Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria.

The rumen is a complex ecosystem. It is the primary site for microbial fermentation of ingested feed allowing conversion of a low nutritional feed source into high quality meat and milk products. However, digestive inefficiencies lead to production of high amounts of environmental pollutants; methane and nitrogenous waste. These inefficiencies could be overcome by development of forages which better match the requirements of the rumen microbial population. Although challenging, the application of meta-proteomics has potential for a more complete understanding of the rumen ecosystem than sequencing approaches alone. Here, we have implemented a meta-proteomic approach to determine the association between taxonomies of microbial sources of the most abundant proteins in the rumens of forage-fed dairy cows, with taxonomic abundances typical of those previously described by metagenomics. Reproducible proteome profiles were generated from rumen samples. The most highly abundant taxonomic phyla in the proteome were Bacteriodetes, Firmicutes and Proteobacteria, which corresponded with the most abundant taxonomic phyla determined from 16S rRNA studies. Meta-proteome data indicated differentiation between metabolic pathways of the most abundant phyla, which is in agreement with the concept of diversified niches within the rumen microbiota.

The effects of PPO activity on the proteome of ingested red clover and implications for improving the nutrition of grazing cattle.

UNLABELLED: Increasing the rumen-stable protein content of feed would lead to improved nitrogen utilisation in cattle, and less nitrogenous waste. Red clover (Trifolium pratense L.) is a high protein ruminant feed containing high polyphenol oxidase (PPO) activity. PPO mediated protein-quinone binding has been linked to protecting plant proteins from proteolysis. To explore the mechanism underlying the effect of PPO on protein protection in fresh forage feeds, proteomic components of feed down-boli produced from wild-type red clover and a low PPO mutant, at point of ingestion and after 4h in vitro incubation with rumen inoculum were analysed. Significant differences in proteomic profiles between wild-type and mutant red clover were determined after 4h incubation, with over 50% less spots in mutant than wild-type proteomes, indicating decreased proteolysis in the latter. Protein identifications revealed preferentially retained proteins localised within the chloroplast, suggesting that PPO mediated protection in the wild-type operates due to the proximity of target proteins to the enzyme and substrates, either diffusing into this compartment from the vacuole or are present in the chloroplast. This increased understanding of protein targets of PPO indicates that wider exploitation of the trait could contribute to increased protein use efficiency in grazing cattle. BIOLOGICAL SIGNIFICANCE: One of the main challenges for sustainable livestock farming is improving capture of dietary nitrogen by ruminants. Typically up to 70% of ingested protein-N is excreted representing a loss of productivity potential and a serious environmental problem in terms of nitrogenous pollution of lands and water. Identification of key characteristics of rumen-protected protein will deliver target traits for selection in forage breeding programmes. The chloroplastic enzyme PPO catalyzes the oxidation of phenols to quinones, which react with protein. Little is currently known about the intracellular protein targets of the products of PPO activity or the mechanism underlying protein complexing, including whether there is any specificity to the reaction. Here we have determined significant differences in the proteomes of freshly ingested down boli corresponding to the presence or absence of active PPO. These results show that in the presence of PPO the forage protein is less amenable to proteolysis and provide the novel information that the protected proteins are putatively chloroplastically located. These data also contribute to a growing evidence base that a chloroplastic PPO substrate exists in red clover in addition to the currently known vacuolar substrates.

Breeding for genetic improvement of forage plants in relation to increasing animal production with reduced environmental footprint.

