Massey Documents by Type
Permanent URI for this communityhttps://mro.massey.ac.nz/handle/10179/294
Browse
9 results
Search Results
Item Genomic insights into the physiology of Quinella, an iconic uncultured rumen bacterium.(Nature Portfolio, 2022-10-20) Kumar S; Altermann E; Leahy SC; Jauregui R; Jonker A; Henderson G; Kittelmann S; Attwood GT; Kamke J; Waters SM; Patchett ML; Janssen PHQuinella is a genus of iconic rumen bacteria first reported in 1913. There are no cultures of these bacteria, and information on their physiology is scarce and contradictory. Increased abundance of Quinella was previously found in the rumens of some sheep that emit low amounts of methane (CH4) relative to their feed intake, but whether Quinella contributes to low CH4 emissions is not known. Here, we concentrate Quinella cells from sheep rumen contents, extract and sequence DNA, and reconstruct Quinella genomes that are >90% complete with as little as 0.20% contamination. Bioinformatic analyses of the encoded proteins indicate that lactate and propionate formation are major fermentation pathways. The presence of a gene encoding a potential uptake hydrogenase suggests that Quinella might be able to use free hydrogen (H2). None of the inferred metabolic pathways is predicted to produce H2, a major precursor of CH4, which is consistent with the lower CH4 emissions from those sheep with high abundances of this bacterium.Item Mathematical modelling supports the existence of a threshold hydrogen concentration and media-dependent yields in the growth of a reductive acetogen.(Springer Nature Limited, 2020-05-01) Smith NW; Shorten PR; Altermann E; Roy NC; McNabb WCThe bacterial production of acetate via reductive acetogenesis along the Wood-Ljungdahl metabolic pathway is an important source of this molecule in several environments, ranging from industrial bioreactors to the human gastrointestinal tract. Here, we contributed to the study of reductive acetogens by considering mathematical modelling techniques for the prediction of bacterial growth and acetate production. We found that the incorporation of a hydrogen uptake concentration threshold into the models improves their predictions and we calculated this threshold as 86.2 mM (95% confidence interval 6.1-132.6 mM). Monod kinetics and first-order kinetics models, with the inclusion of two candidate threshold terms or reversible Michaelis-Menten kinetics, were compared to experimental data and the optimal formulation for predicting both growth and metabolism was found. The models were then used to compare the efficacy of two growth media for acetogens. We found that the recently described general acetogen medium was superior to the DSMZ medium in terms of unbiased estimation of acetogen growth and investigated the contribution of yeast extract concentration to acetate production and bacterial growth in culture. The models and their predictions will be useful to those studying both industrially and environmentally relevant reductive acetogenesis and allow for straightforward adaptation to similar cases with different organisms.Item Hydrogen cross-feeders of the human gastrointestinal tract.(Taylor & Francis Group, 2019-01-01) Smith NW; Shorten PR; Altermann EH; Roy NC; McNabb WCHydrogen plays a key role in many microbial metabolic pathways in the human gastrointestinal tract (GIT) that have an impact on human nutrition, health and wellbeing. Hydrogen is produced by many members of the GIT microbiota, and may be subsequently utilized by cross-feeding microbes for growth and in the production of larger molecules. Hydrogenotrophic microbes fall into three functional groups: sulfate-reducing bacteria, methanogenic archaea and acetogenic bacteria, which can convert hydrogen into hydrogen sulfide, methane and acetate, respectively. Despite different energy yields per molecule of hydrogen used between the functional groups, all three can coexist in the human GIT. The factors affecting the numerical balance of hydrogenotrophs in the GIT remain unconfirmed. There is increasing evidence linking both hydrogen sulfide and methane to GIT diseases such as irritable bowel syndrome, and strategies for the mitigation of such health problems through targeting of hydrogenotrophs constitute an important field for further investigation.Item Aristaeella hokkaidonensis gen. nov. sp. nov. and Aristaeella lactis sp. nov., two rumen bacterial species of a novel proposed family, Aristaeellaceae fam. nov.(Microbiology Society, 2023-05-12) Mahoney-Kurpe SC; Palevich N; Noel SJ; Gagic D; Biggs PJ; Soni P; Reid PM; Koike S; Kobayashi Y; Janssen PH; Attwood GT; Moon CDTwo strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order 'Christensenellales', were phylogenetically and phenotypically characterized. These strains, designated R-7T and WTE2008T, shared 98.6-99.0 % sequence identity between their 16S rRNA gene sequences. R-7T and WTE2008T clustered together on a distinct branch from other Christensenellaceae strains and had <88.1 % sequence identity to the closest type-strain sequence from Luoshenia tenuis NSJ-44T. The genome sequences of R-7T and WTE2008T had 83.6 % average nucleotide identity to each other, and taxonomic assignment using the Genome Taxonomy Database indicates these are separate species within a novel family of the order 'Christensenellales'. Cells of R-7T and WTE2008T lacked any obvious appendages and their cell wall ultra-structures were characteristic of Gram-negative bacteria. The five most abundant cellular