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Korbel KL, Hose GC, Karwautz C, Greenfield P, Wang H, Chariton AA, Griebler C. Detection, movement and persistence of invertebrate eDNA in groundwater. Sci Rep 2024; 14:17151. [PMID: 39060364 PMCID: PMC11282260 DOI: 10.1038/s41598-024-67349-3] [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: 11/10/2023] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Sampling groundwater biodiversity is difficult because of limited access and issues with species identification. Environmental DNA (eDNA) provides a viable alternative to traditional sampling approaches, however limited knowledge of the abundance and fate of DNA in groundwater hinders the interpretation of data from these environments. Groundwater environments are dark and have lower oxygen concentrations and microbial activity than surface waters. Consequently, assumptions about DNA fate in surface ecosystems may not apply to groundwaters. Here, we test the longevity and transport of eDNA in groundwater within a static microcosm and a flow-through mesocosm. A variety of invertebrates were placed within a mesocosm and microcosm to enable DNA shedding, and then removed. DNA persisted for up to 5 weeks after their removal in the static experiment and was detected between 9 and 33 days in the flow-through experiment. Sediments and water both proved important for eDNA detection. Crustacean DNA was detected sporadically and unpredictably, whereas non-crustacean DNA was detected more frequently despite their lower densities. We suggest that detecting crustaceans poses a challenge to utilising eDNA approaches for stygofauna monitoring. This is confounded by the scarcity of sequences for stygofauna in reference databases. Further research is needed before eDNA alone can be routinely employed for stygofauna detection.
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Affiliation(s)
- K L Korbel
- School of Natural Sciences, Macquarie University, Sydney, Australia.
| | - G C Hose
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - C Karwautz
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - P Greenfield
- Energy Business Unit, Common wealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - H Wang
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Workgroup of Limnology and Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
| | - A A Chariton
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - C Griebler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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Tingga RCT, Gani M, Osman NA, Aifat NR, Chan E, Khamis S, Rohani ER, Mohd-Daut N, Mohd-Ridwan AR, Md-Zain BM. Interspecific variation in the diet of Symphalangussyndactylus and Macacanemestrina at Genting Highlands, Pahang, Peninsular Malaysia. Biodivers Data J 2024; 12:e122453. [PMID: 38817270 PMCID: PMC11137372 DOI: 10.3897/bdj.12.e122453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/08/2024] [Indexed: 06/01/2024] Open
Abstract
Primate communities in the Genting Highlands consist of a single species of Hylobatidae and four species of Cercopithecidae, which are known to exhibit social interaction behaviour. Thus, a study on the diets of Symphalangussyndactylus (siamang; family Hylobatidae) and Macacanemestrina (pig-tailed macaque; family Cercopithecidae) was carried out at Genting Highlands, in order to compare the dietary preferences and interspecific competition between the two primate families. A DNA metabarcoding approach was used to analyse diet intake using non-invasive samples based on the trnL region. Based on the 140 amplicon sequence variants (ASVs) generated, 26 plant orders, 46 different families, 60 genera and 49 species were identified from 23 different plant classes. Fabaceae and Moraceae were classified as the most preferred plants at the family level for S.syndactylus; meanwhile, Piperaceae and Arecaceae were classified as the most preferred for M.nemestrina. Only six out of the 60 different plant genera classified in this study, were found to be consumed by both species. Therefore, the low similarity of preferred plants in the diets between the two families suggests that there is little interspecific competition. These findings are important for future conservation management of highland primates, especially in the Genting Highlands.
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Affiliation(s)
- Roberta Chaya Tawie Tingga
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan MalaysiaBangi, 43600, SelangorMalaysia
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota Samarahan, SarawakMalaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan MalaysiaBangi, 43600, SelangorMalaysia
- National Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras, 56100 Kuala Lumpur, MalaysiaNational Wildlife Forensic Laboratory (NWFL), Department of Wildlife and National Parks (PERHILITAN), KM 10 Jalan Cheras56100 Kuala LumpurMalaysia
| | - Nur Azimah Osman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan MalaysiaBangi, 43600, SelangorMalaysia
- School of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000, Kuala Pilah, Negeri Sembilan, MalaysiaSchool of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000Kuala Pilah, Negeri SembilanMalaysia
| | - Nor Rahman Aifat
- Faculty of Tropical Forestry, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, MalaysiaFaculty of Tropical Forestry, Universiti Malaysia Sabah, 88400Kota Kinabalu, SabahMalaysia
| | - Eddie Chan
- Genting Nature Adventure, Resorts World Awana Hotel, 69000, Genting Highlands, Pahang, MalaysiaGenting Nature Adventure, Resorts World Awana Hotel, 69000, Genting HighlandsPahangMalaysia
| | - Shamsul Khamis
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan MalaysiaBangi, 43600, SelangorMalaysia
| | - Emelda Rosseleena Rohani
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, MalaysiaInstitute of Systems Biology, Universiti Kebangsaan MalaysiaBangi, 43600, SelangorMalaysia
| | - Norlinda Mohd-Daut
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan MalaysiaBangi, 43600, SelangorMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak, 94300Kota Samarahan, SarawakMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan MalaysiaBangi, 43600, SelangorMalaysia
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Bell KL, Turo KJ, Lowe A, Nota K, Keller A, Encinas‐Viso F, Parducci L, Richardson RT, Leggett RM, Brosi BJ, Burgess KS, Suyama Y, de Vere N. Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding. Mol Ecol 2023; 32:6345-6362. [PMID: 36086900 PMCID: PMC10947134 DOI: 10.1111/mec.16689] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.
