Coastal and wetland ecosystems provide critical habitat to birds, fish, wildlife, and a suite of other organisms, clean our water and mitigate flooding events, and offer tremendous recreational opportunities to visitors. However, the majority of coastal and wetland ecosystems in the Great Lakes basin have been significantly degraded or destroyed by ditching, draining, development, invasive species, and other human impacts over the past two centuries. The restoration and management of these systems is a high priority for resource managers of public and private lands. Therefore, the USGS Great Lakes Science Center wetlands research team and its many collaborators are conducting research that supports the restoration and sustainable management of Great Lakes coastal wetlands, including the development of new restoration approaches and innovative treatments for invasive plant species. Extensive collaborations with federal, state, academic, and non-profit partners are the foundation of our cutting-edge science and support our work with managers to apply site-specific results at national scales.
Wetland restoration
The restoration or rehabilitation of Great Lakes coastal wetlands is a high priority for management agencies in the Great Lakes basin. Although some wetlands are degraded by ditching or filling, many are isolated from the Great Lakes and tributaries by earthen dikes and present opportunities for restoration. Therefore, our research team is working with US Fish and Wildlife Service and many other partners to study how wetlands respond to being reconnected back to their parent water body. We look at biotic (fish, invertebrates, vegetation), abiotic (water quality, nutrient loads, flow), and ecosystem-level factors and work closely with the management community to share results and help guide future restoration efforts.
Cutting-edge technology to develop innovative invasive species treatments
Recent scientific advancements in the fields of genetics and interactions between host plants and the micro-organisms associated with them create a unique opportunity to develop cutting-edge technologies to control invasive and promote native species establishment, further improving the efficiency and results of management actions. Sequencing and describing a plant’s genome opens the door to development of species-specific treatments that limit the expression of specific traits that help non-native plants outcompete native plants and invade critical habitats. Testing of new non-toxic bioherbicides that target the relationship between invasive plants and bacteria, fungi, and other microbes advance our understanding of how microbes contribute to plant invasiveness. However, these lines of research are novel and still full of many unknowns. We are working collaboratively with many partners to develop new treatments for the non-native Phragmites australis (common reed) and set a foundation that supports adaptation of the treatments for other invasive plant species.
Regional coordination
Lack of regional communication among people working to manage invasive species and restore functional ecosystems often contributes to inefficient use of resources, uncoordinated research efforts, and missed opportunities to maximize the collective impact on the problem. We work collaboratively with government, tribal, non-profit, and academic partners to fill regional communication gaps and link science and natural resource management. For example, a close partnership with the Great Lakes Commission helped create the Great Lakes Phragmites Collaborative to improve the flow of information about the invasive Phragmites australis and subsequently the Phragmites Adaptive Management Framework (see below) to reduce uncertainty about which management treatment worked best as site conditions vary. The Great Lakes Coastal Wetland Monitoring Program is another example of region-wide collaboration to evaluate the ecological health of Great Lakes coastal wetlands.
Adaptive Management
Adaptive management is an iterative, structured decision-making process designed to reduce uncertainty by monitoring and making changes to the process through time. USGS, the Great Lakes Commission, the University of Georgia, and other partners used principles of adaptive management to stand up the Phragmites Adaptive Management Framework and reduce uncertainty about which treatments work best. Without coordinated adaptive management, management actions are often performed using a trial-and-error approach. Our goal is to use adaptive management to facilitate a shift in management strategy for Phragmites to reduce treatment uncertainty, increase management efficiency, and improve invasive species management at both the local and regional scales.
Fostering Collaboration
Collective Impact is a structured form of collaboration that pulls together a diverse group of participants around a common agenda that often tackles a large societal problem. USGS, the Great Lakes Commission, and many other partners have adapted this approach to reduce the impact of invasive Phragmites australis throughout the basin. Structured collaborations through the Great Lakes Phragmites Collaborative, the Collaborative on Symbiosis and Phragmites Management (i.e., Phragmites Symbiosis Collaborative), and the European Frogbit Collaborative are maximizing the impact of research on and management of non-native plants.
