Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

Abstract

Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one§ enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as “Candidatus Nitrosocaldus islandicus,” is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. “Ca. N. islandicus” encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation§. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as “Ca. N. islandicus” is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that “Ca. N. islandicus” has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes§ – one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.

Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay

“…) further supports a central role for nirK in ammonia oxidation. Although the absence of nirK in a handful of the thermophilic AOA genomes is perplexing, two likely explanations exist: (i) as suggested previously, a hitherto unidentified protein performs the role of nirK in these organisms (Daebeler et al ., ); or (ii) ammonia oxidation is tightly coupled to the metabolism of a co‐occurring organism, as postulated in the case of Ca . Nitrosocaldus cavascerensis and Ca .…”

“…Putative nirK genes were found in all but three of the screened AOA isolate/enrichment genomes, corroborating the postulated pivotal role of this gene in the core metabolism of mesophilic Thaumarchaeota. Exceptions were the uncultivated sponge symbiont Cenarchaeum symbiosum (Hallam et al, 2006b;Bartossek et al, 2010) and genomically characterized members of the thermophilic lineage Nitrosocaldus (Abby et al, 2018;Daebeler et al, 2018). Interestingly, some members of the mesophilic thaumarchaeal lineage -Nitrosopumilus maritimus SCM1 and Ca.…”

“…Nitrosocaldus cavascerensis and Ca. Nitrosocaldus islandicus (Abby et al, 2018;Daebeler et al, 2018).…”

Integrated mobile genetic elements in Thaumarchaeota

“…However, in the GenBank database it is affiliated to the phylum Thaumarchaeota and was, thus, retained in our analysis. The analysed organisms were isolated from a wide range of environments, including a subsurface gold mine (Nunoura et al, 2011), thermal springs (Spang et al, 2012;Lebedeva et al, 2013;Abby et al, 2018;Daebeler et al, 2018), wastewater treatment plant (Li et al, 2016), marine waters (Santoro et al, 2015;Bayer et al, 2016;Ahlgren et al, 2017) and sediments (Park et al, 2014) and various soil samples (Kim et al, 2011;Lehtovirta-Morley et al, 2011;Tourna et al, 2011;Zhalnina et al, 2014;Lehtovirta-Morley et al, 2016;Herbold et al, 2017). Although most of these organisms are mesophiles, some are psychrophilic (Hallam et al, 2006), thermophilic (Nunoura et al, 2011;Spang et al, 2012;Lebedeva et al, 2013;Abby et al, 2018;Daebeler et al, 2018) or acidophilic (Lehtovirta-Morley et al, 2011).…”

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

“…Following the initial description of Nitrosopumilus maritimus SCM1 (Könneke et al, 2005), analysis of the supporting physiology of AOA has been aided by the cultivation of additional ecotypes. 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).…”