Profiling of microbial community during in situ remediation of volatile sulfide compounds in river sediment with nitrate by high throughput sequencing

International Biodeterioration and Biodegradation

Volumn 85, Issue , 2013, Pages 429-437

  Chen, Lei ^a   Wang, Ling yun ^a   Liu, Shu juan ^a   Hu, Jiang yong ^b   He, Yan ^c   Zhou, Hong wei ^c   Zhang, Xi hui ^a  

^a TSINGHUA UNIVERSITY   (China)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c SOUTHERN MEDICAL UNIVERSITY   (China)

Author keywords

16S rRNA V6; High throughput sequencing; Microbial community; Odor control; Sediment remediation

Indexed keywords

16S RRNA; HIGH-THROUGHPUT SEQUENCING; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY STRUCTURES; NITRATE-REDUCING BACTERIA; OXIDATION-REDUCTION POTENTIALS; SEDIMENT REMEDIATION; SULFATE REDUCING BACTERIA;

BACTERIA; BIOLOGY; NITRATES; ODOR CONTROL; POLLUTION; REDOX REACTIONS; RIVER POLLUTION; RIVERS; RNA; SULFUR COMPOUNDS; THROUGHPUT; WELL STIMULATION;

SEDIMENTS;

ABUNDANCE; BACTERIUM; BIODEGRADATION; BIOREMEDIATION; COMMUNITY STRUCTURE; FLUVIAL DEPOSIT; INHIBITION; MICROBIAL COMMUNITY; NITRATE; ODOR; PHYLOGENY; REDOX POTENTIAL; RIVER BED; RIVER POLLUTION; SEDIMENT POLLUTION; SOIL MICROORGANISM; VOLATILE SUBSTANCE;

CHINA;

EID: 84885082373     PISSN: 09648305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ibiod.2013.08.015     Document Type: Article

References (46)

