Bioremediation of contaminated marine sediments can enhance metal mobility due to changes of bacterial diversity

Water Research

Volumn 68, Issue , 2015, Pages 637-650

  Fonti, Viviana ^a   Beolchini, Francesca ^a   Rocchetti, Laura ^a   Dell'Anno, Antonio ^a  

^a UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

Author keywords

Bacterial diversity; Bioremediation; Marine sediments; Metals

Indexed keywords

BACTERIA; BIOGEOCHEMISTRY; BIOREMEDIATION; BIOTECHNOLOGY; CONTAMINATION; ECOSYSTEMS; INORGANIC COMPOUNDS; METALS; SUBMARINE GEOLOGY; SULFUR COMPOUNDS;

BACTERIAL DIVERSITY; BIOGEOCHEMICAL INTERACTIONS; CONTAMINATED MARINE SEDIMENTS; MARINE SEDIMENTS; MOLECULAR FINGERPRINTING; NEXT-GENERATION SEQUENCING; SEDIMENTARY ORGANIC MATTER; SULFATE REDUCING BACTERIA;

SEDIMENTS;

ACETIC ACID; ARSENIC; BACTERIAL DNA; HYDROCARBON; INORGANIC COMPOUND; LACTOSE; METAL; NITROGEN; ORGANIC COMPOUND; ORGANIC MATTER; PHOSPHORUS; RNA 16S; RNA 23S; ACETIC ACID DERIVATIVE; SEA WATER; SULFATE;

ABUNDANCE; BACTERIUM; BIOREMEDIATION; ELEMENT MOBILITY; MARINE SEDIMENT; SEDIMENT POLLUTION; SOLUBILIZATION; SPECIES DIVERSITY;

ARTICLE; BACTERIAL DIVERSITY; BACTERIAL GROWTH; BIODIVERSITY; BIOREMEDIATION; DESULFOBACTERACEAE; DESULFOBULBACEAE; ECOSYSTEM HEALTH; FLAVOBACTERIACEAE; GRAIN; INORGANIC NUTRIENT; ITALY; POLYMERASE CHAIN REACTION; SEASHORE; SEDIMENT; TAXONOMIC IDENTIFICATION; TOTAL ORGANIC CARBON; WATER CONTAMINATION; X RAY POWDER DIFFRACTION; ANALYSIS OF VARIANCE; BACTERIUM; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; METABOLISM; MICROBIOLOGY; PROCEDURES; TIME; X RAY DIFFRACTION;

BACTERIA (MICROORGANISMS);

ACETATES; ANALYSIS OF VARIANCE; BACTERIA; BIODEGRADATION, ENVIRONMENTAL; BIODIVERSITY; GENETIC VARIATION; GEOLOGIC SEDIMENTS; LACTOSE; METALS; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA; SULFATES; TIME FACTORS; X-RAY DIFFRACTION;

EID: 84911390618     PISSN: 00431354     EISSN: 18792448     Source Type: Journal    
DOI: 10.1016/j.watres.2014.10.035     Document Type: Article

References (71)

