The ntrB and ntrC genes are involved in the regulation of poly-3-hydroxybutyrate biosynthesis by ammonia in Azospirillum brasilense Sp7

Ethylene signals through an ethylene receptor to modulate biofilm formation and root colonization in a beneficial plant-associated bacterium

Ethylene is a plant hormone involved in many aspects of plant growth and development as well as responses to stress. The role of ethylene in plant-microbe interactions has been explored from the perspective of plants. However, only a small number of studies have examined the role of ethylene in microbes. We demonstrated that Azospirillum brasilense contains a functional ethylene receptor that we call Azospirillum Ethylene Response1 (AzoEtr1) after the nomenclature used in plants. AzoEtr1 directly binds ethylene with high affinity. Treating cells with ethylene or disrupting the receptor reduces biofilm formation and colonization of plant root surfaces. Additionally, RNA sequencing and untargeted metabolomics showed that ethylene causes wide-spread metabolic changes that affect carbon and nitrogen metabolism. One result is the accumulation of poly-hydroxybutyrate. Our data suggests a model in which ethylene from host plants alters the density of colonization by A. brasilense and re-wires its metabolism, suggesting that the bacterium implements an adaptation program upon sensing ethylene. These data provide potential new targets to regulate beneficial plant-microbe interactions.

Ectoine hyperproduction by engineered Halomonas bluephagenesis

Ectoine, a crucial osmoprotectant for salt adaptation in halophiles, has gained growing interest in cosmetics and medical industries. However, its production remains challenged by stringent fermentation process in model microorganisms and low production level in its native producers. Here, we systematically engineered the native ectoine producer Halomonas bluephagenesis for ectoine production by overexpressing ectABC operon, increasing precursors availability, enhancing product transport system and optimizing its growth medium. The final engineered H. bluephagenesis produced 85 g/L ectoine in 52 h under open unsterile incubation in a 7 L bioreactor in the absence of plasmid, antibiotic or inducer. Furthermore, it was successfully demonstrated the feasibility of decoupling salt concentration with ectoine synthesis and co-production with bioplastic P(3HB-co-4HB) by the engineered H. bluephagenesis. The unsterile fermentation process and significantly increased ectoine titer indicate that H. bluephagenesis as the chassis of Next-Generation Industrial Biotechnology (NGIB), is promising for the biomanufacturing of not only intracellular bioplastic PHA but also small molecular compound such as ectoine.

Polyhydroxybutyrate Metabolism in Azospirillum brasilense and Its Applications, a Review

Gram-negative Azospirillum brasilense accumulates approximately 80% of polyhydroxybutyrate (PHB) as dry cell weight. For this reason, this bacterium has been characterized as one of the main microorganisms that produce PHB. PHB is synthesized inside bacteria by the polymerization of 3-hydroxybutyrate monomers. In this review, we are focusing on the analysis of the PHB production by A. brasilense in order to understand the metabolism during PHB accumulation. First, the carbon and nitrogen sources used to improve PHB accumulation are discussed. A. brasilense accumulates more PHB when it is grown on a minimal medium containing a high C/N ratio, mainly from malate and ammonia chloride, respectively. The metabolic pathways to accumulate and mobilize PHB in A. brasilense are mentioned and compared with those of other microorganisms. Next, we summarize the available information to understand the role of the genes involved in the regulation of PHB metabolism as well as the role of PHB in the physiology of Azospirillum. Finally, we made a comparison between the properties of PHB and polypropylene, and we discussed some applications of PHB in biomedical and commercial areas.