Animal production is a fundamental component of the food supply chain, and with an increasing global population production levels are set to increase. Ruminant animals in particular are valuable in their ability to convert a fibre-rich forage diet into a high-quality protein product for human consumption, although this benefit is offset by inefficiencies in rumen fermentation that contribute to emission of significant quantities of methane and nitrogenous waste. Through co-operation between plant and animal sciences, we can identify how the nutritional requirements of ruminants can be satisfied by high-quality forages for the future. Selective forage plant breeding has supported crop improvement for nearly a century. Early plant breeding programmes were successful in terms of yield gains (4% to 5% per decade), with quality traits becoming increasingly important breeding targets (e.g. enhanced disease resistance and digestibility). Recently, demands for more sustainable production systems have required high yielding, high-quality forages that enable efficient animal production with minimal environmental impact. Achieving this involves considering the entire farm system and identifying opportunities for maximising nutrient use efficiency in both forage and animal components. Forage crops of the future must be able to utilise limited resources (water and nutrients) to maximise production on a limited land area and this may require us to consider alternative plant species to those currently in use. Furthermore, new breeding targets will be identified as the interactions between plants and the animals that consume them become better understood. This will ensure that available resources are targeted at delivering maximum benefits to the animal through enhanced transformation efficiency.

Successional colonization of perennial ryegrass by rumen bacteria.

UNLABELLED: This study investigated successional colonization of perennial ryegrass (PRG) by the rumen microbiota. PRG grown for 6 weeks in a greenhouse was incubated in sacco in the rumens of three Holstein × Freisian cows over a period of 24 h. PRG incubated within the rumen was subsequently harvested at various time intervals postincubation to assess colonization over time. DGGE-based dendograms revealed the presence of distinct primary (0-2 h) and secondary (4 h onwards) attached bacterial communities. Moving window analysis, band number and Shannon-Wiener diversity indices suggest that after 2 h a proportion of primary colonizing bacteria detach, to be replaced with a population of secondary colonizing bacteria between 2 and 4 h after entry of PRG into the rumen. Sequencing and classification of bands lost and gained between 2 and 4 h showed that the genus Prevotella spp. was potentially more prevalent following 4 h of incubation, and Prevotella spp. 16S rDNA-based QPCR supported this finding somewhat, as 2- to 4-h Prevotella QPCR data were greater but not significantly so. Low-temperature scanning electron microscopy showed that attached bacteria were predominantly enveloped in extracellular polymeric substances. In conclusion, colonization of fresh PRG is biphasic with primary colonization completed within 2 h and secondary colonization commencing after 4 h of attachment in this study. SIGNIFICANCE AND IMPACT OF THE STUDY: We investigated, over a 24-h period in sacco, whether attachment of rumen microbiota to perennial ryegrass (PRG) showed successional changes in diversity. Knowledge of the bacterial species that attach to PRG over time may aid our understanding of the temporal function of the attached microbiota and ultimately permit the development of novel strategies for improving animal production to meet the future demands for meat and milk.

Ruminal protozoal contribution to the duodenal flow of fatty acids following feeding of steers on forages differing in chloroplast content.

Ruminant products are criticised for their SFA content relative to PUFA, although n-6:n-3 PUFA is desirable for human health ( < 4). Rumen protozoa are rich in unsaturated fatty acids due to engulfment of PUFA-rich chloroplasts. Increasing the chloroplast content of rumen protozoa offers a potentially novel approach to enhance PUFA flow to the duodenum and subsequent incorporation into meat and milk. We evaluated protozoal contribution to duodenal n-3 PUFA flow due to intracellular chloroplast content. A total of six Holstein × Friesian steers were fed, in a two-period changeover design, either straw:concentrate (S:C, 60:40; DM basis; S:C, low chloroplast) or fresh perennial ryegrass (PRG; high chloroplast). Following 12 d adaptation to diet, ruminal protozoal and whole duodenal samples were obtained. N and fatty acid content of whole duodenum and rumen protozoal samples were assessed and protozoal 18S rDNA quantitative PCR performed, enabling calculation of protozoal N flow. The ratio of individual fatty acids:N in rumen protozoal samples was calculated to obtain protozoal fatty acid flows. Based on total fatty acid flow, contribution (%) of protozoa to individual fatty acid flows was calculated. Protozoal fatty acid data and microscopical observations revealed that protozoa were enriched with 18 : 3n-3 following PRG feeding, compared with the S:C diet, due to increased intracellular chloroplast content. However, duodenal protozoal 18S rDNA concentration post PRG feeding was low, indicating rumen retention of the protozoa. Nutrition influences the 18 : 3n-3 content of protozoa; the challenge is to increase protozoal flow to the small intestine, while maintaining sustainable rumen densities.

