Metagenomic approaches to develop biological control strategies for aquatic invasive species

Project manager: Michael Sadowsky

Funded by: Environment and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources

Description: Microorganisms are closely associated with aquatic invasive species, possibly including harmless commensal bacteria as well as enteric bacteria and pathogens. This project aims to characterize the total microbial community structures associated with zebra mussels and Eurasian watermilfoil to determine if they contain any potential biocontrols for managing these AIS.

Zebra mussels, quagga mussels, and Eurasian watermilfoil samples will be collected from several water bodies where there are new AIS invasions, sudden changes of population density, or die-off events occurring. After dissection and observation, DNA will be obtained from all organs and tissues using DNA extraction kits. Water and sediment samples will also be collected near the sites to determine their influence on the microbial community.

In addition to providing valuable information on potential biocontrols for zebra mussels, quagga mussels, and Eurasian watermilfoil, this study may also allow us to develop molecular marker methods to ascertain the presence/absence of these AIS and quantify their abundance in lakes.

Project start date: 2015

Estimated end date: 2019



Aquatic invasive species, including Eurasian watermilfoil (EWM) and invasive mussels pose a serious threat to the health, structure, and function of aquatic ecosystems. Traditional approaches for AIS control, including the use of chemicals and manual removal, have been ineffective. This requires development of new management and eradication strategies, such as the use of (micro)biological control agents. Some microorganisms have evolved to live in close association with aquatic organisms and such relationships could potentially be exploited to develop microbe-mediated AIS management strategies. As a first step in identifying potential biocontrols, this project (Phase I) had proposed to characterize the microbial communities (bacterial and fungal) associated with invasive mussels and EWM, across time and space, using amplicon-based high-throughput sequencing approaches. To accomplish this, zebra mussels (ZMs), water, and sediment samples were obtained from 15 lakes twice a year, whereas EWM were sampled from 10 lakes, once a month for six months. Field samples were processed, DNA extracted and high-throughput sequencing was performed on all field samples using the Illumina platform. Sequencing analysis (188 million reads) showed a distinct clustering of each sample type, irrespective of sampling time and location. Core microbial communities were characterized and several taxonomic groups were identified that were either specific or present in high relative abundance in ZMs and EWM, when compared to sediment and water samples. This gives us a promising lead on microbes to purse in Phase II of this study, which will evaluate potential pathogenic characteristics and species-specificity of any pathogens. In addition, our results also indicated that EWM was associated with elevated concentrations of fecal indicator bacteria, such as E. coli and Enterococcus. This means that not only are these aquatic plants a nuisance, but they may present a hazard to human health as well, especially if they harbor known human pathogens in addition to fecal indicator bacteria. Overall, the results obtained in Phase I have helped to define the distribution of microbes associated with these AIS, and will be useful for the development of future microbiological control strategies (Phase II).

Phase II: Development of potential microbiological control agents for AIS

This phase, which is built on the research conducted in phase I, will identify and isolate microbes that are potentially pathogenic to AIS, and evaluate the specificity and effectiveness of potential biocontrol agents in the laboratory. Work will consist of sample collection and processing, isolation and characterization of potential pathogens, and challenge/infectivity experiments.


Field sampling coccurred around the state in 2017 and 2018. Sequence analyses have now been completed for all samples of native and invasive plants, and results look promising. An experimental setup was designed, constructed, and has been completed to conduct stress
experiments on zebra mussels. Zebra mussels were collected from Lake Minnetonka for preliminary survival experiments. The effect of environmental variables (e.g., water temperature, pH, dissolved oxygen, and salinity) on the structure of zebra mussel-associated microbiota will be evaluated during summer and fall. This data will be used for targeted microbe experiments.

Microbes that show potential to be pathogenic will be isolated using multiple cultivation strategies, and extensive laboratory screening will be conducted for the desired traits and potential interactions.