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Abstract Background The isolation of highly pure copper-free methanobactin is a prerequisite for the investigation of the biogeochemical functions of this chalkophore molecule produced by methane oxidizing bacteria. Here, we report a purification method for methanobactin from Methylosinus trichosporium OB3b cultures based on reversed-phase HPLC fractionation used in combination with a previously reported resin extraction. HPLC eluent fractions of the resin extracted product were collected and characterized with UV-vis, FT-IR, and C-1s NEXAFS spectroscopy, as well as with elemental analysis and ESI-MS. Results The results showed that numerous compounds other than methanobactin were present in the isolate obtained with resin extraction. Molar C/N ratios, mass spectrometry measurements, and UV-vis spectra indicated that methanobactin was only present in one of the HPLC fractions. On a mass basis, methanobactin carbon contributed only 32% to the total organic carbon isolated with resin extraction. Our spectroscopic results implied that besides methanobactin, the organic compounds in the resin extract comprised breakdown products of methanobactin as well as polysaccharide-like substances. Conclusion Our results demonstrate that a purification step is indispensable in addition to resin extraction in order to obtain pure methanobactin. The proposed HPLC purification procedure is suitable for semi-preparative work and provides copper-free methanobactin.

As the interest in plant-based alternative food products has increased significantly in the last years, it is also important to investigate these products regarding microbiological aspects. The aim of this study was to assess the microbiological quality and the occurrence of selected foodborne pathogens in plant-based meat alternative products (PBMA) collected at retail level in Switzerland. A total of 100 PBMA (84 vegan and 16 vegetarian products) was analyzed qualitatively for the presence of Salmonella, Listeria monocytogenes and quantitatively for Staphylococcus aureus, Bacillus cereus group members, Enterobacteriaceae and the total viable count. Furthermore, pH measurements were carried out and the a w -value was determined. Isolates were further analyzed with Whole Genome Sequencing. The total viable count before the expiration date was between < 2 log and 7 log CFU/g (median: 5.97 log CFU/g). In six (6 %) samples Enterobacteriaceae with 2 log to 3 log CFU/g were detected. No Salmonella and no Listeria monocytogenes were detected. However, seven products (7 %) were contaminated with other Listeria spp. (six L. innocua and one L. seeligeri). Further findings were two (2 %) Staphylococcus aureus ST8 with the presence of selx and tsst-1 genes, and five (5 %) Bacillus cereus group members (three B. paranthracis, one B. cereus sensu stricto, and one B. cytotoxicus) which all were diarrhea-associated strains. This study provides data that are relevant for HACCP concepts of companies that produce plant-based meat alternative products and helps to define microbiological parameters that should be included when testing such products., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

The mobility and bioavailability of phosphate in paddy soils are closely coupled to redox-driven Fe-mineral dynamics. However, the role of phosphate during Fe-mineral dissolution and transformations in soils remains unclear. Here, we investigated the transformations of ferrihydrite and lepidocrocite and the effects of phosphate pre-adsorbed to ferrihydrite during a 16-week field incubation in a flooded sandy rice paddy soil in Thailand. For the deployment of the synthetic Fe-minerals in the soil, the minerals were contained in mesh bags either in pure form or after mixing with soil material. In the latter case, the Fe-minerals were labeled with 57 Fe to allow the tracing of minerals in the soil matrix with 57 Fe Mössbauer spectroscopy. Porewater geochemical conditions were monitored, and changes in the Fe-mineral composition were analyzed using 57 Fe Mössbauer spectroscopy and/or X-ray diffraction analysis. Reductive dissolution of ferrihydrite and lepidocrocite played a minor role in the pure mineral mesh bags, while in the 57 Fe-mineral-soil mixes more than half of the minerals was dissolved. The pure ferrihydrite was transformed largely to goethite (82-85%), while ferrihydrite mixed with soil only resulted in 32% of all remaining 57 Fe present as goethite after 16 weeks. In contrast, lepidocrocite was only transformed to 12% goethite when not mixed with soil, but 31% of all remaining 57 Fe was found in goethite when it was mixed with soil. Adsorbed phosphate strongly hindered ferrihydrite transformation to other minerals, regardless of whether it was mixed with soil. Our results clearly demonstrate the influence of the complex soil matrix on Fe-mineral transformations in soils under field conditions and how phosphate can impact Fe oxyhydroxide dynamics under Fe reducing soil conditions.

