Extracellular Polymeric Material Research Articles

IMAC application of extracellular polymeric substances doped composite membranes for α-amylase immobilization and kinetic studies

Immobilized metal affinity chromatography (IMAC), extensively utilized technique in affinity chromatography, has proven to be highly effective in purifying α-amylase, a crucial enzyme in industrial applications. Here, Poly (2-hydroxyethyl methacrylate) (PHEMA) based composite membranes were fabricated using the radical copolymerization technique in a petri dish. Extracellular polymeric materials (EPS) as the metal binding agent. The attachment of Cu2+ ions to the membranes occurred through the utilization of EPSs (Cu2+-EPS). The membranes having Cu2+-EPS (Cu2+-EPS-PM) were subjected to various characterization techniques, including scanning electron microscopy (SEM), attenuated total reflectance-fourier transform infrared spectroscopy (ATR-FTIR), swelling tests, and surface area measurements. The investigation also encompassed the examination of various factors, including pH, initial α-amylase concentration, temperature, and ionic strength, that exert an influence on the adsorption of α-amylase from an aqueous medium. The Cu2+-EPS-PMs demonstrated maximum adsorption capacity with a value of 54.2 mg/g polymer (pH 5.0 sodium acetate buffer, temperature: 25°C, initial α-amylase concentration of 2 mg/mL). Additionally, it has been observed that the enzyme is able to be used in adsorption and desorption cycles on Cu2+-EPS-PM many times. The investigation also focused on examining the impact of pH, temperature, storage, and operational stability over the activities of both free and immobilized α-amylase. The outcomes showed that immobilization had positive effects on activity.

Investigating Biofilms: Advanced Methods for Comprehending Microbial Behavior and Antibiotic Resistance.

Biofilms, which consist of microorganisms enclosed in an extracellular polymeric material (EPS), hold immense importance in the fields of environmental research, industry, and medicine. They play a significant role in ecosystem dynamics and stability, but they also pose issues such as biofouling, corrosion, and pollution. Biofilms in medical environments are linked to persistent infections and elevated healthcare expenses. The EPS matrix plays a crucial role in maintaining the structural integrity and antibiotic resistance of these structures. The research primarily investigates the role of the EPS matrix in facilitating horizontal gene transfer among biofilm communities, with a particular emphasis on EPS and its impact on this process. The process is recognized as a pivotal mechanism in the emergence of antibiotic resistance, underscoring the crucial function of EPS in the dynamics of biofilms. The analysis also highlights the significant financial constraints caused by biofilms in several industries. Biofilm-associated infections in the healthcare sector result in escalated treatment expenses and extended hospitalization periods. In an industrial context, biofilms have a role in increasing maintenance expenses and product contamination, emphasizing the need for efficient management solutions. This review presents the most recent progress in biofilm research, emphasizing the utilization of sophisticated imaging tools and molecular methodologies. In addition to conventional imaging techniques, the research explores the utilization of sophisticated molecular tools, such as DNA and RNA sequencing, in conjunction with proteomics. These approaches are essential for assessing the genetic and metabolic mechanisms that regulate biofilm development and antibiotic resistance. The review underscores the significance of employing an interdisciplinary methodology in the study of biofilms. By incorporating a range of approaches, such as sophisticated imaging and molecular analysis, a comprehensive understanding of biofilm dynamics may be achieved. This approach also opens up possibilities for developing novel solutions to address the negative impacts of biofilms on health, industry, and the environment.

Microbial community evolution in the biofilm attached to sponge carriers in pulp mill effluent treatment

This study investigates the evolution of the biofilm matrix responsible for treating effluent from a pulp mill and identifies the microbial community by 16S rRNA gene sequencing. In addition, a biocarrier promising a functional structure with better specific features for biofilm formation than traditional polyurethane carriers was explored. The average removal efficiencies were 43.7% for chemical oxygen demand (COD) and 62.7% for biochemical oxygen demand (BOD5). The color increased during the treatment, indicating anoxic zones being formed in the inner part of this type of carrier. Periodic micrographs showed the evolution of extracellular polymeric substances and materials like fungi and bacteria adhered to the carriers. Genetic sequencing confirmed the presence of Bacillus sp. and Paenibacillus glucanolyticus, species with the potential to degrade and discolor pulp industrial effluents. Results offer a potential basis to enhance treatment facilities of pulp and paper mills based on microbial activities.

Biosurfactant derived from probiotic Lactobacillus acidophilus exhibits broad-spectrum antibiofilm activity and inhibits the quorum sensing-regulated virulence.

