The impact of maize silage production and supplementary feed use on the carbon balance of New Zealand dairy farms

Globally, agriculture contributes 10-12% to anthropogenic greenhouse gas (GHG) emissions. Consequently, mitigation of agricultural GHGs has taken on increased importance, particularly in countries like New Zealand where agriculture accounts for almost half of national emissions. Sequestration of atmospheric CO₂ in the soil by altering land management practices has been identified as a potential mitigation option for anthropogenic GHG emissions. However, implementing management practices as a mitigation option first requires an understanding of their effect on soil C stocks. Often the effects of cropping and grassland management on soil C stocks are studied individually, but these practices are linked when the resulting crop is supplied to grazing animals as supplemental feed. This is important for the New Zealand dairy industry, which has been traditionally pasture-based, but increasingly is supported by supplemental feed to compensate for periods of low pasture growth and to boost productivity. To understand the impact of supplemental feed use on soil C stocks and, therefore, on any mitigation potential, both the production of the feed and its use need to be considered together. The overarching aim of this thesis was to experimentally determine the impacts of supplemental feed production and use on soil C by using the net ecosystem carbon balance (NECB) methodology to quantify changes in ecosystem carbon (C) stocks (assumed synonymous to the change in soil C). A secondary aim of this thesis was to advance NECB methodology in complex grazed pasture systems, primarily through examination of the scale at which measurements were made. Improved methodology and understanding are needed to allow a greater number of management practices to be tested. Conceptually, importation of supplemental feed and its embodied C can lead to an increase in ecosystem C because consumption of supplemental feed C by the animals results in additional excreta deposition on the pasture during grazing that can be stored as soil C. This hypothesis was tested by determining the NECB for three years on a dairy farm where imported supplemental feed accounted for >40% of the cows’ diet. A positive NECB (indicating a gain of ecosystem C) was calculated for all three years, but consideration of uncertainties resulted in only one year having a definitive gain of C. The three-year average NECB was 71 ± 77 g C m⁻² y⁻¹ (mean ± uncertainty) and was not considered different from zero. Theoretical calculations based on the imported quantity of supplemental feed C (average 526 g C m⁻² y⁻¹) coupled with the digestibility of the feed and manure retention rates suggest gains of around 25 g C m⁻² y⁻¹ could be expected. The results of this study were of the same order of magnitude to what was expected from modelling and manure C retention literature, and although experimentally a gain in C associated with a large import of supplemental feed could not be definitively concluded, the results confirmed that large gains of ecosystem C are unlikely. A broad range of supplemental feed is used within the New Zealand dairy industry including grazed and harvested feeds, with maize harvested for silage being one of the more common. Internationally, sites where maize cropping with full biomass harvest occurs have been identified as a large source of C, but these studies tend to be from long-term cropping systems. Within New Zealand dairy farm systems, maize silage is often grown as part of the pasture renewal process and, consequently, findings from studies within long-term cropping systems may not apply. In this study, NECBs were calculated for a system where a long-term pasture site was converted to maize silage cropping for two years before a return to permanent pasture. To isolate the C balance of the maize crop alone, NECBs were calculated for the period of maize crop establishment through to seedling emergence of the subsequent sward (~190 days). The Year 1 maize crop NECB was –850 g C m⁻² (a loss of C), while the Year 2 maize crop lost a further –415 g C m⁻². Concurrent grazed pasture NECBs from the same farm were 11 g C m⁻² and –115 g C m⁻² over the same two periods. Above-ground biomass production was around three times greater from the maize crop than adjacent pastures, with more than 90% of this production exported from the site, compared to around 60% net export of the pasture biomass after accounting for returned excreta. The hypothesis that a large loss of ecosystem C could be expected from maize silage cropping for supplement feed was supported. Future research to determine whether the return to permanent pasture results in recovery of previously lost C are required to understand the long-term impacts of periodic cropping for supplemental feed production. Consideration of the effect that all types of supplemental feed production have on ecosystem C stocks was beyond the scope of this thesis, but conclusions can be drawn on systems which use maize silage. Dairy farms which import supplemental feed (maize silage or other) are likely to see small increases (<50 g C m⁻² y⁻¹) in the ecosystem C stocks regardless of the quantity imported, while the production site would be expected to have large losses when producing maize silage. Results from this thesis suggest that where production and use occur within the same dairy farm system a net loss would be expected, and if averaged across the entire farm would be in the order of –40 g C m⁻² y⁻¹. Losses during maize silage production may be reduced by minimising the time that soil is bare during establishment, and although not tested, possibly by decreasing tillage intensity. Moreover, if ecosystem C losses during production are recovered longer-term when returned to grazed pasture (i.e. in the several years following cropping), on-farm production of periodically cropped maize silage may lead to small, but consistent gains in soil C and provide the potential for GHG mitigation. A key unresolved question is the rate of C recovery following a return to permanent pasture relative to the cropping return period. While determining the effect of supplemental feed on ecosystem C, the opportunity also arose to investigate two aspects of NECB measurement scale. Firstly, NECBs were compared when calculated with an ecosystem boundary equivalent to (i) the paddocks included within the eddy covariance (EC) flux footprint (NECBFootprint), and (ii) the farm boundary (NECBFarm). Both calculated NECBs were similar (NECBFootprint was 56 ± 77 g C m⁻² y⁻¹ and NECBFarm was 71 ± 77 g C m⁻² y⁻¹) and the selection of the best boundary definition was dependent on the quality of the available data with NECBFarm considered best in this study. Furthermore, components contributing to the NECB differ with system boundary location and, therefore, can influence interpretation. When choosing a system boundary, the assumption that the measured CO₂ exchange is representative of the entire area within the defined boundary needs to be cautiously considered. The second methodology investigation calculated paddock-specific NECBs for two adjacent paddocks with a single EC system located between them. Provided regular EC data are available from both paddocks (i.e. due to regularly changing wind directions), paddock-specific NECBs can be calculated. Advantages of this approach include eliminating inherent management heterogeneity (e.g. asynchronous grazing), and the ability to allow for treatment comparisons or provide replication while minimising spatial variability and potentially reducing equipment requirements. Key disadvantages were a reduction in data coverage (from 49.1% for the full footprint to 25.9% and 15.7% for each paddock), an increase in uncertainty (by about 25%), and the need for prior assessment of site suitability (i.e. the need for regular wind from both paddocks). Comparisons of NECBs from adjacent rotationally grazed paddocks identified large inter-annual and between-paddock variability, with the latter often due to subtle management differences despite the same overall management regimes. Finally, due to the spatial and temporal variability, several measurement years would be needed to (i) determine the true trajectory of ecosystem C balances and (ii) determine similarity or differences between the two paddocks

