Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

• Published in: Ecological indicators Vol. 46; pp. 379 - 389
• Main Authors: Yang, Chenxue, Wang, Xiaoyang, Miller, Jeremy A., de Blécourt, Marleen, Ji, Yinqiu, Yang, Chunyan, Harrison, Rhett D., Yu, Douglas W.
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier Ltd 01.11.2014; Elsevier
• Subjects: Animal and plant ecology; Animal, plant and microbial ecology; Applied ecology; Arthropoda; arthropods; Biodiversity; Biological and medical sciences; Biological diversity; canopy; China; Climate change; Climatology. Bioclimatology. Climate change; Conservation, protection and management of environment and wildlife; DNA barcoding; Earth, ocean, space; Ecology; Environmental degradation: ecosystems survey and restoration; environmental monitoring; eukaryotic cells; Exact sciences and technology; External geophysics; Forestry; Fundamental and applied biological sciences. Psychology; General aspects; General forest ecology; Generalities. Production, biomass. Quality of wood and forest products. General forest ecology; genetic markers; habitats; Indicators; Leaf litter; Malaise traps; Metabarcoding; Meteorology; plant litter; rapid methods; Restoration ecology; Sampling; Sequencing; Soil (material); Soil fauna; soil sampling; species diversity; Surveillance monitoring; Synecology; Systematic conservation planning; Targeted monitoring; terrestrial ecosystems; Tropical forest; Vietnam; Vietnam; China, People's Rep; China; Climate change; Metabarcoding; Soil fauna; DNA barcoding; Surveillance monitoring; Leaf litter; Tropical forest; Systematic conservation planning; Biodiversity; Targeted monitoring; Restoration ecology; Litter; Ecological indicator; Dynamical climatology; DNA; Ecological recovery; Environmental monitoring; Environmental protection
• DOI: 10.1016/j.ecolind.2014.06.028
• ISSN: 1470-160X

•Metabarcoding removes the taxonomic impediment from large-scale arthropod samples.•However, sampling itself continues to be slow, costly, and vulnerable to contamination.•Metabarcoding recovers valid ecological information from soil and leaf litter.•Soil and leaf litter are easy to collect.•Metabarcoded leaf-litter samples show great promise for biodiversity measurement. The targeted sequencing of taxonomically informative genetic markers, sometimes known as metabarcoding, allows eukaryote biodiversity to be measured rapidly, cheaply, comprehensively, repeatedly, and verifiably. Metabarcoding helps to remove the taxonomic impediment, which refers to the great logistical difficulties of describing and identifying species, and thus promises to improve our ability to detect and respond to changes in the natural environment. Now, sampling has become a rate-limiting step in biodiversity measurement, and in an effort to reduce turnaround time, we use arthropod samples from southern China and Vietnam to ask whether soil, leaf litter, and aboveground samples provide similar ecological information. A soil or leaf-litter sample can be collected in minutes, whereas an aboveground sample, such as from Malaise traps or canopy fogging, can require days to set up and run, during which time they are subject to theft, damage, and deliberate contamination. Here we show that while the taxonomic compositions of soil and leaf-litter samples are very different from aboveground samples, both types of samples provide similar ecological information, in terms of ranking sites by species richness and differentiating sites by beta diversity. In fact, leaf-litter samples appear to be as or more powerful than Malaise-trap and canopy-fogging samples at detecting habitat differences. We propose that metabarcoded leaf-litter and soil samples be widely tested as a candidate method for rapid environmental monitoring in terrestrial ecosystems.