Domestic plant food loss and waste in the United States: Environmental footprints and mitigation strategies.

The United States (U.S.) aims to reduce half of food loss and waste (FLW) by 2030. To achieve this goal, the public, academic, and political attentions on FLW have been increasing, and a series of actions have been implemented. However, the actions lack consideration on the categorical priority of FLW mitigation in relation to environmental footprints. In this article, we compare the FLW of three main plant food categories (i.e., grains, vegetables, and fruits) and their water and carbon footprints during 1970-2017. The vegetable FLW doubled during the period, reaching 3.39 × 1010 kg in 2017, which was 5- and 2-fold higher than the FLW of grains and fruits, respectively. The FLW of vegetables, grains, and fruits contributed 29%, 47%, and 24% to the total blue water wasted through FLW. The total carbon dioxide emissions generated by plant FLW were contributed by vegetables with 50%, grains with 31%, and fruits with 19%. Canonical correspondence analysis indicates that vegetable FLW had a higher positive correlation with urbanization, household incomes, gross domestic product, and high-income population than grain FLW, whereas fruit FLW was not influenced by these socioeconomic factors. Therefore, we suggest that the FLW mitigation should be prioritized on vegetables. Specific strategies include local food sourcing, shortening food miles, building food belts, and developing controlled-environment agriculture. Our data-based comparisons provide valuable insights into food policy improvement for achieving the 2030 reduction goal of the U.S., but the insights could be improved by considering the influences of foods imported from other nations.

Bayesian estimation and sensitivity analysis of toluene and trichloroethylene biodegradation kinetic parameters.

Parameter estimation is needed for process management, design, and reactor scaling when values from the literature vary tremendously or are unavailable. A Bayesian approach, implemented via Markov chain Monte Carlo (MCMC) simulations using SAS software, was used to estimate the kinetic parameters of toluene and trichloroethylene (TCE) biodegradation by the microorganism Pseudomonas putida F1 in batch cultures. The prediction capabilities of Bayesian estimation were illustrated by comparing predicted and observed data and reported in goodness-of-fit statistics. The sensitivity analysis showed that the parameters obtained using this approach were consistent under the designated toluene and TCE concentration range. Moreover, the impact of TCE on toluene degradation kinetics was numerically exhibited, verifying the fact that TCE was able to stimulate toluene degradation; hence, TCE's presence increased the apparent maximum toluene-specific rate. Various kinetic models were explored at different degrees of complexity. At a low TCE concentration range (e.g., <2 mg L-1 ), a simplified Michaelis-Menten model (i.e., substrate half-saturation parameters approximated the inhibition parameters) was adequate to describe the reaction kinetics. However, at a higher TCE range (e.g., 5 mg L-1 ), a full-scale Michaelis-Menten model was needed to discriminate among the inhibition parameters in the model. The results demonstrated that a Bayesian estimation method is particularly useful for determining complex bioreaction kinetic parameters in the presence of a small volume of experimental data.

Surface-Adsorbed Contaminants Mediate the Importance of Chemotaxis and Haptotaxis for Bacterial Transport Through Soils.

Chemotaxis and haptotaxis are important biological mechanisms that influence microbial movement toward concentrated chemoattractants in mobile liquids and along immobile surfaces, respectively. This study investigated their coupled effect, as induced by naphthalene (10 mg L-1), on the transport and retention of two pollutant-degrading bacteria, Pseudomonas fluorescens 5RL (Pf5RL) and Pseudomonas stutzeri DQ1 (PsDQ1), in quartz sand and natural soil. The results demonstrated that PsDQ1 was not chemotactic, whereas Pf5RL was chemotactic at 25°C but not at 4°C due to the restricted movement. In a quartz sand column, haptotaxis did not play a role in increasing the transport of Pf5RL as compared with chemotaxis. Compared with a naphthalene-free soil column, Pf5RL broke through naphthalene-presaturated soil columns to reach a stable effluent concentration 0.5 pore volumes earlier due to advective chemotaxis occurring behind the plume front in the bulk solution. Pf5RL also demonstrated greater retention (e.g., a doubled rate of attachment and a one-third smaller breakthrough percentage) due to along-surface haptotaxis and near-surface chemotaxis occurring in less mobile water near the soil surface. However, both chemotaxis and haptotaxis were weakened when Pf5RL co-transported with naphthalene due to reduced adsorption of naphthalene on the soil. This study suggests that surface adsorption of naphthalene can mediate the relative importance of advective chemotaxis (facilitating initial breakthrough), near-surface chemotaxis (increasing bacterial collision), and haptotaxis (increasing bacterial residence time).

