Utilization Of Nitrogen Sources Research Articles

Efficient utilization of winter nitrogen sources by soil microorganisms and plants in a temperate grassland

In seasonal snow-covered regions, the soil microbial community remains highly active, enabling nitrogen (N) mineralization processes to occur even during the winter. Therefore, winter N accumulation is likely to be a primary N source for plant growth in the subsequent spring. However, the availability of winter N resources (i.e., ammonium and nitrate N) to soil microorganisms and plants in temperate grasslands remains unclear. Here, we applied 15NH4Cl and K15NO3 tracers before autumn-winter freezing, and then investigated the retention of both 15N tracers in soil microorganisms and different plants during the winter and spring period in a typical steppe. The results showed that approximately 33 % and 27 % of 15NH4Cl and K15NO3 tracers were immobilized by soil microorganisms, while little had been uptake by plants during winter. In the subsequent spring, soil retained 32 % and 34 %, microorganisms immobilized 5.1 % and 5.2 %, plant acquired 40 % and 28 % of the 15NH4Cl and K15NO3 tracers, respectively. At a temporal scale, perennial bunch grasses first acquired 15N in the winter-spring transition, followed by perennial rhizome grasses and forbs in early spring, while legumes utilized little 15N. In contrast, the 15N absorption capacity of perennial rhizome grasses and perennial forbs was similar to that of bunch grasses. Additionally, only dominant bunch grasses showed a preference for ammonium N over nitrate N, while other plant species did not exhibit a clear preference for different forms of N. Our results suggest that the temporal differentiation of N utilization between plants and microorganisms enhances the availability of winter N sources. Importantly, the differences among plant species in the timing and quantity of winter N resource utilization contribute to species coexistence in temperate grasslands. This study highlights the crucial role of winter N accumulation as a primary N source for plant growth in temperate grasslands. Understanding the availability of winter N sources for plant and microbial growth is essential for predicting plant community dynamics and species coexistence in these ecosystems.

Nitrogen Availability and Utilisation of Oligopeptides by Yeast in Industrial Scotch Grain Whisky Fermentation

Scotch grain whisky is produced with a substantial proportion of unmalted grains, which can result in nitrogen deficiency for yeast in the fermentable grain mash. This study examined nitrogen source availability and utilisation by three commercial whisky strains (Saccharomyces cerevisiae) during Scotch grain whisky fermentation, focusing on oligopeptides. Peptide uptake kinetics in synthetic whisky mash with defined peptides showed that oligopeptides of up to nine amino acids were taken up by the strains, albeit with some variability between the strains. The study found that peptides with appropriate molecular weights could replace free amino acids without negatively affecting fermentation kinetics. Moreover, fermentation performance improved when additional nitrogen was provided via peptides rather than diammonium phosphate. Analysis of industrial grain mash indicated that despite low initial yeast assimilable nitrogen, residual proteolytic activity from malt increased nitrogen availability during fermentation. Approximately 30% of the nitrogen consumed by yeast during grain mash fermentation was derived from peptides. LC-HRMS peptide analysis revealed complex dynamics of peptide formation, degradation, and utilisation. This study highlights the importance of oligopeptides in ensuring optimal fermentation efficiency in Scotch grain mash and similar substrates.

VmSom1 is essential for growth, development, maintenance of cell wall integrity and virulence in Valsa mali

