Environmental impacts of freshwater use and suspended solids in life cycle assessment

Perturbation of natural ecosystems, namely by increasing freshwater use and its degradative use, as well as topsoil erosion by water of land-use production systems, have been emerging as topics of high environmental concern. Freshwater use has become a focus of attention in the last few years for all stakeholders involved in the production of goods, mainly agro-industrial and forest-based products, which are freshwater-intensive consumers, requiring large inputs of green and blue water. This thesis presents a global review on the available Water Footprint Assessment and Life Cycle Assessment (LCA)-based methods for measuring and assessing the environmental relevance of freshwater resources use, based on a life cycle perspective. Using some of the available midpoint LCA-based methods, the freshwater use-related impacts of a Portuguese wine (white ‘vinho verde’) were assessed. However, the relevance of environmental green water has been neglected because of the absence of a comprehensive impact assessment method associated with green water flows. To overcome this constraint, this thesis helps to improve and enhance the LCA-based methods by providing a midpoint and spatially explicit Life Cycle Impact Assessment (LCIA) method for assessing impacts on terrestrial green water flow and addressing reductions in surface blue water production caused by reductions in surface runoff due to land-use production systems. The applicability of the proposed method is illustrated by a case study on Eucalyptus globulus conducted in Portugal, as the growth of short rotation forestry is largely dependent on local precipitation. Topsoil erosion by water has been characterised as one of the most upsetting problems for rivers. Because of this, this thesis also focuses on the ecosystem impacts caused by suspended solids (SS) from topsoil erosion that reach freshwater systems. A framework to conduct a spatially distributed SS delivery to freshwater streams and a fate and effect LCIA method to derive site-specific characterisation factors (CFs) for endpoint damage on aquatic ecosystem diversity, namely on algae, macrophyte, and macroinvertebrates organisms, were developed. The applicability of this framework, combined with the derived site-specific CFs, is shown by conducting a case study on E. globulus stands located in Portugal as an example of a land use based system. A spatially explicit LCA assessment was shown to be necessary, since the impacts associated with both green water flows and SS vary greatly as a function of spatial location.

Revisiting molecular diagnostics of Streptococcus pneumoniae

Streptococcus pneumoniae is a human pathobiont that colonizes the nasopharynx. S. pneumoniae is responsible for causing non-invasive and invasive disease such as otitis, pneumonia, meningitis, and sepsis, being a leading cause of infectious diseases worldwide. Due to similarities with closely related species sharing the same niche, it may be a challenge to correctly distinguish S. pneumoniae from its relatives when using only non-culture based methods such as real time PCR (qPCR). In 2007, a molecular method targeting the major autolysin (lytA) of S. pneumoniae by a qPCR assay was proposed by Carvalho and collaborators to identify pneumococcus. Since then, this method has been widely used worldwide. In 2013, the gene encoding for the ABC iron transporter lipoprotein PiaA, was proposed by Trzcinzki and collaborators to be used in parallel with the lytA qPCR assay. However, the presence of lytA gene homologues has been described in closely related species such as S. pseudopneumoniae and S. mitis and the presence of piaA gene is not ubiquitous between S. pneumoniae. The hyaluronate lyase gene (hylA) has been described to be ubiquitous in S. pneumoniae. This gene has not been used so far as a target for the identification of S. pneumoniae. The aims of our study were to evaluate the specificity, sensitivity, positive predicted value (PPV) and negative predicted value (NPV) of the lytA and piaA qPCR methods; design and implement a new assay targeting the hylA gene and evaluate the same parameters above described; analyze the assays independently and the possible combinations to access what is the best approach using qPCR to identify S. pneumoniae. A total of 278 previously characterized strains were tested: 61 S. pseudopneumoniae, 37 Viridans group strains, 30 type strains from other streptococcal species and 150 S. pneumoniae strains. The collection included both carriage and disease isolates. By Mulilocus Sequence Analysis (MLSA) we confirmed that strains of S. pseudopneumoniae could be misidentified as S. pneumoniae when lytA qPCR assay is used. The results showed that as a single target, lytA had the best combination of specificity, sensitivity, PPV and NPV being, 98.5%, 100.0%, 98.7% and 100.0% respectively. The combination of targets with the best values of specificity, sensibility, PPV and NPV were lytA and piaA, with 100.0%, 93.3%, 97.9% and 92.6%, respectively. Nonetheless by MLSA we confirmed that strains of S. pseudopneumoniae could be misidentified as S. pneumoniae and some capsulated (23F, 6B and 11A) and non-capsulated S. pneumoniae were not Identified using this assay. The hylA gene as a single target had the lowest PPV. Nonetheless it was capable to correctly identify all S. pneumoniae.