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Environmental Science & Technology Jun 2024Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide (CO) budget. Partitioning of organic carbons into biomass relative to CO...
Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide (CO) budget. Partitioning of organic carbons into biomass relative to CO efflux, termed carbon-use efficiency (CUE), is widely used to characterize organic carbon cycling by soil microorganisms. Recent studies challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in , a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our C-metabolomics data captured substrate carbons into different metabolic pathways: cellulose-derived sugar carbons in glycolytic and pentose-phosphate pathways; lignin-related aromatic carbons in the tricarboxylic acid cycle. Subsequent C-metabolic flux analysis revealed a 3-fold lower investment of sugar carbons in CO efflux compared to aromatic carbons, in agreement with reported substrate-dependent CUE. Proteomics analysis revealed enzyme-level regulation only for substrate uptake and initial catabolism, which dictated downstream fluxes through CO-producing versus biomass-synthesizing reactions. Metabolic partitioning as shown here explained the substrate-dependent CUE calculated from reported metabolic flux analyses of other bacteria, further supporting a metabolism-guided perspective for predicting the microbial conversion of accessible organic matter to CO efflux.
Topics: Carbon Dioxide; Carbon; Metabolic Networks and Pathways; Pseudomonas putida; Biomass
PubMed: 38860668
DOI: 10.1021/acs.est.4c01328 -
Genome Biology and Evolution Jun 2024Many nonsporulating bacterial species survive prolonged resource exhaustion, by entering a state termed long-term stationary phase. Here, we performed long-term...
Many nonsporulating bacterial species survive prolonged resource exhaustion, by entering a state termed long-term stationary phase. Here, we performed long-term stationary phase evolutionary experiments on the bacterium Pseudomonas putida, followed by whole-genome sequencing of evolved clones. We show that P. putida is able to persist and adapt genetically under long-term stationary phase. We observed an accumulation of mutations within the evolving P. putida populations. Within each population, independently evolving lineages are established early on and persist throughout the 4-month-long experiment. Mutations accumulate in a highly convergent manner, with similar loci being mutated across independently evolving populations. Across populations, mutators emerge, that due to mutations within mismatch repair genes developed a much higher rate of mutation than other clones with which they coexisted within their respective populations. While these general dynamics of the adaptive process are quite similar to those we previously observed in the model bacterium Escherichia coli, the specific loci that are involved in adaptation only partially overlap between P. putida and E. coli.
Topics: Pseudomonas putida; Adaptation, Physiological; Mutation; Genome, Bacterial; Evolution, Molecular
PubMed: 38849986
DOI: 10.1093/gbe/evae117 -
PloS One 2024Cellular metabolic activity can be detected by tetrazolium-based colorimetric assays, which rely on dehydrogenase enzymes from living cells to reduce tetrazolium...
Cellular metabolic activity can be detected by tetrazolium-based colorimetric assays, which rely on dehydrogenase enzymes from living cells to reduce tetrazolium compounds into colored formazan products. Although these methods have been used in different fields of microbiology, their application to the detection of bacteria with plastic-degrading activity has not been well documented. Here, we report a microplate-adapted method for the detection of bacteria metabolically active on the commercial polyester polyurethane (PU) Impranil®DLN using the tetrazolium salt 2,3-bis [2-methyloxy-4-nitro-5-sulfophenyl]-2H-tetrazolium-5-carboxanilide (XTT). Bacterial cells that are active on PU reduce XTT to a water-soluble orange dye, which can be quantitatively measured using a microplate reader. We used the Pseudomonas putida KT2440 strain as a study model. Its metabolic activity on Impranil detected by our novel method was further verified by Fourier-transform infrared spectroscopy (FTIR) analyses. Measurements of the absorbance of reduced XTT at 470 nm in microplate wells were not affected by the colloidal properties of Impranil or cell density. In summary, we provide here an easy and high-throughput method for screening bacteria active on PU that can be adapted to other plastic substrates.
Topics: Polyurethanes; Pseudomonas putida; Tetrazolium Salts; Spectroscopy, Fourier Transform Infrared; Water; Colorimetry
PubMed: 38843174
DOI: 10.1371/journal.pone.0303210 -
Metabolic Engineering Jun 2024Sunscreen has been used for thousands of years to protect skin from ultraviolet radiation. However, the use of modern commercial sunscreen containing oxybenzone, ZnO,...
