Changes in the ratio of tetraether to diether lipids in cattle feces in response to altered dietary ratio of grass silage and concentrates.

The distinctive membrane lipids of the archaea can contain a wide range of chemical structures. The membrane lipid composition of ruminal methanogenic archaea has not yet been characterized. In this study, we analyzed proportions of the core archaeal membrane lipids dialkyl glycerol diethers (DGDG) and glycerol dialkyl glycerol tetraether (GDGT). We analyzed the feces of beef steers consuming diets that promoted differences in ruminal conditions that were either favorable (i.e., grass silage) or challenging (i.e., concentrates) for the methanogenic archaea. There was significantly less total ether lipid in the feces of cattle consuming the concentrate diet in comparison to the grass silage diet (97 vs. 218 mg/kg DM, respectively), reflecting the inhibitory effect of dietary concentrate on methanogens. Additionally, the proportion of fecal ether lipids as GDGT was much greater in feces from cattle consuming the concentrate diet than in feces from cattle fed grass silage (90% vs. 67% GDGT). A possible explanation for this adaptation is that membrane lipids composited of GDGT lipids are less permeable to protons, thereby protecting the methanogens against low ruminal pH and helping to maintain the chemiosmotic potential (which is important for ATP production, methanogenesis, and growth). The greater proportion of fecal ether lipids as GDGT may reflect adaptation of membrane lipids within the same species, a shift toward methanogens that have a greater proportion of GDGT (e.g., Thermoplasmata), or both. The effect of ruminal environment on membrane composition means that it will be important to consider the production of both DGDG and GDGT lipids when developing a proxy for methanogenesis.

Technical note: Comparison of biomarker and molecular biological methods for estimating methanogen abundance.

Quantitative real-time PCR (qPCR) has become a popular method for estimation of methanogen abundance in the ruminant digestive tract. However, there is no established method in terms of primer choice and quantification, which means that results are variable and not directly comparable between studies. Archaeol has been proposed as an alternative marker for methanogen abundance, as it is ubiquitous in methanogenic Archaea, and can be quantified by gas chromatography-mass spectrometry (GC-MS). The aim of this experiment was to compare total methanogen populations estimated using the new archaeol approach with estimates based on qPCR. Specific primer sets and probes were used to detect dominant ruminal methanogen species Methanobrevibacter ruminantium, Methanobrevibacter smithii, Methanosphaera stadtmanae, and total methanogen populations. There was variation in the relationships among total methanogen abundance estimates based on archaeol and qPCR. In addition, the universal methanogen primers appeared to preferentially amplify genes from M. smithii. Archaeol had the strongest relationship with the dominant rumen methanogen M. ruminantium, whereas the total methanogen primers had a comparatively weak relationship with archaeol. Archaeol analysis was a useful adjunct to molecular biology methods, but it seems that a valid specific primer for M. ruminantium would be more useful than a biased primer for total methanogens.

Chemical markers for rumen methanogens and methanogenesis.

The targeting of mcrA or 16S rRNA genes by quantitative PCR (qPCR) has become the dominant method for quantifying methanogens in rumen. There are considerable discrepancies between estimates based on different primer sets, and the literature is equivocal about the relationship with methane production. There are a number of problems with qPCR, including low primer specificity, multiple copies of genes and multiple genomes per cell. Accordingly, we have investigated alternative markers for methanogens, on the basis of the distinctive ether lipids of archaeal cell membranes. The membranes of Archaea contain dialkyl glycerol ethers such as 2,3-diphytanayl-O-sn-glycerol (archaeol), and glycerol dialkyl glycerol tetraethers (GDGTs) such as caldarchaeol (GDGT-0) in different proportions. The relationships between estimates of methanogen abundance using qPCR and archaeol measurements varied across primers. Studies in other ecosystems have identified environmental effects on the profile of ether lipids in Archaea. There is a long history of analysing easily accessible samples, such as faeces, urine and milk, to provide information about digestion and metabolism in livestock without the need for intrusive procedures. Purine derivatives in urine and odd-chain fatty acids in milk have been used to study rumen function. The association between volatile fatty acid proportions and methane production is probably the basis for empirical relationships between milk fatty acid profiles and methane production. However, these studies have not yet identified consistent predictors. We have evaluated the relationship between faecal archaeol concentration and methane production across a range of diets in studies on beef and dairy cattle. Faecal archaeol is diagnostic for ruminant faeces being below the limit of detection in faeces from non-ruminant herbivores. The relationship between faecal archaeol and methane production was significant when comparing treatment means across diets, but appears to be subject to considerable between-animal variation. This variation was also evident in the weak relationship between archaeol concentrations in rumen digesta and faeces. We speculate that variation in the distribution and kinetics of methanogens in the rumen may affect the survival and functioning of Archaea in the rumen and therefore contribute to genetic variation in methane production. Indeed, variation in the relationship between the numbers of micro-organisms present in the rumen and those leaving the rumen may explain variation in relationships between methane production and both milk fatty acid profiles and faecal archaeol. As a result, microbial markers in the faeces and milk are unlikely to relate well back to methanogenesis in the rumen. This work has also highlighted the need to describe methanogen abundance in all rumen fractions and this may explain the difficulty interpreting results on the basis of samples taken using stomach tubes or rumenocentesis.

Assessment of archaeol as a molecular proxy for methane production in cattle.

The objective of this study was to assess archaeol, a membrane lipid present in methanogenic Archaea, in cattle feces as a molecular proxy for methanogenesis in the rumen. Feces from 16 heifers either in early lactation [71 d in milk (DIM)] or mid lactation (120 DIM), consuming a diet consisting of 30/70 grass silage/concentrates [dry matter (DM) basis], were analyzed for archaeol. To prepare the feces for analysis, total lipids were obtained by Bligh-Dyer extraction, polar head groups were removed by acid methanolysis, an alcohol fraction was obtained by column chromatography, and finally, the alcohol fraction was trimethylsilylated before analysis by gas chromatography-mass spectrometry. Archaeol was quantified by comparison to an internal standard. A highly significant positive relationship was found between fecal archaeol concentration (mg/kg of DM) and methane output (g/kg of DM intake). A highly significant effect of stage of lactation on this relationship was observed. The significant relationship was surprising, given the lack of agreement between methane and total methanogens in previous studies using molecular biology techniques. Variation in the relationship between fecal archaeol concentrations and methane output could be attributed to differences in the methane-producing capability per cell and the selective retention of methanogens in the rumen. The effect of stage of lactation may have been due to differences in DM intake, affecting rumen passage rates and, thus, methanogen populations and activities.

Molecular mass ranges of coal tar pitch fractions by mass spectrometry and size-exclusion chromatography.

A coal tar pitch was fractionated by solvent solubility into heptane-solubles, heptane-insoluble/toluene-solubles (asphaltenes), and toluene-insolubles (preasphaltenes). The aim of the work was to compare the mass ranges of the different fractions by several different techniques. Thermogravimetric analysis, size-exclusion chromatography (SEC) and UV-fluorescence spectroscopy showed distinct differences between the three fractions in terms of volatility, molecular size ranges and the aromatic chromophore sizes present. The mass spectrometric methods used were gas chromatography/mass spectrometry (GC/MS), pyrolysis/GC/MS, electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) and laser desorption time-of-flight mass spectrometry (LD-TOFMS). The first three techniques gave good mass spectra only for the heptane-soluble fraction. Only LDMS gave signals from the toluene-insolubles, indicating that the molecules were too involatile for GC and too complex to pyrolyze into small molecules during pyrolysis/GC/MS. ESI-FTICRMS gave no signal for toluene-insolubles probably because the fraction was insoluble in the methanol or acetonitrile, water and formic acid mixture used as solvent to the ESI source. LDMS was able to generate ions from each of the fractions. Fractionation of complex samples is necessary to separate smaller molecules to allow the use of higher laser fluences for the larger molecules and suppress the formation of ionized molecular clusters. The upper mass limit of the pitch was determined as between 5000 and 10,000 u. The pitch asphaltenes showed a peak of maximum intensity in the LDMS spectra at around m/z 400, in broad agreement with the estimate from SEC. The mass ranges of the toluene-insoluble fraction found by LDMS and SEC (400-10,000 u with maximum intensity around 2000 u by LDMS and 100-9320 u with maximum intensity around 740 u by SEC) are higher than those for the asphaltene fraction (200-4000 u with maximum intensity around 400 u by LDMS and 100-2680 u with maximum intensity around 286 u by SEC) and greater than values considered appropriate for petroleum asphaltenes (300-1200 u with maximum intensity near 700 u).

The location and ordering of fluoride ions in pure silica zeolites with framework types IFR and STF; implications for the mechanism of zeolite synthesis in fluoride media.

Single-crystal X-ray diffraction studies carried out at a synchrotron radiation source have allowed the structure solution and location of fluoride ions inside as-made pure silica zeolites with the IFR and STF framework structures. The local environment of the fluoride has been identified, and unusual ordering of the fluoride ions has been discovered in both cases. The details of the crystal structures are used to suggest structural features that are important in determining the ordering of fluoride ions in zeolites. A mechanism for how the fluoride ordering occurs is suggested for IFR and STF based on the local structure of small cages that make up these zeolites, and the implications for the mechanism of crystal growth are discussed.

Detection and classification of atmospheric methane oxidizing bacteria in soil.

Well-drained non-agricultural soils mediate the oxidation of methane directly from the atmosphere, contributing 5 to 10% towards the global methane sink. Studies of methane oxidation kinetics in soil infer the activity of two methanotrophic populations: one that is only active at high methane concentrations (low affinity) and another that tolerates atmospheric levels of methane (high affinity). The activity of the latter has not been demonstrated by cultured laboratory strains of methanotrophs, leaving the microbiology of methane oxidation at atmospheric concentrations unclear. Here we describe a new pulse-chase experiment using long-term enrichment with 12CH4 followed by short-term exposure to 13CH4 to isotopically label methanotrophs in a soil from a temperate forest. Analysis of labelled phospholipid fatty acids (PLFAs) provided unambiguous evidence of methane assimilation at true atmospheric concentrations (1.8-3.6 p.p.m.v.). High proportions of 13C-labelled C18 fatty acids and the co-occurrence of a labelled, branched C17 fatty acid indicated that a new methanotroph, similar at the PLFA level to known type II methanotrophs, was the predominant soil micro-organism responsible for atmospheric methane oxidation.

Substances with affinity to a monoclonal aflatoxin B1 antibody in Danish urine samples.

Using a competitive enzyme immunoassay, one or more substances recognized by a monoclonal antibody against aflatoxin B1 were detected in human urine samples collected in Denmark. The concentration of urinary aflatoxin-like substances was equivalent to 0.0-6.5 ng aflatoxin B1/mg creatinine. A truly competitive interaction in the immunoassay was found between aflatoxin-like substances and aflatoxin B1. Aflatoxin-like substances could be isolated in small quantities from urine by affinity chromatography. The quantity of urinary aflatoxin-like compounds in the samples collected showed a skewed normal distribution (80 individuals). In order to explain the seemingly high level of aflatoxin-like material in urine samples from people living in a cold temperate climate, the source of aflatoxin-like compounds was investigated. In a dietary restriction study, potential dietary factors leading to excretion of aflatoxin-like compounds were investigated. Our data indicate that the excretion of these compounds by healthy Danes depends mainly on the food ingested 24-48 hr before urine samples were collected. In particular, the excretion of aflatoxin-like substances was increased when diets include beer, dairy products or meat. A map of the epitope recognized by the antibody was constructed from the results of competition studies with several AFB1 analogues. The epitope map was used to draw chemical structures representing the minimal requirements for antibody recognition. An on-line search was conducted among the 98.2 x 10(6) structures in the Chemical Abstracts and Registry Databases (STN, Columbus, OH) and provided strong evidence that only aflatoxins or aflatoxin derivatives are recognized by the antibody. The possible chemical structures of the aflatoxin-like substances are discussed.