본문 바로가기
KERD
논문KCI 등재

Current methodologies in construction of plant-pollinator network with emphasize on the application of DNA metabarcoding approach

0

조회

0

다운로드

3

인용

0

참고문헌

키워드

주제분류생물학

초록

Background: Pollinators are important ecological elements due to their role in the maintenance of ecosystem health, wild plant reproduction, crop production and food security. The pollinator-plant interaction supports the preservation of plant and animal populations and it also improves the yield in pollination dependent crops. Having knowledge about the plant-pollinator interaction is necessary for development of pesticide risk assessment of pollinators and conservation of endangering species. Results: Traditional methods to discover the relatedness of insects and plants are based on tracing the visiting pollinators by field observations as well as palynology. These methods are time-consuming and needs expert taxonomists to identify different groups of pollinators such as insects or identify flowering plants through palynology. With pace of technology, using molecular methods become popular in identification and classification of organisms. DNA metabarcoding, which is the combination of DNA barcoding and high throughput sequencing, can be applied as an alternative method in identification of mixed origin environmental samples such as pollen loads attached to the body of insects and has been used in DNA-based discovery of plant-pollinator relationship. Conclusions: DNA metabarcoding is practical for plant-pollinator studies, however, lack of reference sequence in online databases, taxonomic resolution, universality of primers are the most crucial limitations. Using multiple molecular markers is preferable due to the limitations of developed universal primers, which improves taxa richness and taxonomic resolution of the studied community.

Abstract

Background: Pollinators are important ecological elements due to their role in the maintenance of ecosystem health, wild plant reproduction, crop production and food security. The pollinator-plant interaction supports the preservation of plant and animal populations and it also improves the yield in pollination dependent crops. Having knowledge about the plant-pollinator interaction is necessary for development of pesticide risk assessment of pollinators and conservation of endangering species. Results: Traditional methods to discover the relatedness of insects and plants are based on tracing the visiting pollinators by field observations as well as palynology. These methods are time-consuming and needs expert taxonomists to identify different groups of pollinators such as insects or identify flowering plants through palynology. With pace of technology, using molecular methods become popular in identification and classification of organisms. DNA metabarcoding, which is the combination of DNA barcoding and high throughput sequencing, can be applied as an alternative method in identification of mixed origin environmental samples such as pollen loads attached to the body of insects and has been used in DNA-based discovery of plant-pollinator relationship. Conclusions: DNA metabarcoding is practical for plant-pollinator studies, however, lack of reference sequence in online databases, taxonomic resolution, universality of primers are the most crucial limitations. Using multiple molecular markers is preferable due to the limitations of developed universal primers, which improves taxa richness and taxonomic resolution of the studied community.

참고문헌 (99)

