Biofilms: implications in bioremediation

Wimpenny, 2000, Heterogeneity in biofilms, FEMS Microbiol. Rev., 24, 661, 10.1111/j.1574-6976.2000.tb00565.x Costerton, 1999, Bacterial biofilms: a common cause of persistent infections, Science, 284, 1318, 10.1126/science.284.5418.1318 Sutherland, 2001, The biofilm matrix – an immobilized but dynamic microbial environment, Trends Microbiol., 9, 222, 10.1016/S0966-842X(01)02012-1 Flemming, 1995, Sorption sites in biofilms, Water. Sci. Technol., 32, 27, 10.1016/0273-1223(96)00004-2 Horn, 2006, Transport of oxygen, sodium chloride, and sodium nitrate in biofilms, Chem. Eng. Sci., 61, 1347, 10.1016/j.ces.2005.08.027 Paul, 2005, Accessing microbial diversity for bioremediation and environmental restoration, Trends Biotechnol., 23, 135, 10.1016/j.tibtech.2005.01.001 Pandey, 2002, Bacterial chemotaxis toward environmental pollutants: role in bioremediation, Appl. Environ. Microbiol., 68, 5789, 10.1128/AEM.68.12.5789-5795.2002 Decho, 2000, Microbial biofilms in intertidal systems: an overview, Cont. Shelf Res., 20, 1257, 10.1016/S0278-4343(00)00022-4 Akinson, 1981, Immobilized biomass-a basis for process development in wastewater treatment, 22 Aoi, 2002, In situ identification of microorganisms in biofilm communities, J. Biosci. Bioeng., 94, 552, 10.1016/S1389-1723(02)80194-3 Woese, 1977, Phylogenetic structure of the prokaryotic domain: the primary kingdoms, Proc. Natl. Acad. Sci. U. S. A., 74, 5088, 10.1073/pnas.74.11.5088 Ito, 2002, Phylogenetic identification and substrate uptake patterns of sulfate reducing bacteria inhabiting an oxicanoxic sewer biofilm determined by combining microautoradiography and fluorescent in situ hybridization, Appl. Environ. Microbiol., 68, 356, 10.1128/AEM.68.1.356-364.2002 Chalfie, 1994, Green fluorescent protein as a marker for gene expression, Science, 263, 802, 10.1126/science.8303295 Tani, 1995, Development of a direct in situ PCR method for detection of specific bacteria in natural environments, Appl. Environ. Microbiol., 61, 4074 Pratt, 1999, Genetic analysis of bacterial biofilm formation, Curr. Opin. Microbiol., 2, 598, 10.1016/S1369-5274(99)00028-4 Stanley, 2004, Environmental signals and regulatory pathways that influence biofilm formation, Mol. Microbiol., 52, 917, 10.1111/j.1365-2958.2004.04036.x Allegrucci, 2006, Phenotypic characterization of Streptococcus pneumoniae biofilm development, J. Bacteriol., 188, 2325, 10.1128/JB.188.7.2325-2335.2006 Kjelleberg, 2002, Is there a role for quorum sensing signals in bacterial biofilms?, Curr. Opin. Microbiol., 5, 254, 10.1016/S1369-5274(02)00325-9 Stanley, 2003, Identification of catabolite repression as a physiological regulator of biofilm formation by Bacillus subtilis by use of DNA microarrays, J. Bacteriol., 185, 1951, 10.1128/JB.185.6.1951-1957.2003 Whiteley, 2001, Gene expression in Pseudomonas aeruginosa biofilms, Nature, 413, 860, 10.1038/35101627 Lazazzera, 2005, Lessons from DNA microarray analysis: the gene expression profile of biofilms, Curr. Opin. Microbiol., 8, 222, 10.1016/j.mib.2005.02.015 Schembri, 2003, Global gene expression in Escherichia coli biofilms, Mol. Microbiol., 48, 253, 10.1046/j.1365-2958.2003.03432.x Parsek, 2005, Sociomicrobiology: the connections between quorum sensing and biofilms, Trends Microbiol., 13, 27, 10.1016/j.tim.2004.11.007 Labbate, 2004, Quorum sensing-controlled biofilm development