Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms

Environment International

Volumn 85, Issue , 2015, Pages 189-205

  Brandt, Kristian K ^a,b   Amézquita, Alejandro ^c   Backhaus, Thomas ^d   Boxall, Alistair ^e   Coors, Anja ^f   Heberer, Thomas ^g   Lawrence, John R ^h   Lazorchak, James ⁱ   Schönfeld, Jens ^j   Snape, Jason R ^k   Zhu, Yong Guan ^l   Topp, Edward ^m  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b Sino Danish Center for Education and Research   (China)

^c UNILEVER RESEARCH   (United Kingdom)

^d UNIVERSITY OF GOTHENBURG   (Sweden)

^e UNIVERSITY OF YORK   (United Kingdom)

^f ECT OEKOTOXIKOLOGIE GMBH   (Germany)

^g Federal Office of Consumer Protection and Food Safety   (Germany)

^h ENVIRONMENT CANADA   (Canada)

ⁱ U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^j UMWELTBUNDESAMT   (Germany)

^k ASTRAZENECA   (United Kingdom)

^l INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^m AGRICULTURE AND AGRI FOOD CANADA   (Canada)

more..

Author keywords

Antimicrobials; Ecosystem services; Ecotoxicology; Environmental risk assessment; Microbial ecology; Pharmaceuticals

Indexed keywords

AGRICULTURE; ANTIBIOTICS; AQUATIC ECOSYSTEMS; DRUG PRODUCTS; ENVIRONMENTAL IMPACT; MICROORGANISMS;

ANTIMICROBIALS; ECO-TOXICOLOGY; ECOSYSTEM SERVICES; ENVIRONMENTAL RISK ASSESSMENT; MICROBIAL ECOLOGY;

RISK ASSESSMENT;

ANTIBIOTIC AGENT; RIBOSOME RNA; ANTIINFECTIVE AGENT; POLLUTANT;

ANTIBIOTICS; ECOSYSTEM SERVICE; ECOTOXICOLOGY; ENVIRONMENTAL FATE; ENVIRONMENTAL RISK; MICROBIAL COMMUNITY; MICROORGANISM; RISK ASSESSMENT; SPECIES DIVERSITY;

ANTIBIOTIC RESISTANCE; ECOTOXICOLOGY; ENVIRONMENTAL PROTECTION; ENVIRONMENTAL RISK ASSESSMENT; ENZYME ACTIVITY; FATTY ACID ANALYSIS; HUMAN ACTIVITIES; INHIBITORY CONCENTRATION; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIAL GROWTH; MICROBIAL RESPIRATION; NONHUMAN; POLLUTION MONITORING; PRIORITY JOURNAL; REVIEW; RISK ASSESSMENT; ANALYSIS; ANIMAL; DRUG EFFECTS; ECOLOGY; ECOSYSTEM; HUMAN; MICROBIAL CONSORTIUM; MICROBIOLOGY; POLLUTANT; STANDARDS; TOXICITY;

ANIMALIA; BACTERIA (MICROORGANISMS);

ANIMALS; ANTI-BACTERIAL AGENTS; ECOLOGY; ECOSYSTEM; ECOTOXICOLOGY; ENVIRONMENTAL POLLUTANTS; HUMANS; MICROBIAL CONSORTIA; RISK ASSESSMENT; SOIL MICROBIOLOGY; WATER MICROBIOLOGY;

EID: 84942567944     PISSN: 01604120     EISSN: 18736750     Source Type: Journal    
DOI: 10.1016/j.envint.2015.09.013     Document Type: Review

References (249)

