Abstract
In this study, the sulfate-reducing bacteria, (SRB) were identified and reported for the first time through analysis of functional gene dsrAB, from the DNA of sediment samples collected from 10 sites of the Chilika lake. The finding illustrates Forty six Operational Taxonomic Units (OTUs), identified from the DGGE which were obtained from the 10 sediment samples. Of these, 34 OTUs exhibited around 78–96% sequence similarity and 12 OTUs showed 97 to 100% sequence similarity to the dsrAB gene of reported type strains of SRB. The sequence information obtained revealed the presence and distribution of diverse types of SRB which include phylotypes related to Desulfovibrio, Desulfonatronovibrio, Desulfomicrobium, Desulfobotulous and Desulfobacca. Upon comparison of dsrAB gene sequences of SRB obtained through this study with those collected from the GenBank, and through the dendrogram constructed, it was observed that except 13 OTUs that clustered closely with the reported type strains, all other 36 OTUs clustered distantly and had no representative member of SRB. This indicated the presence of phylogenetically diverse groups of SRB inhabiting the lake Chilika.
Similar content being viewed by others
References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Barnes SP, Bradbrook SD, Cragg BA (1998) Isolation of sulfate reducing bacteria from deep sea sediment layers of Pacific Ocean. Geomicrobiol J 15:67–83. https://doi.org/10.1080/01490459809378066
Barton LL (1995) Sulfate reducing bacteria. In: Atkinson T, Sherwood RF Biotechnology handbooks-8. Series Kluwer Academic/ Plenum Publishers, New York
Bidle KA, Kastner M, Bartlett DH (1999) A phylogenetic analysis of microbial communities associated with the methane hydrate containing marine fluids and sediments in the Cascadia Margin (ODP site 892B). FEMS Microbiol Lett 177:101–108. https://doi.org/10.1111/j.1574-6968.1999.tb13719.x
Bussmann I, Reichirdt W (1991) Sulfate-reducing bacteria in temporarily oxic sediments with bivalves. Mar Ecol Prog Ser 78:97–102
Coolen MJL, Cypionka H, Sass AM, Sass, Overmann J (2002) Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296:2407–2410. https://doi.org/10.1126/science.1071893
Crill PM, Martens CS (1987) Biogeochemical cycling in an organic rich coastal marine basin. Temporal and spatial variations in sulfate reduction rates. Geochim Cosmochim Acta 51:1175–1186. https://doi.org/10.1016/0016-7037(87)90210-9
D’Hondt S, Jørgensen BB, Miller DJ (2004) Distribution of microbial activity in deep sub seafloor sediments. Science 306:2216–2221. https://doi.org/10.1126/science.1101155
Eaton AD, Clesceri LS, Greenberg AE, Franson MAH (2005) Standard methods for the examination of water and wastewater. Am Public Health Assoc 21:1600
Edgcomb VP, McDonald JH, Devereux R, Smith DW (1999) Estimation of bacterial cell numbers in humic-rich salt marsh sediments using probes to 16S rDNA. Appl Environ Microbiol 164:271–279
Fowler CMR (1990) The solid earth, an introduction to global geophysics. Cambridge University Press, Cambridge
Fröhlich-Nowoisky J, Kampf CJ, Weber B, Huffman JA, Pöhlker C, Andreae MO, Su H (2016) Bioaerosols in the Earth system: Climate, health, and ecosystem interactions. Atmos Res 182:346–376. https://doi.org/10.1038/ismej.2016.45
Hansen TA (1993) Carbon metabolism of sulfate reducing bacteria. In: Odum JM, Singleton R (eds) The sulfate reducing bacteria. Springer Verlag, New York, pp 21–40
Henrichs SM, Reeburgh WS (1987) Anaerobic mineralization of marine sediment organic matter: rates and the role of anaerobic processes in the oceanic carbon economy. Geo Microbiol J 5:191–237. https://doi.org/10.1080/01490458709385971
Hill KD, Dauphinee TM, Woods DJ (1989) The uniqueness of the practical salinity scale (1978): testing the scale with natural seawaters. IEEE J Oceanic Eng 14:265–267. https://doi.org/10.1109/48.29606
Hines ME, Evans RS, Genthner BRS, Willis SG, Friedman S, Rooney-Verga JN, Devereux R (1999) Molecular phylogenetic and biogeochemical studies of Sulfate reducing bacteria in the rhizosphere of Spartina alterniflora. Appl Environ Microbiol 65:2209–2216
