# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 8471 | 0 | 0.9816 | Effects of Klebsiella michiganensis LDS17 on Codonopsis pilosula growth, rhizosphere soil enzyme activities, and microflora, and genome-wide analysis of plant growth-promoting genes. Codonopsis pilosula is a perennial herbaceous liana with medicinal value. It is critical to promote Codonopsis pilosula growth through effective and sustainable methods, and the use of plant growth-promoting bacteria (PGPB) is a promising candidate. In this study, we isolated a PGPB, Klebsiella michiganensis LDS17, that produced a highly active 1-aminocyclopropane-1-carboxylate deaminase from the Codonopsis pilosula rhizosphere. The strain exhibited multiple plant growth-promoting properties. The antagonistic activity of strain LDS17 against eight phytopathogenic fungi was investigated, and the results showed that strain LDS17 had obvious antagonistic effects on Rhizoctonia solani, Colletotrichum camelliae, Cytospora chrysosperma, and Phomopsis macrospore with growth inhibition rates of 54.22%, 49.41%, 48.89%, and 41.11%, respectively. Inoculation of strain LDS17 not only significantly increased the growth of Codonopsis pilosula seedlings but also increased the invertase and urease activities, the number of culturable bacteria, actinomycetes, and fungi, as well as the functional diversity of microbial communities in the rhizosphere soil of the seedlings. Heavy metal (HM) resistance tests showed that LDS17 is resistant to copper, zinc, and nickel. Whole-genome analysis of strain LDS17 revealed the genes involved in IAA production, siderophore synthesis, nitrogen fixation, P solubilization, and HM resistance. We further identified a gene (koyR) encoding a plant-responsive LuxR solo in the LDS17 genome. Klebsiella michiganensis LDS17 may therefore be useful in microbial fertilizers for Codonopsis pilosula. The identification of genes related to plant growth and HM resistance provides an important foundation for future analyses of the molecular mechanisms underlying the plant growth promotion and HM resistance of LDS17. IMPORTANCE: We comprehensively evaluated the plant growth-promoting characteristics and heavy metal (HM) resistance ability of the LDS17 strain, as well as the effects of strain LDS17 inoculation on the Codonopsis pilosula seedling growth and the soil qualities in the Codonopsis pilosula rhizosphere. We conducted whole-genome analysis and identified lots of genes and gene clusters contributing to plant-beneficial functions and HM resistance, which is critical for further elucidating the plant growth-promoting mechanism of strain LDS17 and expanding its application in the development of plant growth-promoting agents used in the environment under HM stress. | 2024 | 38563743 |
| 8765 | 1 | 0.9814 | Pseudomonas chlororaphis IRHB3 assemblies beneficial microbes and activates JA-mediated resistance to promote nutrient utilization and inhibit pathogen attack. INTRODUCTION: The rhizosphere microbiome is critical to plant health and resistance. PGPR are well known as plant-beneficial bacteria and generally regulate nutrient utilization as well as plant responses to environmental stimuli. In our previous work, one typical PGPR strain, Pseudomonas chlororaphis IRHB3, isolated from the soybean rhizosphere, had positive impacts on soil-borne disease suppression and growth promotion in the greenhouse, but its biocontrol mechanism and application in the field are not unclear. METHODS: In the current study, IRHB3 was introduced into field soil, and its effects on the local rhizosphere microbiome, disease resistance, and soybean growth were comprehensively analyzed through high-throughput sequencing and physiological and molecular methods. RESULTS AND DISCUSSION: We found that IRHB3 significantly increased the richness of the bacterial community but not the structure of the soybean rhizosphere. Functional bacteria related to phosphorus solubilization and nitrogen fixation, such as Geobacter, Geomonas, Candidatus Solibacter, Occallatibacter, and Candidatus Koribacter, were recruited in rich abundance by IRHB3 to the soybean rhizosphere as compared to those without IRHB3. In addition, the IRHB3 supplement obviously maintained the homeostasis of the rhizosphere microbiome that was disturbed by F. oxysporum, resulting in a lower disease index of root rot when compared with F. oxysporum. Furthermore, JA-mediated induced resistance was rapidly activated by IRHB3 following PDF1.2 and LOX2 expression, and meanwhile, a set of nodulation genes, GmENOD40b, GmNIN-2b, and GmRIC1, were also considerably induced by IRHB3 to improve nitrogen fixation ability and promote soybean yield, even when plants were infected by F. oxysporum. Thus, IRHB3 tends to synergistically interact with local rhizosphere microbes to promote host growth and induce host resistance in the field. | 2024 | 38380096 |