1. Ågerstrand M., Berg C., Björlenius B., Breitholtz M., Brunström B., Fick J., Gunnarsson L., Larsson D.G.J., Sumpter J.P., Tysklind M., Rudén C. Improving environmental risk assessment of human pharmaceuticals. Environ. Sci. Technol. 2015, 49:5336-5345.
2. Allison K.R., Brynildsen M.P., Collins J.J. Metabolite-enabled eradication of bacterial persisters by aminoglycosides. Nature 2011, 473:216-220.
3. Allison S.D., Martiny J.B.H. Resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci. 2008, 105:11512-11519.
4. Almås Å.R., Mulder J., Bakken L.R. Trace metal exposure of soil bacteria depends on their position in the soil matrix. Environ. Sci. Technol. 2005, 39:5927-5932.
5. Altenburger R., Scholz S., Schmitt-Jansen M., Busch W., Escher B.I. Mixture toxicity revisited from a toxicogenomic perspective. Environ. Sci. Technol. 2012, 46:2508-2522.
6. Altenburger R., Ait-Aissa S., Antczak P., Backhaus T., Barceló D., Seiler T.B., Brion F., Busch W., Chipman K., de Alda M.L., de Aragão Umbuzeiro G., Escher B.I., Falciani F., Faust M., Focks A., Hilscherova K., Hollender J., Hollert H., Jäger F., Jahnke A., Kortenkamp A., Krauss M., Lemkine G.F., Munthe J., Neumann S., Schymanski E.L., Scrimshaw M., Segner H., Slobodnik J., Smedes F., Kughathas S., Teodorovic I., Tindall A.J., Tollefsen K.E., Walz K.H., Williams T.D., van den Brink P.J., van Gils J., Vrana B., Zhang X., Brack W. Future water quality monitoring - adapting tools to deal with mixtures of pollutants in water resource management. Sci. Total Environ. 2015, 512-513:540-551.
7. Aminov R.I. The role of antibiotics and antibiotic resistance in nature. Environ. Microbiol. 2009, 11:2970-2988.
8. Andersson D.I., Hughes D. Microbiological effects of sublethal levels of antibiotics. Nat. Rev. Microbiol. 2014, 12:465-478.
9. Ankley G.T., Bennett R.S., Erickson R.J., Hoff D.J., Hornung M.W., Johnson R.D., Mount D.R., Nichols J.W., Russom C.L., Schmieder P.K., Serrrano J.A., Tietge J.E., Villeneuve D.L. Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment. Environ. Toxicol. Chem. 2010, 29:730-741.
10. Arbejdsgruppen vedrørende Kærgård Plantage Delrapport nr. 1. Jord- og grundvandsforurening ved Kærgård Plantage 2006, 1-91. Danish Environmental Protection Agency (in Danish).
11. Aristilde L., Melis A., Sposito G. Inhibition of photosynthesis by a fluoroquinolone antibiotic. Environ. Sci. Technol. 2010, 44:1444-1450.
12. Armengaud J. Microbiology and proteomics, getting the best of both worlds!. Environ. Microbiol. 2013, 15:12-23.
13. Ashbolt N.J., Amézquita A., Backhaus T., Borriello S.P., Brandt K.K., Collignon P., Coors A., Finley R., Gaze W.H., Heberer T., Lawrence J.R., Larsson D.G.J., McEwen S.A., Ryan J.J., Schönfeld J., Silley P., Snape J.R., van den Eede C., Topp E. Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance. Environ. Health Perspect. 2013, 121:993-1001.
14. Bååth E. Measurement of heavy metal tolerance of soil bacteria using thymidine incorporation into bacteria extracted after homogenization centrifugation. Soil Biol. Biochem. 1992, 24:1167-1172.
15. Bååth E., Pettersson M., Söderberg K.H. Adaptation of a rapid and economical microcentrifugation method to measure thymidine and leucine incorporation by soil bacteria. Soil Biol. Biochem. 2001, 33:1571-1574.
16. Backhaus T. Medicines, shaken and stirred: a critical review on the ecotoxicology of pharmaceutical mixtures. Philos. Trans. R. Soc. B Biol. Sci. 2014, 369. 10.1098/rstb.2013.0585.
17. Backhaus T., Froehner K., Altenburger R., Grimme L.H. Toxicity testing with Vibrio fischeri: a comparison between the long term (24h) and the short term (30min) bioassay. Chemosphere 1997, 35:2925-2938.
18. Backhaus T., Snape J., Lazorchak J. The impact of chemical pollution on biodiversity and ecosystem services: the need for an improved understanding. Integr. Environ. Assess. Manag. 2012, 8:575-576.
19. Baho D.L., Peter H., Tranvik L.J. Resistance and resilience of microbial communities - temporal and spatial insurance against perturbations. Environ. Microbiol. 2012, 14:2283-2292.
20. Bardgett R.D., Freeman C., Ostle N.J. Microbial contributions to climate change through carbon cycle feedbacks. ISME J. 2008, 2:805-814.
21. Bastviken D., Tranvik L. The leucine incorporation method estimates bacterial growth equally well in both oxic and anoxic lake waters. Appl. Environ. Microbiol. 2001, 67:2916-2921.
22. Bent S.J., Forney L.J. The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J. 2008, 2:689-695.
23. Berg J., Brandt K.K., Al-Soud W.A., Holm P.E., Hansen L.H., Sørensen S.J., Nybroe O. Selection for Cu-tolerant bacterial communities with altered composition, but unaltered richness, via long-term Cu exposure. Appl. Environ. Microbiol. 2012, 78:7438-7446.
24. Berg J., Thorsen M.K., Holm P.E., Jensen J., Nybroe O., Brandt K.K. Cu exposure under field conditions coselects for antibiotic resistance as determined by a novel cultivation-independent bacterial community tolerance assay. Environ. Sci. Technol. 2010, 44:8724-8728.
25. Bernier S.P., Létoffé S., Delepierre M., Ghigo J.M. Biogenic ammonia modifies antibiotic resistance at a distance in physically separated bacteria. Mol. Microbiol. 2011, 81:705-716.
26. Bernier S.P., Surette M.G. Concentration-dependent activity of antibiotics in natural environments. Front. Microbiol. 2013, 4. 10.3389/fmicb.2013.00020.
27. Binh C.T.T., Heuer H., Gomes N.C.M., Kotzerke A., Fulle M., Wilke B.M., Schloter M., Smalla K. Short-term effects of amoxicillin on bacterial communities in manured soil. FEMS Microbiol. Ecol. 2007, 62:290-302.
28. Birtel J., Walser J.C., Pichon S., Bürgmann H., Matthews B. Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions. PLoS One 2015, 10. 10.1371/journal.pone.0125356.
29. Bitton G. Wastewater microbiology 2010, Wiley-Blackwell, Online ISBN: 9780470901243. 10.1002/9780470901243.
30. Blanck H. A critical review of procedures and approaches used for assessing pollution-induced community tolerance (PICT) in biotic communities. Hum. Ecol. Risk. Assess. 2002, 8:1003-1034.
31. Boxall A.B.A., Rudd M.A., Brooks B.W., Caldwell D.J., Choi K., Hickmann S., Innes E., Ostapyk K., Staveley J.P., Verslycke T., Ankley G.T., Beazley K.F., Belanger S.E., Berninger J.P., Carriquiriborde P., Coors A., DeLeo P.C., Dyer S.D., Ericson J.F., Gagne F., Giesy J.P., Gouin T., Hallstrom L., Karlsson M.V., Larsson D.G.J., Lazorchak J.M., Mastrocco F., McLaughlin A., McMaster M.E., Meyerhoff R.D., Moore R., Parrott J.L., Snape J.R., Murray-Smith R., Servos M.R., Sibley P.K., Straub J.O., Szabo N.D., Topp E., Tetreault G.R., Trudeau V.L., Van Der Kraak G. Pharmaceuticals and personal care products in the environment: what are the big questions?. Environ. Health Perspect. 2012, 120:1221-1229.
32. Brandt K.K., Pedersen A., Sørensen J. Solid phase-contact assay that uses a lux-marked Nitrosomonas europaea reporter strain to estimate toxicity of bioavailable linear alkylbenzene sulfonate in soil. Appl. Environ. Microbiol. 2002, 68:3502-3508.