Apple Valsa canker disease, caused by Valsa mali Miyabe et Yamada, severely endangers the healthy growth of apple trees. The Som1, located downstream of the cyclic AMP-dependent protein kinase A (cAMP-PKA) pathway, plays crucial roles in the growth, development, morphological differentiation, and virulence of filamentous fungi. In this study, we identify and functionally characterize VmSom1, a homolog of Som1, in Valsa mali. The VmSom1 gene is located on chromosome 12, encoding an 824 amino acid protein. Phylogenetic analysis reveals VmSom1 as a fungal Som1 homolog. The VmSom1 deletion mutants exhibit slower growth rates and fail to produce pycnidia. Additionally, their hyphal growth is significantly inhibited on media containing Calcofluor White, Congo Red, NaCl, and sorbitol. The growth rate of VmSom1 deletion mutants is reduced on maltose, lactose, sucrose and fructose media but increases on glucose medium. Moreover, the mycelial growth rate of the VmSom1 deletion mutant is significantly lower than that of the wild-type strain in peptone, NH4SO4, NaNO3, and no nitrogen. Notably, the distances between the septa increase, and chitin concentration shifts to the hyphal tip in the VmSom1 deletion mutant. Furthermore, compared with the wild-type strain, the VmSom1 deletion mutant exhibits fewer diseased spots on apple fruit and branches. Overall, our findings demonstrate that VmSom1 is involved in regulating the growth and development, colony surface hydrophobicity, osmotic stress, cell wall integrity maintenance, carbon and nitrogen source utilization, septa formation, and virulence of V. mali.

Regulation of nitrogen utilization and mycotoxin biosynthesis by the GATA transcription factor AaAreA in Alternaria alternata.

Alternaria alternata is a prevalent postharvest pathogen that generates diverse mycotoxins, notably alternariol (AOH) and alternariol monomethyl ether (AME), which are recurrent severe contaminants. Nitrogen sources modulate fungal growth, development, and secondary metabolism, including mycotoxin production. The GATA transcription factor AreA regulates nitrogen source utilization. However, little is known about its involvement in the regulation of nitrogen utilization in A. alternata. To examine the regulatory mechanism of AaAreA on AOH and AME biosynthesis in A. alternata, we analyzed the impact of diverse nitrogen sources on the fungal growth, conidiation and mycotoxin production. The use of a secondary nitrogen source (NaNO3) enhanced mycelial elongation and sporulation more than the use of a primary source (NH4Cl). NaNO3 favored greater mycotoxin accumulation than did NH4Cl. The regulatory roles of AaAreA were further clarified through gene knockout. The absence of AaAreA led to an overall reduction in growth in minimal media containing any nitrogen source except NH4Cl. AaAreA positively regulates mycotoxin biosynthesis when both NH4Cl and NaNO3 are used as nitrogen sources. Subcellular localization analysis revealed abundant nuclear transport when NaNO3 was the sole nitrogen source. The regulatory pathway of AaAreA was systematically revealed through comprehensive transcriptomic analyses. The deletion of AaAreA significantly impedes the transcription of mycotoxin biosynthetic genes, including aohR, pksI and omtI. The interaction between AaAreA and aohR, a pathway-specific transcription factor gene, demonstrated that AaAreA binds to the aohR promoter sequence (5'-GGCTATGGAAA-3'), activating its transcription. The expressed AohR regulates the expression of downstream synthase genes in the cluster, ultimately impacting mycotoxin production. This study provides valuable information to further understand how AreA regulates AOH and AME biosynthesis in A. alternata, thereby enabling the effective design of control measures for mycotoxin contamination.

Mrvam7, a conserved SNARE gene involved in vacuolar fusion, is required for development and secondary metabolism in Monascus ruber M7

Vam7 (vacuolar morphogenesis 7), a Qc-soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) that mediates vacuolar fusion, is involved in vacuolar morphogenesis, vegetative growth, sexual and asexual reproduction, and compartmentalized biosynthesis of secondary metabolites in various filamentous fungi. In this study, the homolog of vam7 gene, mrvam7, in Monascus ruber M7 was functionally characterized through gene modification and transcriptome analysis. The results showed that the mrvam7 complementation and overexpression strains exhibited phenotypic similarities to M. ruber M7, whereas the mrvam7 null strain exhibited fragmented vacuoles, slowed growth and diminished sexual and asexual sporulation. Furthermore, the mrvam7 knockout strain displayed a notable increase in citrinin production alongside a significant decrease in Monascus pigments production. Transcriptome data revealed that the deletion of mrvam7 altered the expression levels of several genes involved in sexual and asexual reproduction, carbon and nitrogen source utilization, and secondary metabolites biosynthetic gene clusters. Collectively, these findings underscore the critical role of mrvam7-mediated vacuolar fusion in growth, development, and the compartmentalized biosynthesis and distribution of secondary metabolites in M ruber M7. This study provides novel insights into the mechanisms underlying of compartmentalized secondary metabolites biosynthesis in Monascus species.

