Arid
DOI10.3389/fmicb.2014.00698
Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria
Lynch, Ryan C.1; Darcy, John L.1; Kane, Nolan C.1; Nemergut, Diana R.2,3,4; Schmidt, Steve K.1
通讯作者Lynch, Ryan C.
来源期刊FRONTIERS IN MICROBIOLOGY
ISSN1664-302X
出版年2014
卷号5
英文摘要

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 (H-2, CO and several organic Cl 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.


英文关键词aerobiology Atacama Desert methylotrophy Pseudonocardia trace gas oxidation
类型Article
语种英语
国家USA
收录类别SCI-E
WOS记录号WOS:000347259400001
WOS关键词MULTIPLE SEQUENCE ALIGNMENT ; FREEZE-THAW CYCLES ; ATACAMA DESERT ; CARBON-MONOXIDE ; BACTERIAL COMMUNITIES ; MICROBIAL COMMUNITIES ; SOIL-MICROORGANISMS ; OXIDIZING BACTERIA ; ARID SOILS ; SP NOV.
WOS类目Microbiology
WOS研究方向Microbiology
来源机构Arizona State University
资源类型期刊论文
条目标识符http://119.78.100.177/qdio/handle/2XILL650/182151
作者单位1.Univ Colorado, Dept Ecol & Evolutionary Biol, Boulder, CO 80309 USA;
2.Univ Colorado, Environm Studies Program, Boulder, CO 80309 USA;
3.Univ Colorado, Inst Arctic & Alpine Res, Boulder, CO 80309 USA;
4.Duke Univ, Dept Biol, Durham, NC USA
推荐引用方式
GB/T 7714
Lynch, Ryan C.,Darcy, John L.,Kane, Nolan C.,et al. Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria[J]. Arizona State University,2014,5.
APA Lynch, Ryan C.,Darcy, John L.,Kane, Nolan C.,Nemergut, Diana R.,&Schmidt, Steve K..(2014).Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria.FRONTIERS IN MICROBIOLOGY,5.
MLA Lynch, Ryan C.,et al."Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria".FRONTIERS IN MICROBIOLOGY 5(2014).
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