Production of polyhydroxyalkanoate by mixed cultivation of Brevundimonas diminuta R79 and Pseudomonas balearica R90

The microflora in the activated sludge of propylene oxide saponification wastewater is characterized by a clear succession after enrichment and domestication, and the specifically enriched strains can significantly increase the yield of polyhydroxyalkanoate. In this study, Pseudomonas balearica R90 and Brevundimonas diminuta R79, which are dominant strain after domestication, were selected as models to examine the interactive mechanisms associated with the synthesis of polyhydroxyalkanoate by co-cultured strains. RNA-Seq analysis revealed the up-regulated expression of the acs and phaA genes of strains R79 and R90 in the co-culture group, which enhanced their utilization of acetic acid and synthesis of poly-β-hydroxybutyrate. Cell dry weight and the yield of poly-β-hydroxybutyrate in the co-culture group were accordingly considerably higher than those in the respective pure culture groups. In addition, two-component system, quorum-sensing, flagellar synthesis-related, and chemotaxis-related genes were enriched in strain R90, thereby indicating that compared with the R79 strain, R90 can adapt more rapidly to a domesticated environment. Expression of the acs gene was higher in R79 than in R90, and consequently, strain R79 could more efficiently assimilate acetate in the domesticated environment, and thus predominated in the culture population at the end of the fermentation period.

Boosting nitrogen fertilization by a slow releasing nitrate-intercalated biocompatible layered double hydroxide-hydrogel composite loaded with Azospirillum brasilense

Indiscriminate use of chemical fertilizers leads to soil environmental disbalance and therefore, preparation and application of environment-friendly slow-release multifunctional fertilizers are of paramount importance for sustainable crop production in the present scenario. In this study, we propose a slow-release multifunctional composite nitrogen (N) fertilizer, which possesses the ability to supply plant accessible N in the form of ammonium (NH4 +) and nitrate (NO3 -) to improve nitrate assimilation coupled with zinc (Zn, a major micronutrient for plants in the soil) after its degradation. For this purpose, NO3 --intercalated zinc-aluminum (Zn-Al) layered double hydroxide (LDH) was synthesized using a co-precipitation protocol. The prepared LDH was added as 25.45% of total polymer weight to a sodium carboxymethyl cellulose/hydroxyethyl cellulose citric acid (NaCMC/HEC-CA) biodegradable hydrogel. A. brasilense, commonly used nitrogen-fixing bacteria in soils, was added to the LDH-hydrogel composite along with LDH alone to augment the availability of NH4 + and NO3 -. Adjusting the pH under acidic (pH 5.25) and neutral (pH 7) conditions, the release pattern of NO3 - from LDH and the composite was monitored for 30 days at normal temperature. The pH was selected based on the soil analysis data of North East India. The LDH-composite released 90% (w/w) and 85.45% (w/w) of intercalated NO3 - at pH 5.25 and 7.00 respectively in 30 days. However, 100% (w/w) and 87% (w/w) of intercalated NO3 - at pH 5.25 and 7.00 respectively were released in 30 days when only LDH was applied, which indicated the lower performance of LDH alone in comparison to the LDH-composite for the nitrate holding pattern. The pH of the bacteria-loaded system was observed to be acidic (pH = 5-6) during the study of nitrate assimilation and Zn2+ release. A. brasilense improved nitrate assimilation and increased the NH4 + ion concentration in the studied system. A significant increase in Zn2+ release was observed from day 5 in the presence of A. brasilense in the LDH-composite compared with that in the absence of A. brasilense. In conclusion, the prepared LDH-hydrogel-A. brasilense composite fertilizer system increases the availability of plant accessible N form (both NO3 - and NH4 +) and can potentially improve soil fertility with the addition of Zn and bacteria to the soil in the extended course.

An updated overview on the regulatory circuits of polyhydroxyalkanoates synthesis

Polyhydroxyalkanoates (PHA) are a promising and sustainable alternative to the petroleum‐based synthetic plastics. Regulation of PHA synthesis is receiving considerable importance as engineering the regulatory factors might help developing strains with improved PHA‐producing abilities. PHA synthesis is dedicatedly regulated by a number of regulatory networks. They tightly control the PHA content, granule size and their distribution in cells. Most PHA‐accumulating microorganisms have multiple regulatory networks that impart a combined effect on PHA metabolism. Among them, several factors ranging from global to specific regulators, have been identified and characterized till now. This review is an attempt to categorically summarize the diverse regulatory circuits that operate in some important PHA‐producing microorganisms. However, in several organisms, the detailed mechanisms involved in the regulation of PHA synthesis is not well‐explored and hence further research is needed. The information presented in this review might help researcher to identify the prevailing research gaps in PHA regulation.