Antimicrobial resistance by pathogenic bacteria has become a global risk to human health in recent years. The most promising approach to combating antimicrobial resistance is to target virulent traits of bacteria. In the present study, a biosurfactant derived from the probiotic strain Lactobacillus acidophiluswas tested against three Gram-negative bacteria to evaluate its inhibitory potential on their biofilms, and whether it affected the virulence factors controlled by quorum sensing (QS). A reduction in the virulence factors of Chromobacterium violaceum (violacein production), Serratia marcescens (prodigiosin production) and Pseudomonas aeruginosa (pyocyanin, total protease, LasB elastase and LasA protease production) was observed at different sub-MIC concentrations in a dose-dependent manner. Biofilm development was reduced by 65.76%, 70.64% and 58.12% at the highest sub-MIC levels for C. violaceum, P. aeruginosa and S. marcescens, respectively. Biofilm formation on glass surfaces exhibited significant reduction, with less bacterial aggregation and reduced formation of extracellular polymeric materials. Additionally, swimming motility and exopolysaccharides (EPS) production were shown to be reduced in the presence of the L. acidophilus-derived biosurfactant. Furthermore, molecular docking analysis performed on compounds identified through gas chromatography-mass spectrometry (GC-MS) analysis of QS and biofilm proteins yielded further insights into the mechanism underlying the anti-QS activity. Therefore, the present study has clearly demonstrated that a biosurfactant derived from L. acidophilus can significantly inhibit virulence factors of Gram-negative pathogenic bacteria. This could provide an effective method to inhibit the formation of biofilms and QS in Gram-negative bacteria.

Biofilm Formation in Acute and Chronic Infections with Special Emphasis on Common Chronic and Nosocomial Infections

Biofilm is defined as a community of microorganisms that are adhered to living or non-living solid surfaces and embedded in a common, self-made matrix, comprising of exopolysaccharide material. The role of biofilm in chronic diseases deserves special importance as these extracellular polymeric materials developed with quorum sensing support both the primary criteria of infection development namely adhesion and colonisation. Due to their structural and physiological changes, microorganisms present in the biofilm are difficult to treat or eradicate. The presence of a protective layer of extracellular polymers, changes in metabolic activity or a high rate of mutation make them tolerant or resistant to conventional treatment. The persistence of pathogenic microorganisms mostly renders biofilm to be associated with several acute and chronic infections and various nosocomial or healthcare-related infections. Furthermore, cancer development may also result due to biofilm formation. Biofilm may contribute to inflammation. This study deals with molecular aspects of biofilm formation and its role in different disease formations.

Biofilm Formation by Chromoblastomycosis Fungi Fonsecaea pedrosoi and Phialophora verrucosa: Involvement with Antifungal Resistance.

Patients with chromoblastomycosis (CBM) suffer chronic tissue lesions that are hard to treat. Considering that biofilm is the main growth lifestyle of several pathogens and it is involved with both virulence and resistance to antimicrobial drugs, we have investigated the ability of CBM fungi to produce this complex, organized and multicellular structure. Fonsecaea pedrosoi and Phialophora verrucosa conidial cells were able to adhere on a polystyrene abiotic substrate, differentiate into hyphae and produce a robust viable biomass containing extracellular matrix. Confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) showed the tridimensional architecture of the mature biofilms, revealing a dense network of interconnected hyphae, inner channels and amorphous extracellular polymeric material. Interestingly, the co-culture of each fungus with THP-1 macrophage cells, used as a biotic substrate, induced the formation of a mycelial trap covering and damaging the macrophages. In addition, the biofilm-forming cells of F. pedrosoi and P. verrucosa were more resistant to the conventional antifungal drugs than the planktonic-growing conidial cells. The efflux pump activities of P. verrucosa and F. pedrosoi biofilms were significantly higher than those measured in conidia. Taken together, the data pointed out the biofilm formation by CBM fungi and brought up a discussion of the relevance of studies about their antifungal resistance mechanisms.

