Low flow sampling

Our ESR Olha Nikolenko is focused on the study of the dynamics of GHGs in groundwater. During her field investigations Olha applied low flow sampling technique in order to collect representative groundwater samples from the specific depths minimizing the mixing between different water layers. The collected samples were analyzed for a range of hydrochemical parameters and isotopes (15N, 18O, 11B, 13C, 34S and 3H). In addition, sampled groundwater was used to perform laboratory incubation experiments using NO3- and NH4+ compounds labelled with heavy 15N isotope to quantify the rates of denitrification and nitrification processes.

Collection of groundwater samples

Such approach can help to obtain better insight into the extent of oxic and anoxic zones, occurrence of biochemical processes along the vertical profile of the aquifer and accumulation of GHGs in different hydrogeochemical conditions.

Field set-up for low flow sampling procedure

ESR 13 at the International Phosphorus Workshop 9 (IPW9) – Putting phosphorus first? How to address current and future challenges

The International Phosphorus Workshop is a unique event that brings together experts working on phosphorus in terrestrial and aquatic systems. The workshop is organized every three years in a different location; the first IPW was carried out in Wexford, Ireland, in 1995. This year the event took place at ETH Zurich, Switzerland, from 8th to 12th of July and had an additional relevance since it is the 350th anniversary of the discovery of phosphorus. Our fellow Domiziana Cristini (ESR13) is currently working on stable isotopes of phosphate in freshwater ecosystems, hence the IPW9 was a great opportunity to discuss her project. She presented a poster in the session dedicated to theme 5 (Environmental phosphorus problems).

1. Main campus of ETH Zurich, Switzerland

The workshop arose from the awareness that phosphorus (P) is a key element to all organisms and that an inappropriate use of it causes environmental problems. P is largely applied as fertilizer all over the world and its excess in soils results in dissipation into freshwater ecosystems. The enrichment of P in water bodies is termed eutrophication and has diverse negative consequences like the deterioration of water quality, toxic algal blooms, anoxia (Sondergaard & Jeppesen, 2007). Furthermore, the P surplus that remains in soil may threaten terrestrial biodiversity (Lambers et al., 2013).

2. Booklet of the IPW9 programme

The IPW9 was attended by experts from different fields: natural, engineering and social science, to offer a deeper view on all the aspects that concern P. The activities took place in plenary and parallel oral presentations, poster sessions, interactive workshops and excursions. During these activities five themes were investigated: 1. Phosphorus scarcity, 2. Optimizing regional and national phosphorus cycles, 3. Sourcing phosphorus fertilizers, 4. Efficient phosphorus use in agroecosystems, 5. Environmental phosphorus problems. The oral and poster presentations gave an insight on the advancements in P knowledge and technology, as well as on the concepts that drove the P-related research so far. On the other hand, the interactive workshops offered the possibility to discuss future research address and actions to solve P-derived problems.

3. ESR13 and her poster


Lambers, H., Ahmedi, I., Berkowitz, O., Dunne, C., Finnegan, P.M., Hardy, G.E.St J., Jost, R., Laliberté, E., Pearse, S.J., Teste, F.P., 2013. Phosphorus nutrition of phosphorus-sensitive Australian native plants: threats to plant communities in a global biodiversity hotspot. Conserv Physiol 1: (1).

Sondergaard M., Jeppesen E., 2007. Anthropogenic impacts on lake and stream ecosystems, and approaches to restoration. J. Appl. Ecol. 44: 1089-1094.

FRET Biosensors for measuring the bioavailability of metals

One of our INSPIRATION-ITN fellows (Bastian Saputra) had opportunity to present his work in the Department of Animal and Plant Science, University of Sheffield, UK on 21st Nov 2019 (Fig 1). This event is part of regular meeting for some research groups in this department.

Fig. 1 Bastian is presenting his research in the Dept.of Animal and Plant Science, University of Sheffield, UK.

Bastian presented the progress of his experiment about developing Forster Resonance Energy Transfer (FRET) biosensors for measuring bioavailable heavy metals in soil remediation. The biosensors exploit the fusion of a metal binding protein, metallothionein (MT) to fluorescent proteins (FPs) – in this case, enhanced Cyan FP (eCFP) and the yellow Venus FP (Rajamani et al., 2014). Binding of heavy metals by MT changes the molecular distance between eCFP and Venus, bringing them closer to each other (Fig 2). This proximity enables energy transfer from eCFP (donor) to Venus (acceptor) changing the fluorescent properties of the system (Tsien, 1998; Carter et al, 2014). The occurrence of FRET, and hence binding of metals to MT, can be measured by changes in the ratio of fluorescence emission of eCFP and Venus – metal binding enhances Venus fluorescence at the expense of eCFP. The expression of a FRET sensor inside a host bacterial cell allows direct, rapid measurement of intracellular metal concentrations (Fig 2).

Fig. 2 Concept of biosensor: FRET sensor as a fusion of eCFP-MT-Venus protein is expressed inside the bacteria host cell

Bastian has constructed FRET biosensors inside two different types of bacteria; Escherichia coli and Pseudomonas putida. These modified bacteria can respond directly to the presence of heavy metals potentially to be used to assess the bioavailable fraction in a soil. As the site of action of heavy metals is inside the bacterial cell, bacteria-based biosensors that report cytoplasmic metal concentration directly can be developed as a more appropriate indicator. This biosensor is an alternative approach to measure the toxic effect of metals on cell physiology.

Bastian is currently working with the application of this biosensor as monitoring tools to measure the change of bioavailable heavy metals due to biochar amendment in contaminated soil (in collaboration with Rosa Soria, ESR 8). This is being conducted by extracting the soil pore water from the contaminated soil samples and adding them to the biosensor assay and monitoring results using a spectrofluorometer. Alternatively, microbes can be mixed directly with the soil and metal concentrations monitored using fluorescence microscopy. The measurement of metal concentrations from the biosensors will be integrated with an analysis of plant-bioavailable metal concentrations and changes in soil microbial community to assess the remediation performance. The outcomes of these analysis are expected to provide information about the conditions that can improve the soil quality to support plant growth and microbial activity for the restoration of contaminated land.


Carter, K. P., Young, A. M. and Palmer, A. E. (2014) ‘Fluorescent Sensors for Measuring Metal Ions in Living Systems’. doi: 10.1021/cr400546e.

Rajamani, S. et al. (2014) ‘Noninvasive Evaluation of Heavy Metal Uptake and Storage in Micoralgae Using a Fluorescence Resonance Energy Transfer-Based Heavy Metal Biosensor’, Plant Physiology, 164(2), pp. 1059–1067. doi: 10.1104/pp.113.229765.

Tsien, R. Y. (1998) ‘the Green Fluorescent’, Annual Review of Biochemistry, 199(2), pp. 293–306. doi: 10.1146/annurev.biochem.67.1.509.