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Pollution and Environmental Stressors Modulate the Microbiome in Estuarine Mangroves:A Metagenome Analysis


Affiliations
1 Molecular Biology Research Laboratory, Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune 411 007, India
 

The microbial communities of mangroves which form important links in elemental cycling and bioremediation have not been elucidated in most parts of the world. Due to urbanization and deforestation mangroves are also under threat. In the present study, high throughput next generation sequencing technology, based on 16S rRNA amplicon analysis using Illumina platform, was employed to unravel the microbial diversity present in different mangrove areas in the west coast of India. It could be seen that in mangroves, Proteobacteria and Bacteroidetes were most common, followed by taxon such as Firmicutes, Spirochaetes, Chloroflexi and Verrucomicrobia. In proteobacteria group, Gammaproteobacteria, Alphaproteobacteria and Deltaproteobacteria were most abundant. Interestingly, bacteria having the capacity to utilize sulphate were present along with methanogens in all samples, suggesting that anaerobic and sulphur- based metabolic pathways play an important role in these mangrove ecosystems. The differences in bacterial diversity can be partly attributed to biotic and abiotic factors such as physico-chemical characteristics of the samples, geographical location and natural and human-induced changes in the locality. The metagenomics analysis of mangrove sediment samples has helped in elucidating the baseline data on bacterial diversity along mangroves in Maharashtra along the west coast of India and can provide pointers for effective measures of conservation.

Keywords

Anthropogenic Stressors, Bacterial Communities, Metagenomics, Microbial Ecology, Pollution.
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  • Alongi, D. M., Present state and future of the world’s mangrove forests. Environ. Conserv., 2002, 29(3), 331-349.

  • Beck, M. W. et al., The identification, conservation, and management of estuarine and marine nurseries for fish and invertebrates: a better understanding of the habitats that serve as nurseries for marine species and the factors that create site-specific variability in nursery quality will improve conservation and management of these areas. Bioscience, 2001, 51, 633-641.

  • McLusky, D., The Estuarine Ecosystem, Springer Science and Business Media, 2013.

  • Field, C. et al., Mangrove biodiversity and ecosystem function. Global Ecol. Biogeogr. Lett., 1998, 7, 3-14.

  • Duke, N. C. et al., A world without mangroves. Science, 2007, 317, 41.

  • Gomes, N. C. M., Borges, L. R., Paranhos, R., Pinto, F. N., MendonjaHagler, L. C. and Smalla, K., Exploring the diversity of bacterial communities in sediments o f urban mangrove forests. FEMS Microbiol. Ecol., 2008, 66(1), 96-109.

  • DeLong, E. F. et al., Community genomics among stratified microbial assemblages in the ocean’s interior. Science, 2006, 311, 496-503.

  • Konstantinidis, K. T., Braff, J., Karl, D. M. and DeLong, E. F., Comparative metagenomic analysis of a microbial community residing at a depth of 4000 meters at station ALOHA in the North Pacific subtropical gyre. Appl. Environ. Microbiol., 2009, 75(16), 5345-5355.

  • Shi, Y., Tyson, G. W., Eppley, J. M. and DeLong, E. F., Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J., 2010, 5(6), 9991013.

  • Quaiser, A., Zivanovic, Y., Moreira, D. and Lopez-Garcia, P., Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara. ISME J., 2011, 5(2), 285-304.

  • Kimes, N. E. et al., Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill. Front. Microbiol., 2013, 4, 50; doi:10.3389/fmicb.2013.00050.

  • Tringe, S. G. et al., Comparative metagenomics of microbial communities. Science, 2005, 308, 554-557.

  • De Angelis, K. M. et al., Strategies for enhancing the effectiveness of metagenomic based enzyme discovery in lignocellulolytic microbial communities. Bioenergy Res., 2010, 3(2), 146-158.

  • Baldrian, P. et al., Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J , 2012, 6, 248-258.

  • Fierer, N. et al., Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl. Acad. Sci. USA, 2012, 109, 21390-21395.

  • Simon, C., Wiezer, A., Strittmatter, A. W. and Daniel, R., Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Appl. Environ. Microbiol., 2009, 75(23), 75197526.

