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

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

Simple Summary

The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance.

Abstract

The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.

Multi-marker DNA metabarcoding detects suites of environmental gradients from an urban harbour

There is increasing need for biodiversity monitoring, especially in places where potential anthropogenic disturbance may significantly impact ecosystem health. We employed a combination of traditional morphological and bulk macroinvertebrate metabarcoding analyses to benthic samples collected from Toronto Harbour (Ontario, Canada) to compare taxonomic and functional diversity of macroinvertebrates and their responses to environmental gradients. At the species rank, sites assessed using COI metabarcoding showed more variation than sites assessed using morphological methods. Depending on the assessment method, we detected gradients in magnesium (morphological taxa), ammonia (morphological taxa, COI sequence variants), pH (18S sequence variants) as well as gradients in contaminants such as metals (COI & 18S sequence variants) and organochlorines (COI sequence variants). Observed responses to contaminants such as aromatic hydrocarbons and metals align with known patchy distributions in harbour sediments. We determined that the morphological approach may limit the detection of macroinvertebrate responses to lake environmental conditions due to the effort needed to obtain fine level taxonomic assignments necessary to investigate responses. DNA metabarcoding, however, need not be limited to macroinvertebrates, can be automated, and taxonomic assignments are associated with a certain level of accuracy from sequence variants to named taxonomic groups. The capacity to detect change using a scalable approach such as metabarcoding is critical for addressing challenges associated with biodiversity monitoring and ecological investigations.

Detecting gold mining impacts on insect biodiversity in a tropical mining frontier with SmallSat imagery

Gold mining is a major driver of Amazonian forest loss and degradation. As mining activity encroaches on primary forest in remote and inaccessible areas, satellite imagery provides crucial data for monitoring mining-related deforestation. High-resolution imagery, in particular, has shown promise for detecting artisanal gold mining at the forest frontier. An important next step will be to establish relationships between satellite-derived land cover change and biodiversity impacts of gold mining. In this study, we set out to detect artisanal gold mining using high-resolution imagery and relate mining land cover to insects, a taxonomic group that accounts for the majority of faunal biodiversity in tropical forests. We applied an object-based image analysis (OBIA) to classify mined areas in an Indigenous territory in Guyana, using PlanetScope imagery with ~3.7 m resolution. We complemented our OBIA with field surveys of insect family presence or absence in field plots (n = 105) that captured a wide range of mining disturbances. Our OBIA was able to identify mined objects with high accuracy (>90% balanced accuracy). Field plots with a higher proportion of OBIA-derived mine cover had significantly lower insect family richness. The effects of mine cover on individual insect taxa were highly variable. Insect groups that respond strongly to mining disturbance could potentially serve as bioindicators for monitoring ecosystem health during and after gold mining. With the advent of global partnerships that provide universal access to PlanetScope imagery for tropical forest monitoring, our approach represents a low-cost and rapid way to assess the biodiversity impacts of gold mining in remote landscapes.

A novel approach for reliable qualitative and quantitative prey spectra identification of carnivorous plants combining DNA metabarcoding and macro photography

Prey spectra (the number and composition of captured arthropods) represent a crucial aspect of carnivorous plant ecology, yet remain poorly studied. Traditional morphology-based approaches for prey identification are time-intensive, require specialists with considerable knowledge of arthropod taxonomy, and are hampered by high numbers of unidentifiable (i.e., heavily digested) prey items. We examined prey spectra of three species of closely-related annual Drosera (Droseraceae, sundews) from tropical northern Australia using a novel DNA metabarcoding approach with in-situ macro photography as a plausibility control and to facilitate prey quantity estimations. This new method facilitated accurate analyses of carnivorous plant prey spectra (even of heavily digested prey lacking characteristic morphological features) at a taxonomic resolution and level of completeness far exceeding morphology-based methods and approaching the 100% mark at arthropod order level. Although the three studied species exhibited significant differences in detected prey spectra, little prey specialisation was observed and habitat or plant population density variations were likely the main drivers of prey spectra dissimilarity.

