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Laha RC, De Mandal S, Ralte L, Ralte L, Kumar NS, Gurusubramanian G, Satishkumar R, Mugasimangalam R, Kuravadi NA. Meta-barcoding in combination with palynological inference is a potent diagnostic marker for honey floral composition. AMB Express 2017; 7:132. [PMID: 28651381 PMCID: PMC5483214 DOI: 10.1186/s13568-017-0429-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/12/2017] [Indexed: 11/10/2022] Open
Abstract
Identification of floral samples present in honey is important in order to determine the medicinal value, enhance the production of honey as well as to conserve the honey bees. Traditional approaches for studying pollen samples are based on microscopic observation which is laborious, time intensive and requires specialized palynological knowledge. Present study compares two composite honey metagenome collected from 20 samples in Mizoram, Northeast India using three gene loci- rbcL, matK and ITS2 that was sequenced using a next-generation sequencing (NGS) platform (Illumina Miseq). Furthermore, a classical palynology study for all 20 samples was carried out to evaluate the NGS approach. NGS based approach and pollen microscopic studies were able to detect the most abundant floral components of honey. We investigated the plants that were frequently used by honey bees by examining the results obtained from both the techniques. Microscopic examination of pollens detected plants with a broad taxonomic range covering 26 families. NGS based multigene approach revealed diverse plant species, which was higher than in any other previously reported techniques using a single locus. Frequently found herbaceous species were from the family Poaceae, Myrtaceae, Fabaceae and Asteraceae. The future NGS based approach using multi-loci target, with the help of an improved and robust plant database, can be a potential replacement technique for tedious microscopic studies to identify the polleniferous plants.
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Affiliation(s)
- Rama Chandra Laha
- Departments of Botany, Biotechnology and Zoology, School of Life Sciences, Mizoram University, Aizawl, Mizoram 796004 India
| | - Surajit De Mandal
- Departments of Botany, Biotechnology and Zoology, School of Life Sciences, Mizoram University, Aizawl, Mizoram 796004 India
| | - Lalhmanghai Ralte
- Departments of Botany, Biotechnology and Zoology, School of Life Sciences, Mizoram University, Aizawl, Mizoram 796004 India
| | - Laldinfeli Ralte
- Departments of Botany, Biotechnology and Zoology, School of Life Sciences, Mizoram University, Aizawl, Mizoram 796004 India
| | - Nachimuthu Senthil Kumar
- Departments of Botany, Biotechnology and Zoology, School of Life Sciences, Mizoram University, Aizawl, Mizoram 796004 India
| | - Guruswami Gurusubramanian
- Departments of Botany, Biotechnology and Zoology, School of Life Sciences, Mizoram University, Aizawl, Mizoram 796004 India
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102
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Twyford AD, Ness RW. Strategies for complete plastid genome sequencing. Mol Ecol Resour 2017; 17:858-868. [PMID: 27790830 PMCID: PMC6849563 DOI: 10.1111/1755-0998.12626] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/14/2016] [Accepted: 10/21/2016] [Indexed: 12/01/2022]
Abstract
Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation-sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short-range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.
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Affiliation(s)
- Alex D. Twyford
- Institute of Evolutionary BiologyAshworth LaboratoriesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Rob W. Ness
- Department of BiologyUniversity of Toronto MississaugaMississaugaONCanada
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103
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Honey bee foraging ecology: Season but not landscape diversity shapes the amount and diversity of collected pollen. PLoS One 2017; 12:e0183716. [PMID: 28854210 PMCID: PMC5576699 DOI: 10.1371/journal.pone.0183716] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 08/09/2017] [Indexed: 11/19/2022] Open
Abstract
The availability of pollen in agricultural landscapes is essential for the successful growth and reproduction of honey bee colonies (Apis mellifera L.). The quantity and diversity of collected pollen can influence the growth and health of honey bee colonies, but little is known about the influence of landscape structure on pollen diet. In a field experiment, we rotated 16 honey bee colonies across 16 agricultural landscapes, used traps to collect samples of collected pollen and observed intra-colonial dance communication to gain information about foraging distances. DNA metabarcoding was applied to analyze mixed pollen samples. Neither the amount of collected pollen nor pollen diversity was related to landscape diversity. However, we found a strong seasonal variation in the amount and diversity of collected pollen in all sites independent of landscape diversity. The observed increase in foraging distances with decreasing landscape diversity suggests that honey bees compensated for lower landscape diversity by increasing their pollen foraging range in order to maintain pollen amount and diversity. Our results underscore the importance of a diverse pollen diet for honey bee colonies. Agri-environmental schemes aiming to support pollinators should focus on possible spatial and temporal gaps in pollen availability and diversity in agricultural landscapes.
