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882200.9908Proteomics Analysis Reveals Bacterial Antibiotics Resistance Mechanism Mediated by ahslyA Against Enoxacin in Aeromonas hydrophila. Bacterial antibiotic resistance is a serious global problem; the underlying regulatory mechanisms are largely elusive. The earlier reports states that the vital role of transcriptional regulators (TRs) in bacterial antibiotic resistance. Therefore, we have investigated the role of TRs on enoxacin (ENX) resistance in Aeromonas hydrophila in this study. A label-free quantitative proteomics method was utilized to compare the protein profiles of the ahslyA knockout and wild-type A. hydrophila strains under ENX stress. Bioinformatics analysis showed that the deletion of ahslyA triggers the up-regulated expression of some vital antibiotic resistance proteins in A. hydrophila upon ENX stress and thereby reduce the pressure by preventing the activation of SOS repair system. Moreover, ahslyA directly or indirectly induced at least 11 TRs, which indicates a complicated regulatory network under ENX stress. We also deleted six selected genes in A. hydrophila that altered in proteomics data in order to evaluate their roles in ENX stress. Our results showed that genes such as AHA_0655, narQ, AHA_3721, AHA_2114, and AHA_1239 are regulated by ahslyA and may be involved in ENX resistance. Overall, our data demonstrated the important role of ahslyA in ENX resistance and provided novel insights into the effects of transcriptional regulation on antibiotic resistance in bacteria.202134168639
904710.9901Comparison of transcriptomes of wild-type and isothiazolone-resistant Pseudomonas aeruginosa by using RNA-seq. Isothiazolone biocides (such as Kathon) are widely used in a variety of industrial and domestic applications. However, the mechanisms through which bacteria develop resistance to these biocides are not completely clear. A better understanding of these mechanisms can contribute to optimal use of these biocides. In this study, transcription profiles of a Kathon-resistant strain of Pseudomonas aeruginosa (Pa-R) and the wild-type strain were determined using RNA sequencing (RNA-Seq) with the Illumina HiSeq 2000 platform. RNA-Seq generated 18,657,896 sequence reads aligned to 7093 genes. In all, 1550 differently expressed genes (DEGs, log2 ratio ≥1, false discovery rate (FDR) ≤0.001) were identified, of which 482 were up-regulated and 1068 were down-regulated. Most Kathon-induced genes were involved in metabolic and cellular processes. DEGs significantly enriched nitrogen metabolism and oxidative phosphorylation pathways. In addition, Pa-R showed cross-resistance to triclosan and ciprofloxacin and showed repressed pyocyanin production. These results may improve our understanding of the resistance mechanisms of P. aeruginosa against isothiazolones, and provide insight into the development of more efficient isothiazolones.201627072374
25120.9900Deep sequencing analysis of the Kineococcus radiotolerans transcriptome in response to ionizing radiation. Kineococcus radiotolerans is a gram-positive, radiation-resistant bacterium that was isolated from a radioactive environment. The synergy of several groups of genes is thought to contribute to the radio-resistance of this species of bacteria. Sequencing of the transcriptome, RNA sequencing (RNA-seq), using deep sequencing technology can reveal the genes that are differentially expressed in response to radiation in this bacterial strain. In this study, the transcriptomes of two samples (with and without irradiation treatment) were sequencing by deep sequencing technology. After the bioinformatics process, 143 genes were screened out by the differential expression (DE) analysis. In all 143 differentially expressed genes, 20 genes were annotated to be related to the radio-resistance based on the cluster analysis by the cluster of orthologous groups of proteins (COG) annotation which were validated by the quantitative RT-PCR. The pathway analysis revealed that these 20 validated genes were related to DNA damage repair, including recA, ruvA and ruvB, which were considered to be the key genes in DNA damage repair. This study provides the foundation to investigate the regulatory mechanism of these genes.201525467197