| 8767 | 2 | 0.9807 | Poly-γ-glutamic acid enhanced the drought resistance of maize by improving photosynthesis and affecting the rhizosphere microbial community. BACKGROUND: Compared with other abiotic stresses, drought stress causes serious crop yield reductions. Poly-γ-glutamic acid (γ-PGA), as an environmentally friendly biomacromolecule, plays an important role in plant growth and regulation. RESULTS: In this project, the effect of exogenous application of γ-PGA on drought tolerance of maize (Zea mays. L) and its mechanism were studied. Drought dramatically inhibited the growth and development of maize, but the exogenous application of γ-PGA significantly increased the dry weight of maize, the contents of ABA, soluble sugar, proline, and chlorophyll, and the photosynthetic rate under severe drought stress. RNA-seq data showed that γ-PGA may enhance drought resistance in maize by affecting the expression of ABA biosynthesis, signal transduction, and photosynthesis-related genes and other stress-responsive genes, which was also confirmed by RT-PCR and promoter motif analysis. In addition, diversity and structure analysis of the rhizosphere soil bacterial community demonstrated that γ-PGA enriched plant growth promoting bacteria such as Actinobacteria, Chloroflexi, Firmicutes, Alphaproteobacteria and Deltaproteobacteria. Moreover, γ-PGA significantly improved root development, urease activity and the ABA contents of maize rhizospheric soil under drought stress. This study emphasized the possibility of using γ-PGA to improve crop drought resistance and the soil environment under drought conditions and revealed its preliminary mechanism. CONCLUSIONS: Exogenous application of poly-γ-glutamic acid could significantly enhance the drought resistance of maize by improving photosynthesis, and root development and affecting the rhizosphere microbial community. | 2022 | 34979944 |
| 8725 | 3 | 0.9807 | CuO nanoparticles facilitate soybean suppression of Fusarium root rot by regulating antioxidant enzymes, isoflavone genes, and rhizosphere microbiome. BACKGROUND: Fusarium root rot is a widespread soil-borne disease severely impacting soybean yield and quality. Compared to traditional fertilizers' biological and environmental toxicity, CuO nanoparticles (NPs) hold promise for disease control in a low dose and high efficiency manner. METHODS: We conducted both greenhouse and field experiments, employing enzymatic assays, elemental analysis, qRT-PCR, and microbial sequencing (16S rRNA, ITS) to explore the potential of CuO NPs for sustainable controlling Fusarium-induced soybean disease. RESULTS: Greenhouse experiments showed that foliar spraying of CuO NPs (10, 100, and 500 mg L(-1)) promoted soybean growth more effectively than EDTA-CuNa(2) at the same dose, though 500 CuO NPs caused mild phytotoxicity. CuO NPs effectively controlled root rot, while EDTA-CuNa(2) worsened the disease severity by 0.85-34.04 %. CuO NPs exhibited more substantial antimicrobial effects, inhibiting F. oxysporum mycelial growth and spore germination by 5.04-17.55 % and 10.24-14.41 %, respectively. 100 mg L(-1) CuO NPs was the optimal concentration for balancing soybean growth and disease resistance. Additionally, CuO NPs boosted antioxidant enzyme activity (CAT, POD, and SOD) in leaves and roots, aiding in ROS clearance during pathogen invasion. Compared to the pathogen control, 100 mg L(-1) CuO NPs upregulated the relative expression of seven isoflavone-related genes (Gm4CL, GmCHS8, GmCHR, GmCHI1a, GmIFS1, GmUGT1, and GmMYB176) by 1.18-4.51 fold, thereby enhancing soybean disease resistance in place of progesterone-receptor (PR) genes. Field trials revealed that CuO NPs' high leaf-to-root translocation modulated soybean rhizosphere microecology. Compared to the pathogen control, 100 mg L(-1) CuO NPs increased nitrogen-fixing bacteria (Rhizobium, Azospirillum, Azotobacter) and restored disease-resistant bacteria (Pseudomonas, Burkholderia) and fungi (Trichoderma, Penicillium) to healthy levels. Furthermore, 100 mg L(-1) CuO NPs increased beneficial bacteria (Pedosphaeraceae, Xanthobacteraceae, SCI84, etc.) and fungi (Trichoderma, Curvularia, Hypocreales, etc.), which negatively correlated with F. oxysporum, while recruiting functional microbes to enhance soybean yield. CONCLUSION: 100 mg L(-1) CuO NPs effectively promoting soybean growth and providing strong resistance against root rot disease by improving antioxidant enzyme activity, regulating the relative expression of isoflavone-related genes, increasing beneficial bacteria and fungi and restoring disease-resistant. Our findings suggest that CuO NPs offer an environmentally sustainable strategy for managing soybean disease, with great potential for green production. | 2025 | 40096759 |
