Strategies for Natural Products Discovery from Uncultured Microorganisms

Microorganisms are highly regarded as a prominent source of natural products that have significant importance in many fields such as medicine, farming, environmental safety, and material production. Due to this, only tiny amounts of microorganisms can be cultivated under standard laboratory conditions, and the bulk of microorganisms in the ecosystems are still unidentified, which restricts our knowledge of uncultured microbial metabolism. However, they could hypothetically provide a large collection of innovative natural products. Culture-independent metagenomics study has the ability to address core questions in the potential of NP production by cloning and analysis of microbial DNA derived directly from environmental samples. Latest advancements in next generation sequencing and genetic engineering tools for genome assembly have broadened the scope of metagenomics to offer perspectives into the life of uncultured microorganisms. In this review, we cover the methods of metagenomic library construction, and heterologous expression for the exploration and development of the environmental metabolome and focus on the function-based metagenomics, sequencing-based metagenomics, and single-cell metagenomics of uncultured microorganisms.     

Prediction of isocratic nonaqueous reversed-phase high-performance liquid chromatography retention parameters and response factors of triacylglycerols detected by an ultraviolet-diode array-evaporative light-scattering on-line system

Nonaqueous reversed-phase high-performance liquid chromatography of 10 homogeneous triacylglycerol molecular species (TAG), both saturated and unsaturated, is carried out. The eluate from the column is detected by an ultraviolet diode array detector (DAD) on-line with an evaporative light-scattering detector (ELSD). The retention parameters (as selectivities, alpha) for 220 TAGs are determined, and the obtained values are related to the following structural parameters: total carbon number; mono-, di-, and triunsaturated fatty acid residues number/molecule; and monounsaturated fatty acid carbon number. Multiple regression analysis is carried out to obtain a relationship for the prediction of alpha values of any TAG when the same experimental conditions are used. In regard to the quantitative analysis of the separated TAG species, the dependence of response of the two on-line detectors on the aforementioned structural parameters is studied. Three different wavelengths (205, 210, and 215 nm) are considered for TAG detection by DAD; in each case, the obtained multiple regression model shows a good correlation between the dependent variable and predictive values of the TAG species (response factors and considered structural parameters, respectively). The ELSD gives responses exponentially related to injected amounts. Also, in this case, an attempt to relate the response factors of each considered detector to some structural parameters of TAG species is carried out. The results of this study are used to analyze the TAG fraction from an olive oil.     

Research Progress of the Biosynthesis of Natural Bio-Antibacterial Agent Pulcherriminic Acid in Bacillus

Pulcherriminic acid is a cyclic dipeptide found mainly in Bacillus and yeast. Due to the ability of pulcherriminic acid to chelate Fe³⁺ to produce reddish brown pulcherrimin, microorganisms capable of synthesizing pulcherriminic acid compete with other microorganisms for environmental iron ions to achieve bacteriostatic effects. Therefore, studying the biosynthetic pathway and their enzymatic catalysis, gene regulation in the process of synthesis of pulcherriminic acid in Bacillus can facilitate the industrial production, and promote the wide application in food, agriculture and medicine industries. After initially discussing, this review summarizes current research on the synthesis of pulcherriminic acid by Bacillus, which includes the crystallization of key enzymes, molecular catalytic mechanisms, regulation of synthetic pathways, and methods to improve efficiency in synthesizing pulcherriminic acid and its precursors. Finally, possible applications of pulcherriminic acid in the fermented food, such as Chinese Baijiu, applying combinatorial biosynthesis will be summarized.     

Poly-β-hydroxybutyrate and Exopolysaccharide Biosynthesis by Bacterial Isolates from Pigeonpea [<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millsp] Root Nodules

The bacterial strains that are able to produce biopolymers that are applied in industrial sectors present a source of renewable resources. Some microorganisms are already applied at several industrial sectors, but the prospecting of new microbes must bring microorganisms that are feasible to produce interesting biopolymers more efficiently and in cheaper conditions. Among the biopolymers applied industrially, polyhydroxybutyrate (PHB) and exopolysaccharides (EPS) stand out because of its applications, mainly in biodegradable plastic production and in food industry, respectively. In this context, the capacity of bacteria isolated from pigeonpea root nodules to produce EPS and PHB was evaluated, as well as the cultural characterization of these isolates. Among the 38 isolates evaluated, the majority presented fast growth and ability to acidify the culture media. Regarding the biopolymer production, five isolates produced more than 10 mg PHB per liter of culture medium. Six EPS producing bacteria achieved more than 200 mg EPS per liter of culture medium. Evaluating different carbon sources, the PHB productivity of the isolate 24.6b reached 69% of cell dry weight when cultured with starch as sole carbon source, and the isolate 8.1c synthesized 53% PHB in dry cell biomass and more than 1.3 g L⁻¹ of EPS when grown using xylose as sole carbon source.     

