Dataset

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

The University of Western Australia
Krüger, Manuela ; Teste, François P. ; Laliberté, Etienne ; Lambers, Hans ; Coghlan, Megan ; Zemunik, Graham ; Bunce, Michael
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.5061/dryad.tq0ft&rft.title=Data from: The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression&rft.identifier=10.5061/dryad.tq0ft&rft.publisher=Dryad Digital Repository&rft.description=Ecosystem retrogression following long-term pedogenesis is attributed to phosphorus (P) limitation of primary productivity. Arbuscular mycorrhizal fungi (AMF) enhance P acquisition for most terrestrial plants, but it has been suggested that this strategy becomes less effective in strongly weathered soils with extremely low P availability. Using next generation sequencing of the large subunit ribosomal RNA gene in roots and soil, we compared the composition and diversity of AMF communities in three contrasting stages of a retrogressive >2-million-year dune chronosequence in a global biodiversity hotspot. This chronosequence shows a ~60-fold decline in total soil P concentration, with the oldest stage representing some of the most severely P-impoverished soils found in any terrestrial ecosystem. The richness of AMF operational taxonomic units was low on young (1000's of years), moderately P-rich soils, greatest on relatively old (~120 000 years) low-P soils, and low again on the oldest (>2 000 000 years) soils that were lowest in P availability. A similar decline in AMF phylogenetic diversity on the oldest soils occurred, despite invariant host plant diversity and only small declines in host cover along the chronosequence. Differences in AMF community composition were greatest between the youngest and the two oldest soils, and this was best explained by differences in soil P concentrations. Our results point to a threshold in soil P availability during ecosystem regression below which AMF diversity declines, suggesting environmental filtering of AMF insufficiently adapted to extremely low P availability.,Roche GS Junior amplicon sequencing reads from rootsTrimmed 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.fastafiles_allroots.zipRoche GS Junior amplicon sequencing reads from soilTrimmed 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.fastafiles_allsoil.zipAMF-OTU consensus sequencesFinal consensus sequences created after the second clustering (0.97 sequence similarity) using the iterative refinement method (L-INS-i) of MAFFT.consensus_files_AMF-OTUs.fasTable A1GPS 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).Table A2Phylogenetic 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.Phylogenetic tree filePhylogenetic 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.phylogenetictree_NTI&NRIAlignmentAlignment 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.Figure 1 RAxML_bipartitions_rootsamples.trePhylogenetic 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.Fig1_RAxML_bipartitions_rootsamples.tre.resultFigure 2 RAxML_bipartitions_soilsamples.trePhylogenetic 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.Fig2_RAxML_bipartitions_soilsamples.tre.resultDataset AMF-OTUsDataset 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).amf2.csvDataset Plant-SoilDataset 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).plantSoil.csv,&rft.creator=Krüger, Manuela &rft.creator=Teste, François P. &rft.creator=Laliberté, Etienne &rft.creator=Lambers, Hans &rft.creator=Coghlan, Megan &rft.creator=Zemunik, Graham &rft.creator=Bunce, Michael &rft.date=2015&rft.relation=http://research-repository.uwa.edu.au/en/publications/771de3ee-8911-4184-9bba-0fa272ff29cc&rft.type=dataset&rft.language=English Access the data

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Ecosystem retrogression following long-term pedogenesis is attributed to phosphorus (P) limitation of primary productivity. Arbuscular mycorrhizal fungi (AMF) enhance P acquisition for most terrestrial plants, but it has been suggested that this strategy becomes less effective in strongly weathered soils with extremely low P availability. Using next generation sequencing of the large subunit ribosomal RNA gene in roots and soil, we compared the composition and diversity of AMF communities in three contrasting stages of a retrogressive >2-million-year dune chronosequence in a global biodiversity hotspot. This chronosequence shows a ~60-fold decline in total soil P concentration, with the oldest stage representing some of the most severely P-impoverished soils found in any terrestrial ecosystem. The richness of AMF operational taxonomic units was low on young (1000's of years), moderately P-rich soils, greatest on relatively old (~120 000 years) low-P soils, and low again on the oldest (>2 000 000 years) soils that were lowest in P availability. A similar decline in AMF phylogenetic diversity on the oldest soils occurred, despite invariant host plant diversity and only small declines in host cover along the chronosequence. Differences in AMF community composition were greatest between the youngest and the two oldest soils, and this was best explained by differences in soil P concentrations. Our results point to a threshold in soil P availability during ecosystem regression below which AMF diversity declines, suggesting environmental filtering of AMF insufficiently adapted to extremely low P availability.,Roche GS Junior amplicon sequencing reads from rootsTrimmed 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.fastafiles_allroots.zipRoche GS Junior amplicon sequencing reads from soilTrimmed 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.fastafiles_allsoil.zipAMF-OTU consensus sequencesFinal consensus sequences created after the second clustering (0.97 sequence similarity) using the iterative refinement method (L-INS-i) of MAFFT.consensus_files_AMF-OTUs.fasTable A1GPS 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).Table A2Phylogenetic 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.Phylogenetic tree filePhylogenetic 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.phylogenetictree_NTI&NRIAlignmentAlignment 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.Figure 1 RAxML_bipartitions_rootsamples.trePhylogenetic 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.Fig1_RAxML_bipartitions_rootsamples.tre.resultFigure 2 RAxML_bipartitions_soilsamples.trePhylogenetic 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.Fig2_RAxML_bipartitions_soilsamples.tre.resultDataset AMF-OTUsDataset 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).amf2.csvDataset Plant-SoilDataset 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).plantSoil.csv,

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Associated Persons
Graham Zemunik (Creator)Manuela Krüger (Creator); Megan Coghlan (Creator); Michael Bunce (Creator)

Issued: 2015-08-28

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