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At least 1,495 records · Page 83

Electron Tomography of Cryo-Immobilized Plant Tissue: A Novel Approach to Studying 3D Macromolecular Architecture of Mature Plant Cell Walls In Situ

Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (~2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the primary cell walls of a mutant (cob-6) and wild type Arabidopsis hypocotyl parenchyma cells by RT-tomography of HPF-FS-resin sections, and detected a small but significant difference in spatial organization of cellulose microfibrils in the mutant walls.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancement of Synthetic Trichoderma -Based Enzyme Mixtures for Biomass Conversion with an Alternative Family 5 Glycosyl Hydrolase from Sporotrichum thermophile

Enzymatic conversion of lignocellulosic materials to fermentable sugars is a limiting step in the production of biofuels from biomass. We show here that combining enzymes from different microbial sources is one way to identify superior enzymes. Extracts of the thermophilic fungus Sporotrichum thermophile (synonym Myceliophthora thermophila) gave synergistic release of glucose (Glc) and xylose (Xyl) from pretreated corn stover when combined with an 8-component synthetic cocktail of enzymes from Trichoderma reesei. The S. thermophile extracts were fractionated and an enhancing factor identified as endo-β1,4- glucanase (StCel5A or EG2) of subfamily 5 of Glycosyl Hydrolase family 5 (GH5_5). In multi-component optimization experiments using a standard set of enzymes and either StCel5A or the ortholog from T. reesei (TrCel5A), reactions containing StCel5A yielded more Glc and Xyl. In a five-component optimization experiment (i.e., varying four core enzymes and the source of Cel5A), the optimal proportions for TrCel5A vs. StCel5A were similar for Glc yields, but markedly different for Xyl yields. Both enzymes were active on lichenan, glucomannan, and oat β-glucan; however, StCel5A but not TrCel5A was also active on β1,4-mannan, two types of galactomannan, and β1,4-xylan. Phylogenetically, fungal enzymes in GH5_5 sorted into two clades, with StCel5A and TrCel5A belonging to different clades. Structural differences with the potential to account for the differences in performance were deduced based on the known structure of TrCel5A and a homology-based model of StCel5A, including a loop near the active site of TrCel5A and the presence of four additional Trp residues in the active cleft of StCel5A. The results indicate that superior biomass-degrading enzymes can be identified by exploring taxonomic diversity combined with assays in the context of realistic enzyme combinations and realistic substrates. Substrate range may be a key factor contributing to superior performance within GH5_5.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of Hydrogen Metabolism in the Multicellular Green Alga Volvox carteri

Hydrogen gas functions as a key component in the metabolism of a wide variety of microorganisms, often acting as either a fermentative end-product or an energy source. The number of organisms reported to utilize hydrogen continues to grow, contributing to and expanding our knowledge of biological hydrogen processes. Here we demonstrate that Volvox carteri f. nagariensis, a multicellular green alga with differentiated cells, evolves H 2 both when supplied with an abiotic electron donor and under physiological conditions. The genome of Volvox carteri contains two genes encoding putative [FeFe]-hydrogenases (HYDA1 and HYDA2), and the transcripts for these genes accumulate under anaerobic conditions. The HYDA1 and HYDA2 gene products were cloned, expressed, and purified, and both are functional [FeFe]-hydrogenases. Additionally, within the genome the HYDA1 and HYDA2 genes cluster with two putative genes which encode hydrogenase maturation proteins. This gene cluster resembles operon-like structures found within bacterial genomes and may provide further insight into evolutionary relationships between bacterial and algal [FeFe]-hydrogenase genes.

08 HYDROGEN↗

In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum " Latescibacteria " (WS3)

