Using surface environmental DNA to assess arthropod biodiversity within a forested ecosystem

Allen, Michael C.; Lockwood, Julie L.; Kwait, Robert; Vastano, Anthony R.; Peterson, Donnie L.; Tkacenko, Leon; Angle, Jordan C.; Jaffe, Benjamin D

doi:10.22541/au.166723594.46081923/v1

Cited by 4 publications

(6 citation statements)

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“…These results could have been due to the larger number of species‐level reference sequences available for COI compared with 16S (e.g., 58,323 species for COI vs. 33,540 for 16S in our curated reference database; available in Allen, Lockwood, et al. 2023). In contrast, the two primer sets have very similar representation of higher taxonomic groups in the reference database (e.g., 90 orders for COI and 92 for 16S).…”

Section: Resultsmentioning

confidence: 99%

“…Detailed information on taxonomic assignments, including the match level and taxa identified by each approach, as well as the amplicon sequences, are available in Allen, Lockwood, et al. (2023).…”

Section: Methodsmentioning

confidence: 99%

“…All data and code associated with this study are archived and are openly available (Allen, Lockwood, et al. 2023).…”

Section: Methodsmentioning

confidence: 99%

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Using surface environmental DNA to assess arthropod biodiversity within a forested ecosystem

Allen,

Lockwood,

Kwait

et al. 2023

Environmental DNA

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Terrestrial arthropods are a diverse taxonomic group of significant ecological and economic importance. Our ability to understand the diversity that comprises this group is hampered by the variety of sampling techniques and high level of taxonomic expertise required to identify individual species. DNA metabarcoding approaches have potential to overcome these challenges but have been mainly limited to studies where DNA is directly extracted from trapped individuals. We posit that collection of environmental DNA (eDNA) deposited on vegetation surfaces could provide an alternative method of conducting metabarcoding‐based arthropod inventories. In this study, we illustrate the promise of characterizing arthropod biodiversity based on eDNA collected from terrestrial plant surfaces. We collected 40 paired samples using two novel eDNA sampling techniques—tree bark and foliage sampling—in a New Jersey, USA, pine barrens forest. Metabarcoding using two primer sets revealed significantly higher taxonomic richness for the 16S versus COI primer set (1077 vs. 650 molecular operational taxonomic units; MOTUs), as well as higher richness and diversity in foliage versus bark samples. Accumulation curves suggest that our samples captured about half of the available MOTU‐level diversity. Matching to reference databases revealed 28 arthropod orders, 181 families, 353 genera, and 292 species. Despite having lower MOTU‐level richness, the COI primer set revealed more taxa that were identified to species (197 vs. 115) and genus (227 vs. 173) thanks to a more complete reference database. The two primer sets and sampling substrates showed distinct community compositions that differed in important ecological traits (feeding guild, body size), demonstrating the utility of a multi‐faceted sampling and analytical approach. Our study highlights the value of exploiting eDNA left on plant surfaces via metabarcoding for contributing to rapid arthropod inventories, and thus realizing a range of ecological research and management goals.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Using surface environmental DNA to assess arthropod biodiversity within a forested ecosystem

Allen,

Lockwood,

Kwait

et al. 2023

Environmental DNA

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“…eDNA is typically recovered from plant surfaces by washing it off with water and filtering the wash‐off (Allen et al., 2022; Macher et al., 2023; Valentin et al., 2020). However, washes are probably limited to taxa from the surface of the plant.…”

Section: Introductionmentioning

confidence: 99%

Plant‐derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant–arthropod interactions

Weber,

Stothut,

Mahla

et al. 2023

Molecular Ecology Resources

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Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with plants are barely understood. A promising strategy to overcome this shortfall is environmental DNA (eDNA) metabarcoding from plant material on which arthropods leave DNA traces through direct or indirect interactions. However, the accuracy of this approach has not been sufficiently tested. In four experiments, we exhaustively test the comparative performance of plant‐derived eDNA from surface washes of plants and homogenized plant material against traditional monitoring approaches. We show that the recovered communities of plant‐derived eDNA and traditional approaches only partly overlap, with eDNA recovering various additional taxa. This suggests eDNA as a useful complementary tool to traditional monitoring. Despite the differences in recovered taxa, estimates of community α‐ and β‐diversity between both approaches are well correlated, highlighting the utility of eDNA as a broad scale tool for community monitoring. Last, eDNA outperforms traditional approaches in the recovery of plant‐specific arthropod communities. Unlike traditional monitoring, eDNA revealed fine‐scale community differentiation between individual plants and even within plant compartments. Especially specialized herbivores are better recovered with eDNA. Our results highlight the value of plant‐derived eDNA analysis for large‐scale biodiversity assessments that include information about community‐level interactions.

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“…However, surveys using environmental DNA (eDNA) detection tools offer a solution to aid in finding target populations at low or rare abundance. These methods have advanced aquatic sampling research for decades by reliably increasing detection probabilities through their ability to pick up DNA signatures left behind by target organisms without ever having to see them (Darling & Blum, 2007; Jerde et al., 2011) and have also gained traction in invasive species detection (Allen et al., 2021; Valentin et al., 2018; Valentin, Fonseca, et al., 2020; 2021) and biodiversity monitoring of terrestrial landscapes more recently (Allen et al., 2023).…”

Section: Introductionmentioning

confidence: 99%

Development of novel LAMP and qPCR assays for rapid and specific identification of Bronze birch borer (Agrilus anxius)

Peterson,

Pecori,

Luchi

et al. 2023

Environmental DNA

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Buprestids are an emerging threat to broadleaf forests across the world. Bronze birch borer (Agrilus anxius, BBB) poses a serious threat to European birch species if the insect were to be introduced. Due to their cryptic lifestyle feeding on the vascular tissue of their host plants, buprestids and other wood borers can be difficult to observe or detect. Early detection tools are vital to swiftly implement eradication measures and prevent the establishment of introduced species. In this study, we developed novel qPCR and LAMP assays for BBB and investigated the specificity and sensitivity for their use as early detection tools in European forests. Plant chemicals may limit these assays, so we conducted sensitivity testing with extracted foliage and plant vascular tissues to determine potential inhibition effects on DNA amplification. Both assays were specific to the target species when tested against the DNA of 17 other European Agrilus/buprestid species, two Scolytinae, and five Cerambycids (N = 24). Both assays varied in sensitivity with the qPCR assay amplifying at a concentration as low as 20 fg/μL, whereas the LAMP assay amplified as low as 3.2 pg/μL. Plant chemicals in DNA extracts from leaves did not impact the sensitivity of either assay, reaching similar detection levels. In contrast, vascular tissue reduced the sensitivity of the LAMP assay, amplifying as low as 0.04 ng/μL compared with 0.008 ng/μL in the control. These results demonstrate that both assays are highly specific and sensitive tools that can be used to detect frass and identify larvae as well as monitor the spread of A. anxius. qPCR resulted in more sensitive than LAMP overall. Thus, if results are needed quickly to make fast management decisions or as an initial screening of samples, the LAMP method is optimal. However, if fine detection is critical, then qPCR is preferential.

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Using surface environmental DNA to assess arthropod biodiversity within a forested ecosystem

Cited by 4 publications

References 0 publications

Using surface environmental DNA to assess arthropod biodiversity within a forested ecosystem

Using surface environmental DNA to assess arthropod biodiversity within a forested ecosystem

Plant‐derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant–arthropod interactions

Development of novel LAMP and qPCR assays for rapid and specific identification of Bronze birch borer (Agrilus anxius)

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