614530.9900Arsenic-resistance mechanisms in bacterium Leclercia adecarboxylata strain As3-1: Biochemical and genomic analyses. Microbial arsenic transformation is important in As biogeochemical cycles in the environment. In this study, a new As-resistant bacterial strain Leclercia adecarboxylata As3-1 was isolated and its associated mechanisms in As resistance and detoxification were evaluated based on genome sequencing and gene annotations. After subjecting strain As3-1 to medium containing arsenate (AsV), AsV reduction occurred and an AsV-enhanced bacterial growth was observed. Strain As3-1 lacked arsenite (AsIII) oxidation ability and displayed lower AsIII resistance than AsV, probably due to its higher AsIII accumulation. Polymerase chain reaction and phylogenetic analysis showed that strain As3-1 harbored a typical AsV reductase gene (arsC) on the plasmids. Genome sequencing and gene annotations identified four operons phoUpstBACS, arsHRBC, arsCRDABC and ttrRSBCA, with 8 additional genes outside the operons that might have involved in As resistance and detoxification in strain As3-1. These included 5 arsC genes explaining why strain As3-1 tolerated high AsV concentrations. Besides ArsC, TtrB, TtrC and TtrA proteins could also be involved in AsV reduction and consequent energy acquisition for bacterial growth. Our data provided a new example of diverse As-regulating systems and AsV-enhanced growth without ArrA in bacteria. The information helps to understand the role of As in selecting microbial systems that can transform and utilize As.201931470481
360940.9899Genomic insights into the antibiotic resistance pattern of the tetracycline-degrading bacterium, Arthrobacter nicotianae OTC-16. Although many bacteria have the potential to remove antibiotic residues from environmental niches, the benefits of using antibiotic-degrading bacteria to manage antibiotic pollution should be assessed against the risk of the potential expansion of antimicrobial resistance. This study investigated the antibiotic resistance pattern of the bacterium Arthrobacter nicotianae OTC-16, which shows substantial biodegradation of oxytetracycline (OTC)/tetracycline. The results showed that this strain could be resistant to at least seven categories of 15 antibiotics, based on antimicrobial susceptibility testing. The genome of A. nicotianae OTC-16 contains one chromosome (3,643,989 bp) and two plasmids (plasmid1, 123,894 bp and plasmid2, 29,841 bp). Of the 3,561 genes isolated, eight were related to antibiotic resistance. During OTC degradation by the strain OTC-16, the expression of ant2ia, sul1, tet33, and cml_e8 in the plasmid, and one gene (tetV) in the chromosome were tracked using real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Only the plasmid-derived resistance genes were up-regulated in the presence of OTC. The presence of OTC increased the tolerance of strain OTC-16 to streptomycin sulphate. The findings of this study can help deepen our understanding of the behavioural characteristics of resistance genes and adaptive evolution of drug-resistant bacteria.202134341372
844650.9899Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica. Bacteria halo blight (BHB), a coffee plant disease caused by Pseudomonas syringae pv. garcae, has been gaining importance in producing mountain regions and mild temperatures areas as well as in coffee nurseries. Most Coffea arabica cultivars are susceptible to this disease. In contrast, a great source of genetic diversity and resistance to BHB are found in C. arabica Ethiopian accessions. Aiming to identify quantitative trait nucleotides (QTNs) associated with resistance to BHB and the influence of these genomic regions during the domestication of C. arabica, we conducted an analysis of population structure and a Genome-Wide Association Study (GWAS). For this, we used genotyping by sequencing (GBS) and phenotyping for resistance to BHB of a panel with 120 C. arabica Ethiopian accessions from a historical FAO collection, 11 C. arabica cultivars, and the BA-10 genotype. Population structure analysis based on single-nucleotide polymorphisms (SNPs) markers showed that the 132 accessions are divided into 3 clusters: most wild Ethiopian accessions, domesticated Ethiopian accessions, and cultivars. GWAS, using the single-locus model MLM and the multi-locus models mrMLM, FASTmrMLM, FASTmrEMMA, and ISIS EM-BLASSO, identified 11 