Biological, Earth and Environmental Sciences - Masters by Research Theses

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    Photoperiod and circadian regulation of early development in Lolium perenne (L.) varieties
    (University College Cork, 2022-09-28) Richards, Michael; Henriques, Rossana
    This research describes a protocol for the rapid assessment of early growth photoperiodic performance of the agronomically important perennial ryegrass Lolium perenne, within long-day (LD) and short-day (SD) photoperiods, and provides a preliminary assessment of candidate primer sequences for genes involved in ryegrass circadian regulation. The in-vitro screening process allowed us to compare the effects of LD and SD photoperiods upon both germination rates and root and shoot development. We were able to show a correlation between the performance in vitro with traits from the field based agricultural Pasture Profit Index (PPI), which would allow for a faster screening process for plant breeders. Working in-vitro and being able to control environmental parameters such as temperature would speed the process of screening ryegrass genotypes for useful traits within Irish agriculture and facilitate the exploration of circadian rhythm in ryegrass fitness and its adaptability to climate change.
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    Establishing the Citizen Science Stream Index (CSSI) to monitor water quality in freshwaters
    (University College Cork, 2022-03-01) McSorley, Brendan; Harrison, Simon; Sullivan, Timothy
    Streams and rivers are amongst the most endangered ecosystems in the world. Water quality is an important measure for maintaining ecosystem function. Despite several decades of the EU Nitrates and Water Framework Directives, inputs of nutrient-rich organic matter of both agricultural and municipal origin continue to pollute many waterways in Ireland, most of which are not routinely monitored in terms of water quality. This lack of data hampers efforts to improve water quality. Citizen science projects involve non-experts contributing to scientific data voluntarily and have been identified by the EU as a growing field of practice that is likely to yield significant outcomes for water quality and data capture. In this thesis a biotic index called the Citizen Science Stream Index (CSSI) was established using a principal component analysis of an EPA data set of macroinvertebrates. A further analysis was made using the provided Q-Values in this data set to find the most indicative macroinvertebrates for a citizen science index. The CSSI uses six easily identifiable and common benthic macroinvertebrates with narrow pollution tolerances that indicate water quality, to give a rapid indication of the ecological status of a stream in a sampled area. The CSSI is an easily taught and simple to use biomonitoring index that enables non-experts to identify where pollution has affected the macroinvertebrate community. The protocol involves taking a thirty second kick sample and checking it for the presence or absence of the six taxa, giving a score from -3 to +3. This is repeated three times and the resulting three scores are summed to give a CSSI score between -9 and +9. From this score the sampler can band the water quality of the stream into three water quality bands, red (poor), orange (moderate) and green (good). This thesis validates the CSSI’s indicator taxa, protocol and scoring system by using multiple data sets with varying spatial distribution, water quality and seasonality, comparing the CSSI with contemporary metrics such as the EPA Quality-Values (Q-Values), the Biological Monitoring working Party’s (BMWP) Average Score Per Taxon (ASPT) and the Small Stream Risk Score (SSRS). A pilot study to further test the quality, accuracy and feasibility of the index in the field was carried out on the Nore River catchment with volunteers from the NoreVision project. It was found that the CSSI compared sufficiently with the contemporary metrics tested and provided accurate results in the field study. Therefore, it is fit for purpose as a rapid biomonitoring citizen science index. The CSSI is currently being rolled out in volunteer initiatives around Ireland. The CSSI has received a positive response from participants and provided consistently reliable data capture when compared to existing data points thus far.
