Abarenkov K, Somervuo P, Nilsson R H, Kirk P M, Huotari T, Abrego N, Ovaskainen O. 2018. Protax-fungi: A web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences. The New Phytologist, 220, 517–525.

Allen M C, Nielsen A L, Peterson D L, Lockwood J L. 2021. Terrestrial eDNA survey outperforms conventional approach for detecting an invasive pest insect within an agricultural ecosystem. Environmental DNA, 3, 1102–1112.

Altschul S F, Gish W, Miller W, Myers E W, Lipman D J. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.

Anderson M J. 2017. Permutational multivariate analysis of variance (PERMANOVA). In: Balakrishnan N, Colton T, Everitt B, Piegorsch W, Ruggeri F, Teugels J L, eds., Wiley StatsRef: Statistics Reference Online. John Wiley & Sons, Hoboken.

Andrews S. 2010. FastQC: A quality control tool for high throughput sequence data. Babraham Institute. [2020-12-22]. https://www.bioinformatics.babraham.ac.uk/projects/fastqc

Arribas P, Andújar C, Salces-Castellano A, Emerson B C, Vogler A P. 2021. The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding. Molecular Ecology, 30, 48–61.

Bell K L, Turo K J, Lowe A, Nota K, Keller A, Encinas-Viso F, Parducci L, Richardson R T, Leggett R M, Brosi B J, Burgess K S, Suyama Y, De Vere N. 2022. Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding. Molecular Ecology, 32, 6345–6362.

Berry O, Jarman S, Bissett A, Hope M, Paeper C, Bessey C, Schwartz M K, Hale J, Bunce M. 2021. Making environmental DNA (eDNA) biodiversity records globally accessible. Environmental DNA, 3, 699–705.

Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E. 2015. obitools: A unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources, 16, 176–182.

Brown B V. 2021. Sampling methods for adult flies (Diptera). In: Santos J C, Fernandes G W, eds., Measuring Arthropod Biodiversity. Springer, Cham. pp. 187–204.

Brown E A, Chain F J J, Zhan A, Macisaac H J, Cristescu M E. 2016. Early detection of aquatic invaders using metabarcoding reveals a high number of non-indigenous species in Canadian ports. Diversity and Distributions, 22, 1045–1059.

Carino F O, Kenmore P E, Dyck V A. 1979. The farmcop suction sampler for hoppers and predators in flooded rice field. International Rice Research Newsletter, 4, 21–22.

Chen H, Zhang G, Zhang Q, Lin Y. 2008. Effect of transgenic Bacillus thuringiensis rice lines on mortality and feeding behavior of rice stem borers (Lepidoptera: Crambidae). Journal of Economic Entomology, 101, 182–189.

Cheng Z, Li Q, Deng J, Liu Q, Huang X. 2023. The devil is in the details: Problems in DNA barcoding practices indicated by systematic evaluation of insect barcodes. Frontiers in Ecology and Evolution, 11, 1149839.

Dang C, Lu Z, Wang L, Chang X, Wang F, Yao H, Peng Y, Stanley D, Ye G. 2017. Does Bt rice pose risks to non-target arthropods? Results of a meta-analysis in China. Plant Biotechnology Journal, 15, 1047–1053.

Dirzo R, Young H S, Galetti M, Ceballos G, Isaac N J B, Collen B. 2014. Defaunation in the Anthropocene. Science, 345, 401–406.

Djurhuus A, Closek C J, Kelly R P, Pitz K J, Michisaki R P, Starks H A, Walz K R, Andruszkiewicz E A, Olesin E, Hubbard K, Montes E, Otis D, Muller-Karger F E, Chavez F P, Boehm A B, Breitbart M. 2020. Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nature Communications, 11, 254.

Dunn J C, Stockdale J E, Moorhouse-Gann R J, Mccubbin A, Hipperson H, Morris A J, Grice P V, Symondson W O C. 2018. The decline of the Turtle Dove: Dietary associations with body condition and competition with other columbids analysed using high-throughput sequencing. Molecular Ecology, 27, 3386–3407.

Edgar R C. 2016. UNOISE2: Improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv, doi: 10.1101/081257.

Elbrecht V, Taberlet P, Dejean T, Valentini A, Usseglio-Polatera P, Beisel J N, Coissac E, Boyer F, Leese F. 2016. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects. PeerJ, 4, e1966.

Ficetola G F, Taberlet P, Coissac E. 2016. How to limit false positives in environmental DNA and metabarcoding? Molecular Ecology Resources, 16, 604–607.

Finn C, Grattarola F, Pincheira-Donoso D. 2023. More losers than winners: Investigating Anthropocene defaunation through the diversity of population trends. Biological Reviews of the Cambridge Philosophical Society, 98, 1732–1748.

Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294–299.

Gamonal Gomez N, Sørensen D H, Chua P Y S, Sigsgaard L. 2023. Assessing flower-visiting arthropod diversity in apple orchards through metabarcoding of environmental DNA from flowers and visual census. Environmental DNA, 5, 117–131.

Gervais A, Chagnon M, Fournier V. 2018. Diversity and pollen loads of flower flies (Diptera: Syrphidae) in cranberry crops. Annals of the Entomological Society of America, 111, 326–334.

Gurr G M, Lu Z, Zheng X, Xu H, Zhu P, Chen G, Yao X, Cheng J, Zhu Z, Catindig J L, Villareal S, Van Chien H, Cuong L Q, Channoo C, Chengwattana N, Lan L P, Hai L H, Chaiwong J, Nicol H I, Perovic D J, et al. 2016. Multi-country evidence that crop diversification promotes ecological intensification of agriculture. Nature Plants, 2, 16014.

Van Der Heyde M, Bunce M, Wardell-Johnson G, Fernandes K, White N E, Nevill P. 2020. Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding. Molecular Ecology Resources, 20, 732–745.

Johnson M D, Katz A D, Davis M A, Tetzlaff S, Edlund D, Tomczyk S, Molano-Flores B, Wilder T, Sperry J H. 2023. Environmental DNA metabarcoding from flowers reveals arthropod pollinators, plant pests, parasites, and potential predator–prey interactions while revealing more arthropod diversity than camera traps. Environmental DNA, 5, 551–569.

Kestel J H, Bateman P W, Field D L, White N E, Lines R, Nevill P. 2023. eDNA metabarcoding of avocado flowers: ‘Hass’ it got potential to survey arthropods in food production systems? Molecular Ecology Resources, 23, 1540–1555.

Kestel J H, Field D L, Bateman P W, White N E, Allentoft M E, Hopkins A J M, Gibberd M, Nevill P. 2022. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. Science of the Total Environment, 847, 157556.

Leray M, Yang J Y, Meyer C P, Mills S C, Agudelo N, Ranwez V, Boehm J T, Machida R J. 2013. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: Application for characterizing coral reef fish gut contents. Frontiers in Zoology, 10, 34.

Letourneau D K, Armbrecht I, Rivera B S, Lerma J M, Carmona E J, Daza M C, Escobar S, Galindo V, Gutiérrez C, López S D, Mejía J L, Rangel A M A, Rangel J H, Rivera L, Saavedra C A, Torres A M, Trujillo A R. 2011. Does plant diversity benefit agroecosystems? A synthetic review. Ecological Applications, 21, 9–21.

Li F, Zhang Y, Altermatt F, Zhang X, Cai Y, Yang Z. 2022. Gap analysis for DNA-based biomonitoring of aquatic ecosystems in China. Ecological Indicators, 137, 108732.

Li Y, Zhang Q, Liu Q, Meissle M, Yang Y, Wang Y, Hua H, Chen X, Peng Y, Romeis J. 2017. Bt rice in China - focusing the nontarget risk assessment. Plant Biotechinology Journal, 15, 1340–1345.

Lu Z, Dang C, Han N, Shen Z, Peng Y, Stanley D, Ye G. 2016. The new transgenic cry1Ab/vip3H rice poses no unexpected ecological risks to arthropod communities in rice agroecosystems. Environmental Entomology, 45, 518–525.

