A portion of the bacteria on plant foliage may be washed off during rain events. The fraction washed off is a function of plant morphology, bacteria characteristics, and the timing and intensity of the rainfall event. Wash-off will occur when the amount of precipitation on a given day exceeds 2.54 mm.

The amount of bacteria washing off plant foliage during a precipitation event on a given day is calculated:

$bact_{lp,wsh}=fr_{wsh,lp}*bact_{lp,fol}$ 3:4.1.1

$bact_{p,wsh}=fr_{wsh,p}*bact_{p,fol}$ 3:4.1.2

where $bact_{lp,wsh}$ is the amount of less persistent bacteria on foliage that is washed off the plant and onto the soil surface on a given day (# cfu/m$^2$), $bact_{p,wsh}$ is the amount of persistent bacteria on foliage that is washed off the plant and onto the soil surface on a given day (# cfu/m$^2$), $fr_{wsh,lp}$ is the wash-off fraction for the less persistent bacteria, $fr_{wsh,p}$ is the wash-off fraction for the persistent bacteria, $bact_{lp,fol}$ is the amount of less persistent bacteria attached to the foliage (# cfu/m$^2$), and $bact_{p,fol}$ is the amount of persistent bacteria attached to the foliage (# cfu/m$^2$). The wash-off fraction represents the portion of the bacteria on the foliage that is dislodgable.

Bacteria that washes off the foliage is assumed to remain in solution in the soil surface layer.

Table 3:4-1: SWAT+ input variables that pertain to bacteria wash-off.

Contamination of drinking water by pathogenic organisms is a major environmental concern. Similar to water pollution by excess nutrients, water pollution by microbial pathogens can also be caused by point and nonpoint sources. Point source water contamination normally results from a direct entry of wastewater from municipal or water treatment systems into a drinking water supply. Nonpoint sources of bacterial pollution can be difficult to identify as they can originate from animal production units, land application of different manure types, and wildlife.

Although there are many potential sources of pathogenic loadings to streams, agronomic practices that utilize animal manures contaminated with pathogenic or parasitic organisms appear to be the major source of nonpoint contamination in watersheds. In recent years, a concentration of animal feeding operations has occurred in the cattle, swine and poultry production industries. These operations generate substantial amounts of animal manure that are normally applied raw to relatively limited land areas. Even though animal manure can be considered a beneficial fertilizer and soil amendment, high rates of land applied raw manure increase the risk of surface or groundwater contamination, both from excess nutrients and pathogenic organisms such as Cryptosporidium, Salmonella, or Escherichia coli 0157:H7.

Fecal coliforms (generic forms of bacteria) have customarily been used as indicators of potential pathogen contamination for both monitoring and modeling purposes (Baudart et al., 2000; Hunter et al., 2000; Pasquarell and Boyer, 1995; Walker et al., 1990; Stoddard et al., 1998; Moore et al., 1988). However, recent studies have documented waterborne disease outbreaks caused by Cryptosporidium, Norwalk and hepatitis A viruses, and salmonella despite acceptably low levels of indicator bacteria (Field et al, 1996).

SWAT+ considers fecal coliform an indicator of pathogenic organism contamination. However, to account for the presence of serious pathogens that may follow different growth/die-off patterns, SWAT+ allows two species or strains of pathogens with distinctly different die-off/re-growth rates to be defined. The two-population modeling approach is used to account for the long-term impacts of persistent bacteria applied to soils, whose population density when initially applied may be insignificant compared to that of less persistent bacteria.

One or two bacteria populations may be introduced into an HRU through one of the three types of fertilizer applications reviewed in Chapter 6:1. When bacteria in manure are applied to an HRU, some fraction is intercepted by plant foliage with the remainder reaching the soil. SWAT+ monitors the two bacteria populations on foliage and in the top 10 mm of soil that interacts with surface runoff. Bacteria in the surface soil layer may be in solution or associated with the solid phase. Bacteria incorporated deeper into the soil through tillage or transport with percolating water is assumed to die.

Chick’s Law first order decay equation is used to determine the quantity of bacteria removed from the system through die-off and added to the system by regrowth. The equation for die-off/re-growth was taken from Reddy et al. (1981) as modified by Crane and Moore (1986) and later by Moore et al. (1989). The equation was modified in SWAT+ to include a user-defined minimum daily loss. Die-off/re-growth is modeled for the two bacteria populations on foliage, in the surface soil solution and sorbed to surface soil particles. The equations used to calculate daily bacteria levels in the different pools are:

$bact_{lpfol,i}=bact_{lpfol,i-1}*exp(-\mu _{lpfol,net})-bact_{min,lp}$ 3:4.2.1

$bact_{pfol,i}=bact_{pfol,i-1}*exp(-\mu _{pfol,net})-bact_{min,p}$ 3:4.2.2

$bact_{lpsol,i}=bact_{lpsol,i-1}*exp(-\mu _{lpsol,net})-bact_{min,lp}$ 3:4.2.3

$bact_{psol,i}=bact_{psol,i-1}*exp(-\mu _{psol,net})-bact_{min,p}$ 3:4.2.4

$bact_{lpsorb,i}=bact_{lpsord,i-1}*exp(-\mu _{lpsorb,net})-bact_{min,lp}$ 3:4.2.5

$bact_{psorb,i}=bact_{psorb,i-1}*exp(-\mu _{psorb,net})-bact_{min,p}$ 3:4.2.6

where $bact_{lpfol,i}$ is the amount of less persistent bacteria present on foliage on day $i$ (#cfu/m$^2$), $bact_{lpfol,i-1}$ is the amount of less persistent bacteria present on foliage on day $i-1$ (#cfu/m$^2$), $\mu _{lpfol,net}$ is the overall rate constant for die-off/re-growth of less persistent bacteria on foliage (1/day), $bact_{min,lp}$ is the minimum daily loss of less persistent bacteria (#cfu/m$^2$), $bact_{pfol,i}$ is the amount of persistent bacteria present on foliage on day $i$ (#cfu/m$^2$), $bact_{pfol,i-1}$ is the amount of persistent bacteria present on foliage on day $i-1$(#cfu/m$^2$), $\mu_{pfol,net}$ is the overall rate constant for die-off/re-growth of persistent bacteria on foliage (1/day), $bact_{min,p}$ is the minimum daily loss of persistent bacteria (#cfu/m$^2$), $bact_{lpsol,i}$ is the amount of less persistent bacteria present in soil solution on day $i$ (#cfu/m$^2$), $bact_{lpsol,i-1}$ is the amount of less persistent bacteria present in soil solution on day $i-1$ (#cfu/m$^2$), $\mu_{lpsol,net}$ is the overall rate constant for die-off/re-growth of less persistent bacteria in soil solution (1/day), $bact_{psol,i}$ is the amount of persistent bacteria present in soil solution on day $i$ (#cfu/m$^2$), $bact_{psol,i-1}$ is the amount of persistent bacteria present in soil solution on day $i-1$(#cfu/m$^2$), $\mu_{psol,net}$ is the overall rate constant for die-off/re-growth of persistent bacteria in soil solution (1/day), $bact_{lpsorb,i}$ is the amount of less persistent bacteria sorbed to the soil on day $i$ (#cfu/m$^2$), $bact_{lpsorb,i-1}$ is the amount of less persistent bacteria sorbed to the soil on day $i-1$ (#cfu/m$^2$), $\mu _{lpsorb,net}$ is the overall rate constant for die-off/re-growth of less persistent bacteria sorbed to the soil (1/day), $bact_{psorb,i}$ is the amount of persistent bacteria sorbed to the soil on day $i$ (#cfu/m$^2$), $bact_{psorb,i-1}$ is the amount of persistent bacteria sorbed to the soil on day $i-1$ (#cfu/m$^2$), and $\mu_{psorb,net}$ is the overall rate constant for die-off/re-growth of persistent bacteria sorbed to the soil (1/day).

The overall rate constants define the net change in bacterial population for the different pools modeled. The impact of temperature effects on bacteria die-off/re-growth were accounted for using equations proposed by Mancini (1978). The user defines the die-off and growth factors for the two bacterial populations in the different pools at 20°C. The overall rate constants at 20°C are then calculated:

$\mu_{lpfol,net,20}=\mu_{lpfol,die,20}-\mu_{lpfol,grw,20}$ 3:4.2.7

$\mu_{pfol,net,20}=\mu_{pfol,die,20}-\mu_{pfol,grw,20}$ 3:4.2.8

$\mu_{lpsol,net,20}=\mu_{lpsol,die,20}-\mu_{lpsol,grw,20}$ 3:4.2.9

$\mu_{psol,net,20}=\mu_{psol,die,20}-\mu_{psol,grw,20}$ 3:4.2.10

$\mu_{lpsorb,net,20}=\mu_{lpsorb,die,20}-\mu_{lpsorb,grw,20}$ 3:4.2.11

$\mu_{psorb,net,20}=\mu_{psorb,die,20}-\mu_{psorb,grw,20}$ 3:4.2.12

where $\mu_{lpfol,net,20}$ is the overall rate constant for die-off/re-growth of less persistent bacteria on foliage at 20°C (1/day), $\mu_{lpfol,die,20}$ is the rate constant for die-off of less persistent bacteria on foliage at 20°C (1/day), $\mu_{lpfol,grw,20}$ is the rate constant for re-growth of less persistent bacteria on foliage at 20°C (1/day), $\mu_{pfol,net,20}$ is the overall rate constant for die-off/re-growth of persistent bacteria on foliage at 20°C (1/day), $\mu_{pfol,die,20}$ is the rate constant for die-off of persistent bacteria on foliage at 20°C (1/day), $\mu_{pfol,grw,20}$ is the rate constant for re-growth of persistent bacteria on foliage at 20°C (1/day), $\mu_{lpsol,net,20}$ is the overall rate constant for die-off/re-growth of less persistent bacteria in soil solution at 20°C (1/day), $\mu_{lpsol,die,20}$ is the rate constant for die-off of less persistent bacteria in soil solution at 20°C (1/day), $\mu_{lpsol,grw,20}$ is the rate constant for re-growth of less persistent bacteria in soil solution at 20°C (1/day), $\mu_{psol,net,20}$ is the overall rate constant for die-off/re-growth of persistent bacteria in soil solution at 20°C (1/day), $\mu_{psol,die,20}$ is the rate constant for die-off of persistent bacteria in soil solution at 20°C (1/day), $\mu_{psol,grw,20}$ is the rate constant for re-growth of persistent bacteria in soil solution at 20°C (1/day), $\mu_{lpsorb,net,20}$ is the overall rate constant for die-off/re-growth of less persistent bacteria attached to soil particles at 20°C (1/day), $\mu_{lpsorb,die,20}$ is the rate constant for die-off of less persistent bacteria attached to soil particles at 20°C (1/day), $\mu_{lpsorb,grw,20}$ is the rate constant for re-growth of less persistent bacteria attached to soil particles at 20°C (1/day), $\mu_{psorb,net,20}$ is the overall rate constant for die-off/re-growth of persistent bacteria attached to soil particles at 20°C (1/day), $\mu_{psorb,die,20}$ is the rate constant for die-off of persistent bacteria attached to soil particles at 20°C (1/day), and $\mu_{psorb,grw,20}$ is the rate constant for re-growth of persistent bacteria attached to soil particles at 20°C (1/day).

The overall rate constants are adjusted for temperature using the equations:

$\mu_{lpfol,net}=\mu_{lpfol,net,20}*\theta_{bact}^{(\overline T_{av}-20)}$ 3:4.2.13

$\mu_{pfol,net}=\mu_{pfol,net,20}*\theta_{bact}^{(\overline T_{av}-20)}$ 3:4.2.14

$\mu_{lpsol,net}=\mu_{lpsol,net,20}*\theta_{bact}^{(\overline T_{av}-20)}$ 3:4.2.15

$\mu_{psol,net}=\mu_{psol,net,20}*\theta_{bact}^{(\overline T_{av}-20)}$ 3:4.2.16

$\mu_{lpsorb,net}=\mu_{lpsorb,net,20}*\theta_{bact}^{(\overline T_{av}-20)}$ 3:4.2.17

$\mu_{psorb,net}=\mu_{psorb,net,20}*\theta_{bact}^{(\overline T_{av}-20)}$ 3:4.2.18

where $\theta_{bact}$ is the temperature adjustment factor for bacteria die-off/re-growth, $\overline T_{av}$ is the mean daily air temperature, and all other terms are as previously defined.

Table 3:4-2: SWAT+ input variables that pertain to bacteria die-off/re-growth.

Bacteria can be transported with percolation into the soil profile. Only bacteria present in the soil solution is susceptible to leaching. Bacteria removed from the surface soil layer by leaching are assumed to die in the deeper soil layers.

The amount of bacteria transported from the top 10 mm into the first soil layer is:

$bact_{lp,perc}=\frac{bact_{lpsol}*w_{perc,surf}}{10*\rho_b*depth_{surf}*k_{bact,perc}}$ 3:4.3.1

$bact_{p,perc}=\frac{bact_{psol}*w_{perc,surf}}{10*\rho_b*depth_{surf}*k_{bact,perc}}$ 3:4.3.2

where $bact_{lp,perc}$ is the amount of less persistent bacteria transported from the top 10 mm into the first soil layer (#cfu/m$^2$), $bact_{lpsol}$ is the amount of less persistent bacteria present in soil solution (#cfu/m$^2$), $w_{perc,surf}$ is the amount of water percolating to the first soil layer from the top 10 mm on a given day (mm H$_2$O), $\rho_b$ is the bulk density of the top 10 mm (Mg/m$^3$) (assumed to be equivalent to bulk density of first soil layer), $depth_{surf}$ is the depth of the “surface” layer (10 mm), $k_{bact,perc}$ is the bacteria percolation coefficient (10 m$^3$/Mg), $bact_{p,perc}$ is the amount of persistent bacteria transported from the top 10 mm into the first soil layer (#cfu/m$^2$), and $bact_{psol}$ is the amount of persistent bacteria present in soil solution (#cfu/m$^2$).

Table 3:4-3: SWAT+ input variables that pertain to bacteria transport in percolate.