Flood-induced transport of PAHs from streambed coal tar deposits.

We assessed whether coal tar present in contaminated streambed sediments can be mobilized by flood events and be re-deposited in an adjacent floodplain. The study was conducted within a contaminated urban stream where coal tar wastes were released into a 4-km reach from a coke plant in Chattanooga, Tennessee, USA. Sediments containing visible amounts of coal tar were dredged from the streambed in 1997-98 and 2007 as part of a cleanup effort. However, post-dredging sampling indicated that very high concentrations of polycyclic aromatic hydrocarbons (PAHs) remained in streambed sediments. Sampling of sediments in the floodplain at two sites downstream of the coke plant indicated that high concentrations of PAHs were also present in the floodplain, even though no coal tar was observed in the samples. Age-dating of the floodplain sediments using 137Cs indicated that peak PAH concentrations were contemporary with coke plant operations. While there was little or any direct contamination of the floodplain sediments by coal tar, sediment contamination was likely a result of deposition of suspended streambed sediments containing sorbed PAHs. A flood model developed to delineate the extent of flooding in various flood recurrence scenarios confirmed the potential for contaminated streambed sediments to be transported into the adjacent floodplain. It was hypothesized that coal tar, which was visibly "sticky" during dredging-based stream cleanup, may act as a binding agent for streambed sediments, decreasing mobility and transport in the stream. Therefore, coal tar is likely to remain a persistent contaminant source for downstream reaches of the stream and the adjacent floodplain during flood events. This study also showed that even after excavation of tar-rich streambed sediments, PAH contaminated non-tarry sediments may be a source of flood-related contamination in the adjacent flood plain. A conceptual framework was developed to delineate specific mechanisms that can mobilize contamination from stream sources.

Fate and toxic effects of environmental stressors: environmental control.

The potential for toxicants to harm organisms in the environment is influenced by the physicochemistry of the substances and their environmental behaviors and transformation within ecosystems. This special issue is composed of 20 papers that report on studies which have investigated the fate and toxicity of various toxicants including engineered nanoparticles, pharmaceuticals and personal care products, antibiotics, pathogens, heavy metals, and agricultural nutrients. The environmental transformations of these substances and how these processes affect their toxicity are emphasized. This paper highlights the important findings and perspectives of the selected papers in this special edition, with an aim of providing insights into full-scale evaluation on the toxicity of various contaminants that exist in ecosystems. General suggestions are provided for the future directions of toxicological research.

Metagenomes of microbial communities in arsenic- and pathogen-contaminated well and surface water from bangladesh.

The contamination of drinking water from both arsenic and microbial pathogens occurs in Bangladesh. A general metagenomic survey of well water and surface water provided information on the types of pathogens present and may help elucidate arsenic metabolic pathways and potential assay targets for monitoring surface-to-ground water pathogen transport.

Metagenomes from thawing low-soil-organic-carbon mineral cryosols and permafrost of the canadian high arctic.

Microbial release of greenhouse gases from thawing permafrost is a global concern. Seventy-six metagenomes were generated from low-soil-organic-carbon mineral cryosols from Axel Heiberg Island, Nunavut, Canada, during a controlled thawing experiment. Permafrost thawing resulted in an increase in anaerobic fermenters and sulfate-reducing bacteria but not methanogens.

Integrated metagenomics and metatranscriptomics analyses of root-associated soil from transgenic switchgrass.

The benefits of using transgenic switchgrass with decreased levels of caffeic acid 3-O-methyltransferase (COMT) as biomass feedstock have been clearly demonstrated. However, its effect on the soil microbial community has not been assessed. Here we report metagenomic and metatranscriptomic analyses of root-associated soil from COMT switchgrass compared with nontransgenic counterparts.

