Dataset Information

Investigating the autotrophic and mixotrophic metabolism of an anammox bacterium

ABSTRACT: Anaerobic ammonium oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and mixotrophy beyond genome predictions. Here, we experimentally resolved the central carbon metabolism using metabolomics (LC-MS and GC-MS), metabolic flux analysis and proteomics (shot-gun proteomics).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Candidatus Kuenenia Stuttgartiensis

TISSUE(S): Cell Culture

SUBMITTER: Martin Pabst

LAB HEAD: Martin Pabst

PROVIDER: PXD016171 | Pride | 2021-07-30

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Amx_merged_rfmt_mp_clustered_repl.fasta	Fasta
	Kust_uniprot_174633.fasta	Fasta
	MP13122018_Kust10_DDA01.mzML	Mzml
	MP13122018_Kust10_DDA01.raw	Raw
	MP13122018_Kust20_DDA01.mzML	Mzml

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Publications

Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo <sup>13</sup>C and <sup>2</sup>H metabolic network mapping.

Lawson Christopher E CE Nuijten Guylaine H L GHL de Graaf Rob M RM Jacobson Tyler B TB Pabst Martin M Stevenson David M DM Jetten Mike S M MSM Noguera Daniel R DR McMahon Katherine D KD Amador-Noguez Daniel D Lücker Sebastian S

The ISME journal 20201020 3

Anaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and use of different carbon and energy substrates beyond genome-based predictions. Here, we experimentally resolved the central carbon metabolism of the anammox bacterium Can ...[more]

PMID: 33082573

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Project description:The community composition (in terms of abundance, distribution and contribution of diverse clades) of bacteria involved in nitrogen transformations in the oxygen minimum zones may be related to the rates of fixed N loss in these systems. The abundance of both denirifying and anammox bacteria, and the assemblage composition of denitrifying bacteria were investigated in the Eastern Tropical South Pacific and the Arabian Sea using assays based on molecular markers for the two groups of bacteria. The abundance and distribution of bacteria associated with the fixed N removal processes denitrification and anammox were investigated using quantitative PCR for genes encoding nitrite reductase (nirK and nirS) in denitrifying bacteria and hydrazine oxidase(hzo) and 16S rRNA genesin anammox bacteria. All of these genes had depth distributions with maxima associated with the secondary nitrite maximum in low oxygen waters. NirS was mch more abundant than nirK, and much more abundant than the 16S rRNA gene from anammox bacteria. The ratio of hzo:16S rRNA for anammox was low and variable implying greater unexplored diversity in the the hzo gene. Assemblage composition of the abundant nirS-type denitrifiers was evaluated using a funcitonal gene microarray. Of the nirS archetypes represented on the microarray, very few occurred speficically in one region or depth interval, but the assemblages varied significantly. Community composition of denitrifiers based on microarray analysis of the nirS gene was most different between geographical regions. Within each region, the surface layer and OMZ assemblages clustered distinctly. Thus, in addition to spatial and temporal variation in denitrificaiton and anammox rates, both microbial abundance and community composition also vary between OMZ regions and depths. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.