Effects Of Defaunation Research Articles

Interacting effects of wildlife loss and climate on ticks and tick-borne disease.

Both large-wildlife loss and climatic changes can independently influence the prevalence and distribution of zoonotic disease. Given growing evidence that wildlife loss often has stronger community-level effects in low-productivity areas, we hypothesized that these perturbations would have interactive effects on disease risk. We experimentally tested this hypothesis by measuring tick abundance and the prevalence of tick-borne pathogens (Coxiella burnetii and Rickettsia spp.) within long-term, size-selective, large-herbivore exclosures replicated across a precipitation gradient in East Africa. Total wildlife exclusion increased total tick abundance by 130% (mesic sites) to 225% (dry, low-productivity sites), demonstrating a significant interaction of defaunation and aridity on tick abundance. When differing degrees of exclusion were tested for a subset of months, total tick abundance increased from 170% (only mega-herbivores excluded) to 360% (all large wildlife excluded). Wildlife exclusion differentially affected the abundance of the three dominant tick species, and this effect varied strongly over time, likely due to differences among species in their host associations, seasonality, and other ecological characteristics. Pathogen prevalence did not differ across wildlife exclusion treatments, rainfall levels, or tick species, suggesting that exposure risk will respond to defaunation and climate change in proportion to total tick abundance. These findings demonstrate interacting effects of defaunation and aridity that increase disease risk, and they highlight the need to incorporate ecological context when predicting effects of wildlife loss on zoonotic disease dynamics.

A pantropical assessment of vertebrate physical damage to forest seedlings and the effects of defaunation

Many of the forces that shape tropical forest plant communities are facilitated by interactions with animals, which can either promote or inhibit plant reproduction and survival across ontogenetic stages. Hunting-induced defaunation can disrupt these interactions, altering tree recruitment, forest structure, and carbon storage, with strong effects at the seed and seedling stages. Research to date has largely focused on how changes to prominent interactions (especially seed dispersal) affect plant species and communities, while concurrent disruptions to less-studied processes may have opposing effects. With a particularly limited understanding of non-trophic interactions – such as physical damage to seedlings by vertebrate trampling, rooting, and digging – it remains difficult to predict the outcomes of defaunation for tropical forest plant communities. We established 1800 artificial seedlings in 18 intact and disturbed sites across the three main tropical forest regions – the Neotropics (Peru), the Afrotropics (Gabon) and the Indo-Malayan tropics (Malaysian Borneo) – to isolate non-trophic vertebrate physical damage from other causes of seedling mortality (herbivory, pathogens, abiotic desiccation, etc.), and to understand its effects in intact and anthropogenically-disturbed forests. We found that vertebrate physical damage is a consistent force in forests across the tropics, and that hunting significantly alters its strength, with a ∼70% decrease in damage in hunted vs. intact sites that resulted in a ∼3.5-fold (350%) increase in artificial seedling survival. Our results reveal an understudied mechanism that may contribute to changes in seedling survival, stem density, and plant community composition in tropical forests subjected to hunting.

Defaunation effects on plant recruitment depend on size matching and size trade-offs in seed-dispersal networks.

Defaunation by humans causes a loss of large animals in many ecosystems globally. Recent work has emphasized the consequences of downsizing in animal communities for ecosystem functioning. However, no study so far has integrated network theory and life-history trade-offs to mechanistically evaluate the functional consequences of defaunation in plant-animal networks. Here, we simulated an avian seed-dispersal network and its derived ecosystem function seedling recruitment to assess the relative importance of different size-related mechanisms. Specifically, we considered size matching (between bird size and seed size) and size trade-offs, which are driven by differences in plant or animal species abundance (negative size-quantity relationship) as well as in recruitment probability and disperser quality (positive size-quality relationship). Defaunation led to impoverished seedling communities in terms of diversity and seed size, but only if models accounted for size matching. In addition, size trade-off in plants, in concert with size matching, provoked rapid decays in seedling abundance in response to defaunation. These results underscore a disproportional importance of large animals for ecosystem functions. Downsizing in ecological networks will have severe consequences for ecosystem functioning, especially in interaction networks that are structured by size matching between plants and animals.

Cascading effects of defaunation on the coexistence of two specialized insect seed predators.

