Evidence for catabolite inhibition in regulation of pentose utilization and transport in the ruminal bacterium Selenomonas ruminantium

Xylose Metabolism in Bacteria—Opportunities and Challenges towards Efficient Lignocellulosic Biomass-Based Biorefineries

In a sustainable society based on circular economy, the use of waste lignocellulosic biomass (LB) as feedstock for biorefineries is a promising solution, since LB is the world’s most abundant renewable and non-edible raw material. LB is available as a by-product from agricultural and forestry processes, and its main components are cellulose, hemicellulose, and lignin. Following suitable physical, enzymatic, and chemical steps, the different fractions can be processed and/or converted to value-added products such as fuels and biochemicals used in several branches of industry through the implementation of the biorefinery concept. Upon hydrolysis, the carbohydrate-rich fraction may comprise several simple sugars (e.g., glucose, xylose, arabinose, and mannose) that can then be fed to fermentation units. Unlike pentoses, glucose and other hexoses are readily processed by microorganisms. Some wild-type and genetically modified bacteria can metabolize xylose through three different main pathways of metabolism: xylose isomerase pathway, oxidoreductase pathway, and non-phosphorylative pathway (including Weimberg and Dahms pathways). Two of the commercially interesting intermediates of these pathways are xylitol and xylonic acid, which can accumulate in the medium either through manipulation of the culture conditions or through genetic modification of the bacteria. This paper provides a state-of-the art perspective regarding the current knowledge on xylose transport and metabolism in bacteria as well as envisaged strategies to further increase xylose conversion into valuable products.

Zeolite addition to improve biohydrogen production from dark fermentation of C5/C6-sugars and Sargassum sp. biomass

Thermophilic biohydrogen production by dark fermentation from a mixture (1:1) of C5 (arabinose) and C6 (glucose) sugars, present in lignocellulosic hydrolysates, and from Sargassum sp. biomass, is studied in this work in batch assays and also in a continuous reactor experiment. Pursuing the interest of studying interactions between inorganic materials (adsorbents, conductive and others) and anaerobic bacteria, the biological processes were amended with variable amounts of a zeolite type-13X in the range of zeolite/inoculum (in VS) ratios (Z/I) of 0.065–0.26 g g⁻¹. In the batch assays, the presence of the zeolite was beneficial to increase the hydrogen titer by 15–21% with C5 and C6-sugars as compared to the control, and an increase of 27% was observed in the batch fermentation of Sargassum sp. Hydrogen yields also increased by 10–26% with sugars in the presence of the zeolite. The rate of hydrogen production increased linearly with the Z/I ratios in the experiments with C5 and C6-sugars. In the batch assay with Sargassum sp., there was an optimum value of Z/I of 0.13 g g⁻¹ where the H₂ production rate observed was the highest, although all values were in a narrow range between 3.21 and 4.19 mmol L⁻¹ day⁻¹. The positive effect of the zeolite was also observed in a continuous high-rate reactor fed with C5 and C6-sugars. The increase of the organic loading rate (OLR) from 8.8 to 17.6 kg m⁻³ day⁻¹ of COD led to lower hydrogen production rates but, upon zeolite addition (0.26 g g⁻¹ VS inoculum), the hydrogen production increased significantly from 143 to 413 mL L⁻¹ day⁻¹. Interestingly, the presence of zeolite in the continuous operation had a remarkable impact in the microbial community and in the profile of fermentation products. The effect of zeolite could be related to several properties, including the porous structure and the associated surface area available for bacterial adhesion, potential release of trace elements, ion-exchanger capacity or ability to adsorb different compounds (i.e. protons). The observations opens novel perspectives and will stimulate further research not only in biohydrogen production, but broadly in the field of interactions between bacteria and inorganic materials.

