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The temporary storage of wet algae concentrates enables the decoupling in time of algae harvests and their biorefinery. However, the impact of cultivation and of the harvest conditions on algae quality during preservation is largely unknown. This study aimed to determine the impact of nutrient limitation and of harvest methods on the preservation of Chlorella vulgaris biomass. Algae were either well-fed until harvest or received no nutrients for one week, and were harvested by either batch or continuous centrifugation. The organic acid formation, lipid levels, and lipolysis were monitored. Nutrient limitation had a large impact and resulted in lower pH values (4.9 ± 0.4), high levels of lactic acid and acetic acid, and a slightly higher degree of lipid hydrolysis. Concentrates of well-fed algae had a higher pH (7.4 ± 0.2) and another pattern of fermentation products with mainly acetic acid, succinic acid, and, to a smaller extent, lactic acid and propionic acid. The effect of the harvest method was smaller, with, most often, higher lactic acid and acetic acid levels for algae harvested by continuous centrifugation than for those obtained by batch centrifugation. In conclusion, nutrient limitation, a well-known method to enhance algae lipid levels, can impact several quality attributes of algae during their wet storage.

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Gene transfer agents (GTAs) are virus-like elements that are encoded by some bacterial and archaeal genomes. The production of GTAs can be induced by carbon depletion and results in host lysis and the release of virus-like particles that contain mostly random fragments of the host DNA. The remaining members of a GTA-producing population act as GTA recipients by producing proteins needed for GTA-mediated DNA acquisition. Here, we detected a codon usage bias toward codons with more readily available tRNAs in the RcGTA-like GTA genes of alphaproteobacterial genomes. Such bias likely improves the translational efficacy during GTA gene expression. While the strength of codon usage bias fluctuates substantially among individual GTA genes and across taxonomic groups, it is especially pronounced in Sphingomonadales, whose members are known to inhabit nutrient-depleted environments. By screening genomes for gene families with trends in codon usage biases similar to those in GTA genes, we found a gene that likely encodes head completion protein in some GTAs where it appeared missing, and 13 genes previously not implicated in the GTA life cycle. The latter genes are involved in various molecular processes, including the homologous recombination and transport of scarce organic matter. Our findings provide insights into the role of selection for translational efficiency in the evolution of GTA genes and outline genes that are potentially involved in the previously hypothesized integration of GTA-delivered DNA into the host genome. IMPORTANCE Horizontal gene transfer (HGT) is a fundamental process that drives evolution of microorganisms. HGT can result in a rapid dissemination of beneficial genes within and among microbial communities and can be achieved via multiple mechanisms. One peculiar HGT mechanism involves viruses "domesticated" by some bacteria and archaea (their hosts). These so-called gene transfer agents (GTAs) are encoded in hosts' genomes, produced under starvation conditions, and cannot propagate themselves as viruses. We show that GTA genes are under selection to improve the efficiency of their translation when the host activates GTA production. The selection is especially pronounced in bacteria that occupy nutrient-depleted environments. Intriguingly, several genes involved in incorporation of DNA into a genome are under similar selection pressure, suggesting that they may facilitate the integration of GTA-delivered DNA into the host genome. Our findings underscore the potential importance of GTAs as a mechanism of HGT under nutrient-limited conditions, which are widespread in microbial habitats.

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The soil bacterium Burkholderia pseudomallei is the causative agent of melioidosis and a significant cause of human morbidity and mortality in many tropical and subtropical countries. The species notoriously survives harsh environmental conditions but the genetic architecture for these adaptations remains unclear. Here we employed a powerful combination of genome-wide epistasis and co-selection studies (2,011 genomes), condition-wide transcriptome analyses (82 diverse conditions), and a gene knockout assay to uncover signals of "co-selection"-that is a combination of genetic markers that have been repeatedly selected together through B. pseudomallei evolution. These enabled us to identify 13,061 mutation pairs under co-selection in distinct genes and noncoding RNA. Genes under co-selection displayed marked expression correlation when B. pseudomallei was subjected to physical stress conditions, highlighting the conditions as one of the major evolutionary driving forces for this bacterium. We identified a putative adhesin (BPSL1661) as a hub of co-selection signals, experimentally confirmed a BPSL1661 role under nutrient deprivation, and explored the functional basis of co-selection gene network surrounding BPSL1661 in facilitating the bacterial survival under nutrient depletion. Our findings suggest that nutrient-limited conditions have been the common selection pressure acting on this species, and allelic variation of BPSL1661 may have promoted B. pseudomallei survival during harsh environmental conditions by facilitating bacterial adherence to different surfaces, cells, or living hosts.

