A descriptive model is presented that can explain changes in the amount of methane (CH
4) formed in the rumen in relation to passage rate, feed type, and the effects of pH and inhibitors of ...methanogenesis. The model is based on methanogen growth kinetics in continuous systems. The growth rate of hydrogen (H
2) utilising methanogens in the rumen and the prevailing H
2 concentration are dynamically linked. Higher H
2 concentrations are required to permit a growth rate sufficient to prevent washout of methanogens from the rumen at higher ruminal passage rates, at suboptimal ruminal pH values, or in the presence of inhibitors. Lower H
2 concentrations are possible when the passage rate is lower, when the pH is near optimum, or when methanogens are less affected by inhibitors. Analysis of the literature confirms that increased particulate passage rate is associated with higher rumen H
2 concentrations, less CH
4 formation, and increased importance of propionate as a fermentation endproduct. Published data also show that partial inhibition of methanogens results in higher H
2 concentrations, less CH
4 formation, and more propionate formation. The model suggests that the prevailing H
2 concentration influences the thermodynamics of rumen fermentation. H
2 producing fermentation pathways are favoured at low H
2 concentrations. Therefore, feeds and conditions that result in low H
2 partial pressures will result in more H
2 formation, and less propionate formation, and so more CH
4 is formed per mole of feed monomer fermented in the rumen. Conversely, feeds and additives that favour high H
2 concentrations result in less H
2 formation per mole of feed monomer fermented in the rumen, and so result in production of less CH
4 and more propionate.
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In 1909, H. Joel Conn expressed the hope that methods would soon be at hand by which the significance of the different bacteria present in any soil could be determined. However, by 1918 he was ...pointing out that the methods available to him, which relied on cultivation of bacteria on artificial media, resulted in the formation of colonies by only 1.5 to 10% of the bacterial cells in soil. Fifty years later, Vagn Jensen concluded a review of cultivation-based methodologies by stating his suspicion that those cells that were forming colonies were unrepresentative of the total bacterial community . This was confirmed when cultivation-independent methods began to be used to study soil bacteria. Even so, in the absence of better methods, the pure cultures derived from the colonies that did form were extensively and successfully studied throughout the 20th century. Much of our basic knowledge of soil bacteria, as well as the discovery of many important antibiotics, came from investigations of pure cultures. Cultured isolates are still very important in developing our understanding of bacterial physiology, genetics, and ecology.
Abstract
Based on Monte Carlo simulations of the nonlinear Schrödinger equation in two horizontal dimensions, the dependence of the kurtosis on the directional energy distribution of the initial ...conditions is examined. The parametric survey is carried out to obtain the behavior of the kurtosis as function of the Benjamin–Feir index and directional spread in directional sea states. As directional dispersion effect becomes significant, the kurtosis monotonically decreases in comparison with the unidirectional waves. A parameterization of the kurtosis estimated from directional spectra is proposed here; the error of the parameterization is at most 10%. The parameterization is verified against laboratory data, and good agreement is obtained.
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Approximate Stokes Drift Profiles in Deep Water Breivik, Øyvind; Janssen, Peter A. E. M.; Bidlot, Jean-Raymond
Journal of physical oceanography,
09/2014, Volume:
44, Issue:
9
Journal Article
Peer reviewed
Open access
A deep-water approximation of the Stokes drift velocity profile is explored as an alternative to the monochromatic profile. The alternative profile investigated relies on the same two quantities ...required for the monochromatic profile, namely, the Stokes transport and the surface Stokes drift velocity. Comparisons with parametric spectra and profiles under wave spectra from the Interim ECMWF Re-Analysis (ERA-Interim) and buoy observations reveal much better agreement than the monochromatic profile even for complex sea states. That the profile gives a closer match and a more correct shear has implications for ocean circulation models since the Coriolis-Stokes force depends on the magnitude and direction of the Stokes drift profile, and Langmuir turbulence parameterizations depend sensitively on the shear of the profile. The alternative profile comes at no added numerical cost compared to the monochromatic profile.
