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Scientific Reports May 2024Phosphorus (P) use efficiency in alkaline/calcareous soils is only 20% due to precipitation of PO with calcium and magnesium. However, coating Diammonium Phosphate (DAP)...
Phosphorus (P) use efficiency in alkaline/calcareous soils is only 20% due to precipitation of PO with calcium and magnesium. However, coating Diammonium Phosphate (DAP) with phosphorus solubilizing bacteria (PSB) is more appropriate to increase fertilizer use efficiency. Therefore, with the aim to use inorganic fertilizers more effectively present study was conducted to investigate comparative effect of coated DAP with PSB strains Bacillus subtilis ZE15 (MN003400), Bacillus subtilis ZR3 (MN007185), Bacillus megaterium ZE32 (MN003401) and Bacillus megaterium ZR19 (MN007186) and their extracted metabolites with uncoated DAP under axenic conditions. Gene sequencing was done against various sources of phosphorus to analyze genes responsible for phosphatase activity. Alkaline phosphatase (ALP) gene amplicon of 380bp from all tested strains was showed in 1% w/v gel. Release pattern of P was also improved with coated fertilizer. The results showed that coated phosphatic fertilizer enhanced shoot dry weight by 43 and 46% under bacterial and metabolites coating respectively. Shoot and root length up to 44 and 42% with metabolites coated DAP and 41% with bacterial coated DAP. Physiological attributes also showed significant improvement with coated DAP over conventional. The results supported the application of coated DAP as a useful medium to raise crop yield even at lower application rates i.e., 50 and 75% DAP than non-coated 100% DAP application which advocated this coating technique a promising approach for advancing circular economy and sustainable development in modern agriculture.
Topics: Zea mays; Phosphorus; Fertilizers; Soil; Soil Microbiology; Bacillus megaterium; Phosphates; Bacillus subtilis
PubMed: 38762518
DOI: 10.1038/s41598-024-61817-6 -
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 -
Communications Biology May 2024Although a low temperature limit for life has not been established, it is thought that there exists a physical limit imposed by the onset of intracellular vitrification,...
Although a low temperature limit for life has not been established, it is thought that there exists a physical limit imposed by the onset of intracellular vitrification, typically occurring at ~-20 °C for unicellular organisms. Here, we show, through differential scanning calorimetry, that molar concentrations of magnesium perchlorate can depress the intracellular vitrification point of Bacillus subtilis cells to temperatures much lower than those previously reported. At 2.5 M Mg(ClO), the peak vitrification temperature was lowered to -83 °C. Our results show that inorganic eutectic salts can in principle maintain liquid water in cells at much lower temperatures than those previously claimed as a lower limit to life, raising the prospects of active biochemical processes in low temperature natural settings. Our results may have implications for the habitability of Mars, where perchlorate salts are pervasive and potentially other terrestrial and extraterrestrial, cryosphere environments.
Topics: Bacillus subtilis; Perchlorates; Cold Temperature; Vitrification; Calorimetry, Differential Scanning
PubMed: 38755264
DOI: 10.1038/s42003-024-06277-4 -
PLoS Genetics May 2024Regulation of transcription is a fundamental process that allows bacteria to respond to external stimuli with appropriate timing and magnitude of response. In the soil...
Regulation of transcription is a fundamental process that allows bacteria to respond to external stimuli with appropriate timing and magnitude of response. In the soil bacterium Bacillus subtilis, transcriptional regulation is at the core of developmental processes needed for cell survival. Gene expression in cells transitioning from exponential phase to stationary phase is under the control of a group of transcription factors called transition state regulators (TSRs). TSRs influence numerous developmental processes including the decision between biofilm formation and motility, genetic competence, and sporulation, but the extent to which TSRs influence bacterial physiology remains to be fully elucidated. Here, we demonstrate two TSRs, ScoC and AbrB, along with the MarR-family transcription factor PchR negatively regulate production of the iron chelator pulcherrimin in B. subtilis. Genetic analysis of the relationship between the three transcription factors indicate that all are necessary to limit pulcherrimin production during exponential phase and influence the rate and total amount of pulcherrimin produced. Similarly, expression of the pulcherrimin biosynthesis gene yvmC was found to be under control of ScoC, AbrB, and PchR and correlated with the amount of pulcherrimin produced by each background. Lastly, our in vitro data indicate a weak direct role for ScoC in controlling pulcherrimin production along with AbrB and PchR. The layered regulation by two distinct regulatory systems underscores the important, role for pulcherrimin in B. subtilis physiology.
PubMed: 38753885
DOI: 10.1371/journal.pgen.1011283 -
EFSA Journal. European Food Safety... May 2024Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety of the feed additive consisting of endo-1,4-β-xylanase...
Safety of the feed additive consisting of endo-1,4-β-xylanase (produced with CBS 143953), subtilisin (produced with CBS 143946) and α-amylase (produced with CBS 143954) (Avizyme® 1505) for all poultry species (Danisco (UK) Ltd.).
Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety of the feed additive consisting of endo-1,4-β-xylanase (produced with CBS 143953), subtilisin (produced with CBS 143946) and α-amylase (produced with CBS 143954) (Avizyme® 1505) as a zootechnical feed additive for all poultry species. The additive is authorised in feed for chickens and turkeys for fattening, ducks and laying hens. In 2020, the FEEDAP Panel issued an opinion for the renewal of the authorisation of the additive for the species/categories for which there is an authorisation, a reduction of the minimum recommended level in turkeys for fattening and the extension of use to all poultry species. In that assessment, the Panel could not conclude on the safety of the additive due to uncertainties on the characterisation of the production strains and the possible presence of their viable cells and DNA in the final product. Moreover, limitations were identified in the xylanase specifications and xylanase method of analysis. The applicant submitted information to address the limitations previously identified. The Panel concluded that the additive is safe for the target species under the proposed conditions of use. The use of Avizyme® 1505 in animal nutrition is considered safe for the consumer and the environment. The additive is a mild irritant to skin and eyes; it is not a dermal sensitiser but should be considered a respiratory sensitiser. The additive is efficacious in ducks at 75 U endo-1,4-β-xylanase, 1000 U subtilisin and 100 U α-amylase/kg of complete feed. In other poultry species for fattening (including turkeys), reared for breeding and reared for laying, the additive is efficacious at 187.5 U endo-1,4-β-xylanase, 2500 U subtilisin and 250 U α-amylase per kg of complete feed and at 300 U endo-1,4-β-xylanase, 4000 U subtilisin and 400 U α-amylase per kg of complete feed for all poultry species for laying (except for ducks).
PubMed: 38751508
DOI: 10.2903/j.efsa.2024.8797 -
Scientific Reports May 2024Biodegradable plastics are those subjected easily to a degradation process, in which they can be decomposed after disposal in the environment through microbial activity....
Biodegradable plastics are those subjected easily to a degradation process, in which they can be decomposed after disposal in the environment through microbial activity. 30 bioplastic film formulations based only on chitosan film were used in the current investigation as a positive control together with chitosan film recovered from chitin-waste of locally obtained Aristeus antennatus. Additionally, castor oil was used as a plasticizer. While the yield of chitosan was 18% with 7.65% moisture content and 32.27% ash in the shells, the isolated chitin had a degree of deacetylation (DD) of 86%. The synthesized bioplastic films were characterized via numerous criteria. Firstly, the swelling capacity of these biofilms recorded relatively high percentages compared to polypropylene as synthetic plastic. Noticeably, the FTIR profiles, besides DSC, TGA, and XRD, confirmed the acceptable characteristics of these biofilms. In addition, their SEM illustrated the homogeneity and continuity with a few straps of the chitosan film and showed the homogeneous mixes of chitosan and castor oil with 5 and 20%. Moreover, data detected the antibacterial activity of different bioplastic formulas against some common bacterial pathogens (Enterococcus feacalis, Kelbsiella pnumina, Bacillus subtilis, and Pseudomonas aeruginosa). Amazingly, our bioplastic films have conducted potent antimicrobial activities. So, they may be promising in such a direction. Further, the biodegradability efficacy of bioplastic films formed was proved in numerous environments for several weeks of incubation. However, all bioplastic films decreased in their weights and changed in their colors, while polypropylene, was very constant all the time. The current findings suggest that our biofilms may be promising for many applications, especially in the field of food package protecting the food, and preventing microbial contamination, consequently, it may help in extending the shelf life of products.
Topics: Chitosan; Castor Oil; Biodegradable Plastics; Plasticizers; Starch; Animals; Biofilms; Anti-Bacterial Agents; Moths; Microbial Sensitivity Tests
PubMed: 38750054
DOI: 10.1038/s41598-024-61377-9 -
Brazilian Journal of Biology = Revista... 2024The use of fertilizers affects not only the soil fertility and crop yield, but also significantly changes the taxonomic structure of the soil microbiocenosis. Here,...
Responses of soil physico-chemical properties, structure of the microbial community and crop yields to different fertilization practices in Russia's conventional farming system.
The use of fertilizers affects not only the soil fertility and crop yield, but also significantly changes the taxonomic structure of the soil microbiocenosis. Here, based on stationary field experiment, we studied the influence of organo-mineral fertilizer (ОМF), modified by bacteria Bacillus subtilis, H-13 in comparison with different fertilizer systems (organic, mineral, organo-mineral) on (i) crop yield, (ii) physical and chemical properties, and (iii) alpha and beta diversity of the microbial community Albic Retisol (Loamic, Aric, Cutanic, Differentic, Ochric). The studies were carried out against the background of liming (рНКCl - 5.9) and without it (рНКCl - 5.1). The use of only one cattle farmyard manure was less effective than its co-application with mineral fertilizers in half doses. A similar effect was obtained when applying ОМF. In addition, the use of OMF contributes to a significant increase in the reserves of soil organic carbon in the soil layer 0-20 cm by 18%-32%. Using high-throughput sequencing of the 16S rRNA variable V4 gene sequence libraries, 10.759 taxa from 456 genera were identified, assigned to 34 fila (31 bacterial and 3 archaeotic. Unilateral application of mineral fertilizers leads to a significant decrease in the alpha diversity of the structure of soil microbial communities (OTE (other things equal) and Shannon index). A clear clustering of the microbiota was found in the variants with and without the introduction of сattle farmyard manure. It is revealed that the taxonomic structure of the microbiocenosis is formed under the influence of two main factors: crop rotation culture and applied fertilizers. The type of cultivated crop determines the dynamics of the microbiota at the level of larger taxa, such as domains, and fertilizers affect the structure of the microbial community at a lower taxonomic level (phyla, orders, bloodlines). On the basis of the Deseq analysis, marker taxa were identified, according to the share participation of which it is possible to determine the type of cultivated crop and fertilizers used in the experiment. Understanding the dynamics of taxa association and other influential factors can lead to the creation of universal systems of metagenomic indication, where tracking the dynamics of microbial communities will allow for a comprehensive assessment of the agroecological state of soils and timely decisions to prevent their degradation.
