16S rDNA analysis of microbial communities in a highly polluted region of the Marmara Sea

Abstract

The Marmara Sea is a small (size 70 x 250 km) intercontinental basin connecting Black Sea and Mediterranean Sea. The population of Marmara region reaches to 25 million and therefore there is large number of domestic and industrial wastewater discharges to the Marmara Sea from different points. Also large quantities of Central Asian oil and gas are transported to the west through the Marmara Sea. Combining effect of pollution sources create a chronic pollution at the Marmara Sea and formed several anoxic sediments in highly polluted sites. One of the areas is Küçükçekmece region. The region is populated by both residential and industrial sites and takes domestic and industrial effluent of more than 3 million people. Industrial sites mainly composed of metal industry, textile and leather industry, medicine industry, paper industry, chemical industry, rubber and plastic industry. Also in 1999 due to tanker accident at Küçükçekmece beach, the region was polluted with more than 3000 tones of petroleum. Sediment is a carbon and nutrient pool for aquatic environments. The presence of hydrocarbon compounds creates a suitable environment for the growth of anaerobic bacteria. Anaerobic biodegradation processes are slower than aerobic biodegradation. However, anaerobic processes can be a significant factor in removal of organic contaminants owing to the abundance of anaerobic electron acceptors relative to dissolved xygen; therefore promising a stable and long term removal of contaminants. It has been estimated that less than 1% of the total microbial population in the land environment and even less in the marine environment have been successfully isolated in pure culture. Marmara Sea has great importance not only because of geological position but also its composition of microbial life which still remains in darkness. The microbial diversity in this unique ecosystem has not been studied using culture-independent molecular techniques yet. Microbial community analyses together with chemical analyses of the sediments will undoubtly form a base to develop bioremediation strategies to overcome chronic pollution at the Küçükçekmece coast. Main aim of this study is to find a suitable microbial community in anoxic sediments taken from Marmara Sea for a bioremediation strategy depending on anaerobic biodegradation. The microbial diversity and community structure were analyzed by Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rDNA Clone Library method. The results were evaluated with sediment quality parameters along the sampling point. Established results will be used with other information from the literature to analyze the suitability of any of the community in the anoxic sediments from the Küçükçekmeçe coast for bioremediation purposes. Suitable communities will be marked and used as a cornerstone for a bioremediation strategy based on anaerobic biodegradation. DGGE results indicate presence of 34 different bands for bacterial community and 15 different bands for archaeal community with each band representing a different organism. Clone library results are parallel to results of DGGE. In bacterial clone library there are 23 different clones and 26 different clones for September 05 and December 06 respectively. In archaeal 16S rDNA clone library, 19 different clones and 20 different clones were found in September 05 and December 06 respectively. The result of sequencing of bacterial dominant clones indicate presence of Trichococcus pasteurii, Clostridium glycolicum in September 05 and Elbe River snow isolate Iso26, Xanthomonas sp. CC-FH5, and Gallicola barnesae in December 06. Archaeal dominant clones are Methanoplanus petrolearius, Methanoplanus limicola, Methanogenium organophilum in September 05 and Methanogenium frigidum and Methanosaeta sp. in December 06. Results of clone library generation show that syntrophic relations are running in both times. In September 05, fermentation and hydrogenotrophic methanogenesis dominated pathway. In December 06, anaerobic respiration and fermentation coupled with acetoclastic and hydrogenotrophic methanogenesis dominated the pathway.