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The biosynthesis of nitrous oxide in the green algae Chlamydomonas reinhardtii

ABSTRACT: This data was generated to identify the molecular pathways responsible for nitrous oxide synthesis by the green algae Chlamydomonas reinhardtii, when supplied with nitrite under aerobic conditions (oxia). RNA samples were collected at three time points, 15 min, 3 hours, and 24 hours after the start of the experiment. The control and treatment groups were grown under the same conditions, except treatment group was supplied with 10mM nitrite at time 0. Illumina TruSeq stranded RNA libraries were synthesised from the resulting RNA before sequencing on a HiSeq2500 (125bp). The resulting sequence run generated 241,151,809 paired-end 125bp reads, of which 200,946,839 remained following quality filtering. The short data was mapped to the published genome and read counts were generated with HT-Seq count with the default settings. The raw read count data was analysed by DESeq2 in order to identify genes differentially expressed during nitrous oxide production.

ORGANISM(S): Chlamydomonas reinhardtii

PROVIDER: GSE90609 | GEO | 2017/07/01

SECONDARY ACCESSION(S): PRJNA355168

REPOSITORIES: GEO

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Project description:Purpose: Free nitrous acid (FNA) has recently been demonstrated as an antimicrobial agent to a range of microorganisms. However, its antimicrobial mechanism is largely unknown. For this study Desulfovibrio vulgaris Hildenborough was selected to gain a systematic understanding of the antimicrobial mechanism of FNA. Methods: D. vulgaris was grown under anaerobic denitrifying conditions and when FNA was added (4 Î¼g-N/L) growth temporarily stopped. From cultures with and without added FNA, RNA was extracted and the abundance of gene transcripts was detected by sequencing. Transcripts exhibiting â¥1 or â¤-1 fold abundance change in the presence of FNA were designated as differentially expressed. Results:The results imply that FNA exerted multiple antimicrobial effects. Growth of the culture was inhibited by FNA and significant proportions of the cells were killed during the exposure. Respiration by sulfate reduction and lactate oxidation was shut down along with ATP production when exposed to FNA. Correspondingly, decreased transcript levels of genes involved in these metabolic pathways were detected. Detoxification of FNA was evident by nitrite reduction and the genes coding both nitrite reductase (NrfA) and hydroxylamine reductase were highly up regulated. During the FNA induced energy depleted state, there was evidence that D. vulgaris lowered both ribosome activity and protein production. Conditions within the cells were more oxidizing and genes coding for proteins providing resistance to oxidative stress were up regulated. Culture thiol levels increased during the exposure, suggesting that FNA had caused protein structures to alter. Furthermore, genes for motility were up regulated possibly as an attempt to avoid FNA stress. These findings provide new insight for understanding the response of D. vulgaris to FNA exposure. Conclusion: In this study, we performed genome-wide high throughput RNA sequencing (RNA-Seq) analysis on D. vulgaris in the absence and presence of a bacteriostatic-level of FNA (4 Î¼g-N/L). By combining the global activated/suppressed gene profiles and detected physiological responses, we detected the microbial response to FNA exposure and revealed potential antimicrobial mechanisms of FNA on this prevalent model sulfate reducing bacteria. mRNA profiles of D. vulgaris Hildenborough towards FNA stress were generated by next generation sequencing in triplicate via Illumina 2000.

Project description:Oxygen deficient zones (ODZs) are major sites of net natural oceanic nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ of the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N-tracer experiments in combination with qPCR and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. Denitrification was responsible for the highest N2O production with mean 8.7 nmol L-1 d-1 but up to 118 Â± 27.8 nmol L-1 d-1 just below the oxic-anoxic interface. Highest N2O production from AO of 0.16 Â± 0.003 nmol L-1 d-1 occurred in the upper oxycline at O2 concentrations of 10 - 30 Âµmol L-1 which coincided with highest archaeal amoA transcripts/genes. Oxygen responses of N2O production varied with substrate, but production and yields were generally highest below 10 Âµmol L-1 O2. Particulate organic matter additions increased N2O production by denitrification up to 5-fold suggesting increased N2O production during times of high particulate organic matter export. High N2O yields from ammonium oxidation of 2.1% were measured, but the overall contribution to N2O production stays an order of magnitude behind denitrification as an N2O source. Hence, these findings show that denitrification is the most important N2O production process in low oxygen conditions fueled by organic carbon supply which implies a positive feedback of the total oceanic N2O sources in response to increasing oceanic deoxygenation. [SUBMITTER_CITATION]: Frey, C., Bange, H. W., Achterberg, E. P., Jayakumar, A., Löscher, C. R., Arévalo-Martínez, D. L., León-Palmero, E., Sun, M., Sun, X., Xie, R. C., Oleynik, S., and Ward, B. B.: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru, Biogeosciences, 17, 2263-2287

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The biosynthesis of nitrous oxide in the green algae Chlamydomonas reinhardtii

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