Bio-immobilization of dark fermentative bacteria for enhancing continuous hydrogen production from cornstalk hydrolysate

Mycelia pellets were employed as biological carrier in a continuous stirred tank reactor to reduce biomass washout and enhance hydrogen production from cornstalk hydrolysate. Hydraulic retention time (HRT) and influent substrate concentration played critical roles on hydrogen production of the bioreactor. The maximum hydrogen production rate of 14.2mmol H₂L^-1h^-1 was obtained at optimized HRT of 6h and influent concentration of 20g/L, 2.6 times higher than the counterpart without mycelia pellets. With excellent immobilization ability, biomass accumulated in the reactor and reached 1.6g/L under the optimum conditions. Upon further energy conversion analysis, continuous hydrogen production with mycelia pellets gave the maximum energy conversion efficiency of 17.8%. These results indicate mycelia pellet is an ideal biological carrier to improve biomass retention capacity of the reactor and enhance hydrogen recovery efficiency from lignocellulosic biomass, and meanwhile provides a new direction for economic and efficient hydrogen production process.

Aeromonas surface glucan attached through the O-antigen ligase represents a new way to obtain UDP-glucose

We previously reported that A. hydrophila GalU mutants were still able to produce UDP-glucose introduced as a glucose residue in their lipopolysaccharide core. In this study, we found the unique origin of this UDP-glucose from a branched α-glucan surface polysaccharide. This glucan, surface attached through the O-antigen ligase (WaaL), is common to the mesophilic Aeromonas strains tested. The Aeromonas glucan is produced by the action of the glycogen synthase (GlgA) and the UDP-Glc pyrophosphorylase (GlgC), the latter wrongly indicated as an ADP-Glc pyrophosphorylase in the Aeromonas genomes available. The Aeromonas glycogen synthase is able to react with UDP or ADP-glucose, which is not the case of E. coli glycogen synthase only reacting with ADP-glucose. The Aeromonas surface glucan has a role enhancing biofilm formation. Finally, for the first time to our knowledge, a clear preference on behalf of bacterial survival and pathogenesis is observed when choosing to produce one or other surface saccharide molecules to produce (lipopolysaccharide core or glucan).

Biohydrogen production from arabinose and glucose using extreme thermophilic anaerobic mixed cultures

BACKGROUND

Second generation hydrogen fermentation technologies using organic agricultural and forestry wastes are emerging. The efficient microbial fermentation of hexoses and pentoses resulting from the pretreatment of lingocellulosic materials is essential for the success of these processes.

RESULTS

Conversion of arabinose and glucose to hydrogen, by extreme thermophilic, anaerobic, mixed cultures was studied in continuous (70°C, pH 5.5) and batch (70°C, pH 5.5 and pH 7) assays. Two expanded granular sludge bed (EGSB) reactors, Rarab and Rgluc, were continuously fed with arabinose and glucose, respectively. No significant differences in reactor performance were observed for arabinose and glucose organic loading rates (OLR) ranging from 4.3 to 7.1 kgCOD m-3 d-1. However, for an OLR of 14.2 kgCOD m-3 d-1, hydrogen production rate and hydrogen yield were higher in Rarab than in Rgluc (average hydrogen production rate of 3.2 and 2.0 LH2 L-1 d-1 and hydrogen yield of 1.10 and 0.75 molH2 mol-1substrate for Rarab and Rgluc, respectively). Lower hydrogen production in Rgluc was associated with higher lactate production. Denaturing gradient gel electrophoresis (DGGE) results revealed no significant difference on the bacterial community composition between operational periods and between the reactors. Increased hydrogen production was observed in batch experiments when hydrogen partial pressure was kept low, both with arabinose and glucose as substrate. Sugars were completely consumed and hydrogen production stimulated (62% higher) when pH 7 was used instead of pH 5.5.

CONCLUSIONS

Continuous hydrogen production rate from arabinose was significantly higher than from glucose, when higher organic loading rate was used. The effect of hydrogen partial pressure on hydrogen production from glucose in batch mode was related to the extent of sugar utilization and not to the efficiency of substrate conversion to hydrogen. Furthermore, at pH 7.0, sugars uptake, hydrogen production and yield were higher than at pH 5.5, with both arabinose and glucose as substrates.

Characterization of lateral flagella of Selenomonas ruminantium

Selenomonas ruminantium produces a tuft of flagella near the midpoint of the cell body and swims by rotating the cell body along the cell's long axis. The flagellum is composed of a single kind of flagellin, which is heavily glycosylated. The hook length of S. ruminantium is almost double that of Salmonella.

