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At least 865 records · Page 48

Cyanobacteria as cell factories for the photosynthetic production of sucrose

Biofuels and other biologically manufactured sustainable goods are growing in popularity and demand. Carbohydrate feedstocks required for industrial fermentation processes have traditionally been supplied by plant biomass, but the large quantities required to produce replacement commodity products may prevent the long-term feasibility of this approach without alternative strategies to produce sugar feedstocks. Cyanobacteria are under consideration as potential candidates for sustainable production of carbohydrate feedstocks, with potentially lower land and water requirements relative to plants. Several cyanobacterial strains have been genetically engineered to export significant quantities of sugars, especially sucrose. Sucrose is not only naturally synthesized and accumulated by cyanobacteria as a compatible solute to tolerate high salt environments, but also an easily fermentable disaccharide used by many heterotrophic bacteria as a carbon source. In this review, we provide a comprehensive summary of the current knowledge of the endogenous cyanobacterial sucrose synthesis and degradation pathways. We also summarize genetic modifications that have been found to increase sucrose production and secretion. Finally, we consider the current state of synthetic microbial consortia that rely on sugar-secreting cyanobacterial strains, which are co-cultivated alongside heterotrophic microbes able to directly convert the sugars into higher-value compounds (e.g., polyhydroxybutyrates, 3-hydroxypropionic acid, or dyes) in a single-pot reaction. We summarize recent advances reported in such cyanobacteria/heterotroph co-cultivation strategies and provide a perspective on future developments that are likely required to realize their bioindustrial potential.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic diversity, population structure and anthracnose resistance response in a novel sweet sorghum diversity panel

Sweet sorghum is an attractive feedstock for the production of renewable chemicals and fuels due to the readily available fermentable sugars that can be extracted from the juice, and the additional stream of fermentable sugars that can be obtained from the cell wall polysaccharides in the bagasse. An important selection criterion for new sweet sorghum germplasm is resistance to anthracnose, a disease caused by the fungal pathogen Colletotrichum sublineolum. The identification of novel anthracnose-resistance sources present in sweet sorghum germplasm offers a fast track towards the development of new resistant sweet sorghum germplasm. We established a sweet sorghum diversity panel (SWDP) of 272 accessions from the USDA-ARS National Plant Germplasm (NPGS) collection that includes landraces from 22 countries and advanced breeding material, and that represents ~15% of the NPGS sweet sorghum collection. Genomic characterization of the SWDP identified 171,954 single nucleotide polymorphisms (SNPs) with an average of one SNP per 4,071 kb. Population structure analysis revealed that the SWDP could be stratified into four populations and one admixed group, and that this population structure could be aligned to sorghum’s racial classification. Results from a two-year replicated trial of the SWDP for anthracnose resistance response in Texas, Georgia, Florida, and Puerto Rico showed 27 accessions to be resistant across locations, while 145 accessions showed variable resistance response against local pathotypes. A genome-wide association study identified 16 novel genomic regions associated with anthracnose resistance. Four resistance loci on chromosomes 3, 6, 8 and 9 were identified against pathotypes from Puerto Rico, and two resistance loci on chromosomes 3 and 8 against pathotypes from Texas. In Georgia and Florida, three resistance loci were detected on chromosomes 4, 5, 6 and four on chromosomes 4, 5 (two loci) and 7, respectively. One resistance locus on chromosome 2 was effective against pathotypes from Texas and Puerto Rico and a genomic region of 41.6 kb at the tip of chromosome 8 was associated with resistance response observed in Georgia, Texas, and Puerto Rico. This publicly available SWDP and the extensive evaluation of anthracnose resistance represent a valuable genomic resource for the improvement of sorghum.

