Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils

• Published in: mBio 2023-12, Vol.14 (6), p.e0215023
• Main Authors: Liu, Guo-Hong, Yang, Shang, Han, Shuang, Xie, Cheng-Jie, Liu, Xing, Rensing, Christopher, Zhou, Shun-Gui
• Format: Article
• Language: English
• Subjects: Environmental Microbiology; new diazotrophic Geomonas; nitrogen fixation; nitrogenase; paddy soil; Research Article; RT-qPCR; transcriptome analysis
• ISSN: 2150-7511; 2150-7511
• DOI: 10.1128/mbio.02150-23

Nitrogen gas (N ) fixation driven by diazotrophs is a crucial process for supplying nitrogen to paddy soil ecosystems. The genus has been considered to be an important potential diazotroph in paddy soils, but direct experimental evidence of the nitrogen-fixing ability of in pure culture is still lacking. Hence, we aimed to demonstrate this nitrogen-fixing capability and shed light on how this process was regulated in response to ammonium (NH ) in . In this study, we determined that a key nitrogenase gene ( ) was present in 50 isolates from paddy soils. Members of contained the minimum nitrogen fixation gene cluster ( ) based on genomic analysis, implying species had the potential to fix nitrogen. Acetylene reduction assay (ARA), N isotope labeling, and total nitrogen accumulation assays validated that was, indeed, able to fix nitrogen in pure culture. Under nitrogen-fixing conditions, the cell morphology of changed from short rod-shaped (with NH ) to long rod-shaped and flagella became longer and thicker. The expression of genes correlated to nitrogen fixation in the transcriptome was quantified in response to NH . Expression of genes associated with nitrogenase, flavin-based electron bifurcation complexes (such as the FixAB system), NH uptake, and transformation (e.g., glutamine and glutamate synthetases) were significantly upregulated under nitrogen-fixing conditions, suggesting these mechanisms might be involved in N fixation in . These results were verified by RT-qPCR. Taken together, our results demonstrate that species possess the ability to fix N and expand our understanding on the ecological significance and potential applications of in paddy soil ecosystems. IMPORTANCE The ability of species to fix nitrogen gas (N ) is an important metabolic feature for its application as a plant growth-promoting rhizobacterium. This research is of great importance as it provides the first comprehensive direct experimental evidence of nitrogen fixation by the genus in pure culture. We isolated a number of strains from paddy soils and determined that was present in these strains. This study demonstrated that these species harbored genes encoding nitrogenase, as do and in the same class of . We demonstrated N -dependent growth of and determined regulation of gene expression associated with nitrogen fixation. The research establishes and advances our understanding of nitrogen fixation in .