Here, we report the genome sequences of four Escherichia albertii isolates that were recovered from hunted wild boars in Switzerland in 2022 and 2023. The genome sizes of KBWS15i, KBWS35i, KBWS50i, and KBSW171i were 4.4 Mbp, 4.5 Mbp, 4.5 Mbp, and 4.7 Mbp, respectively., Competing Interests: The authors declare no conflict of interest.

Here, we report the genome sequences of two Escherichia albertii isolates recovered from a healthy dog (KBD171i) and cat (KBK128i) in Switzerland in 2022. The genome sizes of KBK128i and KBD171i were 4.7 Mbp and 4.9 Mbp, respectively.

Escherichia albertii , a zoonotic pathogen, has sporadically been associated with infectious diarrhea in humans. Poultry and wild birds are considered potential reservoirs. We assessed the occurrence of E. albertii in 280 fecal samples from wild birds ( n = 130) and pooled fecal samples collected at slaughterhouse level from poultry flocks ( n = 150) in Switzerland. Using an E. albertii -specific PCR targeting the Eacdt gene, 23.8% (31/130) of the samples from wild birds, but not from the pooled poultry fecal samples, tested positive for Eacdt . The positive samples originated from 11 bird species belonging to eight families. Strain isolation was attempted on the PCR-positive samples by subculturing the broth cultures onto xylose-MacConkey plates. Isolation was possible on 12 of the 31 Eacdt -PCR-positive samples. Whole-genome sequencing revealed that the strains belonged to nine distinct sequence types, with ST13420 and ST5967 being represented by two and three isolates, respectively. All strains harbored the eae gene, while two strains were also positive for stx2f . Our study thus shows that E. albertii is present in the Swiss wild bird population, which can potentially act as a source of this pathogen to humans, other animals, and the environment.

Escherichia albertii , a close relative of E. coli , is an emerging zoonotic foodborne pathogen associated with watery diarrhea mainly in children and immunocompromised individuals. E. albertii was initially classified as eae -positive Hafnia alvei , however, as more genetic and biochemical information became available it was reassigned to its current novel taxonomy. Its infections are common under conditions of poor hygiene with confirmed transmission via contaminated water and food, mainly poultry-based products. This pathogen has been isolated from various domestic and wild animals, with most isolates being derived from birds, implying that birds among other wild animals might act as its reservoir. Due to the absence of standardized isolation and identification protocols, E. albertii can be misidentified as other Enterobacteriaceae . Exploiting phenotypes such as its inability to ferment rhamnose and xylose and PCR assays targeting E. albertii -specific genes such as the cytolethal distending toxin and the DNA-binding transcriptional activator of cysteine biosynthesis encoding genes can be used to accurately identify this pathogen. Several gaps exist in our knowledge of E. albertii and need to be bridged. A deeper understanding of E. albertii epidemiology and physiology is required to allow the development of effective measures to control its transmission and infections. Overall, current data suggest that E. albertii might play a more significant role in global infectious diarrhea cases than previously assumed and is often overlooked or misidentified. Therefore, simple, and efficient diagnostic tools that cover E. albertii biodiversity are required for effective isolation and identification of this elusive agent of diarrhea.