Applied Research
As an applied research agency, USGS continues to work closely with partner management agencies to identify high priority research needs and implement wetland and invasive species projects. From electrofishing in hydrologically reconnected wetland habitat to testing innovative treatment methods on Phragmites, our research directly supports decision making and resource management on the landscape.
Data related to this research
Phragmites australis Transcriptome Assembly Optimization
Histochemical study of nitrogen-transfer endosymbiosis
Wetland vegetation and elevation of Arcadia Marsh, Michigan (1995-2010)
Effects of fungal endophytes on invasive Phragmites australis (ssp. australis) performance in growth chamber and field experiments at the Indiana University Research and Teaching Preserve (N 39.217, W −86.540) (2018)
Reference genome for Phragmites australis (Poaceae, subfamily Arundinoideae) and comparison of North American invasive genotype (ssp. australis) and native (ssp. americanus)
Data collected to support research on grass crop growth promotion and biostimulation by endophytic bacteria
Land cover classifications and associated data from treatment areas enrolled in the Phragmites Adaptive Management Framework, 2018
The effects of North American fungi and bacteria on Phragmites australis leaves 2017-2019, with comparisons to the global Phragmites microbiome
DIDSON video collection of Coastal Lake Erie Wetland, Lucas Co, Ohio in 2011
Total phosphorus and water flux at a restored hydrologic connection at Ottawa National Wildlife Refuge in 2013 and 2014
Land cover map including wetlands and invasive Phragmites circa 2017
Using turbidity measurements to estimate phosphorus and sediment flux in a Great Lakes Coastal Marsh, in Ohio
Publications related to this research
Optimization and application of non-native Phragmites australis transcriptome assemblies
Genetic analysis of North American Phragmites australis guides management approaches
Turbidity and estimated phosphorus retention in a reconnected Lake Erie coastal wetland
Histochemical evidence for nitrogen‐transfer Endosymbiosis in non‐photosynthetic cells of leaves and inflorescence bracts of angiosperms
Fungal endophyte effects on invasive Phragmites australis performance in field and growth chamber environments
Extent of sedge-grass meadow in a Lake Michigan drowned river mouth wetland dictated by topography and lake level
Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed)
Endophytic bacteria in grass crop growth promotion and biostimulation
Enhancing Great Lakes coastal ecosystems research by initiating engagement between scientists and decision-makers
Using uncrewed aerial vehicles for identifying the extent of invasive Phragmites australis in treatment areas enrolled in an adaptive management program
Differences in rhizosphere microbial communities between native and non‐native Phragmites australis may depend on stand density
Improved fish counting method accurately quantifies high‐density fish movement in dual‐frequency identification sonar data files from a coastal wetland environment
Software related to this research
Data analysis and figures for Differences in Rhizosphere Microbial Communities Between Native and Non-Native Phragmites australis May Depend on Stand Density
Annual Management Unit Summary Code
News related to this research
The following are partners in this research
- Overview
Coastal and wetland ecosystems provide critical habitat to birds, fish, wildlife, and a suite of other organisms, clean our water and mitigate flooding events, and offer tremendous recreational opportunities to visitors. However, the majority of coastal and wetland ecosystems in the Great Lakes basin have been significantly degraded or destroyed by ditching, draining, development, invasive species, and other human impacts over the past two centuries. The restoration and management of these systems is a high priority for resource managers of public and private lands. Therefore, the USGS Great Lakes Science Center wetlands research team and its many collaborators are conducting research that supports the restoration and sustainable management of Great Lakes coastal wetlands, including the development of new restoration approaches and innovative treatments for invasive plant species. Extensive collaborations with federal, state, academic, and non-profit partners are the foundation of our cutting-edge science and support our work with managers to apply site-specific results at national scales.
Wetland restoration
Wetlands restoration and invasive species approaches. Credit Taaja Tucker-Silva, USGS. The restoration or rehabilitation of Great Lakes coastal wetlands is a high priority for management agencies in the Great Lakes basin. Although some wetlands are degraded by ditching or filling, many are isolated from the Great Lakes and tributaries by earthen dikes and present opportunities for restoration. Therefore, our research team is working with US Fish and Wildlife Service and many other partners to study how wetlands respond to being reconnected back to their parent water body. We look at biotic (fish, invertebrates, vegetation), abiotic (water quality, nutrient loads, flow), and ecosystem-level factors and work closely with the management community to share results and help guide future restoration efforts.