Expression of a humanized viral 2A-mediated lux operon efficiently generates autonomous bioluminescence in human cells.

BACKGROUND: Expression of autonomous bioluminescence from human cells was previously reported to be impossible, suggesting that all bioluminescent-based mammalian reporter systems must therefore require application of a potentially influential chemical substrate. While this was disproven when the bacterial luciferase (lux) cassette was demonstrated to function in a human cell, its expression required multiple genetic constructs, was functional in only a single cell type, and generated a significantly reduced signal compared to substrate-requiring systems. Here we investigate the use of a humanized, viral 2A-linked lux genetic architecture for the efficient introduction of an autobioluminescent phenotype across a variety of human cell lines. METHODOLOGY/PRINCIPAL FINDINGS: The lux cassette was codon optimized and assembled into a synthetic human expression operon using viral 2A elements as linker regions. Human kidney, breast cancer, and colorectal cancer cell lines were both transiently and stably transfected with the humanized operon and the resulting autobioluminescent phenotype was evaluated using common imaging instrumentation. Autobioluminescent cells were screened for cytotoxic effects resulting from lux expression and their utility as bioreporters was evaluated through the demonstration of repeated monitoring of single populations over a prolonged period using both a modified E-SCREEN assay for estrogen detection and a classical cytotoxic compound detection assay for the antibiotic Zeocin. Furthermore, the use of self-directed bioluminescent initiation in response to target detection was assessed to determine its amenability towards deployment as fully autonomous sensors. In all cases, bioluminescent measurements were supported with traditional genetic and transcriptomic evaluations. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that the viral 2A-linked, humanized lux genetic architecture successfully produced autobioluminescent phenotypes in all cell lines tested without the induction of cytotoxicity. This autobioluminescent phenotype allowed for repeated interrogation of populations and self-directed control of bioluminescent activation with detection limits and EC50 values similar to traditional reporter systems, making the autobioluminescent cells amenable to automated monitoring and significantly reducing the time and cost required to perform bioluminescent workflows.

Temporal dynamics of oocyte growth and vitellogenin gene expression in zebrafish (Danio rerio).

Little is known about how hepatic vitellogenin gene (vtg) expression relates to oogenesis in fish, especially among fractional spawners. The objective of this study was to relate hepatic vtg 1A/B expression to stage-specific oocyte development in zebrafish (Danio rerio), an asynchronous spawning fish. Liver samples were collected at seven time points postspawning (1-32 days) and fish were preserved for subsequent histological analyses. Relative vtg 1A/B expression among liver samples was quantified by reverse transcription-quantitative PCR and oogenesis was evaluated following standard hematoxylin and eosin staining of serial ovarian sections. Histological analyses indicate that a subset of previtellogenic oocytes (stages 1-2) transitioned into postvitellogenic oocytes (stages 3-4) within 4 days (96 h) postspawning. By 8 days postspawning (192 h), the majority of the ovary was occupied by mature (stage 4) oocytes, a trend that continued through 32 days postspawning. Hepatic vtg 1A/B gene expression was upregulated 3.89-fold 1-h postspawning relative to the average gene expression across all time points, but was not correlated to stage-specific oogenesis. Follicular atresia among fish sampled 32 days postspawning highlights the importance of regular spawning in zebrafish and suggests that the event of spawning itself may be integral to the regulation of oocyte development.

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples.

The total community genomic DNA (gDNA) from permafrost was extracted using four commercial DNA extraction kits. The gDNAs were compared using quantitative real-time PCR (qPCR) targeting 16S rRNA genes and bacterial diversity analyses obtained via 454 pyrosequencing of the 16S rRNA (V3 region) amplified in single or nested PCR. The FastDNA(®) SPIN (FDS) Kit provided the highest gDNA yields and 16S rRNA gene concentrations, followed by MoBio PowerSoil(®) (PS) and MoBio PowerLyzer™ (PL) kits. The lowest gDNA yields and 16S rRNA gene concentrations were from the Meta-G-Nome™ (MGN) DNA Isolation Kit. Bacterial phyla identified in all DNA extracts were similar to that found in other soils and were dominated by Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Acidobacteria. Weighted UniFrac and statistical analyses indicated that bacterial community compositions derived from FDS, PS, and PL extracts were similar to each other. However, the bacterial community structure from the MGN extracts differed from other kits exhibiting higher proportions of easily lysed ß- and γ-Proteobacteria and lower proportions of Actinobacteria and Methylocystaceae important in carbon cycling. These results indicate that gDNA yields differ between the extraction kits, but reproducible bacterial community structure analysis may be accomplished using gDNAs from the three bead-beating lysis extraction kits.