Iron-rich organic flocs are frequently observed in surface waters of wetlands and show a high affinity for trace metal(loid)s. To date, spectroscopic speciation analyses of Fe and trace elements in these mineral-organic matter (OM) associations are missing. In this study, we investigated the speciation and distribution of Fe and As in flocs collected from low-flow streams (pH 5.3-6.3) of the naturally As-enriched peatland Gola di Lago (Switzerland) using (57)Fe Mössbauer spectroscopy and synchrotron X-ray techniques. The flocs were rich in acid carbohydrates and contained up to 22.1 wt % Fe, 34.9 wt % C, and 2620 mg/kg As. Mössbauer analyses revealed small quantities (<5%) of Fe(II) and Fe(III)-OM complexes and the predominance of ferrihydrite (∼ Fe(5)HO(8) · 4H2O, 51-59%) and lepidocrocite (γ-FeOOH, 34-46%). The latter was not observed by synchrotron X-ray diffraction, implying a coherent scattering domain size of <10 nm. Iron X-ray absorption spectroscopy (XAS) confirmed the Mössbauer results, and bulk As XAS indicated the prevalence of arsenate (71-84%) in the flocs. Shell-fit analyses showed that As was entirely sorbed to Fe(III)-(oxyhydr)oxides and that both arsenate and arsenite exclusively formed monodentate-binuclear ("bridging") complexes (R(As-Fe) = 3.31-3.34 Å). Microfocused X-ray fluorescence spectrometry documented a strong correlation between As and Fe in the flocs. These analyses also revealed intense As hotspots coinciding with abundant freshwater green algae (Closterium spp.). Microfocused As X-ray absorption near-edge structure spectra collected at algae-specific points identified up to 29% As(III), which, in combination with ∼ 5% As(III) detected at Fe-rich points, suggests As(V) bioreduction in the algae. Our findings imply that floc (bio)organics serve primarily as nucleation sites for the precipitation of nanocrystalline Fe(III)-(oxyhydr)oxides, rendering flocs effective sorbents for trace metal(loid)s. Thus, Fe-rich freshwater flocs likely play a pivotal role for the speciation and cycling of trace elements in wetlands.

Arsenic is a toxic trace element, which commonly occurs as contaminant in riverine floodplains and associated wetlands affected by mining and ore processing. In this study, we investigated the solid-phase speciation of As in river floodplain soils characterized by circumneutral pH (5.7-7.1) and As concentrations of up to 40.3 g/kg caused by former mining of arsenopyrite-rich ores. Soil samples collected in the floodplain of Ogosta River (Bulgaria) were size-fractionated and subsequently analyzed using a combination of X-ray fluorescence (XRF) spectrometry, powder X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), and selective chemical extraction of poorly crystalline mineral phases. Arsenic and Fe were found to be spatially correlated and both elements were strongly enriched in the fine soil particle size fractions (<2 μm and 2-50 μm). Between 14 and 82% of the total As was citrate-ascorbate extractable. Molar As/Fe ratios were as high as 0.34 in the bulk soil extracts and increased up to 0.48 in extracts of the fine particle size fractions. Arsenic K-edge XAS spectra showed the predominance of As(V) and were well fitted with a reference spectrum of As(V) adsorbed to ferrihydrite. Whereas no As(III) was detected, considerable amounts of As(-I) were present and identified as arsenopyrite originating from the mining waste. Iron K-edge XAS revealed that in addition to As(V) adsorbed to ferrihydrite, X-ray amorphous As(V)-rich hydrous ferric oxides ("As-HFO") with a reduced number of corner-sharing FeO6 octahedra relative to ferrihydrite were the dominating secondary As species in the soils. The extremely high concentrations of As in the fine particle size fractions (up to 214 g/kg) and its association with poorly crystalline Fe(III) oxyhydroxides and As-HFO phases suggest a high As mobilization potential under both oxic and anoxic conditions, as well as a high bioaccessibility of As upon ingestion, dermal contact, or inhalation by humans or animals.

