Comparative Metabologenomics Analysis of Polar Actinomycetes

Biosynthetic and chemical datasets are the two major pillars for microbial drug discovery in the omics era. Despite the advancement of analysis tools and platforms for multi-strain metabolomics and genomics, linking these information sources remains a considerable bottleneck in strain prioritisation and natural product discovery. In this study, molecular networking of the 100 metabolite extracts derived from applying the OSMAC approach to 25 Polar bacterial strains, showed growth media specificity and potential chemical novelty was suggested. Moreover, the metabolite extracts were screened for antibacterial activity and promising selective bioactivity against drug-persistent pathogens such as Klebsiella pneumoniae and Acinetobacter baumannii was observed. Genome sequencing data were combined with metabolomics experiments in the recently developed computational approach, NPLinker, which was used to link BGC and molecular features to prioritise strains for further investigation based on biosynthetic and chemical information. Herein, we putatively identified the known metabolites ectoine and chrloramphenicol which, through NPLinker, were linked to their associated BGCs. The metabologenomics approach followed in this study can potentially be applied to any large microbial datasets for accelerating the discovery of new (bioactive) specialised metabolites.     

Antimicrobial and Antibiofilm Activities of the Fungal Metabolites Isolated from the Marine Endophytes Epicoccum nigrum M13 and Alternaria alternata 13A

Epicotripeptin (1), a new cyclic tripeptide along with four known cyclic dipeptides (2–5) and one acetamide derivative (6) were isolated from seagrass-associated endophytic fungus Epicoccum nigrum M13 recovered from the Red Sea. Additionally, two new compounds, cyclodidepsipeptide phragamide A (7) and trioxobutanamide derivative phragamide B (8), together with eight known compounds (9–16), were isolated from plant-derived endophyte Alternaria alternata 13A collected from a saline lake of Wadi El Natrun depression in the Sahara Desert. The structures of the isolated compounds were determined based on the 1D and 2D NMR spectroscopic data, HRESIMS data, and a comparison with the reported literature. The absolute configurations of 1 and 7 were established by advanced Marfey’s and Mosher’s ester analyses. The antimicrobial screening indicated that seven of the tested compounds exhibited considerable (MIC range of 2.5–5 µg/mL) to moderate (10–20 µg/mL) antibacterial effect against the tested Gram-positive strains and moderate to weak (10–30 µg/mL) antibacterial effect against Gram-negative strains. Most of the compounds exhibited weak or no activity against the tested Gram-negative strains. On the other hand, four of the tested compounds showed considerable antibiofilm effects against biofilm forming Gram-positive and Gram-negative strains.     

Responses of oaks and tanoaks to the sudden oak death pathogen after 8 y of monitoring in two coastal California forests

Sudden oak death, caused by Phytophthora ramorum, is widely established in mesic forests of coastal central and northern California. In 2000, we placed 18 plots in two Marin County sites to monitor disease progression in coast live oaks (Quercus agrifolia), California black oaks (Q. kelloggii), and tanoaks (Lithocarpus densiflorus), the species that are most consistently killed by the pathogen in these areas. Through early 2008, the numbers of newly infected trees increased for all species. The infection rate for trees that were asymptomatic in 2000 was 5.0% y⁻¹ for coast live oaks, 4.1% y⁻¹ for black oaks and 10.0% y⁻¹ for tanoaks. Mortality rates were 3.1% y⁻¹ for coast live oaks, 2.4% y⁻¹ for black oaks, and 5.4% y⁻¹ for tanoaks. Mortality not attributed to P. ramorum was 0.54% y⁻¹ for coast live oaks, and 0.75% y⁻¹ for tanoaks. Weibull survival models of trees that were asymptomatic in 2000 provided overall median survival times of 13.7 y for coast live oaks, 13.8 y for black oaks, and 8.8 y for tanoaks. Survival of infected (bleeding) trees declined to 9.7 y for coast live oaks, 6.2 y for black oaks, and 5.8 y for tanoaks. Ambrosia beetle attacks on bleeding trees further reduced modeled survival times by 65–80%, reaffirming the earlier finding that beetle attacks on bleeding cankers considerably reduce survival. Across all plots, the modeled time for 90% of trees that were asymptomatic in 2000 to become infected is 36.5 y for coast live oaks and 15.4 y for tanoaks. There was a trend toward higher infection rates as tree diameter increased. Greater than 90% of living coast live oaks that failed during the study had extensive beetle tunneling at the site of the break. Disease intensity in coast live oaks at the plot level was positively associated with bay laurel (Umbellularia californica) basal area and negatively associated with Pacific madrone (Arbutus menziesii) basal area. This study demonstrates the use of survival modeling to characterize the effects of epidemic disease on different species and to project the future of forests infected with tree pathogens.     

