Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites
Data files
Apr 17, 2024 version files 53.66 GB
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180328_SND405_A_L001_GWM-1320_R1.fastq.gz
1.47 GB
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180328_SND405_A_L001_GWM-1320_R2.fastq.gz
1.61 GB
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180328_SND405_A_L001_GWM-1321_R1.fastq.gz
2.89 GB
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180328_SND405_A_L001_GWM-1321_R2.fastq.gz
3.12 GB
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180328_SND405_A_L001_GWM-1322_R1.fastq.gz
4.21 GB
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180328_SND405_A_L001_GWM-1322_R2.fastq.gz
4.42 GB
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180328_SND405_A_L001_GWM-1323_R1.fastq.gz
4.36 GB
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180328_SND405_A_L001_GWM-1323_R2.fastq.gz
4.55 GB
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180328_SND405_A_L002_GWM-1320_R1.fastq.gz
1.47 GB
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180328_SND405_A_L002_GWM-1320_R2.fastq.gz
1.61 GB
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180328_SND405_A_L002_GWM-1321_R1.fastq.gz
2.95 GB
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180328_SND405_A_L002_GWM-1321_R2.fastq.gz
3.19 GB
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180328_SND405_A_L002_GWM-1322_R1.fastq.gz
4.27 GB
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180328_SND405_A_L002_GWM-1322_R2.fastq.gz
4.50 GB
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180328_SND405_A_L002_GWM-1323_R1.fastq.gz
4.43 GB
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180328_SND405_A_L002_GWM-1323_R2.fastq.gz
4.62 GB
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README.md
3.80 KB
Abstract
Soil microbial communities play a key role in plant nutrition and stress tolerance. This is particularly true in sites contaminated by trace metals, which often have low fertility and stressful conditions for woody plants in particular. However, we have limited knowledge of the abiotic and biotic factors affecting the richness and composition of microbial communities inhabiting the rhizosphere of plants in contaminated sites. Using high-throughput amplicon sequencing, we studied the rhizospheric bacterial and fungal community structures of 14 woody plant families planted in three contrasting sites contaminated by metals (Pb, Cd, Zn, Mn, Fe, S). The rhizospheric bacterial communities in the given sites showed no significant difference between the various woody species but did differ significantly between sites. The Proteobacteria phylum was dominant, with over 25% of the overall relative abundance, followed by Actinobacteria, Bacteroidetes, and Gemmatimonadetes. Sites were also the main driver in fungal community composition, yet, unlike bacteria, tree species identity significantly affected fungal communities. The Betulaceae, Salicaceae, and Fagaceae families had a high proportion of Basidiomycota, particularly ectomycorrhizal fungi, and the lowest diversity and richness. The other tree families and the unplanted soil harbored a greater abundance of Ascomycota and Mucoromycota. Consequently, for both bacteria and fungi, the site effect significantly impacted their community richness and composition, while the influence of plants on the richness and composition of rhizospheric microbial communities stayed consistent across sites and was dependent on the microbial kingdom. Finally, we highlighted the importance of considering this contrasting response of plant rhizospheric microbial communities in relation to their host identity, particularly to improve assisted revegetation efforts at contaminated sites.
https://doi.org/10.5061/dryad.prr4xgxsp
This Readme file lists the raw sequencing fastq files obtained for the Bact02 and Fung02 markers, explains how they were obtained and the structure of the descriptor files that can be used to assign each sequence read to the right PCR replicate. Finally, the last section explains the structure of the
Description of the data and file structure
Bact02 marker
After PCR amplification, amplicons were pooled in equal volumes in two separate batches A and B. Each batch was used to prepare a sequencing library.
Library GWM-1320 corresponds to batch A, and library GWM-1321 corresponds to batch B. Each library was sequenced on two different Illumina HiSeq2500 sequencing lanes.
Ultimately, this resulted in 4 R1 fastq sequence files, and 4 R2 fastq sequences files listed below:
180328_SND405_A_L001_GWM-1320_R1.fastq.gz (Batch A)
180328_SND405_A_L001_GWM-1320_R2.fastq.gz (Batch A)
180328_SND405_A_L001_GWM-1321_R1.fastq.gz (Batch B)
180328_SND405_A_L001_GWM-1321_R2.fastq.gz (Batch B)
180328_SND405_A_L002_GWM-1320_R1.fastq.gz (Batch A)
180328_SND405_A_L002_GWM-1320_R2.fastq.gz (Batch A)
180328_SND405_A_L002_GWM-1321_R1.fastq.gz (Batch B)
180328_SND405_A_L002_GWM-1321_R2.fastq.gz (Batch B)
The following files can be used to assign each assembled sequence to the corresponding PCR replicate based on the forward an reverse tag combination:
Bact02_A.ngsfilter (Batch A)
Bact02_B.ngsfilter (Batch B)
These files have the following structure:
First column: name of the experiment
Second column: name of the PCR replicate
Third column: forward and reverse tags (separated by a colon)
Fourth column: forward PCR primer
Fifth column: reverse PCR primer
Sixth column: optional extra information, before a semi-colon
Fung02 marker
After PCR amplification, amplicons were pooled in equal volumes in two separate batches A and B. Each batch was used to prepare a sequencing library. Library GWM-1322 corresponds to batch A, and library GWM-1323 corresponds to batch B. Each library was sequenced on two different Illumina HiSeq2500 sequencing lanes.
Ultimately, this resulted in 4 R1 fastq sequence files, and 4 R2 fastq sequences files listed below:
180328_SND405_A_L001_GWM-1322_R1.fastq.gz (Batch A)
180328_SND405_A_L001_GWM-1322_R2.fastq.gz (Batch A)
180328_SND405_A_L001_GWM-1323_R1.fastq.gz (Batch B)
180328_SND405_A_L001_GWM-1323_R2.fastq.gz (Batch B)
180328_SND405_A_L002_GWM-1322_R1.fastq.gz (Batch A)
180328_SND405_A_L002_GWM-1322_R2.fastq.gz (Batch A)
180328_SND405_A_L002_GWM-1323_R1.fastq.gz (Batch B)
180328_SND405_A_L002_GWM-1323_R2.fastq.gz (Batch B)
The following files can be used to assign each assembled sequence to the corresponding PCR replicate based on the forward an reverse tag combination:
Fung02_A.ngsfilter (Batch A)
Fung02_B.ngsfilter (Batch B)
These files have the same structure as the corresponding files for Bact02.
PCR replicate names
LetterNumber-3Letters-Number_Letter (for example C5-FOX-1_a)
First letter = site symbol. C stands for Carrières, L for Leforest and T for Thann.
First number = bloc number
Group of three letters = species name (see abbreviations in Table S1, CON stands for the control)
Second number = replicate number
Second letter = PCR replicate code (“a”, “b”, “c”, “d”)
For controls, the PCR replicate names start with “CTL_Extra”, and “CTL-PCR-neg” for the extraction and PCR negative controls, respectively.
Prefix “Blancs_” indicates a combination of forward and reverse tags absent from the experiment, and used to monitor the level of tag jumps.