59 BASIC BIOLOGICAL SCIENCES↗

Optimizing dietary rumen-degradable starch to rumen-degradable protein ratio improves lactation performance and nitrogen utilization efficiency in mid-lactating Holstein dairy cows

The dietary rumen-degradable starch (RDS) to rumen-degradable protein (RDP) ratio, denoted as the RDS-to-RDP ratio (SPR), has been proven to enhance in vitro rumen fermentation. However, the effects of dietary SPR in vivo remain largely unexplored. This study was conducted to investigate the effect of dietary SPR on lactation performance, nutrient digestibility, rumen fermentation patterns, blood indicators, and nitrogen (N) partitioning in mid-lactating Holstein cows. Seventy-two Holstein dairy cows were randomly assigned to three groups (24 head/group), balanced for (mean ± standard deviation) days in milk (116 ± 21.5), parity (2.1 ± 0.8), milk production (42 ± 2.1 kg/d), and body weight (705 ± 52.5 kg). The cows were fed diets with low (2.1, control), medium (2.3), or high (2.5) SPR, formulated to be isoenergetic, isonitrogenous, and iso-starch. The study consisted of a one-week adaptation phase followed by an eight-week experimental period. The results indicated that the high SPR group had a lower dry matter intake compared to the other groups ( p < 0.05). A quadratic increase in milk yield and feed efficiency was observed with increasing dietary SPR ( p < 0.05), peaking in the medium SPR group. The medium SPR group exhibited a lower milk somatic cell count and a higher blood total antioxidant capacity compared to other groups ( p < 0.05). With increasing dietary SPR, there was a quadratic improvement ( p < 0.05) in the total tract apparent digestibility of crude protein, ether extract, starch, neutral detergent fiber, and acid detergent fiber. Although no treatment effect was observed in rumen pH, the rumen total volatile fatty acids concentration and microbial crude protein synthesis increased quadratically ( p < 0.05) as dietary SPR increased. The molar proportion of propionate linearly increased ( p = 0.01), while branched-chain volatile fatty acids linearly decreased ( p = 0.01) with increasing dietary SPR. The low SPR group (control) exhibited higher concentration of milk urea N, rumen ammonia N, and blood urea N than other groups ( p < 0.05). Despite a linear decrease ( p < 0.05) in the proportion of urinary N to N intake, increasing dietary SPR led to a quadratic increase ( p = 0.01) in N utilization efficiency and a quadratic decrease ( p < 0.05) in the proportion of fecal N to N intake. In conclusion, optimizing dietary SPR has the potential to enhance lactation performance and N utilization efficiency. Based on our findings, a medium dietary SPR (with SPR = 2.3) is recommended for mid-lactating Holstein dairy cows. Nevertheless, further research on rumen microbial composition and metabolites is warranted to elucidate the underlying mechanisms of the observed effects.

Chen, Panliang↗

Converting Sugars to Biofuels: Ethanol and Beyond

To date, the most significant sources of biofuels are starch- or sugarcane-based ethanol, which have been industrially produced in large quantities in the USA and Brazil, respectively. However, the ultimate goal of biofuel production is to produce fuels from lignocellulosic biomass-derived sugars with optimal fuel properties and compatibility with the existing fuel distribution infrastructure. To achieve this goal, metabolic pathways have been constructed to produce various fuel molecules that are categorized into fermentative alcohols (butanol and isobutanol), non-fermentative alcohols from 2-keto acid pathways, fatty acids-derived fuels and isoprenoid-derived fuels. This review will focus on current metabolic engineering efforts to improve the productivity and the yield of several key biofuel molecules. Strategies used in these metabolic engineering efforts can be summarized as follows: (1) identification of better enzymes; (2) flux control of intermediates and precursors; (3) elimination of competing pathways; (4) redox balance and cofactor regeneration; and (5) bypassing regulatory mechanisms. In addition to metabolic engineering approaches, host strains are optimized by improving sugar uptake and utilization, and increasing tolerance to toxic hydrolysates, metabolic intermediates and/or biofuel products.

metabolic engineering↗

Integrated Biorefinery of Brewer’s Spent Grain for Second-Generation Ethanol, Mycoprotein, and Bioactive Vinasse Production

Brewer’s spent grain (BSG), the main lignocellulosic by-product of the beer industry, represents an abundant yet underutilized resource with high potential for valorization. This study presents an integrated biorefinery approach to convert BSG into second-generation (2G) ethanol, bioactive vinasse for plant growth promotion, and fungal biomass as a potential mycoprotein source. The biomass was first subjected to biological delignification using the white-rot fungus Ganoderma lucidum, after which two valorization routes were explored: (i) evaluation of the fungal biomass as a mycoprotein candidate and (ii) alcoholic fermentation for ethanol production. For the latter, three pretreatment strategies were assessed (diluted sulfuric acid and two deep eutectic solvents (DESs) based on choline chloride combined with either glycerol or lactic acid) followed by a one-pot enzymatic saccharification and fermentation using Kluyveromyces marxianus SLP1. The highest ethanol yield on substrate (YP/S) was achieved with [Ch]Cl:lactic acid pretreatment (0.46 g/g, 89.32% of theoretical). Vinasse, recovered after distillation, was characterized for organic acid content and tested on Solanum lycopersicum seed germination, showing promising biostimulant activity. Overall, this work highlights the potential of BSG as a sustainable feedstock within circular economy models, enabling the production of multiple bio-based products from a single residue.