fatty acids of both strains were C16 : 0, C16 : 0 iso, C17 : 0 anteiso, C18 : 0 and C15 : 0 anteiso. The strains used a wide range of the 23 soluble carbon sources tested, and grew best on cellobiose, but not on sugar-alcohols. Xylan and pectin were fermented by both strains, but not cellulose. Acetate, hydrogen, ethanol and lactate were the major fermentation end products. R-7T produced considerably more hydrogen than WTE2008T, which produced more lactate. Based on these analyses, Aristaeellaceae fam. nov. and Aristaeella gen. nov., with type species Aristaeella hokkaidonensis sp. nov., are proposed. Strains R-7T (=DSM 112795T=JCM 34733T) and WTE2008T (=DSM 112788T=JCM 34734T) are the proposed type strains for Aristaeella hokkaidonensis sp. nov. and Aristaeella lactis sp. nov., respectively.Item Public response to decarbonisation through alternative shipping fuels(Springer Nature, 2023-06-24) Carlisle DP; Feetham PM; Wright M; Teagle DAlthough shipping is the most energy efficient method of transporting trade goods it is held accountable for 2-3% of global greenhouse gas (GHG) emissions. The shipping industry is exploring pathways to carbon-neutral fuels to help eliminate GHG emissions by 2050. To date research on alternative fuels has not considered public opinion; it remains unclear whether the public will support alternative shipping fuels, or whether public opposition might prevent or defer their deployment. To fill this knowledge gap and help the industry and policy makers arrive at publicly acceptable decisions our research examines UK public perceptions of six shipping fuels using a mixed-method approach. Our findings reveal that biofuels and hydrogen are clearly favoured, owing to biofuel’s perceived low risk and hydrogen’s lack of negative by-products. Perceptions of liquid natural gas are somewhat positive, suggesting that it provides an acceptable near-term option while other fuels are developed. Despite lingering stigma, nuclear is preferred over the incumbent heavy fuel oil, though both are perceived negatively. However, the UK public strongly dislike ammonia, perceiving it as unproven, risky, and lacking availability. A third support use of alternative shipping fuels, with support greater from those living near ports - a “yes in my back yard” (YIMBY) effect. The results demonstrate that different alternative fuels are likely to elicit different public reactions as they become more widely known and show how the overall evaluations arise from specific positive or negative associations with each fuel.Item Examination of hydrogen cross-feeders using a colonic microbiota model(BioMed Central Ltd, 2021-12) Smith NW; Shorten PR; Altermann E; Roy NC; McNabb WCBACKGROUND: Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing. RESULTS: An existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version. CONCLUSIONS: Although the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.Item Homoacetogenesis as an alternative hydrogen sink in the rumen : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Microbiology and Genetics at Massey University, Palmerston North, New Zealand.(Massey University, 2016) Raju, PreetiRuminant livestock contribute significantly to global greenhouse gas emissions. This is due to microorganisms, known as methanogens that generate methane from hydrogen and carbon dioxide during feed fermentation in the rumen. Mitigation strategies are being developed to reduce methane emissions from ruminants. However, inhibiting methane production may cause accumulation of unused hydrogen in the rumen, which may slow down rumen fermentation and affect animal productivity. Homoacetogens, microbes known to reside in the rumen, can use hydrogen and carbon dioxide to form acetate. Homoacetogens could take over the role of ruminal hydrogen disposal following inhibition of methanogens. The aims of this study were to quantify the involvement of alternative hydrogen utilisers, such as homoacetogens, in hydrogen or electron utilisation. Chemical compounds were screened to identify specific inhibitors of methanogens (BES, acetylene), and both methanogens and homoacetogens (chloroform). Homoacetogenesis was measured via incorporation of 13CO2 into 13C-acetate using a short-term in vitro assay. This short-term in vitro assay measured and confirmed the occurrence of homoacetogenesis in sheep rumen fluid, and it accounted for 1.67% of electron utilisation in fresh rumen fluid. Homoacetogenesis increased in the assay when BES was added, suggesting homoacetogens could increase their activity in the absence of methanogens. Homoacetogenesis decreased with the addition of chloroform, which is known to partially inhibit homoacetogens. Methane formation was inhibited by acetylene in an in vitro serial batch fermentation inoculated with sheep rumen fluid. Homoacetogenesis did not increase, but the homoacetogens were able to grow and maintain themselves as the rumen material was repeatedly diluted and supplemented with fresh feed. Their activity accounted for 2.32% of electron utilisation. To study their significance in the rumen, methane formation was inhibited in sheep using acetylene. Homoacetogenesis increased and accounted for 6.53% of electron utilisation. However, propionate appeared to be the major electron sink (58-88%) in the absence of methanogenesis both in vitro and in vivo. In the future, knowledge of these hydrogen-utilising microorganisms could be used to divert hydrogen or electrons into more beneficial end-products, leading