Ontology highlight
ABSTRACT:
PROVIDER: PRJNA890149 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21915405_1.fastq.gz | Fastqsanger.gz | |||
| SRR21915405_2.fastq.gz | Fastqsanger.gz | |||
| SRR21915406_1.fastq.gz | Fastqsanger.gz | |||
| SRR21915406_2.fastq.gz | Fastqsanger.gz | |||
| SRR21915407_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Nitrite-oxidizing bacteria are vital players in the global nitrogen cycle that convert nitrite to nitrate during the 2nd step of nitrification. Within this functional guild, the genus Nitrospira is among the most widespread and phylogenetically and physiologically diverse nitrite oxidizers and its members drive nitrite oxidation in many natural and biotechnological ecosystems. Despite their ecological and biotechnological importance, our understanding of Nitrospira’s energy metabolism is still limited. The main bottleneck for a detailed biochemical characterization of Nitrospira is biomass production, since they are slow-growing organisms and fastidious to culture. In this study, we cultured Nitrospira moscoviensis in a continuous stirred tank reactor system (CSTR) allowing constant biomass harvesting. Additionally, this cultivation setup enabled accurate control of physicochemical parameters and thus avoided fluctuating levels of nitrite and accumulation of nitrate. We performed transcriptome analysis and confirmed constant gene expression profiles in the chemostat culture over a period of two weeks. The transcriptomic data supports the predicted core metabolism of N. moscoviensis, including the reductive TCA cycle as a CO2 fixation pathway, the novel bd-like oxidase as terminal oxidase and the octaheme nitrite reductase involved in nitrogen assimilation. Additionally, the expression of multiple copies of respiratory complexes suggests functional differentiation of these copies within the respiratory chain. Transcriptome analysis also suggests a soluble and a membrane-bound gamma subunit as part of the nitrite oxidoreductase (NXR), the enzyme catalyzing nitrite oxidation. Overall, the transcriptome data provided novel insights into the metabolism of Nitrospira supporting the genome-based prediction of key pathways. Moreover, the application of a CSTR to cultivate Nitrospira is an important foundation for future proteomic and biochemical characterizations, which are crucial for a better understanding of canonical and complete nitrifying microorganisms.
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