Glycogen Formation by the Ruminal Bacterium Prevotella ruminicola

Prevotella ruminicola is an important ruminal bacteria. In maltose-grown cells, nearly 60% of cell dry weight consisted of high-molecular-weight (>2 x 10(sup6)) glycogen. The ratio of glycogen to protein (grams per gram) was relatively low (1.3) during exponential growth, but when cell growth slowed during the transition to the stationary phase, the ratio increased to 1.8. As much as 40% of the maltose was converted to glycogen during cell growth. Glycogen accumulation in glucose-grown cells was threefold lower than that in maltose-grown cells. In continuous cultures provided with maltose, much less glycogen was synthesized at high (>0.2 per h) than at low dilution rates, where maltose was limiting (28 versus 60% of dry weight, respectively). These results indicated that glycogen synthesis was stimulated at low growth rates and was also influenced by the growth substrate. In permeabilized cells, glycogen was synthesized from [(sup14)C]glucose-1-phosphate but not radiolabelled glucose, indicating that glucose-1-phosphate is the initial precursor of glycogen formation. Glycogen accumulation may provide a survival mechanism for P. ruminicola during periods of carbon starvation and may have a role in controlling starch fermentation in the rumen.

Xylose anaerobic conversion by open-mixed cultures

Xylose is, after glucose, the dominant sugar in agricultural wastes. In anaerobic environments, carbohydrates are converted into volatile fatty acids and alcohols. These can be used as building blocks in biotechnological or chemical processes, e.g., to produce bioplastics. In this study, xylose fermentation by mixed microbial cultures was investigated and compared with glucose under the same conditions. The product spectrum obtained with both substrates was comparable. It was observed that, in the case of xylose, a higher fraction of the carbon was converted into catabolic products (butyrate, acetate, and ethanol) and the biomass yield was approximately 20% lower than on glucose, 0.16 versus 0.21 Cmol X/Cmol S. This lower yield is likely related to the need of an extra ATP during xylose uptake. When submitted to a pulse of glucose, the population cultivated on xylose could instantaneously convert the glucose. No substrate preference was observed when glucose and xylose were fed simultaneously to the continuously operated bioreactor.

Transport of D-xylose in Lactobacillus pentosus, Lactobacillus casei, and Lactobacillus plantarum: evidence for a mechanism of facilitated diffusion via the phosphoenolpyruvate:mannose phosphotransferase system

We have identified and characterized the D-xylose transport system of Lactobacillus pentosus. Uptake of D-xylose was not driven by the proton motive force generated by malolactic fermentation and required D-xylose metabolism. The kinetics of D-xylose transport were indicative of a low-affinity facilitated-diffusion system with an apparent K(m) of 8.5 mM and a V(max) of 23 nmol min(-1) mg of dry weight(-1). In two mutants of L. pentosus defective in the phosphoenolpyruvate:mannose phosphotransferase system, growth on D-xylose was absent due to the lack of D-xylose transport. However, transport of the pentose was not totally abolished in a third mutant, which could be complemented after expression of the L. curvatus manB gene encoding the cytoplasmic EIIB(Man) component of the EII(Man) complex. The EII(Man) complex is also involved in D-xylose transport in L. casei ATCC 393 and L. plantarum 80. These two species could transport and metabolize D-xylose after transformation with plasmids which expressed the D-xylose-catabolizing genes of L. pentosus, xylAB. L. casei and L. plantarum mutants resistant to 2-deoxy-D-glucose were defective in EII(Man) activity and were unable to transport D-xylose when transformed with plasmids containing the xylAB genes. Finally, transport of D-xylose was found to be the rate-limiting step in the growth of L. pentosus and of L. plantarum and L. casei ATCC 393 containing plasmids coding for the D-xylose-catabolic enzymes, since the doubling time of these bacteria on D-xylose was proportional to the level of EII(Man) activity.