基于微生物作为智能模板的电催化剂制备与应用研究进展

通过电催化实现可再生能源的存储与转化对于改善能源结构、保护生态环境、实现碳达峰和碳中和的国家战略具有重大意义。而开发低成本、高效的电催化剂成为全世界科学家共同面对的挑战。微生物在自然界中广泛存在,具有结构、组成和代谢丰富的特点,可以成为电催化剂的模板以及碳、磷、硫等非金属元素以及金属元素的来源,而且具有无毒、生产可重复性好、易于规模化等优点,已成为电催化剂制备的新趋势。对此,本文综述了微生物“智能”引导制备电催化剂的发展及在电催化析氢(HER)、电催化析氧(OER)、氧还原反应(ORR)、二氧化碳还原(CO₂RR)、锂电池(LBs)等领域的应用现状。希望有助于推动微生物代谢与催化剂微纳结构关系以及与催化反应的构效关系的深入理解,最后针对这类材料的问题挑战及其未来发展方向进行了探讨与展望。     

Effect of Biodiesel-derived Raw Glycerol on 1,3-Propanediol Production by Different Microorganisms

The microbial production of 1,3-propanediol (1,3-PD) from raw glycerol, a byproduct of biodiesel production, is economically and environmentally advantageous. Although direct use of raw glycerol without any pretreatment is desirable, previous studies have reported that this could cause inhibition of microbial growth. In this study, we investigated the effects of raw glycerol type, different microorganisms, and pretreatment of raw glycerol on the production of 1,3-PD. Raw glycerol from waste vegetable-oil-based biodiesel production generally caused more inhibition of 1,3-PD production and microbial growth compared to raw glycerol from soybean-oil-based biodiesel production. In addition, two raw glycerol types produced from two biodiesel manufacturers using waste vegetable oil exhibited different 1,3-PD production behavior, partially due to different amounts of methanol included in the raw glycerol from the two biodiesel manufacturers. Klebsiella strains were generally resistant to all types of raw glycerol while the growth of Clostridium strains was variably inhibited depending on the type of raw glycerol. The 1,3-PD production of the Clostridium strains using acid-pretreated raw glycerol was significantly enhanced compared to that with raw glycerol, demonstrating the feasibility of using raw glycerol for 1,3-PD production by various microorganisms.     

Bioconversion of Corncob Acid Hydrolysate into Microbial Oil by the Oleaginous Yeast Lipomyces starkeyi

For the first time, corncob acid hydrolysate was used for microbial oil production by the oleaginous yeast Lipomyces starkeyi. After hydrolysis by dilute sulfuric acid, corncob could turn into an acid hydrolysate with a sugar concentration of about 42.3 g/L. Detoxified by overliming and absorption with activated carbon, the corncob hydrolysate could be used by L. starkeyi efficiently that a total biomass of 17.2 g/L with a lipid content of 47.0 % (corresponding to a lipid yield of 8.1 g/L) and a lipid coefficient of 20.9 could be obtained after cultivation on the corncob hydrolysate for 8 days. Therefore, L. starkeyi is a promising strain for microbial oil production from lignocellulosic biomass. Glucose and xylose were used by L. starkeyi simultaneously during lipid fermentation while arabinose could not be utilized by it. Besides, the lipid composition of L. starkeyi was similar to that of vegetable oils; thus, it is a promising feedstock for biodiesel production.     

Compositional Shift in Fatty Acid Profiles of Lipids Obtained from Oleaginous Yeasts upon the Addition of Essential Oil from <Emphasis Type="Italic">Citrus sinensis</Emphasis> L.

