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Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification

ABSTRACT: Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification

PROVIDER: PRJNA691925 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13429077.fastq.gz	Fastqsanger.gz
	SRR13429078.fastq.gz	Fastqsanger.gz
	SRR13429079.fastq.gz	Fastqsanger.gz
	SRR13429080.fastq.gz	Fastqsanger.gz
	SRR13429081.fastq.gz	Fastqsanger.gz

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Similar Datasets

Adaptive responses of Trichlorobacter lovleyi to nitrite detoxification reveal overlooked contributions of Geobacterales to nitrate ammonification

Project description:Poorly understood microorganisms "short-circuit" the nitrogen cycle via the dissimilatory nitrate reduction to ammonium to retain the element in agricultural lands and stimulate crop productivity. The prevalence of Geobacterales closely related to Trichlorobacter lovleyi in nitrate ammonification hotspots motivated us to investigate adaptive responses contributing to ammonification rates in the laboratory type strain T. lovleyi SZ. Here we describe the identification of tightly regulated pathways for efficient nitrate foraging and respiration with acetate, an important intermediate of organic matter degradation that Geobacterales efficiently assimilate and oxidize. Challenging the established dogma that high carbon/nitrate ratios stimulate the reduction of nitrate to ammonium, T. lovleyi doubled rapidly across a wide range of ratios provided nitrate concentrations were low enough to prevent the accumulation of the toxic nitrite intermediate. Yet, excess electrons during hydrogenotrophic growth alleviated nitrite toxicity and stimulated the reduction of nitrate to ammonium even under conditions of severe acetate limitation. These findings underscore the importance of nitrite toxicity in the ammonification of nitrate by Geobacterales and provide much needed mechanistic understanding of microbial adaptations contributing to soil nitrogen conservation. This information is critical to enhance the predictive value of genomic-based traits in environmental surveys and to guide strategies for sustainable management of nitrogen fertilization as well as mitigation of green-house emissions and agrochemical leaching from agricultural lands.

2024-12-31 | GSE164776 | GEO

Trichlorobacter lovleyi strain:LYY

Project description:Trichlorobacter lovleyi strain:LYY Genome sequencing

| PRJNA626355 | ENA

Trichlorobacter lovleyi isolate:J2

Project description:Trichlorobacter lovleyi isolate:J2 Genome sequencing

| PRJNA1255882 | ENA

Trichlorobacter lovleyi strain:IAE

Project description:Trichlorobacter lovleyi strain:IAE Genome sequencing

| PRJNA562098 | ENA

Trichlorobacter lovleyi

Project description:Geobacter lovleyi overview

| PRJNA35945 | ENA

Trichlorobacter lovleyi strain:IAE | isolate:Sediment | cultivar:DCB-1

Project description:Trichlorobacter lovleyi strain:IAE | isolate:Sediment | cultivar:DCB-1 Genome sequencing

| PRJNA771489 | ENA

Trichlorobacter lovleyi SZ strain:SZ

Project description:A delta-proteobacterium capable of chlororespiration

| PRJNA17423 | ENA

Trichlorobacter thiogenes strain:ATCC BAA-34

Project description:Trichlorobacter thiogenes strain:ATCC BAA-34 Genome sequencing

| PRJNA245580 | ENA

Cytochrome <i>c</i> nitrite reductase from the bacterium <i>Geobacter lovleyi</i> represents a new NrfA subclass.

Project description:Cytochrome c nitrite reductase (NrfA) catalyzes the reduction of nitrite to ammonium in the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a process that competes with denitrification, conserves nitrogen, and minimizes nutrient loss in soils. The environmental bacterium Geobacter lovleyi has recently been recognized as a key driver of DNRA in nature, but its enzymatic pathway is still uncharacterized. To address this limitation, here we overexpressed, purified, and characterized G. lovleyi NrfA. We observed that the enzyme crystallizes as a dimer but remains monomeric in solution. Importantly, its crystal structure at 2.55-Å resolution revealed the presence of an arginine residue in the region otherwise occupied by calcium in canonical NrfA enzymes. The presence of EDTA did not affect the activity of G. lovleyi NrfA, and site-directed mutagenesis of this arginine reduced enzymatic activity to <3% of the WT levels. Phylogenetic analysis revealed four separate emergences of Arg-containing NrfA enzymes. Thus, the Ca2+-independent, Arg-containing NrfA from G. lovleyi represents a new subclass of cytochrome c nitrite reductase. Most genera from the exclusive clades of Arg-containing NrfA proteins are also represented in clades containing Ca2+-dependent enzymes, suggesting convergent evolution.

| S-EPMC7450111 | biostudies-literature

Discover of overlooked differentially expressed gene regions from single-cell RNA-seq data with neural stem cell derived from human induced pluripotent stem

Project description:Single-cell RNA sequencing has enabled researchers to quantify the transcriptomes of individual cells, infer cell types, and investigate differential expression among cell types, which will lead to a better understanding of the regulatory mechanisms of cell states. Transcript diversity caused by phenomena such as aberrant splicing events have been revealed, and the differential expression of previously unannotated transcripts might be overlooked by annotation-based analyses. Accordingly, we have developed an approach to discover overlooked differentially expressed (DE) gene regions that complements annotation-based methods. We applied our algorithm to two datasets and discovered several intriguing DE transcripts, including a transcript related to the modulation of neural stem/progenitor cell differentiation.

2019-09-19 | GSE125288 | GEO

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