Blast furnace sludge (BFS), an industrial waste generated in pig iron production, typically contains high contents of iron and various trace metals of environmental concern, including Zn, Pb, and Cd. The chemical speciation of these metals in BFS is largely unknown. Here, we used a combination of synchrotron X-ray diffraction, micro-X-ray fluorescence, and X-ray absorption spectroscopy at the Zn K-edge for solid-phase Zn speciation in 12 BFS samples collected on a former BFS sedimentation pond site. Additionally, one fresh BFS was analyzed for comparison. We identified five major types of Zn species in the BFS, which occurred in variable amounts: (1) Zn in the octahedral sheets of phyllosilicates, (2) Zn sulfide minerals (ZnS, sphalerite, or wurtzite), (3) Zn in a KZn-ferrocyanide phase (K(2)Zn(3)[Fe(CN)(6)](2)·9H(2)O), (4) hydrozincite (Zn(5)(OH)(6)(CO(3))(2)), and (5) tetrahedrally coordinated adsorbed Zn. The minerals franklinite (ZnFe(2)O(4)) and smithsonite (ZnCO(3)) were not detected, and zincite (ZnO) was detected only in traces. The contents of ZnS were positively correlated with the total S contents of the BFS. Similarly, the abundance of the KZn-ferrocyanide phase was closely correlated with the total CN contents, with the stoichiometry suggesting this as the main cyanide phase. This study provides the first quantitative Zn speciation in BFS deposits, which is of great relevance for environmental risk assessment, the development of new methods for recovering Zn and Fe from BFS, and potential applications of BFS as sorbent materials in wastewater treatment.

Background: The isolation of highly pure copper-free methanobactin is a prerequisite for the investigation of the biogeochemical functions of this chalkophore molecule produced by methane oxidizing bacteria. Here, we report a purification method for methanobactin from Methylosinus trichosporium OB3b cultures based on reversed-phase HPLC fractionation used in combination with a previously reported resin extraction. HPLC eluent fractions of the resin extracted product were collected and characterized with UV-vis, FT-IR, and C-1s NEXAFS spectroscopy, as well as with elemental analysis and ESI-MS., Results: The results showed that numerous compounds other than methanobactin were present in the isolate obtained with resin extraction. Molar C/N ratios, mass spectrometry measurements, and UV-vis spectra indicated that methanobactin was only present in one of the HPLC fractions. On a mass basis, methanobactin carbon contributed only 32% to the total organic carbon isolated with resin extraction. Our spectroscopic results implied that besides methanobactin, the organic compounds in the resin extract comprised breakdown products of methanobactin as well as polysaccharide-like substances., Conclusion: Our results demonstrate that a purification step is indispensable in addition to resin extraction in order to obtain pure methanobactin. The proposed HPLC purification procedure is suitable for semi-preparative work and provides copper-free methanobactin.

The long-term speciation of Zn in contaminated soils is strongly influenced by soil pH, clay, and organic matter content as well as Zn loading. In addition, the type of Zn-bearing contaminant entering the soil may influence the subsequent formation of pedogenic Zn species, but systematic studies on such effects are currently lacking. We therefore conducted a soil incubation study in which four soils, ranging from strongly acidic to calcareous, were spiked with 2000 mg/kg Zn using either ZnO (zincite) or ZnS (sphalerite) as the contamination source. The soils were incubated under aerated conditions in moist state for up to four years. The extractability and speciation of Zn were assessed after one, two, and four years using extractions with 0.01 M CaCl(2) and Zn K-edge X-ray absorption fine structure (XAFS) spectroscopy, respectively. After four years, more than 90% of the added ZnO were dissolved in all soils, with the fastest dissolution occurring in the acidic soils. Contamination with ZnO favored the formation of Zn-bearing layered double hydroxides (LDH), even in acidic soils, and to a lesser degree Zn-phyllosilicates and adsorbed Zn species. This was explained by locally elevated pH and high Zn concentrations around dissolving ZnO particles. Except for the calcareous soil, ZnS dissolved more slowly than ZnO, reaching only 26 to 75% of the added ZnS after four years. ZnS dissolved more slowly in the two acidic soils than in the near-neutral and the calcareous soil. Also, the resulting Zn speciation was markedly different between these two pairs of soils: Whereas Zn bound to hydroxy-interlayered clay minerals (HIM) and octahedrally coordinated Zn sorption complexes prevailed in the two acidic soils, Zn speciation in the neutral and the calcareous soil was dominated by Zn-LDH and tetrahedrally coordinated inner-sphere Zn complexes. Our results show that the type of Zn-bearing contaminant phase can have a significant influence on the formation of pedogenic Zn species in soils. Important factors include the rate of Zn release from the contaminant phases and effects of the contaminant phase on bulk soil properties and on local chemical conditions around weathering contaminant particles.

