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From Microbial Ecology to Microbial Ecotoxicology

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Microbial Ecotoxicology

Abstract

Because of their ubiquity, abundance and metabolic activities, microorganisms play a crucial role in the biogeochemical cycling of elements in the environment. Any perturbations in the activity and diversity of the microbial community are likely to lead to significant impacts in terms not only of biogeochemical cycling but also ecosystem resilience . Human activities and industrialization have resulted in the release of millions of tonnes of chemicals and pollutants into the environments; some of these are toxic to living organisms. However there is a lack of information about the toxicity effects at the ecosystem level; where toxicity tests have been included in studies the basis has been the use of target species including plants (e.g. radish germination), worms (e.g. earthworm survival) and microbes (e.g. the Microtox bioassay test) to evaluate the effect of the pollutant on the target organisms. Microbial ecotoxicology represents an emerging discipline that encompasses microbial ecology, microbial toxicology, chemistry and physics and that offers great potential in the assessment of the fate and impact of environmental pollutants at the ecosystem level. In this introduction we discuss the importance of microbial ecology together with some of the advantages of the application of the recently established microbial ecotoxicology discipline in order to reliably assess the impact of contamination on the resilience and the functionality of the microbial community.

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References

  • Abd-El-Haleem D, Ripp S, Scott C, Sayler SG (2002) A luxCDABE-based bioluminescent bioreporter for the detection of phenol. J Ind Microbiol Biotechnol 29(5):233–237. doi:10.1038/sj.jim.7000309

  • Aburto-Medina A, Adetutu E, Aleer S, Weber J, Patil S, Sheppard P, Ball A, Juhasz A (2012) Comparison of indigenous and exogenous microbial populations during slurry phase biodegradation of long-term hydrocarbon-contaminated soil. Biodegradation 23(6):813–822. doi:10.1007/s10532-012-9563-8

    Article  CAS  PubMed  Google Scholar 

  • Aburto A, Ball AS (2009) Bacterial population dynamics and separation of active degraders by stable isotope probing during benzene degradation in a BTEX-impacted aquifer. Rev Int Contaminacion Ambiental 25(3)

    Google Scholar 

  • Aburto A, Fahy A, Coulon F, Lethbridge G, Timmis KN, Ball AS, McGenity TJ (2009) Mixed aerobic and anaerobic microbial communities in benzene-contaminated groundwater. J Appl Microbiol 106(1):317–328

    Article  CAS  PubMed  Google Scholar 

  • Adetutu E, Weber J, Aleer S, Dandie CE, Aburto-Medina A, Ball AS, Juhasz AL (2013) Assessing impediments to hydrocarbon biodegradation in weathered contaminated soils. J Hazard Mater 261(0):847–853. doi:10.1016/j.jhazmat.2013.01.052

  • Adetutu EM, Gundry TD, Patil SS, Golneshin A, Adigun J, Bhaskarla V, Aleer S, Shahsavari E, Ross E, Ball AS (2015) Exploiting the intrinsic microbial degradative potential for field-based in situ dechlorination of trichloroethene contaminated groundwater. J Hazard Mater 300:48–57. doi:10.1016/j.jhazmat.2015.06.055

  • Ahtiainen J, Valo R, Järvinen M, Joutti A (2002) Microbial toxicity tests and chemical analysis as monitoring parameters at composting of creosote-contaminated soil. Ecotoxicol Environ Saf 53(2):323–329. doi:10.1006/eesa.2002.2225

    Article  CAS  PubMed  Google Scholar 

  • Aleer S, Adetutu EM, Makadia TH, Patil S, Ball AS (2011) Harnessing the hydrocarbon-degrading potential of contaminated soils for the bioremediation of waste engine oil. Water Air Soil Pollut 218(1–4):121–130

    Article  CAS  Google Scholar 

  • Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1):143–169

    CAS  PubMed  PubMed Central  Google Scholar 

  • Arias ME, Gonzalez-Perez JA, Gonzalez-Vila FJ, Ball AS (2005) Soil health—a new challenge for microbiologists and chemists. Int Microbiol 8(1):13–21

    CAS  PubMed  Google Scholar 

  • Bachmann T (2003) Transforming cyanobacteria into bioreporters of biological relevance. Trends Biotechnol 21(6):247–249. doi:10.1016/S0167-7799(03)00114-8

    Article  CAS  PubMed  Google Scholar 

  • Bastiaens L, Springael D, Dejonghe W, Wattiau P, Verachtert H, Diels L (2001) A transcriptional luxAB reporter fusion responding to fluorene in Sphingomonas sp. LB126 and its initial characterisation for whole-cell bioreporter purposes. Res Microbiol 152(10):849–859. doi:10.1016/S0923-2508(01)01268-2

    Article  CAS  PubMed  Google Scholar 

  • Bechor O, Smulski DR, Van Dyk TK, LaRossa RA, Belkin S (2002) Recombinant microorganisms as environmental biosensors: pollutants detection by Escherichia coli bearing fabA′:lux fusions. J Biotechnol 94(1):125–132. doi:10.1016/S0168-1656(01)00423-0

