Agnieszka Mrozik

Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds

The contamination of soil with aromatic compounds is of particular environmental concern as they exhibit carcinogenic and mutagenic properties. One of the methods of their removal from soil is bioaugmentation, defined as a technique for improvement of the degradative capacity of contaminated areas by introduction of specific competent strains or consortia of microorganisms. The efficiency of bioaugmentation is determined by many abiotic and biotic factors discussed in this paper. The first include chemical structure, concentration and availability of pollutants as well as physico-chemical properties of soil. In turn, among biotic factors the most important is the selection of proper microorganisms that can not only degrade contaminants but can also successfully compete with indigenous microflora. Several strategies are being developed to make augmentation a successful technology particularly in soils without degrading indigenous microorganisms. These approaches involve the use of genetically engineered microorganisms and gene bioaugmentation. The enhancement of bioaugmentation may be also achieved by delivering suitable microorganisms immobilized on various carriers or use of activated soil.

Bioaugmentation as a strategy for the remediation of pesticide-polluted soil: A review.

Bioaugmentation, a green technology, is defined as the improvement of the degradative capacity of contaminated areas by introducing specific microorganisms, has emerged as the most advantageous method for cleaning-up soil contaminated with pesticides. The present review discusses the selection of pesticide-utilising microorganisms from various sources, their potential for the degradation of pesticides from different chemical classes in liquid media as well as soil-related case studies in a laboratory, a greenhouse and field conditions. The paper is focused on the microbial degradation of the most common pesticides that have been used for many years such as organochlorinated and organophosphorus pesticides, triazines, pyrethroids, carbamate, chloroacetamide, benzimidazole and derivatives of phenoxyacetic acid. Special attention is paid to bacterial strains from the genera Alcaligenes, Arthrobacter, Bacillus, Brucella, Burkholderia, Catellibacterium, Pichia, Pseudomonas, Rhodococcus, Serratia, Sphingomonas, Stenotrophomonas, Streptomyces and Verticillum, which have potential applications in the bioremediation of pesticide-contaminated soils using bioaugmentation technology. Since many factors strongly influence the success of bioaugmentation, selected abiotic and biotic factors such as pH, temperature, type of soil, pesticide concentration, content of water and organic matter, additional carbon and nitrogen sources, inoculum size, interactions between the introduced strains and autochthonous microorganisms as well as the survival of inoculants were presented.

Microbial diversity in waters, sediments and microbial mats evaluated using fatty acid-based methods

The review summarises recent advances towards a greater comprehensive assessment of microbial diversity in aquatic environments using the fatty acid methyl esters and phospholipid fatty acids approaches. These methods are commonly used in microbial ecology because they do not require the culturing of micro-organisms, are quantitative and reproducible and provide valuable information regarding the structure of entire microbial communities. Because some fatty acids are associated with taxonomic and functional groups of micro-organisms, they allow particular groups of micro-organisms to be distinguished. The integration of fatty acid-based methods with stable isotopes, RNA and DNA analyses enhances our knowledge of the role of micro-organisms in global nutrient cycles, functional activity and phylogenetic lineages within microbial communities. Additionally, the analysis of fatty acid profiles enables the shifts in the microbial diversity in pristine and contaminated environments to be monitored. The main objective of this review is to present the use of lipid-based approaches for the characterisation of microbial communities in water columns, sediments and biomats.

Facilitation of Co-Metabolic Transformation and Degradation of Monochlorophenols by Pseudomonas sp. CF600 and Changes in Its Fatty Acid Composition