Metabolic circuits and gene regulators in polyhydroxyalkanoate producing organisms: Intervention strategies for enhanced production

Worldwide worries upsurge concerning environmental pollutions triggered by the accumulation of plastic wastes. Biopolymers are promising candidates for resolving these difficulties by replacing non-biodegradable plastics. Among biopolymers, polyhydroxyalkanoates (PHAs), are natural polymers that are synthesized and accumulated in a range of microorganisms, are considered as promising biopolymers since they have biocompatibility, biodegradability, and other physico-chemical properties comparable to those of synthetic plastics. Consequently, considerable research have been attempted to advance a better understanding of mechanisms related to the metabolic synthesis and characteristics of PHAs and to develop native and recombinant microorganisms that can proficiently produce PHAs comprising desired monomers with high titer and productivity for industrial applications. Recent developments in metabolic engineering and synthetic biology applied to enhance PHA synthesis include, promoter engineering, ribosome-binding site (RBS) engineering, development of synthetic constructs etc. This review gives a brief overview of metabolic routes and regulators of PHA production and its intervention strategies.

The Modification of Regulatory Circuits Involved in the Control of Polyhydroxyalkanoates Metabolism to Improve Their Production

Poly-(3-hydroxyalkanoates) (PHAs) are bacterial carbon and energy storage compounds. These polymers are synthesized under conditions of nutritional imbalance, where a nutrient is growth-limiting while there is still enough carbon source in the medium. On the other side, the accumulated polymer is mobilized under conditions of nutrient accessibility or by limitation of the carbon source. Thus, it is well known that the accumulation of PHAs is affected by the availability of nutritional resources and this knowledge has been used to establish culture conditions favoring high productivities. In addition to this effect of the metabolic status on PHAs accumulation, several genetic regulatory networks have been shown to drive PHAs metabolism, so the expression of the PHAs genes is under the influence of global or specific regulators. These regulators are thought to coordinate PHAs synthesis and mobilization with the rest of bacterial physiology. While the metabolic and biochemical knowledge related to the biosynthesis of these polymers has led to the development of processes in bioreactors for high-level production and also to the establishment of strategies for metabolic engineering for the synthesis of modified biopolymers, the use of knowledge related to the regulatory circuits controlling PHAs metabolism for strain improvement is scarce. A better understanding of the genetic control systems involved could serve as the foundation for new strategies for strain modification in order to increase PHAs production or to adjust the chemical structure of these biopolymers. In this review, the regulatory systems involved in the control of PHAs metabolism are examined, with emphasis on those acting at the level of expression of the enzymes involved and their potential modification for strain improvement, both for higher titers, or manipulation of polymer properties. The case of the PHAs producer Azotobacter vinelandii is taken as an example of the complexity and variety of systems controlling the accumulation of these interesting polymers in response to diverse situations, many of which could be engineered to improve PHAs production.

Physical-Chemical Properties of Biogenic Selenium Nanostructures Produced by Stenotrophomonas maltophilia SeITE02 and Ochrobactrum sp. MPV1

