Transcriptome Analysis of Gene Expression in Dermacoccus abyssi HZAU 226 under Lysozyme Stress

Transcriptome of Kurthia gibsonii TYL-A1 Revealed the Biotransformation Mechanism of Tylosin

Tylosin (TYL) pollution has aroused widespread concern, and its existence poses a serious threat to the environment and human health. Microbial degradation of antibiotics is considered to be an effective strategy to reduce the environmental impact of antibiotics, but its degradation mechanism is still unclear. In this study, transcriptome analysis was combined to explore the response mechanism of K. gibsonii strain TYL-A1 under TYL stress. The results showed that the strain showed a significant antioxidant response under TYL stress to cope with TYL-induced cell damage. TYL also increased the level of intracellular reactive oxygen species (ROS), damaged the integrity of the cell membrane, and inhibited the growth of strain TYL-A1. Transcriptome sequencing showed that under TYL exposure conditions, 1650 DEGs in strain TYL-A1 showed expression changes, of which 806 genes were significantly up-regulated and 844 genes were significantly down-regulated. Differentially expressed DEGs were significantly enriched in pathways related to metabolism, biosynthesis, and stress response, and tricarboxylic acid cycle, oxidative phosphorylation, and carbon metabolism genes were significantly up-regulated. In conclusion, this study provides novel insights regarding the degradation of TYL by K. gibsonii TYL-A1.

Comparative Analysis of Hulless Barley Transcriptomes to Regulatory Effects of Phosphorous Deficiency

Hulless barley is a cold-resistant crop widely planted in the northwest plateau of China. It is also the main food crop in this region. Phosphorus (P), as one of the important essential nutrient elements, regulates plant growth and defense. This study aimed to analyze the development and related molecular mechanisms of hulless barley under P deficiency and explore the regulatory genes so as to provide a basis for subsequent molecular breeding research. Transcriptome analysis was performed on the root and leaf samples of hulless barley cultured with different concentrations of KH2PO4 (1 mM and 10 μM) Hoagland solution. A total of 46,439 genes were finally obtained by the combined analysis of leaf and root samples. Among them, 325 and 453 genes had more than twofold differences in expression. These differentially expressed genes (DEGs) mainly participated in the abiotic stress biosynthetic process through Gene Ontology prediction. Moreover, the Kyoto Encyclopedia of Genes and Genomes showed that DEGs were mainly involved in photosynthesis, plant hormone signal transduction, glycolysis, phenylpropanoid biosynthesis, and synthesis of metabolites. These pathways also appeared in other abiotic stresses. Plants initiated multiple hormone synergistic regulatory mechanisms to maintain growth under P-deficient conditions. Transcription factors (TFs) also proved these predictions. The enrichment of ARR-B TFs, which positively regulated the phosphorelay-mediated cytokinin signal transduction, and some other TFs (AP2, GRAS, and ARF) was related to plant hormone regulation. Some DEGs showed different values in their FPKM (fragment per kilobase of transcript per million mapped reads), but the expression trends of genes responding to stress and phosphorylation remained highly consistent. Therefore, in the case of P deficiency, the first response of plants was the expression of stress-related genes. The effects of this stress on plant metabolites need to be further studied to improve the relevant regulatory mechanisms so as to further understand the importance of P in the development and stress resistance of hulless barley.

Comparative Transcriptome Analysis Reveals the Molecular Mechanisms of Acetic Acid Reduction by Adding NaHSO3 in Actinobacillus succinogenes GXAS137

Acetic acid (AC) is a major by-product from fermentation processes for producing succinic acid (SA) using Actinobacillus succinogenes. Previous experiments have demonstrated that sodium bisulfate (NaHSO3) can significantly decrease AC production by A. succinogenes GXAS137 during SA fermentation. However, the mechanism of AC reduction is poorly understood. In this study, the transcriptional profiles of the strain were compared through Illumina RNA-seq to identify differentially expressed genes (DEGs). A total of 210 DEGs were identified by expression analysis: 83 and 127 genes up-regulated and down-regulated, respectively, in response to NaHSO3 treatment. The functional annotation analysis of DEGs showed that the genes were mainly involved in carbohydrates, inorganic ions, amino acid transport, metabolism, and energy production and conversion. The mechanisms of AC reduction might be related to two aspects: (i) the lipoic acid synthesis pathway (LipA, LipB) was significantly down-regulated, which blocked the pathway catalyzed by pyruvate dehydrogenase complex to synthesize acetyl-coenzyme A (acetyl-CoA) from pyruvate; (ii) the expression level of the gene encoding bifunctional acetaldehyde-alcohol dehydrogenase was significantly up-regulated, and this effect facilitated the synthesis of ethanol from acetyl-CoA. However, the reaction of NaHSO3 with the intermediate metabolite acetaldehyde blocked the production of ethanol and consumed acetyl-CoA, thereby decreasing AC production. Thus, our study provides new insights into the molecular mechanism of AC decreased underlying the treatment of NaHSO3 and will deepen the understanding of the complex regulatory mechanisms of A. succinogenes.

