Nutrient-limited Environments Research Articles

Single-Cell Technologies to Understand the Mechanisms of Cellular Adaptation in Chemostats.

There is a growing interest in continuous manufacturing within the bioprocessing community. In this context, the chemostat process is an important unit operation. The current application of chemostat processes in industry is limited although many high yielding processes are reported in literature. In order to reach the full potential of the chemostat in continuous manufacture, the output should be constant. However, adaptation is often observed resulting in changed productivities over time. The observed adaptation can be coupled to the selective pressure of the nutrient-limited environment in the chemostat. We argue that population heterogeneity should be taken into account when studying adaptation in the chemostat. We propose to investigate adaptation at the single-cell level and discuss the potential of different single-cell technologies, which could be used to increase the understanding of the phenomena. Currently, none of the discussed single-cell technologies fulfill all our criteria but in combination they may reveal important information, which can be used to understand and potentially control the adaptation.

Role of Hibernation Promoting Factor in Ribosomal Protein Stability during Pseudomonas aeruginosa Dormancy.

Pseudomonas aeruginosa is an opportunistic pathogen that causes biofilm-associated infections. P. aeruginosa can survive in a dormant state with reduced metabolic activity in nutrient-limited environments, including the interiors of biofilms. When entering dormancy, the bacteria undergo metabolic remodeling, which includes reduced translation and degradation of cellular proteins. However, a supply of essential macromolecules, such as ribosomes, are protected from degradation during dormancy. The small ribosome-binding proteins, hibernation promoting factor (HPF) and ribosome modulation factor (RMF), inhibit translation by inducing formation of inactive 70S and 100S ribosome monomers and dimers. The inactivated ribosomes are protected from the initial steps in ribosome degradation, including endonuclease cleavage of the ribosomal RNA (rRNA). Here, we characterized the role of HPF in ribosomal protein (rProtein) stability and degradation during P. aeruginosa nutrient limitation. We determined the effect of the physiological status of P. aeruginosa prior to starvation on its ability to recover from starvation, and on its rRNA and rProtein stability during cell starvation. The results show that the wild-type strain and a stringent response mutant (∆relA∆spoT strain) maintain high cellular abundances of the rProteins L5 and S13 over the course of eight days of starvation. In contrast, the abundances of L5 and S13 reduce in the ∆hpf mutant cells. The loss of rProteins in the ∆hpf strain is dependent on the physiology of the cells prior to starvation. The greatest rProtein loss occurs when cells are first cultured to stationary phase prior to starvation, with less rProtein loss in the ∆hpf cells that are first cultured to exponential phase or in balanced minimal medium. Regardless of the pre-growth conditions, P. aeruginosa recovery from starvation and the integrity of its rRNA are impaired in the absence of HPF. The results indicate that protein remodeling during P. aeruginosa starvation includes the degradation of rProteins, and that HPF is essential to prevent rProtein loss in starved P. aeruginosa. The results also indicate that HPF is produced throughout cell growth, and that regardless of the cellular physiological status, HPF is required to protect against ribosome loss when the cells subsequently enter starvation phase.

Integrating Mathematical Modeling with High-Throughput Imaging Explains How Polyploid Populations Behave in Nutrient-Sparse Environments.

Breast cancer progresses in a multistep process from primary tumor growth and stroma invasion to metastasis. Nutrient-limiting environments promote chemotaxis with aggressive morphologies characteristic of invasion. It is unknown how coexisting cells differ in their response to nutrient limitations and how this impacts invasion of the metapopulation as a whole. In this study, we integrate mathematical modeling with microenvironmental perturbation data to investigate invasion in nutrient-limiting environments inhabited by one or two cancer cell subpopulations. Subpopulations were defined by their energy efficiency and chemotactic ability. Invasion distance traveled by a homogeneous population was estimated. For heterogeneous populations, results suggest that an imbalance between nutrient efficacy and chemotactic superiority accelerates invasion. Such imbalance will spatially segregate the two populations and only one type will dominate at the invasion front. Only if these two phenotypes are balanced, the two subpopulations compete for the same space, which decelerates invasion. We investigate ploidy as a candidate biomarker of this phenotypic heterogeneity and discuss its potential to inform the dose of mTOR inhibitors (mTOR-I) that can inhibit chemotaxis just enough to facilitate such competition. SIGNIFICANCE: This study identifies the double-edged sword of high ploidy as a prerequisite to personalize combination therapies with cytotoxic drugs and inhibitors of signal transduction pathways such as mTOR-Is. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/22/5109/F1.large.jpg.