We show that two species of insect seed predators relying on the same host plant species are niche differentiated in their reproductive strategies such that one species has the advantage when fruits are handled promptly by vertebrates and the other when they are not. Defaunation disrupts this mediating influence of vertebrates and strongly favours one species at the expense of the other, providing a case study of the cascading effects of defaunation and its potential to disrupt coexistence of non-target species, including the hyperdiverse phytophagous insects of tropical forests.

Effects of defaunation on rumen fermentation features, feed intake, digestibility and animal performance

The objective of the review was to provide compiled information on the effects of defaunation on rumen fermentation features, feed intake, digestibility and animal performance for development workers, academic user’s, researchers and other interested readers. Defaunation is the selective removal of protozoa from the rumen of animals. Based on the most of information reviewed defaunation decreases rumen pH, ruminal ammonia concentration, methane emissions, fibre carbohydrate digestibility and organic matter digestibility, and it increases total volatile fatty acids concentration, numbers of bacteria, feed conversion efficiency and weight gain but it did not affect dry matter intake.

Effects of defaunation and dietary coconut oil distillate on fermentation, digesta kinetics and methane production of Brahman heifers.

A 2×2 factorial experiment was conducted to assess the effects of presence or absence of rumen protozoa and of dietary coconut oil distillate (COD) supplementation on rumen fermentation characteristics, digesta kinetics and methane production in Brahman heifers. Twelve Brahman heifers were selected to defaunate, with 6 being subsequently refaunated. After defaunation and refaunation, heifers were randomly allocated to COD supplement or no supplement treatments while fed an oaten chaff-based diet. Methane production (MP; 94.17 v 104.72g CH4 /d) and methane yield [MY; 19.45 v 21.64g CH4 /kg dry matter intake (DMI)] were reduced in defaunated heifers compared with refaunated heifers when measured at 5weeks after refaunation treatment (p<0.01). Supplement of COD similarly reduced MP and MY (89.36 v 109.53g/d and 18.46 v 22.63g/kg DMI, respectively; p<0.01), and there were no significant interactions of defaunation and COD effects on rumen fermentation or methane emissions. Concentration of total volatile fatty acid (VFA) and molar proportions of acetate, propionate and butyrate was not affected by defaunation or by COD. Microbial crude protein (MCP; g/d) outflow was increased by defaunation (p<0.01) in the absence of COD but was unaffected by defaunation in COD-supplemented heifers. There was a tendency towards a greater average daily gain (ADG) in defaunated heifers (p=0.09), but COD did not increase ADG (p>0.05). The results confirmed that defaunation and COD independently reduced enteric MP even though the reduced emissions were achieved without altering rumen fermentation VFA levels or gut digesta kinetics.

Contrasting effects of defaunation on aboveground carbon storage across the global tropics.

Defaunation is causing declines of large-seeded animal-dispersed trees in tropical forests worldwide, but whether and how these declines will affect carbon storage across this biome is unclear. Here we show, using a pan-tropical data set, that simulated declines of large-seeded animal-dispersed trees have contrasting effects on aboveground carbon stocks across Earth's tropical forests. In our simulations, African, American and South Asian forests, which have high proportions of animal-dispersed species, consistently show carbon losses (2–12%), but Southeast Asian and Australian forests, where there are more abiotically dispersed species, show little to no carbon losses or marginal gains (±1%). These patterns result primarily from changes in wood volume, and are underlain by consistent relationships in our empirical data (∼2,100 species), wherein, large-seeded animal-dispersed species are larger as adults than small-seeded animal-dispersed species, but are smaller than abiotically dispersed species. Thus, floristic differences and distinct dispersal mode–seed size–adult size combinations can drive contrasting regional responses to defaunation.

How do primates affect seed germination? A meta‐analysis of gut passage effects on neotropical plants