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104
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Willcox BK, Aizen MA, Cunningham SA, Mayfield MM, Rader R. Deconstructing pollinator community effectiveness. CURRENT OPINION IN INSECT SCIENCE 2017; 21:98-104. [PMID: 28822496 DOI: 10.1016/j.cois.2017.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
Effective pollination is a complex, context-dependent phenomenon determined by both species-level and community-level factors. While pollinator communities are constituted by interacting organisms in a shared environment, these factors are often simplified or overlooked when quantifying species-level pollinator effectiveness alone. Here, we review the recent literature on pollinator effectiveness to identify the pros and cons of existing methods and outline three important areas for future research: plant-pollinator interactions, heterospecific pollen transfer and variation in pollination outcomes. We conclude that pollinator community effectiveness needs to be acknowledged as a key property of pollination effectiveness in order to fully account for the suite of plant, pollinator and environmental factors known to influence different stages of successful pollination.
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Affiliation(s)
- Bryony K Willcox
- School of Environmental and Rural Science, University of New England, Armidale, 2350, NSW, Australia
| | - Marcelo A Aizen
- Laboratorio Ecotono, INIBIOMA-CONICET and Centro Regional Bariloche, Universidad Nacional del Comahue, Quintral 1250, 8400 San Carlos de Bariloche, Río Negro, Argentina
| | - Saul A Cunningham
- Fenner School of Environment and Society, The Australian National University, Canberra Australian Capital Territory 2601, Australia
| | - Margaret M Mayfield
- The University of Queensland, School of Biological Sciences, Brisbane, Queensland 4072, Australia
| | - Romina Rader
- School of Environmental and Rural Science, University of New England, Armidale, 2350, NSW, Australia.
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105
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Bell KL, Fowler J, Burgess KS, Dobbs EK, Gruenewald D, Lawley B, Morozumi C, Brosi BJ. Applying pollen DNA metabarcoding to the study of plant-pollinator interactions. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1600124. [PMID: 28690929 PMCID: PMC5499302 DOI: 10.3732/apps.1600124] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/09/2017] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY To study pollination networks in a changing environment, we need accurate, high-throughput methods. Previous studies have shown that more highly resolved networks can be constructed by studying pollen loads taken from bees, relative to field observations. DNA metabarcoding potentially allows for faster and finer-scale taxonomic resolution of pollen compared to traditional approaches (e.g., light microscopy), but has not been applied to pollination networks. METHODS We sampled pollen from 38 bee species collected in Florida from sites differing in forest management. We isolated DNA from pollen mixtures and sequenced rbcL and ITS2 gene regions from all mixtures in a single run on the Illumina MiSeq platform. We identified species from sequence data using comprehensive rbcL and ITS2 databases. RESULTS We successfully built a proof-of-concept quantitative pollination network using pollen metabarcoding. DISCUSSION Our work underscores that pollen metabarcoding is not quantitative but that quantitative networks can be constructed based on the number of interacting individuals. Due to the frequency of contamination and false positive reads, isolation and PCR negative controls should be used in every reaction. DNA metabarcoding has advantages in efficiency and resolution over microscopic identification of pollen, and we expect that it will have broad utility for future studies of plant-pollinator interactions.