Bryophytes Harbor Cultivable Actinobacteria With Plant Growth Promoting Potential.

This study was designed to investigate the cultivable actinobacteria associated with bryophytes and their plant growth promoting ability. Thirteen actinobacteria were isolated and tested for their ability to promote growth of plant in vitro and in planta. All isolates were able to produce IAA and siderophores. Six isolates were identified as members of the genus Micromonospora. Five isolates belonged to the genus Streptomyces and one each of Microbispora and Mycobacterium. Micromonospora sp. CMU55-4 was inoculated to rare moss [Physcomitrium sphaericum (C. Ludw.) Fürnr.] and could increase the amount of carotenoid, fresh weight, and dry weight of this moss. In addition, this strain promoted capsule production, and rescued P. sphaericum’s gametophytes during acclimatization to land. Strain CMU55-4 was identified as Micromonospora chalcea based on whole genome sequence analysis. Its plant growth promoting potential was further characterized through genome mining. The draft genome size was 6.6 Mb (73% GC). The genome contained 5,933 coding sequences. Functional annotation predicted encoded genes essential for siderophore production, phosphate solubilization that enable bacteria to survive under nutrient limited environment. Glycine-betaine accumulation and trehalose biosynthesis also aid plants under drought stress. M. chalcea CMU55-4 also exhibited genes for various carbohydrate metabolic pathways indicating those for efficient utilization of carbohydrates inside plant cells. Additionally, predictive genes for heat shock proteins, cold shock proteins, and oxidative stress such as glutathione biosynthesis were identified. In conclusion, our results demonstrate that bryophytes harbor plant growth promoting actinobacteria. A representative isolate, M. chalcea CMU55-4 promotes the growth of P. sphaericum moss and contains protein coding sequences related to plant growth promoting activities in its genome.

Short rotation coppice of leguminous tree Leucaena spp. improves soil fertility while producing high biomass yields in Mediterranean environment

The use of woody nitrogen-fixing plant species as multipurpose and energy crops aims to enhance biomass yield while improving soil properties. Yet, the effectiveness of this option is still under debate especially the use of short rotation cropping in water and nutrient limited environments. This study investigated whether short rotation coppicing of four taxa of multipurpose biomass woody legume Leucaena spp. can improve soil conditions when grown for biomass under a Mediterranean environment. Biomass yield, mineral composition and heat value of the biomass and the mineral and organic matter content of soil were evaluated. Under favorable growing conditions, woody dry biomass production was up to 29 Mg ha−1 year−1 with slight but significant differences between the four taxa that were tested. After 11 years of cropping, the soil showed higher fertility and microbial activity compared to the uncropped plot. Leucaena cultivation increased soil nitrogen by 35 %, dehydrogenase activity by 98 %, and organic matter and carbon content (by 41 %). Annual cuttings resulted in the highest biomass production, followed by two and three year cuttings. The mineral composition and the calorific capacity of woody biomass make it suitable for commercial use as an energy source (generating on average 151 MW h ha-1 year-1). In conclusion, short rotation coppicing of nitrogen-fixing woody species results in high biomass production rates with the restoration of degraded soils, constituting a sustainable agroforestry system for rural areas.

Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition.

