JEP  Vol.3 No.12 , December 2012
Prokaryotic Horizontal Gene Transfer in Freshwater Lakes: Implications of Dynamic Biogeochemical Zonation
ABSTRACT
The highly adaptive nature of prokaryotic communities in the face of changing environmental conditions reflects in part their ability to share advantageous genetic information through horizontal gene transfer (HGT). Natural freshwater lacustrine (lake) systems are a vital and finite resource, and the influence of HGT on their quality (e.g. enabling the spread of antibiotic resistance and xenobiotic catabolism genes) is likely significant. Laboratory and in situ studies indicate that the dynamic physical, chemical, and biological conditions that structure freshwater systems can influence HGT within freshwater prokaryotic communities. Thus, understanding how biogeochemical parameters impact HGT in freshwater lakes is an emerging knowledge gap with potential implications for ecosystem and human health on a global scale. In this review, we provide a general synopsis of what is known about HGT in freshwater prokaryotic communities, followed by an integrated summary of current knowledge identifying how biogeochemical factors may influence prokaryotic HGT in freshwater lacustrine systems.

Cite this paper
C. Drudge and L. Warren, "Prokaryotic Horizontal Gene Transfer in Freshwater Lakes: Implications of Dynamic Biogeochemical Zonation," Journal of Environmental Protection, Vol. 3 No. 12, 2012, pp. 1634-1654. doi: 10.4236/jep.2012.312181.
References
[1]   E. V. Koonin and Y. I. Wolf, “Genomics of Bacteria and Archaea: The Emerging Dynamic View of the Prokary otic World,” Nucleic Acids Research, Vol. 36, No. 21, 2008, pp. 6688-6719. doi:10.1093/nar/gkn668

[2]   O. Zhaxybayeva and W. F. Doolittle, “Lateral Gene Transfer,” Current Biology, Vol. 21, No. 7, 2011, pp. R242-R246. doi:10.1016/j.cub.2011.01.045

[3]   A. O. Summers, “Genetic Linkage and Horizontal Gene Transfer, the Roots of the Antibiotic Multi-Resistance Problem,” Animal Biotechnology, Vol. 17, No. 2, 2006, pp. 125-135. doi:10.1080/10495390600957217

[4]   D. Springael and E. M. Top, “Horizontal Gene Transfer and Microbial Adaptation to Xenobiotics: New Types of Mobile Genetic Elements and Lessons from Ecological Studies,” Trends in Microbiology, Vol. 12, No. 2, 2004, pp. 53-58. doi:10.1016/j.tim.2003.12.010

[5]   B. Liang, G. Wang, Y. Zhao, K. Chen, S. Li and J. Jiang, “Facilitation of Bacterial Adaptation to Chlorothalo nil-Contaminated Sites by Horizontal Transfer of the Chlorothalonil Hydrolytic Dehalogenase Gene,” Applied and Environmental Microbiology, Vol. 77, No. 12, 2011, pp. 4268-4272. doi:10.1128/AEM.02457-10

[6]   J. M. Monier, D. Bernillon, E. Kay, A. Faugier, O. Ry balka, Y. Dessaux, P. Simonet and T. M. Vogel, “Detection of Potential Transgenic Plant DNA Recipients among Soil Bacteria,” Environmental Biosafety Research, Vol. 6, No. 1-2, 2007, pp. 71-83. doi:10.1051/ebr:2007036

[7]   F. Donnarumma, D. Paffetti, G. Stotzky, R. Giannini and C. Vettori, “Potential Gene Exchange between Bacillus thuringiensis subsp. kurstaki and Bacillus spp. in Soil in Situ,” Soil Biology and Biochemistry, Vol. 42, No. 8, 2010, pp. 1329-1337. doi:10.1016/j.soilbio.2010.03.014

[8]   J. B. Cotner and B. A. Biddanda, “Small Players, Large Role: Microbial Influence on Biogeochemical Processes in Pelagic Aquatic Ecosystems,” Ecosystems, Vol. 5, No. 2, 2002, pp. 105-121. doi:10.1007/s10021-001-0059-3

[9]   US Environmental Protection Agency, “Great Lakes,” 2011. http://www.epa.gov/greatlakes/statsrefs.html

[10]   A. Pruden, R. Pei, H. Storteboom and K. H. Carlson, “Antibiotic Resistance Genes as Emerging Contaminants: Studies in Northern Colorado,” Environmental Science and Technology, Vol. 40, No. 23, 2006, pp. 7445-7450. doi:10.1021/es060413l

[11]   J. L. Martinez, “Environmental Pollution by Antibiotics and by Antibiotic Resistance Determinants,” Environ mental Pollution, Vol. 157, No. 11, 2009, pp. 2893-2902. doi:10.1016/j.envpol.2009.05.051

[12]   H. K. Allen, J. Donato, H. H. Wang, K. A. Cloud-Hansen, J. Davies and J. Handelsman, “Call of the Wild: Antibiotic Resistance Genes in Natural Environments,” Nature Reviews Microbiology, Vol. 8, No. 4, 2010, pp. 251-259. doi:10.1038/nrmicro2312

[13]   N. G. Taylor, D. W. Verner-Jeffreys and C. Baker-Austin, “Aquatic Systems: Maintaining, Mixing and Mobilising Antimicrobial Resistance?” Trends in Ecology and Evolution, Vol. 26, No. 6, 2011, pp. 278-284. doi:10.1016/j.tree.2011.03.004

[14]   A. Lupo, S. Coyne and T. U. Berendonk, “Origin and Evolution of Antibiotic Resistance: The Common Mechanisms of Emergence and Spread in Water Bodies,” Frontiers in Microbiology, Vol. 3, 2012, p. 18. doi:10.3389/fmicb.2012.00018

[15]   L. S. Frost and G. Koraimann, “Regulation of Bacterial Conjugation: Balancing Opportunity with Adversity,” Future Microbiology, Vol. 5, No. 7, 2010, pp. 1057-1071. doi:10.2217/fmb.10.70

[16]   O. Johnsborg, V. Eldholm and L. S. H?varstein, “Natural Genetic Transformation: Prevalence, Mechanisms and Function,” Research in Microbiology, Vol. 158, No. 10, 2007, pp. 767-778. doi:10.1016/j.resmic.2007.09.004

[17]   C. Canchaya, G. Fournous, S. Chibani-Chennoufi, M. L. Dillmann and H. Brüssow, “Phage as Agents of Lateral Gene Transfer,” Current Opinion in Microbiology, Vol. 6, No. 4, 2003, pp. 417-424. doi:10.1016/S1369-5274(03)00086-9

[18]   M. Martinez-Garcia, B. K. Swan, N. J. Poulton, M. L. Gomez, D. Masland, M. E. Sieracki and R. Stepanauskas, “High-Throughput Single-Cell Sequencing Identifies Photo heterotrophs and Chemoautotrophs in Freshwater Bacte rioplankton,” The ISME Journal, Vol. 6, No. 1, 2012, pp. 113-123. doi:10.1038/ismej.2011.84

[19]   D. J. Saye, O. Ogunseitan, G. S. Sayler and R. V. Miller, “Potential for Transduction of Plasmids in a Natural Freshwater Environment: Effect of Plasmid Donor Concentration and a Natural Microbial Community on Transduction in Pseudomonas aeruginosa,” Applied and Environmental Microbiology, Vol. 53, No. 5, 1987, pp. 987-995.

[20]   S. B. O’Morchoe, O. Ogunseitan, G. S. Sayler and R. V. Miller, “Conjugal Transfer of R68.45 and FP5 between Pseudomonas aeruginosa Strains in a Freshwater Envi ronment,” Applied and Environmental Microbiology, Vol. 54, No. 8, 1988, pp. 1923-1929.

[21]   H. G. Williams, M. J. Day, J. C. Fry and G. J. Stewart, “Natural Transformation in River Epilithon,” Applied and Environmental Microbiology, Vol. 62, No. 8, 1996, pp. 2994-2998.

