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Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria.

Lynch RC, Darcy JL, Kane NC, Nemergut DR, Schmidt SK - Front Microbiol (2014)

Bottom Line: The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9-98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection.We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs.Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA.

ABSTRACT
Previous surveys of very dry Atacama Desert mineral soils have consistently revealed sparse communities of non-photosynthetic microbes. The functional nature of these microorganisms remains debatable given the harshness of the environment and low levels of biomass and diversity. The aim of this study was to gain an understanding of the phylogenetic community structure and metabolic potential of a low-diversity mineral soil metagenome that was collected from a high-elevation Atacama Desert volcano debris field. We pooled DNA extractions from over 15 g of volcanic material, and using whole genome shotgun sequencing, observed only 75-78 total 16S rRNA gene OTUs3%. The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9-98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection. Due to this low diversity and uneven community composition, we assembled and analyzed the metabolic pathways of the most abundant genome, a Pseudonocardia sp. (56-72% of total 16S genes). Our assembly and binning efforts yielded almost 4.9 Mb of Pseudonocardia sp. contigs, which accounts for an estimated 99.3% of its non-repetitive genomic content. This genome contains a limited array of carbohydrate catabolic pathways, but encodes for CO2 fixation via the Calvin cycle. The genome also encodes complete pathways for the catabolism of various trace gases (H2, CO and several organic C1 compounds) and the assimilation of ammonia and nitrate. We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs. Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions.

No MeSH data available.


Related in: MedlinePlus

Distribution of Ka:Ks ratios for 1260 pairwise orthologous protein coding sequences between the best volcano Pseudonocardia sp. assembly and its closest fully-sequenced relative, Pseudonocardia asaccharolytica, showing the majority of genes (95.3%) to be under purifying or relaxed selection regimes, where synonymous substitutions that do not alter the amino acid coding potential dominate the gene. However, some outliers (4.7%) display higher levels of non-synonymous mutations (≥1 Ka:Ks) likely driven by divergent selection from the harsh high-elevation desert conditions. This analysis was limited to 23% of total volcano Pseudonocardia sp. genes due to the high degree of overall genomic divergence between these two species.
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Figure 4: Distribution of Ka:Ks ratios for 1260 pairwise orthologous protein coding sequences between the best volcano Pseudonocardia sp. assembly and its closest fully-sequenced relative, Pseudonocardia asaccharolytica, showing the majority of genes (95.3%) to be under purifying or relaxed selection regimes, where synonymous substitutions that do not alter the amino acid coding potential dominate the gene. However, some outliers (4.7%) display higher levels of non-synonymous mutations (≥1 Ka:Ks) likely driven by divergent selection from the harsh high-elevation desert conditions. This analysis was limited to 23% of total volcano Pseudonocardia sp. genes due to the high degree of overall genomic divergence between these two species.

Mentions: Of the 5024 annotated CDS from the draft P. asaccharolytica genome we were able to initially align 1722 orthologous coding sequences from our best metagenome Pseudonocardia sp. assembly with at least 70% nucleotide identity. Of these, manual inspection filtered out 462 gene pairs that were poorly aligned or were not true homologs across the entire sequence. There were 59 remaining ortholog pairs (4.7%) with estimated Ka:Ks ratios ≥ 1, which reflects elevated rates of non-synonymous mutations brought about through strong divergent selection acting upon the amino acid sequences (Figure 4, Supplementary Table 2).


Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria.

Lynch RC, Darcy JL, Kane NC, Nemergut DR, Schmidt SK - Front Microbiol (2014)

Distribution of Ka:Ks ratios for 1260 pairwise orthologous protein coding sequences between the best volcano Pseudonocardia sp. assembly and its closest fully-sequenced relative, Pseudonocardia asaccharolytica, showing the majority of genes (95.3%) to be under purifying or relaxed selection regimes, where synonymous substitutions that do not alter the amino acid coding potential dominate the gene. However, some outliers (4.7%) display higher levels of non-synonymous mutations (≥1 Ka:Ks) likely driven by divergent selection from the harsh high-elevation desert conditions. This analysis was limited to 23% of total volcano Pseudonocardia sp. genes due to the high degree of overall genomic divergence between these two species.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4269115&req=5

Figure 4: Distribution of Ka:Ks ratios for 1260 pairwise orthologous protein coding sequences between the best volcano Pseudonocardia sp. assembly and its closest fully-sequenced relative, Pseudonocardia asaccharolytica, showing the majority of genes (95.3%) to be under purifying or relaxed selection regimes, where synonymous substitutions that do not alter the amino acid coding potential dominate the gene. However, some outliers (4.7%) display higher levels of non-synonymous mutations (≥1 Ka:Ks) likely driven by divergent selection from the harsh high-elevation desert conditions. This analysis was limited to 23% of total volcano Pseudonocardia sp. genes due to the high degree of overall genomic divergence between these two species.
Mentions: Of the 5024 annotated CDS from the draft P. asaccharolytica genome we were able to initially align 1722 orthologous coding sequences from our best metagenome Pseudonocardia sp. assembly with at least 70% nucleotide identity. Of these, manual inspection filtered out 462 gene pairs that were poorly aligned or were not true homologs across the entire sequence. There were 59 remaining ortholog pairs (4.7%) with estimated Ka:Ks ratios ≥ 1, which reflects elevated rates of non-synonymous mutations brought about through strong divergent selection acting upon the amino acid sequences (Figure 4, Supplementary Table 2).

Bottom Line: The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9-98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection.We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs.Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA.

ABSTRACT
Previous surveys of very dry Atacama Desert mineral soils have consistently revealed sparse communities of non-photosynthetic microbes. The functional nature of these microorganisms remains debatable given the harshness of the environment and low levels of biomass and diversity. The aim of this study was to gain an understanding of the phylogenetic community structure and metabolic potential of a low-diversity mineral soil metagenome that was collected from a high-elevation Atacama Desert volcano debris field. We pooled DNA extractions from over 15 g of volcanic material, and using whole genome shotgun sequencing, observed only 75-78 total 16S rRNA gene OTUs3%. The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9-98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection. Due to this low diversity and uneven community composition, we assembled and analyzed the metabolic pathways of the most abundant genome, a Pseudonocardia sp. (56-72% of total 16S genes). Our assembly and binning efforts yielded almost 4.9 Mb of Pseudonocardia sp. contigs, which accounts for an estimated 99.3% of its non-repetitive genomic content. This genome contains a limited array of carbohydrate catabolic pathways, but encodes for CO2 fixation via the Calvin cycle. The genome also encodes complete pathways for the catabolism of various trace gases (H2, CO and several organic C1 compounds) and the assimilation of ammonia and nitrate. We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs. Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions.

No MeSH data available.


Related in: MedlinePlus