A hallmark of metastasis is the adaptation of tumor cells to new environments. Metabolic constraints imposed by the serine and glycine-limited brain environment restrict metastatic tumor growth. How brain metastases overcome these growth-prohibitive conditions is poorly understood. Here, we demonstrate that 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the rate-limiting step of glucose-derived serine synthesis, is a major determinant of brain metastasis in multiple human cancer types and preclinical models. Enhanced serine synthesis proved important for nucleotide production and cell proliferation in highly aggressive brain metastatic cells. In vivo, genetic suppression and pharmacologic inhibition of PHGDH attenuated brain metastasis, but not extracranial tumor growth, and improved overall survival in mice. These results reveal that extracellular amino acid availability determines serine synthesis pathway dependence, and suggest that PHGDH inhibitors may be useful in the treatment of brain metastasis. SIGNIFICANCE: Using proteomics, metabolomics, and multiple brain metastasis models, we demonstrate that the nutrient-limited environment of the brain potentiates brain metastasis susceptibility to serine synthesis inhibition. These findings underscore the importance of studying cancer metabolism in physiologically relevant contexts, and provide a rationale for using PHGDH inhibitors to treat brain metastasis.This article is highlighted in the In This Issue feature, p. 1241.

Short-Chain Fatty Acids Promote Mycobacterium avium subsp. hominissuis Growth in Nutrient-Limited Environments and Influence Susceptibility to Antibiotics.

Mycobacterium avium subsp. hominissuis (MAH) is a common intracellular pathogen that infects immunocompromised individuals and patients with pre-existing chronic lung diseases, such as cystic fibrosis, who develop chronic and persistent pulmonary infections. The metabolic remodeling of MAH in response to host environmental stresses or within biofilms formed in bronchial airways plays an important role in development of the persistence phenotype contributing to the pathogen’s tolerance to antibiotic treatment. Recent studies suggest a direct relationship between bacterial metabolic state and antimicrobial susceptibility, and improved antibiotic efficacy has been associated with the enhanced metabolism in bacteria. In the current study, we tested approximately 200 exogenous carbon source-dependent metabolites and identified short-chain fatty acid (SCFA) substrates (propionic, butyric and caproic acids) that MAH can utilize in different physiological states. Selected SCFA enhanced MAH metabolic activity in planktonic and sessile states as well as in the static and established biofilms during nutrient-limited condition. The increased bacterial growth was observed in all conditions except in established biofilms. We also evaluated the influence of SCFA on MAH susceptibility to clinically used antibiotics in established biofilms and during infection of macrophages and found significant reduction in viable bacterial counts in vitro and in cultured macrophages, suggesting improved antibiotic effectiveness against persistent forms of MAH.

Abstract 5712: Nutrient scarcity confers breast cancer brain metastasis sensitivity to serine synthesis pathway inhibition

Abstract The metabolic milieu of the brain is severely deprived of nutrients, including the amino acids serine and its catabolite glycine. The metabolic rewiring required for tumor cells to survive in the nutrient-limited environment of the brain and the metabolic vulnerabilities this confers are poorly understood. Here we demonstrate that cell-intrinsic de novo serine synthesis is a major determinant of triple-negative breast cancer (TNBC) brain metastasis. Whole proteome comparison of TNBC cells that differ in their capacity to colonize the brain reveals that 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the rate-limiting step of glucose-derived serine synthesis, is the most significantly upregulated protein in cells that efficiently metastasize to the brain. Expression of catalytically active PHGDH in a non-brain trophic cell line promoted brain metastasis. Furthermore, genetic silencing or pharmacological inhibition of PHGDH attenuated brain metastasis burden in mice. These findings indicate that nutrient availability determines serine synthesis pathway dependence in brain metastasis, and suggest that PHGDH inhibitors may be useful in the treatment of patients with cancers that have spread to the brain. Citation Format: Bryan Ngo, Eugenie Kim, Sophia Doll, Sophia Bustraan, Alba Luengo, Shawn M. Davidson, Ahmed Ali, Gino Ferraro, Diane Kang, Jing Ni, Roger Liang, Ariana Plasger, Edward R. Kastenhuber, Roozbeh Eskandari, Sarah Bacha, Roshan Sriram, Benjamin D. Stein, Samuel F. Bakhoum, Edouard Mullarky, Matija Snuderl, Nello Mainolfi, Vipin Suri, Adam Friedman, Mark Manfredi, David M. Sabatini, Drew Jones, Min Yu, Jean J. Zhao, Rakesh K. Jain, Matthew G. Vander Heiden, Matthias Mann, Lewis C. Cantley, Michael E. Pacold. Nutrient scarcity confers breast cancer brain metastasis sensitivity to serine synthesis pathway inhibition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5712.

