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866300.9004CPR 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.202438246077
638710.9003Insights into the Evolutionary and Ecological Roles of Bathyarchaeia in Arsenic Detoxification. Arsenic (As) is a prevalent toxic element, posing significant risks to organisms, including microbes. While microbial arsenic detoxification has been extensively studied in bacteria, archaeal mechanisms remain understudied. Here, we investigated arsenic resistance genes in Bathyarchaeia, one of the most abundant archaeal lineages on Earth. Comprehensive genomic analysis of 318 Bathyarchaeia representatives revealed a widespread distribution of arsenic resistance genes, with 60% of genomes harboring genes for arsenate reduction (arsR1 and arsC2), arsenite methylation (arsM), and arsenic transport (acr3, arsP, and arsB). Phylogenetic analysis revealed that these genes are widely distributed across 14 archaeal phyla, including Asgardarchaeota, Thermoproteota, and Thermoplasmatota, with close evolutionary relationships among these archaeal lineages. In situ investigation of sediment columns and laboratory microcosm experiments demonstrated a strong positive correlation between Bathyarchaeia abundance and arsenic concentrations, suggesting their adaptation to arsenic-rich environments. Molecular dating analysis placed the emergence of Bathyarchaeia at approximately 3.01 billion years ago, with the evolution of their arsenic resistance mechanisms closely tracking major geological events, including the Great Oxidation Event (2.4-2.1 Gya), Huronian Glaciation (2.29-2.25 Gya), and Cryogenian Glaciation (∼700 Mya). Our findings highlight the critical role of Archaea in the arsenic cycle and provide insights into the evolutionary history of arsenic resistance associated with paleogeochemical changes in Bathyarchaeia.202540921195
50920.8997A novel toxoflavin-quenching regulation in bacteria and its application to resistance cultivars. The toxoflavin (Txn), broad host range phytotoxin produced by a variety of bacteria, including Burkholderia glumae, is a key pathogenicity factor of B. glumae in rice and field crops. Two bacteria exhibiting Txn-degrading activity were isolated from healthy rice seeds and identified as Sphingomonas adhaesiva and Agrobacterium sp. respectively. The genes stdR and stdA, encoding proteins responsible for Txn degradation of both bacterial isolates, were identical, indicating that horizontal gene transfer occurred between microbial communities in the same ecosystem. We identified a novel Txn-quenching regulation of bacteria, demonstrating that the LysR-type transcriptional regulator (LTTR) StdR induces the expression of the stdA, which encodes a Txn-degrading enzyme, in the presence of Txn as a coinducer. Here we show that the bacterial StdR(Txn) -quenching regulatory system mimics the ToxR(Txn) -mediated biosynthetic regulation of B. glumae. Substrate specificity investigations revealed that Txn is the only coinducer of StdR and that StdA has a high degree of specificity for Txn. Rice plants expressing StdA showed Txn resistance. Collectively, bacteria mimic the mechanism of Txn biosynthesis regulation, employ it in the development of a Txn-quenching regulatory system and share it with neighbouring bacteria for survival in rice environments full of Txn.202134009736
864430.8992Biotic 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.202540054196
813340.8990Symbiotic bacteria confer insecticide resistance by metabolizing buprofezin in the brown planthopper, Nilaparvata lugens (Stål). Buprofezin, a chitin synthesis inhibitor, is widely used to control several economically important insect crop pests. However, the overuse of buprofezin has led to the evolution of resistance and exposed off-target organisms present in agri-environments to this compound. As many as six different strains of bacteria isolated from these environments have been shown to degrade buprofezin. However, whether insects can acquire these buprofezin-degrading bacteria from soil and enhance their own resistance to buprofezin remains unknown. Here we show that field strains of the brown planthopper, Nilaparvata lugens, have acquired a symbiotic bacteria, occurring naturally in soil and water, that provides them with resistance to buprofezin. We isolated a symbiotic bacterium, Serratia marcescens (Bup_Serratia), from buprofezin-resistant N. lugens and showed it has the capacity to degrade buprofezin. Buprofezin-susceptible N. lugens inoculated with Bup_Serratia became resistant to buprofezin, while antibiotic-treated N. lugens became susceptible to this insecticide, confirming the important role of Bup_Serratia in resistance. Sequencing of the Bup_Serratia genome identified a suite of candidate genes involved in the degradation of buprofezin, that were upregulated upon exposure to buprofezin. Our findings demonstrate that S. marcescens, an opportunistic pathogen of humans, can metabolize the insecticide buprofezin and form a mutualistic relationship with N. lugens to enhance host resistance to buprofezin. These results provide new insight into the mechanisms underlying insecticide resistance and the interactions between bacteria, insects and insecticides in the environment. From an applied perspective they also have implications for the control of highly damaging crop pests.202338091367
