Combination of Pseudo-LC-NMR and HRMS/MS-Based Molecular Networking for the Rapid Identification of Antimicrobial Metabolites From .

An endophytic fungal strain isolated from a seagrass endemic to the Mediterranean Sea () was studied in order to identify its antimicrobial constituents and further characterize the composition of its metabolome. It was identified as by in-depth phylogenetic analyses. The ethyl acetate extract of that strain exhibited antimicrobial activities and an ability to inhibit quorum sensing of .

Optimized Prediction of Reducing Sugars and Dry Matter of Potato Frying by FT-NIR Spectroscopy on Peeled Tubers.

Dry matter content (DMC) and reducing sugars (glucose, fructose) contents of three potato varieties for frying (Innovator, Lady Claire, and Markies) were determined by applying Fourier-transform near-infrared spectrometry (FT-NIR), with paying particular attention to tubers preparation (unpeeled, peeled, and transversally cut tubers) before spectral acquisitions. Potatoes were subjected to normal storage temperature as it is processed in the industry (8 °C) and lower temperature inducing sugar accumulations (5 °C) for 195 and 48 days, respectively. Prediction of DMC has been successfully modeled for all varieties.

A clay-based formulation of the herbicide imazaquin containing exclusively the biologically active enantiomer.

Background: Imazaquin is a chiral herbicide which displays high mobility in soils. Like other imidazolinones, imazaquin is available for use only as racemic mixture of its enantiomers. In this work, several clay materials were assayed as adsorbents of imazaquin, and then the most suitable material was selected to prepare a clay-based slow release imazaquin nanoformulation containing exclusively the biologically active R-enantiomer.

Singular approach to penetrometry by preprocessing of digitized force-displacement curves and chemometry: A case study of 12 tomato varieties.

Unlabelled: This study evaluated a singular approach to the analysis of digitized force-displacement curves from penetrometry performed on tomatoes. Penetrometry is commonly used to evaluate the texture properties of fresh fruits and vegetables. Currently, the parameters are computed from force-displacement curves.

Complete genome sequence of P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites.

is a Gram negative, motile gammaproteobacterium belonging to the order and the family . We isolated strain P3B5 from the phyllosphere of basil plants ( L.).

Frequency of a natural truncated allele of in the germplasm of .

is the causal agent of powdery mildew (PM) in apple. To reduce the amount of fungicides required to control this pathogen, the development of resistant apple cultivars should become a priority. Resistance to PM was achieved in various crops by knocking out specific members of the gene family that are responsible for PM susceptibility (S-genes).

Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi.

Background: While recent advances in next generation sequencing technologies have enabled researchers to readily identify countless microbial species in soil, rhizosphere, and phyllosphere microbiomes, the biological functions of the majority of these species are unknown. Functional studies are therefore urgently needed in order to characterize the plethora of microorganisms that are being identified and to point out species that may be used for biotechnology or plant protection. Here, we used a dual culture assay and growth analyses to characterise yeasts (40 different isolates) and their antagonistic effect on 16 filamentous fungi; comprising plant pathogens, antagonists, and saprophytes.

UHPLC-MS-based HDAC Assay Applied to Bio-guided Microfractionation of Fungal Extracts.

Introduction: Histone deacetylases (HDAC) are considered as promising targets for cancer treatment. Today, four HDAC inhibitors, vorinostat, romidepsin, belinostat, and panobinostat, have been approved by the Food and Drug Administration (FDA) for cancer treatment, while others are in clinical trials. Among them, several are naturally occurring fungal metabolites.

Short communication: Heat-resistant Escherichia coli as potential persistent reservoir of extended-spectrum β-lactamases and Shiga toxin-encoding phages in dairy.

Here we report the isolation of heat-resistant Escherichia coli from raw milk cheeses. Detection of the heat-resistance markers clpK and orfI by PCR was followed by phenotypical confirmation of increased heat-resistance. These strains were Shiga toxin-negative and, although several were found to be multidrug resistant, no plasmids encoding extended-spectrum β-lactamases (ESBL) were found in any of the isolates.

Is the risk for soil arthropods covered by new data requirements under the EU PPP Regulation No. 1107/2009?

Testing of effects on earthworms and non-target foliar arthropods is an integral part of the ecotoxicological risk assessment for the authorization of plant protection products. According to the new data requirements, which came into force in 2014 for active substances and in 2016 for plant protection products, the chronic earthworm toxicity test with Eisenia fetida based on reproductive, growth, and behavioral effects instead of the acute earthworm toxicity test based on mortality, has to be conducted routinely. Additional testing of effects on soil arthropods (Folsomia candida, Hyposaspis aculeifer) is required if the risk assessment of foliar applications raises concerns regarding non-target foliar arthropods (Aphidius rhopalosiphi, Typhlodromus pyri) or if the product is applied directly on or into the soil.

