# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 8628 | 0 | 0.9894 | Biofertilizer microorganisms accompanying pathogenic attributes: a potential threat. Application of biofertilizers containing living or dormant plant growth promoting bacterial cells is considered to be an ecofriendly alternative of chemical fertilizers for improved crop production. Biofertilizers opened myriad doors towards sustainable agriculture as they effectively reduce heavy use of chemical fertilizers and pesticides by keeping soils profuse in micro and macronutrients, regulating plant hormones and restraining infections caused by the pests present in soil without inflicting environmental damage. Generally, pathogenicity and biosafety testing of potential plant growth promoting bacteria (PGPB) are not performed, and the bacteria are reported to be beneficial solely on testing plant growth promoting characteristics. Unfortunately, some rhizosphere and endophytic PGPB are reported to be involved in various diseases. Such PGPB can also spread virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Therefore, deployment of such microbial populations in open fields could lead to disastrous side effects on human health and environment. Careless declaration of bacteria as PGPB is more pronounced in research publications. Here, we present a comprehensive report of declared PGPB which are reported to be pathogenic in other studies. This review also suggests the employment of some additional safety assessment protocols before reporting a bacteria as beneficial and product development. | 2022 | 35221573 |
| 8630 | 1 | 0.9894 | Environmental fate and behaviour of antibiotic resistance genes and small interference RNAs released from genetically modified crops. Rising global populations have amplified food scarcity across the world and ushered in the development of genetically modified (GM) crops to overcome these challenges. Cultivation of major crops such as corn and soy has favoured GM crops over conventional varieties to meet crop production and resilience needs. Modern GM crops containing small interference RNA molecules and antibiotic resistance genes have become increasingly common in the United States. However, the use of these crops remains controversial due to the uncertainty regarding the unintended release of its genetic material into the environment and possible downstream effects on human and environmental health. DNA or RNA transgenes may be exuded from crop tissues during cultivation or released during plant decomposition and adsorbed by soil. This can contribute to the persistence and bioavailability in soil or water environment and possible uptake by soil microbial communities and further passing of this information to neighbouring bacteria, disrupting microbial ecosystem services such as nutrient cycling and soil fertility. In this review, transgene mechanisms of action, uses in crops, and knowledge regarding their environmental fate and impact to microbes are evaluated. This aims to encapsulate the current knowledge and promote further research regarding unintended effects transgenes may cause. | 2022 | 35892194 |
| 8644 | 2 | 0.9894 | Biotic and abiotic drivers of soil carbon, nitrogen and phosphorus and metal dynamic changes during spontaneous restoration of Pb-Zn mining wastelands. The biotic and abiotic mechanisms that drive important biogeochemical processes (carbon, nitrogen, phosphorus and metals dynamics) in metal mine revegetation remains elusive. Metagenomic sequencing was used to explored vegetation, soil properties, microbial communities, functional genes and their impacts on soil processes during vegetation restoration in a typical Pb-Zn mine. The results showed a clear niche differentiation between bacteria, fungi and archaea. Compared to bacteria and fungi, the archaea richness were more tightly coupled with natural restoration changes. The relative abundances of CAZyme-related, denitrification-related and metal resistance genes reduced, while nitrification, urease, inorganic phosphorus solubilisation, phosphorus transport, and phosphorus regulation -related genes increased. Redundancy analysis, hierarchical partitioning analysis, relative-importance analysis and partial least squares path modelling, indicated that archaea diversity, primarily influenced by available lead, directly impacts carbon dynamics. Functional genes, significantly affected by available cadmium, directly alter nitrogen dynamics. Additionally, pH affects phosphorus dynamics through changes in bacterial diversity, while metal dynamics are directly influenced by vegetation. These insights elucidate natural restoration mechanisms in mine and highlight the importance of archaea in soil processes. | 2025 | 40054196 |
| 8647 | 3 | 0.9892 | Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades. With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change. | 2024 | 39019914 |
| 8625 | 4 | 0.9891 | Marine viruses: truth or dare. Over the past two decades, marine virology has progressed from a curiosity to an intensely studied topic of critical importance to oceanography. At concentrations of approximately 10 million viruses per milliliter of surface seawater, viruses are the most abundant biological entities in the oceans. The majority of these viruses are phages (viruses that infect bacteria). Through lysing their bacterial hosts, marine phages control bacterial abundance, affect community composition, and impact global biogeochemical cycles. In addition, phages influence their hosts through selection for resistance, horizontal gene transfer, and manipulation of bacterial metabolism. Recent work has also demonstrated that marine phages are extremely diverse and can carry a variety of auxiliary metabolic genes encoding critical ecological functions. This review is structured as a scientific "truth or dare," revealing several well-established "truths" about marine viruses and presenting a few "dares" for the research community to undertake in future studies. | 2012 | 22457982 |
