Abstract
The soil oligochaete Enchytraeus albidus is a standard test organism used in biological testing for Environmental Risk Assessment (ERA). Although effects are known at acute and chronic level through survival, reproduction and avoidance behaviour endpoints, very little is known at the sub-cellular and molecular levels. In this study, the effects of soil properties (clay, organic matter and pH) and of the chemicals copper and phenmedipham were studied on E. albidus gene expression, during exposure periods of 2, 4 and 21 days, using DNA microarrays based on a normalised cDNA library for this test species (Amorim et al. 2011). The main objectives of this study were: (1) to assess changes in gene expression of E. albidus over time, and (2) to identify molecular markers for natural and chemical exposures. Results showed an influence of exposure time on gene expression. Transcriptional responses to phenmedipham were seen at 2 days while the responses to copper and the different soils were more pronounced at 4 days of exposure. Some genes were differentially expressed in a stress specific manner and, in general, the responses were related with effects in the energy metabolism and cell growth.
Similar content being viewed by others
References
Alexa A, Rahnenfuhrer J, Lengauer T (2006) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22(13):1600–1607
Altschul S, Gish W, Miller W, Meyers E, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Amorim M, Rombke J, Schallnass H, Mortagua A, Soares V (2005a) Effect of soil properties and aging on the toxicity of copper for Enchytraeus albidus, Enchytraeus luxuriosus, and Folsomia candida. Environ Toxicol Chem 24(8):1875–1885
Amorim M, Rombke J, Scheffczyk A, Soares A (2005b) Effect of different soil types on the enchytraeids Enchytraeus albidus and Enchytraeus luxuriosus using the herbicide Phenmedipham. Chemosphere 61(8):1102–1114
Amorim M, Rombke J, Soares A (2005c) Avoidance behaviour of Enchytraeus albidus: effects of Benomyl, Carbendazim, phenmedipham and different soil types. Chemosphere 59(4):501–510
Amorim MJB, Novais S, Römbke J, Soares AMVM (2008a) Avoidance test with Enchytraeus albidus (Enchytraeidae): effects of different exposure time and soil properties. Environ Pollut 155(1):112–116
Amorim MJB, Novais S, Römbke J, Soares AMVM (2008b) Enchytraeus albidus (Enchytraeidae): a test organism in a standardised avoidance test? Effects of different chemical substances. Environ Int 34(3):363–371
Amorim MJB, Novais SC, Van der Ven K, Vandenbrouck T, Soares AMVM, De Coen W (2011) Development of a microarray for Enchytraeus albidus (Oligochaeta): preliminary tool with diverse applications. Environ Toxicol Chem 30(6):1395–1402
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rates—a practical and powerful approach to multiple testing. J R Stat Soc B Met 57:289–300
Bundy JG, Sidhu JK, Rana F, Spurgeon DJ, Svendsen C, Wren JF, Sturzenbaum SR, Morgan AJ et al (2008) ‘Systems toxicology’ approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm Lumbricus rubellus. BMC Biol 6:25
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676
Gomes SIL, Novais SC, Gravato C, Guilhermino L, Scott-Fordsmand JJ, Soares AMVM, Amorim MJB (2011) Effect of Cu-nanoparticles versus one Cu-salt: analysis of stress biomarkers response in Enchytraeus albidus (Oligochaeta). Nanotoxicology. doi: 10.3109/17435390.2011.562327
Gong P, Guan X, Inouye LS, Pirooznia M, Indest KJ, Athow RS, Deng YP, Perkins EJ (2007) Toxicogenomic analysis provides new insights into molecular mechanisms of the sublethal toxicity of 2, 4, 6-trinitrotoluene in Eisenia fetida. Environ Sci Technol 41(23):8195–8202
Gong P, Guan X, Inouye LS, Deng YP, Pirooznia M, Perkins EJ (2008) Transcriptomic analysis of RDX and TNT interactive sublethal effects in the earthworm Eisenia fetida. BMC Genomics 9(Suppl 1):S15
Gracey AY, Cossins AR (2003) Application of microarray technology in environmental and comparative physiology. Annu Rev Physiol 65:231–259
Henle FGJ (1837) Ueber Enchytraeus, eine neue Anneliden-Gattung. Arch Anat Physiol Med 74–90
Howcroft CF, Amorim MJB, Gravato C, Guilhermino L, Soares AMVM (2009) Effects of natural and chemical stressors on Enchytraeus albidus: can oxidative stress parameters be used as fast screening tools for the assessment of different stress impacts in soils? Environ Int 35(2):318–324
Howcroft C, Gravato C, Amorim M, Novais S, Soares A, Guilhermino L (2011) Biochemical characterization of cholinesterases in Enchytraeus albidus and assessment of in vivo and in vitro effects of different soil properties, copper and phenmedipham. Ecotoxicology 20(1):119–130
