Ester Eckert
 Associated Researcher


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+39 0323 518321 (Telephone)
+39 0323 556513 (Fax)
Research Interests: Bacterial diversity and ecophysiology; Interactions of bacteria with organisms of other trophic levels; Organic carbon transfer through the food web mediated by bacteria; Microbial collaboration and competition. My former projects have mainly centred on the development and diversity of bacteria during phytoplankton blooms. I have studied the ecophysiology of various aquatic phylotypes and the impact of microbial carbon uptake on the aquatic food web. Currently I am involved in a multidisciplinary project evaluating the presents of antibiotic resistant bacteria in the human gut of people with different dietary habits. Therein my part consist of evaluating the bacterial diversity using NGS and relating bacterial phylotypes to potential functions in the gut.
I manage the NGS facility of the MEG.
Education: Oct 2005 – Nov 2008, Bachelor studies in biology at the Unversity of Zurich, Zurich, Switzerland
Jul – Sep 2008, Research internship in microbial ecology, Under the supervision of Prof. Dr. Hans-Peter Grossart, Leibniz Institute for Freshwater Ecology and Inland Fishery Neuglobsow, Germany
Nov 2008 – Jan 2012, Master thesis in Biology (Microbiology) entitled: Dynamics and ecophysiology of bacteria during a phytoplankton spring bloom in Lake Zurich Under the supervision of Prof. Dr. Jakob Pernthaler, Limnological Station, Institute of Plant Biology University of Zurich, Zurich, Switzerland
Mar 2010 – Oct 2013, PhD studies in Natural Sciences (Biology, Microbiology) entitled: Organic carbon uptake by bacteria with different live strategies – Successions and unexplored food web interactions Under the supervision of Prof. Dr. Jakob Pernthaler, Limnological Station, Institute of Plant Biology University of Zurich, Switzerland
Mar 2014-Gen 2015, Post-doc position at the MEG of the CNR - Institute of Ecosystem Study Verbania in the research group of Dr. Gianluca Corno
Feb 2015 - Nov 2017 Marie Curie Fellow at the MEG, with Dr. Diego Fontaneto. From Dec 2017 Associated researcher at he MEG.
Extramural Activities: Member of the local organizing committee of the 1st EMBO Conference on Aquatic Microbial Ecology (SAME13), 2013, Stresa, Italy; Member of the local organizing committee of the 33rd Congress of the International Society of Limnology (SIL 33), 2016, Turin, Italy; External expert within the category 'biology and environment' for the national competition of the foundation Schweizer Jugend Forscht (the Swiss youth in science foundation), 2013 & 2014.


  • EM Eckert, A Di Cesare, MT Kettner, M Arias, D Fontaneto, HP Grossart, G Corno. Microplastics increase impact of treated wastewater on freshwater microbial community. Environmental Pollution. 234: 495-502.
  • C Losasso, EM Eckert, E Mastrorilli, J Villiger, M Mancin, I Patuzzi, A Di Cesare, V Cibin, F Barrucci, J Pernthaler, G Corno, A Ricci. Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study. Frontiers in Microbiology. 9: 317.
  • EM Eckert, A Di Cesare, M Coci, G Corno. Persistence of antibiotic resistance genes in large subalpine lakes: the role of anthropogenic pollution and ecological interactions. Hydrobiologia.


  • A Di Cesare, EM Eckert, M Rogora, G Corno. Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community. Environmental Pollution. pii: S0269-7491(16)32742-7. DOI: 10.1016/j.envpol.2017.04.036.
  • A Turolla, R Sabatino, D Fontaneto, EM Eckert, N Colinas, G Corno, B Citterio, F Biavasco, M Antonelli, A Mauro, G Mangiaterra, A Di Cesare. Defence strategies and antibiotic resistance gene abundance in enterococci under stress by exposure to low doses of peracetic acid. Chemosphere. 185: 480-488.
  • S Amalfitano, G Corno, EM Eckert, S Fazi, S Ninio, C Callieri, HP Grossart, W Eckert. Tracing particulate matter and associated microorganisms in freshwaters. Hydrobiologia. 800: 145-154.
  • C Callieri, S Amalfitano, G Corno, A Di Cesare, R Bertoni, EM Eckert. The microbiome associated with two Synechococcus ribotypes at different levels of ecological interaction. Journal of Phycology. 53: 1151-1158.


  • EM Eckert, A Di Cesare, B Stenzel, D Fontaneto, G Corno. Daphnia as a refuge for an antibiotic resistance gene in an experimental freshwater community. Science of the Total Environment. 571: 77-81.
  • A Di Cesare, C Losasso, L Barco, EM Eckert, D Conficoni, G Sarasini, G Corno, A Ricci. Diverse distribution of Toxin-Antitoxin II systems in Salmonella enterica serovars. Scientific Report 6: 28759; doi: 10.1038/srep28759.
  • A Di Cesare, EM Eckert, G Corno. Co-selection of antibiotic and heavy metal resistance in freshwater bacteria. Journal of Limnology 75(S2): 59-66.
  • A Di Cesare, EM Eckert, S D'Urso, R Bertoni, DC Gillan, R Wattiez, G Corno Co-occurrence of integrase 1, antibiotic and heavy metal resistance genes in municipal wastewater treatment plants. Water Research 94: 208-214.


  • A Di Cesare, EM Eckert, A. Teruggi, D Fontaneto, R Bertoni, C Callieri, G Corno. Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake. Molecular Ecology 24: 3888-3900.
  • T Posch, B Eugster, F Pomati, J Pernthaler, G Pitsch, EM Eckert. Network of interactions between ciliates and phytoplankton during spring. Frontiers in Microbiology 6
  • EM Eckert, D Fontaneto, M Coci, C Callieri. Does a Barcoding Gap Exist in Prokaryotes? Evidences from Species Delimitation in Cyanobacteria. Life 5(1): 50-64.


  • Eckert EM and Pernthaler J. Bacterial epibionts of Daphnia are a potential route for the efficient transfer of dissolved organic carbon within freshwater food webs. ISME Journal doi: 10.1038/ismej.2014.39
  • Callieri C, Coci M, Eckert EM, Salcher MM, and Bertoni R. Archaea and Bacteria in deep lake hypolimnion: in situ dark inorganic carbon uptake. Journal of Limnology 73: 31-38


  • Eckert EM, Baumgartner M, Huber IM, and Pernthaler J. Grazing resistant freshwater bacteria profit from chitin and cell-wall-derived organic carbon. Environmental Microbiology 15: 2019-2030


  • Eckert EM, Salcher MM, Posch T, Eugster B, and Pernthaler J. Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom. Environmental Microbiology 14: 794-806