Soil biodiversity and DNA barcodes: opportunities and challenges

By A. Orgiazzi, M. B. Dunbar, Panos Panagos, G. A. D. Groot, P. Lemanceau. 2015

152 citations recorded by the source corpus.

Soils encompass a huge diversity of organisms which mostly remains to be characterized due to a number of methodological and logistical issues. Nonetheless, remarkable progress has been made in recent years toward developing strategies to characterize and describe soil biodiversity, especially thanks to the development of molecular approaches relying on direct DNA extraction from the soil matrix. Metabarcoding can be applied to DNA from any environment or organism, and is gaining increasing prominence in biodiversity studies. This approach is already commonly used to characterize soil microbial communities and its application is now being extended to other soil organisms, i.e. meso- and macro-fauna. These developments offer unprecedented scientific and operational opportunities in order to better understand soil biodiversity distribution and dynamics, and to propose tools and strategies for biodiversity diagnosis. However, these opportunities also come with challenges that the scientific community must face. Such challenges are related to i) clarification of terminology, (ii) standardisation of methods and further methodological development for additional taxonomic groups, (iii) development of a common database, and (iv) ways to avoid waste of information and data derived from metabarcoding. In order to facilitate common application of metabarcoding in soil biodiversity assessment, we discuss these opportunities and challenges and propose solutions towards a more homogeneous framework. © 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c52cf52d94408d1c0e69161d092e5ec77f867323

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In Ecology

In Molecular Biology

Citations in the corpus

An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability. (2016, background): “While technology to detect and quantify soil organisms in high phylogenetic resolution is developing rapidly [12,46], knowledge of the ecological significance of this information is incomplete and ecological theory is lagging behind [47].”
Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil (2016, methodology): “…these approaches mainly have been applied to the study of microbial communities of the soil, mostly for metabarcoding of bacterial and archaeal biodiversity (Orgiazzi et al. 2015), which is usually performed by DNA extractions directly on the soil matrix and amplification of the 16S rRNA gene.”