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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Date
2016
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Massey University
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Abstract
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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Keywords
Methanotrophs, Environmental aspects, Dairy waste, Purification, Filters and filtration, New Zealand, Research Subject Categories::TECHNOLOGY::Bioengineering