Microbial conversion of sugars from plant biomass to lactic acid or ethanol

Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment

Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.

Spectral Unmixing for Label-Free, In-Liquid Characterization of Biomass Microstructure and Biopolymer Content by Coherent Raman Imaging

Characterization of lignocellulosic biomass microstructure with chemical specificity and under physiological conditions could provide invaluable insights to our understanding of plant tissue development, microstructure, origins of recalcitrance, degradation, and solubilization. However, most methods currently available are either destructive, are not compatible with hosting a physiological environment, or introduces exogenous probes, complicating their use for studying changes in microstructure and mechanisms of plant development, recalcitrance, or degradation in situ. To address these challenges, we here present a multi-modal chemically specific imaging technique based on coherent anti-Stokes Raman scattering (CARS) microspectroscopy with simplex maximization and entropy-based spectral unmixing enabling label-free, chemically specific characterization of plant microstructure in liquid. We describe how spatial drift of samples suspended in liquid can introduce artifacts in spectral unmixing procedures for single-frequency CARS and propose a mitigative strategy toward these effects using simultaneously acquired forward-scattered CARS signals and epi-detected autofluorescence. We further apply the technique for chemical and microstructural characterization of untreated and liquid hot water pretreated rapeseed straw by CARS and show how the framework can be extended for 3D imaging with chemical specificity. Finally, we provide examples of the intricate chemical and microstructural details recovered by this hybrid imaging technique, including discerning between primary and secondary cell walls, localization of aqueous components to cell lumina, and the presence of funnel-type pits in samples ofBrassica napus.

Chromohalobacter salixigens Uronate Dehydrogenase: Directed Evolution for Improved Thermal Stability and Mutant CsUDH-inc X-ray Crystal Structure

Chromohalobacter salixigens contains a uronate dehydrogenase termed CsUDH that can convert uronic acids to their corresponding C1,C6-dicarboxy aldaric acids, an important enzyme reaction applicable for biotechnological use of sugar acids. To increase the thermal stability of this enzyme for biotechnological processes, directed evolution using gene family shuffling was applied, and the hits selected from 2-tier screening of a shuffled gene family library contained in total 16 mutations, only some of which when examined individually appreciably increased thermal stability. Most mutations, while having minimal or no effect on thermal stability when tested in isolation, were found to exhibit synergy when combined; CsUDH-inc containing all 16 mutations had ΔK _t ^0.5 +18 °C, such that k _cat was unaffected by incubation for 1 hr at ~70 °C. X-ray crystal structure of CsUDH-inc showed tight packing of the mutated residue side-chains, and comparison of rescaled B-values showed no obvious differences between wild type and mutant structures. Activity of CsUDH-inc was severely depressed on glucuronic and galacturonic acids. Combining select combinations of only three mutations resulted in good or comparable activity on these uronic acids, while maintaining some improved thermostability with ΔK _t ^0.5 ~+ 10 °C, indicating potential to further thermally optimize CsUDH for hyperthermophilic reaction environments.

A novel colorimetric indicator for ethanol detection in preserved baby mangoes

A colorimetric indicator cube for use in smart packaging was designed and fabricated to detect ethanol produced by microbial fermentation in preserved baby mangoes. The presence and level of ethanol was indicated by color variations of the indicator cube, which consists of porous melamine foam (MF) that entraps an indicator solution of potassium dichromate and sulfuric acid. Within the packaging, the cube sits behind a gas-permeable membrane. The morphological structure of MF was studied by digital microscope and X-ray fluorescence analysis. In the optimal condition, the indicator cube exhibited distinct color changes from yellow to brown, green and blue over an ethanol concentration range from 0.25% to 5.0%. Color changes were clearly visible to the naked eye. The repeatability of the ethanol indicator cube was good and storage stability was maintained for up to 19 and 74 days at room and refrigeration temperatures, respectively. The smart packaging was applied to detect ethanol in preserved baby mangoes at different storage times.

Metataxonomic analysis of bacterial communities and mycotoxin reduction during processing of three millet varieties into ogi, a fermented cereal beverage

