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The vast majority of antibiotic resistant genes (ARG) acquired by human pathogens have originated from the natural environment. Therefore, understanding factors that influence intrinsic levels of ARG in the environment could be epidemiologically significant. The selection for metal resistance often promotes AR in exposed organisms; however, the relationship between metal levels in nature and the intrinsic presence of ARG has not been fully assessed. Here, we quantified, using qPCR, the abundance of eleven ARG and compared their levels with geochemical conditions in randomly selected soils from a Scottish archive. Many ARG positively correlated with soil copper levels, with approximately half being highly significant (p<0.05); whereas chromium, nickel, lead, and iron also significantly correlated with specific ARG. Results show that geochemical metal conditions innately influence the potential for AR in soil. We suggest soil geochemical data might be used to estimate baseline gene presence on local, regional and global scales within epidemiological risk studies related to AR transmission from the environment.

The experiments presented here are based on the reconfiguration of an ancient medicine, Lemnian Earth (LE) ( terra sigillata , stamped earth , sphragis ), an acclaimed therapeutic clay with a 2500-year history of use. Based on our hypothesis that LE was not a natural material but an artificially modified one involving a clay-fungus interaction, we present results from experiments involving the co-culture of a common fungus, Penicillium purpurogenum ( Pp ), with two separate clay slurries, smectite and kaolin, which are the principal constituents of LE. Our results show: (a) the leachate of the Pp +smectite co-culture is antibacterial in vitro , inhibiting the growth of both Gram-positive and Gram-negative bacteria; (b) in vivo , supplementation of regular mouse diet with leachates of Pp +smectite increases intestinal microbial diversity; (c) Pp+ kaolin does not produce similar results; (d) untargeted metabolomics and analysis of bacterial functional pathways indicates that the Pp +smectite-induced microbiome amplifies production of short-chain fatty acids (SCFAs) and amino acid biosynthesis, known to modulate intestinal and systemic inflammation. Our results suggest that the combination of increased microbial diversity and SCFA production indicates beneficial effects on the host microbiome, thus lending support to the argument that the therapeutic properties of LE may have been based on the potential for modulating the gut microbiome. Our experiments involving reconfigured LE open the door to future research into small molecule-based sources for promoting gut health.

Lactobacillus pentosus MP-10, isolated from brines of naturally fermented Aloreña green table olives, exhibited high probiotic potential. The genome sequence of L. pentosus MP-10 is currently considered the largest genome among lactobacilli, highlighting the microorganism's ecological flexibility and adaptability. Here, we analyzed the complete genome sequence for the presence of acquired antibiotic resistance and virulence determinants to understand their defense mechanisms and explore its putative safety in food. The annotated genome sequence revealed evidence of diverse mobile genetic elements, such as prophages, transposases and transposons involved in their adaptation to brine-associated niches. In-silico analysis of L. pentosus MP-10 genome sequence identified a CRISPR (clustered regularly interspaced short palindromic repeats)/cas (CRISPR-associated protein genes) as an immune system against foreign genetic elements, which consisted of six arrays (4-12 repeats) and eleven predicted cas genes [CRISPR1 and CRISPR2 consisted of 3 (Type II-C) and 8 (Type I) genes] with high similarity to L. pentosus KCA1. Bioinformatic analyses revealed L. pentosus MP-10 to be absent of acquired antibiotic resistance genes, and most resistance genes were related to efflux mechanisms; no virulence determinants were found in the genome. This suggests that L. pentosus MP-10 could be considered safe and with high-adaptation potential, which could facilitate its application as a starter culture and probiotic in food preparations.