Advances in microbial ecosystem concepts and their consequences for ruminant agriculture.

Microbial transformations in the rumen ecosystem have a major impact on our ability to meet the challenge of reducing the environmental footprint of ruminant livestock agriculture, as well as enhancing product quality. Current understanding of the rumen microbial ecosystem is limited, and affects our ability to manipulate rumen output. The view of ruminal fermentation as the sum of activities of the dominant rumen microbiota is no longer adequate, with a more holistic approach required. This paper reviews rumen functionality in the context of the microbiota of the rumen ecosystem, addressing ruminal fermentation as the product of an ecosystem while highlighting the consequences of this for ruminant agriculture. Microbial diversity in the rumen ecosystem enhances the resistance of the network of metabolic pathways present, as well as increasing the potential number of new pathways available. The resulting stability of rumen function is further promoted by the existence of rumen microbiota within biofilms. These protected, structured communities offer potential advantages, but very little is currently known about how ruminal microorganisms interact on feed-surfaces and how these communities develop. The temporal and spatial development of biofilms is strongly linked to the availability of dietary nutrients, the dynamics of which must also be given consideration, particularly in fresh-forage-based production systems. Nutrient dynamics, however, impact not only on pathway inputs but also the turnover and output of the whole ecosystem. Knowledge of the optimal balance of metabolic processes and the corresponding microbial taxa required to provide a stable, balanced ecosystem will enable a more holistic understanding of the rumen. Future studies should aim to identify key ecosystem processes and components within the rumen, including microbial taxa, metabolites and plant-based traits amenable to breeding-based modification. As well as gaining valuable insights into the biology of the rumen ecosystem, this will deliver realistic and appropriate novel targets for beneficial manipulation of rumen function.

Evidence in support of a role for plant-mediated proteolysis in the rumens of grazing animals.

The present work aimed to differentiate between proteolytic activities of plants and micro-organisms during the incubation of grass in cattle rumens. Freshly cut ryegrass was placed in bags of varying permeability and incubated for 16 h in the rumens of dairy cows that had previously grazed a ryegrass sward, supplemented with 4 kg dairy concentrate daily. Woven polyester bags (50 microm pore size) permitted direct access of the micro-organisms and rumen fluid enzymes to the plant material. The polythene was impermeable even to small molecules such as NH(3). Dialysis tubing excluded micro-organisms and rumen enzymes/metabolites larger than 10 kDa. DM loss was 46.3 % in polyester, 36.2 % in polythene and 38.1 % in dialysis treatments. It is possible that the DM loss within polythene bags occurred due to a solubilisation of plant constituents (e.g. water-soluble carbohydrates) rather than microbial attachment/degradation processes. The final protein content of the herbage residues was not significantly different between treatments. Regardless of bag permeability, over 97 % of the initial protein content was lost during incubations in situ. Electrophoretic separation showed that Rubisco was extensively degraded in herbage residues whereas the membrane-associated, light-harvesting protein remained relatively undegraded. Protease activity was detected in herbage residues and bathing liquids after all incubation in situ treatments. Although rumen fluid contains proteases (possibly of plant and microbial origin), our results suggest that, owing to cell compartmentation, their activity against the proteins of intact plant cells is limited, supporting the view that plant proteases are involved in the degradation of proteins in freshly ingested herbage.

Proteolysis and cell death in clover leaves is induced by grazing.