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Affiliation(s)
- Karen L. Bell
- Department of Environmental Sciences, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia 6008, Australia
- CSIRO Land and Water and CSIRO Health and Biosecurity, 147 Underwood Avenue, Floreat, Western Australia 6014, Australia
| | - Julie Fowler
- Department of Environmental Sciences, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
| | - Kevin S. Burgess
- Department of Biology, Columbus State University, Columbus, Georgia 31907-5645 USA
| | - Emily K. Dobbs
- Department of Environmental Sciences, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
| | - David Gruenewald
- Department of Environmental Sciences, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
| | - Brice Lawley
- Department of Environmental Sciences, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
| | - Connor Morozumi
- Department of Environmental Sciences, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
| | - Berry J. Brosi
- Department of Environmental Sciences, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
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106
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Raclariu AC, Paltinean R, Vlase L, Labarre A, Manzanilla V, Ichim MC, Crisan G, Brysting AK, de Boer H. Comparative authentication of Hypericum perforatum herbal products using DNA metabarcoding, TLC and HPLC-MS. Sci Rep 2017; 7:1291. [PMID: 28465563 PMCID: PMC5431008 DOI: 10.1038/s41598-017-01389-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/29/2017] [Indexed: 12/03/2022] Open
Abstract
Many herbal products have a long history of use, but there are increasing concerns over product efficacy, safety and quality in the wake of recent cases exposing discrepancies between labeling and constituents. When it comes to St. John’s wort (Hypericum perforatum L.) herbal products, there is limited oversight, frequent off-label use and insufficient monitoring of adverse drug reactions. In this study, we use amplicon metabarcoding (AMB) to authenticate 78 H. perforatum herbal products and evaluate its ability to detect substitution compared to standard methods using thin-layer chromatography (TLC) and high performance liquid chromatography coupled with mass spectrometry (HPLC-MS). Hypericum perforatum was detected in 68% of the products using AMB. Furthermore, AMB detected incongruence between constituent species and those listed on the label in all products. Neither TLC nor HPLC-MS could be used to unambiguously identify H. perforatum. They are accurate methods for authenticating presence of the target compounds, but have limited efficiency in detecting infrageneric substitution and do not yield any information on other plant ingredients in the products. Random post-marketing AMB of herbal products by regulatory agencies could raise awareness among consumers of substitution and would provide an incentive to manufacturers to increase quality control from raw ingredients to commercialized products.
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Affiliation(s)
- Ancuta Cristina Raclariu
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway.,NIRDBS/"Stejarul" Research Centre for Biological Sciences, Alexandru cel Bun Street, 6, 610004, Piatra, Neamt, Romania
| | - Ramona Paltinean
- Department of Pharmaceutical Botany, University of Medicine and Pharmacy "Iuliu Haţieganu", Faculty of Pharmacy, Gheorghe Marinescu Street, 23, 400337, Cluj-Napoca, Romania
| | - Laurian Vlase
- Department of Pharmaceutical Technology and Biopharmaceutics, "Iuliu Hatieganu" University of Medicine and Pharmacy, Ion Creanga Street, 8-10, 400010, Cluj-Napoca, Romania
| | - Aurélie Labarre
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway
| | - Vincent Manzanilla
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway
| | - Mihael Cristin Ichim
- NIRDBS/"Stejarul" Research Centre for Biological Sciences, Alexandru cel Bun Street, 6, 610004, Piatra, Neamt, Romania
| | - Gianina Crisan
- Department of Pharmaceutical Botany, University of Medicine and Pharmacy "Iuliu Haţieganu", Faculty of Pharmacy, Gheorghe Marinescu Street, 23, 400337, Cluj-Napoca, Romania
| | - Anne Krag Brysting
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway
| | - Hugo de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway.
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107
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Krauss SL, Phillips RD, Karron JD, Johnson SD, Roberts DG, Hopper SD. Novel Consequences of Bird Pollination for Plant Mating. TRENDS IN PLANT SCIENCE 2017; 22:395-410. [PMID: 28412035 DOI: 10.1016/j.tplants.2017.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 02/12/2017] [Accepted: 03/07/2017] [Indexed: 06/07/2023]
Abstract
Pollinator behaviour has profound effects on plant mating. Pollinators are predicted to minimise energetic costs during foraging bouts by moving between nearby flowers. However, a review of plant mating system studies reveals a mismatch between behavioural predictions and pollen-mediated gene dispersal in bird-pollinated plants. Paternal diversity of these plants is twice that of plants pollinated solely by insects. Comparison with the behaviour of other pollinator groups suggests that birds promote pollen dispersal through a combination of high mobility, limited grooming, and intra- and interspecies aggression. Future opportunities to test these predictions include seed paternity assignment following pollinator exclusion experiments, single pollen grain genotyping, new tracking technologies for small pollinators, and motion-triggered cameras and ethological experimentation for quantifying pollinator behaviour.