Ganoderma lucidum↗

In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi

Lignocellulose is an abundant and renewable resource that holds great promise for sustainable bioprocessing. However, unpretreated lignocellulose is recalcitrant to direct utilization by most microbes. Current methods to overcome this barrier include expensive pretreatment steps to liberate cellulose and hemicellulose from lignin. Anaerobic gut fungi possess complex cellulolytic machinery specifically evolved to decompose crude lignocellulose, but they are not yet genetically tractable and have not been employed in industrial bioprocesses. Here, we aim to exploit the biomass-degrading abilities of anaerobic fungi by pairing them with another organism that can convert the fermentable sugars generated from hydrolysis into bioproducts. By combining experiments measuring the amount of excess fermentable sugars released by the fungal enzymes acting on crude lignocellulose, and a novel dynamic flux balance analysis algorithm, we screened potential consortia partners by qualitative suitability. Microbial growth simulations reveal that the fungus Anaeromyces robustus is most suited to pair with either the bacterium Clostridia ljungdahlii or the methanogen Methanosarcina barkeri—both organisms also found in the rumen microbiome. By capitalizing on simulations to screen six alternative organisms, valuable experimental time is saved towards identifying stable consortium members. This approach is also readily generalizable to larger systems and allows one to rationally select partner microbes for formation of stable consortia with non-model microbes like anaerobic fungi.

59 BASIC BIOLOGICAL SCIENCES↗

Ammonia Fiber Expansion (AFEX) Pretreatment of Lignocellulosic Biomass

Lignocellulosic materials are plant-derived feedstocks, such as crop residues (e.g., corn stover, rice straw, and sugar cane bagasse) and purpose-grown energy crops (e.g., miscanthus, and switchgrass) that are available in large quantities to produce biofuels, biochemicals, and animal feed. Plant polysaccharides (i.e., cellulose, hemicellulose, and pectin) embedded within cell walls are highly recalcitrant towards conversion into useful products. Ammonia fiber expansion (AFEX) is a thermochemical pretreatment that increases accessibility of polysaccharides to enzymes for hydrolysis into fermentable sugars. These released sugars can be converted into fuels and chemicals in a biorefinery. Here, we describe a laboratory-scale batch AFEX process to produce pretreated biomass on the gram-scale without any ammonia recycling. The laboratory-scale process can be used to identify optimal pretreatment conditions (e.g., ammonia loading, water loading, biomass loading, temperature, pressure, residence time, etc.) and generates sufficient quantities of pretreated samples for detailed physicochemical characterization and enzymatic/microbial analysis. The yield of fermentable sugars from enzymatic hydrolysis of corn stover pretreated using the laboratory-scale AFEX process is comparable to pilot-scale AFEX process under similar pretreatment conditions. This paper is intended to provide a detailed standard operating procedure for the safe and consistent operation of laboratory-scale reactors for performing AFEX pretreatment of lignocellulosic biomass.

09 BIOMASS FUELS↗

Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGAT)

Anaerobaculum mobile Menes and Muxí 2002 is one of three described species of the genus Anaerobaculum , family Synergistaceae , phylum Synergistetes . This anaerobic and motile bacterium ferments a range of carbohydrates and mono-and dicarboxylic acids with acetate, hydrogen and CO2 as end products. A. mobile NGAT is the first member of the genus Anaerobaculum and the sixth member of the phylum Synergistetes with a completely sequenced genome. Here we describe the features of this bacterium, together with the complete genome sequence, and annotation. The 2,160,700 bp long single replicon genome with its 2,053 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

59 BASIC BIOLOGICAL SCIENCES↗

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans

Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to p

Peptococcaceae↗

CAZyme domain architectures suggest fine-scale functional differentiation among anaerobic fungi and bacteria during lignocellulose conversion to volatile fatty acids

