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.

Sulfide oxidizing bacteria in the context of acid mine drainage formation in former uranium mine

Acid mine drainage (AMD) results from outflow of acidic water from waste rock and tailings and occurs naturally in microbiologically active environments containing sulphide minerals. On air exposed sulphide minerals (often pyrite), bacterially catalysed oxidation results on formation of sulphuric acid. The most common bacteria responsible for acid generation include iron oxidizers (FOB), like Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans. In addition, Sulphate Reducing Bacteria (SRB) and Sulphur oxidizing Bacteria (SOB), like Thiobacillus thioparus play an important role in the acid formation.

In this study the leaching and uptake of polonium and radium by SOB bacteria and bacteria isolated from Paukkajanvaaran former uranium mine soil is examined. In addition soil microbiome on the former uranium mine area is mapped using next-generation sequencing.

Bacterial sequences