Data from: The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression

Krüger M, Teste FP, Laliberté E, Lambers H, Coghlan M, Zemunik G, Bunce M

Date Published: August 28, 2015

DOI: http://dx.doi.org/10.5061/dryad.tq0ft

 

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Title Roche GS Junior amplicon sequencing reads from roots
Downloaded 5 times
Description Trimmed and pre-processed sequence reads from amplicon sequencing with the Roche GS Junior system using Lib-A chemistry from roots. Pre-processing was performed as described in Coghlan et al. (2012) and involved searching for exact MID-tags and primer sequences.
Download fastafiles_allroots.zip (553.1 Kb)
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Title Roche GS Junior amplicon sequencing reads from soil
Downloaded 3 times
Description Trimmed and pre-processed sequence reads from amplicon sequencing with the Roche GS Junior system using Lib-A chemistry from soil. Pre-processing was performed as described in Coghlan et al. (2012) and involved searching for exact MID-tags and primer sequences.
Download fastafiles_allsoil.zip (375.3 Kb)
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Title AMF-OTU consensus sequences
Downloaded 7 times
Description Final consensus sequences created after the second clustering (0.97 sequence similarity) using the iterative refinement method (L-INS-i) of MAFFT.
Download consensus_files_AMF-OTUs.fas (32.55 Kb)
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Title Table A1
Downloaded 1 time
Description GPS data of the 15 plots sampled within the three different dunes systems (Quindalup = Young, Spearwood = Middle and Bassendean = Old) of the Jurien Bay chronosequence (Zemunik et al. 2015).
Download Table A1_GPSdata.docx (12.82 Kb)
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Title Table A2
Downloaded 36 times
Description Phylogenetic divsersity (PD, NRI and NTI) for all 15 plots, the dune system (Quindalup=Young, Spearwood=Middle, Bassendean=Old), all root and soil samples along the Jurien Bay chronosequence.
Download Table A2_PD_NRI&NTI.xlsx (13.93 Kb)
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Title Phylogenetic tree file
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Description Phylogenetic Maximum-Likelihood tree file (RAxML) including both, root and soil OTUs, used for the calculation of NRI and NTI with the QIIME relatedness.py python script.
Download phylogenetictree_NTI&NRI (14.03 Kb)
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Title Alignment
Downloaded 3 times
Description Alignment file (fasta) of the AMF-OTUs detected at the Jurien Bay chronosequence, with part of the sequence dataset published in Krüger et al. (2012) as reference, sequences of the Young (Quindalup) dunes from Shi et al. (2012) and other environmental sequences.
Download Alignment_JurienBaychronosequence.fas (635.5 Kb)
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Title Figure 1 RAxML_bipartitions_rootsamples.tre
Downloaded 5 times
Description Phylogenetic Maximum-Likelihood tree (RAxML) with accession numbers only of all AMF-OTUs detected in roots at the Jurien Bay chronosequence. The phylip file used for this phylogenetic tree is uploaded as ReadMe file.
Download Fig1_RAxML_bipartitions_rootsamples.tre.result (10.68 Kb)
Download README.int (633.3 Kb)
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Title Figure 2 RAxML_bipartitions_soilsamples.tre
Downloaded 7 times
Description Phylogenetic Maximum-Likelihood tree (RAxML) with accession numbers only of all AMF-OTUs detected in soil at the Jurien Bay chronosequence. The phylip file used for this phylogenetic tree is uploaded as ReadMe file.
Download Fig2_RAxML_bipartitions_soilsamples.tre.result (2.381 Kb)
Download README.int (142.3 Kb)
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Title Dataset AMF-OTUs
Downloaded 5 times
Description Dataset of the operational taxonomix units (OTUs) for arbuscular mycorrhizal fungi (AMF) of all 15 plots at the Jurien Bay chronosequence from soil and roots. This dataset was used to calculate the rarefied richness, phylogenetic diversity, the non-parametric multidimensional scaling (NMDS) plot and the regression analyses of rarified AMF-OTU richness (for more details, see the Material and Method section of the paper).
Download amf2.csv (18.14 Kb)
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Title Dataset Plant-Soil
Downloaded 5 times
Description Dataset used for the Redundancy analysis (RDA) biplot with fitted plot and forward-selected soil nutrient variables, rarefied richness of arbuscular mycorrhiza (AM) host-plant communities along the Jurien Bay dune chronosequence based on the number of individuals per plot and the relative cover (for details see Material and Method section of the paper).
Download plantSoil.csv (3.407 Kb)
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When using this data, please cite the original publication:

Krüger M, Teste FP, Laliberté E, Lambers H, Coghlan M, Zemunik G, Bunce M (2015) The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression. Molecular Ecology 24(19): 4912–4930. http://dx.doi.org/10.1111/mec.13363

Additionally, please cite the Dryad data package:

Krüger M, Teste FP, Laliberté E, Lambers H, Coghlan M, Zemunik G, Bunce M (2015) Data from: The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.tq0ft
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