A fundamental shift in our understanding – scientists unravel the global nitrogen mystery

A study led by the University of Oklahoma advances scientific understanding of ammonia oxidation.

Assistant Professor Wei Qin of the University of Oklahoma led new research that fundamentally changes the understanding of ammonia oxidation, a key component of the global nitrogen cycle. The study was recently published in the journal Natural Microbiology.

Ammonia-oxidizing microbes, commonly known as AOM, use ammonia for energy and are responsible for the annual oxidation of about 2.3 trillion kilograms of nitrogen in soil, freshwater, subsurface, and man-made ecosystems. A major question that has remained unanswered for decades is how the different lineages of AOM species Living in the same environment: do they compete for ammonia or do they instead use other alternative compounds for their energy needs?

„Different lineages of AOM were growing simultaneously in the same environment and were thought to compete primarily for ammonia,” said Qin. „Our collaborative research focused on determining why and how these metabolically conserved lineages can coexist without direct competition for inorganic nitrogen (ammonia), and we examined their abilities to use organic nitrogen (urea) instead.”

Role of urea in AOM diversity and coexistence

More than half of AOM species have adapted to use urea, a widely available organic nitrogen compound that accounts for approximately 40 percent of all nitrogen in fertilizers, as an alternative energy source. However, this process requires AOM to use additional energy because urea is a very complex molecular structure and must first be broken down into ammonia inside AOM cells before use. Knowing this, Kin's team sought to understand how AOM acquires and metabolizes ammonia and urea when both are available simultaneously.

„We've always called urea an alternative substrate for ammonia,” Kin said. „Now, we realize that the main lineage of AOM actually prefers urea and suppresses ammonia utilization when urea is present. This discovery challenges dominant assumptions that have persisted for more than 100 years since the first AOM species were cultivated.

Research results show that different AOM lineages use different regulatory strategies for ammonia or urea use, thereby reducing direct competition with each other and allowing coexistence. These differential preferences reveal hidden physiological heterogeneity and have real-world consequences that warrant further investigation.

„AOM produces nitrate, which leaches into groundwater and surrounding water bodies, causing eutrophication, or Nitrous oxide, which is a potent greenhouse gas,” said Qin. „Once we determine which AOM progenitors prefer urea, we can investigate their contribution to nitrate leaching and greenhouse gas production in the environment. This is necessary to develop sustainable and practical approaches to reduce these nitrogen pollutants in natural and engineered ecosystems. This will be the focus of future research.”

Reference: Wei Qin, Stephanie B. Wei, Yu Zheng, Yunkyung Choi, Xiangpeng Li, Juliet Johnston, Xianhui Wan, Britt Abrahamson, Zachary Flinkstrom, Payan Linkstrom, “Ammonia-oxidizing bacteria and archaea exhibit different nitrogen source preferences”, Lei Hou, Qing Tao, Wyatt W. Chlouber. , Xin Sun, Michael Wells, Long Ngo, Kristopher A. Hunt, Hidetoshi Urakawa, Xuanyu Tao, Dongyu Wang, Xiaoyuan Yan, Dazhi Wang, Chongle Pan, Peter K. Weber, Jiandong Jiang, Jisong Cho, Yao Zhang, David A. Stahl, Bess B. Ward, Xavier Mayali, Willem Martens-Habena, and Marie-Carolina H. Winkler, 31 Jan. 2024, Natural Microbiology.
DOI: 10.1038/s41564-023-01593-7