Molecular approaches to the study of aquatic microbial communities

Application of Nanodiamonds in Modelled Bioremediation of Phenol Pollution in River Sediments

The pollution of aquatic ecosystems is a big problem that has its impact on river sediments. In recent decades, an effective solution to this problem has been the application of bioremediation technologies. Nanoremediation is an innovative part of these technologies. We still know little about the efficiency of nanoparticles, especially nanodiamonds, in modelled conditions. The aim of the present study is to investigate the effect of nanodiamonds on the key parameters of modelled bioremediation of river sediments that are polluted with phenol, as well their effect on the structures and functions of microbial communities. An important indicative mechanism that was used is the application of fluorescent in situ hybridization for sediment microbial communities. The results of this study revealed the positive role of nanodiamonds that is associated with their intoxication with high concentrations of phenol. Readaptation was also found, in which the xenobiotic biodegradation potential evolved by increasing the relative proportions of non-culturable bacteria, namely Acinetobacter (at the 144th hour) and Pseudomonas (at the 214th hour). The results can help to find an effective solution to the question of how information from such precise molecular methods and the application of nanodiamonds can be translated into the accessible language of management and bioremediation technologies.

Method for collecting air-water interface microbes suitable for subsequent microscopy and molecular analysis in both research and teaching laboratories

A method has been developed for collecting air-water interface (AWI) microbes and biofilms that enables analysis of the same sample with various combinations of bright-field and fluorescence light microscopy optics, scanning and transmission electron microscopy (TEM), and atomic force microscopy. The identical sample is then subjected to molecular analysis. The sampling tool consists of a microscope slide supporting appropriate substrates, TEM grids, for example, that are removable for the desired protocols. The slide with its substrates is then coated with a collodion polymer membrane to which in situ AWI organisms adhere upon contact. This sampling device effectively separates the captured AWI bacterial community from the bulk water community immediately subtending. Preliminary data indicate that the AWI community differs significantly from the water column community from the same sample site when both are evaluated with microscopy and with 16S ribosomal DNA sequence-based culture-independent comparisons. This microbe collection method can be used at many levels in research and teaching.

Evidence for a dynamic cycle between Mn and Co in the water column of a stratified lake

The geochemical behavior of Co in aquatic systems has often been related to the presence of Fe and Mn particles. A few studies have shown that Co is exclusively associated with particulate Mn, but the dynamics of Co and Mn cycling have never been determined in real time under natural conditions. In this study, we used a combination of analytical techniques to study the temporal and spatial evolution of Mn microparticles (MnOx) over 2 weeks in the water column of a shallow stratified lake (Paul Lake, MI). We report a temporal accumulation of dissolved Mn at the oxic-anoxic transition, and we show that this accumulation is due to the reductive dissolution of Mn particles. The reductant has not been identified, but abiotic reduction by sigmaH2S and ferrous iron is excluded because they are produced below the zone of MnOx reduction. Hybridization of RNA isolated from Paul Lake with oligonucleotide probes targeting the delta proteobacteria, which include metal-reducing species, suggests that their activity is greatest at and just below the oxic-anoxic transition, so that Mn reduction may be influenced by bacterial activity. Mn-oxidizing bacteria were isolated from this zone as well. We also demonstrate that the dynamic evolution of MnOx has a direct influence on the distribution of Co in the water column of this lake: dissolved Co is released during the reductive dissolution of MnOx and accumulates at the redox interface.

Distribution and abundance of Gram-positive bacteria in the environment: development of a group-specific probe

We developed a 16S rRNA-targeted oligonucleotide probe (S-P-GPos-1200-a-A-13) for the Gram-positive bacteria, confirmed its specificity by database searches and hybridization studies, and investigated the effects of humic acids on membrane hybridizations with this probe. S-P-GPos-1200-a-A-13 was used to estimate the abundance of Gram-positive populations in the bovine rumen and Lake Michigan sediments. This probe should be useful for studies of the environmental distribution of Gram-positive bacteria and the detection of uncultured, phylogenetically Gram-positive bacteria with variable or negative Gram staining reactions, and could serve for Gram staining in some diagnostic settings.