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

Abstract

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.

Responses of grassland snakes to tallgrass prairie restoration

“…Analyses of faunal responses to ecological restoration are accumulating rapidly and increasingly include responses to created habitat (Andrews et al ; Goldspiel et al ), often utilizing a chronosequence approach (van Noordwijck et al ; Fernandes et al ), including the Nachusa Grasslands chronosequence (Wodika & Baer ; Griffin et al ; Barber et al 2017 a ). We present several lines of evidence to suggest that snakes have responded positively to created habitat at Nachusa Grasslands.…”

Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

“…Due to the degraded nature of eDNA, all primers used targeted short amplicons (72–157 bp) to improve amplification success from samples. ZBJ‐ArtF1c/ZBJ‐ArtR2c (~157 bp, Zeale, Butlin, Barker, Lees, & Jones, 2011) was chosen as a general arthropod primer, with addition of Ant236/361 (~72 bp, Fernandes et al, 2019) to target arthropod orders such as Hymenoptera, against which ZBJ‐ArtF1c/ZBJ‐ArtR2c has shown some bias (Clarke, Soubrier, Weyrich, & Cooper, 2014; Fernandes et al, 2019). Primer bias may differentially affect sites with different community composition, so the combination of the two invertebrate primers was chosen to control for this bias.…”

“…The reduction in the cost of high‐throughput sequencing has led to a rapid increase in the number of eDNA studies, as well as commercial interest (supporting information in Koziol et al, 2019). Soil microbial researchers have been using eDNA metabarcoding for over two decades (Anderson & Cairney, 2004) and there is now growing evidence that barcoding may be useful to monitor plant communities (Fahner, Shokralla, Baird, & Hajibabaei, 2016; de Mattia et al, 2012; Thompson & Newmaster, 2014), vertebrates (Andersen et al, 2012; Calvignac‐Spencer, Merkel, & Kutzner, 2013; Fernandes et al, 2019) and invertebrates (Ji et al, 2013; Yang et al, 2014). Researchers have successfully sequenced: topsoil (Andersen et al, 2012; Fahner et al, 2016), scat (De Barba et al, 2014), ancient middens (Murray et al, 2012), air (Kraaijeveld et al, 2015), bulk arthropods (Ji et al, 2013; Yu et al, 2012), leaf material (Thompson & Newmaster, 2014), flowers (Thomsen & Sigsgaard, 2019) and more.…”

DNA-Based Arthropod Diversity Assessment in Amazonian Iron Mine Lands Show Ecological Succession Towards Undisturbed Reference Sites

“…Moreover, the high biodiversity present in the study areas and the lack of a complete reference database, which makes taxonomic assignment to the OTUs difficult, makes this type of study challenging. Nevertheless, DNA metabarcoding of bulk arthropod samples has proven to be an efficient method to study changes in ecosystems (Edwards et al, 2014;Zhang et al, 2016;Barsoum et al, 2019;Fernandes et al, 2019;Gervan et al, 2020). Although DNA metabarcoding of bulk arthropod samples has been used for environmental monitoring purposes and has been recently applied to study arthropod communities after mining (Fernandes et al, 2019;Gervan et al, 2020), we are far from defining baselines and understanding the multiple factors that influence arthropod diversity detected within bulk arthropod samples.…”

“…However, the choice of metabarcoding primer set is an important decision, as PCR amplification bias can occur when having mismatches between the primer and the target sequences (Krehenwinkel et al, 2017). Metabarcoding of bulk arthropod samples has been used to quantify the biological impacts of logging and planting oil palm (Edwards et al, 2014); to characterise the diversity of insect samples in montane landscapes in tropical southern China (Zhang et al, 2016); to monitor temporal changes in arthropod communities in different forest types (Brandon-Mong et al, 2018); to measure biodiversity response to subtle differences in forest environmental condition (Barsoum et al, 2019); to follow changes in an invertebrate community in an ecosystem under restoration after sand mining (Fernandes et al, 2019); and to assess reclamation trajectories after mining (Gervan et al, 2020) [i.e., when the area again has a useful function (SER, 2004)]. However, we are far from defining baselines for assessing rehabilitation and from understanding the multiple factors that influence arthropod diversity in post-mining areas under rehabilitation, such as the season in which samples were collected and primer bias.…”