Phenotypic microarray characterization of hemolytic and non-hemolytic strains of Listeria monocytogenes

Limited information is available on the phenotypic characteristics of Listeriamonocytogenes that may affect its virulence of L.monocytogenes. The study focused on comparing the differences between two strains of L. monocytogenes, one hemolytic (LLO+) and one non-hemolytic (tLLO). Using Phenotype Microarray (PM) technology, carbon, nitrogen, and phosphorus-sulfur source utilization by the strains was performed and the KEGG pathway involvement in substrate utilization was analyzed. Of the 285 substrates screened, the results suggested that d-gluconic acid and l-serine may play a role in L. monocytogenes hemolytic activity towards LLO production by generating pyruvate as an intermediate and amino acid biosynthesis, which may play an important role in virulence protein translation. d-gluconic acid and l-serine showed no effect on the tLLO strain in PM analysis and validation tests. Notably, the scope of this study was limited to these two strains of L. monocytogenes. While these findings provide valuable insights into the metabolic differences between hemolytic and non-hemolytic strains, further research is necessary to expand this understanding to a broader range of strains and explore additional factors that may influence LLO functionality.

Oligotrophic characteristics and genomic analysis of the Rhodoligotrophos defluvii lm1T isolated from activated sludge

Oligotrophic conditions have important role in the evolution of life and also the study of ecological status and ecological functions of oligotrophic bacteria in such ecosystems. In this study, the oligotrophic characteristics of the experimental strain Rhodoligotrophos defluvii lm1T (hereinafter referred to as lm1T) isolated from activated sludge were investigated. The results indicated that lm1T was able to grow normally in Luria-Bertani (LB) and diluted LB solid agar plates, demonstrating it to be a facultative oligotrophic bacterium. Research about carbon source and genome analysis revealed that lm1T lacks 6-phosphofructokinase in the glycolysis process, resulting in the inability to convert glucose-6-phosphate to fructose-6-phosphate, which prevented lm1T from utilizing glucose. And in line with that, lm1T can utilize 1,6-diphosphofructose, acetate, propionate, and butyrate to meet its growth requirements. lm1T possesses a wide range of nitrogen sources utilization, including NaNO3, urea, NH4Cl, (NH4)2SO4, peptone, and yeast extract, enabling its adaptation to various complex environments. Additionally, comparative genomic analysis of lm1T and the model strain Rhodoligotrophos appendicifer 120-1T revealed that lm1T had more genes related to degradation metabolism, which aided its adaptation to complex environments.

Introduction of soybean into maize field reduces N2O emission intensity via optimizing nitrogen source utilization

The application of synthetic nitrogen (N) fertilizer has increased anthropogenic N2O emission in global croplands. Due to the advantage of biological nitrogen fixation (BNF), the introduction of legume may lessen N2O emission intensity (emission/yield) in cereal field. Yet, this speculation lacks strong evidences and the relevant mechanistic explanations. A two-year field study was conducted using static chamber method (15N isotope labeling in fertilizer) in the mono- and inter-cropping fields with soybean introduced in maize field in semiarid rainfed Loess Plateau. The results indicated that maize-soybean intercropping showed 13 % lower N2O emission intensity than monocropping, attributed to 14 % and 20 % lower annually N2O emissions in intercropped zone than that of sole maize and soybean zones respectively. Also, a 15 % higher grain yield was observed in intercropped maize relative to that in sole maize. Particularly, during the peak time of emission following N fertilization and BNF within growing season, soybean introduction reduced 25 % and 24 % of N2O emissions in intercropped zone than sole maize and soybean zone respectively. It also favored maize plant with an additional 17 % more fertilizer-derived N, 21 % less soil-derived N and 30 kg N ha−1 soybean transferred-N from BNF. The contributions of N fertilization, BNF and soil initial organic N to N2O production were lessened in intercropping. In this case, the capacity of substrates N transformation into N2O emissions was lowered. Critically, soybean introduction reduced soil ammonia oxidation (as evidenced from amoA AOA and AOB gene abundance) in intercrops’ rhizosphere, and increased soil nitrite reduction (nirS and nirK gene abundance) in maize rhizosphere, and improved soil N2O reduction to N2 (nosZ gene abundance) in soybean rhizosphere. Therefore, soybean introduction optimized N source use for lower N2O emission intensity, via reducing the transformation of substrate N into N2O, and modifying the expression of nitrification and denitrification functional genes.