A simple dependence between protein evolution rate and the number of protein-protein interactions

BACKGROUND: It has been shown for an evolutionarily distant genomic comparison that the number of protein-protein interactions a protein has correlates negatively with their rates of evolution. However, the generality of this observation has recently been challenged. Here we examine the problem using protein-protein interaction data from the yeast Saccharomyces cerevisiae and genome sequences from two other yeast species. RESULTS: In contrast to a previous study that used an incomplete set of protein-protein interactions, we observed a highly significant correlation between number of interactions and evolutionary distance to either Candida albicans or Schizosaccharomyces pombe. This study differs from the previous one in that it includes all known protein interactions from S. cerevisiae, and a larger set of protein evolutionary rates. In both evolutionary comparisons, a simple monotonic relationship was found across the entire range of the number of protein-protein interactions. In agreement with our earlier findings, this relationship cannot be explained by the fact that proteins with many interactions tend to be important to yeast. The generality of these correlations in other kingdoms of life unfortunately cannot be addressed at this time, due to the incompleteness of protein-protein interaction data from organisms other than S. cerevisiae. CONCLUSIONS: Protein-protein interactions tend to slow the rate at which proteins evolve. This may be due to structural constraints that must be met to maintain interactions, but more work is needed to definitively establish the mechanism(s) behind the correlations we have observed

3q26 Amplification is Rarely Present in Women Whose LSIL Cytology does not Represent CIN 2+ Disease

Comparative Medicine - OneHealth and Comparative Medicine Poster SessionObjective: 10-17% of women with LSIL cytology truly have CIN 2+ disease at colposcopically directed biopsy and 20% of the CIN 2+ lesions derive from women with LSIL cytology. No molecular marker has yet been able to triage LSIL cytology effectively. If possible, the triage would spare women the referral to colposcopy. Irreversible chromosomal damage occurs during oncogenesis. Increasing cervical dysplastic severity occurs with increasing amplification of the 3q26 chromosomal region. The purpose of this study is to evaluate the test characteristics of 3q26 amplification in women whose routine cytology is reported as LSIL with emphasis on the negative predictive value for reassurance. Methods: We conducted a retrospective study using the available SurePath™ liquid cytology LSIL archival samples from women 17-59 years old which were linked to colposcopically directed biopsy samples taken on average 36 days after cytology sampling (3-90 day range). Nuclei from the LSIL samples were hybridized with a single-copy probe for the chromosome 3q26 region and a control probe for the centromeric alpha repeat sequence of chromosome 7, using standard FISH methods. Amplification was defined as five or more signals present in at least 2 cells. Results: Of the 68 paired cytology/biopsy samples, 3q26 amplification occurred in 40% of the women with CIN 2+ disease (sensitivity 95% CI: 12, 74). There was no amplification in 91% of women with less than CIN 2 disease (specificity 95% CI: 81, 97); and the negative predictive value was 90% (79, 96). Conclusions: The lack of 3q26 amplification in women with screening cytology LSIL results offers reassurance that CIN 2+ disease has not developed. Future prospective studies are ongoing

Implementing Primordial Binaries in Simulations of Star Cluster Formation with a Hybrid MHD and Direct N-Body Method

The fraction of stars in binary systems within star clusters is important for their evolution, but what proportion of binaries form by dynamical processes after initial stellar accretion remains unknown. In previous work, we showed that dynamical interactions alone produced too few low-mass binaries compared to observations. We therefore implement an initial population of binaries in the coupled MHD and direct N-body star cluster formation code Torch. We compare simulations with, and without, initial binary populations and follow the dynamical evolution of the binary population in both sets of simulations, finding that both dynamical formation and destruction of binaries take place. Even in the first few million years of star formation, we find that an initial population of binaries is needed at all masses to reproduce observed binary fractions for binaries with mass ratios above the $q \geq 0.1$ detection limit. Our simulations also indicate that dynamical interactions in the presence of gas during cluster formation modify the initial distributions towards binaries with smaller primary masses, larger mass ratios, smaller semi-major axes and larger eccentricities. Systems formed dynamically do not have the same properties as the initial systems, and systems formed dynamically in the presence of an initial population of binaries differ from those formed in simulations with single stars only. Dynamical interactions during the earliest stages of star cluster formation are important for determining the properties of binary star systems.Comment: 15 pages, 14 figures, submitted to MNRAS and edited to address positive referee's repor