    Article  CAS  PubMed  Google Scholar 

  • Benitez L, Martin-Gonzalez A, Gilardi P, Soto T, de Lecea JR, Gutiérrez JC (1994) The ciliated protozoa Tetrahymena thermophila as a bionsensor to detect mycotoxins. Lett Appl Microbiol 19(6):489–491. doi:10.1111/j.1472-765X.1994.tb00989.x

    Article  CAS  Google Scholar 

  • Boehm MJ, Wu T, Stone AG, Kraakman B, Iannotti DA, Wilson GE, Madden LV, Hoitink HAJ (1997) Cross-polarized magic-angle spinning 13C nuclear magnetic resonance spectroscopic characterization of soil organic matter relative to culturable bacterial species composition and sustained biological control of pythium root rot. Appl Environ Microbiol 63(1):162–168

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bonnet JL, Bonnemoy F, Dusser M, Bohatier J (2007) Assessment of the potential toxicity of herbicides and their degradation products to nontarget cells using two microorganisms, the bacteria Vibrio fischeri and the ciliate Tetrahymena pyriformis. Environ Toxicol 22(1):78–91. doi:10.1002/tox.20237

    Article  CAS  PubMed  Google Scholar 

  • Bonnet JL, Bonnemoy F, Dusser M, Bohatier J (2008) Toxicity assessment of the herbicides sulcotrione and mesotrione toward two reference environmental microorganisms: Tetrahymena pyriformis and Vibrio fischeri. Arch Environ Contam Toxicol 55(4):576–583. doi:10.1007/s00244-008-9145-2

    Article  CAS  PubMed  Google Scholar 

  • Broos K, Warne MSJ, Heemsbergen DA, Stevens D, Barnes MB, Correll RL, McLaughlin MJ (2007) Soil factors controlling the toxicity of copper and zinc to microbial processes in Australian soils. Environ Toxicol Chem 26(4):583–590

    Article  CAS  PubMed  Google Scholar 

  • Brussaard CPD, Peperzak L, Beggah S, Wick LY, Wuerz B, Weber J, Samuel Arey J, van der Burg B, Jonas A, Huisman J, van der Meer JR (2016) Immediate ecotoxicological effects of short-lived oil spills on marine biota. Nat Commun 7. doi:10.1038/ncomms11206

  • Bundy JG, Paton GI, Campbell CD (2004) Combined microbial community level and single species biosensor responses to monitor recovery of oil polluted soil. Soil Biol Biochem 36(7):1149–1159. doi:10.1016/j.soilbio.2004.02.025

    Article  CAS  Google Scholar 

  • Burns A, Ryder DS (2001) Potential for biofilms as biological indicators in Australian riverine systems. Ecol Manage Restor 2(1):53–64. doi:10.1046/j.1442-8903.2001.00069.x

    Article  Google Scholar 

  • Campanella L, Cubadda F, Sammartino MP, Saoncella A (2001) An algal biosensor for the monitoring of water toxicity in estuarine environments. Water Res 35(1):69–76. doi:10.1016/S0043-1354(00)00223-2

    Article  CAS  PubMed  Google Scholar 

  • Cho J-C, Park K-J, Ihm H-S, Park J-E, Kim S-Y, Kang I, Lee K-H, Jahng D, Lee D-H, Kim S-J (2004) A novel continuous toxicity test system using a luminously modified freshwater bacterium. Biosens Bioelectron 20(2):338–344. doi:10.1016/j.bios.2004.02.001

    Article  CAS  PubMed  Google Scholar 

  • Cornelissen G, Rigterink H, Ferdinandy MMA, van Noort PCM (1998) Rapidly desorbing fractions of PAHs in contaminated sediments as a predictor of the extent of bioremediation. Environ Sci Technol 32(7):966–970. doi:10.1021/es9704038

  • Costa PS, Reis MP, Ávila MP, Leite LR, de Araújo FMG, Salim ACM, Oliveira G, Barbosa F, Chartone-Souza E, Nascimento AMA (2015) Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment. PLoS ONE 10(3):e0119465. doi:10.1371/journal.pone.0119465

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cupples AM (2011) The use of nucleic acid based stable isotope probing to identify the microorganisms responsible for anaerobic benzene and toluene biodegradation. J Microbiol Methods 85(2):83–91. doi:10.1016/j.mimet.2011.02.011

    Article  CAS  PubMed  Google Scholar 

  • Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci 99(16):10494–10499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • D’Souza SF (2001) Microbial biosensors. Biosens Bioelectron 16(6):337–353. doi:10.1016/S0956-5663(01)00125-7

    Article  PubMed  Google Scholar 

  • Durrieu C, Tran-Minh C (2002) Optical algal biosensor using alkaline phosphatase for determination of heavy metals. Ecotoxicol Environ Saf 51(3):206–209. doi:10.1006/eesa.2001.2140

    Article  CAS  PubMed  Google Scholar 

  • Dutka BJ, Kwan KK (1981) Comparison of three microbial toxicity screening tests with the microtox test. Bull Environ Contam Toxicol 27(1):753–757. doi:10.1007/BF01611091

    Article  CAS  PubMed  Google Scholar 

  • Dykhuizen DE (1998) Santa rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73(1):25–33. doi:10.1023/a:1000665216662

