Alanine synthesized by alanine dehydrogenase enables ammonium-tolerant nitrogen fixation in Paenibacillus sabinae T27

Precipitation affects soil nitrogen fixation by regulating active diazotrophs and nitrate nitrogen in an alpine grassland of Qinghai-Tibetan Plateau

Soil asymbiotic nitrogen (N) fixation provides a critical N source to support plant growth in alpine grasslands, and precipitation change is expected to lead to shifts in soil asymbiotic N fixation. However, large gaps remain in understanding the response of soil asymbiotic N fixation to precipitation gradients. Here we simulated five precipitation gradients (10 % (0.1P), 50 % (0.5P), 70 % (0.7P), 100 % (1.0P) and 150 % (1.5P) of the natural precipitation) in an alpine grassland of Qinghai-Tibetan Plateau and examined the soil nitrogenase activity and N fixation rate for each gradient. Quantitative PCR and high-throughput sequencing were used to measure the abundance and community composition of the soil nifH DNA (total diazotrophs) and nifH RNA reverse transcription (active diazotrophs) gene. Our results showed that the soil diazotrophic abundance, diversity and nifH gene expression rate peaked under the 0.5P. Soil nitrogenase activity and N fixation rate varied in the range 0.032-0.073 nmol·C2H4·g-1·h-1 and 0.008-0.022 nmol·N2·g-1·h-1 respectively, being highest under the 0.5P. The 50 % precipitation reduction enhanced the gene expression rates of Azospirillum and Halorhodospira which were likely responsible for the high N fixation potential. The 0.5P treatment also possessed a larger and more complex active diazotrophic network than the other treatments, which facilitated the resistance of diazotrophic community to environmental stress and thus maintained a high N fixation potential. The active diazotrophic abundance had the largest positive effect on soil N fixation, while nitrate nitrogen had the largest negative effect. Together, our study suggested that appropriate precipitation reduction can enhance soil N fixation through promoting the abundance of the soil active diazotrophs and decreasing soil nitrate nitrogen, and soil active diazotrophs and nitrate nitrogen should be considered in predicting soil N inputs in the alpine grassland of Qinghai-Tibetan Plateau under precipitation change.

Non-targeted effects of nitrification inhibitors on soil free-living nitrogen fixation modified with weed management

Biological nitrogen fixation and nitrification inhibitor applications contribute to improving soil nitrogen (N) availability, however, free-living N fixation affected by nitrification inhibitors has not been effectively evaluated in soils under different weed management methods. In this study, the effects of the nitrification inhibitors dicyandiamide (DCD) and 3, 4-dimethylpyrazole phosphate (DMPP) on the nitrogenase, nifH gene，and diazotrophic communities in soils under different weed management methods (AMB, weeds growth without mowing or glyphosate spraying; GS, glyphosate spraying; MSG, mowing and removing weeds and glyphosate spraying; and WM, mowing aboveground weeds) were investigated. Compared to the control counterparts, the DCD application decreased soil nitrogenase activity and nifH gene abundance by 4.5 % and 37.9 %, respectively, under the GS management method, and the DMPP application reduced soil nitrogenase activity by 20.4 % and reduced the nifH gene abundance by 83.4 % under the MSG management method. The application of nitrification inhibitors significantly elevated soil NH4+-N contents but decreased NO3--N contents, which had adverse impacts on soil nifH gene abundance and nitrogenase activity. The nifH gene abundances were also negatively impacted by dissolved organic N and Geobacter but were positively affected by available phosphorus and diazotrophic community structures. Nitrification inhibitors significantly inhibited Methylocella but stimulated Rhizobiales and affected soil diazotrophic communities. The nitrification inhibitors DCD and DMPP significantly altered soil diazotrophic community structures, but weed management outweighed nitrification inhibitors in reshaping soil diazotrophic community structures. The non-targeted effects of the nitrification inhibitors DMPP and DCD on soil free-living N fixation were substantially influenced by the weed management methods.

Effects of nitrogen supply on hydrogen-oxidizing bacterial enrichment to produce microbial protein: Comparing nitrogen fixation and ammonium assimilation

To investigate the effects of nitrogen source supply on microbial protein (MP) production by hydrogen-oxidizing bacteria (HOB) under continuous feed gas provision, a sequencing batch culture comparison (N2 fixation versus ammonium assimilation) was performed. The results confirmed that even under basic cultivation conditions, N2-fixing HOB (NF-HOB) communities showed higher levels of CO2 and N2 fixation (190.45 mg/L Δ CODt and 11.75 mg/L Δ TNbiomass) than previously known, with the highest biomass yield being 0.153 g CDW/g COD-H2. Rich ammonium stimulated MP synthesis and the biomass accumulation of communities (increased by 7.4 ～ 14.3 times), presumably through the enhancement of H2 and CO2 absorption. The micro mechanism may involve encouraging the enrichment of species like Xanthobacter and Acinetobacter then raising the abundance of nitrogenase and glutamate synthase to facilitate the nitrogen assimilation. This would provide NF-HOB with ideas for optimizing their MP synthesis activity.