Ogi is a fermented cereal beverage, made primarily from maize (Zea mays) and rarely from millets. Unlike maize-based ogi, little is known about the bacterial community and mycotoxin profile during the production of millet-based ogi. Therefore, the bacterial community dynamics and mycotoxin reduction during ogi processing from three millet varieties were investigated using next-generation sequencing of the 16S rRNA gene and liquid chromatography-tandem mass spectrometry, respectively. A total of 1163 amplicon sequence variants (ASVs) were obtained, with ASV diversity across time intervals influenced by processing stage and millet variety. ASV distribution among samples suggested that the souring stage was more influenced by millet variety than the steeping stage, and that souring may be crucial for the quality attributes of the ogi. Furthermore, bacterial community structure during steeping and souring was significantly differentiated (PERMANOVA, P < 0.05) between varieties, with close associations observed for closely-related millet varieties. Taxonomically, Firmicutes, followed by Actinobacteria, Bacteroidetes, Cyanobacteria and Proteobacteria phyla were relatively abundant (>1%). Lactic acid bacteria, such as Burkholderia-Caballeronia-Paraburkholderia, Lactobacillus, Lactococcus and Pediococcus, dominated most fermentation stages, suggesting their roles as key fermentative and functional bacteria in relation to mycotoxin reduction. About 52-100%, 58-100% and 100% reductions in mycotoxin (aflatoxins, beauvericin, citrinin, moniliformin, sterigmatocystin and zearalenone) concentrations were recorded after processing of white fonio, brown fonio and finger millet, respectively, into ogi. This study provides new knowledge of the dominant bacterial genera vital for the improvement of millet-based ogi through starter culture development and as well, elucidates the role of processing in reducing mycotoxins in millet ogi.

Non-sterile fermentation of food waste using thermophilic and alkaliphilic Bacillus licheniformis YNP5-TSU for 2,3-butanediol production

Conversion of food waste into 2,3-butanediol (2,3-BDO) via microbial fermentation provides a promising way to reduce waste disposal to landfills and produce sustainable chemicals. However, sterilization of food waste, an energy- and capital-costly process, is generally required before fermentation to avoid any contamination, which reduces the energy net output and economic feasibility of food waste fermentation. In this study, we investigated the non-sterile fermentation of food waste to produce 2,3-BDO using a newly isolated thermophilic and alkaliphilic B. licheniformis YNP5-TSU. Three unitary food waste samples (i.e., pepper, pineapple, cabbage wastes) and one miscellaneous food waste mixture were respectively inoculated with B. licheniformis YNP5-TSU under non-sterile conditions. At 50 °C and an initial pH of 9.0, B. licheniformis YNP5-TSU was able to consume all sugars in food waste and produce 5.2, 5.9, 5.9 and 4.3 g/L of 2,3-BDO within 24 h from pepper, pineapple, cabbage and miscellaneous wastes, respectively, corresponding to a yield of 0.40, 0.38, 0.41 and 0.41 g 2,3-BDO/g sugar. These 2,3-BDO concentrations and yields from the non-sterile fermentations were comparable to those from the traditional sterile fermentations, which produced 4.0-6.8 g/L of 2,3-BDO with yields of 0.31-0.48 g 2,3-BDO/g sugar. Moreover, B. licheniformis was able to ferment various food wastes (pepper, pineapple and miscellaneous wastes) without any external nutrient addition and produce similar 2,3-BDO quantities. The non-sterile fermentation of food waste using novel thermophilic and alkaliphilic B. licheniformis YNP5-TSU provides a robust and energy-efficient approach to convert food waste to high-value chemicals.

Microbial extraction of chitin from seafood waste using sugars derived from fruit waste-stream

Chitin and chitosan are natural amino polysaccharides that have exceptional biocompatibility in a wide range of applications such as drug delivery carriers, antibacterial agents and food stabilizers. However, conventional chemical extraction methods of chitin from marine waste are costly and hazardous to the environment. Here we report a study where shrimp waste was co-fermented with Lactobacillus plantarum subsp. plantarum ATCC 14917 and Bacillus subtilis subsp. subtilis ATCC 6051 and chitin was successfully extracted after deproteinization and demineralization of the prawn shells. The glucose supplementation for fermentation was replaced by waste substrates to reduce cost and maximize waste utilization. A total of 10 carbon sources were explored, namely sugarcane molasses, light corn syrup, red grape pomace, white grape pomace, apple peel, pineapple peel and core, potato peel, mango peel, banana peel and sweet potato peel. The extracted chitin was chemically characterized by Fourier Transform Infrared Spectroscopy (FTIR) to measure the degree of acetylation, elemental analysis (EA) to measure the carbon/nitrogen ratio and X-ray diffraction (XRD) to measure the degree of crystallinity. A comparison of the quality of the crude extracted chitin was made between the different waste substrates used for fermentation and the experimental results showed that the waste substrates generally make a suitable replacement for glucose in the fermentation process. Red grape pomace resulted in recovery of chitin with a degree of deacetylation of 72.90%, a carbon/nitrogen ratio of 6.85 and a degree of crystallinity of 95.54%. These achieved values were found to be comparable with and even surpassed commercial chitin.

