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As natural metabolites, organic acids have been widely applied in food, pharmaceutical, and bio-based materials industries. Particularly, the short-chain organic acids, including C2, C3, C4, C5, and C6 organic acids, are necessary intermediate metabolites in cells and are also alternatives to some commercial chemical products. As the necessary metabolites in cells, most major short-chain organic acids can be produced through microbial fermentation. Specifically, with the development of synthetic biology, metabolic engineering could endow cells with the ability to produce more short-chain organic acid products including propionic acid, pyruvate, lactic acid, 3-hydroxypropionic acid, malic acid, succinic acid, fumaric acid, butyric acid, itaconic acid, α-ketoglutaric acid, glutaric acid, citric acid, gluconic acid, muconic acid, adipic acid, xylonic acid, and so on. The recent advances in the biological production of short-chain organic acids, as well as the challenges and perspectives, are summarized in this review to promote the generation of microbial cell factories for the production of short-chain organic acids.Key points• Outlines the production strategy of short-chain organic acids• Provide guidance for efficient synthesis of short-chain organic acids• Impacts the necessary factor of acid resistance on the successful production of host cells

Following the huge success of the first edition, which has become THE reference source for everyone working in the field, this long-awaited, completely updated edition features almost 50% new content.

Microorganisms encounter acid stress during multiple bioprocesses. Microbial species have therefore developed a variety of resistance mechanisms. The damage caused by acidic environments is mitigated through the maintenance of pH homeostasis, cell membrane integrity and fluidity, metabolic regulation, and macromolecule repair. The acid tolerance mechanisms can be used to protect probiotics against gastric acids during the process of food intake, and can enhance the biosynthesis of organic acids. The combination of systems and synthetic biology technologies offers new and wide prospects for the industrial applications of microbial acid tolerance mechanisms. In this review, we summarize acid stress response mechanisms of microbial cells, illustrate the application of microbial acid tolerance in industry, and prospect the introduction of systems and synthetic biology to further explore the acid tolerance mechanisms and construct a microbial cell factory for valuable chemicals.

Soil contamination with toxic heavy metals [such as arsenic (As)] is becoming a serious global problem due to rapid development of social economy. Silicon (Si), being an important fertilizer element, has been found effective in enhancing plant tolerance against biotic and abiotic stresses. For this purpose, we have designed the current experiment to explore the contribution of Si in mediating growth and eco-physiology by alleviating As stress in a leafy vegetable spinach ( Spinacia oleracea L.). Fifteen days old seedlings of S. oleracea were subjected to the different concentrations of As, i.e., 0 (no As), 50, and 100 µM in the soil which were also supplied with the different exogenous levels of Si, i.e., 0 (no Si), 1.5, and 3 mM. Results from the present study revealed that the As toxicity induced a substantial decreased in shoot length, root length, number of leaves, leaf area, shoot fresh weight, root fresh weight, shoot dry weight, root dry weight, chlorophyll-a, chlorophyll-b, total chlorophyll, carotenoid content, net photosynthesis, stomatal conductance, transpiration rate, soluble sugar, reducing sugar, non-reducing sugar contents, calcium (Ca 2+ ), magnesium (Mg 2+ ), iron (Fe 2+ ), and phosphorus (P) contents in the roots and shoots of the plants. In contrast, increasing levels of As in the soil significantly ( P  < 0.05) increased As concentration in the roots and shoots of the plants, phenolic content, malondialdehyde (MDA), hydrogen peroxide (H 2 O 2 ), electrolyte leakage (EL), fumaric acid, acetic acid, citric acid, formic acid, malic acid, oxalic acid contents in the roots of the plants. Although, the activities of enzymatic antioxidants such as superoxidase dismutase, peroxidase, catalase, ascorbate peroxidase in the roots and shoots of the plants and non-enzymatic such as phenolic, flavonoid, ascorbic acid, and anthocyanin contents were initially increased with the exposure of 50 µM As, but decreased by the increasing the As concentration 100 µM in the soil. Addition of Si into the soil significantly alleviated As toxicity effects on S . oleracea by improving photosynthetic capacity and ultimately plant growth. Increased activities of antioxidant enzymes in Si-treated plants seem to play a role in capturing stress-induced reactive oxygen species as was evident from lower level of MDA, H 2 O 2 , MDA, and EL in Si-treated plants. Research findings, therefore, suggested that Si application can ameliorate As toxicity in S . oleracea seedlings and resulted in improved plant growth and composition under metal stress as depicted by balanced exudation of organic acids.

