Uptake and export of citric acid by Aspergillus niger is reciprocally regulated by manganese ions

Transcriptomics identify the triggering of citrate export as the key event caused by manganese deficiency in Aspergillus niger

For over a century, the filamentous Ascomycete fungus Aspergillus niger has played a pivotal role in the industrial production of citric acid. A critical fermentation parameter that sustains high-yield citric acid accumulation is the suboptimal concentration of manganese(II) ions in the culture broth at the early stages of the process. However, the requirement for this deficiency has not been investigated on a functional genomics level. In this study, we compared the transcriptome of the citric acid hyper-producer A. niger NRRL2270 strain grown under citric acid-producing conditions in 6-L scale bioreactors at Mn2+ ion-deficient (5 ppb) and Mn2+ ion-sufficient (100 ppb) conditions at three early time points of cultivation. Of the 11,846 genes in the genome, 963 genes (8.1% of the total) were identified as significantly differentially expressed under these conditions. Disproportionately high number of differentially regulated genes encode predicted extracellular and membrane proteins. The most abundant gene group that was upregulated in Mn2+ ion deficiency condition encodes enzymes acting on polysaccharides. In contrast, six clusters of genes encoding secondary metabolites showed downregulation under manganese deficiency. Mn2+ deficiency also triggers upregulation of the cexA gene, which encodes the citrate exporter. We provide functional evidence that the upregulation of cexA is caused by the intracellular accumulation of citrate or acetyl-CoA and is a major factor in triggering citrate overflow.

IMPORTANCE

Citric acid is produced on industrial scale by batch fermentation of the filamentous fungus Aspergillus niger. High-yield citric acid production requires a low (<5 ppb) manganese(II) ion concentration in the culture broth. However, the requirement for this deficiency has not been investigated on a functional genomics level. Here, we compared the transcriptome of a citric acid hyper-producer A. niger strain grown under citric acid-producing conditions in 6-L scale bioreactors at Mn2+ ion-deficient (5 ppb) and Mn2+ ion-sufficient (100 ppb) conditions at three early time points of cultivation. We observed that Mn2+ deficiency triggers an upregulation of the citrate exporter gene cexA and provides functional evidence that this event is responsible for citrate overflow. In addition to the industrial relevance, this is the first study that examined the role of Mn2+ ion deficiency in a heterotrophic eukaryotic cell on a genome-wide scale.

Exploiting Micrometer-Scale Replication of Fungal Biotemplates for Multifunctional Uses in Electrochemistry and SERS Substrates

In this paper, filamentous fungi have been used as biotemplates to integrate gold nanoparticles (Au-NPs) into the cell wall. A new chemical mechanism has been proposed to elucidate the assimilation of Au-NPs by fungi, considering the ionic current that arises in the function of fungal metabolism. After biological components were eliminated, mycelium-like gold microtubes have been obtained using different fungal species as precursors. Mycelium-like gold microtubes replicate the biological shape of fungi, presenting inherent multifunctionality. This work presents two promising applications for this material: high surface area electrodes for electrochemical experiments and substrates for SERS detection of organic molecules such as Rhodamine 6G.

Bioreactor as the root cause of the “manganese effect” during Aspergillus niger citric acid fermentations

High-yield citric acid production by the filamentous Ascomycete fungus Aspergillus niger requires a combination of extreme nutritional conditions, of which maintaining a low manganese (II) ion concentration (<5 μg L⁻¹) is a key feature. Technical-scale production of citric acid predominantly uses stainless-steel tank fermenters, but glass bioreactors used for strain improvement and manufacturing process development also contain stainless steel components, in which manganese is an essential alloying element. We show here that during citric acid fermentations manganese (II) ions were leaching from the bioreactor into the growth media, resulting in altered fungal physiology and morphology, and significant reduction of citric acid yields. The leaching of manganese (II) ions was dependent on the fermentation time, the acidity of the culture broth and the sterilization protocol applied. Manganese (II) ion leaching was partially mitigated by electrochemical polishing of stainless steel components of the bioreactor. High concentrations of manganese (II) ions during early cultivation led to a reduction in citric acid yield. However, the effect of manganese (II) ions on the reduction of citric acid yield diminished towards the second half of the fermentation. Since maintaining low concentrations of manganese (II) ions is costly, the results of this study can potentially be used to modify protocols to reduce the cost of citric acid production.

The Role of Metal Ions in Fungal Organic Acid Accumulation

Organic acid accumulation is probably the best-known example of primary metabolic overflow. Both bacteria and fungi are capable of producing various organic acids in large amounts under certain conditions, but in terms of productivity-and consequently, of commercial importance-fungal platforms are unparalleled. For high product yield, chemical composition of the growth medium is crucial in providing the necessary conditions, of which the concentrations of four of the first-row transition metal elements, manganese (Mn2+), iron (Fe2+), copper (Cu2+) and zinc (Zn2+) stand out. In this paper we critically review the biological roles of these ions, the possible biochemical and physiological consequences of their influence on the accumulation of the most important mono-, di- and tricarboxylic as well as sugar acids by fungi, and the metal ion-related aspects of submerged organic acid fermentations, including the necessary instrumental analytics. Since producing conditions are associated with a cell physiology that differs strongly to what is observed under "standard" growth conditions, here we consider papers and patents only in which organic acid accumulation levels achieved at least 60% of the theoretical maximum yield, and the actual trace metal ion concentrations were verified.