    Article  CAS  PubMed  Google Scholar 

  • Fahy A, McGenity TJ, Timmis KN, Ball AS (2006) Heterogeneous aerobic benzene-degrading communities in oxygen-depleted groundwaters. FEMS Microbiol Ecol 58(2):260–270

    Article  CAS  PubMed  Google Scholar 

  • Fang H, Cai L, Yang Y, Ju F, Li X, Yu Y, Zhang T (2014) Metagenomic analysis reveals potential biodegradation pathways of persistent pesticides in freshwater and marine sediments. Sci Total Environ 470–471:983–992. doi:10.1016/j.scitotenv.2013.10.076

    Article  PubMed  CAS  Google Scholar 

  • Fang H, Cai L, Yu Y, Zhang T (2013) Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge. Biores Technol 129:209–218. doi:10.1016/j.biortech.2012.11.054

    Article  CAS  Google Scholar 

  • Farré M, Barceló D (2009) Biosensors for aquatic toxicology evaluation. In: Barceló D, Hansen P-D (eds) Biosensors for environmental monitoring of aquatic systems: bioanalytical and chemical methods for endocrine disruptors. Springer, Berlin, pp 115–160. doi:10.1007/978-3-540-36253-1_5

  • Farré M, Fernandez J, Paez M, Granada L, Barba L, Gutierrez H, Pulgarin C, Barceló D (2014) Analysis and toxicity of methomyl and ametryn after biodegradation. Anal Bioanal Chem 373(8):704–709. doi:10.1007/s00216-002-1413-9

    Article  CAS  Google Scholar 

  • Ghiglione J-F, Martin-Laurent F, Pesce S (2016) Microbial ecotoxicology: an emerging discipline facing contemporary environmental threats. Environ Sci Pollut Res 23(5):3981–3983. doi:10.1007/s11356-015-5763-1

  • Ghiglione J-F, Martin-Laurent F, Stachowski-Haberkorn S, Pesce S, Vuilleumier S (2014) The coming of age of microbial ecotoxicology: report on the first two meetings in France. Environ Sci Pollut Res 21(24):14241–14245. doi:10.1007/s11356-014-3390-x

    Article  Google Scholar 

  • Gołębiewski M, Deja-Sikora E, Cichosz M, Tretyn A, Wróbel B (2014) 16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils. Microb Ecol 67(3):635–647. doi:10.1007/s00248-013-0344-7

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gong P, Hawari J, Thiboutot S, Ampleman G, Sunahara GI (2001) Ecotoxicological effects of hexahydro-1,3,5-trinitro-1,3,5-triazine on soil microbial activities. Environ Toxicol Chem 20(5):947–951. doi:10.1002/etc.5620200502

    Article  CAS  PubMed  Google Scholar 

  • González-Barreiro O, Rioboo C, Herrero C, Cid A (2006) Removal of triazine herbicides from freshwater systems using photosynthetic microorganisms. Environ Pollut 144(1):266–271. doi:10.1016/j.envpol.2005.12.014

    Article  PubMed  CAS  Google Scholar 

  • Green SJ, Leigh MB, Neufeld JD (2010) Denaturing Gradient Gel Electrophoresis (DGGE) for microbial community analysis. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 4137–4158. doi:10.1007/978-3-540-77587-4_323

  • Gu J-D, Wang Y (2014) Geomicrobial ecotoxicology as a new subject in environmental sciences is proposed. Ecotoxicology 23(10):1823–1825. doi:10.1007/s10646-014-1359-7

    Article  CAS  PubMed  Google Scholar 

  • Gu MB, Chang ST (2001) Soil biosensor for the detection of PAH toxicity using an immobilized recombinant bacterium and a biosurfactant. Biosens Bioelectron 16(9–12):667–674. doi:10.1016/S0956-5663(01)00230-5

    Article  CAS  PubMed  Google Scholar 

  • Gutiérrez JC, Martín-González A, Díaz S, Ortega R (2003) Ciliates as a potential source of cellular and molecular biomarkers/biosensors for heavy metal pollution. Eur J Protistol 39(4):461–467. doi:10.1078/0932-4739-00021

    Article  Google Scholar 

  • Guzzo J, Guzzo A, DuBow MS (1992) Characterization of the effects of aluminum on luciferase biosensors for the detection of ecotoxicity. Toxicol Lett 64:687–693. doi:10.1016/0378-4274(92)90248-I

    Article  PubMed  Google Scholar 

  • Hansen P-D, Usedom A (1997) New biosensors for environmental analysis. In: Scheller FW, Schubert F, Fedrowitz J (eds) Frontiers in biosensorics II: practical applications. Birkhäuser Basel, Basel, pp 109–120. doi:10.1007/978-3-0348-9045-8_8

  • Hansen PD (2008) Biosensors and eco-toxicology. Eng Life Sci 8(1):26–31. doi:10.1002/elsc.200720228

    Article  CAS  Google Scholar 

  • Herrmann S, Kleinsteuber S, Chatzinotas A, Kuppardt S, Lueders T, Richnow H-H, Vogt C (2010) Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing. Environ Microbiol 12(2):401–411. doi:10.1111/j.1462-2920.2009.02077.x

