Ecology of Novel Nitrite-Oxidizers in the Phylum Chloroflexi

Bacteria in waste water who would want to stick their noses into that topic? Most will turn their heads, but Austrian scientists Dr. Anne Daebeler and Assoc.-Prof Holger Daims from the University of Vienna loose their appetite. Quite the contrary, and their scientific hunger for more knowledge about the bacteria that drive waste water treatment processes has very recently lead to a surprising discovery. Chloroflexi bacteria, which have so far mostly been seen in the context of operational disturbances in waste water plants, participate in an important part of the water cleaning process. They are capable of converting toxic nitrite to nitrate by oxidation. This conversion is a crucial milestone in waste water treatment, because only the product nitrate can be removed from the water by other bacteria. As a consequence of this exciting discovery, the role of Chloroflexi bacteria in waste water treatment plants and other environments has to be reconsidered. The project Ecoflex Understanding the Ecology of Newly Discovered Nitrite-Oxidizing Bacteria in the Phylum Chloroflexi aims to answer pressing questions about their ecological life style. Such answers are necessary to correctly evaluate the function of the newly discovered Chloroflexi bacteria in order to use it to its full potential. So far, nothing is known about the best conditions for nitrite oxidation by the new Chloroflexi bacteria for example. However, Daebeler and Daims expect the right amounts of oxygen and nitrite, but also temperature to be essential. Their experiments with waste water sludge in the laboratory under strictly regulated circumstances, but also a search for the new bacteria in various waste water treatment plants and natural environments will deliver the first answers. Another line of research will employ ways of cultivation and genomic analysis. Here, the Austrian scientists will especially focus on potential metabolic processes and the comparison to known nitrite oxidizers. The combination of these research lines has the potential to deliver holistic answers that will not only reveal the relationship of the new bacteria with their surroundings but also convey explanations.

Nitrification, the oxidation of ammonia to nitrate, is a key process of the nitrogen cycle in nature. Moreover, it is important for biological wastewater treatment and drinking water treatment, but on the other hand causes massive loss of nitrogen from fertilized arable soils. Nitrification is a two-step process: ammonia is oxidized by ammonia-oxidizing microorganisms to nitrite, which is further transformed to nitrate by nitrite-oxidizing bacteria. Little is known about the biology of nitrifiers, because only very few species can be cultured in the laboratory. In this project, we used cultivation-independent molecular biological methods detecting nitrifiers directly in environmental samples next to classical cultivation-based experiments. Their use led to the discovery of a hitherto unknown, ammonia-oxidizing archaeon in Icelandic hot springs and a nitrite-oxidizing bacterium that is able to withstand uncommonly high pH levels from a saline-alkaline lake in the Austrian national park Neusiedler See-Seewinkel. With these new cultures in hand we were able to discover unexpected features about their metabolic functions and adaptive mechanisms to their extreme habitats. We were further surprised to reveal that other nitrite-oxidizing bacteria and comammox of the genus Nitrospira exist that are adapted to a high salinity and pH values up to 11. A combination of genome analyses with laboratory experiments revealed that Nitrospira moscoviensis, a model organism for the most wide-spread nitrite-oxidizers in nature, is capable of consuming atmospheric concentrations of hydrogen for energy generation. So far, scientists assumed that nitrifiers would be specialized microorgansims which show a very limited set of other activities. This project has demonstrated that nitrifiers are adapted to diverse environmental conditions and have unexpected ecological functions. This knowledge is important for a better understanding of the nitrogen cycle and can help optimize the efficiency of fertilization, wastewater treatment, and drinking water preparation.