scispace - formally typeset
Search or ask a question

Showing papers in "Applied Microbiology and Biotechnology in 2013"


Journal ArticleDOI
TL;DR: The study of microbial interactions among multispecies leaching consortia, including cell-to-cell communication mechanisms, must be considered in order to reveal more insights into the biology of bioleaching microorganisms and their potential biotechnological use.
Abstract: Bioleaching of metal sulfides is performed by a diverse group of microorganisms. The dissolution chemistry of metal sulfides follows two pathways, which are determined by the mineralogy and the acid solubility of the metal sulfides: the thiosulfate and the polysulfide pathways. Bacterial cells can effect this metal sulfide dissolution via iron(II) ion and sulfur compound oxidation. Thereby, iron(III) ions and protons, the metal sulfide-attacking agents, are available. Cells can be active either in planktonic state or in forming biofilms on the mineral surface; however, the latter is much more efficient in terms of bioleaching kinetics. In the case of Acidithiobacillus ferrooxidans, bacterial exopolymers contain iron(III) ions, each complexed by two uronic acid residues. The resulting positive charge allows an electrostatic attachment to the negatively charged pyrite. Thus, the first function of complexed iron(III) ions is the mediation of cell attachment, while their second function is oxidative dissolution of the metal sulfide, similar to the role of free iron(III) ions in non-contact leaching. In both cases, the electrons extracted from the metal sulfide reduce molecular oxygen via a redox chain forming a supercomplex spanning the periplasmic space and connecting both outer and inner membranes. In this review, we summarize some recent discoveries relevant to leaching bacteria which contribute to a better understanding of these fascinating microorganisms. These include surface science, biochemistry of iron and sulfur metabolism, anaerobic metabolism, and biofilm formation. The study of microbial interactions among multispecies leaching consortia, including cell-to-cell communication mechanisms, must be considered in order to reveal more insights into the biology of bioleaching microorganisms and their potential biotechnological use.

474 citations


Journal ArticleDOI
TL;DR: This review highlights the enormous use of harsh surfactants in agricultural soil and agrochemical industries and there is need to explore novel biosurfactant from uncultured microbes in soil biosphere by using advanced methodologies like functional metagenomics.
Abstract: Agricultural productivity to meet growing demands of human population is a matter of great concern for all countries. Use of green compounds to achieve the sustainable agriculture is the present necessity. This review highlights the enormous use of harsh surfactants in agricultural soil and agrochemical industries. Biosurfactants which are reported to be produced by bacteria, yeasts, and fungi can serve as green surfactants. Biosurfactants are considered to be less toxic and eco-friendly and thus several types of biosurfactants have the potential to be commercially produced for extensive applications in pharmaceutical, cosmetics, and food industries. The biosurfactants synthesized by environmental isolates also has promising role in the agricultural industry. Many rhizosphere and plant associated microbes produce biosurfactant; these biomolecules play vital role in motility, signaling, and biofilm formation, indicating that biosurfactant governs plant–microbe interaction. In agriculture, biosurfactants can be used for plant pathogen elimination and for increasing the bioavailability of nutrient for beneficial plant associated microbes. Biosurfactants can widely be applied for improving the agricultural soil quality by soil remediation. These biomolecules can replace the harsh surfactant presently being used in million dollar pesticide industries. Thus, exploring biosurfactants from environmental isolates for investigating their potential role in plant growth promotion and other related agricultural applications warrants details research. Conventional methods are followed for screening the microbial population for production of biosurfactant. However, molecular methods are fewer in reaching biosurfactants from diverse microbial population and there is need to explore novel biosurfactant from uncultured microbes in soil biosphere by using advanced methodologies like functional metagenomics.

363 citations


Journal ArticleDOI
TL;DR: Probiotic strains which are capable to limit excessive amounts of reactive radicals in vivo may contribute to prevent and control several diseases associated with oxidative stress.
Abstract: Thirty-four strains of lactic acid bacteria (seven Bifidobacterium, 11 Lactobacillus, six Lactococcus, and 10 Streptococcus thermophilus) were assayed in vitro for antioxidant activity against ascorbic and linolenic acid oxidation (TAA(AA) and TAA(LA)), trolox-equivalent antioxidant capacity (TEAC), intracellular glutathione (TGSH), and superoxide dismutase (SOD). Wide dispersion of each of TAA(AA), TAA(LA), TEAC, TGSH, and SOD occurred within bacterial groups, indicating that antioxidative properties are strain specific. The strains Bifidobacterium animalis subsp. lactis DSMZ 23032, Lactobacillus acidophilus DSMZ 23033, and Lactobacillus brevis DSMZ 23034 exhibited among the highest TAA(AA), TAA(LA), TEAC, and TGSH values within the lactobacilli and bifidobacteria. These strains were used to prepare a potentially antioxidative probiotic formulation, which was administered to rats at the dose of 10(7), 10(8), and 10(9) cfu/day for 18 days. The probiotic strains colonized the colon of the rats during the trial and promoted intestinal saccharolytic metabolism. The analysis of plasma antioxidant activity, reactive oxygen molecules level, and glutathione concentration, revealed that, when administered at doses of at least 10(8) cfu/day, the antioxidant mixture effectively reduced doxorubicin-induced oxidative stress. Probiotic strains which are capable to limit excessive amounts of reactive radicals in vivo may contribute to prevent and control several diseases associated with oxidative stress.

