Genomic surveillance for antimicrobial resistance - a One Health perspective.

Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.

Genomic analysis of diverse environmental Acinetobacter isolates identifies plasmids, antibiotic resistance genes, and capsular polysaccharides shared with clinical strains.

Acinetobacter baumannii, an important pathogen known for its widespread antibiotic resistance, has been the focus of extensive research within its genus, primarily involving clinical isolates. Consequently, data on environmental A. baumannii and other Acinetobacter species remain limited. Here, we utilized Illumina and Nanopore sequencing to analyze the genomes of 10 Acinetobacter isolates representing 6 different species sourced from aquatic environments in South Australia. All 10 isolates were phylogenetically distinct compared to clinical and other non-clinical Acinetobacter strains, often tens of thousands of single-nucleotide polymorphisms from their nearest neighbors. Despite the genetic divergence, we identified pdif modules (sections of mobilized DNA) carrying clinically important antimicrobial resistance genes in species other than A. baumannii, including carbapenemase oxa58, tetracycline resistance gene tet(39), and macrolide resistance genes msr(E)-mph(E). These pdif modules were located on plasmids with high sequence identity to those circulating in globally distributed A. baumannii ST1 and ST2 clones. The environmental A. baumannii isolate characterized here (SAAb472; ST350) did not possess any native plasmids; however, it could capture two clinically important plasmids (pRAY and pACICU2) with high transfer frequencies. Furthermore, A. baumannii SAAb472 possessed virulence genes and a capsular polysaccharide type analogous to clinical strains. Our findings highlight the potential for environmental Acinetobacter species to acquire and disseminate clinically important antimicrobial resistance genes, underscoring the need for further research into the ecology and evolution of this important genus.IMPORTANCEAntimicrobial resistance (AMR) is a global threat to human, animal, and environmental health. Studying AMR in environmental bacteria is crucial to understand the emergence and dissemination of resistance genes and pathogens, and to identify potential reservoirs and transmission routes. This study provides novel insights into the genomic diversity and AMR potential of environmental Acinetobacter species. By comparing the genomes of aquatic Acinetobacter isolates with clinical and non-clinical strains, we revealed that they are highly divergent yet carry pdif modules that encode resistance to antibiotics commonly used in clinical settings. We also demonstrated that an environmental A. baumannii isolate can acquire clinically relevant plasmids and carries virulence factors similar to those of hospital-associated strains. These findings suggest that environmental Acinetobacter species may serve as reservoirs and vectors of clinically important genes. Consequently, further research is warranted to comprehensively understand the ecology and evolution of this genus.

Comparison of kits for SARS-CoV-2 extraction in liquid and passive samples.

Effective extraction and detection of viral nucleic acids from sewage are fundamental components of a successful SARS-CoV-2 sewage surveillance programme. As there is no standard method employed in sewage surveillance, understanding the performance of different extraction kits in the recovery of SARS-CoV-2 and the impact that PCR inhibitors have on quantification is essential to minimize data discrepancies caused by sample extraction. Three commercial nucleic acid extraction kits: the RNeasy PowerSoil Total RNA Kit (PS), the RNeasy PowerMicrobiome Kit (PMB), and the MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit (MM), with minor modifications, were evaluated. Their efficacy in recovering viral ribonucleic acid and removal of PCR inhibitors was assessed using two South Australian wastewater matrices-one from a major metropolitan site and one from a regional centre. Both had SARS-CoV-2 present due to active COVID-19 cases in these communities. Overall, the MM kit had a higher recovery of SARS-CoV-2 from the samples tested, followed by PMB and PS. The PMB kit performance was strongly influenced by the sample matrix when compared to the MM kit. It is recommended to assess the performance of extraction kits using different local wastewater matrices to ensure the accuracy and reliability of monitoring results to avoid false reporting.

Genomic Analysis of Carbapenem-Resistant Comamonas in Water Matrices: Implications for Public Health and Wastewater Treatments.

