Bacterial Diversity of a Microbial Mat from Hot Spring at Wartawan Beach, Lampung and Its Potential as a Source of Hydrogenases

Gintung Patantis, Ekowati Chasanah, Yusro Nuri Fawzya, He Pe Qing, Zhang Xue Lei

Abstract


Biohydrogen produced from thermophilic hydrogenases is an ideal and clean energy sources. As the biggest tectonic area in the world, Indonesia is potential for thermophile isolation. The aims of this study were to analyze the bacterial diversity of a microbial mat from hot spring at Wartawan beach, Lampung and to analyze the potency of microbial mat for hydrogenases, using clone library method. The diversity of 16S rRNA showed that the microbial mat sample contained 9 phyla of bacteria, and dominated by Cyanobacteria and Proteobacteria. These phyla indicate that the bacterial community of the microbial mat consisted of phototrophic and heterotrophic groups. In addition, a microbial mat of Wartawan beach environment might be influenced by marine environment and hydrothermal vent which was indicated by detection of both associated bacteria. The diversity of hydrogenase genes using NiFe hydrogenase (NiFe) and FeFe hydrogenase (FeFe) genes showed that Cyanobacteria was specifically related to NiFe, while Firmicutes was associated with FeFe. Proteobacteria and Bacteroidetes, however, were detected for both genes. The detected hydrogenase genes indicate that the microbial mat from hot spring at Wartawan beach is a promising source for hydrogenases isolation and further applications for biohydrogen production as a renewable energy. 


Keywords


diversity, bacteria, hydrogenases, microbial mat, hot spring Wartawan beach

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Alain, K., Tindall, B. J., Catala, P., Intertaglia, L., & Lebaron, P. (2010). Ekhidna lutea gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from the South East Pacific Ocean. Int. J. Syst. Evol. Microbiol., 60(12), 2972-2978. doi:10.1099/ijs.0.018804-0

Amin, A., Ahmed, I., Salam, N., Kim, B.-Y., Singh, D., Zhi, X.-Y., . . . Li, W.-J. (2017). Diversity and distribution of thermophilic bacteria in hot springs of Pakistan. Microbial Ecol., 74(1), 116-127. doi:10.1007/s00248-017-0930-1

Arun, A., Chen, W.-M., Lai, W.-A., Chou, J.-H., Rekha, P., Shen, F.-T., . . . Young, C.-C. (2009). Parvularcula lutaonensis sp. nov., a moderately thermotolerant marine bacterium isolated from a coastal hot spring. Int. J. Syst. Evol. Microbiol., 59(5), 998-1001. doi:10.1099/ijs.0.004481-0

Baba, R., Asakawa, S., & Watanabe, T. (2016). H2-producing bacterial community during rice straw decomposition in paddy field soil: Estimation by an analysis of [FeFe]-hydrogenase gene transcripts. Microb. Environ., 31(3), 226-233. doi:10.1264/jsme2.ME16036

Barz, M., Beimgraben, C., Staller, T., Germer, F., Opitz, F., Marquardt, C., . . . Schmitz, R. (2010). Distribution analysis of hydrogenases in surface waters of marine and freshwater environments. PLoS One, 5(11), e13846. doi:10.1371/journal.pone.0013846

Boyd, E. S., Spear, J. R., & Peters, J. W. (2009). [FeFe] hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community. Appl. Environ. Microbiol., 75(13), 4620-4623. doi:10.1128/AEM.00582-09

Caires, T. A., de Mattos Lyra, G., Hentschke, G. S., de Gusmão Pedrini, A., Sant'Anna, C. L., & de Castro Nunes, J. M. (2018). Neolyngbya gen. nov.(Cyanobacteria, Oscillatoriaceae): A new filamentous benthic marine taxon widely distributed along the Brazilian coast. Mol. Phylo. Evol., 120, 196-211. doi:10.1016/j.ympev.2017.12.009

Calusinska, M., Happe, T., Joris, B., & Wilmotte, A. (2010). The surprising diversity of clostridial hydrogenases: a comparative genomic perspective. Microbiology, 156(6), 1575-1588. doi:10.1099/mic.0.032771-0

Canganella, F., & Wiegel, J. (2011). Extremophiles: from abyssal to terrestrial ecosystems and possibly beyond. Naturwissenschaften, 98(4), 253-279. doi:10.1007/s00114-011-0775-2

