Enrichment and Characterization of a Nitric Oxide-reducing Microbial Community in a Continuous Bioreactor

Overview

Journal Nat Microbiol

Specialties Microbiology
Parasitology

Date 2023 Jul 10

PMID 37429908

Authors

Paloma Garrido-Amador

Niek Stortenbeker

Hans J C T Wessels

Daan R Speth

Inmaculada Garcia-Heredia

Boran Kartal

Affiliations

Soon will be listed here.

Abstract

Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.

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References

Xu T, Park S, Venable J, Wohlschlegel J, Diedrich J, Cociorva D . ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity. J Proteomics. 2015; 129:16-24. PMC: 4630125. DOI: 10.1016/j.jprot.2015.07.001. View

Gerbling K, Steup M, Latzko E . Fructose 1,6-Bisphosphatase Form B from Synechococcus leopoliensis Hydrolyzes both Fructose and Sedoheptulose Bisphosphate. Plant Physiol. 1986; 80(3):716-20. PMC: 1075189. DOI: 10.1104/pp.80.3.716. View

Parks D, Imelfort M, Skennerton C, Hugenholtz P, Tyson G . CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015; 25(7):1043-55. PMC: 4484387. DOI: 10.1101/gr.186072.114. View

Hassan J, Bergaust L, Molstad L, de Vries S, Bakken L . Homeostatic control of nitric oxide (NO) at nanomolar concentrations in denitrifying bacteria - modelling and experimental determination of NO reductase kinetics in vivo in Paracoccus denitrificans. Environ Microbiol. 2015; 18(9):2964-78. DOI: 10.1111/1462-2920.13129. View

Suenaga T, Riya S, Hosomi M, Terada A . Biokinetic Characterization and Activities of NO-Reducing Bacteria in Response to Various Oxygen Levels. Front Microbiol. 2018; 9:697. PMC: 5902568. DOI: 10.3389/fmicb.2018.00697. View

Kemmer G, Keller S . Nonlinear least-squares data fitting in Excel spreadsheets. Nat Protoc. 2010; 5(2):267-81. DOI: 10.1038/nprot.2009.182. View

van der Oost J, de Boer A, de Gier J, Zumft W, Stouthamer A, Van Spanning R . The heme-copper oxidase family consists of three distinct types of terminal oxidases and is related to nitric oxide reductase. FEMS Microbiol Lett. 1994; 121(1):1-9. DOI: 10.1111/j.1574-6968.1994.tb07067.x. View

Zumft W . Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme-copper oxidase type. J Inorg Biochem. 2004; 99(1):194-215. DOI: 10.1016/j.jinorgbio.2004.09.024. View

Fish J, Chai B, Wang Q, Sun Y, Brown C, Tiedje J . FunGene: the functional gene pipeline and repository. Front Microbiol. 2013; 4:291. PMC: 3787254. DOI: 10.3389/fmicb.2013.00291. View

10.

Dijkhuizen L, Harder W . Current views on the regulation of autotrophic carbon dioxide fixation via the Calvin cycle in bacteria. Antonie Van Leeuwenhoek. 1984; 50(5-6):473-87. DOI: 10.1007/BF02386221. View

11.

Vosswinkel R, Neidt I, Bothe H . The production and utilization of nitric oxide by a new, denitrifying strain of Pseudomonas aeruginosa. Arch Microbiol. 1991; 156(1):62-9. DOI: 10.1007/BF00418189. View

12.

Bell L, Richardson D, Ferguson S . Identification of nitric oxide reductase activity in Rhodobacter capsulatus: the electron transport pathway can either use or bypass both cytochrome c2 and the cytochrome bc1 complex. J Gen Microbiol. 1992; 138(3):437-43. DOI: 10.1099/00221287-138-3-437. View

13.

Cole J . Anaerobic bacterial response to nitric oxide stress: Widespread misconceptions and physiologically relevant responses. Mol Microbiol. 2021; 116(1):29-40. DOI: 10.1111/mmi.14713. View

14.

Jain C, Rodriguez-R L, Phillippy A, Konstantinidis K, Aluru S . High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018; 9(1):5114. PMC: 6269478. DOI: 10.1038/s41467-018-07641-9. View

15.

Kopylova E, Noe L, Touzet H . SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012; 28(24):3211-7. DOI: 10.1093/bioinformatics/bts611. View

16.

Yilmaz P, Parfrey L, Yarza P, Gerken J, Pruesse E, Quast C . The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res. 2013; 42(Database issue):D643-8. PMC: 3965112. DOI: 10.1093/nar/gkt1209. View

17.

Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar . ARB: a software environment for sequence data. Nucleic Acids Res. 2004; 32(4):1363-71. PMC: 390282. DOI: 10.1093/nar/gkh293. View

18.

Amann R, Binder B, Olson R, Chisholm S, Devereux R, Stahl D . Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol. 1990; 56(6):1919-25. PMC: 184531. DOI: 10.1128/aem.56.6.1919-1925.1990. View

19.

Dalsgaard T, Bak F . Nitrate Reduction in a Sulfate-Reducing Bacterium, Desulfovibrio desulfuricans, Isolated from Rice Paddy Soil: Sulfide Inhibition, Kinetics, and Regulation. Appl Environ Microbiol. 1994; 60(1):291-7. PMC: 201302. DOI: 10.1128/aem.60.1.291-297.1994. View

20.

Vollack K, Zumft W . Nitric oxide signaling and transcriptional control of denitrification genes in Pseudomonas stutzeri. J Bacteriol. 2001; 183(8):2516-26. PMC: 95168. DOI: 10.1128/JB.183.8.2516-2526.2001. View