    Article  CAS  PubMed  Google Scholar 

  • Hill GT, Mitkowski NA, Aldrich-Wolfe L, Emele LR, Jurkonie DD, Ficke A, Maldonado-Ramirez S, Lynch ST, Nelson EB (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15(1):25–36. doi:10.1016/S0929-1393(00)00069-X

    Article  Google Scholar 

  • Hirsch PR, Mauchline TH, Clark IM (2010) Culture-independent molecular techniques for soil microbial ecology. Soil Biol Biochem 42(6):878–887

    Article  CAS  Google Scholar 

  • Ingham ER, Cambardella C, Coleman DC (1986) Manipulation of bacteria, fungi and protozoa by biocides in lodgepole pine forest soil microcosms: effects on organism interactions and nitrogen mineralization. Can J Soil Sci 66(2):261–272. doi:10.4141/cjss86-028

    Article  Google Scholar 

  • Jones RJ, Muller J, Haynes D, Schreiber U (2003) Effects of herbicides diuron and atrazine on corals of the great barrier reef, Australia. Mar Ecol Prog Ser 251:153–167

    Article  CAS  Google Scholar 

  • Juneau P, Popovic R (1999) Evidence for the rapid phytotoxicity and environmental stress evaluation using the PAM fluorometric method: importance and future application. Ecotoxicology 8(6):449–455. doi:10.1023/a:1008955819527

  • Kahru A, Ivask A, Kasemets K, Pollumaa L, Kurvet I, François M, Dubourguier H-C (2005) Biotests and biosensors in ecotoxicological risk assessment of field soils polluted with zinc, lead, and cadmium. Environ Toxicol Chem 24(11):2973–2982. doi:10.1897/05-002R1.1

    Article  CAS  PubMed  Google Scholar 

  • Kallmeyer J, Pockalny R, Adhikari RR, Smith DC, D’Hondt S (2012) Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci 109(40):16213–16216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kamlet MJ, Doherty RM, Veith GD, Taft RW, Abraham MH (1986) Solubility properties in polymers and biological media. 7. An analysis of toxicant properties that influence inhibition of bioluminescence in Photobacterium phosphoreum (the Microtox test). Environ Sci Technol 20(7):690–695. doi:10.1021/es00149a007

    Article  CAS  PubMed  Google Scholar 

  • Kao C-M, Liao H-Y, Chien C-C, Tseng Y-K, Tang P, Lin C-E, Chen S-C (2016) The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis. J Hazard Mater 302:144–150. doi:10.1016/j.jhazmat.2015.09.047

    Article  CAS  PubMed  Google Scholar 

  • Kasai Y (2011) Molecular Technologies for Analysis of Petroleum Bioremediation. In: Koukkou A-I (ed) Microbial bioremediation of non-metals: current research. Caister Academic Press, Norfolk, UK, pp 233–252

    Google Scholar 

  • Khudur L, Shahsavari E, Miranda A, Morrison P, Nugegoda D, Ball A (2015) Evaluating the efficacy of bioremediating a diesel-contaminated soil using ecotoxicological and bacterial community indices. Environ Sci Pollut Res 1–11. doi:10.1007/s11356-015-4624-2

  • King J, DiGrazia P, Applegate B, Burlage R, Sanseverino J, Dunbar P, Larimer F, Sayler Ga (1990) Rapid, sensitive bioluminescent reporter technology for naphthalene exposure and biodegradation. Science(Washington) 249(4970):778–781

    Google Scholar 

  • Kováts N, Horváth E (2016) Bioluminescence‐based assays for assessing eco‐and genotoxicity of airborne emissions. Luminescence

    Google Scholar 

  • Kumpiene J, Guerri G, Landi L, Pietramellara G, Nannipieri P, Renella G (2009) Microbial biomass, respiration and enzyme activities after in situ aided phytostabilization of a Pb- and Cu-contaminated soil. Ecotoxicol Environ Saf 72(1):115–119. doi:10.1016/j.ecoenv.2008.07.002

    Article  CAS  PubMed  Google Scholar 

  • Kunapuli U, Lueders T, Meckenstock RU (2007) The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation. ISME J\ 1\ (7\):643\-653\

    Google Scholar 

  • Lanno R, Wells J, Conder J, Bradham K, Basta N (2004) The bioavailability of chemicals in soil for earthworms. Ecotoxicol Environ Saf 57(1):39–47. doi:10.1016/j.ecoenv.2003.08.014

    Article  CAS  PubMed  Google Scholar 

  • Lehman RM, Colwell FS, Ringelberg DB, White DC (1995) Combined microbial community-level analyses for quality assurance of terrestrial subsurface cores. J Microbiol Methods 22(3):263–281. doi:10.1016/0167-7012(95)00012-A

    Article  Google Scholar 

  • Liu F, Ying G-G, Yang L-H, Zhou Q-X (2009) Terrestrial ecotoxicological effects of the antimicrobial agent triclosan. Ecotoxicol Environ Saf 72(1):86–92. doi:10.1016/j.ecoenv.2008.06.009

    Article  CAS  PubMed  Google Scholar 

  • Lors C, Damidot D, Ponge J-F, Périé F (2012) Comparison of a bioremediation process of PAHs in a PAH-contaminated soil at field and laboratory scales. Environ Pollut 165:11–17. doi:10.1016/j.envpol.2012.02.004

