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Microbiology and Biotechnology Letters


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Molecular and Cellular Microbiology (MCM)  |  Microbial Genetics, Physiology and Metabolism

Microbiol. Biotechnol. Lett. 2021; 49(3): 432-439

Received: November 30, 2020; Revised: April 27, 2021; Accepted: May 18, 2021

Characterization of Denitrifying and Dissimilatory Nitrate Reduction to Ammonium Bacteria Isolated from Mud Crab Culture Environment

Yuni Puji Hastuti1*, Iman Rusmana2, Kukuh Nirmala1, Ridwan Affandi3, and Yuli Siti Fatma2

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

Correspondence to :
Yuni Puji Hastuti,

Microbial community plays important roles in the culture environment of mud crab Scylla serrata. One of the environmental management efforts for the cultivation of S.serrata is by stabilizing microorganisms involved in nitrogen cycle process. The availability of dissolved inorganic nitrogen 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 processes, i.e., denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This study aimed to identify denitrifying and DNRA bacteria isolated from the recirculating cultivation of S. serrata. The water samples were collected from anaerobic filters called close filter system, which is anaerobically conditioned with the addition of varying physical filter materials in the recirculating mud crab cultures. The results showed that three denitrifying bacterial isolates and seven DNRA bacterial isolates were successfully identified. The phylogenetic analysis based on 16S rRNA gene of the denitrifying bacteria revealed that HIB_7a had the closest similarity to Stenotrophomonas daejeonensis strain MJ03. Meanwhile, DNRA bacterial isolate of HIB_92 showed a 100% similarity to Bacillus sonorensis strain N3, Bacillus vallismortis 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 denitrifying and DNRA bacterial isolates identity which might have the potential to be applied as probiotics in aquaculture systems in order to maintain optimal environmental conditions.

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

Graphical Abstract

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