Fermentation Strategies to Improve Soil Bio-Inoculant Production and Quality

The application of plant beneficial microorganisms has been widely accepted as an efficient alternative to chemical fertilizers and pesticides. Isolation and selection of efficient microorganisms, their characterization and testing in soil-plant systems are well studied. However, the production stage and formulation of the final products are not in the focus of the research, which affects the achievement of stable and consistent results in the field. Recent analysis of the field of plant beneficial microorganisms suggests a more integrated view on soil inoculants with a special emphasis on the inoculant production process, including fermentation, formulation, processes, and additives. This mini-review describes the different groups of fermentation processes and their characteristics, bearing in mind different factors, both nutritional and operational, which affect the biomass/spores yield and microbial metabolite activity. The characteristics of the final products of fermentation process optimization strategies determine further steps of development of the microbial inoculants. Submerged liquid and solid-state fermentation processes, fed-batch operations, immobilized cell systems, and production of arbuscular mycorrhiza are presented and their advantages and disadvantages are discussed. Recommendations for further development of the fermentation strategies for biofertilizer production are also considered.

Global Transcriptional Response of Aspergillus niger to Blocked Active Citrate Export through Deletion of the Exporter Gene

Aspergillus niger is the major industrial citrate producer worldwide. Export as well as uptake of citric acid are believed to occur by active, proton-dependent, symport systems. Both are major bottlenecks for industrial citrate production. Therefore, we assessed the consequences of deleting the citT gene encoding the A. niger citrate exporter, effectively blocking active citrate export. We followed the consumption of glucose and citrate as carbon sources, monitored the secretion of organic acids and carried out a thorough transcriptome pathway enrichment analysis. Under controlled cultivation conditions that normally promote citrate secretion, the knock-out strain secreted negligible amounts of citrate. Blocking active citrate export in this way led to a reduced glucose uptake and a reduced expression of high-affinity glucose transporter genes, mstG and mstH. The glyoxylate shunt was strongly activated and an increased expression of the OAH gene was observed, resulting in a more than two-fold higher concentration of oxalate in the medium. Deletion of citT did not affect citrate uptake suggesting that citrate export and citrate uptake are uncoupled from the system.

Carbon-Source Dependent Interplay of Copper and Manganese Ions Modulates the Morphology and Itaconic Acid Production in Aspergillus terreus

The effects of the interplay of copper(II) and manganese(II) ions on growth, morphology and itaconic acid formation was investigated in a high-producing strain of Aspergillus terreus (NRRL1960), using carbon sources metabolized either mainly via glycolysis (D-glucose, D-fructose) or primarily via the pentose phosphate shunt (D-xylose, L-arabinose). Limiting Mn²⁺ concentration in the culture broth is indispensable to obtain high itaconic acid yields, while in the presence of higher Mn²⁺ concentrations yield decreases and biomass formation is favored. However, this low yield in the presence of high Mn²⁺ ion concentrations can be mitigated by increasing the Cu²⁺ concentration in the medium when D-glucose or D-fructose is the growth substrate, whereas this effect was at best modest during growth on D-xylose or L-arabinose. A. terreus displays a high tolerance to Cu²⁺ which decreased when Mn²⁺ availability became increasingly limiting. Under such conditions biomass formation on D-glucose or D-fructose could be sustained at concentrations up to 250 mg L^–1 Cu²⁺, while on D-xylose- or L-arabinose biomass formation was completely inhibited at 100 mg L^–1. High (>75%) specific molar itaconic acid yields always coincided with an “overflow-associated” morphology, characterized by small compact pellets (<250 μm diameter) and short chains of “yeast-like” cells that exhibit increased diameters relative to the elongated cells in growing filamentous hyphae. At low concentrations (≤1 mg L^–1) of Cu²⁺ ions, manganese deficiency did not prevent filamentous growth. Mycelial- and cellular morphology progressively transformed into the typical overflow-associated one when external Cu²⁺ concentrations increased, irrespective of the available Mn²⁺. Our results indicate that copper ions are relevant for overflow metabolism and should be considered when optimizing itaconic acid fermentation in A. terreus.

Identification of the citrate exporter Cex1 of Yarrowia lipolytica

Yarrowia lipolytica is a yeast with many talents, one of them being the production of citric acid. Although the citrate biosynthesis is well studied, little is known about the transport mechanism by which citrate is exported. To gain better insight into this mechanism, we set out to identify a transporter involved in citrate export of Y. lipolytica. A total of five proteins were selected for analysis based on their similarity to a known citrate exporter, but neither a citrate transport activity nor any other phenotypic function could be attributed to them. Differential gene expression analysis of two strains with a distinct citrate productivity revealed another three putative transporters, one of which is YALI0D20196p. Disrupting YALI0D20196g in Y. lipolytica abolished citrate production, while extrachromosomal expression enhanced citrate production 5.2-fold in a low producing wildtype. Furthermore, heterologous expression of YALI0D20196p in the non-citrate secreting yeast Saccharomyces cerevisiae facilitated citrate export. Likewise, expression of YALI0D20196p complemented the ability to secrete citrate in an export-deficient strain of Aspergillus niger, confirming a citrate export function of YALI0D20196p. This report on the identification of the first citrate exporter in Y. lipolytica, termed Cex1, represents a valuable starting point for further investigations of the complex transport processes in yeasts.