33. Brandt K.K., Frandsen R.J.N., Holm P.E., Nybroe O. Development of pollution-induced community tolerance is linked to structural and functional resilience of a soil bacterial community following a five-year field exposure to copper. Soil Biol. Biochem. 2010, 42:748-757.
34. Brandt K.K., Sjøholm O.R., Krogh K.A., Halling-Sørensen B., Nybroe O. Increased pollution-induced bacterial community tolerance to sulfadiazine in soil hotspots amended with artificial root exudates. Environ. Sci. Technol. 2009, 43:2963-2968.
35. Brodie E.L., DeSantis T.Z., Joyner D.C., Baek S.M., Larsen J.T., Andersen G.L., Hazen T.C., Richardson P.M., Herman D.J., Tokunaga T.K., Wan J.M., Firestone M.K. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol. 2006, 72:6288-6298.
36. Brosche S., Backhaus T. Toxicity of five protein synthesis inhibiting antibiotics and their mixture to limnic bacterial communities. Aquat. Toxicol. 2010, 99:457-465.
37. Bull A.T. Microbial Diversity and Bioprospecting 2004, ASM Press, Washington DC, (1-496 pp.).
38. Cabello F.C., Godfrey H.P., Tomova A., Ivanova L., Dölz H., Millanao A., Buschmann A.H. Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health. Environ. Microbiol. 2013, 15:1917-1942.
39. Campbell C.D., Chapman S.J., Cameron C.M., Davidson M.S., Potts J.M. A rapid microtiter plate method to measure carbon dioxide evolved from carbon substrate amendments so as to determine the physiological profiles of soil microbial communities by using whole soil. Appl. Environ. Microbiol. 2003, 69:3593-3599.
40. Cardinale B.J., Duffy J.E., Gonzalez A., Hooper D.U., Perrings C., Venail P., Narwani A., Mace G.M., Tilman D., Wardle D.A., Kinzig A.P., Daily G.C., Loreau M., Grace J.B., Larigauderie A., Srivastava D.S., Naeem S. Biodiversity loss and its impact on humanity. Nature 2012, 486:59-67.
41. Cermák L., Kopecký J., Novotná J., Omelka M., Parkhomenko N., Plhácková K., Ságová-Marecková M. Bacterial communities of two contrasting soils reacted differently to lincomycin treatment. Appl. Soil Ecol. 2008, 40:348-358.
42. Chapman S.J., Campbell C.D., Artz R.R.E. Assessing CLPPs using MicroResp (TM) - a comparison with biolog and multi-SIR. J. Soils Sediments 2007, 7:406-410.
43. Chee-Sanford J.C., Mackie R.I., Koike S., Krapac I.G., Lin Y.F., Yannarell A.C., Maxwell S., Aminov R.I. Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste. J. Environ. Qual. 2009, 38:1086-1108.
44. Chin-Leo G. Bacterial secondary productivity. Manual of Environmental Microbiology 2002, 354-363. ASM Press, Washington DC. C.J. Hurst, R.L. Crawford, M.J. McInerney, G.R. Knudsen, L.D. Stetzenbach (Eds.).
45. Committee for Medicinal Products for Human Use Guideline on the environmental risk assessment of medicinal products for human use 2006, 1-12. European Medicines Agency, London, UK.
46. Cordova-Kreylos A.L., Scow K.M. Effects of ciprofloxacin on salt marsh sediment microbial communities. ISME J. 2007, 1:585-595.
47. Cui H., Wang S.P., Jia S.G., Zhang N., Zhou Z.Q. Influence of ciprofloxacin on the microbial catabolic diversity in soil. J. Environ. Sci. Health B 2013, 48:869-877.
48. Cullen J.J. Primary production methods. Encyclopedia of Ocean Sciences 2001, 2277-2284. Academic Press, London. J. Steele, S. Thorpe, K. Turekian (Eds.).
49. Dalkmann P., Broszat M., Siebe C., Willaschek E., Sakinc T., Huebner J., Amelung W., Grohmann E., Siemens J. Accumulation of pharmaceuticals, Enterococcus, and resistance genes in soils irrigated with wastewater for zero to 100years in central Mexico. PLoS ONE 2012, 7.
50. Dantas G., Sommer M.O.A., Oluwasegun R.D., Church G.M. Bacteria subsisting on antibiotics. Science 2008, 320:100-103.
51. Davies J., Davies D. Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 2010, 74:417-433.
52. Davies J., Spiegelman G.B., Yim G. The world of subinhibitory antibiotic concentrations. Curr. Opin. Microbiol. 2006, 9:445-453.
53. de Klevit T.R. Quorum sensing in Pseudomonas aeruginosa biofilms. Environ. Microbiol. 2009, 11:279-288.
54. Degens B.P., Harris J.A. Development of a physiological approach to measuring the catabolic diversity of soil microbial communities. Soil Biol. Biochem. 1998, 29:1309-1320.
55. Delcour A.H. Outer membrane permeability and antibiotic resistance. Biochim. Biophys. Acta Protein Proteomics 2009, 1794:808-816.
56. Delmont T.O., Robe P., Cecillon S., Clark I.M., Constancias F., Simonet P., Hirsch P.R., Vogel T.M. Accessing the soil metagenome for studies of microbial diversity. Appl. Environ. Microbiol. 2011, 77:1315-1324.
57. Delmont T.O., Simonet P., Vogel T.M. Describing microbial communities and performing global comparisons in the 'omic era'. ISME J. 2012, 6:1625-1628.
58. Demoling L.A., Bååth E., Greve G., Wouterse M., Schmitt H. Effects of sulfamethoxazole on soil microbial communities after adding substrate. Soil Biol. Biochem. 2009, 41:840-848.
59. Dias E., Oliveira M., Jones-Dias D., Vasconcelos V., Ferreira E., Manageiro V., Canica M. Assessing the antibiotic susceptibility of freshwater cyanobacteria spp. Front. Microbiol. 2015, 6. 10.3389/fmicb.2015.00799.
60. Ding C., He J. Effect of antibiotics in the environment on microbial populations. Appl. Microbiol. Biotechnol. 2010, 87:925-941.
61. Ding G.C., Radl V., Schloter-Hai B., Jechalke S., Heuer H., Smalla K., Schloter M. Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine. PLoS ONE 2014, 9. 10.1371/journal.pone.0092958.
62. Dynes J.J., Lawrence J.R., Korber D.R., Swerhone G.D.W., Leppard G.G., Hitchcock A.P. Morphological and biochemical changes in Pseudomonas fluorescens biofilms induced by sub-inhibitory exposure to antimicrobial agents. Can. J. Microbiol. 2009, 55:163-178.
63. Ebert I., Bachmann J., Kühnen U., Küster A., Kussatz C., Maletzki D., Schlüter C. Toxicity of the fluoroquinolone antibiotics enrofloxacin and ciprofloxacin to photoautotrophic aquatic organisms. Environ. Toxicol. Chem. 2011, 30:2786-2792.
64. EFSA Panel on Plant Protection Products and their residues (PPR) Scientific opinion on the development of specific protection goal options for environmental risk assessment of pesticides, in particular in relation to the revision of the guidance documents on aquatic and terrestrial ecotoxicology. EFSA J. 2010, 8:1821.
65. Eng R.H., Padberg F.T., Smith S.M., Tan E.N., Cherubin C.E. Bactericidal effects of antibiotics on slowly growing and nongrowing bacteria. Antimicrob. Agents Chemother. 1991, 35:1824-1828.
66. Faber J.H., van Wensem J. Elaborations on the use of the ecosystem services concept for application in ecological risk assessment for soils. Sci. Total Environ. 2012, 415:3-8.
67. Fai P.B., Grant A. An assessment of the potential of the microbial assay for risk assessment (Mara) for ecotoxicological testing. Ecotoxicology 2010, 19:1626-1633.
68. Fajardo A., Martínez J.L. Antibiotics as signals that trigger specific bacterial responses. Curr. Opin. Microbiol. 2008, 11:161-167.
69. Falkowski P.G., Fenchel T., DeLong E.F. The microbial engines that drive earth's biogeochemical cycles. Science 2008, 320:1034-1039.