  1. Armbruster WS, "The specialization continuum in pollination systems : diversity of concepts and implications for ecology, evolution and conservation", Funct Ecol, 31(1), pp.88~100 (2017)[DOI]
  2. Bailes EJ, "How can an understanding of plant-pollinator interactions contribute to global food security?", Curr Opin Plant Biol, 26, pp.72~79 (2015)[DOI]
  3. Baksay S, "Experimental quantification of pollen with DNA metabarcoding using ITS1 and trnL", Sci Rep, 10(1), pp.4202~ (2020)[DOI]
  4. "Reconstructing great basin butterfly-pollen interaction networks over the past century" (2020)[URL]
  5. Bascompte J, "Asymmetric coevolutionary networks facilitate biodiversity maintenance", Science, 312(5772), pp.431~433 (2006)[DOI]
  6. Bascompte J, "Plant-animal mutualistic networks : the architecture of biodiversity", Annu Rev Ecol Evol Syst, 38, pp.567~593 (2007)[DOI]
  7. Batuecas I, "Development of a multi-primer metabarcoding approach to understand trophic interactions in agroecosystems", Insect Science (2022)[DOI]
  8. Beattie AJ, "A technique for the study of insect-borne pollen", Pan-Pac Entomol, 47(1), pp.82~ (1971)
  9. Bell KL, "Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures", Mol Ecol, 28(2), pp.431~455 (2019)[DOI]
  10. Bell KL, "Review and future prospects for DNA barcoding methods in forensic palynology", Forensic Sci Int Genet, 21, pp.110~116 (2016)[DOI]
  11. Bell KL, "Applying pollen DNA metabarcoding to the study of plant-pollinator interactions", Appl Plant Sci, 5(6) (2017)[DOI]
  12. Bell KL, "An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding", Appl Plant Sci, 5(3) (2017)[DOI]
  13. Bengtsson-Palme J, "Metaxa2 Database Builder : enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker", Bioinformatics, 34(23), pp.4027~4033 (2018)[DOI]
  14. Bovo S, "Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity", Sci Rep, 10(1), pp.9279~ (2020)[DOI]
  15. Boyer F, "obitools : a unix-inspired software package for DNA metabarcoding", Mol Ecol Resour, 16(1), pp.176~182 (2016)[DOI]
  16. Bruni I, "A DNA barcoding approach to identify plant species in multiflower honey", Food Chem, 170, pp.308~315 (2015)[DOI]
  17. Chagnon PL, "Using ecological network theory to evaluate the causes and consequences of arbuscular mycorrhizal community structure", New Phytol, 194(2), pp.307~312 (2012)[DOI]
  18. Chen S, "Validation of the ITS2region as a novel DNA barcode for identifying medicinal plant species", PLoS One, 5(1), pp.e8613~ (2010)[DOI]
  19. Cheng T, "Barcoding the kingdom Plantae : new PCR primers for ITS regions of plants with improved universality and specificity", Mol Ecol Resour, 16(1), pp.138~149 (2016)[DOI]
  20. Corriveau JL, "Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species", Am J Bot, 75(10), pp.1443~1458 (1988)[DOI]
  21. Danieli-Silva A, "Do pollination syndromes cause modularity and predict interactions in a pollination network in tropical high-altitude grasslands?", Oikos, 121(1), pp.35~43 (2012)[DOI]
  22. de Vere N, "Using DNA metabarcoding to investigate honey bee foraging reveals limited flower use despite high floral availability", Sci Rep, 7, pp.42838~ (2017)[DOI]
  23. de Vere N, "DNA barcoding the native flowering plants and conifers of Wales", PLoS One, 7(6), pp.e37945~ (2012)[DOI]
  24. Dodd ME, "Phylogenetic analysis of trait evolution and species diversity variation among angiosperm families", Evolution, 53(3), pp.732~744 (1999)[DOI]
  25. Dormann CF, "A method for detecting modules in quantitative bipartite networks", Methods Ecol Evol, 5(1), pp.90~98 (2014)[DOI]
  26. Dufresne Y, "SLIM : a flexible web application for the reproducible processing of environmental DNA metabarcoding data", BMC Bioinformatics, 20(1), pp.88~ (2019)[DOI]
  27. "UTAX algorithm" (2015)[URL]
  28. Elbrecht V, "Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass--sequence relationships with an innovative metabarcoding protocol", PLoS One, 10(7), pp.e0130324~ (2015)[DOI]
  29. Elton CS, "Animal ecology", Sidgwick and Jackson, ~ (1927)
  30. Forup ML, "The restoration of ecological interactions : plant-pollinator networks on ancient and restored heathlands", J Appl Ecol, 45(3), pp.742~752 (2008)[DOI]
  31. Frost CM, "Using network theory to understand and predict biological invasions", Trends Ecol Evol, 34(9), pp.831~843 (2019)[DOI]
  32. Fründ J, "Pollinator diversity and specialization in relation to flower diversity", Oikos, 119(10), pp.1581~1590 (2010)
  33. Galal-Khallaf A, "Towards more sustainable surimi? PCR-cloning approach for DNA barcoding reveals the use of species of low trophic level and aquaculture in Asian surimi", Food Control, 61, pp.62~69 (2016)[DOI]
  34. Galimberti A, "A DNA barcoding approach to characterize pollen collected by honeybees", PLoS One, 9(10), pp.e109363~ (2014)[DOI]