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Affiliation(s)
- Siegfried L Krauss
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Fraser Avenue, Kings Park, WA 6005, Australia; School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - Ryan D Phillips
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Fraser Avenue, Kings Park, WA 6005, Australia; School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Jeffrey D Karron
- Department of Biological Sciences, PO Box 413, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | - Steven D Johnson
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
| | - David G Roberts
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Fraser Avenue, Kings Park, WA 6005, Australia; Centre of Excellence in Natural Resource Management and School of Plant Biology, University of Western Australia, 35 Stirling Terrace, Albany, WA 6330, Australia
| | - Stephen D Hopper
- Centre of Excellence in Natural Resource Management and School of Plant Biology, University of Western Australia, 35 Stirling Terrace, Albany, WA 6330, Australia
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108
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Ghosh JS, Bhattacharya S, Pal A. Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure. Genetica 2017; 145:319-333. [PMID: 28439758 DOI: 10.1007/s10709-017-9967-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 04/20/2017] [Indexed: 11/27/2022]
Abstract
The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.
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Affiliation(s)
- Jayadri Sekhar Ghosh
- Division of Plant Biology, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata, 700054, India
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Samik Bhattacharya
- Division of Plant Biology, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata, 700054, India
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany
| | - Amita Pal
- Division of Plant Biology, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata, 700054, India.
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109
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Wilkinson MJ, Szabo C, Ford CS, Yarom Y, Croxford AE, Camp A, Gooding P. Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants. Sci Rep 2017; 7:46040. [PMID: 28401958 PMCID: PMC5388885 DOI: 10.1038/srep46040] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/08/2017] [Indexed: 01/08/2023] Open
Abstract
We estimate the global BOLD Systems database holds core DNA barcodes (rbcL + matK) for about 15% of land plant species and that comprehensive species coverage is still many decades away. Interim performance of the resource is compromised by variable sequence overlap and modest information content within each barcode. Our model predicts that the proportion of species-unique barcodes reduces as the database grows and that 'false' species-unique barcodes remain >5% until the database is almost complete. We conclude the current rbcL + matK barcode is unfit for purpose. Genome skimming and supplementary barcodes could improve diagnostic power but would slow new barcode acquisition. We therefore present two novel Next Generation Sequencing protocols (with freeware) capable of accurate, massively parallel de novo assembly of high quality DNA barcodes of >1400 bp. We explore how these capabilities could enhance species diagnosis in the coming decades.
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Affiliation(s)
- Mike J. Wilkinson
- Pwllpeiran Upland Research Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 4AB, UK
| | - Claudia Szabo
- School of Computer Science, The University of Adelaide, SA 5005, Australia
| | - Caroline S. Ford
- Pwllpeiran Upland Research Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 4AB, UK
| | - Yuval Yarom
- School of Computer Science, The University of Adelaide, SA 5005, Australia
| | - Adam E. Croxford
- School of Agriculture, Food and Wine, Waite Campus, The University of Adelaide, SA 5064, Australia
| | - Amanda Camp
- School of Animal & Veterinary Sciences, Roseworthy Campus, The University of Adelaide, SA 5371, Australia
| | - Paul Gooding
- Australian Genome Research Facility, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
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Vamosi JC, Gong YB, Adamowicz SJ, Packer L. Forecasting pollination declines through DNA barcoding: the potential contributions of macroecological and macroevolutionary scales of inquiry. THE NEW PHYTOLOGIST 2017; 214:11-18. [PMID: 27901268 DOI: 10.1111/nph.14356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
While pollinators are widely acknowledged as important contributors to seed production in plant communities, we do not yet have a good understanding of the importance of pollinator specialists for this ecosystem service. Determination of the prevalence of pollinator specialists is often hindered by the occurrence of cryptic species and the limitations of observational data on pollinator visitation rates, two areas where DNA barcoding of pollinators and pollen can be useful. Further, the demonstrated adequacy of pollen DNA barcoding from historical records offers opportunities to observe the effects of pollinator loss over longer timescales, and phylogenetic approaches can elucidate the historical rates of extinction of specialist lineages. In this Viewpoint article, we review how advances in DNA barcoding and metabarcoding of plants and pollinators have brought important developments to our understanding of specialization in plant-pollinator interactions. We then put forth several lines of inquiry that we feel are especially promising for providing insight on changes in plant-pollinator interactions over space and time. Obtaining estimates of the effects of reductions in specialists will contribute to forecasting the loss of ecosystem services that will accompany the erosion of plant and pollinator diversity.
