# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 8654 | 0 | 0.9978 | Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake. Cueva de la Mora (CM) is an acidic, meromictic pit lake in the Iberian Pyrite Belt characterized by extremely high metal(loid) concentrations and strong gradients in oxygen, metal, and nutrient concentrations. We hypothesized that geochemical variations with depth would result in differences in community composition and in metal resistance strategies among active microbial populations. We also hypothesized that metal resistance gene (MRG) expression would correlate with toxicity levels for dissolved metal species in the lake. Water samples were collected in the upper oxic layer, chemocline, and deep anoxic layer of the lake for shotgun metagenomic and metatranscriptomic sequencing. Metagenomic analyses revealed dramatic differences in the composition of the microbial communities with depth, consistent with changing geochemistry. Based on relative abundance of taxa identified in each metagenome, Eukaryotes (predominantly Coccomyxa) dominated the upper layer, while Archaea (predominantly Thermoplasmatales) dominated the deep layer, and a combination of Bacteria and Eukaryotes were abundant at the chemocline. We compared metal resistance across communities using a curated list of protein-coding MRGs with KEGG Orthology identifiers (KOs) and found that there were broad differences in the metal resistance strategies (e.g., intracellular metal accumulation) expressed by Eukaryotes, Bacteria, and Archaea. Although normalized abundances of MRG and MRG expression were generally higher in the deep layer, expression of metal-specific genes was not strongly related to variations in specific metal concentrations, especially for Cu and As. We also compared MRG potential and expression in metagenome assembled genomes (MAGs) from the deep layer, where metal concentrations are highest. Consistent with previous work showing differences in metal resistance mechanisms even at the strain level, MRG expression patterns varied strongly among MAG populations from the same depth. Some MAG populations expressed very few MRG known to date, suggesting that novel metal resistance strategies remain to be discovered in uncultivated acidophiles. | 2020 | 32899650 |
| 8659 | 1 | 0.9978 | Phage phylogeny, molecular signaling, and auxiliary antimicrobial resistance in aerobic and anaerobic membrane bioreactors. Phage emit communication signals that inform their lytic and lysogenic life cycles. However, little is known regarding the abundance and diversity of the genes associated with phage communication systems in wastewater treatment microbial communities. This study focused on phage communities within two distinct biochemical wastewater environments, specifically aerobic membrane bioreactors (AeMBRs) and anaerobic membrane bioreactors (AnMBRs) exposed to varying antibiotic concentrations. Metagenomic data from the bench-scale systems were analyzed to explore phage phylogeny, life cycles, and genetic capacity for antimicrobial resistance and quorum sensing. Two dominant phage families, Schitoviridae and Peduoviridae, exhibited redox-dependent dynamics. Schitoviridae prevailed in anaerobic conditions, while Peduoviridae dominated in aerobic conditions. Notably, the abundance of lytic and lysogenic proteins varied across conditions, suggesting the coexistence of both life cycles. Furthermore, the presence of antibiotic resistance genes (ARGs) within viral contigs highlighted the potential for phage to transfer ARGs in AeMBRs. Finally, quorum sensing genes in the virome of AeMBRs indicated possible molecular signaling between phage and bacteria. Overall, this study provides insights into the dynamics of viral communities across varied redox conditions in MBRs. These findings shed light on phage life cycles, and auxiliary genetic capacity such as antibiotic resistance and bacterial quorum sensing within wastewater treatment microbial communities. | 2024 | 38677036 |
| 8647 | 2 | 0.9977 | 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 |
| 8649 | 3 | 0.9977 | Antibiotic-Induced Recruitment of Specific Algae-Associated Microbiome Enhances the Adaptability of Chlorella vulgaris to Antibiotic Stress and Incidence of Antibiotic Resistance. Insights into the symbiotic relation between eukaryotic hosts and their microbiome lift the curtain on the crucial roles of microbes in host fitness, behavior, and ecology. However, it remains unclear whether and how abiotic stress shapes the microbiome and further affects host adaptability. This study first investigated the effect of antibiotic exposure on behavior across varying algae taxa at the community level. Chlorophyta, in particular Chlorella vulgaris, exhibited remarkable adaptability to antibiotic stress, leading to their dominance in phytoplankton communities. Accordingly, we isolated C. vulgaris strains and compared the growth of axenic and nonaxenic ones under antibiotic conditions. The positive roles of antibiotics in algal growth