864550.8988Resilience mechanisms of rhizosphere microorganisms in lead-zinc tailings: Metagenomic insights into heavy metal resistance. This study investigates the impact of heavy metal contamination in lead-zinc tailings on plant and soil microbial communities, focusing on the resilience mechanisms of rhizosphere microorganisms in these extreme environments. Utilizing metagenomic techniques, we identified a significant association between Coriaria nepalensis Wall. rhizosphere microbial communities and metal(loid) resistance genes. Our results reveal a notable diversity and abundance of bacteria within the rhizosphere of tailings, primarily consisting of Proteobacteria, Actinobacteria, and Chloroflexi. The presence of metal-resistant bacterial taxa, including Afipia, Bradyrhizobium, Sphingomonas, and Miltoncostaea, indicates specific evolutionary adaptations to metal-rich, nutrient-deficient environments. Elevated expression of resistance genes such as znuD, zntA, pbrB, and pbrT underscores the microorganisms' ability to endure these harsh conditions. These resistance genes are crucial for maintaining biodiversity, ecosystem stability, and adaptability. Our findings enhance the understanding of interactions between heavy metal contamination, microbial community structure, and resistance gene dynamics in lead-zinc tailings. Additionally, this research provides a theoretical and practical foundation for employing plant-microbial synergies in the in-situ remediation of contaminated sites.202540056745
638660.8981Distribution of antibiotic and metal resistance genes in two glaciers of North Sikkim, India. Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understand the impact of climate change. Mapquesting the glaciers led to the discovery of concealed world of "psychrophiles" harboring in it. In the present study, the antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) were evaluated through both the culture-dependent and culture-independent methods. Samples were collected from two different glaciers, i.e., debris-covered glacier (Changme Khangpu) and debris-free glacier (Changme Khang). Functional metagenomics of both the glacier samples, provided evidence of presence of resistant genes against various antibiotic groups. Bacitracin resistant gene (bacA) was the predominant ARG in both the glaciers. MRGs in both the glacier samples were diversified as the genes detected were resistant against various heavy metals such as arsenic, tungsten, mercury, zinc, chromium, copper, cobalt, and iron. Unique MRGs identified from Changme Khangpu glacier were resistant to copper (cutA, cutE, cutC, cutF, cueR, copC, and copB) and chromium (yelf, ruvB, nfsA, chrR, and chrA) whereas, from Changme Khang glacier they showed resistance against cobalt (mgtA, dmef, corD, corC, corB, and cnrA), and iron (yefD, yefC, yefB, and yefA) heavy metals. ARGs aligned maximum identity with Gram-negative psychrotolerant bacteria. The cultured bacterial isolates showed tolerance to high concentrations of tested heavy metal solutions. Interestingly, some of the antibiotic resistant bacterial isolates also showed tolerance towards the higher concentrations of heavy metals. Thus, an introspection of the hypothesis of co-occurrence and/co-selection of ARGs and MRGs in such environments has been highlighted here.202032888596
638870.8980A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota. Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.202337504286