Fleshy fruit acidity is an important component of fruit organoleptic quality and is mainly due to the presence of malic and citric acids, the main organic acids found in most ripe fruits. The accumulation of these two acids in fruit cells is the result of several interlinked processes that take place in different compartments of the cell and appear to be under the control of many factors. This review combines analyses of transcriptomic, metabolomic, and proteomic data, and fruit process-based simulation models of the accumulation of citric and malic acids, to further our understanding of the physiological mechanisms likely to control the accumulation of these two acids during fruit development. The effects of agro-environmental factors, such as the source:sink ratio, water supply, mineral nutrition, and temperature, on citric and malic acid accumulation in fruit cells have been reported in several agronomic studies. This review sheds light on the interactions between these factors and the metabolism and storage of organic acids in the cell.

This research was supported by King Abdullah University of Science and Technology (KAUST) through baseline funding and workshop funding to C.M.D. Support from the Australian Research Council through grants LIEF Project LE170100219, DE160100443, DE170101524, DP150103286, DP150102092, DP160100248, DE130101084, LP160100242 and LE140100083 is acknowledged. J.J.M. was supported by the Netherlands Earth System Science Center. J.W.F. was supported by the US National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research programme under Grant Number DEB-1237517. D.K.-J. received financial support from the Independent Research Fund Denmark (8021-00222B, CARMA) and the COCOA project under the BONUS programme, funded by the EU 7th Framework Programme and the Danish Research Council. A.A.-O. was supported by an “Obra Social la Caixa” fellowship (LCF/BQ/ES14/10320004). A.A.-O. and P.M. acknowledge the support by the Generalitat de Catalunya (grant 2017 SGR-1588). This work is contributing to the ICTA ‘Unit of Excellence’ (MinECo, MDM2015-0552). H.K.’s input is a contribution to the CESEA project (NE/L001535/1) funded by NERC. T.K., K.W. and T.T. were supported by JSPS KAKENHI (18H04156) and the Environment Research and Technology Development Fund (S-14) of the Ministry of the Environment, Japan. J.M.S. was supported by the National Science Foundation under South Florida Water, Sustainability and Climate grant EAR-1204079. I.M. was supported by a Juan de la Cierva Formación post-doctoral fellowship from the Spanish Ministry of Science, Innovation and Universities.

Among the most important factors influencing beer quality is the presence of well-adjusted amounts of higher alcohols and esters. Thus, a heavy body of literature focuses on these substances and on the parameters influencing their production by the brewing yeast. Additionally, the complex metabolic pathways involved in their synthesis require special attention. More than a century of data, mainly in genetic and proteomic fields, has built up enough information to describe in detail each step in the pathway for the synthesis of higher alcohols and their esters, but there is still place for more. Higher alcohols are formed either by anabolism or catabolism (Ehrlich pathway) of amino acids. Esters are formed by enzymatic condensation of organic acids and alcohols. The current paper reviews the up-to-date knowledge in the pathways involving the synthesis of higher alcohols and esters by brewing yeasts. Fermentation parameters affecting yeast response during biosynthesis of these aromatic substances are also fully reviewed.

Background Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates. Methods The compositions of bacterial and fungal communities from the roots and rhizosphere of wheat ( Triticum aestivum L. ) under four levels of long-term inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified. Results ROC levels varied dramatically across wheat growth stages and correlated more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including Arthrobacter , Bacillus and Devosia , correlated significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels. Conclusions Our results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage demostrated a stronger influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to N fertilization, and their abundance correlated significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.

