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Scientific Reports Feb 2024Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the...
Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (10 and 10 cfu.g soil). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.
Topics: Agricultural Inoculants; Soil; Nitrates; Agriculture; Pseudomonas fluorescens; Soil Microbiology
PubMed: 38378706
DOI: 10.1038/s41598-024-54069-x -
MicroLife 2024Pyoverdin is a water-soluble metal-chelator synthesized by members of the genus and used for the acquisition of insoluble ferric iron. Although freely diffusible in...
Pyoverdin is a water-soluble metal-chelator synthesized by members of the genus and used for the acquisition of insoluble ferric iron. Although freely diffusible in aqueous environments, preferential dissemination of pyoverdin among adjacent cells, fine-tuning of intracellular siderophore concentrations, and fitness advantages to pyoverdin-producing versus nonproducing cells, indicate control of location and release. Here, using time-lapse fluorescence microscopy to track single cells in growing microcolonies of SBW25, we show accumulation of pyoverdin at cell poles. Accumulation occurs on cessation of cell growth, is achieved by cross-feeding in pyoverdin-nonproducing mutants and is reversible. Moreover, accumulation coincides with localization of a fluorescent periplasmic reporter, suggesting that pyoverdin accumulation at cell poles is part of the general cellular response to starvation. Compatible with this conclusion is absence of non-accumulating phenotypes in a range of pyoverdin mutants. Analysis of the performance of pyoverdin-producing and nonproducing cells under conditions promoting polar accumulation shows an advantage to accumulation on resumption of growth after stress. Examination of pyoverdin polar accumulation in a multispecies community and in a range of laboratory and natural species of , including PAO1 and KT2440, confirms that the phenotype is characteristic of .
PubMed: 38370141
DOI: 10.1093/femsml/uqae001 -
Scientific Reports Feb 2024The aim of this study was to produce mutant strains of Bacillus subtilis with high probiotic performance for use in the aquaculture of rainbow trout Oncorhynchus mykiss....
The aim of this study was to produce mutant strains of Bacillus subtilis with high probiotic performance for use in the aquaculture of rainbow trout Oncorhynchus mykiss. The main strain of B. subtilis (MS) was irradiated with gamma rays (5.3 KGy). Subsequently, the B. subtilis mutant strain no. 45 (MS. 45) was selected for bacterial growth performance, resistance to acidic conditions, resistance to bile salts and antibacterial activity against Aeromonas hydrophila and Pseudomonas fluorescens. After 60 days, the rainbow trout (70.25 ± 3.89 g) fed with MS. 45 and MS were exposed to hypoxia stress (dissolved oxygen = 2 ppm). Subsequently, immune indices (lysozyme, bacterial activity and complement activity), hematological indices [hematocrit, hemoglobin, WBC, RBC, mean corpuscular volume (MCV)] and antioxidant factors (T-AOC, SOD and MDA)) were analyzed after and before hypoxia exposure. The expression of immunological genes (IFN-γ, TNF-α, IL-1β, IL-8) in the intestine and the expression of hypoxia-related genes (HIF-1α, HIF-2α, FIH1) in the liver were compared between the different groups under hypoxia and normoxia conditions. Growth, immunological and antioxidant indices improved in group MS. 45 compared to the other groups. Stress indices and associated immunologic and hypoxia expressions under hypoxia and normoxia conditions improved in MS. 45 compared to the other groups. This resulted in improved growth, immunity and stress responses in fish fed with the microbial supplement of MS. 45 (P < 0.05) under hypoxia and normoxia conditions, (P < 0.05), resulting in a significant improvement in trout aquaculture.
Topics: Animals; Diet; Oncorhynchus mykiss; Antioxidants; Bacillus subtilis; Probiotics; Aquaculture; Hypoxia; Animal Feed; Fish Diseases
PubMed: 38355704
DOI: 10.1038/s41598-024-54380-7 -
Green Chemistry : An International... Feb 2024Novel synthetic strategies for the production of high-value chemicals based on the 12 principles of green chemistry are highly desired. Herein, we present a proof of...
Novel synthetic strategies for the production of high-value chemicals based on the 12 principles of green chemistry are highly desired. Herein, we present a proof of concept for two novel chemo-enzymatic one-pot cascades allowing for the production of valuable fragrance and flavor aldehydes. We utilized renewable phenylpropenes, such as eugenol from cloves or estragole from estragon, as starting materials. For the first strategy, Pd-catalyzed isomerization of the allylic double bond and subsequent enzyme-mediated (aromatic dioxygenase, ADO) alkene cleavage were performed to obtain the desired aldehydes. In the second route, the double bond was oxidized to the corresponding ketone a copper-free Wacker oxidation protocol followed by enzymatic Baeyer-Villiger oxidation (phenylacetone monooxygenase from ), esterase-mediated (esterase from , PfeI) hydrolysis and subsequent oxidation of the primary alcohol (alcohol dehydrogenase from , AlkJ) to the respective aldehyde products. Eight different phenylpropene derivatives were subjected to these reaction sequences, allowing for the synthesis of seven aldehydes in up to 55% yield after 4 reaction steps (86% for each step).