Studying the surface-tethered AaaA as a virulence factor and anti-P. aeruginosa drug target

P. aeruginosa is a leading cause of bacterial wound infections, and is associated with a disproportionally high level of mortality in burn patients especially. Because of its wide arsenal of virulence factors and biofilm formation ability, infections with P. aeruginosa are often chronic and extremely difficult to treat. This study uses an ex-vivo skin model to study the role of the virulence factor AaaA (PA0328) in chronic wound infections. AaaA, or the Arginine-specific aminopeptidase of Pseudomonas aeruginosa A, is a surface-tethered autotransporter which cleaves N-terminal arginine from peptides. In the oxygen and nutrient-limited environments of chronic wounds, this free arginine could serve as a nutrient source for P. aeruginosa via alternative metabolic pathways. Changes in local arginine concentrations may also alter host iNOS and Arginase immune responses which influence inflammation and wound healing, in order to favour a chronic infection. Being surface-tethered and immunogenic, AaaA is also of interest as a potential antimicrobial drug or vaccine target. This study aims to probe the role of AaaA on both pathogen survival and host response in the wound context, using a combination of in situ transcriptional reporters, immunofluorescence and laser-scanning microscopy, and RT-qPCR to localise and quantify P. aeruginosa survival and aaaA expression, as well as resident immune cell invasion, and expression of immune factor genes, in wounds over time. Here, we present preliminary data examining AaaA expression and function in P. aeruginosa biofilm cultures and ex-vivo skin wound infections, as well as the results of preliminary inhibitor screens.

Little giants: a rapidly invading seagrass alters ecosystem functioning relative to native foundation species

The spread of invasive species is a major component of global ecological change and how and when to manage particular species is a difficult empirical question. Ideally, these decisions should be based on the specific impacts of invading species including both their effects on native competitors and how they may or may not play similar roles in broader ecosystem functioning. Halophila stipulacea is an invasive seagrass currently spreading through the Caribbean, and as seagrasses are foundation species, the effects of invasion have the potential to be particularly far-reaching. To evaluate the impacts of H. stipulacea we quantified spread and potential for displacement of native seagrasses as well as the effects of invasion on multiple ecosystem processes, particularly resource support for higher trophic levels and habitat creation. Long-term monitoring suggested that H. stipulacea likely displaces some native seagrasses (Syringodium filiforme and Halodule wrightii), but not others. Halophila stipulacea had lower N and protein levels and higher C:N ratios than native seagrasses, and as such is a poorer quality resource for consumers. We also observed significantly lower consumption of H. stipulacea than the native S. filiforme but limited differences compared to Thalassia testudinum. We found H. stipulacea created a more nutrient limited environment than T. testudinum and there were significantly distinct invertebrate assemblages in native- and invasive-dominated seagrass beds, but no difference in species richness or invertebrate biomass. These results suggest that the spread of H. stipulacea would impact a variety of ecological processes, potentially restructuring seagrass ecosystems through both direct impacts on environmental conditions (e.g., nutrient availability) and indirect food web interactions.

Metabolism of Gluconeogenic Substrates by an Intracellular Fungal Pathogen Circumvents Nutritional Limitations within Macrophages.

