Ontology highlight
ABSTRACT:
PROVIDER: PRJNA889081 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21878137_1.fastq.gz | Fastqsanger.gz | |||
| SRR21878137_2.fastq.gz | Fastqsanger.gz | |||
| SRR21878138_1.fastq.gz | Fastqsanger.gz | |||
| SRR21878138_2.fastq.gz | Fastqsanger.gz | |||
| SRR21878139_1.fastq.gz | Fastqsanger.gz |
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Project description:Geobacter sulfurreducens is a widely explored microorganism recognized by its metabolic versatility able to reduce a number of external electron acceptors. In the present study the capacity of this strain to reduce nitrate was evaluated along with its transcriptomic profile under nitrate-reducing conditions and the catalytic role of Pd nanoparticles on the reductive pathway. Results demonstrated that G. sulfurreducens was able to reduce nitrate and important kinetic differences related to the time response were found among the electron donors used (acetate and hydrogen). When using acetate, a delay response on nitrate reduction of 4 days and reduction of 94% of nitrate was achieved, while nitrite was not detected, and all the nitrogen was recovered as ammonium (79.6 ± 5.7 %). The use of hydrogen as electron donor increased 2-fold the maximum rate of nitrate reduction, leading to 93% reduction of nitrate during the first 20 h with recovery of 45% as ammonium, while nitrite was not detected. In addition, transcriptome profiling analysis of G. sulfurreducens under nitrate-reducing conditions using hydrogen or acetate as an electron donor at 2 and 6 days reveals that a core of 146 genes (69 upregulated and 77 downregulated) are differentially expressed in all conditions. Genes related to nitrogen metabolism, such as nrfA and nrfH, gdhA, and amtB, were upregulated in the incubations and RT-qPCR data confirmed upregulations of these genes. Experiments performed with biologically synthesized Pd (Bio-Pd) + G. sulfurreducens cells demonstrated synergistic input of Bio-Pd and the metabolic capacity of G. sulfurreducens. These results expand the metabolic versatility of G. sulfurreducens, which may have important implications in nitrogen cycling in natural environments and engineered systems.
2023-06-01 | GSE179298 | GEO
Project description:We compared global transcriptional patterns in Pyrobaculum aerophilum cultures with oxygen, nitrate, arsenate and ferric iron as respiratory electron acceptors to identify genes and regulatory patterns that differentiate these pathways. Keywords: Time course study with different respiratory electron acceptors
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Project description:Alicycliphilus denitrificans is a versatile, ubiquitous, facultative anaerobic bacterium. A. denitrificans strain BC can use chlorate, nitrate and oxygen as electron acceptor for growth. Cells display a prolonged lag-phase when transferred from nitrate to chlorate and vice versa. Furthermore, cells adapted to aerobic growth do not easily use nitrate or chlorate as electron acceptor. We further investigated these responses of strain BC by differential proteomics, transcript analysis and enzyme activity assays. In nitrate-adapted cells transferred to chlorate and vice versa, appropriate electron acceptor reduction pathways need to be activated. In oxygen-adapted cells, adaptation to the use of chlorate or nitrate is likely difficult due to the poorly active nitrate reduction pathway and low active chlorate reduction pathway. We deduce that the Nar-type nitrate reductase of strain BC also reduces chlorate, which may result in toxic levels of chlorite if cells are transferred to chlorate. Furthermore, the activities of nitrate reductase and nitrite reductase appear to be not balanced when oxygen-adapted cells a shifted to nitrate as electron acceptor, leading to the production of a toxic amount of nitrite. These data suggest that strain BC encounters metabolic challenges in environments with fluctuations in the availability of electron acceptors. Proteomic samples were prepared from Alicycliphilus denitrificans grown in the presence of different electron acceptors: chlorate, nitrate and oxygen. Proteins were separated by a short SDS gel and for each sample 4 in-gel digest slices were prepared. Peptide samples were measured by nLC LTQ-Orbitrap and the data were analysed with MaxQuant using default settings (1% FDR on peptide and protein level) and filtered extra to keep only proteins identified with at least 2 peptides and 1 unique and 1 unmodified peptide.