344 citations


Journal ArticleDOI
TL;DR: A review of a variety of well-known biodeterioration phenomena observed on different materials, such as stone and building materials, objects exhibited in museums and libraries, as well as human remains and burial-related materials and some prominent examples of successful and unsuccessful conservation treatments are given.
Abstract: Microorganisms (bacteria, archaea and fungi), in addition to lichens and insect pests, cause problems in the conservation of cultural heritage because of their biodeteriorative potential. This holds true for all types of historic artefacts, and even for art made of modern materials, in public buildings, museums and private art collections. The variety of biodeterioration phenomena observed on materials of cultural heritage is determined by several factors, such as the chemical composition and nature of the material itself, the climate and exposure of the object, in addition to the manner and frequency of surface cleaning and housekeeping in museums. This study offers a review of a variety of well-known biodeterioration phenomena observed on different materials, such as stone and building materials, objects exhibited in museums and libraries, as well as human remains and burial-related materials. The decontamination of infected artefacts, exhibition rooms and depots incurs high expenditure for museums. Nevertheless, the question has to be raised: whether the process of biodeterioration of cultural heritage can or should be stopped under all circumstances, or whether we have to accept it as a natural and an implicit consecution of its creation. This study also highlights critically the pros and cons of biocide treatments and gives some prominent examples of successful and unsuccessful conservation treatments. Furthermore, an outlook on the future research needs and developments in this highly interesting field is given.

340 citations


Journal ArticleDOI
TL;DR: Data on macro and trace elements and radionuclides in edible wild-grown and cultivated mushrooms is reviewed and updates and the problem of erroneous data on mineral compounds determined in mushrooms is discussed.
Abstract: This article reviews and updates data on macro and trace elements and radionuclides in edible wild-grown and cultivated mushrooms. A huge biodiversity of mushrooms and spread of certain species over different continents makes the study on their multi-element constituents highly challenging. A few edible mushrooms are widely cultivated and efforts are on to employ them (largely Agaricus spp., Pleurotus spp., and Lentinula edodes) in the production of selenium-enriched food (mushrooms) or nutraceuticals (by using mycelia) and less on species used by traditional medicine, e.g., Ganoderma lucidum. There are also attempts to enrich mushrooms with other elements than Se and a good example is enrichment with lithium. Since minerals of nutritional value are common constituents of mushrooms collected from natural habitats, the problem is however their co-occurrence with some hazardous elements including Cd, Pb, Hg, Ag, As, and radionuclides. Discussed is also the problem of erroneous data on mineral compounds determined in mushrooms.

314 citations


Journal ArticleDOI
TL;DR: There have been notable developments in the areas of catalysis, cell biology, and proteomics in addition to continued applications in the more established areas of detection, labeling and drug delivery.
Abstract: Streptavidin and its homologs (together referred to as streptavidin) are widely used in molecular science owing to their highly selective and stable interaction with biotin. Other factors also contribute to the popularity of the streptavidin–biotin system, including the stability of the protein and various chemical and enzymatic biotinylation methods available for use with different experimental designs. The technology has enjoyed a renaissance of a sort in recent years, as new streptavidin variants are engineered to complement native proteins and novel methods of introducing selective biotinylation are developed for in vitro and in vivo applications. There have been notable developments in the areas of catalysis, cell biology, and proteomics in addition to continued applications in the more established areas of detection, labeling and drug delivery. This review summarizes recent advances in streptavidin engineering and new applications based on the streptavidin–biotin interaction.

295 citations


Journal ArticleDOI
TL;DR: This review summarizes the effects of actinobacteria as BCA, PGPA, and its beneficial associations with plants.
Abstract: Biological control and plant growth promotion by plant beneficial microbes has been viewed as an alternative to the use of chemical pesticides and fertilizers. Bacteria and fungi that are naturally associated with plants and have a beneficial effect on plant growth by the alleviation of biotic and abiotic stresses were isolated and developed into biocontrol (BCA) and plant growth-promoting agents (PGPA). Actinobacteria are a group of important plant-associated spore-forming bacteria, which have been studied for their biocontrol, plant growth promotion, and interaction with plants. This review summarizes the effects of actinobacteria as BCA, PGPA, and its beneficial associations with plants.