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions

Currently, there is no consensus regarding the mechanism underlying Aspergillus niger citrate biosynthesis and secretion. We hypothesise that depending on the experimental setup, extracellular citrate accumulation can have fundamentally different underlying transcriptomic landscapes. We show that varying the amount and type of supplement of an arginine auxotrophic A. niger strain results in transcriptional down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations when increased citrate production is triggered by iron limitation. By combining gene expression data obtained from these two very distinct experimental setups with hidden Markov models and transporter homology approaches, we were able to compile a shortlist of the most likely citrate transporter candidates. Two candidates (An17g01710 and An09g06720m.01) were heterologously expressed in the yeast Saccharomyces cerevisiae, and one of the resultant mutants showed the ability to secrete citrate. Our findings provide steps in untangling the complex interplay of different mechanisms underlying A. niger citrate accumulation, and we demonstrate how a comparative transcriptomics approach complemented with further bioinformatics analyses can be used to pinpoint a fungal citrate exporter.

The effects of external Mn2+ concentration on hyphal morphology and citric acid production are mediated primarily by the NRAMP-family transporter DmtA in Aspergillus niger

Background

Citric acid, a commodity product of industrial biotechnology, is produced by fermentation of the filamentous fungus Aspergillus niger. A requirement for high-yield citric acid production is keeping the concentration of Mn²⁺ ions in the medium at or below 5 µg L⁻¹. Understanding manganese metabolism in A. niger is therefore of critical importance to citric acid production. To this end, we investigated transport of Mn²⁺ ions in A. niger NRRL2270.

Results

we identified an A. niger gene (dmtA; NRRL3_07789), predicted to encode a transmembrane protein, with high sequence identity to the yeast manganese transporters Smf1p and Smf2p. Deletion of dmtA in A. niger eliminated the intake of Mn²⁺ at low (5 µg L⁻¹) external Mn²⁺ concentration, and reduced the intake of Mn²⁺ at high (> 100 µg L⁻¹) external Mn²⁺ concentration. Compared to the parent strain, overexpression of dmtA increased Mn²⁺ intake at both low and high external Mn²⁺ concentrations. Cultivation of the parent strain under Mn²⁺ ions limitation conditions (5 µg L⁻¹) reduced germination and led to the formation of stubby, swollen hyphae that formed compact pellets. Deletion of dmtA caused defects in germination and hyphal morphology even in the presence of 100 µg L⁻¹ Mn²⁺, while overexpression of dmtA led to enhanced germination and normal hyphal morphology at limiting Mn²⁺ concentration. Growth of both the parent and the deletion strains under citric acid producing conditions resulted in molar yields (Y_p/s) of citric acid of > 0.8, although the deletion strain produced ~ 30% less biomass. This yield was reduced only by 20% in the presence of 100 µg L⁻¹ Mn²⁺, whereas production by the parent strain was reduced by 60%. The Y_p/s of the overexpressing strain was 17% of that of the parent strain, irrespective of the concentrations of external Mn²⁺.

Conclusions

Our results demonstrate that dmtA is physiologically important in the transport of Mn²⁺ ions in A. niger, and manipulation of its expression modulates citric acid overflow.

Efficient itaconic acid production by Aspergillus terreus: Overcoming the strong inhibitory effect of manganese

Itaconic acid (IA), a building block platform chemical, is produced industrially by Aspergillus terreus utilizing glucose. Lignocellulosic biomass can serve as a low cost source of sugars for IA production. However, the fungus could not produce IA from dilute acid pretreated and enzymatically saccharified wheat straw hydrolyzate even at 100-fold dilution. Furfural, hydroxymethyl furfural and acetic acid were inhibitory, as is typical, but Mn²⁺ was particularly problematic for IA production. It was present in the hydrolyzate at a level that was 230 times over the inhibitory limit (50 ppb). Recently, it was found that PO₄ ^3- limitation decreased the inhibitory effect of Mn²⁺ on IA production. In the present study, a novel medium was developed for production of IA by varying PO₄ ^3- , Fe³⁺ and Cu²⁺ concentrations using response surface methodology, which alleviated the strong inhibitory effect of Mn²⁺ . The new medium contained 0.08 g KH₂ PO₄ , 3 g NH₄ NO₃ , 1 g MgSO₄ ·7H₂ O, 5 g CaCl₂ ·2 H₂ O, 0.83 mg FeCl₃ ·6H₂ O, 8 mg ZnSO₄ ·7H₂ O, and 45 mg CuSO₄ ·5H₂ O per liter. The fungus was able to produce IA very well in the presence of Mn²⁺ up to 100 ppm in the medium. This medium will be extremely useful for IA production in the presence of Mn²⁺ . This is the first report on the development of Mn²⁺ tolerant medium for IA production by A. terreus.

Autophagy is important to the acidogenic metabolism of Aspergillus niger

Significant phenotypic overlaps exist between autophagy and acidogenesis in Aspergillus niger. The possible role of autophagy in the acidogenic growth and metabolism of this fungus was therefore examined and the movement of cytosolic EGFP to vacuoles served to monitor this phenomenon. An autophagy response to typical as well as a metabolic inhibitor-induced nitrogen starvation was observed in A. niger mycelia. The vacuolar re-localization of cytosolic EGFP was not observed upon nitrogen starvation in the A. niger Δatg1 strain. The acidogenic growth of the fungus consisted of a brief log phase followed by an extended autophagy-like state throughout the idiophase of fermentation. Mycelia in the idiophase were highly vacuolated and EGFP was localized to the vacuoles but no autolysis was observed. Both autophagy and acidogenesis are compromised in Δatg1 and Δatg8 strains of A. niger. The acidogenic growth of the fungus thus appears to mimic a condition of nutrient limitation and is associated with an extended autophagy-like state. This crucial role of autophagy in acidogenic A. niger physiology could be of value in improving citric acid fermentation.