Glycogen biosynthesis via UDP-glucose in the ruminal bacterium Prevotella bryantii B1(4)

Prevotella bryantii is an important amylolytic bacterium in the rumen that produces considerable amounts of glycogen when it is grown on maltose. Radiolabel studies indicated that glucose-1-phosphate was converted to UDP-glucose, and this latter intermediate served as the immediate precursor for glycogen synthesis. High levels of UDP-glucose pyrophosphorylase activities (> 1,492 nmol/min/mg of protein) were detected in cells grown on maltose, cellobiose, glucose, or sucrose, and activity was greatly stimulated (by approximately 60-fold) by the addition of fructose-1,6-bis phosphate (half-maximal activation concentration was 240 microM). However, ADP-glucose pyrophosphorylase activity was not detected in any of the cultures. Glycogen synthase activity in maltose-grown cultures (48 nmol/min/mg of protein) was higher than that in cellobiose-, sucrose-, and glucose-grown cultures (< 26 nmol/min/mg of protein). This is the first report of a bacterium that exclusively uses UDP-glucose to synthesize glycogen. The elucidation of this unique glycogen biosynthesis pathway provides information necessary to further investigate the role of bacterial glycogen accumulation in rumen metabolism.

Hexose phosphorylation by the ruminal bacterium Selenomonas ruminantium

Three strains of Selenomonas ruminantium (D, GA192, and H18) were surveyed for phosphorylation of D-glucose and 2-deoxyglucose by phosphoenolpyruvate and ATP. Cells of all three strains that had been treated with toluene had high rates of hexose phosphorylation with either phosphoryl donor; this activity was constitutive in strain D. Glucose phosphorylation that was dependent on phosphoenolpyruvate was maximal at pH 7.2, remained fairly high at pH 6.5, but decreased (> or = 65%) at pH 5.0 for all strains. Cell extracts were used to evaluate the involvement of soluble kinases in 2-deoxyglucose phosphorylation. Both glucose and 2-deoxyglucose were phosphorylated by ATP, but phosphorylation of either hexose was negligible with phosphoenolpyruvate in each bacterium. Because phosphoenolpyruvate could not serve as a phosphoryl donor, the activity dependent on phosphoenolpyruvate in cells treated with toluene might have been due to a phosphotransferase system associated with the membrane. Unlabeled 2-deoxyglucose was a strong inhibitor (> or = 59%) of [14C]glucose phosphorylation with ATP by cell extracts of all S. ruminantium strains, and unlabeled glucose was a strong inhibitor (> or = 78%) of [14C]2-deoxyglucose phosphorylation with ATP. Based on Lineweaver-Burk kinetics, 2-deoxyglucose was a competitive inhibitor of initial rates of kinase activity in strains D, GA192, and H18. These results collectively suggest that glucose phosphorylation with phosphoenolpyruvate and 2-deoxyglucose phosphorylation with ATP are common traits in these strains of S. ruminantium.

Ecology, metabolism, and genetics of ruminal selenomonads

Selenomonas ruminantium is one of the more prominent and functionally diverse bacteria present in the rumen and can survive under a wide range of nutritional fluctuations. Selenomonas is not a degrader of complex polysaccharides associated with dietary plant cell wall components, but is important in the utilization of soluble carbohydrates released from initial hydrolysis of these polymers by other ruminal bacteria. Selenomonads have multiple carbon flow routes for carbohydrate catabolism and ATP generation, and subspecies differ in their ability to use lactate. Some soluble carbohydrates (glucose, sucrose) appear to be transported via the phosphoenolpyruvate phosphotransferase system, while arabinose and xylose are transported by proton symport. High cell yields and the presence of electron transport components in Selenomonas strains has been documented repeatedly and this may partially account for the energy partitioning observed between energy consumed for growth and maintenance functions. Most strains can utilize ammonia, protein, and/or amino acids as a nitrogen source. Some strains can hydrolyze urea and/or reduce nitrate and use the ammonia for the biosynthesis of amino acids. Experimental evidence suggests that ammonia assimilatory enzymes in some strains may possess unique properties with respect to other presumably similar bacteria. Little is known about the genetics of ruminal selenomonads. Plasmid DNA has been isolated from some strains, but it is unknown what physiological functions may be encoded on these extrachromosomal elements. Due to the predominance of S. ruminantium in the rumen, it is an ideal candidate for genetic manipulation. Once the genetics of this bacterium are better understood, it may be possible to amplify its role in the rumen.

