@phdthesis{Mahata2021,
  author    = {Mahata, Khadak Singh},
  title     = {Spatiotemporal variations of key air pollutants and greenhouse gases in the Himalayan foothills},
  doi       = {10.25932/publishup-51991},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-519910},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xv, 144},
  year      = {2021},
  abstract  = {South Asia is a rapidly developing, densely populated and highly polluted region that is facing the impacts of increasing air pollution and climate change, and yet it remains one of the least studied regions of the world scientifically. In recognition of this situation, this thesis focuses on studying (i) the spatial and temporal variation of key greenhouse gases (CO2 and CH4) and air pollutants (CO and O3) and (ii) the vertical distribution of air pollutants (PM, BC) in the foothills of the Himalaya. Five sites were selected in the Kathmandu Valley, the capital region of Nepal, along with two sites outside of the valley in the Makawanpur and Kaski districts, and conducted measurements during the period of 2013-2014 and 2016. These measurements are analyzed in this thesis. The CO measurements at multiple sites in the Kathmandu Valley showed a clear diurnal cycle: morning and evening levels were high, with an afternoon dip. There are slight differences in the diurnal cycles of CO2 and CH4, with the CO2 and CH4 mixing ratios increasing after the afternoon dip, until the morning peak the next day. The mixing layer height (MLH) of the nocturnal stable layer is relatively constant (~ 200 m) during the night, after which it transitions to a convective mixing layer during the day and the MLH increases up to 1200 m in the afternoon. Pollutants are thus largely trapped in the valley from the evening until sunrise the following day, and the concentration of pollutants increases due to emissions during the night. During afternoon, the pollutants are diluted due to the circulation by the valley winds after the break-up of the mixing layer. The major emission sources of GHGs and air pollutants in the valley are transport sector, residential cooking, brick kilns, trash burning, and agro-residue burning. Brick industries are influential in the winter and pre-monsoon season. The contribution of regional forest fires and agro-residue burning are seen during the pre-monsoon season. In addition, relatively higher CO values were also observed at the valley outskirts (Bhimdhunga and Naikhandi), which indicates the contribution of regional emission sources. This was also supported by the presence of higher concentrations of O3 during the pre-monsoon season. The mixing ratios of CO2 (419.3 ±6.0 ppm) and CH4 (2.192 ±0.066 ppm) in the valley were much higher than at background sites, including the Mauna Loa observatory (CO2: 396.8 ± 2.0 ppm, CH4:1.831 ± 0.110 ppm) and Waligaun (CO2: 397.7 ± 3.6 ppm, CH4: 1.879 ± 0.009 ppm), China, as well as at an urban site Shadnagar (CH4: 1.92 ± 0.07 ppm) in India. The daily 8 hour maximum O3 average in the Kathmandu Valley exceeds the WHO recommended value during more than 80\% of the days during the pre-monsoon period, which represents a significant risk for human health and ecosystems in the region. Moreover, in the measurements of the vertical distribution of particulate matter, which were made using an ultralight aircraft, and are the first of their kind in the region, an elevated polluted layer at around ca. 3000 m asl. was detected over the Pokhara Valley. The layer could be associated with the large-scale regional transport of pollution. These contributions towards understanding the distributions of key air pollutants and their main sources will provide helpful information for developing management plans and policies to help reduce the risks for the millions of people living in the region.},
  language  = {en}
}
@phdthesis{Hoffmann2019,
  author    = {Hoffmann, Mathias},
  title     = {Improving measurement and modelling approaches of the closed chamber method to better assess dynamics and drivers of carbon based greenhouse gas emissions},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-421302},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xx, 204, xxix},
  year      = {2019},
  abstract  = {The trace gases CO2 and CH4 pertain to the most relevant greenhouse gases and are important exchange fluxes of the global carbon (C) cycle. Their atmospheric quantity increased significantly as a result of the intensification of anthropogenic activities, such as especially land-use and land-use change, since the mid of the 18th century. To mitigate global climate change and ensure food security, land-use systems need to be developed, which favor reduced trace gas emissions and a sustainable soil carbon management. This requires the accurate and precise quantification of the influence of land-use and land-use change on CO2 and CH4 emissions. A common method to determine the trace gas dynamics and C sink or source function of a particular ecosystem is the closed chamber method. This method is often used assuming that accuracy and precision are high enough to determine differences in C gas emissions for e.g., treatment comparisons or different ecosystem components. However, the broad range of different chamber designs, related operational procedures and data-processing strategies which are described in the scientific literature contribute to the overall uncertainty of closed chamber-based emission estimates. Hence, the outcomes of meta-analyses are limited, since these methodical differences hamper the comparability between studies. Thus, a standardization of closed chamber data acquisition and processing is much-needed. Within this thesis, a set of case studies were performed to: (I) develop standardized routines for an unbiased data acquisition and processing, with the aim of providing traceable, reproducible and comparable closed chamber based C emission estimates; (II) validate those routines by comparing C emissions derived using closed chambers with independent C emission estimates; and (III) reveal processes driving the spatio-temporal dynamics of C emissions by developing (data processing based) flux separation approaches. The case studies showed: (I) the importance to test chamber designs under field conditions for an appropriate sealing integrity and to ensure an unbiased flux measurement. Compared to the sealing integrity, the use of a pressure vent and fan was of minor importance, affecting mainly measurement precision; (II) that the developed standardized data processing routines proved to be a powerful and flexible tool to estimate C gas emissions and that this tool can be successfully applied on a broad range of flux data sets from very different ecosystem; (III) that automatic chamber measurements display temporal dynamics of CO2 and CH4 fluxes very well and most importantly, that they accurately detect small-scale spatial differences in the development of soil C when validated against repeated soil inventories; and (IV) that a simple algorithm to separate CH4 fluxes into ebullition and diffusion improves the identification of environmental drivers, which allows for an accurate gap-filling of measured CH4 fluxes. Overall, the proposed standardized data acquisition and processing routines strongly improved the detection accuracy and precision of source/sink patterns of gaseous C emissions. Hence, future studies, which consider the recommended improvements, will deliver valuable new data and insights to broaden our understanding of spatio-temporal C gas dynamics, their particular environmental drivers and underlying processes.},