[22]   A. Caro-Quintero, J. Deng, J. Auchtung, I. Brettar, M. G. H?fle, J. Klappenbach and K. T. Konstantinidis, “Un precedented Levels of Horizontal Gene Transfer among Spatially Co-Occurring Shewanella Bacteria from the Baltic Sea,” The ISME Journal, Vol. 5, No. 1, 2011, pp. 131-140. doi:10.1038/ismej.2010.93

[23]   K. E. Ashelford, J. C. Fry, M. J. Day, K. E. Hill, M. A. Learner, J. R. Marchesi, C. D. Perkins and A. J. Weight man, “Using Microcosms to Study Gene Transfer in Aquatic Habitats,” FEMS Microbiology Ecology, Vol. 23, No. 2, 1997, pp. 81-94. doi:10.1111/j.1574-6941.1997.tb00393.x

[24]   J. D. van Elsas, J. Fry, P. Hirsch and S. Molin, “Ecology of Plasmid Transfer and Spread,” In: C. M. Thomas, Ed., The Horizontal Gene Pool, Harwood, Amsterdam, 2000, pp. 175-206. doi:10.4324/9780203304334_chapter_4

[25]   M. Shintani, N. Fukushima, M. Tezuka, H. Yamane and H. Nojiri, “Conjugative Transfer of the IncP-7 Carbazole Degradative Plasmid, pCAR1, in River Water Samples,” Biotechnology Letters, Vol. 30, No. 1, 2008, pp. 117-122. doi:10.1007/s10529-007-9519-y

[26]   T. Kenzaka, K. Tani and M. Nasu, “High-Frequency Phage-Mediated Gene Transfer in Freshwater Environ ments Determined at Single-Cell Level,” The ISME Journal, Vol. 4, No. 5, 2010, pp. 648-659. doi:10.1038/ismej.2009.145

[27]   F. Maruyama, K. Tani, T. Kenzaka, N. Yamaguchi and M. Nasu, “Quantitative Determination of Free-DNA Uptake in River Bacteria at the Single-Cell Level by in Situ Roll ing-Circle Amplification,” Applied and Environmental Microbiology, Vol. 72, No. 9, 2006, pp. 6248-6256. doi:10.1128/AEM.03035-05

[28]   F. Maruyama, K. Tani, T. Kenzaka, N. Yamaguchi and M. Nasu, “Application of Real-Time Long and Short Polymerase Chain Reaction for Sensitive Monitoring of the Fate of Extracellular Plasmid DNA Introduced into River Waters,” Microbes and Environments, Vol. 23, No. 3, 2008, pp. 229-236. doi:10.1264/jsme2.23.229

[29]   G. W. Jones, L. Baines and F. J. Genthner, “Heterotrophic Bacteria of the Freshwater Neuston and Their Ability to Act as Plasmid Recipients under Nutrient Deprived Conditions,” Microbial Ecology, Vol. 22, No. 1, 1991, pp. 15 25. doi:10.1007/BF02540210

[30]   M. J. Bale, J. C. Fry and M. J. Day, “Plasmid Transfer between Strains of Pseudomonas aeruginosa on Membrane Filters Attached to River Stones,” Journal of General Microbiology, Vol. 133, No. 11, 1987, pp. 3099 3107.

[31]   M. J. Bale, M. J. Day and J. C. Fry, “Novel Method for Studying Plasmid Transfer in Undisturbed River Epilithon,” Applied and Environmental Microbiology, Vol. 54, No. 11, 1988, pp. 2756-2758.

[32]   M. J. Bale, J. C. Fry and M. J. Day, “Transfer and Occurrence of Large Mercury Resistance Plasmids in River Epilithon,” Applied and Environmental Microbiology, Vol. 54, No. 4, 1988b, pp. 972-978.

[33]   M. G. Jobling, S. E. Peters and D. A. Ritchie, “Plas mid-Borne Mercury Resistance in Aquatic Bacteria,” FEMS Microbiology Letters, Vol. 49, No. 1, 1988, pp. 31-37.

[34]   J. C. Fry and M. J. Day, “Plasmid Transfer in the Epilithon,” In: J. C. Fry and M. J. Day, Eds., Bacterial Genetics in Natural Environments, Chapman and Hall, London, 1990, pp. 172-181. doi:10.1007/978-94-009-1834-4_5

[35]   M. G. Weinbauer, “Ecology of Prokaryotic Viruses,” FEMS Microbiology Reviews, Vol. 28, No. 2, 2004, pp. 127-181. doi:10.1016/j.femsre.2003.08.001

[36]   K. E. Wommack and R. R. Colwell, “Virioplankton: Vi ruses in Aquatic Ecosystems,” Microbiology and Mo lecular Biology Reviews, Vol. 64, No. 1, 2000, pp. 69-114. doi:10.1128/MMBR.64.1.69-114.2000

[37]   R. V. Miller, “Environmental Bacteriophage-Host Inter actions: Factors Contribution to Natural Transduction,” Antonie Van Leeuwenhoek, Vol. 79, No. 2, 2001, pp. 141 147. doi:10.1023/A:1010278628468

[38]   W. D. Morrison, R. V. Miller and G. S. Sayler, “Fre quency of F116-Mediated Transduction of Pseudomonas aeruginosa in a Freshwater Environment,” Applied and Environmental Microbiology, Vol. 36, No. 5, 1978, pp. 724-730.

[39]   D. J. Saye, O. Ogunseitan, G. S. Sayler and R. V. Miller, “Transduction of Linked Chromosomal Genes between Pseudomonas aeruginosa Strains during Incubation in Situ in a Freshwater Habitat,” Applied and Environmental Microbiology, Vol. 56, No. 1, 1990, pp. 140-145.

[40]   S. Ripp and R. V. Miller, “Effects of Suspended Particulates on the Frequency of Transduction among Pseudomonas aeruginosa in a Freshwater Environment,” Applied and Environmental Microbiology, Vol. 61, No. 4, 1995, pp. 1214-1219.

[41]   M. K. Amin and M. J. Day, “Donor and Recipient Effects on Transduction Frequency in Situ,” REGEM 1 Programme for the 1st International Conference on the Release of Genetically Engineered Microorganisms, Cardiff, 5-8 April 1988, p. 11.

[42]   K. M. Nielsen, P. J. Johnsen, D. Bensasson and D. Daffonchio, “Release and Persistence of Extracellular DNA in the Environment,” Environmental Biosafety Research, Vol. 6, No. 1-2, 2007, pp. 37-53. doi:10.1051/ebr:2007031

[43]   D. M. Karl and M. D. Bailiff, “The Measurement and Distribution of Dissolved Nucleic Acids in Aquatic Environments,” Limnology and Oceanography, Vol. 34, No. 3, 1989, pp. 543-558. doi:10.4319/lo.1989.34.3.0543

[44]   J. H. Paul, S. C. Jiang and J. B. Rose, “Concentration of Viruses and Dissolved DNA from Aquatic Environments by Vortex Flow Filtration,” Applied and Environmental Microbiology, Vol. 57, No. 8, 1991b, pp. 2197-2204.

[45]   W. Siuda, R. J. Chróst and H. Güde, “Distribution and Origin of Dissolved DNA in Lakes of Different Trophic States,” Aquatic Microbial Ecology, Vol. 15, No. 1, 1998, pp. 89-96. doi:10.3354/ame015089

[46]   S. C. Jiang and J. H. Paul, “Viral Contribution to Dissolved DNA in the Marine Kingdom as Determined by Differential Centrifugation and Kingdom Probing,” Applied and Environmental Microbiology, Vol. 61, No. 1, 1995, pp. 317-325.

[47]   H. C. Flemming and J. Wingender, “The Biofilm Matrix,” Nature Reviews Microbiology, Vol. 8, No. 9, 2010, pp. 623-633. doi:10.1038/nrmicro2415

[48]   T. Hara and S. Ueda, “A Study on the Mechanism of DNA Excretion from P. aeruginosa KYU-1. Effect of Mitomycin C on Extracellular DNA Production,” Agricultural Chemistry and Biotechnology, Vol. 45, No. 11, 1981, pp. 2457-2461. doi:10.1271/bbb1961.45.2457

[49]   M. G. Lorenz, D. Gerjets and W. Wackernagel, “Release of Transforming Plasmid and Chromosomal DNA from Two Cultured Soil Bacteria,” Archives of Microbiology, Vol. 156, No. 4, 1991, pp. 319-326. doi:10.1007/BF00263005

[50]   G. J. Stewart, “Transformation in Natural Environments,” In: E. M. H. Wellington and J. D. van Elsas, Eds., Genetic Interactions among Microorganisms in the Natural Environment, Pergamon Press, Oxford, 1992, pp. 216-234.

[51]   G. Romanowski, M. G. Lorenz and W. Wackernagel, “Adsorption of Plasmid DNA to Mineral Surfaces and Protection against DNase I,” Applied and Environmental Microbiology, Vol. 57, No. 4, 1991, pp. 1057-1061.