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Affiliation(s)
- Karen L. Bell
- CSIRO Health & Biosecurity and CSIRO Land & WaterFloreatWAAustralia
- School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Katherine J. Turo
- Department of Ecology, Evolution, and Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
| | | | - Kevin Nota
- Department of Ecology and GeneticsEvolutionary Biology Centre, Uppsala UniversityUppsalaSweden
| | - Alexander Keller
- Organismic and Cellular Networks, Faculty of BiologyBiocenter, Ludwig‐Maximilians‐Universität MünchenPlaneggGermany
| | - Francisco Encinas‐Viso
- Centre for Australian National Biodiversity ResearchCSIROBlack MountainAustralian Capital TerritoryAustralia
| | - Laura Parducci
- Department of Ecology and GeneticsEvolutionary Biology Centre, Uppsala UniversityUppsalaSweden
- Department of Environmental BiologySapienza University of RomeRomeItaly
| | - Rodney T. Richardson
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMarylandUSA
| | | | - Berry J. Brosi
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Kevin S. Burgess
- Department of BiologyCollege of Letters and Sciences, Columbus State University, University System of GeorgiaAtlantaGeorgiaUSA
| | - Yoshihisa Suyama
- Field Science CenterGraduate School of Agricultural Science, Tohoku UniversityOsakiMiyagiJapan
| | - Natasha de Vere
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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Bleke CA, Gese EM, Roberts SB, Villalba JJ. Seasonal shifts in pronghorn antelope (Antilocapra americana) diets under a new lens: Examining diet composition using a molecular technique. PLoS One 2023; 18:e0292725. [PMID: 37819912 PMCID: PMC10566741 DOI: 10.1371/journal.pone.0292725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
Foraging is one of the most fundamental activities contributing to the maximization of an animal's fitness, and thus herbivores must optimize their diet selection and intake to meet their nutrient demands for survival, growth, and reproduction. Using plant DNA barcoding, we determined diet composition of five subpopulations of adult female pronghorn antelope (Antilocapra americana) grazing rangelands in southern and southeastern Idaho, USA. Fecal samples were collected for two years (2018-2019), and across metabolically-important adult female life history stages (late gestation, early lactation, breeding season). Plant DNA barcoding yielded 137 detected species within pronghorn diets across subpopulations and sampling periods with forbs being the most abundant. Pronghorn dietary functional group composition ranged from 52.2-60.3% from forbs followed by shrubs (22.6-28.2%), graminoids (8.7-15.7%), and legumes (5.5-9.6%). Dietary protein intake was also highest from forbs and ranged from 32.4-62.4% followed by graminoids (1.2-43.1%), shrubs (18.7-21.3%), and legumes (2.6-7.4%). We found significant intra- and interannual differences in the mean number of genera-based plant detections in pronghorn diets. Dietary protein intake of cultivated legumes (e.g., alfalfa [Medicago sativa] and sainfoin [Onobrychis viciifolia]) was lower than expected, ranging from <1.0-30.8%, suggesting that even within an agricultural-dominated landscape, factors other than plant nutritional composition contributed to pronghorn diets. Although the plant DNA barcoding technique exhibits limitations, it demonstrated potential for elucidating pronghorn dietary species richness, particularly for plants consumed in small proportions, as well as for observing temporal fluctuations in functional group composition and dietary protein intake explained through the interplay between environmental factors, plant chemical composition, and the animals' physiological needs.
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Affiliation(s)
- Cole A. Bleke
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
| | - Eric M. Gese
- U.S. Department of Agriculture, Wildlife Services, National Wildlife Research Center, Utah Field Station, Logan, Utah, United States of America
| | - Shane B. Roberts
- Idaho Department of Fish and Game, Boise, Idaho, United States of America
| | - Juan J. Villalba
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
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Shah AP, Travadi T, Sharma S, Pandit R, Joshi C, Joshi M. Comprehensive analysis using DNA metabarcoding, SCAR marker based PCR assay, and HPLC unveils the adulteration in Brahmi herbal products. Mol Biol Rep 2023; 50:7605-7618. [PMID: 37532919 DOI: 10.1007/s11033-023-08653-5] [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: 03/17/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Brahmi is one of the important nootropic botanicals, widely sold in the market, with the name "Brahmi'' being used to describe both Bacopa monnieri and Centella asiatica species. The Brahmi herbal products market is expanding; hence, economically motivated adulteration is highly prevalent. METHODS AND RESULTS This study aimed to develop DNA-based methods, including SCAR marker-based PCR and metabarcoding, to authenticate Brahmi herbal products and compare these methods with HPLC. These methods have been validated using mock controls (in-house blended formulations). All targeted plant species in mock controls were detected successfully with all three methods, whereas, in market samples, only 22.2%, 55.6%, and 50.0% were found positive for Brahmi by PCR assay, DNA metabarcoding, and HPLC, respectively. Metabarcoding can detect the presence of non-labeled plants together with targeted species, which is an advantage over PCR assay or HPLC. CONCLUSION SCAR marker-based PCR is a rapid and cost-effective method for detecting the presence of B. monnieri and C. asiatica. However, in this study, the success rate of PCR amplification was relatively low because the primers targeted either RAPD or ITS-based SCAR markers. HPLC assay, although an alternative, was unable to detect the presence of other botanicals, just like the SCAR marker-based PCR assay. On the other hand, metabarcoding can be utilized to identify the target plants, even in very small quantities, while also providing simulated identification of other botanicals. This study successfully addressed the need for quality control of Brahmi herbal products and provided the first-time report of DNA metabarcoding for such products.
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Affiliation(s)
- Abhi P Shah
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Tasnim Travadi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Sonal Sharma
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India.
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Raclariu-Manolică AC, Mauvisseau Q, Paranaiba R, De Boer HJ, Socaciu C. Authentication of milk thistle commercial products using UHPLC-QTOF-ESI + MS metabolomics and DNA metabarcoding. BMC Complement Med Ther 2023; 23:257. [PMID: 37480124 PMCID: PMC10360273 DOI: 10.1186/s12906-023-04091-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Milk thistle is one of the most popular hepatoprotectants, and is often sold in combination with other ingredients. Botanical supplements are known to be vulnerable to contamination and adulteration, and emerging technologies show promise to improve their quality control. METHODS Untargeted and semi-targeted metabolomics based on UHPLC-QTOF-ESI+MS techniques, UV spectrometry, and DNA metabarcoding using Illumina MiSeq were used to authenticate eighteen milk thistle botanical formulations (teas, capsules, tablets, emulsion). RESULTS Untargeted metabolomics separated 217 molecules and by multivariate analysis the discrimination between the different preparations was established. The semi-targeted metabolomics focused on 63 phytochemicals, mainly silymarin flavonolignans and flavonoids, that may be considered as putative biomarkers of authenticity. All formulations contained molecules from silymarin complexes at different levels. The quantitative evaluation of silybins was done using in parallel UV spectrometry and UHPLC-QTOF-ESI+MS and their correlations were compared. DNA metabarcoding detected milk thistle in eleven out of sixteen retained preparations, whereas two others had incomplete evidence of milk thistle despite metabolomics validating specific metabolites, e.g., silymarin complex, identified and quantified in all samples. Meanwhile, the DNA metabarcoding provided insights into the total species composition allowing the interpretation of the results in a broad context. CONCLUSION Our study emphasizes that combining spectroscopic, chromatographic, and genetic techniques bring complementary information to guarantee the quality of the botanical formulations.