BACKGROUND AND AIM: Recycled sources of phosphorus (P), such as struvite extracted from wastewater, have potential to substitute for more soluble manufactured fertilisers and help reduce the long-term threat to food security from dwindling finite reserves of phosphate rock (PR). This study aimed to determine whether struvite could be a component of a sustainable P fertiliser management strategy for arable crops. METHODS: A combination of laboratory experiments, pot trials and mathematical modelling of the root system examined the P release properties of commercial fertiliser-grade struvite and patterns of P uptake from a low-P sandy soil by two different crop types, in comparison to more soluble inorganic P fertilisers (di-ammonium phosphate (DAP) and triple super phosphate (TSP)). RESULTS: Struvite had greatly enhanced solubility in the presence of organic acid anions; buckwheat, which exudes a high level of organic acids, was more effective at mobilising struvite P than the low level exuder, spring wheat. Struvite granules placed with the seed did not provide the same rate of P supply as placed DAP granules for early growth of spring wheat, but gave equivalent rates of P uptake, yield and apparent fertiliser recovery at harvest, even though only 26 % of struvite granules completely dissolved. Fertiliser mixes containing struvite and DAP applied to spring wheat have potential to provide both optimal early and late season P uptake and improve overall P use efficiency. CONCLUSIONS: We conclude that the potential resource savings and potential efficiency benefits of utilising a recycled slow release fertiliser like struvite offers a more sustainable alternative to only using conventional, high solubility, PR-based fertilisers.

peels are usually discarded as wastes; however, they are rich sources of Vitamin C, fibre, and many nutrients, including phenolics and flavonoids which are also good antioxidant agents. This study aimed to examine phytochemical composition and antioxidant capabilities of peel extracted conventionally with different methanol/water, ethanol/water, and acetone/water solvents. peels were subjected to extraction with 100%, 70% and 50% of methanol, ethanol, and acetone, respectively, as well as hot water extraction. Antioxidant activities of the peel extracts were examined via the 2,2-diphenylpicrylhydrazyl (DPPH) free radical scavenging activity, ferric reducing antioxidant power (FRAP) assay, and oxygen radical absorbance capacity (ORAC) assay. Total phenolic content and total flavonoid content of the extracts were measured via the Folin-Ciocalteau method and the aluminium chloride colorimetric method, respectively. Phenolic acid and organic acid composition of the peel extracts were further determined via high performance liquid chromatography (HPLC) while flavonoid content was identified via ultra performance liquid chromatography (UPLC). DPPH radical scavenging activity of peel extracts varied from 8.35 to 18.20 mg TE/g, FRAP ranged from 95.00 to 296.61 mmol Fe(II)/g, while ORAC value ranged from 0.31 to 0.92 mol TE/g. Significant level of association between the assays was observed especially between TPC and FRAP (R-square = 0.95,  < 0.0001). TPC of various peel extracts ranged from 12.08 to 38.24 mg GAE/g, with 70% acetone/water extract (AEC) showing the highest TPC. TFC ranged from 1.90 to 5.51 mg CE/g. Extraction yield ranged from 0.33 to 0.54 g/g DW and tended to increase with increasing water concentration in the solvent. In the phytochemical investigation, five phenolic acids were identified using HPLC, including gallic acid, protocatechuic acid, 4-hydroxybenzoic acid, caffeic acid and ferulic acid. A total of five organic acids including lactic acid, citric acid, L-mallic acid, kojic acid and ascorbic acid were quantified via HPLC. In addition, concentrations of six flavonoids including catechin, epigallocatechin, vitexin, rutin, luteolin and apigenin were determined via UPLC. Phytochemicals including phenolics and flavonoids in peel extracts exhibited good antioxidant properties. Among the extracts, 70% AEC with highest TPC and high TFC content showed greatest antioxidant activity in all three assays. Different phenolic acids, organic acids and flavonoids were also identified from the extracts. This study indicated that peels contained potential antioxidant compounds which could be exploited as value added products in the food industry.