| 8651 | 4 | 0.9806 | Repercussions of Prolonged Pesticide Use on Natural Soil Microbiome Dynamics Using Metagenomics Approach. The residual pesticides in soil can affect the natural microbiome composition and genetic profile that drive nutrient cycling and soil fertility. In the present study, metagenomic approach was leveraged to determine modulations in nutrient cycling and microbial composition along with connected nexus of pesticide, antibiotic, and heavy metal resistance in selected crop and fallow soils having history of consistent pesticide applications. GC-MS analysis estimated residuals of chlorpyrifos, hexachlorbenzene, and dieldrin showing persistent nature of pesticides that pose selective pressure for microbial adaptation. Taxonomic profiling showed increased abundance of pesticide degrading Streptomyces, Xanthomonas, Cupriavidus, and Pseudomonas across the selected soils. Genes encoding for pesticide degrading cytochrome p450, organophosphorus hydrolase, aldehyde dehydrogenase, and oxidase were predominant and positively correlated with Bacillus, Sphingobium, and Burkholderia. Nitrogen-fixing genes (nifH, narB, and nir) were relatively less abundant in crop soils, correlating to the decrease in nitrogen-fixing bacteria (Anabaena, Pantoea, and Azotobacter). Microbial enzymes involved in carbon (pfkA, gap, pgi, and tpiA) and phosphorus cycle (gmbh and phnJ) were significantly higher in crop soils indicating extensive utilization of pesticide residuals as a nutrient source by the indigenous soil microbiota. Additionally, presence of antibiotic and heavy metal resistance genes suggested potential cross-resistance under pressure from pesticide residues. The results implied selective increase in pesticide degrading microbes with decrease in beneficial bacteria that resulted in reduced soil health and fertility. The assessment of agricultural soil microbial profile will provide a framework to develop sustainable agriculture practices to conserve soil health and fertility. | 2025 | 39096471 |
| 8814 | 5 | 0.9803 | Alleviation of Cadmium and Nickel Toxicity and Phyto-Stimulation of Tomato Plant L. by Endophytic Micrococcus luteus and Enterobacter cloacae. Cadmium (Cd) and nickel (Ni) are two of the most toxic metals, wreaking havoc on human health and agricultural output. Furthermore, high levels of Cd and Ni in the soil environment, particularly in the root zone, may slow plant development, resulting in lower plant biomass. On the other hand, endophytic bacteria offer great promise for reducing Cd and Ni. Moreover, they boost plants' resistance to heavy metal stress. Different bacterium strains were isolated from tomato roots. These isolates were identified as Micrococcus luteus and Enterobacter cloacae using 16SrDNA and were utilized to investigate their involvement in mitigating the detrimental effects of heavy metal stress. The two bacterial strains can solubilize phosphorus and create phytohormones as well as siderophores. Therefore, the objective of this study was to see how endophytic bacteria (Micrococcus luteus and Enterobactercloacae) affected the mitigation of stress from Cd and Ni in tomato plants grown in 50 μM Cd or Ni-contaminated soil. According to the findings, Cd and Ni considerably lowered growth, biomass, chlorophyll (Chl) content, and photosynthetic properties. Furthermore, the content of proline, phenol, malondialdehyde (MDA), H(2)O(2), OH, O(2), the antioxidant defense system, and heavy metal (HM) contents were significantly raised under HM-stress conditions. However, endophytic bacteria greatly improved the resistance of tomato plants to HM stress by boosting enzymatic antioxidant defenses (i.e., catalase, peroxidase, superoxide dismutase, glutathione reductase, ascorbate peroxidase, lipoxygenase activity, and nitrate reductase), antioxidant, non-enzymatic defenses, and osmolyte substances such as proline, mineral content, and specific regulatory defense genes. Moreover, the plants treated had a higher value for bioconcentration factor (BCF) and translocation factor (TF) due to more extensive loss of Cd and Ni content from the soil. To summarize, the promotion of endophytic bacterium-induced HM resistance in tomato plants is essentially dependent on the influence of endophytic bacteria on antioxidant capacity and osmoregulation. | 2022 | 35956496 |