Microbial production of high value molecules using rayon waste material as carbon-source

Rayon filaments composed of regenerated cellulose are used as reinforcement materials in tires and to a lower extent in the clothing industry as personal protective equipment e.g. flame retardant cellulosic based materials. After use, these materials are currently transferred to landfills while chemical degradation does not allow the recovery of the cellulose (as glucose) nor the separation of the high valuable flame-retardant pigment. In this study, rayon fibers were enzymatically hydrolyzed to allow recovery of glucose and valuable additives. The glucose was successfully used as carbon source for the production of high value compounds such as itaconic acid, lactic acid and chitosan. 14.2 g/L of itaconic acid, 36.5 g/L of lactic acid and 39.2 g/L of chitosan containing biomass were produced from Escherichia coli, Lactobacillus paracasei and Aspergillus niger, respectively, comparable to yields obtained when using commercial glucose as carbon source.

Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

INTRODUCTION

Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies.

MATERIALS AND METHODS

The uptake of metabolites by microorganisms is well studied, but our knowledge of how and why they secrete different intracellular compounds is poor. The secretion of metabolites by microbial cells has traditionally been regarded as a consequence of intracellular metabolic overflow.

CONCLUSIONS

Here, we provide evidence based on time-series metabolomics data that microbial cells eliminate some metabolites in response to environmental cues, independent of metabolic overflow. Moreover, we review the different mechanisms of metabolite secretion and explore how this knowledge can benefit metabolic modeling and engineering.

Aspergillus niger Secretes Citrate to Increase Iron Bioavailability

Aspergillus niger has an innate ability to secrete various organic acids, including citrate. The conditions required for A. niger citrate overproduction are well described, but the physiological reasons underlying extracellular citrate accumulation are not yet fully understood. One of the less understood culture conditions is the requirement of growth-limiting iron concentrations. While this has been attributed to iron-dependent citrate metabolizing enzymes, this straightforward relationship does not always hold true. Here, we show that an increase in citrate secretion under iron limited conditions is a physiological response consistent with a role of citrate as A. niger iron siderophore. We found that A. niger citrate secretion increases with decreasing amounts of iron added to the culture medium and, in contrast to previous findings, this response is independent of the nitrogen source. Differential transcriptomics analyses of the two A. niger mutants NW305 (gluconate non-producer) and NW186 (gluconate and oxalate non-producer) revealed up-regulation of the citrate biosynthesis gene citA under iron limited conditions compared to iron replete conditions. In addition, we show that A. niger can utilize Fe(III) citrate as iron source. Finally, we discuss our findings in the general context of the pH-dependency of A. niger organic acid production, offering an explanation, besides competition, for why A. niger organic acid production is a sequential process influenced by the external pH of the culture medium.

Emerging biotechnologies for production of itaconic acid and its applications as a platform chemical

Recently, itaconic acid (IA), an unsaturated C5-dicarboxylic acid, has attracted much attention as a biobased building block chemical. It is produced industrially (&gt;80 g L−1) from glucose by fermentation with Aspergillus terreus. The titer is low compared with citric acid production (&gt;200 g L−1). This review summarizes the latest progress on enhancing the yield and productivity of IA production. IA biosynthesis involves the decarboxylation of the TCA cycle intermediate cis-aconitate through the action of cis-aconitate decarboxylase (CAD) enzyme encoded by the CadA gene in A. terreus. A number of recombinant microorganisms have been developed in an effort to overproduce it. IA is used as a monomer for production of superabsorbent polymer, resins, plastics, paints, and synthetic fibers. Its applications as a platform chemical are highlighted. It has a strong potential to replace petroleum-based methylacrylic acid in industry which will create a huge market for IA.

Evaluación de factores que afectan la bioacidulación de roca fosfórica bajo condiciones in vitro

El fósforo (P) es un nutriente esencial para el desarrollo de las plantas, desafortunadamente, su disponibilidad en muchos suelos es baja. Consecuentemente, los agricultores aplican altas cantidades de fertilizantes fosfóricos solubles, pero esto es ineficiente y costoso. El uso directo de roca fosfórica (RP) es muy atractivo por su bajo costo; sin embargo, es poco soluble y de baja eficiencia agronómica. Para superar esta limitación, hay un creciente interés en el uso de microorganismos del suelo capaces de disolverla y mejorar su valor como fertilizante. El objetivo de este trabajo fue evaluar el efecto que tienen algunos factores sobre la capacidad del hongo Mortierella sp. para disolver RP bajo condiciones in vitro. Estos factores son: (i) tiempo de incubación, (ii) tipo de RP, (iii) concentración inicial de P soluble y (iv) adición de vitaminas y micronutrientes. Despues del periodo de incubación se midió P en solución y pH. Los resultados indican que producto de la biodisolución de RP la más alta concentración de P en solución se alcanzó al día 5. Por otro lado, la biodisolución de RP fue reducida por la adición de vitaminas y micronutrientes y por el incremento en la concentración inicial de P soluble en el medio. Aunque la disolución microbiana fue más efectiva con la RP de Carolina del Norte, las RP del Huila y Santander presentaron un buen nivel de disolución en un periodo de tiempo corto. La bioacidulación mejorara la efectividad agronómica de la RP para su uso directo o a través de un proceso biotecnológico previo.