Biological nitrification (that is, NH3 → NO2− → NO3−) is a key reaction in the global nitrogen cycle (N-cycle); however, it is also known anecdotally to be unpredictable and sometimes fails inexplicably. Understanding the basis of unpredictability in nitrification is critical because the loss or impairment of this function might influence the balance of nitrogen in the environment and also has biotechnological implications. One explanation for unpredictability is the presence of chaotic behavior; however, proving such behavior from experimental data is not trivial, especially in a complex microbial community. Here, we show that chaotic behavior is central to stability in nitrification because of a fragile mutualistic relationship between ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), the two major guilds in nitrification. Three parallel chemostats containing mixed microbial communities were fed complex media for 207 days, and nitrification performance, and abundances of AOB, NOB, total bacteria and protozoa were quantified over time. Lyapunov exponent calculations, supported by surrogate data and other tests, showed that all guilds were sensitive to initial conditions, suggesting broad chaotic behavior. However, NOB were most unstable among guilds and displayed a different general pattern of instability. Further, NOB variability was maximized when AOB were most unstable, which resulted in erratic nitrification including significant NO2− accumulation. We conclude that nitrification is prone to chaotic behavior because of a fragile AOB–NOB mutualism, which must be considered in all systems that depend on this critical reaction.

Potentially toxic elements (PTE) from industrial activities remain a global concern for their environmental hazards. In particular, strontium is found in drinking water and food, primarily from contamination from the nuclear industry, petroleum extractions, fireworks, and electronics. Its carbonate form is bioavailable and closely resembles calcium; thus, it has become a health concern, and phytoremediation has often been considered for Sr2+. We toxicologically determined Sr2+ tolerance in Festuca rubra (red fescue) and Trifolium pratense (red clover), and their ability to bio-accumulate strontium was compared to the sorption capacity of the soils. These plants were chosen for their ubiquity and as primary colonisers in soils. Experimentally uncontaminated farm soils from Lanarkshire, Scotland, were used, along with these two common plants. Further, seed-germination and plant-growth assays demonstrated that strontium chloride exposures impact both species (0–40mM; p < 0.05). Moreover, translocation factors suggest that T. pratense more efficiently accumulated strontium, and F. rubra has the potential to be the excluder species, which restricts strontium to the roots. This knowledge is relevant to how strontium contamination may be phytoremediated, and suggests using clover during the early stages of ecological succession to sequester strontium from soils.

Multidrug resistant bacteria in water supply systems have been emerging as a growing public health concern. Many factors affect the source and fate of these bacteria. However, conditions in the plumbing systems may contribute to the dispersion of resistance genes among bacterial populations. Through the process of lateral gene transfer, resistance genetic material can be exchanged between species in the microbial population, intensifying the problem of resistance genes. The main aim of this study was to investigate the diversity of microorganisms in tap water in Glasgow, Scotland, and the occurrence of certain antibiotic resistance genes and gene-transfer mechanisms. Results show that antibiotic resistant bacteria exist at the consumers’ end of the distribution system, some of which also contain integrase genes, which can aid in the dispersion of resistance genes. Presence of such microorganisms indicates that further investigations should be taken to assess the risks to public health.

Antibiotic resistance (AR) is a growing health concern worldwide and the Arctic represents an understudied region in terms of AR. This study aimed to quantify AR genes (ARGs) from effluent released from a wastewater treatment plant (WWTP) in Iqaluit, Nunavut, Canada, thus creating a baseline reference for future evaluations. Water, sediment, and truncate softshell clam ( Mya truncata) tissue samples were compared from the wastewater, the receiving environment of Frobisher Bay, and nearby undisturbed freshwaters. The pharmaceuticals and personal care products (PPCPs) atenolol, carbamazepine, metoprolol, naproxen, sulfapyridine, and trimethoprim were found in the wastewater, but the PPCPs were undetectable in the receiving environment. However, the relative abundances of ARGs were significantly higher in wastewater than in the receiving environment or reference sites. Abundances did not significantly differ in Frobisher Bay compared to undisturbed reference sites. ARGs in clams near the WWTP had similar relative abundances as those from pristine areas. The lack of ARG detection is likely due to Frobisher Bay tides flushing inputs to levels below detection. These data suggest that the WWTP infrastructure does not influence the receiving environment based on the measured parameters; more importantly, further research must elucidate the impact and fate of AR and PPCPs in Arctic communities.

