## 1 Introduction  
Southwest China hosts the world's largest exposed karst region, where karst water resources, totaling 2039.67 \(\times\) 10\({}^{4}\) m\({}^{3}\)/year, comprise 23.39% of the nation's groundwater [1]. However, challenges such as high population density, uneven spatial and temporal distribution of these resources, intricate storage and burial dynamics, and significant pollution reduce per capita water availability [2, 3]. Karst areas, characterized by rocky desertification, present a complex and diverse range of underground water pollution. This leads to a highly sensitive and vulnerable groundwater system, which is particularly susceptible to pathogen-microbiota pollution [4, 5]. Research indicates that pathogen-microbiota indicators in groundwater are not merely detrimental to human health but also potentially harbor or transmit other harmful microbes. These indicators serve as proxies for microbial virusesposing threats to human health [6; 7; 8; 9]. Consequently, investigating the response changes of pathogen-microbiota indicators in groundwater within rocky desertification areas holds substantial theoretical and practical significance. The soil-water matrix environment plays a pivotal role in exploring the response mechanisms of groundwater to pathogen-microbiota pollution. The sequence of interactions, spanning from groundwater contamination through infiltration to microbial pollution, culminates in the response of pathogen toxicology indicators. This sequence is intimately linked with the evolutionary processes of microbes [4; 5]. Soil, as a three-phase porous medium, exhibits substantial purification capabilities attributed to its unique structure and the presence of mineral ions. Within this porous matrix environment, the evolution and migration of groundwater microbes are influenced by the soil's self-purification capacities, which play a crucial role in retaining microbes, thereby substantially diminishing the microbial content that enters the groundwater [10; 11]. The factors affecting microbial evolution in soil solid porous media can be classified into three categories: microbial factors, soil medium factors, and soil environmental factors [12; 13]. Microbial factors encompass the microbe type, strain size, surface charge, hydrophobicity, and chemotactic nature of the community. The surface charge of microbes significantly influences their adsorption within the soil-water matrix environment [14]. Moreover, their migration and attenuation are associated with factors such as microbial type [8; 15; 16; 17], surface hydrophobicity [18], individual size [19], community chemotaxis [12; 20], and population heterogeneity [21; 22]. Soil medium factors encompass soil particle size, pore structure, moisture content, mineral composition, and overall content. The dynamics of solute movement in the soil-water matrix environment adhere to mechanisms such as interception, leaching, and physicochemical filtration, as delineated in previous studies [23; 24]. The ionic content of clay minerals demonstrates pronounced adsorption [25; 26] and desorption [27; 28] effects on microbes. Microbial mobility is enhanced in larger pores [29; 30]. An increase in moisture content correlates with greater microbial retention [29; 31], and smaller effective particle sizes are associated with higher microbial retention [32; 33; 34]. Soil environmental factors encompass pH, temperature, flow rate, and ionic strength. Within certain limits, elevated temperatures enhance the activity of microbial pathogens [35; 36]. The migration capacity of microbes notably increases with the environmental pH [11; 13]. Enhanced hydrodynamic conditions facilitate microbial migration capacity while diminishing retention effects [32; 36]. An increased ion concentration amplifies microbial migration and penetration capabilities [37; 38]. However, molecular diffusion effects are generally inconsequential in most microbial transport processes [39; 40].