The “Latescibacteria” (formerly WS3), member of the Fibrobacteres–Chlorobi–Bacteroidetes (FCB) superphylum, represents a ubiquitous candidate phylum found in terrestrial, aquatic, and marine ecosystems. Recently, single-cell amplified genomes (SAGs) representing the “Latescibacteria” were obtained from the anoxic monimolimnion layers of Sakinaw Lake (British Columbia, Canada), and anoxic sediments of a coastal lagoon (Etoliko lagoon, Western Greece). Here, we present a detailed in-silico analysis of the four SAGs to gain some insights on their metabolic potential and apparent ecological roles. Metabolic reconstruction suggests an anaerobic fermentative mode of metabolism, as well as the capability to degrade multiple polysaccharides and glycoproteins that represent integral components of green (Charophyta and Chlorophyta) and brown (Phaeophycaea) algae cell walls (pectin, alginate, ulvan, fucan, hydroxyproline-rich glycoproteins), storage molecules (starch and trehalose), and extracellular polymeric substances (EPSs). The analyzed SAGs also encode dedicated transporters for the uptake of produced sugars and amino acids/oligopeptides, as well as an extensive machinery for the catabolism of all transported sugars, including the production of a bacterial microcompartment (BMC) to sequester propionaldehyde, a toxic intermediate produced during fucose and rhamnose metabolism. Finally, genes for the formation of gas vesicles, flagella, type IV pili, and oxidative stress response were found, features that could aid in cellular association with algal detritus. Collectively, these results indicate that the analyzed “Latescibacteria” mediate the turnover of multiple complex organic polymers of algal origin that reach deeper anoxic/microoxic habitats in lakes and lagoons. The implications of such process on our understanding of niche specialization in microbial communities mediating organic carbon turnover in stratified water bodies are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

Selection signatures in four lignin genes from switchgrass populations divergently selected for in vitro dry matter digestibility

Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. Fermentation of lignocellulosic biomass to ethanol in a bioenergy system or to volatile fatty acids in a livestock production system is strongly and negatively influenced by lignification of cell walls. This study detects specific loci that exhibit selection signatures across switchgrass breeding populations that differ in in vitro dry matter digestibility (IVDMD), ethanol yield, and lignin concentration. Allele frequency changes in candidate genes were used to detect loci under selection. Out of the 183 polymorphisms identified in the four candidate genes, twenty-five loci in the intron regions and four loci in coding regions were found to display a selection signature. All loci in the coding regions are synonymous substitutions. Selection in both directions were observed on polymorphisms that appeared to be under selection. Genetic diversity and linkage disequilibrium within the candidate genes were low. The recurrent divergent selection caused excessive moderate allele frequencies in the cycle 3 reduced lignin population as compared to the base population. As a result, this study provides valuable insight on genetic changes occurring in short-term selection in the polyploid populations, and discovered potential markers for breeding switchgrass with improved biomass quality.

09 BIOMASS FUELS↗

Draft genome sequence of Actinotignum schaalii DSM 15541 T : Genetic insights into the lifestyle, cell fitness and virulence

The permanent draft genome sequence of Actinotignum schaalii DSM 15541 T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor

Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading anaerobic bioreactor. The bioreactor was seeded with bovine rumen fluid and operated with a 4 days hydraulic retention time on cellulose (avicel) as sole carbon and energy source. The reactor performance and microbial community structure was monitored during the establishment of the cellulose-degrading community. After stable operation was established in the bioreactor, the mixing intensity was increased in order to investigate the effect of a physical disruption of the microbial community structure. Lastly, the original conditions were re-established to understand the stability of the microbial community after a perturbation. All factors measured were found to be inter-correlated during these three distinct phases of operation (establishment, perturbation and re-establishment). In particular, the return of community structure and function to pre-perturbed conditions suggests that propionate fermentation and acetate utilization were the explanatory factors for community establishment and re-establishment.

09 BIOMASS FUELS↗

Constraints-based analysis identifies NAD + recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum

