Abstract
Environmental DNA (eDNA) analysis is an efficient and easy-to-standardise molecular tool that has gained widespread importance during the past 10 years, as part of the worldwide campaign to investigate and monitor biodiversity by using globally accessible DNA-based systems (iBOL; https://ibol.org). Genetic methods are increasingly used to assess species diversity, as they are faster and often allow better taxonomic resolution than manual identification methods. However, eDNA is a fast-moving research field and needs continuous updating. In recent times, with the application of new sequencing technologies and the emergence of public bio-informatic databases, eDNA analyses have gained enormous potential not only for monitoring common species but also for investigating endangered taxa without the need for collecting living organisms, or revealing rare or cryptic species that are not visible when using conventional approaches. The success of the method is also due to its versatility, as eDNA can be isolated from environments as diverse as water (marine and freshwater), air, soil (tundra and permafrost), aquatic sediments (river, lake and ocean), ice, gut content, bulk insect and pollen samples, carcasses, shed skin and hairs. The method can also be applied in extreme environments like deep ocean trenches, deserts and geysers, where standard sampling procedures are problematic and sometimes impossible. After the first report of an extraction protocol for eDNA found in sediments (Ogram et al., 1987), eDNA analyses have grown very rapidly, even in the ancient DNA research field (Willerslev et al., 2003), where DNA from sediments often turned out to reveal more detailed information on plant palaeo-communities than could be achieved with pollen and macrofossils (Pedersen et al., 2015).
This book presents a comprehensive account of practices and protocols dealing with the analysis of eDNA samples, starting from recommendations during field sampling and building towards the more general aspects related to future developments of the field. It provides also an updated review of the current state-of-the-art, comprehensive bibliographic summary for researchers and a practical appendix with examples of primer pairs available for DNA metabarcoding. Although bits and pieces of all this information can be found in numerous recent papers, this book offers the opportunity to find all this information in one place.
The book is primarily aimed at ecologists who do not have a strong background in molecular genetics. Because of its clear and simple writing style, it is also suitable for wider readerships and scientists from other disciplines. The book is also technically oriented, providing practical suggestions for protocols, methods and workflows, but also providing the background ecological information necessary to enable the design of sound experiments in different fields. The title of the book, Environmental DNA for Biodiversity Research and Monitoring, suggests a very broad coverage, as eDNA can originate from an extraordinary variety of substrates and can be analysed using two major molecular approaches (metabarcoding and shotgun sequencing). However, three broad types of environments (soil, water faeces and air) and one molecular approach (metabarcoding) are extensively presented and discussed in the key part of the book (Chapters 2–10). Some later chapters are dedicated to analyses of host associations (microbiota), faeces, gut contents and bulk samples, but overall the central part of the book has a strong focus on soil and water environments, with little mention of studies conducted on other substrates like insects, pollen, snow, ice cores or leftovers from large organisms such as hair, shed skin or carcasses.
The book consists of two main parts. The first part (Chapters 1–10) presents the history of eDNA providing important information on the origin and the recent rapid evolution of this field of research (Chapter 1). This first chapter also briefly introduces the most common approaches used in eDNA analysis: those that are polymerase chain reaction (PCR)-based (quantitative PCR and metabarcoding) and those that are PCR-free (shotgun sequencing). Chapters 2–10 deal with theories, methods, protocols and workflows used in metabarcoding. After the barcode concept is introduced, the authors present all the steps necessary to select and design appropriate metabarcoding markers. Most of the book’s examples are based on the in-house package OBItools distributed as an open-source software and developed by the same authors. Successive chapters are dedicated to taxonomic identification using major public bioinformatics databases (Chapter 3) and the steps to go through field and laboratory sampling (Chapter 4). Importantly, the first part of Chapter 4 is dedicated to taphonomy with accurate coverage of the processes and factors responsible for the release, persistence, and degradation of the DNA molecules in the environment. Taphonomy is unglamorous work, but really vital for sound inference in modern and ancient biodiversity investigation using DNA and it is therefore pleasing to see this topic thoroughly discussed in the book. Chapters 5–10 deal with DNA extraction, amplification, sequencing and data analysis, focussing on metabarcoding examples.
The second part of the book, Chapters 11–19, deals with general topics in ecology. The authors discuss landmark studies in the eDNA field and present questions and concepts relating to freshwater, marine, terrestrial and palaeoenvironments. While metabarcoding may be most commonly used by researchers in the field, it is also clear that many researchers today are looking to move towards shotgun sequencing as a way to characterise the communities in an unbiased way. The book discusses the shotgun sequencing approach at several points but devotes only a few paragraphs to this topic in the final chapter, which discusses the future of the research field. Here, the authors describe the potential of the shotgun sequencing approach, with and without enrichment capture. It is good but – in a way – also a pity to see that the focus of this book is metabarcoding, as shotgun sequencing is now rapidly evolving and has recently gained enormous importance (e.g. Slon et al., 2017). In many of the cases presented in the book, methods that rely on hybridisation-based enrichment in combination with shotgun sequencing to characterise biodiversity or animal diet can be also easily implemented by designing DNA capture probes for the taxonomic orders of interests. However, given that the book came out in 2018, it is understandable that not so much weight was given to this novel approach. Overall, the book reflects the authors’ view of eDNA analyses with a clear emphasis on metabarcoding analyses and the use of in-house protocols, workflows and software. The authors are world-leading researchers in the metabarcoding field and, as they state in the preface of the book, their major aim was to provide simple and robust solutions with minimal inputs for all researchers, allowing molecular biodiversity monitoring worldwide (metabarcoding is currently much cheaper than shotgun sequencing).
With these very few limitations in mind, the book is an excellent example of a well-structured and comprehensive work, which makes a significant contribution to the research field of eDNA. It will undoubtedly become essential reading when planning and conducting experimental research for scientists worldwide and a must-read textbook for undergraduate students who wish to enter the eDNA field. The paperback version is also very affordable and well worth the £36.99.