637980.8978Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India. Anthropogenic activities mediated antibiotic resistance genes (ARGs) in the pristine aquatic bodies (lakes) is raising concern worldwide. Long read shotgun sequencing was used to assess taxonomic diversity, distribution of ARGs and metal resistance genes (MRGs) and mobile genetic elements (MGEs) in six sites within hypersaline Lonar soda lake (India) prone to various anthropogenic activities. Proteobacteria and Euryarchaeota were dominant phyla under domain Bacteria and Archaea respectively. Higher abundance of Bacteroidetes was pragmatic at sites 18LN5 and 18LN6. Functional analysis indicated 26 broad-spectrum ARGs types, not reported earlier in this ecosystem. Abundant ARG types identified were multidrug efflux, glycopepetide, bacitracin, tetracycline and aminogylcoside resistance. Sites 18LN1 and 18LN5 depicted 167 and 160 different ARGs subtypes respectively and rpoB2, bcrA, tetA(48), mupA, ompR, patA, vanR and multidrug ABC transporter genes were present in all samples. The rpoB2 gene was dominant in 18LN1, whereas bcrA gene in 18LN2-18LN6 sites. Around 24 MRGs types were detected with higher abundance of arsenic in 18LN1 and copper in 18LN2-18LN6, signifying metal contamination linked to MRGs. The bacterial taxa Pseudomonas, Thioalkalivibrio, Burkholderia, Clostridium, Paenibacillus, Bacillus and Streptomyces were significantly associated with ARGs. This study highlights the resistomic hotspots in the lake for deploying policies for conservation efforts.202032155479
867190.8974Adapting to UV: Integrative Genomic and Structural Analysis in Bacteria from Chilean Extreme Environments. Extremophilic bacteria from extreme environments, such as the Atacama Desert, Salar de Huasco, and Antarctica, exhibit adaptations to intense UV radiation. In this study, we investigated the genomic and structural mechanisms underlying UV resistance in three bacterial isolates identified as Bacillus velezensis PQ169, Pseudoalteromonas sp. AMH3-8, and Rugamonas violacea T1-13. Through integrative genomic analyses, we identified key genes involved in DNA-repair systems, pigment production, and spore formation. Phylogenetic analyses of aminoacidic sequences of the nucleotide excision repair (NER) system revealed conserved evolutionary patterns, indicating their essential role across diverse bacterial taxa. Structural modeling of photolyases from Pseudoalteromonas sp. AMH3-8 and R. violacea T1-13 provided further insights into protein function and interactions critical for DNA repair and UV resistance. Additionally, the presence of a complete violacein operon in R. violacea T1-13 underscores pigment biosynthesis as a crucial protective mechanism. In B. velezensis PQ169, we identified the complete set of genes responsible for sporulation, suggesting that sporulation may represent a key protective strategy employed by this bacterium in response to environmental stress. Our comprehensive approach underscores the complexity and diversity of microbial adaptations to UV stress, offering potential biotechnological applications and advancing our understanding of microbial resilience in extreme conditions.202540565314
7947100.8973Molecular insights into linkages among free-floating macrophyte-derived organic matter, the fate of antibiotic residues, and antibiotic resistance genes. Macrophyte rhizospheric dissolved organic matter (ROM) served as widespread abiotic components in aquatic ecosystems, and its effects on antibiotic residues and antibiotic resistance genes (ARGs) could not be ignored. However, specific influencing mechanisms for ROM on the fate of antibiotic residues and expression of ARGs still remained unclear. Herein, laboratory hydroponic experiments for water lettuce (Pistia stratiotes) were carried out to explore mutual interactions among ROM, sulfamethoxazole (SMX), bacterial community, and ARGs expression. Results showed ROM directly affect SMX concentrations through the binding process, while CO and N-H groups were main binding sites for ROM. Dynamic changes of ROM molecular composition diversified the DOM pool due to microbe-mediated oxidoreduction, with enrichment of heteroatoms (N, S, P) and decreased aromaticity. Microbial community analysis showed SMX pressure significantly stimulated the succession of bacterial structure in both bulk water and rhizospheric biofilms. Furthermore, network analysis further confirmed ROM bio-labile compositions as energy sources and electron shuttles directly influenced microbial structure, thereby facilitating proliferation of antibiotic resistant bacteria (Methylotenera, Sphingobium, Az spirillum) and ARGs (sul1, sul2, intl1). This investigation will provide scientific supports for the control of antibiotic residues and corresponding ARGs in aquatic ecosystems.202438653136
