DOI: 10.5061/dryad.vt4b8gtx9
title: Soil microbial influences over coexistence in multispecies plant communities in a subtropical forest

description: Soil microbes have long been recognized to substantially affect the
 coexistence of pairwise plant species across terrestrial ecosystems.
 However, projecting their impacts on the coexistence of multi-species
 plant systems remains a pressing challenge. To address this challenge, we
 conducted a greenhouse experiment with 540 seedlings of five tree species
 in a subtropical forest in China and evaluated microbial effects on
 multispecies coexistence using the structural method, which quantifies how
 the structure of species interactions influences the likelihood of
 multiple species to persist. Specifically, we grew seedlings alone or with
 competitors in different microbial contexts and fitted individual biomass
 to a population dynamic model to calculate intra- and inter-specific
 interaction strength with and without soil microbes. We then used these
 interaction structures to calculate two metrics of multispecies
 coexistence, structural niche differences (which promote coexistence) and
 structural fitness differences (which drive exclusion), for all possible
 communities comprising two to five plant species. We found that the soil
 microbes generally increased both the structural niche and fitness
 differences across all communities, with a much stronger effect on
 structural fitness differences. A further examination of functional traits
 between plant species pairs found that trait differences are stronger
 predictors of structural niche differences than structural fitness
 differences and that soil microbes have the potential to change
 trait-mediated plant interactions. Our findings underscore that soil
 microbes strongly influence the coexistence of multispecies plant systems,
 and also add to the experimental evidence that the influence is more on
 fitness differences rather than niche differences.
description: We conducted the experiment in a greenhouse located at the
 Heishiding Natural Reserve (111°53′ E, 23°27′ N, 150–927 m elevation),
 Guangdong Province, south China. Our experiment included five species that
 vary in their relative abundance in the reserve and in mycorrhizal types:
 <em>Artocarpus styracifolius </em>(ASTY),<em>
 Cryptocarya concinna </em>(CCON), <em>Cyclobalanopsis hui
 </em>(CHUI), <em>Castanopsis hystrix
 </em>(CHYS)<em> </em>and<em> Cyclobalanopsis
 pachyloma </em>(CPAC) (Appendix S1: Table S1). Briefly, ASTY and
 CCON form root associations with arbuscular mycorrhizal fungi, and the
 others associate with ectomycorrhizal fungi. In our
 experiment, we grew either a single individual (to measure the intrinsic
 growth rate) or two conspecific individuals (to measure intraspecific
 interaction coefficients) of each species in pots inoculated with soil
 from conspecific adult trees, or in pots with only sterile soil (5 species
 × 2 soils × 2 density levels = 20 treatments; Figure 1). Additionally, we
 grew each pairwise combination of species (10 combinations) to obtain the
 interspecific interaction coefficients. To do so, we grew each pair of
 species (<em>i</em>/<em>j</em>) in inoculated soil
 with species <em>i</em>’s soil microbes and separately with
 species <em>j</em>’s soil microbes (to quantify interaction
 coefficients in the presence of microbes)<em>,</em> and in
 sterile soil (to quantify interaction coefficients in the absence of
 microbes), which led to a total of 30 treatments (10 species pairs × 3
 soil microbial treatments = 30 treatments; Figure 1). For each treatment,
 we established six replicate blocks. To generate
 allometric equations for estimating the initial biomass of experimental
 seedlings, we grew an additional 20 seedlings per species in the same
 greenhouse conditions in sterilized soils. In September 2020, we harvested
 these seedlings and measured each individual’s height, basal diameter,
 leaf count, and total biomass. We performed linear regression models of
 the total biomass with these three predictors for each species (Appendix
 S1: Table S2). Using this linear regression, we estimated the initial
 biomass of seedlings based on height, basal diameter, and leaf count
 measurements from the beginning of the experiment. In May 2021, after 12
 months of growth, we harvested the total (above- and below-ground) biomass
 for each seedling dried for 48 h at 60 ℃, and weighed.