[52]   V. Torsvik, L. ?vre?s and T. F. Thingstad, “Prokaryotic Diversity—Magnitude, Dynamics, and Controlling Factors,” Science, Vol. 296, No. 5570, 2002, pp. 1064-1066. doi:10.1126/science.1071698

[53]   E. J. Biers, S. Sun and E. C. Howard, “Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome,” Applied and Environmental Microbiology, Vol. 75, No. 7, 2009, pp. 2221-2229. doi:10.1128/AEM.02118-08

[54]   R. J. Newton, S. E. Jones, A. Eiler, K. D. McMahon and S. Bertilsson, “A Guide to the Natural History of Fresh water Lake Bacteria,” Microbiology and Molecular Biology Reviews, Vol. 75, No. 1, 2011, pp. 14-49. doi:10.1128/MMBR.00028-10

[55]   L. A. Warren and E. A. Haack, “Biogeochemical Controls on Metal Behaviour in Freshwater Environments,” Earth-Science Reviews, Vol. 54, No. 4, 2001, pp. 261-320. doi:10.1016/S0012-8252(01)00032-0

[56]   A. Bissett, A. Reimer, D. de Beer, F. Shiraishi and G. Arp, “Metabolic Microenvironmental Control by Photosynthetic Biofilms under Changing Macroenvironmental Temperature and pH Conditions,” Applied and Environmental Microbiology, Vol. 74, No. 20, 2008, pp. 6306 6312. doi:10.1128/AEM.00877-08

[57]   D. A. Fike, C. L. Gammon, W. Ziebis and V. J. Orphan, “Micron-Scale Mapping of Sulfur Cycling across the Oxycline of a Cyanobacterial Mat: A Paired nanoSIMS and CARD-FISH Approach,” The ISME Journal, Vol. 2, No. 7, 2008, pp. 749-759. doi:10.1038/ismej.2008.39

[58]   T. Borch, R. Kretzschmar, A. Kappler, P. Van Cappellen, M. Ginder-Vogel, A. Voegelin and K. Campbell, “Bio geochemical Redox Processes and Their Impact on Contaminant Dynamics,” Environmental Science and Technology, Vol. 44, No. 1, 2010, pp. 15-23. doi:10.1021/es9026248

[59]   T. Lawley, B. M. Wilkins and L. S. Frost, “Bacterial Conjugation in Gram-Negative Bacteria,” In: B. E. Funnell and G. J. Philips, Eds., Plasmid Biology, ASM Press, Washington DC, 2004, pp. 203-226.

[60]   G. Alonso, K. Baptista, T. Ngo and D. E. Taylor, “Tran scriptional Organization of the Temperature-Sensitive Transfer System from the IncHI1 Plasmid R27,” Micro biology, Vol. 151, No. 11, 2005, pp. 3563-3573. doi:10.1099/mic.0.28256-0

[61]   F. W. Shiah and H. W. Ducklow, “Temperature Regulation of Heterotrophic Bacterioplankton Abundance, Pro duction, and Specific Growth Rate in Chesapeake Bay,” Limnology and Oceanography, Vol. 39, No. 6, 1994, pp. 1243-1258. doi:10.4319/lo.1994.39.6.1243

[62]   A. S. P. Ram, D. Boucher, T. Sime-Ngando, D. Debroas and J. C. Romagoux, “Phage Bacteriolysis, Protistan Bacterivory Potential, and Bacterial Production in a Fresh water Reservoir: Coupling with Temperature,” Microbial Ecology, Vol. 50, No. 1, 2005, pp. 64-72. doi:10.1007/s00248-004-0110-y

[63]   W. F. Yue, M. Du and M. J. Zhu, “High Temperature in Combination with UV Irradiation Enhances Horizontal Transfer of stx2 Gene from E. coli O157:H7 to Non Pathogenic E. coli,” PLoS ONE, Vol. 7, No. 2, 2012, Ar ticle ID: e31308. doi:10.1371/journal.pone.0031308

[64]   I. Ahrenholtz, M. G. Lorenz and W. Wackernagel, “The Extracellular Nuclease of Serratia marcescens: Studies on the Activity in Vitro and Effect on Transforming DNA in a Groundwater Aquifer Microcosm,” Archives of Microbiology, Vol. 161, No. 2, 1994, pp. 176-183.

[65]   K. Matsui, M. Honjo and Z. Kawabata, “Estimation of the Fate of Dissolved DNA in Thermally Stratified Lake Water from the Stability of Exogenous Plasmid DNA,” Aquatic Microbial Ecology, Vol. 26, No. 1, 2001, pp. 95 102. doi:10.3354/ame026095

[66]   I. Auzat, S. Chapuy-Regaud, G. Le Bras, D. D. Santos, A. D. Ogunniyi, I. L. Thomas, J. R. Garel, J. C. Paton and M. C. Trombe, “The NADH Oxidase of Streptococcus pneumoniae: Its Involvement in Competence and Virulence,” Molecular Microbiology, Vol. 34, No. 5, 1999, pp. 1018-1028. doi:10.1046/j.1365-2958.1999.01663.x

[67]   D. R. Stallions and R. Curtiss, “Bacterial Conjugation under Anaerobic Conditions,” Journal of Bacteriology, Vol. 111, No. 1, 1972, pp. 294-295.

[68]   J. E. Król, H. D. Nguyen, L. M. Rogers, H. Beyenal, S. M. Krone and E. M. Top, “Increased Transfer of a Multidrug Resistance Plasmid in Escherichia coli Biofilms at the Air-Liquid Interface,” Applied and Environmental Microbiology, Vol. 77, No. 15, 2011, pp. 5079-5088. doi:10.1128/AEM.00090-11

[69]   L. S. Frost and J. Simon, “Studies on the Pili of the Promiscuous Plasmid RP4,” In: C. I. Kado and J. H. Crosa, Eds., Molecular Mechanisms of Bacterial Virulence, Kluwer Academic Publishers, Dordrecht, 1994, pp. 47-65. doi:10.1007/978-94-011-0746-4_4

[70]   P. Viljanen and J. Boratynski, “The Susceptibility of Conjugative Resistance Transfer in Gram-Negative Bacteria to Physicochemical and Biochemical Agents,” FEMS Microbiology Letters, Vol. 88, No. 1, 1991, pp. 43-54. doi:10.1111/j.1574-6968.1991.tb04956.x

[71]   C. A. Pinedo and B. F. Smets, “Conjugal TOL Transfer from Pseudomonas putida to Pseudomonas aeruginosa: Effects of Restriction Proficiency, Toxicant Exposure, Cell Density Ratios, and Conjugation Detection Method on Observed Transfer Efficiencies,” Applied and Environmental Microbiology, Vol. 71, No. 1, 2005, pp. 51-57. doi:10.1128/AEM.71.1.51-57.2005

[72]   A. Sch?fer, J. Kalinowski and A. Pühler, “Increased Fertility of Corynebacterium glutamicum Recipients in Intergeneric Matings with Escherichia coli after Stress Ex posure,” Applied and Environmental Microbiology, Vol. 60, No. 2, 1994, pp. 756-759.

[73]   R. A. Edwards, R.A. Helm and S. R. Maloy, “Increasing DNA Transfer Efficiency by Temporary Inactivation of Host Restriction,” Biotechniques, Vol. 26, No. 5, 1999, pp. 892-900.

[74]   J. P. Claverys, M. Prudhomme and B. Martin, “Induction of Competence Regulons as a General Response to Stress in Gram-Positive Bacteria,” Annual Review of Microbi ology, Vol. 60, 2006, pp. 451-475. doi:10.1146/annurev.micro.60.080805.142139

[75]   M. Prudhomme, L. Attaiech, G. Sanchez, B. Martin and J. P. Claverys, “Antibiotic Stress Induces Genetic Trans formability in the Human Pathogen Streptococcus pneumonia,” Science, Vol. 313, No. 5783, 2006, pp. 89-92. doi:10.1126/science.1127912

[76]   C. úbeda, E. Maiques, E. Knecht, í. Lasa, R. P. Novick and J. R. Penadés, “Antibiotic-Induced SOS Response Promotes Horizontal Dissemination of Pathogenicity Is land-Encoded Virulence Factors in Staphylococci,” Molecular Microbiology, Vol. 56, No. 3, 2005, pp. 836-844. doi:10.1111/j.1365-2958.2005.04584.x

[77]   E. Maiques, C. úbeda, S. Campoy, N. Salvador, í. Lasa, R. P. Novick, J. Barbé and J. R. Penadés, “β-Lactam Antibiotics Induce the SOS Response and Horizontal Transfer of Virulence Factors in Staphylococcus aureus,” Journal of Bacteriology, Vol. 188, No. 7, 2006, pp. 2726 2729. doi:10.1128/JB.188.7.2726-2729.2006

[78]   J. W. Beaber, B. Hochhut and M. K. Waldor, “SOS Re sponse Promotes Horizontal Dissemination of Antibiotic Resistance Genes,” Nature, Vol. 427, No. 6969, 2004, pp. 72-74. doi:10.1038/nature02241

[79]   T. G. Rossman, M. Molina and L. W. Meyer, “The Genetic Toxicology of Metal Compounds: I. Induction of λ Prophage in E coli WP2S (λ),” Environmental Mutagenesis, Vol. 6, No. 1, 1984, pp. 59-69. doi:10.1002/em.2860060108