Biotic seed dispersal is a key process maintaining biodiversity in tropical forests where most trees produce vertebrate‐dispersed seeds. Existing meta‐analyses suggest an overall positive effect of vertebrate gut passage on seed germination, but no significant effects for non‐flying mammals. However, previous meta‐analyses combined rodents (seed predators) and primates (seed dispersers) into the non‐flying mammals category, which may confound specific effects of each group on seed germination. However positive effects of monkeys on germination had previously been found in some studies. Here we disentangle the role of Neotropical primates as contributors to seed dispersal in tropical forests by running a meta‐analysis to determine the overall magnitude of gut passage effects on seed germination percentage and mean time to germination. We also compare effect sizes as a function of different feeding guilds, gut complexities, and seed size. Our results show a strong, positive effect of primates on seed germination percentage and on the number of days to first germination. Strictly frugivorous monkeys, the group most threatened by extinction, showed the highest dispersal quality, increasing germination percentage by 75%. Primates that include insects in their diets had no average effect on germination percentage or time. Gut passage had different outcomes on seeds with different sizes; both large and small seeds showed similar increases in germination percentages after gut passage, but only large seeds germinated faster than control seeds after gut passage. Our results show a relevant role for primates in providing high seed dispersal quality and as drivers of forest regeneration. The combined effects of defaunation and forest fragmentation may result in decreased regeneration of trees, which has the potential to affect negatively both forest structure and ecosystem processes. Finally, we provide general guidelines for standardizing research on seed dispersal by primates.SynthesisConsuming fleshy fruits and dispersing seeds is the main ecological service provided by vertebrates to plants. Vertebrate increases seed germination due to treatment given during digestive system passage. Previous meta‐analyses suggest an overall positive effect of vertebrate gut passage on germination, but no insights are available on its variation among different functional groups of mammals. Our analyses indicated that gut passage by Neotropical primates increased seed germination. Strict frugivores, the ones most threatened by extinction, were the most efficient. Our results show a relevant role for primates in providing high seed dispersal quality and as drivers of forest regeneration, which can be meaningful for conservation in a community scale.

Hunting alters seedling functional trait composition in a Neotropical forest.

Defaunation alters trophic interactions between plants and vertebrates, whichmay disrupt trophic cascades, thereby favoring a subset of plant species and reducing diversity. If particular functional traits characterize the favored plant species,.then defaunation may alter community-wide patterns of functional trait composition. Changes in plant functional traits occurring with defaunation may help identify the species interactions affected by defaunation and the potential for other cascading effects of defaunation. We tested the hypotheses that defaunation would (1) disrupt seed dispersal, thereby favoring species whose dispersal agents are not affected (e.g., small birds, bats, and abiotic agents), (2) reduce seed predation, thereby favoring larger-seeded species, and (3) reduce herbivory, thereby favoring species with lower leaf mass per area (LMA), leaf toughness, and wood density. We examined how these six traits responded to vertebrate defaunation caused by hunters or by experimental exclosures among more than-30 000 woody seedlings in a lowland tropical moist forest. Exclosures reduced terrestrial frugivores, granivores, and herbivores, while hunters also reduced volant and arboreal frugivores and granivores. The comparison of exclosures and hunting allowed us to parse the impacts of arboreal and volant species (reduced by hunters only) and terrestrial species (reduced by both hunters and exclosures). The loss of terrestrial vertebrates alone had limited effects on plant trait composition. The additional loss of volant and arboreal vertebrates caused significant shifts in plant species composition towards communities with more species dispersed abiotically, including lianas and low wood-density tree species, and fewer species dispersed by large vertebrates. In contrast to previous studies, community seed mass did not decline significantly in hunted sites. Our exclosure results suggest this is because reducing seed predators disproportionately benefits large-seeded species,.partially compensating for the reduction of seed dispersers at hunted sites. Our result9sdemonstrate that decreased seed dispersal and seed predation are important determinants of seedling community compositional change as a consequence of defaunation. Defaunation may also negatively impact carbon storage in tropical forests, by favoring lianas and low wood density tree species.

Spatial Pattern of Pindó Palm (Syagrus romanzoffiana) Recruitment in Argentinian Atlantic Forest: The Importance of Tapir and Effects of Defaunation

AbstractHunting pressure, fragmentation and deforestation have caused global declines in animal abundance, and the consequences for plant communities are poorly understood. Many large‐seeded plants, for instance, depend on large and endangered vertebrates for seed dispersal. In some Semi‐deciduous Atlantic Forests, endangered tapirs (Tapirus terrestris) are major dispersers of pindó palms (Syagrus romanzoffiana). Here, we compare recruitment patterns of pindó palms between protected and disturbed (defaunated) Atlantic Forest areas in Argentina and evaluate the potential consequences of the lack of the main disperser for pindó palm regeneration. We analyzed the number and spatial pattern of pindó adults, offspring, and tapir dung piles within ten plots established in an area spanning tapir latrines inside Iguazú National Park and in a fragmented forest area outside the park where tapir is locally extinct. In both areas, we evaluated recruitment levels beneath 24 adult palms in circular plots centered on adult stems. We found lower pindó palm recruitment outside the park where offspring tended to be aggregated around adult palms. In contrast, in Iguazú National Park offspring were spatially associated with tapir dung‐piles, in which most offspring were registered. Recruitment under adults was higher outside the park suggesting a lower rate of seed removal in disturbed areas. Our results show that tapir dispersal promotes higher recruitment levels of pindó offspring and shapes their spatial pattern, breaking the spatial association with adult (presumably maternal) palms. These results are useful for predicting the impact of local tapir extinction on this palm.

