Paul J. Weimer

Cellulolytic and physiological properties of Clostridium thermocellum

Three strains of Clostridium thermocellum obtained from various sources were found to have nearly identical deoxyribonucleic acid guanosine plus cytosine contents that ranged from 38.1–39.5 mole-%. All strain examined fermented only cellulose and cellulose derivatives, but not glucose, or xylose or other sugars. The principal cellulose fermentation products were ethanol, lactate, acetate, hydrogen and carbon dioxide. Growth of C. thermocellum on cellulose resulted in the production of extracellular cellulase that was non-oxygen labile, was thermally stable at 70° C for 45 min and adsorbed strongly on cellulose. Production of cellulase during fermentation correlated linearly with growth and cellulose degradation. Both the yield and specific activity of crude cellulase varied considerably with the specific growth substrates. Highest cellulase yield was obtained when grown on native cellulose, α-cellulose and low degree of polymerization cellulose but not carboxymethylcellulose or other carbohydrate sources. Cellulase activity was not detected when cells were grown on cellobiose. Crude extracellular protein preparations lacked proteolytic and cellobiase activity. The pH and temperafure optima for endoglucanase activity were 5.2 and 65° C, respectively, while that of the exoglucanase activity were 5.4 and 64° C, respectively. The specific activity at 60° c for exoglucanase and endoglucanase of crude cellulase obtained from cells grown on cellulose (MN 300) was 3.6 μmoles reducing sugar equivalents released per h (unit)/mg of protein and 1.5 μmole reducing sugar equivalent released per min (unit)/mg of protein, respectively. The yield of endoglucanase was 125 units per g of cellulose MN 300 degraded and that of exoglucanase was 300 units per g of cellulose MN 300 degraded. Glucose and cellobiose were the hydrolytic end products of crude cellulase action on cellulose, cellotraose and cellotriose in vitro.

Symbiotic Nitrogen Fixation in the Fungus Gardens of Leaf-Cutter Ants

Gardening for Ants and Termites Among the social insects, ants and termites are the most diverse and ecologically dominant. Termites are known to engage in a mutualism with nitrogen-fixing bacteria, and Pinto-Tomás et al. (p. 1120) have identified similar relationships occurring among leaf-cutter ants, which maintain specialized nitrogen-fixing bacteria in their fungus gardens. Together, these mutualisms are a major source of nitrogen in terrestrial ecosystems. How is the evolutionary stability of such mutualistic cooperation maintained? Aanen et al. (p. 1103) show that the Termitomyces fungus cultured by termites remains highly related because mycelia of the same clone fuse together and grow more efficiently to out-compete rare clones. Leaf-cutting ants engage in a mutualism with nitrogen-fixing bacteria that help fertilize their fungus gardens. Bacteria-mediated acquisition of atmospheric N2 serves as a critical source of nitrogen in terrestrial ecosystems. Here we reveal that symbiotic nitrogen fixation facilitates the cultivation of specialized fungal crops by leaf-cutter ants. By using acetylene reduction and stable isotope experiments, we demonstrated that N2 fixation occurred in the fungus gardens of eight leaf-cutter ant species and, further, that this fixed nitrogen was incorporated into ant biomass. Symbiotic N2-fixing bacteria were consistently isolated from the fungus gardens of 80 leaf-cutter ant colonies collected in Argentina, Costa Rica, and Panama. The discovery of N2 fixation within the leaf-cutter ant−microbe symbiosis reveals a previously unrecognized nitrogen source in neotropical ecosystems.

An Insect Herbivore Microbiome with High Plant Biomass-Degrading Capacity

Herbivores can gain indirect access to recalcitrant carbon present in plant cell walls through symbiotic associations with lignocellulolytic microbes. A paradigmatic example is the leaf-cutter ant (Tribe: Attini), which uses fresh leaves to cultivate a fungus for food in specialized gardens. Using a combination of sugar composition analyses, metagenomics, and whole-genome sequencing, we reveal that the fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity. Comparison of this microbiomes predicted carbohydrate-degrading enzyme profile with other metagenomes shows closest similarity to the bovine rumen, indicating evolutionary convergence of plant biomass degrading potential between two important herbivorous animals. Genomic and physiological characterization of two dominant bacteria in the fungus garden microbiome provides evidence of their capacity to degrade cellulose. Given the recent interest in cellulosic biofuels, understanding how large-scale and rapid plant biomass degradation occurs in a highly evolved insect herbivore is of particular relevance for bioenergy.

