# Bacteria Sediment

In sediment channel routing, the maximum concentration of sediment that can be transported by the water, $$conc\_{sed,ch,mx}$$, (ton/m$$^3$$ or kg/L) is compared to the concentration of sediment in the reach at the beginning of the time step, $$conc\_{sed,ch,i}$$ (Neitsch et al., 2005).

&#x20;              If $$conc\_{sed,ch,i}$$ < $$conc\_{sed,ch,mx}$$, resuspension is the dominant process in the reach segment and the net amount of sediment reentrained is calculated:

&#x20;              $$sed\_{deg}=(conc\_{sed,ch,mx}-conc\_{sed,ch,i})\*V\_{ch}\*K\_{ch}\*C\_{ch}$$               7:5.2.1

where $$sed\_{deg}$$ is the amount of sediment reentrained in the reach segment (metric tons), $$conc\_{sed,ch,mx}$$ is the maximum concentration of sediment that can be transported by the water (ton sediment/m$$^3$$ H$$\_2$$O or kg sediment/L H$$*2$$O), $$conc*{sed,ch,i}$$ is the initial sediment concentration in the reach (ton sediment/m$$^3$$ H$$*2$$O or kg sediment/L H$$*2$$O), $$V*{ch}$$ is the volume of water in the reach segment (m$$^3$$ H$$*2$$O), $$K*{ch}$$ is the channel erodibility factor (cm/hr/Pa), and $$C*{ch}$$ is the channel cover factor. When sediment resuspends, both bacteria in sediment solution and on sediment particles are released, and the net amount of bacteria released from streambed is calculated:

&#x20;                $$bact\_{deg}=sed\_{deg} \*conc\_{bact,sed}$$                                                           7:5.2.2

where $$bact\_{deg}$$ is the amount of bacteria released from streambed in the reach segment (# cfu), $$sed\_{deg}$$ is the amount of sediment reentrained in the reach segment (metric tons), and $$conc\_{bact,sed}$$ is the concentration of bacteria in streambed in the reach segment (# cfu/ton sediment). Bacteria concentration in streambed is calculated by the empirical regression equation, logarithmic sine function of the days of year:

&#x20;                $$log(conc\_{bact,sed})=bsc\_1*sin(bsc\_2*\frac{day-bsc\_3}{366}\*\pi)+bsc\_4$$            7:5.2.3

where $$conc\_{bact,sed}$$ is the concentration of bacteria in streambed (# cfu/ton sediment), *day* is the days of year, and $$bsc\_1$$ through $$bsc\_4$$ are the regression coefficients in streambed bacteria concentration equation.

&#x20;               If $$conc\_{sed,ch,i}$$ > $$conc\_{sed,ch,mx}$$, deposition is the dominant process in the reach segment and the net amount of sediment deposited is calculated:

&#x20;               $$sed\_{dep}=(conc\_{sed,ch,i}-conc\_{sed,ch,mx})\*V\_{ch}$$                                  7:5.2.4

where $$sed\_{dep}$$ is the amount of sediment deposited in the reach segment (metric tons), $$conc\_{sed,ch,i}$$ is the initial sediment concentration in the reach (ton sediment/m$$^3$$ H$$\_2$$O or kg sediment/L H$$*2$$O), $$conc*{sed,ch,mx}$$ is the maximum concentration of sediment that can be transported by the water (ton sediment/m$$^3$$ H$$\_2$$O or kg sediment/L H$$*2$$O), and $$V*{ch}$$is the volume of water in the reach segment (m$$^3$$ H$$\_2$$O). When suspended sediment deposits, bacteria on settling sediment particles are deposited, and the net amount of bacteria settled from stream water is calculated (Bai and Lung, 2005):

&#x20;             $$bact\_{dep}=bact\_{ch,i}*\frac{K\_p*sed\_{dep}}{V\_{ch}+K\_p\*(conc\_{sed,ch,i}\*V\_{ch})}$$                                         7:5.2.5

where  $$bact\_{dep}$$ is the amount of bacteria settled from stream water in the reach segment (# cfu), $$bact\_{ch,i}$$ is the amount of bacteria in the stream water in the reach segment at the beginning of the time period (# cfu), $$K\_p$$ is the linear partitioning coefficient of bacteria between the suspended sediment and water (m$$^3$$ H$$*2$$O/ton sediment or L H$$*2$$O/kg sediment), $$sed*{dep}$$ is the amount of sediment deposited in the reach segment (metric tons), $$V*{ch}$$ is the volume of water in the reach segment (m$$^3$$ H$$*2$$O), and $$conc*{sed,ch,i}$$ is the initial sediment concentration in the reach (ton sediment/m$$^3$$ H$$\_2$$O or kg sediment/L H$$\_2$$O). The linear partitioning coefficient is calculated from the empirical regression equation (Pachepsky et al., 2006):

&#x20;                  $$K\_p=10^{-1.6}\*clay^{1.98}$$                                                             7:5.2.6

where $$K\_p$$ is the linear partitioning coefficient of bacteria onto the suspended sediment (m$$^3$$ H$$\_2$$O/ton sediment or L H$$\_2$$O/kg sediment) and $$clay$$ is the percentage of clay in suspended sediment in stream water in the reach segment (%). *clay* normally varies between 2 and 50%.

&#x20;           Once the amount of bacteria released and settled has been calculated, the final amount of sediment in the reach is determined:

&#x20;             $$bact\_{ch}=bact\_{ch,i}+bact\_{deg}-bact\_{dep}$$                                     7:5.2.7

where $$bact\_{ch}$$ is the amount of bacteria in the stream water in the reach segment (# cfu), $$bact\_{ch,i}$$ is the amount of bacteria in the stream water in the reach segment at the beginning of the time period (# cfu), $$bact\_{deg}$$ is the amount of bacteria released from streambed in the reach segment (# cfu), and $$bact\_{dep}$$ is the amount of bacteria settled from stream water in the reach segment (# cfu).

&#x20;        The final bacteria concentration in the reach is calculated:

&#x20;               $$conc\_{bact,ch}=\frac{bact\_{ch}}{V\_{ch}}\*10^{-4}$$                                                    7:5.2.8

where $$conc\_{bact,ch}$$ is the concentration of bacteria in the stream water in the reach segment (# cfu/100 mL), $$bact\_{ch}$$ is the amount of bacteria in the stream water in the reach segment (# cfu), and $$V\_{ch}$$ is the volume of water in the reach segment (m$$^3$$ H$$\_2$$O).