    Article  CAS  PubMed  Google Scholar 

  • Maderova L, Paton GI (2013) Deployment of microbial sensors to assess zinc bioavailability and toxicity in soils. Soil Biol Biochem 66:222–228. doi:10.1016/j.soilbio.2013.07.017

    Article  CAS  Google Scholar 

  • Maderova L, Watson M, Paton GI (2011) Bioavailability and toxicity of copper in soils: integrating chemical approaches with responses of microbial biosensors. Soil Biol Biochem 43(6):1162–1168. doi:10.1016/j.soilbio.2011.02.004

    Article  CAS  Google Scholar 

  • Malik S, Beer M, Megharaj M, Naidu R (2008) The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ Int 34(2):265–276

    Article  CAS  PubMed  Google Scholar 

  • Manefield M, Whiteley AS, Griffiths RI, Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68(11):5367–5373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Margesin R, Zimmerbauer A, Schinner F (2000) Monitoring of bioremediation by soil biological activities. Chemosphere 40(4):339–346. doi:10.1016/S0045-6535(99)00218-0

    Article  CAS  PubMed  Google Scholar 

  • Marty JL, Olive D, Asano Y (1997) Measurement of BOD: correlation between 5-day BOD and commercial BOD biosensor values. Environ Technol 18(3):333–337. doi:10.1080/09593331808616544

    Article  CAS  Google Scholar 

  • Mateo P, Leganés F, Perona E, Loza V, Fernández-Piñas F (2015) Cyanobacteria as bioindicators and bioreporters of environmental analysis in aquatic ecosystems. Biodivers Conserv 24(4):909–948. doi:10.1007/s10531-015-0903-y

    Article  Google Scholar 

  • Mejáre M, Bülow L (2001) Metal-binding proteins and peptides in bioremediation and phytoremediation of heavy metals. Trends Biotechnol 19(2):67–73. doi:10.1016/S0167-7799(00)01534-1

    Article  PubMed  Google Scholar 

  • Mekki A, Dhouib A, Feki F, Sayadi S (2008) Assessment of toxicity of the untreated and treated olive mill wastewaters and soil irrigated by using microbiotests. Ecotoxicol Environ Saf 69(3):488–495. doi:10.1016/j.ecoenv.2007.04.008

    Article  CAS  PubMed  Google Scholar 

  • Metzker ML (2010) Sequencing technologies [mdash] the next generation. Nat Rev Genet 11(1):31–46

    Article  CAS  PubMed  Google Scholar 

  • Min J, Pham CH, Gu MB (2003) Specific responses of bacterial cells to dioxins. Environ Toxicol Chem 22(2):233–238. doi:10.1002/etc.5620220201

    Article  CAS  PubMed  Google Scholar 

  • Molina-Barahona L, Vega-Loyo L, Guerrero M, Ramírez S, Romero I, Vega-Jarquín C, Albores A (2005) Ecotoxicological evaluation of diesel-contaminated soil before and after a bioremediation process. Environ Toxicol 20(1):100–109. doi:10.1002/tox.20083

    Article  CAS  PubMed  Google Scholar 

  • Mora APd, Ortega-Calvo JJ, Cabrera F, Madejón E (2005) Changes in enzyme activities and microbial biomass after “in situ” remediation of a heavy metal-contaminated soil. Appl Soil Ecol 28(2):125–137. doi:10.1016/j.apsoil.2004.07.006

    Article  Google Scholar 

  • Mueller DC, Bonner JS, McDonald SJ, Autenrieth RL, Donnelly KC, Lee K, Doe K, Anderson J (2003) The use of toxicity bioassays to monitor the recovery of oiled wetland sediments. Environ Toxicol Chem 22(9):1945–1955. doi:10.1897/02-325

    Article  CAS  PubMed  Google Scholar 

  • Muñoz-Leoz B, Ruiz-Romera E, Antigüedad I, Garbisu C (2011) Tebuconazole application decreases soil microbial biomass and activity. Soil Biol Biochem 43(10):2176–2183. doi:10.1016/j.soilbio.2011.07.001

    Article  CAS  Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59(3):695–700

    CAS  PubMed  PubMed Central  Google Scholar 

  • Naessens M, Leclerc JC, Tran-Minh C (2000) Fiber optic biosensor using chlorella vulgaris for determination of toxic compounds. Ecotoxicol Environ Saf 46(2):181–185. doi:10.1006/eesa.1999.1904

    Article  CAS  PubMed  Google Scholar 

  • Naidu R (2011) Chemical bioavailability in terrestrial environments. Elsevier Science

    Google Scholar 

  • Nakatsu C (2007) Soil microbial community analysis using denaturing gradient gel electrophoresis. Soil Sci Soc Am J 71(2):562–571

    Article  CAS  Google Scholar 

  • Nomura Y, Ikebukuro K, Yokoyama K, Takeuchi T, Arikawa Y, Ohno S, Karube I (1998) Application of a linear alkylbenzene sulfonate biosensor to river water monitoring1. Biosens Bioelectron 13(9):1047–1053. doi:10.1016/S0956-5663(97)00077-8

