Liu Liangting, Liu Mengfan, Jiang Yiming, Lin Weitie, Luo Jianfei
School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People's Republic of China.
School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People's Republic of China
mSystems. 2021 Feb 16;6(1):e01003-20. doi: 10.1128/mSystems.01003-20.
Ammonia tolerance is a universal characteristic among the ammonia-oxidizing bacteria (AOB); in contrast, the known species of ammonia-oxidizing archaea (AOA) have been regarded as ammonia sensitive, until the identification of the genus " Nitrosocosmicus." However, the mechanism of its ammonia tolerance has not been reported. In this study, the AOA species " Nitrosocosmicus agrestis," obtained from agricultural soil, was determined to be able to tolerate high concentrations of NH (>1,500 μM). In the genome of this strain, which was recovered from metagenomic data, a full set of genes for the pathways of polysaccharide metabolism, urea hydrolysis, arginine synthesis, and polyamine synthesis was identified. Among them, the genes encoding cytoplasmic carbonic anhydrase (CA) and a potential polyamine transporter (drug/metabolite exporter [DME]) were found to be unique to the genus " Nitrosocosmicus." When " Nitrosocosmicus agrestis" was grown with high levels of ammonia, the genes that participate in CO/HCO conversion, glutamate/glutamine syntheses, arginine synthesis, polyamine synthesis, and polyamine excretion were significantly upregulated, and the polyamines, including putrescine and spermidine, had significant levels of production. Based on genome analysis, gene expression quantification, and polyamine determination, we propose that the production and excretion of polyamines is probably one of the reasons for the ammonia tolerance of " Nitrosocosmicus agrestis," and even of the genus " Nitrosocosmicus." Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global NO emission. Recently, some AOA species from the genus " Nitrosocosmicus" were also found to have high ammonia tolerance. However, the reported mechanism for the ammonia tolerance is very rare and indeterminate for AOB and for AOA species. In this study, an ammonia-tolerant AOA strain of the species " Nitrosocosmicus agrestis" was identified and its potential mechanisms for ammonia tolerance were explored. This study will be of benefit for determining more of the ecological role of AOA in agricultural soils or other environments.
耐氨性是氨氧化细菌（AOB）的一个普遍特征；相比之下，在“亚硝化宇宙菌属”被鉴定出来之前，已知的氨氧化古菌（AOA）物种一直被认为对氨敏感。然而，其耐氨机制尚未见报道。在本研究中，从农业土壤中获得的AOA物种“田野亚硝化宇宙菌”被确定能够耐受高浓度的NH（>1500μM）。在从宏基因组数据中恢复的该菌株基因组中，鉴定出了多糖代谢、尿素水解、精氨酸合成和多胺合成途径的全套基因。其中，编码细胞质碳酸酐酶（CA）和一种潜在多胺转运蛋白（药物/代谢物输出蛋白[DME]）的基因被发现是“亚硝化宇宙菌属”所特有的。当“田野亚硝化宇宙菌”在高浓度氨环境中生长时，参与CO/HCO转化、谷氨酸/谷氨酰胺合成、精氨酸合成、多胺合成和多胺排泄的基因显著上调，腐胺和亚精胺等多胺有显著的产量。基于基因组分析、基因表达定量和多胺测定，我们提出多胺的产生和排泄可能是“田野亚硝化宇宙菌”乃至“亚硝化宇宙菌属”耐氨的原因之一。AOA的耐氨性通常远低于AOB，这使得AOB而非AOA成为农业土壤中主要的氨氧化菌，导致全球一氧化氮排放。最近，还发现一些“亚硝化宇宙菌属”的AOA物种具有高耐氨性。然而，所报道的耐氨机制对于AOB和AOA物种来说都非常罕见且不明确。在本研究中，鉴定出了一个耐氨的AOA菌株“田野亚硝化宇宙菌”，并探索了其潜在的耐氨机制。本研究将有助于确定AOA在农业土壤或其他环境中更多的生态作用。
