Megasphaera elsdenii: Its Role in Ruminant Nutrition and Its Potential Industrial Application for Organic Acid Biosynthesis

The Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of M. elsdenii usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). M. elsdenii has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of M. elsdenii to produce C2-C7 carboxylic acids-potential precursors for industrial fuel and chemical production-is examined.

Microbial communities for valorizing biomass using the carboxylate platform to produce volatile fatty acids: A review

The carboxylate platform employs a diverse microbial consortium of anaerobes in which the methanogens are inhibited. Nearly all biomass components are digested to a mixture of C1-C8 monocarboxylic acids and their corresponding salts. The methane-arrested anaerobic digestion proceeds readily without needing to sterilize biomass or equipment. It accepts a wide range of feedstocks (e.g., agricultural residues, municipal solid waste, sewage sludge, animal manure, food waste, algae, and energy crops), and produces high product yields. This review highlights several important aspects of the platform, including its thermodynamic underpinnings, influences of inoculum source and operating conditions on product formation, and downstream chemical processes that convert the carboxylates to hydrocarbon fuels and oxygenated chemicals. This review further establishes the carboxylate platform as a viable and economical route to industrial biomass utilization.

Effects of preservation of rumen inoculum on volatile fatty acids production and the community dynamics during batch fermentation of fruit pomace

Rumen fluid (RF) as inocula is useful for evaluating biomass digestibility and has potential for producing volatile fatty acids (VFA) via the carboxylate platform. However, RF is not readily available, necessitating evaluation of potential preservation methods. Glycerol (50% v/v) and DMSO (5% v/v) were used to preserve rumen inocula for 3 months at -80 °C. Effects of cryo-preservation on digestibility, VFA production and community composition with β-diversity distance metrics were compared to fresh RF using apple, citrus and grape pomace as substrates. For all substrates, DMSO cryo-preserved rumen digestibility parameters, VFA yield and product distribution were more significantly comparable to fresh RF (P > 0.05) than was glycerol cryo-preserved RF. Similarly, β-diversity coefficient (unweighted unifrac) between DMSO cryo-preserved RF and fresh RF was 0.250 while the coefficient was 0.359 for the glycerol cryo-preserved RF compared to fresh RF. This showed that a DMSO cryo-preserved RF is less affected by preservation effects and is a more promising alternative to fresh RF.

166 Altering the ruminal microbiota in dairy calves using rumen contents dosing

A major goal in dairy research is to improve milk production efficiency (MPE). With the advent of next-generation sequencing, efforts are underway to improve MPE by manipulating the rumen microbiota. MPE correlates to ruminal bacterial community composition (BCC), but the adult rumen microbiota is highly stable and returns to a baseline BCC after heavy perturbation. We seek to influence rumen BCC by early intervention in pre-weaning calves. Two cannulated Holstein donors of disparate MPE were selected. Three cohorts of 6 bull calves were established and dosed by gavage with a rumen inoculum sourced from the high-efficiency donor (HE), the low-efficiency donor (LE), or an autoclaved 50:50 mix as a microbe-free control (C). Dosing occurred at birth, then biweekly through 6 weeks. Feces were collected at each dosing. Daily preweaning intake of calf starter, which correlates to downstream feed efficiency, was greatest in HE calves and lowest in C calves (P &lt; 0.05), though preweaning average daily gain did not differ between cohorts (P = 0.210). Calves were sacrificed at 8 weeks to access rumen contents and rumen wall sections were collected to assess papillation. Fecal and rumen samples were subjected to 16S rRNA amplicon sequencing. BCC differed by cohort in fecal and rumen samples (P &lt; 0.05), with HE calf samples most similar to adult rumen samples and C calves least similar. Additionally, HE calves tended to have elongated papillae (P =0.062), the development of which is dependent on byproducts of microbial metabolism in the rumen and which points to differences in potential absorptive capacity of the epithelium. These data demonstrate that the rumen BCC can be influenced by early intervention. Future work includes expansion of this dosing protocol to a cohort of 60 female calves, following rumen BCC development and the impact on MPE in through the first lactation.

Valorisation of the invasive species, Prosopis juliflora, using the carboxylate platform to produce volatile fatty acids

Biomass derived from low-value, high-volume invasive plant species is an attractive, alternative feedstock to produce biofuels and biochemicals. This study aimed to use the carboxylate platform to valorize the invasive leguminous shrub, Prosopis juliflora (Mesquite), by utilizing in vitro rumen fermentations without chemical pretreatment to produce volatile fatty acids. The three fractions of the mesquite: leaves (ProL), stems (ProS) and branches (ProB) were compared regarding chemical composition, neutral detergent fiber (NDF) digestibility at 7 time points and VFA production after 72 h with sugarcane bagasse (SCB) as a reference. NDF digestibility was significantly (P < 0.05) higher in ProL (35.8%) than ProS (30.4%) and ProB (20.9%) compared to SCB (21.9%). VFA concentrations from 20 g biomass L^-1 showed significant differences with 8.07, 6.71 and 6.51 g L^-1 for ProL, ProS and ProB respectively, while SCB yielded 4.02 g L^-1. These concentrations were comparable with other platforms that employ chemically pretreated biomass for VFA production.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

Shifts in fermentation end products and bacterial community composition in long-term, sequentially transferred in vitro ruminal enrichment cultures fed switchgrass with and without ethanol as a co-substrate

In vitro ruminal fermentations resemble in vivo fermentations with respect to substrate consumption and distribution of fermentation products in short term (1-5 d) incubations. However, little is known regarding changes in in vitro fermentations over prolonged incubation or multiple transfers. Gas production, pH, fermentation products, and bacterial community composition were examined in duplicate in vitro fermentations of switchgrass plus distillers grains that were transferred at 3-4 d intervals over 900 d. Additionally, duplicate fermentations inoculated from 160 d-old enrichments into the same medium but supplemented with ethanol, and transferred at 3-4 d over a 730 d period were characterized. SWG and SWG + E fermentation showed marked differences in community composition, pH, total product concentrations and ratios, relative to each other and to the original inoculum. The results have implications for the use of ruminal inocula for industrial production of short- and medium-chain fatty acids via the carboxylate platform.

A global analysis of gene expression in Fibrobacter succinogenes S85 grown on cellulose and soluble sugars at different growth rates

BACKGROUND

Cellulose is the most abundant biological polymer on earth, making it an attractive substrate for the production of next-generation biofuels and commodity chemicals. However, the economics of cellulose utilization are currently unfavorable due to a lack of efficient methods for its hydrolysis. Fibrobacter succinogenes strain S85, originally isolated from the bovine rumen, is among the most actively cellulolytic mesophilic bacteria known, producing succinate as its major fermentation product. In this study, we examined the transcriptome of F. succinogenes S85 grown in continuous culture at several dilution rates on cellulose, cellobiose, or glucose to gain a system-level understanding of cellulose degradation by this bacterium.