We studied the fractionation of zinc (Zn) in 49 contaminated soils as influenced by Zn content and soil properties using a seven-step sequential extraction procedure (F1: NH4NO3; F2: NH4-acetate, pH 6; F3: NH3OHCl, pH 6; F4: NH4-EDTA, pH 4.6; F5: NH4-oxalate, pH 3; F6: NH4-oxalate/ascorbic acid, pH 3; F7: residual). The soils had developed from different geologic materials and covered a wide range in soil pH (4.0-7.3), organic C content (9.3-102 g kg(-1)), and clay content (38-451 g kg(-1)). Input of aqueous Zn with runoff water from electricity towers during 26 to 74 yr resulted in total soil Zn contents of 3.8 to 460 mmol kg(-1). In acidic soils (n = 24; pH <6.0), Zn was mainly found in the mobile fraction (F1) and the last two fractions (F6 and F7). In neutral soils (n = 25; pH > or =6.0), most Zn was extracted in the mobilizable fraction (F2) and the intermediate fractions (F4 and F5). The extractability of Zn increased with increasing Zn contamination of the soils. The sum of mobile (F1) and mobilizable (F2) Zn was independent of soil pH, the ratio of Zn in F1 over F1+F2 plotted against soil pH, exhibited the typical shape of a pH sorption edge and markedly increased from pH 6 to pH 5, reflecting the increasing lability of mobilizable Zn with decreasing soil pH. In conclusion, the extractability of Zn from soils contaminated with aqueous Zn after decades of aging under field conditions systematically varied with soil pH and Zn content. The same trends are expected to apply to aqueous Zn released from decomposing Zn-bearing contaminants, such as sewage sludge or smelter slag. The systematic trends in Zn fractionation with varying soil pH and Zn content indicate the paramount effect of these two factors on molecular scale Zn speciation. Further research is required to characterize the link between the fractionation and speciation of Zn and to determine how Zn loading and soil physicochemical properties affect Zn speciation in soils.

We investigated the effect of 4 yr of aging of a noncalcareous soil contaminated with filter dust from a brass foundry (80% w/w ZnO, 15% w/w Cu0.6Zn0.4) on the chemical extractability of Zn and Cu and their uptake by barley (Hordeum vulgare L.), pea (Pisum sativum L.), and sunflower (Helianthus annus L.). Pot experiments were conducted with the freshly contaminated soil (2250 mg kg-1 Zn; 503 mg kg-1 Cu), with the contaminated soil aged for 4 yr in the field (1811 mg kg-1 Zn; 385 mg kg-1 Cu), and with the uncontaminated control soil (136 mg kg-1 Zn; 32 mg kg-1 Cu). In comparison with the uncontaminated soil, the growth of barley and pea was clearly reduced in both contaminated soils, while toxicity symptoms did not systematically vary from the freshly contaminated to the 4 yr aged soil. The sunflower did not grow in the contaminated soils. The slow oxidative dissolution of the brass platelets led to an increase in the solubility and the plant uptake of Cu from the freshly contaminated to the 4 yr aged soil. In an earlier study, we found that the fine-grained ZnO dissolved in the field soil within 9 mo and that about half of the released Zn was incorporated into a layered double hydroxide phase and about half was adsorbed to the soil matrix. These changes in Zn speciation did not lead to a reduction of the Zn contents in the shoots and roots of barley and pea grown in the aged soil as compared with the freshly contaminated soil.