Degradation and utilization of xylan by the ruminal bacteria Butyrivibrio fibrisolvens and Selenomonas ruminantium

The cross-feeding of xyland hydrolysis products between the xylanolytic bacterium Butyrivibrio fibrisolvens H17c and the xylooligosaccharide-fermenting bacterium Selenomonas ruminantium GA192 was investigated. Cultures were grown anaerobically in complex medium containing oat spelt xylan, and the digestion of xylan and the generation and subsequent utilization of xylooligosaccharide intermediates were monitored over time. Monocultures of B. fibrisolvens rapidly degraded oat spelt xylan, and a pool of extracellular degradation intermediates composed of low-molecular-weight xylooligosaccharides (xylobiose through xylopentaose and larger, unidentified oligomers) accumulated in these cultures. The ability of S. ruminantium to utilize the products of xylanolysis by B. fibrisolvens was demonstrated by its ability to grow on xylan that had first been digested by the extracellular xylanolytic enzymes of B. fibrisolvens. Although enzymatic hydrolysis converted the xylan to soluble products, this alone was not sufficient to assure complete utilization by S. ruminantium, and considerable quantities of oligosaccharides remained following growth. Stable xylan-utilizing cocultures of S. ruminantium and B. fibrisolvens were established, and the utilization of xylan was monitored. Despite the presence of an oligosaccharide-fermenting organism, accumulations of acid-alcohol soluble products were still noted; however, the composition of carbohydrates present in these cultures differed from that seen when B. fibrisolvens was cultivated alone. Residual carbohydrates present at various times during growth were of higher average degree of polymerization in cocultures than in cultures of B. fibrisolvens alone. Structural characterization of these residual products may help define the limitations on the assimilation of xylooligosaccharides by ruminal bacteria.

Cyclic AMP in ruminal and other anaerobic bacteria

An examination of cAMP levels in predominant species of ruminal bacteria and other anaerobic bacteria was conducted. Cellular cAMP concentrations of glucose-grown cultures of Butyrivibrio fibrisolvens 49, Prevotella ruminicola D31d, Selenomonas ruminantium HD4 and D, Megasphaera elsdenii B159, Streptococcus bovis JB1, Bacteroides thetaiotaomicron 5482, and Clostridium acetobutylicum ATCC 824 were determined at various times during growth by a competitive binding radioimmunoassay procedure. The results were compared to those for Escherichia coli NRRL B3704. The levels of cAMP ranged from undetectable for B. thetaiotaomicron to approximately 15 pmol/mg cell protein for P. ruminicola D31d. Varying the growth substrate in a manner previously shown to elicit regulatory response did not alter the level of cAMP in these organisms. In general, cAMP concentrations present in these organisms were much lower than the 6-25 pmol/mg cell protein observed for E. coli. The levels of cAMP in P. ruminicola were consistently higher than levels in other anaerobes, particularly during the early exponential and stationary phases of growth. Based on these data it seems unlikely that cAMP is involved in regulation of substrate catabolism in the anaerobic bacteria examined except in P. ruminicola where it may have an unknown regulatory function.

Pentose transport by the ruminal bacterium Butyrivibrio fibrisolvens

Butyrivibrio fibrisolvens is a fibrolytic ruminal bacterium that degrades hemicellulose and ferments the resulting pentose sugars. Washed cells of strain D1 accumulated radiolabelled xylose (Km = 1.5 microM) and arabinose (Km = 0.2 microM) when the organism was grown on xylose, arabinose, or glucose, but cultures grown on sucrose or cellobiose had little capacity to transport pentose. Glucose and xylose inhibited transport of each other non-competitively. Both sugars were utilized preferentially over arabinose, but since they did not inhibit transport of arabinose, it appeared that the preference was related to an internal metabolic step. Although the protonmotive force was completely abolished by ionophores, cells retained some ability to transport pentose. In contrast, the metabolic inhibitors iodoacetate, arsenate, and fluoride had little effect on protonmotive force but caused a large decrease in intracellular ATP and xylose and arabinose uptake. These results suggested that high-affinity, ATP-dependent mechanisms were responsible for pentose transport and hexose sugars affected the utilization of xylose and arabinose.