Stenotrophomonas maltophilia SeITE02 and Ochrobactrum sp. MPV1 were isolated from the rhizosphere soil of the selenium-hyperaccumulator legume Astragalus bisulcatus and waste material from a dumping site for roasted pyrites, respectively. Here, these bacterial strains were studied as cell factories to generate selenium-nanostructures (SeNS) under metabolically controlled growth conditions. Thus, a defined medium (DM) containing either glucose or pyruvate as carbon and energy source along with selenite () was tested to evaluate bacterial growth, oxyanion bioconversion and changes occurring in SeNS features with respect to those generated by these strains grown on rich media. Transmission electron microscopy (TEM) images show extra- or intra-cellular emergence of SeNS in SeITE02 or MPV1 respectively, revealing the presence of two distinct biological routes of SeNS biogenesis. Indeed, the stress exerted by upon SeITE02 cells triggered the production of membrane vesicles (MVs), which surrounded Se-nanoparticles (SeNPs_{SeITE02-G_e} and SeNPs_{SeITE02-P_e} with average diameter of 179 ± 56 and 208 ± 60 nm, respectively), as highlighted by TEM and scanning electron microscopy (SEM), strongly suggesting that MVs might play a crucial role in the excreting mechanism of the SeNPs in the extracellular environment. On the other hand, MPV1 strain biosynthesized intracellular inclusions likely containing hydrophobic storage compounds and SeNPs (123 ± 32 nm) under pyruvate conditioning, while the growth on glucose as the only source of carbon and energy led to the production of a mixed population of intracellular SeNPs (118 ± 36 nm) and nanorods (SeNRs; average length of 324 ± 89). SEM, fluorescence spectroscopy, and confocal laser scanning microscopy (CLSM) revealed that the biogenic SeNS were enclosed in an organic material containing proteins and amphiphilic molecules, possibly responsible for the high thermodynamic stability of these nanomaterials. Finally, the biogenic SeNS extracts were photoluminescent upon excitation ranging from 380 to 530 nm, whose degree of fluorescence emission (λ_em = 416–640 nm) was comparable to that from chemically synthesized SeNPs with L-cysteine (L-cys SeNPs). This study offers novel insights into the formation, localization, and release of biogenic SeNS generated by two different Gram-negative bacterial strains under aerobic and metabolically controlled growth conditions. The work strengthens the possibility of using these bacterial isolates as eco-friendly biocatalysts to produce high quality SeNS targeted to possible biomedical applications and other biotechnological purposes.

Poly(3-hydroxybutyrate) hyperproduction by a global nitrogen regulator NtrB mutant strain of Paracoccus denitrificans PD1222

Paracoccus denitrificans PD1222 accumulates short-length polyhydroxyalkanoates, poly(3-hydroxybutyrate), under nitrogen-deficient conditions. Polyhydroxybutyrate metabolism requires the 3-ketoacyl-CoA thiolase PhaA, the acetoacetyl-CoA dehydrogenase/reductase PhaB and the synthase PhaC for polymerization. Additionally, P. denitrificans PD1222 grows aerobically with nitrate as sole nitrogen source. Nitrate assimilation is controlled negatively by ammonium through the two-component NtrBC system. NtrB is a sensor kinase that autophosphorylates a histidine residue under low-nitrogen concentrations and, in turn, transfers a phosphoryl group to an aspartate residue of the response regulator NtrC protein, which acts as a transcriptional activator of the P. denitrificans PD1222 nasABGHC genes. The P. denitrificans PD1222 NtrB mutant was unable to use nitrate efficiently as nitrogen source when compared to the wild-type strain, and it also overproduced poly(3-hydroxybutyrate). Acetyl-CoA concentration in the P. denitrificans PD1222 NtrB mutant strain was higher than in the wild-type strain. The expression of the phaC gene was also increased in the NtrB mutant when compared to the wild-type strain. These results suggest that accumulation of poly(3-hydroxybutyrate) in the NtrB mutant strain of PD1222 responds to the high levels of acetyl-CoA that accumulate in the cytoplasm as consequence of its inability to efficiently use nitrate as nitrogen source.

Expression of the small regulatory RNA gene mmgR is regulated negatively by AniA and positively by NtrC in Sinorhizobium meliloti 2011

In the N2-fixing symbiont of alfalfa root nodules, Sinorhizobium meliloti 2011, the mmgR gene encodes a 77 nt small untranslated RNA (sRNA) that negatively regulates the accumulation of polyhydroxybutyrate (PHB) when the bacterium is grown under conditions of surplus carbon (C) in relation to nitrogen (N). We previously showed that the expression of mmgR is primarily controlled at the transcriptional level and that it depends on the cellular N status, although the regulatory mechanism and the factors involved were unknown. In this study, we provide experimental data supporting that: (a) mmgR is induced upon N limitation with the maximum expression found at the highest tested C/N molar ratio in the growth medium; (b) a conserved heptamer TTGTGCA located between the -35 and -10 mmgR promoter elements is necessary and sufficient for induction by N limitation; (c) induction of mmgR requires the N-status regulator NtrC; (d) under C limitation, mmgR transcription is repressed by AniA, a global regulator of C flow; (e) the mmgR promoter contains a conserved dyadic motif (TGC[N3]GCA) partially overlapping the heptamer TTGTGCA, which was also found in the promoters of the PHB-related genes phaP1, phaP2, phaZ and phaR (aniA) of S. meliloti and other alpha-proteobacteria. Taken together, these results suggest that the mmgR promoter would integrate signals from the metabolism of C and N through - at least - the global regulators NtrC and AniA, to provide an optimal level of the MmgR sRNA to fine-tune gene expression post-transcriptionally according to varying C and N availability.