Comamonas spp. are Gram-negative bacteria that catabolize a wide range of organic and inorganic substrates. Comamonas spp. are abundant in aquatic and soil environments, including wastewater, and can cause opportunistic infections in humans. Because of their potential in wastewater bioaugmentation and bioremediation strategies, the identification of Comamonas species harboring genes encoding carbapenemases and other clinically important antibiotic resistance genes warrant further investigation. Here, we present an analysis of 39 whole-genome sequences comprising three Comamonas species from aquatic environments in South Australia that were recovered on media supplemented with carbapenems. The analysis includes a detailed description of 33 Comamonas denitrificans isolates, some of which carried chromosomally acquired blaGES-5, blaOXA, and aminoglycoside resistance (aadA) genes located on putative genomic islands (GIs). All blaGES-5- and blaOXA-containing GIs appear to be unique to this Australian collection of C. denitrificans. Notably, most open reading frames (ORFs) within the GIs, including all antimicrobial resistance (AMR) genes, had adjacent attC sites, indicating that these ORFs are mobile gene cassettes. One C. denitrificans isolate carried an IncP-1 plasmid with genes involved in xenobiotic degradation and response to oxidative stress. Our assessment of the sequences highlights the very distant nature of C. denitrificans to the other Comamonas species and its apparent disposition to acquire antimicrobial resistance genes on putative genomic islands. IMPORTANCE Antimicrobial resistance (AMR) poses a global public health threat, and the increase in resistance to "last-resort drugs," such as carbapenems, is alarming. Wastewater has been flagged as a hot spot for AMR evolution. Comamonas spp. are among the most common bacteria in wastewater and play a role in its bioaugmentation. While the ability of Comamonas species to catabolize a wide range of organic and inorganic substrates is well documented, some species are also opportunistic pathogens. However, data regarding AMR in Comamonas spp. are limited. Here, through the genomic analyses of 39 carbapenem-resistant Comamonas isolates, we make several key observations, including the identification of a subset of C. denitrificans isolates that harbored genomic islands encoding carbapenemase blaGES-5 or extended-spectrum ß-lactamase blaOXA alleles. Given the importance of Comamonas species in potential wastewater bioaugmentation and bioremediation strategies, as well as their status as emerging pathogens, the acquisition of critically important antibiotic resistance genes on genomic islands warrants future monitoring.

Assessing the Lability and Environmental Mobility of Organically Bound Copper by Stable Isotope Dilution.

The environmental mobility of Cu and therefore its potential toxicity are closely linked to its attachment to natural organic matter (NOM). Geochemical models assume full lability of metals bound to NOM, especially under strong oxidizing conditions, which often leads to an overestimation of the lability of soil metals. Stable isotope dilution (SID) has been successfully applied to estimate the labile (isotopically exchangeable) pool of soil metals. However, its application to study the lability of NOM-Cu required development of a robust separation and detection approach so that free Cu ions can be discriminated from (the also soluble) NOM-Cu. We developed a SID protocol (with enriched 65Cu) to quantify the labile pool of NOM-Cu using size exclusion chromatography coupled to a UV detector (for the identification of different NOM molecular weights) and ICP-MS (for 65Cu/63Cu ratio measurement). The Cu isotopic-exchange technique was first characterized and verified using standard NOM (SR-NOM) before applying the developed technique to an "organic-rich" podzol soil extract. The developed protocol indicated that, in contrast to the common knowledge, significant proportions of SR-NOM-Cu (25%) and soil organic-Cu (55%) were not labile, i.e., permanently locked into inaccessible organic structures. These findings need to be considered in defining Cu interactions with the reactive pool of NOM using geochemical models and risk evaluation protocols in which complexed Cu has always been implicitly assumed to be fully labile and exchangeable with free Cu ions.

Maintaining a social license to operate for wastewater-based monitoring: The case of managing infectious disease and the COVID-19 pandemic.