Microbial pathogens exploit host nutrients to proliferate and cause disease. Intracellular pathogens, particularly those exclusively living in the phagosome such as Histoplasma capsulatum, must adapt and acquire nutrients within the nutrient-limited phagosomal environment. In this study, we investigated which host nutrients could be utilized by Histoplasma as carbon sources to proliferate within macrophages. Histoplasma yeasts can grow on hexoses and amino acids but not fatty acids as the carbon source in vitro Transcriptional analysis and metabolism profiling showed that Histoplasma yeasts downregulate glycolysis and fatty acid utilization but upregulate gluconeogenesis within macrophages. Depletion of glycolysis or fatty acid utilization pathways does not prevent Histoplasma growth within macrophages or impair virulence in vivo However, loss of function in Pck1, the enzyme catalyzing the first committed step of gluconeogenesis, impairs Histoplasma growth within macrophages and severely attenuates virulence in vivo, indicating that Histoplasma yeasts rely on catabolism of gluconeogenic substrates (e.g., amino acids) to proliferate within macrophages.IMPORTANCEHistoplasma is a primary human fungal pathogen that survives and proliferates within host immune cells, particularly within the macrophage phagosome compartment. The phagosome compartment is a nutrient-limited environment, requiring Histoplasma yeasts to be able to assimilate available carbon sources within the phagosome to meet their nutritional needs. In this study, we showed that Histoplasma yeasts do not utilize fatty acids or hexoses for growth within macrophages. Instead, Histoplasma yeasts consume gluconeogenic substrates to proliferate in macrophages. These findings reveal the phagosome composition from a nutrient standpoint and highlight essential metabolic pathways that are required for a phagosomal pathogen to proliferate in this intracellular environment.

Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar.

Plant-associated microbial communities play a central role in the plant response to biotic and abiotic stimuli, improving plant fitness under challenging growing conditions. Many studies have focused on the characterization of changes in abundance and composition of root-associated microbial communities as a consequence of the plant response to abiotic factors such as altered soil nutrients and drought. However, changes in composition in response to abiotic factors are still poorly understood concerning the endophytic community associated to the phyllosphere, the above-ground plant tissues. In the present study, we applied high-throughput 16S rDNA gene sequencing of the phyllosphere endophytic bacterial communities colonizing wild Populus trichocarpa (black cottonwood) plants growing in native, nutrient-limited environments characterized by hot-dry (xeric) riparian zones (Yakima River, WA), riparian zones with mid hot-dry (Tieton and Teanaway Rivers, WA) and moist (mesic) climates (Snoqualmie, Skykomish and Skagit Rivers, WA). From sequencing data, 587 Amplicon Sequence Variants (ASV) were identified. Surprisingly, our data show that a core microbiome could be found in phyllosphere-associated endophytic communities in trees growing on opposite sides of the Cascades Mountain Range. Considering only taxa appearing in at least 90% of all samples within each climatic zone, the core microbiome was dominated only by two ASVs affiliated Pseudomonadaceae and two ASVs of the Enterobacteriaceae family. Alpha-diversity measures indicated that plants colonizing hot-dry environments showed a lower diversity than those from mid hot-dry and moist climates. Beta-diversity measures showed that bacterial composition was significantly different across sampling sites. Accordingly, we found that specific ASV affiliated to Pseudomonadaceae and Enterobacteriaceae were significantly more abundant in the phyllosphere endophytic community colonizing plants adapted to the xeric environment. In summary, this study highlights that sampling site is the major driver of variation and that only a few ASV showed a distribution that significantly correlated to climate variables.

Plant diversity effect on water quality in wetlands: a meta-analysis based on experimental systems.

The ecological literature reports little empirical evidence from biodiversity-ecosystem functioning (BEF) experiments in wetland systems, even though wetlands are widely known for their water filtering capacity. Experiments comparing the effect of plant monocultures and mixtures on water quality to improve pollutant removal efficiency in treatment wetlands share the characteristics of classical BEF experiments, and so could provide insights for wetland management. To add to our understanding of BEF relationships in wetlands, we evaluated plant diversity effects on water purification through a meta-analysis of freshwater experimental wetlands comparing monocultures to mixtures. We found 28 studies that matched our criteria for BEF analysis, for a total of 561 diversity effects on pollutant removal. Overall, the meta-analysis shows no significant effect of plant richness on removal of total suspended solids, but a positive effect on chemical oxygen demand and total nitrogen removal, and a marginal effect on phosphorus removal. Thus, the results of this meta-analysis are consistent with reports of an overall positive biodiversity effect on ecosystem properties. An analysis of moderator variables shows that the experimental context (size of the experimental units, nutrient load, duration of the experiment) does not explain much of the residual variance. For pollutants that benefit from a positive plant richness effects on removal, mixtures do not perform better than the best monoculture. We found no evidence that plant richness effects are due to functional complementarity among species rather than to the presence of particularly efficient species. Complementarity effects may be less prevalent in highly productive, nutrient-rich wetlands, compared to nutrient-limited environments such as natural grasslands. Although findings must be confirmed by long-term field experiments under natural conditions, result from experimental wetland systems may contribute to a better understanding of biodiversity effect on ecosystem functions in wetlands, in addition to guide practices in natural wetland restoration and the use of constructed wetlands for water treatment.