70. Fang H., Han Y.L., Yin Y.M., Jin X.X., Wang S.Y., Tang F.F., Cai L., Yu Y.L. Microbial response to repeated treatments of manure containing sulfadiazine and chlortetracycline in soil. J. Environ. Sci. Health B 2014, 49:609-615.
71. Fechner L., Gourlay-Francé C., Uher E., Tusseau-Vuillemin M.-H. Adapting an enzymatic toxicity test to allow comparative evaluation of natural freshwater biofilms' tolerance to metals. Ecotoxicology 2010, 19:1302-1311.
72. Fernández-Calvino D., Bååth E. Co-selection for antibiotic tolerance in Cu-polluted soil is detected at higher Cu-concentrations than increased Cu-tolerance. Soil Biol. Biochem. 2013, 57:953-956.
73. Fierer N., Ladau J., Clemente J.C., Leff J.W., Owens S.M., Pollard K.S., Knight R., Gilbert J.A., McCulley R.L. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 2013, 342:621-624.
74. Finley R.L., Collignon P., Larsson D.G.J., McEwen S.A., Li X.Z., Gaze W.H., Reid-Smith R., Timinouni M., Graham D.W., Topp E. The scourge of antibiotic resistance: the important role of the environment. Clin. Infect. Dis. 2013, 57:704-710.
75. Focks A., Klasmeier J., Matthies M. Mechanistic link between uptake of sulfonamides and bacteriostatic effect: model development and application to experimental data from two soil microorganisms. Environ. Toxicol. Chem. 2010, 29:1445-1452.
76. Frostegård Å., Petersen S.O., Bååth E., Nielsen T.H. Dynamics of a microbial community associated with manure hot spots as revealed by phospholipid fatty acid analysis. Appl. Environ. Microbiol. 1997, 63:2224-2231.
77. Frostegård Å., Tunlid A., Bååth E. Use and misuse of PLFA measurements in soils. Soil Biol. Biochem. 2011, 43:1621-1625.
78. Garcia-Reyero N., Perkins E.J. Systems biology: leading the revolution in ecotoxicology. Environ. Toxicol. Chem. 2011, 30:265-273.
79. Garland J.L. Analysis and interpretation of community-level physiological profiles in microbial ecology. FEMS Microbiol. Ecol. 1997, 24:289-300.
80. Garmendia L., Hernandez A., Sanchez M.B., Martínez J.L. Metagenomics and antibiotics. Clin. Microbiol. Infect. 2012, 18:27-31.
81. Gaze W.H., Krone S.M., Larsson D.G., Li X.Z., Robinson J.A., Simonet P., Smalla K., Timinouni M., Topp E., Wellington E.M., Wright G.D., Zhu Y.G. Influence of humans on evolution and mobilization of environmental antibiotic resistome. Emerg. Infect. Dis. 2013, 19. 10.3201/eid1907.120871.
82. 2 and ZnO nanoparticles. Appl. Environ. Microbiol. 2012, 78:6749-6758.
83. Gihring T.M., Green S.J., Schadt C.W. Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ. Microbiol. 2012, 14:285-290.
84. Gilbert J.A., Meyer F., Bailey M.J. The future of microbial metagenomics (or is ignorance bliss?). ISME J. 2011, 5:777-779.
85. Gillings M.R. Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome. Front. Microbiol. 2013, 4. 10.3389/fmicb.2013.00004.
86. Gillings M.R. Integrons: past, present, and future. Microbiol. Mol. Biol. Rev. 2014, 78:257-277.
87. Girardi C., Greve J., Lamshöft M., Fetzer I., Miltner A., Schäffer A., Kästner M. Biodegradation of ciprofloxacin in water and soil and its effects on the microbial communities. J. Hazard. Mater. 2011, 198:22-30.
88. Goebel N.L., Edwards C.A., Follows M.J., Zehr J.P. Modeled diversity effects on microbial ecosystem functions of primary production, nutrient uptake, and remineralization. Ecology 2013, 95:153-163.
89. Goh E.B., Yim G., Tsui W., McClure J., Surette M.G., Davies J. Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:17,025-17,030.
90. Gorokhova E., Rivetti C., Furuhagen S., Edlund A., Ek K., Breitholtz M. Bacteria-mediated effects of antibiotics on Daphnia nutrition. Environ. Sci. Technol. 2015, 49:5759-5787.
91. Granados-Chinchilla F., Arias-Andres M., Rodriguez C. Tetracycline and 4-epitetracycline modified the in vitro catabolic activity and structure of a sediment microbial community from a tropical tilapia farm idiosyncratically. J. Environ. Sci. Health B 2013, 48:291-301.
92. Grant A. Pollution-tolerant species and communities: intriguing toys or invaluable monitoring tools?. Hum. Ecol. Risk. Assess. 2002, 8:955.
93. Griffiths B.S., Philippot L. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol. Rev. 2013, 37:112-129.
94. Gullberg E., Cao S., Berg O.G., Ilbäck C., Sandegren L., Hughes D., Andersson D.I. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog. 2011, 7.
95. Haegeman B., Hamelin J., Moriarty J., Neal P., Dushoff J., Weitz J.S. Robust estimation of microbial diversity in theory and in practice. ISME J. 2013, 7:1092-1101.
96. Hamasaki K. Comparison of bromodeoxyuridine immunoassay with tritiated thymidine radioassay for measuring bacterial productivity in oceanic waters. J. Oceanogr. 2006, 62:793-799.
97. Hamasaki K., Taniguchi A., Tada Y., Long R.A., Azam F. Actively growing bacteria in the Inland Sea of Japan, identified by combined bromodeoxyuridine immunocapture and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 2007, 73:2787-2798.
98. Hammesfahr U., Bierl R., Thiele-Bruhn S. Combined effects of the antibiotic sulfadiazine and liquid manure on the soil microbial-community structure and functions. J. Plant Nutr. Soil Sci. 2011, 174:614-623.
99. Hammesfahr U., Heuer H., Manzke B., Smalla K., Thiele-Bruhn S. Impact of the antibiotic sulfadiazine and pig manure on the microbial community structure in agricultural soils. Soil Biol. Biochem. 2008, 40:1583-1591.
100. Händel N., Schuurmans J.M., Brul S., ter Kuile B.H. Compensation of the metabolic costs of antibiotic resistance by physiological adaptation in Escherichia coli. Antimicrob. Agents Chemother. 2013, 57:3752-3762.
101. Harris S.J., Cormican M., Cummins E. Antimicrobial residues and antimicrobial-resistant bacteria: impact on the microbial environment and risk to human health - a review. Hum. Ecol. Risk. Assess. 2012, 18:767-809.
102. Hazen T.C., Rocha A.M., Techtmann S.M. Advances in monitoring environmental microbes. Curr. Opin. Biotechnol. 2013, 24:526-533.
103. He Z., Deng Y., Van Nostrand J.D., Tu Q., Xu M., Hemme C.L., Li X., Wu L., Gentry T.J., Yin Y., Liebich J., Hazen T.C., Zhou J. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J. 2010, 4:1167-1179.
104. He Z., Deng Y., Zhou J. Development of functional gene microarrays for microbial community analysis. Curr. Opin. Biotechnol. 2012, 23:49-55.
105. Heberer T., Massmann G., Fanck B., Taute T., Dünnbier U. Behaviour and redox sensitivity of antimicrobial residues during bank filtration. Chemosphere 2008, 73:451-460.
106. Heipieper H.J., Fischer J., Meinhardt F. Cis-trans isomerase of unsaturated fatty acids: an immediate bacterial adaptive mechanism to cope with emerging membrane perturbation caused by toxic hydrocarbons. Handbook of Hydrocarbon and Lipid Microbiology 2010, 1605-1613. Springer-Verlag, Berlin. K.N. Timmis (Ed.).
107. Hellman M., Berg J., Brandt K.K., Hallin S. Survey of bromodeoxyuridine uptake among environmental bacteria and variation in uptake rates in a taxonomically diverse set of bacterial isolates. J. Microbiol. Methods 2011, 86:376-378.
108. Helt C.D., Weber K.P., Legge R.L., Slawson R.M. Antibiotic resistance profiles of representative wetland bacteria and faecal indicators following ciprofloxacin exposure in lab-scale constructed mesocosms. Ecol. Eng. 2012, 39:113-122.