Phenotypes of gene disruptants in relation to a putative mitochondrial malate–citrate shuttle protein in citric acid-producing Aspergillus niger

The mitochondrial citrate transport protein (CTP) functions as a malate–citrate shuttle catalyzing the exchange of citrate plus a proton for malate between mitochondria and cytosol across the inner mitochondrial membrane in higher eukaryotic organisms. In this study, for functional analysis, we cloned the gene encoding putative CTP (ctpA) of citric acid-producing Aspergillus niger WU-2223L. The gene ctpA encodes a polypeptide consisting 296 amino acids conserved active residues required for citrate transport function. Only in early-log phase, the ctpA disruptant DCTPA-1 showed growth delay, and the amount of citric acid produced by strain DCTPA-1 was smaller than that by parental strain WU-2223L. These results indicate that the CTPA affects growth and thereby citric acid metabolism of A. niger changes, especially in early-log phase, but not citric acid-producing period. This is the first report showing that disruption of ctpA causes changes of phenotypes in relation to citric acid production in A. niger.

Contribution of arginase to manganese metabolism of Aspergillus niger

Aspects of manganese metabolism during normal and acidogenic growth of Aspergillus niger were explored. Arginase from this fungus was a Mn[II]-enzyme. The contribution of the arginase protein towards A. niger manganese metabolism was investigated using arginase knockout (D-42) and arginase over-expressing (ΔXCA-29) strains of A. niger NCIM 565. The Mn[II] contents of various mycelial fractions were found in the order: D-42 strain < parent strain < ΔXCA-29 strain. While the soluble fraction forms 60% of the total mycelial Mn[II] content, arginase accounted for a significant fraction of this soluble Mn[II] pool. Changes in the arginase levels affected the absolute mycelial Mn[II] content but not its distribution in the various mycelial fractions. The A. niger mycelia harvested from acidogenic growth media contain substantially less Mn[II] as compared to those from normal growth media. Nevertheless, acidogenic mycelia harbor considerable Mn[II] levels and a functional arginase. Altered levels of mycelial arginase protein did not significantly influence citric acid production. The relevance of arginase to cellular Mn[II] pool and homeostasis was evaluated and the results suggest that arginase regulation could occur via manganese availability.

Impact of butyric acid on butanol formation by Clostridium pasteurianum

The butanol yield of the classic fermentative acetone-butanol-ethanol (ABE) process has been enhanced in the past decades through the development of better strains and advanced process design. Nevertheless, by-product formation and the incomplete conversion of intermediates still decrease the butanol yield. This study demonstrates the potential of increasing the butanol yield from glycerol though the addition of small amounts of butyric acid. The impact of butyric acid was investigated in a 7L stirred tank reactor. The results of this study show the positive impact of butyric acid on butanol yield under pH controlled conditions and the metabolic stages were monitored via online measurement of carbon dioxide formation, pH value and redox potential. Butyric acid could significantly increase the butanol yield at low pH values if sufficient quantities of primary carbon source (glycerol) were present.

Direct fungal fermentation of lignocellulosic biomass into itaconic, fumaric, and malic acids: current and future prospects

Various economic and environmental sustainability concerns as well as consumer preference for bio-based products from natural sources have paved the way for the development and expansion of biorefining technologies. These involve the conversion of renewable biomass feedstock to fuels and chemicals using biological systems as alternatives to petroleum-based products. Filamentous fungi possess an expansive portfolio of products including the multifunctional organic acids itaconic, fumaric, and malic acids that have wide-ranging current applications and potentially addressable markets as platform chemicals. However, current bioprocessing technologies for the production of these compounds are mostly based on submerged fermentation, which necessitates physicochemical pretreatment and hydrolysis of lignocellulose biomass to soluble fermentable sugars in liquid media. This review will focus on current research work on fungal production of itaconic, fumaric, and malic acids and perspectives on the potential application of solid-state fungal cultivation techniques for the consolidated hydrolysis and organic acid fermentation of lignocellulosic biomass.

Comparing phosphorus mobilization strategies using Aspergillus niger for the mineral dissolution of three phosphate rocks

Phosphorus deficiencies are limiting crop production in agricultural soils worldwide. Locally available sources of raw phosphate rock (PR) are being recognized for their potential role in soil fertility improvement. Phosphorus bioavailability is essential for the efficiency of PRs and can be increased by acid treatments. The utilization of organic acid producing micro-organisms, notably Aspergillus niger, presents a sustainable alternative to the use of strong inorganic acids, but acid production of A. niger strongly depends on the mineral content of the growth media. This study compared the phosphorus mobilization efficiency of two biological treatments, namely addition of acidic cell-free supernatants from A. niger cultivations to PRs and the direct cultivation of A. niger with PRs. The results show that addition of PR to cultivations leads to significant differences in the profile of organic acids produced by A. niger. Additions of PR, especially igneous rocks containing high amounts of iron and manganese, lead to reduced citric acid concentrations. In spite of these differences, phosphorus mobilization was similar between treatments, suggesting that the simpler direct cultivation method was not inferior. In addition to citric acid, it is suggested that oxalic acid contributes to PR solubilization in direct cultivations with A. niger, which would benefit farmers in developing countries where conventional fertilizers are not adequately accessible.