in Serratia liquefaciens MG1, J. Bacteriol., 186, 692, 10.1128/JB.186.3.692-698.2004 Puskas, 1997, A quorum-sensing system in the free-living photosynthetic bacterium Rhodobacter sphaeroides, J. Bacteriol., 179, 7530, 10.1128/jb.179.23.7530-7537.1997 Jefferson, 2004, What drives bacteria to produce a biofilm?, FEMS Microbiol. Lett., 236, 163, 10.1111/j.1574-6968.2004.tb09643.x Davey, 2000, Microbial biofilms: from ecology to molecular genetics, Microbiol. Mol. Biol. Rev., 64, 847, 10.1128/MMBR.64.4.847-867.2000 Ghigo, 2001, Natural conjugative plasmids induce bacterial biofilm development, Nature, 412, 442, 10.1038/35086581 Roberts, 2001, Gene transfer in bacterial biofilms, Methods Enzymol., 336, 60, 10.1016/S0076-6879(01)36578-3 Fux, 2005, Survival strategies of infectious biofilms, Trends Microbiol., 13, 34, 10.1016/j.tim.2004.11.010 Roberts, 1999, Transfer of a conjugative transposon, Tn5397 in a model oral biofilm, FEMS Microbiol. Lett., 177, 63, 10.1111/j.1574-6968.1999.tb13714.x Gorisa, 2003, Diversity of activated sludge bacteria receiving the 3-chloroaniline-degradative plasmid pC1gfp, FEMS Microbiol. Ecol., 46, 221, 10.1016/S0168-6496(03)00231-9 Molin, 2003, Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilization of the biofilms structure, Curr. Opin. Biotechnol., 14, 255, 10.1016/S0958-1669(03)00036-3 Aspiras, 2004, ComX activity of Streptococcus mutans growing in biofilms, FEMS Microbiol. Lett., 238, 167 Whitchurch, 2002, Extracellular DNA required for bacterial biofilm formation, Science, 295, 1487, 10.1126/science.295.5559.1487 Springael, 2002, Community shifts in a seeded 3-chlorobenzoate degrading membrane biofilm reactor: indications for involvement of in situ horizontal transfer of the clc-element from inoculum to contaminant bacteria, Environ. Microbiol., 4, 70, 10.1046/j.1462-2920.2002.00267.x Licht, 1999, Plasmid transfer in the animal intestine and other dynamic bacterial populations: the role of community structure and environment, Microbiology, 145, 2615, 10.1099/00221287-145-9-2615 Top, 1998, Enhancement of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation in soil by dissemination of catabolic plasmids, Antonie Van Leeuwenhoek, 73, 87, 10.1023/A:1000663619522 Dejonghe, 2000, Effect of dissemination 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmid on 2,4-D degradation and on bacterial community structure in two different soil horizons, Appl. Environ. Microbiol., 66, 3297, 10.1128/AEM.66.8.3297-3304.2000 Barkay, 2001, Metal and radionuclide bioremediation: issues, considerations and potentials, Curr. Opin. Microbiol., 4, 318, 10.1016/S1369-5274(00)00210-1 Nicolella, 2000, Particle based biofilm reactor technology, Trends Biotechnol., 18, 312, 10.1016/S0167-7799(00)01461-X Stelmack, 1999, Bacterial adhesion to soil contaminants in the presence of surfactants, Appl. Environ. Microbiol., 65, 163, 10.1128/AEM.65.1.163-168.1999 Law, 2003, Bacterial chemotaxis to naphthalene desorbing from a nonaqueous liquid, Appl. Environ. Microbiol., 69, 5968, 10.1128/AEM.69.10.5968-5973.2003 O’Toole, 1998, Flagella and twitching motility are necessary for Pseudomonas aeruginosa biofilm development, Mol. Microbiol., 30, 295, 10.1046/j.1365-2958.1998.01062.x McCarter, 1988, Flagellar dynamometer controls swarmer cell differentiation of V. parahaemolyticus, Cell, 54, 345, 10.1016/0092-8674(88)90197-3 Watnick, 1999, Steps