Diversity of Bacterial Community that Contribute in Nitrogen Cycle at Lake of Situ Sawangan-Bojongsari, West Java.
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One of the problems in freshwater management is the declining of water quality due to pollution of nitrogen compound. Mechanisms of nitrogen transformation by indigenous bacteria in water body have been considered to solve this problem. Situ Sawangan-Bojongsari is the largest lake at Depok city, West Java. Antrophogenic activities on the lake have been accused to cause nitrogen pollution. Accordingly, the aim of this research is to investigate the abundance and diversity of bacterial community that contribute in N cycle as well as to study the profile of physical and chemical parameters that influence the bacterial community. Water and sediment samples were collected from three sampling station, each with three replicate. Water samples were collected from the surface of the water column (0 cm), secchi depth (110) and the bottom (230 cm). Sediment samples were collected by sediment core and divided to three section depth (0-2 cm, 2-5 cm, and 5-10 cm). Analysis of physical factors was fermormed at the time of sampling which included temperature, pH, and DO. Wheter analysis of chemical factors from water and pore water sediment covered some parameters: TN, TOM, DOM, TOC, N-NH3, N-NO3, dan N-NO2. Analysis of the bacterial abundance that contribute in N cycle was done using MPN method. The community structure of the bacteria was analyzed using DGGE method. Amplification product of nifH, amoA, and nosZ gene were targeted for DGGE analysis. The most abundance of nitrogen fixing bacteria was found at the sediment in the depth of 2-5 cm (4.43 log cell/mL) and the less abundance was found at the water coloumn in the depth of 0 cm (2.46 log cell/mL). The most abundance of ammonia oxidizing bacteria was found in the depth of 0 cm (270 cell/mL). The less abundance of the bacteria was found in the depth of 230 cm (73 cells/Ml). The most abundance of nitrite oxidizing bacteria was found at the water column in the depth of 0 cm (2.87 log cell/mL) and the less abundance of the bacteria was found in the depth of 230 cm. There was no ammonia and nitrite oxidizing bacteria found in the sediment. The most abundance of nitrate reducing bacteria (denitrification) was found at the sediment in the depth of 2-5 and 5-10 cm (6.04 log cell/mL) and the less abundance of the bacteria was found at the water column in the depth of 0 cm (1.32 log cell/mL). The most abundance of nitrate reducing bacteria (DNRA) was found at the sedimen in the depth of 5-10 cm (4.32 log cell/ml) and the less abundance of the bacteria was found at the water column in the depth of 0 and 110 cm (1.56 log cell/mL). The most abundance of amonifying bacteria was found at the sediment in the depth of 5-10 cm (4.43 log cell/mL) and the less abundance of the bacteria was found at the water column in the depth of 0 cm (1.86 cell/mL). A total of 11 unique bands of nifH gene generated after DGGE analysis. Six of eleven unique bands of the gene selected, sequenced and identified by searching against Genbank using BlastN, and the highest identity and score values of the six isolated sequences were the nifH gene of uncultured bacterium in non-redundant database of Genbank (80-90%). Analysis of amino acid sequence from the six isolated of nifH gene showed similarity between 65 and 92% with the functional protein of nifH (nitrogenase). A total of 5 isolated nifH gene were nitrogenase reductase of uncultured bacterium and one isolated nifH gene was nitrogenase reductase of Methylomonas sp. MKI. However, the most probable affiliations of the bacteria harboring the nifH gene were the nitrogen fixing bacteria from α- or β-proteobacteria, including Bradyrhizobium sp. ORS324, Azospirillum brasilense, and Azotobacter vinelandii. Fragment of amoA gene was amplified from water samples. There was no fragment amoA gene from sediment samples. Total of 10 unique bands of amoA gene can be detected after DGGE anaysis. Six of teen bands of amoA genes according to BlastN analysis were the amoA of uncultured bacterium (86-97 %). Amino acid sequences analysis of the six isolated of amoA genes revealed similarity between 56 and 93 % with functional protein of amoA (ammonia monooxygenase). Total of five isolated of the gene were as ammonia monooxygenase of uncultured bacterium and one isolated was as ammonia monooxygenase of Nitrosospira sp.III7. However based on phylogenetic analysis, the six isolated of amoA gene was belong to the genus Nitrosospira. Fragment of nosZ gene was amplified from sediment samples and there was no fragment nosZ gene from water samples. A total of 12 unique bands of nosZ gene were detected after DGGE analysis. Seven of twelve unique bands were isolated and BlastN analysis of the isolated gene showed that the seven isolated were nosZ of uncultured bacterium (91-98%). Amino acid sequence of the seven isolated of nosZ gene revealed similarity between 87 dan 99% with functional protein of nosZ (nitrous oxide reductase) and the seven isolated of nosZ gene were as nitrous oxide reductase of uncultured bacterium. Interestingly, phylogenetic analysis showed that the seven genes of amoA was belong to the genus Azospirillum.