水稻根圈細菌 Oryzomicrobium terrae strain TPP412 之全基因體序列分析及其對於水稻生長之影響

Abstract

Oryzomicrobium terrae strain TPP412 (簡稱TPP412)為一株分離自北台灣水田的新屬新種土壤細菌。本研究藉由次世代定序以及生物資訊技術分析TPP412菌株之全基因體序列，並利用盆栽試驗探討施用該菌株對於水稻生長之影響，亦評估該菌株對於緩和水稻幼苗遭受鹽分逆境的效果。定序結果顯示TPP412的基因體大小為3,526,415 bp，含有3,120條蛋白質編碼基因 (protein-coding gene)。經序列比對與功能註解(annotation)發現，TPP412具有多數與促進植物生長相關的基因，例如生長素(Indole acetic acid, IAA)生合成(ALDH; NIT)、抗菌化合物(4-hydroxybenzoate)生合成(ubiC)，以及抗非生物逆境，例如超氧歧化酶 (superoxide dismutase, SOD)、過氧化氫酶(catalase, CAT)等(sodB, katG)基因。在水稻盆栽試驗發現，將TPP412菌肥接種至未滅菌的全量化肥土壤中，其穀粒產量比施用在滅菌土壤組高。在鹽分逆境試驗發現，水稻幼苗若預先處理TPP412菌液，不僅能促進生長，還可緩解濃度100mM的氯化鈉水耕液對作物的傷害。綜合上述結果，TPP412具有促進植物生長、緩解鹽分逆境的功效，也因並具有完整的基因體資訊，將會是一株兼具應用以及研究潛力的土壤根圈益生菌。

Oryzomicrobium terrae strain TPP412 (abbreviated as TPP412) is a novel genus and species of eubacterium that was isolated from paddy field soil in northern Taiwan. The first objective of this study was to analyze the complete genome of TPP412 by Next Generation Sequencing (NGS) and bioinformatics technologies. I elucidated the role of this bacterium in plant growth-promotion by pot experiments with rice plants cultivated under non-sterile and sterile soils. I also evaluated the effects of TPP412 on rice seedling growth under saline condition (100mM NaCl) in hydroponic environment. The results of whole genome sequencing indicated that TPP412 has one circular chromosome that is 3,526,415 bp in size with 3,120 protein-coding genes. Through sequences alignment and functional annotation, I found that many genes related to plant growth-promotion involved in indole acetic acid (IAA) biosynthesis (ALDH; NIT); antimicrobial compound, 4-hydroxybenzoate biosynthesis (ubiC); and antioxidants resist to abiotic stress, such as superoxide dismutase (SOD) (sodB) and catalase (CAT) (katG). The results of pot experiments showed that inoculation with single inoculum TPP412 at full amount of recommended chemical fertilizer in non-sterile soil condition had a more stimulating effect on grain yield in non-sterile soil condition than that in sterile soil condition. I also found that treating the rice seedlings with TPP412 in advance can enhance plant growth and alleviate the damage from salt stress. Taken together, TPP412 is a beneficial bacterium for plant growth promotion and alleviation in salt stress. Furthermore, the complete genomic information of TPP412 will be a potentially powerful tool for studying the mode of action.