Long-Term Survival of Synechococcus and Heterotrophic Bacteria without External Nutrient Supply after Changes in Their Relationship from Antagonism to Mutualism

Phytoplankton and heterotrophic bacteria have a close but usually changeable relationship. Uncovering the dynamic changes and driving factors of their interrelationships is of great significance for an in-depth understanding of the ecological processes and functions of marine microorganisms.

Nitrates increase abscisic acid levels to regulate haustoria formation in the parasitic plant Phtheirospermum japonicum

Parasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. Some, the obligate parasites are entirely dependent on their hosts for survival, whereas others, the facultative parasites, are independent of their hosts and infect depending on environmental conditions and the presence of the host. How parasitic plants regulate their haustoria in response to their environment is largely unknown. Using the facultative root parasite Phtheirospermum japonicum, we found that external nutrient levels modified haustorial numbers. This effect was independent of phosphate and potassium but nitrates were sufficient and necessary to block haustoria formation. Elevated nitrate levels prevented the activation of hundreds of genes associated with haustoria formation, downregulated genes associated with xylem development and increased levels of abscisic acid (ABA). Enhancing ABA levels independently of nitrates blocked haustoria formation whereas reducing ABA biosynthesis allowed haustoria to form in the presence of nitrates suggesting that nitrates mediated haustorial regulation in part via ABA production. Nitrates also inhibited haustoria formation and reduced infectivity of the obligate root parasite Striga hermonthica, suggesting a more widely conserved mechanism by which parasitic plants adapt their extent of parasitism according to nitrogen availability in the external environment.

Metabolic adaptations to hypoxia in the neonatal mouse forebrain can occur independently of the transporters SLC7A5 and SLC3A2

Neonatal encephalopathy due to hypoxia–ischemia is associated with adverse neurodevelopmental effects. The involvement of branched chain amino acids (BCAAs) in this is largely unexplored. Transport of BCAAs at the plasma membrane is facilitated by SLC7A5/SLC3A2, which increase with hypoxia. We hypothesized that hypoxia would alter BCAA transport and metabolism in the neonatal brain. We investigated this using an organotypic forebrain slice culture model with, the SLC7A5/SLC3A2 inhibitor, 2-Amino-2-norbornanecarboxylic acid (BCH) under normoxic or hypoxic conditions. We subsequently analysed the metabolome and candidate gene expression. Hypoxia was associated with increased expression of SLC7A5 and SLC3A2 and an increased tissue abundance of BCAAs. Incubation of slices with 13C-leucine confirmed that this was due to increased cellular uptake. BCH had little effect on metabolite abundance under normoxic or hypoxic conditions. This suggests hypoxia drives increased cellular uptake of BCAAs in the neonatal mouse forebrain, and membrane mediated transport through SLC7A5 and SLC3A2 is not essential for this process. This indicates mechanisms exist to generate the compounds required to maintain essential metabolism in the absence of external nutrient supply. Moreover, excess BCAAs have been associated with developmental delay, providing an unexplored mechanism of hypoxia mediated pathogenesis in the developing forebrain.

Assessing Impacts of Changes in External Nutrient Loadings on a Temperate Chinese Drinking Water Reservoir

The safety of drinking water is constantly being evaluated. In the last few decades, however, many drinking waters sources in the world, including in China, have undergone serious eutrophication and consequently water quality deterioration due to anthropogenic induced stressors such as elevated external nutrient inputs. In this study, we used the state-of-the-art complex, dynamic, mechanistic model GOTM-FABM-PCLake (a coupled one-dimensional hydrodynamic-lake ecosystem model) to quantitatively assess the impacts of external nutrient loading on the temperate Jihongtan reservoir in Shandong Province, China. Simulated values of all variables targeted in calibration (water temperature, dissolved oxygen, total nitrogen, total phosphorus, and chlorophyll a) agreed well with observations throughout the entire calibration and validation period and generally mimicked seasonal dynamics and inter-annual variations as found in the monitoring data. A series of scenarios, representing changed external nutrient loadings (both increasing and decreasing compared to the current nutrient load), were set up to quantify the effects on the reservoir water quality. Changes relative to the current external nutrient load had a significant effect on the simulated TN and TP concentrations in the reservoir. Our impact assessment indicate that TN will meet the Chinese water quality requirements of the water source (Class III) when the external nitrogen load is reduced by 70%, whereas TP will meet the requirements even if the external phosphorus load is increased by 100% relative to current loads. The model predicts progressively higher summer and autumn phytoplankton biomasses in the scenarios with increasing external phosphorus loading and potential toxic cyanobacteria will become more dominant at the expense of diatoms and other algae. Strict control of the external nutrient loading is therefore needed to maintain good drinking water quality in the reservoir.