1. Ahlf W., Förstner U. Managing contaminated sediments. J. Soils Sediments 2001, 1:30-36.
2. Akcil A., Erust C., Ozdemiroglu S., Fonti V., Beolchini F. A review of approaches and techniques used in aquatic contaminated sediments: metal removal and stabilization by chemical and biotechnological processes. J. Clean. Prod. 2014, (in press).
3. Baumann Z., Fisher N.S. Modeling metal bioaccumulation in a deposit-feeding polychaete from labile sediment fractions and from pore water. Sci. Total Environ. 2011, 409:2607-2615.
4. Beolchini F., Rocchetti L., Regoli F., Dell'Anno A. Bioremediation of marine sediments contaminated by hydrocarbons: experimental analysis and kinetic modeling. J. Hazard. Mater. 2010, 182:403-407.
5. Bernardet J.F., Yasuyoshi N. An introduction to the family flavobacteriaceae. Prokaryotes 2006, 455-480.
6. Brehm U., Gorbushina A., Mottershead D. The role of microorganisms and biofilms in the breakdown and dissolution of quartz and glass. Palaeogeogr. Palaeoclimatol. Palaeoecol. 2005, 219:117-129.
7. Buchanan J., Kain K., Holme W., McIntyre A. The Determination of Organic Matter in Sediments. Methods Study Mar 1971, 49-50. Blackwell Sci. Oxford, Benthos.
8. Calmano W., Hong J., Fostner U. Binding and mobilization of heavy metals in contaminated sediments afected by pH and redox potential. Water Sci. Technol. 1993, 28:223-235.
9. Chao A., Chazdon R.L., Colwell R.K., Shen T.-J. Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics 2006, 62:361-371.
10. Chapman P.M., Wang F. Assessing sediment contamination in estuaries. Environ. Toxicol. Chem. 2001, 20:3-22.
11. Chen Z., Chen Z., Mayer L.M. Sedimentary Metal Bioavailability Determined by the Digestive Constraints of Marine Deposit Feeders: Gut Retention Time and Dissolved Amino Acids 1999.
12. Cicero A.M., Mecozzi M., Morlino R., Pellegrini D., Veschetti E. Distribution of chlorinated organic pollutants in harbor sediments of Livorno (Italy): a multivariate approach to evaluate dredging sediments. Environ. Monit. Assess. 2001, 71:297-316.
13. Connon S.A., Giovannoni S.J. High-Throughput Methods for Culturing Microorganisms in Very-Low-Nutrient Media Yield Diverse New Marine Isolates 2002.
14. Danovaro R., Manini E., Fabiano M. Exoenzymatic activity and organic matter composition in sediments of the Northern Adriatic Sea: response to a river plume. Microb. Ecol. 2001, 44:235-251.
15. Danovaro R., Luna G.M., Dell'Anno A., Pietrangeli B. Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments. Appl. Environ. Microbiol. 2006, 72:5982-5989.
16. Dell'Anno A., Mei M.L., Pusceddu A., Danovaro R. Assessing the trophic state and eutrophication of coastal marine systems: a new approach based on the biochemical composition of sediment organic matter. Mar. Pollut. Bull. 2002, 44:611-622.
17. Dell'Anno A., Mei M.L., Ianni C., Danovaro R. Impact of bioavailable heavy metals on bacterial activities in coastal marine sediments. W. J. Microbiol. Biotechnol. 2003, 19:93-100.
18. Dell'Anno A., Beolchini F., Gabellini M., Rocchetti L., Pusceddu A., Danovaro R. Bioremediation of petroleum hydrocarbons in anoxic marine sediments: consequences on the speciation of heavy metals. Mar. Pollut. Bull. 2009, 58:1808-1814.
19. Dos Santos H.F., Cury J.C., do Carmo F.L., dos Santos A.L., Tiedje J., van Elsas J.D., Rosado A.S., Peixoto R.S. Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. PLoS One 2011, 6:e16943.
20. Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
21. Eggleton J., Thomas K.V. A review of factors affecting the release and bioavailability of contaminants during sediment disturbance events. Environ. Int. 2004, 30:973-980.
22. Evangelou V.P. Environmental Soil and Water Chemistry 1998, Principles and Applications, New York.
23. Fenchel T., Blackburn H., King G.M. Bacterial Biogeochemistry: the Ecophysiology of Mineral Cycling 2012, Academic Press.
24. Fernández-Gómez B., Richter M., Schüler M., Pinhassi J., Acinas S.G., González J.M., Pedrós-Alió C. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J. 2013, 7:1026-1037.