Interaction of temperature, salinity and extracellular polymeric substances controls trace element incorporation into tufa calcite

AbstractThe influence of extracellular polymeric substances on carbonate mineral growth in natural settings remains one of the most poorly understood contributors to the growth of non‐marine carbonate sediments. The influences of these materials are complicated by their association with living cells creating local microenvironments via metabolism and enzyme production, and by our uncertainty about the extracellular polymeric substances materials themselves. Different mixtures of extracellular polymeric substance molecules may behave in different ways, and differences in the local physical environment may alter how the mixtures influence mineral formation, and even result in different patterns of polymerization. Here, the influence of extracellular polymeric substances on calcite precipitation rate and Mg/Cacalcite in the absence of cells is investigated using extracts of extracellular polymeric substances from temperate fluvial tufa biofilm. The influence is complex, with the concentration of extracellular polymeric substances in solution altering deposition rate and trace element incorporation. Moreover, the results show interaction of the presence/absence of extracellular polymeric substances and both temperature and salinity. However, despite extracting extracellular polymeric substances from the same parent sample, a uniform influence was not found in these experiments, implying that the mixture is sufficiently variable within a sample for microenvironments within the biofilm to either promote or inhibit mineralization. As sedimentologists, we can no longer take the view that extracellular polymeric substances are a bystander material, or that they have a single set of coherent and predictable or intuitive influences. Rather, the emphasis must be on investigating the specific mixtures present in nature, and their complex and dynamic interaction with both mineral surfaces and hydrochemical conditions.

Developing Nano-Delivery Systems for Agriculture and Food Applications with Nature-Derived Polymers.

The applications of nanotechnology are wide ranging, and developing functional nanomaterials for agri-food applications from nature-derived polymers is widely conceived as a sustainable approach that is safer for human and animal consumption. In light of this, this review focuses on the advances in the development of nano-delivery systems using nature-derived polymers for agri-food applications. The review opens with a section detailing the different types of nature-derived polymers currently being used in various applications in the agri-food industry with a special mention on microbial extracellular polymeric materials. The major applications of nano-delivery systems in the food sector, such as food fortification and food preservation, as well as in the agricultural sector for controlled release of agrochemicals using nature-derived polymers are discussed. The review ends with a perspective on the safety and public perception of nano-enabled foods with a concluding remark on future directions of incorporating nano-delivery systems for agri-food purposes.

Reserve, structural and extracellular polysaccharides of Chlorella vulgaris: A holistic approach

Chlorella vulgaris is a green microalga approved for human consumption with high biological value due to its high protein content and polyunsaturated fatty acids composition. Moreover, this microalga is rich in starch and structural polysaccharides that could have potential to be valued as food ingredients. To fulfill this hypothesis, starch digestibility was evaluated in raw and boiled biomass, showing 43% and 71% of glucose released, respectively. The low extraction yield of starch obtained with water (13%) allowed to infer protein hindrance. This was overcome by 1 M and 4 M KOH aqueous solutions that allowed to obtain an additional 51% of starch. The final residue left showed that only 16% of total starch remained unextracted. KOH solutions allowed also to obtain galactans composed by 1,3-, 1,6- and 1,3,6-linked galactose residues. These linkages were also observed in the polysaccharides recovered from the growth medium, showing similarity between the exopolysaccharides and those present in the cell wall. The extracellular polymeric material revealed immunostimulatory effect on B lymphocytes. This opens the possibility of the use of both starch and exopolysaccharides of C. vulgaris as food ingredients.

Advanced strategies for combating bacterial biofilms.

Biofilms are communities of microorganisms that are formed on and attached to living or nonliving surfaces and are surrounded by an extracellular polymeric material. Biofilm formation enjoys several advantages over the pathogens in the colonization process of medical devices and patients' organs. Unlike planktonic cells, biofilms have high intrinsic resistance to antibiotics and sanitizers, and overcoming them is a significant problematic challenge in the medical and food industries. There are no approved treatments to specifically target biofilms. Thus, it is required to study and present innovative and effective methods to combat a bacterial biofilm. In this review, several strategies have been discussed for combating bacterial biofilms to improve healthcare, food safety, and industrial process.

Response of natural phytoplankton communities exposed to crude oil and chemical dispersants during a mesocosm experiment

