Table 1.
Characteristics of soils used in metagenomic analysis.
Figure 1.
Rarefaction curve of annotated species richness as a function of the number of sequences sampled.
Table 2.
Characteristics of metagenomes.
Figure 2.
Percent abundance of sequences in the metagenomes with similarities to genes from various respiratory pathways.
Anaerobic respiratory reductases include the SEED subsystem of the same name plus other anaerobic respiration-related genes (denitrification, sulfate reduction, reductive dechlorination, tetrathionate respiration, TMAO reduction and decaheme cytochromes). Methanogenesis genes include all related functions in SEED, including methanopterin biosynthesis. Acetogenesis genes are CO dehydrogenases and related functions. χ2 results were highly significant (P<0.001) for anaerobic reductases (χ2 = 33.14), cytochrome C oxidases (χ 2 = 41.99) and methanogenesis (χ 2 = 61.28), significant for cytochrome d oxidases (χ 2 = 8.16, P = 0.043) and non-significant for acetogenesis (χ2 = 0.411, P = 0.938).
Table 3.
Relative abundance (%) and total number of sequences matching genes from various anaerobic respiratory pathways.
Figure 3.
Percent abundance of sequences in the metagenomes with similarities to oxidative stress genes.
Aerotolerance refers to the SEED subsystem known as “Aerotolerance operon in Bacteroides and potentially orthologous operons in other organisms.” χ2 results were highly significant for peroxidase (χ2 = 21.37, P<0.001), significant for aerotolerance (χ2 = 10.03, P<0.018) and SOD (χ2 = 11.08, P = 0.0113), and marginally significant for catalase (χ2 = 6.41, P = 0.093).
Figure 4.
Percent abundance of sequences with similarities to genes within SEED fermentation subsystems (χ2 = 30.88, P<0.001).
Figure 5.
Percent abundance of genomic sequences from selected taxa with known respiratory pathways.
FeRB, Fe-reducing bacteria consist of Geobacteraceae (incuding Pelobacter and Desulfomonas), Rhodoferax (Albidiferax) ferrireducens, Shewanella, Carboxydothermus and Anaeromyxobacter. SRB, sulfate reducing bacteria include the Desulfobacterales, Desulfovibrionales and Desulfurococcales. Dehalo, Dehalorespirers include Anaeromyxobacter, Carboxydothermus, Dechloromonas, and Dehalococcoides. Strict fermenters (Strict Ferm) include Clostridiales and Bacteroides. Syntrophic bacteria include Syntrophaceae, Syntrophobacteraceae and Syntrophomonadaceae. All the taxa shown varied significantly with depth (P<0.001) by the Pearson chi-square test.
Figure 6.
Percent abundance of sequences from methanogenic Archaea genomes with depth (χ2 = 61.29, P<0.001).
Table 4.
Comparison of Barrow soil metagenomes presented in this study (all layers combined) with published Waseca farm soil metagenome [6].
Table 5.
Taxonomic representation of key genes in fermentative pathways found in all four metagenomes.
Figure 7.
Maximum likelihood phylogenetic tree of decaheme cytochrome protein sequences with high similarity to metagenomic sequences.
(Mean log E value = −13.3, mean % identity = 70.5%, mean alignment length = 47.7). The code in square brackets represents the number of similar sequences (superscript) from the four layers, with A-D corresponding to shallow-deep. Different sequences from the same genome are differentiated by the last 4 digits of the MD5 number in the M5nr database (http://tools.metagenomics.anl.gov/m5nr/m5nr.cgi). Sequences were aligned based on the ten CxxCH heme-binding domains. MtrA Opitutus has only 7–8 canonical heme-binding domains (eighth domain = TxxCH), and so this sequence was used as an outgroup.
Figure 8.
Maximum likelihood tree of PilA genes with highest similarity to metagenomic sequences.
Sequences from the same genome are differentiated by the last 5 digits of the MD5 number in the M5nr database (http://tools.metagenomics.anl.gov/m5nr/m5nr.cgi).