Effects of Defaunation on Fermentation Characteristics, Degradation of Ryegrass Hay and Methane Production by Rumen Microbes In Vitro When Incubated with Plant Oils

This study was conducted to examine the effects of defaunation (removal of live protozoa) on fermentation characteristics, degradation of ryegrass hay and CH4 (methane) production by rumen microbes when incubated with plant oils (SO, sunflower oil and LO, linseed oil) in vitro. Sodium lauryl sulfate (0.000375 g/ml) as a defaunation reagent was added into the culture solution and incubated anaerobically up to 24 h at 39℃. pH from defaunation was increased for all treatments from 6 h incubation times (p<0.01-0.001) compared with those from fauantion. Concentration of ammonia-N from defaunation is higher than that from faunation at 3 h (p<0.001), 12 h (p<0.05) and 24 h (p<0.001) incubation times. Defaunation decreased (p<0.01-0.001) total volatile fatty acid concentration at all incubation times. Molar proportions of C2 (acetate, p<0.05-0.001) and butyrate (p<0.01-0.001) were also decreased by defaunation at all incubation times. Molar proportion of C3 (propionate), however, was increased by defaunation at all incubation times (p<0.001). Thus the rate of C2 to C3 was decreased by defaunation at all incubation times (p<0.001). Defaunation decreased ED (effective degradability) of dry matter (p<0.001) and ED of neutral detergent fiber (p<0.001) of ryegrass hay. Defaunation decreased total gas, CH4 production, CH4 % in total gas and CH4/CO2 at all incubation times (p<0.001). Oil supplementation decreased total gas (p<0.05-0.001), CH4 production (p<0.001) and CH4 % in total gas (p<0.001) compared with control at all incubation times. The result of this study showed that defaunation combined with oil supplementation may cause an alteration of microbial communities and further medicate the fermentation pattern, resulting in both reduction of degradation of ryegrass hay and CH4 production. No difference, however, was observed in all the examinations between SO and LO.

A dynamic mechanistic model of lactic acid metabolism in the rumen

Current feed evaluation systems for ruminants are too imprecise to describe diets in terms of their acidosis risk. The dynamic mechanistic model described herein arises from the integration of a lactic acid (La) metabolism module into an extant model of whole-rumen function. The model was evaluated using published data from cows and sheep fed a range of diets or infused with various doses of La. The model performed well in simulating peak rumen La concentrations (coefficient of determination = 0.96; root mean square prediction error = 16.96% of observed mean), although frequency of sampling for the published data prevented a comprehensive comparison of prediction of time to peak La accumulation. The model showed a tendency for increased La accumulation following feeding of diets rich in nonstructural carbohydrates, although less-soluble starch sources such as corn tended to limit rumen La concentration. Simulated La absorption from the rumen remained low throughout the feeding cycle. The competition between bacteria and protozoa for rumen La suggests a variable contribution of protozoa to total La utilization. However, the model was unable to simulate the effects of defaunation on rumen La metabolism, indicating a need for a more detailed description of protozoal metabolism. The model could form the basis of a feed evaluation system with regard to rumen La metabolism.