Phage treatment of Pseudomonas aeruginosa yields a phage-resistant population with different susceptibility to innate immune responses and mild effects on metabolic profiles

In this study, we have investigated innate immune activation capacity and metabolic features of a population of P. aeruginosa PAO1 phage-resistant mutants with diverse genetic modification (large genomic deletions and point mutations) arising after exposure to phages targetting lipopolysaccharide (LPS) or Type-4 pili (T4P). Deletions led to the loss of genes involved in LPS synthesis, cell envelope permeability, efflux systems, biofilm production, oxidative stress tolerance, and DNA repair. Loss of LPS O antigen resulted in bacterial sensitivity to serum complement and stimulation of inflammatory cascades but did not cause increased phagocytosis, while T4P phage-resistant mutants were more effectively phagocytized than LPS-defective mutants. Changes in the utilization of different carbon, nitrogen, sulphur, and phosphorus sources were identified, especially in mutants where the two phage DNA persisted in the bacterial population (pseudolysogeny). However, the metabolic changes did not directly correlate with single-gene mutations or the large gene deletions, suggesting they reflect adaptive changes to the gene modifications that arise during the selection of resistant mutants. In contrast, phage-resistant mutants were susceptible to humoral innate immune responses, suggesting that phage resistance may be a beneficial outcome of phage therapy.

Dissolved nitrogen uptake versus nitrogen fixation: Mode of nitrogen acquisition affects stable isotope signatures of a diazotrophic cyanobacterium and its grazer.

Field studies suggest that changes in the stable isotope ratios of phytoplankton communities can be used to track changes in the utilization of different nitrogen sources, i.e., to detect shifts from dissolved inorganic nitrogen (DIN) uptake to atmospheric nitrogen (N2) fixation by diazotrophic cyanobacteria as an indication of nitrogen limitation. We explored changes in the stable isotope signature of the diazotrophic cyanobacterium Trichormus variabilis in response to increasing nitrate (NO3-) concentrations (0 to 170 mg L-1) under controlled laboratory conditions. In addition, we explored the influence of nitrogen utilization at the primary producer level on trophic fractionation by studying potential changes in isotope ratios in the freshwater model Daphnia magna feeding on the differently grown cyanobacteria. We show that δ 15N values of the cyanobacterium increase asymptotically with DIN availability, from -0.7 ‰ in the absence of DIN (suggesting N2 fixation) to 2.9 ‰ at the highest DIN concentration (exclusive DIN uptake). In contrast, δ 13C values of the cyanobacterium did not show a clear relationship with DIN availability. The stable isotope ratios of the consumer reflected those of the differently grown cyanobacteria but also revealed significant trophic fractionation in response to nitrogen utilization at the primary producer level. Nitrogen isotope turnover rates of Daphnia were highest in the absence of DIN as a consequence of N2 fixation and resulting depletion in 15N at the primary producer level. Our results highlight the potential of stable isotopes to assess nitrogen limitation and to explore diazotrophy in aquatic food webs.

