Isolation of ‘CandidatusNitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration

Abstract

Studies of the distribution of ammonia oxidising archaea (AOA) and bacteria (AOB) suggest distinct ecological niches characterised by ammonia concentration and pH, arising through differences in substrate affinity and ammonia tolerance. AOA form five distinct phylogenetic clades, one of which, the ‘Nitrososphaera sister cluster’, has no cultivated isolate. A representative of this cluster, named ‘Candidatus Nitrosocosmicus franklandus’, was isolated from a pH 7.5 arable soil and we propose a new cluster name: ‘Nitrosocosmicus’. While phylogenetic analysis of amoA genes indicates its association with the Nitrososphaera sister cluster, analysis of 16S rRNA genes provided no support for a relative branching that is consistent with a ‘sister cluster’, indicating placement within a lineage of the order Nitrososphaerales. ‘Ca. N. franklandus’ is capable of ureolytic growth and its tolerances to nitrite and ammonia are higher than in other AOA and similar to those of typical soil AOB. Similarity of other growth characteristics of ‘Ca. N. franklandus’ with those of typical soil AOB isolates reduces support for niche differentiation between soil AOA and AOB and suggests that AOA have a wider physiological diversity than previously suspected. In particular, the high ammonia tolerance of ‘Ca. N. franklandus’ suggests potential contributions to nitrification in fertilised soils.

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics

“…Urea can be used by Thaumarchaeota members as source of ammonia, as shown by biochemical assays of cultivated species (Lehtovirta-Morley et al, 2016), and as carbon source, as inferred from 14 C-labeled urea incorporation of prokaryotic communities of Artic waters (Alonso-Saez et al, 2012). The genes encoding for urease subunits, as well as auxiliary proteins, were present in two separate contigs of CcThau but lowly expressed (TPM av .…”

Geospatial variation in co‐occurrence networks of nitrifying microbial guilds

“…Moreover, Nitrospira lineage I OTUs, which are competitive Nitrospira NOBs in environments with higher NO 2 − concentrations (Maixner et al., ), were most prevalent in module 5 and co‐occurred with AOA OTUs within the Nitrososphaera “sister cluster” (Figure ). Isolates and enrichment cultures of this previously undefined AOA lineage have recently been shown to prefer neutral pH conditions and can tolerate NH 3 and NO 2 − concentration levels typically associated with AOB (Lehtovirta‐Morley et al., ; Sauder et al., ). Other notable patterns, such as the co‐occurrence of Nitrososphaera subcluster 11 and the Namibian soil lineage of Nitrospira exclusively in module 4, may also be of potential significance from an ecophysiological perspective, especially considering the significant positive correlation of the abundance of this module with soil Cu concentrations.…”

A plea for linguistic accuracy – also for Candidatus taxa

“…Nitros(o)archaeum has the neuter gender, and therefore the ending of the 'geographical' epithet must be -ense Nitrosoarchaeum limnia [69] Nitrosarchaeum limnae According to Appendix 9, the connecting vowel is dropped when the following word element starts with a vowel. The source of the proposed epithet limnia is not clear; if based on Greek linh, genitive linh& the transliteration of the genitive case is limnae Nitrosocaldus yellowstonii [71] Nitrosocaldus yellowstonensis The name Yellowstone with the ending for 'geographical' adjectives -ensis gives yellowstonensis Nitrosocosmicus franklandus [72] Nitrosocosmicus franklandianus Appendix 9 gives two ways to form specific epithets named in honour of persons.…”