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This research aimed to investigate the suitability of the filamentous microalga Zygnema heydrichii as a biodiesel feedstock. Under ambient culture conditions, biomass yield, lipid content, and fatty acid composition were measured. The effects of nutrient deprivation, pH, and salinity on biomass and lipid production were also investigated. Z. heydrichii under nutrient-enriched medium showed specific growth rate (µ) 0.31 day-1 and lipid content 14.75% DW. The most abundant fatty acids were C16:0, C18:1, C18:2 and C18:3, all of which are considered appropriate for biodiesel production. Nitrogen and phosphorus depletion from the growth medium further increased lipid content to 21.45% and 15.35% DW, respectively. The N depletion of the medium remarkably increased TAG content of the culture. Z. heydrichii possess great ability to grow in salty water (40 Mm NaCl). A low-cost, semi-continuous outdoor culture yielded biomass and lipid productivity of 0.208 g day-1and 0.038 g L-1 day-1, respectively.

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Due to the diverse applications, graphene-family nanomaterials (GFNs) have a high probability of release into the aquatic system, potentially posing risks to the aquatic environment. The acute effects on single-celled Microcystis aeruginosa by graphene oxide (GO) or graphene oxide quantum dots (GOQDs) were compared in the present study. GOQDs dispersed more effectively in water than GO at all pH values tested. The 96-hour median effective concentration (EC50) of GO and GOQDs were determined to be 49.32 and 22.46 mg/L, respectively. Both GO and GOQDs were internalized by heteroagglomeration and envelopment processes, with GOQDs inducing stronger upregulation of cell permeability, plasmolysis and lipid bodies than GO. Cracking of thylakoid layers, disappearance of nucleoid, and disintegration of cell infrastructure were observed at higher concentrations. In comparison to GO, GOQDs induced higher reactive oxygen species (ROS) and malondialdehyde (MDA) and disrupted antioxidant enzymes, leading to the inhibition of cellular contents such as chlorophyll a and proteins. Furthermore, both GO and GOQDs adsorbed nutrients from the algal medium, resulting in nutrient depletion-induced indirect toxicity, with GOQDs depleting more nutrients than GO. The current study provides new understanding of nanotoxicity of GO and GOQD and aids in the potential risks of nanomaterials in aquatic environments.

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Metabolic reprogramming of cancer cells generates a tumour microenvironment (TME) characterised by nutrient restriction, hypoxia, acidity and oxidative stress. While these conditions are unfavourable for infiltrating effector T cells, accumulating evidence suggests that regulatory T cells (Tregs) continue to exert their immune-suppressive functions within the TME. The advantages of Tregs within the TME stem from their metabolic profile. Tregs rely on oxidative phosphorylation for their functions, which can be fuelled by a variety of substrates. Even though Tregs are an attractive target to augment anti-tumour immune responses, it remains a challenge to specifically target intra-tumoral Tregs. We provide a comprehensive review of distinct mechanistic links and pathways involved in regulation of Treg metabolism under the prevailing conditions within the tumour. We also describe how these Tregs differ from the ones in the periphery, and from conventional T cells in the tumour. Targeting pathways responsible for adaptation of Tregs in the tumour microenvironment improves anti-tumour immunity in preclinical models. This may provide alternative therapies aiming at reducing immune suppression in the tumour.

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An inadequate supply of amino acids leads to accumulation of uncharged tRNAs, which can bind and activate GCN2 kinase to reduce translation. Here, we show that glutamine-specific tRNAs selectively become uncharged when extracellular amino acid availability is compromised. In contrast, all other tRNAs retain charging of their cognate amino acids in a manner that is dependent upon intact lysosomal function. In addition to GCN2 activation and reduced total translation, the reduced charging of tRNAGln in amino-acid-deprived cells also leads to specific depletion of proteins containing polyglutamine tracts including core-binding factor α1, mediator subunit 12, transcriptional coactivator CBP and TATA-box binding protein. Treating amino-acid-deprived cells with exogenous glutamine or glutaminase inhibitors restores tRNAGln charging and the levels of polyglutamine-containing proteins. Together, these results demonstrate that the activation of GCN2 and the translation of polyglutamine-encoding transcripts serve as key sensors of glutamine availability in mammalian cells.

