Monilinia spp., which causes brown rot, is one of the most damaging pathogens in stone fruits. Researchers are exploring epiphytic and endophytic microorganisms with the potential to suppress pathogens, control pathogenic microorganisms, and/or promote plant growth. In this study, microorganisms with antagonistic activity against three Monilinia species were isolated from plum orchard soil and plum fruits. Antagonism tests in vitro showed strong antagonistic properties of six strains of bacteria and two yeast-like fungi against M. fructigena, M. fructicola, and M. laxa, with growth inhibition from 45.5 to 84.6%. The antagonists were identified and characterized at the genetic level using whole genome sequencing (WGS). Genes involved in antibiotic resistance, virulence, secondary metabolite synthesis, and plant growth promotion were identified and characterized through genome mapping, gene prediction, and annotation. None of the microorganisms studied were predicted to be pathogenic to humans. The results of this study indicate that the bacteria Bacillus pumilus, B. velezensis, two strains of Lysinibacillus agricola, Pseudomonas chlororaphis isolated from stone fruit orchard soil, and the yeast-like fungus Aureobasidium pullulans, isolated from plums, are promising candidates for the biological control of Monilinia spp.

For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as plant probiotics for sustainable agriculture.

The exopolysaccharide (EPS) produced by Pantoea alhagi NX-11, referred to as alhagan, enhances plant stress resistance, improves soil properties, and exhibits notable rheological properties. Despite these benefits, the exact bio-synthetic process of alhagan by P. alhagi NX-11 remains unclear. This study focused on sequencing the complete genome of P. alhagi NX-11 and identifying an alhagan synthesis gene cluster (LQ939_RS12550 to LQ939_RS12700). Gene annotation revealed that alhagan biosynthesis in P. alhagi NX-11 follows the Wzx/Wzy-dependent pathway. Furthermore, transcriptome analysis of P. alhagi NX-11 highlighted significant upregulation of four glycosyltransferase genes (alhH, wcaJ, alhK, and alhM) within the alhagan synthesis gene cluster. These glycosyltransferases are crucial for alhagan synthesis. To delve deeper into this process, two upregulated and uncharacterized glycosyltransferase genes, alhH and alhK, were knocked out. The resulting mutants, Delta alhH and Delta alhK, showed a notable decrease in EPS yield, reduced molecular weight, and altered monosaccharide compositions. These findings contribute to a better understanding of the alhagan biosynthesis mechanism in P. alhagi NX-11.

Vanillic acid (VA) is a phenolic compound frequently present in wastewater and agricultural soil. High concentrations of VA will increase the burden of sewage treatment and pose toxicity to crop plants. Although advanced oxidation has been successfully used to remove VA, green and sustainable treatments for VA pollution with efficient VA-degrading microbes, especially about the full pathways of VA degradation, are not well documented. In this study, a full investigation of VA degradation ability and associated metabolic mechanisms in the new VA-degrading bacterium Herbaspirillum aquaticum KLS-1 was performed. Results showed that strain KLS1 completely removed 500 mg/L VA within 36 h following a zero-order degradation kinetic model with a degradation half-time of 15.01 h. An efficient VA degradation occurred under the conditions with pH values of 7-9, temperatures of 30-40 degrees C, and shaking speeds of 150-200 rpm. A fed-batch experiment and SEM analysis showed that strain KLS-1 exhibited a good ability to remove up to 46.8 mg VA without cellular damage. The protocatechuate ortho-cleavage pathway was probably associated with efficient VA degradation in strain KLS-1 according to the whole genome sequencing and transcriptomic analysis. This study has offered a comprehensive understanding of full VA degradation mechanisms in microbes by using genomic sequencing coupled with transcriptomic analysis and provided a new VA-degrading bacterium for potential bioremediation of VA pollution.

Tobacco bacterial wilt (TBW) caused by Ralstonia solanacearum is a serious soil -borne disease, which seriously damages the growth of tobacco crops. Bacillus velezensis A5 was isolated from 3000 m deep-sea sediments of the Pacific Ocean, and was found to be antagonistic to TBW. Here, we report the complete genome sequence of strain A5, which has a 4,000,699 -bp single circular chromosome with 3827 genes and a G + C content of 46.44%, 87 tRNAs, and 27 rRNAs. A total of 12 gene clusters were identified in the genome of strain A5, which were responsible for the biosynthesis of antibacterial compounds, including surfactin, bacillaene, fengycin, difficidin, bacillibactin, and bacilysin. Additionally, strain A5 was found to contain a series of genes related to the biosynthesis of carbohydrate -active enzymes and secreted proteins. Our results indicate that strain A5 can be considered a promising biocontrol agent against TBW in agricultural fields.

Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59(T) and S8-45(T). (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59(T) and S8-45(T) were summed as feature 3 (comprising C16:1 omega 6c and/or C16:1 omega 7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59(T) and S8-45(T) harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59(T) and S8-45(T) strains. Additionally, strain S5-59(T) possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59(T) (=JCM 35564T =GDMCC 1.3193T) and S8-45(T) (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59(T) and S8-45(T), were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.

Background: MicroRNA (miRNA) plays an important role in hepatic stellate cell (HSCs) activation and liver fibrosis. The purpose of this study is to explore the effect of hypoxia on the differential expression of mRNAs and miRNAs in rat HSCs. Methods: HSC-T6 cells were treated with cobalt chloride (CoCl2), and the activity of HSC-T6 cells was measured by the CCK-8 assay. The mRNA expression levels of hypoxia inducible factor-1 alpha (HIF-1 alpha), collagen type I, transforming growth factor-131 (TGF-131), and Smad7 were measured by RT-qPCR. The protein expression levels of HIF-1 alpha, Bax, Bcl-2, and caspase-3 were assayed by western blot. We used basal medium and 400 mu mol/L CoCl2 medium to treat HSC-T6 cells for 48 h. Cells were harvested after 48 h to extract RNA. Transcriptome sequencing was performed to investigate differentially expressed miRNAs and mRNAs (fold change >2; P<0.05). Bioinformatics analysis was performed to predict the functions of differentially expressed miRNAs and mRNAs. Further, we used RT-qPCR to detect the expression of mRNAs and miRNAs to confirm the accuracy of sequencing. Results: With the increase of CoCl2 concentration, the activity of HSC-T6 cells decreased (P<0.05). The mRNA expression levels of HIF-1 alpha, collagen I, TGF-131, and Smad7, and the protein expressions levels of HIF-1 alpha, Bax, caspase-3, and the Bcl-2/Bax ratio were increased compared with the control group (P<0.05), while the expression of Bcl-2 decreased. A total of 54 miRNAs (20 upregulated and 34 downregulated) and 1,423 mRNAs (685 upregulated and 738 downregulated) were differentially expressed in the 400 mu mol/L CoCl2 medium group compared to the control basal medium group. Further bioinformatics analysis demonstrated that the differentially expressed mRNAs and miRNAs were mainly enriched in the synthesis of extracellular matrix. In addition, we used RT-qPCR to detect the expression of mRNAs and miRNAs to confirm the accuracy of sequencing. Conclusions: Our results presented the profiles of mRNAs and miRNAs in hypoxia-induced HSC-T6 cells in rats, the signaling pathways, and co-expression networks. These findings may suggest novel insights for the early diagnosis and treatment of HSC activation and liver fibrosis.