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Supplemental Information

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%).

DOI: 10.7287/peerj.preprints.2473v1/supp-1

Phylogenetic Trees

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).

DOI: 10.7287/peerj.preprints.2473v1/supp-2

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).

DOI: 10.7287/peerj.preprints.2473v1/supp-3

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.

DOI: 10.7287/peerj.preprints.2473v1/supp-4

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).

DOI: 10.7287/peerj.preprints.2473v1/supp-5

Metagenome assembly statistics

DOI: 10.7287/peerj.preprints.2473v1/supp-6

Organism Table

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.

DOI: 10.7287/peerj.preprints.2473v1/supp-7

Proteomics Data

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%).

DOI: 10.7287/peerj.preprints.2473v1/supp-8

Plant assemblage

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.

DOI: 10.7287/peerj.preprints.2473v1/supp-9

Metabolite Information

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.

DOI: 10.7287/peerj.preprints.2473v1/supp-10

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.

DOI: 10.7287/peerj.preprints.2473v1/supp-11

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.

DOI: 10.7287/peerj.preprints.2473v1/supp-12

PQQ dependent methanol dehydrogenase protein alignment

DOI: 10.7287/peerj.preprints.2473v1/supp-14

Ribosomal protein S3 protein alignment

DOI: 10.7287/peerj.preprints.2473v1/supp-15

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Cristina N Butterfield conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Zhou Li conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Peter F Andeer conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Susan Spaulding performed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables.

Brian C Thomas performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Andrea Singh performed the experiments, contributed reagents/materials/analysis tools.

Robert L Hettich conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Kenwyn B Suttle performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Alexander J Probst performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables.

Susannah G Tringe contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Trent Northen conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Chongle Pan conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Jillian F Banfield conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Angelo Coast Range Reserve Permission APP#27790

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The sequencing reads have been deposited as “Meadow soil samples from Angelo, CA genome sequencing and assembly”: SRA302421 – 2015-10-05T12:25:59.383. Genomes are currently being processed for submission to NCBI. All data are also available in ggKbase (http://ggkbase.berkeley.edu/angelo_ncbi_2016/organisms).

Data Deposition

The following information was supplied regarding data availability:

The raw data has been supplied as a supplementary file.

Funding

This work is supported by the Office of Science, Office of Biological and Environmental Research, of the U. S. Department of Energy Grant DOE-SC10010566. The sequencing was conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, and Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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