Cutting-edge technology to develop innovative invasive species treatments
Recent scientific advancements in the fields of genetics and interactions between host plants and the micro-organisms associated with them create a unique opportunity to develop cutting-edge technologies to control invasive and promote native species establishment, further improving the efficiency and results of management actions. Sequencing and describing a plant’s genome opens the door to development of species-specific treatments that limit the expression of specific traits that help non-native plants outcompete native plants and invade critical habitats. Testing of new non-toxic bioherbicides that target the relationship between invasive plants and bacteria, fungi, and other microbes advance our understanding of how microbes contribute to plant invasiveness. However, these lines of research are novel and still full of many unknowns. We are working collaboratively with many partners to develop new treatments for the non-native Phragmites australis (common reed) and set a foundation that supports adaptation of the treatments for other invasive plant species.
Regional coordination
Lack of regional communication among people working to manage invasive species and restore functional ecosystems often contributes to inefficient use of resources, uncoordinated research efforts, and missed opportunities to maximize the collective impact on the problem. We work collaboratively with government, tribal, non-profit, and academic partners to fill regional communication gaps and link science and natural resource management. For example, a close partnership with the Great Lakes Commission helped create the Great Lakes Phragmites Collaborative to improve the flow of information about the invasive Phragmites australis and subsequently the Phragmites Adaptive Management Framework (see below) to reduce uncertainty about which management treatment worked best as site conditions vary. The Great Lakes Coastal Wetland Monitoring Program is another example of region-wide collaboration to evaluate the ecological health of Great Lakes coastal wetlands.
Adaptive Management
Adaptive management is an iterative, structured decision-making process designed to reduce uncertainty by monitoring and making changes to the process through time. USGS, the Great Lakes Commission, the University of Georgia, and other partners used principles of adaptive management to stand up the Phragmites Adaptive Management Framework and reduce uncertainty about which treatments work best. Without coordinated adaptive management, management actions are often performed using a trial-and-error approach. Our goal is to use adaptive management to facilitate a shift in management strategy for Phragmites to reduce treatment uncertainty, increase management efficiency, and improve invasive species management at both the local and regional scales.
Fostering Collaboration
Collective Impact is a structured form of collaboration that pulls together a diverse group of participants around a common agenda that often tackles a large societal problem. USGS, the Great Lakes Commission, and many other partners have adapted this approach to reduce the impact of invasive Phragmites australis throughout the basin. Structured collaborations through the Great Lakes Phragmites Collaborative, the Collaborative on Symbiosis and Phragmites Management (i.e., Phragmites Symbiosis Collaborative), and the European Frogbit Collaborative are maximizing the impact of research on and management of non-native plants.
Applied Research
As an applied research agency, USGS continues to work closely with partner management agencies to identify high priority research needs and implement wetland and invasive species projects. From electrofishing in hydrologically reconnected wetland habitat to testing innovative treatment methods on Phragmites, our research directly supports decision making and resource management on the landscape.