109. Herndl G.J., Reinthaler T., Teira E., van Aken H., Veth C., Pernthaler A., Pernthaler J. Contribution of archaea to total prokaryotic production in the deep Atlantic Ocean. Appl. Environ. Microbiol. 2005, 71:2303-2309.
110. Heuer H., Kopmann C., Binh C.T.T., Top E.M., Smalla K. Spreading antibiotic resistance through spread manure: characteristics of a novel plasmid type with low %G+C content. Environ. Microbiol. 2009, 11:937-949.
111. Heuer H., Schmitt H., Smalla K. Antibiotic resistance gene spread due to manure application on agricultural fields. Curr. Opin. Microbiol. 2011, 14:236-243.
112. Heuer H., Smalla K. Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months. Environ. Microbiol. 2007, 9:657-666.
113. Heuer H., Smalla K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol. Rev. 2012, 36:1083-1104.
114. 2O release in estuarine and coastal sediments. Environ. Sci. Technol. 2015, 49:326-333.
115. Iizumi T., Mizumoto M., Nakamura K. A bioluminescence assay using Nitrosomonas europaea for rapid and sensitive detection of nitrification inhibitors. Appl. Environ. Microbiol. 1998, 64:3656-3662.
116. Ishii S., Sadowsky M.J. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environ. Microbiol. 2009, 11:733-740.
117. Jansson J.K. Towards "Tera-Terra": Terabase sequencing of terrestrial metagenomes. Microbe 2011, 6:309-315.
118. Jechalke S., Focks A., Rosendahl I., Groeneweg J., Siemens J., Heuer H., Smalla K. Structural and functional response of the soil bacterial community to application of manure from difloxacin-treated pigs. FEMS Microbiol. Ecol. 2014, 87:78-88.
119. Jechalke S., Kopmann C., Richter M., Moenickes S., Heuer H., Smalla K. Plasmid-mediated fitness advantage of Acinetobacter baylyi in sulfadiazine-polluted soil. FEMS Microbiol. Lett. 2013, 348:127-132.
120. Jones O.A.H., Sdepanian S., Lofts S., Svendsen C., Spurgeon D.J., Maguire M.L., Griffin J.L. Metabolomic analysis of soil communities can be used for pollution assessment. Environ. Toxicol. Chem. 2014, 33:61-64.
121. Juhler S., Revsbech N.P., Schramm A., Herrmann M., Ottosen L.D.M., Nielsen L.P. Distribution and rate of microbial processes in an ammonia-loaded air filter biofilm. Appl. Environ. Microbiol. 2009, 75:3705-3713.
122. Keller M., Zengler K. Tapping into microbial diversity. Nat. Rev. Microbiol. 2004, 2:141-150.
123. Kleineidam K., Sharma S., Kotzerke A., Heuer H., Thiele-Bruhn S., Smalla K., Wilke B.M., Schloter M. Effect of sulfadiazine on abundance and diversity of denitrifying bacteria by determining nirK and nirS genes in two arable soils. Microb. Ecol. 2010, 60:703-707.
124. Knapp C.W., Dolfing J., Ehlert P.A.I., Graham D.W. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environ. Sci. Technol. 2010, 44:580-587.
125. Kong W.D., Zhu Y.G., Fu B.J., Marschner P., He J.Z. The veterinary antibiotic oxytetracycline and Cu influence functional diversity of the soil microbial community. Environ. Pollut. 2006, 143:129-137.
126. Kostich M.S., Batt A.L., Lazorchak J.M. Concentrations of prioritized pharmaceuticals in effluents from 50 large wastewater treatment plants in the US and implications for risk estimation. Environ. Pollut. 2014, 184:354-359.
127. Kotzerke A., Sharma S., Schauss K., Heuer H., Thiele-Bruhn S., Smalla K., Wilke B.M., Schloter M. Alterations in soil microbial activity and N-transformation processes due to sulfadiazine loads in pig-manure. Environ. Pollut. 2008, 153:315-322.
128. Kowalczyk A., Martin T.J., Price O.R., Snape J.R., van Egmond R.A., Finnegan C.J., Schäfer H., Davenport R.J., Bending G.D. Refinement of biodegradation tests methodologies and the proposed utility of new microbial ecology techniques. Ecotoxicol. Environ. Saf. 2015, 111:9-22.
129. Kristiansen I.B., De Jonge H., Nørnberg P., Mather-Christiansen O., Elsgaard L. Sorption of linear alkylbenzene sulfonate to soil components and effects on microbial iron reduction. Environ. Toxicol. Chem. 2003, 22:1221-1228.
130. Kümmerer K., Alexy R., Hüttig J., Schöll A. Standardized tests fail to assess the effects of antibiotics on environmental bacteria. Water Res. 2004, 38:2111-2116.
131. Lalor B.M., Cookson W.R., Murphy D.V. Comparison of two methods that assess soil community level physiological profiles in a forest ecosystem. Soil Biol. Biochem. 2007, 39:454-462.
132. Lankadurai B.P., Nagato E.G., Simpson M.J. Environmental metabolomics: an emerging approach to study organism responses to environmental stressors. Environ. Rev. 2013, 21:180-205.
133. Larsson D.G.J., de Pedro C., Paxeus N. Effluent from drug manufactures contains extremely high levels of pharmaceuticals. J. Hazard. Mater. 2007, 148:751-755.
134. Lekfeldt J.D.S., Magid J., Holm P.E., Nybroe O., Brandt K.K. Evaluation of the leucine incorporation technique for detection of pollution-induced community tolerance to copper in a long-term agricultural field trial with urban waste fertilizers. Environ. Pollut. 2014, 194:78-85.
135. Levin B.R., Rozen D.E. Non-inherited antibiotic resistance. Nat. Rev. Microbiol. 2006, 4:556-562.
136. Linares J.F., Gustafsson I., Baquero F., Martínez J.L. Antibiotics as intermicrobial signaling agents instead of weapons. Proc. Natl. Acad. Sci. 2006, 103:19,484-19,489.
137. Liu B., Li Y., Zhang X., Wang J., Gao M. Combined effects of chlortetracycline and dissolved organic matter extracted from pig manure on the functional diversity of soil microbial community. Soil Biol. Biochem. 2014, 74:148-155.
138. Liu B.Y., Nie X.P., Liu W.Q., Snoeijs P., Guan C., Tsui M.T.K. Toxic effects of erythromycin, ciprofloxacin and sulfamethoxazole on photosynthetic apparatus in Selenastrum capricornutum. Ecotoxicol. Environ. Saf. 2011, 74:1027-1035.
139. Loman N.J., Misra R.V., Dallman T.J., Constantinidou C., Gharbia S.E., Wain J., Pallen M.J. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 2012, 30:434-439.
140. Luck G.W., Daily G.C., Ehrlich P.R. Population diversity and ecosystem services. Trends Ecol. Evol. 2003, 18:331-336.
141. Martiny A.C., Treseder K., Pusch G. Phylogenetic conservatism of functional traits in microorganisms. ISME J. 2013, 7:830-838.
142. Matthews R.A., Landis W.G., Matthews G.B. The community conditioning hypothesis and its application to environmental toxicology. Environ. Toxicol. Chem. 1996, 15:597-603.
143. Maul J.D., Schuler L.J., Belden J.B., Whiles M.R., Lydy M.J. Effects of the antibiotic ciprofloxacin on stream microbial communities and detritivorous macroinvertebrates. Environ. Toxicol. Chem. 2006, 25:1598-1606.
144. McClellan K., Altenburger R., Schmitt-Jansen M. Pollution-induced community tolerance as a measure of species interaction in toxicity assessment. J. Appl. Ecol. 2008, 45:1514-1522.
145. Melamed S., Lalush C., Elad T., Yagur-Kroll S., Belkin S., Pedahzur R. A bacterial reporter panel for the detection and classification of antibiotic substances. Microb. Biotechnol. 2012, 5:536-548.