QTNs associated with resistance to BHB. Among these QTNs, the four with the highest values of association for resistance to BHB are linked to g000 (Chr_0_434_435) and g010741 genes, which are predicted to encode a serine/threonine-kinase protein and a nucleotide binding site leucine-rich repeat (NBS-LRR), respectively. These genes displayed a similar transcriptional downregulation profile in a C. arabica susceptible cultivar and in a C. arabica cultivar with quantitative resistance, when infected with P. syringae pv. garcae. However, peaks of upregulation were observed in a C. arabica cultivar with qualitative resistance, for both genes. Our results provide SNPs that have potential for application in Marker Assisted Selection (MAS) and expand our understanding about the complex genetic control of the resistance to BHB in C. arabica. In addition, the findings contribute to increasing understanding of the C. arabica domestication history.202236330243
904360.9899The Bifunctional Enzyme SpoT Is Involved in the Clarithromycin Tolerance of Helicobacter pylori by Upregulating the Transporters HP0939, HP1017, HP0497, and HP0471. Clarithromycin (CLA) is a commonly recommended drug for Helicobacter pylori eradication. However, the prevalence of CLA-resistant H. pylori is increasing. Although point mutations in the 23S rRNA are key factors for CLA resistance, other factors, including efflux pumps and regulation genes, are also involved in the resistance of H. pylori to CLA. Guanosine 3'-diphosphate 5'-triphosphate and guanosine 3',5'-bispyrophosphate [(p)ppGpp)], which are synthesized by the bifunctional enzyme SpoT in H. pylori, play an important role for some bacteria to adapt to antibiotic pressure. Nevertheless, no related research involving H. pylori has been reported. In addition, transporters have been found to be related to bacterial drug resistance. Therefore, this study investigated the function of SpoT in H. pylori resistance to CLA by examining the shifts in the expression of transporters and explored the role of transporters in the CLA resistance of H. pylori A ΔspoT strain was constructed in this study, and it was shown that SpoT is involved in H. pylori tolerance of CLA by upregulating the transporters HP0939, HP1017, HP0497, and HP0471. This was assessed using a series of molecular and biochemical experiments and a cDNA microarray. Additionally, the knockout of genes hp0939, hp0471, and hp0497 in the resistant strains caused a reduction or loss (the latter in the Δhp0497 strain) of resistance to CLA. Furthermore, the average expression levels of these four transporters in clinical CLA-resistant strains were considerably higher than those in clinical CLA-sensitive strains. Taken together, our results revealed a novel molecular mechanism of H. pylori adaption to CLA stress.201728242673
853170.9898Biotransformation mechanism of Vibrio diabolicus to sulfamethoxazole at transcriptional level. Sulfamethoxazole (SMX) has attracted much attention due to its high probability of detection in the environment. Marine bacteria Vibrio diabolicus strain L2-2 has been proven to be able to transform SMX. In this study, the potential resistance and biotransformation mechanism of strain L2-2 to SMX, and key genes responses to SMX at environmental concentrations were researched. KEGG pathways were enriched by down-regulated genes including degradation of L-Leucine, L-Isoleucine, and fatty acid metabolism. Resistance mechanism could be concluded as the enhancement of membrane transport, antioxidation, response regulator, repair proteins, and ribosome protection. Biotransformation genes might involve in arylamine N-acetyltransferases (nat), cytochrome c553 (cyc-553) and acyl-CoA synthetase (acs). At the environmental concentration of SMX (0.1-10 μg/L), nat was not be activated, which meant the acetylation of SMX might not occur in the environment; however, cyc-553 was up-regulated under SMX stress of 1 μg/L, which indicated the hydroxylation of SMX could occur in the environment. Besides, the membrane transport and antioxidation of strain L2-2 could be activated under SMX stress of 10 μg/L. The results provided a better understanding of resistance and biotransformation of bacteria to SMX and would support related researches about the impacts of environmental antibiotics.202133429311