- Data
Data related to this research
Filter Total Items: 17Phragmites australis Transcriptome Assembly Optimization
Nonnative Phragmites australis (common reed) is widely distributed across North America and insufficient knowledge of P. australis has impeded the efficiency of management. To aid in Phragmites management and future studies, we used RNA-seq data from multiple types of plant tissue to construct forty-nine P. australis transcriptomes via different assembly tools and multiple parameter settings, resuHistochemical study of nitrogen-transfer endosymbiosis
Plant roots have the best-understood mutualisms with microbes, but leaf and bract cell endosymbiosis have not been previously reported. Leaf and bract cells of more than 30 species in 18 families of seed plants were surveyed for the presence of intracellular bacteria and several experiments were designed to find and analyze nutrient exchanges between bacteria and plant cells. This dataset containsWetland vegetation and elevation of Arcadia Marsh, Michigan (1995-2010)
Vegetation sampling and elevation data were collected to characterize the sedge-grass meadow of Arcadia Marsh, Arcadia, Michigan (USA), a drowned river mouth wetland near Lake Michigan. Wetland vegetation community data were collected by quadrat sampling in 1995, 2002, and 2010 and topographic data were collected via GPS and LIDAR positional data in 2010.Effects of fungal endophytes on invasive Phragmites australis (ssp. australis) performance in growth chamber and field experiments at the Indiana University Research and Teaching Preserve (N 39.217, W −86.540) (2018)
These data tables contain data collections from field experiments of Phragmites australis (ssp. australis) treated with known fungal endophytes. Tiller counts, tiller diameter, and tiller height measurements were taken every two weeks over an eight-week study period. Clones of Phragmites plants were collected from three different locations: Sandusky, Michigan; Bloomington, Indiana; and the OttawaReference genome for Phragmites australis (Poaceae, subfamily Arundinoideae) and comparison of North American invasive genotype (ssp. australis) and native (ssp. americanus)
These data represent the first reference genome for the invasive Phragmites australis ssp. australis (1.14 giga base pairs (Gbp)), as well as output from comparative genomic and transcriptomic analyses for invasive and native genotypes coexisting in the Great Lakes region of North America. Genome sequencing data used tillers and associated rhizome tissues collected from a single P. australis patchData collected to support research on grass crop growth promotion and biostimulation by endophytic bacteria
These data show grass crop and model species response to toxic chemicals (Arsenic (As)) and humic acids. Experiments were performed by collaboration between the U.S. Geological Survey, Rutgers University, and Rey Juan Carlos University. A series of individual experiments investigated beneficial effects of endophytic bacteria on grass crop growth and resilience to known plant toxicity.Land cover classifications and associated data from treatment areas enrolled in the Phragmites Adaptive Management Framework, 2018
During 2018, uncrewed aerial vehicles (UAVs or 'drones') were used to collect spatially referenced aerial imagery from 20 management units (sites) enrolled in the Phragmites Adaptive Management Framework, a collective learning program developed by the Great Lakes Phragmites Collaborative. Management units were located in Michigan, Ohio, and Wisconsin (USA). Invasive Phragmites australis (hereafterThe effects of North American fungi and bacteria on Phragmites australis leaves 2017-2019, with comparisons to the global Phragmites microbiome
The data document the results of several microbe bioassays performed by the USGS on Phragmites australis plants, including those performed on mature leaves, seedlings, and dead leaf tissues exploration of the literature to find accounts of microbes associated with Phragmites worldwide. For the bioassays, we prepared 162 pure cultures isolated from Phragmites plants in North America along the eastDIDSON video collection of Coastal Lake Erie Wetland, Lucas Co, Ohio in 2011
The data set includes quantitative fish abundance counts estimated from video data files collected by a Dual-frequency IDentification SONar (DIDSON) placed at the junction of a water control structure located between Pool 2B and Crane Creek (41.62133N, -83.20769W) within Ottawa National Wildlife Refuge (Lucas County, Ohio). One-hour-long video data files were used to estimate fish activity in a reTotal phosphorus and water flux at a restored hydrologic connection at Ottawa National Wildlife Refuge in 2013 and 2014
This tabular data set contains estimates of total phosphorus concentration and mass, as well as measurements of water discharge and volume at a diked wetland pool (Pool 2B) that was reconnected to a Lake Erie tributary (Crane Creek) via a water control structure in March 2011. Sampling occurred during 2013 and 2014. In addition, this data set contains evaluations of movement of total phosphorus anLand cover map including wetlands and invasive Phragmites circa 2017