  35. Galtier N, "Mitochondrial DNA as a marker of molecular diversity : a reappraisal", Mol Ecol, 18(22), pp.4541~4550 (2009)[DOI]
  36. Garrido-Sanz L, "Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics", MBMG, 4, pp.e48281~ (2020)[DOI]
  37. Ghosh S, "Metagenomics and microbial ecology: techniques and applications", pp.105~116 (2021), CRC Press
  38. Gómez JM, "The functional consequences of mutualistic network architecture", PLoS One, 6(1), pp.e16143~ (2011)[DOI]
  39. Gous A, "Plant-pollinator interactions over time : pollen metabarcoding from bees in a historic collection", Evol Appl, 12(2), pp.187~197 (2019)[DOI]
  40. Hawkins J, "Using DNA metabarcoding to identify the floral composition of honey : a new tool for investigating honey bee foraging preferences", PLoS One, 10(8), pp.e0134735~ (2015)[DOI]
  41. Hebert PD, "Ten species in one : DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator", Proc Natl Acad Sci U S A, 101(41), pp.14812~14817 (2004)[DOI]
  42. Hebert PD, "Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species", Proc Biol Sci, 270(Suppl 1), pp.S96~99 (2003)[DOI]
  43. Hegland SJ, "How does climate warming affect plant-pollinator interactions?", Ecol Lett, 12(2), pp.184~195 (2009)[DOI]
  44. x. Hu Y, "Occurrence of plastids in the sperm cells of Caprifoliaceae : biparental plastid inheritance in angiosperms is unilaterally derived from maternal inheritance", Plant Cell Physiol, 49(6), pp.958~968 (2008)[DOI]
  45. Isbell F, "High plant diversity is needed to maintain ecosystem services", Nature, 477(7363), pp.199~202 (2011)[DOI]
  46. Jordano P, "Specialization and generalization in plantpollinator interactions", pp.173~199 (2006), University of Chicago Press
  47. Kaiser-Bunbury CN, "The robustness of pollination networks to the loss of species and interactions : a quantitative approach incorporating pollinator behaviour", Ecol Lett, 13(4), pp.442~452 (2010)[DOI]
  48. Keller A, "Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples", Plant Biol(Stuttg), 17(2), pp.558~566 (2015)[DOI]
  49. Khansari E, "Pollen morphology of Campanula(Campanulaceae)and allied genera in Iran with special focus on its systematic implication", Flora, 207(3), pp.203~211 (2012)[DOI]
  50. Khansaritoreh E, "Employing DNA metabarcoding to determine the geographical origin of honey", Heliyon, 6(11), pp.e05596~ (2020)[DOI]
  51. King C, "Why flower visitation is a poor proxy for pollination : measuring single-visit pollen deposition, with implications for pollination networks and conservation", Methods Ecol Evol, 4(9), pp.811~818 (2013)[DOI]
  52. Klein AM, "Importance of pollinators in changing landscapes for world crops", Proc Biol Sci, 274(1608), pp.303~313 (2007)[DOI]
  53. Kraaijeveld K, "Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing", Mol Ecol Resour, 15(1), pp.8~16 (2015)[DOI]
  54. Laha RC, "Meta-barcoding in combination with palynological inference is a potent diagnostic marker for honey floral composition", AMB Express, 7(1), pp.189~ (2017)[DOI]
  55. Leontidou K, "DNA metabarcoding of airborne pollen : new protocols for improved taxonomic identification of environmental samples", Aerobiologia, 34(1), pp.63~74 (2018)[DOI]
  56. Lopezaraiza-Mikel ME, "The impact of an alien plant on a native plant-pollinator network : an experimental approach", Ecol Lett, 10(7), pp.539~550 (2007)[DOI]
  57. Lucas A, "Floral resource partitioning by individuals within generalised hoverfly pollination networks revealed by DNA metabarcoding", Sci Rep, 8(1), pp.5133~ (2018)[DOI]
  58. McGinnis S, "BLAST: at the core of a powerful and diverse set of sequence analysis tools", Nucleic Acids Res, 32(Web Server), pp.W20~25 (2004)[DOI]
  59. Memmott J, "Tolerance of pollination networks to species extinctions", Proc Biol Sci, 271(1557), pp.2605~2611 (2004)[DOI]
  60. Saeed Mohamadzade Namin, "Genetic diversity of genus Vespa including an invaded species of V. velutina (Hymenoptera: Vespidae) in Korea inferred from DNA barcoding data", Journal of Asia-Pacific Entomology, 23(2), pp.540~545 (2020), 한국응용곤충학회[DOI]
  61. Mohamadzade Namin S, "Molecular characteristics of Bombus(Alpinobombus)polaris from North Greenland with comments on its general biology and phylogeography", Polar Biol, 44, pp.2209~2216 (2021)[DOI]
  62. Moorhouse-Gann RJ, "New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones", Sci Rep, 8(1), pp.8542~ (2018)[DOI]
  63. Nagata N, "The selective increase or decrease of organellar DNA in generative cells just after pollen mitosis one controls cytoplasmic inheritance", Planta, 209(1), pp.53~65 (1999)[DOI]
  64. Novella-Fernandez R, "Interaction strength in plant-pollinator networks: are we using the right measure?", PLoS One, 14(12), pp.e0225930~ (2019)[DOI]
  65. Olesen JM, "The modularity of pollination networks", Proc Natl Acad Sci U S A, 104(50), pp.19891~19896 (2007)[DOI]