Tailoring lipids from oleaginous yeasts to contain specific types of fatty acid is of considerable interest to food, fuel, and pharmaceutical industries. In this study, the essential oil obtained from Citrus sinesus L. has been used to alter the fatty acid composition of two common oleaginous yeasts, Rhodosporidium toruloides and Cryptococcus curvatus. With increasing levels of essential oil in the medium, the metabolic flux of the fatty acid biosynthesis pathway shifted towards saturated fatty acid production. Essential oil reduced the activities of elongase and ?9 desaturase. This made the lipid obtained from both these yeasts rich in saturated fatty acids. At certain specific concentrations of the essential oil in the medium, the lipid obtained from R. toruloides and C. curvatus cultures was similar to mahuwa butter and palm oil, respectively. Limonene is the major constituents of orange essential oil. Its effect on one of the oleaginous yeasts, R. toruloides, was also studied separately. Effects similar to orange essential oil were obtained with limonene. Thus, we can conclude that limonene in orange essential oil brings about compositional change of microbial lipid produced in this organism.     

A Review of Hydrogen Production by Photosynthetic Organisms Using Whole-Cell and Cell-Free Systems

Molecular hydrogen is a promising currency in the future energy economy due to the uncertain availability of finite fossil fuel resources and environmental effects from their combustion. It also has important uses in the production of fertilizers and platform chemicals as well as in upgrading conventional fuels. Conventional methods for producing molecular hydrogen from natural gas produce carbon dioxide and use a finite resource as feedstock. However, these issues can be overcome by using light energy from the Sun combined with microorganisms and their molecular machinery capable of photosynthesis. In the presence of light, the proteins involved in photosynthesis coupled with appropriate catalysts in higher plants, algae, and cyanobacteria can produce molecular hydrogen, and optimization via genetic modifications and biomolecular engineering further improves production rates. In this review, we will discuss techniques that have been utilized to improve rates of hydrogen production in biological systems based on the protein machinery of photosynthesis coupled with appropriate catalysts. We will also suggest areas for improvement and future directions for work in the field.     

Bacterial production of PHA from lactose and cheese whey permeate

Due to the large availability of agro-industry wastes containing potentially exploitable substrates, such as whey from dairy industry, a study on the bacterial conversion of lactose and whey permeate to poly(β-hydroxyalkanoate) (PHA) was undertaken. A first approach was carried out on culture collection strains. Among a number of strains tested, Hydrogenophaga pseudoflava DSM 1034 and Sinorhizobium meliloti 41 were found to grow on lactose and produce PHA. These findings suggested to investigate among a wider range of microorganisms by directly isolating new strains from soil. A number of soil bacteria were first isolated on a minimal medium containing lactose as unique carbon source and PHA-accumulating traits were then investigated. Three isolates, identified by 16S rDNA sequence analysis as Sinorhizobium sp., Bacillus megaterium and Bacillus sp., were selected for their efficient growth and PHA production using lactose as carbon source. The same strains were also tested for their ability to accumulate PHA by direct fermentation of whey and whey permeate. Our results suggest that production of the polymer from cheese whey or whey permeate may be possible, although further research is needed to determine whether these microorganisms have the potential for commercial production of such biodegradable polymers.     

Old chromophores, new photoactivation paradigms, trendy applications: flavins in blue light-sensing photoreceptors

The knowledge on the mechanisms by which blue light (BL) is sensed by diverse and numerous organisms, and of the physiological responses elicited by the BL photoreceptors, has grown remarkably during the last two decades. The basis for this "blue revival" was set by the identification and molecular characterization of long sought plant BL sensors, employing flavins as chromophores, chiefly cryptochromes and phototropins. The latter photosensors are the foundation members of the so-called light, oxygen, voltage (LOV)-protein family, largely spread among archaea, bacteria, fungi and plants. The accumulation of sequenced microbial genomes during the last years has added the BLUF (Blue Light sensing Using FAD) family to the BL photoreceptors and yielded the opportunity for intense "genome mining," which has presented to us the intriguing wealth of BL sensing in prokaryotes. In this contribution we provide an update of flavin-based BL sensors of the LOV and BLUF type, from prokaryotic microorganisms, with special emphasis to their light-activation pathways and molecular signal-transduction mechanisms. Rather than being a fully comprehensive review, this research collects the most recent discoveries and aims to unveil and compare signaling pathways and mechanisms of BL sensors.     

Cryptic Chemical Communication: Secondary Metabolic Responses Revealed by Microbial Co‐culture

Microbial secondary metabolites (SMs) have long been viewed as a significant source of novel pharmaceutical and agrochemical molecules. With the increasing availability of genomic data, numerous biosynthetic gene clusters (BGCs) have been discovered. Despite the presence of tens of thousands of BGCs that can theoretically produce extremely diverse SMs, many gene clusters remain in a silent state under axenic culture conditions. Co‐culture is a promising research approach as it stimulates the expression of cryptic BGCs to produce novel metabolites and also mimics natural interspecies interactions in a laboratory environment. In recent years, the roles of SMs in microbial communication have caught the attention of researchers and our understanding of microbes and their production of remarkable SMs has improved. SMs may be extensively involved in a variety of communication events among microorganisms. We herein summarize certain representative findings in the field of chemical communication involving SMs in co‐culture systems.     