During the 2010 Deepwater Horizon oil spill, the chemical dispersant Corexit was applied over vast areas of the Gulf of Mexico. Marine phytoplankton play a key role in aggregate formation through the production of extracellular polymeric materials (EPS), an important step in the biological carbon pump. This study examined the impacts of oil and dispersants on the composition and physiology of natural marine phytoplankton communities from the Gulf of Mexico during a 72-hour mesocosm experiment and consequences to carbon export. The communities were treated using the water accommodated fraction (WAF) of oil, which was produced by adding Macondo surrogate oil to natural seawater and mixed for 24 h in the dark. A chemically enhanced WAF (CEWAF) was made in a similar manner, but using a mixture of oil and the dispersant Corexit in a 20:1 ratio as well as a diluted CEWAF (DCEWAF). Phytoplankton communities exposed to WAF showed no significant changes in PSII quantum yield (Fv/Fm) or electron transfer rates (ETRmax) compared to Control communities. In contrast, both Fv/Fm and ETRmax declined rapidly in communities treated with either CEWAF or DCEWAF. Analysis of other photophysiological parameters showed that photosystem II (PSII) antenna size and PSII connectivity factor were not altered by exposure to DCEWAF, suggesting that processes downstream of PSII were affected. The eukaryote community composition in each experimental tank was characterized at the end of the 72 h exposure time using 18S rRNA sequencing. Diatoms dominated the communities in both the control and WAF treatments (52 and 56% relative abundance respectively), while in CEWAF and DCEWAF treatments were dominated by heterotrophic Euglenozoa (51 and 84% respectively). Diatoms made up the largest relative contribution to the autotrophic eukaryote community in all treatments. EPS concentration was four times higher in CEWAF tanks compared to other treatments. Changes in particle size distributions (a proxy for aggregates) over time indicated that a higher degree of particle aggregation occurred in both the CEWAF and DCEWAF treatments than the WAF or Controls. Our results demonstrate that chemically dispersed oil has more negative impacts on photophysiology, phytoplankton community structure and aggregation dynamics than oil alone, with potential implications for export processes that affect the distribution and turnover of carbon and oil in the water column.

Intravascular catheters and biofilm control.

Intravascular catheters are the most common cause of nosocomially acquired bloodstream infections. Bacteria found adhering to the intraluminal surfaces of catheters are the principal source and cause of these infections. Adherent bacteria overtime are known to form multicellular communities which become encased within a three dimensional matrix of extracellular polymeric material known as biofilms, which are thought to be responsible for persistent infections. Consequently, a number of technologies have been developed to help prevent and control biofilms in intravascular catheters. One such approach involves impregnating catheter material with antimicrobial agents. Unfortunately these methods are not universally effective in preventing catheter-related biofilm infections. Technologies that utilise antimicrobials, as catheter locks have been shown to have more potential for preventing biofilm formation and reducing the incidences of catheter related bloodstream infections (CRBSI). This article discusses the significance of biofilms in intravascular catheters and determines whether the treatments available today are proving to be effective for controlling biofilms and draws attention to future avenues which are being investigated to control biofilms and therefore CRBSI.

Bacteriophages as Weapons Against Bacterial Biofilms in the Food Industry

Microbiological contamination in the food industry is often attributed to the presence of biofilms in processing plants. Bacterial biofilms are complex communities of bacteria attached to a surface and surrounded by an extracellular polymeric material. Their extreme resistance to cleaning and disinfecting processes is related to a unique organization, which implies a differential bacterial growth and gene expression inside the biofilm. The impact of biofilms on health, and the economic consequences, has promoted the development of different approaches to control or remove biofilm formation. Recently, successful results in phage therapy have boosted new research in bacteriophages and phage lytic proteins for biofilm eradication. In this regard, this review examines the environmental factors that determine biofilm development in food-processing equipment. In addition, future perspectives for the use of bacteriophage-derived tools as disinfectants are discussed.

The ultrastructure of subgingival dental plaque, revealed by high-resolution field emission scanning electron microscopy

Objectives/Aims:To explore the ultrastructure of subgingival dental plaque using high-resolution field emission scanning electron microscopy (FE-SEM) and to investigate whether extracellular DNA (eDNA) could be visualised in ex vivo samples.Materials and Methods:Ten patients were recruited who fulfilled the inclusion criteria (teeth requiring extraction with radiographic horizontal bone loss of over 50% and grade II/III mobility). In total, 12 teeth were extracted using a minimally traumatic technique. Roots were sectioned using a dental air turbine handpiece, under water cooling to produce 21 samples. Standard fixation and dehydration protocols were followed. For some samples, gold-labelled anti-DNA antibodies were applied before visualising biofilms by FE-SEM.Results:High-resolution FE-SEMs of subgingival biofilm were obtained in 90% of the samples. The sectioning technique left dental plaque biofilms undisturbed. Copious amounts of extracellular material were observed in the plaque, which may have been eDNA as they had a similar appearance to labelled eDNA from in vitro studies. There was also evidence of membrane vesicles and open-ended tubular structures. Efforts to label eDNA with immune-gold antibodies were unsuccessful and eDNA was not clearly labelled.Conclusions:High-resolution FE-SEM images were obtained of undisturbed subgingival ex vivo dental plaque biofilms. Important structural features were observed including extracellular polymeric material, vesicles and unusual open tubule structures that may be remnants of lysed cells. The application of an eDNA immune-gold-labelling technique, previously used successfully in in vitro samples, did not clearly identify eDNA in ex vivo samples. Further studies are needed to characterise the molecular composition of the observed extracellular matrix material.