| 8423 | 5 | 0.9891 | Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis. Arbuscular mycorrhizal fungi (AMF) belong to Glomeromycotina, and are mutualistic symbionts of many land plants. Associated bacteria accompany AMF during their lifecycle to establish a robust tripartite association consisting of fungi, plants and bacteria. Physical association among this trinity provides possibilities for the exchange of genetic materials. However, very few horizontal gene transfer (HGT) from bacteria or plants to AMF has been reported yet. In this study, we complement existing algorithms by developing a new pipeline, Blast2hgt, to efficiently screen for putative horizontally derived genes from a whole genome. Genome analyses of the glomeromycete Rhizophagus irregularis identified 19 fungal genes that had been transferred between fungi and bacteria/plants, of which seven were obtained from bacteria. Another 18 R. irregularis genes were found to be recently acquired from either plants or bacteria. In the R. irregularis genome, gene duplication has contributed to the expansion of three foreign genes. Importantly, more than half of the R. irregularis foreign genes were expressed in various transcriptomic experiments, suggesting that these genes are functional in R. irregularis. Functional annotation and available evidence showed that these acquired genes may participate in diverse but fundamental biological processes such as regulation of gene expression, mitosis and signal transduction. Our study suggests that horizontal gene influx through endosymbiosis is a source of new functions for R. irregularis, and HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus. | 2018 | 29887874 |
| 8361 | 6 | 0.9891 | Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts. Symbiotic microorganisms are crucial for the survival of corals and their resistance to coral bleaching in the face of climate change. However, the impact of microbe-microbe interactions on coral functioning is mostly unknown but could be essential factors for coral adaption to future climates. Here, we investigated interactions between cultured dinoflagellates of the Symbiodiniaceae family, essential photosymbionts of corals, and associated bacteria. By assessing the genomic potential of 49 bacteria, we found that they are likely beneficial for Symbiodiniaceae, through the production of B vitamins and antioxidants. Additionally, bacterial genes involved in host-symbiont interactions, such as secretion systems, accumulated mutations following long-term exposure to heat, suggesting symbiotic interactions may change under climate change. This highlights the importance of microbe-microbe interactions in coral functioning. | 2023 | 37909753 |
| 6934 | 7 | 0.9891 | Impact of protist predation on bacterial community traits in river sediments. Sediment-associated microbial communities are pivotal in driving biogeochemical processes and serve as key indicators of ecosystem health and function. However, the ecological impact of protist predation on these microbial communities remains poorly understood. Here, sediment microcosms were established with varying concentrations of indigenous protists. Results revealed that protist predation exerted strong and differential effects on the bacterial community composition, functional capabilities, and antibiotic resistance profiles. Higher levels of protist predation pressure increased bacterial alpha diversity and relative abundance of genera associated with carbon and nitrogen cycling, such as Fusibacter, Methyloversatilis, Azospirillum, and Holophaga. KEGG analysis indicated that protist predation stimulated microbial processes related to the carbon, nitrogen, and sulfur cycles. Notably, the relative abundance and associated health risks of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and mobile genetic elements (MGEs) were affected by predation pressure. Medium protist predation pressure increased the relative abundance and potential risks associated with ARGs, whereas high protist concentrations led to a reduction in both, likely due to a decrease in the relative abundance of ARG-hosting pathogenic bacteria such as Pseudomonas, Acinetobacter, and Aeromonas. These findings provide comprehensive insights into the dynamics of bacterial communities under protist predation in river sediment ecosystems. | 2025 | 40885182 |
| 6439 | 8 | 0.9890 | A review: Marine aquaculture impacts marine microbial communities. Marine aquaculture is key for protein production but disrupts marine ecosystems by releasing excess feed and pharmaceuticals, thus affecting marine microbes. Though vital, its environmental impact often remains overlooked. This article delves into mariculture's effects on marine microbes, including bacteria, fungi, viruses, and antibiotic-resistance genes in seawater and sediments. It highlights how different mariculture practices-open, pond, and cage culture-affect these microbial communities. Mariculture's release of nutrients, antibiotics, and heavy metals alters the microbial composition, diversity, and functions. Integrated multi-trophic aquaculture, a promising sustainable approach, is still developing and needs refinement. A deep understanding of mariculture's impact on microbial ecosystems is crucial to minimize pollution and foster sustainable practices, paving the way for the industry's sustainable advancement. | 2024 | 38919720 |