Ma W, Lin L, Peng Q. 2023. Origin, selection, and succession of coastal intertidal zone-derived bacterial communities associated with the degradation of various lignocellulose substrates. Microbial Ecology, 86, 1589–1603.

Macher J N, Macher T H, Leese F. 2017. Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger. Metabarcoding and Metagenomics, 1, e22262.

McCravy K W. 2018. A review of sampling and monitoring methods for beneficial arthropods in agroecosystems. Insects, 9, 170.

Meiklejohn K A, Damaso N, Robertson J M. 2019. Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials. PLoS ONE, 14, e0217084.

Mousavi-Derazmahalleh M, Stott A, Lines R, Peverley G, Nester G, Simpson T, Zawierta M, De La Pierre M, Bunce M, Christophersen C T. 2021. eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity. Molecular Ecology Resources, 21, 1697–1704.

Newton J P, Bateman P W, Heydenrych M J, Kestel J H, Dixon K W, Prendergast K S, White N E, Nevill P. 2023. Monitoring the birds and the bees: Environmental DNA metabarcoding of flowers detects plant–animal interactions. Environmental DNA, 5, 488–502.

Oksanen J, Simpson G, Blanchet F G, Kindt R, Legendre P, Minchin P, Hara R, Solymos P, Stevens H, Szöcs E, Wagner H, Barbour M, Bedward M, Bolker B, Borcard D, Carvalho G, Chirico M, De Cáceres M, Durand S, Weedon J. 2022. Vegan: Community ecology package. R package version 2.6-4. [2024-9-27]. https://CRAN.R-project.org/package=vegan

Orr M C, Ferrari R R, Hughes A C, Chen J, Ascher J S, Yan Y H, Williams P H, Zhou X, Bai M, Rudoy A, Zhang F, Ma K P, Zhu C D. 2021. Taxonomy must engage with new technologies and evolve to face future challenges. Nature Ecology & Evolution, 5, 3–4.

Pentinsaari M, Blagoev G A, Hogg I D, Levesque-Beaudin V, Perez K, Sobel C N, Vandenbrink B, Borisenko A. 2020. A DNA barcoding survey of an arctic arthropod community: Implications for future monitoring. Insects, 11, 46.

Porter T M, Hajibabaei M. 2018. Automated high throughput animal CO1 metabarcode classification. Scientific Reports, 8, 4226.

Prado S G, Ngo H T, Florez J A, Collazo J A. 2017. Sampling bees in tropical forests and agroecosystems: A review. Journal of Insect Conservation, 21, 753–770.

R Core Team. 2023. R: A language and environment for statistical computing. R foundation for statistical computing. Vienna, Austria. [2023-4-19]. https://www.R-project.org/

Reilly J R, Artz D R, Biddinger D, Bobiwash K, Boyle N K, Brittain C, Brokaw J, Campbell J W, Daniels J, Elle E, Ellis J D, Fleischer S J, Gibbs J, Gillespie R L, Gundersen K B, Gut L, Hoffman G, Joshi N, Lundin O, Mason K, et al. 2020. Crop production in the USA is frequently limited by a lack of pollinators. Proceedings of the Royal Society (B: Biological Sciences), 287, 20200922.

Saccò M, Guzik M T, Van Der Heyde M, Nevill P, Cooper S J B, Austin A D, Coates P J, Allentoft M E, White N E. 2022. eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. Science of the Total Environment, 820, 153223.

Senapathi D, Fründ J, Albrecht M, Garratt M P D, Kleijn D, Pickles B J, Potts S G, An J, Andersson G K S, Bänsch S, Basu P, Benjamin F, Bezerra A D M, Bhattacharya R, Biesmeijer J C, Blaauw B, Blitzer E J, Brittain C A, Carvalheiro L G, Cariveau D P, et al. 2021. Wild insect diversity increases inter-annual stability in global crop pollinator communities. Proceedings of the Royal Society (B: Biological Sciences), 288, 20210212.