RESULTS

Several patterns of gene expression were observed for the major cellulases produced by F. succinogenes S85. A large proportion of cellulase genes were constitutively expressed, including the gene encoding for Cel51A, the major cellulose-binding endoglucanase produced by this bacterium. Moreover, other cellulase genes displayed elevated expression during growth on cellulose relative to growth on soluble sugars. Growth rate had a strong effect on global gene expression, particularly with regard to genes predicted to encode carbohydrate-binding modules and glycoside hydrolases implicated in hemicellulose degradation. Expression of hemicellulase genes was tightly regulated, with these genes displaying elevated expression only during slow growth on soluble sugars. Clear differences in gene expression were also observed between adherent and planktonic populations within continuous cultures growing on cellulose.

CONCLUSIONS

This work emphasizes the complexity of the fiber-degrading system utilized by F. succinogenes S85, and reinforces the complementary role of hemicellulases for accessing cellulose by these bacteria. We report for the first time evidence of global differences in gene expression between adherent and planktonic populations of an anaerobic bacterium growing on cellulose at steady state during continuous cultivation. Finally, our results also highlight the importance of controlling for growth rate in investigations of gene expression.

Camelina Seed Supplementation at Two Dietary Fat Levels Change Ruminal Bacterial Community Composition in a Dual-Flow Continuous Culture System

This experiment aimed to determine the effects of camelina seed (CS) supplementation at different dietary fat levels on ruminal bacterial community composition and how it relates to changes in ruminal fermentation in a dual-flow continuous culture system. Diets were randomly assigned to 8 fermenters (1,200–1,250 mL) in a 2 × 2 factorial arrangement of treatments in a replicated 4 × 4 Latin square with four 10-day experimental periods that consisted of 7 days for diet adaptation and 3 days for sample collection. Treatments were: (1) no CS at 5% ether extract (EE, NCS5); (2) no CS at 8% EE (NCS8); (3) 7.7% CS at 5% EE (CS5); and (4) 17.7% CS at 8% EE (CS8). Megalac was used as a control to adjust EE levels. Diets contained 55% orchardgrass hay and 45% concentrate, and fermenters were equally fed a total of 72 g/day (DM basis) twice daily. The bacterial community was determined by sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Sequencing data were analyzed using mothur and statistical analyses were performed in R and SAS. The most abundant phyla across treatments were the Bacteroidetes and Firmicutes, accounting for 49 and 39% of the total sequences, respectively. The bacterial community composition in both liquid and solid fractions of the effluent digesta changed with CS supplementation but not by dietary EE. Including CS in the diets decreased the relative abundances of Ruminococcus spp., Fibrobacter spp., and Butyrivibrio spp. The most abundant genus across treatments, Prevotella, was reduced by high dietary EE levels, while Megasphaera and Succinivibrio were increased by CS supplementation in the liquid fraction. Correlatively, the concentration of acetate was decreased while propionate increased; C18:0 was decreased and polyunsaturated fatty acids, especially C18:2 n-6 and C18:3 n-3, were increased by CS supplementation. Based on the correlation analysis between genera and fermentation end products, this study revealed that CS supplementation could be energetically beneficial to dairy cows by increasing propionate-producing bacteria and suppressing ruminal bacteria associated with biohydrogenation. However, attention should be given to avoid the effects of CS supplementation on suppressing cellulolytic bacteria.

Transient changes in milk production efficiency and bacterial community composition resulting from near-total exchange of ruminal contents between high- and low-efficiency Holstein cows

The objectives of this study were to determine if milk production efficiency (MPE) is altered by near-total exchange of ruminal contents between high- (HE) and low-MPE (LE) cows and to characterize ruminal bacterial community composition (BCC) before exchange and over time postexchange. Three pairs of ruminally cannulated, third-lactation cows were selected whose MPE (energy-corrected milk per unit of dry matter intake) differed over their first 2 lactations. Approximately 95% of ruminal contents were exchanged between cows within each pair. Ruminal pH and volatile fatty acid (VFA) profiles, along with BCC (characterized by sequencing of the variable 4 region of 16S rRNA genes), were assessed just before feeding on d -8, -7, -5, -4, -1, 1, 2, 3, 7, 10, 14, 21, 28, 35, 42, and 56, relative to the exchange date. High-MPE cows had higher total ruminal VFA concentrations, higher molar percentages of propionate and valerate, and lower molar percentages of acetate and butyrate than did LE cows, and re-established these differences 1 d after contents exchange. Across all LE cows, MPE increased during 7 d postexchange but declined thereafter. Two of the 3 HE cows displayed decreases in MPE following introduction of the ruminal contents from the corresponding LE cow, but MPE increased in the third HE cow, which was determined to be an outlier. For all 6 cows, both liquid- and solids-associated BCC differed between individuals within a pair before contents exchange. Upon exchange, BCC of both phases in all 3 pairs was more similar to that of the donor inoculum than to preexchange host BCC. For 5 of 6 cows, the solids-associated community returned within 10 d to more resemble the preexchange community of that host than that of the donor community. Individual variability before the exchange was greater in liquids than in solids, as was the variability in response of bacterial communities to the exchange. Individual cows varied in their response, but generally moved toward re-establishment of their preexchange communities by 10 d after contents exchange. By contrast, ruminal pH and VFA profiles returned to preexchange levels within 1 d. Despite the small number of cows studied, the data suggest an apparent role for the ruminal bacterial community as a determinant of MPE.

In vitro ruminal fermentation of treated alfalfa silage using ruminal inocula from high and low feed-efficient lactating cows

AIMS

To assess the effect of two additives on alfalfa silage and on in vitro ruminal fermentation when using ruminal inocula from high feed-efficient (HE) and low feed-efficient (LE) lactating cows.

METHODS AND RESULTS

First- and second-cut alfalfa was harvested at 40% bloom stage, treated with control (no additive), Lactobacillus plantarum (LP) or formic acid (Formic), ensiled in 1·0 l minisilos, and fermented for 60 days. Fermented alfalfa was incubated in vitro for 24 h using ruminal inoculum from HE and LE lactating cows. The pH was lower in alfalfa silage treated with LP and Formic, and produced lower ammonia-N than did the control. In vitro true dry matter digestibility (IVTDMD) was higher with ruminal inoculum from HE than LE cows, but there was no consistent effect of treated alfalfa on microbial biomass yield and in vitro volatile fatty acids.

CONCLUSIONS

The IVTDMD was numerically greater with ruminal inoculum from higher feed-efficient cows although statistical significance was only demonstrated with the first-cut alfalfa. However, treated alfalfa silage did not show the effect expected on in vitro microbial biomass yield.

SIGNIFICANCE AND IMPACT OF THE STUDY

The feed efficiency of cows used as a source of ruminal inocula may affect IVTDMD and be a source of variation across in vitro runs. Differences in ruminal fermentation between cows of different feed efficiency could help to explain differences in milk yield and other parameters of dairy cattle performance.