Tritrophic interactions follow phylogenetic escalation and climatic adaptation

One major goal in plant evolutionary ecology is to address how and why tritrophic interactions mediated by phytochemical plant defences vary across species, space, and time. In this study, we tested three classical hypotheses about plant defences: (i) the resource-availability hypothesis, (ii) the altitudinal/elevational gradient hypothesis and (iii) the defence escalation hypothesis. For this purpose, predatory soil nematodes were challenged to hunt for root herbivores based on volatile cues from damaged or intact roots of 18 Alpine Festuca grass species adapted to distinct climatic niches spanning 2000 meters of elevation. We found that adaptation into harsh, nutrient-limited alpine environments coincided with the production of specific blends of volatiles, highly attractive for nematodes. We also found that recently-diverged taxa exposed to herbivores released higher amounts of volatiles than ancestrally-diverged species. Therefore, our model provides evidence that belowground indirect plant defences associated with tritrophic interactions have evolved under two classical hypotheses in plant ecology. While phylogenetic drivers of volatile emissions point to the defence-escalation hypothesis, plant local adaptation of indirect defences is in line with the resource availability hypothesis.

A light-limited growth model considering the nutrient effect for improved understanding and prevention of macroalgae bloom.

A useful growth process model for Ulva prolifera with light limitation considering the nutrient effect was proposed to better understand the development of macroalgae bloom. The interrelationship between light and nutrient limitation was demonstrated to obtain the mechanism. As a case study, thresholds of light and nutrients for different stages of Ulva prolifera growth were estimated using the proposed model. Limits of light intensity, nitrate, and phosphate concentration on the initial growth were found to be 40.0Wm-2, 6.5μmolL-1, and 0.27μmolL-1, respectively. The minimal light intensity for initial growth was found to increase monotonously with decrease in the nutrient concentration. It was also observed that the minimal light intensity for growth increases as the density of Ulva prolifera increases and the nutrient concentration decreases. Similarly, the minimal nutrient concentration for initial growth increases monotonously with decrease in the light intensity. In addition, the minimal nutrient concentration for growth increases with increase in the density of Ulva prolifera and decrease in the light intensity. It was demonstrated that the phosphate limitation on the initial growth of Ulva prolifera seedling can occur in most coastal waters of the southern Yellow Sea and a tendency of approaching the phosphate limitation on the growth of the floating thalli of Ulva prolifera exists. Evidence was provided to support the argument that the macroalgae thalli from aquaculture rafts, rather than that from seedlings or spores, can contribute to the original biomass of the floating green Ulva prolifera in the southern Yellow Sea. The model presented in this study can provide new insights into the interrelationship between the light and nutrient limitation, as well as into the growth mechanism of floating seaweeds. It can also provide a more accurate prediction of seaweed growth in light- and nutrient-limited environments.

