and abiotic legacies (changes in chemical properties) of three pioneer grass species, and examined feedback effects of three grasses, two legumes and two woody plants with different root traits.
The soils for the experiment were collected from several patches of REE mine tailings that had been abandoned since 2007. The grass species, comprising M. sinensis, Paspalum thunbergii and Digitaria sanguinalis, were planted in both the conditioning and feedback phases.Besides grasses, the legume species, comprising of Tephrosia candida and Cajanus cajan, and the woody species, comprising of P. massoniana and C. lanceolate, were planted in the feedback phase.
The conditioning phase lasted for 18 weeks. At the end of this phase, the shoots and coarse roots were removed, soil samples were collected for chemical properties (abiotic legacies) and microbial communities(biotic legacies) measurement. [The collection of data in "SoilAbioticData" and "SoilBioticData"]
The feedback phase lasted for 16 weeks. At the end of this phase, the plant shoots and roots were harvested for plant functional trait analyses. [The collection of data in "PlantTraitData"]
More details about materials and methods can be found in the paper.