Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land.

Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.

Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils.

Arctic soils are marked by cryoturbic features, which impact soil-atmosphere methane (CH4 ) dynamics vital to global climate regulation. Cryoturbic diapirism alters C/N chemistry within frost boils by introducing soluble organic carbon and nutrients, potentially influencing microbial CH4 oxidation. CH4 oxidation in soils, however, requires a spatio-temporal convergence of ecological factors to occur. Spatial delineation of microbial activity with respect to these key microbial and biogeochemical factors at relevant scales is experimentally challenging in inherently complex and heterogeneous natural soil matrices. This work aims to overcome this barrier by spatially linking microbial CH4 oxidation with C/N chemistry and metagenomic characteristics. This is achieved by using positron-emitting radiotracers to visualize millimeter-scale active CH4 uptake areas in Arctic soils with and without diapirism. X-ray absorption spectroscopic speciation of active and inactive areas shows CH4 uptake spatially associates with greater proportions of inorganic N in diapiric frost boils. Metagenomic analyses reveal Ralstonia pickettii associates with CH4 uptake across soils along with pertinent CH4 and inorganic N metabolism associated genes. This study highlights the critical relationship between CH4 and N cycles in Arctic soils, with potential implications for better understanding future climate. Furthermore, our experimental framework presents a novel, widely applicable strategy for unraveling ecological relationships underlying greenhouse gas dynamics under global change.

The role of monodentate tetrahedral borate complexes in boric acid binding to a soil organic matter analogue.

Boron is an essential plant micronutrient responsible for several important functions. Boron availability in soils may be influenced by binding with soil organic matter (SOM), particularly with aromatic diol and polyphenol groups on SOM. The mechanism by which aromatic diols bind boron, however, remains unclear. The objective of this work is to further investigate interaction between boric acid and varying concentrations of an aromatic, polyphenolic SOM analogue (tannic acid at 5, 10 and 20 g L-1) from pH = 5-9. UV/Visible spectroscopy showed boric acid enhanced tannic acid deprotonation at pH = 7.0 and 9.0, resulting in singly deprotonated tannic acid subunits. Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) showed boric acid/tannic acid binding for all concentrations at pH = 7 and 9, whereas binding at pH = 5.0 was observed only at 20 g L-1 tannic acid. Uncomplexed boron species were not evident at pH = 9.0, but were detectable at pH = 7.0 at lower tannic acid concentrations and prevalent at pH = 5.0, qualitatively indicating binding affinity increases from pH = 5.0 to 9.0. ATR-FTIR results indicated tetrahedral coordination of boron upon complexation to tannic acid with a monodentate mechanism. These results collectively highlight a transition of solution planar boric acid to a tetrahedral, monodentate coordination with a single phenol group in tannic acid polyphenols. This contrasts with previous spectroscopic studies, which indicated bidentate tetrahedral or monodentate trigonal planar orientations prevail at aromatic diol sites. This work presents a previously unobserved boric acid coordination mechanism to an SOM analogue and, therefore, may better inform prediction and modeling of boron behavior in soils.

From the Outside in: An Overview of Positron Imaging of Plant and Soil Processes.

Positron-emitting nuclides have long been used as imaging agents in medical science to spatially trace processes non-invasively, allowing for real-time molecular imaging using low tracer concentrations. This ability to non-destructively visualize processes in real time also makes positron imaging uniquely suitable for probing various processes in plants and porous environmental media, such as soils and sediments. Here, we provide an overview of historical and current applications of positron imaging in environmental research. We highlight plant physiological research, where positron imaging has been used extensively to image dynamics of macronutrients, signalling molecules, trace elements, and contaminant metals under various conditions and perturbations. We describe how positron imaging is used in porous soils and sediments to visualize transport, flow, and microbial metabolic processes. We also address the interface between positron imaging and other imaging approaches, and present accompanying chemical analysis of labelled compounds for reviewed topics, highlighting the bridge between positron imaging and complementary techniques across scales. Finally, we discuss possible future applications of positron imaging and its potential as a nexus of interdisciplinary biogeochemical research.

Oxalate-enhanced solubility of lead (Pb) in the presence of phosphate: pH control on mineral precipitation.

Here we study the precipitation of lead (Pb)-phosphate minerals over the pH range of 4.0 to 8.0 with and without oxalate, a ubiquitous and abundant low-molecular-weight organic acid derived from plants and microorganisms in environmental matrices. In the aqueous Pb-phosphate systems, phosphate precipitated Pb efficiently, reducing the dissolved Pb concentration below 1 µM at all the tested pH values, with the minimum solubility of about 0.1 µM measured at the intermediate pH of 6.0. The measured dissolved Pb and free Pb2+ ion activity were not in agreement with predictions from generally-accepted solubility products of the Pb phosphate minerals, particularly hydroxypyromorphite [Pb5(PO4)3OH]. Discrepancies between our measured Pb phosphate solubility products and older reported values are attributed to non-ideal behavior of these minerals (incongruent dissolution) as well as uncertainties in stability constants for soluble Pb-phosphate ion pairs. The presence of equimolar levels of oxalate and phosphate resulted in up to 250-fold increase in Pb solubility at acidic pH and about a 4-fold increase at pH 7.0, due to the strong suppression of Pb phosphate precipitation by oxalate and formation of soluble Pb-oxalate complexes. At pH 4.0 and 5.0, Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) identified a Pb-oxalate mineral phase as the only precipitate despite the presence of phosphate; in the absence of oxalate, Pb hydrogen phosphate, PbHPO4, stably formed under these acidic conditions. At pH 6.0 and greater, FTIR and XRD data revealed that Pb-phosphate [Pb3(PO4)2], and hydroxypyromorphite [Pb5(PO4)3OH] to a lesser extent, were the predominant precipitates both in the absence and presence of oxalate. Therefore, oxalate did not strongly interfere with Pb-phosphate mineral formation at aqueous pH greater than 6.0 but oxalate controlled Pb solubility at acidic pH values.