Mixotrophic ciliates in North-Patagonian Andean lakes: stoichiometric balances in nutrient limited environments

espanolLos lagos andinos nord-patagonicos son ultraoligotroficos, muy transparentes y poseen una red trofica microbiana particular, con la presencia de grandes ciliados mixotroficos. Estos organismos exhiben diferentes caracteristicas que les permiten colonizar el epilimnion (Stentor araucanus) o el metalimnion (Ophrydium naumanni). S. araucanus es una especie pigmentada oscura (stentorina) resistente a la radiacion ultravioleta y que necesita un alto suministro de luz para mantener la fotosintesis de sus algas endosimbioticas. En contraste, O. naumanni domina la biomasa fotosintetica en los niveles de clorofila maxima profunda (metalimnion) de estos lagos, siendo fotosinteticamente eficiente a bajas intensidades de luz, pero susceptible a la fotoinhibicion en el epilimnion. El analisis de las vacuolas alimentarias revelo una baja superposicion de nichos, sin embargo, el clima optico, modulado por variaciones temporales o espaciales en la profundidad de la termoclina, resulto un factor clave para la alternancia de estas dos especies. En general, estas especies son estequiometricas mas balanceadas (carbono:nutrientes) que el seston, pero los mecanismos por los cuales cada especie regula el equilibrio elemental difieren. O. naumanni aumenta la bacterivoria con la luz, lo que aumenta la incorporacion de fosforo, mientras que S. araucanus regula la fijacion de carbono. La baja proporcion de carbono: nutrientes de estos organismos representa una muy buena fuente de alimento para el zooplancton. Finalmente, senalamos que los diferentes efectos de cambios locales y globales afectaran negativamente esta particular biota de ciliados mixotrofos de los lagos andinos del norte de la Patagonia EnglishTransparent ultraoligotrophic lakes in the North-Patagonian Andes have a particular microbial food web, with the presence of large mixotrophic ciliates. These organisms exhibit different features that allow them to colonize either the epilimnion (Stentor araucanus) or the metalimnion (Ophrydium naumanni). S. araucanus is a dark pigmented (stentorin) species resistant to ultraviolet radiation and needs high light supply to maintain endosymbiotic algal photosynthesis. In contrast, O. naumanni dominates the phothosynthetic biomass in the deep chlorophyll maxima (metalimnion) of these lakes, being photosynthetically efficient at low light intensities but susceptible to photoinhibition at epilimnetic light irradiances. Analysis of food vacuoles revealed a weak niche overlap, however light climate, shaped by temporal or spatial variations in thermocline depth, resulted in a key factor modulating the relative success of these mixotrophic ciliate species. Overall, these species are stoichiometrically, carbon to nutrients, more balanced than the bulk seston, but the mechanisms by which each species regulates the elemental balance differ. O. naumanni increases bacterivory with light, thus increasing phosphorus uptake, while S. araucanus regulates carbon fixation. The low carbon:nutrient ratio of these organisms would represent a very good food source for zooplankton. Finally, we pointed out that different effects of local and global changes will affect negatively the particular ciliate assemblage of North-Patagonian Andean lakes

Digging Deeper: In Search of the Mechanisms of Carbon and Nitrogen Exchange in Ectomycorrhizal Symbioses.

Symbiosis with ectomycorrhizal (ECM) fungi is an advantageous partnership for trees in nutrient-limited environments. Ectomycorrhizal fungi colonize the roots of their hosts and improve their access to nutrients, usually nitrogen (N) and, in exchange, trees deliver a significant portion of their photosynthetic carbon (C) to the fungi. This nutrient exchange affects key soil processes and nutrient cycling, as well as plant health, and is therefore central to forest ecosystem functioning. Due to their ecological importance, there is a need to more accurately understand ECM fungal mediated C and N movement within forest ecosystems such that we can better model and predict their role in soil processes both now and under future climate scenarios. There are a number of hurdles that we must overcome, however, before this is achievable such as understanding how the evolutionary history of ECM fungi and their inter- and intra- species variability affect their function. Further, there is currently no generally accepted universal mechanism that appears to govern the flux of nutrients between fungal and plant partners. Here, we consider the current state of knowledge on N acquisition and transport by ECM fungi and how C and N exchange may be related or affected by environmental conditions such as N availability. We emphasize the role that modern genomic analysis, molecular biology techniques and more comprehensive and standardized experimental designs may have in bringing cohesion to the numerous ecological studies in this area and assist us in better understanding this important symbiosis. These approaches will help to build unified models of nutrient exchange and develop diagnostic tools to study these fungi at various scales and environments.