ISO (2003) Soil quality—effects of pollutants on enchytraeidae (Enchytraeus sp.)—determination of effects on reproduction and survival. Guideline no. 16387. ISO (International Organization for Standardization), Geneva
Kobeticova K, Hofman J, Holoubek I (2009) Avoidance response of Enchytraeus albidus in relation to carbendazim ageing. Environ Pollut 157(2):704–706
Løkke H, van Gestel CAM (1998) Handbook of soil invertebrate toxicity tests. Wiley, Chichester
McLaughlin MJ, Hamon RE, Parker DR, Pierzynski GM, Smolders E, Thornton I, Welp G (2002) Soil chemistry. In: Fairbrother A, Glazebrook PW, Tarazona JV, Straalen NMV (eds) Test methods to determine hazards of sparingly soluble metal compounds in soils. Society of Environmental Toxicology and Chemistry (SETAC) Press, Pensacola, Florida, pp 5–85
Nota B, Timmermans MJTN, Franken C, Montagne-Wajer K, Marien J, De Boer ME, De Boer TE, Ylstra B et al (2008) Gene expression analysis of collembola in cadmium containing soil. Environ Sci Technol 42(21):8152–8157
Novais SC, Soares AMVM, Amorim MJB (2010) Can avoidance in Enchytraeus albidus be used as a screening parameter for pesticides testing? Chemosphere 79(2):233–237
Novais SC, Gomes SIL, Gravato C, Guilhermino L, de Coen W, Soares AMVM, Amorim MJB (2011) Reproduction and biochemical responses in Enchytraeus albidus (Oligochaeta) exposed to metals: effects of zinc and cadmium. Environ Pollut 159(7):1836–1843
OECD (1984) Guideline for testing chemicals. Earthworm, acute toxicity tests. No. 207. OECD (Organization for Economic Cooperation and Development), Paris
OECD (2004) Guidelines for the testing of chemicals. Enchytraeid reproduction test. No. 220. OECD (Organization for Economic Cooperation and Development), Paris
Owen J, Hedley BA, Svendsen C, Wren J, Jonker MJ, Hankard PK, Lister LJ, Sturzenbaum SR et al (2008) Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus. BMC Genomics 9:266
Reynders H, van der Ven K, Moens LN, van Remortel P, De Coen WM, Blust R (2006) Patterns of gene expression in carp liver after exposure to a mixture of waterborne and dietary cadmium using a custom-made microarray. Aquat Toxicol 80(2):180–193
Ritchie M, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth G (2007) A comparison of background correction methods for two-colour microarrays. Bioinformatics 23:2700–2707
Rombke J, Moser T (2002) Validating the enchytraeid reproduction test: organisation and results of an international ringtest. Chemosphere 46(7):1117–1140
Saint-Denis M, Narbonne JF, Arnaud C, Ribera D (2001) Biochemical responses of the earthworm Eisenia fetida andrei exposed to contaminated artificial soil: effects of lead acetate. Soil Biol Biochem 33(3):395–404
SAS (2003) SAS 9.1.3. Version 9.1.3 edn. SAS Institute Inc., Cary
Shi LM, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F et al (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24(9):1151–1161
Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3(1): article 3
Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W (eds) Bioinformatics and computational biology solutions using R and bioconductor. Springer, New York, pp 397–420
Smyth GK, Speed T (2003) Normalization of cDNA microarray data. Methods 31(4):265–273
Soetaert A, van der Ven K, Moens LN, Vandenbrouck T, van Remortel P, De Coen WM (2007) Daphnia magna and ecotoxicogenomics: gene expression profiles of the anti-ecdysteroidal fungicide fenarimol using energy-, molting- and life stage-related cDNA libraries. Chemosphere 67(1):60–71
Steibel JP, Rosa GJM (2005) On reference designs for microarray experiments. Stat Appl Genet Mol Biol 4
Suzuki I, Simon WJ, Slabas AR (2006) The heat shock response of Synechocystis sp PCC 6803 analysed by transcriptomics and proteomics. J Exp Bot 57(7):1573–1578
Vandegehuchte MB, Vandenbrouck T, Coninck DD, De Coen WM, Janssen CR (2010) Can metal stress induce transferable changes in gene transcription in Daphnia magna? Aquat Toxicol 97(3):188–195
Vandenbrouck T, Jones OAH, Dom N, Griffin JL, De Coen W (2010) Mixtures of similarly acting compounds in Daphnia magna: from gene to metabolite and beyond. Environ Int 36(3):254–268
Wettenhall JM, Smyth GK (2004) limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20(18):3705–3706
Acknowledgments
This study was sponsored by Fundação para a Ciência e Tecnologia (Portugal), through a PhD grant to Sara Novais (SFRH/BD/36253/2007) and through the project reference PTDC/BIA-BCM/64745/2006 (REDE).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Novais, S.C., Howcroft, C.F., Carreto, L. et al. Differential gene expression analysis in Enchytraeus albidus exposed to natural and chemical stressors at different exposure periods. Ecotoxicology 21, 213–224 (2012). https://doi.org/10.1007/s10646-011-0780-4
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10646-011-0780-4