Sunscreen has been used for thousands of years to protect skin from ultraviolet radiation. However, the use of modern commercial sunscreen containing oxybenzone, ZnO, and TiO has raised concerns due to their negative effects on human health and the environment. In this study, we aim to establish an efficient microbial platform for production of shinorine, a UV light absorbing compound with anti-aging properties. First, we methodically selected an appropriate host for shinorine production by analyzing central carbon flux distribution data from prior studies alongside predictions from genome-scale metabolic models (GEMs). We enhanced shinorine productivity through CRISPRi-mediated downregulation and utilized shotgun proteomics to pinpoint potential competing pathways. Simultaneously, we improved the shinorine biosynthetic pathway by refining its design, optimizing promoter usage, and altering the strength of ribosome binding sites. Finally, we conducted amino acid feeding experiments under various conditions to identify the key limiting factors in shinorine production. The study combines meta-analysis of C-metabolic flux analysis, GEMs, synthetic biology, CRISPRi-mediated gene downregulation, and omics analysis to improve shinorine production, demonstrating the potential of Pseudomonas putida KT2440 as platform for shinorine production.
PubMed: 38839037
DOI: 10.1016/j.ymben.2024.06.001 -
Chemosphere Aug 2024The widespread and inevitable use of plastic has led to prospective ecological problems through Bisphenol A (BPA), a synthetic chemical in plastic manufacturing. The...
The widespread and inevitable use of plastic has led to prospective ecological problems through Bisphenol A (BPA), a synthetic chemical in plastic manufacturing. The present study addresses a unique methodology for eliminating BPA using the assistance of Pseudomonas putida. In the present work, biomass was torrefied to generate biochar with highly porous networks that could accommodate the bacterial species for effective colonization and multiplication. The designed biochar-bacterial globules demonstrated the ability to effectively remove BPA (96.88%) at a concentration of up to 2 g/L. The biochar-bacterial globules could effectively adsorb BPA at a low concentration of 20 mg/L. The alteration in pH did not impact the globule's performance, providing additional support for the practical utilization of these globules in polluted water bodies. In addition, the biochar-bacterial globules exhibited superior effectiveness in degradation compared to the standard levels, particularly in saline conditions. The simplicity and effectiveness of the approach make it promising for real-world implementation in addressing ecological problems associated with BPA contamination.
Topics: Benzhydryl Compounds; Phenols; Pseudomonas putida; Charcoal; Water Pollutants, Chemical; Biodegradation, Environmental; Adsorption
PubMed: 38825245
DOI: 10.1016/j.chemosphere.2024.142496 -
Environmental Science and Pollution... Jun 2024Simultaneous application of modified FeO with biological treatments in remediating multi-metal polluted soils, has rarely been investigated. Thus, a pioneering approach...
Simultaneous application of modified FeO with biological treatments in remediating multi-metal polluted soils, has rarely been investigated. Thus, a pioneering approach towards sustainable environmental remediation strategies is crucial. In this study, we aimed to improve the efficiency of FeO as adsorbents for heavy metals (HMs) by applying protective coatings. We synthesized core-shell magnetite nanoparticles coated with modified nanocellulose, nanohydrochar, and nanobiochar, and investigated their effectiveness in conjunction with bacteria (Pseudomonas putida and Bacillus megaterium) for remediating a multi-metal contamination soil. The results showed that the coatings significantly enhanced the immobilization of heavy metals in the soil, even at low doses (0.5%). The coating of nanocellulose had the highest efficiency in stabilizing metals due to the greater variety of surface functional groups and higher specific surface area (63.86 m g) than the other two coatings. Interestingly, uncoated FeO had lower performance (113.6 m g) due to their susceptibility to deformation and oxidation. The use of bacteria as a biological treatment led to an increase in the stabilization of metals in soil. In fact, Pseudomonas putida and Bacillus megaterium increased immobilization of HMs in soil successfully because of extracellular polymeric substances and intensive negative charges. Analysis of metal concentrations in plants revealed that Ni and Zn accumulated in the roots, while Pb and Cd were transferred from the roots to the shoots. Treatment FeO coated with modified nanocellulose at rates of 0.5 and 1% along with Pseudomonas putida showed the highest effect in stabilizing metals. Application of coated FeO for in-situ immobilization of HMs in contamination soils is recommendable due to their high metal stabilization efficiency and suitability to apply in large quantities.
Topics: Metals, Heavy; Soil Pollutants; Magnetite Nanoparticles; Soil; Pseudomonas putida; Bacillus megaterium; Environmental Restoration and Remediation; Adsorption
PubMed: 38822962
DOI: 10.1007/s11356-024-33808-7 -
Frontiers in Microbiology 2024Chinese cabbage, scientifically known as subsp is a highly popular vegetable in China for its delectable taste. However, the occurrence of bacterial soft rot disease...
