Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability

Effects of swine manure dilution with lagoon effluent on microbial communities and odor formation in pit recharge systems

Pit recharge systems (PRS) control odor by managing organic solids in swine manure. However, there needs to be more understanding of PRS's effect on the microbiome composition and its impact on odor formation. A study was conducted to understand how recharge intervals used in PRS impact manure microbiome and odor formation. Bioreactors dynamically loaded simulated recharge intervals of 14, 10, and 4 days by diluting swine manure with lagoon effluent at varying ratios. Treatment ratios tested included 10:0 (control), 7:3 (typical Korean PRS), 5:5 (enhanced PRS #1), and 2:8 (enhanced PRS #2). Manure microbial membership, chemical concentrations, and odorant concentrations were used to identify the interactions between microbiota, manure, and odor. The initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent, respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9% or increased by 17.6%, respectively, with each unit dilution. Microbial community composition was controlled by both treatment (i.e., manure dilution ratio and barn source material) and environmental factors (i.e., solids and pH). Microbiome composition was correlated with manure odor formation profiles, but this effect was inseparable from environmental factors, which explained over 75% of the variance in odor profiles. Consequently, monitoring solids and pH in recharge waters will significantly impact odor control in PRS.

Fingolimod Inhibits Exopolysaccharide Production and Regulates Relevant Genes to Eliminate the Biofilm of K. pneumoniae

Klebsiella pneumoniae (K. pneumoniae) exhibits the ability to form biofilms as a means of adapting to its adverse surroundings. K. pneumoniae in this biofilm state demonstrates remarkable resistance, evades immune system attacks, and poses challenges for complete eradication, thereby complicating clinical anti-infection efforts. Moreover, the precise mechanisms governing biofilm formation and disruption remain elusive. Recent studies have discovered that fingolimod (FLD) exhibits biofilm properties against Gram-positive bacteria. Therefore, the antibiofilm properties of FLD were evaluated against multidrug-resistant (MDR) K. pneumoniae in this study. The antibiofilm activity of FLD against K. pneumoniae was assessed utilizing the Alamar Blue assay along with confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM), and crystal violet (CV) staining. The results showed that FLD effectively reduced biofilm formation, exopolysaccharide (EPS), motility, and bacterial abundance within K. pneumoniae biofilms without impeding its growth and metabolic activity. Furthermore, the inhibitory impact of FLD on the production of autoinducer-2 (AI-2) signaling molecules was identified, thereby demonstrating its notable anti-quorum sensing (QS) properties. The results of qRT-PCR analysis demonstrated that FLD significantly decreased the expression of genes associated with the efflux pump gene (AcrB, kexD, ketM, kdeA, and kpnE), outer membrane (OM) porin proteins (OmpK35, OmpK36), the quorum-sensing (QS) system (luxS), lipopolysaccharide (LPS) production (wzm), and EPS production (pgaA). Simultaneously, FLD exhibited evident antibacterial synergism, leading to an increased survival rate of G. mellonella infected with MDR K. pneumoniae. These findings suggested that FLD has substantial antibiofilm properties and synergistic antibacterial potential for colistin in treating K. pneumoniae infections.

Lysinibacillus irui sp. nov., isolated from Iru, fermented African locust beans

A Gram-positive, motile, aerobic, rod-shaped, endospore-forming strain designated IRB4-01T was isolated from fermented African locust beans (Iru) obtained from Bodija market in the city of Ibadan, southwestern Nigeria, during a screening process from food-related sources. IRB4-01T grew at 10-50 °C (optimum, 35-37 °C), pH 6-10 (optimum, pH 7) and in 0-6 % NaCl (optimum, 1-3 %). Phylogenetic analyses based on 16S rRNA and combined short- and long-read genome sequencing revealed that IRB4-01T is closely related to Lysinibacillus cavernae SYSU K30005T and Lysinibacillus boronitolerans 10aT. The cell-wall peptidoglycan type was A4α (Lys-Asp), containing the diagnostic diamino acid lysine. The major polar lipids in strain IRB4-01T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid, while the predominant menaquinone was MK-7. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. Genomic DNA G+C content was 37.4  mol%, while the digital DNA-DNA hybridization revealed 33.6 and 32.3 % relatedness to L. cavernae SYSU K30005T and L. boronitolerans 10aT, respectively. Based on phenotypic, physiological and chemotaxonomic characteristics, as well as genome comparisons, strain IRB4-01T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus irui sp. nov. is proposed. The type strain is IRB4-01T (NCIMB 15452T=LMG 32887T). Hybrid genome data are provided on the NCBI database using the Bioproject number PRJNA906010 and accession numbers CP113527 and CP113528. Additionally, a representative 16S rRNA sequence is available with the GenBank accession number OQ566940.

Response to Cold Adaption in Acinetobacter johnsonii XY27 from Spoiled Bigeye Tuna (Thunnus obesus): Membrane Protein Composition and Protein Biomarker Identification by Proteomics

Acinetobacter johnsonii is one of the major food-spoilage bacteria and can survive under cold stress. In this study, the membrane composition, membrane permeability, and energy transduction of A. johnsonii XY27 cultured at 4 and 30 °C were examined comparatively by flow cytometry combined with liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. The Na⁺/K⁺ATPase activity, alkaline phosphatase and ATPase activity, fluorescence intensity, and cell viability in A. johnsonii XY27 increased with the decrease in cultivation temperature. The polyunsaturated fatty acid and monounsaturated fatty acids have a higher content in A. johnsonii XY27 cultured at 4 °C compared to that cultured at 30 °C, in which the contents of methyl palmitoleate, methyl myristoleate, and methyl oleate increased dramatically with decreasing temperature. Comparative proteomics analysis revealed that 31 proteins were downregulated and 4 proteins were upregulated, in which catalase-peroxidase 1 and cold shock proteins as biomarker proteins could effectively control A. johnsonii during cold adaptation.