Effect of Defaunation on In Vitro Fermentation Characteristics and Methane Emission When Incubated with Forages

An in vitro study was conducted to determine the effects of defaunation (removal of protozoa) and forage sources (rice straw, ryegrass and tall fescue) on ruminal fermentation characteristics, methane (<TEX>$CH_4$</TEX>) production and degradation by rumen microbes. Sodium lauryl sulfate, as a defaunation reagent, was added into the mixed culture solution to remove ruminal protozoa at a concentration of 0.375 mg/ml. Pure cellulose (0.64 g, Sigma, C8002) and three forage sources were incubated in the bottle of culture solution of mixed rumen microbes (faunation) or defaunation for up to 24 h. The concentration of ammonia-N was high under condition of defaunation compared to that from faunation in all incubations (p<0.001). Total VFA concentration was increased at 3, 6 and 12 h (p<0.05~p<0.01) but was decreased at 24 h incubation (p<0.001) under condition of defaunation. Defaunation decreased acetate (p<0.001) and butyrate (p<0.001) proportions at 6, 12 and 24 h incubation times, but increased propionate (p<0.001) proportion at all incubation times for forages. Effective degradability of dry matter was decreased by defaunation (p<0.001). Defaunation not only decreased total gas (p<0.001) and <TEX>$CO_2$</TEX> (p<0.01~0.001) production at 12 and 24 h incubations, but reduced <TEX>$CH_4$</TEX> production (p<0.001) at all incubation times for all forages. The <TEX>$CH_4$</TEX> production, regardless of defaunation, in order of forage sources were rice straw > tall fescue > ryegrass > cellulose (p<0.001) up to 24 h incubation.

No changes in seedling recruitment when terrestrial mammals are excluded in a partially defaunated Atlantic rainforest

One of the most intriguing questions in ecology is how to identify which and how many species will be able to inhabit human-modified landscapes. Large-bodied mammals structure plant communities by trampling, herbivory, seed dispersal and predation, and their local extinction may have pervasive consequences in plant communities due to the breakdown of key interactions. Although much attention has been given to understanding the effects of defaunation on plant communities, information on the potential impacts on plant functional groups (seed dispersal, seed size and seedling leaves defense) inhabiting continuous forests after defaunation is scarce. We conducted mammal surveys (line transects and camera trapping) to determine the defaunation status of a continuous Atlantic forest in Brazil. Then, we evaluated the effects of defaunation on seedling diversity, richness and abundance of functional groups using 15 plot-pairs (each pair with one open and one exclusion plot) monitored over 36months. We found that the studied area is partially defaunated because it exhibits high abundance of primates, while terrestrial mammals, such as large rodents and ungulates, are rare. We found no significant changes in either seedling richness and diversity or in the seedling composition of plant functional groups in response to mammal exclosure. Seedling mortality and recruitment were similar between plot types. Our findings suggest that at semi-defaunated areas, where arboreal species are still present, terrestrial mammals have low impacts on the plant community reassembly.

Long-term exclosure of large terrestrial vertebrates: Implications of defaunation for seedling demographics in the Amazon rainforest

“Empty forests” in which humans have driven large vertebrate species to extinction lack myriad direct and indirect species interactions. This may alter key ecosystem processes, including trophic cascades, disturbance regimes, and nutrient cycling. Past research concerning the effects of tropical forest defaunation mainly compared sites with an intact fauna with sites having degraded faunal communities. However, experimental studies on seedling demographics at individual sites, with the same abiotic and biotic conditions, over a long period of time are still scarce. In this research we conducted a 7-year experiment within a completely intact and pristine forest in Manu National Park, Peru to elucidate the effects of defaunation on tree seedling demographics and densities. We constructed semipermeable exclosures that prevented access of large terrestrial vertebrates, but allowed free passage of small- and medium-sized species. New tree seedlings taller than 5cm were tagged and followed. Jolly–Seber mark-recapture models were used to estimate density, survival, and recruitment of seedlings. Seedling density in the exclosures continued to increase significantly after the first year of the study. Only during the first 2years was seedling survival higher in the exclosures. The numbers of new recruits were consistently higher in exclosures when compared to open control plots throughout the study. In accord with increased density, survival, and recruitment in exclosure plots, we also observed increased understory vegetation cover. Our results suggest that defaunation can have long-term effects on seedling demographics and density, which could ultimately influence the composition and diversity of the canopy tree community.