were apparent only in the presence of bacteria. Results of 16S rRNA sequencing further revealed that antibiotic challenges resulted in the recruitment of specific bacterial consortia in the phycosphere, whose functions were tightly linked to the host growth promotion and adaptability enhancement. In addition, the algal phycosphere was characterized with 47-fold higher enrichment capability of antibiotic resistance genes (ARGs) than the surrounding water. Under antibiotic stress, specific ARG profiles were recruited in C. vulgaris phycosphere, presumably driven by the specific assembly of bacterial consortia and mobile genetic elements induced by antibiotics. Moreover, the antibiotics even enhanced the dissemination potential of the bacteria carrying ARGs from the algal phycosphere to broader environmental niches. Overall, this study provides an in-depth understanding into the potential functional significance of antibiotic-mediated recruitment of specific algae-associated bacteria for algae adaptability and ARG proliferation in antibiotic-polluted waters. | 2023 | 37642958 |
| 8565 | 4 | 0.9977 | Deciphering the transfers of antibiotic resistance genes under antibiotic exposure conditions: Driven by functional modules and bacterial community. Antibiotics can exert selective pressures on sludge as well as affect the emergence and spread of antibiotic resistance genes (ARGs). However, the underlying mechanisms of ARGs transfers are still controversial and not fully understood in sludge system. In present study, two anaerobic sequence batch reactors (ASBR) were constructed to investigate the development of ARGs exposed to two sulfonamide antibiotics (SMs, sulfadiazine SDZ and sulfamethoxazole SMX) with increasing concentrations. The abundance of corresponding ARGs and total ARGs obviously increased with presence of SMs. Functional analyses indicated that oxidative stress response, signal transduction and type IV secretion systems were triggered by SMs, which would promote ARGs transfers. Network analysis revealed 18 genera were possible hosts of ARGs, and their abundances increased with SMs. Partial least-squares path modeling suggested functional modules directly influenced mobile genetic elements (MGEs) as well as the ARGs might be driven by both functional modules and bacteria community, while bacteria community composition played a more key role. Sludge with refractory antibiotics (SDZ) may stimulate the relevant functions and shift the microbial composition to a greater extent, causing more ARGs to emerge and spread. The mechanisms of ARGs transfers are revealed from the perspective of functional modules and bacterial community in sludge system for the first time, and it could provide beneficial directions, such as oxidative stress reduction, cellular communication control, bacterial composition directional regulation, for ARGs spread controlling in the future. | 2021 | 34563930 |
| 8662 | 5 | 0.9976 | Relationships between Phyllosphere Bacterial Communities and Leaf Functional Traits in a Temperate Forest. As a vital component of biodiversity, phyllosphere bacteria in forest canopy play a critical role in maintaining plant health and influencing the global biogeochemical cycle. There is limited research on the community structure of phyllosphere bacteria in natural forests, which creates a gap in our understanding of whether and/or how phyllosphere bacteria are connected to leaf traits of their host. In this study, we investigated the bacterial diversity and composition of the canopy leaves of six dominant tree species in deciduous broad-leaved forests in northeastern China, using high-throughput sequencing. We then compare the differences in phyllosphere bacterial community structure and functional genes of dominant tree species. Fourteen key leaf functional traits of their host trees were also measured according to standard protocols to investigate the relationships between bacterial community composition and leaf functional traits. Our result suggested that tree species with closer evolutionary distances had similar phyllosphere microbial alpha diversity. The dominant phyla of phyllosphere bacteria were Proteobacteria, Actinobacteria, and Firmicutes. For these six tree species, the functional genes of phyllosphere bacteria were mainly involved in amino acid metabolism and carbohydrate metabolism processes. The redundancy and envfit analysis results showed that the functional traits relating to plant nutrient acquisition and resistance to diseases and pests (such as leaf area, isotope carbon content, and copper content) were the main factors influencing the community structure of phyllosphere bacteria. This study highlights the key role of plant interspecific genetic relationships and plant attributes in shaping phyllosphere bacterial diversity. | 2023 | 38005751 |
| 8664 | 6 | 0.9976 | Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system. BACKGROUND: Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system. RESULTS: We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes. CONCLUSIONS: These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. Video Abstract. | 2023 | 36945052 |