Effects of inorganic nanoparticles on viability and catabolic activities of Agrobacterium sp. PH-08 during biodegradation of dibenzofuran.

This study investigated the cytotoxicity, genotoxicity, and growth inhibition effects of four different inorganic nanoparticles (NPs) such as aluminum (nAl), iron (nFe), nickel (nNi), and zinc (nZn) on a dibenzofuran (DF) degrading bacterium Agrobacterium sp. PH-08. NP (0-1,000 mg L(-1)) -treated bacterial cells were assessed for cytotoxicity, genotoxicity, growth and biodegradation activities at biochemical and molecular levels. In an aqueous system, the bacterial cells treated with nAl, nZn and nNi at 500 mg L(-1) showed significant reduction in cell viability (30-93.6 %, p < 0.05), while nFe had no significant inhibition on bacterial cell viability. In the presence of nAl, nZn and nNi, the cells exhibited elevated levels of reactive oxygen species (ROS), DNA damage and cell death. Furthermore, NP exposure showed significant (p < 0.05) impairment in DF and catechol biodegradation activities. The reduction in DF biodegradation was ranged about 71.7-91.6 % with single NPs treatments while reached up to 96.3 % with a mixture of NPs. Molecular and biochemical investigations also clearly revealed that NP exposure drastically affected the catechol-2,3-dioxygenase activities and its gene (c23o) expression. However, no significant inhibition was observed in nFe treatment. The bacterial extracellular polymeric materials and by-products from DF degradation can be assumed as key factors in diminishing the toxic effects of NPs, especially for nFe. This study clearly demonstrates the impact of single and mixed NPs on the microbial catabolism of xenobiotic-degrading bacteria at biochemical and molecular levels. This is the first study on estimating the impact of mixed NPs on microbial biodegradation.

Uncovering a microbial enigma: isolation and characterization of the streamer-generating, iron-oxidizing, acidophilic bacterium "Ferrovum myxofaciens".

A betaproteobacterium, shown by molecular techniques to have widespread global distribution in extremely acidic (pH 2 to 4) ferruginous mine waters and also to be a major component of "acid streamer" growths in mine-impacted water bodies, has proven to be recalcitrant to enrichment and isolation. A modified "overlay" solid medium was devised and used to isolate this bacterium from a number of mine water samples. The physiological and phylogenetic characteristics of a pure culture of an isolate from an abandoned copper mine ("Ferrovum myxofaciens" strain P3G) have been elucidated. "F. myxofaciens" is an extremely acidophilic, psychrotolerant obligate autotroph that appears to use only ferrous iron as an electron donor and oxygen as an electron acceptor. It appears to use the Calvin-Benson-Bassham pathway to fix CO2 and is diazotrophic. It also produces copious amounts of extracellular polymeric materials that cause cells to attach to each other (and to form small streamer-like growth in vitro) and to different solid surfaces. "F. myxofaciens" can catalyze the oxidative dissolution of pyrite and, like many other acidophiles, is tolerant of many (cationic) transition metals. "F. myxofaciens" and related clone sequences form a monophyletic group within the Betaproteobacteria distantly related to classified orders, with genera of the family Nitrosomonadaceae (lithoautotrophic, ammonium-oxidizing neutrophiles) as the closest relatives. On the basis of the phylogenetic and phenotypic differences of "F. myxofaciens" and other Betaproteobacteria, a new family, "Ferrovaceae," and order, "Ferrovales," within the class Betaproteobacteria are proposed. "F. myxofaciens" is the first extreme acidophile to be described in the class Betaproteobacteria.

The role of biofilms in reprocessing medical devices

Biofilms are communities of microorganisms within extracellular polymeric material attached to surfaces. Within a biofilm, cells have some protection from drying and other stress factors in their environment, including antimicrobial agents. In this article, the challenges to medical device reprocessing posed by biofilms are addressed. Biofilm formation on reusable medical device surfaces is a risk that can be controlled. By ensuring prompt device cleaning and reprocessing either by high-level disinfection or sterilization and proper drying, biofilms will not have a chance to form. Reusable medical devices like flexible endoscopes that are promptly cleaned and disinfected, rinsed and dried pose little risk to patients.