| 6089 | 6 | 0.9801 | Genomic analyses of metal resistance genes in three plant growth promoting bacteria of legume plants in Northwest mine tailings, China. To better understand the diversity of metal resistance genetic determinant from microbes that survived at metal tailings in northwest of China, a highly elevated level of heavy metal containing region, genomic analyses was conducted using genome sequence of three native metal-resistant plant growth promoting bacteria (PGPB). It shows that: Mesorhizobium amorphae CCNWGS0123 contains metal transporters from P-type ATPase, CDF (Cation Diffusion Facilitator), HupE/UreJ and CHR (chromate ion transporter) family involved in copper, zinc, nickel as well as chromate resistance and homeostasis. Meanwhile, the putative CopA/CueO system is expected to mediate copper resistance in Sinorhizobium meliloti CCNWSX0020 while ZntA transporter, assisted with putative CzcD, determines zinc tolerance in Agrobacterium tumefaciens CCNWGS0286. The greenhouse experiment provides the consistent evidence of the plant growth promoting effects of these microbes on their hosts by nitrogen fixation and/or indoleacetic acid (IAA) secretion, indicating a potential in-site phytoremediation usage in the mining tailing regions of China. | 2015 | 25597676 |
| 8726 | 7 | 0.9797 | CRISPR-dCpf1 mediated whole genome crRNA inhibition library for high-throughput screening of growth characteristic genes in Bacillus amyloliquefaciens LB1ba02. Bacillus amyloliquefaciens LB1ba02 is generally recognized as food safe (GRAS) microbial host and important enzyme-producing strain in the industry. However, autolysis affects the growth of bacteria, further affecting the yield of target products. Besides, the restriction-modification system, existed in B. amyloliquefaciens LB1ba02, results in a low transformation efficiency, which further leads to a lack of high-throughput screening tools. Here, we constructed a genome-wide crRNA inhibition library based on the CRISPR/dCpf1 system and high-throughput screening of related genes affecting the cell growth and autolysis using flow cytometry in B. amyloliquefaciens LB1ba02. The whole genome crRNA library was first validated for resistance to the toxic chemical 5-fluorouracil, and then used for validation of essential genes. In addition, seven gene loci (oppD, flil, tuaA, prmA, sigO, hslU, and GE03231) that affect the growth characteristics of LB1ba02 were screened. Among them, the Opp system had the greatest impact on growth. When the expression of operon oppA-oppB-oppC-oppD-oppF was inhibited, the cell growth difference was most significant. Inhibition of other sites could also promote rapid growth of bacteria to varying degrees; however, inhibition of GE03231 site accelerated cell autolysis. Therefore, the whole genome crRNA inhibition library is well suited for B. amyloliquefaciens LB1ba02 and can be further applied to high-throughput mining of other functional genes. | 2023 | 37802457 |
| 8543 | 8 | 0.9793 | Soil bacteria, genes, and metabolites stimulated during sulfur cycling and cadmium mobilization under sodium sulfate stress. Sodium sulfate stress is known to improve cadmium (Cd) mobilization in soil and microbial sulfur oxidation, Cd resistance, and the accumulation of stress tolerance-associated metabolites has been correlated with increased soil Cd availability and toxicity. In this study, aerobic soil microcosms with Cd-contamination were stimulated with sodium sulfate to investigate its effects on soil microbial community structure, functional genes, and associated metabolite profiles. Metagenomic analysis revealed that sulfur oxidizing and Cd-resistant bacteria carried gene clusters encoding sox, dsr, and sqr genes, and znt, czc, and cad genes, respectively. Exposure to sodium sulfate resulted in the reprogram of soil metabolites. In particular, intensification of sulfur metabolism triggered an up-regulation in the tricarboxylic acid (TCA) cycle, which promoted the secretion of carboxylic acids and their precursors by soil bacteria. The accumulation of organic acids induced in response to high sodium sulfate dosages potentially drove an observed increase in Cd mobility. Pseudomonas and Erythrobacter spp. exhibited a high capacity for adaptation to heavy metal- or sulfur-induced stress, evident by an increased abundance of genes and metabolites for sulfur cycling and Cd resistance. These results provide valuable insights towards understanding the microbial mechanisms of sulfur transformation and Cd dissolution under saline stress. | 2021 | 34214562 |