Multidisziplinäre Untersuchungen zur nachhaltigen Stickstoffdüngung unter Berücksichtigung der Möglichkeiten der satellitengestützten Präzisionslandwirtschaft

Zusammenfassung Im Forschungsprojekt FATIMA (FArming Tools for external nutrient Inputs and water MAnagement) wurde ein integrierter Ansatz für die Optimierung des Stickstoffmanagements in der Landwirtschaft gewählt. Neben der technischen Komponente, die die Verarbeitung von Sentinel-2-Satellitendaten umfasste, wurden auch die sozio-ökonomischen Aspekte eines verbesserten Nährstoff-managements untersucht. Die Ergebnisse zeigen, dass LandwirtInnen vor allem an zeitnahen Applikationskarten zur teilflächenspezifischen Stickstoffausbringung interessiert sind. Im Zuge des Projekts wurde nicht nur ein Feldversuch für die Validierung der Satellitendaten als Grundlage einer ökonomischen Analyse angelegt, sondern auch eine funktionierende Online-Anwendung für teilflächenspezifische Stickstoffdüngung, basierend auf aktuellen und historischen Satellitenbildern, entwickelt und getestet.

Computational study on ratio-sensing in yeast galactose utilization pathway

Metabolic networks undergo gene expression regulation in response to external nutrient signals. In microbes, the synthesis of enzymes that are used to transport and catabolize less preferred carbon sources is repressed in the presence of a preferred carbon source. For most microbes, glucose is a preferred carbon source, and it has long been believed that as long as glucose is present in the environment, the expression of genes related to the metabolism of alternative carbon sources is shut down, due to catabolite repression. However, recent studies have shown that the induction of the galactose (GAL) metabolic network does not solely depend on the exhaustion of glucose. Instead, the GAL genes respond to the external concentration ratio of galactose to glucose, a phenomenon of unknown mechanism that we termed ratio-sensing. Using mathematical modeling, we found that ratio-sensing is a general phenomenon that can arise from competition between two carbon sources for shared transporters, between transcription factors for binding to communal regulatory sequences of the target genes, or a combination of the aforementioned two levels of competition. We analyzed how the parameters describing the competitive interaction influenced ratio-sensing behaviors in each scenario and found that the concatenation of both layers of signal integration could expand the dynamical range of ratio-sensing. Finally, we investigated the influence of circuit topology on ratio-sensing and found that incorporating negative auto-regulation and/or coherent feedforward loop motifs to the basic signal integration unit could tune the sensitivity of the response to the external nutrient signals. Our study not only deepened our understanding of how ratio-sensing is achieved in yeast GAL metabolic regulation, but also elucidated design principles for ratio-sensing signal processing that can be used in other biological settings, such as being introduced into circuit designs for synthetic biology applications.

Microbial communities of soda lakes and pans in the Carpathian Basin: a review

In this review, I would like to summarize the current knowledge on the microbiology of soda lakes and pans of the Carpathian Basin. First, the characteristic physical and chemical features of these sites are described. Most of the microbiological information presented deals with prokaryotes and algae, but protists and viruses are also mentioned. Planktonic bacterial communities are dominated by members of the phyla Actinobacteria, Bacteroidetes and Proteobacteria; small-sized trebouxiophycean green algae and Synechococcus/Cyanobium picocyanobacteria are the most important components of phytoplankton. Based on the current knowledge, it seems that mainly temperature, salinity, turbidity and grazing pressure regulate community composition and the abundance of individual microbial groups, but the external nutrient load from birds also has a significant impact on the ecological processes.

Computational study on ratio-sensing in yeast galactose utilization pathway

Metabolic networks undergo gene expression regulation in response to external nutrient signals. In microbes, the synthesis of enzymes that are used to transport and catabolize less preferred carbon sources is repressed in the presence of a preferred carbon source. For most microbes, glucose is a preferred carbon source, and it has long been believed that as long as glucose is present in the environment, the expression of genes related to the metabolism of alternative carbon sources is shut down, due to catabolite repression. However, recent studies have shown that the induction of the galactose (GAL) metabolic network does not solely depend on the exhaustion of glucose. Instead, the GAL genes respond to the external concentration ratio of galactose to glucose, a phenomenon of unknown mechanism that we termed ratio-sensing. Using mathematical modeling, we found that ratio-sensing is a general phenomenon that can arise from competition between two carbon sources for shared transporters, between transcription factors for binding to communal regulatory sequences of the target genes, or a combination of the aforementioned two levels of competition. We analyzed how the parameters describing the competitive interaction influenced ratio-sensing behaviors in each scenario and found that the concatenation of both layers of signal integration can expand the dynamical range of ratio-sensing. Finally, we investigated the influence of circuit topology on ratio-sensing and found that incorporating negative auto-regulation and/or coherent feedforward loop motifs to the basic signal integration unit can tune the sensitivity of the response to the external nutrient signals. Our study not only deepened our understanding of how ratio-sensing is achieved in yeast GAL metabolic regulation, but also elucidated design principles for ratio-sensing signal processing that can be used in other biological settings, such as being introduced into circuit designs for synthetic biology applications.Author summaryMicrobes make sophisticated choices about the uptake and metabolism of nutrients depending on the variety of nutrient choices available to them in their environment. In the well-studied yeast galactose utilization network, a recent study has shown that galactose metabolic genes respond to the external concentration ratio of galactose to glucose. Using computational models, we showed that this type of phenomenon could arise from a competition between galactose and glucose for transporters, a competition between transcription factors for promoters, or a combination of these two mechanisms. We further revealed the controlling parameters that determined the system sensitivity towards competing input signals and that determined the concentration ratio required to induce the metabolic network in each scenario. Combining competition inhibition at both the transporter level and the transcriptional level can enlarge the ratio-sensing regime, resulting a robust signal integration module. We suspect that modules of this kind may be common in many areas of biology.