Project description:In this experiment, we used advanced proteomics techniques to discern differences in energy allocation between three strains of ammonia oxidizing bacteria: Nitrosomonas europaea, Nitrosomonas ureae, and Nitrosospira multiformis, during ammonia starved and ammonia replete conditions. Replicate cultures in late log phase from the three strains were starved of ammonia for 24 hours and compared to replicate control cultures grown for the same period. All three species were grown with three biological replicates for each condition and species with the exception of two replicates from the N. ureae starved cultures due to sample processing loss. This study has, to our knowledge, produced the first complete proteomes of Nitrosospira multiformis and Nitrosomonas ureae.

2018-05-16 | PXD008954 | Pride

Growth of complete ammonia oxidizers on guanidine

Project description:The nitrogen rich compound guanidine occurs widely in nature and is used by microbes as a nitrogen source, but microorganisms that grow on guanidine have not yet been discovered. Here we show that complete ammonia-oxidizing microbes (comammox), but no other known nitrifiers, encode homologues of a guanidinase and that the comammox isolate Nitrospira inopinata grows on guanidine as sole source of energy and reductant. Proteomics, kinetic enzyme characterization, and the crystal structure of the N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Transcription of comammox guanidinases was induced in wastewater treatment plant microbiomes upon incubation with guanidine, and guanidine degradation was detected in these systems. The discovery of guanidine as a selective growth substrate for comammox shows a unique niche of these globally important nitrifiers and offers new options for their isolation as well as for targeted manipulation of nitrifier communities.

2024-08-03 | PXD038826 | Pride

Comammox - Complete nitrification by Nitrospira bacteria

Project description:Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.

2019-03-15 | PXD013103 | Pride

Plant tissue ammonia oxidizing bacteria

Project description:Plant tissue ammonia oxidizing bacteria Raw sequence reads

| PRJNA796717 | ENA

Hypoosmolarity inhibits archaeal ammonia oxidation

Project description:Salinity strongly influences the physiology and distribution of nitrifying microorganisms, yet the effects of low salinity on these key players in nitrogen cycling remain understudied. This study investigates the impact of hypoosmolarity on different groups of ammonia oxidizers in soil and lake environments, as well as in pure culture isolates. In soil microcosms amended with ammonium, at low salinity levels (~120 µS/cm), which are comparable to values commonly found in pristine terrestrial and aquatic environments, the abundance of ammonia-oxidizing bacteria (AOB), dominated by Nitrosomonas oligotropha, significantly increased. In contrast, the growth of ammonia-oxidizing archaea (AOA), dominated by “Ca. Nitrosotenuis” of the Nitrosopumilaceae family, was stimulated by high salinity (~760 µS/cm). In ammonium-fed lake microcosms, the abundance of AOB, dominated by N. oligotropha, significantly increased under both low (~170 µS/cm) and high salinity (~850 µS/cm) conditions. In the presence of allylthiourea, a bacterial nitrification inhibitor, AOA were found to be sensitive to low salinity in both soil and lake microcosms. Consistently, pure culture studies revealed marked growth inhibition of AOA, especially of members of the Nitrosopumilaceae, under hypoosmolarity, unlike AOB and complete ammonia oxidizers (comammox) strains. Comparative genomic analyses with AOB and comammox, along with transcriptomic studies, suggested that the sensitivity of AOA to hypoosmolarity stress is attributed to a lack of sophisticated osmoregulatory transport systems and their S-layer cell wall structure. Overall, this study highlights the importance of hypoosmolarity as a key factor shaping the ecological niches and distribution of ammonia oxidizers as well as nitrification activities in terrestrial and aquatic environments increasingly affected in their salinities by intensified water cycles due to climate change.

2026-04-06 | PXD064500 | Pride

ammonia oxidizing bacteria of reservoir sediment

Project description:ammonia oxidizing bacteria of sediment Raw sequence reads

| PRJNA609392 | ENA