The transcriptional regulator NtrC controls glucose-6-phosphate dehydrogenase expression and polyhydroxybutyrate synthesis through NADPH availability in Herbaspirillum seropedicae

The NTR system is the major regulator of nitrogen metabolism in Bacteria. Despite its broad and well-known role in the assimilation, biosynthesis and recycling of nitrogenous molecules, little is known about its role in carbon metabolism. In this work, we present a new facet of the NTR system in the control of NADPH concentration and the biosynthesis of molecules dependent on reduced coenzyme in Herbaspirillum seropedicae SmR1. We demonstrated that a ntrC mutant strain accumulated high levels of polyhydroxybutyrate (PHB), reaching levels up to 2-fold higher than the parental strain. In the absence of NtrC, the activity of glucose-6-phosphate dehydrogenase (encoded by zwf) increased by 2.8-fold, consequently leading to a 2.1-fold increase in the NADPH/NADP⁺ ratio. A GFP fusion showed that expression of zwf is likewise controlled by NtrC. The increase in NADPH availability stimulated the production of polyhydroxybutyrate regardless the C/N ratio in the medium. The mutant ntrC was more resistant to H₂O₂ exposure and controlled the propagation of ROS when facing the oxidative condition, a phenotype associated with the increase in PHB content.

Maize Inoculation with Azospirillum brasilense Ab-V5 Cells Enriched with Exopolysaccharides and Polyhydroxybutyrate Results in High Productivity under Low N Fertilizer Input

Although Azospirillum strains used in commercial inoculant formulations presents diazotrophic activity, it has been reported that their ability to produce phytohormones plays a pivotal role in plant growth-promotion, leading to a general recommendation of its use in association with regular N-fertilizer doses. In addition, a high variability in the effectiveness of Azospirillum inoculants is still reported under field conditions, contributing to the adoption of the inoculation technology as an additional management practice rather than its use as an alternative practice to the use of chemical inputs in agriculture. To investigate whether the content of stress-resistance biopolymers would improve the viability and performance of Azospirillum inoculants when used as substitute of N-fertilizers, biomass of A. brasilense strain Ab-V5 enriched in exopolysaccharides (EPS) and polyhydroxybutirate (PHB) was produced using a new culture medium developed by factorial mixture design, and the effectiveness of resulting inoculants was evaluated under field conditions. The culture medium formulation extended the log phase of A. brasilense cultures, which presented higher cell counts and increased EPS and PHB contents than observed in the cultures grown in the OAB medium used as control. An inoculation trial with maize conducted under greenhouse conditions and using the biopolymers-enriched Ab-V5 cells demonstrated the importance of EPS and PHB to the long term bacterial viability in soil and to the effectiveness of inoculation. The effectiveness of liquid and peat inoculants prepared with Ab-V5 cells enriched with EPS and PHB was also evaluated under field conditions, using maize as target crop along different seasons, with the inoculants applied directly over seeds or at topdressing under limiting levels of N-fertilization. No additive effect on yield resulted from inoculation under high N fertilizer input, while inoculated plants grown under 80% reduction in N fertilizer showed yields at levels compared to fully fertilized plants, regardless the inoculation method. The presented data highlights the feasibility to partially substitute the N-fertilizer demand in non-legume crops using high-quality inoculant formulations, prepared with diazotrophic bacteria enriched with stress-resistance biopolymers that confer increased viability an effectiveness to the bacterial cells.

Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti

The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to the cell. The impact of carbon storage on cellular metabolism would be reflected in global transcription patterns. By investigating the transcriptomic effects of genetically disrupting genes involved in the PHB carbon storage cycle, we revealed a relationship between intracellular carbon storage and nitrogen metabolism. This work demonstrates the utility of combining transcriptome sequencing with metabolic pathway mutations for identifying underlying gene regulatory mechanisms.

Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti, we investigated the global transcriptomic response to the genetic disruption of key genes in PHB synthesis and degradation and in glycogen synthesis. Under both nitrogen-limited and balanced growth conditions, transcriptomic analysis was performed with genetic mutants deficient in PHB synthesis (phbA, phbB, phbAB, and phbC), PHB degradation (bdhA, phaZ, and acsA2), and glycogen synthesis (glgA1). Three distinct genomic regions of the pSymA megaplasmid exhibited altered expression in the wild type and the PHB cycle mutants that was not seen in the glycogen synthesis mutant. An Fnr family transcriptional motif was identified in the upstream regions of a cluster of genes showing similar transcriptional patterns across the mutants. This motif was found at the highest density in the genomic regions with the strongest transcriptional effect, and the presence of this motif upstream of genes in these regions was significantly correlated with decreased transcript abundance. Analysis of the genes in the pSymA regions revealed that they contain a genomic overrepresentation of Fnr family transcription factor-encoding genes. We hypothesize that these loci, containing mostly nitrogen utilization, denitrification, and nitrogen fixation genes, are regulated in response to the intracellular carbon/nitrogen balance. These results indicate a transcriptional regulatory association between intracellular carbon levels (mediated through the functionality of the PHB cycle) and the expression of nitrogen metabolism genes.

IMPORTANCE The ability of bacteria to store carbon and energy as intracellular polymers uncouples cell growth and replication from nutrient uptake and provides flexibility in the use of resources as they are available to the cell. The impact of carbon storage on cellular metabolism would be reflected in global transcription patterns. By investigating the transcriptomic effects of genetically disrupting genes involved in the PHB carbon storage cycle, we revealed a relationship between intracellular carbon storage and nitrogen metabolism. This work demonstrates the utility of combining transcriptome sequencing with metabolic pathway mutations for identifying underlying gene regulatory mechanisms.

Author Video: An author video summary of this article is available.

Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans

Transcriptional adaptation to nitrate-dependent anabolism by Paracoccus denitrificans PD1222 was studied. A total of 74 genes were induced in cells grown with nitrate as N-source compared with ammonium, including nasTSABGHC and ntrBC genes. The nasT and nasS genes were cotranscribed, although nasT was more strongly induced by nitrate than nasS. The nasABGHC genes constituted a transcriptional unit, which is preceded by a non-coding region containing hairpin structures involved in transcription termination. The nasTS and nasABGHC transcripts were detected at similar levels with nitrate or glutamate as N-source, but nasABGHC transcript was undetectable in ammonium-grown cells. The nitrite reductase NasG subunit was detected by two-dimensional polyacrylamide gel electrophoresis in cytoplasmic fractions from nitrate-grown cells, but it was not observed when either ammonium or glutamate was used as the N-source. The nasT mutant lacked both nasABGHC transcript and nicotinamide adenine dinucleotide (NADH)-dependent nitrate reductase activity. On the contrary, the nasS mutant showed similar levels of the nasABGHC transcript to the wild-type strain and displayed NasG protein and NADH–nitrate reductase activity with all N-sources tested, except with ammonium. Ammonium repression of nasABGHC was dependent on the Ntr system. The ntrBC and ntrYX genes were expressed at low levels regardless of the nitrogen source supporting growth. Mutational analysis of the ntrBCYX genes indicated that while ntrBC genes are required for nitrate assimilation, ntrYX genes can only partially restore growth on nitrate in the absence of ntrBC genes. The existence of a regulation mechanism for nitrate assimilation in P. denitrificans, by which nitrate induction operates at both transcriptional and translational levels, is proposed.