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Affiliation(s)
- Jana C Vamosi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Yan-Bing Gong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Laurence Packer
- Department of Biology, York University, Toronto, ON, M3J 1P3, Canada
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111
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Kaluza BF, Wallace H, Keller A, Heard TA, Jeffers B, Drescher N, Blüthgen N, Leonhardt SD. Generalist social bees maximize diversity intake in plant species-rich and resource-abundant environments. Ecosphere 2017. [DOI: 10.1002/ecs2.1758] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Benjamin F. Kaluza
- Department of Ecology; Leuphana University; 21335 Lüneburg Germany
- Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore Queensland 4558 Australia
- Department of Animal Ecology and Tropical Biology; University of Würzburg; 97074 Würzburg Germany
| | - Helen Wallace
- Faculty of Science, Health, Education and Engineering; University of the Sunshine Coast; Maroochydore Queensland 4558 Australia
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology; University of Würzburg; 97074 Würzburg Germany
- DNA Analytics Core Facility; University of Würzburg; 97074 Würzburg Germany
| | - Tim A. Heard
- CSIRO Ecosystem Sciences; Brisbane Queensland 4001 Australia
| | | | - Nora Drescher
- Department of Ecology; Leuphana University; 21335 Lüneburg Germany
| | - Nico Blüthgen
- Department of Biology; University of Darmstadt; 64287 Darmstadt Germany
| | - Sara D. Leonhardt
- Department of Animal Ecology and Tropical Biology; University of Würzburg; 97074 Würzburg Germany
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112
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Bell KL, Loeffler VM, Brosi BJ. An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1600110. [PMID: 28337390 PMCID: PMC5357121 DOI: 10.3732/apps.1600110] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/30/2017] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY DNA metabarcoding has broad-ranging applications in ecology, aerobiology, biosecurity, and forensics. A bioinformatics pipeline has recently been published for identification using a comprehensive database of ITS2, one of the common plant DNA barcoding markers. There is, however, no corresponding database for rbcL, the other primary marker used in plants. METHODS Using publicly available data, we compiled a reference library of rbcL sequences and trained databases for use with UTAX and RDP classifier algorithms. We used this reference library, along with the existing bioinformatics pipeline and ITS2 reference library, to identify species in an artificial mixture of nine species of pollen. We have made this database publicly available in multiple formats, to allow use with multiple bioinformatics pipelines, now and in the future. RESULTS Using the rbcL database, in addition to the ITS2 database, we succeeded in making species-level identifications for eight species and a family-level identification of the ninth species. This is an improvement on ITS2 sequence alone. DISCUSSION The reference library described here will assist with identification of plant species using rbcL. By making another gene region available for standard barcoding, this will increase the resolution and accuracy of identifications.