[80]   T. G. Rossman, M. Molina, L. Meyer, P. Boone, C. B. Klein, Z. Wang, F. Li, W. C. Lin and P. L. Kinney, “Performance of 133 Compounds in the Lambda Prophage Induction Endpoint of the Microscreen Assay and a Comparison with S. typhimurium Mutagenicity and Ro dent Carcinogenicity Assays,” Mutation Research, Vol. 260, No. 4, 1991, pp. 349-367. doi:10.1016/0165-1218(91)90021-D

[81]   D. M. DeMarini and H. G. Brooks, “Induction of Pro phage Lambda by Chlorinated Organics: Detection of Some Single-Species/Single-Site Carcinogens,” Environmental and Molecular Mutagenesis, Vol. 19, No. 2, 1992, pp. 98-111. doi:10.1002/em.2850190204

[82]   N. Soberón, R. Martín and J. E. Suárez, “New Method for Evaluation of Genotoxicity, Based on the Use of Real Time PCR and Lysogenic Gram-Positive and Gram Negative Bacteria,” Applied and Environmental Microbiology, Vol. 73, No. 9, 2007, pp. 2815-2819. doi:10.1128/AEM.00407-07

[83]   L. R. Mesak, V. Miao and J. Davies, “Effects of Subinhibitory Concentrations of Antibiotics on SOS and DNA Repair Gene Expression in Staphylococcus aureus,” Antimicrobial Agents and Chemotherapy, Vol. 52, No. 9, 2008, pp. 3394-3397. doi:10.1128/AAC.01599-07

[84]   Z. Baharoglu and D. Mazel, “Vibrio cholerae Triggers SOS and Mutagenesis in Response to a Wide Range of Antibiotics: A Route towards Multiresistance,” Antimicrobial Agents and Chemotherapy, Vol. 55, No. 5, 2011, pp. 2438-2441. doi:10.1128/AAC.01549-10

[85]   V. M. F. Vargas, S. B. Migliavacca, A. C. de Melo, R. C. Horn, R. R. Guidobono, I. C. F. de Sá Ferreira and M. H. D. Pestana, “Genotoxicity Assessment in Aquatic Environments under the Influence of Heavy Metals and Organic Contaminants,” Mutation Research, Vol. 490, No. 2, 2001, pp. 141-158. doi:10.1016/S1383-5718(00)00159-5

[86]   E. Kristiansson, J. Fick, A. Janzon, R. Grabic, C. Rut gersson, B. Weijdeg?rd, H. S?derstr?m and D. G. J. Larsson, “Pyrosequencing of Antibiotic-Contaminated River Sediments Reveals High Levels of Resistance and Gene Transfer Elements,” PLoS ONE, Vol. 6, No. 2, 2011, e17038. doi:10.1371/journal.pone.0017038

[87]   K. Smalla, A. S. Haines, K. Jones, E. Kr?gerrecklenfort, H. Heuer, M. Schloter and C. M. Thomas, “Increased Abundance of IncP-1β Plasmids and Mercury Resistance Genes in Mercury-Polluted River Sediments: First Discovery of IncP-1β Plasmids with a Complex mer Trans poson as the Sole Accessory Element,” Applied and Environmental Microbiology, Vol. 72, No. 11, 2006, pp. 7253-7259. doi:10.1128/AEM.00922-06

[88]   M. S. Wright, C. Baker-Austin, A. H. Lindell, R. Ste panauskas, H. W. Stokes and J. V. McArthur, “Influence of Industrial Contamination on Mobile Genetic Elements: Class 1 Integron Abundance and Gene Cassette Structure in Aquatic Bacterial Communities,” The ISME Journal, Vol. 2, No. 4, 2008, pp. 417-428. doi:10.1038/ismej.2008.8

[89]   C. P. Rosewarne, V. Pettigrove, H. W. Stokes and Y. M. Parsons, “Class 1 Integrons in Benthic Bacterial Communities: Abundance, Association with Tn402-Like Trans position Modules and Evidence for Coselection with Heavy-Metal Resistance,” FEMS Microbiology Ecology, Vol. 72, No. 1, 2010, pp. 35-46. doi:10.1111/j.1574-6941.2009.00823.x

[90]   N. F. Burton, M. J. Day and A. T. Bull, “Distribution of Bacterial Plasmids in Clean and Polluted Sites in a South Wales River,” Applied and Environmental Microbiology, Vol. 44, No. 5, 1982, pp. 1026-1029.

[91]   R. P. Schwarzenbach, B. I. Escher, K. Fenner, T. B. Hofstetter, C. A. Johnson, U. von Gunten and B. Wehrli, “The Challenge of Micropollutants in Aquatic Systems,” Science, Vol. 313, No. 5790, 2006, pp. 1072-1077. doi:10.1126/science.1127291

[92]   K. Kümmerer, “Antibiotics in the Aquatic Environment A Review Part I,” Chemosphere, Vol. 75, No. 4, 2009, pp. 417-434. doi:10.1016/j.chemosphere.2008.11.086

[93]   B. L. Skjelkv?le, T. Andersen, E. Fjeld, J. Mannio, A. Wilander, K. Johansson, J. P. Jensen and T. Moiseenko, “Heavy Metal Surveys in Nordic Lakes; Concentrations, Geographic Patterns and Relation to Critical Limits,” Ambio, Vol. 30, No. 1, 2001, pp. 2-10.

[94]   A. C. Alder, A. Bruchet, M. Carballa, M. Clara, A. Joss, D. L?ffler, C. S. McArdell, K. Miksch, F. Omil, T. Tuhkanen and T. A. Ternes, “Consumption and Occurrence,” In: T. A. Ternes and A. Joss, Eds., Human Pharmaceuticals, Hormones and Fragrances: The Challenge of Micropollutants in Urban Water Management, IWA Publishing, London, 2009, pp. 15-54.

[95]   D. E. Armstrong and A. W. Elzerman, “Trace Metal Ac cumulation in Surface Microlayers,” Journal of Great Lakes Research, Vol. 8, No. 2, 1982, pp. 282-287. doi:10.1016/S0380-1330(82)71966-5

[96]   J. Eggleton and K. V. Thomas, “A Review of Factors Affecting the Release and Bioavailability of Contaminants during Sediment Disturbance Events,” Environment International, Vol. 30, No. 7, 2004, pp. 973-980. doi:10.1016/j.envint.2004.03.001

[97]   O. Wurl and J. P. Obbard, “A Review of Pollutants in the Sea-Surface Microlayer (SML): A Unique Habitat for Marine Organisms,” Marine Pollution Bulletin, Vol. 48, No. 11-12, 2004, pp. 1016-1030. doi:10.1016/j.marpolbul.2004.03.016

[98]   E. Haack and L. A. Warren, “Biofilm Hydrous Manganese Oxyhydroxides and Metal Dynamics in Acid Rock Drainage,” Environmental Science and Technology, Vol. 37, No. 18, 2003, pp. 4138-4147. doi:10.1021/es026274z

[99]   D. B. Wunder, V. A. Bosscher, R. C. Cok and R. M. Ho zalski, “Sorption of Antibiotics to Biofilm,” Water Research, Vol. 45, No. 6, 2011, pp. 2270-2280. doi:10.1016/j.watres.2010.11.013

[100]   J. M. Harrington, S. E. Fendorf and R. F. Rosenzweig, “Biotic Generation of Arsenic(III) in Metal(loid)-Contaminated Freshwater Lake Sediments,” Environmental Science and Technology, Vol. 32, No. 16, 1998, pp. 2425 2430. doi:10.1021/es971129k

[101]   R. P. Rastogi, Richa, A. Kumar, M. B. Tyagi and R. P. Sinha, “Molecular Mechanisms of Ultraviolet Radia tion-Induced DNA Damage and Repair,” Journal of Nucleic Acids, 2010, 592980. doi:10.4061/2010/592980

[102]   R. Maranger, P. A. del Giorgio and D. F. Bird, “Accumulation of Damaged Bacteria and Viruses in Lake Water Exposed to Solar Radiation,” Aquatic Microbial Ecology, Vol. 28, No. 3, 2002, pp. 213-227. doi:10.3354/ame028213

[103]   K. E. Wommack, R. T. Hill, T. A. Muller and R. R. Colwell, “Effects of Sunlight on Bacteriophage Viability and Structure,” Applied and Environmental Microbiology, Vol. 62, No. 4, 1996, pp. 1336-1341.

