Plasma Optimization as a Novel Tool to Explore Plant-Microbe Interactions in Climate Smart Agriculture

Plasma treatment has emerged as a promising tool for manipulating plant microbiomes and metabolites. This review explores the diverse applications and effects of plasma on these biological systems. It is hypothesized that plasma treatment will not induce substantial changes in the composition of plant microbiomes or the concentration of plant metabolites. We delve into the mechanisms by which plasma can regulate microbial communities, enhance antimicrobial activity, and recruit beneficial microbes to mitigate stress. Furthermore, we discuss the optimization of plasma parameters for effective microbiome interaction and the role of plasmids in plant-microbe interactions. By characterizing plasmidome responses to plasma exposure and investigating transcriptional and metabolomic shifts, we provide insights into the potential of plasma as a tool for engineering beneficial plant-microbe interactions. The review presented herein demonstrates that plasma treatment induces substantial changes in both microbial community composition and metabolite levels, thereby refuting our initial hypothesis. Finally, we integrate plasmidome, transcriptome, and metabolome data to develop a comprehensive understanding of plasma's effects on plant biology and explore future perspectives for agricultural applications.

The source and dissemination of ARGs in pristine environments: Elucidating the role of migratory birds in the Arctic

Antibiotic resistance genes (ARGs) are a class of emerging contaminants that significantly threaten public health. In this work, the profiles of ARGs and microbial communities in the soil, sediment, migratory bird, and local deer fecal samples collected from the Arctic were characterized using a metagenomic approach. The results retrieved the baseline profiles of ARGs and identified the role of migratory birds in disseminating ARGs in the Arctic. A total of 26 ARG types and 718 subtypes were determined, and 131 core ARGs were identified. All the samples were dominated by multidrug resistance genes, and some genes resistant to antibiotics commonly used in anthropogenic were also detected. Characterization of ARGs in bird fecal samples was significantly distinct from other media, with higher abundance, richness, and unique ARGs detected. Proteobacteria was the most predominant phylum in soil and fecal samples, while Thaumarchaeota was prevalent in sediment samples. Firmicutes harbored the majority of ARGs in all samples. The results of FEAST indicated that migratory birds were crucial allochthonous ARG sources in the Arctic. These significant findings shed light on the global spread of ARGs and should facilitate efforts to map baseline levels of ARGs before the era of antibiotics.

Plasmid-Mediated Transfer of Antibiotic Resistance Genes in Soil

Due to selective pressure from the widespread use of antibiotics, antibiotic resistance genes (ARGs) are found in human hosts, plants, and animals and virtually all natural environments. Their migration and transmission in different environmental media are often more harmful than antibiotics themselves. ARGs mainly move between different microorganisms through a variety of mobile genetic elements (MGEs), such as plasmids and phages. The soil environment is regarded as the most microbially active biosphere on the Earth’s surface and is closely related to human activities. With the increase in human activity, soils are becoming increasingly contaminated with antibiotics and ARGs. Soil plasmids play an important role in this process. This paper reviews the current scenario of plasmid-mediated migration and transmission of ARGs in natural environments and under different antibiotic selection pressures, summarizes the current methods of plasmid extraction and analysis, and briefly introduces the mechanism of plasmid splice transfer using the F factor as an example. However, as the global spread of drug-resistant bacteria has increased and the knowledge of MGEs improves, the contribution of soil plasmids to resistance gene transmission needs to be further investigated. The prevalence of multidrug-resistant bacteria has also made the effective prevention of the transmission of resistance genes through the plasmid-bacteria pathway a major research priority.