Advances in citric acid fermentation by Aspergillus niger: biochemical aspects, membrane transport and modeling

Citric acid is regarded as a metabolite of energy metabolism, of which the concentration will rise to appreciable amounts only under conditions of substantive metabolic imbalances. Citric acid fermentation conditions were established during the 1930s and 1940s, when the effects of various medium components were evaluated. The biochemical mechanism by which Aspergillus niger accumulates citric acid has continued to attract interest even though its commercial production by fermentation has been established for decades. Although extensive basic biochemical research has been carried out with A. niger, the understanding of the events relevant for citric acid accumulation is not completely understood. This review is focused on citric acid fermentation by A. niger. Emphasis is given to aspects of fermentation biochemistry, membrane transport in A. niger and modeling of the production process.

Citric acid production

Citric acid is a commodity chemical produced and consumed throughout The World. It is used mainly in the food and beverage industry, primarily as an acidulant. Although it is one of the oldest industrial fermentations, its World production is still in rapid increasing. Global production of citric acid in 2007 was over 1.6 million tones. Biochemistry of citric acid fermentation, various microbial strains, as well as various substrates, technological processes and product recovery are presented. World production and economics aspects of this strategically product of bulk biotechnology are discussed.

Plant- and microbial-based mechanisms to improve the agronomic effectiveness of phosphate rock: a review

Deficiency in plant-available phosphorus is considered to be a major limiting factor to food production in many agricultural soils. Mineral resources are necessary to restore soil phosphorus content. In regions where conventional fertilizers are not used due to cost limitations or to mitigate adverse environmental effects, local sources of phosphate rock are being increasingly recognized for potential use as alternative phosphorus fertilizers. The main obstacle associated with using directly applied ground phosphate rock is that the phosphate released is often unable to supply sufficient plant-available phosphorus for crop uptake. Plantand microbial-based mechanisms are low-cost, appropriate technologies to enhance the solubilization and increase the agronomic effectiveness of phosphate rock. Common mechanisms of phosphate rock dissolution including proton and organic acid production will be reviewed for both plants and microorganisms. This review will also address possibilities for future research directions and applications to agriculture, as well as highlight ongoing research at the University of Guelph, Guelph, Canada.

Thermodynamic boundary conditions suggest that a passive transport step suffices for citrate excretion in Aspergillus and Penicillium

Excretion of organic acids, e.g. citrate, by anamorphic fungi is a frequent phenomenon in natural habitats and in laboratory cultures. In biotechnological processes for citrate production with Aspergillus niger extracellular citrate concentrations up to 1 mol l(-1) are achieved. Intracellular citrate concentrations are in the millimolar range. Therefore the question arises whether citrate excretion depends on active transport. In this article thermodynamic calculations are presented for citrate excretion by A. niger at an extracellular pH of 3 and by Penicillium simplicissimum at an extracellular pH of 7. From the results of these calculations it is concluded that in both cases a passive transport step suffices for citrate excretion.

Identification of genes associated with morphology in Aspergillus niger by using suppression subtractive hybridization

The morphology of citric acid production strains of Aspergillus niger is sensitive to a variety of factors, including the concentration of manganese (Mn(2+)). Upon increasing the Mn(2+) concentration in A. niger (ATCC 11414) cultures to 14 ppb or higher, the morphology switches from pelleted to filamentous, accompanied by a rapid decline in citric acid production. The molecular mechanisms through which Mn(2+) exerts effects on morphology and citric acid production in A. niger cultures have not been well defined, but our use of suppression subtractive hybridization has identified 22 genes responsive to Mn(2+). Fifteen genes were differentially expressed when A. niger was grown in media containing 1,000 ppb of Mn(2+) (filamentous form), and seven genes were expressed in 10 ppb of Mn(2+) (pelleted form). Of the 15 filament-associated genes, seven are novel and eight share 47 to 100% identity with genes from other organisms. Five of the pellet-associated genes are novel, and the other two genes encode a pepsin-type protease and polyubiquitin. All 10 genes with deduced functions are either involved in amino acid metabolism-protein catabolism or cell regulatory processes. Northern blot analysis showed that the transcripts of all 22 genes were rapidly enhanced or suppressed by Mn(2+). Steady-state mRNA levels of six selected filament-associated genes remained high during 5 days of culture in a filamentous state and remained low under pelleted growth conditions. The opposite behavior was observed for four selected pellet-associated genes. The full-length cDNA of the filament-associated clone, Brsa-25, was isolated. Antisense expression of Brsa-25 permitted pelleted growth and increased citrate production at concentrations of Mn(2+) that were higher than the parent strain could tolerate. These results suggest the involvement of the newly isolated genes in the regulation of A. niger morphology.