[104]   S. W. Wilhelm, M. G. Weinbauer, C. A. Suttle and W. H. Jeffrey, “The Role of Sunlight in the Removal and Repair of Viruses in the Sea,” Limnology and Oceanography, Vol. 43, No. 4, 1998, pp. 586-592. doi:10.4319/lo.1998.43.4.0586

[105]   J. L. Ravanat, T. Douki and J. Cadet, “Direct and Indirect Effects of UV Radiation on DNA and Its Components,” Journal of Photochemistry and Photobiology B: Biology, Vol. 63, No. 1-3, 2001, pp. 88-102. doi:10.1016/S1011-1344(01)00206-8

[106]   M. A. Tapper and R. E. Hicks, “Temperate Viruses and Lysogeny in Lake Superior Bacterioplankton,” Limnology and Oceanography, Vol. 43, No. 1, 1998, pp. 95-103. doi:10.4319/lo.1998.43.1.0095

[107]   S. W. Wilhelm and R. E. H. Smith, “Bacterial Carbon Production in Lake Erie is Influenced by Viruses and Solar Radiation,” Canadian Journal of Fisheries and Aquatic Sciences, Vol. 57, No. 2, 2000, pp. 317-326. doi:10.1139/f99-202

[108]   D. P. H?der, H. D. Kumar, R. C. Smith and R. C. Worrest, “Effects of Solar UV Radiation on Aquatic Ecosystems and Interactions with Climate Change,” Photochemical and Photobiological Sciences, Vol. 6, No. 3, 2007, pp. 267-285. doi:10.1039/b700020k

[109]   D. P. Morris, H. Zagarese, C. E. Williamson, E. G. Bal seiro, B. R. Hargreaves, B. Modenutti, R. Moeller and C. Queimalinos, “The Attenuation of Solar UV Radiation in Lakes and the Role of Dissolved Organic Carbon,” Limnology and Oceanography, Vol. 40, No. 8, 1995, pp. 1381-1391. doi:10.4319/lo.1995.40.8.1381

[110]   N. M. Scully and D. R. S. Lean, “The Attenuation of Ultraviolet Radiation in Temperate Lakes,” Archiv für Hydrobiologie, Vol. 43, 1994, pp. 135-144.

[111]   M. G. Lorenz, B. W. Aardema and W. Wackernagel, “Highly Efficient Genetic Transformation of Bacillus subtilis Attached to Sand Grains,” Journal of General Microbiology, Vol. 134, No. 1, 1988, pp. 107-112.

[112]   B. Chamier, M. G. Lorenz and W. Wackernagel, “Natural Transformation of Acinetobacter calcoaceticus by Plas mid DNA Adsorbed on Sand and Groundwater Aquifer Material,” Applied and Environmental Microbiology, Vol. 59, No. 5, 1993, pp. 1662-1667.

[113]   C. Vettori, G. Stotzky, M. Yoder and E. Gallori, “Interaction between Bacteriophage PBS1 and Clay Minerals and Transduction of Bacillus subtilis by Clay-Phage Complexes,” Environmental Microbiology, Vol. 1, No. 4, 1999, pp. 347-355. doi:10.1046/j.1462-2920.1999.00044.x

[114]   C. Vettori, E. Gallori and G. Stotzky, “Clay Minerals Protect Bacteriophage PBS1 of Bacillus subtilis Against Inactivation and Loss of Transducing Ability by UV Ra diation,” Canadian Journal of Microbiology, Vol. 46, No. 8, 2000, pp. 770-773.

[115]   D. Kirchman and R. Mitchell, “Contribution of Particle-Bound Bacteria to Total Microheterotrophic Activity in Five Ponds and Two Marshes,” Applied and Environ mental Microbiology, Vol. 43, No. 1, 1982, pp. 200-209.

[116]   B. C. Crump, J. A. Baross and C. A. Simenstad, “Dominance of Particle-Attached Bacteria in the Columbia River Estuary, USA,” Aquatic Microbial Ecology, Vol. 14, No. 1, 1998, pp. 7-18. doi:10.3354/ame014007

[117]   N. D. Seeley and S. B. Primrose, “A Review: The Isolation of Bacteriophages from the Environment,” Journal of Applied Bacteriology, Vol. 53, No. 1, 1982, pp. 1-17. doi:10.1111/j.1365-2672.1982.tb04729.x

[118]   L. Kernegger, I. Zweimüller and P. Peduzzi, “Effects of Suspended Matter Quality and Virus Abundance on Microbial Parameters: Experimental Evidence from a Large European River,” Aquatic Microbial Ecology, Vol. 57, No. 2, 2009, pp. 161-173. doi:10.3354/ame01341

[119]   G. Pietramellara, J. Ascher, F. Borgogni, M. T. Cec cherini, G. Guerri and P. Nannipieri, “Extracellular DNA in Soil and Sediment: Fate and Ecological Relevance,” Biology and Fertility of Soils, Vol. 45, No. 3, 2009, pp. 219-235. doi:10.1007/s00374-008-0345-8

[120]   G. Romanowski, M. G. Lorenz and W. Wackernagel, “Plasmid DNA in a Groundwater Aquifer Microcosm— Adsorption, DNAase Resistance and Natural Genetic Transformation of Bacillus subtilis,” Molecular Ecology, Vol. 2, No. 3, 1993, pp. 171-181. doi:10.1111/j.1365-294X.1993.tb00106.x

[121]   C. Crecchio and G. Stotzky, “Binding of DNA on Humic Acids: Effect on Transformation of Bacillus subtilis and Resistance to DNase,” Soil Biology and Biochemistry, Vol. 30, No. 8-9, 1998, pp. 1061-1067. doi:10.1016/S0038-0717(97)00248-4

[122]   N. Lu, J. L. Zilles and T. H. Nguyen, “Adsorption of Extracellular Chromosomal DNA and Its Effects on Natural Transformation of Azotobacter vinelandii,” Applied and Environmental Microbiology, Vol. 76, No. 13, 2010, pp. 4179-4184. doi:10.1128/AEM.00193-10

[123]   P. Cai, Q. Huang, W. Chen, D. Zhang, K. Wang, D. Jiang and W. Liang, “Soil Colloids-Bound Plasmid DNA: Effect on Transformation of E. coli and Resistance to DNase I Degradation,” Soil Biology and Biochemistry, Vol. 39, No. 5, 2007a, pp. 1007-1013. doi:10.1016/j.soilbio.2006.11.010

[124]   K. E. Hill and E. M. Top, “Gene Transfer in Soil Systems Using Microcosms,” FEMS Microbiology Ecology, Vol. 25, No. 4, 1998, pp. 319-329. doi:10.1111/j.1574-6941.1998.tb00483.x

[125]   J. M. Plach, A. V. C. Elliott, I. G. Droppo and L. A. Warren, “Physical and Ecological Controls on Freshwater Floc Trace Metal Dynamics,” Environmental Science and Technology, Vol. 45, No. 6, 2011, pp. 2157-2164. doi:10.1021/es1031745

[126]   A. V. C. Elliott, J. M. Plach, I. G. Droppo and L. A. Warren, “Comparative Floc-Bed Sediment Trace Element Partitioning across Variably Contaminated Aquatic Eco systems,” Environmental Science and Technology, Vol. 46, No. 1, 2012, pp. 209-216. doi:10.1021/es202221u

[127]   Z. Qiu, Y. Yu, Z. Chen, M. Jin, D. Yang, Z. Zhao, J. Wang, Z. Shen, X. Wang, D. Qian, A. Huang, B. Zhang and J. W. Li, “Nanoalumina Promotes the Horizontal Transfer of Multiresistance Genes Mediated by Plasmids across Genera,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 109, No. 13, 2012, pp. 4944-4949. doi:10.1073/pnas.1107254109

[128]   A. S?dergren, “Role of Aquatic Surface Microlayer in the Dynamics of Nutrients and Organic Compounds in Lakes, with Implications for the Ecotones,” Hydrobiologia, Vol. 251, No. 1-3, 1993, pp. 217-225. doi:10.1007/BF00007181

[129]   G. A. Weyhenmeyer, L. Hakanson and M. Meili, “A Validated Model for Daily Variations in the Flux, Origin, and Distribution of Settling Particles Within Lakes,” Limnology and Oceanography, Vol. 42, No. 7, 1997, pp. 1517-1529. doi:10.4319/lo.1997.42.7.1517

[130]   M. K. Amin and M. J. Day, “Influence of pH Value on Viability and Transduction Frequency of Pseudomonas aeruginosa Phage F116,” Letters in Applied Microbiology, Vol. 6, No. 4, 1988b, pp. 93-96. doi:10.1111/j.1472-765X.1988.tb01222.x

[131]   P. A. Rochelle, M. J. Day and J. C. Fry, “Occurrence, Transfer and Mobilization in Epilithic Strains of Acine tobacter of Mercury-Resistance Plasmids Capable of Transformation,” Journal of General Microbiology, Vol. 134, No. 11, 1988, pp. 2933-2941.

