PXD039573-2

PXD039573 is an original dataset announced via ProteomeXchange.

Title	Differential contribution of nitrifying prokaryotes to nitrification in groundwater
Description	The ecophysiology of complete ammonia oxidizing Nitrospira (CMX) and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the relevance of their activity from the ecosystem-level process perspective has remained unclear. We investigated oligotrophic carbonate rock aquifers as a model system to assess the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen. CMX accounted for up to 95% of the ammonia oxidizer communities. Nitrification rates were positively correlated to CMX clade A-associated phylotypes and AOB affiliated with Nitrosomonas ureae. Surprisingly, short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed more than 90% to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOA and AOB was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater is primarily governed by AOB. Higher growth yields at lower NH4+ turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations. Activity measurements combined with differential inhibition allowed a refined understanding of ammonia oxidizer coexistence, competition and cooperation beyond the insights from molecular data alone.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:07:53.770.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nico Jehmlich
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-20 02:27:04	ID requested
1	2023-10-24 11:50:55	announced
⏵ 2	2023-11-14 09:07:55	announced	2023-11-14: Updated project metadata.
3	2024-10-22 06:09:14	announced	2024-10-22: Updated project metadata.

Kr, ü, ger M, Chaudhari N, Thamdrup B, Overholt WA, Bristow LA, Taubert M, K, ü, sel K, Jehmlich N, von Bergen M, Herrmann M, Differential contribution of nitrifying prokaryotes to groundwater nitrification. ISME J, 17(10):1601-1611(2023) [pubmed]

submitter keyword: Prokaryotes, Metaproteomics,Nitrification, Ammonia-oxidizing bacteria, Groundwater

Nico Jehmlich
contact affiliation	Helmholtz-Centre for Environmental Research - UFZ GmbH Department of Molecular Systems Biology Permoserstrasse 15 04318 Leipzig, Germany
contact email	nico.jehmlich@ufz.de
lab head
Nico Jehmlich
contact affiliation	Helmholtz-Centre for Environmental Research - UFZ
contact email	nico.jehmlich@ufz.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD039573
     1. Label: PRIDE project
     2. Name: Differential contribution of nitrifying prokaryotes to nitrification in groundwater