Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest
Data files
Oct 10, 2023 version files 284.77 KB
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Phylogeny.data
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README.md
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Root.community.data.csv
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Root.trait.data.csv
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Soil.topographical.variables.csv
Nov 06, 2023 version files 284.87 KB
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Phylogeny.data
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README.md
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Root.community.data.csv
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Root.trait.data.csv
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Soil.topographical.variables.csv
Abstract
Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e. β diversity), which can reflect the degree of community-wide biotic homogenization, remains largely unknown, hindering better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0–30 cm soil profiles in a subtropical forest in China. Root segments were identified into 143 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw) and mean nearest neighbor distance (Dnn) to quantify species ecological differences, we tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes, examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Both functional and phylogenetic Dpw (e.g. interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, phylogenetic Dnn (e.g. intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.
README: Beta diversity among root neigbourhoods
In this study, we looked at the functional and phylogenetic turnover rate (e.g., dissimilarity of functional traits and phylogenetic relatedness among species ) of root-centric species among root neighbourhoods (e.g., soil patches where multiple heterospecific roots cooccur) in a subtropical forest in southern China. The study aimed to compare the turnover rate of functions and phylogeny with that of plant taxonomy. Trait dissimilarity among species was quantified based on six root functional traits with species phylogenetic relatedness quantified based on a phylogeny. Multiple abiotic variables were measured at the soil core level such as topographical variables (e.g., elevation) and soil variables (e.g., soil nitrogen and phosphorus content).
Description of the data and file structure
- the [Root.trait.data] file is composed of 138 rows and 7 columns. Each row indicates one species named as "species", and the remaining rows indicate six functional traits of fine roots as explained below. 1. Average diameter: Averaged diameter of fine roots (mm). 2. Specific root length: Length per unit dry mass of fine roots (cm/mg). 3. Specific root tip abundance: Number of root tips per unit dry mass of fine roots (tips/mg). 4. Specific root surface area: Surface area per unit dry mass of fine roots (cm2/mg). 5. Root tissue density: Mass per unit volume of fine roots (mg/cm3). 6. Root branching intensity: Number of root tips per unit cm of fine roots (tips/cm).
- the [Soil.topographical.variables] file is composed of 625 rows and 22 columns. Each row indicates one sampling location named as “site”, and the remaining 21 rows indicate the measured topographical and soil variables as explained below. 1. Site: sampling location 2. gx: the x coordinate of the sampling location in the 500 by 1000 m forest plot. 3. gy: the y coordinate of the sampling location in the 500 by 1000 m forest plot. 4. Altitude: altitude of the sampling location (m). 5. Slope: slope of the sampling location (degree). 6. Aspect: aspect of the sampling location (degree). 7. Curvature: curvature of the sampling location. 8. Soil pH: soil pH of the sampling location. 9. Soil total nitrogen: soil total nitrogen content of the sampling location (g/kg). 10. Total phosphorus: soil total phosphorus content of the sampling location (g/kg). 11. Total potassium: soil total potassium content of the sampling location (g/kg). 12. Available phosphorus:soil available phosphorus content of the sampling location (mg/kg). 13. Available potassium: soil available potassium of the sampling location (mg/kg). 14. Soil volumetric sand content: soil volumetric sand content of the sampling location (%). 15. Available copper: soil available copper of the sampling location (mg/kg). 16. Available zinc: soil available zinc of the sampling location (mg/kg). 17. Available iron: soil available iron of the sampling location (mg/kg). 18. Available manganese: soil available manganese of the sampling location (mg/kg). 19. Exchangeable magnesium: soil exchangeable magnesium of the sampling location (mg/kg). 20. Exchangeable base cations: soil exchangeable base cations of the sampling location (cmol/kg). 21. Available boron: soil available boron of the sampling location (mg/kg). 22. Exchangeable aluminum: soil exchangeable aluminum of the sampling location (cmol/kg).
- the [Root.community.data] file is composed of 609 rows and 138 columns. Each row indicates one sampling location names as “site”, and the remaining 138 rows indicate the presence/ absence of the study138 species in a root neighbourhoods (e.g. soil patches).
- the [Phylogeny.data] file stores phylogeny of 152 species including the study 138 species. The file can be opened with “TexEdit”.
Code/Software
Data files are processed with R.
Methods
We randomly collected root materials from 625 soil cores (i.e., root neigbourhoods) in a subtropical forest. Species were identified with DNA-barcoding and their morphologies. Soil variables were measued within a distance of 10 cm from the root-sampling core.The spatial distances of soil cores were quantified based on the coordinates of the cores. Species phylogeny was onstructed based on DNA sequence. Species root morphological and archetectural traits were measured with WinRHIZO.
Usage notes
These datasets were collected in the Guangdong Heishiding Dynamic Forest Plot in Southern China (2016). Details for each dataset are provided in the README file.