Ontology highlight
ABSTRACT:
PROVIDER: PRJEB91801 | ENA |
REPOSITORIES: ENA
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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
Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone.
2013-08-24 | GSE50164 | GEO
Project description:<p>While irrigation and fertilization are basic cultivation practices in poplar plantations on a global scale, the impact of these practices on the environment is not well understood. Here, we demonstrate that water-urea coupling and water-compound fertilizer coupling differentially impact soil ecosystems. We report that water-fertilizer coupling did not significantly alter taxonomic diversity indices (richness, evenness), but it did drive significant shifts in microbial community composition, reflected by changes in the relative abundance of specific taxa (e.g., core phyla) and their functional profiles. Water-urea coupling reduced Proteobacteria and Actinobacteria in non-rhizosphere soils while increasing Acidobacteria and Chloroflexi. In contrast, water-compound fertilizer coupling amplified Proteobacteria and Actinobacteria dominance in rhizosphere soils. Water-fertilizer coupling reshaped microbial composition and functional gene abundance linked to nitrogen and sulfur cycling, indicating a potential shift in microbial-mediated N and S transformation processes. Water-urea treatment enriched denitrification genes and dissimilatory nitrate reduction genes (napABC) in rhizosphere soil, while water-compound fertilizer treatment enhanced nitrification (amoABC, HAO) and denitrification gene abundance in both soils. For sulfur (S) cycling, water-urea treatment favored thiosulfate oxidation genes (SOX complex), whereas water-compound fertilizer treatment increased assimilatory sulfate reduction genes. Multi-omics integration linked these microbial dynamics to metabolic reprogramming—water-urea increased lipid and secondary metabolites in rhizosphere soils, while water-compound fertilizers elevated amino acid-associated metabolites in non-rhizosphere soils.</p>
2025-06-17 | MTBLS12375 | MetaboLights