Anaerobic fermentation with microbial communities (microbiomes) is an emerging platform for conversion of lignocellulosic biomass to biofuels and bioproducts. The process relies on diverse anaerobic microbes that interact to deconstruct and convert lignocellulosic biomass into a range of products, such as volatile fatty acids (VFAs), which can be achieved by arresting methanogenesis during fermentation. However, defining the distinct functional roles played by various fungi and bacteria during anaerobic biodegradation remains poorly understood. Here, we performed parallel enrichment experiments from cow faeces, goat faeces, and anaerobic digester sludge, selecting for fungal or bacterial dominated communities that convert sorghum biomass into VFAs. Subsequently we reconstructed metabolic networks across these enrichments based on recovered bacterial metagenome-assembled genomes (MAGs) and fungal isolate genomes and profiled their metabolic activity using metatranscriptomics to identify potential functional niches. Our findings implicate diverse bacteria affiliated with the Bacteroidales and Lachnospiraceae in the direct conversion of lignocellulosic biomass to propionate and butyrate, respectively, whereas Neocallimastix-dominated fungal enrichments converted lignocellulose to lactate, acetate and formate. Analysis of carbohydrate-active enzymes (CAZymes) revealed fine-scale differences between microbes that expressed unique multi-functional enzymes linking two or more CAZymes together with distinct carbohydrate binding motifs, implicating lignocellulose structure as a key driver of selection and niche differentiation. Most of these multi-functional enzymes localized complementary degradation functions together, likely conferring synergistic degradation effects within and between microbiome members. We anticipate that these findings will help inform efforts to develop synthetic microbiomes with tailored functionality for low-cost conversion of lignocellulosic biomass to fuels and bio-based chemicals.

Lawson, Christopher E [University of Toronto;]↗

Diets with and without edible cricket support a similar level of diversity in the gut microbiome of dogs

The gut microbiome plays an important role in the health of dogs. Both beneficial microbes and overall diversity can be modulated by diet. Fermentable sources of fiber in particular often increase the abundance of beneficial microbes. Banded crickets ( Gryllodes sigillatus ) contain the fermentable polysaccharides chitin and chitosan. In addition, crickets are an environmentally sustainable protein source. Considering crickets as a potential source of both novel protein and novel fiber for dogs, four diets ranging from 0% to 24% cricket content were fed to determine their effects on healthy dogs’ ( n = 32) gut microbiomes. Fecal samples were collected serially at 0, 14, and 29 days, and processed using high-throughput sequencing of 16S rRNA gene PCR amplicons. Microbiomes were generally very similar across all diets at both the phylum and genus level, and alpha and beta diversities did not differ between the various diets at 29 days. A total of 12 ASVs (amplicon sequence variants) from nine genera significantly changed in abundance following the addition of cricket, often in a dose-response fashion with increasing amounts of cricket. A net increase was observed in Catenibacterium , Lachnospiraceae [ Ruminococcus ], and Faecalitalea , whereas Bacteroides , Faecalibacterium , Lachnospiracaeae NK4A136 group and others decreased in abundance. Similar changes in Catenibacterium and Bacteroides have been associated with gut health benefits in other studies. However, the total magnitude of all changes was small and only a few specific taxa changed in abundance. Overall, we found that diets containing cricket supported the same level of gut microbiome diversity as a standard healthy balanced diet. These results support crickets as a potential healthy, novel food ingredient for dogs.

60 APPLIED LIFE SCIENCES↗

Genome assembly PYCC 8100

The yeast Torulaspora delbrueckii is gaining importance for biotechnology due to its ability to increase wine sensorial complexity and for enhancing pre-frozen bread dough leavening. However, little is known about its population structure, and variation in gene content, or possible domestication routes have not been investigated. Here, we address these issues and update the circumscription of T. delbrueckii, which is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked with anthropic environments, one to wine fermentations and the other one to diverse sources including dairy products and bread dough (Mix- Anthropic clade). Using 62 genomes we identified 5629 genes in the pangenome of T. delbrueckii and 270 genes in the cloud genome. A pangenome tree analysis showed that wine strains have a genome composition were more similar to European wild arboreal strains than to those of the Mix Anthropic clade, in contradiction with the phylogenetic analysis. An association of gene content and ecology gave further support to the hypothesis that the Mix - Anthropic clade has the most specialized genome content and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. Contrary to S. cerevisiae, domestication in T. delbrueckii is not primed by alcoholic fermentation and appears to be a recent event.