in the development of a Vibrio cholerae El Tor biofilm, Mol. Microbiol., 34, 586, 10.1046/j.1365-2958.1999.01624.x Lee, 2004, Role of flagellum and motility in pathogenesis of Vibrio vulnificus, Infect. Immun., 72, 4905, 10.1128/IAI.72.8.4905-4910.2004 Stanley, 1983, Factors affecting the irreversible attachment of Pseudomonas aeruginosa to stainless steel, Can. J. Microbiol., 29, 1493, 10.1139/m83-230 Kargi, 2005, Removal of 2,4-dichlorophenol and toxicity from synthetic wastewater in a rotating perforated tube biofilm reactor, Process Biochem., 40, 2105, 10.1016/j.procbio.2004.07.013 Puhakka, 1995, Fluidized bed biofilms for chlorophenol mineralization, Water. Sci. Technol., 31, 227, 10.1016/0273-1223(95)00170-R Johnsen, 2005, Principles of microbial PAH-degradation in soil, Environ. Pollut., 133, 71, 10.1016/j.envpol.2004.04.015 Bastiaens, 2000, Isolation of adherent polycyclic aromatic hydrocarbon-degrading bacteria using PAH-sorbing carriers, Appl. Environ. Microbiol., 66, 1834, 10.1128/AEM.66.5.1834-1843.2000 Wolfaardt, 1995, Bioaccumulation of the herbicide diclofop in extracellular polymers and its utilization by a biofilm community during starvation, Appl. Environ. Microbiol., 61, 152, 10.1128/AEM.61.1.152-158.1995 Gisi, 1997, Biodegradation of the pesticide 4, 6-dinitro-ortho-cresol by microorganisms in batch cultures and in fixed-bed column reactors, Appl. Microbiol. Biotechnol., 48, 441, 10.1007/s002530051077 Lendenmann, 1998, Simultaneous biodegradation of 2,4-dinitrotoluene and 2,6-dinitrotoluene in an aerobic fluidized-bed biofilm reactor, Environ. Sci. Technol., 32, 82, 10.1021/es970281j Perumbakkam, S. et al. A bioremediation approach using natural transformation in pure-culture and mixed-population biofilms. Biodegradation (in press) DOI:10.1007/s10532-005-9025-7 (http://www.springerlink.com) Castonguay, 2006, Biofilm formation by Escherichia coli is stimulated by synergistic interactions and co-adhesion mechanisms with adherence-proficient bacteria, Res. Microbiol., 157, 471, 10.1016/j.resmic.2005.10.003 Kuboniwa, 2006, Streptococcus gordonii utilizes several distinct gene functions to recruit Porphyromonas gingivalis into a mixed community, Mol. Microbiol., 60, 121, 10.1111/j.1365-2958.2006.05099.x Cheng, C. et al. Thermophilic aerobic wastewater treatment of waste metal working fluids. Wat. Env. J. (in press) DOI:10.1111/j.1747-6593.2005.00010.x (http://www.blackwellpublishing.com) Lloyd, 2003, Microbial reduction of metals and radionuclides, FEMS Microbiol. Rev., 27, 411, 10.1016/S0168-6445(03)00044-5 White, 2000, Copper accumulation by sulfate-reducing bacterial biofilms, FEMS Microbiol. Lett., 183, 313, 10.1111/j.1574-6968.2000.tb08977.x Macaskie, 2000, Enzymatically mediated bioprecipitation of uranium by Citrobacter sp.: a concerted role for exocellular lipopolysaccharide and associated phosphatase in biomineral formation, Microbiology, 146, 1855, 10.1099/00221287-146-8-1855 Labrenz, 2000, Formation of sphalerite (ZnS) deposits in natural biofilms of sulfate-reducing bacteria, Science, 290, 1744, 10.1126/science.290.5497.1744 Costley, 2001, Bioremediation of heavy metals in a synthetic wastewater using a rotating biological contactor, Water Res., 35, 3715, 10.1016/S0043-1354(01)00072-0 Valls, 2002, Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution, FEMS Microbiol. Rev., 26, 327, 10.1111/j.1574-6976.2002.tb00618.x