| 6447 | 9 | 0.9889 | Climate warming fuels the global antibiotic resistome by altering soil bacterial traits. Understanding the implications of global warming on the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) within soil ecosystems is crucial for safeguarding human well-being and sustaining ecosystem health. However, there is currently a lack of large-scale, systematic underpinning data needed to examine this issue. Here, using an integrative approach that combines field experiments, extensive global metagenomic data and microbial culturing, we show that warming enriches bacteria with ARGs and VFGs, increases metabolic complexity and adaptability in bacteria, and accelerates genetic alterations related to ARG and VFGs development. Our validation experiments confirm that the warming effect is more pronounced in colder regions. Machine learning predictions further suggest that warming will increase the soil ARG abundance, especially in some areas that rely heavily on fossil fuels. These results suggest another major negative consequence of global warming, highlighting the importance of developing and implementing sustainability policies that simultaneously combat climate change and antibiotic resistance. | 2025 | 40468041 |
| 6440 | 10 | 0.9889 | Fate and transport of biological microcontaminants bound to microplastics in the soil environment. Microplastics, fragmented plastic particles with a maximum dimension <5 mm, are an emerging contaminant of concern that can also serve as a vector of other chemical and biological contaminants. Compared to chemical contaminants, the potential of microplastics to adsorb biological microcontaminants such as antibiotic resistance genes, small interference RNAs, and pathogenic viruses is not well understood. Many current microplastic studies are based in the aquatic environment (freshwater, seawater, and wastewater), even though the terrestrial environment is considered both an important sink and source of microplastics. Microplastics co-occur with biological microcontaminants in many terrestrial environments including agricultural soils, where biosolids containing both contaminants are often applied as a soil amendment. Recent research suggests that microplastics in these environments can increase gene persistence and flow, which could have unintended downstream consequences for environmental microbiome health and resilience. Antibiotic resistance genes and silencing RNAs bound to microplastics, for example, have the potential to increase resistance and alter gene expression in environmental bacteria, respectively. This review evaluates the sources and pathways of microplastics and biological microcontaminants in the terrestrial environment as well as potential sorption mechanisms that can encourage long-range transport and persistence. Novel sources of biological microcontaminants are considered, and the role of microplastics in promoting the persistence and flow of biological microcontaminants evaluated. Finally, future research directions are suggested to increase understanding of the mechanisms that drive the fate and transport of microplastic-biological microcontaminant complexes in the terrestrial environment and better inform risk management. | 2023 | 37247742 |
| 9583 | 11 | 0.9889 | Bacteriophages presence in nature and their role in the natural selection of bacterial populations. Phages are the obligate parasite of bacteria and have complex interactions with their hosts. Phages can live in, modify, and shape bacterial communities by bringing about changes in their abundance, diversity, physiology, and virulence. In addition, phages mediate lateral gene transfer, modify host metabolism and reallocate bacterially-derived biochemical compounds through cell lysis, thus playing an important role in ecosystem. Phages coexist and coevolve with bacteria and have developed several antidefense mechanisms in response to bacterial defense strategies against them. Phages owe their existence to their bacterial hosts, therefore they bring about alterations in their host genomes by transferring resistance genes and genes encoding toxins in order to improve the fitness of the hosts. Application of phages in biotechnology, environment, agriculture and medicines demands a deep insight into the myriad of phage-bacteria interactions. However, to understand their complex interactions, we need to know how unique phages are to their bacterial hosts and how they exert a selective pressure on the microbial communities in nature. Consequently, the present review focuses on phage biology with respect to natural selection of bacterial populations. | 2020 | 33170167 |
| 6438 | 12 | 0.9888 | The influence of heavy metals, polyaromatic hydrocarbons, and polychlorinated biphenyls pollution on the development of antibiotic resistance in soils. The minireview is devoted to the analysis of the influence of soil pollution with heavy metals, polyaromatic hydrocarbons (PAHs), and the polychlorinated biphenyls (PCBs) on the distribution of antibiotics resistance genes (ARGs) in soil microbiomes. It is shown that the best understanding of ARGs distribution process requires studying the influence of pollutants on this process in natural microbiocenoses. Heavy metals promote co-selection of genes determining resistance to them together with ARGs in the same mobile elements of a bacterial genome, but the majority of studies focus on agricultural soils enriched with ARGs originating from manure. Studying nonagricultural soils would clear mechanisms of ARGs transfer in natural and anthropogenically transformed environments and