PubMed: 38323304
DOI: 10.1039/d3gc04191c -
Meat Science May 2024This study assessed the bioprotective effect of Carnobacterium maltaromaticum (CM) against Pseudomonas fluorescens (PF) and Brochothrix thermosphacta (BT) in ground beef...
This study assessed the bioprotective effect of Carnobacterium maltaromaticum (CM) against Pseudomonas fluorescens (PF) and Brochothrix thermosphacta (BT) in ground beef and sliced cooked ham stored in high- and low-oxygen-modified atmospheres (66/4/30% O/N/CO and 70/30% N/CO respectively). Both meat products were inoculated with CM, PF, and BT individually or in combination and stored for 7 days (3 days at 4 °C + 4 days at 8 °C) for ground beef and 28 days (10 days at 4 °C + 18 days at 8 °C) for sliced cooked ham. Each food matrix was assigned to 6 treatments: NC (no bacterial inoculation, representing the indigenous bacteria of meat), CM, BT, PF, CM + BT, and CM + PF. Bacterial growth, pH, instrumental color, and headspace gas composition were assessed during storage. CM counts remained stable from inoculation and throughout the shelf-life. CM reduced the population of inoculated and indigenous spoilage bacteria, including BT, PF, and enterobacteria, and showed a negligible impact on the physicochemical quality parameters of the products. Furthermore, upon simulating the shelf-life of ground beef and cooked ham, a remarkable extension could be observed with CM. Therefore, CM could be exploited as a biopreservative in meat products to enhance quality and shelf-life.
Topics: Animals; Cattle; Food Packaging; Food Microbiology; Meat; Bacteria; Colony Count, Microbial; Carnobacterium
PubMed: 38301298
DOI: 10.1016/j.meatsci.2024.109441 -
Nucleic Acids Research Mar 2024The complement of tRNA genes within a genome is typically considered to be a (relatively) stable characteristic of an organism. Here, we demonstrate that bacterial tRNA...
The complement of tRNA genes within a genome is typically considered to be a (relatively) stable characteristic of an organism. Here, we demonstrate that bacterial tRNA gene set composition can be more flexible than previously appreciated, particularly regarding tRNA gene copy number. We report the high-rate occurrence of spontaneous, large-scale, tandem duplication events in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The identified duplications are up to ∼1 Mb in size (∼15% of the wildtype genome) and are predicted to change the copy number of up to 917 genes, including several tRNA genes. The observed duplications are inherently unstable: they occur, and are subsequently lost, at extremely high rates. We propose that this unusually plastic type of mutation provides a mechanism by which tRNA gene set diversity can be rapidly generated, while simultaneously preserving the underlying tRNA gene set in the absence of continued selection. That is, if a tRNA set variant provides no fitness advantage, then high-rate segregation of the duplication ensures the maintenance of the original tRNA gene set. However, if a tRNA gene set variant is beneficial, the underlying duplication fragment(s) may persist for longer and provide raw material for further, more stable, evolutionary change.
Topics: Gene Dosage; Gene Duplication; Genes, Bacterial; Mutation; Pseudomonas fluorescens; RNA, Transfer
PubMed: 38296823
DOI: 10.1093/nar/gkae049 -
BioRxiv : the Preprint Server For... Jan 2024Swarming motility in pseudomonads typically requires both a functional flagellum and production/secretion of a biosurfactant. Published work has shown that the wild-type...
Swarming motility in pseudomonads typically requires both a functional flagellum and production/secretion of a biosurfactant. Published work has shown that the wild-type Pf0-1 is swarming-deficient due to a point mutation in the gene, which until recently, was thought to inactivate rather than attenuate the Gac/Rsm pathway. As a result, little is known about the underlying mechanisms that regulate swarming motility by Pf0-1. Here, we demonstrate that a Δ Δ Δ mutant, which phenotypically mimics Gac/Rsm pathway overstimulation, is proficient at swarming motility. RsmA and RsmE appear to play a key role in this regulation. Transposon mutagenesis of the Δ Δ Δ mutant identified multiple factors that impact swarming motility, including pathways involved in flagellar synthesis and biosurfactant production/secretion. We find that loss of genes linked to biosurfactant Gacamide A biosynthesis or secretion impact swarming motility, as does loss of the alternative sigma factor FliA, which results in a defect in flagellar function. Collectively, these findings provide evidence that Pf0-1 can swarm if the Gac/Rsm pathway is activated, highlight the regulatory complexity of swarming motility in this strain, and demonstrate that the cyclic lipopeptide Gacamide A is utilized as a biosurfactant for swarming motility.
