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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

Community profile (A) All OTU3% taxonomic assignments from each site that represent at least 1% of the total metagenome 16S gene reads. These 12 OTUs constitute 94.3 and 92.6% of the total 16S gene reads from sites 1 (gray bars) and 3 (black bars) respectively and are all members of Actinomycetales other than the single Acidimicrobiales OTU3%. (B) Maximum likelihood phylogeny of the most abundant Pseudonocardia OTU3%, split into sub OTUs1%. The scale bar represents 1% divergence between nucleic acid sequences.
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Figure 1: Community profile (A) All OTU3% taxonomic assignments from each site that represent at least 1% of the total metagenome 16S gene reads. These 12 OTUs constitute 94.3 and 92.6% of the total 16S gene reads from sites 1 (gray bars) and 3 (black bars) respectively and are all members of Actinomycetales other than the single Acidimicrobiales OTU3%. (B) Maximum likelihood phylogeny of the most abundant Pseudonocardia OTU3%, split into sub OTUs1%. The scale bar represents 1% divergence between nucleic acid sequences.

Mentions: After trimming we were left with 3.85 million reads that total 1.3 Gb of DNA sequence data for downstream analysis. Each of the two site libraries contained nearly identical distributions of bacterial (99.2%), eukaryotic (0.5%) and archaeal (0.3%) reads, based on all MG RAST annotation databases. We found a low diversity community populated mostly by Actinobacteria (Table 1), which make up 98.6 and 97.9% of the 16S rRNA genes from the site 1 and 3 libraries, respectively. This highly uneven community structure is significantly under dispersed (P < 0.001 and 0.01 for the phylogenetic randomization tests on the two samples), indicating a likely non-random assemblage of bacterial lineages. All lineages shown in Figure 1 belong within the Actinomycetales, other than an OTU3% belonging to the Acidimicrobiales order (Supplementary Figure 1) that makes up 15.6% of the site 3 library, but only 1.9% of the site 1 library. The Pseudonocardia are by far the most abundant lineages (72.2% of site 1 and 56.3% of site 3 total 16S reads) and the Saccharopolyspora (Pseudonocardiaceae) also make up 8.8% and 12.6% of total 16S rRNA gene reads from sites 1 and 3, respectively.


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)

Community profile (A) All OTU3% taxonomic assignments from each site that represent at least 1% of the total metagenome 16S gene reads. These 12 OTUs constitute 94.3 and 92.6% of the total 16S gene reads from sites 1 (gray bars) and 3 (black bars) respectively and are all members of Actinomycetales other than the single Acidimicrobiales OTU3%. (B) Maximum likelihood phylogeny of the most abundant Pseudonocardia OTU3%, split into sub OTUs1%. The scale bar represents 1% divergence between nucleic acid sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Community profile (A) All OTU3% taxonomic assignments from each site that represent at least 1% of the total metagenome 16S gene reads. These 12 OTUs constitute 94.3 and 92.6% of the total 16S gene reads from sites 1 (gray bars) and 3 (black bars) respectively and are all members of Actinomycetales other than the single Acidimicrobiales OTU3%. (B) Maximum likelihood phylogeny of the most abundant Pseudonocardia OTU3%, split into sub OTUs1%. The scale bar represents 1% divergence between nucleic acid sequences.
Mentions: After trimming we were left with 3.85 million reads that total 1.3 Gb of DNA sequence data for downstream analysis. Each of the two site libraries contained nearly identical distributions of bacterial (99.2%), eukaryotic (0.5%) and archaeal (0.3%) reads, based on all MG RAST annotation databases. We found a low diversity community populated mostly by Actinobacteria (Table 1), which make up 98.6 and 97.9% of the 16S rRNA genes from the site 1 and 3 libraries, respectively. This highly uneven community structure is significantly under dispersed (P < 0.001 and 0.01 for the phylogenetic randomization tests on the two samples), indicating a likely non-random assemblage of bacterial lineages. All lineages shown in Figure 1 belong within the Actinomycetales, other than an OTU3% belonging to the Acidimicrobiales order (Supplementary Figure 1) that makes up 15.6% of the site 3 library, but only 1.9% of the site 1 library. The Pseudonocardia are by far the most abundant lineages (72.2% of site 1 and 56.3% of site 3 total 16S reads) and the Saccharopolyspora (Pseudonocardiaceae) also make up 8.8% and 12.6% of total 16S rRNA gene reads from sites 1 and 3, respectively.

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