highlight the role of antibiotic-producing bacteria. PAHs make a considerable shift in soil microbiomes leading to an increase in the number of Actinobacteria which are the source of antibiotics formation and bear multiple ARGs. The soils polluted with PAHs can be a selective medium for bacteria resistant to antibiotics, and the level of ARGs expression is much higher. PCBs are accumulated in soils and significantly alter the specific structure of soil microbiocenoses. In such soils, representatives of the genera Acinetobacter, Pseudomonas, and Alcanivorax dominate, and the ability to degrade PCBs is connected to horizontal gene transfer (HGT) and high level of genomic plasticity. The attention is also focused on the need to study the properties of the soil having an impact on the bioavailability of pollutants and, as a result, on resistome of soil microorganisms. | 2018 | 29453715 |
| 9728 | 13 | 0.9888 | Metagenomic analysis of metal(loid)s resistance genes and its environmental applications. Heavy metals are widely used to satiate the demands of growing industrialization and modern life. However, the presence of metal in large quantities in the ecosystem significantly impacts all life forms, particularly microorganisms. Many bacterial strains have developed metal resistance genes (MRG) to survive in extreme conditions through various mechanisms, such as active efflux, sequestration, permeability barriers, or co-resistance with antibiotic resistance genes. Metagenomic analysis is a powerful approach that enables the exploration of the functional repertoire and diversity of microorganisms, providing deeper insights into the mechanisms underlying the development of MRGs, and the active metabolites they produce to adapt to the polluted environments. With the advancement of these techniques, the knowledge can be further applied to environmental applications, such as bioremediation, biomonitoring, and synthetic biology. Bacteria with metal toxicity tolerance can be employed to enhance environmental sustainability and mitigate potential hazards. | 2025 | 40992856 |
| 8629 | 14 | 0.9888 | Antibiotic resistance in plant growth promoting bacteria: A comprehensive review and future perspectives to mitigate potential gene invasion risks. Plant growth-promoting bacteria (PGPB) are endowed with several attributes that can be beneficial for host plants. They opened myriad doors toward green technology approach to reduce the use of chemical inputs, improve soil fertility, and promote plants' health. However, many of these PGPB harbor antibiotic resistance genes (ARGs). Less attention has been given to multi-resistant bacterial bioinoculants which may transfer their ARGs to native soil microbial communities and other environmental reservoirs including animals, waters, and humans. Therefore, large-scale inoculation of crops by ARGs-harboring bacteria could worsen the evolution and dissemination of antibiotic resistance and aggravate the negative impacts on such ecosystem and ultimately public health. Their introduction into the soil could serve as ARGs invasion which may inter into the food chain. In this review, we underscore the antibiotic resistance of plant-associated bacteria, criticize the lack of consideration for this phenomenon in the screening and application processes, and provide some recommendations as well as a regulation framework relating to the development of bacteria-based biofertilizers to aid maximizing their value and applications in crop improvement while reducing the risks of ARGs invasion. | 2022 | 36204627 |
| 6396 | 15 | 0.9888 | Interaction between microplastic biofilm formation and antibiotics: Effect of microplastic biofilm and its driving mechanisms on antibiotic resistance gene. As two pollutants with similar transport pathways, microplastics (MPs) and antibiotics (ATs) inevitably co-exist in water environments, and their interaction has become a topic of intense research interest for scholars over the past few years. This paper comprehensively and systematically reviews the current interaction between MPs and ATs, in particular, the role played by biofilm developed MPs (microplastic biofilm). A summary of the formation process of microplastic biofilm and its unique microbial community structure is presented in the paper. The formation of microplastic biofilm can enhance the adsorption mechanisms of ATs on primary MPs. Moreover, microplastic biofilm system is a diverse and vast reservoir of genetic material, and this paper reviews the mechanisms by which microplastics with biofilm drive the production of antibiotic resistance genes (ARGs) and the processes that selectively enrich for more ARGs. Meanwhile, the enrichment of ARGs may lead to the development of microbial resistance and the gradual loss of the antimicrobial effect of ATs. The transfer pathways of ARGs affected by microplastic biofilm are outlined, and ARGs dependent transfer of antibiotic resistance bacteria (ARB) is mainly through horizontal gene transfer (HGT). Furthermore, the ecological implications of the interaction between microplastic biofilm and ATs and perspectives for future research are reviewed. This review contributes to a new insight into the aquatic ecological environmental risks and the fate of contaminants (MPs, ATs), and is of great significance for controlling the combined pollution of these two pollutants. | 2023 | 37517232 |