PubMed: 38293239
DOI: 10.1101/2024.01.17.576057 -
World Journal of Microbiology &... Jan 2024Pseudomonas fluorescens complex consists of environmental and some human opportunistic pathogenic bacteria. It includes mainly beneficial and few phytopathogenic species... (Review)
Review
Pseudomonas fluorescens complex consists of environmental and some human opportunistic pathogenic bacteria. It includes mainly beneficial and few phytopathogenic species that are common inhabitants of soil and plant rhizosphere. Many members of the group are in fact known as effective biocontrol agents of plant pathogens and as plant growth promoters and for these attitudes they are of great interest for biotechnological applications. The antagonistic activity of fluorescent Pseudomonas is mainly related to the production of several antibiotic compounds, lytic enzymes, lipopeptides and siderophores. Several volatile organic compounds are also synthesized by fluorescent Pseudomonas including different kinds of molecules that are involved in antagonistic interactions with other organisms and in the induction of systemic responses in plants. This review will mainly focus on the volatile compounds emitted by some members of P. fluorescens complex so far identified, with the aim to highlight the role played by these molecules in the interaction of the bacteria with phytopathogenic micro and macro-organisms and plants.
Topics: Humans; Pseudomonas; Pseudomonas fluorescens; Plants; Rhizosphere; Plant Development; Plant Diseases
PubMed: 38281212
DOI: 10.1007/s11274-023-03873-0 -
Journal of Molecular Biology Mar 2024Light-Oxygen-Voltage (LOV) flavoproteins transduce a light signal into variable signaling outputs via a structural rearrangement in the sensory core domain, which is...
Light-Oxygen-Voltage (LOV) flavoproteins transduce a light signal into variable signaling outputs via a structural rearrangement in the sensory core domain, which is then relayed to fused effector domains via α-helical linker elements. Short LOV proteins from Pseudomonadaceae consist of a LOV sensory core and N- and C-terminal α-helices of variable length, providing a simple model system to study the molecular mechanism of allosteric activation. Here we report the crystal structures of two LOV proteins from Pseudomonas fluorescens - SBW25-LOV in the fully light-adapted state and Pf5-LOV in the dark-state. In a comparative analysis of the Pseudomonadaceae short LOVs, the structures demonstrate light-induced rotation of the core domains and splaying of the proximal A'α and Jα helices in the N and C-termini, highlighting evidence for a conserved signal transduction mechanism. Another distinguishing feature of the Pseudomonadaceae short LOV protein family is their highly variable dark recovery, ranging from seconds to days. Understanding this variability is crucial for tuning the signaling behavior of LOV-based optogenetic tools. At 37 °C, SBW25-LOV and Pf5-LOV exhibit adduct state lifetimes of 1470 min and 3.6 min, respectively. To investigate this remarkable difference in dark recovery rates, we targeted three residues lining the solvent channel entrance to the chromophore pocket where we introduced mutations by exchanging the non-conserved amino acids from SBW25-LOV into Pf5-LOV and vice versa. Dark recovery kinetics of the resulting mutants, as well as MD simulations and solvent cavity calculations on the crystal structures suggest a correlation between solvent accessibility and adduct lifetime.
Topics: Light; Oxygen; Signal Transduction; Solvents; Flavoproteins; Protein Domains; Protein Conformation, alpha-Helical; Pseudomonas fluorescens; Bacterial Proteins; Optogenetics; Photoreceptors, Microbial; Mutation; Crystallography, X-Ray
PubMed: 38280482
DOI: 10.1016/j.jmb.2024.168458 -
Microorganisms Dec 2023Coal mining has caused significant soil nitrogen loss in mining areas, limiting reclamation and reuse in agriculture. This article studies the effects of organic...
Coal mining has caused significant soil nitrogen loss in mining areas, limiting reclamation and reuse in agriculture. This article studies the effects of organic fertilizer, inorganic fertilizer, and the combined application of with the ability of nitrogen fixation on soil nitrogen accumulation and composition in the reclamation area of the Tunlan Coal Mine from 2016 to 2022 under the conditions of equal nitrogen application, providing a scientific basis for microbial fertilization and the rapid increase in nitrogen content in the reclaimed soil of mining areas. The results showed that as the reclamation time increased, the nitrogen content and the composition and structure of the soil treated with fertilization rapidly evolved toward normal farmland soil. The soil nitrogen content increased most rapidly in the presence of added + organic fertilizer (MB). Compared to other treatments (inorganic fertilizer (CF), organic fertilizer (M), and + inorganic fertilizer (CFB)), MB increased total nitrogen (TN) to normal farmland soil levels 1-3 years earlier. The comprehensive scores of MB and CFB on the two principal components increased by 1.58 and 0.79 compared to those of M and CF treatments, respectively. This indicates that the combination of and organic fertilizer improves soil nitrogen accumulation more effectively than the combination of and inorganic fertilizer. In addition, the application of increases the content of unknown nitrogen (UN) in acid-hydrolysable nitrogen (AHN) and decreases the content of amino acid nitrogen (AAN) and ammonia nitrogen (AN). However, there was no significant effect on the content of ammonium nitrogen (NH-N) and nitrate nitrogen (NO-N) in soil-mineralized nitrogen (SMN). When combined with inorganic fertilizer, the contribution of SMN to TN increased by 14.78%, while when combined with organic fertilizer, the contribution of AHN to TN increased by 44.77%. In summary, the use of is beneficial for nitrogen recovery in the reclaimed soil of coal-mining areas. The optimal fertilization method under the experimental conditions is the combination of and organic fertilizer.
PubMed: 38276177
DOI: 10.3390/microorganisms12010009