Pentose utilization by the ruminal bacterium Ruminococcus albus

Ruminococcus albus is an important fibrolytic ruminal bacteria which degrades hemicellulose and ferments the resulting pentose sugars. However, little information is available on the utilization of pentoses by this organism or the effect of hexose sugars on pentose metabolism. Enzymatic studies indicated that R. albus metabolized pentoses via the pentose phosphate pathway and possessed constitutive transketolase activity. Cellobiose was preferred over xylose and arabinose, and it appeared that the disaccharide decreased pentose metabolism by repression of transport activity and catabolic enzymes (isomerases and kinases). Glucose and xylose were co-utilized, and transport studies suggested that there was a common transport system for both sugars. In contrast, glucose was preferred over arabinose and the hexose noncompetitively inhibited the transport of arabinose. Since R. albus lacks a glucose phosphotransferase system, the inhibition of arabinose uptake could not be explained by previously described models of inducer exclusion involving such a system. Because accumulation of radiolabeled xylose, arabinose, and glucose proceeded in the absence of a proton motive force and since transport was correlated with the intracellular ATP concentration, it appeared that monosaccharide uptake was driven by ATP hydrolysis.

Xylose and Glucose Utilization by Bacteroides xylanolyticus X5-1 Cells Grown in Batch and Continuous Culture

During cultivation on a mixture of xylose and glucose, Bacteroides xylanolyticus X5-1 showed neither diauxic growth nor a substrate preference. Xylose-limited continuous-culture cells were able to consume xylose and glucose both as single substrates and as mixed substrates without any lag phase. When glucose was the growth-limiting substrate, the microorganism was unable to consume xylose. However, in the presence of a small amount of glucose or pyruvate, xylose was utilized after a short lag phase. In glucose-limited cells, xylose isomerase was present at low activity but xylulose kinase activity could not be detected. On addition of a mixture of xylose and glucose, xylose isomerase was induced immediately and xylulose kinase was induced after about 30 min. The induction of the two enzymes was sensitive to chloramphenicol, showing de novo synthesis. Xylose uptake in glucose-grown cells was very low, but the uptake rate could be increased when incubated with a xylose-glucose mixture. The increase in the uptake rate was not affected by chloramphenicol, indicating that a constitutive uptake system had to be activated. The inability of B. xylanolyticus X5-1 cells undergoing glucose-limited continuous culture to induce the xylose catabolic pathway after the addition of only xylose probably was caused by energy limitation.

Xylose and arabinose utilization by the rumen bacterium Butyrivibrio fibrisolvens

The rumen bacterium Butyrivibrio fibrisolvens strain D1 co-utilized xylose and glucose in batch culture, but there was a marked preference for glucose over arabinose. When both pentoses were provided, xylose was preferred over arabinose. Strain D1 co-utilized a combination of either pentose and cellobiose, but preferred over maltose. Pentose sugars were depleted less rapidly in the presence of sucrose than controls containing only pentose. In contrast, B. fibrisolvens strain A38 exhibited a strong preference for disaccharides, including maltose, over either xylose or arabinose. Theoretical maximum growth yields for strain D1 in single-substrate continuous culture were highest for sucrose and cellobiose and the maintenance energy coefficient for arabinose was at least 3.8-fold greater than for other substrates. We suggest that B. fibrisolvens may have evolved a mechanism to utilize certain sugars before arabinose in order to avoid this high maintenance energy expenditure.

Pentose utilization and transport by the ruminal bacterium Prevotella ruminicola

Plant cell wall polysaccharides are primarily composed of hexose or hexose derivatives, but a significant fraction is hemicellulose which contains pentose sugars. Prevotella ruminicola B14, a predominant ruminal bacterium, simultaneously metabolized pentoses and glucose or maltose, but the organism preferentially fermented pentoses over cellobiose and preferred xylose to sucrose. Xylose and arabinose transport at either low (2 microM) or high (1 mM) substrate concentrations were observed only in the presence of sodium and if oxygen was excluded during the harvest and assay procedures. An artificial electrical potential (delta psi) or chemical gradient of sodium (delta pNa) drove transport in anaerobically prepared membrane vesicles. Because (i) transport was electrogenic, (ii) a delta pNa drove uptake, and (iii) the number of sodium binding sites was approximately 1, it appeared that P. ruminicola possessed pentose/sodium support mechanisms for the transport of arabinose and xylose at low substrate concentrations. Pentose uptake exhibited a low affinity for xylose or arabinose (> 300 microM), and transport of xylose exhibited bi-phasic kinetics which suggested that a second sodium-dependent xylose transport system was present. Little study has been made on solute transport by Prevotella (Bacteroides) species and this work represents the first use of isolated membrane vesicles from these organisms.