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Project description:We report here a methanotroph, Methylotuvimicrobium buryatense 5GB1C, that consumes methane at 500ppm at rates several times higher than any previously published. Analyses of bioreactor-based performance and RNAseq based transcriptomics suggest that this superior ability to utilize low methane is based at least in part on an extremely low non-growth associated maintenance energy and on a 5-fold higher methane specific affinity than previous reports.
2023-08-02 | GSE221011 | GEO
Project description:We compared global transcriptional patterns in Pyrobaculum aerophilum cultures with oxygen, nitrate, arsenate and ferric iron as respiratory electron acceptors to identify genes and regulatory patterns that differentiate these pathways. Keywords: Time course study with different respiratory electron acceptors To focus the microarrays on genes that are specifically affected by changes in terminal electron acceptors we analyzed gene expression in time courses with cultures shifted from aerobic growth to either NO3-, As(V), Fe(III)-citrate, or additional O2. Gene expression and substrate usage were measured at three time points (2.5, 4.5, and 7.5 hours), allowing sufficient time for changes in gene expression, while restricting cultures to a maximum of one or two cell divisions.
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Project description:Nitrite-oxidizing bacteria are vital players in the global nitrogen cycle that convert nitrite to nitrate during the 2nd step of nitrification. Within this functional guild, the genus Nitrospira is among the most widespread and phylogenetically and physiologically diverse nitrite oxidizers and its members drive nitrite oxidation in many natural and biotechnological ecosystems. Despite their ecological and biotechnological importance, our understanding of Nitrospira’s energy metabolism is still limited. The main bottleneck for a detailed biochemical characterization of Nitrospira is biomass production, since they are slow-growing organisms and fastidious to culture. In this study, we cultured Nitrospira moscoviensis in a continuous stirred tank reactor system (CSTR) allowing constant biomass harvesting. Additionally, this cultivation setup enabled accurate control of physicochemical parameters and thus avoided fluctuating levels of nitrite and accumulation of nitrate. We performed transcriptome analysis and confirmed constant gene expression profiles in the chemostat culture over a period of two weeks. The transcriptomic data supports the predicted core metabolism of N. moscoviensis, including the reductive TCA cycle as a CO2 fixation pathway, the novel bd-like oxidase as terminal oxidase and the octaheme nitrite reductase involved in nitrogen assimilation. Additionally, the expression of multiple copies of respiratory complexes suggests functional differentiation of these copies within the respiratory chain. Transcriptome analysis also suggests a soluble and a membrane-bound gamma subunit as part of the nitrite oxidoreductase (NXR), the enzyme catalyzing nitrite oxidation. Overall, the transcriptome data provided novel insights into the metabolism of Nitrospira supporting the genome-based prediction of key pathways. Moreover, the application of a CSTR to cultivate Nitrospira is an important foundation for future proteomic and biochemical characterizations, which are crucial for a better understanding of canonical and complete nitrifying microorganisms.
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Project description:Desulfitobacterium hafniense DCB-2, a halo-respirer and versatile inorganic ion reducer, grows in hazardous waste contaminated environments. M-BM- Gene expression changes were determined when the strain was grown in the presence of high concentrations of Fe(+3), Se(+6), U(+6), or NO3(-) as alternative electron acceptors. (Thesis by Christina L. Harzman at Michigan State University, 2009) RNA was used to directly compare gene expression in control samples of pyruvate fermentation (20 mM) to fermentation in the presence inorganic electron acceptors or respiration-inducing conditions. M-BM- The inorganic electron acceptors added to media for fermentation were 1 mM selenate or 0.5 mM uranyl acetate. The respiration-inducing conditions were 50 mM ferric citrate (20 mM lactate carbon source) or 10 mM nitrate (20 mM lactate carbon source). Microarray hybridizations were performed with a dye swap and 3 biological replicates for a total of 6 slides per condition for comparison.
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