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Metaproteomic analysis of bacterial communities in marine mudflat aquaculture sediment

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Abstract

Bacteria living in marine sediment play crucial roles in the benthic–pelagic interface coupling process. However, the complexity of the marine environment and the abundance of interfering materials hamper metaproteomic research of the marine mudflat environment. In this study, a modified sequential protein extraction method was used for marine mudflat sediment metaproteomic investigation. For marine sediment samples in cultured clam mudflat, more than 1000 protein spots were visualized in a two-dimensional gel electrophoresis map and 78 % of 194 randomly selected spots were successfully identified by mass spectrometry. We further applied this method to compare long-term clam aquaculture and natural mudflat sediment and identified 53 altered proteins from different microbe resources, which belonged to different functional categories or metabolic pathways. We found that proteins involved in stress/defense response process, ATP regeneration and protein folding more inclined to increase abundance while arginine biosynthesis and signal transduction process related proteins preferred to decrease in clam cultured mudflat sediment. Meanwhile, proteins were abundant in pathogens of bivalves, such as Vibrio and Photobacterium, and decreased in Acinetobacter, after about 8 months clam cultured. Furthermore, the terminal restriction fragment length polymorphism assay was performed to compare microbial community composition between sediments mentioned above. Results showed that the top three enrich genera in natural sediment were Cytophaga, Butyrivibrio and Spirochaeta, while Cytophaga, Spirochaeta and Azoarcus were found enrichment in long-term mudflat aquaculture sediment.

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Acknowledgments

This work was sponsored by the National Natural Science Foundation of China (No. 31200105 41276133, 31470238 and J1210050), the Fujian Agricultural and Forestry University Foundation for Distinguished Young Scholars (No. XJQ201201), the Fundamental Research Funds for the Central Universities (CXB2011020) and the Special Research Foundation for Public Welfare Marine Program (No. 201005012).

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    Authors and Affiliations

    1. Marine Biodiversity and Global Change Research Center (MBiGC), College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People’s Republic of China

      Rui Lin & Wenjing Zhang

    2. Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University), Fuzhou, 350002, People’s Republic of China

      Rui Lin, Xiangmin Lin, Tingting Guo, Linkun Wu & Wenxiong Lin

    3. Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, People’s Republic of China

      Xiangmin Lin, Tingting Guo, Linkun Wu & Wenxiong Lin

    4. National Institute of Biological Sciences, Beijing, 102206, People’s Republic of China

      Rui Lin

    5. Agroecological Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People’s Republic of China

      Wenxiong Lin

    6. College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, People’s Republic of China

      Wenjing Zhang

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    1. Rui Lin
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    Rui Lin and Xiangmin Lin have contributed equally to this work.

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    Lin, R., Lin, X., Guo, T. et al. Metaproteomic analysis of bacterial communities in marine mudflat aquaculture sediment. World J Microbiol Biotechnol 31, 1397–1408 (2015). https://doi.org/10.1007/s11274-015-1891-5

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