Competition mode and soil nutrient status shape the role of soil microbes in the diversity–invasibility relationship
Data files
Apr 29, 2024 version files 618.47 MB
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Li_et_al.__FUN_Guild.xlsx
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Li_et_al.__Fungi.xlsx
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Li_et_al.__plant_biomass.xlsx
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README.md
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README.txt.txt
Abstract
Understanding the relationship between plant diversity and invasibility is essential in invasion ecology. Species-rich communities are hypothesized to be more resistant to invasions than species-poor communities. However, while soil microorganisms play a crucial role in regulating this diversity–invasibility relationship, the effects of plant competition mode and soil nutrient status on their role remain unclear. To address this, we conducted a two-stage greenhouse experiment. Soils were first conditioned by growing nine native species separately in them for 1 year, then mixed in various configurations with soils conditioned using one, three, or six species, respectively. Next, we inoculated the mixed soil into sterilized substrate soil and planted the alien species Rhus typhina and native species Ailanthus altissima as test plants. We set up two competition modes (intraspecific and interspecific) and two nutrient levels (fertilization using slow-release fertilizer and non-fertilization). Under intraspecific competition, regardless of fertilization, the biomass of the alien species was higher in soil conditioned by six native species. By contrast, under interspecific competition, the biomass increased without fertilization but remained stable with fertilization in soil conditioned by six native species. Analysis of soil microbes suggests that pathogens and symbiotic fungi in diverse plant communities influenced R. typhina growth, which varied with competition mode and nutrient status. Our findings suggest that the soil microbiome is pivotal in mediating the diversity–invasibility relationship, and this influence varies according to competition mode and nutrient status.
README: Competition mode and soil nutrient status shape the role of soil microbes in the diversity–invasibility relationship
https://doi.org/10.5061/dryad.wh70rxww6
Description of the data and file structure
Data usage bootstrap:
See plant biomass data at: Li et al._ plant biomass
See soil fungi community data at: Li et al._ Fungi
See soil FUNGuild function prediction at: Li et al._ FUN Guid
DATA-SPECIFIC INFORMATION FOR: Li et al._ plant biomass
1. Number of variables: 6
2. Number of cases/rows: 763
3. Variable List:
"species" refers to the classification of plants as either alien or native.
"diversity" refers to the level of plant diversity.
"soil mixture types" refers to the types of soil mixtures.
"interspecific competition" and "intraspecific competition" refer to the modes of competition.
"fertilization" and "non-fertilization" refer to the nutrient levels.
"total biomass" refers to the total plant biomass (g) under a specific treatment.
DATA-SPECIFIC INFORMATION FOR: Li et al._ Fungi
1. Number of variables: 28
2. Number of cases/rows: 2940
3. Variable List:
OTU: operational taxonomic unit
sample1: Experimental soil sample naming
sample2: Experimental soil sample naming
sample4: Experimental soil sample naming
sample5: Experimental soil sample naming
sample6: Experimental soil sample naming
sample7: Experimental soil sample naming
sample8: Experimental soil sample naming
sample9: Experimental soil sample naming
sample10: Experimental soil sample naming
sample11: Experimental soil sample naming
sample12: Experimental soil sample naming
sample13: Experimental soil sample naming
sample14: Experimental soil sample naming
sample15: Experimental soil sample naming
sample16: Experimental soil sample naming
sample17: Experimental soil sample naming
sample18: Experimental soil sample naming
sample19: Experimental soil sample naming
sample20: Experimental soil sample naming
sample21: Experimental soil sample naming
sample22: Experimental soil sample naming
sample23: Experimental soil sample naming
sample24: Experimental soil sample naming
sample25: Experimental soil sample naming
sample26: Experimental soil sample naming
sample27: Experimental soil sample naming
taxonomy: Microbial classification level
DATA-SPECIFIC INFORMATION FOR: Li et al._ FUN Guid
1. Number of variables: 29
2. Number of cases/rows: 2940
3. Variable List:
Functional type:
sample1: Experimental soil sample naming
sample2: Experimental soil sample naming
sample4: Experimental soil sample naming
sample5: Experimental soil sample naming
sample6: Experimental soil sample naming
sample7: Experimental soil sample naming
sample8: Experimental soil sample naming
sample9: Experimental soil sample naming
sample10: Experimental soil sample naming
sample11: Experimental soil sample naming
sample12: Experimental soil sample naming
sample13: Experimental soil sample naming
sample14: Experimental soil sample naming
sample15: Experimental soil sample naming
sample16: Experimental soil sample naming
sample17: Experimental soil sample naming
sample18: Experimental soil sample naming
sample19: Experimental soil sample naming
sample20: Experimental soil sample naming
sample21: Experimental soil sample naming
sample22: Experimental soil sample naming
sample23: Experimental soil sample naming
sample24: Experimental soil sample naming
sample25: Experimental soil sample naming
sample26: Experimental soil sample naming
sample27: Experimental soil sample naming
Methods
At 8 weeks after the start of the test phase, all aboveground and belowground parts of the test plants were harvested and rinsed with water. Owing to the death of some seedlings during the growth period, 502 R. typhina individuals (interspecific: 239, intraspecific: 263) and 259 A. altissima individuals were harvested. The collected plant tissue was placed in a 70 °C oven to dry for a week and was weighed. The biomass of two R. typhina plants was measured together under intraspecific competition, and the biomass of R. typhina and A. altissima was measured separately under interspecific competition.
Soil sampling, DNA extraction, amplicon sequencing, and bioinformatics analysis
The 27 mixed fresh soil samples, collected from various diversity treatments and subsequently stored in a refrigerator at −80 °C, were analyzed for soil fungal community composition. The total microbial community DNA was extracted according to the instructions of the E.Z.N.A. Soil DNA Kit (Omega Bio-tek, Norcross, GA). The quality of the extracted DNA was verified using 1% agarose gel electrophoresis, and DNA concentration and purity were measured using a NanoDrop 2000 device (Thermo Fisher Scientific, Waltham, MA). The fungal rRNA internal transcribed spacer (ITS) region was amplified using the primer set ITS1F (5′-CTTGGTCATTTAGAGGAAGTAA-3′) and ITS2R (5′-GCTGCGTTCTTCATCGATGC-3′). Sequencing was performed using a MiSeq PE300/NovaSeq PE250 platform (Illumina, San Diego, CA). The Illumina MiSeq platform has a higher throughput and lower error rate than other high-throughput sequencers (Loman et al., 2012; Frey et al., 2014).
Fungal sequences were classified using the UNITE database (version 8.0) and using the USEARCH11-uparse algorithm for clustering. Operational taxonomic unit (OTU) sequence similarity was 0.97. Species classification was performed using the unite8.0/its fungi database, and classification confidence was 0.7. As fungal DNA extraction failed for one sample, we obtained 26 samples of ITS rDNA.