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Glutamine and glucose are both oxidized in the mitochondria to supply the majority of usable energy for processes of cellular function. Low levels of plasma and skeletal muscle glutamine are associated with severe illness. We hypothesized that glutamine deficiency would disrupt mitochondrial integrity and impair cell function. C2C12 mouse myoblasts were cultured in control media supplemented with 5.6 mmol/L glucose and 2 mmol/L glutamine, glutamine depletion (Gln-) or glucose depletion (Glc-) media. We compared mitochondrial morphology and function, as well as cell proliferation, myogenic differentiation, and heat-shock response in these cells. Glc- cells exhibited slightly elongated mitochondrial networks and increased mitochondrial mass, with normal membrane potential (ΔΨm). Mitochondria in Gln- cells became hyperfused and swollen, which were accompanied by severe disruption of cristae and decreases in ΔΨm, mitochondrial mass, the inner mitochondrial membrane remodeling protein OPA1, electron transport chain complex IV protein expression, and markers of mitochondrial biogenesis and bioenergetics. In addition, Gln- increased the autophagy marker LC3B-II on the mitochondrial membrane. Notably, basal mitochondrial respiration was increased in Glc- cells as compared to control cells, whereas maximal respiration remained unchanged. In contrast, basal respiration, maximal respiration and reserve capacity were all decreased in Gln- cells. Consistent with the aforementioned mitochondrial deficits, Gln- cells had lower growth rates and myogenic differentiation, as well as a higher rate of cell death under heat stress conditions than Glc- and control cells. We conclude that glutamine is essential for mitochondrial integrity and function; glutamine depletion impairs myoblast proliferation, differentiation, and the heat-shock response.

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Macropinocytosis is increasingly recognized for its versatile adaptations and functions as a highly conserved, ubiquitous pathway for the bulk uptake of fluid, particulate cargo, and membranes. Innate immune cells and transformed cancer cells share the capacity for both constitutive and induced macropinocytosis, which is used for immune surveillance, ingestion of pathogens, immune response shaping, and enhancement of scavenging for nutrients as fuel for cell survival and proliferation. Immunology and cancer biology are leading a resurgence of interest in defining the molecular and physiological regulation of macropinocytosis, partly in pursuit of ways to control macropinocytic uptake in disease settings. New approaches, including high-resolution live imaging, screening of cell surface molecular inventories, biophysics, and exploration of cell microenvironments, have converged to provide new insights into macropinosome induction, formation, and maturation. Recent studies reveal mechanisms for fluid control in and by macrophage macropinosomes that impinge on membrane trafficking and cell migration. EGFR, PTEN, V-ATPase, syndecan 1, and galectin-3 have roles variably in the metabolic regulation of Ras or PI3K signaling for Rac1-mediated macropinocytosis in cancer. These molecular pathways and mechanisms contribute to the impressive adaptability of macropinocytosis in many cells and tissues and in disease.