[132]   P. A. Rochelle, J. C. Fry and M. J. Day, “Factors Affecting Conjugal Transfer of Plasmids Encoding Mercury Resistance from Pure Cultures and Mixed Natural Suspensions of Epilithic Bacteria,” Journal of General Microbiology, Vol. 135, No. 2, 1989, pp. 409-424.

[133]   A. Fernandez-Astorga, A. Muela, R. Cisterna, J. Iriberri and I. Barcina, “Biotic and Abiotic Factors Affecting Plasmid Transfer in Escherichia coli Strains,” Applied and Environmental Microbiology, Vol. 58, No. 1, 1992, pp. 392-398.

[134]   L. J. Tranvik, W. Graneli and G. Gahnstroem, “Microbial Activity in Acidified and Limed Humic Lakes,” Canadian Journal of Fisheries and Aquatic Sciences, Vol. 51, No. 11, 1994, pp. 2529-2536. doi:10.1139/f94-252

[135]   S. C. Maberly, “Diel, Episodic and Seasonal Changes in pH and Concentrations of Inorganic Carbon in a Productive Lake,” Freshwater Biology, Vol. 35, No. 3, 1996, pp. 579-598. doi:10.1111/j.1365-2427.1996.tb01770.x

[136]   A. L. Mills, J. S. Herman, G. M. Hornberger and T. H. DeJesús, “Effect of Solution Ionic Strength and Iron Coatings on Mineral Grains on the Sorption of Bacterial Cells to Quartz Sand,” Applied and Environmental Microbiology, Vol. 60, No. 9, 1994, pp. 3300-3306.

[137]   T. H. Nguyen and K. L. Chen, “Role of Divalent Cations in Plasmid DNA Adsorption to Natural Organic Mat ter-Coated Silica Surface,” Environmental Science and Technology, Vol. 41, No. 15, 2007, pp. 5370-5375. doi:10.1021/es070425m

[138]   X. Wang, M. Li, Q. Yan, X. Chen, J. Geng, Z. Xie and P. Shen, “Across Genus Plasmid Transformation between Bacillus subtilis and Escherichia coli and the Effect of Escherichia coli on the Transforming Ability of Free Plasmid DNA,” Current Microbiology, Vol. 54, No. 6, 2007, pp. 450-456. doi:10.1007/s00284-006-0617-1

[139]   W. J. Page and M. von Tigerstrom, “Optimal Conditions for Transformation of Azotobacter vinelandii,” Journal of Bacteriology, Vol. 139, No. 3, 1979, pp. 1058-1061.

[140]   B. Baur, K. Hanselmann, W. Schlimme and B. Jenni, “Genetic Transformation in Freshwater: Escherichia coli Is Able to Develop Natural Competence,” Applied and Environmental Microbiology, Vol. 62, No. 10, 1996, pp. 3673-3678.

[141]   J. M. Solomon and A. D. Grossman, “Who’s Competent and When: Regulation of Natural Genetic Competence in Bacteria,” Trends in Genetics, Vol. 12, No. 4, 1996, pp. 150-155. doi:10.1016/0168-9525(96)10014-7

[142]   M. C. Trombe, C. Clavé and J. M. Manias, “Calcium Regulation of Growth and Differentiation in Streptococcus pneumonia,” Journal of General Microbiology, Vol. 138, No. 1, 1992, pp. 77-84. doi:10.1099/00221287-138-1-77

[143]   C. M. Thomas and K. M. Nielsen, “Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria,” Nature Reviews Microbiology, Vol. 3, No. 9, 2005, pp. 711-721. doi:10.1038/nrmicro1234

[144]   J. Replicon, A. Frankfater and R. V. Miller, “A Continuous Culture Model to Examine Factors that Affect Transduction among Pseudomonas aeruginosa Strains in Freshwater Environments,” Applied and Environmental Microbiology, Vol. 61, No. 9, 1995, pp. 3359-3366.

[145]   P. Tuomi, T. Torsvik, M. Heldal and G. Bratbak, “Bacterial Population Dynamics in a Meromictic Lake,” Applied and Environmental Microbiology, Vol. 63, No. 6, 1997, pp. 2181-2188.

[146]   M. G. Weinbauer and M. G. H?fle, “Significance of Viral Lysis and Flagellate Grazing as Factors Controlling Bacterioplankton Production in a Eutrophic Lake,” Applied and Environmental Microbiology, Vol. 64, No. 2, 1998a, pp. 431-438.

[147]   M. G. Weinbauer and M. G. H?fle, “Size-Specific Mortality of Lake Bacterioplankton by Natural Virus Com munities,” Aquatic Microbial Ecology, Vol. 15, No. 2, 1998b, pp. 103-113. doi:10.3354/ame015103

[148]   Y. Bettarel, T. Sime-Ngando, C. Amblard and J. Dolan, “Viral Activity in Two Contrasting Lake Ecosystems,” Applied and Environmental Microbiology, Vol. 70, No. 5, 2004, pp. 2941-2951. doi:10.1128/AEM.70.5.2941-2951.2004

[149]   J. W. Costerton, Z. Lewandowski, D. E. Caldwell, D. R. Korber and H. M. Lappin-Scott, “Microbial Biofilms,” Annual Review of Microbiology, Vol. 49, 1995, pp. 711 745. doi:10.1146/annurev.mi.49.100195.003431

[150]   S. J. S?rensen, M. Bailey, L. H. Hansen, N. Kroer and S. Wuertz, “Studying Plasmid Horizontal Transfer in Situ: A Critical Review,” Nature Reviews Microbiology, Vol. 3, No. 9, 2005, pp. 700-710. doi:10.1038/nrmicro1232

[151]   K. B. Barken, S. J. Pamp, L. Yang, M. Gjermansen, J. J. Bertrand, M. Klausen, M. Givskov, C. B. Whitchurch, J. N. Engel and T. Tolker-Nielsen, “Roles of Type IV Pili, Flagellum-Mediated Motility and Extracellular DNA in the Formation of Mature Multicellular Structures in Pseudomonas aeruginosa Biofilms,” Environmental Microbiology, Vol. 10, No. 9, 2008, pp. 2331-2343. doi:10.1111/j.1462-2920.2008.01658.x

[152]   J. M. Ghigo, “Natural Conjugative Plasmids Induce Bacterial Biofilm Development,” Nature, Vol. 412, No. 6845, 2001, pp. 442-445. doi:10.1038/35086581

[153]   J. G?deke, K. Paul, J. Lassak and K. M. Thormann, “Phage-Induced Lysis Enhances Biofilm Formation in Shewanella oneidensis MR-1,” The ISME Journal, Vol. 5, No. 4, 2011, pp. 613-626. doi:10.1038/ismej.2010.153

[154]   M. Hausner and S. Wuertz, “High Rates of Conjugation in Bacterial Biofilms as Determined by Quantitative in Situ Analysis,” Applied and Environmental Microbiology, Vol. 65, No. 8, 1999, pp. 3710-3713.

[155]   S. Molin and T. Tolker-Nielsen, “Gene Transfer Occurs with Enhanced Efficiency in Biofilms and Induces Enhanced Stabilisation of the Biofilm Structure,” Current Opinion in Biotechnology, Vol. 14, No. 3, 2003, pp. 255 261. doi:10.1016/S0958-1669(03)00036-3

[156]   S. Maeda, M. Ito, T. Ando, Y. Ishimoto, Y. Fujisawa, H. Takahashi, A. Matsuda, A. Sawamura and S. Kato, “Ho rizontal Transfer of Nonconjugative Plasmids in a Colony Biofilm of Escherichia coli,” FEMS Microbiology Letters, Vol. 255, No. 1, 2006, pp. 115-120. doi:10.1111/j.1574-6968.2005.00072.x

[157]   R. E. Fox, X. Zhong, S. M. Krone and E. M. Top, “Spatial Structure and Nutrients Promote Invasion of IncP-1 Plasmids in Bacterial Populations,” The ISME Journal, Vol. 2, No. 10, 2008, pp. 1024-1039. doi:10.1038/ismej.2008.53

[158]   M. L. Angles, K. C. Marshall and A. E. Goodman, “Plasmid Transfer between Marine Bacteria in the Aqueous Phase and Biofilms in Reactor Microcosms,” Applied and Environmental Microbiology, Vol. 59, No. 3, 1993, pp. 843-850.