Arbuscular mycorrhizal symbiosis stimulates key genes of the phenylpropanoid biosynthesis and stilbenoid production in grapevine leaves in response to downy mildew and grey mould infection.

Grapevine (Vitis spp) is susceptible to serious fungal diseases usually controlled by chemical treatments. Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts which can stimulate plant defences. We investigated the effect of mycorrhization on grapevine stilbenoid defences.

BMC Ecology Image Competition 2016: the winning images.

The 2016 BMC Ecology Image Competition marked another celebration of the astounding biodiversity, natural beauty, and biological interactions documented by talented ecologists worldwide. For our fourth annual competition, we welcomed guest judge Dr. Matthew Palmer of Columbia University, who chose the winning image from over 140 entries.

Production of Fusaric Acid by Fusarium spp. in Pure Culture and in Solid Medium Co-Cultures.

The ability of fungi isolated from nails of patients suffering from onychomycosis to induce de novo production of bioactive compounds in co-culture was examined. Comparison between the metabolite profiles produced by Sarocladium strictum, by Fusarium oxysporum, and by these two species in co-culture revealed de novo induction of fusaric acid based on HRMS. Structure confirmation of this toxin, using sensitive microflow NMR, required only three 9-cm Petri dishes of fungal culture.

Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication.

Dereplication represents a key step for rapidly identifying known secondary metabolites in complex biological matrices. In this context, liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is increasingly used and, via untargeted data-dependent MS/MS experiments, massive amounts of detailed information on the chemical composition of crude extracts can be generated. An efficient exploitation of such data sets requires automated data treatment and access to dedicated fragmentation databases.

Antifungal Quinoline Alkaloids from Waltheria indica.

Chemical investigation of a dichloromethane extract of the aerial parts of Waltheria indica led to the isolation and characterization of five polyhydroxymethoxyflavonoids, namely, oxyanin A (1), vitexicarpin (3), chrysosplenol E (4), flindulatin (5), 5-hydroxy-3,7,4'-trimethoxyflavone (6), and six quinolone alkaloids, waltheriones M-Q (2, 7, 8, 10, 11) and 5(R)-vanessine (9). Among these, compounds 2, 7, 8, 10, and 11 have not yet been described in the literature. Their chemical structures were established by means of spectroscopic data interpretation including (1)H and (13)C, HSQC, HMBC, COSY, and NOESY NMR experiments and UV, IR, and HRESIMS.

Anti-Candida Cassane-Type Diterpenoids from the Root Bark of Swartzia simplex.

A dichloromethane extract of the roots from the Panamanian plant Swartzia simplex exhibited a strong antifungal activity in a bioautography assay against a genetically modified hypersusceptible strain of Candida albicans. At-line HPLC activity based profiling of the crude extract enabled a precise localization of the antifungal compounds, and dereplication by UHPLC-HRESIMS indicated the presence of potentially new metabolites. Transposition of the HPLC reversed-phase analytical conditions to medium-pressure liquid chromatography (MPLC) allowed an efficient isolation of the major constituents.

Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study.

Background: The intestinal microbiome is a complex community and its role in influencing human health is poorly understood. While conventional microbiology commonly attributes digestive disorders to a single microorganism, a metagenomic approach can detect multiple pathogens simultaneously and might elucidate the role of microbial communities in the pathogenesis of intestinal diseases. We present a proof-of-concept that a shotgun metagenomic approach provides useful information on the diverse composition of intestinal pathogens and antimicrobial resistance profiles in human stool samples.

Composition of fungal soil communities varies with plant abundance and geographic origin.

Interactions of belowground fungal communities with exotic and native plant species may be important drivers of plant community structure in invaded grasslands. However, field surveys linking plant community structure with belowground fungal communities are missing. We investigated whether a selected number of abundant and relatively rare plants, either native or exotic, from an old-field site associate with different fungal communities.

Development and Validation of LNA-Based Quantitative Real-Time PCR Assays for Detection and Identification of the Root-Knot Nematode Meloidogyne enterolobii in Complex DNA Backgrounds.

Meloidogyne enterolobii is a quarantine root-knot nematode posing a major threat to agricultural production systems worldwide. It attacks many host plants, including important agricultural crops, ornamentals, and trees. M.

Online solid phase extraction LC-MS/MS method for the analysis of succinate dehydrogenase inhibitor fungicides and its applicability to surface water samples.

A sensitive and selective analytical method, based on online solid phase extraction coupled to LC-MS/MS, was developed and validated to determine traces of several recently introduced fungicides in surface water and wastewater. The list of target analytes included eight succinate dehydrogenase inhibitors (bixafen, boscalid, fluopyram, flutolanil, fluxapyroxad, isopyrazam, penflufen, and penthiopyrad), and two other fungicides with different modes of action, fenpyrazamine and fluopicolide. Detection and quantification limits in various matrices were in the range of 0.

Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery.

Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions.