Oxygen consumption by ruminal microorganisms: protozoal and bacterial contributions

Interaction between methanotrophy and gastrointestinal nematodes infection on the rumen microbiome of lambs

Complex cross-talk occurs between gastrointestinal nematodes and gut symbiotic microbiota, with consequences for animal metabolism. To investigate the connection between methane production and endoparasites, this study evaluated the effect of mixed infection with Haemonchus contortus and Trichostrongylus colubriformis on methanogenic and methanotrophic community in rumen microbiota of lambs using shotgun metagenomic and real-time quantitative PCR (qPCR). The rumen content was collected from six Santa Inês lambs, (7 months old) before and after 42 days infection by esophageal tube. The metagenomic analysis showed that the infection affected the microbial community structure leading to decreased abundance of methanotrophs bacteria, i.e. α-proteobacteria and β-proteobacteria, anaerobic methanotrophic archaea (ANME), protozoa, sulfate-reducing bacteria, syntrophic bacteria with methanogens, geobacter, and genes related to pyruvate, fatty acid, nitrogen, and sulfur metabolisms, ribulose monophosphate cycle, and Entner-Doudoroff Pathway. Additionally, the abundance of methanogenic archaea and the mcrA gene did not change. The co-occurrence networks enabled us to identify the interactions between each taxon in microbial communities and to determine the reshaping of rumen microbiome associations by gastrointestinal nematode infection. Besides, the correlation between ANMEs was lower in the animal's postinfection. Our findings suggest that gastrointestinal parasites potentially lead to decreased methanotrophic metabolism-related microorganisms and genes.

Evaluation of Nanaerobic Digestion as a Mechanism to Explain Surplus Methane Production in Animal Rumina and Engineered Digesters

Nanaerobes are a newly described class of microorganisms that use a unique cytochrome bd oxidase to achieve nanaerobic respiration at <2 μM dissolved oxygen (∼1% of atmospheric oxygen) but are not viable above this value due to the lack of other terminal oxidases. Although sharing an overlapping ecological niche with methanogenic archaea, the role of nanaerobes in methanogenic systems has not been studied so far. To explore their occurrence and significance, we re-analyzed published meta-omic datasets from animal rumina and waste-to-energy digesters, including conventional anaerobic digesters and anaerobic digesters with ultra-low oxygenation. Results show that animal rumina share broad similarities in the microbial community and system performance with oxygenated digesters, rather than with conventional anaerobic digesters, implying that trace levels of oxygen drive the efficient digestion in ruminants. The rumen system serves as an ideal model for the newly named nanaerobic digestion, as it relies on the synergistic co-occurrence of nanaerobes and methanogens for methane yield enhancement. The most abundant ruminal bacterial family Prevotellaceae contains many nanaerobes, which perform not only anaerobic fermentation but also nanaerobic respiration using cytochrome bd oxidase. These nanaerobes generally accompany hydrogenotrophic methanogens to constitute a thermodynamically and physiologically consistent framework for efficient methane generation. Our findings provide new insights into ruminal methane emissions and strategies to enhance methane generation from biomass.

The effects of Selenohomolanthionine supplementation on the rumen eukaryotic diversity of Shaanbei white cashmere wether goats

Selenium (Se) is an important microelement for animal health. However, the knowledge about the effects of Se supplementation on rumen eukaryotic community remains less explored. In this study, the ruminal eukaryotic diversity in three months old Shaanbei white cashmere wether goats, with body weight (26.18 ± 2.71) kg, fed a basal diet [0.016 mg/kg Se dry matter (DM), control group (CG)] were compared to those animals given basal diet supplemented with different levels of organic Se in the form of Selenohomolanthionine (SeHLan), namely low Se group (LSE, 0.3 mg/kg DM), medium Se group (MSE, 0.6 mg/kg Se DM) and high Se group (HSE, 1.2 mg/kg DM) using 18S rRNA amplicon sequencing. Illumina sequencing generated 2,623,541 reads corresponding to 3123 operational taxonomic units (OTUs). Taxonomic analysis revealed that Eukaryota (77.95%) and Fungi (14.10%) were the dominant eukaryotic kingdom in all samples. The predominant rumen eukaryotic phylum was found to be Ciliophora (92.14%), while fungal phyla were dominated by Ascomycota (40.77%), Basidiomycota (23.77%), Mucoromycota (18.32%) and unidentified_Fungi (13.89%). The dominant eukaryotic genera were found to be Entodinium (55.44%), Ophryoscolex (10.51%) and Polyplastron (10.19%), while the fungal genera were dominanted by Mucor (15.39%), Pichia (9.88%), Aspergillu (8.24%), Malassezia (7.73%) and unidentified_Neocallimastigaceae (7.72%). The relative abundance of eukaryotic genera Ophryoscolex, Enoploplastron and fungal genus Mucor were found to differ significantly among the four treatment groups (P < 0.05). Moreover, Spearman correlation analysis revealed that the ciliate protozoa and fungi were negatively correlated with each other. The results of this study provided newer information about the effects of Se on rumen eukaryotic diversity patterns using 18s rRNA high-throughput sequencing technology.

Some Aspects of the Physiology of the Nyctotherus velox, a Commensal Ciliated Protozoon Taken from the Hindgut of the Tropical Millipede Archispirostreptus gigas

In this paper, the growth requirements, fermentation pattern, and hydrolytic enzymatic activities of anaerobic ciliates collected from the hindgut of the African tropical millipede Archispirostreptus gigas are described. Single-cell molecular analysis showed that ciliates from the millipede hindgut could be assigned to the Nyctotherus velox and a new species named N. archispirostreptae n. sp. The ciliate N. velox can grow in vitro with unspecified prokaryotic populations and various plant polysaccharides (rice starch-RS, xylan, crystalline cellulose20-CC, carboxymethylcellulose-CMC, and inulin) or without polysaccharides (NoPOS) in complex reduced medium with soluble supplements (peptone, glucose, and vitamins). Specific catalytic activity (nkat/g of protein) of α amylase of 300, xylanase of 290, carboxymethylcellulase of 190, and inulinase of 170 was present in the crude protein extract of N. velox. The highest in vitro dry matter digestibility was observed in RS and inulin after 96 h of fermentation. The highest methane concentration was observed in xylan and inulin substrates. The highest short-chain fatty acid concentration was observed in RS, inulin, and xylan. In contrast, the highest ammonia concentration was observed in NoPOS, CMC, and CC. The results indicate that starch is the preferred substrate of the N. velox. Hydrolytic enzyme activities of N. velox showed that the ciliates contribute to the fermentation of plant polysaccharides in the gut of millipedes.

Effect of rumen microbiota transfaunation on the growth, rumen fermentation, and microbial community of early separated Japanese Black cattle

This study aimed to investigate the effect of rumen microbiota transfaunation on the growth, rumen fermentation, and the microbial community of Japanese Black cattle that were separated early from their dams. Here, 24 calves were separated from their dams immediately after calving, 12 of which were transfaunated via inoculation with rumen fluid from adult cattle at the age of 2 months while the remaining 12 were kept unfaunated (not-inoculated). Feed efficiency monitoring was performed during 7-10 months of age. Body weight and feed intake were not significantly different between the transfaunated and unfaunated cattle. Transfaunation increased the relative levels of acetate and butyrate but decreased those of propionate, which increased the non-glucogenic/glucogenic short-chain fatty acid ratio. Microbial 16S, 18S, and ITS ribosomal RNA gene amplicon analysis showed that rumen microbial diversity and composition differed between transfaunated and unfaunated cattle; transfaunation increased the abundance of acetate- and butyrate-producing bacteria, and decreased the abundance of bacterial genera associated with propionate production. Transfaunation also increased the abundance of Methanomassiliicoccaceae_group10 (1.94% vs. 0.05%) and Neocallimastix (27.1% vs. 6.8%) but decreased that of Methanomicrobium (<0.01% vs. 0.06%). Our findings indicate that rumen microbiota transfaunation shifts rumen fermentation toward acetate and butyrate production through a change in the rumen microbial composition in Japanese Black cattle.

Oxygen levels are key to understanding "Anaerobic" protozoan pathogens with micro-aerophilic lifestyles

Publications abound on the physiology, biochemistry and molecular biology of "anaerobic" protozoal parasites as usually grown under "anaerobic" culture conditions. The media routinely used are poised at low redox potentials using techniques that remove O₂ to "undetectable" levels in sealed containers. However there is growing understanding that these culture conditions do not faithfully resemble the O₂ environments these organisms inhabit. Here we review for protists lacking oxidative energy metabolism, the oxygen cascade from atmospheric to intracellular concentrations and relevant methods of measurements of O₂, some well-studied parasitic or symbiotic protozoan lifestyles, their homeodynamic metabolic and redox balances, organism-drug-oxygen interactions, and the present and future prospects for improved drugs and treatment regimes.

The macronuclear genome of anaerobic ciliate Entodinium caudatum reveals its biological features adapted to the distinct rumen environment

Entodinium caudatum is an anaerobic binucleated ciliate representing the most dominant protozoal species in the rumen. However, its biological features are largely unknown due to the inability to establish an axenic culture. In this study, we primally sequenced its macronucleus (MAC) genome to aid the understanding of its metabolism, physiology, ecology. We isolated the MAC of E. caudatum strain MZG-1 and sequenced the MAC genome using Illumina MiSeq, MinION, and PacBio RSII systems. De novo assembly of the MiSeq sequence reads followed with subsequent scaffolding with MinION and PacBio reads resulted in a draft MAC genome about 117 Mbp. A large number of carbohydrate-active enzymes were likely acquired through horizontal gene transfer. About 8.74% of the E. caudatum predicted proteome was predicted as proteases. The MAC genome of E. caudatum will help better understand its important roles in rumen carbohydrate metabolism, and interaction with other members of the rumen microbiome.

Effects of Multi-Species Direct-Fed Microbial Products on Ruminal Metatranscriptome and Carboxyl-Metabolome of Beef Steers

We examined the effects of two direct-fed microbial (DFM) products containing multiple microbial species and their fermentation products on ruminal metatranscriptome and carboxyl-metabolome of beef steers. Nine ruminally-cannulated Holstein steers were assigned to 3 treatments arranged in a 3 × 3 Latin square design with three 21-d periods. Dietary treatments were (1) Control (CON; basal diet without additive), (2) Commence (PROB; basal diet plus 19 g/d of Commence), and (3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both S. cerevisiae-based DFM products containing several microbial species and their fermentation products. Mixed ruminal contents collected multiple times after feeding on day 21 were used for metatranscriptome and carboxyl-metabolome analysis. Partial least squares discriminant analysis revealed a distinct transcriptionally active taxonomy profiles between CON and each of the PROB and SYNB samples. Compared to CON, the steers fed supplemental PROB had 3 differential (LDA ≥ 2.0; p ≤ 0.05) transcriptionally active taxa, none of which were at the species level, and those fed SYNB had eight differential (LDA > 2.0, p ≤ 0.05) transcriptionally active taxa, but there was no difference (p > 0.05) between PROB and SYNB. No functional microbial genes were differentially expressed among the treatments. Compared with CON, 3 metabolites (hydroxylpropionic acid and 2 isomers of propionic acid) were increased (FC ≥ 1.2, FDR ≤ 0.05), whereas 15 metabolites, including succinic acid and fatty acid peroxidation and amino acid degradation products were reduced (FC ≤ 0.83, FDR ≤ 0.05) by supplemental PROB. Compared with CON, 2 metabolites (2 isomers of propionic acid) were increased (FC ≥ 1.2, FDR ≤ 0.05), whereas 2 metabolites (succinic acid and pimelate) were reduced (FC ≤ 0.83, FDR ≤ 0.05) by supplemental SYNB. Compared to SYNB, supplemental PROB reduced (FC ≤ 0.83, FDR ≤ 0.05) the relative abundance of four fatty acid peroxidation products in the rumen. This study demonstrated that dietary supplementation with either PROB or SYNB altered the ruminal fermentation pattern. In addition, supplemental PROB reduced concentrations of metabolic products of fatty acid peroxidation and amino acid degradation. Future studies are needed to evaluate the significance of these alterations to ruminal fatty acid and amino acid metabolisms, and their influence on beef cattle performance.

Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing

In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson's correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.

Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine

A network analysis including relative abundances of all ruminal microbial genera (archaea, bacteria, fungi, and protists) and their genes was performed to improve our understanding of how the interactions within the ruminal microbiome affects methane emissions (CH4). Metagenomics and CH4 data were available from 63 bovines of a two-breed rotational cross, offered two basal diets. Co-abundance network analysis revealed 10 clusters of functional niches. The most abundant hydrogenotrophic Methanobacteriales with key microbial genes involved in methanogenesis occupied a different functional niche (i.e., "methanogenesis" cluster) than methylotrophic Methanomassiliicoccales (Candidatus Methanomethylophylus) and acetogens (Blautia). Fungi and protists clustered together and other plant fiber degraders like Fibrobacter occupied a seperate cluster. A Partial Least Squares analysis approach to predict CH4 variation in each cluster showed the methanogenesis cluster had the best prediction ability (57.3%). However, the most important explanatory variables in this cluster were genes involved in complex carbohydrate degradation, metabolism of sugars and amino acids and Candidatus Azobacteroides carrying nitrogen fixation genes, but not methanogenic archaea and their genes. The cluster containing Fibrobacter, isolated from other microorganisms, was positively associated with CH4 and explained 49.8% of its variability, showing fermentative advantages compared to other bacteria and fungi in providing substrates (e.g., formate) for methanogenesis. In other clusters, genes with enhancing effect on CH4 were related to lactate and butyrate (Butyrivibrio and Pseudobutyrivibrio) production and simple amino acids metabolism. In comparison, ruminal genes negatively related to CH4 were involved in carbohydrate degradation via lactate and succinate and synthesis of more complex amino acids by γ-Proteobacteria. When analyzing low- and high-methane emitters data in separate networks, competition between methanogens in the methanogenesis cluster was uncovered by a broader diversity of methanogens involved in the three methanogenesis pathways and larger interactions within and between communities in low compared to high emitters. Generally, our results suggest that differences in CH4 are mainly explained by other microbial communities and their activities rather than being only methanogens-driven. Our study provides insight into the interactions of the rumen microbial communities and their genes by uncovering functional niches affecting CH4, which will benefit the development of efficient CH4 mitigation strategies.

The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features

Background

Rumen ciliates play important roles in rumen function by digesting and fermenting feed and shaping the rumen microbiome. However, they remain poorly understood due to the lack of definitive direct evidence without influence by prokaryotes (including symbionts) in co-cultures or the rumen. In this study, we used RNA-Seq to characterize the transcriptome of Entodinium caudatum, the most predominant and representative rumen ciliate species.

Results

Of a large number of transcripts, > 12,000 were annotated to the curated genes in the NR, UniProt, and GO databases. Numerous CAZymes (including lysozyme and chitinase) and peptidases were represented in the transcriptome. This study revealed the ability of E. caudatum to depolymerize starch, hemicellulose, pectin, and the polysaccharides of the bacterial and fungal cell wall, and to degrade proteins. Many signaling pathways, including the ones that have been shown to function in E. caudatum, were represented by many transcripts. The transcriptome also revealed the expression of the genes involved in symbiosis, detoxification of reactive oxygen species, and the electron-transport chain. Overall, the transcriptomic evidence is consistent with some of the previous premises about E. caudatum. However, the identification of specific genes, such as those encoding lysozyme, peptidases, and other enzymes unique to rumen ciliates might be targeted to develop specific and effective inhibitors to improve nitrogen utilization efficiency by controlling the activity and growth of rumen ciliates. The transcriptomic data will also help the assembly and annotation in future genomic sequencing of E. caudatum.

Conclusion

As the first transcriptome of a single species of rumen ciliates ever sequenced, it provides direct evidence for the substrate spectrum, fermentation pathways, ability to respond to various biotic and abiotic stimuli, and other physiological and ecological features of E. caudatum. The presence and expression of the genes involved in the lysis and degradation of microbial cells highlight the dependence of E. caudatum on engulfment of other rumen microbes for its survival and growth. These genes may be explored in future research to develop targeted control of Entodinium species in the rumen. The transcriptome can also facilitate future genomic studies of E. caudatum and other related rumen ciliates.

Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

Ruminants are unique among livestock due to their ability to efficiently convert plant cell wall carbohydrates into meat and milk. This ability is a result of the evolution of an essential symbiotic association with a complex microbial community in the rumen that includes vast numbers of bacteria, methanogenic archaea, anaerobic fungi and protozoa. These microbes produce a diverse array of enzymes that convert ingested feedstuffs into volatile fatty acids and microbial protein which are used by the animal for growth. Recent advances in high-throughput sequencing and bioinformatic analyses have helped to reveal how the composition of the rumen microbiome varies significantly during the development of the ruminant host, and with changes in diet. These sequencing efforts are also beginning to explain how shifts in the microbiome affect feed efficiency. In this review, we provide an overview of how meta-omics technologies have been applied to understanding the rumen microbiome, and the impact that diet has on the rumen microbial community.

Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle

Future growth in demand for meat and milk, and the socioeconomic and environmental challenges that farmers face, represent a “grand challenge for humanity”. Improving the digestibility of crop residues such as straw could enhance the sustainability of ruminant production systems. Here, we investigated if transfer of rumen contents from bison to cattle could alter the rumen microbiome and enhance total tract digestibility of a barley straw-based diet. Beef heifers were adapted to the diet for 28 days prior to the experiment. After 46 days, ~70 percent of rumen contents were removed from each heifer and replaced with mixed rumen contents collected immediately after slaughter from 32 bison. This procedure was repeated 14 days later. Intake, chewing activity, total tract digestibility, ruminal passage rate, ruminal fermentation, and the bacterial and protozoal communities were examined before the first and after the second transfer. Overall, inoculation with bison rumen contents successfully altered the cattle rumen microbiome and metabolism, and increased protein digestibility and nitrogen retention, but did not alter fiber digestibility.

The effect of rumen ciliates on chitinolytic activity, chitin content and the number of fungal zoospores in the rumen fluid of sheep

The objective of this study was to investigate the effect of selected protozoa on the degradation and concentration of chitin and the numbers of fungal zoospores in the rumen fluid of sheep. Three adult ewes were fed a hay-concentrate diet, defaunated, then monofaunated with Entodinium caudatum or Diploplastron affine alone and refaunated with natural rumen fauna. The average density of the protozoa population varied from 6.1 · 10(4) (D. affine) to 42.2 · 10(4) cells/ml rumen fluid (natural rumen fauna). The inoculation of protozoa in the rumen of defaunated sheep increased the total activity of chitinolytic enzymes from 2.9 to 3.6 μmol N-acetylglucosamine/g dry matter (DM) of rumen fluid per min, the chitin concentration from 6.3 to 7.2 mg/g DM of rumen fluid and the number of fungal zoospores from 8.1 to 10.9 · 10(5) cells/ml rumen fluid. All examined indices showed diurnal variations. Ciliate population density was highest immediately prior to feeding and lowest at 4 h thereafter. The opposite effects were observed for the numbers of fungal zoospores, the chitin concentration and chitinolytic activity. Furthermore, it was found that chitin from zoospores may account for up to 95% of total microbial chitin in the rumen fluid of sheep. In summary, the examined ciliate species showed the ability of chitin degradation as well as a positive influence on the development of the ruminal fungal population.

Response of lactating cows to live yeast supplementation during summer

Dairy cows experiencing heat stress have reduced intake and increased reliance on glucose, making feeding strategies capable of improving diet digestibility plausible for improving postrumen nutrient flow and performance. The effect of yeast on digestion and performance of lactating cows during the warm summer months of southeastern Brazil was evaluated. Cows were individually fed in tie stalls and temperature-humidity index was above 68 during 75.6% of the experiment. Twenty-eight Holstein cows (207±87 d in milk) received a standard diet for 14 d and then a treatment for 70 d, in a covariate-adjusted, randomized block design with repeated measures over time. Treatments were yeast (Saccharomyces cerevisiae) or control. Yeast was top dressed to the diet in the morning, equivalent to 25×10(10) cfu of live cells and 5×10(10) cfu of dead cells. The diet contained corn silage (37.7%), Tifton silage (7.1%), raw soybeans (4.1%), soybean meal (16.5%), finely ground corn (20.7%), and citrus pulp (11.9%). Yeast increased milk (26.7 vs. 25.4 kg/d) and solids yield (3.06 vs. 2.92 kg/d), especially lactose. Response in milk yield was consistent over time and started at d 5. The daily intake of digestible OM, total-tract digestibility of nutrients, urinary allantoin excretion, chewing pattern throughout the day, and dry matter intake did not respond to yeast. A trend was observed for increased plasma glucose with yeast (62.9 vs. 57.3mg/dL), lowered respiratory frequency (48 vs. 56 breaths/min), and increased plasma niacin content (1.31 vs. 1.22 µg/mL), though cows had similar rectal temperature. Ruminal lactate and butyrate as proportions of ruminal organic acids were reduced by yeast, but no effects on other organic acids, ruminal pH, or protozoa content were detected. Plasma urea N over 24h was increased by yeast. On d 72 to 74, citrus pulp was abruptly replaced with finely ground corn to induce acidosis. The increased load of starch increased dry matter intake between 0700 and 1300 h, jugular blood partial pressure of CO2, HCO3-, and base excess, and decreased blood pH for both treatments. The yeast treatment had a higher blood pH compared with the control, 7.34, and 7.31, respectively. Yeast supplementation improved lactation performance of dairy cows under heat stress. Improvement in lactation performance apparently involved the regulation of body homeothermia, rather than improved digestibility.

Phylogeny of intestinal ciliates, including Charonina ventriculi, and comparison of microscopy and 18S rRNA gene pyrosequencing for rumen ciliate community structure analysis

The development of high-throughput methods, such as the construction of 18S rRNA gene clone or pyrosequencing libraries, has allowed evaluation of ciliate community composition in hundreds of samples from the rumen and other intestinal habitats. However, several genera of mammalian intestinal ciliates have been described based only on morphological features and, to date, have not been identified using molecular methods. Here, we isolated single cells of one of the smallest but widely distributed intestinal ciliates, Charonina ventriculi, and sequenced its 18S rRNA gene. We verified the sequence in a full-cycle rRNA approach using fluorescence in situ hybridization and thereby assigned an 18S rRNA gene sequence to this species previously known only by its morphology. Based on its full-length 18S rRNA gene sequence, Charonina ventriculi was positioned within the phylogeny of intestinal ciliates in the subclass Trichostomatia. The taxonomic framework derived from this phylogeny was used for taxonomic assignment of trichostome ciliate 18S rRNA gene sequence data stemming from high-throughput amplicon pyrosequencing of rumen-derived DNA samples. The 18S rRNA gene-based ciliate community structure was compared to that obtained from microscopic counts using the same samples. Both methods allowed identification of dominant members of the ciliate communities and classification of the rumen ciliate community into one of the types first described by Eadie in 1962. Notably, each method is associated with advantages and disadvantages. Microscopy is a highly accurate method for evaluation of total numbers or relative abundances of different ciliate genera in a sample, while 18S rRNA gene pyrosequencing represents a valuable alternative for comparison of ciliate community structure in a large number of samples from different animals or treatment groups.

Effect of progressive inoculation of fauna-free sheep with holotrich protozoa and total-fauna on rumen fermentation, microbial diversity and methane emissions

Rumen methanogenesis represents an energy waste for the ruminant and an important source of greenhouse gas; thus, integrated studies are needed to fully understand this process. Eight fauna-free sheep were used to investigate the effect of successive inoculation with holotrich protozoa then with total fauna on rumen methanogenesis. Holotrichs inoculation neither altered rumen fermentation rate nor diet digestibility, but increased concentrations of acetate (+15%), butyrate (+57%), anaerobic fungi (+0.82 log), methanogens (+0.41 log) and methanogenesis (+54%). Further inoculation with total fauna increased rumen concentrations of protozoa (+1.0 log), bacteria (+0.29 log), anaerobic fungi (+0.78 log), VFA (+8%), ammonia and fibre digestibility (+17%) without affecting levels of methanogens or methanogenesis. Rumen methanogens population was fairly stable in terms of structure and diversity, while the bacterial community was highly affected by the treatments. Inoculation with holotrich protozoa increased bacterial diversity. Further inoculation with total fauna lowered bacterial diversity but increased concentrations of certain propionate and lactate-producing bacteria, suggesting that alternative H2 sinks could be relevant. This experiment suggests that holotrich protozoa have a greater impact on rumen methanogenesis than entodiniomorphids. Thus, further research is warranted to understand the effect of holotrich protozoa on methane formation and evaluate their elimination from the rumen as a potential methane mitigation strategy.

Study of methanogen communities associated with different rumen protozoal populations

Protozoa-associated methanogens (PAM) are considered one of the most active communities in the rumen methanogenesis. This experiment investigated whether methanogens are sequestrated within rumen protozoa, and structural differences between rumen free-living methanogens and PAM. Rumen protozoa were harvested from totally faunated sheep, and six protozoal fractions (plus free-living microorganisms) were generated by sequential filtration. Holotrich-monofaunated sheep were also used to investigate the holotrich-associated methanogens. Protozoal size determined the number of PAM as big protozoa had 1.7–3.3 times more methanogen DNA than smaller protozoa, but also more endosymbiotic bacteria (2.2- to 3.5-fold times). Thus, similar abundance of methanogens with respect to total bacteria were observed across all protozoal fractions and free-living microorganisms, suggesting that methanogens are not accumulated within rumen protozoa in a greater proportion to that observed in the rumen as a whole. All rumen methanogen communities had similar diversity (22.2 ± 3.4 TRFs). Free-living methanogens composed a conserved community (67% similarity within treatment) in the rumen with similar diversity but different structures than PAM (P < 0.05). On the contrary, PAM constituted a more variable community (48% similarity), which differed between holotrich and total protozoa (P < 0.001). Thus, PAM constitutes a community, which requires further investigation as part of methane mitigation strategies.

In vitro methane formation and carbohydrate fermentation by rumen microbes as influenced by selected rumen ciliate species

Ciliate protozoa contribute to ruminal digestion and emission of the greenhouse gas methane. Individual species of ciliates co-cultured with mixed prokaryote populations were hypothesized to utilize carbohydrate types differently. In an in vitro batch culture experiment, 0.6 g of pure cellulose or xylan was incubated for 24 h in 40-mL cultures of Entodinium caudatum, Epidinium ecaudatum, and Eudiplodinium maggii with accompanying prokaryotes. Irrespective of ciliate species, gas formation (mL) and short-chain fatty acids (SCFA) concentrations (mmol L(-1)) were higher with xylan (71; 156) than with cellulose (52; 105). Methane did not differ (7.9% of total gas). The SCFA profiles resulting from fermentation of the carbohydrates were similar before and after removing the ciliates from the mixed microbial population. However, absolute methane production (mL 24 h(-1)) was lower by 50% on average after removing E. caudatum and E. maggii. Methanogen copies were less without E. maggii, but not without E. ecaudatum. Within 3 weeks part of this difference was compensated. Butyrate proportion was higher in cultures with E. maggii and E. ecaudatum than with E. caudatum and only when fermenting xylan. In conclusion, the three ciliate species partly differed in their response to carbohydrate type and in supporting methane formation.

The biology of free-living anaerobic ciliates

Anaerobic ciliates are incapable of using oxidative phosphorylation in their energy metabolism and they are more or less sensitive to oxygen. All anaerobic ciliates possess mitochondria-like organelles (with a double outer membrane and often a few cristae) but these do not contain typical mitochondrial enzymes (e.g., cytochromes, cytochrome oxidase). In some species these organelles are capable of fermenting pyruvate into acetate and H2 and they are then referred to as hydrogenosomes. At least six orders of ciliates include anaerobic species. It is concluded that the evolution of anaerobic forms has taken place independently within different taxonomic groups and that hydrogenosomes are modified mitochondria. Many anaerobic ciliates harbour ecto- or endosymbiotic bacteria. Several ciliate species which produce hydrogen as a metabolic waste product harbour endosymbiotic methanogenic bacteria; in some cases this symbiosis represents a mutualistic relationship in which the host controls the life cycle of the symbionts and gains from their presence in terms of growth rate and growth efficiency. Many marine anaerobic ciliates harbour ectosymbiotic bacteria, but the nature of these bacteria and the significance of the association is not yet understood. The present paper reviews what is known about the biology of anaerobic ciliates with special emphasis on free-living forms, including a discussion of their habitats and their role in the microbial communities of anoxic environments.

Comparisons of Salmonella conjugation and virulence gene hyperexpression mediated by rumen protozoa from domestic and exotic ruminants

Recent studies have identified a phenomenon in which ciliated protozoa engulf Salmonella and the intra-protozoal environment hyperactivates virulence gene expression and provides a venue for conjugal transfer of antibiotic resistance plasmids. The former observation is relegated to Salmonella bearing the SGI1 multiresistance integron while the latter phenomenon appears to be a more generalized event for recipient Salmonella. Our previous studies have assessed virulence gene hyperexpression only with protozoa from the bovine rumen while conjugal transfer has been demonstrated in rumen protozoa from cattle and goats. The present study examined virulence gene hyperexpression for Salmonella exposed to rumen protozoa obtained from cattle, sheep, goats, or two African ruminants (giraffe and bongo). Conjugal transfer was also assessed in these protozoa using Salmonella as the recipient. Virulence gene hyperexpression was only observed following exposure to the rumen protozoa from cattle and sheep while elevated virulence was also observed in these animals. Conjugal transfer events were, however, observed in all protozoa evaluated. It therefore appears that the protozoa-based hypervirulence is not universal to all ruminants while conjugal transfer is more ubiquitous.

L3 and adult Ostertagia (Teladorsagia) circumcincta exhibit cyanide sensitive oxygen uptake

Oxygen consumption by L3 and adult Ostertagia (Teladorsagia) circumcincta was examined in vitro to determine whether oxygen can be utilised in metabolism. The oxygen concentration in the abomasal fluid of sheep infected with O. circumcincta was also measured. Rates of consumption (in nmol O2/h/1000 worms) were 13+/-1 in sheathed L3, 34+/-6 in ex-sheathed L3, and 1944+/-495 in adult worms. Constant rates of consumption were maintained until media oxygen concentration dropped to between 10 and 20 microM. Consumption was inhibited 95% by cyanide in L3 and 74% in adults. Oxygen concentration in abomasal fluid varied between 10 and 30 microM in both infected and uninfected animals. During infection, oxygen concentration decreased slightly with increased abomasal pH, though the correlation between the two was poor (r=-0.30). In conclusion, O. circumcincta can consume oxygen and oxygen concentration at the infection site is sufficient to support at least some aerobic metabolism.

Carbohydrate and Amino Acid Fermentation in the Free-Living Primitive Protozoon Hexamita sp

Hexamita sp. is an amitochondriate free-living diplomonad which inhabits O(2)-limited environments, such as the deep waters and sediments of lakes and marine basins. C nuclear magnetic resonance spectroscopy reveals ethanol, lactate, acetate, and alanine as products of glucose fermentation under microaerobic conditions (23 to 34 muM O(2)). Propionic acid and butyric acid were also detected and are believed to be the result of fermentation of alternative substrates. Production of organic acids was greatest under microaerobic conditions (15 muM O(2)) and decreased under anaerobic (<0.25 muM O(2)) and aerobic (200 to 250 muM O(2)) conditions. Microaerobic incubation resulted in the production of high levels of oxidized end products (70% acetate) compared to that produced under anoxic conditions (20% acetate). In addition, data suggest that Hexamita cells contain the arginine dihydrolase pathway, generating energy from the catabolism of arginine to citrulline, ornithine, NH(4), and CO(2). The rate of arginine catabolism was higher under anoxic conditions than under microaerobic conditions. Hexamita cells were able to grow in the absence of a carbohydrate source, albeit with a lower growth rate and yield.