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Gene transfer agents (GTAs) are virus-like elements integrated into bacterial genomes, particularly, those of Alphaproteobacteria The GTAs can be induced under conditions of nutritional stress, incorporate random fragments of bacterial DNA into miniphage particles, lyse the host cells, and infect neighboring bacteria, thus enhancing horizontal gene transfer. We show that GTA genes evolve under conditions of pronounced positive selection for the reduction of the energy cost of protein production as shown by comparison of the amino acid compositions with those of both homologous viral genes and host genes. The energy saving in GTA genes is comparable to or even more pronounced than that in the genes encoding the most abundant, essential bacterial proteins. In cases in which viruses acquire genes from GTAs, the bias in amino acid composition disappears in the course of evolution, showing that reduction of the energy cost of protein production is an important factor of evolution of GTAs but not bacterial viruses. These findings strongly suggest that GTAs represent bacterial adaptations rather than selfish, virus-like elements. Because GTA production kills the host cell and does not propagate the GTA genome, it appears likely that the GTAs are retained in the course of evolution via kin or group selection. Therefore, we hypothesize that GTAs facilitate the survival of bacterial populations under energy-limiting conditions through the spread of metabolic and transport capabilities via horizontal gene transfer and increases in nutrient availability resulting from the altruistic suicide of GTA-producing cells.IMPORTANCE Kin selection and group selection remain controversial topics in evolutionary biology. We argue that these types of selection are likely to operate in bacterial populations by showing that bacterial gene transfer agents (GTAs), but not related viruses, evolve under conditions of positive selection for the reduction of the energy cost of GTA particle production. We hypothesize that GTAs are dedicated devices mediating the survival of bacteria under conditions of nutrient limitation. The benefits conferred by GTAs under nutritional stress conditions appear to include horizontal dissemination of genes that could provide bacteria with enhanced capabilities for nutrient utilization and increases of nutrient availability occurring through the lysis of GTA-producing bacteria.

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Bacillus subtilis cells can mount a number of responses to nutritional deprivation but ultimately either form dormant spores or enter a metabolically quiescent state. In a recent article (mBio 10:e01414-19, https://doi.org/10.1128/mBio.01414-19, 2019), R. Hashuel and S. Ben-Yehuda report on a novel means by which nutrient-starved B. subtilis cells escape from aging (days-old) colonies by accumulating mutations enabling them to continue growth under nutrient-limited conditions. They postulate that such a strategy may be a major factor determining the dynamics of bacterial populations in natural environments.

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Burgeoning use of segregated microfluidic platforms that parse somas and neurites into discrete compartments is fueling unique examinations of neuronal structure and physiology in a manner impossible to achieve with non-compartmentalized systems. However, even though this line of axon-soma polarizing microfluidic devices stems from the same general design of a Campenot chamber set-up, slight deviations in device geometry appear to induce vastly different nutrient transport profiles that influence neuron survival and maturation. Here we examine the uptake of nerve growth factor (NGF) by a pheochromocytoma PC12 cell line cultured using two Campenot-like device designs, a "Standard" layout, representative of a commercial device, and a custom "Notch" layout, predicted to encourage more efficient nutrient transfer that gives rise to sustained neuron viability and extensive neurite elaboration. Exploiting in vitro culture schemes coupled with computational analyses, we identify the influence of device design geometry on the interplay between neuronal survival and maturation, gauged from morphometric assessments and the spatiotemporal distribution of NGF. Computer simulations of NGF transport within the devices revealed that the microfluidic neuron culture system is highly sensitive to change, where nutrient transport is intricately linked to device geometry and cell plating density, and premature depletion of nutrients is observed if specific design criteria are not met. This study underscores the importance of validating specific device geometries for a particular neuro-based assessment, while showcasing computational modeling as a powerful tool to achieve this goal.

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Low fertilizer application rates for several decades have depleted soil nutrients in Sub-Saharan Africa (SSA) and contributed to relatively stagnant maize (Zea mays L.) yields. As maize is a staple crop, nutrient depletion has resulted in major food insecurity. While one potential solution is to apply more nitrogen (N) fertilizer, previous studies in SSA have found maize yield responses to be variable, likely because N is often not the only limiting nutrient. This study aimed to determine the impact of consecutive N fertilizer applications on plant uptake and available soil reserves of non-N nutrients. Maize was grown continuously in 3 sites that were representative of the ecosystem variability found in East/Southern Africa (Embu, Kenya; Kiboko, Kenya; Harare, Zimbabwe) at 4 different N fertilizer rates (0-160 kg N ha-1) from 2010 to 2015. Following the final season, grain, stover, and soil (sampled at different depths to 0.9 m) samples were analyzed for essential plant nutrients. Nitrogen fertilizer increased plant uptake of P, S, Cu, and Zn by up to 280%, 320%, 420%, and 210%, respectively, showing potential for mitigating non-N nutrient deficiencies in 2 of the 3 sites. Cumulatively, however, there was a net negative effect of higher N rates on the P, K, and S soil-plant balances in all sites and on the Mn and Cu soil-plant balance in Kiboko, indicating that applying N fertilizer depletes non-N soil nutrients. While N fertilizer enhances the uptake of non-N nutrients, a balanced application of multiple essential nutrients is needed to sustainably increase yields in SSA.