287 citations


Journal ArticleDOI
TL;DR: In this study, it is successfully demonstrated that 454 pyrosequencing was a powerful approach for investigating the bacterial communities in the activated sludge, digestionSludge, influent, and effluent samples of a full scale wastewater treatment plant treating saline sewage.
Abstract: In this study, we successfully demonstrated that 454 pyrosequencing was a powerful approach for investi- gating the bacterial communities in the activated sludge, digestion sludge, influent, and effluent samples of a full scale wastewater treatment plant treating saline sewage. For each sample, 18,808 effective sequences were selected and utilized to do the bacterial diversity and abundance analysis. In total, 2,455, 794, 1,667, and 1,932 operational taxonomic units were obtained at 3 % distance cutoff in the activated sludge, digestion sludge, influent, and effluent samples, respectively. The corresponding most dominant classes in the four samples are Alphaproteobacteria, Ther- motogae, Deltaproteobacteria, and Gammaproteobacteria. About 67 % sequences in the digestion sludge sample were found to be affiliated with the Thermotogales order. Also, these sequences were assigned into a recently proposed genus Kosmotoga by the Ribosomal Database Project clas- sifier. In the effluent sample, we found high abundance of Mycobacterium and Vibrio, which are genera containing pathogenic bacteria. Moreover, in this study, we proposed a method to differentiate the "gene percentage" and "cell per- centage" by using Ribosomal RNA Operon Copy Number

281 citations


Journal ArticleDOI
TL;DR: Bacterial communities involved in the anaerobic digestion of conventional substrates such as maize silage combined with cattle manure were relatively stable and similar to each other, whereas special waste materials were digested by very distinct and less diverse communities, indicating partial ammonia inhibition or the influence of other inhibiting factors.
Abstract: The influence of the feedstock type on the microbial communities involved in anaerobic digestion was investigated in laboratory-scale biogas reactors fed with different agricultural waste materials. Community composition and dynamics over 2 months of reactors’ operation were investigated by amplicon sequencing and profiling terminal restriction fragment length polymorphisms of 16S rRNA genes. Major bacterial taxa belonged to the Clostridia and Bacteroidetes, whereas the archaeal community was dominated by methanogenic archaea of the orders Methanomicrobiales and Methanosarcinales. Correlation analysis revealed that the community composition was mainly influenced by the feedstock type with the exception of a temperature shift from 38 to 55 °C which caused the most pronounced community shifts. Bacterial communities involved in the anaerobic digestion of conventional substrates such as maize silage combined with cattle manure were relatively stable and similar to each other. In contrast, special waste materials such as chicken manure or Jatropha press cake were digested by very distinct and less diverse communities, indicating partial ammonia inhibition or the influence of other inhibiting factors. Anaerobic digestion of chicken manure relied on syntrophic acetate oxidation as the dominant acetate-consuming process due to the inhibition of aceticlastic methanogenesis. Jatropha as substrate led to the enrichment of fiber-degrading specialists belonging to the genera Actinomyces and Fibrobacter.

280 citations


Journal ArticleDOI
TL;DR: Progress has been made in understanding and developing bioleaching of copper from primary copper sulfide minerals, chalcopyrite, covellite, and enargite, which point to low oxidation–reduction potential in concert with thermophilic bacteria and archaea as a potential key to the leaching of these minerals.
Abstract: This review presents developments and applications in bioleaching and mineral biooxidation since publication of a previous mini review in 2003 (Olson et al. Appl Microbiol Biotechnol 63:249–257, 2003). There have been discoveries of newly identified acidophilic microorganisms that have unique characteristics for effective bioleaching of sulfidic ores and concentrates. Progress has been made in understanding and developing bioleaching of copper from primary copper sulfide minerals, chalcopyrite, covellite, and enargite. These developments point to low oxidation–reduction potential in concert with thermophilic bacteria and archaea as a potential key to the leaching of these minerals. On the commercial front, heap bioleaching of nickel has been commissioned, and the mineral biooxidation pretreatment of sulfidic-refractory gold concentrates is increasingly used on a global scale to enhance precious metal recovery. New and larger stirred-tank reactors have been constructed since the 2003 review article. One biooxidation–heap process for pretreatment of sulfidic-refractory gold ores was also commercialized. A novel reductive approach to bioleaching nickel laterite minerals has been proposed.

269 citations


Journal ArticleDOI
TL;DR: The nanopattern on the surface of Clanger cicada wings represents the first example of a new class of biomaterials that can kill bacteria on contact based solely on its physical surface structure, and provides a model for the development of novel functional surfaces that possess an increased resistance to bacterial contamination and infection.
Abstract: The nanopattern on the surface of Clanger cicada (Psaltoda claripennis) wings represents the first example of a new class of biomaterials that can kill bacteria on contact based solely on its physical surface structure. As such, they provide a model for the development of novel functional surfaces that possess an increased resistance to bacterial contamination and infection. Their effectiveness against a wide spectrum of bacteria, however, is yet to be established. Here, the bactericidal properties of the wings were tested against several bacterial species, possessing a range of combinations of morphology and cell wall type. The tested species were primarily pathogens, and included Bacillus subtilis, Branhamella catarrhalis, Escherichia coli, Planococcus maritimus, Pseudomonas aeruginosa, Pseudomonas fluorescens, and Staphylococcus aureus. The wings were found to consistently kill Gram-negative cells (i.e., B. catarrhalis, E. coli, P. aeruginosa, and P. fluorescens), while Gram-positive cells (B. subtilis, P. maritimus, and S. aureus) remained resistant. The morphology of the cells did not appear to play any role in determining cell susceptibility. The bactericidal activity of the wing was also found to be quite efficient; 6.1 ± 1.5 × 106 P. aeruginosa cells in suspension were inactivated per square centimeter of wing surface after 30-min incubation. These findings demonstrate the potential for the development of selective bactericidal surfaces incorporating cicada wing nanopatterns into the design.

