5 Transport of Microbes in Groundwater

Microorganisms in groundwater systems can be classified based on their origin and degree of isolation from surface environments. Autochthonous microbes are those that are permanent long-term subsurface residents, whereas allochthonous species come from other environments such as surface waters or the soil zone. The physical isolation and adaptation of autochthonous microorganisms to life underground is a stark example of allopatric (non-overlapping) speciation and evolution over long periods of time, perhaps billions of years in the case of some deep groundwater environments (> 1000 m depth; Magnabosco et al., 2018). Allochthonous microorganisms are transported into the subsurface most often with recharge through downward surface water percolation. Over time, allochthonous microorganisms may become part of the autochthonous microbial community as they adapt to living conditions underground.

In groundwater systems, free-floating planktonic microorganisms undergo advective transport as suspended particulate species that move along with the pore water. Their transport velocity is governed by the hydraulic pressure gradient, porosity, and permeability distribution in accordance with Darcy’s law. Groundwater transport of microorganisms is also subject to the effects of diffusion and hydrodynamic dispersion. The movement of dissolved nutrients and electron acceptors are coupled to the same processes, which are described by the advection-dispersion equation (Equation 37) for the rate of mass transport (Brun and Engesgaard, 2002; Steefel et al., 2005; Tufenkji, 2007).

\displaystyle \frac{\partial C}{\partial t}=\left [ D_{x}\frac{\partial ^{2}C}{\partial x^{2}}+D_{y}\frac{\partial ^{2}C}{\partial y^{2}}+D_{z}\frac{\partial ^{2}C}{\partial z^{2}} \right ] \displaystyle -\left [ v_{x}\frac{\partial C}{\partial x}+v_{y}\frac{\partial C}{\partial y}+v_{z}\frac{\partial C}{\partial z} \right ] (37)


x, y, z = principle directions of transport in three dimensions (L)
C = concentration of dissolved solute or suspended particulate (M/L3)
D = hydrodynamic dispersion coefficients (L2/T)
v = average linear velocity (L/T)
t = time (T)

Microorganisms are subject to a transport phenomenon known as size exclusion. When this happens, transported suspended particles appear to move faster and experience less dispersion than conservative (non-reacting) solutes. Size exclusion in the transport of microorganisms is evident in breakthrough curves from a smaller range of normalized concentrations (C/C0) and shorter retention times of microbes compared to a dissolved tracer (Figure 19). Field experiments indicate microbial cells may be transported at velocities as much as 70 percent greater than the average linear velocity of pore water.

Graphs showing breakthrough curves of normalized concentrations over time.

Figure 19 Breakthrough curves of normalized concentrations over time: a) after a slug injection and: b) during continuous injection (right) of a bacterial suspension with a dissolved tracer.

The reason for faster transport of microorganisms as a result of size exclusion relates to the hyperbolic distribution of water velocities inside pores. Maximum velocity occurs along the centerline, whereas friction and other forces reduce water velocity at the pore walls to zero. On the molecular scale of dissolved solutes, the full distribution of water velocities is sampled in transport processes. Conversely, by virtue of their larger size, microbes and other suspended particulates experience higher velocities near the centerline of pores, leading to an average velocity that is faster than that of a dissolved tracer.

The removal of suspended bacteria from groundwater is mediated by straining and filtration processes. Straining involves the trapping of microorganisms in pore throats or facture apertures that are too small to allow passage. This process is a not only a function of porosity but also depends on pore geometry and the tortuosity of groundwater flow paths. Physical filtration refers to the removal of suspended bacteria from groundwater by collision and deposition on pore wall surfaces. The probability of resuspension after filtration depends on the interplay between hydrodynamic shear and adhesive interfacial forces (sorption affinity). After deposition, microbial cells may secrete large amounts of EPS to increase adherence and initiate biofilm formation.

As suspended bacterial cells are transported in groundwater, they can sorb dissolved substances from solution and carry them along, in effect masquerading as particulate solids. This piggyback process is known as facilitated transport. If the sorbed chemical species happens to come from a point source such as a contaminant spill, size exclusion processes in bacterial transport may decrease the time and increase the distance over which a contaminant moves. In the same way, facilitated transport has considerable potential to aid in the transfer of nutrients from a nutrient-rich area to a nutrient-poor area, thereby stimulating microbial activity over longer groundwater flow paths.

A significant fraction of waterborne disease worldwide is caused by the introduction and transport of allochthonous pathogenic microorganisms (protozoa, bacteria, viruses) in groundwater systems. Many, if not most, of the microbial pathogens in groundwater are contaminants derived from human and animal fecal waste. Primary sources of these disease-causing microbes include failed septic tanks, seepage from waste lagoons, leaky sewer lines, and old or improperly sealed landfills (Macler and Merkle, 2000). Shallow unconfined aquifers are particularly at risk because of their closer proximity to surface sources of microbial contamination (Jin and Flury, 2002; Pandey et al., 2014).

The large size of pathogenic protozoa such as Giardia and Cryptosporidium is a feature that contributes to straining, which limits transport to short distances through groundwater systems (Figure 20). For this reason, the presence of protozoa in deeper aquifers implies a direct introduction of surface water from downward flow through fractured rock or karst with limited unconsolidated overlying soil layers (Jin and Flury, 2002). On the other hand, smaller microbial pathogens such as bacteria and viruses are more likely to experience size exclusion and be transported over greater distances in groundwater than protozoa (Figure 20; Taylor et al., 2004; Tufenkji, 2007).

Straining, filtration, and size exclusion processes emphasize the importance of considering the nature and relative pore space of geological media when evaluating the fate and transport of pathogens and the vulnerability of groundwater. Additional factors such as solution chemistry, virus and cell surface characteristics, soil properties, and temperature influence the survival, transport, and sorption of microbial pathogens in porous media (Jin and Flury, 2002; United States Environmental Protection Agency [USEPA], 2002; Pang et al., 2004). These considerations are particularly relevant when assessing the setback distance of septic tanks from source water wells and shorelines. More information regarding management of septic systems to prevent contamination of groundwater is available on the USEPA website and from Pang et al. (2004).

Figure showing examples of microbial pathogens found in surface and groundwater that are of concern for human and ecological health.

Figure 20 – Examples of microbial pathogens found in surface and groundwater that are of concern for human and ecological health. Because of their large size and susceptibility to straining, protozoa are general indicators of surface water contamination. Alternatively, smaller bacteria and viruses can be transported to groundwater (McKay et al., 1993; Taylor et al., 2004). The presence of microbial pathogens in groundwater is often inferred by the detection of fecal indicator bacteria including total coliform bacteria, Escherichia coli, Enterococci, and coliphage (viruses infecting coliform bacteria). These indicator microorganisms, similar to other pathogens, generally do not grow outside their natural environments in groundwater. Their ability to survive in groundwater environments is limited by conditions such as temperature, competition with other bacteria, predation by other organisms, and entrapment in pore spaces (Macler and Merkle, 2000; Jin and Flury, 2002). Therefore, finding fecal indicator bacteria in groundwater in measurable numbers means there is an increased likelihood of pathogens being present as well.


Groundwater Microbiology Copyright © 2021 by F. Grant Ferris, Natalie Szponar, and Brock A. Edwards. All Rights Reserved.