The first basin-wide map of large stands of invasive Phragmites australis (common reed) in the coastal zone was created through a collaboration between the U.S. Geological Survey and Michigan Tech Research Institute (Bourgeau-Chavez et al 2013). This data set represents a revised version of that map and was created using multi-temporal PALSAR data and Landsat images from 2016-2017. In addition toUsing turbidity measurements to estimate phosphorus and sediment flux in a Great Lakes Coastal Marsh, in Ohio
Great Lakes coastal marshes have the potential to filter water coming off of the landscape and remove sediments and nutrients before they reach the lakes. However, this ability has largely been neutralized as vast areas of coastal wetlands have been isolated behind dikes; while at the same time the Great Lakes continue to suffer from excess phosphorus loading. In this study we used high-frequency - Publications
Publications related to this research
Filter Total Items: 33Optimization and application of non-native Phragmites australis transcriptome assemblies
Phragmites australis (common reed) has a cosmopolitan distribution and has been suggested as a model organism for the study of invasive plant species. In North America, the non-native subspecies (ssp. australis) is widely distributed across the contiguous 48 states in the United States and large parts of Canada. Even though millions of dollars are spent annually on Phragmites management, insufficiAuthorsFeng Tao, Chuanzhu Fan, Yimin Liu, Subashini Sivakumar, Kurt P. Kowalski, Edward M GolenbergGenetic analysis of North American Phragmites australis guides management approaches
Phragmites australis subsp. australis is an invasive and ecologically detrimental plant in multiple regions of North America. Its co-occurrence with the native subspecies, and multiple instances of hybridization, has created the need to differentiate Phragmites subspecies or haplotypes so that management can be appropriately targeted to the invader. We compiled a review of current genetic discrimiAuthorsDenise L. Lindsay, Joanna Freeland, Ping Gong, Xin Guan, Nathan E Harms, Kurt P. Kowalski, Richard F. Lance, Dong-Ha Oh, Bradley T Sartain, Douglas L WendellTurbidity and estimated phosphorus retention in a reconnected Lake Erie coastal wetland
Nearly all of the wetlands in the coastal zone of Lake Erie have been degraded or destroyed since the 1860s, and most of those that remain are separated from their watersheds by earthen dikes. Hydrologic isolation of these wetlands disrupts ecosystem benefits typical to Great Lakes coastal wetlands, particularly the ability to trap sediments and retain nutrients when inundated by runoff and lake wAuthorsGlenn Carter, Kurt P. Kowalski, Michael EgglestonHistochemical evidence for nitrogen‐transfer Endosymbiosis in non‐photosynthetic cells of leaves and inflorescence bracts of angiosperms
We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. Through histochemical analysis, we detected hormones (including ethylene and nitric oxide), superoxide, and nitrogenous chemicals (including nitric oxide and nitrate) around bacteria within plant cells. Bacteria were observed in epidermal cells, various filamenAuthorsApril Micci, Qiuwei Zhang, Xiaoqian Chang, Kathryn Kingsley, Linsey Park, Peerapol Chiaranunt, Raquele Strickland, Fernando Velazquez, Sean Lindert, Matthew T. Elmore, Philip L. Vines, Sharron Crane, Ivelisse Irizarry, Kurt P. Kowalski, David Johnston-Monje, James F. WhiteFungal endophyte effects on invasive Phragmites australis performance in field and growth chamber environments
Manipulating plant microbiomes may provide control of invasive species. Invasive Phragmites australis has spread rapidly in North American wetlands, causing significant declines in native biodiversity. To test microbiome effects on host growth, we inoculated four common fungal endophytes into replicated Phragmites genotypes and monitored their growth in field and growth chamber environments. InocuAuthorsQuynh N Quach, Thomas T Thrasher, Kurt P. Kowalski, Keith ClayExtent of sedge-grass meadow in a Lake Michigan drowned river mouth wetland dictated by topography and lake level
Water-level fluctuations are critical in maintaining diversity of plant communities in Great Lakes wetlands. Sedge-grass meadows are especially sensitive to such fluctuations. We conducted vegetation sampling in a sedge-grass dominated Lake Michigan drowned river mouth wetland in 1995, 2002, and 2010 following high lake levels in 1986 and 1997. We also conducted photointerpretation studies in 16 yAuthorsDouglas A. Wilcox, John A Bateman, Kurt P. Kowalski, James E Meeker, Nicole DunnNovel genome characteristics contribute to the invasiveness of Phragmites australis (common reed)
