Article Figures & Data
Figures
- FIG 1
Sequence and functional compositional differences between two agricultural sites. (A) Distributions of coefficients of variation of SEED subsystems related to secondary metabolism in Havana and Urbana. (B) Nonmetric multidimensional scaling (NMDS) analysis based on MinHash distances determined by Mash showed independent clustering by site and depth. The lengths of the gold arrows are proportional to the correlations between measured metadata and determined ordination values. The directions of the arrows point to increasing changes in the values of the corresponding metadata.
- FIG 2
Abundance and diversity of nitrification genes in sandy (Havana) and silt loam (Urbana) soils. (A) The top shows the concentration of NH4+ at both sites and depths. The arrow shows the point in time when N fertilizer (UAN28, 180 lb N/acre) was applied to the Havana site. Heatmaps represent calculated relative abundances of nitrification genes (genome equivalents) for Havana (left) and Urbana (right) soil samples. Values for the 20- to 30-cm layer in June represent the averages of the three soil cores. Gene abundance comparisons between soil layers were performed using two-sided t tests, and P values are shown in black, to the side of the heatmaps. Right panels show the phylogenetic reconstruction of archaeal (B) and bacterial (C) AmoA protein sequences recovered from contigs. Names in parentheses indicate the corresponding MAGs. Both trees include reference protein sequences and assembled sequences from both soil metagenomes. The pie charts represent the placing of Havana metagenomic reads for archaeal and bacterial amoA genes using RAxML EPA. Pie chart radii represent the read abundances for each node (calculated as genome equivalents), and the colors of the slices represent the depths and months the metagenomic reads originated from.
- FIG 3
Nitrogen cycle genes present in selected metagenome-assembled genomes and population abundance dynamics during the year in Havana. (A and B) MAGs obtained from Havana (A) and Urbana (B) were queried for the presence of N cycle gene markers using HMM models. Colors represent individual MAGs and the shapes depict the predicted taxonomies at the phylum level. Arrows show predicted N cycle pathways. (C) Bar plots show the relative abundances (y axis, reads per kilobase per million reads [RPKM]) for nitrifier MAGs (x axis) obtained from Havana soil metagenomes. Bright colors represent samples from the 0- to 5-cm soil layer, whereas darker color equivalents correspond to samples from the 20- to 30-cm layer (see figure key).
- FIG 4
Recovery of indigenous archaeal and bacterial ammonia-oxidizing populations. (A and B) Phylogenetic reconstruction of archaeal (A) and bacterial (B) MAGs harboring amoA genes. Concatenated alignments of conserved genes for bacterial or archaeal genomes were used to build maximum-likelihood trees in RAxML. Colored circles on the right of each tree show the presence of selected nitrification genes. Strikethrough circles indicate incomplete sequences detected in MAGs. (C) Comparison of the genomic context for the amoA genes found in “Ca. Nitrospira inopinata” and nitrifier bacterial MAGs recovered from both sites. Colors denote different gene operons.
Additional Files
Supplemental material
- Supplemental file 1 -
Supplemental methods and results; alpha-diversity values determined for metagenomic samples (Fig. S1); distributions of coefficients of variation (Fig. S2); functional clustering and taxonomy (Fig. S3); differential abundance of SEED subsystems (Fig. S4); abundance of N-cycle genes (Fig. S5); abundance and diversity for hao and nxrA (Fig. S6); abundance and diversity for archaeal and bacterial genes (Fig. S7); changes in abundance of metagenomic populations (Fig. S8); relative abundances of categories for glycoside hydrolases in both agricultural soils (Fig. S9); soil metadata (Table S1); agricultural management (Table S2); metagenomic sequences and Nonpareil estimations (Table S3); summaries for coassemblies (Table S4) and ROCker models (Table S5).
PDF, 1.1M
- Supplemental file 2 -
Summary for obtained bins (Table S6).
XLSX, 496K
- Supplemental file 3 -
Summary for glycoside hydrolase enzymes found in metagenomic bins (Table S7).
XLSX, 500K
- Supplemental file 1 -