Blockage of methylcitrate cycle inhibits polyketide production in Aspergillus nidulans

Aspergillus nidulans produces the polyketide toxin sterigmatocystin (ST) of which the biosynthetic and pathway specific regulatory genes compose a stc gene cluster. A previous mutagenesis screen identified 23 mutants defective in production of ST. Five mutants constitute a single locus. Genetic complementation and sequencing analysis revealed the mutant locus to be mcsA encoding methylcitrate synthase that converts propionyl-CoA to methylcitrate. Feeding downstream products of methylcitrate synthase, methylcitrate and pyruvate, did not restore ST production in mcsA mutants, indicating that loss of methylcitrate cycle products is not the cause of the ST defect. However, propionate, a precursor for propionyl-CoA, inhibited ST production and induced transcription of mcsA in the wild type. Furthermore, propionate impaired formation of two polyketide spore pigments whereas overexpression of mcsA relieved inhibition of ST production by propionate. Transcription analyses revealed that disruption of mcsA did not affect expression of the specialized fatty acid synthase genes (stcJ and stcK) or polyketide synthase gene (stcA) required for formation of norsolorinic acid (NOR), the first stable intermediate in the ST biosynthetic pathway. Feeding studies showed that NOR but not hexanoic acid (the fatty acid produced by StcJ/StcK and primer unit of StcA) or malonate (source of the extender unit of StcA) restored ST production in the mcsA mutant. We hypothesize that excess buildup of propionyl-CoA in mcsA mutants interferes with polyketide synthase activity.

Aspergillus niger citric acid accumulation: do we understand this well working black box?

This Mini-Review summarizes the current knowledge on the biochemical and physiological events leading to massive citric acid accumulation by Aspergillus niger under industrially comparable conditions, thereby particularly emphasizing the roles of glycolytic flux and its control, excretion of citric acid from the mitochondria and the cytosol, and the critical fermentation variables. The potential of novel techniques for metabolic analysis and genomic approaches in understanding this fermentation is also discussed.

Characterization of an inducible citrate uptake system in Penicillium simplicissimum

When citrate was used as a sole source of carbon, citrate uptake by Penicillium simplicissimum increased 267-fold (if glucose-grown mycelium was adapted to citrate) or 1400-fold (if the fungus was grown on citrate) compared to glucose-grown mycelium. Inhibition of macromolecular synthesis prevented this stimulation of citrate uptake. Citrate uptake by glucose-grown mycelium was low (0.0015 nmol min(-1) (mg DW)(-1)) and most probably due to diffusion of undissociated citric acid. Citrate-adapted mycelium had a K(M) of 65 micromol l(-1) and a V(max) of 0.34 nmol min(-1) (mg DW)(-1). In citrate-grown mycelium K(M) was 318 micromol l(-1) and V(max) was 8.5 nmol min(-1) (mg DW)(-1). Citrate uptake was inhibited by sodium azide and uncouplers (TCS, 3,3',4',5-tetrachlorosalicylanilide; FCCP, carbonyl cyanide p-trifluoromethoxyphenyl-hydrazone). Because of this we postulate that the induced citrate uptake must be an active transport process. The pH optimum of citrate uptake was between pH 6 and 7. EDTA and Mg2+, Mn2+, Cu2+, Zn2+, Fe2+, Ca2+ only weakly influenced the induced citrate uptake. The properties of citrate uptake by Aspergillus niger and P. simplicissimum are compared.

The biochemistry of citric acid accumulation by Aspergillus niger

Fungi, in particular Aspergilli, are well known for their potential to overproduce a variety of organic acids. These microorganisms have an intrinsic ability to accumulate these substances and it is generally believed that this provides the fungi with an ecological advantage, since they grow rather well at pH 3 to 5, while some species even tolerate pH values as low as 1.5. Organic acid production can be stimulated and in a number of cases conditions have been found that result in almost quantitative conversion of carbon substrate into acid. This is exploited in large-scale production of a number of organic acids like citric-, gluconic- and itaconic acid. Both in production volume as well as in knowledge available, citrate is by far the major organic acid. Citric acid (2-hydroxy-propane-1,2,3-tricarboxylic acid) is a true bulk product with an estimated global production of over 900 thousand tons in the year 2000. Till the beginning of the 20th century, it was exclusively extracted from lemons. Since the global market was dominated by an Italian cartel, other means of production were sought. Chemical synthesis was possible, but not suitable due to expensive raw materials and a complicated process with low yield. The discovery of citrate accumulation by Aspergillus niger led to a rapid development of a fermentation process, which only a decade later accounted for a large part of the global production. The application of citric acid is based on three of its properties: (1) acidity and buffer capacity, (2) taste and flavour, and (3) chelation of metal ions. Because of its three acid groups with pKa values of 3.1, 4.7 and 6.4, citrate is able to produce a very low pH in solution, but is also useful as a buffer over a broad range of pH values (2 to 7). Citric acid has a pleasant acid taste which leaves little aftertaste. It sometimes enhances flavour, but is also able to mask sweetness, such as the aspartame taste in diet beverages. Chelation of metal ions is a very important property that has led to applications such as antioxidant and preservative. Moreover, it is a "natural" substance and fully biodegradable.