7950110.8969Fate and removal of fluoroquinolone antibiotics in mesocosmic wetlands: Impact on wetland performance, resistance genes and microbial communities. The fate of fluoroquinolone antibiotics norfloxacin and ofloxacin were investigated in mesocosmic wetlands, along with their effects on nutrients removal, antibiotic resistance genes (ARGs) and epiphytic microbial communities on Hydrilla verticillate using bionic plants as control groups. Approximately 99% of norfloxacin and ofloxacin were removed from overlaying water, and H. verticillate inhibited fluoroquinolones accumulation in surface sediments compared to bionic plants. Partial least squares path modeling showed that antibiotics significantly inhibited the nutrient removal capacity (0.55) but had no direct effect on plant physiology. Ofloxacin impaired wetland performance more strongly than norfloxacin and more impacted the primary microbial phyla, whereas substrates played the most decisive role on microbial diversities. High antibiotics concentration shifted the most dominant phyla from Proteobacteria to Bacteroidetes and inhibited the Xenobiotics biodegradation function, contributing to the aggravation in wetland performance. Dechloromonas and Pseudomonas were regarded as the key microorganisms for antibiotics degradation. Co-occurrence network analysis excavated that microorganisms degrade antibiotics mainly through co-metabolism, and more complexity and facilitation/reciprocity between microbes attached to submerged plants compared to bionic plants. Furthermore, environmental factors influenced ARGs mainly by altering the community dynamics of differential bacteria. This study offers new insights into antibiotic removal and regulation of ARGs accumulation in wetlands with submerged macrophyte.202438569335
6792120.8969Parity in bacterial communities and resistomes: Microplastic and natural organic particles in the Tyrrhenian Sea. Petroleum-based microplastic particles (MPs) are carriers of antimicrobial resistance genes (ARGs) in aquatic environments, influencing the selection and spread of antimicrobial resistance. This research characterized MP and natural organic particle (NOP) bacterial communities and resistomes in the Tyrrhenian Sea, a region impacted by plastic pollution and climate change. MP and NOP bacterial communities were similar but different from the free-living planktonic communities. Likewise, MP and NOP ARG abundances were similar but different (higher) from the planktonic communities. MP and NOP metagenome-assembled genomes contained ARGs associated with mobile genetic elements and exhibited co-occurrence with metal resistance genes. Overall, these findings show that MPs and NOPs harbor potential pathogenic and antimicrobial resistant bacteria, which can aid in the spread of antimicrobial resistance. Further, petroleum-based MPs do not represent novel ecological niches for allochthonous bacteria; rather, they synergize with NOPs, collectively facilitating the spread of antimicrobial resistance in marine ecosystems.202438759465
7665130.8967Metagenomic 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.202335113183
8631140.8965Bacterial metal(loid) resistance genes (MRGs) and their variation and application in environment: A review. Toxic metal(loid)s are widespread and permanent in the biosphere, and bacteria have evolved a wide variety of metal(loid) resistance genes (MRGs) to resist the stress of excess metal(loid)s. Via active efflux, permeability barriers, extracellular/intracellular sequestration, enzymatic detoxification and reduction in metal(loid)s sensitivity of cellular targets, the key components of bacterial cells are protected from toxic metal(loid)s to maintain their normal physiological functions. Exploiting bacterial metal(loid) resistance mechanisms, MRGs have been applied in many environmental fields. Based on the specific binding ability of MRGs-encoded regulators to metal(loid)s, MRGs-dependent biosensors for monitoring environmental metal(loid)s are developed. MRGs-related biotechnologies have been applied to environmental remediation of metal(loid)s by using the metal(loid) tolerance, biotransformation, and biopassivation abilities of MRGs-carrying microorganisms. In this work, we review the historical evolution, resistance mechanisms, environmental variation, and environmental applications of bacterial MRGs. The potential hazards, unresolved problems, and future research directions are also discussed.202336758696
7663150.8965Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance. Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.202236423774
