Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” Representing a Clade Globally Distributed in Thermal Habitats

Elena V Lebedeva,Michael Wagner,Sandra Hauzmayer,Eric Pelletier,Nathalie Schuster,Markus Schmid,Denis Le Paslier,Holger Daims,Alexander Galushko,Roland Hatzenpichler,Marton Palatinszky,Aleksandr Bulaev,Nadezhda V Grigor’Eva,Leo Eberl

doi:10.1371/journal.pone.0080835

Abstract

The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called “marine” group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as “Candidatus Nitrosotenuis uzonensis”, is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, “Candidatus N. uzonensis” also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in “Ca. N. uzonensis”, which potentially include genetic determinants of ecological niche differentiation.

Highlights

The discovery of ammonia-oxidizing archaea revealed a new microbial group involved in nitrogen cycling [1,2,3]
We demonstrate that this thaumarchaeote, which we designate as “Candidatus Nitrosotenuis uzonensis”, represents a lineage of ammonia-oxidizing archaea (AOA) that is globally distributed in terrestrial high temperature environments, but was not brought into culture previously
At the time of manuscript submission, only one morphotype was visible in the enrichment culture by phase microscopy, but PCR screening with three different primer sets (Table S10 in File S1) targeting bacterial 16S rRNA genes revealed a cryptic bacterial contamination as these primer pairs still yielded an amplification product of the expected size

Summary

Introduction

The discovery of ammonia-oxidizing archaea revealed a new microbial group involved in nitrogen cycling [1,2,3]. Enrichment cultures of thermophilic (at 74°C) [18] and moderately thermophilic (at 46°C) [22] AOA have become available, and the widespread presence of archaeal ammonia monooxygenase subunit A (amoA)-like genes in high temperature habitats up to 97°C has been demonstrated. Such amoA-like gene sequences have been found in subsurface thermal springs [23,24], many terrestrial hot springs [19,20,25,26,27] and deep-sea hydrothermal vents [28,29]. The presence of crenarchaeol (more accurately named thaumarchaeol [5]), which is a signature lipid component of both mesophilic [31,32] and thermophilic AOA [18,33], in terrestrial hot springs lends additional support to the importance of AOA in thermal habitats [34,35,36,37]

Methods

Results

Conclusion