Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species

Sire, Lucas; Yáñez, Paul Schmidt; Cai, Wei; Bézier, Annie; Courtial, Béatrice; Cours, Jérémy; Fontaneto, Diego; Larrieu, Laurent; Bouget, Christophe; Thorn, Simon; Müller, Jörg; Yu, Douglas W.; Monaghan, Michael T.; Herniou, Elisabeth A.; Lopez-Vaamonde, Carlos

doi:10.1038/s42003-021-02968-4

Cited by 16 publications

(20 citation statements)

References 85 publications

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“…Homogenization of bulk samples and subsequent DNA extraction from destructed tissue is widely applied when insect biodiversity is assessed using DNA metabarcoding (Beermann et al, 2021 ; Hardulak et al, 2020 ; Mata et al, 2021 ). This destructive approach is known to be highly efficient for bulk sample analysis at a lesser cost compared with nondestructive protocols (Marquina et al, 2019 ; Persaud et al, 2021 ; Sire et al, 2022 ; Zenker et al, 2020 ). However, the application of DNA extraction from ethanol fixative or lysis buffer has the advantage of ensuring sample integrity, and the evaluation of various protocols is ongoing.…”

Section: Discussionmentioning

confidence: 99%

“…Since drying and homogenizing result in a fine powder, it requires more careful handing than wet material due to the increased chance of cross‐contamination. Most DNA extraction protocols are limited to low amounts of starting tissue per reaction, and only a subsample of complete material is usually processed, ranging between 1 and 100 mg (Hausmann et al, 2020 ; Marquina et al, 2019 ; Mata et al, 2021 ; Sire et al, 2022 ). Higher tissue volume during DNA extraction requires multiple reactions or more voluminous DNA extraction kits resulting in an increased effort and cost.…”

Section: Introductionmentioning

confidence: 99%

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Repeated subsamples during DNA extraction reveal increased diversity estimates in DNA metabarcoding of Malaise traps

Zizka

Geiger

Hörren³

et al. 2022

Ecology and Evolution

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With increased application of DNA metabarcoding in biodiversity assessment, various laboratory protocols have been optimized, and their further evaluation is subject of current research. Homogenization of bulk samples and subsequent DNA extraction from a subsample of destructed tissue is a common first stage of the metabarcoding process. This can either be conducted using sample material soaked in a storage fixative, e.g., ethanol (here referred to as “wet” treatment) or from dried individuals (“dry”). However, it remains uncertain if perfect mixing and equal distribution of DNA within the tube is ensured during homogenization and to what extent incomplete mixing and resulting variations in tissue composition affect diversity assessments if only a fraction of the destructed sample is processed in the downstream metabarcoding workflow. Here we investigated the efficiency of homogenization under wet and dry conditions and tested how variations in destructed tissue composition might affect diversity assessments of complex arthropod samples. We considered five time intervals of Malaise trap bulk samples and process nine different subsamples of homogenized tissue (20 mg each) in both treatments. Results indicate a more consistent diversity assessment from dried material, but at the cost of a higher processing time. Both approaches detected comparable OTU diversity and revealed similar taxa compositions in a single tissue extraction. With an increased number of tissue subsamples during DNA extraction, OTU diversity increased for both approaches, especially for highly diverse samples obtained during the summer. Here, particularly the detection of small and low‐biomass taxa increased. The processing of multiple subsamples in the metabarcoding protocol can therefore be a helpful procedure to enhance diversity estimates and counteract taxonomic bias in biodiversity assessments. However, the process induces higher costs and time effort and the application in large‐scale biodiversity assessment, e.g., in monitoring schemes needs to be considered on project‐specific prospects.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Repeated subsamples during DNA extraction reveal increased diversity estimates in DNA metabarcoding of Malaise traps

Zizka

Geiger

Hörren³

et al. 2022

Ecology and Evolution

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“…Arthropod communities were sampled between May 15th and June 15th of 2017, in 28 silver fir-dominated forest stands in the French Pyrenees, by following two categorical gradients of climate-induced tree dieback and post-disturbance salvage logging (Sire et al . 2022).…”