The rapid invasion of the non-native Phragmites australis (Poaceae, subfamily Arundinoideae) is a major threat to native wetland ecosystems in North America and elsewhere. We describe the first reference genome for P. australis and compare invasive (ssp. australis) and native (ssp. americanus) genotypes collected from replicated populations across the Laurentian Great Lakes to deduce genomic basesAuthorsDong-Ha Oh, Kurt P. Kowalski, Quynh Quach, Chathura Wijesinghege, Philippa Tanford, Maheshi Dassanayake, Keith ClayEndophytic bacteria in grass crop growth promotion and biostimulation
Plants naturally carry microbes on seeds and within seeds that may facilitate development and early survival of seedlings. Some crops have lost seed-vectored microbes in the process of domestication or during seed storage and seed treatment. Biostimulant microbes from wild plants were used by pre-modern cultures to re-acquire beneficial seed microbes. Today some companies have developed or are deAuthorsJames F. White, Xiaoqian Chang, Kathryn L. Kingsley, Qiuwei Zhang, Peerapol Chiaranunt, April Micci, Fernando Velazquez, Matthew T. Elmore, Sharron Crane, Shanjia Li, Jiaxin Lu, Maria Molina Cobos, Natalia Gonzalez-Benitez, Miguel J Beltran-Garcia, Kurt P. KowalskiEnhancing Great Lakes coastal ecosystems research by initiating engagement between scientists and decision-makers
A disconnect between scientific research and environmental management communities can be a detriment to both. In the case of Great Lakes coastal ecosystems, which are inherently complex and subject to uncertain effects of future climatic, environmental, and anthropogenic drivers, greater collaboration could be beneficial to their sustainability. We capture the challenges and opportunities identifiAuthorsCharlotte B. Weinstein, Laura Bourgeau-Chavez, S. L. Martin, W. S. Currie, K. Grantham, Q. F. Hamlin, David W Hyndman, Kurt P. Kowalski, J. P. Martina, D. PearsallUsing uncrewed aerial vehicles for identifying the extent of invasive Phragmites australis in treatment areas enrolled in an adaptive management program
Higher spatial and temporal resolutions of remote sensing data are likely to be useful for ecological monitoring efforts. There are many different treatment approaches for the introduced European genotype of Phragmites australis, and adaptive management principles are being integrated in at least some long-term monitoring efforts. In this paper, we investigated how natural color and a smaller setAuthorsColin N. Brooks, Charlotte B. Weinstein, Andrew F. Poley, Amanda G. Grimm, Nicholas P. Marion, Laura Bourgeau-Chavez, Dana Hansen, Kurt P. KowalskiDifferences in rhizosphere microbial communities between native and non‐native Phragmites australis may depend on stand density
Microorganisms surrounding plant roots may benefit invasive species through enhanced mutualism or decreased antagonism, when compared to surrounding native species. We surveyed the rhizosphere soil microbiome of a prominent invasive plant, Phragmites australis, and its co‐occurring native subspecies for evidence of microbial drivers of invasiveness. If the rhizosphere microbial community is importAuthorsWesley A. Bickford, Donald R. Zak, Kurt P. Kowalski, Deborah E. GoldbergImproved fish counting method accurately quantifies high‐density fish movement in dual‐frequency identification sonar data files from a coastal wetland environment
There are many ways to quantify fish movement through shallow‐water habitats, but most noninvasive methods (e.g., visual counts) are not effective in turbid coastal wetland waters of the Great Lakes. Dual‐frequency identification sonar (DIDSON) technology (Sound Metrics) offers a noninvasive, hydroacoustic‐based approach to characterize fish movement in wetlands and other habitats by collecting hiAuthorsMichael R. Eggleston, Scott W. Milne, Maxwell Ramsay, Kurt P. Kowalski - Software
Software related to this research
Data analysis and figures for Differences in Rhizosphere Microbial Communities Between Native and Non-Native Phragmites australis May Depend on Stand Density
This repository holds the code to reproduce the data analyses and figures found in "Differences in Rhizosphere Microbial Communities Between Native and Non-Native Phragmites australis May Depend on Stand Density" published in Ecology and Evolution written by Wesley A. Bickford, Donald R. Zak, Kurt P. Kowalski, and Deborah E. Goldberg.Annual Management Unit Summary Code
The Phragmites Adaptive Management Framework (PAMF) is an adaptive management program created to improve the efficacy and efficiency of Phragmites management efforts throughout the Great Lakes region. Managers enroll Phragmites stands, report the management techniques they used, and monitor the invasion status of Phragmites on their site (management unit - MU). Through a systematic approach, PAMF - News
News related to this research
Filter Total Items: 19 - Partners
The following are partners in this research
Filter Total Items: 18