Invasive Phragmites Science: Management Tools for the Control of Invasive Phragmites to Foster the Restoration of the Great Lakes

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The USGS is developing innovative Phragmites control measures to keep this rapidly spreading invasive plant from further expanding its range into new wetland habitats and to aid in the development of successful restoration strategies. Scientists are conducting studies and field tests to determine if fungi that live within the Phragmites are enabling the plant to take over habitat used by native plants. Gene silencing is another technology scientists have been testing that will help control the spread of invasive plants by 'switching off' a gene that, for example, contributes to the plants ability to spread.

microbial symbiosis of phragmites

Beneficial endophytes (microbes living in plants) have been shown to enhance Phragmites performance compared to those grown without (Ernst et al. 2003). (Public domain.)

All plants host a diverse suite of microbes, such as fungi and bacteria, throughout all stages of their life cycle. Some of these microbes live inside plants (i.e., endophytes) and form relationships that are beneficial to both the microbes and the host plants. Microbes also are thought to confer many benefits to plants, thereby increasing their growth, stress tolerance, and competitive ability. The non-native Phragmites australis (common reed) continues to invade fish and wildlife habitats across the Great Lakes Region, but it isn’t clear what role microbes play in its ability to outcompete native plants. We also don’t know if microbes can be part of a new sustainable management approach for Phragmites. Therefore, researchers at the USGS Great Lakes Science Center (GLSC), Indiana University, and Rutgers University are examining the role of endophytes in both the success of invasive Phragmites and as a potential mechanism for restoring native plant assemblages. Scientists are seeking to better understand the microbes associated with invasive Phragmites and the benefits they confer to their host. The ultimate goal of this research is to identify new control methods based on microbial symbiosis that give land managers another tool in their toolbox for managing this invasive species. To maximize the collective impact of research efforts, the GLSC is using a collaborative approach to coordinate research efforts that explore the relationships between microbes and Phragmites, as well as to develop a comprehensive microbe-based Phragmites control approach.

Microbial Symbiosis of Phragmites

Microbes can perform as both mutualists (mutually beneficial) andpathogens (disease causing). The role they play can have an important impact on a plant’s performancein the field. (Public domain.)

Additionally, scientists at the GLSC, Wayne State University, and the U.S. Army Corps of Engineers are developing an approach for controlling Phragmites that limits the expression of certain traits (i.e., gene silencing) that help Phragmites be so competitive. The gene silencing approach uses a natural defense mechanism within plant cells known as RNA interference (RNAi), whereby a cell breaks down RNA that appears to be viral. Researchers have discovered that if they insert “suspicious looking” RNA into a cell, the cell’s natural defenses are triggered and all RNA with the same code as the suspicious strand will be broken down, disrupting protein formation and preventing trait expression. Researchers are working to adapt this technology as a form of control for invasive Phragmites. Their work is focused on identifying and silencing genes important to the plant’s competitive advantage, such as those for flowering, meristem growth, seed set, and photosynthesis. The gene silencing approach to controlling Phragmites could have advantages beyond traditional strategies, because the technology targets genetic messages specific to the target plant. This means that it would only work on the species being targeted. For land managers, this means that treating rapidly expanding or dense Phragmites stands could take place with minimal detrimental effects on non-target plants or animals.


Shearin, Z. R. C., M. Filipek, R. Desai, W. A. Bickford, K. P. Kowalski, and K. Clay. 2017. Fungal endophytes from seeds of invasive, non-native Phragmites australis and their potential role in germination and seedling growth. Plant and Soil doi:10.1007/s11104-017-3241-x

Bickford, W.A., D.E. Goldberg, K.P. Kowalski, and D.R. Zak. 2018. Root microbes and invasiveness: No difference between native and non-native Phragmites in the Great Lakes. Ecosphere (12):e02526. 10.1002/ecs2.2526

Verma, S. K., K. L. Kingsley, M. S. Bergen, K. P. Kowalski, and J. F. White. 2018. Fungal disease prevention in seedlings of rice (Oryza sativa) and other grasses by growth-promoting seed-associated endophytic bacteria from invasive Phragmites australis. Microorgansims 10.3390/microorganisms6010021

White, J. F. Jr., K. L. Kingsley, S. Butterworth, L. Brindisi, J. W. Gatei, M. T. Elmore, S. K. Verma, X. Yao, and K. P. Kowalski. 2018. Seed-vectored microbes: Their roles in improving seedling fitness and competitor plant suppression. In: S. K. Verma and J. F. White Jr. (eds.). Seed Endophytes: Biology and Biotechnology. Springer International Publishing. doi: 10.1007/978-3-030-10504-4

White, J. F., Jr., K. L. Kingsley, S. K. Verma, and K. P. Kowalski. 2018. Rhizophagy cycle: An oxidative process in plants for nutrient extraction from symbiotic microbes. Microorganisms 6(3):95
White, J. F. Jr., M. S. Torres, S. K. Verma, M. T. Elmore, K. P. Kowalski, and K. L. Kingsley. 2018. Evidence for widespread microbivory of endophytic bacteria in roots of vascular plants through oxidative degradation in root cell periplasmic spaces. In: A. Kumar, A. K. Singh, and V. K. Singh (eds.). PGPR Amelioration in Sustainable Agriculture: Food Security and Environmental Management. Woodhead Publishing

Bell T., K. L. Hockett, R. I. Alcala-Briseno, M. Barbercheck, G. A. Beattie, M. A. Brus, J. E. Carlson, T. Chung, A. Collins, B. Emmett, P. Esker, K. A. Garrett, L. Glena, B. K. Gugino, M. del Mar Jimenez-Gasco, L. Kinkel, J. Kovac, K. P. Kowalski, G. Kuldau, J. H. J. Leveau, M. J. Michalska-Smith, J. Myrick, K. Peter, M. Fernanda Vivanco Salazar, A. Shade, N. Stopnisek, X. Tan, A. T. Welty, K. Wickings, and E. Yergeau. 2019. Manipulating wild and tamed phytobiomes: Challenges and opportunities. Phytobiomes Journal

White, J. F., K. L. Kingsley, Q. Zhang, R. Verma, N. Obi, S. Dvinskikh, M. T. Elmore, S. K. Verma, S. K. Gond, and K. P. Kowalski. 2019. Review: Endopytic microbes and their potential applications in crop management. Pest Management Science


  • Indiana University
  • Rutgers University
  • Wayne State University
  • U.S. Army Corps
Gene silencing in phragmites plants

Gene silencing could be used to disrupt various biological pathways that allow plants to thrive. Here, Phragmites plants in the foreground have been treated with (left) and without (right) a gene silencing spray. Notice the yellowed leaves on the gene silencing plants, resulting in a limited capacity for photosynthesis (Source: Ed Golenberg). (Public domain.)