Cerritos, R., Vinuesa, P., Eguiarte, L. E., Herrera-Estrella, L., Alcaraz-Peraza, L. D., Arvizu-Gomez, J. L., . . . Souza, V. (2008). Bacillus coahuilensis sp. nov., a moderately halophilic species from a desiccation lagoon in the Cuatro Cienegas Valley in Coahuila, Mexico. Int. J. Syst. Evol. Microbiol., 58(4), 919-923. doi:10.1099/ijs.0.64959-0

Chen, J., Hanke, A., Tegetmeyer, H. E., Kattelmann, I., Sharma, R., Hamann, E., . . . Geelhoed, J. S. (2017). Impacts of chemical gradients on microbial community structure. The ISME J., 11(4), 920. doi:10.1038/ismej.2016.175

Crapart, S., Fardeau, M.-L., Cayol, J.-L., Thomas, P., Sery, C., Ollivier, B., & Combet-Blanc, Y. (2007). Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent. Int. J. Syst. Evol. Microbiol., 57(2), 287-292. doi:10.1099/ijs.0.64639-0

Das, D., & Veziroglu, T. N. (2008). Advances in biological hydrogen production processes. Int. J. Hyd. Energy, 33(21), 6046-6057. doi:10.1016/j.ijhydene.2008.07.098

Davidova, I. A., Duncan, K. E., Choi, O. K., & Suflita, J. M. (2006). Desulfoglaeba alkanexedens gen. nov., sp. nov., an n-alkane-degrading, sulfate-reducing bacterium. Int. J. Syst. Evol. Microbiol., 56(12), 2737-2742. doi:10.1099/ijs.0.64398-0

Eberly, J. O., & Ely, R. L. (2008). Thermotolerant hydrogenases: biological diversity, properties, and biotechnological applications. Critical Rev. Microbiol., 34(3-4), 117-130. doi:10.1080/10408410802240893

Engel, A. S., Porter, M. L., Stern, L. A., Quinlan, S., & Bennett, P. C. (2004). Bacterial diversity and ecosystem function of filamentous microbial mats from aphotic (cave) sulfidic springs dominated by chemolithoautotrophic “Epsilonproteobacteria”. FEMS Microbiol. Ecol., 51(1), 31-53. doi:10.1016/j.femsec.2004.07.004

Fang, H. H., Zhang, T., & Li, C. (2006). Characterization of Fe-hydrogenase genes diversity and hydrogen-producing population in an acidophilic sludge. J. Biotechnol., 126(3), 357-364. doi:10.1016/j.jbiotec.2006.04.023

Fourçans, A., Solé, A., Diestra, E., Ranchou‐Peyruse, A., Esteve, I., Caumette, P., & Duran, R. (2006). Vertical migration of phototrophic bacterial populations in a hypersaline microbial mat from Salins‐de‐Giraud (Camargue, France). FEMS Microbiol. Ecol., 57(3), 367-377. doi:10.1111/j.1574-6941.2006.00124.x

Fullerton, H., Hager, K. W., McAllister, S. M., & Moyer, C. L. (2017). Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i. The ISME J., 11(8), 1900. doi:10.1038/ismej.2017.40

Good, I. J. (1953). The population frequencies of species and the estimation of population parameters. Biometrika, 40(3-4), 237-264.

Greening, C., Biswas, A., Carere, C. R., Jackson, C. J., Taylor, M. C., Stott, M. B., . . . Morales, S. E. (2016). Genomic and metagenomic surveys of hydrogenase distribution indicate H 2 is a widely utilised energy source for microbial growth and survival. The ISME J., 10(3), 761. doi:10.1038/ismej.2015.153

Guerrero, R., Piqueras, M., & Berlanga, M. (2002). Microbial mats and the search for minimal ecosystems. Int. Microbiol., 5(4), 177-188. doi:10.1007/s10123-002-0094-8

Hager, K. W., Fullerton, H., Butterfield, D. A., & Moyer, C. L. (2017). Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc. Front. Microbiol., 8, 1578. doi:10.3389/fmicb.2017.01578