Study on the performance of Anerinibacillus sp. in degrading cyanide wastewater and its metabolic mechanism

Cyanide extraction dominates the gold smelting industry, which leads to the generation of large amounts of cyanide-containing wastewater. In this study, Aneurinibacillus tyrosinisolvens strain named JK-1 was used for cyanide wastewater biodegradation. First, we tested the performance of JK-1 in degrading cyanide under different conditions. Then, we screened metabolic compounds and pathways associated with cyanide degradation by JK-1. Finally, we explored the potential JK-1-mediated cyanide degradation pathway. Our results showed that the optimal pH and temperature for cyanide biodegradation were 7.0 and 30 °C, respectively; under these conditions, a degradation rate of >98% was achieved within 48 h. Untargeted metabolomics results showed that increased cyanide concentration decreased the abundance of metabolic compounds by 71.1% but upregulated 32 metabolic pathways. The Kyoto Encyclopedia of Genes and Genomes enrichment results revealed significant changes in amino acid metabolism pathways during cyanide degradation by JK-1, including cyanoamino acid metabolism, β-alanine metabolism, and glutamate metabolism. Differential metabolic compounds included acetyl-CoA, l-asparagine, l-glutamic acid, l-phenylalanine, and l-glutamine. These results confirmed that cyanide degradation by JK-1 occurs through amino acid assimilation. This study provides new insights into the mechanism of cyanide biodegradation, which can be applied in the treatment of cyanide wastewater or tailings.

Glutamine synthetase and GlnR regulate nitrogen metabolism in Paenibacillus polymyxa WLY78

Paenibacillus polymyxa WLY78, a N2-fixing bacterium, has great potential use as a biofertilizer in agriculture. Recently, we have revealed that GlnR positively and negatively regulates the transcription of the nif (nitrogen fixation) operon (nifBHDKENXhesAnifV) in P. polymyxa WLY78 by binding to two loci of the nif promoter according to nitrogen availability. However, the regulatory mechanisms of nitrogen metabolism mediated by GlnR in the Paenibacillus genus remain unclear. In this study, we have revealed that glutamine synthetase (GS) and GlnR in P. polymyxa WLY78 play a key role in the regulation of nitrogen metabolism. P. polymyxa GS (encoded by glnA within glnRA) and GS1 (encoded by glnA1) belong to distinct groups: GSI-α and GSI-β. Both GS and GS1 have the enzyme activity to convert NH4+ and glutamate into glutamine, but only GS is involved in the repression by GlnR. GlnR represses transcription of glnRA under excess nitrogen, while it activates the expression of glnA1 under nitrogen limitation. GlnR simultaneously activates and represses the expression of amtBglnK and gcvH in response to nitrogen availability. Also, GlnR regulates the expression of nasA, nasD1D2, nasT, glnQHMP, and glnS. IMPORTANCE In this study, we have revealed that Paenibacillus polymyxa GlnR uses multiple mechanisms to regulate nitrogen metabolism. GlnR activates or represses or simultaneously activates and inhibits the transcription of nitrogen metabolism genes in response to nitrogen availability. The multiple regulation mechanisms employed by P. polymyxa GlnR are very different from Bacillus subtilis GlnR which represses nitrogen metabolism under excess nitrogen. Both GS encoded by glnA within the glnRA operon and GS1 encoded by glnA1 in P. polymyxa WLY78 are involved in ammonium assimilation, but only GS is required for regulating GlnR activity. The work not only provides significant insight into understanding the interplay of GlnR and GS in nitrogen metabolism but also provides guidance for improving nitrogen fixation efficiency by modulating nitrogen metabolism.

Scripting a new dialogue between diazotrophs and crops

Diazotrophs are bacteria and archaea that can reduce atmospheric dinitrogen (N2) into ammonium. Plant-diazotroph interactions have been explored for over a century as a nitrogen (N) source for crops to improve agricultural productivity and sustainability. This scientific quest has generated much information about the molecular mechanisms underlying the function, assembly, and regulation of nitrogenase, ammonium assimilation, and plant-diazotroph interactions. This review presents various approaches to manipulating N fixation activity, ammonium release by diazotrophs, and plant-diazotroph interactions. We discuss the research avenues explored in this area, propose potential future routes, emphasizing engineering at the metabolic level via biorthogonal signaling, and conclude by highlighting the importance of biocontrol measures and public acceptance.