Soil metagenome
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REPOSITORIES: ENA
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Project description:Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils
| PRJDB2899 | ENA
Project description:Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
2019-03-15 | PXD013103 | Pride
Project description:Archaeal and bacterial ammonia-oxidizers in soil fractions
| PRJNA323757 | ENA
Project description:In the soil the stability of urea is affected by the presence of urease, a ubiquitous enzyme released in the rhizosphere by microbial population and by decomposition of organic matter. To reduce the impact on farmer economies and environmental pollution, a common agronomical practice consists of applying urease inhibitors which delays the hydrolysis of urea and, in turn, ammonia is slowly release in the soil. General aim of the present work was the description of changes in maize root transcriptome occurring in response to treatment with the urease inhibitor NBPT.
2017-02-09 | GSE76828 | GEO
Project description:Marine sponges represent one of the few eukaryotic groups that ubiquitously harbor symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of archaeal ammonia oxidizers (AOA). In this study, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and direct isotope-based functional assays. We demonstrate that the I. basta symbiont is not closely related to other genomically sequenced sponge AOA and is a member of a new genus. “Candidatus Nitrosospongia bastadiensis” is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbor nitrite-oxidizing microbes. Consistently, Ca N. bastadiensis encodes and expresses the genetic repertoire required for chemolithoautotrophic ammonia oxidation. Furthermore, we show that this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system likely involved in defense against foreign DNA, represent important adaptations of AOA to life within these ancient filter-feeding animals.
2019-11-13 | PXD012484 | Pride
Project description:γ-Aminobutyric acid (GABA) is a non-proteinogenic amino acid and widespread in nature from microorganisms to plants and animals. DNA microarray analysis revealed that the transcription of gabTDP was strongly increased in C. glutamicum wild type grown with GABA and urea compared to the same strain cultivated with glucose and urea. Remarkably, the presence of ammonia partially inhibited growth on GABA, and the reasons for it were also investigated in this study.
2020-03-25 | GSE138828 | GEO
Project description:γ-Aminobutyric acid (GABA) is a non-proteinogenic amino acid and widespread in nature from microorganisms to plants and animals. DNA microarray analysis revealed that the transcription of gabTDP was strongly increased in C. glutamicum wild type grown with GABA and urea compared to the same strain cultivated with glucose and urea. Remarkably, the presence of ammonia partially inhibited growth on GABA, and the reasons for it were also investigated in this study.
2020-03-25 | GSE138827 | GEO