Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the “ecology” of eDNA—myriad interactions between extraorganismal genetic material and its environment—and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

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The ecology of environmental DNA and implications for conservation genetics

Fauna Europaea is Europe's main zoological taxonomic index, making the scientific names and distributions of all living, currently known, multicellular, European land and freshwater animals species integrally available in one authoritative database. Fauna Europaea covers about 260,000 taxon names, including 145,000 accepted (sub)species, assembled by a

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Fauna Europaea – all European animal species on the web

NINJA: An automated calculation system for nematode-based biological monitoring

Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

Belowground Microbiota and the Health of Tree Crops

This chapter emphasizes the effects of faunal biodiversity in soil on ecosystem functioning. It covers fauna ranging in size from micro- (protists and rotifers), meso- (nematodes and microarthropods and their roles in detrital food webs), to macrofauna (macroarthropods, earthworms, ants, and termites).

Roles of soil fauna in ecosystems globally are evaluated in terms of their responses to global environmental change. Food web ecology will act as an integrating concept across conservation biology, community and ecosystem ecology, and provision of ecosystem services.

Chapter 5 – Soil Fauna: Occurrence, Biodiversity, and Roles in Ecosystem Function

Soils are among the most complex, diverse and competitive habitats on Earth and soil biota are responsible for ecosystem services such as nutrient cycling, carbon sequestration and remediation of freshwater. The extreme biodiversity prohibits the making of a full inventory of soil life. Hence, an appropriate indicator group should be selected to determine the biological condition of soil systems. Due to their ubiquity and the diverse responses to abiotic and biotic changes, nematodes are suitable indicators for environmental monitoring. However, the time-consuming microscopic analysis of nematode communities has limited the scale at which this indicator group is used. In an attempt to circumvent this problem, a quantitative PCR-based tool for the detection of a consistent part of the soil nematofauna was developed based on a phylum-wide molecular framework consisting of 2,400 full-length SSU rDNA sequences. Taxon-specific primers were designed and tested for specificity. Furthermore, relationships were determined between the quantitative PCR output and numbers of target nematodes. As a first field test for this DNA sequence signature-based approach, seasonal fluctuations of nematode assemblages under open canopy (one field) and closed canopy (one forest) were monitored. Fifteen taxa from four feeding guilds (covering ∼ 65% of the free-living nematode biodiversity at higher taxonomical level) were detected at two trophic levels. These four feeding guilds are composed of taxa that developed independently by parallel evolution and we detected ecologically interpretable patterns for free-living nematodes belonging to the lower trophic level of soil food webs. Our results show temporal fluctuations, which can be even opposite within taxa belonging to the same guild. This research on nematode assemblages revealed ecological information about the soil food web that had been partly overlooked.

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SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations within Evolutionary Heterogeneous Feeding Guilds

Potato cyst nematodes (PCN) are quarantine organisms, and they belong to the economically most relevant pathogens of potato worldwide. Methodologies to assess the viability of their cysts which can contain 200-500 eggs protected by the hardened cuticle of a dead female, are either time and labor intensive, or lack robustness. We present a robust and cost-efficient viability assay based on loss of membrane integrity upon death. This assay uses trehalose, a disaccharide present at a high concentration in the perivitelline fluid of PCN eggs, as a viability marker. Although this assay can detect a single viable egg, the limit of detection for regular field samples was higher, ~ ten viable eggs, due to background signals produced by other soil components. On the basis of thirty non-viable PCN samples from The Netherlands, a threshold level was defined (?Atrehalose= 0.0094) below which the presence of more than ten viable eggs is highly unlikely (true for ~ 99.7% of the observations). This assay can easily be combined with a subsequent DNA-based species determination. As the presence of trehalose is a general phenomenon among cyst nematodes, this method can probably be used for, e.g., soybean, sugar beet and cereal cyst nematodes as well

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-02-11-0051

Renske Landeweert

Papers

SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations within Evolutionary Heterogeneous Feeding Guilds

A rapid, sensitive and cost-efficient assay to estimate viability of potato cyst nematodes

Looking for a needle in a hay-stack: diagnostic kits for the detection of plant parasitic nematodes in complex DNA backgrounds.

Verfahren zur Erkennung von Zystennematoden