| 7476 | 7 | 0.9976 | Bacterial phylogeny structures soil resistomes across habitats. Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny. | 2014 | 24847883 |
| 7982 | 8 | 0.9975 | Decoding the trajectory of antibiotic resistance genes in saline and alkaline soils: Insights from different fertilization regimes. The soil salinity and alkalinity play an important role in the occurrence and proliferation of antibiotic resistance genes (ARGs). Yet, little is known the underlying mechanism by which soil salinity and alkalinity affect antibiotic resistance evolution. Here we investigated the ARGs variation in soil salinity and alkalinity environments created by different fertilization, and explored the biological mechanisms that salinity and alkalinity alter the evolutionary paradigm of antibiotic resistance. The results showed the soil treated by organic fertilizer exhibited a low salinity, neutral level (TSD 239.20 μS/cm, pH 7.17). The ARG abundance in the OF treatment was the highest, keeping an average of 67.83 TPM. Beside the effect of direct input of organic fertilizer at the beginning, it was important to note that, ARGs abundance during planting showed significant correlations with pH and electric conductivity. We observed that changes in microbial survival strategies under different salinity and alkalinity conditions further affected ARG hosts abundance. Indoor experiments demonstrated that there was a survival trade-off between the growth of resistant bacteria and the evolution of antibiotic resistance in salinity and alkalinity environments. Meta-genomic and Meta-transcriptomic analysis consistently demonstrated bacterial antibiotic resistance was primarily associated with pyruvate, energy and lipid metabolic pathways. The functional gene related to salinity and alkalinity, like cysH, cysK, plsB and plsC showed negative correlations with MDR. Prokaryotic transcription assays validated these relations. This study well explains the prevalence of soil ARGs after different fertilization regimes and will give a deeper understanding for the effect of soil salinity and alkalinity on antibiotic resistance evolution. | 2025 | 39765202 |
| 7665 | 9 | 0.9975 | Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs. Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health. | 2023 | 35113183 |
| 8656 | 10 | 0.9975 | Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia. Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence. | 2022 | 36116192 |
| 8648 | 11 | 0.9975 | Host-specific assembly of phycosphere microbiome and enrichment of the associated antibiotic resistance genes: Integrating species of microalgae hosts, developmental stages and water contamination. Phytoplankton-bacteria interactions profoundly impact ecosystem function and biogeochemical cycling, while their substantial potential to carry and disseminate antibiotic resistance genes (ARGs) poses a significant threat to global One Health. However, the ecological paradigm behind the phycosphere assembly of microbiomes and the carrying antibiotic resistomes remains unclear. Our field investigation across various freshwater ecosystems revealed a substantial enrichment of bacteria and ARGs within microalgal niches. Taking account of the influence for species of microalgae hosts, their developmental stages and the stress of water pollution, we characterized the ecological processes governing phycosphere assembly of bacterial consortia and enrichment of the associated ARGs. By inoculating 6 axenic algal hosts with two distinct bacterial consortia from a natural river and the phycosphere of Scenedesmus acuminatus, we observed distinct phycosphere bacteria recruitment among different algal species, yet consistency within the same species. Notably, a convergent bacterial composition was established for the same algae species for two independent inoculations, demonstrating host specificity in phycosphere microbiome assembly. Host-specific signature was discernible as early as the algal lag phase and more pronounced as the algae developed, indicating species types of algae determined mutualism between the bacterial taxa and hosts. The bacteria community dominated the shaping of ARG profiles within the phycosphere and the host-specific phycosphere ARG enrichment was intensified with the algae development. The polluted water significantly stimulated host's directional selection on phycosphere bacterial consortia and increased the proliferation antibiotic resistome. These consortia manifested heightened beneficial functionality, enhancing microalgal adaptability to contamination stress. | 2025 | 40349825 |