 To investigate how functional traits relate to the microbially
 mediated plant coexistence metrics, we measured eight plant functional
 traits that are closely associated with plant life-history: Height (H, the
 shortest distance between the upper boundary of the main photosynthetic
 tissues on a plant and the ground level, cm), specific leaf area (SLA, the
 one-sided area of a fresh leaf divided by its dry mass,
 cm<sup>2</sup>/g), total leaf area (TLA, one-sided or
 projected area of all leaf from the same plant,
 cm<sup>2</sup>), root average diameter (RAD, averaged diameter
 of all roots, mm), root length (RL, total length of all roots, cm), root
 to shoot ratio (RS, the ratio of plant dry mass in root and shoot), root
 surface area (RSA, total surface area of all roots,
 cm<sup>2</sup>), and specific root length (SRL, length per
 unit dry mass of roots, cm/g).
description: ## Description of the data and file structure We have uploaded two
 datasets for statistical analysis: growth_dat.csv and raw_trait_dat.csv.
 The growth_dat.csv is used to construct a Bayesian model to calculate
 intraspecific and interspecific interaction coefficients. The
 raw_trait_dat.csv is employed for Mantel tests to explore the
 relationships between niche differences, fitness differences, and
 traits. NA indicates that the traits of the focal species were not
 measured. ### **growth\_dat.csv** * **block:** The block in which the
 plant is located, ranging from A to F. The differences between the blocks
 are not significant and are not used for analysis. * **soil_origin:** The
 source of the soil microbiota. ASTY, CCON, CHUI, CHYS, CPAC are
 abbreviations for the Latin names of five species. For instance, in the
 case of the species pair 'ASTY-CCON', if the soil_origin is
 "ASTY", this indicates that the soil microbes used for planting
 these two species originate from beneath the trees of ASTY in the field.
 "Sterilized" means that no microbes were inoculated. *
 **species_pair:** The paired species. For example, "ASTY-CCON"
 indicates that individuals of ASTY and CCON are planted together in one
 pot. * **focal_species:** The focal species for which biomass is
 measured. Taking ASTY-CCON as an example, if the focal species is ASTY, it
 means that the subsequent data on growth and neighboring density
 specifically pertain to ASTY. * **treatment:** "Inoculated" or
 "Sterilized". "Inoculated" means that the species pair
 is planted in soil that has been inoculated with soil microbes, while
 "Sterilized" means it is planted in sterilized soil. *
 **growth:** The ratio of the species' biomass at harvest to its
 initial biomass, after a natural logarithm (ln) transformation. * **ASTY,
 CCON, CHUI, CHYS, CPAC:** The number of neighboring species. The column
 names are all species names. A value of 0 indicates that there are no
 neighboring individuals of that species, while a value of 1 indicates that
 the density of neighboring individuals of that species is
 1.![](file:///C:/Users/wwtao/AppData/Local/Temp/msohtmlclip1/01/clip_image002.png) ### **raw\_trait\_dat.csv** * **block:** The block in which the plant is located, ranging from A to F. The differences between the blocks are not significant and are not used for analysis. * **treatment:** "Inoculated" or "Sterilized". "Inoculated" means that the species pair is planted in soil that has been inoculated with soil microbes, while "Sterilized" means it is planted in sterilized soil. * **soil_origin:** The source of the soil microbiota. ASTY, CCON, CHUI, CHYS, CPAC are abbreviations for the Latin names of five species. For instance, in the case of the species pair 'ASTY-CCON', if the soil_origin is "ASTY", this indicates that the soil microbes used for planting these two species originate from beneath the trees of ASTY in the field. "Sterilized" means that no microbes were inoculated. * **species_pair:** The paired species. For example, "ASTY-CCON" indicates that individuals of ASTY and CCON are planted together in one pot. * **focal_species:** The focal species for which traits are measured. Taking ASTY-CCON as an example, if the focal species is ASTY, it means that the subsequent data on traits specifically pertain to ASTY. * **H** (cm): Height. The shortest distance between the upper boundary of the main photosynthetic tissues on a plant and the ground level. * **RL** (cm): Root length. Total length of all roots. * **RSA** (cm2): Root surface area. Total surface area of all roots. * **RAD** (mm): Root average diameter. Averaged diameter of all roots. * **SRL** (cm/g): Specific root length. Length per unit dry mass of roots. * **RS:** Root to shoot ratio. The ratio of plant dry mass in root and shoot. * **SLA** (cm2/g): Specific leaf area. The one-sided area of a fresh leaf divided by its dry mass. * **TLA** (cm2): Total leaf area. One-sided or projected area of all leaf from the same plant. ## Code/Software The Bayesian model fitting was performed using the "rstan" package in R (Stan Development Team, 2020). Code for implementing structural method was from Song et al. (2018). All analyses were implemented in R 4.1.1 (R Development Core Team 2021).