The chromatin remodeler Ino80 regulates yeast stress tolerance and cell metabolism through modulating nitrogen catabolite repression

Chromatin remodelers are important in maintaining the dynamic chromatin state in eukaryotic cells, which is essential for epigenetic regulation. Among the remodelers, the multi-subunits complex INO80 plays crucial roles in transcriptional regulation. However, current knowledge of chromatin regulation of the core subunit Ino80 on stress adaptation remains mysterious. Here we revealed that overexpressing the chromatin remodeler Ino80 elevated tolerance to multiple stresses in budding yeast Saccharomyces cerevisiae. Analyses of differential chromatin accessibility and global transcription levels revealed an enrichment of genes involved in NCR (nitrogen catabolite repression) under acetic acid stress. We demonstrated that Ino80 overexpression reduced the histone H3 occupancy in the promoter region of the glutamate dehydrogenase gene GDH2 and the allantoinase gene DAL1. Consistently, the decreased occupancy of nucleosome was revealed in the Ino80-inactivation mutant. Further analyses showed that Ino80 was recruited to the specific DNA locus in the promoter region of GDH2. Consistently, Ino80 overexpression facilitated the utilization of non-preferred nitrogen source to enhance ethanol yield under prolonged acetic acid stress. These results demonstrate that Ino80 plays a crucial role in coordinating carbon and nitrogen metabolism during stress adaptation.

Fire transforms effects of terrestrial subsidies on aquatic ecosystem structure and function.

Fire can lead to transitions between forest and grassland ecosystems and trigger positive feedbacks to climate warming by releasing CO2 into the atmosphere. Climate change is projected to increase the prevalence and severity of wildfires. However, fire effects on the fate and impact of terrestrial organic matter (i.e., terrestrial subsidies) in aquatic ecosystems are unclear. Here, we performed a gradient design experiment in freshwater pond mesocosms adding 15 different amounts of burned or unburned plant detritus and tracking the chronology of detritus effects at 10, 31, 59, and 89 days. We show terrestrial subsidies had time- and mass-dependent, non-linear impacts on ecosystem function that influenced dissolved organic carbon (DOC), ecosystem metabolism (net primary production and respiration), greenhouse gas concentrations (carbon dioxide [CO2 ], methane [CH4 ]), and trophic transfer. These impacts were shifted by fire treatment. Burning increased the elemental concentration of detritus (increasing %N, %P, %K), with cascading effects on ecosystem function. Mesocosms receiving burned detritus had lower [DOC] and [CO2 ] and higher dissolved oxygen (DO) through Day 59. Fire magnified the effects of plant detritus on aquatic ecosystem metabolism by stimulating photosynthesis and respiration at intermediate detritus-loading through Day 89. The effect of loading on DO was similar for burned and unburned treatments (Day 10); however, burned-detritus in the highest loading treatments led to sustained hypoxia (through Day 31), and long-term destabilization of ecosystem metabolism through Day 89. In addition, fire affected trophic transfer by increasing autochthonous nitrogen source utilization and reducing the incorporation of 15 N-labeled detritus into plankton biomass, thereby reducing the flux of terrestrial subsidies to higher trophic levels. Our results indicate fire chemically transforms plant detritus and alters the role of aquatic ecosystems in processing and storing carbon. Wildfire may therefore induce shifts in ecosystem functions that cross the boundary between aquatic and terrestrial habitats.

The ankyrin repeat-containing protein PlANK1 mediates mycelial growth, oospore development, and virulence in Peronophythora litchii