  • Bodaker, I. et al., Comparative community genomics in the Dead Sea, an increasingly extreme environment. ISME J., 2010, 4, 399407.

  • Inskeep, W. P. et al., Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS ONE, 2010, 5(3), e9773.

  • Amaral-Zettler, L. A. et al., Microbial community structure across the tree of life in the extreme Rio Tinto. ISME J., 2011, 5(1), 4250.

  • Taketani, R. G., Yoshiura, C. A., Dias, A. C. F., Andreote, F. D. and Tsai, S. M., Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove. A van Leeuw J. Microb., 2010, 97(4), 401411.

  • Ghosh, A., Dey, N. and Bera, A., Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarbans, India. Saline Syst., 2010, 6(1), 1; http://dx.doi.org/ 10.1186/1746-1448-6-1.

  • Gomes, N. C. M. et al., Taking ischolar_main, enduring effect of rhizosphere bacterial colonization in mangroves. PLoS ONE, 2010, 5(11), e14065.

  • Mishra, R. R., Swain, M. R., Dangar, T. K. and Thatoi, H., Diversity and seasonal fluctuation of predominant microbial communities in Bhitarkanika, a tropical mangrove ecosystem in India. Rev. Biol. Trop., 2012, 60(2), 909-924.

  • Jiang, X. T., Peng, X., Deng, G. H., Sheng, H. F., Wang, Y. and Zhou, H. W., Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland. Microb. Ecol., 2013, 66, 96-104.

  • Basak, P. et al., Spatiotemporal analysis o f bacterial diversity in sediments of Sundarbans using parallel 16S rRNA gene tag sequencing. Microb. Ecol., 2014, 69, 500-511.

  • Prakash, S. et al., Influence of physicochemical and nutritional factors on bacterial diversity in mangrove sediments along the southwest coast of Tamil Nadu, India. Environ. Monit. Assess., 2015, 187, 562.

  • Basak, P. et al., Bacterial diversity assessment of pristine mangrove microbial community from Dhulibhashani, Sundarbans using 16S rRNA gene tag sequencing. Genom. Data, 2016, 7, 7678.

  • Upadhyay, V. P., Ranjan, R. and Singh, J. S., Human-mangrove conflicts: the way out. Curr. Sci., 2002, 83, 1328-1336.

  • Giri, C. et al., Status and distribution of mangrove forests of the world using earth observation satellite data. Global Ecol. Biogeogr., 2011, 20, 154-159.

  • Sahu, S. C., Suresh, H. S., Murthy, I. K. and Ravindranath, N. H., Mangrove area assessment in India, implications of loss of mangroves. J. Earth Sci. Clim. Change, 2015, 6, 280; doi:10.4172/ 2157-7617.1000280.

  • Kulkarni, R., Deobagkar, D. and Zinjarde, S., Metals in mangrove ecosystems and associated biota: a global perspective. Ecotoxicol. Environ. S a f, 2018, 153, 215-228.

  • Jha, S. K., Chavan, S. B., Pandit, G. G., Negi, B. S. and Sadasivan, S., Behaviour and fluxes of trace and toxic elements in creek sediment near Mumbai, India. Environ. Monit. Assess., 2002, 76, 249-262.

  • Fernandes, L., Nayak, G. N., Ilangovan, D. and Borole, D. V., Accumulation o f sediment, organic matter and trace metals with space and time, in a creek along Mumbai coast, India. Estuar. Coast S h e lf Sci., 2011, 91, 388-399.

  • Kandasamy, K. A., Review o f studies on Pichavaram mangrove, Southeast India. Hydrobiologia, 2000, 430(1), 185-205.

  • Ragavan, P., Mohan, P. M., Saxena, A., Jayaraj, R. S. C., Ravichandran, K. and Saxena, M., Mangrove floristics of the Andaman and Nicobar Islands: critical review and current scenario Mar. Biodivers., 2016, 48, 1291-1311; https://doi.org/10.1007/s12526-0160581-3.