Wastewater monitoring as a public health tool is well-established and the SARS-CoV-2 (COVID-19) pandemic has seen its widespread uptake. Given the significant potential of wastewater monitoring as a public health surveillance and decision support tool, it is important to understand what measures are required to allow the long-term benefits of wastewater monitoring to be fully realized, including how to establish and/or maintain public support. The potential for positive SARS-CoV-2 detections to trigger enforced, community-wide public health interventions (e.g., lockdowns and other impacts on civil liberties) further emphasises the need to better understand the role of public engagement in successful wastewater-based monitoring programs. This paper systematically reviews the processes of building and maintaining the social license to operate wastewater monitoring. We specifically explore the relationship between different stakeholder communities and highlight the information and actions that are required to establish a social license to operate and then prevent its loss. The paper adds to the literature on social license to operate by extending its application to new domains and offers a dynamic model of social license to help guide the agenda for researcher and practitioner communities.

Neutral electrolyzed oxidizing water is effective for pre-harvest decontamination of fresh produce.

Pre-harvest sanitization of irrigation water has potential for reducing pathogen contamination of fresh produce. We compared the sanitizing effects of irrigation water containing neutral electrolyzed oxidizing water (EOW) or sodium hypochlorite (NaClO) on pre-harvest lettuce and baby spinach leaves artificially contaminated with a mixture of Escherichia coli, Salmonella Enteritidis and Listeria innocua (~1 × 108 colony-forming units/mL each resuspended in water containing 100 mg/L dissolved organic carbon, simulating a splash-back scenario from contaminated soil/manure). The microbial load and leaf quality were assessed over 7 days, and post-harvest shelf life evaluated for 10 days. Irrigation with water containing EOW or NaClO at 50 mg/L free chlorine significantly reduced the inoculated bacterial load by ≥ 1.5 log10, whereas tap water irrigation reduced the inoculated bacterial load by an average of 0.5 log10, when compared with untreated leaves. There were no visual effects of EOW or tap water irrigation on baby spinach or lettuce leaf surfaces pre- or post-harvest, whereas there were obvious negative effects of NaClO irrigation on leaf appearance for both plants, including severe necrotic zones and yellowing/browning of leaves. Therefore, EOW could serve as a viable alternative to chemical-based sanitizers for pre-harvest disinfection of minimally processed vegetables.

Optimising the foliar uptake of zinc oxide nanoparticles: Do leaf surface properties and particle coating affect absorption?

Foliar absorption of zinc (Zn) is limited by several barriers, the first of which is the leaf cuticle. In this study, we investigated the absorption of Zn from Zn oxide nanoparticles (ZnO-NPs) in wheat (Triticum aestivum cv Gladius) and sunflower (Helianthus annuus cv Hyoleic 41) to determine the importance of NP surface coating for Zn absorption. Fourier transform infrared (FTIR) spectroscopy showed a higher polysaccharide content in the wheat cuticle than sunflower, indicated by a more pronounced glycosidic bond at 1020 cm-1 , but wax and cutin content were similar. Scanning electron microscopy (SEM) revealed that trichome density was twice as high in wheat (3600 ± 900 cm-2 ) as in sunflower (1600 cm-2 ) and stomatal density four times higher in sunflower (6400 ± 800 cm-2 in wheat and 22 900 cm-2 in sunflower). Suspensions of ZnO-NPs with coatings of different hydrophobicity were applied to leaves to compare Zn absorption using X-ray fluorescence microscopy (XFM) and inductively coupled plasma mass spectroscopy (ICP-MS). Absorption of Zn was similar between wheat and sunflower when Zn was applied at 1000 mg Zn l-1 , but much less Zn was absorbed from all ZnO products than from soluble Zn fertiliser. Particle coating did not affect Zn absorption, but it may facilitate particle adhesion to leaves, providing a longer-term source of resupply of Zn ions to the leaves. Differences in leaf surface characteristics did not affect Zn absorption, indicating that the cuticle is the main pathway of absorption under these conditions.