845380.9898In silico analysis of gene content in tomato genomic regions mapped to the Ty-2 resistance gene. Tomato yellow leaf curl virus is one of the main diseases affecting tomato production worldwide. Previous studies have shown that Ty-2 is an important resistance gene located between molecular markers C2_At2g28250 (82.3 cM) and T0302 (89.0 cM), and exhibits strong resistance to tomato yellow leaf curl virus in Asia. In this study, Ty-2 candidate genes were subjected to bioinformatic analysis for the sequenced tomato genome. We identified 69 genes between molecular markers C2_At2g28250 and T0302, 22 of which were disease-related resistant genes, including nucleotide binding site-leucine-rich repeat disease resistance genes, protease genes (protein kinase, kinase receptor, and protein isomerase), cytochromes, and transcription factors. Expressed sequence tag analysis revealed that 77.3% (17/22) of candidate disease-resistance genes were expressed, involving 143 expressed sequence tags. Based on full-length cDNA sequence analysis, 7 candidate genes were found, 4 of which were involved in tomato responses to pathogens. Microarray expression analysis also showed that most candidate genes were involved in the tomato responses to multiple pathogens, including fungi, viruses, and bacteria. RNA-seq expression analysis revealed that all candidate genes participated in tomato growth and development.201526214476
870490.9898Unraveling nitrogen metabolism, cold and stress adaptation in polar Bosea sp. PAMC26642 through comparative genome analysis. Nitrogen metabolism, related genes, and other stress-resistance genes are poorly understood in Bosea strain. To date, most of the research work in Bosea strains has been focused on thiosulfate oxidation and arsenic reduction. This work aimed to better understand and identify genomic features that enable thiosulfate-oxidizing lichen-associated Bosea sp. PAMC26642 from the Arctic region of Svalbard, Norway, to withstand harsh environments. Comparative genomic analysis was performed using various bioinformatics tools to compare Bosea sp. PAMC26642 with other strains of the same genus, emphasizing nitrogen metabolism and stress adaptability. During genomic analysis of Bosea sp. PAMC26642, assimilatory nitrogen metabolic pathway and its associated enzymes such as nitrate reductase, NAD(P)H-nitrite reductase, ferredoxin-nitrite reductase, glutamine synthetase, glutamine synthase, and glutamate dehydrogenase were identified. In addition, carbonic anhydrase, cyanate lyase, and nitronate monooxygenase were also identified. Furthermore, the strain demonstrated nitrate reduction at two different temperatures (15°C and 25°C). Enzymes associated with various stress adaptation pathways, including oxidative stress (superoxide dismutase, catalase, and thiol peroxidase), osmotic stress (OmpR), temperature stress (Csp and Hsp), and heavy metal resistance, were also identified. The average Nucleotide Identity (ANI) value is found to be below the threshold of 94-95%, indicating this bacterium might be a potential new species. This study is very helpful in determining the diversity of thiosulfate-oxidizing nitrate-reducing bacteria, as well as their ability to adapt to extreme environments. These bacteria can be used in the future for environmental, biotechnological, and agricultural purposes, particularly in processes involving sulfur and nitrogen transformation.202439925882
8826100.9897Transcriptome Analysis of Komagataeibacter europaeus CGMCC 20445 Responses to Different Acidity Levels During Acetic Acid Fermentation. In the industrial production of high-acidity vinegar, the initial ethanol and acetic acid concentrations are limiting factors that will affect acetic acid fermentation. In this study, Komagataeibacter europaeus CGMCC 20445 was used for acetic acid shake flask fermentation at an initial ethanol concentration of 4.3% (v/v). We conducted transcriptome analysis of K. europaeus CGMCC 20445 samples under different acidity conditions to elucidate the changes in differentially expressed genes throughout the fermentation process. We also analyzed the expression of genes associated with acid-resistance mechanisms. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the differentially expressed genes were enriched in ribosomes, citrate cycle, butanoate metabolism, oxidative phosphorylation, pentose phosphate, and the fatty acid biosynthetic pathways. In addition, this study found that K. europaeus CGMCC 20445 regulates the gene expression levels of cell envelope proteins and stress-responsive proteins to adapt to the gradual increase in acidity during acetic acid fermentation. This study improved the understanding of the acid resistance mechanism of K. europaeus and provided relevant reference information for the further genetic engineering of this bacterium.202134584524
