Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.

Environmental Microbiology
Craig W HerboldCécile Gubry-Rangin

Abstract

Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from ac...Continue Reading

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Citations

Jun 7, 2018·FEMS Microbiology Ecology·Michiel H In 't ZandtMike Sm Jetten
Feb 19, 2019·Environmental Microbiology·Mart KrupovicEugene V Koonin
Oct 28, 2019·Environmental Microbiology·Janina HerberMichael Pester
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Methods Mentioned

BETA
PCR

Software Mentioned

FastTree
mafft
BLASTp
RAxML
Blast
Phylobayes
Prodigal
hclust
Opticon Monitor
MicroScope

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