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Affiliation(s)
- Ancuța Cristina Raclariu-Manolică
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Alexandru cel Bun Street, 6, Piatra Neamț, 610004, Romania.
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, Oslo, 0318, Norway.
| | - Quentin Mauvisseau
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, Oslo, 0318, Norway
| | - Renato Paranaiba
- Natural Products Laboratory, School of Health Sciences, University of Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, 70910-900, Brazil
- DNA Laboratory, National Institute of Criminalistics, Brazilian Federal Police, SAIS Quadra 7, Lote 23, Brasília, DF, 70610-200, Brazil
| | - Hugo J De Boer
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, Oslo, 0318, Norway
| | - Carmen Socaciu
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, Mănăştur Street, nr. 3-5, Cluj Napoca, 400372, Romania
- BIODIATECH- Research Center for Applied Biotechnology in Diagnosis and Molecular Therapy, Trifoiului Street 12G, Cluj-Napoca, 400478, Romania
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Frisk CA, Adams-Groom B, Smith M. Isolating the species element in grass pollen allergy: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163661. [PMID: 37094678 DOI: 10.1016/j.scitotenv.2023.163661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Grass pollen is a leading cause of allergy in many countries, particularly Europe. Although many elements of grass pollen production and dispersal are quite well researched, gaps still remain around the grass species that are predominant in the air and which of those are most likely to trigger allergy. In this comprehensive review we isolate the species aspect in grass pollen allergy by exploring the interdisciplinary interdependencies between plant ecology, public health, aerobiology, reproductive phenology and molecular ecology. We further identify current research gaps and provide open ended questions and recommendations for future research in an effort to focus the research community to develop novel strategies to combat grass pollen allergy. We emphasise the role of separating temperate and subtropical grasses, identified through divergence in evolutionary history, climate adaptations and flowering times. However, allergen cross-reactivity and the degree of IgE connectivity in sufferers between the two groups remains an area of active research. The importance of future research to identify allergen homology through biomolecular similarity and the connection to species taxonomy and practical implications of this to allergenicity is further emphasised. We also discuss the relevance of eDNA and molecular ecological techniques (DNA metabarcoding, qPCR and ELISA) as important tools in quantifying the connection between the biosphere with the atmosphere. By gaining more understanding of the connection between species-specific atmospheric eDNA and flowering phenology we will further elucidate the importance of species in releasing grass pollen and allergens to the atmosphere and their individual role in grass pollen allergy.
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Affiliation(s)
- Carl A Frisk
- Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, Norway.
| | - Beverley Adams-Groom
- School of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - Matt Smith
- School of Science and the Environment, University of Worcester, Worcester, United Kingdom
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Dias HQ, Sukumaran S. Are genomic indices effective alternatives to morphology based benthic indices in biomonitoring studies? Perspectives from a major harbour and marine protected area. MARINE POLLUTION BULLETIN 2023; 187:114586. [PMID: 36652865 DOI: 10.1016/j.marpolbul.2023.114586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/01/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Ecological assessments are currently being conducted by traditional morpho-taxonomical identification techniques that are time-consuming and often inaccurate. Biomonitoring programs are increasingly being complemented by the more rapid and efficient DNA barcoding approach. We compared the congruency of morpho-taxonomic (AMBI - AZTI's Marine Biotic Index) and genomic (gAMBI) benthic indices in ecological quality status (EcoQS) assignation in Mumbai harbour and Malvan Marine Protected area (MPA). The study, first of its kind to adopt the gAMBI tool in the selected milieu, contributed substantial number of macrobenthic cytochrome c oxidase subunit I gene (COI) sequences that were previously unavailable in the reference library, adding sufficient genetic resources for establishing ecostatus. AMBI and gAMBI values based on presence/absence data related significantly with those derived from abundance data matrices. Taxonomic and genomic indices derived ecostatus corresponded sufficiently well despite minor discrepancies, underscoring the viability of gAMBI as a superior alternative to AMBI in monitoring studies.
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Affiliation(s)
- Heidy Q Dias
- CSIR-National Institute of Oceanography, Regional Centre Andheri (W), Mumbai 400 053, India
| | - Soniya Sukumaran
- CSIR-National Institute of Oceanography, Regional Centre Andheri (W), Mumbai 400 053, India.
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9
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van der Heyde M, Bunce M, Nevill P. Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157617. [PMID: 35901901 DOI: 10.1016/j.scitotenv.2022.157617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Ecological restoration of terrestrial environments is a globally important process to combat the loss of biodiversity and ecosystem services. Holistic monitoring of restored biota and active management of restoration is necessary to improve restoration processes and outcomes, and provide evidence to stakeholders that targets are being achieved. Increasingly, environmental DNA (eDNA) metabarcoding is used as a restoration monitoring tool because it is able to generate biodiversity data rapidly, accurately, non-destructively, and reliably, on a wide breadth of organisms from soil microbes to mammals. The overall objective of this review is to discuss the key factors to consider in the use of environmental DNA for monitoring of restored terrestrial ecosystems, hopefully improving monitoring, and ultimately, restoration outcomes. We identified that the majority of eDNA based studies of ecosystem restoration are currently conducted in Europe, North America, and Australia, and that almost half of total studies were published in 2021-22. Soil was the most popular sample substrate, soil microbial communities the most targeted taxa, and forests the most studied ecosystem. We suggest there is no 'one size fits all' approach to restoration monitoring using eDNA, and discuss survey design. Factors to consider include substrate selection, sample collection and storage, assay selection, and data interpretation, all of which require careful planning to obtain reliable, and accurate information that can be used for restoration monitoring and decision making. We explore future directions for research and argue that eDNA metabarcoding can be a useful tool in the restoration monitoring 'toolkit', but requires informed application and greater accessibility to data by a wide spectrum of stakeholders.