    Article  CAS  PubMed  Google Scholar 

  • Ogawa T, Shibata M, Yatome C, Idaka E (1988) Growth inhibition ofBacillus subtilis by basic dyes. Bull Environ Contam Toxicol 40(4):545–552. doi:10.1007/bf01688379

  • Oka AR, Phelps CD, McGuinness LM, Mumford A, Young LY, Kerkhof LJ (2008) Identification of critical members in a sulfidogenic benzene-degrading consortium by DNA stable isotope probing. Appl Environ Microbiol 74(20):6476–6480. doi:10.1128/aem.01082-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I (2015) Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights 9:75

    CAS  PubMed  PubMed Central  Google Scholar 

  • Paszczynski A, Crawford RL (1995) Potential for bioremediation of xenobiotic compounds by the white-rot fungus Phanerochaete chrysosporium. Biotechnol Prog 11(4):368–379. doi:10.1021/bp00034a002

    Article  CAS  Google Scholar 

  • Patil SS, Adetutu EM, Aburto-Medina A, Menz IR, Ball AS (2013) Biostimulation of indigenous communities for the successful dechlorination of tetrachloroethene (perchloroethylene)-contaminated groundwater. Biotech Lett 36(1):75–83. doi:10.1007/s10529-013-1369-1

    Article  CAS  Google Scholar 

  • Pimentel D, Whitecraft M, Scott ZR, Zhao L, Satkiewicz P, Scott TJ, Phillips J, Szimak D, Singh G, Gonzalez DO (2010) Will limited land, water, and energy control human population numbers in the future? Hum Ecol 38(5):599–611

    Article  Google Scholar 

  • Płaza GA, Nałęcz-Jawecki G, Pinyakong O, Illmer P, Margesin R (2009) Ecotoxicological and microbiological characterization of soils from heavy-metal- and hydrocarbon-contaminated sites. Environ Monit Assess 163(1):477–488. doi:10.1007/s10661-009-0851-7

    PubMed  Google Scholar 

  • Preston S, Coad N, Townend J, Killham K, Paton GI (2000) Biosensing the acute toxicity of metal interactions: are they additive, synergistic, or antagonistic? Environ Toxicol Chem 19(3):775–780. doi:10.1002/etc.5620190332

    Article  CAS  Google Scholar 

  • Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403(6770):646–649

    Article  CAS  PubMed  Google Scholar 

  • Reid BJ, Jones KC, Semple KT (2000) Bioavailability of persistent organic pollutants in soils and sediments—a perspective on mechanisms, consequences and assessment. Environ Pollut 108(1):103–112. doi:10.1016/S0269-7491(99)00206-7

    Article  CAS  PubMed  Google Scholar 

  • Reith F, Zammit CM, Shar SS, Etschmann B, Bottrill R, Southam G, Ta C, Kilburn M, Oberthür T, Ball AS (2016) Biological role in the transformation of platinum-group mineral grains. Nat Geosci

    Google Scholar 

  • Renella G, Landi L, Ascher J, Ceccherini MT, Pietramellara G, Mench M, Nannipieri P (2008) Long-term effects of aided phytostabilisation of trace elements on microbial biomass and activity, enzyme activities, and composition of microbial community in the Jales contaminated mine spoils. Environ Pollut 152(3):702–712. doi:10.1016/j.envpol.2007.06.053

    Article  CAS  PubMed  Google Scholar 

  • Robbens J, Dardenne F, Devriese L, Coen W, Blust R (2010) Escherichia coli as a bioreporter in ecotoxicology. Appl Microbiol Biotechnol 88(5):1007–1025. doi:10.1007/s00253-010-2826-6

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez-Mozaz S, Marco M-P, de Alda Lopez, Maria J, Barceló D (2003) Biosensors for environmental monitoring of endocrine disruptors: a review article. Anal Bioanal Chem 378(3):588–598. doi:10.1007/s00216-003-2385-0

    PubMed  Google Scholar 

  • Sabater S, Guasch H, Ricart M, Romaní A, Vidal G, Klünder C, Schmitt-Jansen M (2007) Monitoring the effect of chemicals on biological communities. The biofilm as an interface. Anal Bioanal Chem 387(4):1425–1434. doi:10.1007/s00216-006-1051-8

    Article  CAS  PubMed  Google Scholar 

  • Sazykin IS, Sazykina MA, Khmelevtsova LE, Mirina EA, Kudeevskaya EM, Rogulin EA, Rakin AV (2016) Biosensor-based comparison of the ecotoxicological contamination of the wastewaters of Southern Russia and Southern Germany. Int J Environ Sci Technol 13(3):945–954. doi:10.1007/s13762-016-0936-0

    Article  CAS  Google Scholar 

  • Schuster SC (2007) Next-generation sequencing transforms today’s biology. Nature 200(8):16–18

    Google Scholar 

  • Scott C, Pandey G, Hartley CJ, Jackson CJ, Cheesman MJ, Taylor MC, Pandey R, Khurana JL, Teese M, Coppin CW, Weir KM, Jain RK, Lal R, Russell RJ, Oakeshott JG (2008) The enzymatic basis for pesticide bioremediation. Indian J Microbiol 48(1):65–79. doi:10.1007/s12088-008-0007-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Senan RC, Abraham TE (2004) Bioremediation of textile azo dyes by aerobic bacterial consortium aerobic degradation of selected azo dyes by bacterial consortium. Biodegradation 15(4):275–280. doi:10.1023/B:BIOD.0000043000.18427.0a