Foliar application of zinc sulphate and zinc EDTA to wheat leaves: differences in mobility, distribution, and speciation.

Foliar application of zinc (Zn) to crops is an effective way to increase the grain concentration of Zn. However, the development of more efficient foliar Zn fertilizers is limited by a lack of knowledge regarding the distribution, mobility, and speciation of Zn in leaves once it is taken up by the plant. We performed an experiment using radiolabelled Zn (65Zn), and in situ time-resolved elemental imaging using synchrotron X-ray fluorescence microscopy (XFM), to investigate the behaviour of two commonly used Zn foliar fertilizers (Zn sulphate and ZnEDTA) in wheat (Triticum aestivum) leaves. Both experiments showed that Zn had limited mobility in leaves, moving <25 mm from the application point after 24 h. Although limited, the translocation of Zn occurred quickly for both treatments; moving more between 3 h and 12 h after application than between 12 h and 24 h. Speciation analysis using synchrotron-based X-ray absorption near-edge structure (XANES) showed that ZnEDTA was in fact taken up in chelated form and not as ionic Zn (Zn2+). The XANES data also showed that Zn, from both treatments, was then complexed by ligands in the leaf (e.g. phytate and citrate), potentially in response to localized Zn toxicity. The results of the present study provide important insights into the behaviour of commonly used foliar-applied Zn fertilizers, and can be used to optimize current fertilization strategies and contribute to the development of more efficient foliar Zn fertilizers.

Silver Toxicity Thresholds for Multiple Soil Microbial Biomarkers.

Material flow analysis shows that soil is a key repository for silver (Ag) from (nano)silver-functionalized consumer products, but the potential effects of Ag toxicity, via Ag+ release, on soil microbial communities and their ecosystem services remains largely unknown. We examined the responses of multiple microbial biomarkers to increasing Ag+ doses (nine concentrations, 0-2000 mg kg-1) in nine different soils representing a wide range of soil properties. Analyses included substrate-induced microbial respiration, nine different soil enzyme activities, and quantification of bacterial 16S-rRNA (SSU) and fungal intergenic spacer (ITS) copies. The resulting half-maximal effective concentrations (EC50) for Ag ranged from ∼1 to >500 mg kg -1 and showed soil-specific responses, including some hormesis-type responses. Carbon cycle-associated enzyme activities (e.g., cellobiohydrolase, xylosidase, and α/ß-glucosidase) responded similarly to Ag. Sulfatase and leucine-aminopeptidase activities (linked to the sulfur and nitrogen cycles) were the most sensitive to Ag. Total organic carbon, and to a lesser extent pH, were identified as potentially useful response predictors, but only for some biomarkers; this reflects the complexity of soil Ag chemistry. Our results show Ag toxicity is highly dependent on soil characteristics and the specific microbial parameter under investigation, but end point redundancies also indicated that representative parameters for key microbial functions can be identified for risk assessment purposes. Sulfatase activity may be an important Ag toxicity biomarker; its response was highly sensitive and not correlated with that of other biomarkers.

Temporal Evolution of Copper Distribution and Speciation in Roots of Triticum aestivum Exposed to CuO, Cu(OH)2, and CuS Nanoparticles.

Utilization of nanoparticles (NP) in agriculture as fertilizers or pesticides requires an understanding of the NP properties influencing their interactions with plant roots. To evaluate the influence of the solubility of Cu-based NP on Cu uptake and NP association with plant roots, wheat seedlings were hydroponically exposed to 1 mg/L of Cu NPs with different solubilities [CuO, CuS, and Cu(OH)2] for 1 h then transferred to a Cu-free medium for 48 h. Fresh, hydrated roots were analyzed using micro X-ray fluorescence (µ-XRF) and imaging fluorescence X-ray absorption near edge spectroscopy (XANES imaging) to provide laterally resolved distribution and speciation of Cu in roots. Higher solubility Cu(OH)2 NPs provided more uptake of Cu after 1 h of exposure, but the lower solubility materials (CuO and CuS) were more persistent on the roots and continued to deliver Cu to plant leaves over the 48 h depuration period. These results demonstrate that NPs, by associating to the roots, have the potential to play a role in slowly providing micronutrients to plants. Thus, tuning the solubility of NPs may provide a long-term slow delivery of micronutrients to plants and provide important information for understanding mechanisms responsible for plant uptake, transformation, and translocation of NPs.