Technical Note: The effects of five different defaunation methods on biogeochemical properties of intertidal sediment

Abstract. Various methods have been used to remove organisms from sediments to investigate structure and function of faunal assemblages in intertidal habitats. Nevertheless, little is known about how these treatments affect properties of the sediments themselves, although changing these properties may cause changes in the assemblages, independently of other hypotheses being tested. This study assesses the efficacy of defaunation and effect on selected biogeochemical properties of five different methods of defaunating soft muddy sediments in an estuary. The methods were removal and freezing of sediment, removal and oven-heating, freezing in situ with liquid N2, spraying with formalin and spraying with hydrogen peroxide. The first four of these methods have been used in previous studies, whilst the fifth was considered to be a potentially useful defaunator because it does not leave toxic residues. The first two methods required sediment to be brought back to the lab, disrupting the natural structure of the sediment; the last three were done in situ, with much less disturbance. Variables measured to assess effects of the treatments on the sediment were amount of water, grain size, total carbohydrate, suspension index (relative erosion rate), erosion threshold, chlorophyll a and b, colloidal carbohydrate, Fo (minimal fluorescence) and Fv / Fm (photosynthetic yield). There were no significant effects of any treatment on the first four variables. For the others, effects of defaunation varied from treatment to treatment and with time after treatment. Generally, the greatest disturbance was to the microphytobenthos (MPB, measured by chlorophyll and fluorescence) and related variables. For most treatments, recovery was rapid, but the effects of formalin and H2O2 persisted for a few days. Effects on physical properties of the sediment were mostly minor and insignificant. Removal and freezing or heating, however, caused major changes to the sediments because of the disturbances involved. Choosing the appropriate method of defaunation is very important if interpretations are not to be confounded between the effects of defaunation per se and any effects of changes to other biota (such as microphytobenthos) and/or the properties of sediments caused by the method used to defaunate experimental areas.

Effects of Defaunation on Fermentation Characteristics and Methane Production by Rumen Microbes In vitro When Incubated with Starchy Feed Sources.

An in vitro experiment was conducted to examine the effects of defaunation (removal of protozoa) on ruminal fermentation characteristics, CH4 production and degradation by rumen microbes when incubated with cereal grains (corn, wheat and rye). Sodium lauryl sulfate as a defaunation reagent was added into the culture solution at a concentration of 0.000375 g/ml, and incubated anaerobically for up to 12 h at 39°C. Following defaunation, live protozoa in the culture solution were rarely observed by microscopic examination. A difference in pH was found among grains regardless of defaunation at all incubation times (p<0.01 to 0.001). Defaunation significantly decreased pH at 12 h (p<0.05) when rumen fluid was incubated with grains. Ammonia-N concentration was increased by defaunation for all grains at 6 h (p<0.05) and 12 h (p<0.05) incubation times. Total VFA concentration was increased by defaunation at 6 h (p<0.05) and 12 h (p<0.01) for all grains. Meanwhile, defaunation decreased acetate and butyrate proportions at 6 h (p<0.05, p<0.01) and 12 h (p<0.01, p<0.001), but increased the propionate proportion at 3 h, 6 h and 12 h incubation (p<0.01 to 0.001) for all grains. Defaunation increased in vitro effective degradability of DM (p<0.05). Production of total gas and CO2 was decreased by defaunation for all grains at 1 h (p<0.05, p<0.05) and then increased at 6 h (p<0.05, p<0.05) and 12 h (p<0.05, p<0.05). CH4 production was higher from faunation than from defaunation at all incubation times (p<0.05).

Study of the effect of presence or absence of protozoa on rumen fermentation and microbial protein contribution to the chyme1

The aim of this study was to investigate the effect of presence or absence of protozoa on rumen fermentation and efficiency of microbial protein synthesis under different diets. Of 20 twin paired lambs, 1 lamb of each pair was isolated from the ewe within 24 h after birth and reared in a protozoa-free environment (n = 10), whereas their respective twin-siblings remained with the ewe (faunated, n = 10). When lambs reached 6 mo of age, 5 animals of each group were randomly allocated to 1 of 2 experimental diets consisting of either alfalfa hay as the sole diet, or 50:50 mixed with ground barley grain according to a 2 × 2 factorial arrangement of treatments. After 15 d of adaptation to the diet, the animals were euthanized and total rumen and abomasal contents were sampled to estimate rumen microbial synthesis using C(31) alkane as flow marker. Different ((15)N and purine bases) and a novel (recombinant DNA sequences) microbial markers, combined with several microbial reference extracts (rumen protozoa, liquid and solid associated bacteria) were evaluated. Absence of rumen protozoa modified the rumen fermentation pattern and decreased total tract OM and NDF digestibility in 2.0 and 5.1 percentage points, respectively. The effect of defaunation on microbial N flow was weak, however, and was dependent on the microbial marker and microbial reference extract considered. Faunated lambs fed with mixed diet showed the greatest rumen protozoal concentration and the least efficient microbial protein synthesis (29% less than the other treatments), whereas protozoa-free lambs fed with mixed diet presented the smallest ammonia concentration and 34% greater efficiency of N utilization than the other treatments. Although (15)N gave the most precise estimates of microbial synthesis, the use of recombinant DNA sequences represents an alternative that allows separate quantification of the bacteria and protozoa contributions. This marker showed that presence of protozoa decrease the bacterial-N flow through the abomasum by 33%, whereas the protozoa-N contribution to the microbial N flow increased from 1.9 to 14.1% when barley grain was added to the alfalfa hay. Absolute data related to intestinal flow must be treated with caution because the limitations of the sampling and maker system employed.

