Shallot (Allium cepa var. aggregatum L.) is an important commodity in horticulture and Indonesian foods. In Bantul Regency, Yogyakarta, Indonesia, shallot twisted diseases caused by Fusarium spp. significantly reduced yield quality and quantity. Supportive condition for plant-pathogen interaction needed for twisted disease development. This research aimed to measure the twisted disease incidence and observe the cultivation practice applied by shallot farmers in the Bantul coastal area as environmental aspects of the twisted disease to be a pre-study for further research on metagenomic analysis. This research had conducted in three sub-villages with different agroecosystems in the coastal area: Sono, Samiran, and Depok. Data were collected in shallot cultivation period in dry and rainy seasons from three farmers of each area. The higher disease incidence in the rainy season occurred in the Samiran sub-village at 33.97%, while in the dry season, disease incidence occurred in the Depok sub-village at 20.14%. Sono sub-village had the lowest disease incidence in rainy and dry seasons at 12.44% and 0%. Farmer cultivation practice may drive disease incidence due to environmental factors such as shallot variety, spacing between plants, fertilizer, and fungicides. Hence, further study is needed to understand plant-pathogen interaction with metagenomics through samples from 2 and 6 WAP in rainy seasons.

Tiyung cultivar, the consumer preferences of hot pepper in Magelang Regency, is still low in productivity (7 ton.ha-1). This research aimed to determine the growth and yield of hot pepper planted in relay intercropping as affected by biological agent application as a technology to increase productivity. This research was arranged in a Factorial Randomized Complete Block Design with an intercropping pattern of hot pepper (two and three rows model). The second factor was the application of biological agents, consisting of Trichoderma asperellum, Bacillus velezensis B-27 and Arbuscular Mycorrhizal Fungi (with and without biological agents). The control was the monoculture of hot pepper without biological agent application. The data observed were analyzed using Analysis of Variance and followed by the Duncan's Multiple Range Test at α= 5 %. The results showed that the relay intercropping of hot pepper produced less numbers of branches and leaves.  It indicated more efficiency in the use of assimilates for the development of generative organs, thereby resulting in the high values fruits weight per plant, which were as high as those in monoculture. The productivity observed in relay intercropping was 12.93 ton.ha-1, which was 15.8 % higher than in monoculture. The application of biological agents significantly increased the stomatal density, the size of stomatal opening, the number of leaves, weight of fruits per plant and productivity of hot pepper. The productivity of plant applied with biological agents was 16.84 ton.ha-1, which was 86.50 % higher than that without biological agents application.

Plant Growth Promoting Rhizobacteria has been known for its ability to induce plant resistance on shallot against twisted disease. Its ability as a bioprotectant agent is estimated to be comparable to the efficacy of Trichoderma which is currently widely used as a biological control agent.. This study aims to determine the content of jasmonic acid, salicylic acid, peroxidase, and disease suppression in shallot by application of Bacillus velezensis B-27, Bacillus cereus RC76, and application with combination of both rhizobacteria. The application was carried out  with tuber dipping for 30 minutes in each treatment with a bacterial density of 108 CFU mL-1. Application using Trichoderma was used as the comparison treatment, and the control plot was not given any treatment. Pathogen inoculation was carried out simultaneously as planting using Fusarium acutatum with a spore density of 106 CFU mL-1. The jasmonic and salicylic acids content was measured using the High-Performance Liquid Chromatography method, and the peroxidase content was determined using the spectrophotometric method. Disease suppression was measured at 10-day intervals. The results showed that treatment with Bacillus cereus RC76 increased jasmonic and salicylic acid levels, while application with Bacillus velezensis B-27 showed the highest level of peroxidase. Treatments with Bacillus spp. were able to suppress twisted disease by 72.2% to 100%. This study demonstrated that application Bacillus spp. suppressed twisted disease on shallot and increased the jasmonic and salicylic acid content as induced resistance mechanism against pathogens.

Biodiversity has been defined as the range of significantly different types of organisms and their relative abundance in an assemblage of community. The aim of this research was to understand about soil bacterial community after on biological control agents (BCA) treatments with various formulations. This research was conducted at Sleman Regency, Special Region of Yogyakarta and Faculty Agriculture of Universitas Gadjah Mada. The research conducted with culture dependent and culture independent methods to assess soil bacterial diversity. The results showed that soil bacterial diversity before and after treatment of biological control agent were different. Results from this research suggested different molecular methods regarding soil bacterial diversity based on their benefits and challenges.

Phytopythium vexans (de Barry) Abad, de Cock, Bala, Robideau, Lodhi & Lévesque was successfully isolated from the soil of the potatoes field in Ngablak, Magelang. This research aimed to obtain the knowledge and potency of P. vexans as a pathogen in potatoes, identify the morphology and molecular of P. vexans compared with the Oomycetes, Phytophthora and Pythium. The morphological observation was conducted based on a macroscopic colony pattern that grew for five days on the PDA medium and microscopic observation on its hyphae, sporangia, papillate, and chlamydospore. The molecular identification was conducted using multigene analysis, ITS and LSU. The in vitro pathogenicity test was obtained by inoculating P. vexans inoculum to the healthy potatoes leaves and tubers. The results of morphological observation showed that P. vexans had a stellate pattern, aseptate hyphae, and sporangium with an ovoid shape completed with semipapillate. Chlamydospore as a survival form was also found. This research revealed that the morphology of P. vexans was between Pythium and Phytophthora. Whereas, based on the molecular analysis using ITS and LSU, the Phytopythium spp. are more closely related to Phytophthora spp. rather than Pythium spp. The pathogenicity test of P. vexans showed that it could infect the flesh of potato tubers showing a brown lesions symptom