Evaluating restoration trajectories using DNA metabarcoding of ground-dwelling and airborne invertebrates and associated plant communities

Invertebrates are important for restoration processes as they are key drivers of many landscape‐scale ecosystem functions; including pollination, nutrient cycling and soil formation. However, invertebrates are often overlooked in restoration monitoring because they are highly diverse, poorly described, and time‐consuming to survey, and require increasingly scarce taxonomic expertise to enable identification. DNA metabarcoding is a relatively new tool for rapid survey that is able to address some of these concerns, and provide information about the taxa with which invertebrates are interacting via food webs and habitat. Here, we evaluate how invertebrate communities may be used to determine ecosystem trajectories during restoration. We collected ground‐dwelling and airborne invertebrates across chronosequences of mine‐site restoration in three ecologically disparate locations in Western Australia and identified invertebrate and plant communities using DNA metabarcoding. Ground‐dwelling invertebrates showed the clearest restoration signals, with communities becoming more similar to reference communities over time. These patterns were weaker in airborne invertebrates, which have higher dispersal abilities and therefore less local fidelity to environmental conditions. Although we detected directional changes in community composition indicative of invertebrate recovery, patterns observed were inconsistent between study locations. The inclusion of plant assays allowed identification of plant species, as well as potential food sources and habitat. We demonstrate that DNA metabarcoding of invertebrate communities can be used to evaluate restoration trajectories. Testing and incorporating new monitoring techniques such as DNA metabarcoding is critical to improving restoration outcomes.

Changes in soil microbial communities in post mine ecological restoration: Implications for monitoring using high throughput DNA sequencing

The ecological restoration of ecosystem services and biodiversity is a key intervention used to reverse the impacts of anthropogenic activities such as mining. Assessment of the performance of restoration against completion criteria relies on biodiversity monitoring. However, monitoring usually overlooks soil microbial communities (SMC), despite increased awareness of their pivotal role in many ecological functions. Recent advances in cost, scalability and technology has led to DNA sequencing being considered as a cost-effective biological monitoring tool, particularly for otherwise difficult to survey groups such as microbes. However, such approaches for monitoring complex restoration sites such as post-mined landscapes have not yet been tested. Here we examine bacterial and fungal communities across chronosequences of mine site restoration at three locations in Western Australia to determine if there are consistent changes in SMC diversity, community composition and functional capacity. Although we detected directional changes in community composition indicative of microbial recovery, these were inconsistent between locations and microbial taxa (bacteria or fungi). Assessing functional diversity provided greater understanding of changes in site conditions and microbial recovery than could be determined through assessment of community composition alone. These results demonstrate that high-throughput amplicon sequencing of environmental DNA (eDNA) is an effective approach for monitoring the complex changes in SMC following restoration. Future monitoring of mine site restoration using eDNA should consider archiving samples to provide improved understanding of changes in communities over time. Expansion to include other biological groups (e.g. soil fauna) and substrates would also provide a more holistic understanding of biodiversity recovery.

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

Human activities change natural landscapes, and in doing so endanger biodiversity and associated ecosystem services. To reduce the net impacts of these activities, such as mining, disturbed areas are rehabilitated and restored. During this process, monitoring is important to ensure that desired trajectories are maintained. In the Carajás region of the Brazilian Amazon, exploration for iron ores has transformed the original ecosystem; natural forest and a savanna formation with lateritic iron duricrust outcrops named canga. Here, native vegetation is logged and topsoil removed and deposited in waste piles along with mine waste. During rehabilitation, these waste piles are hydroseeded with non-native plant species to achieve rapid revegetation. Further, seeds of native canga and forest plant species are planted to point ecological succession towards natural ecosystems. In this study, we investigate diversity and composition of the arthropod community along a post-mining rehabilitation and restoration gradient, taking seasonality and primer bias into account. We use DNA metabarcoding of bulk arthropod samples collected in both the dry and rainy seasons from waste-pile benches at various stages of revegetation: non-revegetated exposed soils, initial stage with one-to-three-year-old stands, intermediate stage with four-to-five-year-old stands, and advanced stage with six-to-seven-year-old stands. We use samples from undisturbed cangas and forests as reference sites. In addition, we vegetation diversity and structure were measured to investigate relations between arthropod community and vegetation structure. Our results show that, over time, the arthropod community composition of the waste piles becomes more similar to the reference forests, but not to the reference cangas. Nevertheless, even the communities in the advanced-stage waste piles are different from the reference forests, and full restoration in these highly diverse ecosystems is not achieved, even after 6 to 7 years. Finally, our results show seasonal variation in arthropod communities and primer bias.

Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

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.