8542110.9897Transcriptional Activity of Arsenic-Reducing Bacteria and Genes Regulated by Lactate and Biochar during Arsenic Transformation in Flooded Paddy Soil. Organic substrates and biochar are important in controlling arsenic release from sediments and soils; however, little is known about their impact on arsenic-reducing bacteria and genes during arsenic transformation in flooded paddy soils. In this study, microcosm experiments were established to profile transcriptional activity of As(V)-respiring gene (arrA) and arsenic resistance gene (arsC) as well as the associated bacteria regulated by lactate and/or biochar in anaerobic arsenic-contaminated paddy soils. Chemical analyses revealed that lactate as the organic substrate stimulated microbial reduction of As(V) and Fe(III), which was simultaneously promoted by lactate+biochar, due to biochar's electron shuttle function that facilitates electron transfer from bacteria to As(V)/Fe(III). Sequencing and phylogenetic analyses demonstrated that both arrA closely associated with Geobacter (>60%, number of identical sequences/number of the total sequences) and arsC related to Enterobacteriaceae (>99%) were selected by lactate and lactate+biochar. Compared with the lactate microcosms, transcriptions of the bacterial 16S rRNA gene, Geobacter spp., and Geobacter arrA and arsC genes were increased in the lactate+biochar microcosms, where transcript abundances of Geobacter and Geobacter arrA closely tracked with dissolved As(V) concentrations. Our findings indicated that lactate and biochar in flooded paddy soils can stimulate the active As(V)-respiring bacteria Geobacter species for arsenic reduction and release, which probably increases arsenic bioavailability to rice plants.201829188998
7751120.9896A novel hypothermic strain, Pseudomonas reactans WL20-3 with high nitrate removal from actual sewage, and its synergistic resistance mechanism for efficient nitrate removal at 4 °C. Nitrate can be well removed by bacteria at 25-30 °C. However, nitrate removal almost ceases at temperatures lower than 5 °C. In this study, a novel hypothermic strain, Pseudomonas reactans WL20-3 exhibited an excellent aerobic nitrate removal ability at 4 °C. It had high capability for the removal of nitrate, total dissolved nitrogen (TDN), and dissolved organic carbon (DOC) at 4 °C, achieving removal efficiencies of 100%, 87.91%, and 97.48%, respectively. The transcriptome analysis revealed all genes involved in the nitrate removal pathway were significantly up-regulated. Additionally, the up-regulation of ABC transporter genes and down-regulation of respiratory chain genes cooperated with the nitrate metabolism pathway to resist low-temperature stress. In actual sewage, inoculated with WL20-3, the nitrate removal efficiency was found to be 70.70%. Overall, these findings demonstrated the impressive capacity of the novel strain WL20-3 to remove nitrate and provided novel insights into the synergistic resistance mechanism of WL20-3 at low temperature.202337369315
6106130.9896Genomic evidence reveals the extreme diversity and wide distribution of the arsenic-related genes in Burkholderiales. So far, numerous genes have been found to associate with various strategies to resist and transform the toxic metalloid arsenic (here, we denote these genes as "arsenic-related genes"). However, our knowledge of the distribution, redundancies and organization of these genes in bacteria is still limited. In this study, we analyzed the 188 Burkholderiales genomes and found that 95% genomes harbored arsenic-related genes, with an average of 6.6 genes per genome. The results indicated: a) compared to a low frequency of distribution for aio (arsenite oxidase) (12 strains), arr (arsenate respiratory reductase) (1 strain) and arsM (arsenite methytransferase)-like genes (4 strains), the ars (arsenic