  language  = {en}
}
@phdthesis{BysaniKondagari2023,
  author    = {Bysani Kondagari, Viswanada Reddy},
  title     = {Engineering and evolution of saccharomyces cerevisiae for synthetic formatotrophic growth via the reductive glycine pathway},
  doi       = {10.25932/publishup-58222},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-582222},
  school      = {Universit{\"a}t Potsdam},
  pages     = {124},
  year      = {2023},
  abstract  = {Increasing demand for food, healthcare, and transportation arising from the growing world population is accompanied by and driving global warming challenges due to the rise of the atmospheric CO2 concentration. Industrialization for human needs has been increasingly releasing CO2 into the atmosphere for the last century or more. In recent years, the possibility of recycling CO2 to stabilize the atmospheric CO2 concentration and combat rising temperatures has gained attention. Thus, using CO2 as the feedstock to address future world demands is the ultimate solution while controlling the rapid climate change. Valorizing CO2 to produce activated and stable one-carbon feedstocks like formate and methanol and further upgrading them to industrial microbial processes to replace unsustainable feedstocks would be crucial for a future biobased circular economy. However, not all microbes can grow on formate as a feedstock, and those microbes that can grow are not well established for industrial processes. S. cerevisiae is one of the industrially well-established microbes, and it is a significant contributor to bioprocess industries. However, it cannot grow on formate as a sole carbon and energy source. Thus, engineering S. cerevisiae to grow on formate could potentially pave the way to sustainable biomass and value-added chemicals production. The Reductive Glycine Pathway (RGP), designed as the aerobic twin of the anaerobic Reductive Acetyl-CoA pathway, is an efficient formate and CO2 assimilation pathway. The RGP comprises of the glycine synthesis module (Mis1p, Gcv1p, Gcv2p, Gcv3p, and Lpd1p), the glycine to serine conversion module (Shmtp), the pyruvate synthesis module (Cha1p), and the energy supply module (Fdh1p). The RGP requires formate and elevated CO2 levels to operate the glycine synthesis module. In this study, I established the RGP in the yeast system using growth-coupled selection strategies to achieve formate and CO2-dependent biomass formation in aerobic conditions. Firstly, I constructed serine biosensor strains by disrupting the native serine and glycine biosynthesis routes in the prototrophic S288c and FL100 yeast strains and insulated serine, glycine, and one-carbon metabolism from the central metabolic network. These strains cannot grow on glucose as the sole carbon source but require the supply of serine or glycine to complement the engineered auxotrophies. Using growth as a readout, I employed these strains as selection hosts to establish the RGP. Initially, to achieve this, I engineered different serine-hydroxymethyltransferases in the genome of serine biosensor strains for efficient glycine to serine conversion. Then, I implemented the glycine synthesis module of the RGP in these strains for the glycine and serine synthesis from formate and CO2. I successfully conducted Adaptive Laboratory Evolution (ALE) using these strains, which yielded a strain capable of glycine and serine biosynthesis from formate and CO2. Significant growth improvements from 0.0041 h-1 to 0.03695 h-1 were observed during ALE. To validate glycine and serine synthesis, I conducted carbon tracing experiments with 13C formate and 13CO2, confirming that more than 90\% of glycine and serine biosynthesis in the evolved strains occurs via the RGP. Interestingly, labeling data also revealed that 10-15\% of alanine was labelled, indicating pyruvate synthesis from the formate-derived serine using native serine deaminase (Cha1p) activity. Thus, RGP contributes to a small pyruvate pool which is converted to alanine without any selection pressure for pyruvate synthesis from formate. Hence, this data confirms the activity of all three modules of RGP even in the presence of glucose. Further, ALE in glucose limiting conditions did not improve pyruvate flux via the RGP. Growth characterization of these strains showed that the best growth rates were achieved in formate concentrations between 25 mM to 300 mM. Optimum growth required 5\% CO2, and dropped when the CO2 concentration was reduced from 5\% to 2.5\%. Whole-genome sequencing of these evolved strains revealed mutations in genes that encode Gdh1p, Pet9p, and Idh1p. These enzymes might influence intracellular NADPH, ATP, and NADH levels, indicating adjustment to meet the energy demand of the RGP. I reverse-engineered the GDH1 truncation mutation on unevolved serine biosensor strains and reproduced formate dependent growth. To elucidate the effect of the GDH1 mutation on formate assimilation, I reintroduced this mutation in the S288c strain and conducted carbon-tracing experiments to compared formate assimilation between WT and ∆gdh1 mutant strains. Comparatively, enhanced formate assimilation was recorded in the ∆gdh1 mutant strain. Although the 13C carbon tracing experiments confirmed the activity of all three modules of the RGP, the overall pyruvate flux via the RGP might be limited by the supply of reducing power. Hence, in a different approach, I overexpressed the formate dehydrogenase (Fdh1p) for energy supply and serine deaminase (Cha1p) for active pyruvate synthesis in the S288c parental strain and established growth on formate and serine without glucose in the medium. Further reengineering and evolution of this strain with a consistent energy, and formate-derived serine supply for pyruvate synthesis, is essential to achieve complete formatotrophic growth in the yeast system.},
  language  = {en}
}