Playgrounds in City of Pushchino with Different Types of Coating as Reservoir of Antibiotic-Resistant Strains of Pseudomonas spp

In this study, we investigated antibiotic-resistant microorganisms isolated by the direct plating method from 6 playgrounds in the city of Pushchino, Moscow Region, with different types of coating: sand, soil with sand, grass and a modern playground coating made of pressed rubber crumb. According to the results of the study, sand is the cleanest type of coating, both in terms of the total count of cultivated microorganisms (8 × 10⁵/g of substrate) and in terms of the content of resistant strains. The most contaminated both in terms of the total count of cultivated microorganisms (1.2-1.9 × 10⁹/g of substrate) and in terms of the content of antibiotic-resistant strains was the coating of pressed rubber crumb. We isolated 65 antibiotic-resistant strains of fluorescent pseudomonads. Nine Pseudomonas strains were found to contain antibiotic resistance plasmids (one belongs to P-1 incompatibility group, seven to IncP-7 and one to unidentified incompatibility group). For the first time, we discovered a conjugative plasmid pD4A-46 conferring tetracycline resistance and belonging to the P-7 incompatibility group. Taking into account the results obtained under this study, it can be recommended to periodically treat the crumb rubber coating with non-toxic antiseptics, i.e. hydrogen peroxide or chlorhexidine.

Monitoring of distribution of antibiotic-resistant strains of microorganisms in patients with dysbiosis of the urogenital tract

Currently, the problem of the development of resistance to drugs among microorganisms that colonize the urogenital system is becoming especially relevant due to broadly distributed dysbiotic conditions of the reproductive system of men and women. Therefore, there should be constant monitoring of the qualitative and quantitative composition of microbiota of the urogential tract and determination of the levels of antibiotic-resistance of strains of conditionally pathogenic microorganisms in the reproductive system of various layers of the population. We monitored 774,375 people of various age and sex – patients of the independent diagnostic laboratory INVITRO in the city Dnipro in 2017–2019. Among the examined people, 640,783 of the patients were diagnosed with the development of dysbiotic disorders, accounting for 82.7% of the total amount of the applications for medical help. According to the results of identification of the range of dysbiotic conditions of the urogenital system of patients of different ages and sexes, we determined the dominating role of facultative anaerobes in the development of dysbiotic impairments caused by colonizations by large numbers of conditionally-pathogenic microorganisms: in women, Gardnerella accounted for 86.1%, Staphylococcus – 63.2%, Streptococcus – 54.1%, Candida – 69.3%; in men, Streptococcus were found in 83.0%, Staphylococcus – 79.4%, Corynebacterium – 54.2% and Candida – 37.6% of the cases. Share of obligate anaerobes was also quite large: women were diagnosed with Prevotella in 59.7%, Peptostreptococcus in 53.2%, Fusobacterium in 45.4% of the cases cases; men were observed to have Peptostreptococcus 62.4%, Clostridium in 54.3%, Bacteroides in 32.5% of the cases. We determined high parameters of frequency of diagnosing antibiotic-resistant isolates of conditionally pathogenic microorganisms that circulate in the urogenital tract of patients with dysbiotic impairments, belonging to the following families: Mycoplasmataceae – 78.6%, Enterobacteriaceae – 56.0% and genera – Staphylococcus – 76.1%, Gardnerella – 24.3%, Corynebacterium – 21.2%. The research revealed increase in the frequency of detection of strains of urapathogenic bacteria resistant to the applied antibiotic preparations in 2018–2019 compared with the data of 2017: increases of 10.3% and 6.4% in representatives of family Mycoplasmataceae resistant to ciprofloxacin and ofloxacin respectively, 4.8% and 4.0% in Enterobacteriaceae resistant to chloramphenicol and ampicillin respectively, and 8.9% in the genus Staphylococcus resistant to vancomycin.

Diversity and genetic lineages of environmental staphylococci: a surface water overview

Antimicrobial resistance in the environmental dimension is one of the greatest challenges and emerging threats. The presence of resistant bacteria and resistance genes in the environment, especially in aquatic systems, has been a matter of growing concern in the past decade. Monitoring the presence of antimicrobial resistance species, in this particular case, Staphylococcus spp., in natural water environments could lead to a better understanding of the epidemiology of staphylococci infections. Thus, the investigation of natural waters as a potential reservoir and vehicle for transmission of these bacteria is imperative. Only a few studies have investigated the prevalence, antimicrobial resistance and genetic lineages of staphylococci in natural waters. Those studies reported a high diversity of staphylococci species and lineages in surface waters. Methicillin-resistant S. aureus were relatively prevalent in surface waters and, as expected, often presented a multidrug-resistant profile. There was a high diversity of S. aureus lineages in surface waters. The presence of S. aureus CC8 and CC5 suggests a human origin. Among the coagulase-negative staphylococci, the most frequently found in natural waters was S. warneri and S. epidermidis. These studies are extremely important to estimate the contribution of the aquatic environment in the spread of pathogenic bacteria.

