Anne Daebeler

Biology Centre CAS · SoWa Research Infrastructure

Nitrite‐oxidizing bacteria (NOB) catalyze the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical...

Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the ca...

Including information about soil microbial communities into global decomposition models is critical for predicting and understanding how ecosystem functions may shift in response to global change. Here we combined a standardised litter bag method for estimating decomposition rates, the Tea Bag Index (TBI), with high-throughput sequencing of the mic...

Including information about soil microbial communities into global decomposition models is critical for predicting and understanding how ecosystem functions may shift in response to global change. Here we combined a standardised litter bag method for estimating decomposition rates, Tea Bag Index (TBI), with high-throughput sequencing of the microbi...

Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the ca...

Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high p...

Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high p...

Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus "Candidatus Nitrotoga" are widespread in natural and engineered eco...

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...

Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaea 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 Thaumarchaea in terrestrial high-temperature habitats, only one enrichment cultu...

paragraph Nitrification, the oxidation of ammonia (NH3) via nitrite (NO2⁻) to nitrate (NO3⁻), is a key process of the biogeochemical nitrogen cycle. For decades, ammonia and nitrite oxidation were thought to be separately catalyzed by ammonia-oxidizing bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The recent discovery o...

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers (“comammox”), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously as...

The balance of microbial nitrogen (N) transformation processes in sub-arctic terrestrial ecosystems is most likely affected by global change, with potential feedbacks to greenhouse gas emissions and eutrophication. Soil temperature and N availability – their global increases being two of the most pressing global change features - will be prime driv...

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers (‘comammox’), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira , previously k...

Network analysis of 16s rRNA gene sequences derived from the “heavy” fraction of a 13C-CH4 labeled community in a grassland soil (Daebeler et al., 2014). The correlating OTUs with >1% relative abundance are given in the figure, and the corresponding taxonomic affiliation are listed in the Supplementary Information (Table S3).

Co-occurring OTUs with >1% relative abundance derived from the “heavy” fraction of a 13C-CH4 labeled community in a rice paddy soil. Classification of OTUs is as given in Zheng et al. (2014). Bold and gray scripts denote MOB and methylotroph, respectively

Network analysis of 16s rRNA gene sequences derived from the “heavy” fraction of a 13C-CH4 labeled community in a rice paddy soil (Zheng et al., 2014). The correlating OTUs with >1% relative abundance are given in the figure, and the corresponding taxonomic affiliation are listed in the Supplementary Information (Table S4).

Co-occurring OTUs with >1% relative abundance derived from the “heavy” fraction of a 13C-CH4 labeled community in sediments from geothermal springs. Classification of OTUs is as given in Sharp et al. (2014). Bold and gray scripts denote MOB and methylotroph, respectively.

Co-occurring OTUs with >1% relative abundance derived from the “heavy” fraction of a 13C-CH4 labeled community in sediments from an arctic lake. Classification of OTUs is as given in He et al. (2012a,b,c). Bold and gray scripts denote MOB and methylotroph, respectively.

Co-occurring OTUs with >1% relative abundance derived from the “heavy” fraction of a 13C-CH4 labeled community in a grassland soil. Classification of OTUs is as given in Daebeler et al. (2014). Bold and gray scripts denote MOB and methylotroph, respectively.

Venn diagrams showing co-occurring non-MOB community (order level) in all environments (A), as well as the accompanying non-MOB community associated to the alphaproteobacterial (B), and gammaproteobacterial (C) MOB where relevant. MOB and unclassified microorganisms are not included in the Venn diagrams. Blue, green, orange, gray, and turquoise den...

Network analysis of 16s rRNA gene sequences derived from the “heavy” fraction of a 13C-CH4 labeled community in sediments from an arctic lake (He et al., 2012a,b,c). The correlating OTUs with >1% relative abundance are given in the figure, and the corresponding taxonomic affiliation are listed in the Supplementary Information (Table S2).

Network analysis of 16s rRNA gene sequences derived from the “heavy” fraction of a 13C-CH4 labeled community in sediments from oilsands tailings ponds (Saidi-Mehrabad et al., 2013). The correlating OTUs with >1% relative abundance are given in the figure, and the corresponding taxonomic affiliation are listed in the Supplementary Information (Table...

Co-occurring OTUs with >1% relative abundance derived from the “heavy” fraction of a 13C-CH4 labeled community in oilsands tailings ponds. Classification of OTUs is as given in Saidi-Mehrabad et al. (2013). Bold and gray scripts denote MOB and methanol-oxidizer, respectively.

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic c...

The first step of nitrification is carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA). It is largely unknown, by which mechanisms these microbes are capable of coexistence and how their respective contribution to ammonia oxidation may differ with varying soil characteristics. To determine how different levels of ammonium availability...

Ammonium/ammonia is the sole energy substrate of ammonia oxidizers, and is also an essential nitrogen source for other microorganisms. Ammonia oxidizers therefore must compete with other soil microorganisms such as methane-oxidizing bacteria (MOB) in terrestrial ecosystems when ammonium concentrations are limiting. Here we report on the interaction...

The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH(3)F) caused surprisingly little differences in community composition of...

The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental con...