Genomic analysis of cold-active Colwelliaphage 9A and psychrophilic phage–host interactions

The 104kb genome of cold-active bacteriophage 9A, which replicates in the marine psychrophilic gamma-proteobacterium Colwellia psychrerythraea strain 34H (between -12 and 8°C), was sequenced and analyzed to investigate elements of molecular adaptation to low temperature and phage-host interactions in the cold. Most characterized ORFs indicated closest similarity to gamma-proteobacteria and their phages, though no single module provided definitive phylogenetic grouping. A subset of primary structural features linked to psychrophily suggested that the majority of annotated phage proteins were not psychrophilic; those that were, primarily serve phage-specific functions and may also contribute to 9A's restricted temperature range for replication as compared to host. Comparative analyses suggest ribonucleotide reductase genes were acquired laterally from host. Neither restriction modification nor the CRISPR-Cas system appeared to be the predominant phage defense mechanism of Cp34H or other cold-adapted bacteria; we hypothesize that psychrophilic hosts rely more on the use of extracellular polymeric material to block cell surface receptors recognized by phages. The relative dearth of evidence for genome-specific defenses, genetic transfer events or auxiliary metabolic genes suggest that the 9A-Cp34H system may be less tightly coupled than are other genomically characterized marine phage-host systems, with possible implications for phage specificity under different environmental conditions.

Calcium Carbonate Mineralization: Involvement of Extracellular Polymeric Materials Isolated from Calcifying Bacteria

This study highlights the role of specific outer bacterial structures, such as the glycocalix, in calcium carbonate crystallization in vitro. We describe the formation of calcite crystals by extracellular polymeric materials, such as exopolysaccharides (EPS) and capsular polysaccharides (CPS) isolated from Bacillus firmus and Nocardia calcarea. Organic matrices were isolated from calcifying bacteria grown on synthetic medium--in the presence or absence of calcium ions--and their effect on calcite precipitation was assessed. Scanning electron microscopy observations and energy dispersive X-ray spectrometry analysis showed that CPS and EPS fractions were involved in calcium carbonate precipitation, not only serving as nucleation sites but also through a direct role in crystal formation. The utilization of different synthetic media, with and without addition of calcium ions, influenced the biofilm production and protein profile of extracellular polymeric materials. Proteins of CPS fractions with a molecular mass between 25 and 70 kDa were overexpressed when calcium ions were present in the medium. This higher level of protein synthesis could be related to the active process of bioprecipitation.

Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa)*

BackgroundMicroalgae hold promise for yielding a biofuel feedstock that is sustainable, carbon-neutral, distributed, and only minimally disruptive for the production of food and feed by traditional agriculture. Amongst oleaginous eukaryotic algae, the B race of Botryococcus braunii is unique in that it produces large amounts of liquid hydrocarbons of terpenoid origin. These are comparable to fossil crude oil, and are sequestered outside the cells in a communal extracellular polymeric matrix material. Biosynthetic engineering of terpenoid bio-crude production requires identification of genes and reconstruction of metabolic pathways responsible for production of both hydrocarbons and other metabolites of the alga that compete for photosynthetic carbon and energy.ResultsA de novo assembly of 1,334,609 next-generation pyrosequencing reads form the Showa strain of the B race of B. braunii yielded a transcriptomic database of 46,422 contigs with an average length of 756 bp. Contigs were annotated with pathway, ontology, and protein domain identifiers. Manual curation allowed the reconstruction of pathways that produce terpenoid liquid hydrocarbons from primary metabolites, and pathways that divert photosynthetic carbon into tetraterpenoid carotenoids, diterpenoids, and the prenyl chains of meroterpenoid quinones and chlorophyll. Inventories of machine-assembled contigs are also presented for reconstructed pathways for the biosynthesis of competing storage compounds including triacylglycerol and starch. Regeneration of S-adenosylmethionine, and the extracellular localization of the hydrocarbon oils by active transport and possibly autophagy are also investigated.ConclusionsThe construction of an annotated transcriptomic database, publicly available in a web-based data depository and annotation tool, provides a foundation for metabolic pathway and network reconstruction, and facilitates further omics studies in the absence of a genome sequence for the Showa strain of B. braunii, race B. Further, the transcriptome database empowers future biosynthetic engineering approaches for strain improvement and the transfer of desirable traits to heterologous hosts.