Metagenomic insights into the antibiotic resistome of mangrove sediments and their association to socioeconomic status

Mangrove sediments are prone to anthropogenic activities that could enrich antibiotics resistance genes (ARGs). The emergence and dissemination of ARGs are of serious concern to public health worldwide. Therefore, a comprehensive resistome analysis of global mangrove sediment is of paramount importance. In this study, we have implemented a deep machine learning approach to analyze the resistome of mangrove sediments from Brazil, China, Saudi Arabia, India, and Malaysia. Geography (R_ANOSIM = 39.26%; p < 0.005) as well as human intervention (R_ANOSIM = 16.92%; p < 0.005) influenced the ARG diversity. ARG diversity was also inversely correlated to the human development index (HDI) of the host country (R = -0.53; p < 0.05) rather than antibiotics consumption (p > 0.05). Several genes including multidrug efflux pumps were significantly (p < 0.05) enriched in the sites with human intervention. Resistome was consistently dominated by rpoB2 (19.26 ± 0.01%), multidrug ABC transporter (10.40 ± 0.23%), macB (8.84 ± 0.36n%), tetA (4.13 ± 0.35%), mexF (3.26 ± 0.19%), CpxR (2.93 ± 0.2%), bcrA (2.38 ± 0.24%), acrB (2.37 ± 0.18%), mexW (2.19 ± 0.17%), and vanR (1.99 ± 0.11%). Besides, mobile ARGs such as vanA, tet(48), mcr, and tetX were also detected in the mangrove sediments. Comparative analysis against terrestrial and ocean resistomes showed that the ocean ecosystem harbored the lowest ARG diversity (Chao1 = 71.12) followed by mangroves (Chao1 = 258.07) and terrestrial ecosystem (Chao1 = 294.07). ARG subtypes such as abeS and qacG were detected exclusively in ocean datasets. Likewise, rpoB2, multidrug ABC transporter, and macB, detected in mangrove and terrestrial datasets, were not detected in the ocean datasets. This study shows that the socioeconomic factors strongly determine the antibiotic resistome in the mangrove. Direct anthropogenic intervention in the mangrove environment also enriches antibiotic resistome.

The dissemination of antibiotic resistance in various environmental objects (Russia)

Environmental objects (surface and groundwater, soil, bottom sediments, wastewater) are reservoirs in which large-scale multidirectional exchange of determinants of antibiotic resistance between clinical strains and natural bacteria takes place. The review discusses the results of studies on antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG) isolated from environmental objects (water, soil, sewage, permafrost) of the Russian Federation. Despite the relevance of the topic, the number of available publications examining the resistomes of Russian water bodies and soils is small. The most studied environmental objects are surface waters (rivers, lakes), permafrost deposits. Soil resistomes are less studied. Data on ARG and ARB in wastewater are the least covered in publications. In most of the studies, antibiotic resistance of isolated pure bacterial cultures was determined phenotypically. A significant number of publications are devoted to the resistance of natural isolates of Vibrio cholerae, since the lower reaches of the Volga and Don rivers are endemic to cholera. Molecular genetic methods were used in a small number of studies. Geographically, the south of the European part of Russia is the most studied. There are also publications on the distribution of ARG in water bodies of Siberia and the Russian Far East. There are practically no publications on such developed regions of Russia as the center and northwest of the European part of Russia. The territory of the country is very large, anthropogenic and natural factors in its various regions vary significantly; therefore, it seems interesting to combine all available data in one work.