To ensure food security for the ever-increasing world’s population, it is important to explore other alternatives for enhancing plant productivity. This study is aimed at identifying the putative plant growth–promoting (PGP) and endophytic gene clusters in root-associated endophytic microbes from maize root and to also verify if their abundance is affected by different farming practices. To achieve this, we characterize endophytic microbiome genes involved in PGP and endophytic lifestyle inside maize root using the shotgun metagenomic approach. Our results revealed the presence of genes involved in PGP activities such as nitrogen fixation, HCN biosynthesis, siderophore, 4-hydroxybenzoate, ACC deaminase, phenazine, phosphate solubilization, butanediol, methanol utilization, acetoin, nitrogen metabolism, and IAA biosynthesis. We also identify genes involved in stress resistance such as glutathione, catalase, and peroxidase. Our results further revealed the presence of putative genes involved in endophytic behaviors such as aerotaxis, regulator proteins, motility mechanisms, flagellum biosynthesis, nitrogen regulation, regulation of carbon storage, formation of biofilm, reduction of nitric oxide, regulation of beta-lactamase resistance, type III secretion, type IV conjugal DNA, type I pilus assembly, phosphotransferase system (PTS), and ATP-binding cassette (ABC). Our study suggests a high possibility in the utilization of endophytic microbial community for plant growth promotion, biocontrol activities, and stress mitigation. Further studies in ascertaining this claim through culturing of the beneficial isolates as well as pot and field experiments are necessary.

为了确保不断增长的世界人口的粮食安全，探索提高植物生产力的其他替代方法非常重要。本研究旨在确定来自玉米根部的根相关内生微生物中推定的植物生长促进 (PGP) 和内生基因簇，并验证它们的丰度是否受到不同耕作方式的影响。为了实现这一目标，我们使用鸟枪宏基因组学方法表征了玉米根内涉及 PGP 和内生生活方式的内生微生物组基因。我们的结果揭示了参与 PGP 活动的基因的存在，例如固氮、HCN 生物合成、铁载体、4-羟基苯甲酸、ACC 脱氨酶、吩嗪、磷酸盐溶解、丁二醇、甲醇利用、乙偶姻、氮代谢和 IAA 生物合成。我们还鉴定了参与抗逆性的基因，如谷胱甘肽、过氧化氢酶和过氧化物酶。我们的结果进一步揭示了涉及内生行为的假定基因的存在，例如趋氧性、调节蛋白、运动机制、鞭毛生物合成、氮调节、碳储存调节、生物膜形成、一氧化氮减少、β-内酰胺酶抗性调节、 III 型分泌、IV 型结合 DNA、I 型菌毛组装、磷酸转移酶系统 (PTS) 和 ATP 结合盒 (ABC)。我们的研究表明，利用内生微生物群落促进植物生长、生物防治活动和缓解压力的可能性很高。有必要通过培养有益分离株以及盆栽和田间试验来进一步研究以确定这一说法。