Litchi downy blight, caused by Peronophythora litchii, is one of the most serious diseases in major litchi-producing regions worldwide. The ankyrin (ANK) repeat is one of the most common protein-protein interaction motifs found in all kingdoms of life proteins. ANK-containing proteins have been demonstrated to regulate various biological processes in animals, plants, and fungi. However, their functions in phytopathogenic oomycetes remain unknown. Here, we identified 284 non-redundant genes that encode ANK-containing proteins in P. litchii and classified them into 11 subfamilies. Among them, PlANK1 was found to be highly up-regulated in oospores and from zoospores to the infection process. Loss of PlANK1 in P. litchii resulted in impaired mycelial growth and cyst germination, accelerated zoospore encystment, and increased sensitivity to hyperosmotic stresses and Congo red. Furthermore, PlANK1 deletion mutants were defective in oospore formation and development. Inoculation assays showed that the absence of PlANK1 severely diminished the pathogen’s virulence on litchi leaf and fruit. Through transcriptome analysis and nitrogen source utilization assays, we demonstrated that PlANK1 modulates the pathogen’s nitrogen metabolism. Altogether, our findings indicate that PlANK1 is a key regulator of sexual and asexual development, and virulence in P. litchii.

Promoting fucoxanthin accumulation in Phaeodactylum tricornutum by multiple nitrogen supplementation and blue light enhancement

The aim of this study was to promote fucoxanthin accumulation in Phaeodactylum tricornutum by photo-fermentation through optimizing the mode of multiple nitrogen supplementation and blue light enhancement. The results showed that the mixed nitrogen source (tryptone: urea=1:1, N mol/N mol; total nitrogen concentration at 0.02 mol/L) added to the culture system by six times was the best mode in shake flasks. Two-phase culture with light adjustment was then carried out in 5 L photo-fermenter with an enhanced blue light (R: G: B=67.1:16.7:16.3) in the second phase, leading to improved cell density (1.12×108 cells/mL), biomass productivity (330 mg/(d·L)), fucoxanthin content (19.62 mg/g), titer (69.71 mg/L) and productivity (6.97 mg/(d·L)). Compared with one-phase culture under red/blue (R: G: B=70.9:18.3:10.9) light and six-times nitrogen supplementation, the fucoxanthin content was significantly increased by 7.68% (P < 0.05) but the productivity did not change significantly (P > 0.05). Compared with one-phase culture under red/blue (R: G: B=70.9:18.3:10.9) light and one-time nitrogen supplementation, the content and productivity of fucoxanthin were significantly increased by 45.98% and 48.30% (P < 0.05), respectively. This study developed a two-phase culture mode with multiple nitrogen supplementation and blue light enhancement, which effectively promoted the accumulation of fucoxanthin and improved the efficiency of nitrogen source utilization, thus providing a new approach for fucoxanthin accumulation in P. tricornutum by photo-fermentation.

Exploring the potential of Bacillus subtilis as cell factory for food ingredients and special chemicals

BackgroundBacillus subtilis has been established as model microorganism for fundamental research in the laboratory on protein production/secretion and sporulation and as model bacterium for controlling spoilage in the food industry. It has also been used for production of (commercial) enzymes and several secondary metabolites such as vitamins. However, this doesn’t fully reflect the potential of B. subtilis as a cell-factory. Here, various strains of B. subtilis, including food-grade, spore-deficient strains and industrially used strains, were compared for their growth and metabolic potential. Industry-relevant parameters were analyzed for all strains under various aeration regimes, under anaerobic conditions, in various nutritious and nutrient-limited cultivation media, with and without organic nitrogen sources, and with and without sugar.ResultsPractical experiments were conducted to compare industrial relevant properties like growth rates, intracellular components and extracellular metabolite profile of different B. subtilis strains. Based on growth flexibility in different media, we found that some strains like NCIB3610 and DSM1092 are adapted to inorganic or organic nitrogen source utilization, which is highly relevant when considering a biorefinery approach using various cheap and abundant waste/sidestreams. Secondly, spore-deficient strains such as 3NA, 168 S and PY79S, showed advantages in microbial protein and acetolactate pathway expression, which is associated with applications in food industry for protein supplement and diacetyl production. Lastly, WB800 and PY79S exhibited potential for fermentative production of dipicolinic acid, 2,3-butanediol and lactic acid that could serve as precursors for biopolymers.ConclusionThis study demonstrates the broad potential for more extensive industrial use of Bacillus subtilis in the (bio-based) chemical industry for use of sidestreams, in the personal care industry, in the food industry for food additive production, and in the bio-sustainable industry for biofuel and bio-degradable plastic precursors production. In addition, selecting different B. subtilis strains for specific purposes makes full use of the diversity of this species and increases the potential of B. subtilis in its contribution to the bio-based economy.