Penicillium camemberti galacturonate reductase: C-1 oxidation/reduction of uronic acids and substrate inhibition mitigation by aldonic acids

The enzyme galacturonate oxidoreductase PcGOR from Penicillium camemberti reduces the C-1 carbon of D-glucuronate and C-4 epimer D-galacturonate to their corresponding aldonic acids, important reactions in both pectin catabolism and ascorbate biosynthesis. PcGOR was active on both glucuronic acid and galacturonic acid, with similar substrate specificities (k_cat/K_m) using the preferred co-substrate NADPH. Substrate acceptance extended to lactone congeners, and D-glucurono-3,6-lactone was converted to L-gulono-1,4-lactone, an immediate precursor of ascorbate. Reaction with glucuronate showed only minor substrate inhibition, and the product L-gulonate and L-gulono-1,4-lactone were both found to be competitive inhibitors with K_i in the low mM range. In contrast, reaction with C-4 epimer galacturonate displayed marked substrate inhibition. Moreover, the product L-galactonate and L-galactono-1,4-lactone were observed to mitigate substrate inhibition by galacturonate, with the lactone having a greater effect than the acid.

Basidiomycotic Yeast Cryptococcus diffluens Converts l-Galactonic Acid to the Compound on the Similar Metabolic Pathway in Ascomycetes

(1) Background: It has been shown that d-galacturonic acid is converted to l-galactonic acid by the basidiomycotic yeast, Cryptococcus diffluens. However, two pathways are hypothesized for the l-galactonic acid conversion process in C. diffluens. One is similar to the conversion process of the filamentous fungi in d-galacturonic acid metabolism and another is the conversion process to l-ascorbic acid, reported in the related yeast, C. laurentii. It is necessary to determine which, if either, process occurs in C. diffluens in order to produce novel value-added products from d-galacturonic acid using yeast strains. (2) Methods: The diethylaminoethy (DEAE)-fractionated enzyme was prepared from the cell-free extract of C. diffluens by the DEAE column chromatography. The l-galactonic acid conversion activity was assayed using DEAE-fractionated enzyme and the converted product was detected and fractionated by high-performance anion-exchange chromatography. Then, the molecular structure was identified by nuclear magnetic resonance analysis. (3) Results: The product showed similar chemical properties to 2-keto-3-deoxy-l-galactonic acid (l-threo-3-deoxy-hexulosonic acid). (4) Conclusions: It is suggested that l-galactonic acid is converted to 2-keto-3-deoxy-l-galactonic acid by dehydratase in C. diffluens. The l-galactonic acid conversion process of C. diffluens is a prioritized pathway, similar to the pathway of ascomycetes.

Exploring the microbiota and metabolites of traditional rice beer varieties of Assam and their functionalities

Rice beer is traditionally prepared and consumed by various ethnic populations in the Southeast Asian countries. To understand the probable effects of rice beer on human health, present research was aimed to study biochemical parameters, microbial diversity and metabolites of major rice beer varieties of Assam, namely Apong (Poro and Nogin), Xaaj and Joubishi. Alcoholic content of rice beer varieties varied from 9.41 to 19.33% (v/v). Free radical scavenging activity against DPPH· and ABTS⁺ were 1.94-4.14 and 1.69-3.91 mg of ascorbic acid/ml of rice beer, respectively. In relation to antioxidant activities, phenolic content varied from 2.07 to 5.40 mg gallic acid/ml of rice beer. Next-generation sequencing of 16S rDNA showed that 18 genera of bacteria were present irrespective of rice beer varieties in which lactic acid bacteria were the dominant group (90% abundance). Functional predictions based on the bacterial profiles indicated pathways, such as metabolisms of carbohydrate, amino acid, vitamins and cofactors, and xenobiotic biodegradation, to be active in the rice beer varieties. Out of 18 core bacterial genera, 7 had correlations with the predicted functions. Gas chromatography and mass spectroscopy-based metabolite analysis revealed that the metabolite profiles of the rice beer varieties consisted of 18 saccharides, 18 organic acids, 11 sugar alcohols, 8 amino acids, 1 vitamin and nutraceutical compounds thiocoumarine, carotene, oxazolidine-2-one and acetyl tyrosine. Due to the presence of potent prebiotics, probiotics and nutraceuticals, rice beer may have health benefits which need to be studied further.

Galacturonate Metabolism in Anaerobic Chemostat Enrichment Cultures: Combined Fermentation and Acetogenesis by the Dominant sp. nov. "Candidatus Galacturonibacter soehngenii"