Section: Methodsmentioning

confidence: 99%

“…One major shortfall of the metabarcoding approach is the use of destructive DNA extraction from tissue-homogenate after organisms are dried and ground to fine powder (Yu et al . 2012; Sire et al . 2022).…”

Section: Introductionmentioning

confidence: 99%

Non-destructive DNA metabarcoding of arthropods using collection medium from passive traps

Sire

Yáñez

Bézier

et al. 2023

Preprint

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Background: Broad-scale monitoring of arthropods is often carried out with passive traps (e.g. Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates is faster and has been found to be efficient and reliable, but is destructive and prevents a posteriori validation of species occurrences and/or relative abundances. Non-destructive DNA metabarcoding from the collection medium has been applied in a limited number of studies, but further tests of efficiency are required in a broader range of circumstances to assess the consistency of the method. Methods: We quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two types of passive traps and collection media: 1) water with monopropylene glycol (H2O-MPG) used in window-flight traps (WFT, 53 in total); 2) ethanol with monopropylene glycol (EtOH-MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba) stands across a range of climate-induced tree dieback levels and forest management strategies. Results: Of the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total. None of those MOTUs were shared species with the 389 morphological taxa (343 of which were Coleoptera) obtained from the same traps. Metabarcoding of 26 EtOH-MPG samples from MTs detected more arthropod MOTUs (233) and insect orders (11) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders). Arachnida and Collembola were more diverse in EtOH-MPG samples, but Hymenoptera, Coleoptera and Lepidoptera were less represented than in homogenate. Overall, MOTU richness per trap similar for EtOH-MPG (21.81 MOTUs) than for homogenate (32.4 MOTUs). Arthropod communities from EtOH-MPG and homogenate metabarcoding were relatively distinct, with 162 MOTUs (53%) unique to the collection medium and only 71 MOTUs (23%) present in both treatments. Finally, collection medium did not reveal any significant changes in arthropod richness along a disturbance gradient in silver fir forests. We conclude that DNA metabarcoding of collection medium can be used to complement homogenate metabarcoding in inventories to favour the detection of soft-bodied arthropods like spiders.

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“…At the population and ecosystem levels, parasitoid community composition can be estimated through metabarcoding of bulk Malaise trap catches (cf. Kirse et al, 2022;Sire et al, 2022). With appropriate trapping designs, parasitoid community structures can then be contrasted with spatial variation and multi-year trajectories in host densities.…”

Section: Future Prospectsmentioning

confidence: 99%

A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths

Nyman

Wutke

Koivisto

et al. 2022

Ecology and Evolution

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Large areas of forests are annually damaged or destroyed by outbreaking insect pests. Understanding the factors that trigger and terminate such population eruptions has become crucially important, as plants, plant‐feeding insects, and their natural enemies may respond differentially to the ongoing changes in the global climate. In northernmost Europe, climate‐driven range expansions of the geometrid moths Epirrita autumnata and Operophtera brumata have resulted in overlapping and increasingly severe outbreaks. Delayed density‐dependent responses of parasitoids are a plausible explanation for the 10‐year population cycles of these moth species, but the impact of parasitoids on geometrid outbreak dynamics is unclear due to a lack of knowledge on the host ranges and prevalences of parasitoids attacking the moths in nature. To overcome these problems, we reviewed the literature on parasitism in the focal geometrid species in their outbreak range and then constructed a DNA barcode reference library for all relevant parasitoid species based on reared specimens and sequences obtained from public databases. The combined recorded parasitoid community of E. autumnata and O. brumata consists of 32 hymenopteran species, all of which can be reliably identified based on their barcode sequences. The curated barcode library presented here opens up new opportunities for estimating the abundance and community composition of parasitoids across populations and ecosystems based on mass barcoding and metabarcoding approaches. Such information can be used for elucidating the role of parasitoids in moth population control, possibly also for devising methods for reducing the extent, intensity, and duration of outbreaks.

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Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species

Cited by 16 publications

References 85 publications

Repeated subsamples during DNA extraction reveal increased diversity estimates in DNA metabarcoding of Malaise traps

Repeated subsamples during DNA extraction reveal increased diversity estimates in DNA metabarcoding of Malaise traps

Non-destructive DNA metabarcoding of arthropods using collection medium from passive traps

A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths

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