台灣南部地區擁有廣大但崎嶇的地貌，常被稱為「惡地」，其地形條件對農業發展造成極大挑戰。這些地區的土壤通常富含黏土，導致水分滲透與保水性不佳，嚴重限制農業生產力。過往研究指出，施用綠肥，特別是豆科植物，可透過根瘤中固氮菌的作用提供有機質、必需營養素與生物固氮，進而改善土壤健康。本研究旨在評估有機農法中綠肥與植物生長促進根際菌 (plant growth-promoting rhizobacteria, PGPR) 的應用，期望改善惡地土壤性質並促進作物生長。本研究於台南左鎮區一處蘿蔔田進行田間試驗，採用間作策略，設置三種處理組別：單施綠肥 (太陽麻，G組)、單施PGPR (P組)，以及綠肥與PGPR混合施用 (GP組)。根瘤分析顯示，在G與GP組的太陽麻根部均觀察到由Bradyrhizobium屬組成的根瘤菌定殖。微生物總基因體分析 (metagenomics) 結果顯示，各處理組在非度量多維尺度 (NMDS) 中呈現分群，G與GP組相對接近，顯示綠肥施用對土壤微生物群落結構具有較大影響。根據MAG (metagenome-assembled genomes) 分群結果，共分為四大群集，其中 Cluster 1 在 P 組施作下相對豐度較高，且此分群包含的土壤菌相較於其他分群有更高比例持有亞硝酸鹽氧化還原酶的編碼基因，可能與土壤中的硝化能力連動。此結果亦與離子分析中P組未檢測到亞硝酸鹽濃度的結果相符。本研究揭示綠肥與PGPR對惡地微生物生態系的影響機制，有助於深化對微生物介導土壤改善過程的理解，並為惡地地區農業永續發展奠定基礎。

The southern region of Taiwan is characterized by extensive yet rugged landscapes, commonly referred to as "badland" due to their challenging topographical features. Soils in these regions are typically clay-rich, resulting in poor water infiltration and retention, which severely constrains agricultural productivity. Previous research has demonstrated that the incorporation of green manure, particularly from leguminous species, can enhance soil health by providing organic matter, essential nutrients, and biologically fixed nitrogen through the activity of nitrogen-fixing bacteria in root nodules. This study investigated organic farming practices, the applications of green manure and plant growth-promoting rhizobacteria (PGPR), to improve soil properties in nutrient-deficient areas and support crop growth. A field experiment was conducted at a radish cultivation site located in the Zuozhen District of Tainan, employing an intercropping strategy with three treatment groups: green manure (sunn hemp) alone (G), PGPR alone (P), and a combination of green manure and PGPR (GP). Nodulation analysis revealed the presence of Bradyrhizobium in the root nodules of the sunn hemps in both G and GP groups. The findings from the metagenomic analysis indicated that the treatment groups exhibited clustering patterns in non-metric multidimensional scaling (NMDS), with the G and GP groups demonstrating a close proximity. This suggests that that the application of green manure exerts a substantial impact on the composition of soil microbial communities. Furthermore, according to the clustering results of metagenome-assembled genomes (MAGs), four major clusters were identified. Among them, Cluster 1 showed a higher relative abundance in the P treatment group. Compared with the other clusters, the microbial community within this cluster contained a higher proportion of genes encoding nitrite oxidoreductase (narG/H), which may be linked to enhanced nitrification capacity in the soil. This observation aligns with the ion analysis results, which showed no detectable nitrite concentration in the P group. The study elucidates the mechanisms by which green manure and plant growth-promoting rhizobacteria (PGPR) affect the microbial ecosystem in badlands, thereby enhancing the understanding of microbial-mediated soil improvement processes and providing a foundation for sustainable agricultural practices in such environments.

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