Impact of Surface Charge on Cerium Oxide Nanoparticle Uptake and Translocation by Wheat (Triticum aestivum).

Nanoparticle (NP) physiochemical properties, including surface charge, affect cellular uptake, translocation, and tissue localization. To evaluate the influence of surface charge on NP uptake by plants, wheat seedlings were hydroponically exposed to 20 mg/L of ∼4 nm CeO2 NPs functionalized with positively charged, negatively charged, and neutral dextran coatings. Fresh, hydrated roots and leaves were analyzed at various time points over 34 h using fluorescence X-ray absorption near-edge spectroscopy to provide laterally resolved spatial distribution and speciation of Ce. A 15-20% reduction from Ce(IV) to Ce(III) was observed in both roots and leaves, independent of NP surface charge. Because of its higher affinity with negatively charged cell walls, CeO2(+) NPs adhered to the plant roots the strongest. After 34 h, CeO2(-), and CeO2(0) NP exposed plants had higher Ce leaf concentrations than the plants exposed to CeO2(+) NPs. Whereas Ce was found mostly in the leaf veins of the CeO2(-) NP exposed plant, Ce was found in clusters in the nonvascular leaf tissue of the CeO2(0) NP exposed plant. These results provide important information for understanding mechanisms responsible for plant uptake, transformation, and translocation of NPs, and suggest that NP coatings can be designed to target NPs to specific parts of plants.

Application of Synchrotron Radiation-based Methods for Environmental Biogeochemistry: Introduction to the Special Section.

To understand the biogeochemistry of nutrients and contaminants in environmental media, their speciation and behavior under different conditions and at multiple scales must be determined. Synchrotron radiation-based X-ray techniques allow scientists to elucidate the underlying mechanisms responsible for nutrient and contaminant mobility, bioavailability, and behavior. The continuous improvement of synchrotron light sources and X-ray beamlines around the world has led to a profound transformation in the field of environmental biogeochemistry and, subsequently, to significant scientific breakthroughs. Following this introductory paper, this special collection includes 10 papers that either present targeted reviews of recent advancements in spectroscopic methods that are applicable to environmental biogeochemistry or describe original research studies conducted on complex environmental samples that have been significantly enhanced by incorporating synchrotron radiation-based X-ray technique(s). We believe that the current focus on improving the speciation of ultra-dilute elements in environmental media through the ongoing optimization of synchrotron technologies (e.g., brighter light sources, improved monochromators, more efficient detectors) will help to significantly push back the frontiers of environmental biogeochemistry research. As many of the relevant techniques produce extremely large datasets, we also identify ongoing improvements in data processing and analysis (e.g., software improvements and harmonization of analytical methods) as a significant requirement for environmental biogeochemists to maximize the information that can be gained using these powerful tools.

Synchrotron-based X-Ray Approaches for Examining Toxic Trace Metal(loid)s in Soil-Plant Systems.

