A potential central role of Thaumarchaeota in N-Cycling in a semi-arid environment, Fort Stanton Cave, Snowy River passage, New Mexico, USA

Low biomass and productivity of arid-land caves with limited availability of nitrogen (N) raises the question of how microbes acquire and cycle this essential element. Caves are ideal environments for investigating microbial functional capabilities, as they lack phototrophic activity and have near c...

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Bibliographic Details
Published in:FEMS microbiology ecology 2018-11, Vol.94 (11), p.1
Main Authors: Kimble, Jason C, Winter, Ara S, Spilde, Michael N, Sinsabaugh, Robert L, Northup, Diana E
Format: Article
Language:English
Subjects:
Ammonia
Ammonia - metabolism
Archaea - genetics
Archaea - isolation & purification
Archaea - metabolism
Archaeabacteria
Arid environments
Aridity
Bacteria - genetics
Bacteria - isolation & purification
Bacteria - metabolism
Caves
Caves - microbiology
Cycles
Denitrification
Deoxyribonucleic acid
DNA
DNA sequencing
Ecology
Environmental aspects
Ferromanganese
Gene sequencing
Genes
Metagenomics
Microbiology
Microorganisms
Mineral deposits
New Mexico
Nitrate reduction
Nitrates - metabolism
Nitrification
Nitrogen
Nitrogen - metabolism
Nitrogen cycle
Nitrogen Cycle - genetics
Nucleotide sequence
Nutrient cycles
Oxidation
Oxidation-Reduction
Physiological aspects
Reduction
Relative humidity
Rivers
RNA, Ribosomal, 16S - genetics
rRNA 16S
Semi arid environments
Semiarid environments
Taxonomy
Thaumarchaeota
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Summary:Low biomass and productivity of arid-land caves with limited availability of nitrogen (N) raises the question of how microbes acquire and cycle this essential element. Caves are ideal environments for investigating microbial functional capabilities, as they lack phototrophic activity and have near constant temperatures and high relative humidity. From the walls of Fort Stanton Cave (FSC), multicolored secondary mineral deposits of soil-like material low in fixed N, known as ferromanganese deposits (FMD), were collected. We hypothesized that within FMD samples we would find the presence of microbial N cycling genes and taxonomy related to N cycling microorganisms. Community DNA were sequenced using Illumina shotgun metagenomics and 16S rRNA gene sequencing. Results suggest a diverse N cycle encompassing several energetic pathways including nitrification, dissimilatory nitrate reduction and denitrification. N cycling genes associated with assimilatory nitrate reduction were also identified. Functional gene sequences and taxonomic findings suggest several bacterial and archaeal phyla potentially play a role in nitrification pathways in FSC and FMD. Thaumarchaeota, a deep-branching archaeal division, likely play an essential and possibly dominant role in the oxidation of ammonia. Our results provide genomic evidence for understanding how microbes are potentially able to acquire and cycle N in a low-nutrient subterranean environment.
ISSN:1574-6941
0168-6496
1574-6941
DOI:10.1093/femsec/fiy173