Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

This is the final version of the article. Available from the publisher via the DOI in this record.Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.MRG is supported by the Australian Research Council, AP is supported by the Alfred P Sloan Foundation Microbiology of the Built Environment program and the National Science Foundation RAPID award no. 1402651, KS is supported by the Deutsche Forschungsgemeinschaft (DFG) funding the Research Unit FOR 566 ‘Veterinary Medicines in Soil: Basic Research for Risk Analysis’ (Grant No. SM59/5-3) and by the Umweltbundesamt (3713 63 402), JMT is supported by the US National Science Foundation and Y-GZ is supported by the National Science Foundation of China

The nitrogen cycle in the Broadbalk Wheat Experiment : recovery and losses of 15N-labelled fertilizer applied in spring and inputs of nitrogen from the atmosphere

15N-labelled nitrogen fertilizer (containing equal quantities of ammonium-N and nitrate-N) was applied in 4 consecutive years (1980–3) to different microplots located within the Broadbalk Wheat Experiment at Rothamsted, an experiment which has carried winter wheat continuously since 1843. Plots receiving 48, 96, 144 and 192 kg N/ha every year were given labelled fertilizer in mid-April at (nominally) these rates.Grain yields ranged from 1–2 t/ha on plots given no N fertilizer since 1843 to a maximum of 7·3 t/ha with 196 kg N/ha. On plots given adequate P and K fertilizer, between 51 and 68% of the labelled N was recovered in the above-ground crop; only about 40% was recovered where P deficiency limited crop growth. In 1981 fertilizerderived N retained in soil (0–70 cm) at harvest increased from 16 kg/ha, where 48 kg/ha was applied, to 38 kg/ha, where 192 kg/ha was applied. More than 80% of this retained N was in the plough layer (0–23 cm).Overall recovery of fertilizer N in crop plus soil ranged from 70 % to more than 90 % over the 4 years of the experiments. Losses of N were larger in years when spring rainfall was above average and when soil moisture deficits shortly after application were small.Crop uptake of unlabelled N derived from soil increased from 28 kg N/ha on the plot given no fertilizer N to 67 kg N/ha on the plot given 144 kg N/ha. The extra uptake of unlabelled N was mainly, if not entirely, due to greater mineralization of soil N in the plots that had been given N fertilizer for many years. Presumably fertilizer N increased the annual return of crop residues, which in turn led to an accumulation of mineralizable organic N, although there was only a small increase in total soil N content.Wheat given NH4-N grew less well and took up less N than wheat given N08-N in the relatively dry spring of 1980; there was little difference between the two forms of N in the wetter spring of 1981. In both years more fertilizer N was retained in the soil at harvest when fertilizer was applied as NH4-N than as N03-N.The N content of the soil in several plots of the experiment has been constant for many years, so that the annual removal of N is balanced by the annual input. A nitrogen balance for the plot given 144 kg fertilizer N/ha showed an average annual input of non-fertilizer N of at least 48 kg/ha, of which N in rain and seed accounts for about 14 kg/ha. The remainder may come from biological fixation of atmospheric N2 by blue-green algae, or from dry deposition of oxides of nitrogen and/or NH3 onto crop and soil. The overall annual loss of N from the crop–soil system on this particular plot was 54 kg N/ha per year, 28% of the total annual input from fertilizer and nonfertilizer N

Labels direct infants’ attention to commonalities during novel category learning

Recent studies have provided evidence that labeling can influence the outcome of infants’ visual categorization. However, what exactly happens during learning remains unclear. Using eye-tracking, we examined infants’ attention to object parts during learning. Our analysis of looking behaviors during learning provide insights going beyond merely observing the learning outcome. Both labeling and non-labeling phrases facilitated category formation in 12-month-olds but not 8-month-olds (Experiment 1). Non-linguistic sounds did not produce this effect (Experiment 2). Detailed analyses of infants’ looking patterns during learning revealed that only infants who heard labels exhibited a rapid focus on the object part successive exemplars had in common. Although other linguistic stimuli may also be beneficial for learning, it is therefore concluded that labels have a unique impact on categorization

Every fifth published metagenome is not available to science

Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high–impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions—a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.info:eu-repo/semantics/publishedVersio

Tertiary-Treated Municipal Wastewater is a Significant Point Source of Antibiotic Resistance Genes Into Duluth-Superior Harbor

In this study, the impact of tertiary-treated municipal wastewater on the quantity of several antibiotic resistance determinants in Duluth-Superior Harbor was investigated by collecting surface water and sediment samples from 13 locations in Duluth-Superior Harbor, the St. Louis River, and Lake Superior. Quantitative PCR (qPCR) was used to target three different genes encoding resistance to tetracycline (tet(A), tet(X), and tet(W)), the gene encoding the integrase of class 1 integrons (intI1), and total bacterial abundance (16S rRNA genes) as well as total and human fecal contamination levels (16S rRNA genes specific to the genus Bacteroides). The quantities of tet(A), tet(X), tet(W), intI1, total Bacteroides, and human-specific Bacteroides were typically 20-fold higher in the tertiary-treated wastewater than in nearby surface water samples. In contrast, the quantities of these genes in the St. Louis River and Lake Superior were typically below detection. Analysis of sequences of tet(W) gene fragments from four different samples collected throughout the study site supported the conclusion that tertiary-treated municipal wastewater is a point source of resistance genes into Duluth-Superior Harbor. This study demonstrates that the discharge of exceptionally treated municipal wastewater can have a statistically significant effect on the quantities of antibiotic resistance genes in otherwise pristine surface waters

A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants

The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum β-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (<0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 103 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status

A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants

The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum β-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (<0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 10 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status. [Abstract copyright: Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.

Environmental Emission of Pharmaceuticals from Wastewater Treatment Plants in the USA

The residual drugs, drug bioconjugates, and their metabolites, mostly from human and veterinary usage, are routinely flushed down the drain, and enter wastewater treatment plants (WWTP). Increasing population, excessive use of allopathic medicine, continual introduction of novel drugs, and existing inefficient wastewater treatment processes result in the discharge of large volumes of pharmaceuticals and their metabolites from the WWTPs into the environment. The effluent from the WWTPs globally contaminate ~25% of rivers and the lakes. Pharmaceuticals in the environment, as contaminants of emerging concerns, behave as pseudo-persistent despite their relatively short environmental half-lives in the environment. Therefore, residual levels of pharmaceuticals in the environment not only pose a threat to the wildlife but also affect human health through contaminated food and drinking water. This chapter highlights WWTPs as point-sources of their environmental emissions and various effects on the aquatic and terrestrial ecosystem