Harnessing Indigenous Plant Seed Oil for the Production of Bio-fuel by an Oleaginous Fungus,Cunninghamella blakesleeana- JSK2, Isolated from Tropical Soil

Cunninghamella blakesleeana- JSK2, a gamma-linolenic acid (GLA) producing tropical fungal isolate, was utilized as a tool to evaluate the influence of various plant seed oils on biomass, oleagenicity and bio-fuel production. The fungus accumulated 26 % total lipid of their dry biomass (2 g/l) and 13 % of GLA in its total fatty acid. Among the various plant seed oils tested as carbon sources for biotransformation studies, watermelon oil had an effect on biomass and total lipid increasing up to 9.24 g/l and 34 % respectively. Sunflower, pumpkin, and onion oil increased GLA content between 15–18 %. Interestingly, an indigenous biodiesel commodity, Pongamia pinnata oil showed tremendous effect on fatty acid profile in C. blakesleeana- JSK2, when used as a sole source of carbon. There was complete inhibition of GLA from 13 to 0 % and increase in oleic acid content, one of the key components of biodiesel to 70 % (from 20 % in control). Our results suggest the potential application of indigenous plant seed oils, particularly P. pinnata oil, for the production of economically valuable bio-fuel in oleaginous fungi in general, and C. blakesleeana- JSK2, in particular.     

Photothermal catalysis for CO2 conversion

The conversion of carbon dioxide into useful fuels or chemical feedstocks is of great importance for achieving carbon emission peak and carbon neutrality. The harvesting and conversion of solar energy will provide a sustainable and environmentally friendly energy source for human production and living. Very recently, photothermal catalysis has been proved to exhibit great advantages in reducing the reaction temperature, promoting the catalytic activity, and manipulating the reaction pathway in comparison with traditional thermal catalysis. In this review, we firstly introduced the fundamental mechanisms and categories of photothermal catalysis to understand the synergy or the difference between photochemical and thermochemical reaction pathways. Subsequently, the criteria and strategies for photothermal catalyst design are discussed in order to inspire the development of high-efficiency photothermal catalytic route by achieving intense absorption of broadband solar energy spectrum and high conversion capability of solar-to-heat. Recent progress in CO₂ reduction achieved by photothermal catalysis was summarized in terms of production types. In the end, the future challenges and perspectives of photothermal catalytic CO₂ reduction are presented. We hope that this review will not only deepen the understanding of photothermal catalysis, but also inspire the design, preparation and application of high-performance photothermal catalysts, aiming at alleviating non-renewable fossil energy consumption and carbon emissions for early carbon emission peak and carbon neutrality.     

Application of chromatography in purification and structural analysis of natural polysaccharides: A review

Polysaccharides are widely distributed in natural sources from monocytic microorganisms to higher animals, and are found in a variety of biological activities in recent decades. Natural polysaccharides have the characteristics of large molecular weight, diverse composition, and complex structure, so their purification and structural analysis are difficult issues in research. Chromatography as a powerful separation technique, plays an irreplaceable role in the separation and structural analysis of natural polysaccharides, especially in the purification of polysaccharides, the separation of hydrolysates, and the analysis of monosaccharide composition. The separation mechanisms and application of different chromatographic methods in the studies of polysaccharides were summarized in this review. Moreover, the advantages and drawbacks of various chromatography methods were discussed as well.     

Oxygen-controlled Biosurfactant Production in a Bench Scale Bioreactor

Rhamnolipids have been pointed out as promising biosurfactants. The most studied microorganisms for the aerobic production of these molecules are the bacteria of the genus Pseudomonas. The aim of this work was to produce a rhamnolipid-type biosurfactant in a bench-scale bioreactor by one strain of Pseudomonas aeruginosa isolated from oil environments. To study the microorganism growth and production dependency on oxygen, a nondispersive oxygenation device was developed, and a programmable logic controller (PLC) was used to set the dissolved oxygen (DO) concentration. Using the data stored in a computer and the predetermined characteristics of the oxygenation device, it was possible to evaluate the oxygen uptake rate (OUR) and the specific OUR (SOUR) of this microorganism. These rates, obtained for some different DO concentrations, were then compared to the bacterial growth, to the carbon source consumption, and to the rhamnolipid and other virulence factors production. The SOUR presented an initial value of about 60.0 mgO₂/g_DW h. Then, when the exponential growth phase begins, there is a rise in this rate. After that, the SOUR reduces to about 20.0 mgO₂/g_DW h. The carbon source consumption is linear during the whole process.     