  66. Ollerton J, "How many flowering plants are pollinated by animals?", Oikos, 120(3), pp.321~326 (2011)[DOI]
  67. Parducci L, "Shotgun DNA, pollen and biological multi-proxy analysis of Lateglacial lake sediments from Monticchio", EGU General Assembly, ~ (2020)
  68. Peel N, "Semi-quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics(RevMet)", Methods Ecol Evol, 10(10), pp.1690~1701 (2019)[DOI]
  69. Pocock MJ, "The robustness and restoration of a network of ecological networks", Science, 335(6071), pp.973~977 (2012)[DOI]
  70. Pornon A, "DNA metabarcoding data unveils invisible pollination networks", Sci Rep, 7(1), pp.16828~ (2017)[DOI]
  71. Pornon A, "Using metabarcoding to reveal and quantify plant-pollinator interactions", Sci Rep, 6, pp.27282~ (2016)[DOI]
  72. Potter C, "Pollen metabarcoding reveals broad and species-specific resource use by urban bees", PeerJ, 7, pp.e5999~ (2019)[DOI]
  73. Richardson RT, "Quantitative multi-locus metabarcoding and waggle dance interpretation reveal honey bee spring foraging patterns in Midwest agroecosystems", Mol Ecol, 28(3), pp.686~697 (2019)[DOI]
  74. Richardson RT, "Rank-based characterization of pollen assemblages collected by honey bees using a multi-locus metabarcoding approach", Appl Plant Sci, 3(11) (2015)[DOI]
  75. Richardson RT, "Application of ITS2 metabarcoding to determine the provenance of pollen collected by honey bees in an agroecosystem", Appl Plant Sci, 3(1) (2015)[DOI]
  76. Robeson MS, "RESCRIPt : Reproducible sequence taxonomy reference database management", PLoS Comput Biol, 17(11), pp.e1009581~ (2021)[DOI]
  77. Seo E, "Predicting links in plant-pollinator interaction networks using latent factor models with implicit feedback", Proceed AAAI Conf Artif Intell, 32(1), pp.808~815 (2018)
  78. Shokralla S, "Next-generation sequencing technologies for environmental DNA research", Mol Ecol, 21(8), pp.1794~1805 (2012)[DOI]
  79. Sickel W, "Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach", BMC Ecol, 15, pp.20~ (2015)[DOI]
  80. Smart MD, "A comparison of honey bee-collected pollen from working agricultural lands using light microscopy and ITS metabarcoding", Environ Entomol, 46(1), pp.38~49 (2017)[DOI]
  81. 손민웅, "경북과 강원지역 농업생태계에서 여름철 화분매개네트워크 다양성과 상호작용", Journal of Apiculture, 34(3), pp.197~206 (2019), 한국양봉학회
  82. Srivathsan A, "Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate", Front Zool, 13, pp.17~ (2016)[DOI]
  83. Staniczenko PP, "The ghost of nestedness in ecological networks", Nat Commun, 4, pp.1391~ (2013)[DOI]
  84. Swenson SJ, "Testing the effect of pollen exine rupture on metabarcoding with Illumina sequencing", PLoS One, 16(2), pp.e0245611~ (2021)[DOI]
  85. Taberlet P, "Towards next-generation biodiversity assessment using DNA metabarcoding", Mol Ecol, 21(8), pp.2045~2050 (2012)[DOI]
  86. Tylianakis JM, "Ecological networks across environmental gradients", Annu Rev Ecol Evol Syst, 48, pp.25~48 (2017)[DOI]
  87. Tylianakis JM. Ecology, "The global plight of pollinators", Science, 339(6127), pp.1532~1533 (2013)[DOI]
  88. Ulanowicz RE, "Quantitative methods for ecological network analysis", Comput Biol Chem, 28, pp.321~339 (2004)[DOI]
  89. Valdovinos FS, "Adaptive foraging allows the maintenance of biodiversity of pollination networks", Oikos, 122(6), pp.907~917 (2013)[DOI]
  90. Vanbergen AJ, "Network size, structure and mutualism dependence affect the propensity for plant–pollinator extinction cascades", Funct Ecol, 31(6), pp.1285~1293 (2017)[DOI]
  91. Vanbergen AJ, "Insect Pollinators Initiative. Threats to an ecosystem service:pressures on pollinators", Front Ecol Environ, 11(5), pp.251~259 (2013)[DOI]
  92. Wang Q, "Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy", Appl Environ Microbiol, 73(16), pp.5261~5267 (2007)[DOI]
  93. Weiner CN, "Land-use impacts on plant-pollinator networks : interaction strength and specialization predict pollinator declines", Ecology, 95(2), pp.466~474 (2014)[DOI]
  94. Weiner CN, "Land use intensity in grasslands : changes in biodiversity, species composition and specialisation in flower visitor networks", Basic Appl Ecol, 12(4), pp.292~299 (2011)[DOI]
  95. Yohe S, "Review of clinical next-generation sequencing", Arch Pathol Lab Med, 141(11), pp.1544~1557 (2017)[DOI]
  96. Yu DW, "Biodiversity soup : metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring", Methods Ecol Evol, 3(4), pp.613~623 (2012)[DOI]
  97. Zhang Q, "Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species", Plant Cell Physiol, 44(9), pp.941~951 (2003)[DOI]
  98. Zhang Q, "Why does biparental plastid inheritance revive in angiosperms?", J Plant Res, 123(2), pp.201~206 (2010)[DOI]
  99. Zhou X, "Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification", Gigascience, 2(1), pp.4~ (2013)[DOI]

관련 논문AI추천

이 간행물의 다른 논문 (4건)