Transcriptomic profiling permits the identification of pollutant sources and effects in ambient water samples Matthias Hasenbein a,b,f , Inge Werner d , Linda A. Deanovic a , Juergen Geist b , Erika B. Fritsch c , Alireza Javidmehr a , Chris Foe e , Nann A. Fangue f , Richard E. Connon a, ⁎ a Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA b Aquatic Systems Biology Unit, Department of Ecology and Ecosystem Management, Technische Universität München, Mühlenweg 22, D-85354 Freising, Germany c Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA 95616, USA d Swiss Centre for Applied Ecotoxicology, Eawag/EPFL, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland e Central Valley Regional Water Quality Control Board, Rancho Cordova, CA 95670, USA f Department of Wildlife, Fish & Conservation Biology, University of California, Davis, CA 95616, USA HIGHLIGHTS • Ammonia present in effluent is likely acting synergistically with other contaminants. • Transcriptomic profiling differentiates between upstream, downstream and effluent discharge. • Transcription profiling can identify sources of contamination. abstract article info Article history: Received 7 May 2013 Received in revised form 22 August 2013 Accepted 24 August 2013 Available online 21 September 2013 Editor: Christian E.W. Steinberg Keywords: Delta smelt Hypomesus transpacificus Ammonium Wastewater effluent Microarray Quantitative PCR Contaminant exposure is one possible contributor to population declines of endangered fish species in the Sacramento–San Joaquin Estuary, California, including the endangered delta smelt (Hypomesus transpacificus). Herein we investigated transcriptional responses in larval delta smelt resulting from exposure to water samples collected at the Department of Water Resources Field Station at Hood, a site of concern, situated upstream of known delta smelt habitat and spawning sites and downstream of the Sacramento Regional Wastewater Treat- ment Plant (SRWTP). Microarray assessments indicate impacts on energy metabolism, DNA repair mechanisms and RNA processing, the immune system, development and muscle function. Transcription responses of fish exposed to water samples from Hood were compared with exposures to 9% effluent samples from SRWTP, water from the Sacramento River at Garcia Bend (SRGB), upstream of the effluent discharge, and SRGB water spiked with 2 mg/L total ammonium (9% effluent equivalent). Results indicate that transcriptomic profiles from Hood are similar to 9% SRWTP effluent and ammonium spiked SRGB water, but significantly different from SRGB. SRGB samples however were also significantly different from laboratory controls, suggesting that SRWTP effluent is not solely responsible for the responses determined at Hood, that ammonium exposure likely enhances the effect of multiple-contaminant exposures, and that the observed mortality at Hood is due to the combination of both effluent discharge and contaminants arising from upstream of the tested sites. © 2013 Elsevier B.V. All rights reserved. 1. Introduction Aquatic ecosystems are among the most diverse ecosystem types worldwide, however, there have been significant declines in bio- diversity over the past decades; attributed to habitat destruction and degradation, flow modification, invasive species, overexploitation, and overall water quality (Kennish, 2002; Dudgeon et al., 2006; Geist, 2011). The Sacramento–San Joaquin Estuary in California is an example of detrimental effects resulting within an aquatic ecosystem with in- tense anthropogenic impact (Lund et al., 2010; Cloern and Jassby, 2012). Endemic to this system is a pelagic fish species that has exhibited a gradual decline in population since the 1980s (Moyle et al., 1992; Bennett, 2005) with a significant step decline recorded in 2000 (Feyrer et al., 2007; Sommer et al., 2007). The delta smelt (Hypomesus transpacificus) was classified as threatened under the Federal and State Endangered Species Act (ESA), 1993, and listed as endangered under the Californian Endangered Species Act (CESA) in 2010 (DFG, 2011). It is known as a species with an annual life cycle, low fecundity, and a relatively limited habitat range, making it highly susceptible to Science of the Total Environment 468–469 (2014) 688–698 ⁎ Corresponding author at: Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, 2160 Haring Hall, One Shield's Avenue, University of California, Davis, CA 95616, USA. Tel.: +1 530 752 3141; fax: +1 530 752 7690. E-mail address: reconnnon@ucdavis.edu (R.E. Connon). 0048-9697/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.scitotenv.2013.08.081 Contents lists available at ScienceDirect Science of the Total Environment journal homepage: www.elsevier.com/locate/scitotenv