Evaluation of the effects of crude glycerol on the production and properties of novel polyhydroxyalkanoate copolymers containing high 11‐hydroxyoctadecanoate by Cupriavidus necator IPT 029 and Bacillus megaterium IPT 429

Crude glycerol (CG), a by‐product from biodiesel production, is a carbon source with potential as feedstock for polyhydroxyalkanoate (PHA) production. PHAs are biological macromolecules synthesized by microorganisms as intracellular carbon and energy storage granules. PHA production and its properties were investigated using Cupriavidus necator IPT 029 and Bacillus megaterium IPT 429 cultivated with CGs from different origins. The highest PHA extraction percentage (71.56% [w/v]) occurred when C. necator IPT 029 metabolized CG 3 (from the processing of biodiesel from castor bean oil). The gas chromatography–mass spectrometry analyses revealed novel PHA constituents as building blocks of medium (3‐hydroxytetradecanoate) and long (11‐hydroxyoctadecanoate) chains. Molar mass distribution revealed range of 121–6900 kDa. The initial degradation temperature ranged from 181.83 to 287.50°C and the crystallinity ranged from 35.30 to 66.70%. The results obtained indicate that C. necator IPT 029 from CG 3 could produce copolymers with industrially applicable thermophysical properties. Copyright © 2015 John Wiley & Sons, Ltd.     

Systems biology of antibiotic production by microorganisms

The synthesis of secondary metabolites by microorganisms, specifically antibiotics, is of great scientific and economic importance. The onset (control and regulation) of secondary metabolite formation has and still is intriguing scientists both in industry and academia. Despite many studies, there is little known about the molecular mechanisms underlying the regulation of secondary metabolism. With the recent developments in genomics and further development of advanced post-genomic techniques, it will be possible to apply a more holistic analysis to the regulation of antibiotic production in microorganisms. Here we review current knowledge about the control and regulation of secondary metabolites, with a focus on antibiotics. We will also review developments in the genomics of antibiotic-producing microorganisms, and discuss the use of systems biology for gaining a better understanding of the networks involved in regulation of antibiotic production.     

Production and Properties of a Surface-Active Lipopeptide Produced by a New Marine Brevibacterium luteolum Strain

Microbial-derived surfactants are molecules of great interest due to their environmentally friendly nature and low toxicity; however, their production cost is not competitive when compared to synthetics. Marine microorganisms are exposed to extremes of pressure, temperature, and salinity; hence, they can produce stable compounds under such conditions that are useful for industrial applications. A screening program to select marine bacteria able to produce biosurfactant using low-cost substrates (mineral oil, sucrose, soybean oil, and glycerol) was conducted. The selected bacterial strain showed potential to synthesize biosurfactants using mineral oil as carbon source and was identified as Brevibacterium luteolum. The surface-active compound reduced the surface tension of water to 27 mN m^?1 and the interfacial tension (water/hexadecane) to 0.84 mN m^?1 and showed a critical micelle concentration of 40 mg L^?1. The biosurfactant was stable over a range of temperature, pH, and salt concentration and the emulsification index (E₂₄) with different hydrocarbons ranging from 60 to 79 %. Structural characterization revealed that the biosurfactant has a lipopeptide nature. Sand washing removed 83 % of crude oil demonstrating the potential of the biosurfactants (BS) for bioremediation purposes. The new marine B. luteolum strain showed potential to produce high surface-active and stable molecule using a low-cost substrate.     

金属配合物和一氧化碳的反应

一氧化碳是发展可持续化学经济的重要原料。人们希望能够将一氧化碳催化转变成高附加值化学品,从而减少石油等化石资源对人类的束缚。研究均相金属配合物与一氧化碳的反应能够使人们了解一氧化碳转变及利用机理,并开发新催化剂高效地利用一氧化碳资源。本文从金属配合物与一氧化碳反应的活性点出发,分别讨论不同类型的金属配合物与一氧化碳的反应,以求让人们在分子水平上了解一氧化碳的基本反应原理;并总结了该领域存在的难点问题,展望了未来,希望更多的科研工作者投入其中,从而实现利用一氧化碳合成出各种各样的化学品和材料。