Temporally selective modification of the tomato rhizosphere and root microbiome by a dacitic tuff breccia (volcanic ash) containing minerals and trace elements.

Food crops are grown with fertilizers containing nitrogen, phosphorus, and potassium (macronutrients), along with magnesium, calcium, boron, and zinc (micronutrients) at different ratios during their cultivation. Soil and plant associated microbes have been implicated to promote plant growth, stress tolerance, and productivity. However, the high degree of variability across agricultural environments makes it difficult to assess the possible influences of nutrient fertilizers on these microbial communities. Uncovering the underlying mechanisms could lead us to achieving consistently improved food quality and productivity with minimal environmental impacts. For this purpose, we tested a commercially available fertilizer (surface-mined 38-million-year-old volcanic ash deposit AZOMITE®), applied as a supplement to the normal fertilizer program to tomato plants grown in the greenhouse. We examined its impact on the composition of below-ground microbial communities, focusing on those members we identified as "core taxa" that were enriched in the rhizosphere and root endosphere compared to bulk soil, and appeared above their predicted neutral distribution levels in control and treated samples. This analysis revealed that Azomite had little effect on soil or rhizosphere microbial composition overall, but it had a significant, temporally selective influence on the rhizosphere and root associated core taxa. Changes in the composition of the core taxa were correlated to associated functional pathway enrichment of carbohydrate metabolism over shorter chain carbon metabolism, suggesting a conversion of available microbial nutrient source within the roots. This finding exemplifies how the nutrient environment can specifically alter the functional capacity of root-associated bacterial taxa, with potential to improve crop productivity.

Transcriptomic survey reveals multiple adaptation mechanisms in response to nitrogen deprivation in marine Porphyridium cruentum

Single-cell red microalga Porphyridium cruentum is potentially considered to be the bioresource for biofuel and pharmaceutical production. Nitrogen is a kind of nutrient component for photosynthetic P. cruentum. Meanwhile, nitrogen stress could induce to accumulate some substances such as lipid and phycoerythrin and affect its growth and physiology. However, how marine microalga Porphyridium cruentum respond and adapt to nitrogen starvation remains elusive. Here, acclimation of the metabolic reprogramming to changes in the nutrient environment was studied by high-throughput mRNA sequencing in the unicellular red alga P. cruentum. Firstly, to reveal transcriptional regulation, de novo transcriptome was assembled and 8,244 unigenes were annotated based on different database. Secondly, under nitrogen deprivation, 2100 unigenes displayed differential expression (1134 upregulation and 966 downregulation, respectively) and some pathways including carbon/nitrogen metabolism, photosynthesis, and lipid metabolism would be reprogrammed in P. cruentum. The result demonstrated that nitrate assimilation (with related unigenes of 8–493 fold upregulation) would be strengthen and photosynthesis (with related unigenes of 6–35 fold downregulation) be impaired under nitrogen deprivation. Importantly, compared to other green algae, red microalga P. cruentum presented a different expression pattern of lipid metabolism in response to nitrogen stress. These observations will also provide novel insight for understanding adaption mechanisms and potential targets for metabolic engineering and synthetic biology in P. cruentum.

Niche separation in cross-feeding sustains bacterial strain diversity across nutrient environments and may increase chances for survival in nutrient-limited leaf apoplasts

The leaf microbiome plays a crucial role in plant's health and resilience to stress. Like in other hosts, successful colonization is dependent on multiple factors, among them, resource accessibility. The apoplast is an important site of plant-microbe interactions where nutrients are tightly regulated. While leaf pathogens have evolved elaborate strategies to obtain nutrients there, it is not yet clear how commensals survive without most of these adaptations. Resource limitation can promote metabolic interactions, which in turn shape and stabilize microbiomes but this has not been addressed in detail in leaves. Here, we investigated whether and how the nutrient environment might influence metabolic exchange and assembly of bacterial communities in Flaveria trinervia and F. robusta leaves. We enriched bacteria from both plant species in-vitro in minimal media with sucrose as a carbon source, and with or without amino acids. After enrichment, we studied the genetic and metabolic diversity within the communities. Enriched Pseudomonas koreensis strains could cross-feed from diverse leaf bacteria. Although P. koreensis could not utilize sucrose, cross-feeding diverse metabolites from Pantoea sp ensured their survival in the sucrose-only enrichments. The Pseudomonas strains had high genetic similarity (~99.8% ANI) but still displayed clear niche partitioning, enabling them to simultaneously cross-feed from Pantoea. Interestingly, cross-feeders were only enriched from F. robusta and not from F. trinervia. Untargeted metabolomics analysis of the leaf apoplasts revealed contrasting nutrient environments, with greater concentrations of high-cost amino acids in F. trinervia. Additionally, P. koreensis strains were better able to survive without a cross-feeding partner in these richer apoplasts. Thus, cross feeding might arise as an adaptation to cope with nutrient limitations in the apoplast. Understanding how apoplast resources influence metabolic interactions could therefore provide plant breeders targets to manipulate leaf microbiome shape and stability.

