Measurements of soil characteristics
(A) total organic carbon (TOC), (B) soil moisture, (C) soil pH, and (D) particle size. Measurements of TOC, moisture and pH were performed at each depth before and after rain. One inch of rain fell on Day 30 and 3 inches of rain fell on Day 39. TOC decreased by depth and appeared to slightly increase at all depths after the second rainfall. Soil moisture in the upper soil zones was very low before the rainfall and increased with each rain event. Soil pH was fairly uniform between the depths and rose from about 4.6 to 4.9 after the first rain then held steady. The soil was a mixture of clay- and silt-sized particles (~ 45% each) with a minor component of sand-sized particles (8-10%).
a) Bacterial and archaeal16S rRNA phylogenetic tree. b) Bacterial and archaeal rpS3 phylogenetic tree. All rpS3 proteins or 16S rRNA genes from every sample (colored branches) and the references (black branches, chosen based on closest hits to the sample sequences and representatives of in the NCBI database) were aligned and a phylogenetic tree was constructed using RAxML and visualized in Geneious (version 7.0 by Biomatters).
Depiction of the Gemmatimonadetes contig that encodes the methanol utilization proteins
The genetic neighborhood of the methanol dehydrogenase in Gemmatimonadetes encodes for most of the proteins involved in the metabolism of methanol, including the tetrahydromethanopterin (THMPT) biosynthesis (orange), formaldehyde capture (green) pathways, and the methanol dehydrogenase (xoxF) itself and a maturation protein (red). Each of these pathways is represented by at least one known protein in the proteome (indicated by blue star). Gene name abbreviations: formaldehyde activating enzyme (fae); NAD(P)-dependent methylene-tetrahydromethanopterion dehydrogenase (mtdB); formyltransferase/hydroxylating complex (fhc); methenyl-tetrahydromethanopterin cyclohydrolase (mch).
Genome summary of methylotrophic organisms
Rows indicate draft genomes and columns indicate lists of individual genes, with the exception of PQQ biosynthesis where many subunits are represented in a single list.
Emergent self-organizing map of one soil sample
Image of emergent self-organizing map created from time series and coverage patterns of contigs from sample 10 – 20 cm 2 days after 2nd rain. 48 partial to near-complete genomes were defined (colors were assigned randomly).
a) Table listing genomes and megabins generated in the study. The summaries of genome characteristics are listed by sample and include genome completeness, size, GC content, and other genome bin quality information. b) Genomes recovered and the current NCBI and JGI IMG database of genomes for those phyla.
a) Proteomics data: Normalized spectral counts for proteins and their respective scaffolds and genome bins. b) Overview of protein identifications in each sample with the estimated protein false discovery rate. The false discovery rates for each sample are reported. Note: the false discovery rate was strictly controlled at the peptide level (1%).
2013 annual abundance survey and summary of plant species in the Angelo Coast Range Reserve meadow. Introduced species of summer flowering annual grasses and forbs were most abundant during this study.
Chemical formula and neutral mass for each compound in Figure 5 is listed along with LC-MS retention times and the ions associated with that metabolite. The primary ion used for analysis of the metabolite abundance is listed (selected based on detection limits and coefficient of variation across sample extractions) along with secondary ions and primary MS/MS fragments where available. For each ion entry the polarity (POS – positive ionization mode vs NEG – negative ionization mode), adduct (e.g., H+, H-, Na+) and m/z value are presented. Internal extraction and resuspension standards used are listed at the bottom of the table.
Metabolite Peak Areas
Peak areas of each metabolite used to generate Figure 5 and analyzed for significant changes (Table S7). Peak areas correspond to the ‘Ion (m/z) used for Sample Analyses’ column in Table S5.
Post-hoc Tukey tables
Post-hoc Tukey multiple comparison analysis of sugars (A) and nitrogenous compounds (B) demonstrating compounds with significant (α=0.05) differences in peak area across samples displayed in Figure 5.