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Affiliation(s)
- Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia.
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia; Institute of Environmental Science and Research (ESR), Kenepuru, Porirua 5022, New Zealand
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia
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10
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Wanniarachchi S, Swan M, Nevil P, York A. Using eDNA metabarcoding to understand the effect of fire on the diet of small mammals in a woodland ecosystem. Ecol Evol 2022; 12:e9457. [PMID: 36381390 PMCID: PMC9643072 DOI: 10.1002/ece3.9457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022] Open
Abstract
Food acquisition is a fundamental process that drives animal distribution and abundance, influencing how species respond to changing environments. Disturbances such as fire create significant shifts in available dietary resources, yet, for many species, we lack basic information about what they eat, let alone how they respond to a changing resource base. In order to create effective management strategies, faunal conservation in flammable landscapes requires a greater understanding of what animals eat and how this change following a fire. What animals eat in postfire environments has received little attention due to the time-consuming methodologies and low-resolution identification of food taxa. Recently, molecular techniques have been developed to identify food DNA in scats, making it possible to identify animal diets with enhanced resolution. The primary aim of this study was to utilize eDNA metabarcoding to obtain an improved understanding of the diet of three native Australian small mammal species: yellow-footed antechinus (Antechinus flavipes), heath mouse (Pseudomys shortridgei), and bush rat (Rattus fuscipes). Specifically, we sought to understand the difference in the overall diet of the three species and how diet changed over time after fire. Yellow-footed antechinus diets mostly consisted of moths, and plants belonging to myrtles and legume families while bush rats consumed legumes, myrtles, rushes, and beetles. Heath mouse diet was dominated by rushes. All three species shifted their diets over time after fire, with most pronounced shifts in the bush rats and least for heath mice. Identifying critical food resources for native animals will allow conservation managers to consider the effect of fire management actions on these resources and help conserve the species that use them.
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Affiliation(s)
- Saumya Wanniarachchi
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
| | - Matthew Swan
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
| | - Paul Nevil
- Trace and Environmental DNA Laboratory, School of Life and Molecular SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Alan York
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
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11
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Mahima K, Sunil Kumar KN, Rakhesh KV, Rajeswaran PS, Sharma A, Sathishkumar R. Advancements and future prospective of DNA barcodes in the herbal drug industry. Front Pharmacol 2022; 13:947512. [PMID: 36339543 PMCID: PMC9635000 DOI: 10.3389/fphar.2022.947512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/10/2022] [Indexed: 08/04/2023] Open
Abstract
Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
- Department of Pharmacognosy, Siddha Central Research Institute, Chennai, Tamil Nadu, India
| | | | | | | | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Santiago de Queretaro, Queretaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
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12
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Fernandes K, Prendergast K, Bateman PW, Saunders BJ, Gibberd M, Bunce M, Nevill P. DNA metabarcoding identifies urban foraging patterns of oligolectic and polylectic cavity-nesting bees. Oecologia 2022; 200:323-337. [PMID: 36098815 PMCID: PMC9675668 DOI: 10.1007/s00442-022-05254-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 09/01/2022] [Indexed: 12/03/2022]
Abstract
Urbanisation modifies natural landscapes resulting in built-up space that is covered by buildings or hard surfaces and managed green spaces that often substitute native plant species with exotics. Some native bee species have been able to adapt to urban environments, foraging and reproducing in these highly modified areas. However, little is known on how the foraging ecology of native bees is affected by urbanised environments, and whether impacts vary among species with different degrees of specialisation for pollen collection. Here, we aim to investigate the responses of native bee foraging behaviour to urbanisation, using DNA metabarcoding to identify the resources within nesting tubes. We targeted oligolectic (specialist) and polylectic (generalist) cavity-nesting bee species in residential gardens and remnant bushland habitats. We were able to identify 40 families, 50 genera, and 23 species of plants, including exotic species, from the contents of nesting tubes. Oligolectic bee species had higher diversity of plant pollen in their nesting tubes in residential gardens compared to bushland habitats, along with significantly different forage composition between the two habitats. This result implies a greater degree of forage flexibility for oligolectic bee species than previously thought. In contrast, the diversity and composition of plant forage in polylectic bee nesting tubes did not vary between the two habitat types. Our results suggest a complex response of cavity-nesting bees to urbanisation and support the need for additional research to understand how the shifts in foraging resources impact overall bee health.
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Affiliation(s)
- Kristen Fernandes
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia. .,Section for Molecular Ecology and Evolution, Faculty of Health and Medical Sciences, Globe Institute, University of Copenhagen, Copenhagen K, Denmark. .,Food Agility CRC Ltd, 175 Pitt St, Sydney, NSW, 2000, Australia.
| | - Kit Prendergast
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Philip W Bateman
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.,MBioMe - Mine Site Biomonitoring using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Benjamin J Saunders
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Mark Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.,The Institute of Environmental Science and Research (ESR), Kenepuru, Porirua, 5022, New Zealand
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.,MBioMe - Mine Site Biomonitoring using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
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13
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Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B. The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The worldwide rapid declines in insect and plant abundance and diversity that have occurred in the past decades have gained public attention and demand for political actions to counteract these declines are growing. Rapid large-scale biomonitoring can aid in observing these changes and provide information for decisions for land management and species protection. Malaise traps have long been used for insect sampling and when insects are captured in these traps, they carry traces of plants they have visited on the body surface or as digested food material in the gut contents. Metabarcoding offers a promising method for identifying these plant traces, providing insight into the plants with which insects are directly interacting at a given time. To test the efficacy of DNA metabarcoding with these sample types, 79 samples from 21 sites across Germany were analysed with the ITS2 barcode. This study, to our knowledge, is the first examination of metabarcoding plant DNA traces from Malaise trap samples. Here, we report on the feasibility of sequencing these sample types, analysis of the resulting taxa, the usage of cultivated plants by insects near nature conservancy areas and the detection of rare and neophyte species. Due to the frequency of contamination and false positive reads, isolation and PCR negative controls should be used in every reaction. Metabarcoding has advantages in efficiency and resolution over microscopic identification of pollen and is the only possible identification method for the other plant traces from Malaise traps and could provide a broad utility for future studies of plant-insect interactions.