Jørgensen BB (1983) Processes at the sediment water interface. In: Bolin B, Cook RB (eds) The major biochemical cycles and their interactions. Wiley, Chichester, pp 447–515
Karr EA, Sattley WM, Rice MR, Jung DO, Madigan MT, Achenbach LA (2005) Diversity and distribution of sulfate-reducing bacteria in permanently frozen LakeFryxell McMurdo Dry Valleys Antarctica. Appl Environ Microbiol 71:6353–6359. https://doi.org/10.1128/AEM.71.10.6353-6359.2005
Köpke B, Wilms R, Engelen B, Cypionka H, Sass H (2005) Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiol 71:7819–7830. https://doi.org/10.1128/AEM.71.12.7819-7830.2005
Llobet-Brossa E, Rabus R, Bötcher ME, Könneke M, Finke N, Schramm A (2002) Community structure and activity of sulfate reducing bacteria in an inter tidal surface sediment: a multi-method approach. Aquat Microbiol Ecol 29:221–226. https://doi.org/10.3354/ame029211
Manabu F, Susumu T (1996) Microdistribution of sulfate-reducing bacteria in sediments of a hypertrophic lake and their response to the addition of organic matter. Ecol Res 11:257–267
Mohanty PK, Panda B (2009) Circulation & mixing processes in Chilika Lagoon. Indian J Mar Sci 38:205–214. http://nopr.niscair.res.in/handle/123456789/4671
Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700
Sahm K, MacGregor BJ, Jorgensen B, Stahl DA (1999) Sulfate reduction and vertical distribution of sulfate reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment. Environ Microbiol 1:56–74. https://doi.org/10.1046/j.1462-2920.1999.00007.x
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467. https://doi.org/10.1073/pnas.74.12.5463
Schink B, Stams AJ (2013) Syntrophism among prokaryotes. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E , Thompson T (eds) The Prokaryotes-Prokaryotic Communities and Ecophysiology. Springer, Berlin, pp 471–493
Stahl DA, Fishbain S, Klein M, Baker BJ, Wanger W (2002) Origins and diversification of Sulfate-respiring microorganisms. Antonie Leeuwenhoek 81:189–195
Sucharita K, Sasikala C, Ramana CV (2010) Thiorhodococcus modestalkaliphilus sp. nov. a phototrophic gamma proteobacterium from Chilika salt water lagoon, India. J Gen Appl Microbiol 56:93–99. https://doi.org/10.2323/jgam.56.93
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. https://doi.org/10.1093/molbev/mst197
Tanimoto Y, Bak F (1994) Anaerobic degradation of methylmercaptan and dimethyl sulfide by newly isolated thermophilic sulfate reducing bacteria. Appl Environ Microbiol 60:2450–2455
Teske A, Ramsingh NB, Habicht K, Fukui M, Kuver J, Jorgensen BB, CohenY (1998) Sulfate reducing bacteria and their activities in cyanobacterial mats of Solar lake(Sinai, Egypt). Appl Environ Microbiol 64:2943–2951
Throckmorton HM, Heikoop JM, Newman BD, Altmann GL, Conrad MS, Muss JD, Wilson CJ (2015) Pathways and transformations of dissolved methane and dissolved inorganic carbon in Arctic tundra watersheds: Evidence from analysis of stable isotopes. Glob Biogeochem Cycles 29:1893–1910. https://doi.org/10.1002/2014GB005044
Wanger M, Roger AJ, Flax JL, Brusseau GA, Stahl DA (1998) Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacteriol 180:2975–2982
Widdel F, Bak F (1992) Gram-negative mesophilic sulfate-reducing bacteria. In: Balows A, TrIn Balows AHG, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, 2nd edn. Springer, New York, pp 3352–3378. https://doi.org/10.1007/978-1-4757-2191-1_21
Acknowledgements
TS Sasi Jyothsna thanks CSIR for the award of research fellowship. Financial assistance received from DBT and DST (FIST) is acknowledged. We thank Ms. Azmatunnisa for the technical support. Also, I would like to extend my gratitude to Dr. B. Chakradhar, Director, RESPL, for critically reviewing the manuscript and serving as scientific advisor.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors state no conflict of interest for this work.
Rights and permissions
About this article
Cite this article
Tadinada, S.S.J., Kamidi, R., Dutta, S. et al. Phylogenetic diversity of sulfate-reducing bacteria of sediments of Chilika Lake, India, determined through analysis of the dissimilatory sulfite reductase (dsr AB) gene. 3 Biotech 9, 134 (2019). https://doi.org/10.1007/s13205-019-1655-2
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s13205-019-1655-2