In the post genomic era, high throughput data augment stoichiometric flux balance models to compute accurate metabolic flux states, growth and energy phenotypes. Investigating altered metabolism in the context of evolved resistant genotypes potentially provide simple strategies to overcome drug resistance and induce susceptibility to existing antibiotics. A genome-scale metabolic model (GSMM) for Chromobacterium violaceum, an opportunistic human pathogen, was reconstructed using legacy data. Experimental constraints were used to represent antibiotic susceptible and resistant populations. Model predictions were validated using growth and respiration data successfully. Differential flux distribution and metabolic reprogramming were identified as a response to antibiotics, chloramphenicol and streptomycin. Streptomycin resistant populations (StrpR) redirected tricarboxylic acid (TCA) cycle flux through the glyoxylate shunt. Chloramphenicol resistant populations (ChlR) resorted to overflow metabolism producing acetate and formate. This switch to fermentative metabolism is potentially through excess reducing equivalents and increased NADH/NAD ratios. Reduced proton gradients and changed Proton Motive Force (PMF) induced by antibiotics were also predicted and verified experimentally using flow cytometry based membrane potential measurements. Pareto analysis of NADH and ATP maintenance showed the decoupling of electron transfer and ATP synthesis in StrpR. Redox homeostasis and NAD + cycling through rewiring metabolic flux was implicated in re-sensitizing antibiotic resistant C. violaceum. These approaches can be used to probe metabolic vulnerabilities of resistant pathogens. On the verge of a post-antibiotic era, we foresee a critical need for systems level understanding of pathogens and host interaction to extend shelf life of antibiotics and strategize novel therapies.

59 BASIC BIOLOGICAL SCIENCES↗

Isoflavone supplementation, via red clover hay, alters the rumen microbial community and promotes weight gain of steers grazing mixed grass pastures

Biochanin A, an isoflavone present in the pasture legume red clover (Trifloium pratense L.), alters fermentation in the rumen of cattle and other ruminants. Biochanin A inhibits hyperammonia-producing bacteria and promotes cellulolytic bacteria and fiber catalysis in vitro and ex vivo. Consequently, biochanin A supplementation improves weight gain in grazing steers. Red clover contains biologically active isoflavones that may act synergistically. Therefore, the objective was to evaluate the effect of two levels of red clover hay on growth performance and the microbial community in growing steers grazing mixed grass pastures. A grazing experiment was conducted over 2 early growing seasons (2016 and 2017) with 36 cross-bred steers and twelve rumen-fistulated, growing Holstein steers for evaluation of average daily gain and rumen microbiota, respectively. Steers were blocked by body weight and assigned to pastures with one of four treatments: 1) pasture only, 2) pasture + dry distillers’ grains (DDG), 3) pasture + DDG + low level of red clover hay (~15% red clover diet), or 4) pasture + DDG + high level of red clover hay (~30% red clover diet). DDG were added to treatments to meet protein requirements and to balance total protein supplementation between treatments. All supplementation strategies (DDG ± red clover hay) increased average daily gains in comparison to pasture-only controls (P < 0.05), with a low level of red clover supplementation being the most effective (+0.17 kg d-1 > DDG only controls; P < 0.05). Similarly, hyper-ammonia-producing bacteria inhibition (10–100-fold; P < 0.05), fiber catalysis (+10–25%; P < 0.05) and short chain fatty acid concentrations were greatest with the low red clover supplement (+~25%; P < 0.05). These results provide evidence that lower levels or red clover supplementation may be optimal for maximizing overall microbial community function and animal performance in grazing steers.

54 ENVIRONMENTAL SCIENCES↗

A chemically-defined growth medium to support Lactobacillus-Acetobacter sp. community analysis

Lactobacilli and Acetobacter sp. are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in the digestive tract of the fruit fly Drosophila melanogaster. Communities of these bacteria are widespread and prolific, despite numerous strain-specific auxotrophies, suggesting they have evolved nutrient interdependencies that regulate their growth. The use of a chemically-defined medium (CDM) supporting the growth of both groups of bacteria would facilitate the identification of the molecular mechanisms for the metabolic interactions between them. While numerous CDMs have been developed that support specific strains of lactobacilli or Acetobacter , there has not been a medium formulated to support both genera. We developed such a medium, based on a previous CDM designed for growth of lactobacilli, by modifying the nutrient abundances to improve growth yield. We further simplified the medium by substituting casamino acids in place of individual amino acids and the standard Wolfe’s vitamins and mineral stocks in place of individual vitamins and minerals, resulting in a reduction from 40 to 8 stock solutions. These stock solutions can be used to prepare several CDM formulations that support robust growth of numerous lactobacilli and Acetobacter s. Here, we provide the composition and several examples of its use, which is important for tractability in dissecting the genetic and metabolic basis of natural bacterial species interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast

Imidazolium ionic liquids (IILs) have a range of biotechnological applications, including as pretreatment solvents that extract cellulose from plant biomass for microbial fermentation into sustainable bioenergy. However, residual levels of IILs, such as 1-ethyl-3-methylimidazolium chloride ([C 2 C 1 im]Cl), are toxic to biofuel-producing microbes, including the yeast Saccharomyces cerevisiae. S. cerevisiae strains isolated from diverse ecological niches differ in genomic sequence and in phenotypes potentially beneficial for industrial applications, including tolerance to inhibitory compounds present in hydrolyzed plant feedstocks. We evaluated >100 genome-sequenced S. cerevisiae strains for tolerance to [C 2 C 1 im]Cl and identified one strain with exceptional tolerance. By screening a library of genomic DNA fragments from the [C 2 C 1 im]Cl-tolerant strain for improved IIL tolerance, we identified SGE1, which encodes a plasma membrane multidrug efflux pump, and a previously uncharacterized gene that we named ionic liquid tolerance 1 (ILT1), which encodes a predicted membrane protein. Analyses of SGE1 sequences from our panel of S. cerevisiae strains together with growth phenotypes implicated two single nucleotide polymorphisms (SNPs) that associated with IIL tolerance and sensitivity. We confirmed these phenotypic effects by transferring the SGE1 SNPs into a [C 2 C 1 im]Cl-sensitive yeast strain using CRISPR/Cas9 genome editing. Further studies indicated that these SNPs affect Sge1 protein stability and cell surface localization, influencing the amount of toxic IILs that cells can pump out of the cytoplasm. Our results highlight the general potential for discovering useful biotechnological functions from untapped natural sequence variation and provide functional insight into emergent SGE1 alleles with reduced capacities to protect against IIL toxicity.

09 BIOMASS FUELS↗

Microalgae as a feedstock for biofuel precursors and value-added products: Green fuels and golden opportunities

In this study, the prospects of biofuel production from microalgal carbohydrates and lipids coupled with greenhouse gas mitigation due to photosynthetic assimilation of CO 2 have ushered in a renewed interest in algal feedstock. Furthermore, microalgae (including cyanobacteria) have become established as commercial sources of value-added biochemicals such as polyunsaturated fatty acids and carotenoid pigments used as antioxidants in nutritional supplements and cosmetics. This article presents a comprehensive synopsis of the metabolic basis for accumulating lipids as well as applicable methods of lipid and cellulose bioconversion and final applications of these natural or refined products from microalgal biomass. For lipids, one-step in situ transesterification offers a new and more accurate approach to quantify oil content. As a complement to microalgal oil fractions, the utilization of cellulosic biomass from microalgae to produce bioethanol by fermentation, biogas by anaerobic digestion, and bio-oil by hydrothermal liquefaction are discussed. Collectively, a compendium of information spanning green renewable fuels and value-added nutritional compounds is provided.

09 BIOMASS FUELS↗

Investigating the Role of Extensin Proteins in Poplar Biomass Recalcitrance

The biological conversion of cellulosic biomass to biofuel is hindered by cell wall recalcitrance, which can limit the ability of cellulases to access and break down cellulose. The purpose of this study was to investigate whether hydroxyproline-rich cell wall proteins (extensins) are present in poplar stem biomass, and whether these proteins may contribute to recalcitrance. Three classical extensin genes were identified in Populus trichocarpa through bioinformatic analysis of poplar genome sequences, with the following proposed names: PtEXTENSIN1 (Potri.001G019700); PtEXTENSIN2 (Potri.001G020100); PtEXTENSIN3 (Potri.018G050100). Tissue print immunoblots localized the extensin proteins in poplar stems to regions near the vascular cambium. Different thermochemical pretreatments reduced but did not eliminate hydroxyproline (Hyp, a proxy for extensins) from the biomass. Protease treatment of liquid hot water-pretreated poplar biomass reduced Hyp content by a further 16% and increased subsequent glucose yield by 20%. These data suggest that extensins may contribute to recalcitrance in pretreated poplar biomass, and that incorporating protease treatment into pretreatment protocols could result in a small but significant increase in the yield of fermentable glucose.