Agricultural residues such as sugar beet pulp and citrus peel are rich in pectin, which contains galacturonic acid as a main monomer. Pectin-rich residues are underexploited as feedstocks for production of bulk chemicals or biofuels. The anaerobic, fermentative conversion of d-galacturonate in anaerobic chemostat enrichment cultures provides valuable information toward valorization of these pectin-rich feedstocks. Replicate anaerobic chemostat enrichments, with d-galacturonate as the sole limiting carbon source and inoculum from cow rumen content and rotting orange peels, yielded stable microbial communities, which were dominated by a novel Lachnospiraceae species, for which the name "Candidatus Galacturonibacter soehngenii" was proposed. Acetate was the dominant catabolic product, with formate and H₂ as coproducts. The observed molar ratio of acetate and the combined amounts of H₂ and formate deviated significantly from 1, which suggested that some of the hydrogen and CO₂ formed during d-galacturonate fermentation was converted into acetate via the Wood-Ljungdahl acetogenesis pathway. Indeed, metagenomic analysis of the enrichment cultures indicated that the genome of "Candidatus G. soehngenii" encoded enzymes of the adapted Entner-Doudoroff pathway for d-galacturonate metabolism as well as enzymes of the Wood-Ljungdahl pathway. The simultaneous operation of these pathways may provide a selective advantage under d-galacturonate-limited conditions by enabling a higher specific ATP production rate and lower residual d-galacturonate concentration than would be possible with a strictly fermentative metabolism of this carbon and energy source.IMPORTANCE This study on d-galacturonate metabolism by open, mixed-culture enrichments under anaerobic, d-galacturonate-limited chemostat conditions shows a stable and efficient fermentation of d-galacturonate into acetate as the dominant organic fermentation product. This fermentation stoichiometry and population analyses provide a valuable baseline for interpretation of the conversion of pectin-rich agricultural feedstocks by mixed microbial cultures. Moreover, the results of this study provide a reference for studies on the microbial metabolism of d-galacturonate under different cultivation regimes.

Identification and Characterization of 5' Untranslated Regions (5'UTRs) in Zymomonas mobilis as Regulatory Biological Parts

Regulatory RNA regions within a transcript, particularly in the 5' untranslated region (5'UTR), have been shown in a variety of organisms to control the expression levels of these mRNAs in response to various metabolites or environmental conditions. Considering the unique tolerance of Zymomonas mobilis to ethanol and the growing interest in engineering microbial strains with enhanced tolerance to industrial inhibitors, we searched natural cis-regulatory regions in this microorganism using transcriptomic data and bioinformatics analysis. Potential regulatory 5'UTRs were identified and filtered based on length, gene function, relative gene counts, and conservation in other organisms. An in vivo fluorescence-based screening system was developed to confirm the responsiveness of 36 5'UTR candidates to ethanol, acetate, and xylose stresses. UTR_ZMO0347 (5'UTR of gene ZMO0347 encoding the RNA binding protein Hfq) was found to down-regulate downstream gene expression under ethanol stress. Genomic deletion of UTR_ZMO0347 led to a general decrease of hfq expression at the transcript level and increased sensitivity for observed changes in Hfq expression at the protein level. The role of UTR_ZMO0347 and other 5'UTRs gives us insight into the regulatory network of Z. mobilis in response to stress and unlocks new strategies for engineering robust industrial strains as well as for harvesting novel responsive regulatory biological parts for controllable gene expression platforms in this organism.

Environmental impacts of producing bioethanol and biobased lactic acid from standalone and integrated biorefineries using a consequential and an attributional life cycle assessment approach

This study evaluates the environmental impacts of biorefinery products using consequential (CLCA) and attributional (ALCA) life cycle assessment (LCA) approaches. Within ALCA, economic allocation method was used to distribute impacts among the main products and the coproducts, whereas within the CLCA system expansion was adopted to avoid allocation. The study seeks to answer the questions (i) what is the environmental impacts of process integration?, and (ii) do CLCA and ALCA lead to different conclusions when applied to biorefinery?. Three biorefinery systems were evaluated and compared: a standalone system producing bioethanol from winter wheat-straw (system A), a standalone system producing biobased lactic acid from alfalfa (system B), and an integrated biorefinery system (system C) combining the two standalone systems and producing both bioethanol and lactic acid. The synergy of the integration was the exchange of useful energy necessary for biomass processing in the two standalone systems. The systems were compared against a common reference flow: "1MJ_EtOH+1kg_LA", which was set on the basis of products delivered by the system C. Function of the reference flow was to provide service of both fuel (bioethanol) at 99.9% concentration (wt. basis) and biochemical (biobased lactic acid) in food industries at 90% purity; both products delivered at biorefinery gate. The environmental impacts of interest were global warming potential (GWP₁₀₀), eutrophication potential (EP), non-renewable energy (NRE) use and the agricultural land occupation (ALO). Regardless of the LCA approach adopted, system C performed better in most of the impact categories than both standalone systems. The process wise contribution to the obtained environmental impacts also showed similar impact pattern in both approaches. The study also highlighted that the recirculation of intermediate materials, e.g. C₅ sugar to boost bioethanol yield and that the use of residual streams in the energy conversion were beneficial for optimizing the system performance.