Sampaio, Jose P.↗

Single-cell protein from waste cellulose

The recycle, reuse, or reclamation of single cell protein from liquid and solid agricultural waste fibers by a fermentation process is reported. It is shown that cellulose comprises the bulk of the fibers at 50% to 55% of the dry weight of the refuse and that its biodegradability is of prime importance in the choice of a substrate. The application of sodium hydroxide followed by heat and pressure serves to de-polymerize and disrupt lignin structure while swelling the cellulose to increase water uptake and pore volume. Some of the lignin, hemi-celluloses, ash, and cellulose of the material is hydrolized and solubilized. Introduction of microorganisms to the substrate fibers mixed with nutrients produces continuous fermentation of cellulose for further protein extraction and purification.

Dunlap, C. E.↗

Clean fuels from biomass

The paper discusses the U.S. resources to provide fuels from agricultural products, the present status of conversion technology of clean fuels from biomass, and a system study directed to determine the energy budget, and environmental and socioeconomic impacts. Conversion processes are discussed relative to pyrolysis and anaerobic fermentation. Pyrolysis breaks the cellulose molecules to smaller molecules under high temperature in the absence of oxygen, wheras anaerobic fermentation is used to convert biomass to methane by means of bacteria. Cost optimization and energy utilization are also discussed.

Hsu, Y.-Y.↗

Energy from aquatic plant wastewater treatment systems

Water hyacinth (Eichhornia crassipes), duckweed (Spirodela sp. and Lemma sp.), water pennywort (Hydrocotyle ranunculoides), and kudzu (Pueraria lobata) were anaerobically fermented using an anaerobic filter technique that reduced the total digestion time from 90 days to an average of 23 days and produced 0.14-0.28 cu m CH4/kg (dry weight) (2.3-4.5 cu ft/lb) from mature filters. The anaerobic filter provided a large surface area for the anaerobic bacteria to establish and maintain an optimum balance of facultative, acid-forming, and methane-producing bacteria. Consequently the efficiency of the process was greatly improved over prior batch fermentations.

Wolverton, B. C.↗

Coculture Production of Butanol by Clostridium Bacteria

Production of butanol by anaerobic fermentation of sugars enhanced by use of two Clostridium species, one of which feeds on metabolic product of other. Renewed interest in fermentation process for making butanol stimulated by potential use of butanol as surfactant in enhanced oil recovery. Butanol also used as fuel or as chemical feedstock and currently produced synthetically from petroleum.

Bergstrom, S. L.↗

Models of glycolysis: Glyceraldehyde as a source of energy and monomers for prebiotic condensation reactions

All organisms require energy in a chemical form for maintenance and growth. In contemporary life this chemical energy is obtained by the synthesis of the phosphoanhydride bonds of ATP. Among the biological processes that yield ATP, fermentation is generally considered primitive, because it operates under anaerobic conditions by substrate-level phosphorylation which does not require compartmentation by membranes. Fermentation by the glycolytic pathway, which is found in almost every living cell, is an especially attractive energy source for primitive life. Glycolysis not only produces useful chemical energy (ATP), but intermediates of this pathway are also involved in amino acid synthesis and photosynthetic carbon-fixation. It is believed that energy and substrates needed for the origin of life were provided by nonenzymatic chemical reactions that resemble the enzyme-mediated reactions of glycolysis. These nonenzymatic reactions would have provided a starting point for the evolutionary development of glycolysis.

Weber, A. L.↗

Application of gain scheduling to the control of batch bioreactors

The implementation of control algorithms to batch bioreactors is often complicated by the inherent variations in process dynamics during the course of fermentation. Such a wide operating range may render the performance of fixed gain PID controllers unsatisfactory. In this work, a detailed study on the control of batch fermentation is performed. Furthermore, a simple batch controller design is proposed which incorporates the concept of gain-scheduling, a subclass of adaptive control, with oxygen uptake rate as an auxiliary variable. The control of oxygen tension in the biorector is used as a vehicle to convey the proposed idea, analysis and results. Simulation experiments indicate significant improvement in controller performance can be achieved by the proposed approach even in the presence of measurement noise.

Cardello, Ralph↗