| 6017 | 9 | 0.9792 | Selection of lactic acid bacteria to promote an efficient silage fermentation capable of inhibiting the activity of Aspergillus parasiticus and Fusarium gramineraum and mycotoxin production. AIMS: To select lactic acid bacteria with potential silage inoculant properties. The bio-control activity against mycotoxicogenic fungi and the presence of antibiotics resistance gene were also evaluated. METHODS AND RESULTS: Lactobacillus rhamnosus RC007 and Lactobacillus plantarum RC009 were selected on the basis of growth rate and efficacy in reducing the pH of maize extract medium; therefore, they were evaluated for their bio-control ability against Fusarium graminearum and Aspergillus parasiticus. Studies on lag phase, growth rate and aflatoxin B1 (AFB1) and zearalenone (ZEA) production were carried out in vitro under different regimes of aw (0·95 and 0·99); pH (4 and 6); temperature (25 and 37°C); and oxygen availability (normal and reduced). Lactobacillus rhamnosus RC007 was able to completely inhibit the F. graminearum growth at all assayed conditions, while Lact. plantarum RC009 only did it at pH 4. Both Lactobacillus strains were able to significantly reduce the A. parasiticus growth rate mainly at 0·99 aw . A decrease in ZEA production was observed as result of Lactobacillus strains -F. graminearum interaction; however, the A. parasiticus- Lact. plantarum interaction resulted in an increased AFB1 production. Lactobacillus rhamnosus RC007 proved to have no genes for resistance to the tested antibiotics. CONCLUSIONS: The ability of Lact. rhamnosus RC007 to rapidly drop the pH and to inhibit fungal growth and mycotoxin production and the absence of antibiotic resistance genes shows the potential of its application as inoculant and bio-control agent in animal feed. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrated the importance of selecting bacteria for silage inoculants not only for the improvement of silage fermentation but also for their effects on mycotoxicogenic fungi and the resulting mycotoxin production due to the risk that they may involve. | 2013 | 23437822 |
| 8815 | 10 | 0.9792 | Phosphorus-Solubilizing Bacteria Enhance Cadmium Immobilization and Gene Expression in Wheat Roots to Reduce Cadmium Uptake. The application of phosphorus-solubilizing bacteria is an effective method for increasing the available phosphorus content and inhibiting wheat uptake of heavy metals. However, further research is needed on the mechanism by which phosphorus-solubilizing bacteria inhibit cadmium (Cd) uptake in wheat roots and its impact on the expression of root-related genes. Here, the effects of strain Klebsiella aerogenes M2 on Cd absorption in wheat and the expression of root-related Cd detoxification and immobilization genes were determined. Compared with the control, strain M2 reduced (64.1-64.6%) Cd uptake by wheat roots. Cd fluorescence staining revealed that strain M2 blocked the entry of exogenous Cd into the root interior and enhanced the immobilization of Cd by cell walls. Forty-seven genes related to Cd detoxification, including genes encoding peroxidase, chalcone synthase, and naringenin 3-dioxygenase, were upregulated in the Cd+M2 treatment. Strain M2 enhanced the Cd resistance and detoxification activity of wheat roots through the regulation of flavonoid biosynthesis and antioxidant enzyme activity. Moreover, strain M2 regulated the expression of genes related to phenylalanine metabolism and the MAPK signaling pathway to enhance Cd immobilization in roots. These results provide a theoretical basis for the use of phosphorus-solubilizing bacteria to remediate Cd-contaminated fields and reduce Cd uptake in wheat. | 2024 | 39065516 |
| 8707 | 11 | 0.9792 | Bacillus megaterium HgT21: a Promising Metal Multiresistant Plant Growth-Promoting Bacteria for Soil Biorestoration. The environmental deterioration produced by heavy metals derived from anthropogenic activities has gradually increased. The worldwide dissemination of toxic metals in crop soils represents a threat for sustainability and biosafety in agriculture and requires strategies for the recovery of metal-polluted crop soils. The biorestoration of metal-polluted soils using technologies that combine plants and microorganisms has gained attention in recent decades due to the beneficial and synergistic effects produced by its biotic interactions. In this context, native and heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in the development of strategies for sustainable biorestoration of metal-contaminated soils. In this study, we present a genomic analysis and characterization of the rhizospheric bacterium Bacillus megaterium HgT21 isolated from metal-polluted soil from Zacatecas, Mexico. The results reveal that this autochthonous bacterium contains an important set of genes related to a variety of operons associated with mercury, arsenic, copper, cobalt, cadmium, zinc and