1. Allen H.E., Fu G., Boothman W., DiToro D.M., Mahony J.D. Draft Analytical Method for Determination of Acid Volatile Sulfide in Sediment 1991, Environment Protection Agency, US.
2. Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiol. Rev. 1995, 59:143-169.
3. Bai Y.H., Shi Q., Wen D.H., Li Z.X., Jefferson W.A., Feng C.P., Tang X.Y. Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China. PLOS One 2012, 7.
4. 2S in a sewer network and the effects on the subsequent treatment processes. Water Sci. Technol. 1995, 31:293-302.
5. Cetecioglu Z., Ince B.K., Kolukirik M., Ince O. Biogeographical distribution and diversity of bacterial and archaeal communities within highly polluted anoxic marine sediments from the Marmara sea. Mar. Pollut. Bull. 2009, 58:384-395.
6. Chaudhry V., Rehman A., Mishra A., Chauhan P.S., Nautiyal C.S. Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microbial. Ecol. 2012, 64:450-460.
7. Chen S.Y., Liu X.L., Dong X.Z. Syntrophobacter sulfatireducens sp. nov., a novel syntrophic, propionate-oxidizing bacterium isolated from UASB reactors. Int. J. Syst. Evol. Microbiol. 2005, 55:1319-1324.
8. Coates J.D., Phillips E., Lonergan D.J., Jenter H., Lovley D.R. Isolation of geobacter species from diverse sedimentary environments. Appl. Environ. Microbiol. 1996, 62:1531-1536.
9. De Wever H., Cole J.R., Fettig M.R., Hogan D.A., Tiedje J.M. Reductive dehalogenation of trichloroacetic acid by Trichlorobacterthiogenes gen. nov., spnov. Appl. Environ. Microbiol. 2000, 66:2297-2301.
10. Dhote M., Juwarkar A., Kumar A., Kanade G.S., Chakrabarti T. Biodegradation of chrysene by the bacterial strains isolated from oily sludge. World J. Microbiol. Biotechnol. 2010, 26:329-335.
11. Dichristina T.J. Effects of nitrate and nitrite on dissimilatory iron reduction by Shewanellaputrefaciens strain-200. J.Bacteriol. 1992, 174:1891-1896.
12. Di Toro D.M., Mahony J.D., Gonzalez A.M. Particle oxidation model of synthetic FeS and sediment acid-volatile sulfide. Environ. Toxicol. Chem. 1996, 15:2156-2167.
13. Garcia-de-Lomas J., Corzo A., Gonzalez J.M., Andrades J.A., Iglesias E., Montero M.J. Nitrate promotes biological oxidation of sulfide in wastewaters: experiment at plant-scale. Biotechnol. Bioeng. 2006, 93:801-811.
14. Garcia-de-Lomas J., Corzo A., Portillo M.C., Gonzalez J.M., Andrades J.A., Saiz-Jimenez C., Garcia-Robledo E. Nitrate stimulation of indigenous nitrate-reducing, sulfide-oxidising bacterial community in wastewater anaerobic biofilms. Water Res. 2007, 41:3121-3131.
15. Hamady M., Walker J.J., Harris J.K., Gold N.J., Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 2008, 5:235-237.
16. Huber J.A., Mark Welch D.B., Morrison H.G., Huse S.M., Neal P.R., Butterfield D.A., Sogin M.L. Microbial population structures in the deep marine biosphere. Science 2007, 318:97-100.
17. Huse S.M., Dethlefsen L., Huber J.A., Welch D.M., Relman D.A., Sogin M.L. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLOS Genet. 2008, 4.
18. Kelly D.P., Wood A.P. Confirmation of Thiobacillus denitrificans as a species of the genus Thiobacillus, in the beta-subclass of the Proteobacteria, with strain NCIMB 9548 as the type strain. Int. J. Syst. Evol. Microbiol. 2000, 50:547-550.
19. Kjeldsen K.U., Loy A., Jakobsen T.F., Thomsen T.R., Wagner M., Ingvorsen K. Diversity of sulfate-reducing bacteria from an extreme hypersaline sediment, Great Salt Lake (Utah). FEMS Microbiol. Ecol. 2007, 60:287-298.
20. Koizumi Y., Kojima H., Fukui M. Potential sulfur metabolisms and associated bacteria within anoxic surface sediment from saline meromictic Lake Kaiike (Japan). FEMS Microbiol. Ecol. 2005, 52:297-305.
21. Kumaraswamy R., Ebert S., Gray M.R., Fedorak P.M., Foght J.M. Molecular- and cultivation-based analyses of microbial communities in oil field water and in microcosms amended with nitrate to control H2S production. Appl. Microbiol. Biotechnol. 2011, 89:2027-2038.
22. Li J.H., Purdy K.J., Takii S., Hayashi H. Seasonal changes in ribosomal RNA of sulfate-reducing bacteria and sulfate reducing activity in a freshwater lake sediment. FEMS Microbiol. Ecol. 1999, 28:31-39.
23. Lin Y.H., Guo M.X., Zhuang Y. Determination of acid volatile sulfide and simultaneously extrcated metals in sediment. ACTA Sci. Circumst. 1997, 17:353-358.