Effects of nitrogen availability on polymalic acid biosynthesis in the yeast-like fungus Aureobasidium pullulans

Background

Polymalic acid (PMA) is a novel polyester polymer that has been broadly used in the medical and food industries. Its monomer, L-malic acid, is also a potential C4 platform chemical. However, little is known about the mechanism of PMA biosynthesis in the yeast-like fungus, Aureobasidium pullulans. In this study, the effects of different nitrogen concentration on cell growth and PMA biosynthesis were investigated via comparative transcriptomics and proteomics analyses, and a related signaling pathway was also evaluated.

Results

A high final PMA titer of 44.00 ± 3.65 g/L (49.9 ± 4.14 g/L of malic acid after hydrolysis) was achieved in a 5-L fermentor under low nitrogen concentration (2 g/L of NH₄NO₃), which was 18.3 % higher yield than that obtained under high nitrogen concentration (10 g/L of NH₄NO₃). Comparative transcriptomics profiling revealed that a set of genes, related to the ribosome, ribosome biogenesis, proteasome, and nitrogen metabolism, were significantly up- or down-regulated under nitrogen sufficient conditions, which could be regulated by the TOR signaling pathway. Fourteen protein spots were identified via proteomics analysis, and were found to be associated with cell division and growth, energy metabolism, and the glycolytic pathway. qRT-PCR further confirmed that the expression levels of key genes involved in the PMA biosynthetic pathway (GLK, CS, FUM, DAT, and MCL) and the TOR signaling pathway (GS, TOR1, Tap42, and Gat1) were upregulated due to nitrogen limitation. Under rapamycin stress, PMA biosynthesis was obviously inhibited in a dose-dependent manner, and the transcription levels of TOR1, MCL, and DAT were also downregulated.

Conclusions

The level of nitrogen could regulate cell growth and PMA biosynthesis. Low concentration of nitrogen was beneficial for PMA biosynthesis, which could upregulate the expression of key genes involved in the PMA biosynthesis pathway. Cell growth and PMA biosynthesis might be mediated by the TOR signaling pathway in response to nitrogen. This study will help us to deeply understand the molecular mechanisms of PMA biosynthesis, and to develop an effective process for the production of PMA and malic acid chemicals.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0547-y) contains supplementary material, which is available to authorized users.

Metabolic adaptations of Azospirillum brasilense to oxygen stress by cell-to-cell clumping and flocculation

The ability of bacteria to monitor their metabolism and adjust their behavior accordingly is critical to maintain competitiveness in the environment. The motile microaerophilic bacterium Azospirillum brasilense navigates oxygen gradients by aerotaxis in order to locate low oxygen concentrations that can support metabolism. When cells are exposed to elevated levels of oxygen in their surroundings, motile A. brasilense cells implement an alternative response to aerotaxis and form transient clumps by cell-to-cell interactions. Clumping was suggested to represent a behavior protecting motile cells from transiently elevated levels of aeration. Using the proteomics of wild-type and mutant strains affected in the extent of their clumping abilities, we show that cell-to-cell clumping represents a metabolic scavenging strategy that likely prepares the cells for further metabolic stresses. Analysis of mutants affected in carbon or nitrogen metabolism confirmed this assumption. The metabolic changes experienced as clumping progresses prime cells for flocculation, a morphological and metabolic shift of cells triggered under elevated-aeration conditions and nitrogen limitation. The analysis of various mutants during clumping and flocculation characterized an ordered set of changes in cell envelope properties accompanying the metabolic changes. These data also identify clumping and early flocculation to be behaviors compatible with the expression of nitrogen fixation genes, despite the elevated-aeration conditions. Cell-to-cell clumping may thus license diazotrophy to microaerophilic A. brasilense cells under elevated oxygen conditions and prime them for long-term survival via flocculation if metabolic stress persists.