Efflux of organic acids in Penicillium simplicissimum is an energy-spilling process, adjusting the catabolic carbon flow to the nutrient supply and the activity of catabolic pathways

Continuous cultivation was used to study the effect of glucose, ammonium, nitrate or phosphate limitation on the excretion of tricarboxylic acid (TCA) cycle intermediates by Penicillium simplicissimum. Additionally, the effect of benzoic acid, salicylhydroxamic acid (SHAM) and 2,4-dinitrophenol on TCA cycle intermediates was studied. The physiological state of the fungus was characterized by its glucose and O(2) consumption, its CO(2) production, its intra- and extracellular concentrations of TCA cycle intermediates, as well as by its biomass yield, its maintenance coefficient and its respiratory quotient. The excretion of TCA cycle intermediates was observed during ammonium-, nitrate- and phosphate-limited growth. The highest productivity was found with phosphate-limited growth. The respiratory quotient was 1.3 under ammonium limitation and 0.7 under phosphate limitation. Citrate was always the main excreted intermediate. This justifies calling this excretion an energy-spilling process, because citrate excretion avoids the synthesis of too much NADH. The addition of benzoic acid further increased the excretion of TCA cycle intermediates by ammonium-limited hyphae. A SHAM-sensitive respiration was constitutively present during ammonium-limited growth of the fungus. The sum of the excreted organic acids was negatively correlated with the biomass yield (Y(GlcX)).

Metabolism of citric acid production by Aspergillus niger: model definition, steady-state analysis and constrained optimization of citric acid production rate

In an attempt to provide a rational basis for the optimization of citric acid production by A. niger, we developed a mathematical model of the metabolism of this filamentous fungus when in conditions of citric acid accumulation. The present model is based in a previous one, but extended with the inclusion of new metabolic processes and updated with currently available kinetic data. Among the different alternatives to represent the system behavior we have chosen the S-system representation within power-law formalism. This type of representation allows us to verify not only the ability of the model to exhibit a stable steady state of the integrated system but also the robustness and quality of the representation. The model analysis is shown to be self-consistent, with a stable steady state, and in good agreement with experimental evidence. Moreover, the model representation is sufficiently robust, as indicated by sensitivity and steady-state and dynamic analyses. From the steady-state results we concluded that the range of accuracy of the S-system representation is wide enough to model realistic deviations from the nominal steady state. The dynamic analysis indicated a reasonable response time, which provided further indication that the model is adequate. The extensive assessment of the reliability and quality of the model put us in a position to address questions of optimization of the system with respect to increased citrate production. We carried out the constrained optimization of A. niger metabolism with the goal of predicting an enzyme activity profile yielding the maximum rate of citrate production, while, at the same time, keeping all enzyme activities within predetermined, physiologically acceptable ranges. The optimization is based on a method described and tested elsewhere that utilizes the fact that the S-system representation of a metabolic system becomes linear at steady state, which allows application of linear programming techniques. Our results show that: (i) while the present profile of enzyme activities in A. niger at idiophase steady state yields high rates of citric acid production, it still leaves room for changes and suggests possible optimization of the activity profile to over five times the basal rate synthesis; (ii) when the total enzyme concentration is allowed to double its basal value, the citric acid production rate can be increased by more than 12-fold, and even larger values can be attained if the total enzyme concentration is allowed to increase even more (up to 50-fold when the total enzyme concentration may rise up to 10-fold the basal value); and (iii) the systematic search of the best combination of subsets of enzymes shows that, under all conditions assayed, a minimum of 13 enzymes need be modified if significant increases in citric acid are to be obtained. This implies that improvements by single enzyme modulation are unlikely, which is in agreement with the findings of some investigators in this and other fields.

Fungal production of citric and oxalic acid: importance in metal speciation, physiology and biogeochemical processes

The production of organic acids by fungi has profound implications for metal speciation, physiology and biogeochemical cycles. Biosynthesis of oxalic acid from glucose occurs by hydrolysis of oxaloacetate to oxalate and acetate catalysed by cytosolic oxaloacetase, whereas on citric acid, oxalate production occurs by means of glyoxylate oxidation. Citric acid is an intermediate in the tricarboxylic acid cycle, with metals greatly influencing biosynthesis: growth limiting concentrations of Mn, Fe and Zn are important for high yields. The metal-complexing properties of these organic acids assist both essential metal and anionic (e.g. phosphate) nutrition of fungi, other microbes and plants, and determine metal speciation and mobility in the environment, including transfer between terrestrial and aquatic habitats, biocorrosion and weathering. Metal solubilization processes are also of potential for metal recovery and reclamation from contaminated solid wastes, soils and low-grade ores. Such 'heterotrophic leaching' can occur by several mechanisms but organic acids occupy a central position in the overall process, supplying both protons and a metal-complexing organic acid anion. Most simple metal oxalates [except those of alkali metals, Fe(III) and Al] are sparingly soluble and precipitate as crystalline or amorphous solids. Calcium oxalate is the most important manifestation of this in the environment and, in a variety of crystalline structures, is ubiquitously associated with free-living, plant symbiotic and pathogenic fungi. The main forms are the monohydrate (whewellite) and the dihydrate (weddelite) and their formation is of significance in biomineralization, since they affect nutritional heterogeneity in soil, especially Ca, P, K and Al cycling. The formation of insoluble toxic metal oxalates, e.g. of Cu, may confer tolerance and ensure survival in contaminated environments. In semi-arid environments, calcium oxalate formation is important in the formation and alteration of terrestrial subsurface limestones. Oxalate also plays an important role in lignocellulose degradation and plant pathogenesis, affecting activities of key enzymes and metal oxido-reduction reactions, therefore underpinning one of the most fundamental roles of fungi in carbon cycling in the natural environment. This review discusses the physiology and chemistry of citric and oxalic acid production in fungi, the intimate association of these acids and processes with metal speciation, physiology and mobility, and their importance and involvement in key fungal-mediated processes, including lignocellulose degradation, plant pathogenesis and metal biogeochemistry.