DOI: 10.5061/dryad.prr4xgxsp
title: Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites

description: 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.
description: # Differential effects of tree species identity on rhizospheric bacterial
 and fungal community richness and composition across multiple trace
 element-contaminated sites
 [https://doi.org/10.5061/dryad.prr4xgxsp](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.