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Nitrobacter winogradskyi transcriptomic response to ammonia

ABSTRACT: The comparison was done in chemostats. Cultures maintained nitrite. The transcritome responses were compared at three ammonium concentrations. The comparison was done in chemostats. Single cultures maintained with 60 mM nitrite, and the ammonium supllemented as appropiate.

ORGANISM(S): Nitrobacter winogradskyi

SUBMITTER: Luis Sayavedra-Soto

PROVIDER: E-GEOD-58053 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Nitrobacter winogradskyi transcriptomic response to low and high ammonium concentrations.

Sayavedra-Soto Luis L Ferrell Rebecca R Dobie Michael M Mellbye Brett B Chaplen Frank F Buchanan Alex A Chang Jeffrey J Bottomley Peter P Arp Daniel D

FEMS microbiology letters 20141204 3

Nitrobacter winogradskyi Nb-255 is a nitrite-oxidizing bacterium that can grow solely on nitrite (NO2(-)) as a source of energy and nitrogen. In most natural situations, NO2(-) oxidation is coupled closely to ammonium (NH4(+)) oxidation by bacteria and archaea and, conceptually, N. winogradskyi can save energy using NH4(+) to meet its N-biosynthetic requirements. Interestingly, NH4(+) delayed the growth of N. winogradskyi when at concentrations higher than 35 mM, but grew well at concentrations ...[more]

PMID: 25673652

Similar Datasets

Nitrobacter winogradskyi transcriptomic response to ammonia

Project description:The comparison was done in chemostats. Cultures maintained nitrite. The transcritome responses were compared at three ammonium concentrations.

2015-02-20 | GSE58053 | GEO

mRNASeq of Nitrosomonas europaea and Nitrobacter winogradskyi

Project description:N.europaea and N. winogradskyi were grown singly and in co-culture in chemostat to probe for transcriptome diffrences between the two growth conditions. The comparison was done in chemostats. Single cultures maintained with 60 mM ammonium or nitrate, as appropiate, were compared to co-culture maintained with 60 mM ammonium.

2014-12-03 | E-GEOD-58052 | biostudies-arrayexpress

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Project description:Anaerobic ammonium-oxidising (anammox) bacteria, members of the ‘Candidatus Brocadiaceae’ family, play an important role in the nitrogen cycle and are estimated to be responsible for about half of the oceanic nitrogen loss to the atmosphere. Anammox bacteria combine ammonium with nitrite and produce dinitrogen gas via the intermediates nitric oxide and hydrazine (anammox reaction) while nitrate is formed as a by-product. These reactions take place in a specialized, membrane-bound compartment called the anammoxosome. Therefore, the substrates ammonium, nitrite and product nitrate have to cross the outer-, cytoplasmic- and anammoxosome membranes to enter or exit the anammoxosome. The genomes of all anammox species harbour multiple copies of ammonium-, nitrite- and nitrate transporter genes. Here we investigated how the distinct genes for ammonium-, nitrite- and nitrate- transport were expressed during substrate limitation in membrane bioreactors. Transcriptome analysis of Kuenenia stuttgartiensis planktonic cells under ammonium-limitation showed that three of the seven ammonium transporter genes and one of the six nitrite transporter genes were significantly upregulated, while another ammonium and nitrite transporter gene were downregulated in nitrite limited growth conditions. The two nitrate transporters were expressed to similar levels in both conditions. In addition, genes encoding enzymes involved in the anammox reaction were differentially expressed, with those using nitrite as a substrate being upregulated under nitrite limited growth and those using ammonium as a substrate being upregulated during ammonium limitation. Taken together, these results give a first insight in the potential role of the multiple nutrient transporters in regulating transport of substrates and products in and out of the compartmentalized anammox cell.

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Transcription profiling of yeast cells (homozygous deletion mutants of BY4743) grown in chemostats, sampled at steady state. Glucose and ammonium limitation, dilution rates 0.1 and 0.2 hr-1, gene deletions HO and HAP4 applied

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2005-12-31 | E-MEXP-442 | biostudies-arrayexpress

Transcription profiling of G sulfurreducens GGS nitrogen fixation

Project description:G. sulfurreducens (ATCC #51573) was obtained from the laboratory culture collection of Dr. Derek Lovley. Cells were grown under strict anaerobic conditions at 30 °C in chemostats, as previously described (for more information see Esteve-Núñez, A., M. M. Rothermich, M. Sharma, and D. R. Lovley. 2004. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol.:in press.), with acetate (5 mM) as the electron donor and fumarate (27.5 mM) as the electron acceptor. For growth in the absence of fixed nitrogen, the ammonium chloride (4.7 mM) was omitted from the medium and fumarate served as the electron acceptor. Therefore, cultures with ammonium chloride were limited by acetate while cultures without ammonium chloride were limited by nitrogen. Cultures were maintained at a dilution rate of 0.05 h-1 for 5 culture vessel volumes to ensure that cells were at steady-state prior to harvesting. Cells were harvested by centrifugation at 4 °C and the cell pellet was flash-frozen in liquid nitrogen and then stored at -80 °C prior to RNA extraction. Cells grown in the absence of ammonium had acetylene reduction rates of 0.012 nmol/hr compared to 0.003 nmol/hr in ammonium-grown cells, providing evidence that these cells were fixing nitrogen.. The steady-state concentration of cells in the nitrogen-fixing chemostats (0.178 mg/mL + 0.011; mean + standard deviation, n=3) was significantly lower than chemostats provided with ammonium (0.45 mg/mL + 0.007). Three cultures of acetate limited growth with fumarate as the electron acceptor and three cultures of nitrogen limited growth with fumarate as the electron acceptor were grown. Each culture vessel was harvested and extracted for total RNA separately to produce three biological replicates for this experiment.

2005-01-01 | E-TIGR-82 | biostudies-arrayexpress

Steady state growth under inorganic carbon limitation increases energy consumption for maintenance and enhances nitrous oxide production in Nitrosomonas europaea

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Transcription profiling time series of cyanobacteria Prochlorococcus marinus subsp. pastoris str. CCMP1986 (MED4) and str. MIT 9313 grown in media with different levels and sources of nitrogen

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2007-10-11 | E-TABM-91 | biostudies-arrayexpress

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