Metabolomic profiling of Burkholderia cenocepacia in synthetic cystic fibrosis sputum medium reveals nutrient environment-specific production of virulence factors

Infections by Burkholderia cenocepacia lead to life-threatening disease in immunocompromised individuals, including those living with cystic fibrosis (CF). While genetic variation in various B. cenocepacia strains has been reported, it remains unclear how the chemical environment of CF lung influences the production of small molecule virulence factors by these strains. Here we compare metabolomes of three clinical B. cenocepacia strains in synthetic CF sputum medium (SCFM2) and in a routine laboratory medium (LB), in the presence and absence of the antibiotic trimethoprim. Using a mass spectrometry-based untargeted metabolomics approach, we identify several compound classes which are differentially produced in SCFM2 compared to LB media, including siderophores, antimicrobials, quorum sensing signals, and various lipids. Furthermore, we describe that specific metabolites are induced in the presence of the antibiotic trimethoprim only in SCFM2 when compared to LB. Herein, C13-acyl-homoserine lactone, a quorum sensing signal previously not known to be produced by B. cenocepacia as well as pyochelin-type siderophores were exclusively detected during growth in SCFM2 in the presence of trimethoprim. The comparative metabolomics approach described in this study provides insight into environment-dependent production of secondary metabolites by B. cenocepacia strains and suggests future work which could identify personalized strain-specific regulatory mechanisms involved in production of secondary metabolites. Investigations into whether antibiotics with different mechanisms of action induce similar metabolic alterations will inform development of combination treatments aimed at effective clearance of Burkholderia spp. pathogens.

A network-based approach to integrate nutrient environment in the prediction of synthetic lethality in cancer metabolism

Synthetic Lethality (SL) is a promising concept in cancer research. A number of computational methods have been developed to predict SL in cancer metabolism, among which our network-based computational approach, based on genetic Minimal Cut Sets (gMCSs), can be found. A major challenge of these approaches to SL is to systematically consider tumor environment, which is particularly relevant in cancer metabolism. Here, we propose a novel definition of SL for cancer metabolism that integrates genetic interactions and nutrient availability in the environment. We extend our gMCSs approach to determine this new family of metabolic synthetic lethal interactions. A computational and experimental proof-of-concept is presented for predicting the lethality of dihydrofolate reductase inhibition in different environments. Finally, our novel approach is applied to identify extracellular nutrient dependences of tumor cells, elucidating cholesterol and myo-inositol depletion as potential vulnerabilities in different malignancies.

Abstract P514: The Role Of Sweet And Umami Taste Receptors In The Heart

The tongue can distinguish between five different tastes via the taste receptors, which are G-protein coupled receptors (GPCRs). There are two classes of taste receptors, the TAS1 (T1) and TAS2 (T2) families, and the T1R1-T1R3 dimer senses the umami taste and T1R2-T1R3 senses the sweet taste. Recently, the taste receptors have also been found in the brain, lungs, intestine and pancreas, where they sense changes in the nutrient environment and respond through GPCR signalling. Given the importance of glucose and amino acid metabolism in the heart, we hypothesized that the sweet and umami taste receptors have an important function in the heart. Using a variety of technologies and disease states, we have identified that T1R1, T1R2 and T1R3 are expressed in the heart. More specifically, mass spectrometry of a dog model of dyssynchrony has shown the presence of T1R1, T1R3 and T1R2. RNA seq of human patients who received a Left Ventricular Assist device and those who did not also revealed the presence of T1R1 and T1R3. The expression of these proteins was also confirmed using Western blot. We further showed T1R2 and T1R3 protein is localized in the plasma membrane of the cardiomyocytes by immunofluorescence (colocalized with Na/K ATPase) and PM enrichment. When we compared the taste receptor protein levels in dilated cardiomyopathy (DCM) compared to donor heart tissue, we found that T1R2 was overexpressed in DCM, showing that taste receptors may be important in nutrient sensing in disease. Furthermore, when neonatal rat ventricular myocytes were treated with sweet and umami agonists (aspartame for the sweet taste receptor and monosodium glutamate for the umami receptor), they had increased calcium transients as shown by an increase in peak calcium. Cardiomyocytes treated with aspartame also showed a decrease in time to relax. We hypothesize that in the heart, sweet and umami receptors induce positive inotropy upon a change in nutrient environment.