Involvement of Agrobacterium tumefaciens Galacturonate Tripartite ATP-Independent Periplasmic (TRAP) Transporter GaaPQM in Virulence Gene Expression

Monosaccharides capable of serving as nutrients for the soil bacterium Agrobacterium tumefaciens are also inducers of the vir regulon present in the tumor-inducing (Ti) plasmid of this plant pathogen. One such monosaccharide is galacturonate, the predominant monomer of pectin found in plant cell walls. This ligand is recognized by the periplasmic sugar binding protein ChvE, which interacts with the VirA histidine kinase that controls vir gene expression. Although ChvE is also a member of the ChvE-MmsAB ABC transporter involved in the utilization of many neutral sugars, it is not involved in galacturonate utilization. In this study, a putative tripartite ATP-independent periplasmic (TRAP) transporter, GaaPQM, is shown to be essential for the utilization of galacturonic acid; we show that residue R169 in the predicted sugar binding site of the GaaP is required for activity. The gene upstream of gaaPQM (gaaR) encodes a member of the GntR family of regulators. GaaR is shown to repress the expression of gaaPQM, and the repression is relieved in the presence of the substrate for GaaPQM. Moreover, GaaR is shown to bind putative promoter regions in the sequences required for galacturonic acid utilization. Finally, A. tumefaciens strains carrying a deletion of gaaPQM are more sensitive to galacturonate as an inducer of vir gene expression, while the overexpression of gaaPQM results in strains being less sensitive to this vir inducer. This supports a model in which transporter activity is crucial in ensuring that vir gene expression occurs only at sites of high ligand concentration, such as those at a plant wound site.

L-lactic acid production from D-xylose with Candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene

Background

Bioplastics, like polylactic acid (PLA), are renewable alternatives for petroleum-based plastics. Lactic acid, the monomer of PLA, has traditionally been produced biotechnologically with bacteria. With genetic engineering, yeast have the potential to replace bacteria in biotechnological lactic acid production, with the benefits of being acid tolerant and having simple nutritional requirements. Lactate dehydrogenase genes have been introduced to various yeast to demonstrate this potential. Importantly, an industrial lactic acid producing process utilising yeast has already been implemented. Utilisation of D-xylose in addition to D-glucose in production of biochemicals such as lactic acid by microbial fermentation would be beneficial, as it would allow lignocellulosic raw materials to be utilised in the production processes.

Results

The yeast Candida sonorensis, which naturally metabolises D-xylose, was genetically modified to produce L-lactic acid from D-xylose by integrating the gene encoding L-lactic acid dehydrogenase (ldhL) from Lactobacillus helveticus into its genome. In microaerobic, CaCO₃-buffered conditions a C. sonorensis ldhL transformant having two copies of the ldhL gene produced 31 g l⁻¹ lactic acid from 50 g l⁻¹ D-xylose free of ethanol.

Anaerobic production of lactic acid from D-xylose was assessed after introducing an alternative pathway of D-xylose metabolism, i.e. by adding a xylose isomerase encoded by XYLA from Piromyces sp. alone or together with the xylulokinase encoding gene XKS1 from Saccharomyces cerevisiae. Strains were further modified by deletion of the endogenous xylose reductase encoding gene, alone or together with the xylitol dehydrogenase encoding gene. Strains of C. sonorensis expressing xylose isomerase produced L-lactic acid from D-xylose in anaerobic conditions. The highest anaerobic L-lactic acid production (8.5 g l⁻¹) was observed in strains in which both the xylose reductase and xylitol dehydrogenase encoding genes had been deleted and the xylulokinase encoding gene from S. cerevisiae was overexpressed.

Conclusions

Integration of two copies of the ldhL gene in C. sonorensis was sufficient to obtain good L-lactic acid production from D-xylose. Under anaerobic conditions, the ldhL strain with exogenous xylose isomerase and xylulokinase genes expressed and the endogenous xylose reductase and xylitol dehydrogenase genes deleted had the highest L- lactic acid production.

Towards lactic acid bacteria-based biorefineries

Lactic acid bacteria (LAB) have long been used in industrial applications mainly as starters for food fermentation or as biocontrol agents or as probiotics. However, LAB possess several characteristics that render them among the most promising candidates for use in future biorefineries in converting plant-derived biomass-either from dedicated crops or from municipal/industrial solid wastes-into biofuels and high value-added products. Lactic acid, their main fermentation product, is an attractive building block extensively used by the chemical industry, owing to the potential for production of polylactides as biodegradable and biocompatible plastic alternative to polymers derived from petrochemicals. LA is but one of many high-value compounds which can be produced by LAB fermentation, which also include biofuels such as ethanol and butanol, biodegradable plastic polymers, exopolysaccharides, antimicrobial agents, health-promoting substances and nutraceuticals. Furthermore, several LAB strains have ascertained probiotic properties, and their biomass can be considered a high-value product. The present contribution aims to provide an extensive overview of the main industrial applications of LAB and future perspectives concerning their utilization in biorefineries. Strategies will be described in detail for developing LAB strains with broader substrate metabolic capacity for fermentation of cheaper biomass.