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Affiliation(s)
- Karen L. Bell
- Department of Environmental Science, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
- Author for correspondence:
| | - Virginia M. Loeffler
- Department of Environmental Science, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
| | - Berry J. Brosi
- Department of Environmental Science, Emory University, 400 Dowman Drive, Atlanta, Georgia 30322 USA
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113
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Molecular approaches for the analysis of airborne pollen: A case study of Juniperus pollen. Ann Allergy Asthma Immunol 2016; 118:204-211.e2. [PMID: 28024990 DOI: 10.1016/j.anai.2016.11.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/09/2016] [Accepted: 11/17/2016] [Indexed: 11/24/2022]
Abstract
BACKGROUND Pollen monitoring is a common and vital tool in the field of allergy, creating awareness in pollen sensitive individuals. Traditionally, pollen monitoring has been based on conventional microscopic counting techniques that are labor intensive and limited in the identification to the genus or family level. Molecular techniques provide an alternative approach that is less labor intensive and enable identification of any species by its genetic fingerprint. OBJECTIVE To use quantitative polymerase chain reaction (qPCR) to evaluate pollen concentrations in air samples. METHODS Juniperus pollen was selected as our model because of the importance of this pollen in the southcentral United States. We analyzed 105 air samples collected with a Burkard spore trap from 2013 to 2015 using species-specific primers and probes. To evaluate the feasibility of a molecular approach, we used duplicate air samples that allowed us to compare results from classical identification based on light microscopy with our qPCR results. RESULTS Pollen concentrations from the qPCR data were significantly correlated with concentrations determined through light microscopy (R = 0.902, P < .001). We also confirmed an overlap in the pollination seasons between Juniperus ashei and Juniperus pinchotii and between J ashei and Juniperus virginiana. CONCLUSION We found that this method correctly identified different Juniperus species present in mixed air samples in the southcentral United States, an accomplishment that cannot be achieved using microscopic identification. We conclude that the qPCR method is more accurate and sensitive than current pollen monitoring techniques and, therefore, has the potential to be used in various pollen monitoring stations.
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114
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Richardson RT, Bengtsson-Palme J, Johnson RM. Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data. Mol Ecol Resour 2016; 17:760-769. [PMID: 27797448 DOI: 10.1111/1755-0998.12628] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/17/2016] [Accepted: 10/21/2016] [Indexed: 11/29/2022]
Abstract
The taxonomic classification of DNA sequences has become a critical component of numerous ecological research applications; however, few studies have evaluated the strengths and weaknesses of commonly used sequence classification approaches. Further, the methods and software available for sequence classification are diverse, creating an environment in which it may be difficult to determine the best course of action and the trade-offs made using different classification approaches. Here, we provide an in silico evaluation of three DNA sequence classifiers, the rdp Naïve Bayesian Classifier, rtax and utax. Further, we discuss the results, merits and limitations of both the classifiers and our method of classifier evaluation. Our methods of comparison are simple, yet robust, and will provide researchers a methodological and conceptual foundation for making such evaluations in a variety of research situations. Generally, we found a considerable trade-off between accuracy and sensitivity for the classifiers tested, indicating a need for further improvement of sequence classification tools.
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Affiliation(s)
- Rodney T Richardson
- Department of Entomology, The Ohio State University-Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH, 44691, USA
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, Göteborg, SE-413 46, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, PO Box 440, SE-405 30, Gothenburg, Sweden
| | - Reed M Johnson
- Department of Entomology, The Ohio State University-Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH, 44691, USA
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115
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Littlefair JE, Clare EL. Barcoding the food chain: from Sanger to high-throughput sequencing. Genome 2016; 59:946-958. [DOI: 10.1139/gen-2016-0028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace “environmental DNA”, and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.
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Affiliation(s)
- Joanne E. Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
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116
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Hollingsworth PM, Li DZ, van der Bank M, Twyford AD. Telling plant species apart with DNA: from barcodes to genomes. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150338. [PMID: 27481790 PMCID: PMC4971190 DOI: 10.1098/rstb.2015.0338] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 12/17/2022] Open
Abstract
Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, Yunnan 650201, People's Republic of China
| | - Michelle van der Bank
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland park, Johannesburg PO Box 524, South Africa
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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117
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Bell KL, de Vere N, Keller A, Richardson RT, Gous A, Burgess KS, Brosi BJ. Pollen DNA barcoding: current applications and future prospects. Genome 2016; 59:629-40. [DOI: 10.1139/gen-2015-0200] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.
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Affiliation(s)
- Karen L. Bell
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, United Kingdom
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
| | | | - Annemarie Gous
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
- School of Life Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Berry J. Brosi
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
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118
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Pornon A, Escaravage N, Burrus M, Holota H, Khimoun A, Mariette J, Pellizzari C, Iribar A, Etienne R, Taberlet P, Vidal M, Winterton P, Zinger L, Andalo C. Using metabarcoding to reveal and quantify plant-pollinator interactions. Sci Rep 2016; 6:27282. [PMID: 27255732 PMCID: PMC4891682 DOI: 10.1038/srep27282] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/13/2016] [Indexed: 02/02/2023] Open
Abstract
Given the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole.