In this study, co-metabolic degradation of monochlorophenols (2-CP, 3-CP, and 4-CP) by the Pseudomonas sp. CF600 strain in the presence of phenol, sodium benzoate, and 4-hydroxybenzoic acid as an additional carbon source as well as the survival of bacteria were investigated. Moreover, the changes in cellular fatty acid profiles of bacteria depending on co-metabolic conditions were analyzed. It was found that bacteria were capable of degrading 4-CP completely in the presence of phenol, and in the presence of all substrates, they degraded 2-CP and 3-CP partially. The highest 2-CP and 3-CP removal was observed in the presence of sodium benzoate. Bacteria exhibited three various dioxygenases depending on the type of growth substrate. It was also demonstrated that bacteria exposed to aromatic growth substrates earlier degraded monochlorophenols more effectively than unexposed cells. The analysis of fatty acid profiles of bacteria indicated the essential changes in their composition, involving alterations in fatty acid saturation, hydroxylation, and cyclopropane ring formation. The most significant change in bacteria exposed to sodium benzoate and degrading monochlophenols was the appearance of branched fatty acids. The knowledge from this study indicates that Pseudomonas sp. CF600 could be a suitable candidate for the bioaugmentation of environments contaminated with phenolic compounds.

Cellular fatty acid patterns inPseudomonas sp. CF600 during catechol and phenol degradation in media supplemented with glucose as an additional carbon source

Fatty acid composition inPseudomonas sp. CF600 during degradation of catechol and phenol individually and their mixture was investigated. Moreover, the influence of glucose as an additional, easily degradable carbon source on fatty acid profiling in bacteria grown on these aromatic substrates was studied. Both catechol and phenol treatments caused in bacterial cells crucial changes in the distribution of tested groups of fatty acids. The major changes included the increase of fatty acid saturation, decrease in the percentage of cyclopropane fatty acid 17:0cy and the appearance of branched and hydroxy fatty acids. Under catechol, phenol and their mixture exposure saturated/unsaturated ratio showed the value 6.5, 5.68 and 6.38 whereas in control cells this ratio reached the value 3.05. As a response to aromatic compounds bacteria formed fatty acids that were not detected in control cells growing on glucose. It has been demonstrated that the supplementation of cultured media containing single aromatic substrates or/and their mixture with glucose resulted in changes in degradation rates of catechol and phenol. It seemed that glucose influenced some metabolic pathways responsible for the assimilation of aromatic compounds. The incubation of cells in the presence of aromatic compounds and glucose rapidly led to alterations of whole-cell derived fatty acid composition. The most important changes were associated with saturation level of fatty acids and cyclopropane fatty acid contents.

Changes in fatty acid composition of Stenotrophomonas maltophilia KB2 during co-metabolic degradation of monochlorophenols

The changes in the cellular fatty acid composition of Stenotrophomonas maltophilia KB2 during co-metabolic degradation of monochlorophenols in the presence of phenol as well as its adaptive mechanisms to these compounds were studied. It was found that bacteria were capable of degrading 4-chlorophenol (4-CP) completely in the presence of phenol, while 2-chlorophenol (2-CP) and 3-chlorophenol (3-CP) they degraded partially. The analysis of the fatty acid profiles indicated that adaptive mechanisms of bacteria depended on earlier exposure to phenol, which isomer they degraded, and on incubation time. In bacteria unexposed to phenol the permeability and structure of their membranes could be modified through the increase of hydroxylated and cyclopropane fatty acids, and straight-chain and hydroxylated fatty acids under 2-CP, 3-CP and 4-CP exposure, respectively. In the exposed cells, regardless of the isomer they degraded, the most important changes were connected with the increase of the contribution of branched fatty acid on day 4 and the content of hydroxylated fatty acids on day 7. The changes, particularly in the proportion of branched fatty acids, could be a good indicator for assessing the progress of the degradation of monochlorophenols by S. maltophilia KB2. In comparison, in phenol-degrading cells the increase of cyclopropane and straight-chain fatty acid content was established. These findings indicated the degradative potential of the tested strain towards the co-metabolic degradation of persistent chlorophenols, and extended the current knowledge about the adaptive mechanisms of these bacteria to such chemicals.