25. Fonti V., Dell'Anno A., Beolchini F. Influence of biogeochemical interactions on metal bioleaching performance in contaminated marine sediment. Water Res. 2013.
26. Förstner U. Metal speciation-general concepts and applications. Int. J. Environ. Anal. Chem. 1993, 51:5-23.
27. Finke N., Vandieken V., Jørgensen B.B. Acetate, lactate, propionate, and isobutyrate as electron donors for iron and sulfate reduction in Arctic marine sediments, Svalbard. FEMS Microbiol. Ecol. 2007, 59:10-22.
28. Fuchsman C.A., Staley J.T., Oakley B.B., Kirkpatrick J.B., Murray J.W. Free-living and aggregate-associated Planctomycetes in the Black Sea. FEMS Microbiol. Ecol. 2012, 80:402-416.
29. Gadd G.M. Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology 2010, 156:609-643.
30. Gadd G.M. Microbial influence on metal mobility and application for bioremediation. Geoderma 2004, 122:109-119.
31. Gleyzes C., Tellier S., Astruc M. Fractionation studies of trace elements in contaminated soils and sediments: a review of sequential extraction procedures. Trac. Trends Anal. Chem. 2002, 21:451-467.
32. Goh K.-H., Lim T.-T. Arsenic fractionation in a fine soil fraction and influence of various anions on its mobility in the subsurface environment. Appl. Geochem. 2005, 20:229-239.
33. Guo X., Zhang S., Shan X.Q., Luo L.E.I., Pei Z., Zhu Y.-G., Liu T., Xie Y.-N., Gault A. Characterization of Pb, Cu, and Cd adsorption on particulate organic matter in soil. Environ. Toxicol. Chem. 2006, 25:2366-2373.
34. Head I.M., Jones D.M., Röling W.F.M. Marine microorganisms make a meal of oil. Nat. Rev. Microbiol. 2006, 4:173-182.
35. Hewson I., Fuhrman J.A. Richness and diversity of Bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl. Environ. Microbiol. 2004, 70:3425-3433.
36. Hlavay J., Prohaska T., Weisz M., Wenzel W.W., Stingeder G.J. Determination of trace elements bound to soils and sediment fractions. Pure Appl. Chem. 2004, 76:415-442. IUPAC Technical Report.
37. Hollabaugh C.L. Modification of Goldschmidt's geochemical classification of the elements to include arsenic, mercury, and lead as biophile elements. Dev. Environ. Sci. 2007, 5:9-31.
38. Jain C.K. Metal fractionation study on bed sediments of River Yamuna, India. Water Res. 2004, 38:569-578.
39. Jiang W., Fan W. Bioremediation of heavy metal-contaminated soils by sulfate-reducing bacteria. Ann. N. Y. Acad. Sci. 2008, 1140:446-454.
40. Jørgensen B.B. Bacteria and marine biogeochemistry. Marine Geochemistry 2000, 173-207. Springer.
41. Klindworth A., Pruesse E., Schweer T., Peplies J., Quast C., Horn M., Glöckner F.O. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013, 41. e1-e1.
42. Licht S. Aqueous solubilities, solubility products and standard oxidation-reduction potentials of the metal sulfides. J. Electrochem. Soc. 1988, 135:2971-2975.
43. Long E.R., MacDonald D.D., Smith S.L., Calder F.D. Incidence of adverse biological effects within ranges of chemical concentrations in marine and estuarine sediments. Environ. Manag. 1995, 19:81-97.
44. Luna G.M., Dell'Anno A., Danovaro R. DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environ. Microbiol. 2006, 8:308-320.
45. Micheli F., Levin N., Giakoumi S., Katsanevakis S., Abdulla A., Coll M., Fraschetti S., Kark S., Koutsoubas D., Mackelworth P., Maiorano L., Possingham H.P. Setting priorities for regional conservation planning in the Mediterranean Sea. PLoS One 2013, 8:e59038.
46. Morgan P., Watkinson R.J. Factors limiting the supply and efficiency of nutrient and oxygen supplements for the in situ biotreatment of contaminated soil and groundwater. Water Res. 1992, 26:73-78.
47. Okoro H.K., Fatoki O.S. A review of sequential extraction procedures for heavy metals speciation in soil and sediments. J. Environ. Anal. Toxicol. 2012, 01:1-16.
48. Pandey J., Chauhan A., Jain R.K. Integrative approaches for assessing the ecological sustainability of in situ bioremediation. FEMS Microbiol. Rev. 2009, 33:324-375.
49. Parker J.G. A comparison of methods used for the measurement of organic matter in marine sediment. Chem. Ecol. 1983, 1:201-209.