133160.8963Determinants of Copper Resistance in Acidithiobacillus Ferrivorans ACH Isolated from the Chilean Altiplano. The use of microorganisms in mining processes is a technology widely employed around the world. Leaching bacteria are characterized by having resistance mechanisms for several metals found in their acidic environments, some of which have been partially described in the Acidithiobacillus genus (mainly on ferrooxidans species). However, the response to copper has not been studied in the psychrotolerant Acidithiobacillus ferrivorans strains. Therefore, we propose to elucidate the response mechanisms of A. ferrivorans ACH to high copper concentrations (0-800 mM), describing its genetic repertoire and transcriptional regulation. Our results show that A. ferrivorans ACH can grow in up to 400 mM of copper. Moreover, we found the presence of several copper-related makers, belonging to cop and cus systems, as well as rusticyanins and periplasmatic acop protein in the genome. Interestingly, the ACH strain is the only one in which we find three copies of copB and copZ genes. Moreover, transcriptional expression showed an up-regulation response (acop, copZ, cusA, rusA, and rusB) to high copper concentrations. Finally, our results support the important role of these genes in A. ferrivorans copper stress resistance, promoting the use of the ACH strain in industrial leaching under low temperatures, which could decrease the activation times of oxidation processes and the energy costs.202032722087
8646170.8962A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils. Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.202133810508
7737180.8962Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome. BACKGROUND: Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independent metagenomic approaches to explore the virulence and antibiotic resistance in the hadal microbiota of the Mariana Trench. RESULTS: The results indicate that the 10,898 m Challenger Deep bottom sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance, compared with the neighboring but shallower 6038 m steep wall site and the more nearshore 5856 m Pacific basin site. Virulence genes including several famous large translocating virulence genes (e.g., botulinum neurotoxins, tetanus neurotoxin, and Clostridium difficile toxins) were uniquely detected in the trench bottom. However, the shallower and more nearshore site sediment had a higher abundance and richer diversity of known antibiotic resistance genes (ARGs), especially for those clinically relevant ones (e.g., fosX, sul1, and TEM-family extended-spectrum beta-lactamases), revealing resistance selection under anthropogenic stresses. Further analysis of mobilome (i.e., the collection of mobile genetic elements, MGEs) suggests horizontal gene transfer mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria. Notably, contig-level co-occurring and taxonomic analysis shows emerging evidence for substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria. CONCLUSIONS: This study reports the landscape of virulence factors, antibiotic resistome, and mobilome in the sediment and seawater microbiota residing hadal environment of the deepest ocean bottom on earth. Our work unravels the contrasting and unique features of virulence genes, ARGs, and MGEs in the Mariana Trench bottom, providing new insights into the eco-environmental and biological processes underlying microbial pathogenicity, resistance, and adaptative evolution in the hadal environment.202235468809
508190.8962Insights into the chaotropic tolerance of the desert cyanobacterium Chroococcidiopsis sp. 029 (Chroococcidiopsales, Cyanobacteria). The mechanism of perchlorate resistance of the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated by assessing whether the pathways associated with its desiccation tolerance might play a role against the destabilizing effects of this chaotropic agent. During 3 weeks of growth in the presence of 2.4 mM perchlorate, an upregulation of trehalose and sucrose biosynthetic pathways was detected. This suggested that in response to the water stress triggered by perchlorate salts, these two compatible solutes play a role in the stabilization of macromolecules and membranes as they do in response to dehydration. During the perchlorate exposure, the production of oxidizing species was observed by using an oxidant-sensing fluorochrome and determining the expression of the antioxidant defense genes, namely superoxide dismutases and catalases, while the presence of oxidative DNA damage was highlighted by the over-expression of genes of the base excision repair. The involvement of desiccation-tolerance mechanisms in the perchlorate resistance of this desert cyanobacterium is interesting since, so far, chaotropic-tolerant bacteria have been identified among halophiles. Hence, it is anticipated that desert microorganisms might possess an unrevealed capability of adapting to perchlorate concentrations exceeding those naturally occurring in dry environments. Furthermore, in the endeavor of supporting future human outposts on Mars, the identified mechanisms might contribute to enhance the perchlorate resistance of microorganisms relevant for biologically driven utilization of the perchlorate-rich soil of the red planet.202438156502