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14
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Saccò M, Guzik MT, van der Heyde M, Nevill P, Cooper SJB, Austin AD, Coates PJ, Allentoft ME, White NE. eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153223. [PMID: 35063529 DOI: 10.1016/j.scitotenv.2022.153223] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.
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Affiliation(s)
- Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia.
| | - Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Mieke van der Heyde
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, 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; ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide 5000, SA, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Peterson J Coates
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, 1006, Dartmouth, Nova Scotia B2Y 4A2, Canada
| | - 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
| | - Nicole E White
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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15
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Crone MK, Biddinger DJ, Grozinger CM. Wild Bee Nutritional Ecology: Integrative Strategies to Assess Foraging Preferences and Nutritional Requirements. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.847003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bees depend on flowering plants for their nutrition, and reduced availability of floral resources is a major driver of declines in both managed and wild bee populations. Understanding the nutritional needs of different bee species, and how these needs are met by the varying nutritional resources provided by different flowering plant taxa, can greatly inform land management recommendations to support bee populations and their associated ecosystem services. However, most bee nutrition research has focused on the three most commonly managed and commercially reared bee taxa—honey bees, bumble bees, and mason bees—with fewer studies focused on wild bees and other managed species, such as leafcutting bees, stingless bees, and alkali bees. Thus, we have limited information about the nutritional requirements and foraging preferences of the vast majority of bee species. Here, we discuss the approaches traditionally used to understand bee nutritional ecology: identification of floral visitors of selected focal plant species, evaluation of the foraging preferences of adults in selected focal bee species, evaluation of the nutritional requirements of focal bee species (larvae or adults) in controlled settings, and examine how these methods may be adapted to study a wider range of bee species. We also highlight emerging technologies that have the potential to greatly facilitate studies of the nutritional ecology of wild bee species, as well as evaluate bee nutritional ecology at significantly larger spatio-temporal scales than were previously feasible. While the focus of this review is on bee species, many of these techniques can be applied to other pollinator taxa as well.
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16
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Foster NR, Dijk K, Biffin E, Young JM, Thomson VA, Gillanders BM, Jones AR, Waycott M. A targeted capture approach to generating reference sequence databases for chloroplast gene regions. Ecol Evol 2022; 12:e8816. [PMID: 35432922 PMCID: PMC9001157 DOI: 10.1002/ece3.8816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Nicole R. Foster
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Kor‐jent Dijk
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Ed Biffin
- State Herbarium of South Australia Botanic Gardens and State Herbarium Adelaide South Australia Australia
| | - Jennifer M. Young
- College of Science and Engineering Flinders University South Australia Australia
| | - Vicki A. Thomson
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Bronwyn M. Gillanders
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Alice R. Jones
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Michelle Waycott
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
- State Herbarium of South Australia Botanic Gardens and State Herbarium Adelaide South Australia Australia
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17
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van der Heyde M, Bunce M, Dixon KW, Fernandes K, Majer J, Wardell-Johnson G, White NE, Nevill P. Evaluating restoration trajectories using DNA metabarcoding of ground-dwelling and airborne invertebrates and associated plant communities. Mol Ecol 2022; 31:2172-2188. [PMID: 35092102 PMCID: PMC9304231 DOI: 10.1111/mec.16375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 12/05/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
Abstract
Invertebrates are important for restoration processes as they are key drivers of many landscape‐scale ecosystem functions; including pollination, nutrient cycling and soil formation. However, invertebrates are often overlooked in restoration monitoring because they are highly diverse, poorly described, and time‐consuming to survey, and require increasingly scarce taxonomic expertise to enable identification. DNA metabarcoding is a relatively new tool for rapid survey that is able to address some of these concerns, and provide information about the taxa with which invertebrates are interacting via food webs and habitat. Here, we evaluate how invertebrate communities may be used to determine ecosystem trajectories during restoration. We collected ground‐dwelling and airborne invertebrates across chronosequences of mine‐site restoration in three ecologically disparate locations in Western Australia and identified invertebrate and plant communities using DNA metabarcoding. Ground‐dwelling invertebrates showed the clearest restoration signals, with communities becoming more similar to reference communities over time. These patterns were weaker in airborne invertebrates, which have higher dispersal abilities and therefore less local fidelity to environmental conditions. Although we detected directional changes in community composition indicative of invertebrate recovery, patterns observed were inconsistent between study locations. The inclusion of plant assays allowed identification of plant species, as well as potential food sources and habitat. We demonstrate that DNA metabarcoding of invertebrate communities can be used to evaluate restoration trajectories. Testing and incorporating new monitoring techniques such as DNA metabarcoding is critical to improving restoration outcomes.
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Affiliation(s)
- M van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia.,Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - M Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia.,Institute of Environmental Science and Research (ESR), Kenepuru, Porirua, 5022, New Zealand
| | - K W Dixon
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - K Fernandes
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - J Majer
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - G Wardell-Johnson
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - N E White
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia
| | - P Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia, 6845, Australia.,Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPP Box U1987, Perth, Western Australia, 6845, Australia
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18
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Nazar N, Howard C, Slater A, Sgamma T. Challenges in Medicinal and Aromatic Plants DNA Barcoding-Lessons from the Lamiaceae. PLANTS (BASEL, SWITZERLAND) 2022; 11:137. [PMID: 35009140 PMCID: PMC8747715 DOI: 10.3390/plants11010137] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
The potential value of DNA barcoding for the identification of medicinal plants and authentication of traded plant materials has been widely recognized; however, a number of challenges remain before DNA methods are fully accepted as an essential quality control method by industry and regulatory authorities. The successes and limitations of conventional DNA barcoding are considered in relation to important members of the Lamiaceae. The mint family (Lamiaceae) contains over one thousand species recorded as having a medicinal use, with many more exploited in food and cosmetics for their aromatic properties. The family is characterized by a diversity of secondary products, most notably the essential oils (EOs) produced in external glandular structures on the aerial parts of the plant that typify well-known plants of the basil (Ocimum), lavender (Lavandula), mint (Mentha), thyme (Thymus), sage (Salvia) and related genera. This complex, species-rich family includes widely cultivated commercial hybrids and endangered wild-harvested traditional medicines, and examples of potential toxic adulterants within the family are explored in detail. The opportunities provided by next generation sequencing technologies to whole plastome barcoding and nuclear genome sequencing are also discussed with relevant examples.