Regulation of nutrient utilization in filamentous fungi.

Organisms must accurately sense and respond to nutrients to survive. In filamentous fungi, accurate nutrient sensing is important in the establishment of fungal colonies and in continued, rapid growth for the exploitation of environmental resources. To ensure efficient nutrient utilization, fungi have evolved a combination of activating and repressing genetic networks to tightly regulate metabolic pathways and distinguish between preferred nutrients, which require minimal energy and resources to utilize, and nonpreferred nutrients, which have more energy-intensive catabolic requirements. Genes necessary for the utilization of nonpreferred carbon sources are activated by transcription factors that respond to the presence of the specific nutrient and repressed by transcription factors that respond to the presence of preferred carbohydrates. Utilization of nonpreferred nitrogen sources generally requires two transcription factors. Pathway-specific transcription factors respond to the presence of a specific nonpreferred nitrogen source, while another transcription factor activates genes in the absence of preferred nitrogen sources. In this review, we discuss the roles of transcription factors and upstream regulatory genes that respond to preferred and nonpreferred carbon and nitrogen sources and their roles in regulating carbon and nitrogen catabolism. KEY POINTS: • Interplay of activating and repressing transcriptional networks regulates catabolism. • Nutrient-specific activating transcriptional pathways provide metabolic specificity. • Repressing regulatory systems differentiate nutrients in mixed nutrient environments.

Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability.

Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, in coupling codon non-optimality to enhanced degradation, and as a translational repressor, but its functions in cells are incompletely understood. RNA-Seq analyses coupled with CAGE sequencing of all capped mRNAs revealed increased abundance of hundreds of mRNAs in dcp2Δ cells that appears to result directly from impaired decapping rather than elevated transcription. Interestingly, only a subset of mRNAs requires Dhh1 for targeting by Dcp2, and also generally requires the other decapping activators Pat1, Edc3 or Scd6; whereas most of the remaining transcripts utilize NMD factors for Dcp2-mediated turnover. Neither inefficient translation initiation nor stalled elongation appears to be a major driver of Dhh1-enhanced mRNA degradation. Surprisingly, ribosome profiling revealed that dcp2Δ confers widespread changes in relative translational efficiencies (TEs) that generally favor well-translated mRNAs. Because ribosome biogenesis is reduced while capped mRNA abundance is increased by dcp2&Delta, we propose that an increased ratio of mRNA to ribosomes increases competition among mRNAs for limiting ribosomes to favor efficiently translated mRNAs in dcp2Δ cells. Interestingly, genes involved in respiration or utilization of alternative carbon or nitrogen sources are up-regulated, and both mitochondrial function and cell filamentation are elevated in dcp2Δ cells, suggesting that decapping sculpts gene expression post-transcriptionally to fine-tune metabolic pathways and morphological transitions according to nutrient availability.

The Role of luxS in Campylobacter jejuni Beyond Intercellular Signaling.