Bang, 2000, Engineering hydrogen sulfide production and cadmium removal by expression of the thiosulfate reductase gene (phsABC) from Salmonella enterica serovar Typhimurium in Escherichia coli, Appl. Environ. Microbiol., 66, 3939, 10.1128/AEM.66.9.3939-3944.2000 Chang, 2004, Degradation of 2-chlorophenol via a hydrogenotrophic biofilm under different reductive conditions, Chemosphere, 56, 989, 10.1016/j.chemosphere.2004.04.051 Chang, 2003, Reductive dechlorination of 2-chlorophenol in a hydrogenotrophic, gas permeable silicone membrane bioreactor, Bioresour. Technol., 90, 323, 10.1016/S0960-8524(03)00149-4 Caldeira, 1999, 4-chlorophenol degradation by a bacterial consortium: development of a granular activated carbon biofilm reactor, Appl. Microbiol. Biotechnol., 52, 722, 10.1007/s002530051584 Carvalho, 2001, A GAC biofilm reactor for the continuous degradation of 4-chlorophenol: treatment efficiency and microbial analysis, Appl. Microbiol. Biotechnol., 57, 419, 10.1007/s002530100794 Eriksson, 2002, Bacterial growth and biofilm production on pyrene, FEMS Microbiol. Ecol., 40, 21, 10.1111/j.1574-6941.2002.tb00932.x Vayenas, 2002, Visualization experiments of biodegradation in porous media and a calculation of the biodegradation rate, Adv. Water Resour., 25, 203, 10.1016/S0309-1708(01)00023-9 Yamaguchi, 1999, Biodegradation of hydrocarbons by Prototheca zopfii in rotating biological contactors, Process Biochem., 35, 403, 10.1016/S0032-9592(99)00086-2 Jin, 1998, Carbon tetrachloride biodegradation in a fixed biofilm reactor and its kinetic study, Water Sci. Technol, 38, 155, 10.1016/S0273-1223(98)00689-1 Parvatiyar, 1996, Biodegradation of toluene in a membrane biofilter, J. Memb. Sci., 119, 17, 10.1016/0376-7388(96)00021-X Arcangeli, 1995, Growth of an aerobic and an anoxic toluene degrading biofilm: a comparative study, Water Sci. Technol, 32, 125, 10.1016/0273-1223(96)00016-9 Zhang, 1995, Transport and biodegradation of toxic organics in biofilms, J. Hazard. Mater., 41, 267, 10.1016/0304-3894(94)00118-Z Kapdan, 2002, Simultaneous biodegradation and adsorption of textile dyestuff in an activated sludge unit, Process Biochem., 37, 973, 10.1016/S0032-9592(01)00309-0 Oh, 1994, Biodegradation of the phenoxy herbicides MCPP and 2,4-D in fixed-film column reactors, Int. Biodeter. Biodegr., 33, 93, 10.1016/0964-8305(94)90057-4 Chang, 2006, Heavy metal removal from aqueous solution by wasted biomass from a combined AS-biofilm process, Bioresour. Technol., 97, 1503, 10.1016/j.biortech.2005.06.011 Diels, 2003, Heavy metal removal by sand filters inoculated with metal sorbing and precipitating bacteria, Hydrometallurgy, 71, 235, 10.1016/S0304-386X(03)00161-0 Travieso, 2002, BIOALGA reactor: preliminary studies for heavy metals removal, Biochem. Eng. J., 12, 87, 10.1016/S1369-703X(02)00045-1 Scott, 1998, Immobilized biofilms on granular activated carbon for removal and accumulation of heavy metals from contaminated streams, Water Sci. Technol., 38, 197, 10.1016/S0273-1223(98)00725-2 Scott, 1995, Biofilms covered granular activated carbon for decontamination of streams containing heavy metals and organic chemicals, Minerals. Eng., 8, 221, 10.1016/0892-6875(94)00115-S Diels, 1995, The use of bacteria immobilized in tubular membrane reactors for heavy metal recovery and degradation of chlorinated aromatics, J. Memb. Sci., 100, 249, 10.1016/0376-7388(94)00253-U