Transcriptomic and metabolomic analyses to study the key role by which Ralstonia insidiosa induces Listeria monocytogenes to form suspended aggregates

Ralstonia insidiosa can survive in a wide range of aqueous environments, including food processing areas, and is harmful to humans. It can induce Listeria monocytogenes to form suspended aggregates, resulting from the co-aggregation of two bacteria, which allows for more persistent survival and increases the risk of L. monocytogenes contamination. In our study, different groups of aggregates were analyzed and compared using Illumina RNA sequencing technology. These included R. insidiosa under normal and barren nutrient conditions and in the presence or absence of L. monocytogenes as a way to screen for differentially expressed genes (DEGs) in the process of aggregate formation. In addition, sterile supernatants of R. insidiosa were analyzed under different nutrient conditions using metabolomics to investigate the effect of nutrient-poor conditions on metabolite production by R. insidiosa. We also undertook a combined analysis of transcriptome and metabolome data to further investigate the induction effect of R. insidiosa on L. monocytogenes in a barren environment. The results of the functional annotation analysis on the surface of DEGs and qPCR showed that under nutrient-poor conditions, the acdx, puuE, and acs genes of R. insidiosa were significantly upregulated in biosynthetic processes such as carbon metabolism, metabolic pathways, and biosynthesis of secondary metabolites, with Log2FC reaching 4.39, 3.96, and 3.95 respectively. In contrast, the Log2FC of cydA, cyoB, and rpsJ in oxidative phosphorylation and ribosomal pathways reached 3.74, 3.87, and 4.25, respectively. Thirty-one key components were identified while screening for differential metabolites, which mainly included amino acids and their metabolites, enriched to the pathways of biosynthesis of amino acids, phenylalanine metabolism, and methionine metabolism. Of these, aminomalonic acid and Proximicin B were the special components of R. insidiosa that were metabolized under nutrient-poor conditions.

The Metabolomics Changes in Luria-Bertani Broth Medium under Different Sterilization Methods and Their Effects on Bacillus Growth

Luria-Bertani broth (LB) culture medium is a commonly used bacterial culture medium in the laboratory. The nutrient composition, concentration, and culture conditions of LB medium can influence the growth of microbial strains. The purpose of this article is to demonstrate the impact of LB liquid culture medium on microbial growth under different sterilization conditions. In this study, LB medium with four different treatments was used, as follows: A, LB medium without treatments; B, LB medium with filtration; C, LB medium with autoclaving; and D, LB medium with autoclaving and cultured for 12 h. Subsequently, the protein levels and antioxidant capacity of the medium with different treatments were measured, and the effects of the different LB medium treatments on the growth of microorganisms and metabolites were determined via 16s rRNA gene sequencing and metabolomics analysis, respectively. Firmicutes and Lactobacillus were the dominant microorganisms, which were enriched in fermentation and chemoheterotrophy. The protein levels and antioxidant capacity of the LB medium with different treatments were different, and with the increasing concentration of medium, the protein levels were gradually increased, while the antioxidant capacity was decreased firstly and then increased. The growth trend of Bacillus subtilis, Bacillus paralicheniformis, Micrococcus luteus, and Alternaria alternata in the medium with different treatments was similar. Additionally, 220 and 114 differential metabolites were found between B and C medium, and between C and D medium, which were significantly enriched in the "Hedgehog signaling pathway", "biosynthesis of plant secondary metabolites", "ABC transporters", "arginine and proline metabolism", and "linoleic acid metabolism". LB medium may be a good energy source for Lactobacillus growth with unsterilized medium, and LB medium filtered with a 0.22 μm filter membrane may be used for bacterial culture better than culture medium after high-pressure sterilization. LB medium still has the ability for antioxidation and to keep bacteria growth whether or not autoclaved, indicating that there are some substances that can resist a high temperature and pressure and still maintain their functions.