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Affiliation(s)
- André Pornon
- Laboratoire Evolution and Diversité Biologique EDB, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France.,CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - Nathalie Escaravage
- Laboratoire Evolution and Diversité Biologique EDB, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France.,CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - Monique Burrus
- Laboratoire Evolution and Diversité Biologique EDB, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France.,CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - Hélène Holota
- Laboratoire Evolution and Diversité Biologique EDB, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France.,CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - Aurélie Khimoun
- Laboratoire Biogeosciences, Université de Bourgogne 6 bld Gabriel, F-21000 Dijon, France
| | - Jérome Mariette
- Plate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliqués INRA, UR875 Toulouse, F-31320 Castanet-Tolosan, France
| | - Charlène Pellizzari
- Laboratoire Evolution and Diversité Biologique EDB, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France.,CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - Amaia Iribar
- Laboratoire Evolution and Diversité Biologique EDB, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France.,CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - Roselyne Etienne
- Laboratoire Evolution and Diversité Biologique EDB, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France.,CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 43, F-38041 Grenoble, France
| | - Marie Vidal
- GeT-PlaGe, Genotoul, INRA UAR1209, F-31320 Castanet-Tolosan, France
| | - Peter Winterton
- Département de Langues et Gestion, Université Paul Sabatier, F-31062 Toulouse, France
| | - Lucie Zinger
- Laboratoire Evolution and Diversité Biologique EDB, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France.,CNRS, EDB, UMR 5174, F-31062 Toulouse, France
| | - Christophe Andalo
- Laboratoire Evolution and Diversité Biologique EDB, Université Toulouse III Paul Sabatier, F-31062 Toulouse, France.,CNRS, EDB, UMR 5174, F-31062 Toulouse, France
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119
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Hungry for quality—individual bumblebees forage flexibly to collect high-quality pollen. Behav Ecol Sociobiol 2016. [DOI: 10.1007/s00265-016-2129-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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120
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McFrederick QS, Rehan SM. Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee. Mol Ecol 2016; 25:2302-11. [PMID: 26945527 DOI: 10.1111/mec.13608] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/26/2016] [Accepted: 03/02/2016] [Indexed: 11/27/2022]
Abstract
Many insects obtain gut microbes from their diet, but how a mother's foraging patterns influence the microbes found in her offspring's food remains an open question. To address this gap, we studied a bee that forages for pollen from multiple species of plants and may therefore acquire diverse bacteria from different plants. We tested the hypothesis that pollen diversity correlates with bacterial diversity by simultaneously characterizing these two communities in bee brood provisions for the first time. We used deep sequencing of the plant RBCL gene and the bacterial 16S rRNA gene to characterize pollen and bacterial diversity. We then tested for associations between pollen and bacterial species richness and community composition, as well as co-occurrence of specific bacteria and pollen types. We found that both pollen and bacterial communities were extremely diverse, indicating that mother bees visit a wide variety of flowers for pollen and nectar and subsequently bring a diversity of microbes back into their nests. Pollen and bacterial species richness and community composition, however, were not correlated. Certain pollen types significantly co-occurred with the most proportionally abundant bacteria, indicating that the plants these pollen types came from may serve as reservoirs for these bacteria. Even so, the overall diversity of these communities appears to mask these associations at a broader scale. Further study of these pollen and bacteria associations will be important for understanding the complicated relationship between bacteria and wild bees.