Elevated levels of trace metal(loid)s reduce plant growth, both in soils contaminated by industrial activities and in acid agricultural soils. Although the adverse effects of trace metal(loid)s have long been recognized, there remains much unknown both about their behavior in soils, their toxicity to plants, and the mechanisms that plants use to tolerate elevated concentrations. Synchrotron-based approaches are being utilized increasingly in soil-plant systems to examine toxic metal(loid)s. In the present review, brief consideration is given to the theory of synchrotron radiation. Thereafter, we review the use of synchrotron-based approaches for the examination of various trace metal(loid)s in soil-plant systems, including aluminum, chromium, manganese, cobalt, nickel, copper, zinc, arsenic, selenium, and cadmium. Within the context of this review, X-ray absorption spectroscopy (XAS) and X-ray fluorescence microscopy (µ-XRF) are of particular interest. These techniques can provide in situ analyses of the distribution and speciation of metal(loid)s in soil-plant systems. The information presented here serves not only to understand the behavior of trace metals in soil-plant systems, but also to provide examples of the potential applications of synchrotron radiation that can be used to advantage in other studies.

Aging of Dissolved Copper and Copper-based Nanoparticles in Five Different Soils: Short-term Kinetics vs. Long-term Fate.

With the growing availability and use of copper-based nanomaterials (Cu-NMs), there is increasing concern regarding their release and potential impact on the environment. In this study, the short-term (≤5 d) aging profile and the long-term (135 d) speciation of dissolved Cu, copper oxide, and copper sulfide nanoparticles (CuO-NPs and CuS-NPs) were investigated in five different soils using X-ray absorption spectroscopy. Soil pH was found to strongly influence the short-term chemistry of the Cu-NMs added at 100 mg kg above background. Low pH soils promoted rapid dissolution of CuO-NPs that effectively aligned their behavior to that of dissolved Cu within 3 d. In higher pH soils, CuO-NPs persisted longer due to slower dissolution in the soil and resulted in contrasting short-term speciation compared with dissolved Cu, which formed copper hydroxides and carbonates that were reflective of the soil chemistry. Organic matter appeared to slow the dissolution process, but in the long term, the speciation of Cu added as dissolved Cu, CuO-NPs, and CuS-NPs were found to be same for each soil. The results imply that, in the short term, Cu-NMs may exhibit unique behavior in alkaline soils compared with their conventional forms (e.g., in the event of an adverse leaching event), but in the long term (≥135 d), their fates are dictated by the soil properties, are independent of the initial Cu form, and are likely to present minimal risk of nanospecific Cu-NM impact in the soil environment for the concentration studied here.

Element distribution and iron speciation in mature wheat grains (Triticum aestivum L.) using synchrotron X-ray fluorescence microscopy mapping and X-ray absorption near-edge structure (XANES) imaging.

Several studies have suggested that the majority of iron (Fe) and zinc (Zn) in wheat grains are associated with phytate, but a nuanced approach to unravel important tissue-level variation in element speciation within the grain is lacking. Here, we present spatially resolved Fe-speciation data obtained directly from different grain tissues using the newly developed synchrotron-based technique of X-ray absorption near-edge spectroscopy imaging, coupling this with high-definition µ-X-ray fluorescence microscopy to map the co-localization of essential elements. In the aleurone, phosphorus (P) is co-localized with Fe and Zn, and X-ray absorption near-edge structure imaging confirmed that Fe is chelated by phytate in this tissue layer. In the crease tissues, Zn is also positively related to P distribution, albeit less so than in the aleurone. Speciation analysis suggests that Fe is bound to nicotianamine rather than phytate in the nucellar projection, and that more complex Fe structures may also be present. In the embryo, high Zn concentrations are present in the root and shoot primordium, co-occurring with sulfur and presumably bound to thiol groups. Overall, Fe is mainly concentrated in the scutellum and co-localized with P. This high resolution imaging and speciation analysis reveals the complexity of the physiological processes responsible for element accumulation and bioaccessibility.

Novel application of X-ray fluorescence microscopy (XFM) for the non-destructive micro-elemental analysis of natural mineral pigments on Aboriginal Australian objects.

