Refine your search
Collections
Co-Authors
Journals
Year
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z All
Sam, Choon-Kook
- Tropical Mangrove Swamp Metagenome Reveals Unusual Abundance of Ecologically Important Microbes
Abstract Views :264 |
PDF Views:96
Authors
Affiliations
1 Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, MY
2 Natural Sciences and Science Education AG, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, 637616, SG
1 Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, MY
2 Natural Sciences and Science Education AG, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, 637616, SG
Source
Current Science, Vol 112, No 08 (2017), Pagination: 1698-1703Abstract
The tropical ecosystem is extremely rich in flora and fauna, but the tropical mangrove soil microbial diversity remains illusive. To address this knowledge gap, we characterized the metagenome of a Malaysian mangrove soil sample and its microbial ecological roles via next-generation sequencing (NGS). Shotgun NGS data analysis revealed high diversity of ecologically important microbes from bacteria and archaea domains. Also, an unusually high number of archaea was detected together with high abundance of Deltaproteobacteria. In a functional study by the SEED classification in MEGAN, virulence factor genes were abundantly present, implying that the mangrove soil is a potential reservoir of pathogens.Keywords
Mangrove, Metagenomics, Pathogens, Soil.Full Text
References
- Tama, N. F. Y. and Wong, Y. S., Retention and distribution of heavy metals in mangrove soils receiving wastewater. Environ. Pollut., 1996, 94(3), 283–291.
- Holguin, G., Vazquez, P. and Bashan, Y., The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: an overview. Biol. Fertil. Soils, 2001, 33, 265–278.
- Sahoo, K. and Dhal, N. K., Potential microbial diversity in mangrove ecosystems: a review. Indian J. Mar. Sci., 2009, 38(2), 249– 256.
- Sengupta, A. and Chaudhuri, S., Ecology of heterotrophic denitrogen fixation in the rhizosphere of mangrove plant community at the Ganges river estuary in India. Oecologia, 1991, 87, 560–564.
- Holguin, G., Guzman, M. A. and Bashan, Y., Two new nitrogenfixing bacteria from the rhizosphere of mangrove trees: their isolation, identification and in vitro interaction with rhizosphere Staphylococcus sp. FEMS Microbiol. Ecol., 1992, 101, 207–216.
- Alongi, D. M., Christoffersen, P. and Tirendi, F., The influence of forest type on microbial nutrient relationships in tropical mangrove sediments. J. Exp. Mar. Biol. Ecol., 1993, 171(2), 201–223.
- Vazquez, P., Holguin, G., Puente, M. E., Lopez-Cortes, A. and Bashan, Y., Phosphate-solubilizing microorganisms associated with the rhizosphere of mangroves in semiarid coastal lagoon. Biol. Fertil. Soils, 2000, 30, 460–468.
- Andreote, F. D. et al., The microbiome of Brazilian mangrove sediments as revealed by metagenomics. PLoS ONE, 2012; doi: 10.1371/journal.pone.0038600.
- Xu, Z., Hansen, M. A., Hansen, L. H., Jacquiod, S. and Sørensen, S. J., Bioinformatic approaches reveal metagenomic characterization of soil microbial community. PLoS ONE, 2014, 9(4), e93445; doi:10.1371/journal.pone.0093445.
- Paul, E. A., Soil Microbiology, Ecology and Biochemistry, Elsevier Inc., UK, 2007, 3rd edn, pp. 389–430.
- Zhou, J., Bruns, M. A. and Tiedje, J. M., DNA recovery from soils of diverse composition. Appl. Environ. Microbiol., 1996, 62(2), 316–322.
- Hyatt, D., LoCascio, P. F., Hauser, L. J. and Uberbacher, E. C., Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics, 2012, 28(17), 2223–2230.
- Ye, Y, Choi, J. H. and Tang, H., RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinfor., 2011, doi:10.1186/1471-2105-12-159.
- Zhao, Y., Tang, H. and Ye, Y., RAPSearch2: a fast and memoryefficient protein similarity search tool for next generation sequencing data. Bioinformatics, 2012, 28(1), 125–126.
- Huson, D. H., Mitra, S., Weber, N., Ruscheweyh, H. J., Weber, N. and Schuster, S. C., Integrative analysis of environmental sequences using MEGAN4. Genome Res., 2011, 21, 1552–1560.
- Disz, T. et al., Accessing the SEED genome databases via web services API: tools for programmers. BMC Bioinfor., 2010; doi:10.1186/1471-2105-11-319.
- Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knightm R. and Fierer, N., Examining the global distribution of dominant archaeal populations in soil. ISME J., 2011, 5(5), 908– 917.
- Hou, W. et al., A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S RNA gene pyrosequencing. PLoS ONE, 2013; doi: 10.1371/journal.pone.0053350.
- Janssen, P. H., Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol., 2006, 72(3), 1719–1728.
- dos Santos, H. F. et al., Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. PLoS ONE, 2011; doi:10.1371/ journal.pone.0016943.
- Jeffries, T. C. et al., Substrate type determines metagenomic profiles from diverse chemical habitats. PLoS ONE, 2011, 6(9), e25173; doi:10.1371/journal.pone.0025173.
- Ghosh, A., Dey, N., Bera, A., Tiwari, A., Sathyaniranjan, K. B., Chakrabarti, K. and Chattopadhyay, D., Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India. Saline Syst., 2010, 6, 1; doi: 10.1186/1746-1448-6-1.
- Blöthe, M., Akob, D. M., Kostka, J. E., Göschel, K., Drake, H. L. and Küsel, K., pH gradient-induced heterogeneity of Fe(III)reducing microorganisms in coal mining-associated lake sediments. Appl. Environ. Microbiol., 2008, 74(4), 1019–1029.