Journal ArticleDOI
TL;DR: The different components and the major steps involved in the formulation of good quality biofertilizers, including the techniques used to assess the quality of the products following production are presented, emphasizing the need for better quality control systems worldwide.
Abstract: The interest in biofertilizers is increasing and so is the potential for their use in sustainable agriculture. However, many of the products that are currently available worldwide are often of very poor quality, resulting in the loss of confidence from farmers. The formulation of an inoculant is a crucial multistep process that should result in one or several strains of microorganisms included in a suitable carrier, providing a safe environment to protect them from the often harsh conditions during storage and ensuring survival and establishment after introduction into soils. One of the key issues in formulation development and production is the quality control of the products, at each stage of the process. This review presents the different components and the major steps involved in the formulation of good quality biofertilizers, including the techniques used to assess the quality of the products following production. The quality of currently available inoculants is also reviewed, emphasizing the need for better quality control systems worldwide.

Journal ArticleDOI
TL;DR: In inoculation of cytokinin-producing PGPR in container seedlings can alleviate the drought stress and interfere with the suppression of shoot growth, showing a real potential to perform as a drought stress inhibitor in arid environments.
Abstract: One of the proposed mechanisms through which plant growth-promoting rhizobacteria (PGPR) enhance plant growth is the production of plant growth regulators, especially cytokinin. However, little information is available regarding cytokinin-producing PGPR inoculation on growth and water stress consistence of forest container seedlings under drought condition. This study determined the effects of Bacillus subtilis on hormone concentration, drought resistance, and plant growth under water-stressed conditions. Although no significant difference was observed under well-watered conditions, leaves of inoculated Platycladus orientalis (oriental thuja) seedlings under drought stress had higher relative water content and leaf water potential compared with those of noninoculated ones. Regardless of water supply levels, the root exudates, namely sugars, amino acids and organic acids, significantly increased because of B. subtilis inoculation. Water stress reduced shoot cytokinins by 39.14 %. However, inoculation decreased this deficit to only 10.22 %. The elevated levels of cytokinins in P. orientalis shoot were associated with higher concentration of abscisic acid (ABA). Stomatal conductance was significantly increased by B. subtilis inoculation in well-watered seedlings. However, the promoting effect of cytokinins on stomatal conductance was hampered, possibly by the combined action of elevated cytokinins and ABA. B. subtilis inoculation increased the shoot dry weight of well-watered and drought seedlings by 34.85 and 19.23 %, as well as the root by 15.445 and 13.99 %, respectively. Consequently, the root/shoot ratio significantly decreased, indicative of the greater benefits of PGPR on shoot growth than root. Thus, inoculation of cytokinin-producing PGPR in container seedlings can alleviate the drought stress and interfere with the suppression of shoot growth, showing a real potential to perform as a drought stress inhibitor in arid environments.

Journal ArticleDOI
TL;DR: In this paper, the authors review current progress on this topic, describing concepts for activating silent genes, utilization of mutant-type RNA polymerases and rare earth elements, and the applicability of ribosome engineering to myxobacteria and fungi.
Abstract: Genome sequencing of Streptomyces, myxobacteria, and fungi showed that although each strain contains genes that encode the enzymes to synthesize a plethora of potential secondary metabolites, only a fraction are expressed during fermentation. Interest has therefore grown in the activation of these cryptic pathways. We review current progress on this topic, describing concepts for activating silent genes, utilization of “natural” mutant-type RNA polymerases and rare earth elements, and the applicability of ribosome engineering to myxobacteria and fungi, the microbial groups known as excellent searching sources, as well as actinomycetes, for secondary metabolites.

Journal ArticleDOI
TL;DR: Enzymatic approaches that are used for protein crosslinking at the industrial level or have shown promising potential in investigations on the lab-scale are reviewed.
Abstract: The process of protein crosslinking comprises the chemical, enzymatic, or chemoenzymatic formation of new covalent bonds between polypeptides. This allows (1) the site-directed coupling of proteins with distinct properties and (2) the de novo assembly of polymeric protein networks. Transferases, hydrolases, and oxidoreductases can be employed as catalysts for the synthesis of crosslinked proteins, thereby complementing chemical crosslinking strategies. Here, we review enzymatic approaches that are used for protein crosslinking at the industrial level or have shown promising potential in investigations on the lab-scale. We illustrate the underlying mechanisms of crosslink formation and point out the roles of the enzymes in their natural environments. Additionally, we discuss advantages and drawbacks of the enzyme-based crosslinking strategies and their potential for different applications.