Hao, O. J., Chen, J. M., Huang, L., & Buglass, R. L. (1996). Sulfate‐reducing bacteria. Critical Rev. Environ. Sci. Technol., 26(2), 155-187. doi:10.1080/10643389609388489

http://maps.google.co.id/. Retrieved from http://maps.google.co.id/

Jungblut, A. D., Hawes, I., Mackey, T. J., Krusor, M., Doran, P. T., Sumner, D. Y., . . . Goroncy, A. K. (2016). Microbial mat communities along an oxygen gradient in a perennially ice-covered Antarctic lake. Appl. Environ. Microbiol., 82(2), 620-630. doi:10.1128/AEM.02699-15

Karadag, D., Mäkinen, A. E., Efimova, E., & Puhakka, J. A. (2009). Thermophilic biohydrogen production by an anaerobic heat treated-hot spring culture. Bioresource Technol., 100(23), 5790-5795. doi:10.1016/j.biortech.2009.06.035

Khan, S. T., Fukunaga, Y., Nakagawa, Y., & Harayama, S. (2007). Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov. Int. J. Sys. Evol. Microbiol., 57(12), 2946-2951. doi:10.1099/ijs.0.65308-0

Kim, D.-H., & Kim, M.-S. (2011). Hydrogenases for biological hydrogen production. Bioresource Technol., 102(18), 8423-8431. doi:10.1016/j.biortech.2011.02.113

Kothari, A., Potrafka, R., & Garcia-Pichel, F. (2012). Diversity in hydrogen evolution from bidirectional hydrogenases in cyanobacteria from terrestrial, freshwater and marine intertidal environments. J. Biotechnol., 162(1), 105-114. doi:10.1016/j.jbiotec.2012.04.017

Kruse, F. (1999). Mapping hot spring deposits with AVIRIS at Steamboat Springs, Nevada. Paper presented at the Proceedings of the 8th JPL Airborne Earth Science Workshop: Jet Propulsion Laboratory Publication 99.

Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol., 33(7), 1870-1874. doi:10.1093/molbev/msw054

Lau, M. C., Aitchison, J. C., & Pointing, S. B. (2009). Bacterial community composition in thermophilic microbial mats from five hot springs in central Tibet. Extremophiles, 13(1), 139-149. doi:10.1007/s00792-008-0205-3

Lee, S. D. (2007). Lewinella agarilytica sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from beach sediment. Int. J. Sys. Evol. Microbiol., 57(12), 2814-2818. doi:10.1099/ijs.0.65254-0

Lemos, L. N., Fulthorpe, R. R., Triplett, E. W., & Roesch, L. F. (2011). Rethinking microbial diversity analysis in the high throughput sequencing era. J. of Microbiol. Methods, 86(1), 42-51. doi:10.1016/j.mimet.2011.03.014

Li, C., & Fang, H. H. (2007). Fermentative hydrogen production from wastewater and solid wastes by mixed cultures. Critical Rev. Environ. Sci.Technol., 37(1), 1-39. doi:10.1080/10643380600729071

Minnan, L., Jinli, H., Xiaobin, W., Huijuan, X., Jinzao, C., Chuannan, L., . . . Liangshu, X. (2005). Isolation and characterization of a high H2-producing strain Klebsiella oxytoca HP1 from a hot spring. Research Microbiol., 156(1), 76-81. doi:10.1016/j.resmic.2004.08.004

Morris, E. K., Caruso, T., Buscot, F., Fischer, M., Hancock, C., Maier, T. S., . . . Prati, D. (2014). Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories. Ecol. Evol., 4(18), 3514-3524. doi:10.1002/ece3.1155

Moyer, C. L., Dobbs, F. C., & Karl, D. M. (1995). Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol., 61(4), 1555-1562.

Nandi, R., & Sengupta, S. (1998). Microbial production of hydrogen: an overview. Critical Rev. Microbiol., 24(1), 61-84.

Oh, H.-M., Lee, K., & Cho, J.-C. (2009). Lewinella antarctica sp. nov., a marine bacterium isolated from Antarctic seawater. Int. J. Sys. Evol. Microbiol., 59(1), 65-68. doi:10.1099/ijs.0.000794-0

Preisner, E. C., Fichot, E. B., & Norman, R. S. (2016). Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance. Front. Microbiol., 7, 1632. doi:10.3389/fmicb.2016.01632

Puggioni, V., Tempel, S., & Latifi, A. (2016). Distribution of Hydrogenases in Cyanobacteria: A Phylum-Wide Genomic Survey. Front. Genet., 7, 223. doi:10.3389/fgene.2016.00223

Quéméneur, M., Hamelin, J., Benomar, S., Guidici-Orticoni, M.-T., Latrille, E., Steyer, J.-P., & Trably, E. (2011). Changes in hydrogenase genetic diversity and proteomic patterns in mixed-culture dark fermentation of mono-, di-and tri-saccharides. Int. J. Hyd. Energy, 36(18), 11654-11665. doi:10.1016/j.ijhydene.2011.06.010

Schieber, J., Bose, P. K., Eriksson, P., Banerjee, S., Sarkar, S., Altermann, W., & Catuneanu, O. (2007). Atlas of microbial mat features preserved within the siliciclastic rock record (Vol. 2): Elsevier.