Enhanced L-lactic acid production from biomass-derived xylose by a mutant Bacillus coagulans

Xylose effective utilization is crucial for production of bulk chemicals from low-cost lignocellulosic substrates. In this study, an efficient L-lactate production process from xylose by a mutant Bacillus coagulans NL-CC-17 was demonstrated. The nutritional requirements for L-lactate production by B. coagulans NL-CC-17 were optimized statistically in shake flask fermentations. Corn steep liquor powder and yeast exact were identified as the most significant factors by the two-level Plackett-Burman design. Steepest ascent experiments were applied to approach the optimal region of the two factors, and a central composite design was employed to determine their optimal levels. The optimal medium was used to perform batch fermentation in a 3-l bioreactor. A maximum of 90.29 g l(-1)  L-lactic acid was obtained from 100 g l(-1) xylose in 120 h. When using corn stove prehydrolysates as substrates, 23.49 g l(-1)  L-lactic acid was obtained in 36 h and the yield was 83.09 %.

Yamadazyma ubonensis f.a., sp. nov., a novel xylitol-producing yeast species isolated in Thailand

Three hundred and thirty-seven xylose-utilizing yeast strains were isolated from various natural samples. Among these, 68 strains produced xylitol in the range of 0.1-0.69 g xylitol/g xylose. Thirty-nine xylitol-producing strains were identified to be Candida tropicalis. Ten strains were found belonging to 14 known species in the genus Candida, Cyberlindnera, Meyerozyma, Pichia, Wickerhamomyces, Yamadazyma and Cryptococcus. Two strains were identified to be two Candida species and two strains (DMKU-XE142(T) and DMKU-XE332) were found to be a novel species. Strain DMKU-XE142(T) was isolated from tree bark and DMKU-XE332 was obtained from decaying plant leaf collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 region of the large subunit rRNA gene (LSU) and the internal transcribed spacer (ITS) region, the two strains were determined to represent a novel Yamadazyma species although formation of ascospores was not observed. The sequences of the D1/D2 region of the LSU rRNA gene and the ITS region of the two strains were identical but differed from Yamadazyma phyllophila, the closest species in terms of pairwise sequence similarity of the D1/D2 region, by 1.7 % nucleotide substitutions and 3.5 % nucleotide substitutions in the ITS region. The name Yamadazyma ubonensis f.a., sp. nov. is proposed (type strain is DMKU-XE142(T) = BCC 61020(T) = CBS 12859(T)).

Wickerhamomyces xylosica sp. nov. and Candida phayaonensis sp. nov., two xylose-assimilating yeast species from soil

Two strains (NT29T and NT31T) of xylose-assimilating yeasts were obtained from soils collected in northern Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer region, the two strains were found to represent two novel ascomycete yeast species. Strain NT29T was assigned to the genus Candida belonging to the Pichia clade as a representative of Candida phayaonensis sp. nov.; the type strain is NT29T ( = BCC 47634T = NBRC 108868T = CBS 12319T). Strain NT31T represented a novel Wickerhamomyces species, which was named Wickerhamomyces xylosica sp. nov.; the type strain is NT31T ( = BCC 47635T = NBRC 108869T = CBS 12320T).

Engineering filamentous fungi for conversion of D-galacturonic acid to L-galactonic acid

D-Galacturonic acid, the main monomer of pectin, is an attractive substrate for bioconversions, since pectin-rich biomass is abundantly available and pectin is easily hydrolyzed. l-Galactonic acid is an intermediate in the eukaryotic pathway for d-galacturonic acid catabolism, but extracellular accumulation of l-galactonic acid has not been reported. By deleting the gene encoding l-galactonic acid dehydratase (lgd1 or gaaB) in two filamentous fungi, strains were obtained that converted d-galacturonic acid to l-galactonic acid. Both Trichoderma reesei Δlgd1 and Aspergillus niger ΔgaaB strains produced l-galactonate at yields of 0.6 to 0.9 g per g of substrate consumed. Although T. reesei Δlgd1 could produce l-galactonate at pH 5.5, a lower pH was necessary for A. niger ΔgaaB. Provision of a cosubstrate improved the production rate and titer in both strains. Intracellular accumulation of l-galactonate (40 to 70 mg g biomass(-1)) suggested that export may be limiting. Deletion of the l-galactonate dehydratase from A. niger was found to delay induction of d-galacturonate reductase and overexpression of the reductase improved initial production rates. Deletion of the l-galactonate dehydratase from A. niger also delayed or prevented induction of the putative d-galacturonate transporter An14g04280. In addition, A. niger ΔgaaB produced l-galactonate from polygalacturonate as efficiently as from the monomer.

Banana by-products: an under-utilized renewable food biomass with great potential

Banana (Musaceae) is one of the world's most important fruit crops that is widely cultivated in tropical countries for its valuable applications in food industry. Its enormous by-products are an excellent source of highly valuable raw materials for other industries by recycling agricultural waste. This prevents an ultimate loss of huge amount of untapped biomass and environmental issues. This review discusses extensively the breakthrough in the utilization of banana by-products such as peels, leaves, pseudostem, stalk and inflorescence in various food and non-food applications serving as thickening agent, coloring and flavor, alternative source for macro and micronutrients, nutraceuticals, livestock feed, natural fibers, and sources of natural bioactive compounds and bio-fertilizers. Future prospects and challenges are the important key factors discussed in association to the sustainability and feasibility of utilizing these by-products. It is important that all available by-products be turned into highly commercial outputs in order to sustain this renewable resource and provide additional income to small scale farming industries without compromising its quality and safety in competing with other commercial products.