Journal ArticleDOI
TL;DR: Novel nanoscaffold variants employed in the recent past for enzyme immobilisation, namely nanoparticles, nanofibres, nanotubes, nanopores, nanosheets and nanocomposites, are discussed in the context of lipase-mediated nanobiocatalysis.
Abstract: Nanobiotechnology is emerging as a new frontier of biotechnology. The potential applications of nanobiotechnology in bioenergy and biosensors have encouraged researchers in recent years to investigate new novel nanoscaffolds to build robust nanobiocatalytic systems. Enzymes, mainly hydrolytic class of enzyme, have been extensively immobilised on nanoscaffold support for long-term stabilisation by enhancing thermal, operational and storage catalytic potential. In the present report, novel nanoscaffold variants employed in the recent past for enzyme immobilisation, namely nanoparticles, nanofibres, nanotubes, nanopores, nanosheets and nanocomposites, are discussed in the context of lipase-mediated nanobiocatalysis. These nanocarriers have an inherently large surface area that leads to high enzyme loading and consequently high volumetric enzyme activity. Due to their high tensile strengths, nanoscale materials are often robust and resistant to breakage through mechanical shear in the running reactor making them suitable for multiple reuses. The optimisation of various nanosupports process parameters, such as the enzyme type and selection of suitable immobilisation method may help lead to the development of an efficient enzyme reactor. This might in turn offer a potential platform for exploring other enzymes for the development of stable nanobiocatalytic systems, which could help to address global environmental issues by facilitating the production of green energy. The successful validation of the feasibility of nanobiocatalysis for biodiesel production represents the beginning of a new field of research. The economic hurdles inherent in viably scaling nanobiocatalysts from a lab-scale to industrial biodiesel production are also discussed.

Journal ArticleDOI
TL;DR: The strategies being employed to exploit the inherent durability of biofilms and the diverse nutrient cycling of the microbiome for bioremediation are explored, as well as some heavy metals and toxic minerals, as these groups represent the majority of priority pollutants.
Abstract: In this review, the strategies being employed to exploit the inherent durability of biofilms and the diverse nutrient cycling of the microbiome for bioremediation are explored. Focus will be given to halogenated compounds, hydrocarbons, pharmaceuticals, and personal care products as well as some heavy metals and toxic minerals, as these groups represent the majority of priority pollutants. For decades, industrial processes have been creating waste all around the world, resulting in contaminated sediments and subsequent, far-reaching dispersal into aquatic environments. As persistent pollutants have accumulated and are still being created and disposed, the incentive to find suitable and more efficient solutions to effectively detoxify the environment is even greater. Indigenous bacterial communities are capable of metabolizing persistent organic pollutants and oxidizing heavy metal contaminants. However, their low abundance and activity in the environment, difficulties accessing the contaminant or nutrient limitations in the environment all prevent the processes from occurring as quickly as desired and thus reaching the proposed clean-up goals. Biofilm communities provide among other things a beneficial structure, possibility for nutrient, and genetic exchange to participating microorganisms as well as protection from the surrounding environment concerning for instance predation and chemical and shear stresses. Biofilms can also be utilized in other ways as biomarkers for monitoring of stream water quality from for instance mine drainage. The durability and structure of biofilms together with the diverse array of structural and metabolic characteristics make these communities attractive actors in biofilm-mediated remediation solutions and ecosystem monitoring.

Journal ArticleDOI
TL;DR: UPLC-UV-MS data from D. salina is presented consistent with the pathway proposed for carotenoid metabolism in the green microalga Chlamydomonas reinhardtii and it is found that combining red LED (75 %) with blue LED (25 %) allowed growth at a higher total photon flux, and additional blue light instead of red light led to increased β-carotene and lutein accumulation.
Abstract: There is a particularly high interest to derive carotenoids such as β-carotene and lutein from higher plants and algae for the global market. It is well known that β-carotene can be overproduced in the green microalga Dunaliella salina in response to stressful light conditions. However, little is known about the effects of light quality on carotenoid metabolism, e.g., narrow spectrum red light. In this study, we present UPLC-UV-MS data from D. salina consistent with the pathway proposed for carotenoid metabolism in the green microalga Chlamydomonas reinhardtii. We have studied the effect of red light-emitting diode (LED) lighting on growth rate and biomass yield and identified the optimal photon flux for D. salina growth. We found that the major carotenoids changed in parallel to the chlorophyll b content and that red light photon stress alone at high level was not capable of upregulating carotenoid accumulation presumably due to serious photodamage. We have found that combining red LED (75 %) with blue LED (25 %) allowed growth at a higher total photon flux. Additional blue light instead of red light led to increased β-carotene and lutein accumulation, and the application of long-term iterative stress (adaptive laboratory evolution) yielded strains of D. salina with increased accumulation of carotenoids under combined blue and red light.

Journal ArticleDOI
TL;DR: This review summarizes the recent finding in the field of biosurfactant-amended bioremediation, focusing mainly on a critical approach towards potential limitations and causes of failure while investigating the effects of biosURfactants on the efficiency of biodegradation and phytoextraction processes.
Abstract: The number of studies dedicated to evaluating the influence of biosurfactants on bioremediation efficiency is constantly growing. Although significant progress regarding the explanation of mechanisms behind biosurfactant-induced effects could be observed, there are still many factors which are not sufficiently elucidated. This corresponds to the fact that although positive influence of biosurfactants is often reported, there are also numerous cases where no or negative effect was observed. This review summarizes the recent finding in the field of biosurfactant-amended bioremediation, focusing mainly on a critical approach towards potential limitations and causes of failure while investigating the effects of biosurfactants on the efficiency of biodegradation and phytoextraction processes. It also provides a summary of successive steps, which should be taken into consideration when designing biosurfactant-related treatment processes.