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Affiliation(s)
- Nazia Nazar
- Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK;
| | - Caroline Howard
- Tree of Life Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK;
| | - Adrian Slater
- Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK;
| | - Tiziana Sgamma
- Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK;
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19
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Abraham EJ, Kellogg JJ. Chemometric-Guided Approaches for Profiling and Authenticating Botanical Materials. Front Nutr 2021; 8:780228. [PMID: 34901127 PMCID: PMC8663772 DOI: 10.3389/fnut.2021.780228] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/31/2021] [Indexed: 01/08/2023] Open
Abstract
Botanical supplements with broad traditional and medicinal uses represent an area of growing importance for American health management; 25% of U.S. adults use dietary supplements daily and collectively spent over $9. 5 billion in 2019 in herbal and botanical supplements alone. To understand how natural products benefit human health and determine potential safety concerns, careful in vitro, in vivo, and clinical studies are required. However, botanicals are innately complex systems, with complicated compositions that defy many standard analytical approaches and fluctuate based upon a plethora of factors, including genetics, growth conditions, and harvesting/processing procedures. Robust studies rely upon accurate identification of the plant material, and botanicals' increasing economic and health importance demand reproducible sourcing, as well as assessment of contamination or adulteration. These quality control needs for botanical products remain a significant problem plaguing researchers in academia as well as the supplement industry, thus posing a risk to consumers and possibly rendering clinical data irreproducible and/or irrelevant. Chemometric approaches that analyze the small molecule composition of materials provide a reliable and high-throughput avenue for botanical authentication. This review emphasizes the need for consistent material and provides insight into the roles of various modern chemometric analyses in evaluating and authenticating botanicals, focusing on advanced methodologies, including targeted and untargeted metabolite analysis, as well as the role of multivariate statistical modeling and machine learning in phytochemical characterization. Furthermore, we will discuss how chemometric approaches can be integrated with orthogonal techniques to provide a more robust approach to authentication, and provide directions for future research.
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Affiliation(s)
- Evelyn J Abraham
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University (PSU), University Park, PA, United States
| | - Joshua J Kellogg
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University (PSU), University Park, PA, United States.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
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20
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Hu JL, Ci XQ, Liu ZF, Dormontt EE, Conran JG, Lowe AJ, Li J. Assessing candidate DNA barcodes for Chinese and internationally traded timber species. Mol Ecol Resour 2021; 22:1478-1492. [PMID: 34752673 DOI: 10.1111/1755-0998.13546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/22/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH-psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH-psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH-psbA+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.
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Affiliation(s)
- Jian-Lin Hu
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Qin Ci
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Zhi-Fang Liu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Eleanor E Dormontt
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - John G Conran
- Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and Sprigg Geobiology Centre (SGC), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew J Lowe
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
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21
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Vasconcelos S, Nunes GL, Dias MC, Lorena J, Oliveira RRM, Lima TGL, Pires ES, Valadares RBS, Alves R, Watanabe MTC, Zappi DC, Hiura AL, Pastore M, Vasconcelos LV, Mota NFO, Viana PL, Gil ASB, Simões AO, Imperatriz‐Fonseca VL, Harley RM, Giulietti AM, Oliveira G. Unraveling the plant diversity of the Amazonian canga through DNA barcoding. Ecol Evol 2021; 11:13348-13362. [PMID: 34646474 PMCID: PMC8495817 DOI: 10.1002/ece3.8057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 01/04/2023] Open
Abstract
The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harboring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA, and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera, and 115 families of vascular plants from a highly diverse flora in the Amazon basin, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.
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Affiliation(s)
| | | | - Mariana C. Dias
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Renato R. M. Oliveira
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | | | | | | | | | - Daniela C. Zappi
- Instituto Tecnológico ValeBelémBrazil
- Instituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | | | - Mayara Pastore
- Instituto Tecnológico ValeBelémBrazil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - Liziane V. Vasconcelos
- Instituto Tecnológico ValeBelémBrazil
- Programa de Pós‐Graduação em EcologiaUniversidade Federal do ParáBelémBrazil
| | - Nara F. O. Mota
- Instituto Tecnológico ValeBelémBrazil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - Pedro L. Viana
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - André S. B. Gil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - André O. Simões
- Departamento de Biologia VegetalUniversidade Estadual de CampinasCampinasBrazil
| | | | | | - Ana M. Giulietti
- Instituto Tecnológico ValeBelémBrazil
- Programa de Pós‐Graduação em BotânicaUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
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22
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Senthilkumar S, Ulaganathan K, Ghosh Dasgupta M. Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus. 3 Biotech 2021; 11:393. [PMID: 34458062 DOI: 10.1007/s13205-021-02943-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/25/2021] [Indexed: 12/25/2022] Open
Abstract
Chloroplast genome sequencing is an essential tool to understand genome evolution and phylogenetic relationship. The available methods for constructing chloroplast genome include chloroplast enrichment followed by long overlapping PCR or extraction and assembly of chloroplast-specific reads from whole-genome datasets. In the present study, we propose an alternate strategy of extraction and assembly of chloroplast-specific reads from leaf transcriptome data of Pterocarpus santalinus using bowtie2 aligner program. The assembled genome was compared with the published chloroplast genome of P. santalinus for genome size, number of predicted genes, microsatellite repeat motifs, and nucleotide repeats. A near-complete chloroplast genome was assembled from the transcriptome reads. The proposed method requires less computational time and know-how, limited virtual memory, and is cost-effective when compared to whole-genome sequencing. Assembly of Cp genome from transcriptome data will enhance the resolution of phylogenetic studies through comparative plastome analysis, facilitate accurate species/genotype discrimination and accelerate the development of transplastomic plants with enhanced biotic and abiotic tolerance. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02943-0.