146. Mendes R., Kruijt M., de Bruijn I., Dekkers E., van der Voort M., Schneider J.H.M., Piceno Y.M., DeSantis T.Z., Andersen G.L., Bakker P.A.H.M., Raaijmakers J.M. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 2011, 332:1097-1100.
147. Michael I., Rizzo L., Mcardell C.S., Manaia C.M., Merlin C., Schwartz T., Dagot C., Fatta-Kassinos D. Urban wastewater treatment plants as hotspots for the release of antibiotics in the environment: a review. Water Res. 2013, 447:345-360.
148. Millennium Ecosystem Assessment Ecosystems and Human Well-being: Synthesis 2005, Island Press, Washington D.C., USA.
149. Millward R.N., Klerks P.L. Contaminant-adaptation and community tolerance in ecological risk assessment: introduction. Hum. Ecol. Risk. Assess. 2002, 8:921-932.
150. Minz D., Green S.J., Ofek M., Hadar Y. Compost microbial populations and interactions with plants. Microbes at work: from wastes to resources 2010, 231-251. Springer Verlag, Berlin, Germany. H. Insam, I. FrankeWhittle (Eds.).
151. Mitosch K., Bollenbach T. Bacterial responses to antibiotics and their combinations. Environ. Microbiol. Rep. 2014, 6:545-557.
152. Mohapatra S., Chakraborty T., Kumar V., DeBoeck G., Mohanta K.N. Aquaculture and stress management: a review of probiotic intervention. J. Anim. Physiol. Anim. Nutr. 2013, 97:405-430.
153. Molina-Santiago C., Daddaoua A., Fillet S., Duque E., Ramos J.L. Interspecies signalling: Pseudomonas putida efflux pump TtgGHI is activated by indole to increase antibiotic resistance. Environ. Microbiol. 2014, 16:1267-1281.
154. Molina-Santiago C., Daddaoua A., Gómez-Lozano M., Udaondo Z., Molin S., Ramos J.L. Differential transcriptional response to antibiotics by Pseudomonas putida DOT-T1E. Environ. Microbiol. 2015, (in press). 10.1111/1462-2920.12775.
155. Monteiro S., Boxall A. Occurrence and fate of human pharmaceuticals in the environment. Rev. Environ. Contam. Toxicol. 2010, 202:53-154.
156. Moran M.A., Satinsky B., Gifford S.M., Luo H., Rivers A., Chan L.K., Meng J., Durham B.P., Shen C., Varaljay V.A., Smith C.B., Yager P.L., Hopkinson B.M. Sizing up metatranscriptomics. ISME J. 2013, 7:237-243.
157. Mou X.Z., Hodson R.E., Moran M.A. Bacterioplankton assemblages transforming dissolved organic compounds in coastal seawater. Environ. Microbiol. 2007, 9:2025-2037.
158. Näslund J., Hedman J.E., Agestrand C. Effects of the antibiotic ciprofloxacin on the bacterial community structure and degradation of pyrene in marine sediment. Aquat. Toxicol. 2008, 90:223-227.
159. Nelson C.E., Carlson C.A. A nonradioactive assay of bacterial productivity optimized for oligotrophic pelagic environments. Limnol. Oceanogr. Methods 2005, 3:211-220.
160. Nemergut D.R., Schmidt S.K., Fukami T., O'Neill S.P., Bilinski T.M., Stanish L.F., Knelman J.E., Darcy J.L., Lynch R.C., Wickey P., Ferrenberg S. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 2013, 77:342-356.
161. Nesatyy V.J., Suter M.J.F. Proteomics for the analysis of environmental stress responses in organisms. Environ. Sci. Technol. 2007, 41:6891-6900.
162. Nguyen D., Joshi-Datar A., Lepine F., Bauerle E., Olakanmi O., Beer K., McKay G., Siehnel R., Schafhauser J., Wang Y., Britigan B.E., Singh P.K. Active starvation responses mediate antibiotic tolerance in biofilms and nutrient-limited bacteria. Science 2011, 334:982-986.
163. Nocker A., Burr M., Camper A. Genotypic microbial community profiling: a critical technical review. Microb. Ecol. 2007, 54:276-289.
164. Norris K., Potts S.G., Mortimer S.R. Ecosystem services and food production. Issues in Environmental Science and Technology 2010, 52-69. Royal Society of Chemistry, Cambridge. R.E. Hester, R.M. Harrison (Eds.).
165. Ollivier J., Kleineidam K., Reichel R., Thiele-Bruhn S., Kotzerke A., Kindler R., Wilke B.M., Schloter M. Effect of sulfadiazine-contaminated pig manure on the abundances of genes and transcripts involved in nitrogen transformation in the root-rhizosphere complexes of maize and clover. Appl. Environ. Microbiol. 2010, 76:7903-7909.
166. Paerl H.W. Primary productivity and producers. Manual of Environmental Microbiology 2002, 329-341. ASM Press, Washington, D.C. C.J. Hurst, R.L. Crawford, M.J. McInerney, G.R. Knudsen, L.D. Stetzenbach (Eds.).
167. Paton G.I., Rattray E.-A.S., Campbell C.D., Cresser M.S., Glover L.A., Meeussen J.C.L., Killham K. Use of genetically modified microbial biosensors for soil ecotoxicity testing. Biological Indicators of Soil Health 1997, 397-418. CAB International, Wallingford, UK. C. Pankhurst, B.M. Doube, V.V.S.R. Gupta (Eds.).
168. Peng F.J., Zhou L.J., Ying G.G., Liu Y.S., Zhao J.L. Antibacterial activity of the soil-bound antimicrobials oxytetracycline and ofloxacin. Environ. Toxicol. Chem. 2014, 33:776-783.
169. Pérez M.T., Hörtnagl P., Sommaruga R. Contrasting ability to take up leucine and thymidine among freshwater bacterial groups: implications for bacterial production measurements. Environ. Microbiol. 2010, 12:74-82.
170. Pereira e Silva M., Semenov A.V., Schmitt H., van Elsas J.D., Salles J.F. Microbe-mediated processes as indicators to establish the normal operating range of soil functioning. Soil Biol. Biochem. 2013, 57:955-1002.
171. Pernthaler A., Pernthaler J., Schattenhofer M., Amann R. Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl. Environ. Microbiol. 2002, 68:5728-5736.
172. Petric I., Philippot L., Abbate C., Bispo A., Chesnot T., Hallin S., Laval K., Lebeau T., Lemanceau P., Leyval C., Lindström K., Pandard P., Romero E., Sarr A., Schloter M., Simonet P., Smalla K., Wilke B.M., Martin-Laurent F. Inter-laboratory evaluation of the ISO standard 11063 Soil quality - method to directly extract DNA from soil samples. J. Microbiol. Methods 2011, 84:454-460.
173. Philippot L., Ritz K., Pandard P., Hallin S., Martin-Laurent F. Standardisation of methods in soil microbiology: progress and challenges. FEMS Microbiol. Ecol. 2012, 82:1-10.
174. Philippot L., Spor A., Henault C., Bru D., Bizouard F., Jones C.M., Sarr A., Maron P.A. Loss in microbial diversity affects nitrogen cycling in soil. ISME J. 2013, 7:1609-1619.
175. Pillai S., Behra R., Nestler H., Suter M.J.F., Sigg L., Schirmer K. Linking toxicity and adaptive responses across the transcriptome, proteome, and phenotype of Chlamydomonas reinhardtii exposed to silver. Proc. Natl. Acad. Sci. 2014, 111:3490-3495.
176. Pinckney J.L., Hagenbuch I.M., Long R.A., Lovell C.R. Sublethal effects of the antibiotic tylosin on estuarine benthic microalgal communities. Mar. Pollut. Bull. 2013, 68:8-12.
177. Plassart P., Terrat S., Thomson B., Griffiths R., Dequiedt S., Lelievre M., Regnier T., Nowak V., Bailey M., Lemanceau P., Bispo A., Chabbi A., Maron P.A., Mougel C., Ranjard L. Evaluation of the ISO standard 11063 DNA extraction procedure for assessing aoil microbial abundance and community structure. PLoS ONE 2012, 7.
178. Power A.G. Ecosystem services and agriculture: tradeoffs and synergies. Philos. Trans. R. Soc. B Biol. Sci. 2010, 365:2959-2971.
179. Preston-Mafham J., Boddy L., Randerson P.F. Analysis of microbial community functional diversity using sole-carbon-source utilisation profiles - a critique. FEMS Microbiol. Ecol. 2002, 42:1-14.