Fatty acid composition of ruminal bacteria and protozoa, and effect of defaunation on fatty acid profile in the rumen with special reference to conjugated linoleic acid in cattle

Objectives of this study were to compare fatty acid (FA) composition of ruminal bacterial (B) and protozoal (P) cells, and to investigate effect of protozoa on FA profile in the rumen of cattle. Three cows were used to prepare ruminal B and P cells. Four faunated and three defaunated cattle (half-siblings) were used to study effect of protozoa on ruminal FA profile. Proportions of C16:0 and C18:0 in total fatty acids in B cells were 20.7% and 37.4%, whereas those in P cells were 33.4% and 11.6%, respectively. Proportions of trans-vaccenic acid (VA) and cis-9, trans-11 conjugated linoleic acid (CLA) in B cells were 3.9% and 1.0%, and those in P cells were 5.5% and 1.6%, respectively, being higher in P cells. Proportions of C18:1, C18:2 and C18:3 in P cells were two to three times higher than in B cells. Proportions of unsaturated fatty acids, VA and CLA in B cells of faunated cattle were higher than those of defaunated. VA and CLA in the ruminal fluid of faunated were also 1.6 to 2.5 times higher than those of defaunated. This tendency was similar for cell-free fraction of ruminal fluid. These results indicate that protozoa contribute greatly in VA and CLA production in the rumen.

Long-term defaunation increases the abundance of cellulolytic ruminococci and methanogens but does not affect the bacterial and methanogen diversity in the rumen of sheep1

Protozoa are commensal eukaryotes in the rumen of herbivores. Protozoa are large producers of hydrogen, which is utilized by methanogenic archaea to produce methane, a greenhouse gas. The removal of protozoa from the rumen (defaunation) decreases methanogenesis, but also negatively affects fiber digestion, which is the main function of the rumen. The aim of this study was to examine the effect of long-term defaunation on the structure of the microbiota and particularly methanogenic archaea and fibrolytic bacteria to better understand the microbial mechanisms responsible for the decrease in methanogenesis and fibrolysis. The trial was conducted in 5 adult sheep subjected successively to long-term defaunation (2 yr), refaunation (12 wk), and short-term defaunation (10 wk). Methanogens were enumerated by quantitative PCR targeting the rrs (16S ribosomal RNA subunit) and mcrA (methyl coenzyme-M reductase) genes. The rrs gene was used to quantify the 3 major culturable rumen cellulolytic bacterial species (i.e., Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens) and total bacteria. Bacterial and methanogen diversity was also examined by PCR-DGGE (PCR-denaturing gradient gel electrophoresis) analysis targeting the rrs and mcrA genes, respectively. Total rumen bacterial density estimated as rrs copies per gram of DM of rumen content increased in response to long- and short-term defaunation (+1 log, P < 0.001), but without noticeable shifts in diversity. Defaunation increased the rrs copies per gram of DM of rumen content of R. albus and R. flavefaciens (+2 log, P < 0 0.001), but did not affect that of F. succinogenes. Despite a 20% reduction in methane emission in the 2 defaunated periods, the mcrA and rrs copies of methanogens per gram of DM of rumen content increased (+1 log, P < 0.001) in the absence of protozoa, whereas the diversity of the dominant methanogenic community was not modified. This study shows no major difference between long- and short-term defaunation in abundance and diversity of bacteria and archaea. It also provides evidence that monitoring the abundance and diversity of methanogens is not sufficient to comprehend the microbial mechanisms leading to a reduction in methane emissions by ruminants. This study also reports for the first time in sheep a selective effect of defaunation on the abundance of cellulolytic bacterial species.