Quantitative microbial dynamics under climatic stress within the dairy sector

Abstract

The dairy industry is a major contributor to global pollution, with waste disposal negatively impacting ecosystems. It is also known that seasonality affects milk composition and, thus, dairy waste’s microbial quality. However, the impact of climate change on the dairy sector remains unknown. As carbon dioxide levels are expected to rise over the next century, it is crucial to understand the effects of climate change on milk properties and the environmental safety of dairy waste. This dissertation explored the intricate interplay between climate change, the dairy industry, and microbial dynamics. This research employed a multidisciplinary approach, incorporating climatic variables, raw milk quality parameters, microbial responses, and predictive modelling to address the environmental issues facing the dairy sector. Initially, this research assessed the impact of historical climatic conditions on the quality of raw milk, emphasising on the need for a comprehensive understanding of the different farming feeding practices. Recognising the potential risks associated with the microbial contamination and climate change, the research then delved into characterising the effects of environmental stress on the predominant faecal microorganism, i.e., Escherichia coli, focusing on key genes involved in general stress tolerance. Furthermore, the current research introduced a novel spectrophotometric method for estimating pH and dissolved carbon dioxide in various solutions, providing robust estimations under different climatic conditions. The investigation was extended to the growth dynamics of Escherichia coli under varying climatic conditions, developing a predictive model for Escherichia coli growth using temperature and carbon dioxide levels as parameters. RNA sequencing was employed to unravel the genetic and metabolic responses of Escherichia coli to environmental stress, aiming at unravelling the complex adaptive mechanisms activated under climatic changes. Results showed that temperature and solar radiation negatively correlated with raw milk fat, protein, and dry lean percentages. The average environmental temperature had a weakly positive association with the somatic cell levels, while the total bacteria counts were strongly negatively correlated with the global environmental carbon dioxide. This research highlighted the benefits of a diet in order to meet animal nutritional needs that can potentially enhance metabolic tolerance to climate change. Hereafter, a colourimetric method was developed to quantify the concentration of the critical parameter of carbon dioxide in terms of its dissolved concentration in aqueous systems, including dairy waste. This allowed the accurate correlation between environmental conditions and the growth responses of the microbial indicator of Escherichia coli BL21 (DE3) in different simulated culture media. Escherichia coli growth decreased at 42oC and rose at 27oC as dissolved carbon dioxide increased. Moreover, an analysis of the molecular mechanisms has shown that Escherichia coli adapts under high temperatures through various metabolic pathways, while it engages bacterial tolerance to environmental stress at low temperatures and high carbon dioxide levels. In summary, this research has shown that complex genetic and metabolic activities are activated when both temperatures and carbon dioxide levels are combined, affecting antimicrobial resistance, nutrient acquisition, and adaptation strategies, with temperature having a more significant impact on gene expression than carbon dioxide levels. Overall, the current research, which was part of the PROTECT Innovative Training Networks (ITN- Marie Skłodowska), concluded by emphasising the need for adaptive methodologies in dairy waste management, calling for continuous research, proactive strategies, and interdisciplinary collaborations. Recommendations include adopting environmental monitoring and agricultural technologies, sustainable dietary practices, and climate responsive waste management strategies. The dairy industry and policymakers can consider the outcomes of this Thesis to assess the impact of climate change on the dairy industry and develop new intervention strategies to manage resilience in milk production under different climate change scenarios.