Effects of Pulp and Na-Bentonite Amendments on the Mobility of Trace Elements, Soil Enzymes Activity and Microbial Parameters under Ex Situ Aided Phytostabilization

The objective of this study was to explore the potential use of pulp (by-product) from coffee processing and Na-bentonite (commercial product) for minimizing the environmental risk of Zn, Pb and Cd in soil collected from a former mine and zinc-lead smelter. The effects of soil amendments on the physicochemical properties of soil, the structural and functional diversity of the soil microbiome as well as soil enzymes were investigated. Moreover, biomass of Festuca arundinacea Schreb. (cultivar Asterix) and the uptake of trace elements in plant tissues were studied. The outdoor pot set contained the following soils: control soil (initial), untreated soil (without additives) with grass cultivation and soils treated (with additives) with and without plant development. All of the selected parameters were measured at the beginning of the experiment (t0), after 2 months of chemical stabilization (t2) and at the end of the aided phytostabilization process (t14). The obtained results indicated that both amendments efficiently immobilized the bioavailable fractions of Zn (87–91%) and Cd (70–83%) at t14; however, they were characterized by a lower ability to bind Pb (33–50%). Pulp and Na-bentonite drastically increased the activity of dehydrogenase (70- and 12-fold, respectively) at t14, while the activities of urease, acid and alkaline phosphatases differed significantly depending on the type of material that was added into the soil. Generally, the activities of these enzymes increased; however, the increase was greater for pulp (3.5-6-fold) than for the Na-bentonite treatment (1.3–2.2-fold) as compared to the control. Soil additives significantly influenced the composition and dynamics of the soil microbial biomass over the experiment. At the end, the contribution of microbial groups could be ordered as follows: gram negative bacteria, fungi, gram positive bacteria, actinomycetes regardless of the type of soil enrichment. Conversely, the shift in the functional diversity of the microorganisms in the treated soils mainly resulted from plant cultivation. Meanwhile, the highest biomass of plants at t14 was collected from the soil with Na-bentonite (6.7 g dw-1), while it was much lower in a case of pulp treatment (1.43–1.57 g dw-1). Moreover, the measurements of the heavy metal concentrations in the plant roots and shoots clearly indicated that the plants mainly accumulated metals in the roots but that the accumulation of individual metals depended on the soil additives. The efficiency of the accumulation of Pb, Cd and Zn by the roots was determined to be 124, 100 and 26% higher in the soil that was enriched with Na-bentonite in comparison with the soil that was amended with pulp, respectively. The values of the soil indices (soil fertility, soil quality and soil alteration) confirmed the better improvement of soil functioning after its enrichment with the pulp than in the presence of Na-bentonite.

Degradation of 4-chlorophenol and microbial diversity in soil inoculated with single Pseudomonas sp. CF600 and Stenotrophomonas maltophilia KB2

Soil contamination with chlorophenols is a serious problem all over the world due to their common use in different branches of industry and agriculture. The objective of this study was to determine whether bioaugmenting soil with single Pseudomonas sp. CF600 and Stenotrophomonas maltophilia KB2 and additional carbon sources such as phenol (P) and sodium benzoate (SB) could enhance the degradation of 4-chlorophenol (4-CP). During the degradation experiment, the number of bacteria as well as the structural and functional diversity of the soil microbial communities were determined. It was found that the most effective degradation of 4-CP in the soil was observed after it was inoculated with CF600 and the addition of SB. The biodegradation of five doses of 4-CP in this soil proceeded within 100 days. At the same time, the rate of the disappearance of 4-CP in the soil that had been bioaugmented with CF600 and contaminated with 4-CP and P was 5-6.5 times lower compared to its rate of disappearance in the soil that had been contaminated with 4-CP. The biodegradation of 4-CP in all of the treated and untreated soils was accompanied by a systematic decrease in the number of heterotrophic bacteria (THB) ranging between 13 and 40%. It was also proven that the tested aromatic compounds affected the soil microbial community structure through an increase in the marker fatty acids for Gram-negative bacteria (BG-) and fungi (F). The essential changes in the patterns of the fatty acid methyl esters (FAMEs) for the polluted soil included an increase in the fatty acid saturation and hydroxy fatty acid abundance. The obtained results also indicated that the introduction of CF600 into the soil contaminated with 4-CP and SB or P caused an increase in the functional diversity of the soil microorganisms. In contrast, in the soil that had been inoculated with KB2 and in the non-inoculated soil, the addition of 4-CP and P decreased the microbial activity. In conclusion, the inoculation of both strains into contaminated soil with aromatic compounds caused irreversible changes in the functional and structural diversity of the soil microbial communities.