A hydrophobic ammonia‐oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar‐contaminated sediment

Abstract

A wide diversity of ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an ammonia-oxidizing archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically, strain MY3 falls in clade 'Nitrosocosmicus' of the thaumarchaeotal group I.1b. The cells of strain MY3 are large 'walnut-like' cocci, divide by binary fission along a central cingulum, and form aggregates. Strain MY3 is mesophilic and neutrophilic. An assay of C-bicarbonate incorporation into archaeal membrane lipids indicated that strain MY3 is capable of autotrophy. In contrast to some other AOA, TCA cycle intermediates, i.e. pruvate, oxaloacetate and α-ketoglutarate, did not affect the growth rates and yields of strain MY3. The attachment of cells of strain MY3 to XAD-7 hydrophobic beads and to the adsorbent vermiculite demonstrated the potential of strain MY3 to form biofilms. The cell surface was confirmed to be hydrophobic by the extraction of strain MY3 from an aqueous medium with p-xylene. Our finding of a strong potential for surface attachment by strain MY3 may reflect an adaptation to the selective pressures in hydrophobic terrestrial environments.

Genomic adaptation to eutrophication of ammonia‐oxidizing archaea in the Pearl River estuary

“…These include the neutrophilic Nitrososphaera viennensis EN76 (Stieglmeier et al, 2014) and obligately acidophilic Candidatus Nitrosotalea devanaterra Nd1, which were isolated from soils (Lehtovirta-Morley et al, 2014); the thermophilic Nitrosocaldus species, which are enriched in geothermal habitats (Daebeler et al, 2018); and the recently characterized acid-tolerant Ca. Nitrosocosmicus oleophilus MY3 (Jung et al, 2016). Most recently, a new AOA isolate, Candidatus Nitrosomarinus catalina SPOT01, was isolated from the waters off the Californian coast, and the collected data suggest that this new culture might be the dominant ammonia oxidizer in the temperate Pacific (Ahlgren et al, 2017).…”

Physiological and genomic analysis of “CandidatusNitrosocosmicus agrestis”, an ammonia tolerant ammonia-oxidizing archaeon from vegetable soil

“…(iv) Nitrososphaerales: Nitrososphaera, Ca . Nitrosocosmicus and many uncultivated AOA that inhabit in soils (Tourna et al ., 2011; Zhalnina et al ., 2014; Lehtovirta-Morley et al ., 2016), sediments (Jung et al ., 2016), terrestrial hot springs (Hatzenpichler et al ., 2008) and wastewater treatment plants (Sauder et al ., 2017). Up to now, four strains belonging to Nitrososphaera and five strains belonging to Ca .…”

Plant growth‐promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae

“…This shows that N. oleophilus MY3 elicited induced resistance against the hemibiotrophic bacterium, similar to PGPR. To determine the effects of N. oleophilus MY3 on plants grown in soil, 3 week-old soil-grown Arabidopsis seedlings were treated with drench application of 2 week-old N. oleophilus MY3 liquid culture (10 8 cells per ml) (Jung et al, 2016). Leaves of Arabidopsis plants were infiltrated with the necrotrophic and biotrophic pathogens P. carotovorum subsp.…”

“…Several microbial determinants have been shown to elicit plant immunity (Walters et al, 2008), including microbial (fungal and bacterial) cell-wall components and secreted metabolites. Among these secreted metabolites, NO − 2 is a major product released from the AOA (phylum Thaumarchaeota) (Jung et al, 2016). Therefore, we investigated whether the intermediate and final compounds obtained from the association of AOA and AOB with plants are sufficient to elicit ISR against the two pathogens.…”

“…Nitrosocosmicus oleophilus MY3 was first isolated from soil and characterized as AOA (Jung et al, 2016). Therefore, we hypothesized that N. oleophilus MY3 interacts with plant roots like other ammonium-oxidizing bacteria (AOB) (Briones et al, 2003).…”