This manuscript presents the first non-destructive synchrotron micro-X-ray fluorescence study of natural mineral pigments on Aboriginal Australian objects. Our results demonstrate the advantage of XFM (X-ray fluorescence microscopy) of Aboriginal Australian objects for optimum sensitivity, elemental analysis, micron-resolution mapping of pigment areas and the method also has the advantage of being non-destructive to the cultural heritage objects. Estimates of pigment thickness can be calculated. In addition, based on the elemental maps of the pigments, further conclusions can be drawn on the composition and mixtures and uses of natural mineral pigments and whether the objects were made using traditional or modern methods and materials. This manuscript highlights the results of this first application of XFM to investigate complex mineral pigments used on Aboriginal Australian objects.

In situ chemical transformations of silver nanoparticles along the water-sediment continuum.

In order to accurately assess the potential environmental risk posed by silver nanoparticles (Ag-NPs), their transformation and fate must be investigated in natural systems. This has proven to be very challenging due to the difficulties encountered in retrieving/analyzing NPs dispersed in complex and heterogeneous environmental matrices at relevant (i.e., low) concentrations. In this study, we overcame this challenge by immobilizing functionalized Ag-NPs onto plasma polymerized solid substrates to form "nano in situ deployment devices" (nIDDs). This method allowed us to retrieve and analyze the Ag-NPs after 48 h of direct exposure in freshwater-sediment and saltwater-sediment environments. The type and extent of Ag-NPs transformation was expected to vary along the water-sediment continuum as sediments typically contain steep gradients in solute concentrations and redox potential. To trace the distribution of redox sensitive elements (e.g., Fe, Mn), Diffusive Equilibration in Thin-films (DET) devices were inserted into the sediments alongside the nIDDs. Chemical transformation of the immobilized Ag-NPs across the water-sediment continuum was investigated after retrieval by synchrotron radiation X-ray Absorption Spectroscopy. Linear combination fitting of Ag K-edge X-ray absorption spectra indicated that the chemical transformations of Ag-NPs in both freshwater and saltwater sediments were strongly affected by the redox conditions over the investigated range. Silver bound to reduced sulfur was the principal product of Ag-NP transformations but different extents of transformation were observed for Ag-NPs exposed to different depths in the sediment. These field results add important insights about the transformation of Ag-NPs in heterogeneous environments.

In Situ Fixation of Metal(loid)s in Contaminated Soils: A Comparison of Conventional, Opportunistic, and Engineered Soil Amendments.

This study aimed to assess and compare the in vitro and in vivo bioaccessibility/bioavailability of As and Pb in a mining contaminated soil (As, 2267 mg kg(-1); Pb, 1126 mg kg(-1)), after the addition of conventional (phosphoric acid), opportunistic [water treatment residues (WTRs)], and engineered [nano- and microscale zero valent iron (ZVI)] amendments. Phosphoric acid was the only amendment that could significantly decrease Pb bioaccessibility with respect to untreated soil (41 and 47% in the gastric phase and 2.1 and 8.1% in the intestinal phases, respectively), giving treatment effect ratios (TERs, the bioaccessibility in the amended soil divided by the bioaccessibility in the untreated soil) of 0.25 and 0.87 in the gastric and intestinal phase, respectively. The in vivo bioavailability of Pb decreased in the phosphate treatment relative to the untreated soil (6 and 24%, respectively), and also in the Fe WTR 2% (12%) and nZVI-2 (13%) treatments. The ZVI amendments caused a decrease in As bioaccessibility, with the greatest decrease in the nZVI2-treated soil (TERs of 0.59 and 0.64 in the gastric and intestinal phases, respectively). Arsenic X-ray absorption near-edge spectroscopy analysis indicated that most of the As in the untreated soil was present as As(V) associated with Fe mineral phases, whereas in the treated soil, the proportion of arsenosiderite increased. Arsenite was present only as a minor species (3-5%) in the treated soils, with the exception of an nZVI treatment [∼14% of As(III)], suggesting a partial reduction of As(V) to As(III) caused by nZVI oxidation.

Impacts of coprophagic foraging behaviour on the avian gut microbiome.

Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.