A Simple Defined Medium for the Production of True Diketopiperazines in Xylella fastidiosa and Their Identification by Ultra-Fast Liquid Chromatography-Electrospray Ionization Ion Trap Mass Spectrometry

Antimicrobial Cyclic Dipeptides from Japanese Quail (Coturnix japonica) Eggs Supplemented with Probiotic Lactobacillus plantarum

Fifteen cyclic dipeptides (CDPs) containing proline, one cyclo(Phe-Ala) without proline, and a non-peptidyl DL-3-phenyllactic acid were previously identified in the culture filtrates of Lactobacillus plantarum LBP-K10, an isolate from kimchi. In this study, we used Japanese quail (Coturnix japonica) eggs to examine the effects of probiotic supplementation on the antimicrobial CDPs extracted from quail eggs (QE). Eggshell-free QE were obtained from two distinct groups of quails. The first group (K10N) comprised eggs from unsupplemented quails. The second group (K10S) comprised eggs from quails supplemented with Lb. plantarum LBP-K10. The QE samples were extracted using methylene chloride through a liquid-liquid extraction process. The resulting extract was fractionated into 16 parts using semi-preparative high-performance liquid chromatography. Two fractions, Q6 and Q9, were isolated from K10S and identified as cis-cyclo(L-Ser-L-Pro) and cis-cyclo(L-Leu-L-Pro). The Q9 fraction, containing cis-cyclo(L-Leu-L-Pro), has shown significant inhibitory properties against the proliferation of highly pathogenic multidrug-resistant bacteria, as well as human-specific and phytopathogenic fungi. Some of the ten combinations between the remaining fourteen unidentified fractions and two fractions, Q6 and Q9, containing cis-cyclo(L-Ser-L-Pro) and cis-cyclo(L-Leu-L-Pro) respectively, demonstrated a significant increase in activity against multidrug-resistant bacteria only when combined with Q9. The activity was 7.17 times higher compared to a single cis-cyclo(L-Leu-L-Pro). This study presents new findings on the efficacy of proline-containing CDPs in avian eggs. These CDPs provide antimicrobial properties when specific probiotics are supplemented.

Bioactive Metabolites of Serratia sp. NhPB1 Isolated from Pitcher of Nepenthes and its Application to Control Pythium aphanidermatum

Plant-associated bacteria have already been considered as the store house of bioactive compounds that confer the plant growth promotion and disease protection. Hence, the unique plant parts have already been expected to harbor diverse microbial communities with multi-beneficial properties. Based on this, the current study has been designed to identify the potential of Serratia sp. NhPB1 isolated from the pitcher of Nepenthes plant for its activity against the infamous pathogen Pythium aphanidermatum. The in vitro antifungal, plant growth promoting and enzymatic activities of the isolate indicated its promises for agricultural application. The isolate NhPB1 was also demonstrated to have positive effect on Solanum lycopersicum and Capsicum annuum, due to its plant beneficial metabolites. From the results of LC-MS/MS analysis, the isolate has also been revealed to have the ability to synthesize bioactive compounds including salicylic acid, cyclodipeptides, acyl homoserine lactone, indole-3-acetic acid, and serrawettin W1. These identified compounds and their known biological properties make the isolate characterized in the study to have significant promises as an eco-friendly solution for the improvement of agricultural productivity.

Rapid differentiation of graft Citrus sinensis with and without Xylella fastidiosa infection by mass spectrometry

RATIONALE

Xylella fastidiosa causes citrus variegated chlorosis (CVC) in sweet orange trees. A diagnostic method for detecting CVC before the symptoms appear, which would inform citrus producers in advance about when the plant should be removed from the orchard, is essential for reducing pesticide application costs.

METHODS

Chemometrics was applied to high-performance liquid chromatography diode array detector (HPLC-DAD) data to evaluate the similarities and differences between the chromatographic profiles. A liquid chromatography/atmospheric pressure chemical ionization mass spectrometry selected reaction monitoring (LC/APCI-MS-SRM) method was developed to identify the major compounds and to determine their amounts in all samples.