Simultaneous Quantification of Electron Transfer by Carbon Matrices and Functional Groups in Pyrogenic Carbon.

Pyrogenic carbon contains redox-active functional groups and polyaromatic carbon matrices that are both capable of transferring electrons. Several techniques have been explored to characterize the individual electron transfer process of either functional groups or carbon matrices individually. However, simultaneous analysis of both processes remains challenging. Using an approach that employs a four-electrode configuration and dual-interface electron transfer detection, we distinguished the electron transfer by functional groups from the electron transfer by carbon matrices and simultaneously quantified their relative contribution to the total electron transfer to and from pyrogenic carbon. Results show that at low to intermediate pyrolysis temperatures (400-500 °C), redox cycling of functional groups is the major mechanism with a contribution of 100-78% to the total electron transfer; whereas at high temperatures (650-800 °C), direct electron transfer of carbon matrices dominates electron transfer with a contribution of 87-100%. Spectroscopic and diffraction analyses of pyrogenic carbon support the electrochemical measurements by showing a molecular-level structural transition from an enrichment in functional groups to an enrichment in nanosized graphene domains with increasing pyrolysis temperatures. The method described in this study provides a new analytical approach to separately quantify the relative importance of different electron transfer pathways in natural pyrogenic carbon and has potential applications for engineered carbon materials such as graphene oxides.

Supramolecular Association Impacts Biomolecule Adsorption onto Goethite.

Formation of biomolecule-rich supramolecular complexes in dissolved organic matter (DOM) and subsequent adsorption onto minerals is important for the development of mineral-stabilized organic matter, yet the impact of supramolecular association on interfacial behavior is seldom studied. A series of supramolecular complexes of model biomolecules (deoxyribonucleic acid (DNA) and bovine serum albumin (BSA)) are synthesized, characterized, and adsorbed onto goethite. Complexes represent 0.1 mg/mL DNA mixed with BSA concentrations from 0.05 to 0.5 mg/mL in 5 mM KCl at pH = 5.0. Circular dichroism demonstrates strong binding between DNA and BSA, with DNA saturation when (BSA) ≈ 0.4 mg/mL. Dynamic light scattering and electrophoretic mobility measurements suggest DNA-BSA binding reduces DNA-DNA electrostatic repulsion. Spectroscopic studies of DNA/BSA complex adsorption show complexation hinders coordination of DNA phosphodiester groups with goethite. Increasing BSA (≤0.4 mg/mL) in DNA/BSA complexes enhances DNA adsorption, due to reduced repulsion between adsorbed DNA helices. When (BSA) > 0.4 mg/mL, however, DNA adsorption is decreased. We hypothesize this results from blocking of surface sites by fast adsorption of BSA loosely associated with DNA/BSA complexes. We posit an additional mechanism describing multilayered architecture formation of organo-mineral associations in soil, suggesting solution interactions may represent an overlooked factor when considering mineral retention of DOM.

Structures and mechanisms in clay nanopore trapping of structurally-different fluoroquinolone antimicrobials.

Smectite clay nanoparticles are implicated in the retention of antimicrobials within soils and sediments; these clays are also inspected as drug carriers in physiological systems. Cation exchange is considered the primary adsorption mechanism of antimicrobials within smectite nanopores. However, a dual role of acid-base chemistry and adsorptive structures is speculated by recent studies. Using the prototypical smectite clay montmorillonite, we employed a combination of X-ray diffraction (XRD), nuclear magnetic resonance, attenuated total reflectance-Fourier transform infrared spectroscopy, and molecular dynamics simulations to investigate the interlayer nanopore trapping of two structurally-different fluoroquinolone (FQ) antimicrobials with similar acid-base chemistry: ciprofloxacin (a first-generation FQ) and moxifloxacin (a third-generation FQ). Greater sorption at pH 5.0 than at pH 7.0 for both FQs was consistent with cation-exchange of positively-charged species. However, the clay exhibited a near twofold higher sorption capacity for moxifloxacin than for ciprofloxacin. This difference was shown by the XRD data to be accompanied by enhanced trapping of moxifloxacin within the clay interlayers. Using the XRD-determined nanopore sizes, we performed molecular dynamics simulations of thermodynamically-favorable model adsorbates, which revealed that ciprofloxacin was adsorbed parallel to the clay surface but moxifloxacin adopted a tilted conformation across the nanopore. These conformations resulted in more slowly-exchanged than quickly-exchanged Na complexes with ciprofloxacin compared with moxifloxacin. These different Na populations were also captured by 23Na nuclear magnetic resonance. Furthermore, the simulated adsorbates uncovered different complexation interactions that were corroborated by infrared spectroscopy. Therefore, beyond acid-base chemistry, our findings imply that distinct adsorbate structures control antimicrobial trapping within clay nanopores, which can promote persistence in environmental matrices and stable delivery in biological systems.