resistance system)-like genes were identified in 174 strains including 1,051 genes; b) 2/3 ars-like genes were clustered as ars operon and displayed a high diversity of gene organizations (68 forms) which may suggest the rapid movement and evolution for ars-like genes in bacterial genomes; c) the arsenite efflux system was dominant with ACR3 form rather than ArsB in Burkholderiales; d) only a few numbers of arsM and arrAB are found indicating neither As III biomethylation nor AsV respiration is the primary mechanism in Burkholderiales members; (e) the aio-like gene is mostly flanked with ars-like genes and phosphate transport system, implying the close functional relatedness between arsenic and phosphorus metabolisms. On average, the number of arsenic-related genes per genome of strains isolated from arsenic-rich environments is more than four times higher than the strains from other environments. Compared with human, plant and animal pathogens, the environmental strains possess a larger average number of arsenic-related genes, which indicates that habitat is likely a key driver for bacterial arsenic resistance.201424632831
6160140.9896Comparative transcriptional profiling of tildipirosin-resistant and sensitive Haemophilus parasuis. Numerous studies have been conducted to examine the molecular mechanism of Haemophilus parasuis resistance to antibiotic, but rarely to tildipirosin. In the current study, transcriptional profiling was applied to analyse the variation in gene expression of JS0135 and tildipirosin-resistant JS32. The growth curves showed that JS32 had a higher growth rate but fewer bacteria than JS0135. The cell membranes of JS32 and a resistant clinical isolate (HB32) were observed to be smoother than those of JS0135. From the comparative gene expression profile 349 up- and 113 downregulated genes were observed, covering 37 GO and 63 KEGG pathways which are involved in biological processes (11), cellular components (17), molecular function (9), cellular processes (1), environmental information processing (4), genetic information processing (9) and metabolism (49) affected in JS32. In addition, the relative overexpression of genes of the metabolism pathway (HAPS_RS09315, HAPS_RS09320), ribosomes (HAPS_RS07815) and ABC transporters (HAPS_RS10945) was detected, particularly the metabolism pathway, and verified with RT-qPCR. Collectively, the gene expression profile in connection with tildipirosin resistance factors revealed unique and highly resistant determinants of H. parasuis to macrolides that warrant further attention due to the significant threat of bacterial resistance.201728790420
8671150.9896Adapting 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
8727160.9896Transcriptome Analysis of Rice Near-Isogenic Lines Inoculated with Two Strains of Xanthomonas oryzae pv. oryzae, AH28 and PXO99(A). Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a major threat to rice production and food security. Exploring new resistance genes and developing varieties with broad-spectrum and high resistance has been a key focus in rice disease resistance research. In a preliminary study, rice cultivar Fan3, exhibiting high resistance to PXO99(A) and susceptibility to AH28, was developed by enhancing the resistance of Yuehesimiao (YHSM) to BB. This study performed a transcriptome analysis on the leaves of Fan3 and YHSM following inoculation with Xoo strains AH28 and PXO99(A). The analysis revealed significant differential expression of 14,084 genes. Among the transcription factor (TF) families identified, bHLH, WRKY, and ERF were prominent, with notable differences in the expression of OsWRKY62, OsWRKY76, and OsbHLH6 across samples. Over 100 genes were directly linked to disease resistance, including nearly 30 NBS-LRR family genes. Additionally, 11 SWEET family protein genes, over 750 protein kinase genes, 63 peroxidase genes, and eight phenylalanine aminolysase genes were detected. Gene ontology (GO) analysis showed significant enrichment in pathways related to defense response to bacteria and oxidative stress response. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and diterpenoid biosynthesis pathways. Gene expression results from qRT-PCR were consistent with those from RNA-Seq, underscoring the reliability of the findings. Candidate genes identified in this study that may be resistant to BB, such as NBS-LRR family genes LOC_Os11g11960 and LOC_Os11g12350, SWEET family genes LOC_Os01g50460 and LOC_Os01g12130, and protein kinase-expressing genes LOC_Os01g66860 and LOC_Os02g57700, will provide a theoretical basis for further experiments. These results suggest that the immune response of rice to the two strains may be more concentrated in the early stage, and there are more up-regulated genes in the immune response of the high-resistant to PXO99A and medium-resistant to AH28, respectively, compared with the highly susceptible rice. This study offers a foundation for further research on resistance genes and the molecular mechanisms in Fan3 and YHSM.202439599338
5133170.9896Draft genome sequence of Marinobacter sp. DUT-3, a manganese-oxidizing and potential antibiotic-resistant bacterium from Bohai coastal sediments. A manganese-oxidizing bacterium, Marinobacter sp. DUT-3, was isolated from Bohai coastal sediments. A total of 24 contigs with GC content of 57.91% and 3,817 protein-coding genes were obtained by genome sequencing. Isolation of this strain suggests potential for synergistic antibiotics removal via biogenic manganese oxides and intrinsic resistance.202541081498
14180.9895Unraveling Pinus massoniana's Defense Mechanisms Against Bursaphelenchus xylophilus Under Aseptic Conditions: A Transcriptomic Analysis. Pine wilt disease (PWD) is caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus) and significantly impacts pine forest ecosystems globally. This study focuses on Pinus massoniana, an important timber and oleoresin resource in China, which is highly susceptible to PWN. However, the defense mechanism of pine trees in response to PWN remains unclear. Addressing the complexities of PWD, influenced by diverse factors such as bacteria, fungi, and environment, we established a reciprocal system between PWN and P. massoniana seedlings under aseptic conditions. Utilizing combined second- and third-generation sequencing technologies, we identified 3,718 differentially expressed genes post PWN infection. Transcript analysis highlighted the activation of defense mechanisms via stilbenes, salicylic acid and jasmonic acid pathways, terpene synthesis, and induction of pathogenesis-related proteins and resistance genes, predominantly at 72 h postinfection. Notably, terpene synthesis pathways, particularly the mevalonate pathway, were crucial in defense, suggesting their significance in P. massoniana's response to PWN. This comprehensive transcriptome profiling offers insights into P. massoniana's intricate defense strategies against PWN under aseptic conditions, laying a foundation for future functional analyses of key resistance genes. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.202439283201
7526190.9895Fluorescent tag reveals the potential mechanism of how indigenous soil bacteria affect the transfer of the wild fecal antibiotic resistance plasmid pKANJ7 in different habitat soils. Plasmids have increasingly become a point of concern since they act as a vital medium for the dissemination of antibiotic resistance genes (ARGs). Although indigenous soil bacteria are critical hosts for these plasmids, the mechanisms driving the transfer of antibiotic resistance plasmids (ARPs) have not been well researched. In this study, we tracked and visualized the colonization of the wild fecal antibiotic resistance plasmid pKANJ7 in indigenous bacteria of different habitat soils (unfertilized soil (UFS), chemical fertilized soil (CFS), and manure fertilized soil (MFS)). The results showed that plasmid pKANJ7 mainly transferred to the dominant genera in the soil and genera that were highly related to the donor. More importantly, plasmid pKANJ7 also transferred to intermediate hosts which aid in the survival and persistence of these plasmids in soil. Nitrogen levels also raised the plasmid transfer rate (14th day: UFS: 0.09%, CFS: 1.21%, MFS: 4.57%). Lastly, our structural equation model (SEM) showed that dominant bacteria shifts caused by nitrogen and loam were the major driver shaping the difference in the transfer of plasmid pKANJ7. Overall, our findings enhance the mechanistic understanding of indigenous soil bacteria's role in plasmid transfer and inform potential methods to prevent the transmission of plasmid-borne resistance in the environment.202337209559