Multiple dimensions of phylogenetic diversity are needed to explain the complex aboveground-belowground diversity relationships
Data files
Dec 05, 2023 version files 7.84 MB
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bacteria_OTU_table.csv
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bacteria_phylogenetic_tree.tre
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fungi_OTU_table.csv
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fungi_phylogenetic_tree.tre
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plant_phylogenetic_tree.tre
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plant_total_community_table.csv
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README.md
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soil.csv
Abstract
The complex relationship between aboveground and belowground diversity and whether they act as surrogates for one another remains unresolved. Increasing evidence suggests that investigating phylogenetic diversity could provide valuable insights into the interplay between plants and soil microbes, but the proliferation of phylogenetic diversity metrics has hindered comparative studies and the identification of general patterns. To overcome this challenge, we implemented a multi-dimensional framework that classifies phylogenetic diversity metrics into three dimensions: richness, divergence, and regularity, each of which captures different ecological aspects of species differences. Then we applied this framework to investigate the relationship between above and belowground diversity in a subtropical forest in Eastern China. We found that phylogenetic diversity of plant and soil microbes, including bacteria and fungi, were more strongly correlated at the richness and regularity dimension compared with divergence dimension. Further analyses revealed that these observed correlation patterns can be attributed to the influence of soil total phosphorus content, which is the limiting factor of plant and microbial phylogenetic diversity at richness and regularity dimensions. Together, our study demonstrated the necessity of using a multi-dimensional approach to advance our understanding of the complex relationships between plant and soil microbial biodiversity.
README
This README file was generated on 2023-12-02 by Xiaorong Lu.
GENERAL INFORMATION
- This folder contains the data, computer code and document files for the article:
Xiaorong Lu,Marc W.Cadotte,Pandeng Wang,Shan Rao,Xiaoye Shi,Siyuan Ren,Xihua Wang,Shao-peng Li(2023).Multiple dimensions of phylogenetic diversity are needed to explain the complex aboveground-belowground diversity relationships. Oikos.
Author Information
Principal Investigator
Name: Xiaorong Lu
Institution: School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, P.R. China
Email: smilelxr0904@gmail.comCorresponding Investigator Name: Shao-peng Li Institution: School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, P.R. China Email: spli@des.ecnu.edu.cn Co-investigator 1 Name: Prof Marc W. Cadotte Institution: Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada Email: marc.cadotte@utoronto.ca Co-investigator 2 Name: Pandeng Wang Institution: School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China Email: wangpd@mail2.sysu.edu.cn Co-investigator 3 Name: Shan Rao Institution: School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, P.R. China Email:shan.rao@foxmail.com Co-investigator 4 Name: Xiaoye Shi Institution: School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, P.R. China Email: xiaoye.shi@foxmail.com Co-investigator 5 Name: Siyuan Ren Institution: China Aero Geophysical Survey and Remote Sensing Center for Natural Resources, Beijing 100083, China Email: rsy9999ml@163.com Co-investigator 6 Name: Xihua Wang Institution: School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, P.R. China Email: xhwang@des.ecnu.edu.cn
Date of data collection: 2019
Geographic location of data collection: Ningbo City, Zhejiang Province, eastern China
Funding sources that supported the collection of the data: National Natural Science Foundation of China (NSFC3222051, NSFC31971553), the Shanghai Rising-Star Program (20QA1402900), and the Fundamental Research Funds for the Central Universities.
Comments and requests should be addressed to Xiaorong Lu: smilelxr0904@gmail.com. All material is free of use, but I would appreciate being told, and this dataset and the matching paper cited if appropriate.