Divergent utilization patterns of grass fructan, inulin, and other nonfiber carbohydrates by ruminal microbes

Fructans are an important nonfiber carbohydrate in cool season grasses. Their fermentation by ruminal microbes is not well described, though such information is needed to understand their nutritional value to ruminants. Our objective was to compare kinetics and product formation of orchardgrass fructan (phlein; PHL) to other nonfiber carbohydrates when fermented in vitro with mixed or pure culture ruminal microbes. Studies were carried out as randomized complete block designs. All rates given are first-order rate constants. With mixed ruminal microbes, rate of substrate disappearance tended to be greater for glucose (GLC) than for PHL and chicory fructan (inulin; INU), which tended to differ from each other (0.74, 0.62, and 0.33 h(-1), respectively). Disappearance of GLC had almost no lag time (0.04 h), whereas the fructans had lags of 1.4h. The maximum microbial N accumulation, a proxy for cell growth, tended to be 20% greater for PHL and INU than for GLC. The N accumulation rate for GLC (1.31h(-1)) was greater than for PHL (0.75 h(-1)) and INU (0.26 h(-1)), which also differed. More microbial glycogen (+57%) was accumulated from GLC than from PHL, though accumulation rates did not differ (1.95 and 1.44 h(-1), respectively); little glycogen accumulated from INU. Rates of organic acid formation were 0.80, 0.28, and 0.80 h(-1) for GLC, INU, and PHL, respectively, with PHL tending to be greater than INU. Lactic acid production was more than 7-fold greater for GLC than for the fructans. The ratio of microbial cell carbon to organic acid carbon tended to be greater for PHL (0.90) and INU (0.86) than for GLC (0.69), indicating a greater yield of cell mass per amount of substrate fermented with fructans. Reduced microbial yield for GLC may relate to the greater glycogen production that requires ATP, and lactate production that yields less ATP; together, these processes could have reduced ATP available for cell growth. Acetate molar proportion was less for GLC than for fructans, and less for PHL than for INU. In studies with pure cultures, all microbes evaluated showed differences in specific growth rate constants (μ) for GLC, fructose, sucrose, maltose, and PHL. Selenomonas ruminantium and Streptococcus bovis showed the highest μ for PHL (0.55 and 0.67 h(-1), respectively), which were 50 to 60% of the μ achieved for GLC. The 10 other species tested had μ between 0.01 and 0.11h(-1) with PHL. Ruminal microbes use PHL differently than they do GLC or INU.

Redox mediators modify end product distribution in biomass fermentations by mixed ruminal microbes in vitro

The fermentation system of mixed ruminal bacteria is capable of generating large amounts of short-chain volatile fatty acids (VFA) via the carboxylate platform in vitro. These VFAs are subject to elongation to larger, more energy-dense products through reverse β-oxidation, and the resulting products are useful as precursors for liquid fuels production. This study examined the effect of several redox mediators (neutral red, methyl viologen, safranin O, tannic acid) as alternative electron carriers for mixed ruminal bacteria during the fermentation of biomass (ground switchgrass not subjected to other pretreatments) and their potential to enhance elongation of end-products to medium-chain VFAs with no additional run-time. Neutral red (1 mM) in particular facilitated chain elongation, increasing average VFA chain length from 2.42 to 2.97 carbon atoms per molecule, while simultaneously inhibiting methane accumulation by over half yet maintaining total C in end products. The ability of redox dyes to act as alternative electron carriers suggests that ruminal fermentation is inherently manipulable toward retaining a higher fraction of substrate energy in the form of VFA.

Effects of ruminal dosing of Holstein cows with Megasphaera elsdenii on milk fat production, ruminal chemistry, and bacterial strain persistence

Megasphaera elsdenii is a lactate-utilizing bacterium whose ruminal abundance has been shown to be greatly elevated during milk fat depression (MFD). To further examine this association, a total of 23 cannulated multiparous Holstein cows were examined in 3 experiments in which strains of M. elsdenii were directly dosed into the rumen (~2 × 10(12) cells/dose); control cows were dosed with sterile lactate-free culture medium. Cows were fed a total mixed ration (292 g of starch/kg of dry matter) that contained primarily corn silage, alfalfa silage, finely ground high-moisture corn, supplemental protein, and corn oil (3 g/kg of dry matter). Experiments differed in stage of lactation of the cows (early or late), dosing events (single dose, or 4 doses over a 5-d period), timing of dose (prefeed or 4 h postfeed), and M. elsdenii strain (laboratory strain YI9 or 3 strains isolated from cows in the same herd). Dry matter intake and milk yield and composition were measured from 5 to 0 d before dosing and 1 to 7d after first dosing, plus later time points that varied by experiment. Milk yield and composition were not affected by dosing. Megasphaera elsdenii was quantified in the liquid phase of ruminal contents by automated ribosomal intergenic spacer analysis, or by PCR with relative quantification (M. elsdenii 16S rRNA gene copy number as a percentage of total bacterial 16S rRNA gene copies). Neither the M. elsdenii-dosed or control cows displayed MFD after dosing, and in almost all cases M. elsdenii populations returned to low baseline levels (<0.02% of 16S rRNA gene copy number) within 24 h of dosing. This rapid decline in M. elsdenii also occurred in several cows that were dosed with a strain of M. elsdenii that had been isolated from that particular cow during a previous bout of MFD. Ruminal pH and total millimolar volatile fatty acids and lactate did not differ between dosed and control cows, although acetate-to-propionate ratio declined in both groups and butyrate increased after dosing with M. elsdenii. The results confirm that establishing exogenously added bacterial strains in the rumen is difficult, even for strains previously isolated from the recipient cow. The potential role of M. elsdenii as an agent of MFD remains unclear in the absence of successful establishment of the dosed strains.

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.

Production of medium-chain volatile fatty acids by mixed ruminal microorganisms is enhanced by ethanol in co-culture with Clostridium kluyveri

Mixed bacterial communities from the rumen ferment cellulosic biomass primarily to C2-C4 volatile fatty acids, and perform only limited chain extension to produce C5 (valeric) and C6 (caproic) acids. The aim of this study was to increase production of caproate and valerate in short-term in vitro incubations. Co-culture of mixed ruminal microbes with a rumen-derived strain of the bacterium Clostridium kluyveri converted cellulosic biomass (alfalfa stems or switchgrass herbage) plus ethanol to VFA mixtures that include valeric and caproic acids as the major fermentation products over a 48-72h run time. Concentrations of caproate reached 6.1gL(-1), similar to or greater than those reported in most conventional carboxylate fermentations that employ substantially longer run times.

Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay

The rich and diverse microbiota of the rumen provides ruminant animals the capacity to utilize highly fibrous feedstuffs as their energy source, but there is surprisingly little information on the composition of the microbiome of ruminants fed all-forage diets, despite the importance of such agricultural production systems worldwide. In three 28-day periods, three ruminally-cannulated Holstein heifers sequentially grazed orchardgrass pasture (OP), then were fed orchardgrass hay (OH), then returned to OP. These heifers displayed greater shifts in ruminal bacterial community composition (determined by automated ribosomal intergenic spacer analysis and by pyrotag sequencing of 16S rRNA genes) than did two other heifers maintained 84 d on the same OP. Phyla Firmicutes and Bacteroidetes dominated all ruminal samples, and quantitative PCR indicated that members of the genus Prevotella averaged 23% of the 16S rRNA gene copies, well below levels previously reported with cows fed total mixed rations. Differences in bacterial community composition and ruminal volatile fatty acid (VFA) profiles were observed between the OP and OH despite similarities in gross chemical composition. Compared to OP, feeding OH increased the molar proportion of ruminal acetate (P = 0.02) and decreased the proportion of ruminal butyrate (P < 0.01), branched-chain VFA (P < 0.01) and the relative population size of the abundant genus Butyrivibrio (P < 0.001), as determined by pyrotag sequencing. Despite the low numbers of animals examined, the observed changes in VFA profile in the rumens of heifers on OP vs. OH are consistent with the shifts in Butyrivibrio abundance and its known physiology as a butyrate producer that ferments both carbohydrates and proteins.

Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis

BACKGROUND

Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. Moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro. The mechanism of cellulose degradation by R. albus 7 is not well-defined and is thought to involve pilin-like proteins, unique carbohydrate-binding domains, a glycocalyx, and cellulosomes. Here, we used a combination of comparative genomics, fermentation analyses, and transcriptomics to further clarify the cellulolytic and fermentative potential of R. albus 7.

RESULTS

A comparison of the R. albus 7 genome sequence against the genome sequences of related bacteria that either encode or do not encode cellulosomes revealed that R. albus 7 does not encode for most canonical cellulosomal components. Fermentation analysis of R. albus 7 revealed the ability to produce ethanol and acetate on a wide range of fibrous substrates in vitro. Global transcriptomic analysis of R. albus 7 grown at identical dilution rates on cellulose and cellobiose in a chemostat showed that this bacterium, when growing on cellulose, utilizes a carbohydrate-degrading strategy that involves increased transcription of the rare carbohydrate-binding module (CBM) family 37 domain and the tryptophan biosynthetic operon.

CONCLUSIONS

Our data suggest that R. albus 7 does not use canonical cellulosomal components to degrade cellulose, but rather up-regulates the expression of CBM37-containing enzymes and tryptophan biosynthesis. This study contributes to a revised model of carbohydrate degradation by this key member of the rumen ecosystem.

Improving ethanol production from alfalfa stems via ambient-temperature acid pretreatment and washing

The concept of co-production of liquid fuel (ethanol) along with animal feed on farm was proposed, and the strategy of using ambient-temperature acid pretreatment, ensiling and washing to improve ethanol production from alfalfa stems was investigated. Alfalfa stems were separated and pretreated with sulfuric acid at ambient-temperature after harvest, and following ensiling, after which the ensiled stems were subjected to simultaneous saccharification and fermentation (SSF) for ethanol production. Ethanol yield was improved by ambient-temperature sulfuric acid pretreatment before ensiling, and by washing before SSF. It was theorized that the acid pretreatment at ambient temperature partially degraded hemicellulose, and altered cell wall structure, resulted in improved cellulose accessibility, whereas washing removed soluble ash in substrates which could inhibit the SSF. The pH of stored alfalfa stems can be used to predict the ethanol yield, with a correlation coefficient of +0.83 for washed alfalfa stems.

A syndrome of mutualism reinforces the lifestyle of a sloth

Arboreal herbivory is rare among mammals. The few species with this lifestyle possess unique adaptions to overcome size-related constraints on nutritional energetics. Sloths are folivores that spend most of their time resting or eating in the forest canopy. A three-toed sloth will, however, descend its tree weekly to defecate, which is risky, energetically costly and, until now, inexplicable. We hypothesized that this behaviour sustains an ecosystem in the fur of sloths, which confers cryptic nutritional benefits to sloths. We found that the more specialized three-toed sloths harboured more phoretic moths, greater concentrations of inorganic nitrogen and higher algal biomass than the generalist two-toed sloths. Moth density was positively related to inorganic nitrogen concentration and algal biomass in the fur. We discovered that sloths consumed algae from their fur, which was highly digestible and lipid-rich. By descending a tree to defecate, sloths transport moths to their oviposition sites in sloth dung, which facilitates moth colonization of sloth fur. Moths are portals for nutrients, increasing nitrogen levels in sloth fur, which fuels algal growth. Sloths consume these algae-gardens, presumably to augment their limited diet. These linked mutualisms between moths, sloths and algae appear to aid the sloth in overcoming a highly constrained lifestyle.

Fermentation of alfalfa wet-fractionation liquids to volatile fatty acids by Streptococcus bovis and Megasphaera elsdenii

"Green juice", obtained by squeezing fresh alfalfa leaves inoculated with lactic acid bacteria, was fermented at room temperature for 7-21 d to obtain 12-47 g lactic acid L(-1). Inoculation of green juice with Streptococcus bovis and incubation at 39°C reduced fermentation time to 8-12h. The resulting "brown juice" from either fermentation had a pH of ∼4.5 and a protein precipitate. Upon adjustment to pH 5.2-6.8 and inoculation with Megasphaera elsdenii, brown juice was fermented within 48 h to up to 18 g of mixed volatile fatty acids (VFA) L(-1). Single-stage fermentation of green juice by both species in coculture typically resulted in overgrowth of S. bovis and acid inhibition of M. elsdenii, inhibiting VFA production. Because the juice fermentations are conducted without sterilization or supplemental nutrients, they can potentially contribute to an integrated process featuring protein recovery and fermentation of fractionated solids to VFA and other products.

In vitro degradation and fermentation of three dietary fiber sources by human colonic bacteria

Although clinical benefits of dietary fiber supplementation seem to depend partially on the extent of fiber degradation and fermentation by colonic bacteria, little is known about the effect of supplemental fiber type on bacterial metabolism. In an experiment using a nonadapted human bacterial population from three normal subjects, the extent of in vitro fermentation was greater for gum arabic (GA) than for psyllium (PSY), which was greater than that for carboxymethylcellulose (CMC). In a separate experiment, in vitro incubation with feces from 52 subjects with fecal incontinence, before and after random assignment to and consumption of one of three fiber (GA, PSY, or CMC) supplements or a placebo for 20-21 days, indicated that prior consumption of a specific fiber source did not increase its degradation by fecal bacteria. Results suggest that the colonic microbial community enriched on a particular fiber substrate can rapidly adapt to the presentation of a new fiber substrate. Clinical implications of the findings are that intake of a fiber source by humans is not expected to result in bacterial adaptation that would require continually larger and eventually intolerable amounts of fiber to achieve therapeutic benefits.

