Fungal Ecology

Results of wood decay assays involving known wood-decaying fungi and bark beetle-associated fungi.

Full SEM images from multi panel figure 3 in the manuscript.

Supplemental Figures S1 and S2.

Specimens of myxomycetes collected from moist chamber cultures of inner-city and semi-urban parks within the Sydney Basin bioregion in New South Wales. Details of abbreviations are in the 'Supplementary data caption' file

Supplementary table S1 - RNAseq information and statistics of C. quitensis reference transcriptome assembly Supplementary table S2 - Colobanthus quitensis, reference metatranscriptome annotation table, including phylum information and normalized expression (Trimmed means of M-values) Supplementary table S3 - Differential expression between Colobanthus quitensis plants grown in open areas or inside open top chambers Supplementary table S4 - KEGG annotation and KEGG module analysis: Colobanthus quitensis, KEGG analysis of differentially expressed genes, including KEGG module reconstruction and KEGG detailed annotation for all DEGs Supplementary figure S1 - Volcano plot of DE transcripts Article Abstract: Maritime Antarctic is one of the most stressful environments for plant life worldwide. However, two vascular plant species (Deschampsia antarctica and Colobanthus quitensis) have been able to colonize this hostile environment. Although it has been proposed that C. quitensis possesses tolerance mechanisms and adaptations allowing survival and growth under such stressful conditions, the underlying molecular/transcriptional mechanisms are currently unknown. Furthermore, the impact of global warming on the endophytic and epiphytic organisms associated to C. quitensis remains unclear. Here, by using a metatranscriptomic approach, we determined the effect of an in situ simulated global warming scenario on C. quitensis plants. We found a large number of differentially expressed genes successfully annotated (2,997), suggesting that climate change modulates the metatranscriptome of C. quitensis plants and associated endophytes and epiphytes. Interestingly, 50,49% and 26,79% of up- and down-regulated genes, respectively, are from non-plant species (putative endophytic and epiphytic organisms, such as fungi). Interestingly, Gene Ontology analysis pointed out several biological processes differentially enriched in non-plant microorganisms associated with C. quitensis grown in a simulated global warming scenario. Taken together, these results suggest that climatic drivers are shaping plant-microorganism interaction, and that endophytes/epiphytes would play crucial roles on plant adaptation to extreme environmental conditions.

Additional results and data

Raw data and analysis code, compressed into a .zip file. Archived files are: Analysis_and_Figures.R - The R code for all analyses and figure generation Arabidopsis_Data_Sheet_for_R.csv - Raw data of plant growth, seed mass, and flowering time COMPETITION_RESULTS.csv - Fungal growth measurements for culture competition experiments. Reported data are area in pixels of fungal mycelium size

The file contains two sheets, The first sheet contains the fungal community matrix, with species in rows and samples in columns. Data is expressed as read counts. The second sheet contains the environmental data, including soil chemistry data and stand age.

The data set contains Supplemental data sets for the Manuscript entitled "Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi." Environmental sampling: Amplification of nuclear DNA regions (ITS1 and ITS2) were completed using the Fluidigm Access Array and the resulting amplicons were sequenced on an Illumina MiSeq v2 platform runs using rapid 2 × 250 nt paired-end reads. Illumina sequencing run amplicons that were size selected into <500nt and >500nt sub-pools, then remixed together <500nt: >500nt by nM concentration in a 1x:3x proportion. All amplification and sequencing steps were performed at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign. ITS1 region primers consisted of ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3). ITS2 region primers consisted of fITS7 (5'-GTGARTCATCGAATCTTTG-'3) and ITS4 (5'-TCCTCCGCTTATTGATATGC-'3). Supplemental files 1 through 5 contain the raw data files. Supplemental 1 is the ITS1 Illumina MiSeq forward reads and Supplemental 2 is the corresponding index files. Supplemental 3 is the ITS2 Illumina MiSeq forward reads and Supplemental 4 is the corresponding index files. Supplemental 5 is the map file needed to process the forward reads and index files in QIIME. Supplemental 6 and 7 contain the resulting QIIME 1.9.1. OTU tables along with UNITE, NCBI, and CONSTAX taxonomic assignments in addition to the representative OTU sequence. Numeric samples within the OTU tables correspond to the following: 1 Brachythecium sp. 2 Usnea cornuta 3 Dicranum sp. 4 Leucodon julaceus 5 Lobaria quercizans 6 Rhizomnium sp. 7 Dicranum sp. 8 Thuidium delicatulum 9 Myelochroa aurulenta 10 Atrichum angustatum 11 Dicranum sp. 12 Hypnum sp. 13 Atrichum angustatum 14 Hypnum sp. 15 Thuidium delicatulum 16 Leucobryum sp. 17 Polytrichum commune 18 Atrichum angustatum 19 Atrichum angustatum 20 Atrichum crispulum 21 Bryaceae 22 Leucobryum sp. 23 Conocephalum conicum 24 Climacium americanum 25 Atrichum angustatum 26 Huperzia serrata 27 Polytrichum commune 28 Diphasiastrum sp. 29 Anomodon attenuatus 30 Bryoandersonia sp. 31 Polytrichum commune 32 Thuidium delicatulum 33 Brachythecium sp. 34 Leucobryum glaucum 35 Bryoandersonia sp. 36 Anomodon attenuatus 37 Pohlia sp. 38 Cinclidium sp. 39 Hylocomium splendens 40 Polytrichum commune 41 negative control 42 Soil 43 Soil 44 Soil 45 Soil 46 Soil 47 Soil If a sample number is not present within the OTU table; either no sequences were obtained or no sequences passed the quality filtering step in QIIME. Supplemental 8 contains the Summary of unique species per location.