Programmed plant cell death is a widespread phenomenon resulting in the formation of xylem vessels, dissected leaf forms, and aerenchyma. We demonstrate here that some characteristics of programmed cell death can also be observed during the cellular response to biotic and abiotic stress when plant tissue is ingested by grazing ruminants. Furthermore, the onset and progression of plant cell death processes may influence the proteolytic rate in the rumen. This is important because rapid proteolysis of plant proteins in ruminants is a major cause of the inefficient conversion of plant to animal protein resulting in the release of environmental N pollutants. Although rumen proteolysis is widely believed to be mediated by proteases from rumen microorganisms, proteolysis and cell death occurred concurrently in clover leaves incubated in vitro under rumenlike conditions (maintained anaerobically at 39 degrees C) but in the absence of a rumen microbial population. Under rumenlike conditions, both red and white clover cells showed progressive loss of DNA, but this was only associated with fragmentation in white clover. Cell death was indicated by increased ionic leakage and the appearance of terminal deoxynucleotidyl transferase-mediated dUTP-nick-end-labelled nuclei. Foliar protein decreased to 50% of the initial values after 3 h incubation in white clover and after 4 h in red clover, while no decrease was observed in ambient (25 degrees C, aerobic) incubations. In white clover, decreased foliar protein coincided with an increased number of protease isoforms.

Overexpression of Mn-superoxide dismutase in maize leaves leads to increased monodehydroascorbate reductase, dehydroascorbate reductase and glutathione reductase activities.

The effect of increased Mn-superoxide dismutase (SOD) on antioxidant enzymes and metabolites was studied using transformed maize, TG1+ and TG2+. The progeny of the backcross of each of the primary transformants with the parental line generated two populations denoted M6884 and M6885. These were grown at optimal (25 degrees C) and sub-optimal (18, 14 and 10 degrees C) temperatures to assess the impact of elevated SOD activity on cold tolerance and the antioxidant defences in maize. The plants of the M6885 population had similar foliar SOD activities to the untransformed maize plants. Within the segregating M6884 population 50% of the plants had elevated SOD activity (up to four times the activity of the untransformed controls) and 50% of the plants contained the product of the transgene. In untransformed plants grown at 25 degrees C and 18 degrees C, SOD activity was not detectable in mesophyll extracts. Similarly, increased foliar SOD activity in the M6884 transformed maize did not lead to detectable mesophyll SOD activity. Increased foliar KCN-insensitive SOD activities were accompanied by enhancement of monodehydroascorbate reductase, dehydroascorbate reductase and glutathione reductase activities; enzymes which are localized exclusively in the leaf mesophyll tissues. Increased foliar SOD activity had no effect on the hydrogen peroxide, glutathione or ascorbate contents of the leaves. This suggests that increased recycling of reduced ascorbate was required to compensate for enhanced hydrogen peroxide production in transformed plants.

Bundle sheath proteins are more sensitive to oxidative damage than those of the mesophyll in maize leaves exposed to paraquat or low temperatures.

In maize leaves growth at low temperatures causes decreases in maximum catalytic activities of photosynthetic enzymes and reduced amounts of proteins, rather than effects on regulation or co-ordination of the photosynthetic processes. To test the hypothesis that differential localization of antioxidants between the different types of photosynthetic cell in maize leaves is a major determinant of the extreme sensitivity of maize leaves to chilling damage, oxidative damage to proteins, induced by incubation of maize leaves with paraquat, has been measured and compared with the effects incurred by growth at low temperatures. While the increase in protein carbonyl groups caused by paraquat treatment was much greater than that caused by low temperature growth conditions, most carbonyl groups were detected on bundle sheath proteins in both stress conditions. With one or two exceptions proteins located in the mesophyll tissues were free of protein carbonyl groups in both situations. Paraquat treatment caused a complete loss of the psaA gene products, modified the photosystem II reaction centre polypeptide, D1, and increased the number of peptides arising from breakdown of ribulose 1,5-bisphosphate carboxylase oxygenase (Rubisco). In contrast, growth at 15 degrees C increased the abundance (but not number) of Rubisco breakdown products and decreased that of the psaB gene product while the psaA gene product and PEP carboxylase were largely unaffected. Since bundle sheath proteins are more susceptible to oxidative damage than those located in the mesophyll cells, strategies for achieving a more balanced system of antioxidant defence may be effective in improving chilling tolerance in maize.

Tansley Review No. 118: Post-ingestion metabolism of fresh forage.

