Synergistic binding mechanisms of co-contaminants in soil profiles: Influence of iron-bearing minerals and microbial communities.

In contaminated soil sites, the coexistence of inorganic and organic contaminants poses a significant threat to both the surrounding ecosystem and public health. However, the migration characteristics of these co-contaminants within the soil and their interactions with key components, including Fe-bearing minerals, organic matter, and microorganisms, remain unclear. This study involved the collection of a 4.3-m-depth co-contaminated soil profile to investigate the vertical distribution patterns of co-contaminants (namely, arsenic, cadmium, and polychlorinated biphenyls (PCBs)) and their binding mechanisms with environmental factors. The results indicated a notable downward accumulation of inorganic contaminants with increasing soil depth, whereas PCBs were predominantly concentrated in the uppermost layer. Chemical extraction and synchrotron radiation analysis highlighted a positive correlation between the abundance of reactive iron (FeCBD) and both co-contaminants and microbial communities in the contaminated site. Furthermore, Mantel tests and structural equation modeling (SEM) demonstrated the direct impacts of FeCBD and microbial communities on co-contaminants within the soil profile. Overall, these results provided valuable insights into the migration and transformation characteristics of co-contaminants and their binding mechanisms mediated by minerals, organic matter, and microorganisms.

RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria via a cyanobacterial-specific nonapeptide in the noncatalytic region.

RNase E, a central component involved in bacterial RNA metabolism, usually has a highly conserved N-terminal catalytic domain but an extremely divergent C-terminal domain. While the C-terminal domain of RNase E in Escherichia coli recruits other components to form an RNA degradation complex, it is unknown if a similar function can be found for RNase E in other organisms due to the divergent feature of this domain. Here, we provide evidence showing that RNase E forms a complex with another essential ribonuclease-the polynucleotide phosphorylase (PNPase)-in cyanobacteria, a group of ecologically important and phylogenetically ancient organisms. Sequence alignment for all cyanobacterial RNase E proteins revealed several conserved and variable subregions in their noncatalytic domains. One such subregion, an extremely conserved nonapeptide (RRRRRRSSA) located near the very end of RNase E, serves as the PNPase recognition site in both the filamentous cyanobacterium Anabaena PCC7120 and the unicellular cyanobacterium Synechocystis PCC6803. These results indicate that RNase E and PNPase form a ribonuclease complex via a common mechanism in cyanobacteria. The PNPase-recognition motif in cyanobacterial RNase E is distinct from those previously identified in Proteobacteria, implying a mechanism of coevolution for PNPase and RNase E in different organisms.

[Adsorption and desorption of Bt toxin on three kinds of minerals].

This paper studied the characteristics of the adsorption and desorption of Bt (Bacillus thuringiensis) toxin on goethite, kaolinite, and silica. The results showed that in phosphate buffer (pH 8), the adsorption isotherms of Bt toxin on the test minerals followed Langmuir equation (R2 >0. 9661), and the adsorbed amounts were in the order of goethite > kaolinite > silica. The Bt toxin was easily adsorbed on the minerals, and the adsorption could reach equilibrium after 1 hour. Within the range of pH 6-8, the amounts of Bt toxin adsorbed on goethite, kaolinite and silica decreased with increasing pH; in the range of 10 degrees C-50 degrees C, the amounts of the toxin adsorbed on goethite and silica decreased by 8.39% and 47.06%, respectively, while that on kaolinite increased slightly (5.91%). The infrared absorption spectrum showed that there was only a minor alteration of Bt toxin after adsorption. The toxin adsorbed on the minerals was not easily desorbed by deionised water, with the desorption rate ranged from 28.48% to 42.04% after three times washing.

Construction of two lux-tagged Hg2+-specific biosensors and their luminescence performance.

Two Hg2+-specific biosensors were constructed using bacterial luciferase as reporter gene and plasmid-free Pseudomonas putida X4 and Enterobacter aerogenes NTG-01 as host strains. The performance of X4 biosensor was compared with that of NTG-01 biosensor in the same assay conditions. The maximum bioluminescence for X4 (pmerRluxCDABE-Kan) biosensor was found during the midexponential phase and that for NTG-01 (pmerRluxCDABE-Kan) was at the late exponential phase. The shortest induction time of two biosensors was 30 min. The maximum light signal output for NTG-01 and X4 sensors was observed at the incubation time of 5 and 4 h, respectively. The lowest detectable concentration of mercury by the two biosensors were both of 100 pM at 28 degrees C, pH 7 and an initial cell number of 10(6) CFU ml(-1). Cd2+, Zn2+, Co2+, Cu2+, and Pb2 + ions at nanomolar level did not interfere with the measurement by the biosensors. These results show that the sensitivity of the two biosensors is sufficient for the detection of Hg2+ under most contaminated environments.

Amplification of plasmid DNA bound on soil colloidal particles and clay minerals by the polymerase chain reaction.

Polymerase chain reaction (PCR) was used to amplify a 600-base pair (bp) sequence of plasmid pGEX-2T DNA bound on soil colloidal particles from Brown soil (Alfisol) and Red soil (Ultisol), and three different minerals (goethite, kaolinite, montmorillonite). DNA bound on soil colloids, kaolinite, and montmorillonite was not amplified when the complexes were used directly but amplification occurred when the soil colloid or kaolinite-DNA complex was diluted, 10- and 20-fold. The montmorillonite-DNA complex required at least 100-fold dilution before amplification could be detected. DNA bound on goethite was amplified irrespective of whether the complex was used directly, or diluted 10- and 20-fold. The amplification of mineral-bound plasmid DNA by PCR is, therefore, markedly influenced by the type and concentration of minerals used. This information is of fundamental importance to soil molecular microbial ecology with particular reference to monitoring the fate of genetically engineered microorganisms and their recombinant DNA in soil environments.

Interactions of DNA with clay minerals and soil colloidal particles and protection against degradation by DNase.

Adsorption, desorption, and degradation by nucleases of DNA on four different colloidal fractions from a Brown soil and clay minerals were studied. The adsorption of DNase I and the structures of native DNA, adsorbed and desorbed, were also investigated by Fourier Transform Infrared (FTIR), circular dichroism (CD), and fluorescence spectroscopy, to determine the protection mechanism of DNA molecules by soil colloids and minerals against enzymatic degradation. Kaolinite exhibited the highest adsorption affinity for DNA among the examined soil colloids and clay minerals. In comparison with organomineral complexes (organic clays), DNA was tightly adsorbed by H2O2-treated clays (inorganic clays). FTIR spectra showed that the binding of DNA on kaolinite and inorganic clays changed its conformation from the B-form to the Z-form, whereas montmorillonite and organic clays retained the original B-form of DNA. A structural change from the B- to the C-form in DNA molecules desorbed from kaolinite was observed by CD spectroscopy and confirmed by fluorescence spectroscopy. The presence of soil colloids and minerals provided protection to DNA against degradation by DNase I. The higher level of protection was found with montmorillonite and organic clays compared to kaolinite and inorganic clays. The protection of DNA against nuclease degradation by soil colloids and minerals is apparently not controlled by the adsorption affinity of DNA molecules for the colloids and the conformational change of bound DNA. The higher stability of DNA seemed to be attributed mainly to the presence of organic matter in the system and the adsorption of nucleases on soil colloids and minerals. The information obtained in this study is of fundamental significance for the understanding of the behavior of extracellular DNA in soil environment.