The distribution and quantification of tetracycline, sulfonamide and beta-lactam resistance genes were assessed in slaughterhouse zones throughout meat chain production and the meat products; this study represents the first to report quantitatively monitor antibiotic resistance genes (ARG) in goat and lamb slaughterhouse using a culture independent approach, since most studies focused on individual bacterial species and their specific resistance types. Quantitative PCR (qPCR) revealed a high prevalence of tetracycline resistance genes tetA and tetB in almost all slaughterhouse zones. Sulfonamide resistance genes were largely distributed, while beta-lactam resistance genes were less predominant. Statistical analysis revealed that resistant bacteria, in most cases, were spread by the same route in almost all slaughterhouse zones, except for tetB, blaCTX and blaTEM genes, which occurred in few zones as isolated 'hot spots.' The sum of all analyzed ARG indicated that slaughterhouse surfaces and end products act as reservoirs of ARG, mainly tet genes, which were more prevalent in slaughtering room (SR), cutting room (CR) and commercial meat products (MP). Resistance gene patterns suggest they were disseminated throughout slaughterhouse zones being also detected in commercial meat products, with significant correlations between different sampling zones/end products and total resistance in SR, CR and white room (WR) zones, and also refrigerator 4 (F4) and MP were observed. Strategically controlling key zones in slaughterhouse (SR, CR and WR) by adequate disinfection methods could strategically reduce the risks of ARG transmission and minimize the issues of food safety and environment contamination.

The environment disseminates antimicrobial-resistance genes; however, it remains challenging to distinguish whether human activities exacerbate antimicrobial resistance or what is natural. Here, we quantified ~300 resistance-related genes in 200+ Scottish soil samples. Location or land use does not explain gene differences, but nutrient levels reduce gene richness. Elevated levels of metals increased gene richness, and selenium increased transposase levels. Rainfall and persistent organic pollutants also increased transposase relative abundance, possibly promoting conditions conducive to the horizontal transfer of antimicrobial-resistance genes. Selenium and polychlorinated biphenyls were primary factors in gene abundance, while polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pH influenced gene diversity. Polychlorinated biphenyls are derived from anthropogenic activities, highlighting human activities’ potential impact on gene prevalence. This is the first national-scale, high spatial resolution dataset of antimicrobial-resistance genes in Scottish soils and provides a novel resource on which to build future studies.

Methane is a major greenhouse gas linked to global warming; however, patterns of in situ methane oxidation by methane-oxidizing bacteria (methanotrophs), nature's main biological mechanism for methane suppression, are often inconsistent with laboratory predictions. For example, one would expect a strong relationship between methanotroph ecology and Cu level because methanotrophs require Cu to sustain particulate methane monooxygenase (pMMO), the most efficient enzyme for methane oxidation. However, no correlation has been observed in nature, which is surprising because methane monooxygenase (MMO) gene expression has been unequivocally linked to Cu availability. Here we provide a fundamental explanation for this lack of correlation. We propose that MMO expression in nature is largely controlled by solid-phase Cu geochemistry and the relative ability of Cu acquisition systems in methanotrophs, such as methanobactins (mb), to obtain Cu from mineral sources. To test this hypothesis, RT-PCR expression assays were developed for Methylosinus trichosporium OB3b (which produces mb) to quantify pMMO, soluble MMO (the alternate MMO expressed when Cu is \"unavailable\"), and 16S-rRNA gene expression under progressively more stringent Cu supply conditions. When Cu was provided as CuCl₂, pMMO transcript levels increased significantly consistent with laboratory work. However, when Cu was provided as Cu-doped iron oxide, pMMO transcript levels increased only when mb was also present. Finally, when Cu was provided as Cu-doped borosilicate glass, pMMO transcription patterns varied depending on the ambient mb:Cu supply ratio. Cu geochemistry clearly influences MMO expression in terrestrial systems, and, as such, local Cu mineralogy might provide an explanation for methane oxidation patterns in the natural environment.