Chinese cabbage, scientifically known as subsp is a highly popular vegetable in China for its delectable taste. However, the occurrence of bacterial soft rot disease poses a significant threat to its growth and overall development. Consequently, this study aimed to explore the defense mechanisms employed by Chinese cabbage against bacterial soft rot disease. Specifically, the investigation focused on understanding the relationship between the disease and the microbial communities present in the soil surrounding the roots of Chinese cabbage. Significant disparities were observed in the composition of microbial communities present in the root-zone soil of healthy Chinese cabbage plants compared to those affected by -caused soft rot disease. The analysis of 16S rRNA gene high-throughput sequencing results revealed a lower abundance of Proteobacteria (8.39%), Acidobacteriot (0.85), (3.51%), and (1.48%), whereas Firmicutes (113.76%), Bacteroidota (8.71%), Chloroflexi (4.89%), Actinobacteriota (1.71%), A4b (15.52%), (1.62%), and (1.35%) were more prevalent in healthy plant soils. Similarly, the analysis of ITS gene high-throughput sequencing results indicated a reduced occurrence of Chytridiomycota (23.58%), Basidiomycota (21.80%), (86.22%), and (22.57%) in healthy soils. In comparison, Mortierellomycota (50.72%), Ascomycota (31.22%), (485.08%), and (51.59%) were more abundant in healthy plant soils. In addition, a total of 15 bacterial strains were isolated from the root-zone soil of diseased Chinese cabbage plants. These isolated strains demonstrated the ability to fix nitrogen (with the exception of ZT20, ZT26, ZT41, ZT45, and ZT61), produce siderophores and indole acetic acid (IAA), and solubilize phosphate. Notably, ZT14 (), ZT33 (), ZT41 (), ZT52 (), ZT58 (), ZT45 (), and ZT32 () exhibited significant growth-promoting effects as determined by the plant growth promotion (PGP) tests. Consequently, this investigation not only confirmed the presence of the soft rot pathogen in Chinese cabbage plants in Hangzhou, China, but also advanced our understanding of the defense mechanisms employed by Chinese cabbage to combat soft rot-induced stress. Additionally, it identified promising plant-growth-promoting microbes (PGPMs) that could be utilized in the future to enhance the Chinese cabbage industry.
PubMed: 38784798
DOI: 10.3389/fmicb.2024.1401896 -
PloS One 2024[This corrects the article DOI: 10.1371/journal.pone.0299128.].
[This corrects the article DOI: 10.1371/journal.pone.0299128.].
PubMed: 38758818
DOI: 10.1371/journal.pone.0304263 -
Frontiers in Microbiology 2024In natural microbiomes, microorganisms interact with each other and exhibit diverse functions. Microbiome engineering, which enables bacterial knockdown, is a promising...
In natural microbiomes, microorganisms interact with each other and exhibit diverse functions. Microbiome engineering, which enables bacterial knockdown, is a promising method to elucidate the functions of targeted bacteria in microbiomes. However, few methods to selectively kill target microorganisms in the microbiome without affecting the growth of nontarget microorganisms are available. In this study, we focused on the host-specific lytic ability of virulent phages and validated their potency for precise microbiome engineering. In an artificial microbiome consisting of , , , and , the addition of bacteriophages infecting their respective host strains specifically reduced the number of these bacteria more than 10 orders. Remarkably, the reduction in target bacteria did not affect the growth of nontarget bacteria, indicating that bacteriophages were effective tools for precise microbiome engineering. Moreover, a virulent derivative of the λ phage was synthesized from prophage DNA in the genome of λ lysogen by DNA assembly and phage-rebooting techniques, and -targeted microbiome engineering was achieved. These results propose a novel approach for precise microbiome engineering using bacteriophages, in which virulent phages are synthesized from prophage DNA in lysogenic strains without isolating phages from environmental samples.
PubMed: 38756723
DOI: 10.3389/fmicb.2024.1403903 -
Plant Communications May 2024The expression of double-stranded RNAs (dsRNAs) from the plastid genome has been proven to be an effective method for controlling herbivorous pests by targeting...
The expression of double-stranded RNAs (dsRNAs) from the plastid genome has been proven to be an effective method for controlling herbivorous pests by targeting essential insect genes. However, there are limitations to the efficiency of plastid-mediated RNA interference (PM-RNAi) due to the initial damage caused by the insects and their slow response to RNA interference. In this study, we developed transplastomic poplar plants that express dsRNAs targeting the β-Actin (dsACT) and Srp54k (dsSRP54K) genes of Plagiodera versicolora. Feeding experiments showed that transplastomic poplar plants can cause significantly higher mortality in P. versicolora larvae compared with nuclear transgenic or wild-type poplar plants. The efficient killing effect of PM-RNAi on P. versicolora larvae was found to be dependent on the presence of gut bacteria. Importantly, foliar application of a gut bacterial strain, Pseudomonas putida, will induce dysbiosis in the gut bacteria of P. versicolora larvae, leading to a significant acceleration in the speed of killing by PM-RNAi. Overall, our findings suggest that interfering with gut bacteria could be a promising strategy to enhance the effectiveness of PM-RNAi for insect pest control, offering a novel and effective approach for crop protection based on RNAi technology.
PubMed: 38751119
DOI: 10.1016/j.xplc.2024.100974