DNA metabarcoding—a new approach to fauna monitoring in mine site restoration

Fernandes, Kristen; Heyde, Mieke van der; Bunce, Michael; Dixon, Kingsley W.; Harris, Richard J.; Wardell‐Johnson, Grant; Nevill, Paul

doi:10.1111/rec.12868

Cited by 43 publications

(44 citation statements)

References 109 publications

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“…plasticity (Demes, Graham, & Suskiewicz, 2009;Weigand, Jochum, Pfenninger, Steinke, & Klussmann-Kolb, 2011), (b) juveniles with ambiguous morphology (Ji et al, 2013;Richard et al, 2010), and (c) taxa having different levels of detectability according to season and time (Fernandes et al, 2018;Thompson & Newmaster, 2014).…”

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Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

Heyde

Bunce

Wardell‐Johnson

et al. 2020

Molecular Ecology Resources

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Biological surveys based on visual identification of the biota are challenging, expensive and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims to test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap. Samples (n = 200) were collected in the Pilbara (hot desert climate) and Swan Coastal Plain (hot Mediterranean climate) regions of Western Australia. Soil samples yielded little plant or animal DNA, especially in the Pilbara, probably due to conditions not conducive to long-term preservation. In contrast, scat samples contained the highest overall diversity with 131 plant, vertebrate and invertebrate families detected.Invertebrate and plant sequences were detected in the plant (86 families), pitfall (127 families) and vane trap (126 families) samples. In total, 278 families were recovered from the survey, 217 in the Swan Coastal Plain and 156 in the Pilbara. Aside from soil, 22%-43% of the families detected were unique to the particular substrate, and community composition varied significantly between substrates. These results demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys. If the aim is to broadly capture all biota then multiple substrates will be required.

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confidence: 99%

Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

Heyde

Bunce

Wardell‐Johnson

et al. 2020

Molecular Ecology Resources

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“…This is not surprising as previous evidence has shown that land use history or subsequent secondary growth can create changes and differences in the soil decomposer communities that develop under these conditions due to changes in resource input 42 . Moreover, a study using DNA metabarcoding of arthropod orders showed that certain groups of invertebrates were significantly different across land use types in southwest China 43 . In terms of taxonomic resolution, the soil invertebrate community composition at the ESV level was distinctly different across the primary and secondary forests, compared to differences at class, order, and family resolutions.…”

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confidence: 99%

Drivers of tropical soil invertebrate community composition and richness across tropical secondary forests using DNA metasystematics

McGee

Porter

Wright

et al. 2020

Sci Rep

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Tropical forests are fundamental ecosystems, essential for providing terrestrial primary productivity, global nutrient cycling, and biodiversity. Despite their importance, tropical forests are currently threatened by deforestation and associated activities. Moreover, tropical regions are now mostly represented by secondary forest regrowth, with half of the remaining tropical forests as secondary forest. Soil invertebrates are an important component to the functioning and biodiversity of these soil ecosystems. However, it remains unclear how these past land-use activities and subsequent secondary forest developments have altered the soil invertebrate communities and any potential ecological consequences associated with this. DNA metabarcoding offers an effective approach to rapidly monitor soil invertebrate communities under different land-use practices and within secondary forests. In this study, we used DNA metabarcoding to detect community-based patterns of soil invertebrate composition across a primary forest, a 23-year-old secondary forest, and a 33-year-old secondary forest and the associated soil environmental drivers of the soil invertebrate community structure in the Maquenque National Wildlife Refuge of Costa Rica (MNWR). We also used a species contribution analysis (SIMPER) to determine which soil invertebrate groups may be an indication of these soils reaching a pre-disturbed state such as a primary forest. We found that the soil invertebrate community composition at class, order, family, and ESV level were mostly significantly different across that habitats. We also found that the primary forest had a greater richness of soil invertebrates compared to the 23-year-old and 33-year-old secondary forest. Moreover, a redundancy analysis indicated that soil moisture influenced soil invertebrate community structure and explained up to 22% of the total variation observed in the community composition across the habitats; whereas soil invertebrate richness was structured by soil microbial biomass carbon (C) (Cmic) and explained up to 52% of the invertebrate richness across the primary and secondary forests. Lastly, the SIMPER analysis revealed that Naididae, Entomobryidae, and Elateridae could be important indicators of soil and forest recuperation in the MNWR. This study adds to the increasing evidence that soil invertebrates are intimately linked with the soil microbial biomass carbon (Cmic) and that even after 33 years of natural regrowth of a forest, these land use activities can still have persisting effects on the overall composition and richness of the soil invertebrate communities.

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“…There is an increasing call to monitor restoration using the latest molecular approaches (Williams et al 2014;Fernandes et al 2018) but our findings suggest care must be taken in assay selection and optimization to ensure that target groups are identified. Examining fine scale changes to invertebrate communities may be an effective predictor for restoration success.…”

Section: Will a Dna Approach Improve Restoration Monitoring?mentioning

confidence: 96%

Invertebrate DNA metabarcoding reveals changes in communities across mine site restoration chronosequences

Fernandes

Heyde

Coghlan

et al. 2019

Restoration Ecology

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Invertebrate biomonitoring can reveal crucial information about the status of restoration projects; however, it is routinely underused because of the high level of taxonomic expertise and resources required. Invertebrate DNA metabarcoding has been used to characterize invertebrate biodiversity but its application in restoration remains untested. We use DNA metabarcoding, a new approach for restoration assessment, to explore the invertebrate composition from pitfall traps at two mine site restoration chronosequences in southwestern Australia. Invertebrates were profiled using two cytochrome oxidase subunit 1 assays to investigate invertebrate biodiversity. The data revealed differences between invertebrate communities at the two mines and between the different age plots of the chronosequences. Several characteristic taxa were identified for each age within the chronosequence, including springtails within the youngest sites (Order: Collembola) and millipedes within the oldest and reference sites (Order: Julida). This study facilitates development of a molecular “toolkit” for the monitoring of ecological restoration projects. We suggest that a metabarcoding approach shows promise in complementing current monitoring practices that rely on alpha taxonomy.

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DNA metabarcoding—a new approach to fauna monitoring in mine site restoration

Cited by 43 publications

References 109 publications

Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

Drivers of tropical soil invertebrate community composition and richness across tropical secondary forests using DNA metasystematics

Invertebrate DNA metabarcoding reveals changes in communities across mine site restoration chronosequences

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