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Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction ...methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.
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The Zakharov equation describes the evolution of weakly nonlinear surface gravity waves for arbitrary spectral shape. For deep-water waves, results from the Zakharov equation are well established. ...However, for two-dimensional propagation, in intermediate and shallow water, there are problems related to the treatment of apparent singularities in the contribution of the wave-induced set-up to the evolution of the surface gravity waves. More specifically, the kernel in the integral term is characterized by a regular and an apparent singular contribution. Here, we show that the Davey–Stewartson equation can be directly derived from the Zakharov equation, also in the shallow water limit. This result provides guidance on how to treat the singular contribution to the evolution of the action variable. A relevant result that is obtained is that the growth rate obtained from the stability analysis of a plane wave in shallow water does not depend on the singular part of the kernel of the Zakharov equation.
We discuss some consequences of the canonical transformation in the Hamiltonian theory of water waves (Zakharov, J. Appl. Mech. Tech. Phys., vol. 9, 1968, pp. 190–194). Using Krasitskii's canonical ...transformation we derive general expressions for the second-order wavenumber and frequency spectrum and the skewness and the kurtosis of the sea surface. For deep-water waves, the second-order wavenumber spectrum and the skewness play an important role in understanding the so-called sea-state bias as seen by a radar altimeter. According to the present approach but in contrast with results obtained by Barrick & Weber (J. Phys. Oceanogr., vol. 7, 1977, pp. 11–21), in deep water second-order effects on the wavenumber spectrum are relatively small. However, in shallow water in which waves are more nonlinear, the second-order effects are relatively large and help to explain the formation of the observed second harmonics and infra-gravity waves in the coastal zone. The second-order effects on the directional-frequency spectrum are as a rule more important; in particular it is shown how the Stokes-frequency correction affects the shape of the frequency spectrum, and it is also discussed why in the context of the second-order theory the mean-square slope cannot be estimated from time series. The kurtosis of the wave field is a relevant parameter in the detection of extreme sea states. Here, it is argued that in contrast perhaps to one's intuition, the kurtosis decreases while the waves approach the coast. This is related to the generation of the wave-induced current and the associated change in mean sea level.
Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and ...archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.
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The potent greenhouse gas methane (CH4) is produced in the rumens of ruminant animals from hydrogen produced during microbial degradation of ingested feed. The natural animal-to-animal variation in ...the amount of CH4 emitted and the heritability of this trait offer a means for reducing CH4 emissions by selecting low-CH4 emitting animals for breeding. We demonstrate that differences in rumen microbial community structure are linked to high and low CH4 emissions in sheep. Bacterial community structures in 236 rumen samples from 118 high- and low-CH4 emitting sheep formed gradual transitions between three ruminotypes. Two of these (Q and S) were linked to significantly lower CH4 yields (14.4 and 13.6 g CH4/kg dry matter intake DMI, respectively) than the third type (H; 15.9 g CH4/kg DMI; p<0.001). Low-CH4 ruminotype Q was associated with a significantly lower ruminal acetate to propionate ratio (3.7±0.4) than S (4.4±0.7; p<0.001) and H (4.3±0.5; p<0.001), and harbored high relative abundances of the propionate-producing Quinella ovalis. Low-CH4 ruminotype S was characterized by lactate- and succinate-producing Fibrobacter spp., Kandleria vitulina, Olsenella spp., Prevotella bryantii, and Sharpea azabuensis. High-CH4 ruminotype H had higher relative abundances of species belonging to Ruminococcus, other Ruminococcaceae, Lachnospiraceae, Catabacteriaceae, Coprococcus, other Clostridiales, Prevotella, other Bacteroidales, and Alphaproteobacteria, many of which are known to form significant amounts of hydrogen. We hypothesize that lower CH4 yields are the result of bacterial communities that ferment ingested feed to relatively less hydrogen, which results in less CH4 being formed.
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