Understanding physiological responses to pre-treatment inhibitors in ethanologenic fermentations

Alcohol-based liquid fuels feature significantly in the political and social agendas of many countries, seeking energy sustainability. It is certain that ethanol will be the entry point for many sustainable processes. Conventional ethanol production using maize- and sugarcane-based carbohydrates with Saccharomyces cerevisiae is well established, while lignocellulose-based processes are receiving growing interest despite posing greater technical and scientific challenges. A significant challenge that arises from the chemical hydrolysis of lignocellulose is the generation of toxic compounds in parallel with the release of sugars. These compounds, collectively termed pre-treatment inhibitors, impair metabolic functionality and growth. Their removal, pre-fermentation or their abatement, via milder hydrolysis, are currently uneconomic options. It is widely acknowledged that a more cost effective strategy is to develop resistant process strains. Here we describe and classify common inhibitors and describe in detail the reported physiological responses that occur in second-generation strains, which include engineered yeast and mesophilic and thermophilic prokaryotes. It is suggested that a thorough understanding of tolerance to common pre-treatment inhibitors should be a major focus in ongoing strain engineering. This review is a useful resource for future metabolic engineering strategies.

Addition of genes for cellobiase and pectinolytic activity in Escherichia coli for fuel ethanol production from pectin-rich lignocellulosic biomass

Ethanologenic Escherichia coli strain KO11 was sequentially engineered to contain the Klebsiella oxytoca cellobiose phosphotransferase genes (casAB) as well as a pectate lyase (pelE) from Erwinia chrysanthemi, yielding strains LY40A (casAB) and JP07 (casAB pelE), respectively. To obtain an effective secretion of PelE, the Sec-dependent pathway out genes from E. chrysanthemi were provided on a cosmid to strain JP07 to construct strain JP07C. Finally, oligogalacturonide lyase (ogl) from E. chrysanthemi was added to produce strain JP08C. E. coli strains LY40A, JP07, JP07C, and JP08C possessed significant cellobiase activity in cell lysates, while only strains JP07C and JP08C demonstrated extracellular pectate lyase activity. Fermentations conducted by using a mixture of pure sugars representative of the composition of sugar beet pulp (SBP) showed that strains LY40A, JP07, JP07C, and JP08C were able to ferment cellobiose, resulting in increased ethanol production from 15 to 45% in comparison to that of KO11. Fermentations with SBP at very low fungal enzyme loads during saccharification revealed significantly higher levels of ethanol production for LY40A, JP07C, and JP08C than for KO11. JP07C ethanol yields were not considerably higher than those of LY40A; however, oligogalacturonide polymerization studies showed an increased breakdown of biomass to small-chain (degree of polymerization, ≤6) oligogalacturonides. JP08C achieved a further breakdown of polygalacturonate to monomeric sugars, resulting in a 164% increase in ethanol yields compared to those of KO11. The addition of commercial pectin methylesterase (PME) further increased JP08C ethanol production compared to that of LY40A by demethylating the pectin for enzymatic attack by pectin-degrading enzymes.

Candida saraburiensis sp. nov. and Candida prachuapensis sp. nov., xylose-utilizing yeast species isolated in Thailand

Four strains of two novel xylose-utilizing yeast species were obtained from samples collected in Thailand from decaying corncobs (strains KU-Xs13T and KU-Xs18), a decaying grass (KU-Xs20) and estuarine water from a mangrove forest (WB15T). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 domain of the large subunit rRNA gene, the four strains were found to represent two novel species of the genus Candida in the Candida albicans/Lodderomyces elongisporus clade. Three strains (KU-Xs13T, KU-Xs18 and KU-Xs20) were assigned as a single novel species, which was named Candida saraburiensis sp. nov. The type strain is KU-Xs13T (=CBS 11696T=NBRC 106721T=BCC 39601T). Strain WB15T represented another novel species of the genus Candida that was named Candida prachuapensis sp. nov. The type strain is WB15T (=CBS 11024T=NBRC 104881T=BCC 29904T).

