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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

Venn diagram of the shared and unique genes (COGs) among named Pseudonocardia spp. with complete genomes and the volcano Pseudonocardia sp. genome assembly. Although most of the 50 COGs unique to the volcano Pseudonocardia sp. (Supplementary Table 1) are classified as “function unknown” or “general function prediction only,” the six additional defense mechanism related COGs and the nine fewer carbohydrate transport and metabolism COGs in the volcano Pseudonocardia sp. stand out as potentially relevant functional differences with other Pseudonocardia spp.
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Figure 3: Venn diagram of the shared and unique genes (COGs) among named Pseudonocardia spp. with complete genomes and the volcano Pseudonocardia sp. genome assembly. Although most of the 50 COGs unique to the volcano Pseudonocardia sp. (Supplementary Table 1) are classified as “function unknown” or “general function prediction only,” the six additional defense mechanism related COGs and the nine fewer carbohydrate transport and metabolism COGs in the volcano Pseudonocardia sp. stand out as potentially relevant functional differences with other Pseudonocardia spp.

Mentions: COG counts from our highest quality Pseudonocardia sp. assembly (68–115 × coverage bin from site 1) and the three other publicly available genomes for named Pseudonocardia spp. (Supplementary Table 1, Figure 3) highlight some of the specific differences in genome content. We found certain COGs like those needed for CO oxidation are conserved at high copy numbers across all the Pseudonocardia spp., and that COGs such as those required for assimilatory nitrate reduction and carbon fixation (RuBisCO) show relatively higher counts in both our metagenome assembly and P. asaccharolytica. Other highly abundant gene clusters within our metagenome assembly bear resemblance to the more phylogenetically distant Pseudonocardia spp. These clusters include the antibiotic producing non-ribosomal peptide synthesis pathway (NRPS), various ABC peptide importers, cytochrome P450 monooxygenase, and several recombinases.


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)

Venn diagram of the shared and unique genes (COGs) among named Pseudonocardia spp. with complete genomes and the volcano Pseudonocardia sp. genome assembly. Although most of the 50 COGs unique to the volcano Pseudonocardia sp. (Supplementary Table 1) are classified as “function unknown” or “general function prediction only,” the six additional defense mechanism related COGs and the nine fewer carbohydrate transport and metabolism COGs in the volcano Pseudonocardia sp. stand out as potentially relevant functional differences with other Pseudonocardia spp.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Venn diagram of the shared and unique genes (COGs) among named Pseudonocardia spp. with complete genomes and the volcano Pseudonocardia sp. genome assembly. Although most of the 50 COGs unique to the volcano Pseudonocardia sp. (Supplementary Table 1) are classified as “function unknown” or “general function prediction only,” the six additional defense mechanism related COGs and the nine fewer carbohydrate transport and metabolism COGs in the volcano Pseudonocardia sp. stand out as potentially relevant functional differences with other Pseudonocardia spp.
Mentions: COG counts from our highest quality Pseudonocardia sp. assembly (68–115 × coverage bin from site 1) and the three other publicly available genomes for named Pseudonocardia spp. (Supplementary Table 1, Figure 3) highlight some of the specific differences in genome content. We found certain COGs like those needed for CO oxidation are conserved at high copy numbers across all the Pseudonocardia spp., and that COGs such as those required for assimilatory nitrate reduction and carbon fixation (RuBisCO) show relatively higher counts in both our metagenome assembly and P. asaccharolytica. Other highly abundant gene clusters within our metagenome assembly bear resemblance to the more phylogenetically distant Pseudonocardia spp. These clusters include the antibiotic producing non-ribosomal peptide synthesis pathway (NRPS), various ABC peptide importers, cytochrome P450 monooxygenase, and several recombinases.

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