C60 reduces the bioavailability of mercury in aqueous solutions.

The effects of C60 on mercury bioavailability and sorption were investigated at different C60 dosages, reaction times, and pH ranges using the merR::luxCDABE bioluminescent bioreporter Escherichia coli ARL1. The results demonstrated that the bioavailability of mercury (Hg(2+)) decreased with increasing C60 dosage. Approximately 30% of aqueous mercury became biologically unavailable 2h after interaction with C60 at a mass ratio of C60 to mercury as low as 0.01. However, this reduction in bioavailability plateaued at a mass ratio of C60 to mercury of 10 with a further increase in C60 concentrations resulting in only a 20% additional decrease in bioavailability. If this reduction in bioluminescence output is attributable to mercury sorption on C60, then each one log-order increase in C60 concentration resulted in a 0.86 log-order decrease in the mercury partitioning coefficient (Kd). This relationship implies the presence of high mercury-affinitive sites on C60. The length of reaction time was found to play a more important role than C60 dosage in reducing Hg(2+) bioavailability, suggesting an overall slow kinetics of the C60-Hg interactions. In addition, lowering the pH from 7.2 to 5.8 decreased mercury bioavailability due likely to the increase in mercury's association with C60. These results suggest that C60 may be useful in capturing soluble mercury and thus reducing mercury biotoxicity.

Autonomously bioluminescent mammalian cells for continuous and real-time monitoring of cytotoxicity.

Mammalian cell-based in vitro assays have been widely employed as alternatives to animal testing for toxicological studies but have been limited due to the high monetary and time costs of parallel sample preparation that are necessitated due to the destructive nature of firefly luciferase-based screening methods. This video describes the utilization of autonomously bioluminescent mammalian cells, which do not require the destructive addition of a luciferin substrate, as an inexpensive and facile method for monitoring the cytotoxic effects of a compound of interest. Mammalian cells stably expressing the full bacterial bioluminescence (luxCDABEfrp) gene cassette autonomously produce an optical signal that peaks at 490 nm without the addition of an expensive and possibly interfering luciferin substrate, excitation by an external energy source, or destruction of the sample that is traditionally performed during optical imaging procedures. This independence from external stimulation places the burden for maintaining the bioluminescent reaction solely on the cell, meaning that the resultant signal is only detected during active metabolism. This characteristic makes the lux-expressing cell line an excellent candidate for use as a biosentinel against cytotoxic effects because changes in bioluminescent production are indicative of adverse effects on cellular growth and metabolism. Similarly, the autonomous nature and lack of required sample destruction permits repeated imaging of the same sample in real-time throughout the period of toxicant exposure and can be performed across multiple samples using existing imaging equipment in an automated fashion.

An overview on the marine neurotoxin, saxitoxin: genetics, molecular targets, methods of detection and ecological functions.

Marine neurotoxins are natural products produced by phytoplankton and select species of invertebrates and fish. These compounds interact with voltage-gated sodium, potassium and calcium channels and modulate the flux of these ions into various cell types. This review provides a summary of marine neurotoxins, including their structures, molecular targets and pharmacologies. Saxitoxin and its derivatives, collectively referred to as paralytic shellfish toxins (PSTs), are unique among neurotoxins in that they are found in both marine and freshwater environments by organisms inhabiting two kingdoms of life. Prokaryotic cyanobacteria are responsible for PST production in freshwater systems, while eukaryotic dinoflagellates are the main producers in marine waters. Bioaccumulation by filter-feeding bivalves and fish and subsequent transfer through the food web results in the potentially fatal human illnesses, paralytic shellfish poisoning and saxitoxin pufferfish poisoning. These illnesses are a result of saxitoxin's ability to bind to the voltage-gated sodium channel, blocking the passage of nerve impulses and leading to death via respiratory paralysis. Recent advances in saxitoxin research are discussed, including the molecular biology of toxin synthesis, new protein targets, association with metal-binding motifs and methods of detection. The eco-evolutionary role(s) PSTs may serve for phytoplankton species that produce them are also discussed.

