Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation.

Author(s)
Carolina Reyes, Logan Hodgskiss, Melina Kerou, Thomas Pribasnig, Sophie Abby, Barbara Bayer, Stephan Krämer, Christa Schleper
Abstract

Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.

Organisation(s)
Department of Environmental Geosciences, Faculty of Earth Sciences, Geography and Astronomy, Functional and Evolutionary Ecology
External organisation(s)
Université Pierre Mendes-France Grenoble II
Journal
The ISME Journal: multidisciplinary journal of microbial ecology
Volume
14
Pages
2659-2674
No. of pages
16
ISSN
1751-7362
DOI
https://doi.org/10.1038/s41396-020-0715-2
Publication date
07-2020
Peer reviewed
Yes
Austrian Fields of Science 2012
106022 Microbiology, 105906 Environmental geosciences
Keywords
Portal url
https://ucris.univie.ac.at/portal/en/publications/genome-wide-transcriptomic-analysis-of-the-soil-ammonia-oxidizing-archaeon-nitrososphaera-viennensis-upon-exposure-to-copper-limitation(03572219-339c-4f72-a685-4e3e24f28b93).html