| 8658 | 12 | 0.9975 | Microplastic exposure reshapes the virome and virus-bacteria networks with implications for immune regulation in Mytilus coruscus. Microplastic pollution has emerged as a critical environmental concern, yet its impacts on host-associated viral communities and immune balance in marine bivalves remain largely unexplored. In this study, Mytilus coruscus individuals were exposed to microplastics in situ for seven days. Virome sequencing and bioinformatic analyses revealed that microplastic exposure induced divergent responses in DNA and RNA viral communities. DNA viromes exhibited suppressed diversity and downregulation of core viral metabolic pathways, potentially reflecting reduced viral replication capacity under host immune stress. In contrast, RNA viromes displayed metabolic activation and functional shifts, including enriched glycan and nucleotide metabolism, possibly linked to enhanced viral activity or immune evasion. Phage-bacteria interaction networks were also restructured, showing increased associations with opportunistic pathogens such as Vibrio cholerae and Enterobacter, potentially affecting immune surveillance. Furthermore, the expression of antibiotic resistance genes (ARGs) in viral genomes was differentially regulated, suggesting pollutant-induced microbial selection that may challenge host immune resilience. These findings suggest that microplastics not only reshape virome composition and metabolic functions but also influence virus-mediated immune interactions, with important implications for disease susceptibility and immune homeostasis in filter-feeding shellfish. | 2025 | 41056669 |
| 8698 | 13 | 0.9975 | Metagenomics of Virus Diversities in Solid-State Brewing Process of Traditional Chinese Vinegar. Traditional Chinese vinegar offers an exceptional flavor and rich nutrients due to its unique solid-state fermentation process, which is a multiple microbial fermentation system including various bacteria, fungi and viruses. However, few studies on the virus diversities in traditional Chinese vinegar have been reported. In this paper, using Zhenjiang aromatic vinegar as a model system, we systemically explored the viral communities in the solid-state brewing process of traditional Chinese vinegar using bacterial and viral metagenomes. Results showed that the viral diversity in vinegar Pei was extensive and the virus communities varied along with the fermentation process. In addition, there existed some interactions between viral and bacterial communities. Moreover, abundant antibiotic resistance genes were found in viromes, indicating that viruses might protect fermentation bacteria strains from the stress of antibiotics in the fermentation environment. Remarkably, we identified abundant auxiliary carbohydrate metabolic genes (including alcohol oxidases, the key enzymes for acetic acid synthesis) from viromes, implying that viruses might participate in the acetic acid synthesis progress of the host through auxiliary metabolic genes. Taken together, our results indicated the potential roles of viruses in the vinegar brewing process and provided a new perspective for studying the fermentation mechanisms of traditional Chinese vinegar. | 2022 | 37431044 |
| 6940 | 14 | 0.9975 | Higher spreading risk of antibacterial biocide and heavy metal resistance genes than antibiotic resistance genes in aerobic granular sludge. Metagenomic approach was applied to simultaneously reveal the antibiotic resistance genes (ARGs) and antibacterial biocide & metal resistance genes (BMRGs), and the corresponding microbial hosts with high mobility during aerobic granular sludge (AGS) formation process. The results showed that the relative abundance of BMRGs was 88-123 times that of ARGs. AGS process was easier to enrich BMRGs, leading to a greater risk of drug resistance caused by BMRGs than that by ARGs. The enrichments of ARGs and BMRGs in AGS were closely related to several enhanced microbial metabolisms (i.e., cell motility, transposase and ATP-binding cassette transporters) and their corresponding regulatory genes. Several enhanced KEGG Orthologs (KO) functions, such as K01995, K01996, K01997 and K02002, might cause a positive impact on the spread of ARGs and BMRGs, and the main contributors were the largely enriched glycogens accumulating organisms. The first dominant ARGs (adeF) was carried by lots of microbial hosts, which might be enriched and propagated mainly through horizontal gene transfer. Candidatus Competibacter denitrificans simultaneously harbored ARG (cmx) and Cu related RGs (corR). Many enriched bacteria contained simultaneously multiple BMRGs (copR and corR) and mobile genetic elements (integrons and plasmids), granting them high mobility capabilities and contributing to the spread of BMRGs. This study might provide deeper understandings of the proliferation and mobility of ARGs and BMRGs, importantly, highlighted the status of BMRGs, which laid the foundation for the controlling widespread of resistance genes in AGS. | 2022 | 35489476 |