  • Shahi A, Aydin S, Ince B, Ince O (2016) Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach. Ecotoxicol Environ Saf 125:153–160. doi:10.1016/j.ecoenv.2015.11.029

    Article  CAS  PubMed  Google Scholar 

  • Shahsavari E, Aburto-Medina A, Taha M, Ball AS (2016) A quantitative PCR approach for quantification of functional genes involved in the degradation of polycyclic aromatic hydrocarbons in contaminated soils. MethodsX 3:205–211. doi:10.1016/j.mex.2016.02.005

    Article  PubMed  PubMed Central  Google Scholar 

  • Shahsavari E, Adetutu E, Ball A (2015a) Phytoremediation and necrophytoremediation of petrogenic hydrocarbon-contaminated soils. In: Ansari AA, Gill SS, Gill R, Lanza GR, Newman L (eds) Phytoremediation. Springer International Publishing. pp 321–334. doi:10.1007/978-3-319-10969-5_26

  • Shahsavari E, Adetutu EM, Anderson PA, Ball AS (2013) Plant residues—A low cost, effective bioremediation treatment for petrogenic hydrocarbon-contaminated soil. Sci Total Environ 443:766–774. doi:10.1016/j.scitotenv.2012.11.029

    Article  CAS  PubMed  Google Scholar 

  • Shahsavari E, Adetutu EM, Taha M, Ball AS (2015b) Rhizoremediation of phenanthrene and pyrene contaminated soil using wheat. J Environ Manage 155:171–176. doi:10.1016/j.jenvman.2015.03.027

    Article  CAS  PubMed  Google Scholar 

  • Shao CY, Howe CJ, Porter AJR, Glover LA (2002) Novel cyanobacterial biosensor for detection of herbicides. Appl Environ Microbiol 68(10):5026–5033. doi:10.1128/aem.68.10.5026-5033.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simons KL, Sheppard PJ, Adetutu EM, Kadali K, Juhasz AL, Manefield M, Sarma PM, Lal B, Ball AS (2013) Carrier mounted bacterial consortium facilitates oil remediation in the marine environment. Biores Technol 134:107–116. doi:10.1016/j.biortech.2013.01.152

    Article  CAS  Google Scholar 

  • Smolders E, Brans K, Coppens F, Merckx R (2001) Potential nitrification rate as a tool for screening toxicity in metal-contaminated soils. Environ Toxicol Chem 20(11):2469–2474

    Article  CAS  PubMed  Google Scholar 

  • Su L, Jia W, Hou C, Lei Y (2011) Microbial biosensors: A review. Biosens Bioelectron 26(5):1788–1799. doi:10.1016/j.bios.2010.09.005

    Article  CAS  PubMed  Google Scholar 

  • Sütterlin H, Alexy R, Kümmerer K (2008) The toxicity of the quaternary ammonium compound benzalkonium chloride alone and in mixtures with other anionic compounds to bacteria in test systems with Vibrio fischeri and Pseudomonas putida. Ecotoxicol Environ Saf 71(2):498–505. doi:10.1016/j.ecoenv.2007.12.015

    Article  PubMed  CAS  Google Scholar 

  • Sverdrup LE, Ekelund F, Krogh PH, Nielsen T, Johnsen K (2002) Soil microbial toxicity of eight polycyclic aromatic compounds: effects on nitrification, the genetic diversity of bacteria, and the total number of protozoans. Environ Toxicol Chem 21(8):1644–1650. doi:10.1002/etc.5620210815

    Article  CAS  PubMed  Google Scholar 

  • Taranova L, Semenchuk I, Manolov T, Iliasov P, Reshetilov A (2002) Bacteria-degraders as the base of an amperometric biosensor for detection of anionic surfactants. Biosens Bioelectron 17(8):635–640. doi:10.1016/S0956-5663(01)00307-4

    Article  CAS  PubMed  Google Scholar 

  • Thomas DJL, Tyrrel SF, Smith R, Farrow S (2009) Bioassays for the evaluation of landfill leachate toxicity. J Toxicol Environ Health Part B 12(1):83–105. doi:10.1080/10937400802545292

    Article  CAS  Google Scholar 

  • Thomas T, Gilbert J, Meyer F (2012) Metagenomics—a guide from sampling to data analysis. Microb Informatics Exp 2(1):1–12. doi:10.1186/2042-5783-2-3

    Article  Google Scholar 

  • Tscherko D, Kandeler E (1997) Ecotoxicological effects of fluorine deposits on microbial biomass and enzyme activity in grassland. Eur J Soil Sci 48(2):329–335. doi:10.1111/j.1365-2389.1997.tb00553.x

    Article  CAS  Google Scholar 

  • Ulitzur S, Lahav T, Ulitzur N (2002) A novel and sensitive test for rapid determination of water toxicity. Environ Toxicol 17(3):291–296. doi:10.1002/tox.10060