Q‐collect: results of a European Union project to improve the status of reference collections important for plant health

The ability of National Plant Protection Organizations (NPPOs) and their affiliated laboratories to quickly and reliably detect and identify organisms is critical for the effective performance of phytosanitary measures. Plant pest diagnostics is also essential to support the phytosanitary certification of consignments of plants and plant products exported from the EU. Access to reference material has been identified as a limitation on the ability of laboratories to develop and validate diagnostic tests and ensure the reliability of diagnostics. The EU FP7 Q‐collect project worked to establish the state of the art of current phytosanitary collections, to identify gaps and propose minimum quality standards, to facilitate access to specimens and to design and build networks of reference collections. The main results of the project are presented in this paper.     

Chemical Profiling (HPLC-NMR & HPLC-MS), Isolation,and Identification of Bioactive Meroditerpenoids from the Southern Australian Marine Brown Alga Sargassum paradoxum

A phytochemical investigation of a southern Australian marine brown alga, Sargassum paradoxum, resulted in the isolation and identification of four new (5, 9, 10, and 15) and nine previously reported (1, 2, 6–8, and 11–14) bioactive meroditerpenoids. HPLC-NMR and HPLC-MS were central to the identification of a new unstable compound, sargahydroquinal (9), and pivotal in the deconvolution of eight (1, 2, 5–7, and 10–12) other meroditerpenoids. In particular, the complete characterization and identification of the two main constituents (1 and 2) in the crude dichloromethane extract was achieved using stop-flow HPLC-NMR and HPLC-MS. This study resulted in the first acquisition of gHMBCAD NMR spectra in the stop-flow HPLC-NMR mode for a system solely equipped with a 60 μL HPLC-NMR flow cell without the use of a cold probe, microcoil, or any pre-concentration.     

Differential effects of spot blotch on photosynthesis and grain yield in two barley cultivars

Barley spot blotch (SB), caused by Cochliobolus sativus, is an important barley disease which causes extensive grain yield losses. These losses may not always correlate directly with the amount of diseased leaf area. Two barley cultivars, Quebracho (susceptible to SB) and Carumbé (with intermediate susceptibility to SB), were compared in field experiments in 2003, 2004 and 2006. Plots of each cultivar were either inoculated with C. sativus or protected with fungicide under field conditions to generate contrasting treatments: i) diseased, and ii) free of disease, respectively. SB severity over the growing season, photosynthetic rate on leaves with no visible symptoms and grain yield were assessed for each treatment and year. There was no treatment effect on cv. Carumbé, while cv. Quebracho showed a significant yield reduction, even though SB severity during the grain filling period was <10 %. This yield reduction was associated with a reduced photosynthetic rate at the beginning of the grain filling period in cv. Quebracho. A similar experiment was conducted under greenhouse conditions, adding a treatment without inoculum or fungicide. There were no differences in photosynthetic rate or grain yield per plant among treatments. These results suggest a distinct physiological response to SB infection among cultivars affecting leaf photosynthetic rate, and SB severity may not be the best estimator of yield losses caused by SB.     

Anaerobic Bioremediation of a Soil With Mixed Contaminants: Explosives Degradation and Influence on Heavy Metal Distribution,Monitored as Changes in Concentration and Toxicity

Water, Air, & Soil Pollution - The sorption behavior of bisphenol A (BPA) on marine sediments treated using different methods was investigated in batch equilibrium experiments. Adsorption...     

Genetic characterization of <Emphasis Type="Italic">Pelargonium</Emphasis> L’Hér. germplasm

Fifteen species and eight cultivars of the section Pelargonium (DC.) Harv., two species of the section Ligularia (Sweet) Harv. and three species of the section Cortusina (DC.) Harv. were tested for genetic distance to predict successful combinations of interspecific crossings. 156 randomly amplified polymorphic DNA (RAPD)-bands and 485 double primer RAPD-bands were used for distance analysis. Combined with information on the ploidy level, species were clustered in the expected sections except Pelargonium hirtum (Burm. f.) Jacq., which clustered with the species of the section Cortusina. Different accessions of the same wild species showed a high conformity (67–98 %) comparable to the cultivars (66–70 %).