Journal ArticleDOI
TL;DR: This review outlines the general principles and current progress and compares the advantages and challenges for the most widely used biofabrication techniques for printing cells: extrusion, laser, microvalve, inkjet and tissue fragment printing.
Abstract: The development of cell printing is vital for establishing biofabrication approaches as clinically relevant tools. Achieving this requires bio-inks which must not only be easily printable, but also allow controllable and reproducible printing of cells. This review outlines the general principles and current progress and compares the advantages and challenges for the most widely used biofabrication techniques for printing cells: extrusion, laser, microvalve, inkjet and tissue fragment printing. It is expected that significant advances in cell printing will result from synergistic combinations of these techniques and lead to optimised resolution, throughput and the overall complexity of printed constructs.

Journal ArticleDOI
TL;DR: A ‘proof of concept’ has been made, showing that this technology is capable of energy capture as hydrogen gas from low strength domestic wastewaters at ambient temperatures.
Abstract: Addressing the need to recover energy from the treatment of domestic wastewater, a 120-L microbial electrolysis cell was operated on site in Northern England, using raw domestic wastewater to produce virtually pure hydrogen gas (100 ± 6.4 %) for a period of over 3 months. The volumetric loading rate was 0.14 kg of chemical oxygen demand (COD) per cubic metre per day, just below the typical loading rates for activated sludge of 0.2-2 kg COD m(-3) day(-1), at an energetic cost of 2.3 kJ/g COD, which is below the values for activated sludge 2.5-7.2 kJ/g COD. The reactor produced an equivalent of 0.015 LH(2)L(-1) day(-1), and recovered around 70 % of the electrical energy input with a coulombic efficiency of 55 %. Although the reactor did not reach the breakeven point of 100 % electrical energy recovery and COD removal was limited, improved hydrogen capture and reactor design could increase the performance levels substantially. Importantly, for the first time, a 'proof of concept' has been made, showing that this technology is capable of energy capture as hydrogen gas from low strength domestic wastewaters at ambient temperatures.

Journal ArticleDOI
TL;DR: Lactobacillus S-layer proteins show potential for use as antigen carriers in live oral vaccine design because of their adhesive and immunomodulatory properties and the general non-pathogenicity of the species.
Abstract: Bacterial surface (S) layers are the outermost proteinaceous cell envelope structures found on members of nearly all taxonomic groups of bacteria and Archaea. They are composed of numerous identical subunits forming a symmetric, porous, lattice-like layer that completely covers the cell surface. The subunits are held together and attached to cell wall carbohydrates by non-covalent interactions, and they spontaneously reassemble in vitro by an entropy-driven process. Due to the low amino acid sequence similarity among S-layer proteins in general, verification of the presence of an S-layer on the bacterial cell surface usually requires electron microscopy. In lactobacilli, S-layer proteins have been detected on many but not all species. Lactobacillus S-layer proteins differ from those of other bacteria in their smaller size and high predicted pI. The positive charge in Lactobacillus S-layer proteins is concentrated in the more conserved cell wall binding domain, which can be either N- or C-terminal depending on the species. The more variable domain is responsible for the self-assembly of the monomers to a periodic structure. The biological functions of Lactobacillus S-layer proteins are poorly understood, but in some species S-layer proteins mediate bacterial adherence to host cells or extracellular matrix proteins or have protective or enzymatic functions. Lactobacillus S-layer proteins show potential for use as antigen carriers in live oral vaccine design because of their adhesive and immunomodulatory properties and the general non-pathogenicity of the species.

Journal ArticleDOI
TL;DR: In situ biogas upgrading was conducted by introducing H2 directly to the anaerobic reactor, and it was showed that addition of hydrogen had positive effect on the methanogenesis, but had no obvious impact on the acetogenesis.
Abstract: In situ biogas upgrading was conducted by introducing H2 directly to the anaerobic reactor. As H2 addition is associated with consumption of the CO2 in the biogas reactor, pH increased to higher than 8.0 when manure alone was used as substrate. By co-digestion of manure with acidic whey, the pH in the anaerobic reactor with the addition of hydrogen could be maintained below 8.0, which did not have inhibition to the anaerobic process. The H2 distribution systems (diffusers with different pore sizes) and liquid mixing intensities were demonstrated to affect the gas-liquid mass transfer of H2 and the biogas composition. The best biogas composition (75:6.6:18.4) was obtained at stirring speed 150 rpm and using ceramic diffuser, while the biogas in the control reactor consisted of CH4 and CO2 at a ratio of 55:45. The consumed hydrogen was almost completely converted to CH4, and there was no significant accumulation of VFA in the effluent. The study showed that addition of hydrogen had positive effect on the methanogenesis, but had no obvious effect on the acetogenesis. Both hydrogenotrophic methanogenic activity and the concentration of coenzyme F420 involved in methanogenesis were increased. The archaeal community was also altered with the addition of hydrogen, and a Methanothermobacter thermautotrophicus related band appeared in a denaturing gradient gel electrophoresis gel from the sample of the reactor with hydrogen addition. Though the addition of hydrogen increased the dissolved hydrogen concentration, the degradation of propionate was still thermodynamically feasible at the reactor conditions.

