Identification of Nitrobacter isolates and their bacteriophages from swiftlet house environments: implications for nitrate control in edible bird nests

Ningrum, Siti Gusti; Widhowati, Dyah; Nurhidayat, Novik; Yulinery, Titin; Triana, Evi; Soeka, Yati Sudaryati

doi:10.30466/vrf.2025.2061041.4768

Identification of Nitrobacter isolates and their bacteriophages from swiftlet house environments: implications for nitrate control in edible bird nests

Document Type : Original Article

Authors

Siti Gusti Ningrum ¹

Dyah Widhowati ²

Novik Nurhidayat ³

Titin Yulinery ³

Evi Triana ³

Yati Sudaryati Soeka ³

¹ Laboratory of Molecular Genetics Research, Faculty of Veterinary Medicine, Universitas Wijaya Kusuma Surabaya, Surabaya, Indonesia

² Department of Microbiology, Faculty of Veterinary Medicine, Universitas Wijaya Kusuma Surabaya, Surabaya, Indonesia

³ Center for Applied Microbiology Research, The National Research and Innovation Agency, Cibinong, Indonesia

https://doi.org/10.30466/vrf.2025.2061041.4768

Abstract

This study aimed to identify and characterize nitrifying bacteria and their associated bacteriophages from swiftlet house environments as a preliminary step toward developing biological control strategies for nitrate contamination in edible bird nests,a food safety concern due to the excessive nitrite and nitrate accumulation. A total of 80 environmental samples were collected between October and November 2024 from four swiftlet houses in Central Kalimantan, Indonesia, including 20 samples each from feces, pond water, soil, and edible bird nests (Aerodramus fuciphagus). Phenotypic characterization (culture, Gram staining, and biochemical tests) and genotypic identification (PCR and 16S rRNA gene sequencing) were performed. Bacteriophages were screened using spot tests and plaque assays. The study resulted in the isolation and identification of 15 Nitrobacter isolates. Molecular analysis confirmed all isolates belonged to the Nitrobacter genus. One isolate, Nitrobacter AP6, was selected as a representative host for phage screening due to its consistent growth and plaque clarity. Spot tests revealed four bacteriophages capable of lysing Nitrobacter AP6. These findings demonstrate the feasibility of isolating nitrifying bacteria and phages from swiftlet environments and provide a foundation for future biocontrol development, though further in vitro and in situ validation is required to assess effectiveness and safety.

Keywords

Bacteriophage

Edible bird nest

Nitrate contamination

Nitrifying bacteria