    Article  CAS  PubMed  Google Scholar 

  • van Beelen P, Doelman P (1997) Significance and application of microbial toxicity tests in assessing ecotoxicological risks of contaminants in soil and sediment. Chemosphere 34(3):455–499. doi:10.1016/S0045-6535(96)00388-8

    Article  Google Scholar 

  • van der Meer JR, Belkin S (2010) Where microbiology meets microengineering: design and applications of reporter bacteria. Nat Rev Micro 8(7):511–522. doi:10.1038/nrmicro2392

    Article  CAS  Google Scholar 

  • van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30(9):418–426. doi:10.1016/j.tig.2014.07.001

    Article  PubMed  CAS  Google Scholar 

  • Vollmer AC, Belkin S, Smulski DR, Van Dyk TK, LaRossa RA (1997) Detection of DNA damage by use of Escherichia coli carrying recA’:lux, uvrA’:lux, or alkA’:lux reporter plasmids. Appl Environ Microbiol 63(7):2566–2571

    CAS  PubMed  PubMed Central  Google Scholar 

  • Watanabe K (2001) Microorganisms relevant to bioremediation. Curr Opin Biotechnol 12(3):237–241

    Article  CAS  PubMed  Google Scholar 

  • Weitz HJ, Ritchie JM, Bailey DA, Horsburgh AM, Killham K, Glover LA (2001) Construction of a modified mini-Tn5 luxCDABE transposon for the development of bacterial biosensors for ecotoxicity testing. FEMS Microbiol Lett 197(2):159–165. doi:10.1111/j.1574-6968.2001.tb10598.x

    Article  CAS  PubMed  Google Scholar 

  • Whyte LG, Greer CW (2005) Molecular techniques for monitoring and assessing soil bioremediation. In: Margesin R, Schinner F (eds) Monitoring and assessing soil bioremediation, vol 5. Springer, Berlin Heidelberg, pp 201–231

    Chapter  Google Scholar 

  • Widenfalk A, Bertilsson S, Sundh I, Goedkoop W (2008) Effects of pesticides on community composition and activity of sediment microbes—responses at various levels of microbial community organization. Environ Pollut 152(3):576–584. doi:10.1016/j.envpol.2007.07.003

    Article  CAS  PubMed  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87(12):4576–4579. doi:10.1073/pnas.87.12.4576

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu X, McLaren J, Madl R, Wang D (2010) Biofuels from lignocellulosic biomass. In: Sustainable biotechnology. Springer, Berlin, pp 19–41

    Google Scholar 

  • Xu X, Oliff K, Xu T, Ripp S, Sayler G, Zhuang J (2015) Microbial availability of mercury: effective detection and organic ligand effect using a whole-cell bioluminescent bioreporter. Ecotoxicology 24(10):2200–2206. doi:10.1007/s10646-015-1553-2

    Article  CAS  PubMed  Google Scholar 

  • Yergeau E, Sanschagrin S, Beaumier D, Greer CW (2012) Metagenomic analysis of the bioremediation of diesel-contaminated canadian high arctic soils. PLoS ONE 7(1):e30058. doi:10.1371/journal.pone.0030058

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoon Y, Kang Y, Chae Y, Kim S, Lee Y, Jeong S-W, An Y-J (2015) Arsenic bioavailability in soils before and after soil washing: the use of Escherichia coli whole-cell bioreporters. Environ Sci Pollut Res 23(3):2353–2361. doi:10.1007/s11356-015-5457-8

    Article  CAS  Google Scholar 

  • Zhang DC, Mörtelmaier C, Margesin R (2012) Characterization of the bacterial archaeal diversity in hydrocarbon-contaminated soil. Sci Total Environ 421–422:184–196

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. School of Science, Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, VIC, 3083, Australia

    Esmaeil Shahsavari, Arturo Aburto-Medina, Leadin Salah Khudur, Mohamed Taha & Andrew S. Ball

  2. Department of Biochemistry, Faculty of Agriculture, Benha University, Moshtohor, Toukh, 13736, Egypt

    Mohamed Taha

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  1. Esmaeil Shahsavari
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  2. Arturo Aburto-Medina
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  3. Leadin Salah Khudur
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  4. Mohamed Taha
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  5. Andrew S. Ball
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Correspondence to Andrew S. Ball .

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  1. Equipe Environnement et Microbiologie, IPREM UMR 5254, Université de Pau et des Pays de l’Adour, Pau, France

    Cristiana Cravo-Laureau

  2. Equipe Environnement et Microbiologie, IPREM UMR 5254, Université de Pau et des Pays de l’Adour, Pau, France

    Christine Cagnon

  3. Equipe Environnement et Microbiologie, IPREM UMR 5254, Université de Pau et des Pays de l’Adour, Pau, France

    Béatrice Lauga

  4. Equipe Environnement et Microbiologie, IPREM UMR 5254, Université de Pau et des Pays de l’Adour, Pau, France

    Robert Duran

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Shahsavari, E., Aburto-Medina, A., Khudur, L.S., Taha, M., Ball, A.S. (2017). From Microbial Ecology to Microbial Ecotoxicology. In: Cravo-Laureau, C., Cagnon, C., Lauga, B., Duran, R. (eds) Microbial Ecotoxicology. Springer, Cham. https://doi.org/10.1007/978-3-319-61795-4_2

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