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Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

By Paul C. Blainey, Annika C. Mosier, Anastasia Potanina, Christopher A. Francis and Stephen R. Quake

Abstract

Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles

Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:3043068
Provided by: PubMed Central

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Citations

  1. (2008). A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring.
  2. (2008). A role for the ESCRT system in cell division in archaea.
  3. (2008). A unique cell division machinery in the Archaea.
  4. (1999). Abundance and diversity of Archaea in heavy-metal-contaminated soils.
  5. (2010). Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean.
  6. (2009). Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria.
  7. (2004). ARB: a software environment for sequence data.
  8. (1992). Archaea in coastal marine environments.
  9. (2006). Archaea predominate among ammonia-oxidizing prokaryotes in soils.
  10. (2001). Archaeal dominance in the mesopelagic zone of the Pacific Ocean.
  11. (2006). Archaeal nitrification in the ocean.
  12. (2009). Assembling the marine metagenome, one cell at a time. Plos One 4: e5299.
  13. (2001). Autotrophic ammonia oxidation at low pH through urea hydrolysis.
  14. (2000). Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon.
  15. (2007). CC1, a novel crenarchaeal DNA binding protein.
  16. (2000). Closing the ring: links between SMC proteins and chromosome partitioning, condensation, and supercoiling.
  17. (2009). Community-wide analysis of microbial genome sequence signatures.
  18. (2009). Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre.
  19. (2005). Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean.
  20. (2007). CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.
  21. (2010). CRISPR/Cas, the immune system of bacteria and archaea.
  22. (2007). CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.
  23. (2008). Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol.
  24. (1991). Development and application of nucleic acid probes in bacterial systematics.
  25. (2009). Digital PCR provides sensitive and absolute calibration for high throughput sequencing.
  26. (2007). Dissecting biological ‘‘dark matter’’ with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.
  27. (2010). Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota.
  28. (2006). Distribution and activity of Bacteria and Archaea in the deep water masses of the North Atlantic.
  29. (2009). Distribution and diversity of archaeal and bacterial ammonia oxidizers in salt marsh sediments.
  30. (2003). Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR.
  31. (1986). Electron microscopic study of DNA complexes with proteins from the Archaebacterium Sulfolobus acidocaldarius.
  32. (2004). Environmental genome shotgun sequencing of the Sargasso Sea.
  33. (2007). Fluorescence in situ hybridization for the identification of environmental microbes.
  34. (2005). FtsZ and the division of prokaryotic cells and organelles.
  35. (2006). Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum.
  36. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.
  37. (2007). High abundance of Crenarchaeota in a temperate acidic forest soil.
  38. (1992). Identification of individual prokaryotic cells by using enzyme-labeled, rRNA-targeted oligonucleotide probes.
  39. (2009). InterPro: the integrative protein signature database.
  40. (2008). Intracellular organic osmolytes: function and regulation.
  41. (2005). Isolation of an autotrophic ammonia-oxidizing marine archaeon.
  42. (2005). Kinetics of reduction by substrate or dithionite and heme-heme electron transfer in the multiheme hydroxylamine oxidoreductase.
  43. (2008). Latitudinal trends of Crenarchaeota and Bacteria in the meso- and bathypelagic water masses of the Eastern North Atlantic.
  44. (2000). Marine planktonic archaea take up amino acids.
  45. (2007). Mechanosensitive channels in bacteria: signs of closure?
  46. (2008). Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.
  47. (2008). Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California.
  48. (2002). Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea.
  49. (2007). Nanoliter reactors improve multiple displacement amplification of genomes from single cells.
  50. (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes.
  51. (2010). Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea.
  52. (1992). Novel major archaebacterial group from marine plankton.
  53. (1986). Observation of a singlebeam gradient force optical trap for dielectric particles.
  54. (2010). One bacterial cell, one complete genome.
  55. (2004). Optical trapping.
  56. (2006). Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.
  57. (1998). Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils.
  58. (2010). Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight.
  59. (2006). Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon.
  60. (2007). Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre.
  61. (2008). Relative abundance and diversity of ammoniaoxidizing archaea and bacteria in the San Francisco Bay estuary.
  62. (2009). Shifting the genomic gold standard for the prokaryotic species definition.
  63. (2008). Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary.
  64. (2007). Standing stocks and activity
  65. (2000). Testing character correlation using pairwise comparisons on a phylogeny.
  66. (1999). The domainspecific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set.
  67. (2005). Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean.
  68. (2007). Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables.
  69. (2009). Whole genome amplification and de novo assembly of single bacterial cells.