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Kestel JH, Bateman PW, Field DL, White NE, Lines R, Nevill P. eDNA metabarcoding of avocado flowers: 'Hass' it got potential to survey arthropods in food production systems? Mol Ecol Resour 2023; 23:1540-1555. [PMID: 37237427 DOI: 10.1111/1755-0998.13814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/26/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023]
Abstract
In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive, potentially limiting their application in industries such as agriculture, where arthropods often play a critical role in productivity (e.g. pollinators, pests and predators). Environmental DNA (eDNA) metabarcoding of a novel substrate, crop flowers, may offer an accurate and high throughput alternative to aid in the detection of these managed and unmanaged taxa. Here, we compared the arthropod communities detected with eDNA metabarcoding of flowers, from an agricultural species (Persea americana-'Hass' avocado), with two conventional survey techniques: digital video recording (DVR) devices and pan traps. In total, 80 eDNA flower samples, 96 h of DVRs and 48 pan trap samples were collected. Across the three methods, 49 arthropod families were identified, of which 12 were unique to the eDNA dataset. Environmental DNA metabarcoding from flowers revealed potential arthropod pollinators, as well as plant pests and parasites. Alpha diversity levels did not differ across the three survey methods although taxonomic composition varied significantly, with only 12% of arthropod families found to be common across all three methods. eDNA metabarcoding of flowers has the potential to revolutionize the way arthropod communities are monitored in natural and agro-ecosystems, potentially detecting the response of pollinators and pests to climate change, diseases, habitat loss and other disturbances.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Rose Lines
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
- Department of Primary Industries and Regional Development, Perth, Western Australia, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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Yuan B, Hu GX, Zhang XX, Yuan JK, Fan XM, Yuan DY. What Are the Best Pollinator Candidates for Camelia oleifera: Do Not Forget Hoverflies and Flies. INSECTS 2022; 13:insects13060539. [PMID: 35735876 PMCID: PMC9224817 DOI: 10.3390/insects13060539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/29/2022] [Accepted: 06/08/2022] [Indexed: 01/25/2023]
Abstract
Camellia oleifera Abel. is an important woody oil plant, and its pollination success is essential for oil production. We conducted this study to select the best pollinator candidates for C. oleifera using principal component analysis and multi-attribute decision-making. Field observations of the flower-visiting characteristics of candidate pollinators were conducted at three sites. The insect species that visited flowers did not considerably differ between regions or time periods. However, the proportion of each species recorded did vary. We recorded eleven main candidates from two orders and six families at the three sites. The pollen amount carried by Apis mellifera was significantly higher than that of other insects. However, the visit frequency and body length of Apis mellifera were smaller than those of Vespa velutina. Statistical analysis showed that A. mellifera is the best candidate pollinator; Eristaliscerealis is a good candidate pollinator; Phytomia zonata, A. cerana, and V. velutina were ordinary candidate pollinators; and four fly species, Episyrphus balteatus, and Eristalinus arvorum were classified as inefficient candidate pollinators. Our study shows that flies and hoverflies play an important role in the pollination system. Given the global decline in bee populations, the role of flies should also be considered in C. oleifera seed production.
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Affiliation(s)
- Bin Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (B.Y.); (G.-X.H.); (X.-X.Z.); (J.-K.Y.)
- Key Lab of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guan-Xing Hu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (B.Y.); (G.-X.H.); (X.-X.Z.); (J.-K.Y.)
- Key Lab of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiao-Xiao Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (B.Y.); (G.-X.H.); (X.-X.Z.); (J.-K.Y.)
- Key Lab of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jing-Kun Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (B.Y.); (G.-X.H.); (X.-X.Z.); (J.-K.Y.)
- Key Lab of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiao-Ming Fan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (B.Y.); (G.-X.H.); (X.-X.Z.); (J.-K.Y.)
- Key Lab of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha 410004, China
- Correspondence: (X.-M.F.); (D.-Y.Y.)
| | - De-Yi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (B.Y.); (G.-X.H.); (X.-X.Z.); (J.-K.Y.)
- Key Lab of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha 410004, China
- Correspondence: (X.-M.F.); (D.-Y.Y.)
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Borchardt KE, Morales CL, Aizen MA, Toth AL. Plant-pollinator conservation from the perspective of systems-ecology. CURRENT OPINION IN INSECT SCIENCE 2021; 47:154-161. [PMID: 34325080 DOI: 10.1016/j.cois.2021.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Ecosystems are interconnected and complex, but conservation has often focused on rehabilitating individual species. A systems-ecology approach aims to support overall structure and maintain functions of the whole ecosystem, and may be especially pertinent for mutualistic plant-pollinator communities. This approach focuses on species interactions as the units to be conserved within the larger ecosystem. Analyzing species interactions is a more holistic approach because it incorporates a broader web of organisms, and considers the plethora of potential indirect influences from interacting partners. In this article, we suggest pollinator researchers focus on plant-pollinator networks to inform conservation programs and best support the coexistence of pollinators and plants within natural and agricultural systems. We propose that a system-ecology perspective is the most promising way to simultaneously improve pollinator conservation, agricultural sustainability, and human well-being.
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Affiliation(s)
- Kate E Borchardt
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
| | - Carolina L Morales
- Grupo de Ecología de la Polinización, INIBIOMA, Universidad Nacional del Comahue-CONICET, Bariloche, Río Negro, 8400, Argentina
| | - Marcelo A Aizen
- Grupo de Ecología de la Polinización, INIBIOMA, Universidad Nacional del Comahue-CONICET, Bariloche, Río Negro, 8400, Argentina; Wissenschaftskolleg zu Berlin, 14193, Berlin, Germany
| | - Amy L Toth
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA; Department of Entomology, Iowa State University, Ames, IA, 50011, USA.
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