Recommended citation for this dataset: Xiaorong Lu et al. (2023), Data from: Multiple dimensions of phylogenetic diversity are needed to explain the complex aboveground-belowground diversity relationships. Dryad, https://doi.org/10.5061/dryad.cvdncjt9d
DATA & FILE OVERVIEW
1.File List:
"bacteria_OTU table.csv": The OTUs table of bacteria
"fungi_OTU table.csv": The OTUs table of fungi
"plant_community table.csv":The OTUs table of plant
"bacteria_phylogenetic tree.tre": The phylogenetic tree of bacteria
"fungi_phylogenetic tree.tre": The phylogenetic tree of fungi
"plant_phylogenetic tree.tre": The phylogenetic tree of plant
"soil.csv": The soil physicochemical factors
Relationship between files, if important: None
Additional related data collected that was not included in the current data package: None
Are there multiple versions of the dataset? No
A. If yes, name of file(s) that was updated: NA
i. Why was the file updated? NA
ii. When was the file updated? NA
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DATA-SPECIFIC INFORMATION FOR: bacteria_OTU table.csv
Number of variables: 28119
Number of cases/rows: 80
Variable List:
plots:plot code
Zotu xxx: Every Zotus of each column (e.g.,Zotu10) represents the operational taxonomic units (OTUs) at the 100% similarity threshold;Missing data codes:
NoneAbbreviations used:
NoneOther relevant information:
None
#########################################################################
DATA-SPECIFIC INFORMATION FOR: fungi_OTU table.csv
Number of variables: 8997
Number of cases/rows: 80
Variable List:
plots:plot code
Zotu xxx: Every Zotus of each column (e.g.,Zotu6) represents the operational taxonomic units (OTUs) at the 100% similarity thresholdMissing data codes:
NoneAbbreviations used:
NoneOther relevant information:
None
#########################################################################
DATA-SPECIFIC INFORMATION FOR: plant_community table.csv
Number of variables: 59
Number of cases/rows: 16
Variable List:
plots:plot code
Each column represents the scientific name of plant speciesMissing data codes:
NoneAbbreviations used:
NoneOther relevant information:
None
#########################################################################
DATA-SPECIFIC INFORMATION FOR: bacteria_phylogenetic tree.tre
This is a bacterial molecular phylogenetic tree constructed by FastTree software
Missing data codes:
NoneAbbreviations used:
NoneOther relevant information:
None
#########################################################################
DATA-SPECIFIC INFORMATION FOR: fungi_phylogenetic tree.tre
This is a fungal molecular phylogenetic tree constructed by FastTree software
Missing data codes:
NoneAbbreviations used:
NoneOther relevant information:
None
#########################################################################
DATA-SPECIFIC INFORMATION FOR: plant_phylogenetic tree.tre
This is a plant phylogenetic tree produced form a mega-tree (i.e. GBOTB.extended.tre) using R package V.PhyloMaker
Missing data codes:
NoneAbbreviations used:
NoneOther relevant information:
None
#########################################################################
DATA-SPECIFIC INFORMATION FOR: soil.csv
Number of variables: 6
Number of cases/rows: 16
Variable List:
Plots: plot code of soil sampling\
TN: Total nitrogen (g/kg)
TP: Total phosphorus (g/kg)
AP: Available phosphorus (mg/kg)
TOC: Soil total organic carbon (g/kg)
pH: Soil pHMissing data codes:
NoneAbbreviations used:
NoneOther relevant information:
None
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Rcode
The file named "R_code_diversities.R" contains the R source code for all diversity indexes used in the paper (taking plants as an example). It should be processed using the R software.
Methods
This study was conducted in a subtropical forest located in Ningbo City, Zhejiang Province, Eastern China in 2017, with a subtropical monsoon climate characterized by an average annual temperature of 16.2°C and an average annual precipitation of 1700 mm. Dominant tree species in the area include Pinus massoniana, Schima superba, and Cunninghamia lanceolata. Our study comprised 16 plots situated in three different locations, dominated by various tree species ( 40 – 60-year-old stand), including both unmanaged secondary forests and forests that underwent close-to-nature silviculture treatment. In total, we obtained 16 plots, representing a clear diversity gradient and different composition structure across sites. For each plot, five bulk-soil cores (3.8 cm in diameter, 0-10 cm depth), excluding litter and organic horizons, were collected using a five-point sampling method and placed in separate sterile plastic bags. We obtained a total of 80 soil samples from the 16 plots in October 2019. The plant composition of all plots was investigated in August 2019. Every tree stem with a diameter at breast height (DBH) ≥ 5 cm in the plot was sampled. We found 117 plant species in total across all the study plots, both gymnosperms and angiosperms were included.