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Contents Summary 91 I. Introduction 91 II. Primary PSF mechanisms 91 III. Factors mediating the mechanisms of PSF 93 IV. Conclusions and future directions 94 Acknowledgements 95 Author contributions 95 References 95 SUMMARY: Plant-soil feedback (PSF) occurs when plants alter soil properties that influence the performance of seedlings, with consequent effects on plant populations and communities. Many processes influence PSF, including changes in nutrient availability and the accumulation of natural enemies, mutualists or secondary chemicals. Typically, these mechanisms are investigated in isolation, yet no single mechanism is likely to be completely responsible for PSF as these processes can interact. Further, the outcome depends on which resources are limiting and the other plants and soil biota in the surrounding environment. As such, understanding the mechanisms of PSF and their role within plant communities requires quantification of the interactions among the processes influencing PSF and the associated abiotic and biotic contexts.

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BACKGROUND: Individual nutrient depletion is widely used to induce lipid accumulation in microalgae, which also causes cell growth inhibition and decreases the total biomass. Thus, improving the lipid accumulation without biomass loss in the nutrient deficiency cells becomes a potential cost-effective treatment for cheaper biofuels. METHODS: In this study, the effects of different nutritional conditions on the growth and contents of lipids in Chlamydomonas reinhardtii were compared, and the metabolic profiles under different nutritional conditions were also investigated. RESULTS: We showed that similar to other microalgae, nitrogen or phosphorus deficiency inhibited the growth of Chlamydomonas and combined nutrition deficiency reduced biomass by up to 31.7%, though lipid contents in cells (g/g dry weight [DW]) were significantly increased. The addition of sodium acetate countered this growth inhibition that resulted from nitrogen and phosphorus deficiency, with significantly increased biomass. Furthermore, the combination of 4 g/L sodium acetate supplementation with nitrogen and phosphorous deficiency increased total fatty acid yield (mg/L) by 93.0 and 150.1% compared to nutrient-depleted and normal culture conditions, respectively. Metabolite content was affected by the different nutritional conditions, especially metabolites that are involved in lipid metabolism, amino acid metabolism and metabolism of external substances. CONCLUSION: Further research into these metabolites could shed light onto the relationship between cell growth inhibition and fatty acid accumulation in Chlamydomonas.

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In natural environments microorganisms encounter extreme changes in temperature, pH, osmolarities and nutrient availability. The stress response of many bacterial species has been described in detail, however, knowledge in Archaea is limited. Here, we describe the cellular response triggered by nutrient limitation in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. We measured changes in gene transcription and protein abundance upon nutrient depletion up to 4 h after initiation of nutrient depletion. Transcript levels of 1118 of 2223 protein coding genes and abundance of approximately 500 proteins with functions in almost all cellular processes were affected by nutrient depletion. Our study reveals a significant rerouting of the metabolism with respect to degradation of internal as well as extracellular-bound organic carbon and degradation of proteins. Moreover, changes in membrane lipid composition were observed in order to access alternative sources of energy and to maintain pH homeostasis. At transcript level, the cellular response to nutrient depletion in S. acidocaldarius seems to be controlled by the general transcription factors TFB2 and TFEß. In addition, ribosome biogenesis is reduced, while an increased protein degradation is accompanied with a loss of protein quality control. This study provides first insights into the early cellular response of Sulfolobus to organic carbon and organic nitrogen depletion.

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Over the last decades, the vast chemical and biodiversity of marine environment has been identified as an important source of new anticancer drugs. The evolution of marine life is a result of competition among microorganisms for space and nutrients in the marine environment, which drives marine microorganisms to generate diverse enzyme systems with unique properties to adapt to harsh conditions of ocean. Therefore, marine-derived sources offer novel enzymes endowed with extraordinary properties. Recent advances in cancer therapy have facilitated enzyme therapy as a promising tool. But, the available information on the use of enzymes derived from marine sources as therapeutic agents for cancer therapy is scanty. The potential utility of marine enzymes in cancer therapy will be discussed in this chapter.

