Understanding methanotroph ecology in a biofilter for efficiently mitigating methane emissions : a thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Soil Science (Biotechnology) at Massey University, Palmerston North, New Zealand

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2016
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Massey University
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In New Zealand, the majority of the greenhouse gas (GHG), methane (CH4) emissions are from the agriculture sector (enteric fermentation, manure management) and the remainder from solid waste disposal, coal mining and natural gas leaks. A soil-based biofilter made from volcanic pumice soil (isolated from a landfill in Taupo, New Zealand) and perlite has been tested and promoted to mitigate high concentrations (3 300 ppm – 100 000 ppm) of CH4 emissions from a dairy effluent storage pond. This soil-perlite mixture exhibited excellent physical (porosity, water holding capacity and bulk density) characteristics to support the growth and activity of an active methanotroph community. Methanotrophs comprise a diverse group of aerobic alpha and gamma proteobacteria (type I and type II methanotrophs, respectively) that are present naturally in soils where CH4 is produced. However, there is little information on the methanotrophs community structure, population diversity and abundance in this soil-based biofilter. Understanding the activity of these diverse genera under varying soil conditions is essential for optimum use of biofiltration technology, and is the main aim of this thesis. This thesis describes a study to use molecular techniques (PCR, quantitative PCR, T-RFLP and molecular cloning) (Chapter 3) to reveal the population dynamics of methanotrophs (type I, type II and various genera – Methylobacter/Methylomonas/Methylosarcina, Methylococcus and Methylocapsa), in order to build a more efficient CH4 biofiltration system. Methanotroph population dynamics in two fundamentally different prototypes of volcanic pumice soil biofilters – a column and a floating/cover biofilter studied are presented in Chapters 4 and 5. The column biofilter study (Chapter 4) examined the performance of a previously used acidic soil-biofilter medium that was further acidified from pH 5.20 ± 0.20 to 3.72 ± 0.02 by H2S present in the biogas (from the dairy effluent pond).. The more acidic soil biofilter medium (volcanic pumice soil and perlite, 50:50 v/v) was reconstituted with optimal moisture content (110% gravimetric dry wt or ~ 60 % WHC) and achieved a maximum CH4 removal rate of 30.3 g m–3 h–1. In addition, the population of Methylocapsa-like methanotroph increased by 400 %, demonstrating the ability of these soil microorganisms to adapt and grow under acidic pH conditions in the biofilter. The results from this study indicated that (i) when primed with CH4, a soil biofilter can effectively regain efficiency if sufficient moisture levels are maintained, regardless of the soil acidity; (ii) changes in the methanotroph population did not compromise the overall capacity of the volcanic pumice soil to oxidise CH4; and (iii) the more acidic environment (pH 3.72) tends to favour the growth and activity of acid-loving Methylocapsa-like methanotroph while being detrimental to the growth of the Methylobacter / Methylococcus / Methylocystis group of methanotroph. In the floating biofilter (Chapter 5), original acidic soil biofilter medium (pH 5.20) as used in column study was assessed to remove CH4 from the effluent pond surface for a period of one year (December 2013 to November 2014). Field evaluation was supported with a concurrent laboratory study to assess their CH4-oxidising capacity, in addition to identifying and comparing the methanotroph community changes in the soil when exposed to field conditions. Results indicated that (i) irrespective of the season, the floating biofilters in the field were removing 67 ± 6% CH4 throughout the study period with a yearly average rate of 48 ± 23 g CH4 m-3 h-1; however, the highest CH4 removal rate achieved was 101.5 g m-3 h-1 CH4, about 300 % higher than the highest CH4 removal rate by the acidified column biofilter (Chapter 4); (ii) the acidity of the field floating biofilters increased from a pH value of 5.20 to 4.72, but didn’t suppress the genera of methanotrophs (particularly Methylobacter/Methylosinus/Methylocystis); (iii) the laboratory-based floating biofilters experienced biological disturbances with low and high CH4 removal phases during the study period, with an yearly average CH4 oxidation removal of 58%; and (iv) both type I and type II methanotrophs in the field floating biofilters were more abundant, diverse and even compared with the methanotroph community in the laboratory biofilters. This study has demonstrated the ability of the floating biofilters to efficiently mitigate dairy effluent ponds emissions in the field, without requiring any addition of nutrients or water; however, during very dry conditions, occasional addition of water might be needed to keep the biofilter bed moist (≥ 23±4 % dry wt). Earlier New Zealand studies and the current studies (Chapters 4 and 5) were based on the use of a particular volcanic pumice soil as biofilter medium. However, the limited availability of volcanic pumice soil and associated transportation costs limited the wider application of this technology within New Zealand and internationally. This necessitated the assessment of other farm soils and potentially suitable, economical, and locally available biofilter materials that could potentially be used by the farmers to mitigate CH4 emissions (Chapter 6). The potential biofilter materials, viz. farm soil (isolated from a dairy farm effluent pond bank area), pine biochar, garden waste compost, and weathered pine bark mulch were assessed with and without inoculation with a small amount of volcanic pumice soil. All materials supported the growth and activity of methanotrophs. However, the CH4 removal was high (> 80%) and consistent in the inoculated - farm soil and biochar, and was supported by the observed changes in the methanotroph community. The CH4 removal was further enhanced (up to 99%) by the addition of nutrient solution. Field evaluations of these potential materials are now needed to confirm the viability of these materials for recommending them for use on farms. Chapter 7 summarises the molecular results from all the above studies, and describes the future studies. Molecular techniques indicated that a very diverse (Shannon’s diversity, Hʹ = 3.9 to 4.4) group of type I and type II methanotrophs were present in the volcanic pumice soil, which assisted the biofilter materials to perform under varying abiotic conditions. Many novel species and strains of type I and type II methanotrophs were also identified in these soils. For long-term, low cost and efficient and stable CH4 removal, the presence of an even and abundant population (of type I and type II methanotrophs) is however essential. Nevertheless, biofilters offer much promise for mitigating CH4 emissions from dairy ponds, piggeries, and landfills, thereby contributing to the lowering of emissions of this potent greenhouse gas to mitigate the effects of climate change.
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Methanotrophs, Environmental aspects, Dairy waste, Purification, Filters and filtration, New Zealand, Research Subject Categories::TECHNOLOGY::Bioengineering
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