aluminum resistance. Additionally, halotolerance-, beta-lactam resistance-, phosphate solubilization-, and plant growth-promotion-related genes were identified. The analysis of resistance to metal ions revealed resistance to mercury (Hg(II+)), arsenate [AsO(4)]³(-), cobalt (Co(2+)), zinc (Zn(2+)), and copper (Cu(2+)). Moreover, the ability of the HgT21 strain to produce indole acetic acid (a phytohormone) and promote the growth of Arabidopsis thaliana seedlings in vitro was also demonstrated. The genotype and phenotype of Bacillus megaterium HgT21 reveal its potential to be used as a model of both plant growth-promoting and metal multiresistant bacteria. IMPORTANCE Metal-polluted environments are natural sources of a wide variety of PGPB adapted to cope with toxic metal concentrations. In this work, the bacterial strain Bacillus megaterium HgT21 was isolated from metal-contaminated soil and is proposed as a model for the study of metal multiresistance in spore-forming Gram-positive bacteria due to the presence of a variety of metal resistance-associated genes similar to those encountered in the metal multiresistant Gram-negative Cupriavidus metallidurans CH34. The ability of B. megaterium HgT21 to promote the growth of plants also makes it suitable for the study of plant-bacteria interactions in metal-polluted environments, which is key for the development of techniques for the biorestoration of metal-contaminated soils used for agriculture. | 2022 | 35980185 |
| 6121 | 12 | 0.9792 | Complete genome of Sphingomonas paucimobilis ZJSH1, an endophytic bacterium from Dendrobium officinale with stress resistance and growth promotion potential. Sphingomonas paucimobilis ZJSH1 is an endophytic bacterium isolated from the roots of Dendrobium officinale with the ability to promote plant growth. It was found that the genome of strain ZJSH1 had gene fragment rearrangement compared with the genomes of the other four strains of S. paucimobilis, and the genome was integrated with phage genes. Functional analysis showed that the strain contained colonization-related genes, chemotaxis and invasion. A variety of genes encoding active materials, such as hormones (IAA, SA, ABA and zeaxanthin), phosphate cycle, antioxidant enzymes, and polysaccharides were identified which provide the strain with growth promotion and stress-resistant characteristics. Experiments proved that S. paucimobilis ZJSH1 grew well in media containing 80 g/L sodium chloride, 240 g/L polyethylene glycol and 800 μmol/L Cd(2+), indicating its potential for resistance to stresses of salt, drought and cadmium, respectively. S. paucimobilis ZJSH1 is the only endophytic bacterium of this species that has been reported to promote plant growth. The analysis of its genome is conducive to understanding its growth-promoting mechanism and laying a foundation for the development and utilization of this species in the field of agriculture. | 2023 | 36959350 |
| 523 | 13 | 0.9792 | Sulfide-carbonate-mineralized functional bacterial consortium for cadmium removal in flue gas. Sulfide-carbonate-mineralized functional bacterial consortium was constructed for flue gas cadmium biomineralization. A membrane biofilm reactor (MBfR) using the bacterial consortium containing sulfate reducing bacteria (SRB) and denitrifying bacteria (DNB) was investigated for flue gas cadmium (Cd) removal. Cadmium removal efficiency achieved 90%. The bacterial consortium containing Citrobacter, Desulfocurvus and Stappia were dominated for cadmium resistance-nitrate-sulfate reduction. Under flue gas cadmium stress, ten cadmium resistance genes (czcA, czcB, czcC, czcD, cadA, cadB, cadC, cueR, copZ, zntA), and seven genes related to sulfate reduction, increased in abundance; whereas others, nine genes related to denitrification, decreased, indicating that cadmium stress was advantageous to sulfate reduction in the competition with denitrification. A bacterial consortium could capable of simultaneously cadmium resistance, sulfate reduction and denitrification. Microbial induced carbonate precipitation (MICP) and biological adsorption process would gradually yield to sulfide-mineralized process. Flue gas cadmium could transform to Cd-EPS, cadmium carbonate (CdCO(3)) and cadmium sulfide (CdS) bioprecipitate. The functional bacterial consortium was an efficient and eco-friendly bifunctional bacterial consortium for sulfide-carbonate-mineralized of cadmium. This provides a green and low-carbon advanced treatment technology using sulfide-carbonate-mineralized functional bacterial consortium for the removal of cadmium or other hazardous heavy metal contaminants in flue gas. | 2024 | 39019186 |