to the transition from a normal methane-producing rumen to an equally or even more productive low methane one.Item Confined atomic systems : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Mathematical Physics at Massey University, Albany, New Zealand(Massey University, 2015) Hasanbulli, MustafaIn this thesis, we investigate physical properties of various atomic systems such as hydrogen, helium and argon confined in a soft–wall potential of the form Vs(r) = (r=r0)N ; where r0 is the radius of the spherical confinement and N is the stiffness controlling variable. Our main purpose is to introduce a confinement for atomic systems that is flexible in terms of sti ness of the confining walls. However, this brings its complications such as non–existence of analytic solutions to the non–relativistic Schr¨odinger equation for this particular problem, and non– availability of good basis sets for studying electronic properties of such systems. Therefore, at first, we treat the problem in pure numerical fashion. Based on our experience on the numerical data, we then attempt to design basis sets that can be used in quantum chemical software packages. We compare our results to known theoretical and experimental results and, in return, make a decision on the quality of the basis sets. To our knowledge, systems confined in this type of potential has not yet been studied, and, we believe that this study will open up new research areas in this field. Possible applications are in high–pressure simulations of atomic, or molecular systems.Item Modelling and analysis of hydrogen-based wind energy transmission and storage systems : HyLink system at Totara Valley : a thesis presented in partial fulfilment of the requirements for the degree of Master of Technology in Energy Management at Massey University, Palmerston North, New Zealand(Massey University, 2009) Sudol, PeterDistributed generation has the potential to reduce the supply-demand gap emerging in New Zealand’s electricity market. Thereby it can improve the overall network efficiency, harness renewable energy resources and reduce the need for upgrading of existing distribution lines. A typical New Zealand rural community consisting of three adjacent farms at Totara Valley near Woodville represents a demonstration site on distributed generation for Massey University and Industrial Research Limited. Local renewable energy resources are being used for the purpose of sustainable development. Alternative micro-scale technologies are being combined to achieve a valuable network support. This paper is an in-depth report on the implementation process of the HyLink system; a system which utilises hydrogen as an energy carrier to balance and transport the fluctuating wind power. The report documents its development from the laboratory stage to commissioning at Totara Valley, which was carried out under direction of Industrial Research Limited. The PEM electrolyser’s performance at different stack temperatures was investigated. It was found that hydrogen production increases at the same voltage with a higher stack temperature. This is due to the improved kinetics of the electrochemical reactions and decreased thermodynamic energy requirement for water electrolysis. The electrolyser efficiency measurement at the half of its maximal power input (247 W) resulted in 65.3%. Thereby the stack temperature attained less than half of the allowed limit of 80°C. The capture of the excess heat by insulation can improve the electrolyser’s efficiency. Pressure tests were performed on the 2 km long pipeline at Totara Valley using hydrogen and natural gas in order to test their permeability. The results were compared with previous studies at Massey University and with data obtained from the industry. The hydrogen permeability was measured to be 5.5 * 10[to the power of]-16 mol m m[to the power of]-2 s[to the power of]-1 Pa[to the power of]-1 for a 2 km MDPE pipe. This is about half the result obtained from previous studies on hydrogen permeability through MDPE at Massey University which was undertaken at room temperature. The reason for this discrepancy is likely to be the lower ambient temperature during the measurement at Totara Valley, which can be supported with the Arrhenius equation. It was furthermore measured that the power loss due to hydrogen diffusion through the pipeline walls during the fuel cell operation is about 1.5 W at the current system operation mode. A techno-economic analysis of the system was undertaken applying the micro-power optimisation software HOMER as a simulation tool. Two operation modes of the system were investigated, the load following and the peak demand compensating. The simulation results reveal that the durability and the cost of the electrochemical energy conversion devices; electrolyser and fuel cell, are the main hurdles which need to be overcome on the path in introducing hydrogen based energy systems like HyLink. Finally, economic optimisation modelling of the small-scale system by best component alignment was performed. It was found that the electrolyser capacity down-rating of 80% in relation to the wind turbine capacity, leads to a minimal system levelised cost. In addition to this, the impact of various wind turbine/electrolyser subsystems and pipeline storage capacities on the fuel cell capacity factor and on the system levelised cost in the load following operation mode was analysed. The outcomes can be useful for further HyLink related energy system planning.