Comparative study of SPORL and dilute-acid pretreatments of spruce for cellulosic ethanol production

The performance of two pretreatment methods, sulfite pretreatment to overcome recalcitrance of lignocellulose (SPORL) and dilute acid (DA), was compared in pretreating softwood (spruce) for fuel ethanol production at 180 degrees Celsius for 30 min with a sulfuric acid loading of 5% on oven-dry wood and a 5:1 liquor-to-wood ratio. SPORL was supplemented with 9% sodium sulfite (w/w of wood). The recoveries of total saccharides (hexoses and pentoses) were 87.9% (SPORL) and 56.7% (DA), while those of cellulose were 92.5% (SPORL) and 77.7% (DA). The total of known inhibitors (furfural, 5-hydroxymethylfurfural, and formic, acetic and levulinic acids) formed in SPORL were only 35% of those formed in DA pretreatment. SPORL pretreatment dissolved approximately 32% of the lignin as lignosulfonate, which is a potential high-value co-product. With an enzyme loading of 15 FPU (filter paper units) per gram of cellulose, the cellulose-to-glucose conversion yields were 91% at 24h for the SPORL substrate and 55% at 48 h for the DA substrate, respectively.

The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist.

Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which is also one of only two cultivated species in its phylum, is an efficient and prolific degrader of cellulose. Specifically, it has a particularly high activity against crystalline cellulose that requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, it does not degrade cellulose using a cellulosome or by producing high extracellular titers of cellulase enzymes. To better understand the biology of F. succinogenes, we sequenced the genome of the type strain S85 to completion. A total of 3,085 open reading frames were predicted from its 3.84 Mbp genome. Analysis of sequences predicted to encode for carbohydrate-degrading enzymes revealed an unusually high number of genes that were classified into 49 different families of glycoside hydrolases, carbohydrate binding modules (CBMs), carbohydrate esterases, and polysaccharide lyases. Of the 31 identified cellulases, none contain CBMs in families 1, 2, and 3, typically associated with crystalline cellulose degradation. Polysaccharide hydrolysis and utilization assays showed that F. succinogenes was able to hydrolyze a number of polysaccharides, but could only utilize the hydrolytic products of cellulose. This suggests that F. succinogenes uses its array of hemicellulose-degrading enzymes to remove hemicelluloses to gain access to cellulose. This is reflected in its genome, as F. succinogenes lacks many of the genes necessary to transport and metabolize the hydrolytic products of non-cellulose polysaccharides. The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation.

Expression of 17 Genes in Clostridium thermocellum ATCC 27405 during Fermentation of Cellulose or Cellobiose in Continuous Culture

ABSTRACT Clostridium thermocellum is a thermophilic, anaerobic, cellulolytic bacterium that produces ethanol and acetic acid as major fermentation end products. The effect of growth conditions on gene expression in C. thermocellum ATCC 27405 was studied using cells grown in continuous culture under cellobiose or cellulose limitation over a ∼10-fold range of dilution rates (0.013 to 0.16 h−1). Fermentation product distribution displayed similar patterns in cellobiose- or cellulose-grown cultures, including substantial shifts in the proportion of ethanol and acetic acid with changes in growth rate. Expression of 17 genes involved or potentially involved in cellulose degradation, intracellular phosphorylation, catabolite repression, and fermentation end product formation was quantified by real-time PCR, with normalization to two calibrator genes (recA and the 16S rRNA gene) to determine relative expression. Thirteen genes displayed modest (fivefold or less) differences in expression with growth rate or substrate type: sdbA (cellulosomal scaffoldin-dockerin binding protein), cdp (cellodextrin phosphorylase), cbp (cellobiose phosphorylase), hydA (hydrogenase), ldh (lactate dehydrogenase), ack (acetate kinase), one putative type IV alcohol dehydrogenase, two putative cyclic AMP binding proteins, three putative Hpr-like proteins, and a putative Hpr serine kinase. By contrast, four genes displayed >10-fold-reduced levels of expression when grown on cellobiose at dilution rates of >0.05 h−1: cipA (cellulosomal scaffolding protein), celS (exoglucanase), manA (mannanase), and a second type IV alcohol dehydrogenase. The data suggest that at least some cellulosomal components are transcriptionally regulated but that differences in expression with growth rate or among substrates do not directly account for observed changes in fermentation end product distribution.

Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations.

The ruminal microbial community is remarkably diverse, containing 100s of different bacterial and archaeal species, plus many species of fungi and protozoa. Molecular studies have identified a “core microbiome” dominated by phyla Firmicutes and Bacteroidetes, but also containing many other taxa. The rumen provides an ideal laboratory for studies on microbial ecology and the demonstration of ecological principles. In particular, the microbial community demonstrates both redundancy (overlap of function among multiple species) and resilience (resistance to, and capacity to recover from, perturbation). These twin properties provide remarkable stability that maintains digestive function for the host across a range of feeding and management conditions, but they also provide a challenge to engineering the rumen for improved function (e.g., improved fiber utilization or decreased methane production). Direct ruminal dosing or feeding of probiotic strains often fails to establish the added strains, due to intensive competition and amensalism from the indigenous residents that are well-adapted to the historical conditions within each rumen. Known exceptions include introduced strains that can fill otherwise unoccupied niches, as in the case of specialist bacteria that degrade phytotoxins such as mimosine or fluoroacetate. An additional complicating factor in manipulating the ruminal fermentation is the individuality or host specificity of the microbiota, in which individual animals contain a particular community whose species composition is capable of reconstituting itself, even following a near-total exchange of ruminal contents from another herd mate maintained on the same diet. Elucidation of the interactions between the microbial community and the individual host that establish and maintain this specificity may provide insights into why individual hosts vary in production metrics (e.g., feed efficiency or milk fat synthesis), and how to improve herd performance.

