Characterization of glyphosate-resistant Burkholderia anthina and Burkholderia cenocepacia isolates from a commercial Roundup® solution.

Roundup® is the brand name for herbicide solutions containing glyphosate, which specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase of the shikimate pathway. The inhibition of the EPSP synthase causes plant death because EPSP is required for biosynthesis of aromatic amino acids. Glyphosate also inhibits the growth of archaea, bacteria, Apicomplexa, algae and fungi possessing an EPSP synthase. Here, we have characterized two glyphosate-resistant bacteria from a Roundup solution. Taxonomic classification revealed that the isolates 1CH1 and 2CH1 are Burkholderia anthina and Burkholderia cenocepacia strains respectively. Both isolates cannot utilize glyphosate as a source of phosphorus and synthesize glyphosate-sensitive EPSP synthase variants. Burkholderia. anthina 1CH1 and B. cenocepacia 2CH1 tolerate high levels of glyphosate because the herbicide is not taken up by the bacteria. Previously, it has been observed that the exposure of soil bacteria to herbicides like glyphosate promotes the development of antibiotic resistances. Antibiotic sensitivity testing revealed that the only the B. cenocepacia 2CH1 isolate showed increased resistance to a variety of antibiotics. Thus, the adaptation of B. anthina 1CH1 and B. cenocepacia 2CH1 to glyphosate did not generally increase the antibiotic resistance of both bacteria. However, our study confirms the genomic adaptability of bacteria belonging to the genus Burkholderia.

Aminophosphonates in Nanofiltration and Reverse Osmosis Permeates.

Aminophosphonates such as aminotris(methylenephosphonic acid) (ATMP) are common constituents of antiscalants. In nanofiltration (NF) and reverse osmosis (RO) processes, ATMP prevents inorganic scaling leading to more stable membrane performance. So far, little attention has been paid to the possible permeation of aminophosphonates through NF and RO membranes. We have investigated the permeability of these membrane types for ATMP and its potential metabolites iminodi(methylenephosphonic acid) (IDMP) and amino(methylenephosphonic acid) (AMPA) with two different NF membranes (TS40 and TS80) and one RO membrane (ACM2) and three different water compositions (ultra-pure water, synthetic tap water and local tap water). We found traces of phosphonates in all investigated permeates. The highest phosphonate rejection occurred with local tap water for all three membranes investigated. Filtration experiments with a technical antiscalant formulation containing ATMP indicated similar trends of phosphonate permeability through all three membranes. We assume that the separation mechanisms of the membranes are the results of a very complex relationship between physico-chemical properties such as Donnan exclusion, feed pH, feed ionic strength and feed concentration, as well as solute-solute interactions.

Molecular mechanisms underlying glyphosate resistance in bacteria.

Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations.

Supplementary data on rapid sample clean-up procedure of aminophosphonates for LC/MS analysis.

Minimising matrix effects through high sample purity is of major importance for LC/MS analysis. Here we provide supplementary data and protocols related to the article "Rapid sample clean-up procedure of aminophosphonates for LC/MS analysis" (revised article submitted to Talanta) [1]. It is demonstrated that the tested phosphonates iminodi(methylenephosphonic acid) (IDMP), hydroxyethelidene(diphosphonic acid) (HEDP), aminotris(methylenephosphonic acid) (ATMP), ethylenediaminetetra(methyloenephosphonic acid) (EDTMP) and diethylenetriaminepenta(methylenephosphonic acid) (DTPMP) dissolved in tap water are not detectable by LC/MS without sample clean-up. Only the smallest aminophosphonate amino(methylenephosphonic acid) (AMPA) was detectable but the recovery is decreased drastically. The optimised sample clean-up with cation exchange resin (CER) Dowex 50WX8 is described in detail and illustrated. The protocol is provided. The influence of the incubation time, addition of different ammonium acetate concentrations, different samples pHs and different water qualities is demonstrated and preferred clean-up conditions are recommended. Calibration results of all tested aminophosphonates are validated regarding limit of detection, limit of quantification, lower limit of quantification, absolute and relative process standard deviation. A final recommendation for the best clean-up condition for all six tested aminophosphonates is provided.•AMPA analysis without derivatisation is possible with optimised clean-up procedure•Clean-up procedure is combinable with derivatisation method of [2]•Procedure is simple, rapid and highly reproducible.

The influence of selected bivalent metal ions on the photolysis of diethylenetriamine penta(methylenephosphonic acid).

DTPMP is predominantly utilized as scale inhibitor. We investigated the reaction rates and degradation mechanism of DTPMP with and without addition of Fe2+, Mg2+ and Ca2+ by performing LC/MS and 31P NMR analyses. DTPMP undergoes conversion with and without addition of bivalent metal ions. The initial cleavage of DTPMP is initiated at the CN bond leading to release of IDMP as its major breakdown product. The release of smaller quantities of EABMP and AMPA confirmed the nucleophilic attack on the DTPMP amines. Oxidation of Fe2+ to Fe3+ during the initial 30 min indicated an intramolecular electron transfer changing the electron density distribution at the nitrogen centre, which increased the radical attack during UV irradiation. Independent of the fact that Fe2+ acted as catalyst and Mg2+ and Ca2+ acted as reactants, we found no significant differences in their degradation mechanisms. However, the reaction rates were strongly affected by the addition of the bivalent metal ions as Fe2+ accelerated most DTPMP degradation followed by Mg2+ and Ca2+. The UV treatment without metal ion addition was four times slower compared with Fe2+ addition. We conclude that in environments rich in ferrous iron and/or at reduced redox potential, photolysis of DTPMP will be catalysed by iron and will lead to accumulation of IDMP, EABMP and AMPA and several other none-quantifiable breakdown products.