| 155 | 15 | 0.9975 | RNA-Seq transcriptomic analysis reveals gene expression profiles of acetic acid bacteria under high-acidity submerged industrial fermentation process. Acetic acid bacteria (AAB) are Gram-negative obligate aerobics in Acetobacteraceae family. Producing acetic acid and brewing vinegars are one of the most important industrial applications of AAB, attributed to their outstanding ability to tolerate the corresponding stresses. Several unique acid resistance (AR) mechanisms in AAB have been revealed previously. However, their overall AR strategies are still less-comprehensively clarified. Consequently, omics analysis was widely performed for a better understanding of this field. Among them, transcriptome has recently obtained more and more attention. However, most currently reported transcriptomic studies were conducted under lab conditions and even in low-acidity environment, which may be unable to completely reflect the conditions that AAB confront under industrialized vinegar-brewing processes. In this study, we performed an RNA-Seq transcriptomic analysis concerning AAB's AR mechanisms during a continuous and periodical industrial submerged vinegar fermentation process, where a single AAB strain performed the fermentation and the acetic acid concentration fluctuated between ~8% and ~12%, the highest acidity as far we know for transcriptomic studies. Samples were directly taken from the initial (CK), mid, and final stages of the same period of the on-going fermentation. 16S rRNA sequence analysis indicated the participation of Komagataeibacter europaeus in the fermentation. Transcriptomic results demonstrated that more genes were downregulated than upregulated at both mid and final stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrich analysis reflected that the upregulated genes mainly carried out tricarboxylic acid cycle and oxidative phosphorylation processes, probably implying a considerable role of acetic acid overoxidation in AR during fermentation. Besides, upregulation of riboflavin biosynthesis pathway and two NAD(+)-dependent succinate-semialdehyde dehydrogenase-coding genes suggested a critical role of succinate oxidation in AR. Meanwhile, downregulated genes were mainly ribosomal protein-coding ones, reflecting that the adverse impact on ribosomes initiates at the transcription level. However, it is ambiguous whether the downregulation is good for stress responding or it actually reflects the stress. Furthermore, we also assumed that the fermentation stages may have a greater effect on gene expression than acidity. Additionally, it is possible that some physiological alterations would affect the AR to a larger extent than changes in gene expression, which suggests the combination of molecular biology and physiology research will provide deeper insight into the AR mechanisms in AAB. | 2022 | 36246236 |
| 8663 | 16 | 0.9975 | CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater. The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 metagenome-assembled genomes (MAGs) from 66 groundwater samples, we explored the effect of antibiotics on bacterial, archaeal, and fungal communities, and revealed the pivotal microbes and their mechanisms in coping with antibiotic stress. The results indicated that antibiotics had the most significant influence on bacterial and archaeal communities, while the impact on the fungal community was minimal. Analysis of co-occurrence networks between antibiotics and microbes revealed the critical roles of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea, two representative microbial groups in groundwater ecosystem, in coping with antibiotic resistance and enhancing network connectivity and complexity. Further genomic analysis demonstrated that CPR bacteria carried approximately 6 % of the identified antibiotic resistance genes (ARGs), indicating their potential to withstand antibiotics on their own. Meanwhile, the genomes of CPR bacteria and DPANN archaea were found to encode diverse biosynthetic gene clusters (BGCs) responsible for producing antimicrobial metabolites, which could not only assist CPR and DPANN organisms but also benefit the surrounding microbes in combating antibiotic stress. These findings underscore the significant impact of antibiotics on prokaryotic microbial communities in groundwater, and highlight the importance of CPR bacteria and DPANN archaea in enhancing the overall resilience and functionality of the microbial community in the face of antibiotic stress. | 2024 | 38246077 |
| 8812 | 17 | 0.9975 | Discovery of a new genus of anaerobic ammonium oxidizing bacteria with a mechanism for oxygen tolerance. In the past 20 years, there has been a major stride in understanding the core mechanism of anaerobic ammonium-oxidizing (anammox) bacteria, but there are still several discussion points on their survival strategies. Here, we discovered a new genus of anammox bacteria in a full-scale wastewater-treating biofilm system, tentatively named "Candidatus Loosdrechtia aerotolerans". Next to genes of all core anammox metabolisms, it encoded and transcribed genes involved in the dissimilatory nitrate reduction to ammonium (DNRA), which coupled to oxidation of small organic acids, could be used to replenish ammonium and sustain their metabolism. Surprisingly, it uniquely harbored a