Effects of chemical treatments and heating on the crystallinity of celluloses and their implications for evaluating the effect of crystallinity on cellulose biodegradation

Chemical treatments similar to those routinely used to extract cellulose from plant biomass caused significant increases in the relative crystallinity index (RCI) of Sig-macell 100 (a commercial cellulose of moderate crystallinity), as measured by x-ray powder diffraction in both the reflectance and transmittance modes. In general, the largest increases in RCI were observed following higher (rather than lower) temperature treatments. Substantial increases in crystalliity were also observed upon resuspension in water prior to drying, with higher temperatures again resulting in the greatest increases in RCI. Measurement of the RCIs of wetted Sigmacell 100 samples by acid hydrolysis kinetics revealed that most of the increased crystallinity occurred rapidly upon contact with water. In contrast to Sigmacell 100, a cellulose of higher initial crystallinity (the microcrystalline cellulose Sigmacell 50) showed little change in crystallinity following the above treatments. The results provide a partial explanation for the inconsistent relationships reported between cellulose crystallinity and cellulose biodegradation. (c) 1995 John Wiley & Sons, Inc.

Relationship between the fine structure of native cellulose and cellulose degradability by the cellulase complexes of Trichoderma reesei and Clostridium thermocellum

The initial rate of hydrolysis of six commercially available native (type l) celluloses was determined for the crude cellulase complexes of the thermophilic anaerobic bacterium C. thermocellum and the mesophilic fungus T. reesei. These rates were then compared with certain physical features of the substrates in an attempt to determine the role of cellulose structure in its degradability. Within the substrate series tested, the Clostridium system showed a greater relative range in rate of enzymatic hydrolysis than did the Trichoderma system. Average correlation coefficients for the kinetic rates from bacterial and fungal cellulases, respectively, and the following physical parameters were obtained: relative crystallinity index (RCl) from acid hydrolysis, -0.61 and -0.85; RCl from x-ray diffraction, -0.75 and -0.89; accessibility to formylation at 4 degrees C, + 0.49 and +0.60; nonaccessibility to formylation at 65 degrees C, -0.40 and -0.73; fiber saturation point, + 0.83 and + 0.85. Kinetic and pore volume distribution data suggest that the rate-limiting components of both the bacterial and fungal cellulase systems are of similar size, approximately 43 A along one axis.

Changes in ruminal bacterial community composition following feeding of alfalfa ensiled with a lactic acid bacterial inoculant

Some silage inoculants help to improve silage quality and promote an increase in milk production, possibly through altering the rumen microflora. We hypothesized that rumen bacterial community composition (BCC) would be different in cows fed alfalfa ensiled with the inoculant Lactobacillus plantarum MTD/1 (LP) compared with those fed alfalfa ensiled without the inoculant (Ctrl). Eight ruminally cannulated Holstein cows were allotted to 2 diets (Ctrl or LP) in a double crossover design with four 28-d periods. Diets were formulated to contain (% dry matter basis) 28.0% neutral detergent fiber and 16.2% crude protein, and contained alfalfa silage, 50.9; corn silage, 20.6; high-moisture shelled corn, 21.4; soy hulls, 4.7; plus minerals and vitamins, 2.4. Ruminal digesta were collected just before feeding on 3 consecutive days near the end of each period, and were separated into solid and liquid phases. Microbial DNA was extracted from each phase, amplified by PCR using domain-level bacterial primers, and subjected to automated ribosomal intergenic spacer analysis. The pH was 4.56 and 4.86 and the lactate-to-acetate ratio 9.8 and 4.4, respectively, for the treated and untreated alfalfa silages. Dry matter intakes and milk production data were not influenced by diets but showed a cow effect. Total volatile fatty acids (mM) tended to be greater for LP compared with Ctrl. Individual volatile fatty acids were not influenced by diets but showed a significant cow effect. Ruminal acetate (mol/100 mol) and acetate-to-propionate ratio were lower and propionate (mol/100 mol) greater for the 2 milk fat-depressed (MFD; <3.2% fat content) cows compared with the other 6 cows. Correspondence analysis of the 265 peaks in the automated ribosomal intergenic spacer analysis profile across the 188 samples revealed that the first 2 components contributed 7.1 and 3.8% to the total variation in the profile. The ordination points representing the liquid and solid phases clustered separately, indicating that these phases differed in BCC. The analysis of similarity data showed differences between Ctrl and LP. The lactic acid bacterial counts (log(10) cfu/g of wet silage) were 3.94 and 4.53 for the untreated and treated silage, respectively, at ensiling. The relative population size (RPS) of L. plantarum, determined by real-time PCR of 16S rRNA gene copies, was greater in LP compared with Ctrl. The ordination points corresponding to certain individual cows clustered separately, and the most distinctive bacterial communities were those associated with MFD cows. The RPS of Megasphaera elsdenii was greater in 1 of the 2 MFD cows, although mean RPS of M. elsdenii did not differ between the treatments. In addition to the differences in rumen BCC between LP and Ctrl, MFD cows also displayed differences in BCC compared with cows with normal milk fat yield.

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.

End product yields from the extraruminal fermentation of various polysaccharide, protein and nucleic acid components of biofuels feedstocks

"Extraruminal" fermentations employing in vitro incubation of mixed ruminal bacterial consortia, are capable of converting a complex array of biomass materials to mixtures of volatile fatty acids (VFA), methane, and carbon dioxide. Most of the potential energy in the biomass feedstock is retained in the VFA products, which are potential reactants for electrochemical conversion to hydrocarbon fuels. Quantitative data on VFA yields and proportions from biomass components are necessary for determining industrial feasibility, but such measurements have not been systematically reported. VFA yields and proportions were determined for a variety of carbohydrates, proteins and nucleic acids. Carbohydrates yielded primarily acetic and propionic acids, while proteins also yielded a more favorable product mix (longer average chain length and branched chain VFAs). Addition of certain co-substrates (e.g., glycerol) favorably improved the VFA product mix. The results have implications for hydrocarbon fuel generation from biomass materials by hybrid fermentation/chemical processes.

Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents

The purpose of this study was to examine the stability and host specificity of a cow's ruminal bacterial community following massive challenge with ruminal microflora from another cow. In each of 2 experiments, 1 pair of cows was selected on the basis of differences in ruminal bacterial community composition (BCC), determined by automated ribosomal intergenic spacer analysis (ARISA), a culture-independent "community fingerprinting" technique. Each pair of cows was then subjected to a 1-time exchange of >95% of ruminal contents without changing the composition of a corn silage/alfalfa haylage-based TMR. In experiment 1, the 2 cows differed (P<0.01) in prefeed ruminal pH (mean = 6.88 vs. 6.14) and prefeed total VFA concentration (mean = 57 vs. 77 mM), averaged over 3 d. Following exchange of ruminal contents, ruminal pH and total VFA concentration in both cows returned to their preexchange values within 24h. Ruminal BCC also returned to near its original profile, but this change required 14 d for 1 cow and 61 d for the other cow. In experiment 2, the 2 other cows differed in prefeed ruminal pH (mean = 6.69 vs. 6.20) and total VFA concentration (mean = 101 vs. 136 mM). Following exchange of ruminal contents, the first cow returned to its preexchange pH and VFA values within 24h; the second cow's rumen rapidly stabilized to a higher prefeed pH (mean = 6.47) and lower prefeed VFA concentration (mean = 120 mM) that was retained over the 62-d test period. Both cows reached somewhat different BCC than before the exchange. However, the BCC of both cows remained distinct and were ultimately more similar to that of the preexchange BCC than of the donor animal BCC. The data indicate that the host animal can quickly reestablish its characteristic ruminal pH and VFA concentration despite dramatic perturbation of its ruminal microbial community. The data also suggest that ruminal BCC displays substantial host specificity that can reestablish itself with varying success when challenged with a microbial community optimally adapted to ruminal conditions of a different host animal.