Targeting Cell Metabolism as Cancer Therapy.

Significance: Cancer cells exhibit altered metabolic pathways to keep up with biosynthetic and reduction-oxidation needs during tumor proliferation and metastasis. The common induction of metabolic pathways during cancer progression, regardless of cancer histio- or genotype, makes cancer metabolism an attractive target for therapeutic exploitation. Recent Advances: Emerging data suggest that these altered pathways may even result in resistance to anticancer therapies. Identifying specific metabolic dependencies that are unique to cancer cells has proved challenging in this field, limiting the therapeutic window for many candidate drug approaches. Critical Issues: Cancer cells display significant metabolic flexibility in nutrient-limited environments, hampering the longevity of suppressing cancer metabolism through any singular approach. Combinatorial "synthetic lethal" approaches may have a better chance for success and promising strategies are reviewed here. The dynamism of the immune system adds a level of complexity, as various immune populations in the tumor microenvironment often share metabolic pathways with cancer, with successive alterations during immune activation and quiescence. Decoding the reprogramming of metabolic pathways within cancer cells and stem cells, as well as examining metabolic symbiosis between components of the tumor microenvironment, would be essential to further meaningful drug development within the tumor's metabolic ecosystem. Future Directions: In this article, we examine evidence for the therapeutic potential of targeting metabolic alterations in cancer, and we discuss the drawbacks and successes that have stimulated this field.

Transcriptomic Analysis of Aggregatibacter actinomycetemcomitans Core and Accessory Genes in Different Growth Conditions.

Aggregatibacter actinomycetemcomitans genome can be divided into an accessory gene pool (found in some but not all strains) and a core gene pool (found in all strains). The functions of the accessory genes (genomic islands and non-island accessory genes) are largely unknown. We hypothesize that accessory genes confer critical functions for A. actinomycetemcomitans in vivo. This study examined the expression patterns of accessory and core genes of A. actinomycetemcomitans in distinct growth conditions. We found similar expression patterns of island and non-island accessory genes, which were generally lower than the core genes in all growth conditions. The median expression levels of genomic islands were 29%–37% of the core genes in enriched medium but elevated to as high as 63% of the core genes in nutrient-limited media. Several putative virulence genes, including the cytolethal distending toxin operon, were found to be activated in nutrient-limited conditions. In conclusion, genomic islands and non-island accessory genes exhibited distinct patterns of expression from the core genes and may play a role in the survival of A. actinomycetemcomitans in nutrient-limited environments.

Investigating host-bacterial interactions among enteric pathogens

BackgroundIn 2017, World Health Organization (WHO) published a catalogue of 12 families of antibiotic-resistant “priority pathogens” that are posing the greatest threats to human health. Six of these dreaded pathogens are known to infect the human gastrointestinal system. In addition to causing gastrointestinal and systemic infections, these pathogens can also affect the composition of other microbes constituting the healthy gut microbiome. Such aberrations in gut microbiome can significantly affect human physiology and immunity. Identifying the virulence mechanisms of these enteric pathogens are likely to help in developing newer therapeutic strategies to counter them.ResultsUsing our previously published in silico approach, we have evaluated (and compared) Host-Pathogen Protein-Protein Interaction (HPI) profiles of four groups of enteric pathogens, namely, different species of Escherichia, Shigella, Salmonella and Vibrio. Results indicate that in spite of genus/ species specific variations, most enteric pathogens possess a common repertoire of HPIs. This core set of HPIs are probably responsible for the survival of these pathogen in the harsh nutrient-limiting environment within the gut. Certain genus/ species specific HPIs were also observed.ConslusionsThe identified bacterial proteins involved in the core set of HPIs are expected to be helpful in understanding the pathogenesis of these dreaded gut pathogens in greater detail. Possible role of genus/ species specific variations in the HPI profiles in the virulence of these pathogens are also discussed. The obtained results are likely to provide an opportunity for development of novel therapeutic strategies against the most dreaded gut pathogens.