It is generally assumed that breakdown of plant material in the rumen is a process mediated by gut microorganisms. This view arose because of the identification of a pre-gastric fermentation in the rumen, brought about by a large and diverse microbial population. The extensive use of dried and ground feed particles in forage evaluation might have helped to promote this assumption. However, although the assumption might be correct in animals feeding on conserved forage (hay and silage) where the cells of ingested forage are dead, it is possible that with grazed (living) forage, the role played by plant enzymes in the rumen has been overlooked. In a grazing situation, plant cells that remain intact on entering the rumen are not inert, but will respond to the perceived stresses of the rumen environment for as long as they are metabolically viable. Metabolic adjustments could include anaerobic and heat-shock responses that could promote premature senescence, leading to remobilization of cell components, especially proteins. Moreover, contact of plant cells with colonizing microorganisms in the rumen might promote a type of hypersensitive response, in much the same way as it does outside the rumen. After fresh plant material enters the rumen and prior to extensive plant cell-wall degradation, there is often a phase of rapid proteolysis providing N in excess of that required to maintain the rumen microbial population. The inefficient use of this ingested N results in generation of ammonia and urea in exhaled breath and urine, which promotes welfare and environmental pollution concerns. Therefore an important research goal in livestock agriculture is to find ways of decreasing this initial rate of proteolysis in the rumen. This will benefit the farmer financially (through decreased use of feed supplements), but will also benefit the environment, as N pollution can adversely affect pasture diversity and ecology. This review considers the possible responses of plant metabolism to the rumen environment, and how such considerations could alter current thinking in ruminant agriculture. Contents Summary 37 I. INTRODUCTION 37 II. DIGESTION OF PLANTS IN THE RUMEN: OLD AND NEW CONCEPTS 39 III. RUMEN-INDUCED PLANT METABOLISM: CELL DEGRADATION AND DEATH 41 IV. FUTURE PROSPECTS 50 Acknowledgements 51 References 51.

Evidence of a role for plant proteases in the degradation of herbage proteins in the rumen of grazing cattle.

Protein breakdown in the rumen is generally regarded as a two-stage process in which proteases produced by rumen microorganisms cleave plant protein into peptides and amino acids. However, many of the fiber-degrading cellulolytic species in the rumen are not in fact proteolytic, and the proteolytic activity of the entire rumen microbial population is only moderate when compared to the gastric and pancreatic secretions in the abomasum. Moreover, plant cell walls remain largely intact after initial chewing (particularly in cattle), presenting a physical barrier that must be breached prior to their effective colonization. The present study considers the hypothesis that the plant enzymes are at least partly responsible for herbage protein degradation in grazing ruminants. Ryegrass, red clover, white clover, and bird's-foot trefoil were incubated in the presence and absence of rumen microorganisms. The production of volatile fatty acids indicated the level of microbial activity, whereas the relative disappearance of the large subunit of ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco LSU) indicated proteolytic activity. In all incubations, the relative abundance of the Rubisco LSU decreased as the incubation progressed. When rumen microorganisms were absent, low molecular weight peptides (below 20 kDa) accumulated as the incubation progressed. This accumulation was not observed in the presence of rumen microorganisms. Therefore we suggest that the intrinsic plant proteases contribute to the initial stages of proteolysis of grazed herbage.

Ascorbate metabolism in potato leaves supplied with exogenous ascorbate.

Photosynthesis and leaf ascorbate were measured in potato (Solanum tuberosum L.) plants grown in low light and then transferred to high light. Total foliar ascorbate content in low light-grown plants was 4.72+/-0.42 micromol mg(-1)chl. Over 80% of the ascorbate pool was found in the reduced form irrespective of position on the stem. No statistically-significant light-dependent effects were observed. Leaf discs supplied with [14C]-ascorbate in the dark showed significant ascorbate uptake such that after a 16h incubation over half of the total ascorbate pool in the discs was labelled [14C]-ascorbate. No ascorbate efflux from the leaves occurred during the period of [14C]-ascorbate uptake. The total amount of ascorbate did not increase, however, implying modified ascorbate turnover. The turnover of the [14C]-ascorbate in the leaves occurred at similar rates in both light and darkness. Little degradation of labelled ascorbate was observed, suggesting that uptake of exogenous ascorbate leads to inhibition of de novo ascorbate biosynthesis in potato leaf discs.

