Microbial ‘blueprint’ may unlock mysteries of wastewater treatment

A University of Wisconsin–Madison environmental engineer and her graduate student are among researchers on a multi-institutional team who have mapped the metagenome of elusive phosphorous-eating organisms key to thousands of wastewater treatment processes in the developed world.

A genomic blueprint of many organisms within the bacterial species Accumulibacter phosphatis, this metagenome will help researchers learn more about the underlying microbiology of an environmentally friendly wastewater treatment process known as enhanced biological phosphorous removal (EBPR). Increased biochemical understanding of the organism, which for decades scientists have been unable to culture in the laboratory, may enable engineers to optimize wastewater treatment systems.

The researchers published their findings in the Sept. 24 online early edition of the journal Nature Biotechnology.

Scientists’ current understanding of EBPR is based only on empirical evidence, says Katherine McMahon, a UW–Madison assistant professor of civil and environmental engineering who is among the study’s co-authors. “From an engineering perspective, we know how to make the bacteria remove phosphorous from wastewater, but we don’t understand why or how they do it,” she says.

On the surface, the organisms within the A. phosphatis species look like average lake bacteria, yet their physiology is bizarre, she says. Subjected to biphasic conditions in a wastewater treatment plant, the organisms clean sewage by gorging themselves on phosphorous, releasing it, gorging themselves on carbon, extracting energy from it and repeating the process over and over.

Using enriched sludge samples from laboratory-scale bioreactors, seeded from wastewater treatment plants in Madison and Brisbane, Australia, researchers at the Department of Energy Joint Genome Institute in California spent a year and a half mapping the metagenome of different Accumulibacter genera, species and strains.

Among their findings, the researchers discovered that A. phosphatis has a set of genes that would enable it to live in fresh water. They learned the organism can make a novel protein that helps it expel electrons – a finding that may help them understand how A. phosphatis captures energy from its food. They also uncovered clues, including the organism’s ability to fix nitrogen and its dependence on cobalt, that may point to ways researchers can culture A. phosphatis in the laboratory.

Now the group is conducting follow-up experiments using metaproteomics. A new technique not feasible without the metagenome sequence, metaproteomics enables them to study protein content of the entire sludge community. “We want to see, at the level of protein expression, what happens if the organisms don’t have enough food, for example,” says McMahon.

This lack of food can occur when storms overload wastewater treatment plants, releasing phosphorous into the environment and polluting lakes and rivers, she says.

In addition, the researchers are studying each gene in the pathways responsible for phosphorous uptake and storage, as well as how genes turn on or off based on an environmental stimulus like oxygen or oxygen depletion. That knowledge is key, says McMahon, to designing more efficient wastewater treatment processes.

“Engineers have control over the oxygen concentration or the amount of food the bacteria are given, but we do not currently understand how these things impact bacterial gene expression,” she says. “With understanding on a biochemical level, engineers can optimize the process more rationally.”

Other co-authors of the research paper include scientists from the Advanced Wastewater Management Group at the University of Queensland, Australia.