Paralytic shellfish toxins inhibit copper uptake in Chlamydomonas reinhardtii.

Paralytic shellfish toxins are secondary metabolites produced by several species of dinoflagellates and cyanobacteria. Known targets of these toxins, which typically occur at detrimental concentrations during harmful algal blooms, include voltage-gated ion channels in humans and other mammals. However, the effects of the toxins on the co-occurring phytoplankton community remain unknown. The present study examined the molecular mechanisms of the model photosynthetic alga Chlamydomonas reinhardtii in response to saxitoxin exposure as a means of gaining insight into the phytoplankton community response to a bloom. Previous work with yeast indicated that saxitoxin inhibited copper uptake, so experiments were designed to examine whether saxitoxin exhibited a similar mode of action in algae. Expression profiling following exposure to saxitoxin or a copper chelator produced similar profiles in copper homeostasis genes, notably induction of the cytochrome c6 (CYC6) and copper transporter (COPT1, CTR1) genes. Cytochrome c6 is used as an alternative to plastocyanin under conditions of copper deficiency, and immunofluorescence data showed this protein to be present in a significantly greater proportion of saxitoxin-exposed cells compared to controls. Live-cell imaging with a copper-sensor probe for intracellular labile Cu(I) confirmed that saxitoxin blocked copper uptake. Extrapolations of these data to phytoplankton metabolic processes along with the copper transporter as a molecular target of saxitoxin based on existing structural models are discussed.

Continuous, real-time bioimaging of chemical bioavailability and toxicology using autonomously bioluminescent human cell lines.

Bioluminescent imaging is an emerging biomedical surveillance strategy that uses external cameras to detect in vivo light generated in small animal models of human physiology or in vitro light generated in tissue culture or tissue scaffold mimics of human anatomy. The most widely utilized of reporters is the firefly luciferase (luc) gene; however, it generates light only upon addition of a chemical substrate, thus only generating intermittent single time point data snapshots. To overcome this disadvantage, we have demonstrated substrate-independent bioluminescent imaging using an optimized bacterial bioluminescence (lux) system. The lux reporter produces bioluminescence autonomously using components found naturally within the cell, thereby allowing imaging to occur continuously and in real-time over the lifetime of the host. We have validated this technology in human cells with demonstrated chemical toxicological profiling against exotoxin exposures at signal strengths comparable to existing luc systems (~1.33 × 107 photons/second). As a proof-in-principle demonstration, we have engineered breast carcinoma cells to express bioluminescence for real-time screening of endocrine disrupting chemicals and validated detection of 17ß-estradiol (EC50 = ~ 10 pM). These and other applications of this new reporter technology will be discussed as potential new pathways towards improved models of target chemical bioavailability, toxicology, efficacy, and human safety.

Genetically modified whole-cell bioreporters for environmental assessment.

Living whole-cell bioreporters serve as environmental biosentinels that survey their ecosystems for harmful pollutants and chemical toxicants, and in the process act as human and other higher animal proxies to pre-alert for unfavorable, damaging, or toxic conditions. Endowed with bioluminescent, fluorescent, or colorimetric signaling elements, bioreporters can provide a fast, easily measured link to chemical contaminant presence, bioavailability, and toxicity relative to a living system. Though well tested in the confines of the laboratory, real-world applications of bioreporters are limited. In this review, we will consider bioreporter technologies that have evolved from the laboratory towards true environmental applications, and discuss their merits as well as crucial advancements that still require adoption for more widespread utilization. Although the vast majority of environmental monitoring strategies rely upon bioreporters constructed from bacteria, we will also examine environmental biosensing through the use of less conventional eukaryotic-based bioreporters, whose chemical signaling capacity facilitates a more human-relevant link to toxicity and health-related consequences.