[159]   M. K. Kay, T. C. Erwin, R. J. C. McLean and G. M. Aron, “Bacteriophage Ecology in Escherichia coli and Pseudomonas aeruginosa Mixed-Biofilm Communities,” Applied and Environmental Microbiology, Vol. 77, No. 3, 2011, pp. 821-829. doi:10.1128/AEM.01797-10

[160]   A. Resch, B. Fehrenbacher, K. Eisele, M. Schaller and F. G?tz, “Phage Release from Biofilm and Planktonic Staphylococcus aureus Cells,” FEMS Microbiology Letters, Vol. 252, No. 1, 2005, pp. 89-96. doi:10.1016/j.femsle.2005.08.048

[161]   P. S. Stewart and M. J. Franklin, “Physiological Heterogeneity in Biofilms,” Nature Reviews Microbiology, Vol. 6, No. 3, 2008, pp. 199-210. doi:10.1038/nrmicro1838

[162]   G. Hidalgo, A. Burns, E. Herz, A. G. Hay, P. L. Houston, U. Wiesner and L. W. Lion, “Functional Tomographic Fluorescence Imaging of pH Microenvironments in Microbial Biofilms by Use of Silica Nanoparticle Sensors,” Applied and Environmental Microbiology, Vol. 75, No. 23, 2009, pp. 7426-7435. doi:10.1128/AEM.01220-09

[163]   A. P. Hitchcock, J. J. Dynes, J. R. Lawrence, M. Obst, G. D. W. Swerhone, D. R. Korber and G. G. Leppard, “Soft X-Ray Spectromicroscopy of Nickel Sorption in a Natural River Biofilm,” Geobiology, Vol. 7, No. 4, 2009, 432-453. doi:10.1111/j.1472-4669.2009.00211.x

[164]   G. Chen, X. Chen, Y. Yang, A. G. Hay, X. Yu and Y. Chen, “Sorption and Distribution of Copper in Unsaturated Pseudomonas putida CZ1 Biofilms as Determined by X-ray Fluorescence Microscopy,” Applied and Environmental Microbiology, Vol. 77, No. 14, 2011, pp. 4719-4727. doi:10.1128/AEM.00125-11

[165]   J. D. van Elsas and M. J. Bailey, “The Ecology of Transfer of Mobile Genetic Elements,” FEMS Microbiology Ecology, Vol. 42, No. 2, 2002, pp. 187-197.

[166]   M. Hermansson and C. Linberg, “Gene Transfer in the Marine Environment,” FEMS Microbiology Ecology, Vol. 15, No. 1-2, 1994, pp. 47-54. doi:10.1111/j.1574-6941.1994.tb00228.x

[167]   B. F. Smets, B. E. Rittmann and D. A. Stahl, “Quantifica tion of the Effect of Substrate Concentration on the Conjugal Transfer Rate of the TOL Plasmid in Short-Term Batch Mating Experiments,” Letters in Applied Microbiology, Vol. 21, No. 3, 1995, pp. 167-172. doi:10.1111/j.1472-765X.1995.tb01033.x

[168]   M. R. Shakibaie, K. A. Jalilzadeh and S. M. Yamakanamardi, “Horizontal Transfer of Antibiotic Resistance Genes among Gram Negative Bacteria in Sewage and Lake Water and Influence of Some Physico-Chemical Parameters of Water on Conjugation Process,” Journal of Environmental Biology, Vol. 30, No. 1, 2009, pp. 45-49.

[169]   B. Normander, B. B. Christensen, S. Molin and N. Kroer, “Effect of Bacterial Distribution and Activity on Conjugal Gene Transfer on the Phylloplane of the Bush Bean (Phaseolus vulgaris),” Applied and Environmental Microbiology, Vol. 64, No. 5, 1998, pp. 1902-1909.

[170]   A. R. Johnsen and N. Kroer, “Effects of Stress and Other Environmental Factors on Horizontal Plasmid Transfer Assessed by Direct Quantification of Discrete Transfer Events,” FEMS Microbiology Ecology, Vol. 59, No. 3, 2007, pp. 718-728. doi:10.1111/j.1574-6941.2006.00230.x

[171]   T. A. Kokjohn and G. S. Sayler, “Attachment and Replication of Pseudomonas aeruginosa Bacteriophages under Conditions Simulating Aquatic Environments,” Journal of General Microbiology, Vol. 137, No. 3, 1991, pp. 661 666. doi:10.1099/00221287-137-3-661

[172]   S. E. Finkel and R. Kolter, “DNA as a Nutrient: Novel Role for Bacterial Competence Gene Homologs,” Journal of Bacteriology, Vol. 183, No. 21, 2001, pp. 6288-6293. doi:10.1128/JB.183.21.6288-6293.2001

[173]   J. J. Elser, L. B. Stabler and R. P. Hassett, “Nutrient Limitation of Bacterial Growth and Rates of Bacterivory in Lakes and Oceans: A Comparative Study,” Aquatic Microbial Ecology, Vol. 9, No. 2, 1995, pp. 105-110. doi:10.3354/ame009105

[174]   E. M. Smith and Y. T. Prairie, “Bacterial Metabolism and Growth Efficiency in Lakes: The Importance of Phosphorus Availability,” Limnology and Oceanography, Vol. 49, No. 1, 2004, pp. 137-147. doi:10.4319/lo.2004.49.1.0137

[175]   N. E. Melechen and G. Go, “Induction of Lambdoid Pro phages by Amino Acid Deprivation: Differential Inducibility; Role of recA,” Molecular and General Genetics, Vol. 180, No. 1, 1980, pp. 147-155. doi:10.1007/BF00267364

[176]   J. H. Paul, M. E. Frischer and J. M. Thurmond, “Gene Transfer in Marine Water Column and Sediment Microcosms by Natural Plasmid Transformation,” Applied and Environmental Microbiology, Vol. 57, No. 5, 1991a, pp. 1509-1515.

[177]   A. E. Goodman, K. C. Marshall and M. Hermansson, “Gene Transfer among Bacteria under Conditions of Nutrient Depletion in Simulated and Natural Aquatic Envi ronments,” FEMS Microbiology Ecology, Vol. 15, No. 1-2, 1994, pp. 55-60. doi:10.1111/j.1574-6941.1994.tb00229.x

[178]   J. J. Cole, M. L. Pace, N. F. Caraco and G. S. Steinhart, “Bacterial Biomass and Cell Size Distributions in Lakes: More and Larger Cells in Anoxic Waters,” Limnology and Oceanography, Vol. 38, No. 8, 1993, pp. 1627-1632. doi:10.4319/lo.1993.38.8.1627

[179]   P. Carlsson and D. A. Caron, “Seasonal Variation of Phosphorus Limitation of Bacterial Growth in a Small Lake,” Limnology and Oceanography, Vol. 46, No. 1, 2001, pp. 108-120. doi:10.4319/lo.2001.46.1.0108

[180]   U. Münster, E. Heikkinen and J. Knulst, “Nutrient Com position, Microbial Biomass and Activity at the Air-Water Interface of Small Boreal Forest Lakes,” Hydrobiologia, Vol. 363, No. 1-3, 1997, pp. 261-270.

[181]   B. Bostr?m, J. M. Andersen, S. Fleischer and M. Jansson, “Exchange of Phosphorus across the Sediment-Water In terface,” Hydrobiologia, Vol. 170, No. 1, 1988, pp. 229 244. doi:10.1007/BF00024907

[182]   J. E. González and M. M. Marketon, “Quorum Sensing in Nitrogen-Fixing Rhizobia,” Microbiology and Molecular Biology Reviews, Vol. 67, No. 4, 2003, pp. 574-592. doi:10.1128/MMBR.67.4.574-592.2003

[183]   J. P. Ramsay, J. T. Sullivan, N. Jambari, C. A. Ortori, S. Heeb, P. Williams, D. A. Barrett, I. L. Lamont and C. W. Ronson, “A LuxRI-Family Regulatory System Controls Excision and Transfer of the Mesorhizobium loti Strain R7A Symbiosis Island by Activating Expression of Two Conserved Hypothetical Genes,” Molecular Microbiology, Vol. 73, No. 6, 2009, pp. 1141-1155. doi:10.1111/j.1365-2958.2009.06843.x

[184]   D. Ghosh, K. Roy, K. E. Williamson, S. Srinivasiah, K. E. Wommack and M. Radosevich, “Acyl-Homoserine Lac tones Can Induce Virus Production in Lysogenic Bacteria: An Alternative Paradigm for Prophage Induction,” Ap plied and Environmental Microbiology, Vol. 75, No. 22, 2009, pp. 7142-7152. doi:10.1128/AEM.00950-09

[185]   E. S. Antonova and B. K. Hammer, “Quorum-Sensing Autoinducer Molecules Produced by Members of a Multispecies Biofilm Promote Horizontal Gene Transfer to Vibrio cholerae,” FEMS Microbiology Letters, Vol. 322, No. 1, 2011, pp. 68-76. doi:10.1111/j.1574-6968.2011.02328.x

[186]   L. M?lbak, S. Molin and N. Kroer, “Root Growth and Exudate Production Define the Frequency of Horizontal Plasmid Transfer in the Rhizosphere,” FEMS Microbiol ogy Ecology, Vol. 59, No. 1, 2007, pp. 167-176. doi:10.1111/j.1574-6941.2006.00229.x