Community Structure of Nitrifying and Denitrifying Bacteria from Effluents Discharged into Lake Victoria, Kenya

An active microbial community of nitrifying and denitrifying bacteria is needed for efficient utilization of nitrogenous compounds from wastewater. In this study, we explored the bacterial community diversity and structure within rivers, treated and untreated wastewater treatment plants (WWTPs) discharging into Lake Victoria. Water samples were collected from rivers and WWTPs that drain into Lake Victoria. Physicochemical analysis was done to determine the level of nutrients or pollutant loading in the samples. Total community DNA was extracted, followed by Illumina high throughput sequencing to determine the total microbial community and abundance. Enrichment and isolation were then done to recover potential nitrifiers and denitrifiers. Physicochemical analysis pointed to high levels total nitrogen and ammonia in both treated and untreated WWTPs as compared to the samples from the lake and rivers. A total of 1,763 operational taxonomic units (OTUs) spread across 26 bacterial phyla were observed with the most dominant phylum being Proteobacteria. We observed a decreasing trend in diversity from the lake, rivers to WWTPs. The genus Planktothrix constituted 19% of the sequence reads in sample J2 collected from the lagoon. All the isolates recovered in this study were affiliated to three genera: Pseudomonas, Klebsiella and Enterobacter in the phylum Proteobacteria. A combination of metagenomic analysis and a culture-dependent approach helped us understand the relative abundance as well as potential nitrifiers and denitrifiers present in different samples. The recovered isolates could be used for in situ removal of nitrogenous compounds from contaminated wastewater.

Gene Analysis of Listeria monocytogenes Suspended Aggregates Induced by Ralstonia insidiosa Cell-Free Supernatants under Nutrient-Poor Environments

Listeria monocytogenes is a zoonotic food-borne pathogen. The production of food-borne pathogenic bacteria aggregates is considered to be a way to improve their resistance and persistence in the food chain. Ralstonia insidiosa has been shown to induce L. monocytogenes to form suspended aggregates, but induction mechanisms remain unclear. In the study, the effect of R. insidiosa cell-free supernatants cultured in 10% TSB medium (10% RIS) on the formation of L. monocytogenes suspended aggregates was evaluated. Next, the Illumina RNA sequencing was used to compare the transcriptional profiles of L. monocytogenes in 10% TSB medium with and without 10% RIS to identify differentially expressed genes (DEGs). The result of functional annotation analysis of DEGs indicated that these genes mainly participate in two component system, bacterial chemotaxis and flagellar assembly. Then the reaction network of L. monocytogenes suspended aggregates with the presence of 10% RIS was summarized. The gene-deletion strain of L. monocytogenes was constructed by homologous recombination. The result showed that cheA and cheY are key genes in the formation of suspended aggregates. This research is the preliminary verification of suspended aggregates' RNA sequencing and is helpful to analyze the aggregation mechanisms of food-borne pathogenic bacteria from a new perspective.

sRNA23, a novel small RNA, regulates to the pathogenesis of Streptococcus suis serotype 2

ABBREVIATION

sRNA: small noncoding RNA; FBA: fructose diphosphate aldolase; rplB: 50S ribosomal protein L2; RACE: rapid amplification of cDNA ends; EMSA: electrophoretic mobility shift assay; THB: Todd-Hewitt broth; FBS: fetal bovine serum; BIP: 2,2'-Bipyridine.

Nitrogen removal performance, quantitative detection and potential application of a novel aerobic denitrifying strain, Pseudomonas sp. GZWN4 isolated from aquaculture water

A novel Pseudomonas sp. GZWN4 with the aerobic nitrogen removal ability was isolated from aquaculture water, whose removal efficiency of NO₂^--N, NO₃^--N and NH₄⁺-N was 99.72%, 82.54% and 98.62%, respectively. The key genes involved in nitrogen removal, nxr, napA, narI, nirS, norB and nosZ, were successfully amplified and by combination with the results of nitrogen balance analysis, it was inferred that the denitrification pathway of strain GZWN4 was NO₃^--N → NO₂^--N → NO → N₂O → N₂. The strain GZWN4 had excellent nitrite removal performance at pH 7.0-8.5, temperature 25-30 ℃, C/N ratio 5-20, salinity 8-32‰ and dissolved oxygen concentration 2.52-5.73 mg L^-1. The receivable linear correlation (R² = 0.9809) was obtained with the range of quantification between l0³ and 10⁸ CFU mL^-1 of the strain by enzyme-linked immunosorbent assay. Strain GZWN4 could maintain high abundance in the actual water and wastewater of mariculture and the removal efficiency of TN were 52.57% and 63.64%, respectively. The safety evaluation experiment showed that the strain GZWN4 had no hemolysis and high biosecurity toward shrimp Litopenaeus vannamei. The excellent nitrogen removal ability and adaptability to aquaculture environment made strain GZWN4 a promising candidate for treatment of water and wastewater in aquaculture.