Data on DNA gel sample load, gel electrophoresis, PCR and cost analysis.

The data presented in this article provide supporting information to the related research article "Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples" (Kuhn et al., 2017) [1]. In that article, we compared the suitability of ten selected DNA extraction methods based on DNA quality, purity, quantity and applicability to universal PCR. Here we provide the data on the specific DNA gel sample load, all unreported gel images of crude DNA and PCR results, and the complete cost analysis for all tested extraction procedures and in addition two commercial DNA extraction kits for soil and water.

Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples.

DNA extraction for molecular biological applications usually requires target optimized extraction procedures depending on the origin of the samples. For environmental samples, a range of different procedures has been developed. We compared the applicability and efficiency of ten selected DNA extraction methods published in recent literature using four different environmental samples namely: activated sludge from a domestic wastewater treatment plant, river sediment, anaerobic digestion sludge and nitrifying enrichment culture. We assessed the suitability of the extraction procedures based on both DNA yield and quality. DNA quantification was performed by both ultra violet (UV) spectrophotometry and fluorescence spectrophotometry after staining with PicoGreen. In our study, DNA yields based on UV measurement were overestimated in most cases while DNA yields from fluorescence measurements correlated well with the sample load on agarose gels of crude DNA. The quality of the DNA extracts was determined by gel electrophoresis of crude DNA and PCR products from 16S rDNA with the universal primer set 27f/1525r. It was observed that gel electrophoresis of crude DNA was not always suitable to evaluate DNA integrity and purity since interfering background substances (e.g. humic substances) were not visible. Therefore, we strongly recommend examining the DNA quality of both crude DNA and 16S rDNA PCR products by gel electrophoresis when a new extraction method is established. Summarizing, we found four out of ten extraction procedures being applicable to all tested samples without noticeable restrictions. The procedure G (according to the standard method 432_10401 of the Lower Saxony State Office for Consumer Protection and Food Safety) had the broadest application range over procedure J (published by Wilson, 2001). These were followed by procedures F (Singka et al., 2012) and A (Bourrain et al., 1999). All four extraction procedures delivered reliable and reproducible crude DNA and PCR products. From an economical point of view, all procedures tested during this study were cheaper compared to commercial DNA extraction kits.

Metaproteome analysis of sewage sludge from membrane bioreactors.

Microbial dynamics and enzymatic activities of activated sludge processes are not completely understood yet. A better understanding about the biology is indispensable for further process optimization. Since proteins play a key role as catalysts in sludge processes, a protocol for protein extraction and analysis by 2-D PAGE was established. It is based on phenol extraction of alkaline extracts and on a subsequent precipitation with ammonium sulphate. 2-D protein patterns obtained from different sludges collected from membrane bioreactors showed--besides common spots--significant differences. Selected proteins were identified with nano-HPLC-ESI-MS/MS. All membrane biological reactor (MBR) sludge samples investigated in this study contained elastase 3A, which implies that this human serine protease is a significant constituent of municipal wastewater. Although the identification of proteins from ammonia-oxidizing bacterium Nitrosomonas europaea was expected, the detection of a protein with homology to the marine bacterium Saprospira grandis in MBR1 was surprising.

Electrolytic methanogenic-methanotrophic coupling for tetrachloroethylene bioremediation: proof of concept.

Coupling of methanogenic and methanotrophic catabolisms was performed in a single-stage technology equipped with a water electrolysis cell placed in the effluent recirculation loop. The electrolysis-generated hydrogen served as an electron donor for both bicarbonate reduction into CH4 and reductive dechlorination, while the O2 and CH4, supported the cometabolic oxidation of chlorinated intermediates left over by the tetrachloroethylene (PCE) transformation. The electrolytical methanogenic/methanotrophic coupled (eMaMoC) process was tested in a laboratory-scale setup at PCE loads ranging from 5 to 50 micromol/L(rx) x d (inlet concentrations from 4 to 11 mg/L), and at various hydraulic residence times (HRT). Degradation followed essentially a reductive dechlorination pathway from PCE to cis-1,2-dichloroethene (DCE), and an oxidative pathway from DCE to CO2. PCE reductive dechlorination to DCE was consistently over 98% while a maximum oxidative DCE mineralization of 89% was obtained at a load of 4.3 micromol PCE/ L(rx) x d and an HRT of 6 days. Controlling dissolved oxygen concentrations within a relatively low range (2-3 mg/L) seemed instrumental to sustain the overall degradation capacity. Degradation kinetics were further evaluated: the apparent half-saturation constant (K(s)) had to be set relatively high (29 microM) for the simulated data to best fit the experimental ones. In spite of such kinetic limitations, the eMaMoC system, while fueled by water electrolysis, was effective in building and sustaining a functional methanogenic/methanotrophic consortium capable of significant PCE mineralization in a single-stage process. Hence, degradation standards are within reach so long as the methanotrophic DCE-oxidizing potential, including substrate affinity, are optimized and HRT accordingly adjusted.

Bacterial extracellular DNA forming a defined network-like structure.

It is generally assumed that nucleic acids are localized inside of living cells and that their primary function is the storage of information. In contrast, extracellular DNA is mainly considered as a remnant of lysed cells. Here, we report the formation of extracellular bacterial DNA as a spatial structure. An aquatic bacterium, strain F8, was isolated, which produced a stable filamentous network of extracellular DNA. Different staining and enzymatic techniques confirmed that it was DNA. We were able to amplify the 16S rRNA gene from the extracellular DNA. Restriction endonuclease cleavage and randomly amplified polymorphic DNA analysis of extracellular and genomic DNAs revealed major similarities, but also some differences in both sequences. Our data demonstrate a new function and relevance for extracellular DNA.