Oxygen uptake and antioxidant responses of the free-living diplomonad Hexamita sp

The free-living anaerobic flagellate Hexamita sp. was observed to actively consume O2 with a K(m) O2 of 13 microM. Oxygen consumption increased linearly with O2 tension up to a threshold level of 100 microM, above which it was inhibited. Oxygen uptake was supported by a number of substrates but probably not coupled to energy conservation as cytochromes could not be detected spectro-photometrically. In addition, inhibitors specific for respiratory chain components did not significantly affect O2 uptake. Respiration was however, partially inhibited by flavoprotein and iron-sulfur protein inhibitors. NAD(P)H supported O2 consumption was measured in both particulate and soluble fractions; this activity was partially inhibited by quinacrine. A chemosensory response was observed in cells exposed to air, however no response was observed in the presence of superoxide dismutase plus catalase. Catalase and nonspecific peroxidase activity could not be detected, but superoxide dismutase plus catalase. Catalase and nonspecific peroxidase activity could not be detected, but superoxide dismutase activity was present. Superoxide dismutase was sensitive to NaN3, and H2O2 but not KCN, suggesting a Fe prosthetic group. Flow cytometric analysis revealed that thiol levels in live cells were depleted in the presence of t-butyl H2O2. The observed NADPH-driven glutathione reductase activity is believed to recycle oxidized thiols in order to re-establish reduced thiol levels in the cell. The corresponding thiol cycling enzyme glutathione peroxidase could not be detected. The ability to withstand high O2 tensions (100 microM) would enable Hexamita to spend short periods in a wider range of habitats. Prolonged exposure to O2 tensions higher than 100 microM leads to irreversible damage and cell death.

Oxygen affinities of metronidazole-resistant and -sensitive stocks of Giardia intestinalis

The common protozoon, Giardia intestinalis, parasitizes the upper small intestine of man, and is often refractory to treatment by metronidazole. Defective oxygen-scavenging mechanisms have been implicated as a cause of metronidazole resistance of another flagellate Trichomonas vaginalis, where metronidazole is also the most common drug treatment. Oxygen consumption of six clinical isolates of G. intestinalis and one line selected for resistance to metronidazole was measured over 0-50 microM-O2 using an oxygen electrode open for gas exchange. At > 30 microM-O2, inhibition of respiration was demonstrated in all seven stocks. Apparent oxygen affinities (KmO2) were found to range from 0.5 to 5.2 microM-O2; however, isolates from patients who failed to respond to treatment with metronidazole did not have measurably defective O2-scavenging capabilities compared with metronidazole-sensitive isolates. These strains did, however, show elevated NADPH-oxidase activities compared with metronidazole-sensitive strains. Results indicate that biochemical mechanisms of drug resistance in G. intestinalis may be quite different from those operating in T. vaginalis.

Influence of CO2 and low concentrations of O2 on fermentative metabolism of the ruminal ciliate Polyplastron multivesiculatum

The effects of ruminal concentrations of CO2 and oxygen on the end products of endogenous metabolism and fermentation of D-glucose by the ruminal entodiniomorphid ciliate Polyplastron multivesiculatum were investigated. The principal metabolic products were butyric, acetic, and lactic acids, H2, and CO2. 13C nuclear magnetic resonance spectroscopy identified glycerol as a previously unknown major product of D-[1-13C]glucose fermentation by this protozoan. Metabolite formation rates were clearly influenced by the headspace gas composition. In the presence of 1 to 3 microM O2, acetate, H2, and CO2 formation was partially depressed. A gas headspace with a high CO2 content (66 kPa) was found to suppress hydrogenosomal pathways and to favor butyrate accumulation. Cytochromes were not detected (less than 2 pmol/mg of protein) in P. multivesiculatum; protozoal suspensions, however, consumed O2 for up to 3 h at 1 kPa of O2. Under gas phases of greater than 2.6 kPa of O2, the organisms rapidly became vacuolate and the cilia became inactive. The results suggest that fermentative pathways in P. multivesiculatum are influenced by the O2 and CO2 concentrations that prevail in situ in the rumen.

Trichomonas vaginalis requires traces of oxygen and high concentrations of carbon dioxide for optimal growth

The effects of O2 and CO2 on the growth in culture of Trichomonas vaginalis strain C1-NIH were investigated. Growth under pre-purified N2 in the absence of CO2 supplementation gave a doubling time of 4.4 h; when traces of O2 (less than 0.25 microM) were present, the doubling time was 3.5 h. Organisms grew most rapidly (doubling time 2.3 h) with traces of O2 (less than 0.25 microM) and with the CO2 level controlled at 5 mM. The balance of fermentation products from maltose was greatly influenced by supplied gases. Under strictly anaerobic conditions at 5 mM CO2, equimolar glycerol and lactate accounted for more than 95% of the measured products, whereas lower CO2 increased acetate production. Under microaerobic conditions (O2 less than 0.25 microM) acetate was the major product when CO2 was limited to that evolved endogenously; again 5 mM CO2 favoured glycerol and lactate production. Activities of key enzymes measured in cell-free extracts (pyruvate:ferredoxin oxidoreductase, hydrogenase, glycerol kinase, malate dehydrogenase (decarboxylating) and lactate dehydrogenase) altered with growth conditions commensurately with observed changes in metabolic flux patterns. These results suggest that T. vaginalis is optimally adapted to conditions it experiences in situ in the vagina (traces of O2, high CO2).