Quantitative analysis of cellulose degradation and growth of cellulolytic bacteria in the rumen

Ruminant animals digest cellulose via a symbiotic relationship with ruminal microorganisms. Because feedstuffs only remain in the rumen for a short time, the rate of cellulose digestion must be very rapid. This speed is facilitated by rumination, a process that returns food to the mouth to be rechewed. By decreasing particle size, the cellulose surface area can be increased by up to 10(6)-fold. The amount of cellulose digested is then a function of two competing rates, namely the digestion rate (K(d)) and the rate of passage of solids from the rumen (K(p)). Estimation of bacterial growth on cellulose is complicated by several factors: (1) energy must be expended for maintenance and growth of the cells, (2) only adherent cells are capable of degrading cellulose and (3) adherent cells can provide nonadherent cells with cellodextrins. Additionally, when ruminants are fed large amounts of cereal grain along with fiber, ruminal pH can decrease to a point where cellulolytic bacteria no longer grow. A dynamic model based on STELLA software is presented. This model evaluates all of the major aspects of ruminal cellulose degradation: (1) ingestion, digestion and passage of feed particles, (2) maintenance and growth of cellulolytic bacteria and (3) pH effects.

Acetate metabolism inMethanosarcina barkeri

Methanosarcina barkeri was grown by acetate fermentation in complex medium (N2 gas phase). The molar growth yield was 1.6–1.9 g cells/mol methane formed. Under these conditions 63–82% of the methane produced byMethanosarcina strains was derived from the methyl carbon of acetate, indicating that some methane was derived from other media components. Growth was not demonstrated in complex media lacking acetate or mineral acetate medium containing acetate but lacking H2/CO2, methanol, or trypticase and yeast extract. Acetate metabolism byM. barkeri strain MS was further exmined in mineral acetate medium containing H2/CO2 and/or methanol, but lacking cysteine. Under these conditions, more methane was derived from the methyl carbon of acetate than from the carboxyl carbon. Methanogenesis from the methyl group increased with increasing acetate concentration. The methyl carbon contributed up to 42% of the methane formed with H2/CO2 and up to 5% with methanol. Methanol stimulated the oxidation of the methyl group of acetate to CO2. The average rates of methane formation from acetate were 1.3 nomol/min ·ml/culture (0.04mg2 cell dry weight) in defined media (gas phase H2/CO2) and complex media (gas phase N2). Acetate contributed up to 60% of cell carbon formed under the growth conditions examined. Similar quantities of cell carbon were derived from the methyl and carboxyl carbons of acetate, suggesting incorporation of this compound as a two-carbon unit. Incorporated acetate was not preferentially localized in lipid material, as 70% of the incorporated acetate was found in the wall and protein cell fractions. Acetate catabolism was stimulated by pregrowing of cultures in media containing acetate, while acetate anabolism was not influenced. The results are discussed in terms of the differences between the mechanisms of acetate catabolism and anabolism.

Plant species composition and biofuel yields of conservation grasslands

Marginal croplands, such as those in the Conservation Reserve Program (CRP), have been suggested as a source of biomass for biofuel production. However, little is known about the composition of plant species on these conservation grasslands or their potential for ethanol production. Our objective was to assess the potential of CRP and other conservation grasslands for biofuel production, describing the relationships of plant species richness and tall native C4 prairie grass abundance with plant chemical composition and the resulting potential ethanol yield. We determined plant species composition and diversity at multiple scales with the modified Whittaker plot technique, aboveground biomass, plant chemical composition, and potential ethanol yield at 34 sites across the major ecological regions of the northeastern USA. Conservation grasslands with higher numbers of plant species had lower biomass yields and a lower ethanol yield per unit biomass compared with sites with fewer species. Thus, biofuel yield per unit land area decreased by 77% as plant species richness increased from 3 to 12.8 species per m2. We found that, as tall native C4 prairie grass abundance increased from 1.7% to 81.6%, the number of plant species decreased and aboveground biomass per unit land area and ethanol yield per unit biomass increased resulting in a 500% increased biofuel yield per unit land area. Plant species richness and composition are key determinants of biomass and ethanol yields from conservation grasslands and have implications for low-input high-diversity systems. Designing systems to include a large proportion of species with undesirable fermentation characteristics could reduce ethanol yields.