Optimizing on-farm pretreatment of perennial grasses for fuel ethanol production

Switchgrass (Panicum virgatum L.) and reed canarygrass (Phalaris arundinacea L.) were pretreated under ambient temperature and pressure with sulfuric acid and calcium hydroxide in separate experiments. Chemical loadings from 0 to 100g (kg DM)(-1) and durations of anaerobic storage from 0 to 180days were investigated by way of a central composite design at two moisture contents (40% or 60% w.b.). Pretreated and untreated samples were fermented to ethanol by Saccharomyces cerevisiae D5A in the presence of a commercially available cellulase (Celluclast 1.5L) and beta-glucosidase (Novozyme 188). Xylose levels were also measured following fermentation because xylose is not metabolized by S. cerevisiae. After sulfuric acid pretreatment and anaerobic storage, conversion of cell wall glucose to ethanol for reed canarygrass ranged from 22% to 83% whereas switchgrass conversions ranged from 16% to 46%. Pretreatment duration had a positive effect on conversion but was mitigated with increased chemical loadings. Conversions after calcium hydroxide pretreatment and anaerobic storage ranged from 21% to 55% and 18% to 54% for reed canarygrass and switchgrass, respectively. The efficacy of lime pretreatment was found to be highly dependent on moisture content. Moreover, pretreatment duration was only found to be significant for reed canarygrass. Although significant levels of acetate and lactate were observed in the biomass after storage, S. cerevisiae was not found to be inhibited at a 10% solids loading.

Optimizing on-farm pretreatment of perennial grasses for fuel ethanol production

Switchgrass (Panicum virgatum L.) and reed canarygrass (Phalaris arundinacea L.) were pretreated under ambient temperature and pressure with sulfuric acid and calcium hydroxide in separate experiments. Chemical loadings from 0 to 100g (kg DM)(-1) and durations of anaerobic storage from 0 to 180days were investigated by way of a central composite design at two moisture contents (40% or 60% w.b.). Pretreated and untreated samples were fermented to ethanol by Saccharomyces cerevisiae D5A in the presence of a commercially available cellulase (Celluclast 1.5L) and beta-glucosidase (Novozyme 188). Xylose levels were also measured following fermentation because xylose is not metabolized by S. cerevisiae. After sulfuric acid pretreatment and anaerobic storage, conversion of cell wall glucose to ethanol for reed canarygrass ranged from 22% to 83% whereas switchgrass conversions ranged from 16% to 46%. Pretreatment duration had a positive effect on conversion but was mitigated with increased chemical loadings. Conversions after calcium hydroxide pretreatment and anaerobic storage ranged from 21% to 55% and 18% to 54% for reed canarygrass and switchgrass, respectively. The efficacy of lime pretreatment was found to be highly dependent on moisture content. Moreover, pretreatment duration was only found to be significant for reed canarygrass. Although significant levels of acetate and lactate were observed in the biomass after storage, S. cerevisiae was not found to be inhibited at a 10% solids loading.

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.

pH dynamics and bacterial community composition in the rumen of lactating dairy cows

The influence of pH dynamics on ruminal bacterial community composition was studied in 8 ruminally cannulated Holstein cows fitted with indwelling electrodes that recorded pH at 10-min intervals over a 54-h period. Cows were fed a silage-based total mixed ration supplemented with monensin. Ruminal samples were collected each day just before feeding and at 3 and 6h after feeding. Solid and liquid phases were separated at collection, and extracted DNA was subjected to PCR amplification followed by automated ribosomal intergenic spacer analysis (ARISA). Although cows displayed widely different pH profiles (mean pH=6.11 to 6.51, diurnal pH range=0.45 to 1.39), correspondence analysis of the ARISA profiles revealed that 6 of the 8 cows showed very similar bacterial community compositions. The 2 cows having substantially different community compositions had intermediate mean pH values (6.30 and 6.33) and intermediate diurnal pH ranges (averaging 0.89 and 0.81 pH units). Fortuitously, these 2 cows alone also displayed milk fat depression, along with markedly higher ruminal populations of 1 bacterial operational taxonomic unit (OTU) and reduced populations of another ARISA amplicon. Cloning and sequencing of the elevated OTU revealed phylogenetic similarity to Megasphaera elsdenii, a species reportedly associated with milk fat depression. The higher populations of both M. elsdenii and OTU246 in these 2 cows were confirmed using quantitative real-time PCR (qPCR) with species-specific primers, and the fraction of total bacterial rDNA copies contributed by these 2 taxa were very highly correlated within individual cows. By contrast, the fraction of total bacterial rDNA copies contributed by Streptococcus bovis and genus Ruminococcus, 2 taxa expected to respond to ruminal pH, did not differ among cows (mean= <0.01 and 10.6%, respectively, of rRNA gene copies, determined by qPCR). The data indicate that cows with widely differing pH profiles can have similar ruminal bacterial community compositions, and that milk fat depression can occur at intermediate ruminal pH. The results support recent reports that milk fat depression is associated with shifts in bacterial community composition in rumine and is specifically related to the relative abundance of Megasphaera elsdenii.

Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants

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.

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.

Lessons from the cow: what the ruminant animal can teach us about consolidated bioprocessing of cellulosic biomass

Consolidated bioprocessing (CBP) of cellulosic biomass is a promising source of ethanol. This process uses anaerobic bacteria, their own cellulolytic enzymes and fermentation pathways that convert the products of cellulose hydrolysis to ethanol in a single reactor. However, the engineering and economics of the process remain questionable. The ruminal fermentation is a very highly developed natural cellulose-degrading system. We propose that breakthroughs developed by cattle and other ruminant animals in cellulosic biomass conversion can guide future improvements in engineered CBP systems. These breakthroughs include, among others, an elegant and effective physical pretreatment; operation at high solids loading under non-aseptic conditions; minimal nutrient requirements beyond the plant biomass itself; efficient fermentation of nearly all plant components; efficient recovery of primary fermentation end-products; and production of useful co-products. Ruminal fermentation does not produce significant amounts of ethanol, but it produces volatile fatty acids and methane at a rapid rate. Because these alternative products have a high energy content, efforts should be made to recover these products and convert them to other organic compounds, particularly transportation fuels.