24. Liu X.D., Tiquia S.M., Holguin G., Wu L.Y., Nold S.C., Devol A.H., Luo K., Palumbo A.V., Tiedje J.M., Zhou J.Z. Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico. Appl. Environ. Microbiol. 2003, 69:3549-3560.
25. Mansfeldt T. Redox potential of bulk soil and soil solution concentration of nitrate, manganese, iron, and sulfate in two Gleysols. J.Plant Nutr. Soil Sci. 2004, 167:7-16.
26. Moura I., Bursakov S., Costa C., Moura J. Nitrate and nitrite utilization in sulfate-reducing bacteria. Anaerobe 1997, 3:279-290.
27. Murphy T.P., Lawson A., Kumagai M., Babin J. Review of emerging issues in sediment treatment. Aquat. Ecosyst. Health Manage 1999, 2:419-434.
28. Muyzer G., Stams A. The ecology and biotechnology of sulphate-reducing bacteria. Nat. Rev. Microbiol. 2008, 6:441-454.
29. Perelo L.W. Review: in situ and bioremediation of organic pollutants in aquatic sediments. J.Hazard. Mater. 2010, 177:81-89.
30. Pratt B., Riesen R., Johnston C.G. PLFA Analyses of microbial communities associated with PAH-contaminated riverbank sediment. Microbial. Ecol. 2012, 64:680-691.
31. Purdy K.J., Nedwell D.B., Embley T.M., Takii S. Use of 16S rRNA-targeted oligonucleotide probes to investigate the occurrence and selection of sulfate-reducing bacteria in response to nutrient addition to sediment slurry microcosms from a Japanese estuary. FEMS Microbiol. Ecol. 1997, 24:221-234.
32. Roesch L.F., Fulthorpe R.R., Riva A., Casella G., Hadwin A., Kent A.D., Daroub S.H., Camargo F., Farmerie W.G., Triplett E.W. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007, 1:283-290.
33. Schumacher B.A. Methods for the Determination of Total Organic Carbon (TOC) in Soils and Sediments 2002, Environment Protection Agency, US.
34. Schutte U., Abdo Z., Bent S.J., Shyu C., Williams C.J., Pierson J.D., Forney L.J. Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl. Microbiol. Biotechnol. 2008, 80:365-380.
35. Segata N., Izard J., Waldron L., Gevers D., Miropolsky L., Garrett W.S., Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011, 12.
36. Shao K.Q., Gao G., Qin B.Q., Tang X.M., Wang Y.P., Chi K.X., Dai J.Y. Comparing sediment bacterial communities in the macrophyte-dominated and algae-dominated areas of eutrophic Lake Taihu, China. Canad. J. Microbiol. 2011, 57:263-272.
37. Shao M.F., Zhang T., Fang H. Autotrophic denitrification and its effect on metal speciation during marine sediment remediation. Water Res. 2009, 43:2961-2968.
38. Shao M.F., Zhang T., Fang H., Li X.D. The effect of nitrate concentration on sulfide-driven autotrophic denitrification in marine sediment. Chemosphere 2011, 83:1-6.
39. Suarez-Suarez A., Lopez-Lopez A., Tovar-Sanchez A., Yarza P., Orfila A., Terrados J., Arnds J., Marques S., Niemann H., Schmitt-Kopplin P., Amann R., Rossello-Mora R. Response of sulfate-reducing bacteria to an artificial oil-spill in a coastal marine sediment. Environ. Microbiol. 2011, 13:1488-1499.
40. Tamaki H., Sekiguchi Y., Hanada S., Nakamura K., Nomura N., Matsumura M., Kamagata Y. Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl. Environ. Microbiol. 2005, 71:2162-2169.
41. Telang A.J., Ebert S., Foght J.M., Westlake D., Jenneman G.E., Gevertz D., Voordouw G. Effect of nitrate injection on the microbial community in an oil field as monitored by reverse sample genome probing. Appl. Environ. Microbiol. 1997, 63:1785-1793.
42. Torres-Alvarado M. Spatial distribution of sulfate reducing bacteria in the sediment of a coastal lagoon. Hidrobiologica 2007, 17:277-279.
43. Voordouw G., Armstrong S.M., Reimer M.F., Fouts B., Telang A.J., Shen Y., Gevertz D. Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria. Appl. Environ. Microbiol. 1996, 62:1623-1629.
44. Zhang L., De Schryver P., De Gusseme B., De Muynck W., Boon N., Verstraete W. Chemical and biological technologies for hydrogen sulfide emission control in sewer systems: a review. Water Res. 2008, 42:1-12.
45. Zhang M., Zhang T., Shao M.F., Fang H. Autotrophic denitrification in nitrate-induced marine sediment remediation and Sulfurimonasdenitrificans-like bacteria. Chemosphere 2009, 76:677-682.
46. Zhou H.W., Li D.F., Tam N., Jiang X.T., Zhang H., Sheng H.F., Qin J., Liu X., Zou F. BIPES, a cost-effective high-throughput method for assessing microbial diversity. ISME J. 2011, 5:741-749.