  • Andreote, F. D. et al., The microbiome o f Brazilian mangrove sediments as revealed by metagenomics. PLoS ONE, 2012, 7(6), e38600.

  • Alzubaidy, H. et al., Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea. Gene, 2016, 576, 626-636.

  • Salter, S. J. et al., Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol., 2014, 12(1), 87.

  • Bagwell, C. E., La Rocque, J. R., Smith, G. W., Polson, S. W., Friez. M. J., Longshore, J. W. and Lovell, C. R., Molecular diversity of diazotrophs in oligotrophic tropical seagrass bed communities. FEMS Microbiol. E col, 2002, 39, 113-119.

  • Bird, C., Martinez, J. M., O’Donnell, A. G. and Wyman, M., Spatial distribution and transcriptional activity of an uncultured clade of planktonic diazotrophic y-proteobacteria in the Arabian Sea. Appl. Environ. Microbiol., 2005, 71, 2079-2085.

  • Church, M. J., Short, C. M., Jenkins, B. D., Karl, D. M. and Zehr, J. P., Temporal patterns of nitrogenase gene (nifH) expression in the oligotrophic North Pacific Ocean. Appl. Environ. Microbiol., 2005, 71, 5362-5370.

  • Kim, S. J. and Kwon, K. K., Bacteroidetes, Handbook of Hydrocarbon and Lipid Microbiology, 2010, pp. 1813-1817.

  • Lyimo, T. J., Pol, A. and Op den Camp, H. J. M., Methane emission, sulphide concentration and redox potential profiles in Mtoni mangrove sediment, Tanzania. Western Indian Ocean J. Mar. Sci., 2002, 1, 71-80.

  • Lyimo, T. J., Pol, A. and Op den Camp, H. J. M., Sulfate reduction and methanogenesis in sediments of Mtoni mangrove forest, Tanzania. Ambio, 2002, 31, 614-616.

  • Muyzer, G. and Stams, A. J., The ecology and biotechnology of sulphate-reducing bacteria. Nat. Rev. Microbiol., 2008, 6(6), 441-454.

  • Alongi, D. M., Boto, K. G. and Robertson, A. I., Nitrogen and Phosphorus Cycles in Tropical Mangrove Ecosystems, Am Geophys Univ, Washington DC, 1992, vol. 41, pp. 251-292.

  • Rodriguez, H. and Fraga, R., Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol. Adv., 1999, 17(4-5), 319-339.


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  • Pollution and Environmental Stressors Modulate the Microbiome in Estuarine Mangroves:A Metagenome Analysis

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Authors

Mandar S. Paingankar
Molecular Biology Research Laboratory, Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune 411 007, India
Deepti D. Deobagkar
Molecular Biology Research Laboratory, Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune 411 007, India

Abstract


The microbial communities of mangroves which form important links in elemental cycling and bioremediation have not been elucidated in most parts of the world. Due to urbanization and deforestation mangroves are also under threat. In the present study, high throughput next generation sequencing technology, based on 16S rRNA amplicon analysis using Illumina platform, was employed to unravel the microbial diversity present in different mangrove areas in the west coast of India. It could be seen that in mangroves, Proteobacteria and Bacteroidetes were most common, followed by taxon such as Firmicutes, Spirochaetes, Chloroflexi and Verrucomicrobia. In proteobacteria group, Gammaproteobacteria, Alphaproteobacteria and Deltaproteobacteria were most abundant. Interestingly, bacteria having the capacity to utilize sulphate were present along with methanogens in all samples, suggesting that anaerobic and sulphur- based metabolic pathways play an important role in these mangrove ecosystems. The differences in bacterial diversity can be partly attributed to biotic and abiotic factors such as physico-chemical characteristics of the samples, geographical location and natural and human-induced changes in the locality. The metagenomics analysis of mangrove sediment samples has helped in elucidating the baseline data on bacterial diversity along mangroves in Maharashtra along the west coast of India and can provide pointers for effective measures of conservation.

Keywords


Anthropogenic Stressors, Bacterial Communities, Metagenomics, Microbial Ecology, Pollution.

References





DOI: https://doi.org/10.18520/cs%2Fv115%2Fi8%2F1525-1535