RESULTS

We evaluated the effect of this bacterium on the variation in the chemical profile in citrus plants. The organs of C. sinensis grafted on C. limonia were analyzed. Chemometrics was applied to the obtained data, and two major groups were differentiated. Flavonoids were observed in one group (leaves) and coumarins in the second (roots), both at higher concentrations in the plants with CVC symptoms than in those without the symptoms and those in the negative control. The rootstocks also interfered in the metabolism of the scion.

CONCLUSIONS

The developed LC/APCI-MS-SRM method for detecting CVC before the symptoms appear is simple and accurate. It is inexpensive, and many samples can be screened per hour using 1 mg of leaves. Knowledge of the influence of the rootstock on the chemical profile of the graft is limited. This study demonstrates the effect of the rootstock in synthesizing flavonoids and increasing its content in all parts of the graft.

Marine Bacteria from Rocas Atoll as a Rich Source of Pharmacologically Active Compounds

Rocas Atoll is a unique environment in the equatorial Atlantic Ocean, hosting a large number of endemic species, however, studies on the chemical diversity emerging from this biota are rather scarce. Therefore, the present work aims to assess the metabolomic diversity and pharmacological potential of the microbiota from Rocas Atoll. A total of 76 bacteria were isolated and cultured in liquid culture media to obtain crude extracts. About one third (34%) of these extracts were recognized as cytotoxic against human colon adenocarcinoma HCT-116 cell line. 16S rRNA gene sequencing analyses revealed that the bacteria producing cytotoxic extracts were mainly from the Actinobacteria phylum, including Streptomyces, Salinispora, Nocardiopsis, and Brevibacterium genera, and in a smaller proportion from Firmicutes phylum (Bacillus). The search in the spectral library in GNPS (Global Natural Products Social Molecular Networking) unveiled a high chemodiversity being produced by these bacteria, including rifamycins, antimycins, desferrioxamines, ferrioxamines, surfactins, surugamides, staurosporines, and saliniketals, along with several unidentified compounds. Using an original approach, molecular networking successfully highlighted groups of compounds responsible for the cytotoxicity of crude extracts. Application of DEREPLICATOR+ (GNPS) allowed the annotation of macrolide novonestimycin derivatives as the cytotoxic compounds existing in the extracts produced by Streptomyces BRB-298 and BRB-302. Overall, these results highlighted the pharmacological potential of bacteria from this singular atoll.

Structural elucidation and antimicrobial activity of a diketopiperazine isolated from a Bacillus sp. associated with the marine sponge Spongia officinalis

A diketopiperazine (3S, 6S)-3,6-diisobutylpiperazine-2,5-dione was isolated from a sponge-associated microbe for the first time and characterized by FTIR, HRESI-MS, ¹H, ¹³C NMR and 2D NMR. The source is novel for this compound. Single crystal XRD of this diketopiperazine obtained as a natural product was analysed for the first time and its melting point was determined to be 262 °C. MICs of this cyclic dipeptide against Escherichia coli and Staphylococcus aureus subsp. aureus were 16 µg mL^-1 and 22 µg mL^-1 respectively, the first report of antibacterial activity of this diketopiperazine.Supplemental data for this article can be accessed at https://doi.org/10.1080/14786419.2019.1672684.

Whole Genome Sequencing and Metabolomic Study of Cave Streptomyces Isolates ICC1 and ICC4