50. Pastorelli A.A., Baldini M., Stacchini P., Baldini G., Morelli S., Sagratella E., Zaza S., Ciardullo S. Human exposure to lead, cadmium and mercury through fish and seafood product consumption in Italy: a pilot evaluation. Food Addit. Contam. Part A 2012, 29:1913-1921.
51. Polz M.F., Cavanaugh C.M. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 1998, 64:3724-3730.
52. Prica M., Dalmacija B., Dalmacija M., Agbaba J., Krcmar D., Trickovic J., Karlovic E. Changes in metal availability during sediment oxidation and the correlation with the immobilization potential. Ecotoxicol. Environ. Saf. 2010, 73:1370-1377.
53. Quince C., Lanzén A., Curtis T.P., Davenport R.J., Hall N., Head I.M., Read L.F., Sloan W.T. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 2009, 6:639-641.
54. Quevauviller P. Operationally defined extraction procedures for soil and sediment analysis. I. Standardization. Trends Anal. Chem. 1998, 17:289-298.
55. Rajkumar M., Ae N., Freitas H. Endophytic bacteria and their potential to enhance heavy metal phytoextraction. Chemosphere 2009, 77:153-160.
56. Reddy K.R., DeLaune R.D. Biogeochemistry of Wetlands: Science and Applications 2004, Crc Press.
57. Rocchetti L., Beolchini F., Hallberg K.B., Johnson D.B., Dell'Anno A. Effects of prokaryotic diversity changes on hydrocarbon degradation rates and metal partitioning during bioremediation of contaminated anoxic marine sediments. Mar. Pollut. Bullet. 2012, 64:1688-1698.
58. Roesch L.F.W., Fulthorpe R.R., Riva A., Casella G., Hadwin A.K.M., Kent A.D., Daroub S.H., Camargo F.a O., Farmerie W.G., Triplett E.W. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007, 1:283-290.
59. Ryan J.a, Zhang P., Hesterberg D., Chou J., Sayers D.E. Formation of chloropyromorphite in a lead-contaminated soil amended with hydroxyapatite. Environ. Sci. Technol. 2001, 35:3798-3803.
60. Sahu M.K., Sivakumar K., Thangaradjou T., Kannan L. Phosphate solubilizing actinomycetes in the estuarine environment: an inventory. J. Environ. Biol. 2007, 28:795-798.
61. Salomons W. Adoption of common schemes for single and sequential extractions of trace metal in soils and sediments. Int. J. Environ. Anal. Chem. 1993, 51:3-4.
62. Sauvé S., Hendershot W., Allen H.E. Critical review solid-solution partitioning of metals in contaminated Soils: dependence on pH, total metal Burden, and organic matter. Environ. Sci. Technol. 2000, 34:1125-1131.
63. Schloss P.D., Gevers D., Westcott S.L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 2011, 6:e27310.
64. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.a, Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
65. Sogin M.L., Morrison H.G., Huber J.a, Mark Welch D., Huse S.M., Neal P.R., Arrieta J.M., Herndl G.J. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl. Acad. Sci. U. S. A. 2006, 103:12115-12120.
66. Tabak H.H., Lens P., Hullebusch E.D., Dejonghe W. Developments in bioremediation of soils and sediments polluted with metals and radionuclides - 1. Microbial processes and mechanisms affecting bioremediation of metal contamination and influencing metal toxicity and transport. Rev. Environ. Sci. Bio/Technol. 2005, 4:115-156.
67. Tadonléké R.D. Strong coupling between natural Planctomycetes and changes in the quality of dissolved organic matter in freshwater samples. FEMS Microbiol. Ecol. 2007, 59:543-555.
68. Toes A.C.M., Maas B.A., Geelhoed J.S., Kuenen J.G., Muyzer G. Interactions between microorganisms and heavy metals. Proceedings of European Symposium on Environmental Biotechnology 2004, 55-59. ESEB.
69. Van Hullebusch E.D., Lens P.N.L., Tabak H.H. Developments in bioremediation of soils and sediments polluted with metals and Radionuclides. 3. Influence of chemical speciation and bioavailability on contaminants Immobilization/Mobilization bio-processes. Rev. Environ. Sci. Bio/Technol. 2005, 4:185-212.
70. Warren L.A., Haack E.A. Biogeochemical controls on metal behaviour in freshwater environments. Earth-Sci. Rev. 2001, 54:261-320.
71. Yin Y., Impellitteri C.A., You S.-J., Allen H.E. The importance of organic matter distribution and extract soil:solution ratio on the desorption of heavy metals from soils. Sci. Total Environ. 2002, 287:107-119.