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Functional and Systems Biology

Strain-Specific Quantification of Bacteria Associated with Duckweed Could Be Used on Other Host–Microbe Systems

Researchers developed a genomics-based computational pipeline for tracking and quantifying specific strains of bacteria within bacterial communities associated with duckweed. 

duckweed microscopy image

A team of researchers developed a suite of molecular approaches for studying the association between duckweed and bacteria. (Image courtesy of Kenneth Acosta and Eric Lam | Rutgers University)

The Science 

Duckweed is a family of freshwater aquatic plants with short doubling time (the amount of time it takes for an aquatic plant to double in size) and simplified architecture consisting of essentially fronds (leaf-like structures) as well as roots. Similarities between bacterial communities of duckweed and terrestrial plants make duckweed a model system for studying plant–microbe interactions. However, current methods often lack the specificity to differentiate strains in bacterial communities associated with plants. In a recently published study, a multi-institutional research team used polymerase chain reaction (PCR) technology in combination with other molecular and computational approaches to detect and quantify specific strains of bacteria present in bacterial communities associated with duckweed. The molecular methods introduced in this work should enable the tracking and quantification of specific plant–microbe associations within other plant-microbial communities. 

The Impact 

Bacteria are abundant microbes on plants that have the potential to promote plant growth. To harness this potential, researchers need a better understanding of how specific strains of bacteria behave within bacterial communities associated with plants. In this research, scientists used computational approaches to identify DNA sequences unique to specific strains of bacteria, and they employed these sequences to conduct PCR-based research. The multi-institutional team demonstrated the effectiveness of strain-specific PCR to differentiate and monitor specific duckweed–bacterium associations within a community. This study demonstrates that strain-specific approaches can be easily adopted to study how specific bacteria behave in plant-associated bacterial communities. 


In this study, a multi-institutional team of researchers optimized and applied a number of molecular methods to detect duckweed-associated bacteria. The team systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from both Lemna minor (common duckweed) and its associated bacteria. They combined ribosomal intergenic spacer analysis and PCR technology of a plant-specific marker to detect bacteria associated with duckweed. Draft genomes were generated at the Joint Genome Institute, a Department of Energy, Office of Science user facility, for duckweed-associated bacteria and a seaweed-associated bacterial isolate. Using publicly available computational tools, the team developed a genomics-based computational pipeline to generate bacterial strain-specific primers. The primers were then used to detect and quantify the associations of duckweed with each of the selected bacteria in the presence or absence of ambient microbial communities from wastewater samples. Confocal microscopy was then used to confirm some of the PCR results and to describe bacterial colonization patterns on duckweed tissues. The molecular methods and computational pipeline introduced in this work could enable high-resolution, quantitative studies of duckweed-associated bacteria in diverse contexts, as well as other host-plant–microbe interaction studies. 


Eric Lam, Rutgers University, 

Kenneth Acosta, Rutgers University, 


A portion of this research was funded by a Facilities Integrating Collaborations for User Science project, which provided access to instrumentation and expertise at the Environmental Molecular Sciences Laboratory and the Joint Genome Institute, both Department of Energy, Office of Science user facilities sponsored by the Biological and Environmental Research program. 


K. Acosta, et al. "Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria" Plants 12, no. 4: 872 (2023). [DOI: 10.3390/plants12040872]