Unsealed tubewells lead to increased fecal contamination of drinking water.

Bangladesh is underlain by shallow aquifers in which millions of drinking water wells are emplaced without annular seals. Fecal contamination has been widely detected in private tubewells. To evaluate the impact of well construction on microbial water quality 35 private tubewells (11 with intact cement platforms, 19 without) and 17 monitoring wells (11 with the annulus sealed with cement, six unsealed) were monitored for culturable Escherichia coli over 18 months. Additionally, two 'snapshot' sampling events were performed on a subset of wells during late-dry and early-wet seasons, wherein the fecal indicator bacteria (FIB) E. coli, Bacteroidales and the pathogenicity genes eltA (enterotoxigenic E. coli; ETEC), ipaH (Shigella) and 40/41 hexon (adenovirus) were detected using quantitative polymerase chain reaction (qPCR). No difference in E. coli detection frequency was found between tubewells with and without platforms. Unsealed private wells, however, contained culturable E. coli more frequently and higher concentrations of FIB than sealed monitoring wells (p < 0.05), suggestive of rapid downward flow along unsealed annuli. As a group the pathogens ETEC, Shigella and adenovirus were detected more frequently (10/22) during the wet season than the dry season (2/20). This suggests proper sealing of private tubewell annuli may lead to substantial improvements in microbial drinking water quality.

Comparison of fecal indicators with pathogenic bacteria and rotavirus in groundwater.

Groundwater is routinely analyzed for fecal indicators but direct comparisons of fecal indicators to the presence of bacterial and viral pathogens are rare. This study was conducted in rural Bangladesh where the human population density is high, sanitation is poor, and groundwater pumped from shallow tubewells is often contaminated with fecal bacteria. Five indicator microorganisms (E. coli, total coliform, F+RNA coliphage, Bacteroides and human-associated Bacteroides) and various environmental parameters were compared to the direct detection of waterborne pathogens by quantitative PCR in groundwater pumped from 50 tubewells. Rotavirus was detected in groundwater filtrate from the largest proportion of tubewells (40%), followed by Shigella (10%), Vibrio (10%), and pathogenic E. coli (8%). Spearman rank correlations and sensitivity-specificity calculations indicate that some, but not all, combinations of indicators and environmental parameters can predict the presence of pathogens. Culture-dependent fecal indicator bacteria measured on a single date did not predict total bacterial pathogens, but annually averaged monthly measurements of culturable E. coli did improve prediction for total bacterial pathogens. A qPCR-based E. coli assay was the best indicator for the bacterial pathogens. F+RNA coliphage were neither correlated nor sufficiently sensitive towards rotavirus, but were predictive of bacterial pathogens. Since groundwater cannot be excluded as a significant source of diarrheal disease in Bangladesh and neighboring countries with similar characteristics, the need to develop more effective methods for screening tubewells with respect to microbial contamination is necessary.

Global gene expression in larval zebrafish (Danio rerio) exposed to selective serotonin reuptake inhibitors (fluoxetine and sertraline) reveals unique expression profiles and potential biomarkers of exposure.

Larval zebrafish (Danio rerio) were exposed (96 h) to selective serotonin reuptake inhibitors (SSRIs) fluoxetine and sertraline and changes in transcriptomes analyzed by Affymetrix GeneChip Zebrafish Array were evaluated to enhance understanding of biochemical pathways and differences between these SSRIs. The number of genes differentially expressed after fluoxetine exposure was 288 at 25 µg/L and 131 at 250 µg/L; and after sertraline exposure was 33 at 25 µg/L and 52 at 250 µg/L. Same five genes were differentially regulated in both SSRIs indicating shared molecular pathways. Among these, the gene coding for FK506 binding protein 5, annotated to stress response regulation, was highly down-regulated in all treatments (results confirmed by qRT-PCR). Gene ontology analysis indicated at the gene expression level that regulation of stress response and cholinesterase activities were influenced by these SSRIs, and suggested that changes in transcription of these genes could be used as biomarkers of SSRI exposure.