Prerequisites for the development of biotechnology for the production of environmentally friendly products of aquabioculture

Aquaponics is a hybrid food growing technology that combines the best of aquaculture (growing fish in an artificial aquatic environment and hydroponics (growing plants without soil in an aquatic nutrient environment). It is completely organic because the fish produces natural fertilizers used by the plants, which means no exogenous chemicals. Aquaculture has been around for a long time. Throughout the civilized world, aquaculture is one of the most dynamically developing industries, it is considered as a way to ensure food security and a means to combat poverty. Due to the need to provide the world population with high-quality and healthy fish and vegetable products, aquaponics, which is already one of the fastest growing agricultural and food sectors, has great potential for future development.

Protein-Metabolite Interactomics Reveals Novel Regulation of Carbohydrate Metabolism

Metabolism is highly interconnected and also has profound effects on other cellular processes. However, the interactions between metabolites and proteins that mediate this connectivity are frequently low affinity and difficult to discover, hampering our understanding of this important area of cellular biochemistry. Therefore, we developed the MIDAS platform, which can identify protein-metabolite interactions with great sensitivity. We analyzed 33 enzymes from central carbon metabolism and identified 830 protein-metabolite interactions that were mostly novel, but also included known regulators, substrates, products and their analogs. We validated previously unknown interactions, including two atomic-resolution structures of novel protein-metabolite complexes. We also found that both ATP and long-chain fatty acyl-CoAs inhibit lactate dehydrogenase A (LDHA), but not LDHB, at physiological concentrations in vitro. Treating cells with long-chain fatty acids caused a loss of pyruvate/lactate interconversion, but only in cells reliant on LDHA. We propose that these regulatory mechanisms are part of the metabolic connectivity that enables survival in an ever-changing nutrient environment, and that MIDAS enables a broader and deeper understanding of that network.

Impairment of Autophagic Flux Participates in the Antitumor Effects of TAT-Cx43266-283 in Glioblastoma Stem Cells

Autophagy is a physiological process by which various damaged or non-essential cytosolic components are recycled, contributing to cell survival under stress conditions. In cancer, autophagy can have antitumor or protumor effects depending on the developmental stage. Here, we use Western blotting, immunochemistry, and transmission electron microscopy to demonstrate that the antitumor peptide TAT-Cx43266-283, a c-Src inhibitor, blocks autophagic flux in glioblastoma stem cells (GSCs) under basal and nutrient-deprived conditions. Upon nutrient deprivation, GSCs acquired a dormant-like phenotype that was disrupted by inhibition of autophagy with TAT-Cx43266-283 or chloroquine (a classic autophagy inhibitor), leading to GSC death. Remarkably, dasatinib, a clinically available c-Src inhibitor, could not replicate TAT-Cx43266-283 effect on dormant GSCs, revealing for the first time the possible involvement of pathways other than c-Src in TAT-Cx43266-283 effect. TAT-Cx43266-283 exerts an antitumor effect both in nutrient-complete and nutrient-deprived environments, which constitutes an advantage over chloroquine and dasatinib, whose effects depend on nutrient environment. Finally, our analysis of the levels of autophagy-related proteins in healthy and glioma donors suggests that autophagy is upregulated in glioblastoma, further supporting the interest in inhibiting this process in the most aggressive brain tumor and the potential use of TAT-Cx43266-283 as a therapy for this type of cancer.

Metabolomic Profiling of Burkholderia Cenocepacia in Synthetic Cystic Fibrosis Sputum Media Reveals Nutrient Environment-Specific Production of Virulence Factors

Infections by Burkholderia cenocepacia lead to life-threatening disease in immunocompromised individuals, including those living with cystic fibrosis (CF). While genetic variation in various B. cenocepacia strains has been reported, it remains unclear how the chemical environment of CF lung influences the production of small molecule virulence factors by these strains. Here we compare metabolomes of three clinical B. cenocepacia strains in synthetic CF sputum media (SCFM2) and in a routine laboratory media (LB), in the presence and absence of the antibiotic trimethoprim. Using a mass spectrometry based untargeted metabolomics approach, we identify several compound classes which are differentially produced in SCFM2 compared to LB media, including siderophores, antimicrobials, quorum sensing signals, and various lipids. Furthermore, we describe that specific metabolites are induced by the antibiotic trimethoprim only in SCFM2 when compared to LB. Herein, C13-acyl-homoserine lactone, a quorum sensing signal previously not known to be produced by B. cenocepacia as well as pyochelin-type siderophores were exclusively detected during growth in SCFM2 in the presence of trimethoprim. The comparative metabolomics approach described in this study provides insight into environment-dependent production of secondary metabolites by B. cenocepacia strains and suggests future work which could identify personalized strain-specific regulatory mechanisms involved in production of secondary metabolites.