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    Spatiotemporal variability in Antarctic krill (Euphausia superba) around South Georgia from Antarctic fur seal (Arctocephalus gazella) diets at two long term monitoring sites
    (University College Cork, 2022-11-29) Coleman, Jamie; Jessopp, Mark John; Hollyman, Phillip; Collins, Martin; Trathan, Phillip
    Despite its biological, biogeochemical, and economic importance, there is much about Antarctic krill (Euphausia superba Dana, 1852) that is still poorly understood. This is especially true for its recruitment into South Georgia’s waters, which is highly variable and difficult to predict. Krill fluctuations exert bottom-up pressures on the entire ecosystem which can be reflected in changes in the breeding success and diet of dependent higher predators, such as Antarctic fur seals - Arctocephalus gazella (Peters, 1875). This study compares two long-term datasets (2008-2021) of Antarctic fur seal diet from Bird Island and King Edward Point, South Georgia, to investigate year-round krill dynamics. Foraging tracks from breeding female fur seals demonstrated that seals from the two sites forage in distinct regions. Krill length-frequency distributions generally followed a synchronous pattern across both sites with summer increases in length associated with growth, and winter decreases associated with ongoing senescence, mortality and possibly krill shrinkage, coupled with recent recruits with smaller body lengths entering the population. Using a multivariate approach, mixed layer depth, sea surface temperature, chlorophyll a, and salinity together explained 43% of the dissimilarities in krill length-frequency distributions predated by fur seals between seasons. Bird Island seals took significantly larger krill than those at KEP, possibly a result of continued krill growth during advection between the two areas, or differences in local oceanography. Krill cohorts visibly developed across years with large-scale recruitment of smaller krill occurring every 4-5 years. An anomalous period between 2017 and 2020 occurred when synchrony between sites broke down and later re-established. The beginning and end of this anomalous period appears to coincide with switches in the El Niño Southern-Oscillation, however more data are needed to formally test this link. This study highlights the importance of having multiple spatially separated long-term monitoring sites; this is particularly important in this ecological system as it can vary over a range of scales, including local scales, and it is also recognised to be experiencing significant changes.
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    Examining the effects of soil compaction on plant growth and root systems architecture through the development of a simple, lab-based rhizotron system
    (University College Cork, 2022-08-26) Kampff, Zoe; Lettice, Eoin; Doyle Prestwich, Barbara
    Soil compaction concerns have grown as both annual precipitation and machinery weights have increased in many parts of the world. Compact soil is created by the physical degradation of the soil structure by external factors. The negative results of soil compaction have a wide effect across the agricultural sector with serious economic and environmental consequences. Soil compaction is a looming threat to crop productivity exacerbated by intensive agricultural practices worldwide. Increased weight of farming equipment, intensive grazing systems, and a changing climate further increase concerns about soil compaction. Numerous studies conclude that soil compaction can impede root development and alter the root system architecture (RSA) which can impact plant growth and negatively affect yields in a variety of plant species. Other soil compaction concerns include increased flooding, increased run-off, and its contribution to climate change through impacting on greenhouse gas emissions. With research trends suggesting an increased focus on crop productivity, tolerance, and sustainable approaches to keep up with global demands, it seems appropriate and important to include compaction studies. This study focused on the effects of soil compaction on plant growth and root systems of perennial ryegrass (Lolium perenne) and oilseed rape (Brassicaceae napus). Rhizotron experiments examined plant growth in soil with and without induced levels of soil compaction. Soil bulk densities of 0.9, 1.1, and 1.3 g/cm3 were achieved in soil- filled, lab-based rhizotron experiments for both plant species. At final harvest, plant parameter measurements and in situ root images suggest that soil compaction has a negative effect on plant growth and the RSA of the plants examined. Increasing soil bulk density significantly decreased above-ground plant height (p = 0.05) and mean shoot dry weights (p = 0.03) as well as affecting total root lengths of oilseed rape. This study provides evidence that above and below-ground plant traits could effectively be examined within an inexpensive rhizotron system. Although the rhizotron system explored had limitations (root system length is limited to rhizotron size; a soil bulk density greater than 1.3 g/cm3 could not be achieved) the study demonstrates a low-cost highly reproducible experimental design that provides an opportunity to expand these methods for a variety of plant species.
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    Modulation of plant growth by day length dependent regulation of the TOR signaling pathway
    (University College Cork, 2022-07-13) Hamilton, Ferga; Henriques, Rossana; Wingler, Astrid
    Plant growth occurs through cell growth and proliferation, which are high energy demanding processes. Plants need to coordinate growth responses with their environmental conditions to ensure the best use of their resources. This accurate regulation depends on the circadian clock, an internal time keeping mechanism that informs the plant of day length duration (photoperiod). The TOR (Target of Rapamycin) kinase pathway is a central hub where cellular energy levels are perceived and translated into specific growth responses across kingdoms. In plants, the TOR pathway has been associated with rapid growing tissue including embryos, shoot and root meristems. Downstream of TOR, the 40S ribosomal protein S6 Kinase 1 (S6K1) modulates both cell growth and proliferation. Since S6K1 accumulation is modulated by the circadian clock, this thesis investigated how changes in S6K1 levels would affect plant growth when the clock function is impaired by mutation in ZTL (ZEITLUPE) which encodes a F-box protein that targets for degradation several components of the Arabidopsis clock. The findings show that de-regulation of TOR signaling pathway components impacts plant growth and development. This negative effect is reinforced by a defective circadian function, suggesting that plants require a running clock to match the TOR pathway activity with specific environmental conditions.