Identification in Agrobacterium tumefaciens of the D-galacturonic acid dehydrogenase gene

There are at least three different pathways for the catabolism of D-galacturonate in microorganisms. In the oxidative pathway, which was described in some prokaryotic species, D-galacturonate is first oxidised to meso-galactarate (mucate) by a nicotinamide adenine dinucleotide (NAD)-dependent dehydrogenase (EC 1.1.1.203). In the following steps of the pathway mucate is converted to 2-keto-glutarate. The enzyme activities of this catabolic pathway have been described while the corresponding gene sequences are still unidentified. The D-galacturonate dehydrogenase was purified from Agrobacterium tumefaciens, and the mass of its tryptic peptides was determined using MALDI-TOF mass spectrometry. This enabled the identification of the corresponding gene udh. It codes for a protein with 267 amino acids having homology to the protein family of NAD(P)-binding Rossmann-fold proteins. The open reading frame was functionally expressed in Saccharomyces cerevisiae. The N-terminally tagged protein was not compromised in its activity and was used after purification for a kinetic characterization. The enzyme was specific for NAD and accepted D-galacturonic acid and D-glucuronic acid as substrates with similar affinities. NMR analysis showed that in water solution the substrate D-galacturonic acid is predominantly in pyranosic form which is converted by the enzyme to 1,4 lactone of galactaric acid. This lactone seems stable under intracellular conditions and does not spontaneously open to the linear meso-galactaric acid.

The second green revolution? Production of plant-based biodegradable plastics

Biodegradable plastics are those that can be completely degraded in landfills, composters or sewage treatment plants by the action of naturally occurring micro-organisms. Truly biodegradable plastics leave no toxic, visible or distinguishable residues following degradation. Their biodegradability contrasts sharply with most petroleum-based plastics, which are essentially indestructible in a biological context. Because of the ubiquitous use of petroleum-based plastics, their persistence in the environment and their fossil-fuel derivation, alternatives to these traditional plastics are being explored. Issues surrounding waste management of traditional and biodegradable polymers are discussed in the context of reducing environmental pressures and carbon footprints. The main thrust of the present review addresses the development of plant-based biodegradable polymers. Plants naturally produce numerous polymers, including rubber, starch, cellulose and storage proteins, all of which have been exploited for biodegradable plastic production. Bacterial bioreactors fed with renewable resources from plants – so-called ‘white biotechnology’ – have also been successful in producing biodegradable polymers. In addition to these methods of exploiting plant materials for biodegradable polymer production, the present review also addresses the advances in synthesizing novel polymers within transgenic plants, especially those in the polyhydroxyalkanoate class. Although there is a stigma associated with transgenic plants, especially food crops, plant-based biodegradable polymers, produced as value-added co-products, or, from marginal land (non-food), crops such as switchgrass (Panicum virgatum L.), have the potential to become viable alternatives to petroleum-based plastics and an environmentally benign and carbon-neutral source of polymers.

Plant surface lipid biosynthetic pathways and their utility for metabolic engineering of waxes and hydrocarbon biofuels

Due to their unique physical properties, waxes are high-value materials that are used in a variety of industrial applications. They are generated by chemical synthesis, extracted from fossil sources, or harvested from a small number of plant and animal species. As a result, the diversity of chemical structures in commercial waxes is low and so are their yields. These limitations can be overcome by engineering of wax biosynthetic pathways in the seeds of high-yielding oil crops to produce designer waxes for specific industrial end uses. In this review, we first summarize the current knowledge regarding the genes and enzymes generating the chemical diversity of cuticular waxes that accumulate at the surfaces of primary plant organs. We then consider the potential of cuticle biosynthetic genes for biotechnological wax production, focusing on selected examples of wax ester chain lengths and isomers. Finally, we discuss the genes/enzymes of cuticular alkane biosynthesis and their potential in future metabolic engineering of plants for the production of renewable hydrocarbon fuels.

Terpenoid biomaterials

Terpenoids (isoprenoids) encompass more than 40 000 structures and form the largest class of all known plant metabolites. Some terpenoids have well-characterized physiological functions that are common to most plant species. In addition, many of the structurally diverse plant terpenoids may function in taxonomically more discrete, specialized interactions with other organisms. Historically, specialized terpenoids, together with alkaloids and many of the phenolics, have been referred to as secondary metabolites. More recently, these compounds have become widely recognized, conceptually and/or empirically, for their essential ecological functions in plant biology. Owing to their diverse biological activities and their diverse physical and chemical properties, terpenoid plant chemicals have been exploited by humans as traditional biomaterials in the form of complex mixtures or in the form of more or less pure compounds since ancient times. Plant terpenoids are widely used as industrially relevant chemicals, including many pharmaceuticals, flavours, fragrances, pesticides and disinfectants, and as large-volume feedstocks for chemical industries. Recently, there has been a renaissance of awareness of plant terpenoids as a valuable biological resource for societies that will have to become less reliant on petrochemicals. Harnessing the powers of plant and microbial systems for production of economically valuable plant terpenoids requires interdisciplinary and often expensive research into their chemistry, biosynthesis and genomics, as well as metabolic and biochemical engineering. This paper provides an overview of the formation of hemi-, mono-, sesqui- and diterpenoids in plants, and highlights some well-established examples for these classes of terpenoids in the context of biomaterials and biofuels.