Research

We conduct research on diverse topics related to the biosorption and -accumulation of environmental contaminants in bacteria and fungi isolated from the boreal environment. Our techniques include e.g. molecular biology techniques (DNA sequencing including 16S rRNA sequencing and next-generation sequencing, protein isolation and purification, electrophoresis, protein sequencing), spectroscopic and chromatographic methods (ATR-FT-IR, EDX, GC-MS), tracer techniques and imaging techniques (TEM, SEM, autoradiography). For more information, collaboration and training opportunities, please contact M. Lusa.

Exophiala

Uptake and speciation studies of radionuclides and heavy metals in boreal environmental microbiota (surface biosphere)

Soil microorganisms show impressive diversity and one of their most important features is their biochemical versatility.There are several processes found in soil microbiota, which affect the geochemical cycle of elements (figure on the bottom), including native biosorption, oxidation, reduction, enzymatic transformations, accumulation and precipitation. Oxidation-reduction processes are highly significant in the environment and are affected by microorganisms. Microorganisms can use several substances as an electron donor or as an electron acceptor.  The most prevailing electron donor is by far organic carbon. When oxygen is not present, microorganisms can use alternative electron acceptors like nitrate, manganese, iron, arsenic or sulphur. In addition other oxyanions, like SeO32- or TcO4- can be used as electron acceptors . Various micro-organisms have also developed different metal resistance processes which include changes in the oxidation state of toxic metals like As(V), Ag(II) and Tc(VII).

Two types of cellular retardation processes, called bioaccumulation and biosorption, can be found in micro-organisms. Usually an active transport mechanism in which energy is required is referred as bioaccumulation and term biosorption is used when physical adsorption on cell membrane structures residing on the cell surfaces are employed.  Intracellular accumulation is typically metabolism dependent and involves transportation of the substance through the cell membrane, a process which can be significantly affected by the presence of stable or radioactive ions.

In our group various retardation processes (uptake, protein structures involved in uptake, retardation, reduction, oxidation) of radionuclides (i.e. Tc, Np, Se, U, Ra) in soil bacteria isolated from boreal environment are studied.

Interactions of metals with bacteria

Metabolism of selenium oxyanions in Pseudomonads and the effect of selenium reducing bacteria on plant uptake of Se(IV) in Arabidopsis thaliana

Selenium (Se) is an essential micronutrient for humans and animals, but is toxic when taken in excessive amounts. In animals, Se acts as an antioxidant and helps in immune responses and thyroid hormone metabolism. However, especially the higher valence states (selenate, Se(VI)O42-  and selenite, Se(IV)O32-) are toxic and their toxic character is related to their oxidant capacity. Plants are the main source of dietary Se, but the essentiality of Se to plants is still debatable however. At low doses, Se may protect the plants from variety of abiotic stresses like cold, drought, desiccation and metal stress. However, at higher doses Se toxicity causes oxidative stress and distorted protein structure and function in plants, which may impact the crops through impaired plant growth, development and metabolism.

Se enters the food chain through plants which take it up from the soil. We previously found that bacteria affect selenium behaviour and retention in boreal bog environment (see Lusa et al. 2015) and that the Pseudomonas strains isolated from boreal bog environment, remove Se(IV) from solutions under different nutrient conditions. Elemental reduced Se0 is formed after incubation in Se(IV) containing cultures under aerobic conditions and intracellular Se0 granules can be verified using TEM and EDX. We found nitrate, nitrite  and sulfate to enhance Se(IV) uptake, but as Se(IV) uptake sustained also under sulphur and nitrogen starvation two distinct Se(IV) transport mechanisms can be suggested; a low affinity transport system regulated by nitrate, nitrite or sulfate and a distinct Se(IV) regulated transport system. The proteome analysis of Se(IV) supplement and temperature responses showed variations in the protein expression on the 60 – 40 kDa regions following these stress factors, probably through enzymes associated to oxidative stress, uptake or temperature adaptation (see Lusa et al. (2017) AIMS Microbiology, 3(4): 784-800).

In this study the proteins associated in Se(IV) uptake and reduction in Pseudomonads  i.e. by determination of the N-terminal amino acid sequences are further characterized.  In addition, the effect of Pseudomonads on selenium plant uptake (Arabidopsis thaliana) through redox state changes is examined.

Selenium metabolism in Pseudomonads (Boreal bog)

 

The effects of microbiota on carbon speciation in deep biosphere (bedrock)

Deep geological subsurface repositories (Olkiluoto in Finland) are being considered for long-term disposal of spent nuclear fuel. Microbial processes may play a significant role in the long-term stability of such a storage and understanding the role of the microbial communities in these deep terrestial environments is therefore of critical importance for the safety of the spent nuclear fuel repository.

Methane and sulphates are major constituents of Olkiluoto groundwater and a sulphate-methane mixing zone (SMMZ) has been identified between 250 and 350 m depth. On this zone SO42− concentration is elevated and below the SMMZ zone high CH4 concentration exists. Above the SMMZ zone CH4 concentrations decrease sharply and carbon exists mainly in the form of bicarbonate. The bacterial community of SMMZ zone consists mainly of sulphate reducing (SRB) and sulphate oxidizing (SOB) bacteria and below the SMMZ zone archaeal methanogens prevail. Little is known of the activity and function of the microbial communities of these grounwater zones.

In this study the effects of anaerobic SRB and methanogens on the speciation of radiocarbon (14C) in the reducing SMMZ zone conditions is studied.

Microbiota have essential roles in soil biogeochemical cycles and readily respond to the changes occurring in the soil conditions due to toxic compounds, including radionuclides. The level of radiological exposure of humans and other biota to radionuclides from different sources (e.g. uranium mines, disposal of spent nuclear fuel) depends on the environmental dispersion, migration and retention as well as transfer pathways of these radionuclides. Many of these transfer pathways include microbiological steps and mediators, which are however still largely unknown. Therefore, the characterization of microorganisms in such radionuclide-polluted environments is important and improves our understanding of the impacts of radionuclides on microbial ecology and evolution and vice versa. This also helps in the understanding of the mechanisms of microbial radionuclide tolerance. To address these questions, we use amplicon sequencing approaches combined with isolated bacterial strains and batch uptake and leaching
experiments of radionuclides from different type of environmental samples, including former pilot-scale uranium mine and oligotrofic mire envionments.

 

Bacterial sequences

 

Soil bacteria-plant interactions in radionuclide, heavy-metal and trace element plant-uptake

Our research aims to improve future phytoremediation and agricultural practices globally by providing detailed research data on soil microbial and plant interaction processes, especially in the healthy growth of plants as well in the accumulation of agriculturally important trace elements in crops. Heavy-metals, radionuclides and trace elements enter the food chain through plants which take it up from the soil. Plants are in continuous contact with soil microbiota, which can modify soil chemical environment and affect the availability of chemical elements for plant-uptake. Especially because of these interactions, the role of plant-bacterial synergy in reducing regional heavy-metal and radionuclide load or toxic trace element levels is essential and knowledge of the bacterial processes associated with the metabolism of these elements is of importance. The aim of our study is to identify the major metabolic pathways involved in heavy-metal/radionuclide accumulation in plants and the importance of bacterial-plant interactions in the shapeability of these pathways.