Forage quality and composition measurements as predictors of ethanol yield from maize (Zea mays L.) stover

BACKGROUND

Improvement of biofeedstock quality for cellulosic ethanol production will be facilitated by inexpensive and rapid methods of evaluation, such as those already employed in the field of ruminant nutrition. Our objective was to evaluate whether forage quality and compositional measurements could be used to estimate ethanol yield of maize stover as measured by a simplified pretreatment and simultaneous saccharification and fermentation assay. Twelve maize varieties selected to be diverse for stover digestibility and composition were evaluated.

RESULTS

Variation in ethanol yield was driven by glucan convertibility rather than by glucan content. Convertibility was highly correlated with ruminal digestibility and lignin content. There was no relationship between structural carbohydrate content (glucan and neutral detergent fiber) and ethanol yield. However, when these variables were included in multiple regression equations including convertibility or neutral detergent fiber digestibility, their partial regression coefficients were significant and positive. A regression model including both neutral detergent fiber and its ruminal digestibility explained 95% of the variation in ethanol yield.

CONCLUSION

Forage quality and composition measurements may be used to predict cellulosic ethanol yield to guide biofeedstock improvement through agronomic research and plant breeding.

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.

Effect of monensin feeding and withdrawal on populations of individual bacterial species in the rumen of lactating dairy cows fed high-starch rations

Real-time polymerase chain reaction (PCR) was used to quantify 16 procaryotic taxa in the rumina of two lactating dairy cows following supply and subsequent withdrawal of the feed additive monensin (13.9 mg/kg of diet dry matter) in a high-starch, silage-based ration. PCR was conducted on DNA from rumen samples collected 6 h post feeding on two successive days before monensin supplementation, after 30 days of monensin supplementation, and at six weekly intervals after monensin withdrawal. Mean values of relative population size (RPS, the percent of bacterial 16S rRNA copy number) for genus Prevotella increased (P < 0.05) from 41.8% without monensin to 49.2% with monensin and declined to 42.5% after monensin withdrawal. Mean RPS values for two biohydrogenating species (Megasphaera elsdenii and Butyrivibrio fibrisolvens) were low (<0.4%) and declined several-fold in response to monensin. Mean RPS values for the biohydrogenating species Eubacterium ruminantium, four cellulolytic species, four starch- or dextrin-fermenting species, and Domain Archaea were not altered (P > 0.10) upon monensin feeding or withdrawal. The data suggest that monensin in high-starch diets does not suppress populations of classical ruminal Gram-positive bacteria or the availability of H2, though it may affect bacteria involved in biohydrogenation of lipids that regulate bovine mammary lipogenesis.

Sucrose concentration alters fermentation kinetics, products, and carbon fates during in vitro fermentation with mixed ruminal microbes1

Effects of sucrose (Suc) concentration on fermentation kinetics and products were evaluated using 3 concentrations of Suc, with 1 concentration of isolated NDF from Bermudagrass fermented together in batch culture in vitro with rumen inoculum. Fixed amounts of medium and inoculum were the protein sources, so protein:Suc decreased with increasing Suc. Kinetics were calculated from gas production over 48 h in a randomized complete block design (n = 28), and product yield was evaluated with sampling every 4 h for 24 h in a split-split plot in time design (n = 84). Fermentation vial was the experimental unit. Increasing Suc increased the lag time of rapidly (P < 0.01) and slowly fermented (P < 0.01) fractions and tended to decrease the rate of gas production from the rapid fraction (P = 0.07). Gas production from the slow fraction decreased linearly with increasing Suc (P = 0.02), suggesting a decrease in NDF fermentation. Sucrose was the predominant substrate at </=8 h of fermentation. Maxima for microbial CP (MCP) production were detected at </=8 h of fermentation. At detected MCP maxima, MCP production increased linearly (P = 0.02) and total organic acids (sum of lactate, acetate, propionate, and butyrate; mmol) tended to increase linearly (P = 0.07) with increasing Suc. Maximum lactate production at 0 and 4 h increased (P = 0.01), and yield of lactate from Suc tended to increase, linearly (P = 0.09) with increasing Suc. At detected MCP maxima, yield of C in products (total organic acids, MCP, CO(2), CH(4), glycogen) from utilized Suc C declined linearly for total products (P = 0.01) and organic acids (P = 0.01) and tended to decline for MCP (P = 0.12) as Suc increased. This may be a function of increased catabolic inefficiency of microbes with increasing Suc, as evidenced by increasing yields of lactate, or the use of C for products not measured. Product C yields were 1.28, 0.98, and 0.81 from lowest to greatest Suc inclusion, respectively. Values >1 indicate incorporation of C from the medium, likely from AA and peptides. The results support the premises that direct effects of Suc concentration and perhaps protein:Suc alter yields of fermentation products. That substrate concentration altered fermentation products and kinetics, possibly due to interactions with the run conditions, advises the clear definition of substrates and fermentation conditions to determine how the results integrate into our knowledge of ruminant nutrition.

Fermentability of eastern gamagrass, big bluestem and sand bluestem grown across a wide variety of environments

Plant biomass has attracted interest as a feedstock for biofuels production, but much of this work has been focused on relatively few plant species. In this study, three relatively-unstudied species of warm-season perennial grasses, grown at multiple locations in the eastern and central US and harvested over a three year period, were examined for fermentability via in vitro ruminal gas production and dry matter digestibility assays, and near-infrared reflectance calibrations were developed for these fermentation parameters. Big bluestem (Andropogon gerardii Vitman) displayed greater fermentability than did sand bluestem (Andropogon hallii Hack) or eastern gamagrass [Tripsacum dactyloides (L.) L.], but displayed lower biomass yields. The bluestems also displayed lower N contents and less variation in fermentability over different growth environments (geographic locations and harvest years), suggesting a more consistent biomass quality than for eastern gamagrass. Thus, in addition to their use as forage for ruminant animals, bluestems may be of particular interest as feedstocks for bioconversion to ethanol and other products via direct microbial fermentation (consolidated bioprocessing) schemes, and thus merit additional efforts to enhance biomass yield potential.

Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR

Relative quantification real-time PCR was used to quantify several bacterial species in ruminal samples from two lactating cows, each sampled 3 h after feeding on two successive days. Abundance of each target taxon was calculated as a fraction of the total 16S rRNA gene copies in the samples, using taxon-specific and eubacterial domain-level primers. Bacterial populations showed a clear predominance of members of the genus Prevotella, which comprised 42% to 60% of the bacterial rRNA gene copies in the samples. However, only 2% to 4% of the bacterial rRNA gene copies were represented by the classical ruminal Prevotella species Prevotella bryantii, Prevotella ruminicola and Prevotella brevis. The proportion of rRNA gene copies attributable to Fibrobacter succinogenes, Ruminococcus flavefaciens, Selenomonas ruminantium and Succinivibrio dextrinosolvens were each generally in the 0.5% to 1% range. Proportions for Ruminobacter amylophilus and Eubacterium ruminantium were lower (0.1% to 0.2%), while Butyrivibrio fibrisolvens, Streptococcus bovis, Ruminococcus albus and Megasphaera elsdenii were even less abundant, each comprising <0.03% of the bacterial rRNA gene copies. The data suggest that the aggregate abundance of the most intensively studied ruminal bacterial species is relatively low and that a large fraction of the uncultured population represents a single bacterial genus.

