Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review

AoB Plants, vol. 14, pp. plac031

Abstract

Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.

Authors 12

1. Pritam Banerjee

   National Chung Cheng University

   Affiliation as printed

   Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

   Department of Earth and Environmental Sciences, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

2. Kathryn A. Stewart Aachen Institute of Environmental Science

   Leiden University

   Affiliation as printed

   Institute of Environmental Science, Leiden University , 2333 CC Leiden , The Netherlands

3. Gobinda Dey

   National Chung Cheng University

   Affiliation as printed

   Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

   Department of Earth and Environmental Sciences, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

4. Caterina Maria Antognazza

   University of Insubria

   Affiliation as printed

   Department of Theoretical and Applied Science, University of Insubria , Via J.H. Dunant, 3, 21100 Varese , Italy

5. Raju Kumar Sharma

   National Chung Cheng University

   Affiliation as printed

   Department of Chemistry and Biochemistry, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

   Department of Earth and Environmental Sciences, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

6. Jyoti Prakash Maity

   KIIT University

   Affiliation as printed

   Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University , Bhubaneswar, Odisha 751024 , India

7. Hideyuki Doi

   University of Hyogo

   Affiliation as printed

   Graduate School of Information Science, University of Hyogo , 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047 , Japan

8. Natasha de Vere

   University of Copenhagen · Natural History Museum of Denmark

   Affiliation as printed

   Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K

9. Michael W.Y. Chan

   National Chung Cheng University

   Affiliation as printed

   Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

10. Pin-Yun Lin

    National Chung Cheng University

    Affiliation as printed

    Department of Chemistry and Biochemistry, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

    Department of Earth and Environmental Sciences, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

11. Hung-Chun Chao

    National Chung Cheng University

    Affiliation as printed

    Department of Earth and Environmental Sciences, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan

12. Chien‐Yen Chen corresponding

    National Chung Cheng University

    Affiliation as printed

    Center for Nano Bio-Detection, Center for Innovative Research on Aging Society, AIM-HI, National Chung Cheng University , Chiayi 62102 , Taiwan

    Department of Earth and Environmental Sciences, National Chung Cheng University , 168 University Road, Min-Hsiung, Chiayi County 62102 , Taiwan