Positive effect of reduced aeration rate on growth and stereospecificity of DL-malic acid consumption by Azospirillum brasilense: improving the shelf life of a liquid inoculant formulation

Azospirillum brasilense has significance as a growth promoter in plants of commercial interest. Two industrial native strains (Start and Calf), used as a part of an inoculant formulation in Mexico during the last 15 years, were incubated in laboratory-scale pneumatic bioreactors at different aeration rates. In both strains, the positive effect of decreased aeration was observed. At the lowest (0.1 vvm, air volume/liquid volume×minute), the highest biomass were obtained for Calf (7.8 × 10(10)CFU/ml), and Start (2.9 × 10(9)CFU/ml). These were higher in one magnitude order compared to cultures carried out at 0.5 vvm, and two compared to those at 1.0 vvm. At lower aeration, both stereoisomeric forms of malic acid were consumed, but at higher aeration, just L-malate was consumed. A reduction in aeration allows an increase of the shelf life and the microorganism saved higher concentrations of polyhydroxybutyrate. The selected fermentation conditions are closely related to those prevalent in large-scale bioreactors and offer the possibility of achieving high biomass titles with high shelf life at a reduced costs, due to the complete use of a carbon source at low aeration of a low cost raw material as DL-malic acid mixture in comparison with the L-malic acid stereoisomer.

Identification and characterization of PhbF: a DNA binding protein with regulatory role in the PHB metabolism of Herbaspirillum seropedicae SmR1

Background

Herbaspirillum seropedicae SmR1 is a nitrogen fixing endophyte associated with important agricultural crops. It produces polyhydroxybutyrate (PHB) which is stored intracellularly as granules. However, PHB metabolism and regulatory control is not yet well studied in this organism.

Results

In this work we describe the characterization of the PhbF protein from H. seropedicae SmR1 which was purified and characterized after expression in E. coli. The purified PhbF protein was able to bind to eleven putative promoters of genes involved in PHB metabolism in H. seropedicae SmR1. In silico analyses indicated a probable DNA-binding sequence which was shown to be protected in DNA footprinting assays using purified PhbF. Analyses using lacZ fusions showed that PhbF can act as a repressor protein controlling the expression of PHB metabolism-related genes.

Conclusions

Our results indicate that H. seropedicae SmR1 PhbF regulates expression of phb-related genes by acting as a transcriptional repressor. The knowledge of the PHB metabolism of this plant-associated bacterium may contribute to the understanding of the plant-colonizing process and the organism's resistance and survival in planta.

Azospirillum-plant relationships: physiological, molecular, agricultural, and environmental advances (1997-2003)

This review presents a critical and comprehensive documentation and analysis of the developments in agricultural, environmental, molecular, and physiological studies related to Azospirillum cells, and to Azospirillum interactions with plants, based solely on information published between 1997 and 2003. It was designed as an update of previous reviews (Bashan and Levanony 1990; Bashan and Holguin 1997a), with a similar scope of interest. Apart from an update and critical analysis of the current knowledge, this review focuses on the central issues of Azospirillum research today, such as, (i) physiological and molecular studies as a general model for rhizosphere bacteria; (ii) co-inoculation with other microorganisms; (iii) hormonal studies and re-consideration of the nitrogen contribution by the bacteria under specific environmental conditions; (iv) proposed Azospirillum as a non-specific plant-growth-promoting bacterium; (v) re-introduction of the "Additive Hypothesis," which suggests involvement of multiple mechanisms employed by the bacteria to affect plant growth; (vi) comment on the less researched areas, such as inoculant and pesticide research; and (vii) proposes possible avenues for the exploitation of this bacterium in environmental areas other than agriculture.Key words: Azospirillum, plant–bacteria interaction, plant-growth-promoting bacteria, PGPB, PGPR, rhizosphere bacteria.

Involvement of glnB, glnZ, and glnD genes in the regulation of poly-3-hydroxybutyrate biosynthesis by ammonia in Azospirillum brasilense Sp7

The role of three key nitrogen regulatory genes, glnB (encoding the P(II) protein), glnZ (encoding the P(z) protein), and glnD (encoding the GlnD protein), in regulation of poly-3-hydroxybutyrate (PHB) biosynthesis by ammonia in Azospirillum brasilense Sp7 was investigated. It was observed that glnB glnZ and glnD mutants produce substantially higher amounts of PHB than the wild type produces during the active growth phase. glnB and glnZ mutants have PHB production phenotypes similar to that of the wild type. Our results indicate that the P(II)-P(z) system is apparently involved in nitrogen-dependent regulation of PHB biosynthesis in A. brasilense Sp7.