new ferredoxin-dependent nitrate reductase, which has not yet been found in any other anammox genome and might confer a selective advantage to it in nitrate assimilation. Similar to many other microorganisms, superoxide dismutase and catalase related to oxidative stress resistance were encoded and transcribed by "Ca. Loosdrechtia aerotolerans". Interestingly, bilirubin oxidase (BOD), likely involved in oxygen resistance of anammox bacteria under fluctuating oxygen concentrations, was identified in "Ca. Loosdrechtia aerotolerans" and four Ca. Brocadia genomes, and its activity was demonstrated using purified heterologously expressed proteins. A following survey of oxygen-active proteins in anammox bacteria revealed the presence of other previously undetected oxygen defense systems. The novel cbb3-type cytochrome c oxidase and bifunctional catalase-peroxidase may confer a selective advantage to Ca. Kuenenia and Ca. Scalindua that face frequent changes in oxygen concentrations. The discovery of this new genus significantly broadens our understanding of the ecophysiology of anammox bacteria. Furthermore, the diverse oxygen tolerance strategies employed by distinct anammox bacteria advance our understanding of their niche adaptability and provide valuable insight for the operation of anammox-based wastewater treatment systems. | 2022 | 36257158 |
| 6904 | 18 | 0.9975 | Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure. An expanding list of chemicals may permeabilize bacterial cells and facilitate horizontal gene transfer (HGT), which enhances propagation of antibiotic resistance genes (ARGs) in the environment. Previous studies showed that 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), an ionic liquid, can facilitate HGT of some ARGs among bacteria. However, the dynamic response of a wider range of ARGs and associated mobile genetic elements (MGEs) in different environments is unknown. Here, we used metagenomic tools to study shifts of the resistome and microbiome in both sediments and freshwater microcosms exposed to [BMIm][PF6]. Exposure for 16 h to 0.1 or 1.0 g/L significantly enriched more than 207 ARG subtypes primarily encoding efflux pumps in freshwater microcosms as well as cultivable antibiotic-resistant bacteria. This resistome enrichment was attributed to HGT facilitated by MGEs (428 plasmids, 61 integron-integrase genes, and 45 gene cassettes were enriched) as well as to HGT-related functional genes. Interestingly, resistome enrichment occurred fast (within 16 h) after [BMIm][PF6] exposure, before any significant changes in bacterial community structure. Similar ARG enrichment occurred in sediment microcosms exposed to [BMIm][PF6] for 28 d, and this longer exposure affected the microbial community structure (e.g., Proteobacteria abundance increased significantly). Overall, this study suggests that [BMIm][PF6] releases could rapidly enrich the antibiotic resistome in receiving environments by increasing HGT and fortuitously selecting for efflux pump genes, thus contributing to ARG propagation. | 2020 | 31944684 |
| 7636 | 19 | 0.9975 | Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions. A paradoxical impact of high rates of production and consumption of antibiotics is their widespread release in the environment. Consequently, low concentrations of antibiotics and their byproducts have been routinely identified from various environmental settings especially from aquatic environments. However, the impact of such low concentrations of antibiotics on the exposed host especially in early life remains poorly understood. We exposed zebrafish to two different environmental concentrations of oxytetracycline and sulfamethoxazole, from larval stage to adulthood (∼120 days) and characterized their impact on the taxonomic diversity, antibiotic resistance genes, and metabolic pathways of the gut microbiome using metagenomic shotgun sequencing and analysis. Long term exposure of environmental concentrations of oxytetracycline and sulfamethoxazole significantly impacted the taxonomic composition and metabolic pathways of zebrafish gut microbiome. The antibiotic exposed samples exhibited significant enrichment of multiple flavobacterial species, including Flavobacterium sp. F52, Flavobacterium johnsoniae and Flavobacterium sp. Fl, which are well known pathogenic bacteria. The relative abundance of antibiotic resistance genes, especially several tetratcycline and sulfonamide resistance genes were significantly higher in the exposed samples and showed a linear correlation with the antibiotic concentrations. Furthermore, several metabolic pathways, including folate biosynthesis, oxidative phosphorylation, and biotin metabolism pathways, showed significant enrichment in the antibiotic exposed samples. Collectively, our results suggest that early life exposure of the environmental concentrations of antibiotics can increase the abundance of unfavorable bacteria, antibiotic resistance genes and associated pathways in the gut microbiome of zebrafish. | 2021 | 33725532 |