The terrestrial subsurface microbiome has gained considerable amount of interests in the recent years because of its rich potential resource for biomining novel genes coding for metabolites possessing antimicrobial activities. In our previous study, we identified two Streptomyces isolates, designated as ICC1 and ICC4, from the Iron Curtain Cave, Chilliwack, Canada that exhibited antagonistic activities against the multidrug resistant strains of Escherichia coli. In this study, the genomes of these two isolates were sequenced by Illumina MiSeq, assembled and annotated. The genes associated with secondary metabolite production were identified and annotated using the bioinformatics platforms antiSMASH and BAGEL. ICC1 and ICC4 were then cultivated and ICC1 metabolome characterized by UHPLC-ESI-HRMS. The Global Natural Products Social Molecular Networking was used to identify metabolites based on the MS/MS spectral data. ICC1 and ICC4 showed a high level of sequence identity with the terrestrial bacteria Streptomyces lavendulae; however, they possess a greater secondary metabolite potential as estimated by the total number of identified biosynthetic gene clusters (BGCs). In particular, ICC1 and ICC4 had a greater number of polyketide and non-ribosomal peptide BGCs. The most frequently detected BGCs were those predicted to generate terpenes, small and low complexity dipeptides and lipids. Spectral analysis clearly identified a number of diketopiperazine products through matched reference spectra for cyclo (Leu-Pro), cyclo (Pro-Val) and cyclo [(4-hydroxyPro)-Leu]. One of the terpenes gene clusters predicted by antiSMASH possesses a seven-gene pathway consistent with diazepinomicin biosynthesis. This molecule contains a very rare core structure and its BGC, to date, has only been identified from a single bacterial genome. The tetrapeptide siderophore coelichelin BGC was unambiguously identified in the genome, however, the metabolite could not be identified from the culture extracts. Two type III polyketides, 2′, 5′ – dimethoxyflavone and nordentatin, were identified from the UHPLC-HRMS data of the aqueous and n-butanolic fractions of Streptomyces sp. ICC1, respectively. A BGC likely encoding these metabolites was predicted in both genomes. The predicted similarities in molecule production and genome shared by these two strains could be an indicative of a cooperative mode of living in extreme habitats instead of a competitive one. This secondary metabolite potential may contribute to the fitness of ICC1 and ICC4 in the Iron Curtain Cave.

Metabolomic Fingerprinting of Salinispora From Atlantic Oceanic Islands

Salinispora (Micromonosporaceae) is an obligate marine bacterium genus consisting of three species that share over 99% 16S rRNA identity. The genome and biosynthetic pathways of the members of this genus have been widely investigated due to their production of species-specific metabolites. However, despite the species’ high genetic similarity, site-specific secondary metabolic gene clusters have been found in Salinispora strains collected at different locations. Therefore, exploring the metabolic expression of Salinispora recovered from different sites may furnish insights into their environmental adaptation or their chemical communication and, further, may lead to the discovery of new natural products. We describe the first occurrence of Salinispora strains in sediments from the Saint Peter and Saint Paul Archipelago (a collection of islets in Brazil) in the Atlantic Ocean, and we investigate the metabolic profiles of these strains by employing mass-spectrometry-based metabolomic approaches, including molecular networking from the Global Natural Products Social Molecular Networking platform. Furthermore, we analyze data from Salinispora strains recovered from sediments from the Madeira Archipelago (Portugal, Macaronesia) in order to provide a wider metabolomic investigation of Salinispora strains from the Atlantic Oceanic islands. Overall, our study evidences a broader geographic influence on the secondary metabolism of Salinispora than was previously proposed. Still, some biosynthetic gene clusters, such as those corresponding to typical chemical signatures of S. arenicola, like saliniketals and rifamycins, are highly conserved among the assessed strains.

Development of a Chemically Defined Medium for Better Yield and Purification of Enterocin Y31 fromEnterococcus faeciumY31

The macro- and micronutrients in traditional medium, such as MRS, used for cultivating lactic acid bacteria, especially for bacteriocin production, have not been defined, preventing the quantitative monitoring of metabolic flux during bacteriocin biosynthesis. To enhance Enterocin Y31 production and simplify steps of separation and purification, we developed a simplified chemically defined medium (SDM) for the growth ofEnterococcus faeciumY31 and production of its bacteriocin, Enterocin Y31. We found that the bacterial growth was unrelated to Enterocin Y31 production in MRS; therefore, both the growth rate and the Enterocin Y31 production were set as the index for investigation. Single omission experiments revealed that 5 g/L NaCl, five vitamins, two nucleic acid bases, MgSO4·7H2O, MnSO4·4H2O, KH2PO4, K2HPO4, CH3COONa, fourteen amino acids, and glucose were essential for the strain’s growth and Enterocin Y31 production. Thus, a novel simplified and defined medium (SDM) was formulated with 30 components in total. Consequently, Enterocin Y31 production yield was higher in SDM as compared to either MRS or CDM. SDM improved the Enterocin Y31 production and simplified the steps of purification (only two steps), which has broad potential applications.