Smith D P, Peay K G. 2014. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS ONE, 9, e90234.

Smith M R, Singh G M, Mozaffarian D, Myers S S. 2015. Effects of decreases of animal pollinators on human nutrition and global health: A modelling analysis. The Lancet, 386, 1964–1972.

Spafford R D, Lortie C J. 2013. Sweeping beauty: Is grassland arthropod community composition effectively estimated by sweep netting? Ecology and Evolution, 3, 3347–3358.

Strickler K M, Fremier A K, Goldberg C S. 2015. Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms. Biological Conservation, 183, 85–92.

Thomsen P F, Sigsgaard E E. 2019. Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods. Ecology and Evolution, 9, 1665–1679.

Thomsen P F, Willerslev E. 2015. Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation, 183, 4–18.

Tréguier A, Paillisson J M, Dejean T, Valentini A, Schlaepfer M A, Roussel J M. 2014. Environmental DNA surveillance for invertebrate species: Advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds. Journal of Applied Ecology, 51, 871–879.

Valentin R E, Fonseca D M, Gable S, Kyle K E, Hamilton G C, Nielsen A L, Lockwood J L. 2020. Moving eDNA surveys onto land: Strategies for active eDNA aggregation to detect invasive forest insects. Molecular Ecology Resources, 20, 746–755.

Valentin R E, Kyle K E, Allen M C, Welbourne D J, Lockwood J L. 2021. The state, transport, and fate of aboveground terrestrial arthropod eDNA. Environmental DNA, 3, 1081–1092.

Valentin R E, Maslo B, Lockwood J L, Pote J, Fonseca D M. 2016. Real-time PCR assay to detect brown marmorated stink bug, Halyomorpha halys (Stål), in environmental DNA. Pest Management Science, 72, 1854–1861.

Visser F, Merten V J, Bayer T, Oudejans M G, De Jonge D S W, Puebla O, Reusch T B H, Fuss J, Hoving H J T. 2021. Deep-sea predator niche segregation revealed by combined cetacean biologging and eDNA analysis of cephalopod prey. Science Advances, 7, eabf5908.

Vorholt J A. 2012. Microbial life in the phyllosphere. Nature Reviews Microbiology, 10, 828–840.

Wang Y, Chen J, Xiao D, Ma F, Hua H. 2016. Assessing the efficacy of different sampling methods for arthropods in rice field. Journal of Environmental Entomology, 38, 1090–1098. (in Chinese)

Wilson J J, Brandon-Mong G J, Gan H M, Sing K W. 2019. High-throughput terrestrial biodiversity assessments: Mitochondrial metabarcoding, metagenomics or metatranscriptomics? Mitochondrial DNA Part A, 30, 60–67.

Yamamoto S, Masuda R, Sato Y, Sado T, Araki H, Kondoh M, Minamoto T, Miya M. 2017. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific Reports, 7, 40368.

Zafeiropoulos H, Viet H Q, Vasileiadou K, Potirakis A, Arvanitidis C, Topalis P, Pavloudi C, Pafilis E. 2020. PEMA: A flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes. GigaScience, 9, giaa022.

Zeale M R K, Butlin R K, Barker G L A, Lees D C, Jones G. 2011. Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Molecular Ecology Resources, 11, 236–244.

Zenker M M, Specht A, Fonseca V G. 2020. Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol. Ecology and Evolution, 10, 2352–2366.

Zhu H, Zou X, Wang D, Wan S, Wang L, Guo J. 2015. Responses of community-level plant-insect interactions to climate warming in a meadow steppe. Scientific Reports, 5, 18654.

Zinger L, Taberlet P, Schimann H, Bonin A, Boyer F, De Barba M, Gaucher P, Gielly L, Giguet-Covex C, Iribar A, Réjou-Méchain M, Rayé G, Rioux D, Schilling V, Tymen B, Viers J, Zouiten C, Thuiller W, Coissac E, Chave J. 2019. Body size determines soil community assembly in a tropical forest. Molecular Ecology, 28, 528–543.