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Affiliation(s)
- Quinn S McFrederick
- Department of Entomology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, 46 College Road, Durham, NH, 03824, USA
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121
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Sauvage T, Schmidt WE, Suda S, Fredericq S. A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA. BMC Ecol 2016; 16:8. [PMID: 26965054 PMCID: PMC4785743 DOI: 10.1186/s12898-016-0068-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/27/2016] [Indexed: 12/21/2022] Open
Abstract
Background In spite of their ecological importance as primary producers and microbioeroders of marine calcium carbonate (CaCO3) substrata, endolithic phototrophs spanning both prokaryotic (the cyanobacteria) and eukaryotic algae lack established molecular resources for their facilitated survey with high throughput sequencing. Here, the development of a metabarcoding framework for the elongation factor EF-Ttu (tufA) was tested on four Illumina-sequenced marine CaCO3 microfloras for the characterization of their endolithic phototrophs, especially the abundant bioeroding Ostreobium spp. (Ulvophyceae). The framework consists of novel tufA degenerate primers and a comprehensive database enabling Operational Taxonomic Unit (OTU) identification at multiple taxonomic ranks with percent identity thresholds determined herein. Results The newly established tufA database comprises 4057 non-redundant sequences (from 1339 eukaryotic and prokaryotic phototrophs, and 2718 prokaryotic heterotrophs) including 27 classes in 10 phyla of phototrophic diversity summarized from data mining on GenBank®, our barcoding of >150 clones produced from coral reef microfloras, and >300 eukaryotic phototrophs (>230 Ulvophyceae including >100 ‘Ostreobium’ spp., and >70 Florideophyceae, Phaeophyceae and miscellaneous taxa). Illumina metabarcoding with the newly designed primers resulted in 802 robust OTUs including 618 phototrophs and 184 heterotrophs (77 and 23 % of OTUs, respectively). Phototrophic OTUs belonged to 14 classes of phototrophs found in seven phyla, and represented ~98 % of all reads. The phylogenetic profiles of coral reef microfloras showed few OTUs in large abundance (proportion of reads) for the Chlorophyta (Ulvophyceae, i.e. Ostreobium and Phaeophila), the Rhodophyta (Florideophyceae) and Haptophyta (Coccolithophyceae), and a large diversity (richness) of OTUs in lower abundance for the Cyanophyta (Cyanophyceae) and the Ochrophyta (the diatoms, ‘Bacillariophyta’). The bioerosive ‘Ostreobium’ spp. represented four families in a large clade of subordinal divergence, i.e. the Ostreobidineae, and a fifth, phylogenetically remote family in the suborder Halimedineae (provisionally assigned as the ‘Pseudostreobiaceae’). Together they harbor 85–95 delimited cryptic species of endolithic microsiphons. Conclusions The novel degenerate primers allowed for amplification of endolithic phototrophs across a wide phylogenetic breadth as well as their recovery in very large proportions of reads (overall 98 %) and diversity (overall 77 % of OTUs). The established companion tufA database and determined identity thresholds allow for OTU identification at multiple taxonomic ranks to facilitate the monitoring of phototrophic assemblages via metabarcoding, especially endolithic communities rich in bioeroding Ulvophyceae, such as those harboring ‘Ostreobium’ spp., Phaeophila spp. and associated algal diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12898-016-0068-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Sauvage
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, 70503, USA.
| | - William E Schmidt
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, 70503, USA
| | - Shoichiro Suda
- Department of Marine Science, Biology and Chemistry, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Suzanne Fredericq
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, 70503, USA
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122
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Review and future prospects for DNA barcoding methods in forensic palynology. Forensic Sci Int Genet 2016; 21:110-6. [DOI: 10.1016/j.fsigen.2015.12.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/19/2015] [Accepted: 12/15/2015] [Indexed: 11/18/2022]
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123
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Cornman RS, Otto CRV, Iwanowicz D, Pettis JS. Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci. PLoS One 2015; 10:e0145365. [PMID: 26700168 PMCID: PMC4689544 DOI: 10.1371/journal.pone.0145365] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/01/2015] [Indexed: 01/31/2023] Open
Abstract
Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality, further protocol optimization and/or a modest reduction in multiplex scale should offset this difficulty. As small quantities of pollen are sufficient for amplification, our approach might be extendable to other questions or species for which large pollen samples are not available.
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Affiliation(s)
- R Scott Cornman
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Fort Collins, CO, 80526, United States of America
| | - Clint R V Otto
- U.S. Geological Survey, Northern Prairie Wildlife Research Center, 8711 37th Street Southeast, Jamestown, ND, 58401, United States of America
| | - Deborah Iwanowicz
- U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV, 25430, United States of America
| | - Jeffery S Pettis
- U.S. Department of Agriculture-Agriculture Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, MD, 20705, United States of America
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124
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Ankenbrand MJ, Keller A, Wolf M, Schultz J, Förster F. ITS2 Database V: Twice as Much: Table 1. Mol Biol Evol 2015; 32:3030-2. [DOI: 10.1093/molbev/msv174] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 07/25/2015] [Indexed: 11/13/2022] Open
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