| 8635 | 16 | 0.9888 | Techniques for enhancing the tolerance of industrial microbes to abiotic stresses: A review. The diversity of stress responses and survival strategies evolved by microorganism enables them to survive and reproduce in a multitude of harsh environments, whereas the discovery of the underlying resistance genes or mechanisms laid the foundation for the directional enhancement of microbial tolerance to abiotic stresses encountered in industrial applications. Many biological techniques have been developed for improving the stress resistance of industrial microorganisms, which greatly benefited the bacteria on which industrial production is based. This review introduces the main techniques for enhancing the resistance of microorganisms to abiotic stresses, including evolutionary engineering, metabolic engineering, and process engineering, developed in recent years. In addition, we also discuss problems that are still present in this area and offer directions for future research. | 2020 | 31206805 |
| 8335 | 17 | 0.9887 | Implementing Optogenetic-Controlled Bacterial Systems in Drosophila melanogaster for Alleviation of Heavy Metal Poisoning. Drosophila melanogaster (fruit fly) is an animal model chassis in biological and genetic research owing to its short life cycle, ease of cultivation, and acceptability to genetic modification. While the D. melanogaster chassis offers valuable insights into drug efficacy, toxicity, and mechanisms, several obvious challenges such as dosage control and drug resistance still limit its utility in pharmacological studies. Our research combines optogenetic control with engineered gut bacteria to facilitate the precise delivery of therapeutic substances in D. melanogaster for biomedical research. We have shown that the engineered bacteria can be orally administered to D. melanogaster to get a stable density of approximately 28,000 CFUs/per fly, leading to no detectable negative effects on the growth of D. melanogaster. In a model of D. melanogaster exposure to heavy metal, these orally administered bacteria uniformly express target genes under green light control to produce MtnB protein for binding and detoxifying lead, which significantly reduces the level of oxidative stress in the intestinal tract of Pb-treated flies. This pioneering study lays the groundwork for using optogenetic-controlled bacteria in the model chassis D. melanogaster to advance biomedical applications. | 2024 | 39312764 |
| 6449 | 18 | 0.9887 | Microbial regulation of natural antibiotic resistance: Understanding the protist-bacteria interactions for evolution of soil resistome. The emergence, evolution and spread of antibiotic resistance genes (ARGs) in the environment represent a global threat to human health. Our knowledge of antibiotic resistance in human-impacted ecosystems is rapidly growing with antibiotic use, organic fertilization and wastewater irrigation identified as key selection pressures. However, the importance of biological interactions, especially predation and competition, as a potential driver of antibiotic resistance in the natural environment with limited anthropogenic disturbance remains largely overlooked. Stress-affected bacteria develop resistance to maximize competition and survival, and similarly bacteria may develop resistance to fight stress under the predation pressure of protists, an essential component of the soil microbiome. In this article, we summarized the major findings for the prevalence of natural ARGs on our planet and discussed the potential selection pressures driving the evolution and development of antibiotic resistance in natural settings. This is the first article that reviewed the potential links between protists and the antibiotic resistance of bacteria, and highlighted the importance of predation by protists as a crucial selection pressure of antibiotic resistance in the absence of anthropogenic disturbance. We conclude that an improved ecological understanding of the protists-bacteria interactions and other biological relationships would greatly expand our ability to predict and mitigate the environmental antibiotic resistance under the context of global change. | 2020 | 31818598 |
| 8766 | 19 | 0.9887 | Partitioning the Effects of Soil Legacy and Pathogen Exposure Determining Soil Suppressiveness via Induced Systemic Resistance. Beneficial host-associated bacteria can assist plant protection against pathogens. In particular, specific microbes are able to induce plant systemic resistance. However, it remains largely elusive which specific microbial taxa and functions trigger plant immune responses associated with disease suppression. Here, we experimentally studied this by setting up two independent microcosm experiments that differed in the time at which plants were exposed to the pathogen and the soil legacy (i.e., soils with historically suppressive or conducive). Overall, we found soil legacy effects to have a major influence on disease suppression irrespective of the time prior to pathogen exposure. Rhizosphere bacterial communities of tomato plants were significantly different between the two soils, with potential beneficial strains occurring at higher relative abundances in the suppressive soil. Root transcriptome analysis revealed the soil legacy to induce differences in gene expression, most importantly, genes involved in the pathway of phenylpropanoid biosynthesis. Last, we found genes in the phenylpropanoid biosynthesis pathway to correlate with specific microbial taxa, including Gp6, Actinomarinicola, Niastella, Phaeodactylibacter, Longimicrobium, Bythopirellula, Brevundimonas, Ferruginivarius, Kushneria, Methylomarinovum, Pseudolabrys, Sphingobium, Sphingomonas, and Alterococcus. Taken together, our study points to the potential regulation of plant systemic resistance by specific microbial taxa, and the importance of soil legacy on disease incidence and eliciting plant-defense mechanisms. | 2022 | 36365269 |