Studies of the extracellular glycocalyx of the anaerobic cellulolytic bacterium Ruminococcus albus 7

Anaerobic cellulolytic bacteria are thought to adhere to cellulose via several mechanisms, including production of a glycocalyx containing extracellular polymeric substances (EPS). As the compositions and structures of these glycocalyces have not been elucidated, variable-pressure scanning electron microscopy (VP-SEM) and chemical analysis were used to characterize the glycocalyx of the ruminal bacterium Ruminococcus albus strain 7. VP-SEM revealed that growth of this strain was accompanied by the formation of thin cellular extensions that allowed the bacterium to adhere to cellulose, followed by formation of a ramifying network that interconnected individual cells to one another and to the unraveling cellulose microfibrils. Extraction of 48-h-old whole-culture pellets (bacterial cells plus glycocalyx [G] plus residual cellulose [C]) with 0.1 N NaOH released carbohydrate and protein in a ratio of 1:5. Boiling of the cellulose fermentation residue in a neutral detergent solution removed almost all of the adherent cells and protein while retaining a residual network of adhering noncellular material. Trifluoroacetic acid hydrolysis of this residue (G plus C) released primarily glucose, along with substantial amounts of xylose and mannose, but only traces of galactose, the most abundant sugar in most characterized bacterial exopolysaccharides. Linkage analysis and characterization by nuclear magnetic resonance suggested that most of the glucosyl units were not present as partially degraded cellulose. Calculations suggested that the energy demand for synthesis of the nonprotein fraction of EPS by this organism represents only a small fraction (<4%) of the anabolic ATP expenditure of the bacterium.

Use of real time PCR to determine population profiles of individual species of lactic acid bacteria in alfalfa silage and stored corn stover

Real-time polymerase chain reaction (RT-PCR) was used to quantify seven species of lactic acid bacteria (LAB) in alfalfa silage prepared in the presence or absence of four commercial inoculants and in uninoculated corn stover harvested and stored under a variety of field conditions. Species-specific PCR primers were designed based on recA gene sequences. Commercial inoculants improved the quality of alfalfa silage, but species corresponding to those in the inoculants displayed variations in persistence over the next 96 h. Lactobacillus brevis was the most abundant LAB (12 to 32% of total sample DNA) in all of the alfalfa silages by 96 h. Modest populations (up to 10%) of Lactobacillus plantarum were also observed in inoculated silages. Pediococcus pentosaceus populations increased over time but did not exceed 2% of the total. Small populations (0.1 to 1%) of Lactobacillus buchneri and Lactococcus lactis were observed in all silages, while Lactobacillus pentosus and Enterococcus faecium were near or below detection limits. Corn stover generally displayed higher populations of L. plantarum and L. brevis and lower populations of other LAB species. The data illustrate the utility of RT-PCR for quantifying individual species of LAB in conserved forages prepared under a wide variety of conditions.

Interactions between Euphorbia esula toxins and bovine ruminal microbes

Cattle generally avoid grazing leafy spurge (LS; Euphorbia esula), whereas sheep and goats will often eat it. Understanding metabolism of toxic phytochemicals in LS by bovine rumen microflora may help explain why cattle often develop aversions to LS after initially eating it. Toxicity of LS compounds after in vitro fermentation with normal vs. antibiotic-modified bovine rumen digesta was evaluated at different lengths of fermentation. Levels of toxic and aversion-inducing ingenols were determined for fermented and nonfermented mixtures of LS and bovine rumen digesta, and the toxicity of an aversion-inducing extract of LS to rumen microbial species that are common in cattle, sheep, and goats was evaluated. Fermentation of LS with bovine digesta increased the toxicity of extracted compounds. Introduction of neomycin (an antibiotic that preferentially inhibits gram-negative bacteria) into the LS and bovine rumen digesta mixtures did not appear to affect toxicities regardless of fermentation length. Levels of ingenol were observed in LS and bovine digesta mixtures (both fermented and nonfermented) that were consistent with levels of ingenols reported for LS. Finally, a toxic extract of LS had little or no negative effect on the growth of several common species of rumen bacteria. The results indicate that LS is not generally toxic to the ruminal bacteria, but that microbial activity in the rumen may be responsible for enhancing LS toxicity to cattle.

Expression of 17 genes in Clostridium thermocellum ATCC 27405 during fermentation of cellulose or cellobiose in continuous culture

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 approximately 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.

Cultivation of mesophilic soil crenarchaeotes in enrichment cultures from plant roots

Because archaea are generally associated with extreme environments, detection of nonthermophilic members belonging to the archaeal division Crenarchaeota over the last decade was unexpected; they are surprisingly ubiquitous and abundant in nonextreme marine and terrestrial habitats. Metabolic characterization of these nonthermophilic crenarchaeotes has been impeded by their intractability toward isolation and growth in culture. From studies employing a combination of cultivation and molecular phylogenetic techniques (PCR-single-strand conformation polymorphism, sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, and real-time PCR), we present evidence here that one of the two dominant phylotypes of Crenarchaeota that colonizes the roots of tomato plants grown in soil from a Wisconsin field is selectively enriched in mixed cultures amended with root extract. Clones recovered from enrichment cultures were found to group phylogenetically with sequences from clade C1b.A1. This work corroborates and extends our recent findings, indicating that the diversity of the crenarchaeal soil assemblage is influenced by the rhizosphere and that mesophilic soil crenarchaeotes are found associated with plant roots, and provides the first evidence for growth of nonthermophilic crenarchaeotes in culture.

Lactic acid bacteria used in inoculants for silage as probiotics for ruminants

Many studies have shown the beneficial effects on ruminant performance of feeding them with silages inoculated with lactic acid bacteria (LAB). These benefits might derive from probiotic effects. The purpose of the current study was to determine whether LAB included in inoculants for silage can survive in rumen fluid (RF), as the first step in studying their probiotic effects. Experiments were conducted in the United States and Israel with clarified (CRF) and strained RF (SRF) that were inoculated at 10(6)-10(8) microorganisms/mL with and without glucose at 5 g/L. RF with no inoculants served as control. Ten commercial inoculants were used. The RF was incubated at 39 degrees C and sampled in duplicates at 6, 12, 24, 48, 72, and 96 h for pH and LAB counts. The results indicate that with glucose the pH of the RF decreased during the incubation period. In the SRF, the pH of the inoculated samples was higher than that of the controls in most cases. This might be a clue to the mechanism by which LAB elicit the enhancement in animal performance. LAB counts revealed that the inoculants survived in the RF during the incubation period. The addition of glucose resulted in higher LAB counts.