Counting Resistance Genes at the Rushmill Plant

The Rushmill Water Reclamation Facility sits at the low end of town, where the sewers converge before the treated water returns to the Skelt River. Rushmill, its plant, and its river are fictional, and every figure below is invented for this passage. For thirty years the plant's laboratory tracked the same measurements: solids, oxygen demand, nitrogen, phosphorus, and bacteria. Two years ago the staff added a new one. They began counting genes.

The genes they count are resistance genes, stretches of DNA that let a bacterium survive a drug that would otherwise kill it. People and farm animals take antibiotics, and a share of every dose leaves the body unchanged, along with bacteria that have already survived it. A sewer collects that waste from a whole town and delivers it to one place. The plant did not create the problem, and it cannot avoid receiving it.

What makes these genes different from a chemical pollutant is that they can be copied and shared. Some resistance genes sit on the chromosome, the main loop of DNA a bacterium passes to its daughters. Others sit on a plasmid, a much smaller ring of DNA that a bacterium can copy and hand directly to a neighbor, sometimes to a neighbor of a different species. That handoff is called horizontal gene transfer, and it happens most readily where bacteria are crowded, warm, well fed, and in physical contact.

That description also fits the inside of an activated sludge basin. In the biological stage of the plant, billions of bacteria live packed into floating clumps for several hours, mixed with air and supplied with a steady meal. Those conditions are what make the process work, because the community consumes the organic matter and the ammonia that would otherwise reach the river. The same conditions give any plasmid an unusually good chance of moving. So the biological stage is both the plant's largest removal step and its most active site of exchange.

The Rushmill study sampled five points every month for a year: the raw influent, the water leaving secondary treatment, the final effluent after chlorine disinfection, the river a quarter mile above the outfall, and the river two miles below it. The laboratory used a method that counts copies of a target gene in a water sample. The method counts the gene, not the cell. A gene from a bacterium killed an hour earlier still counts, because the DNA remains in the water until something breaks it apart.

The pattern in the table surprised some of the staff. Between the influent and the secondary effluent, gene copies fell by more than a factor of a hundred, which is what the plant is built to do: it grows bacteria, then settles them out as sludge and removes them from the water. Between the secondary effluent and the final effluent, living bacteria dropped by hundreds of times, yet gene copies barely moved. Chlorine is very good at killing cells and much less effective at destroying the DNA inside them. Downstream of the outfall, gene copies were higher than upstream, though far below what the plant received, and repeat sampling farther down the river showed the counts falling with distance as sunlight, dilution, and other organisms broke the free DNA apart.

The results put a choice in front of the utility. Ozone breaks chemical bonds, including bonds in DNA, and a plant that adds an ozone stage would lower the gene count as well as the cell count. So would a membrane, which physically strains out cells and much of the material around them. Both cost money to build and energy to run, and neither is required, because no regulation currently sets a limit for resistance genes in effluent. A different approach starts upstream. A medicine take-back program, prescribing guidelines at the town's clinics, and rules for the two farms on the edge of the sewer district would reduce what arrives at the plant in the first place.

At the town meeting the plant's laboratory director summarized what the study meant. The genes arrive in the sewer from the town's households, clinics, and farms rather than forming in the treatment process, she said, so the plant is not their source. It is the place where the town can measure what it has been sending and decide what to do about it.

1. According to the passage, what is a plasmid?
2. Name the five points where the Rushmill study collected its samples.
3. Using the table, describe what happened to gene copies and to living bacteria between the secondary effluent and the final effluent, and explain why the two changed so differently.
4. The passage calls the activated sludge basin both the plant's largest removal step and its most active site of exchange. Explain how both statements can be true.
5. The table shows more gene copies in the river below the outfall than above it, and the passage says counts fall farther downstream. Give one explanation the passage supports for that decline.
6. Explain the difference between killing a bacterium and removing its resistance gene from the water, and say why that difference matters when a utility chooses a treatment step.
7. The utility can fund an ozone stage or a medicine take-back program, but not both this year. Using the passage and the table, give one advantage of each choice.