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Microbiology and Biotechnology Letters


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Molecular and Cellular Microbiology  |  Microbial Genetics, Physiology and Metabolism

Microbiol. Biotechnol. Lett.

Received: November 30, 2020; Revised: April 27, 2021

Characterization of denitrifying and dissimilatory nitrate reduction to ammonium (DNRA) bacteria isolated from mud crab culture environment

Yuni Puji Hastuti 1*, Iman Rusmana 2, Kukuh Nirmala 1, Ridwan Affandi 3 and Yuli Siti Fatma 2

1Department of Aquaculture, IPB University, Bogor 16680, Indonesia, 2Department of Biology, IPB University, Bogor 16680, Indonesia, 3Department of Aquatic Resources Management, IPB University, Bogor 16680, Indonesia

Correspondence to :
Yuni Puji Hastuti, Jl. Raya Dramaga, Bogor, 16680, West Java, Indonesia [16680]
Tel : +6281310499728, Fax : +622518628755, E-mail :


Culture environmental condition affects the physiological responses of mud crab Scylla serrata which is important for its growth. The availability of dissolved inorganic nitrogen (DIN) in its culture environment under a recirculating system closely relates to the nitrogen cycle, which involves both anaerobic and aerobic bacterial activities. Anaerobically, there are two major nitrogen compound degradation process, i.e., denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This present study aimed to identify denitrifying and DNRA bacteria in mud crabs’ culture environment under recirculating aquaculture system. The water samples were collected from anaerobic filters in the recirculating mud crab cultures. The results showed that three denitrifying bacterial isolates and seven DNRA bacterial isolates were successfully identified, exhibiting the various characteristics based on color, shape, and Gram staining. The phylogenetic analysis based on 16S rRNA gene for the denitrifying bacteria revealed that HIB_7a isolate was found to belong to Stenotrophomonas sp. Meanwhile, HIB_92 isolate, belonging to DNRA bacteria, exhibited 100% similarity to Bacillus sonorensis strain N3, Bacillus strain VITS-17, Bacillus tequlensis strain TY5, Geobacillus sp. strain DB24, Bacillus subtilis strain A1, and Bacillus mojavensis strain SSRAI21. This study provides basic information regarding bacterial isolates identity that could be applied in aquaculture system to maintain optimal environmental condition.

Keywords: Aquaculture environment, bacterial identification, denitrification, DNRA, Scylla serrata, 16S rRNA gene

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