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Affiliation(s)
- Shanmugavel Senthilkumar
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore, 641002 Tamil Nadu India
| | - Kandasamy Ulaganathan
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500007 Andhra Pradesh India
| | - Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore, 641002 Tamil Nadu India
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23
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Milla L, Sniderman K, Lines R, Mousavi‐Derazmahalleh M, Encinas‐Viso F. Pollen DNA metabarcoding identifies regional provenance and high plant diversity in Australian honey. Ecol Evol 2021; 11:8683-8698. [PMID: 34257922 PMCID: PMC8258210 DOI: 10.1002/ece3.7679] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/25/2022] Open
Abstract
Accurate identification of the botanical components of honey can be used to establish its geographical provenance, while also providing insights into honeybee (Apis mellifera L.) diet and foraging preferences. DNA metabarcoding has been demonstrated as a robust method to identify plant species from pollen and pollen-based products, including honey. We investigated the use of pollen metabarcoding to identify the floral sources and local foraging preferences of honeybees using 15 honey samples from six bioregions from eastern and western Australia. We used two plant metabarcoding markers, ITS2 and the trnL P6 loop. Both markers combined identified a total of 55 plant families, 67 genera, and 43 species. The trnL P6 loop marker provided significantly higher detection of taxa, detecting an average of 15.6 taxa per sample, compared to 4.6 with ITS2. Most honeys were dominated by Eucalyptus and other Myrtaceae species, with a few honeys dominated by Macadamia (Proteaceae) and Fabaceae. Metabarcoding detected the nominal primary source provided by beekeepers among the top five most abundant taxa for 85% of samples. We found that eastern and western honeys could be clearly differentiated by their floral composition, and clustered into bioregions with the trnL marker. Comparison with previous results obtained from melissopalynology shows that metabarcoding can detect similar numbers of plant families and genera, but provides significantly higher resolution at species level. Our results show that pollen DNA metabarcoding is a powerful and robust method for detecting honey provenance and examining the diet of honeybees. This is particularly relevant for hives foraging on the unique and diverse flora of the Australian continent, with the potential to be used as a novel monitoring tool for honeybee floral resources.
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Affiliation(s)
- Liz Milla
- Centre for Australian National Biodiversity ResearchCSIROCanberraACTAustralia
| | - Kale Sniderman
- School of Earth SciencesThe University of MelbourneMelbourneVic.Australia
| | - Rose Lines
- eDNA Frontiers LaboratoryCurtin UniversityPerthWAAustralia
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24
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Avanesyan A, Sutton H, Lamp WO. Choosing an Effective PCR-Based Approach for Diet Analysis of Insect Herbivores: A Systematic Review. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:1035-1046. [PMID: 33822094 DOI: 10.1093/jee/toab057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Indexed: 06/12/2023]
Abstract
Identification of ingested plant species using polymerase chain reaction (PCR)-based methods is an increasingly useful yet challenging approach to accurately determine the diet composition of insect herbivores and thus their trophic interactions. A typical process of detection of DNA of ingested plants involves the choice of a DNA extraction method, a genomic target region, and/or the best approach for an accurate plant species identification. The wide range of available techniques makes the choice of the most appropriate method for an accurately and timely identification of ingested plants from insect guts difficult. In our study, we reviewed the commonly used PCR-based approaches in studies published from 1977 to 2019, to provide researchers with the information on the tools which have been shown to be effective for obtaining and identifying ingested plants. Our results showed that among five insect orders used in the retrieved studies Coleoptera and Hemiptera were prevalent (33 and 28% of all the records, respectively). In 79% of the studies a DNA barcoding approach was employed. In a substantial number of studies Qiagen DNA extraction kits and CTAB protocol were used (43 and 23%, respectively). Of all records, 65% used a single locus as a targeted plant DNA fragment; trnL, rbcL, and ITS regions were the most frequently used loci. Sequencing was the dominant type of among DNA verification approaches (70% of all records). This review provides important information on the availability of successfully used PCR-based approaches to identify ingested plant DNA in insect guts, and suggests potential directions for future studies on plant-insect trophic interactions.
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Affiliation(s)
- Alina Avanesyan
- Department of Entomology, University of Maryland, 4291 Fieldhouse Drive, 4112 Plant Sciences, College Park, MD 20742, USA
| | - Hannah Sutton
- Department of Entomology, University of Maryland, 4291 Fieldhouse Drive, 4112 Plant Sciences, College Park, MD 20742, USA
| | - William O Lamp
- Department of Entomology, University of Maryland, 4291 Fieldhouse Drive, 4112 Plant Sciences, College Park, MD 20742, USA
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25
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Shadrin DM. DNA Barcoding: Applications. RUSS J GENET+ 2021. [DOI: 10.1134/s102279542104013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Ishak S, Dormontt E, Young JM. Microbiomes in forensic botany: a review. Forensic Sci Med Pathol 2021; 17:297-307. [PMID: 33830453 DOI: 10.1007/s12024-021-00362-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 11/24/2022]
Abstract
Fragments of botanical material can often be found at crime scenes (on live and dead bodies, or on incriminating objects) and can provide circumstantial evidence on various aspects of forensic investigations such as determining crime scene locations, times of death or possession of illegal species. Morphological and genetic analysis are the most commonly applied methods to analyze plant fragment evidence but are limited by their low capacity to differentiate between potential source locations, especially at local scales. Here, we review the current applications and limitations of current plant fragment analysis for forensic investigations and introduce the potential of microbiome analysis to complement the existing forensic plant fragment analysis toolkit. The potential for plant fragment provenance identification at geographic scales meaningful to forensic investigations warrants further investigation of the phyllosphere microbiome in this context. To that end we identify three key areas of future research: 1) Retrieval of microbial DNA of sufficient quality and quantity from botanical material; 2) Variability of the phyllosphere microbiome at different taxonomic and spatial scales, with explicit reference to assignment capacity; 3) Impacts on assignment capacity of time, seasonality and movement of fragments between locations. The development of robust microbiome analysis tools for forensic purposes in botanical material could increase the evidentiary value of the botanical evidence commonly encountered in casework, aiding in the identification of crime scene locations.