180. Pruden A., Larsson D.G.J., Amézquita A., Collignon P., Brandt K.K., Graham D.W., Lazorchak J.M., Suzuki S., Silley P., Snape J., Topp E., Zhang T., Zhu Y.G. Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment. Environ. Health Perspect. 2013, 121:878-885.
181. Pruden A., Pei R., Storteboom H., Carlson K.H. Antibiotic resistance genes as emerging contaminants: studies in northern Colorado. Environ. Sci. Technol. 2006, 40:7445-7450.
182. Quinlan E.L., Nietch C.T., Blocksom K., Lazorchak J.M., Batt A.L., Griffiths R., Klemm D.J. Temporal dynamics of periphyton exposed to tetracycline in stream mesocosms. Environ. Sci. Technol. 2011, 45:10,684-10,690.
183. Ramette A. Multivariate analysis in microbial ecology. FEMS Microbiol. Ecol. 2007, 62:142-160.
184. Ratcliff W.C., Denison R.F. Alternative actions for antibiotics. Science 2011, 332:547-548.
185. Reichel R., Michelini L., Ghisi R., Thiele-Bruhn S. Soil bacterial community response to sulfadiazine in the soil-root zone. J. Plant Nutr. Soil Sci. 2015, 178:499-506.
186. Reichel R., Patzelt D., Barleben C., Rosendahl I., Ellerbrock R.H., Thiele-Bruhn S. Soil microbial community responses to sulfadiazine-contaminated manure in different soil microhabitats. Appl. Soil Ecol. 2014, 80:15-25.
187. Reichel R., Radl V., Rosendahl I., Albert A., Amelung W., Schloter M., Thiele-Bruhn S. Soil microbial community responses to antibiotic-contaminated manure under different soil moisture regimes. Appl. Microbiol. Biotechnol. 2014, 98:6487-6495.
188. Rocca J.D., Hall E.K., Lennon J.T., Evans S.E., Waldrop M.P., Cotner J.B., Nemergut D.R., Graham E.B., Wallenstein M.D. Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed. ISME J. 2015, 9:1693-1699.
189. Roose-Amsaleg C., Yan C., Hoang A.M., Laverman A.M. Chronic exposure of river sediments to environmentally relevant levels of tetracycline affects bacterial communities but not denitrification rates. Ecotoxicology 2013, 22:1467-1478.
190. Ros M., Goberna M., Pascual J.A., Klammer S., Insam H. 16S rDNA analysis reveals low microbial diversity in community level physiological profile assays. J. Microbiol. Methods 2008, 72:221-226.
191. Rousk J., Demoling L.A., Baath E. Contrasting short-term antibiotic effects on respiration and bacterial growth compromises the validity of the selective respiratory inhibition technique to distinguish fungi and bacteria. Microb. Ecol. 2009, 58:75-85.
192. Rousk J., Bååth E. Growth of saprotrophic fungi and bacteria in soil. FEMS Microbiol. Ecol. 2011, 78:17-30.
193. Rousk J., Demoling L.A., Bahr A., Baath E. Examining the fungal and bacterial niche overlap using selective inhibitors in soil. FEMS Microbiol. Ecol. 2008, 63:350-358.
194. Sapkota A., Sapkota A.R., Kucharski M., Burke J., McKenzie S., Walker P., Lawrence R. Aquaculture practices and potential human health risks: Current knowledge and future priorities. Environ. Int. 2008, 34:1215-1226.
195. Schauss K., Focks A., Heuer H., Kotzerke A., Schmitt H., Thiele-Bruhn S., Smalla K., Wilke B.M., Matthies M., Amelung W., Klasmeier J., Schloter M. Analysis, fate and effects of the antibiotic sulfadiazine in soil ecosystems. Trac Trends Anal. Chem. 2009, 28:612-618.
196. Schauss K., Focks A., Leininger S., Kotzerke A., Heuer H., Thiele-Bruhn S., Sharma S., Wilke B.M., Matthies M., Smalla K., Munch J.C., Amelung W., Kaupenjohann M., Schloter M., Schleper C. Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environ. Microbiol. 2009, 11:446-456.
197. Schirmer K., Fischer B., Madureira D., Pillai S. Transcriptomics in ecotoxicology. Anal. Bioanal. Chem. 2010, 397:917-923.
198. Schloter M., Lebuhn M., Heulin T., Hartmann A. Ecology and evolution of bacterial microdiversity. FEMS Microbiol. Rev. 2000, 24:647-660.
199. Schmidt T.M., Sogin M.L., et al. The rare biosphere 2011, 1-29. American Academy of Microbiology, Washington D.C.
200. Schmitt H., Haapakangas H., van Beelen P. Effects of antibiotics on soil microorganisms: time and nutrients influence pollution-induced community tolerance. Soil Biol. Biochem. 2005, 37:1882-1892.
201. Schmitt H., van Beelen P., Tolls J., van Leeuwen C.J. Pollution-induced community tolerance of soil microbial communities caused by the antibiotic sulfachloropyridazine. Environ. Sci. Technol. 2004, 38:1148-1153.
202. Schmitt H., Martinali B., Van Beelen P., Seinen W. On the limits of toxicant-induced tolerance testing: cotolerance and response variation of antibiotic effects. Environ. Toxicol. Chem. 2006, 25:1961-1968.
203. Segura P.A., Francois M., Gagnon C., Sauvé S. Review of the occurrence of anti-infectives in contaminated wastewaters and natural and drinking waters. Environ. Health Perspect. 2009, 117:675-684.
204. Shade A., Klimowicz A.K., Spear R.N., Linske M., Donato J.J., Hogan C.S., McManus P.S., Handelsman J. Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil. Appl. Environ. Microbiol. 2013, 79:6617-6625.
205. Shade A., Peter H., Allison S.D., Baho D., Berga M., Buergmann H., Huber D.H., Langenheder S., Lennon J.T., Martiny J.B., Matulich K.L., Schmidt T.M., Handelsman J. Fundamentals of microbial community resistance and resilience. Front. Microbiol. 2012, 3.
206. 2S: a universal defense against antibiotics in bacteria. Science 2011, 334:986-990.
207. Simon C., Daniel R. Metagenomic analyses: past and future trends. Appl. Environ. Microbiol. 2011, 77:1153-1161.
208. Singh B.K., Bardgett R.D., Smith P., Reay D.S. Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat. Rev. Microbiol. 2010, 8:779-790.
209. Singh B.K., Quince C., Macdonald C.A., Khachane A., Thomas N., Al-Soud W.A., Sørensen S.J., He Z., White D., Sinclair A., Crooks B., Zhou J., Campbell C.D. Loss of microbial diversity in soils is coincident with reductions in some specialized functions. Environ. Microbiol. 2014, 16:2408-2420.
210. Six J., Frey S.D., Thiet R.K., Batten K.M. Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci. Soc. Am. J. 2006, 70:555-569.
211. Smalla K., Wachtendorf U., Heuer H., Liu W.T., Forney L. Analysis of BIOLOG GN substrate utilization patterns by microbial communities. Appl. Environ. Microbiol. 1998, 64:1220-1225.
212. Stepanauskas R., Glenn T.C., Jagoe C.H., Tuckfield R.C., Lindell A.H., Mcarthur J.V. Elevated microbial tolerance to metals and antibiotics in metal-contaminated industrial environments. Environ. Sci. Technol. 2005, 39:3671-3678.
213. Stepanauskas R., Glenn T.C., Jagoe C.H., Tuckfield R.C., Lindell A.H., King C.J., Mcarthur J.V. Coselection for microbial resistance to metals and antibiotics in freshwater microcosms. Environ. Microbiol. 2006, 8:1510-1514.
214. Su C., Lei L., Duan Y., Zhang K.Q., Yang J. Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl. Microbiol. Biotechnol. 2012, 93:993-1003.
215. Subbiah M., Mitchell S.M., Ullman J.L., Call D.R. β-Lactams and florfenicol antibiotics remain bioactive in soils while ciprofloxacin, neomycin, and tetracycline are neutralized. Appl. Environ. Microbiol. 2011, 77:7255-7260.