Schmidt, O., Drake, H. L., & Horn, M. A. (2010). Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen. Appl. Environ. Microbiol., 76(6), 2027-2031. doi:10.1128/AEM.02895-09

Scott, J. J., Breier, J. A., Luther III, G. W., & Emerson, D. (2015). Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems. PLoS One, 10(3), e0119284. doi:10.1371/journal.pone.0119284

Selvarajan, R., Sibanda, T., & Tekere, M. (2017). Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron‐rich) thermal springs: Diversity and biotechnological analysis. MicrobiologyOpen, 560, 1-12. doi:10.1002/mbo3.560

Show, K., Lee, D., Tay, J., Lin, C., & Chang, J. (2012). Biohydrogen production: current perspectives and the way forward. Int. J. Hyd. Energy, 37(20), 15616-15631. doi:10.1016/j.ijhydene.2012.04.109

Silva, S. M., & Pienaar, R. N. (2000). Benthic Marine Cyanophyceae from Kwa-Zulu Natal,-South Africa. Berlin: J Cramer.

Tamagnini, P., Leitão, E., Oliveira, P., Ferreira, D., Pinto, F., Harris, D. J., . . . Lindblad, P. (2007). Cyanobacterial hydrogenases: diversity, regulation and applications. FEMS Microbiol. Rev., 31(6), 692-720. doi:0.1111/j.1574-6976.2007.00085.x

Vignais, P. M., Billoud, B., & Meyer, J. (2001). Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev., 25(4), 455-501. doi:10.1111/j.1574-6976.2001.tb00587.x

Ward, D. M., Ferris, M. J., Nold, S. C., & Bateson, M. M. (1998). A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol. Mol. Biol. Rev., 62(4), 1353-1370.

Xing, D., Ren, N., & Rittmann, B. E. (2008). Genetic diversity of hydrogen-producing bacteria in an acidophilic ethanol-H2-coproducing system, analyzed using the [Fe]-hydrogenase gene. Appl. Environ. Microbiol., 74(4), 1232-1239. doi:10.1128/AEM.01946-07

Xu, S.-Y., He, P.-Q., Dewi, S.-Z., Zhang, X.-L., Ekowati, C., Liu, T.-J., & Huang, X.-H. (2013). Hydrogen-producing microflora and Fe–Fe hydrogenase diversities in seaweed bed associated with marine hot springs of Kalianda, Indonesia. Curr. Microbiol., 66(5), 499-506. doi:10.1007/s00284-013-0302-0

Yi, H., & Chun, J. (2006). Thalassobius aestuarii sp. nov., isolated from tidal flat sediment. The J. Microbiol., 44(2), 171-176.

Zilda, D. S., Harmayani, E., Widada, J., Asmara, W., Irianto, H. E., Patantis, G., & Fawzya, Y. N. (2012). Screening of thermostable protease producing microorganisms isolated from Indonesian hotspring. Squalen Bull. Mar. Fish. Postharvest Biotech., 7(3), 105-114. doi:10.15578/squalen.v7i3.5

Zilda, D. S., Kusumarini, A., & Chasanah, E. (2008). Penapisan dan Karakterisasi Protease dari Bakteri Termo-Asidofilik P5-A dari Sumber Air Panas Tambarana. Jurnal Pascapanen dan Bioteknologi Kelautan dan Perikanan, 3(2), 113-121. doi:10.15578/jpbkp.v3i2.17

Zilda, D. S., Patantis, G., & Chasanah, E. (2009). The use of restriction fragment length polymorphism (RFLP) technique for assessing genetic diversity of thermophilic bacteria. J. Mar. Fish. Postharvest Biotec., 4, 37-43.




DOI: http://dx.doi.org/10.15578/squalen.v13i1.323

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