The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations

Autor(en)

Anja Spang, Anja Poehlein, Pierre Offre, Sabine Zumbragel, Susanne Haider, Nicolas Rychlik, Boris Nowka, Christel Schmeisser, Elena Lebedeva, Thomas Rattei, Christoph Böhm, Markus Christian Schmid, Alexander Galushko, Roland Hatzenpichler, Thomas Weinmaier, Rolf Daniel, Christa Schleper, Eva Spieck, Wolfgang Streit, Michael Wagner

Abstrakt

The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83?Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N.?gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N.?gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.

Organisation(en)

Externe Organisation(en)

Georg-August-Universität Göttingen, Universität Hamburg, Russian Academy of Sciences

Journal

Environmental Microbiology

Band

14

Seiten

3122-3145

Anzahl der Seiten

24

ISSN

1462-2912

DOI

https://doi.org/10.1111/j.1462-2920.2012.02893.x

Publikationsdatum

2012

Peer-reviewed

Ja

ÖFOS 2012

106013 Genetik

Sustainable Development Goals

SDG 15 – Leben an Land

Link zum Portal

https://ucrisportal.univie.ac.at/de/publications/d5732ff6-999c-48f7-a1d9-a4ec079b2dc9