PXD051979

PXD051979 is an original dataset announced via ProteomeXchange.

Title	Nitrite toxicity drives nitrous oxide accumulation in a cooperative denitrifying synthetic community
Description	Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, have caused unprecedented increases in the emission of nitrous oxide (N2O) in recent decades. As a potent greenhouse gas, and an ozone depleting substance, understanding the sources and sinks of N2O is of vital importance. Nitrate (NO3-) reducing microbes are a primary contributor to the biotic production of N2O in anoxic regions of soil, marine systems, and wastewater treatment facilities through the process of denitrification. Thus, developing a better understanding of denitrifying microbial communities, and the environmental factors that influence N2O emissions may provide strategies to mitigate emissions in agriculture and wastewater treatment. Here, through comprehensive genome analysis, we show that pathway partitioning is a common strategy utilized by microbial communities to perform complete denitrification. Through detailed physiological characterization and kinetic modeling of a cooperative synthetic community (SynCom) assembled by pairing bacterial isolates from a field site heavily contaminated with NO3-, we also provide insight into the controls of N2O emissions. We demonstrate that members of this SynCom cooperate to perform complete denitrification through exchange of nitrite (NO2-) and nitric oxide (NO), and that community context drives global physiological changes in each member. We identify links between amino acid metabolism and denitrification activity as well as indicators of competition and amino acid exchange. We also show that NO2- toxicity with unbalanced growth of community members drives N2O production, suggesting that this SynCom provides a simplified, environmentally relevant, model of pathway partitioning in denitrifying communities. This SynCom should provide a framework with which to further explore how environmental context can impact cooperation and lead to the production of N2O
HostingRepository	PRIDE
AnnounceDate	2025-06-24
AnnouncementXML	Submission_2025-06-24_07:13:06.125.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Petzold
SpeciesList	scientific name: Acidovorax sp.; NCBI TaxID: 1872122; scientific name: Rhodanobacter sp.; NCBI TaxID: 1883446;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-03 13:42:01	ID requested
⏵ 1	2025-06-24 07:13:07	announced

Carr AV, Otwell AE, Hunt KA, Chen Y, Wilson J, Faria JP, Liu F, Edirisinghe JN, Valenzuela JJ, Turkarslan S, Lui LM, Nielsen TN, Arkin AP, Henry CS, Petzold CJ, Stahl DA, Baliga NS, Emergence and disruption of cooperativity in a denitrifying microbial community. ISME J, 19(1):(2025) [pubmed]

10.1093/ismejo/wraf093;

submitter keyword: Nitrogen Cycle,SynCom,Denitrification,Microbial community

Christopher J.Petzold
contact affiliation	Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720
contact email	cjpetzold@lbl.gov
lab head
Christopher Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/06/PXD051979

PRIDE project URI

• PRIDE
  1. PXD051979
     1. Label: PRIDE project
     2. Name: Nitrite toxicity drives nitrous oxide accumulation in a cooperative denitrifying synthetic community