09 BIOMASS FUELS↗

Brazilian CBP - Technoeconomic analysis data

This data is related to the paper entitled "Techno-economic analysis of sugarcane bagasse and straw conversion into cellulosic ethanol via consolidated bioprocessing". That features the evaluation of sugarcane bagasse and straw conversion to ethanol at stand-alone facilities generating electricity from residues. The following scenarios were evaluated: Conventional, featuring hydrothermal pretreatment, fungal cellulase, and yeast fermentation (current commercial standard); Mid-term consolidated bioprocessing (CBP), relying on bagasse solubilization without pretreatment or cotreatment; and Mature CBP, incorporating cotreatment but no pretreatment and considering significant technological advance of the CBP. Available here are the spreadsheets used for Material and Energy balance calculation, Capital and Operational costs estimation and Cash flow analysis. Also available are the description and python code used for Monte Carlo analysis of the ethanol and capital investment variations. This data can be used as a source to implement other techno-economic analysis in the biorefinary context.

09 BIOMASS FUELS↗

Lipid accumulation from glucose and xylose in an engineered, naturally oleaginous strain of Saccharomyces cerevisiae

Saccharomyces cerevisiae, a well-known industrial yeast for alcoholic fermentation, is not historically known to accumulate lipids. Four S. cerevisiae strains used in industrial applications were screened for their ability to accumulate neutral lipids. Only one, D5A, was found to accumulate up to 20% dry cell weight (dcw) lipids. This strain was further engineered by knocking out ADP-activated serine/threonine kinase (SNF1) which increased lipid accumulation to 35% dcw lipids. In addition, we engineered D5A to utilize xylose and found that D5A accumulates up to 37% dcw lipids from xylose as the sole carbon source. Further we over-expressed different diacylglycerol acyltransferase (DGA1) genes and boosted lipid accumulation to 50%. Fatty acid speciation showed that 94% of the extracted lipids consisted of 5 fatty acid species, C16:0 (palmitic), C16:1n7 (palmitoleic), C18:0 (stearic), C18:1n7 (vaccenic), and C18:1n9 (oleic), while the relative distributions changed depending on growth conditions. In addition, this strain accumulated lipids concurrently with ethanol production.

09 BIOMASS FUELS↗

Polysaccharide-catalyzed nucleation and growth of disordered dolomite: A potential precursor of sedimentary dolomite

This paper is about growing dolomite and even Mg-rich dolomite in presence of certain polysaccharides that could be major components in extracellular polymeric substances (EPS) of anaerobic bacteria like sulfate-reducing bacteria, methanogens and fermenters. This paper lays foundation for us to investigate roles of polysaccharide in governing compositions of Ca-Mg-carbonates and dolomite. Polysacchrides may be used as catalysts for enhancing stable Ca-Mg-carbonate (dolomite) in deep surface environment.

58 GEOSCIENCES↗

Potential for Combined Heat and Power with Carbon Capture and Storage at U.S. Ethanol Facilities

Conference paper presented at 17th International Conference on Greenhouse Gas Control Technologies (GHGT-17), Calgary, Alberta, Canada, October 20–24, 2024. Economic conditions in the United States have positioned ethanol producers as early adopters of industrial CO 2 capture and storage (CCS) from fermentation processes, creating an opportunity to further reduce emissions. Replacing fossil fired energy with biogenic combined heat and power (CHP) coupled with CCS could enable ethanol production to achieve net negative CO 2 emissions, with gasification based CHP better matching ethanol facilities’ heat and power needs than combustion based systems. Pilot scale testing showed that while 100% biomass gasification increased tar formation, cofeeding corn stover with coal and optimizing gasifier configurations offered promising pathways to reduce tar and improve operational performance.

09 BIOMASS FUELS↗

Fungal Bioprocess for Upgrading Thin Stillage

In dry mill ethanol plants, thin stillage is a low value liquid stream that remains after recovery of the ethanol. Clarification of the thin stillage (removal of solids) and production of a value-added product would be desirable. Fungi are excellent candidates to explore for such a bioprocess due to their general tolerance to lower pH, ability to utilize a broad range of carbon sources and historical use as single-cell-proteins (SCP) or other foods. The objective of this CRADA project was to identify a fungal strain and develop a fungal bioprocess that would utilize components of the thin stillage to produce a clarified water stream suitable for recycle to the ethanol fermentation and also produce SCP as a valuable by-product for animal feed applications.

agricultural↗