Rapid detection and identification of microorganisms is a challenging and important aspect in a wide range of fields, from medical to industrial, affecting human lives. Unfortunately, classical methods of microorganism identification are based on time-consuming and labor-intensive approaches. Screening techniques require the rapid and cheap grouping of bacterial isolates; however, modern bioanalytics demand comprehensive bacterial studies at a molecular level. Modern approaches for the rapid identification of bacteria use molecular techniques, such as 16S ribosomal RNA gene sequencing based on polymerase chain reaction or electromigration, especially capillary zone electrophoresis and capillary isoelectric focusing. However, there are still several challenges with the analysis of microbial complexes using electromigration technology, such as uncontrolled aggregation and/or adhesion to the capillary surface. Thus, an approach using capillary electrophoresis of microbial aggregates with UV and matrix-assisted laser desorption ionization time-of-flight MS detection is presented.

In the presented work identification of microorganisms isolated from various types of honeys was performed. Martix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing were applied to study environmental bacteria strains.With both approches, problematic spore-forming Bacillus spp, but also Staphylococcus spp., Lysinibacillus spp., Micrococcus spp. and Brevibacillus spp were identified. However, application of spectrometric technique allows for an unambiguous distinction between species/species groups e.g.B. subtilis or B. cereus groups. MALDI TOF MS and 16S rDNA sequencing allow for construction of phyloproteomic and phylogenetic trees of identified bacterial species. Furthermore, the correlation beetween physicochemical properties, geographical and botanical origin and the presence bacterial species in honey samples were investigated.

Phytoremediation is the bioremediation of contaminated soils and waters by using plants and their associated microorganisms. Phytoremediation of heavy metal (HM)-contaminated soils is based on immobilization of metals in rhizosphere soil and roots (phytostabilization) and on mobilization, uptake, and transfer of metals into the aboveground plant organs (phytoextraction). In this review, we aimed to (i) discuss the fundamentals, potential, and limitations of plant-associated microorganisms (bacteria and fungi) to increase the efficiency of phytostabilization and phytoextraction of HM-contaminated soils and (ii) describe promising developments and future challenges to expanding their use. Controlled inoculations of plants with growth-promoting microorganisms can significantly increase their root growth, biomass production, and stress tolerance in HM-contaminated soils. A serious weakness of phytoremediation in general is the usually high and difficult to measure expenditure of time for successful completion. The bioconcentration factors (BCFs) and the translocation factors (TFs) are among the most important measures of the efficiency of phytoremediation. However, an overview of BCFs and TFs for a variety of combinations of plants with defined associated microorganisms is lacking. Moreover, the joint evaluation of model systems would allow an improved cost–benefit calculation of microbial inoculations in phytoremediation systems. For this purpose, the use of in vitro model systems is considered to be preferable to field experiments due to the savings in time and costs and the control of environmental conditions. However, the transferability of in vitro data to field conditions is limited. Currently, attention is focused on the use of artificial neural networks, mainly to avoid formulating any complex relationships between soil inputs (e.g., soil amendments, pH, carbon, nitrogen and hydrogen contents, electrical conductivity, and dissolved organic carbon) and design outputs (e.g., BCFs and TFs) beforehand and because of the high accuracy of the obtained models. The controlled use of associated microorganisms to increase the efficiency of phytoremediation of HM, mainly using combinations of Brassica and Salix spp. and rhizobacteria at contaminated soils, is a promising possibility. A crucial future challenge for the expansion of their use will be to develop well-defined cost- and time-efficient tools for a credible prediction of their effectiveness on contaminated field sites.