Journal ArticleDOI
TL;DR: This review emphasizes the utilization of marine bacteria in the field of bioremediation and understanding the mechanism behind acquiring the characteristic feature of adaptive responses.
Abstract: Bacteria are widespread in nature as they can adapt to any extreme environmental conditions and perform various physiological activities. Marine environments are one of the most adverse environments owing to their varying nature of temperature, pH, salinity, sea surface temperature, currents, precipitation regimes and wind patterns. Due to the constant variation of environmental conditions, the microorganisms present in that environment are more suitably adapted to the adverse conditions, hence, possessing complex characteristic features of adaptation. Therefore, the bacteria isolated from the marine environments are supposed to be better utilized in bioremediation of heavy metals, hydrocarbon and many other recalcitrant compounds and xenobiotics through biofilm formation and production of extracellular polymeric substances. Many marine bacteria have been reported to have bioremediation potential. The advantage of using marine bacteria for bioremediation in situ is the direct use of organisms in any adverse conditions without any genetic manipulation. This review emphasizes the utilization of marine bacteria in the field of bioremediation and understanding the mechanism behind acquiring the characteristic feature of adaptive responses.

Journal ArticleDOI
TL;DR: This article reviews the fundamentals of strategies for reducing PHA production and moves on to the applications of several cheap substrates with a special emphasis on methane, methanol, and CO2.
Abstract: Polyhydroxybutyrate (PHB) is an attractive substitute for petrochemical plastic due to its similar properties, biocompatibility, and biodegradability. The cost of scaled-up PHB production inhibits its widespread usage. Intensive researches are growing to reduce costs and improve thermomechanical, physical, and processing properties of this green biopolymer. Among cheap substrates which are used for reducing total cost of PHB production, some C1 carbon sources, e.g., methane, methanol, and CO2 have received a great deal of attention due to their serious role in greenhouse problem. This article reviews the fundamentals of strategies for reducing PHA production and moves on to the applications of several cheap substrates with a special emphasis on methane, methanol, and CO2. Also, some explanation for involved microorganisms including the hydrogen-oxidizing bacteria and methanotrophs, their history, culture condition, and nutritional requirements are given. After description of some important strains among the hydrogen-oxidizing and methanotrophic producers of PHB, the article is focused on limitations, threats, and opportunities for application and their future trends.

Journal ArticleDOI
TL;DR: This study showed for the first time that total nitrogen removal rates can be maintained when decreasing the temperature and when low nitrogen concentration and moderate COD levels are treated, and a balance should be found in the future between the increased NO and N2O emissions and a decreased energy consumption to justify OLAND mainstream treatment.
Abstract: Energy-positive sewage treatment can be achieved by implementation of oxygen-limited autotrophic nitrification/denitrification (OLAND) in the main water line, as the latter does not require organic carbon and therefore allows maximum energy recovery through anaerobic digestion of organics. To test the feasibility of mainstream OLAND, the effect of a gradual temperature decrease from 29 to 15 °C and a chemical oxygen demand (COD)/N increase from 0 to 2 was tested in an OLAND rotating biological contactor operating at 55–60 mg NH4 +–N L−1 and a hydraulic retention time of 1 h. Moreover, the effect of the operational conditions and feeding strategies on the reactor cycle balances, including NO and N2O emissions were studied in detail. This study showed for the first time that total nitrogen removal rates of 0.5 g N L−1 day−1 can be maintained when decreasing the temperature from 29 to 15 °C and when low nitrogen concentration and moderate COD levels are treated. Nitrite accumulation together with elevated NO and N2O emissions (5 % of N load) were needed to favor anammox compared with nitratation at low free ammonia (<0.25 mg N L−1), low free nitrous acid (<0.9 μg N L−1), and higher DO levels (3–4 mg O2 L−1). Although the total nitrogen removal rates showed potential, the accumulation of nitrite and nitrate resulted in lower nitrogen removal efficiencies (around 40 %), which should be improved in the future. Moreover, a balance should be found in the future between the increased NO and N2O emissions and a decreased energy consumption to justify OLAND mainstream treatment.

Journal ArticleDOI
TL;DR: The results highlight the importance of the cell membrane as a target for future metabolic engineering efforts for enabling resistance and tolerance of desirable biorenewable compounds, such as carboxylic acids.
Abstract: Carboxylic acids are an attractive biorenewable chemical. However, like many other fermentatively produced compounds, they are inhibitory to the biocatalyst. An understanding of the mechanism of toxicity can aid in mitigating this problem. Here, we show that hexanoic and octanoic acids are completely inhibitory to Escherichia coli MG1655 in minimal medium at a concentration of 40 mM, while decanoic acid was inhibitory at 20 mM. This growth inhibition is pH-dependent and is accompanied by a significant change in the fluorescence polarization (fluidity) and integrity. This inhibition and sensitivity to membrane fluidization, but not to damage of membrane integrity, can be at least partially mitigated during short-term adaptation to octanoic acid. This short-term adaptation was accompanied by a change in membrane lipid composition and a decrease in cell surface hydrophobicity. Specifically, the saturated/unsaturated lipid ratio decreased and the average lipid length increased. A fatty acid-producing strain exhibited an increase in membrane leakage as the product titer increased, but no change in membrane fluidity. These results highlight the importance of the cell membrane as a target for future metabolic engineering efforts for enabling resistance and tolerance of desirable biorenewable compounds, such as carboxylic acids. Knowledge of these effects can help in the engineering of robust biocatalysts for biorenewable chemicals production.

Journal ArticleDOI
TL;DR: Production of malic acid by Aspergillus oryzae NRRL 3488 was first improved by overexpression of a native C4-dicarboxylate transporter, leading to a greater than twofold increase in the rate of malate production.
Abstract: Malic acid, a petroleum-derived C4-dicarboxylic acid that is used in the food and beverage industries, is also produced by a number of microorganisms that follow a variety of metabolic routes. Several members of the genus Aspergillus utilize a two-step cytosolic pathway from pyruvate to malate known as the reductive tricarboxylic acid (rTCA) pathway. This simple and efficient pathway has a maximum theoretical yield of 2 mol malate/mol glucose when the starting pyruvate originates from glycolysis. Production of malic acid by Aspergillus oryzae NRRL 3488 was first improved by overexpression of a native C4-dicarboxylate transporter, leading to a greater than twofold increase in the rate of malate production. Overexpression of the native cytosolic alleles of pyruvate carboxylase and malate dehydrogenase, comprising the rTCA pathway, in conjunction with the transporter resulted in an additional 27 % increase in malate production rate. A strain overexpressing all three genes achieved a malate titer of 154 g/L in 164 h, corresponding to a production rate of 0.94 g/L/h, with an associated yield on glucose of 1.38 mol/mol (69 % of the theoretical maximum). This rate of malate production is the highest reported for any microbial system.

Journal ArticleDOI
TL;DR: The structure of airborne bacterial communities in the urban area of Milan suggests that soil and plants are the sources which contribute most to the airborne communities of Milan atmosphere, but the structure of the bacterial community seems to depend mainly on the source of bacteria that predominates in a given period of time.
Abstract: Despite airborne microorganisms representing a relevant fraction of atmospheric suspended particles, only a small amount of information is currently available on their abundance and diversity and very few studies have investigated the environmental factors influencing the structure of airborne bacterial communities. In this work, we used quantitative PCR and Illumina technology to provide a thorough description of airborne bacterial communities in the urban area of Milan (Italy). Forty samples were collected in 10-day sampling sessions, with one session per season. The mean bacterial abundance was about 10⁴ ribosomal operons per m³ of air and was lower in winter than in the other seasons. Communities were dominated by Actinobacteridae, Clostridiales, Sphingobacteriales and few proteobacterial orders (Burkholderiales, Rhizobiales, Sphingomonadales and Pseudomonadales). Chloroplasts were abundant in all samples. A higher abundance of Actinobacteridae, which are typical soil-inhabiting bacteria, and a lower abundance of chloroplasts in samples collected on cold days were observed. The variation in community composition observed within seasons was comparable to that observed between seasons, thus suggesting that airborne bacterial communities show large temporal variability, even between consecutive days. The structure of airborne bacterial communities therefore suggests that soil and plants are the sources which contribute most to the airborne communities of Milan atmosphere, but the structure of the bacterial community seems to depend mainly on the source of bacteria that predominates in a given period of time.

Journal ArticleDOI
Yi Qiao1, Jin Sun1, Yinyi Ding1, Guowei Le1, Yonghui Shi1 
TL;DR: Evidence is provided that modulation of the redox state by an antioxidant has the potential to improve gut microbiota, which has relevance for metabolic health.
Abstract: Alterations of the gut microbiota induced by diet exert a strong influence on the development of metabolic syndrome. In this study, we prove the hypothesis that the long-term high-fat diet (HFD) may influence gut microbiota directly and/or indirectly by changing the redox state. Lipoic acid (LA), as a universal antioxidant, was used to improve the redox state. Reactive oxygen species (ROS), total antioxidant capacity (T-AOC), and malondialdehyde (MDA) were analyzed to profile oxidative stress states. PCR-denaturing gradient gel electrophoresis (DGGE) was used to describe gut flora structures, while plate count was employed for the quantitative analysis of Escherichia coli, lactobacilli, and enterococcus. The influence of redox state on the vitality of gut-derived bacteria was measured in vitro. ROS and MDA, which significantly decreased in LA mice compared with HFD mice, showed a strong positive association with E. coli and enterococcus (P < 0.05) and a negative association with lactobacilli (P < 0.05). Increased T-AOC in LA mice showed a high positive association with lactobacilli (P < 0.05) and a negative correlation with E. coli and enterococcus. These correlations implied that the dietary effects on the gut microbiota were conferred, at least in part, through an effect on oxidative stress. This study provides evidence that modulation of the redox state by an antioxidant has the potential to improve gut microbiota, which has relevance for metabolic health.