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We systematically investigated the toxicity mechanism of three graphene-family materials (GFMs), graphene oxide (GO), reduced graphene oxide (rGO) and multi-layer graphene (MG), to algae (Chlorella pyrenoidosa). GFMs exhibited much higher toxicity than other carbon materials (carbon nanotube and graphite), with the 96 h median effective concentration (EC50) values of 37.3 (GO), 34.0 (rGO), and 62.2 (MG) mg/L. Shading effect contributed approximately 16.4% of growth inhibition by GO due to its higher dispersibility and transformation while the other GFMs did not show any shading effect. Hydrophobic rGO and MG more readily heteroagglomerated with algae than GO, thus likely leading to more direct contacts with algae. Flow cytometry results showed significant decrease of membrane integrity after GFM exposure, and rGO caused the highest membrane damage, which was confirmed by the increased DNA and K+ efflux. The observed membrane damage was caused by a combination of oxidative stress and physical penetration/extraction. Moreover, all the three GFMs could adsorb macronutrients (N, P, Mg, and Ca) from the algal medium, thus leading to nutrient depletion-induced indirect toxicity. GO showed the highest nutrient depletion (53% of total toxicity) due to its abundant functional groups. The information provided in this work will be useful for understanding toxicity mechanism and environmental risk of different GFMs in aquatic environments.

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Research results published regarding the impact of soil and water conservation practices in the highland areas of Ethiopia have been inconsistent and scattered. In this paper, a detailed review and synthesis is reported that was conducted to identify the impacts of soil and water conservation practices on crop yield, surface run-off, soil loss, nutrient loss, and the economic viability, as well as to discuss the implications for an integrated approach and ecosystem services. The review and synthesis showed that most physical soil and water conservation practices such as soil bunds and stone bunds were very effective in reducing run-off, soil erosion and nutrient depletion. Despite these positive impacts on these services, the impact of physical soil and water conservation practices on crop yield was negative mainly due to the reduction of effective cultivable area by soil/stone bunds. In contrast, most agronomic soil and water conservation practices increase crop yield and reduce run-off and soil losses. This implies that integrating physical soil and water conservation practices with agronomic soil and water conservation practices are essential to increase both provisioning and regulating ecosystem services. Additionally, effective use of unutilized land (the area occupied by bunds) by planting multipurpose grasses and trees on the bunds may offset the yield lost due to a reduction in planting area. If high value grasses and trees can be grown on this land, farmers can harvest fodder for animals or fuel wood, both in scarce supply in Ethiopia. Growing of these grasses and trees can also help the stability of the bunds and reduce maintenance cost. Economic feasibility analysis also showed that, soil and water conservation practices became economically more viable if physical and agronomic soil and water conservation practices are integrated.

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Yeast cell wall is a structure that helps yeasts to manage and respond to many environmental stresses. The mannosylphosphorylation is a modification in response to stress that provides the cell wall with negative charges able to bind compounds present in the environment. Phenotypes related to the cell wall modification such as the filamentous growth in Saccharomyces cerevisiae are affected by nutrient depletion. The present work aimed at describing the effect of carbon and/or nitrogen limitation on the aptitude of S. cerevisiae strains to bind coloured polyphenols. Carbon- and nitrogen-rich or deficient media supplemented with grape polyphenols were used to simulate different grape juice conditions-early, mid, 'adjusted' for nitrogen, and late fermentations. In early fermentation condition, the R+G+B values range from 106 (high adsorption, strain Sc1128) to 192 (low adsorption, strain Σ1278b), in mid-fermentation the values range from 111 (high adsorption, strain Sc1321) to 258 (low adsorption, strain Sc2306), in 'adjusted' for nitrogen conditions the values range from 105 (high adsorption, strain Sc1321) to 194 (low adsorption, strain Sc2306) while in late fermentation conditions the values range from 101 (high adsorption, strain Sc384) to 293 (low adsorption, strain Sc2306). The effect of nutrient availability is not univocal for all the strains and the different media tested modified the strains behaviour. In all the media the strains show significant differences. Results demonstrate that wine yeasts decrease/increase their parietal adsorption activity according to the nutrient availability. The wide range of strain variability observed could be useful in selecting wine starters.

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