Differential Localization of Antioxidants in Maize Leaves.

The aim of this work was to determine the compartmentation of antioxidants between the bundle-sheath and mesophyll cells of maize (Zea mays L.) leaves. Rapid fractionation of the mesophyll compartment was used to minimize modifications in the antioxidant status and composition due to extraction procedures. The purity of the mesophyll isolates was assessed via the distribution of enzyme and metabolite markers. Ribulose-1,5 bisphosphate and ribulose-1,5-bisphosphate carboxylase/oxygenase were used as bundle-sheath markers and phosphoenolpyruvate carboxylase was used as the mesophyll marker enzyme. Glutathione reductase and dehydroascorbate reductase were almost exclusively localized in the mesophyll tissue, whereas ascorbate, ascorbate peroxidase, and superoxide dismutase were largely absent from the mesophyll fraction. Catalase, reduced glutathione, and monodehydroascorbate reductase were found to be approximately equally distributed between the two cell types. It is interesting that, whereas H2O2 levels were relatively high in maize leaves, this oxidant was largely restricted to the mesophyll compartment. We conclude that the antioxidants in maize leaves are partitioned between the two cell types according to the availability of reducing power and NADPH and that oxidized glutathione and dehydroascorbate produced in the bundle-sheat tissues have to be transported to the mesophyll for re-reduction to their reduced forms.

Effect of Chilling on Carbon Assimilation, Enzyme Activation, and Photosynthetic Electron Transport in the Absence of Photoinhibition in Maize Leaves.

The relationships between electron transport and photosynthetic carbon metabolism were measured in maize (Zea mays L.) leaves following exposure to suboptimal temperatures. The quantum efficiency for electron transport in unchilled leaves was similar to that previously observed in C3 plants, although maize has two types of chloroplasts, mesophyll and bundle sheath, with PSII being largely absent from the latter. The index of noncyclic electron transport was proportional to the CO2 assimilation rate. Chilled leaves showed decreased rates of CO2 assimilation relative to unchilled leaves, but the integral relationships between the quantum efficiency for electron transport or the index of noncyclic electron transport and CO2 fixation were unchanged and there was no photoinhibition. The maximum catalytic activities of the Benson-Calvin cycle enzymes, fructose-1,6-bisphosphatase and ribulose-1,5-bisphosphate carboxylase, were decreased following chilling, but activation was unaffected. Measurements of thiol-regulated enzymes, particularly NADP-malate dehydrogenase, indicated that chilling induced changes in the stromal redox state so that reducing equivalents were more plentiful. We conclude that chilling produces a decrease in photosynthetic capacity without changing the internal operational, regulatory or stoichiometric relationships between photosynthetic electron transport and carbon assimilation. The enzymes of carbon assimilation are particularly sensitive to chilling, but enhanced activation may compensate for decreases in maximal catalytic activity.

Purification and properties of a phosphatase in French bean (Phaseolus vulgaris L.) leaves that hydrolyses 2'-carboxy-D-arabinitol 1-phosphate.

An enzyme that releases P(i) from 2-carboxy-D-arabinitol 1-phosphate, a naturally occurring tightly binding inhibitor of ribulose 1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39), was purified from leaves of French bean seedlings. It was a monomeric protein of M(r) about 56,000. Catalytic activity was stimulated by increased concentrations of inorganic salts to a maximum at an ionic strength above 0.2. NADPH and D-fructose 1,6-bisphosphate increased the activity of the enzyme in both the presence and absence of 0.2 M-KCl. The pure enzyme did not require dithiothreitol for activity. The pH optimum was 7, the Km for 2-carboxy-D-arabinitol 1-phosphate was 0.43 mM and the specific activity 6.8 mumol/min per mg of protein. The enzyme had little or no activity against phosphate ester intermediates of photosynthetic metabolism and glycolysis but hydrolysed the 1,5-bisphosphates of 2'-carboxy-D-ribitol and 2'-carboxy-D-arabinitol more rapidly than 2'-carboxy-D-arabinitol 1-phosphate.