[187]   N. Kroer, T. Barkay, S. S?rensen and D. Weber, “Effect of Root Exudates and Bacterial Metabolic Activity on Conjugal Gene Transfer in the Rhizosphere of a Marsh Plant,” FEMS Microbiology Ecology, Vol. 25, No. 4, 1998, pp. 375-384. doi:10.1111/j.1574-6941.1998.tb00489.x

[188]   M. Ueki, K. Matsui, K. Choi and Z. Kawabata, “The Enhancement of Conjugal Plasmid pBHR1 Transfer between Bacteria in the Presence of Extracellular Metabolic Prod ucts Produced by Microcystis aeruginosa,” FEMS Micro biology Ecology, Vol. 51, No. 1, 2004, pp. 1-8. doi:10.1016/j.femsec.2004.07.003

[189]   K. Matsui, N. Ishii and Z. Kawabata, “Release of Extracellular Transformable Plasmid DNA from Escherichia coli Cocultivated with Algae,” Applied and Environmental Microbiology, Vol. 69, No. 4, 2003, pp. 2399 2404. doi:10.1128/AEM.69.4.2399-2404.2003

[190]   K. Matsui, N. Ishii and Z. Kawabata, “Microbial Interactions Affecting the Natural Transformation of Bacillus subtilis in a Model Aquatic Ecosystem,” FEMS Microbiology Ecology, Vol. 45, No. 3, 2003b, pp. 211-218. doi:10.1016/S0168-6496(03)00148-X

[191]   J. Matsuo, S. Oguri, S. Nakamura, T. Hanawa, T. Fukumoto, Y. Hayashi, K. Kawaguchi, Y. Mizutani, T. Yao, K. Akizawa, H. Suzuki, C. Simizu, K. Matsuno, S. Kamiya and H. Yamaguchi, “Ciliates Rapidly Enhance the Frequency of Conjugation between Escherichia coli Strains through Bacterial Accumulation in Vesicles,” Research in Microbiology, Vol. 161, No. 8, 2010, pp. 711-719. doi:10.1016/j.resmic.2010.07.004

[192]   T. R. de Kievit, “Quorum Sensing in Pseudomonas aeru ginosa Biofilms,” Environmental Microbiology, Vol. 11, No. 2, 2009, pp. 279-288. doi:10.1111/j.1462-2920.2008.01792.x

[193]   P. Cai, Q. Huang, J. Zhu, D. Jiang, X. Zhou, X. Rong and W. Liang, “Effects of Low-Molecular-Weight Organic Ligands and Phosphate on DNA Adsorption by Soil Colloids and Minerals,” Colloids and Surfaces B: Biointer faces, Vol. 54, No. 1, 2007b, pp. 53-59. doi:10.1016/j.colsurfb.2006.07.013

[194]   K. L. Meibom, M. Blokesch, N. A. Dolganov, C. Y. Wu and G. K. Schoolnik, “Chitin Induces Natural Competence in Vibrio cholerae,” Science, Vol. 310, No. 5755, 2005, pp. 1824-1827. doi:10.1126/science.1120096

[195]   H. W. Paerl and J. L. Pinckney, “A Mini-Review of Microbial Consortia: Their Roles in Aquatic Production and Biogeochemical Cycling,” Microbial Ecology, Vol. 31, No. 3, 1996, pp. 225-247. doi:10.1007/BF00171569

[196]   L. de Gelder, F. P. Vandecasteele, C. J. Brown, L. J. For ney and E. M. Top, “Plasmid Donor Affects Host Range of Promiscuous IncP-1β Plasmid pB10 in an Activated Sludge Microbial Community,” Applied and Environ mental Microbiology, Vol. 71, No. 9, 2005, pp. 5309 5317. doi:10.1128/AEM.71.9.5309-5317.2005

[197]   I. Chen and D. Dubnau, “DNA Uptake during Bacterial Transformation,” Nature Reviews Microbiology, Vol. 2, No. 3, 2004, pp. 241-249. doi:10.1038/nrmicro844

[198]   A. C. Yannarell and E. W. Triplett, “Within and Between-Lake Variability in the Composition of Bacterioplankton Communities: Investigations Using Multiple Spatial Scales,” Applied and Environmental Microbiology, Vol. 70, No. 1, 2004, pp. 214-223. doi:10.1128/AEM.70.1.214-223.2004

[199]   R. C. Crump, H. E. Adams, J. E. Hobbie and G. W. Kling, “Biogeography of Bacterioplankton in Lakes and Streams of an Arctic Tundra Catchment,” Ecology, Vol. 88, No. 6, 2007, pp. 1365-1378. doi:10.1890/06-0387

[200]   K. Dominik and M. G. H?fle, “Changes in Bacterio plankton Community Structure and Activity with Depth in a Eutrophic Lake as Revealed by 5S rRNA Analysis,” Applied and Environmental Microbiology, Vol. 68, No. 7, 2002, pp. 3606-3613. doi:10.1128/AEM.68.7.3606-3613.2002

[201]   A. C. Yannarell, A. D. Kent, G. H. Lauster, T. K. Kratz and E. W. Triplett, “Temporal Patterns in Bacterial Communities in Three Temperate Lakes of Different Trophic Status,” Microbial Ecology, Vol. 46, No. 4, 2003, pp. 391-405. doi:10.1007/s00248-003-1008-9

[202]   W. Zwisler, N. Selje and M. Simon, “Seasonal Patterns of the Bacterioplankton Community Composition in a Large Mesotrophic Lake,” Aquatic Microbial Ecology, Vol. 31, No. 3, 2003, pp. 211-225. doi:10.3354/ame031211

[203]   S. R. Mueller-Spitz, G. W. Goetz and S. L. McLellan, “Temporal and Spatial Variability in Nearshore Bacterio plankton Communities of Lake Michigan,” FEMS Micro biology Ecology, Vol. 67, No. 3, 2009, pp. 511-522. doi:10.1111/j.1574-6941.2008.00639.x

[204]   A. Konopka, T. Bercot and C. Nakatsu, “Bacterioplank ton Community Diversity in a Series of Thermally Stratified Lakes,” Microbial Ecology, Vol. 38, No. 2, 1999, pp. 126-135. doi:10.1007/s002489900166

[205]   D. Boucher, L. Jardillier and D. Debroas, “Succession of Bacterial Community Composition over Two Consecutive Years in Two Aquatic Systems: A Natural Lake and a Lake-Reservoir,” FEMS Microbiology Ecology, Vol. 55, No. 1, 2006, pp. 79-97. doi:10.1111/j.1574-6941.2005.00011.x

[206]   A. Shade, S. E. Jones and K. D. McMahon, “The Influence of Habitat Heterogeneity on Freshwater Bacterial Community Composition and Dynamics,” Environmental Microbiology, Vol. 10, No. 4, 2008, pp. 1057-1067. doi:10.1111/j.1462-2920.2007.01527.x

[207]   E. F. DeLong, D. G. Franks and A. L. Alldredge, “Phylogenetic Diversity of Aggregate-Attached vs. Free-Living Marine Bacterial Assemblages,” Limnology and Oceanography, Vol. 38, No. 5, 1993, pp. 924-934. doi:10.4319/lo.1993.38.5.0924

[208]   B. C. Crump, E. V. Armbrust and J. A. Baross, “Phylogenetic Analysis of Particle-Attached and Free-Living Bacterial Communities in the Columbia River, Its Estuary, and the Adjacent Coastal Ocean,” Applied and Environ mental Microbiology, Vol. 65, No. 7, 1999, pp. 3192 3204.

[209]   D. A. Pearce, C. J. van der Gast, K. Woodward and K. K. Newsham, “Significant Changes in the Bacterioplankton Community Structure of a Maritime Antarctic Freshwater Lake Following Nutrient Enrichment,” Microbiology, Vol. 151, No. 10, 2005, pp. 3237-3248. doi:10.1099/mic.0.27258-0

[210]   J. A. J. Haagensen, S. K. Hansen, T. Johansen and S. Molin, “In Situ Detection of Horizontal Transfer of Mo bile Genetic Elements,” FEMS Microbiology Ecology, Vol. 42, No. 2, 2002, pp. 261-268. doi:10.1111/j.1574-6941.2002.tb01016.x

[211]   M. C. Haug, S. A. Tanner, C. Lacroix, L. Meile and M. J. A. Stevens, “Construction and Characterization of En terococcus faecalis CG110/gfp/pRE25*, a Tool for Mo nitoring Horizontal Gene Transfer in Complex Microbial Ecosystems,” FEMS Microbiology Letters, Vol. 313, No. 2, pp. 111-119. doi:10.1111/j.1574-6968.2010.02

 
 
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