| 6116 | 14 | 0.9791 | Identification of plasmid encoded osmoregulatory genes from halophilic bacteria isolated from the rhizosphere of halophytes. Bacterial plasmids carry genes that code for additional traits such as osmoregulation, CO(2) fixation, antibiotic and heavy metal resistance, root nodulation and nitrogen fixation. The main objective of the current study was to identify plasmid-conferring osmoregulatory genes in bacteria isolated from rhizospheric and non-rhizospheric soils of halophytes (Salsola stocksii and Atriplex amnicola). More than 55% of halophilic bacteria from the rhizosphere and 70% from non-rhizospheric soils were able to grow at 3 M salt concentrations. All the strains showed optimum growth at 1.5-3.0 M NaCl. Bacterial strains from the Salsola rhizosphere showed maximum (31%) plasmid elimination during curing experiments as compared to bacterial strains from the Atriplex rhizosphere and non-rhizospheric soils. Two plasmid cured strains Bacillus HL2HP6 and Oceanobacillus HL2RP7 lost their ability to grow in halophilic medium, but they grew well on LB medium. The plasmid cured strains also showed a change in sensitivity to specific antibiotics. These plasmids were isolated and transformed into E. coli strains and growth response of wild-type and transformed E. coli strains was compared at 1.5-4 M NaCl concentrations. Chromosomal DNA and plasmids from Bacillus filamentosus HL2HP6 were sequenced by using high throughput sequencing approach. Results of functional analysis of plasmid sequences showed different proteins and enzymes involved in osmoregulation of bacteria, such as trehalose, ectoine synthetase, porins, proline, alanine, inorganic ion transporters, dehydrogenases and peptidases. Our results suggested that plasmid conferring osmoregulatory genes play a vital role to maintain internal osmotic balance of bacterial cells and these genes can be used to develop salt tolerant transgenic crops. | 2019 | 31422229 |
| 6080 | 15 | 0.9791 | Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia. Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries. | 2023 | 38276185 |
| 8697 | 16 | 0.9791 | Deciphering the Root Endosphere Microbiome of the Desert Plant Alhagi sparsifolia for Drought Resistance-Promoting Bacteria. Drought is among the most destructive abiotic stresses limiting crop growth and yield worldwide. Although most research has focused on the contribution of plant-associated microbial communities to plant growth and disease suppression, far less is known about the microbes involved in drought resistance among desert plants. In the present study, we applied 16S rRNA gene amplicon sequencing to determine the structure of rhizosphere and root endosphere microbiomes of Alhagi sparsifolia Compared to those of the rhizosphere, endosphere microbiomes had lower diversity but contained several taxa with higher relative abundance; many of these taxa were also present in the roots of other desert plants. We isolated a Pseudomonas strain (LTGT-11-2Z) that was prevalent in root endosphere microbiomes of A. sparsifolia and promoted drought resistance during incubation with wheat. Complete genome sequencing of LTGT-11-2Z revealed 1-aminocyclopropane-1-carboxylate deaminases, siderophore, spermidine, and colanic acid biosynthetic genes, as well as type VI secretion system (T6SS) genes, which are likely involved in biofilm formation and plant-microbe interactions. Together, these results indicate that drought-enduring plants harbor bacterial endophytes favorable to plant drought resistance, and they suggest that novel endophytic bacterial taxa and gene resources may be discovered among these desert plants.IMPORTANCE Understanding microbe-mediated plant resistance to drought is important for sustainable agriculture. We performed 16S rRNA gene amplicon sequencing and culture-dependent functional analyses of Alhagi sparsifolia rhizosphere and root endosphere microbiomes and identified key endophytic bacterial taxa and their genes facilitating drought resistance in wheat. This study improves our understanding of plant drought resistance and provides new avenues for drought resistance improvement in crop plants under field conditions. | 2020 | 32220847 |
| 8768 | 17 | 0.9790 | Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials. BACKGROUND: As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms. RESULTS: WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release. CONCLUSION: All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction. | 2024 | 38178261 |
| 7947 | 18 | 0.9789 | Molecular 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. | 2024 | 38653136 |
| 8646 | 19 | 0.9789 | A 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. | 2021 | 33810508 |