Plant metabarcoding in biomonitoring and ecological inquiry
Year: 2025
Type: article
Abstract: The worldwide rapid decline in plant abundance and diversity that has occurred in the past decades has gained public attention, and the demand for political actions to counteract these declines is growing. Rapid large-scale biomonitoring can aid in observing these changes and provide information for decisions for land management and species protection. DNA metabarcoding is an emerging method that can use environmental DNA to detect plants from all sorts of samples, from faeces to ancient DNA in permafrost. Because of the great potential and various fields of application, this method is continuously being improved. Every step in this work can skew results, and care must be taken in lab protocols and the interpretation of the results. To name only a few complications, DNA extraction methods must be appropriately examined to overcome inhibitors that are often inherent to the sample type, PCR primer choice can exacerbate PCR bias, and sterile methods must be employed to overcome false positives that can occur in these typically very low-quantity or degraded samples. The work detailed here represents both the development of methods as well as illustrating the usefulness of plant DNA metabarcoding in biomonitoring and ecological studies. First, with a study examining pollen exine rupture and its effect on sequencing performance. The results of this study led to more informed choices for bead mill duration and size of beads to maximize the accuracy of results. The next study is a proof-of-concept paper that evaluated the performance of plant metabarcoding from Malaise trap preservative ethanol. It demonstrated that samples of this type can provide information on what plants are in the area and utilized by insects in a particular timeframe, as well as the potential to detect rare and red list plant species. In addition, the method can enhance knowledge of plants in the area with lower effort than large-scale vegetation surveys due to the large foraging range of the insects collected. In the next study, methods were developed to investigate slide-mounted insect body pollen collected from dipteran and hymenopteran visitors to Caraway flowers. The range of pollen grains contained in samples was high, from under 100 grains to well over 10,000. Metabarcoding revealed many more species interactions than morphological identifications and identified several additional potential pollinators of Caraway. However, the methods implemented need adjustment as there is not a “one-size-fits-all” method for a wide range of pollen samples; what works well for the larger quantity samples might not be usable for small quantity samples that are especially prone to false positives and extraction failure. A book chapter was created that detailed protocols for field, laboratory, and data analysis of plant DNA metabarcoding of airborne pollen samples and Malaise trap preservative ethanol. The chapter can serve as a starting point for individuals interested in using this DNA metabarcoding for these sample types in a research program. Lastly, four multiauthor papers are included that represent the incorporation of plant metabarcoding into a large-scale project investigating the multifaceted causes of insect and plant declines in nature-protected areas in Germany. The major outcome from this project was that adjacent agriculture and the methods employed in food production also have a significant effect within the protected areas. These studies led to recommendations for expansion of fallow area borders between agriculture and nature protected areas, as well as reduced application or elimination of pesticides and artificial nutrient enrichment, in agriculture near protected areas. All of these works together have helped to develop methods and increase confidence in the results of studies utilizing the emerging method of plant DNA metabarcoding. They provide new insight into laboratory best practice protocols and illustrate the powerful potential of the method to provide more detailed and faster information on the taxonomic composition of ecosystems in a rapidly changing world.
Author: Swenson-Friedrich, Stephanie
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
SDG: Life on land
Open Access status: green
OpenAlex ID: W7103989776
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