Ironing Out Genes in the Environment: An Experimental Study of the DNA-Goethite Interface.

DNA fate in soil plays an important role in the cycling of genetic information in the environment. Adsorption onto mineral surfaces has great impact on this function. This study probes the kinetics, equilibrium behavior and bonding mechanisms associated with adsorption of DNA onto goethite, a common soil mineral. Surface sensitive ATR-FTIR and XPS approaches are applied to directly characterize the DNA-goethite interface. Adsorption kinetics follow a pseudo-first-order model, suggesting adsorption rate is surface limited. Adsorption rate constants increase with DNA concentration, ranging from 3.29 × 10-3 to 3.55 × 10-1 min-1. Equilibrium adsorption, as monitored by ATR-FTIR and XPS, follows the Langmuir model, with a high affinity of DNA for goethite observed (K = 1.25 × 103 and 9.48 × 102 mL/mg for ATR-FTIR and XPS, respectively). ATR-FTIR and XPS characterization of the structure of surface adsorbed DNA demonstrates inner-sphere coordination between backbone phosphate groups of DNA and goethite. Furthermore, adsorbed DNA retains a B-form, suggesting the DNA helix adsorbs on goethite without degradation or alteration to helical structure, despite binding of backbone phosphate groups. This work advances our understanding of the environmental behavior of DNA by characterizing the mechanism of adsorption onto a prominent soil mineral.

Kinetic and Conformational Insights of Protein Adsorption onto Montmorillonite Revealed Using in Situ ATR-FTIR/2D-COS.

Protein adsorption onto clay minerals is a process with wide-ranging impacts on the environmental cycling of nutrients and contaminants. This process is influenced by kinetic and conformational factors that are often challenging to probe in situ. This study represents an in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopic investigation of the adsorption of a model protein (bovine serum albumin (BSA)) onto a clay mineral (montmorillonite) at four concentrations (1.50, 3.75, 7.50, and 15.0 µM) under environmentally relevant conditions. At all concentrations probed, FTIR spectra show that BSA readily adsorbs onto montmorillonite. Adsorption kinetics follow an Elovich model, suggesting that primary limitations on adsorption rates are surface-related heterogeneous energetic restrictions associated with protein rearrangement and lateral protein-protein interaction. BSA adsorption onto montmorillonite fits the Langmuir model, yielding K = 5.97 × 10(5) M(-1). Deconvolution and curve fitting of the amide I band at the end of the adsorption process (∼120 min) shows a large extent of BSA unfolding upon adsorption at 1.50 µM, with extended chains and turns increasing at the expense of α-helices. At higher concentrations/surface coverages, BSA unfolding is less pronounced and a more compact structure is assumed. Two-dimensional correlation spectroscopic (2D-COS) analysis reveals three different pathways corresponding to adsorbed conformations. At 1.50 µM, adsorption increases extended chains, followed by a loss in α-helices and a subsequent increase in turns. At 3.75 µM, extended chains decrease and then aggregated strands increase and side chains decrease, followed by a decrease in turns. With 7.50 and 15.0 µM BSA, the loss of side-chain vibrations is followed by an increase in aggregated strands and a subsequent decrease in turns and extended chains. Overall, the BSA concentration and resultant surface coverage have a profound impact on the dynamics of BSA adsorption onto montmorillonite. These results enhance our understanding of the molecular-level protein dynamics and stabilization of organic matter at mineral surfaces.

ZnS nanocrystal cytotoxicity is influenced by capping agent chemical structure and duration of time in suspension.

As a result of their characteristic physical and optical properties, including their size, intense fluorescence, broad excitation, narrow emission and resistance to photobleaching, semiconductor nanocrystals are potentially useful for a variety of biological applications including molecular imaging, live-cell labeling, photodynamic therapy and targeted drug delivery. In this study, zinc sulfide (ZnS) semiconductor nanocrystals were synthesized in the 3 to 4 nm size range with selected capping agents intended to protect the nanocrystal core and increase its biological compatibility. We show that the biocompatibility of ZnS nanocrystals with primary murine splenocytes is influenced by the chemical structure of the outer capping agent on the nanocrystal. Additionally, the cytotoxicity of ZnS nanocrystals increases markedly as a function of time spent in suspension in phosphate-buffered saline (PBS). These data suggest that the potential therapeutic and/or biological use of ZnS nanocrystals is inherently dependent upon the proper choice of capping agent, as well as the conditions of nanocrystal preparation and storage.