Heavy metals in soils may adversely affect environmental quality. In this study, we investigated the release of Zn, Cd, Pb, and Cu from four contaminated soils by column leaching and single and sequential batch extractions. Homogeneously packed soil columns were leached with 67 mL/g 10(-2) M CaCl2 to investigate the exchangeable metal pool and subsequently with 1400 mL/g 10(-2) M CaCl2 adjusted to pH 3 to study the potential of metal release in response to soil acidification. In two noncalcareous soils (pH 5.7 and 5.1), exchange by Ca resulted in pronounced release peaks for Zn and Cd that were coupled to the exchange of Mg by Ca, and 40 to 70% of total Zn and Cd contents were rapidly mobilized. These amounts compared well with exchangeable pools determined in single and sequential batch extractions. In two soils with near-neutral pH, the effluent concentrations of Zn and Cd were several orders of magnitude lower and no pronounced elution peaks were observed. This behavior was also observed for Cu and Pb in all four soils. When the soils were leached at pH 3, the column effluent patterns reflected the coupling of CaCO3 dissolution (if present) and other proton buffering reactions, proton-induced metal release, and metal-specific readsorption within the soil column. Varying the flow rate by a factor of five had only minor effects on the release patterns. Overall, Ca exchange and subsequent acidification to pH 3 removed between 65 and 90% of total Zn, Cd, Pb, and Cu from the four contaminated soils.

Recent spectroscopic studies have demonstrated the formation of layered double hydroxides (LDH) and phyllosilicates upon sorption of Zn2+, Ni2+, and Co2+ to clay minerals and aluminum oxides at neutral to alkaline pH and at relatively high initial metal concentrations (>1 mM). The intention of the present study was to investigate whether such phases also form in soil under slightly acidic conditions and at lower metal concentrations. Columns packed with a loamy soil were percolated with aqueous solutions containing 0.1 or 0.2 mM Zn, Ni, Co, and Cd in a 10 mM CaCl2 background at pH 6.5. Metal breakthrough curves indicated a rapid initial sorption step, resulting in retarded breakthrough fronts, followed by further slow metal retention during the entire loading period of 42 days (7000 pore volumes). Total metal sorption and the contribution of slow sorption processes decreased in the order Zn > Ni > Co > Cd. Leaching the reacted soil with 10 mM CaCl2 at pH 6.5 remobilized 8% of the total retained Zn, 15% of Ni, 21% of Co, and 77% of Cd. Subsequent leaching with acidified influent (pH 3.0) remobilized most of the remaining metals. X-ray absorption fine-structure (XAFS) spectroscopy revealed that slow Zn sorption was due to the formation of a Zn-Al LDH precipitate. Although Ni, Co, and Cd concentrations were too low for XAFS analysis, their leaching patterns suggest that part of Ni and Co were also incorporated in solid phases, while most sorbed Cd was still present as exchangeable sorption complex after 42 days. A small but significant percentage of the sorbed metals (2-5%) remained in the soil, even after leaching with more than 3000 pore volumes at pH 3.0, which may suggest micropore diffusion or incorporation into more stable mineral phases.

The transport and deposition dynamics of hematite (alpha-Fe(2)O(3)) colloids in packed quartz sand media are investigated. Column transport experiments were carried out at various solution ionic strengths, colloid concentrations, and flow velocities. A colloid transport model was proposed that includes the dynamics of blocking as well as multilayer deposition that takes place at high ionic strengths where particle-particle interactions are favorable. Blocking dynamics in the model are described by either Langmuirian adsorption (LA) or random sequential adsorption (RSA). Two important model parameters-the particle-matrix collision efficiency and the ionic strength dependent blocking (excluded area) parameter-are estimated from the colloid breakthrough curves using a nonlinear optimization procedure. The collision (attachment) efficiency for particle-particle interactions, on the other hand, was determined independently from colloid aggregation rate measurements. At very low ionic strength, only monolayer deposition is observed and the RSA model gives a better description of the experimental data than the LA model. At higher ionic strengths, multilayer deposition becomes significant and both models yield comparable results. Calculated maximum surface coverages at low ionic strengths were in good agreement with experimentally observed values obtained by scanning electron microscopy. Copyright 2000 Academic Press.