The full role of the luxS gene in the biological processes, such as essential amino acid synthesis, nitrogen and pyruvate metabolism, and flagellar assembly, of Campylobacter jejuni has not been clearly described to date. Therefore, in this study, we used a comprehensive approach at the cellular and molecular levels, including transcriptomics and proteomics, to investigate the key role of the luxS gene and compared C. jejuni 11168ΔluxS (luxS mutant) and C. jejuni NCTC 11168 (wild type) strains. Transcriptomic analysis of the luxS mutant grown under optimal conditions revealed upregulation of luxS mutant metabolic pathways when normalized to wild type, including oxidative phosphorylation, carbon metabolism, citrate cycle, biosynthesis of secondary metabolites, and biosynthesis of various essential amino acids. Interestingly, induction of these metabolic pathways was also confirmed by proteomic analysis, indicating their important role in energy production and the growth of C. jejuni. In addition, genes important for the stress response of C. jejuni, including nutrient starvation and oxidative stress, were upregulated. This was also evident in the better survival of the luxS mutant under starvation conditions than the wild type. At the molecular level, we confirmed that metabolic pathways were upregulated under optimal conditions in the luxS mutant, including those important for the biosynthesis of several essential amino acids. This also modulated the utilization of various carbon and nitrogen sources, as determined by Biolog phenotype microarray analysis. In summary, transcriptomic and proteomic analysis revealed key biological differences in tricarboxylic acid (TCA) cycle, pyruvate, nitrogen, and thiamine metabolism as well as lipopolysaccharide biosynthesis in the luxS mutant. IMPORTANCE Campylobacter jejuni is the world's leading foodborne bacterial pathogen of gastrointestinal disease in humans. C. jejuni is a fastidious but widespread organism and the most frequently reported zoonotic pathogen in the European Union since 2005. This led us to believe that C. jejuni, which is highly sensitive to stress factors (starvation and oxygen concentration) and has a low growth rate, benefits significantly from the luxS gene. The role of this gene in the life cycle of C. jejuni is well known, and the expression of luxS regulates many phenotypes, including motility, biofilm formation, host colonization, virulence, autoagglutination, cellular adherence and invasion, oxidative stress, and chemotaxis. Surprisingly, this study confirmed for the first time that the deletion of the luxS gene strongly affects the central metabolic pathway of C. jejuni, which improves its survival, showing its role beyond the intercellular signaling system.

Optimization of medium composition of Lactobacillus plantarum Y44 using Plackett–Burman and Box–Behnken designs

The biomass of Lactobacillus strains depends on the culture media and culture conditions. The purpose of this study was to optimize the culture medium composition and culture conditions of Lactobacillus plantarum Y44 to improve its biomass. The utilization of different carbon sources and nitrogen sources by L. plantarum Y44 was assessed by single factor experiment to screen out the economical carbon and nitrogen sources for L. plantarum Y44 growth. Through optimization experiments, the optimized culture medium for L. plantarum Y44 growth consists of soybean peptone 44.1 g/L, yeast extract 22.1 g/L, sucrose 35.6 g/L, hydrogen diamine citrate 2 g/L, anhydrous sodium acetate 8.5 g/L, dipotassium hydrogen phosphate 4 g/L, Tween-80 2 mL/L, manganese sulfate 0.25 g/L, and magnesium sulfate 0.58 g/L, and the initial pH 6.7. The concentration of viable bacteria cells of L. plantarum Y44 culturing in the optimized medium at 37 °C for 16 h was up to 3.363 × 1010 CFU/mL, as 6.11 times higher than that in the MRS medium.

Biogeographic patterns in populations of marine Pseudoalteromonas atlantica isolates.

Intra-specific genomic diversity is well documented in microbes. The question, however, remains whether natural selection or neutral evolution is the major contributor to this diversity. We undertook this study to estimate genomic diversity in Pseudoalteromonas atlantica populations and whether the diversity, if present, could be attributed to environmental factors or distance effects. We isolated and sequenced twenty-three strains of P. atlantica from three geographically distant deep marine basins and performed comparative genomic analyses to study the genomic diversity of populations among these basins. Average nucleotide identity followed a strictly geographical pattern. In two out of three locations, the strains within the location exhibited>99.5% identity, whereas, among locations, the strains showed<98.11% identity. Phylogenetic and pan-genome analysis also reflected the biogeographical separation of the strains. Strains from the same location shared many accessory genes and clustered closely on the phylogenetic tree. Phenotypic diversity between populations was studied in ten out of twenty-three strains testing carbon and nitrogen source utilization and osmotolerance. A genetic basis for phenotypic diversity could be established in most cases but was apparently not influenced by local environmental conditions. Our study suggests that neutral evolution may have a substantial role in the biodiversity of P. atlantica.