Опубликована: Янв. 1, 2024
Язык: Английский
Nitrogen, Год журнала: 2025, Номер 6(1), С. 4 - 4
Опубликована: Янв. 10, 2025
Climate change and anthropogenic nitrogen addition alter the soil physicochemical properties microbial activity in oligotrophic forest soil. Unbalanced non-selective fertilizer application is lost as gas emissions (N2O, NO) also contributed to eutrophication through NO3− leachate. Similarly, infiltrates contaminated drinking water sources lead human thyroid dysfunction. In order protect depleting timber growth due deficiency increasing ecological concerns from misapplication, we reviewed effects of different synthetic forms levels on biogeochemical process. this review, focused most recent findings research articles, review meta-analyses followed complementary insights agricultural so that may be able highlight how these observations contribute understanding cycle. Firstly, elaborated role nitrification denitrification transformation Secondly, discussed effect functional gene abundances. Thirdly, analyzed possible abundances conversion Finally, revealed not only pathways by substrate availability but shift dominance, thereby modifying properties, such pH. This collectively changes conditions, which are critical for expression potential involved These create a direction sustainable eco-friendly nitrogen-deficient
Язык: Английский
Процитировано
1
Environmental Research, Год журнала: 2025, Номер unknown, С. 120754 - 120754
Опубликована: Янв. 1, 2025
Язык: Английский
Процитировано
0
Frontiers in Microbiology, Год журнала: 2025, Номер 16
Опубликована: Фев. 26, 2025
The anammox bacteria "Candidatus Kuenenia stuttgartiensis" (Ca. Kuenenia) are able to gain energy by combining ammonium and nitrite produce nitrogen gas, which is an ecologically technically significant activity process. In this reaction, nitric oxide serves as a recognized intermediate in the reduction of nitrite, subsequently combined with hydrazine. However, enzyme that converts remains elusive. study, we investigated nitrite-reducing "Ca. strain CSTR1 identify candidates for such enzyme. An optimized vitro assay was established measure activities, followed protein fractions obtained from various fractionation methods. Separation cell extract size exclusion chromatography yielded active corresponding molecular range 150-200 kDa. Several proteins coeluted activity, including hydroxylamine dehydrogenase HOX, NADP-dependent isopropanol (Adh), electron-transfer 4Fe-4S subunit (Fcp), detoxifying flavorubredoxin (NorVW). further separation anion exchange chromatography, resulted much lower yields, activities were distributed among several fractions. addition, extracts using ultracentrifugation ultrafiltration linked but could not exclude involvement other activity. Overall, our results suggest mechanism Kuenenia" strains more complex than currently described literature. Nitrite appears be strongly associated HOX may additionally require participation proteins.
Язык: Английский
Процитировано
0
Nature Communications, Год журнала: 2025, Номер 16(1)
Опубликована: Апрель 3, 2025
Язык: Английский
Процитировано
0
ISME Communications, Год журнала: 2024, Номер 4(1)
Опубликована: Янв. 1, 2024
Язык: Английский
Процитировано
2
Microorganisms, Год журнала: 2024, Номер 12(4), С. 791 - 791
Опубликована: Апрель 13, 2024
Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds global nitrogen cycle. The major cycle are fixation, nitrification, denitrification, anaerobic ammonium oxidation, ammonification. focus this report is complex biogeochemical process which, complete form, consists a series four enzyme-catalyzed reduction reactions transforms nitrate to gas. Denitrification microbial strain-level ecological trait (characteristic), denitrification potential (functional performance) can be inferred from rules rely on presence or absence genes for denitrifying enzymes genomes. Despite significance associated large-scale genomic scholarly data sources, there lack datasets interactive computational tools investigating genomes according rules. Therefore, our goal categorize archaeal bacterial by based traits defined enzyme involvement steps. We integration genome, taxonomic lineage, ecosystem, provide investigations context strains. constructed an ecosystem annotated dataset 62,624 (866 archaea 61,758 bacteria) at least one twelve four-step canonical pathway. Our four-digit binary-coding scheme categorized sixteen including assigned 3280 260 bacteria genera. strains with pattern included Arcobacteraceae isolated detected diverse ecosystems aquatic, human, plant, Mollusca (shellfish). serve as research resources understanding biochemical, molecular, physiological aspects among others. produced also identifying synthetic communities.
Язык: Английский
Процитировано
1
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Май 17, 2024
Denitrification is a key metabolic process in the global nitrogen cycle and performed by taxonomically diverse microorganisms. Despite widespread importance of this metabolism, challenges remain identifying denitrifying populations predicting their end-products based on genotype. Here, genome-resolved metagenomics was used to explore denitrification genotype Bacillota enriched nitrate-amended high temperature incubations with confirmed N2O N2 production. A set 12 hidden Markov models (HMMs) created target diversity genes members phylum Bacillota. Genomic potential for complete found five metagenome-assembled genomes (MAGs) from enrichments, including two novel Brevibacillaceae family. Genomes denitrifiers encode reductase (nos) gene clusters clade II-type nosZ often include multiple variants nitric oxide (nor) gene. The HMM applied all Genome Taxonomy Database (GTDB) identified 17 genera inferred contain content. Among it common three distinct reductases be present (qNOR, bNOR sNOR) which may reflect adaptability environments variable redox conditions.
Язык: Английский
Процитировано
0
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Июнь 2, 2024
Abstract Microbes use a range of genetic codes and gene structures, yet these are ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding ecosystems. To resolve this, we developed lineage-specific prediction approach that uses the correct code based on taxonomic fragments, removes partial optimises small proteins. Applied to 9,634 metagenomes 3,594 genomes from human gut, this increased landscape captured expressed microbial proteins by 78.9%, including previously hidden groups. Optimised 3,772,658 clusters, many with antimicrobial activity. Integration sequences sample metadata into tool, InvestiGUT, enables association prevalence host parameters. Accurate is critical for functionality microbiomes, hence work will enhance mechanistic interactions between microbes hosts.
Язык: Английский
Процитировано
0
Опубликована: Янв. 1, 2024
Язык: Английский
Процитировано
0