216. Tappe W., Zarfl C., Kummer S., Burauel P., Vereecken H., Groeneweg J. Growth-inhibitory effects of sulfonamides at different pH: dissimilar susceptibility patterns of a soil bacterium and a test bacterium used for antibiotic assays. Chemosphere 2008, 72:836-843.
217. Terrat S., Plassart P., Bourgeois E., Ferreira S., Dequiedt S., Adele-Dit-De-Renseville N., Lemanceau P., Bispo A., Chabbi A., Maron P.A., Ranjard L. Meta-barcoded Evaluation of the ISO Standard 11063 DNA Extraction Procedure to Characterize Soil Bacterial and Fungal Community Diversity And Composition 2014, Microb. Biotechnol., (n/a).
218. Thiele-Bruhn S. Microbial inhibition by pharmaceutical antibiotics in different soils - dose-response relations determined with the iron(III) reduction test. Environ. Toxicol. Chem. 2005, 24:869-876.
219. Thorsen M.K., Brandt K.K., Nybroe O. Abundance and diversity of culturable Pseudomonas constitute sensitive indicators for adverse long-term copper impacts in soil. Soil Biol. Biochem. 2013, 57:933-935.
220. Tlili A., Berard A., Blanck H., Bouchez A., Cássio F., Eriksson K.M., Morin S., Montuelle B., Navarro E., Pascoal C., Pesce S., Schmitt-Jansen M., Behra R. Pollution-induced community tolerance (PICT): towards an ecologically relevant risk assessment of chemicals in aquatic systems. Freshw. Biol. 2015, 10.1111/fwb.12558.
221. Tlili A., Marechal M., Montuelle B., Volat B., Dorigo U., Bérard A. Use of the MicroResp(TM) method to assess pollution-induced community tolerance to metals for lotic biofilms. Environ. Pollut. 2011, 159:18-24.
222. Tobor-Kaplon M.A., Bloem J., Römkens P.F.A.M., de Ruiter P.C. Functional stability of microbial communities in contaminated soils. Oikos 2005, 111:119-129.
223. Toth J.D., Feng Y., Dou Z. Veterinary antibiotics at environmentally relevant concentrations inhibit soil iron reduction and nitrification. Soil Biol. Biochem. 2011, 43:2470-2472.
224. Van Aggelen G., Ankley G.T., Baldwin W.S., Bearden D.W., Benson W.H., Chipman J.K., Collette T.W., Craft J.A., Denslow N.D., Embry M.R., Falciani F., George S.G., Helbing C.C., Hoekstra P.F., Iguchi T., Kagami Y., Katsiadaki I., Kille P., Liu L., Lord P.G., McIntyre T., O'Neill A., Osachoff H., Perkins E.J., Santos E.M., Skirrow R.C., Snape J.R., Tyler C.R., Versteeg D., Viant M.R., Volz D.C., Williams T.D., Yu L. Integrating omic technologies into aquatic ecological risk assessment and environmental monitoring: hurdles, achievements, and future outlook. Environ. Health Perspect. 2010, 118:1-5.
225. van der Grinten E., Pikkemaat M.I.G., van den Brandhof E.-J., Stroomberg G.J., Kraak M.H.S. Comparing the sensitivity of algal, cyanobacterial and bacterial bioassays to different groups of antibiotics. Chemosphere 2010, 80:1-6.
226. van der Meer J.R., Belkin S. Where microbiology meets microengineering: design and applications of reporter bacteria. Nat. Rev. Microbiol. 2010, 8:511-522.
227. van Straalen N.M., Feder M.E. Ecological and evolutionary functional genomics-how can it contribute to the risk assessment of chemicals?. Environ. Sci. Technol. 2012, 46:3-9.
228. VICH.Guidance for industry Environmental Impact Assessment for Veterinary Medicinal Products Phase II Guidance. International Cooperation on Harmonisation of Technical Requirements of Veterinary Medicinal Products. VICH GL 38 2004, 166:1-37.
229. Vulkan R., Zhao F., Barbosa-Jefferson V., Preston S., Paton G.I., Tipping E., McGrath S.P. Copper speciation and impacts on bacterial biosensors in the porewater of copper-contaminated soils. Environ. Sci. Technol. 2000, 34:5115-5120.
230. Wackett L.P., Hershberger C.D. Biocatalysis and Biodegradation: Microbial Transformation of Organic Compounds 2001, 1-250. ASM Press, Washington, DC.
231. Wakelin S., Lombi E., Donner E., MacDonald L., Black A., O'Callaghan M. Application of MicroResp for soil ecotoxicology. Environ. Pollut. 2013, 179:177-184.
232. Wellington E.M.H., Boxall A.B.A., Cross P., Feil E.J., Gaze W.H., Hawkey P.M., Johnson-Rollings A.S., Jones D.L., Lee N.M., Otten W., Thomas C.M., Williams A.P. The role of the natural environment in the emergence of antibiotic resistance in Gram-negative bacteria. Lancet Infect. Dis. 2013, 13:155-165.
233. Wertz S., Degrange V., Prosser J.I., Poly F., Commeaux C., Freitag T., Guillaumaud N., Roux X.L. Maintenance of soil functioning following erosion of microbial diversity. Environ. Microbiol. 2006, 8:2162-2169.
234. Wilson B.A., Smith V.H., deNoyelles F., Larive C.K. Effects of three pharmaceutical and personal care products on natural freshwater algal assemblages. Environ. Sci. Technol. 2003, 37:1713-1719.
235. Wintzingerode F.V., Göbel U.B., Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 1997, 21:213-229.
236. Wright G.D. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat. Rev. Microbiol. 2007, 5:175-186.
237. Wright M.S., Peltier G.L., Stepanauskas R., McArthur J.V. Bacterial tolerances to metals and antibiotics in metal-contaminated and reference streams. FEMS Microbiol. Ecol. 2006, 58:293-302.
238. Xia K., Bhandari A., Das K., Pillar G. Occurrence and fate of pharmaceuticals and personal care products (PPCPs) in biosolids. J. Environ. Qual. 2005, 34:91-104.
239. Yachi S., Loreau M. Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc. Natl. Acad. Sci. 1999, 96:1463-1468.
240. Yergeau E., Lawrence J.R., Waiser M.J., Korber D.R., Greer C.W. Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays. Appl. Environ. Microbiol. 2010, 76:5432-5439.
241. Yergeau E., Sanschagrin S., Waiser M.J., Lawrence J.R., Greer C.W. Sub-inhibitory concentrations of different pharmaceutical products affect the meta-transcriptome of river biofilm communities cultivated in rotating annular reactors. Environ. Microbiol. Rep. 2012, 4:350-359.
242. Youngblut N.D., Shade A., Read J.S., McMahon K.D., Whitaker R.J. Lineage-specific responses of microbial communities to environmental change. Appl. Environ. Microbiol. 2013, 79:39-47.
243. Zarfl C., Matthies M., Klasmeier J. A mechanistical model for the uptake of sulfonamides by bacteria. Chemosphere 2008, 70:753-760.
244. Zearley T.L., Summers R.S. Removal of trace organic micropollutants by drinking water biological filters. Environ. Sci. Technol. 2012, 46:9412-9419.
245. Zelles L. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol. Fertil. Soils 1999, 29:111-129.
246. Zhang Y., Boyd S.A., Teppen B.J., Tiedje J.M., Li H. Role of Tetracycline Speciation in the Bioavailability to Escherichia coli for Uptake and Expression of Antibiotic Resistance 2014, Environmental Science & Technology.
247. Zhu Y.G., Johnson T.A., SU J.Q., Qiao M., Guo G.X., Stedtfeld R.D., Hashsham S.A., Tiedje J.M. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc. Natl. Acad. Sci. 2013, 110:3435-3440.
248. Zielezny Y., Groeneweg J., Vereecken H., Tappe W. Impact of sulfadiazine and chlorotetracycline on soil bacterial community structure and respiratory activity. Soil Biol. Biochem. 2006, 38:2372-2380.
249. Zounková R., Klimesová Z., Nepejchalová L., Hilscherová K., Bláha L. Complex evaluation of ecotoxicity and genotoxicity of antimicrobials oxytetracycline and flumequine used in aquaculture. Environ. Toxicol. Chem. 2011, 30:1184-1189.