Topics: Fertilizers; Soil Microbiology; Soil; Crops, Agricultural; Russia; Agriculture; RNA, Ribosomal, 16S; Animals; Cattle; Microbiota; Manure
PubMed: 38747864
DOI: 10.1590/1519-6984.282493 -
BioRxiv : the Preprint Server For... May 2024is an anaerobic enteric pathogen that disseminates in the environment as a dormant spore. For and other sporulating bacteria, the initiation of sporulation is a...
is an anaerobic enteric pathogen that disseminates in the environment as a dormant spore. For and other sporulating bacteria, the initiation of sporulation is a regulated process that prevents spore formation under favorable growth conditions. In , one such mechanism for preventing sporulation is the Kinase Inhibitory Protein, KipI, which impedes activation of the main sporulation kinase. In addition, KipI functions as part of a complex that detoxifies the intermediate metabolite, 5-oxoproline (OP), a harmful by-product of glutamic acid. In this study, we investigate the orthologous Kip proteins in to determine their roles in the regulation of sporulation and metabolism. Using deletion mutants in and the full operon, we show that unlike in the Kip proteins have no significant impact on sporulation. However, we found that the operon encodes a functional oxoprolinase that facilitates detoxification of OP. Further, our data demonstrate that KipOTIA not only detoxifies OP, but also allows OP to be used as a nutrient source that supports the robust growth of , thereby facilitating the conversion of a toxic byproduct of metabolism into an effective energy source.
PubMed: 38746432
DOI: 10.1101/2024.05.01.592088 -
BioRxiv : the Preprint Server For... Apr 2024The gut microbiome has been proposed to influence many aspects of animal development and physiology. However, both the specific bacterial species and the molecular...
The gut microbiome has been proposed to influence many aspects of animal development and physiology. However, both the specific bacterial species and the molecular mechanisms by which bacteria exert these effects are unknown in most cases. Here, we established a high throughput screening platform using the model animal for identifying bacterial species and mechanisms that influence animal development and physiology. From our initial screens we found that many species can restore normal animal development to insulin signaling mutant animals that otherwise do not develop to adulthood. To determine how influence animal development we screened a complete non-essential gene knockout library of for mutants that no longer restored development to adulthood. We found the gene is required for animal development. In the absence of , produces excess N1-aminopropylagmatine. This polyamine is taken up by animal intestinal cells via the polyamine transporter CATP-5. When this molecule is taken up in sufficient quantities it inhibits animal mitochondrial function and causes diverse species of animals to arrest their development. To our knowledge, these are the first observations that can produce N1-aminopropylagmatine and that polyamines produced by intestinal microbiome species can antagonize animal development and mitochondrial function. Given that species are regularly isolated from animal intestinal microbiomes, including from humans, we propose that altered polyamine production from intestinal is likely to also influence animal development and metabolism in other species and potentially even contribute developmental and metabolic pathologies in humans. In addition, our findings demonstrate that can be used as a model animal to conduct high throughput screens for bacterial species and bioactive molecules that alter animal physiology.
PubMed: 38746390
DOI: 10.1101/2024.04.29.591726 -
Respirology Case Reports May 2024A 70-year-old immunocompetent male with a history of insomnia presented with pneumonia and bacteremia caused by . The patient took benzodiazepines and regularly consumed...
A 70-year-old immunocompetent male with a history of insomnia presented with pneumonia and bacteremia caused by . The patient took benzodiazepines and regularly consumed alcohol and natto (fermented soybeans). Initial antibiotic treatment was not effective, and bronchoalveolar lavage was performed. Bronchoalveolar lavage fluid (BALF) analysis revealed an increased lymphocytes fraction, and was detected in the BALF. Whole-genome sequencing confirmed the congruence of the genetic sequences between the strain in the blood culture of the patient, BALF, and strain isolated from the consumed natto, confirming subsp as the causative pathogen of pneumonia and bacteremia. Vancomycin followed by levofloxacin and systemic corticosteroid were used to treat the condition. This case highlights community-acquired pneumonia and bacteremia caused by subsp, particularly in individuals who consume natto.
PubMed: 38745892
DOI: 10.1002/rcr2.1384