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Affiliation(s)
- Sarah Ishak
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada.
| | - Eleanor Dormontt
- Advanced DNA, Identification and Forensic Facility, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jennifer M Young
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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27
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Jones L, Twyford AD, Ford CR, Rich TCG, Davies H, Forrest LL, Hart ML, McHaffie H, Brown MR, Hollingsworth PM, de Vere N. Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom. Mol Ecol Resour 2021; 21:2050-2062. [PMID: 33749162 DOI: 10.1111/1755-0998.13388] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/09/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022]
Abstract
DNA barcoding and metabarcoding provide new avenues for investigating biological systems. These techniques require well-curated reference libraries with extensive coverage. Generating an exhaustive national DNA barcode reference library can open up new avenues of research in ecology, evolution and conservation, yet few studies to date have created such a resource. In plant DNA barcoding, herbarium collections provide taxonomically robust material but also pose challenges in lab processing. Here, we present a national DNA barcoding resource covering all of the native flowering plants and conifers of the United Kingdom. This represents 1,482 plant species, with the majority of specimens (81%) sourced from herbaria. Using Sanger sequencing of the plant DNA barcode markers, rbcL, matK, and ITS2, at least one DNA barcode was retrieved from 98% of the UK flora. We sampled from multiple individuals, resulting in a species coverage for rbcL of 96% (4,477 sequences), 90% for matK (3,259 sequences) and 75% for ITS2 (2,585 sequences). Sequence recovery was lower for herbarium material compared to fresh collections, with the age of the specimen having a significant effect on the success of sequence recovery. Species level discrimination was highest with ITS2, however, the ability to successfully retrieve a sequence was lowest for this region. Analyses of the genetic distinctiveness of species across a complete flora showed DNA barcoding to be informative for all but the most taxonomically complex groups. The UK flora DNA barcode reference library provides an important resource for many applications that require plant identification from DNA.
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Affiliation(s)
- Laura Jones
- National Botanic Garden of Wales, Llanarthne, UK
| | - Alex D Twyford
- Royal Botanic Garden Edinburgh, Edinburgh, UK.,School of Biological Sciences, Institute of Evolutionary Biology, Edinburgh, UK
| | - Col R Ford
- National Botanic Garden of Wales, Llanarthne, UK
| | | | | | | | | | | | - Max R Brown
- School of Biological Sciences, Institute of Evolutionary Biology, Edinburgh, UK
| | | | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, UK.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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28
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Albani Rocchetti G, Armstrong CG, Abeli T, Orsenigo S, Jasper C, Joly S, Bruneau A, Zytaruk M, Vamosi JC. Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species. THE NEW PHYTOLOGIST 2021; 230:433-450. [PMID: 33280123 DOI: 10.1111/nph.17133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 05/29/2023]
Abstract
Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.
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Affiliation(s)
| | | | - Thomas Abeli
- Department of Science, University Roma Tre, Viale G. Marconi 446, Roma, 00154, Italy
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, 27100, Italy
| | - Caroline Jasper
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Simon Joly
- Montreal Botanical Garden, Montréal, QC, H1X 2B2, Canada
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Anne Bruneau
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Maria Zytaruk
- Department of English, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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29
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Rossmann S, Lysøe E, Skogen M, Talgø V, Brurberg MB. DNA Metabarcoding Reveals Broad Presence of Plant Pathogenic Oomycetes in Soil From Internationally Traded Plants. Front Microbiol 2021; 12:637068. [PMID: 33841362 PMCID: PMC8027490 DOI: 10.3389/fmicb.2021.637068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
Plants with roots and soil clumps transported over long distances in plant trading can harbor plant pathogenic oomycetes, facilitating disease outbreaks that threaten ecosystems, biodiversity, and food security. Tools to detect the presence of such oomycetes with a sufficiently high throughput and broad scope are currently not part of international phytosanitary testing regimes. In this work, DNA metabarcoding targeting the internal transcribed spacer (ITS) region was employed to broadly detect and identify oomycetes present in soil from internationally shipped plants. This method was compared to traditional isolation-based detection and identification after an enrichment step. DNA metabarcoding showed widespread presence of potentially plant pathogenic Phytophthora and Pythium species in internationally transported rhizospheric soil with Pythium being the overall most abundant genus observed. Baiting, a commonly employed enrichment method for Phytophthora species, led to an increase of golden-brown algae in the soil samples, but did not increase the relative or absolute abundance of potentially plant pathogenic oomycetes. Metabarcoding of rhizospheric soil yielded DNA sequences corresponding to oomycete isolates obtained after enrichment and identified them correctly but did not always detect the isolated oomycetes in the same samples. This work provides a proof of concept and outlines necessary improvements for the use of environmental DNA (eDNA) and metabarcoding as a standalone phytosanitary assessment tool for broad detection and identification of plant pathogenic oomycetes.
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Affiliation(s)
- Simeon Rossmann
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Erik Lysøe
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Monica Skogen
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Venche Talgø
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - May Bente Brurberg
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
- Department of Plant Sciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
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30
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Choudhary P, Singh BN, Chakdar H, Saxena AK. DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance. World J Microbiol Biotechnol 2021; 37:54. [PMID: 33604719 DOI: 10.1007/s11274-021-03019-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
DNA barcoding has proven to be a versatile tool for plant disease diagnostics in the genomics era. As the mass parallel and next generation sequencing techniques gained importance, the role of specific barcodes came under immense scrutiny. Identification and accurate classification of phytopathogens need a universal approach which has been the main application area of the concept of barcode. The present review entails a detailed description of the present status of barcode application in plant disease diagnostics. A case study on the application of Internal Transcribed Spacer (ITS) as barcode for Aspergillus and Fusarium spp. sheds light on the requirement of other potential candidates as barcodes for accurate identification. The challenges faced while barcoding novel pathogens have also been discussed with a comprehensive outline of integrating more recent technologies like meta-barcoding and genome skimming for detecting plant pathogens.
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Affiliation(s)
- Prassan Choudhary
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Bansh Narayan Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India.
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
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31
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Banchi E, Ametrano CG, Greco S, Stanković D, Muggia L, Pallavicini A. PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5722079. [PMID: 32016319 PMCID: PMC6997939 DOI: 10.1093/database/baz155] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/11/2019] [Accepted: 12/23/2019] [Indexed: 01/02/2023]
Abstract
DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called 'better clustering for QIIME' (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.
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Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy.,Division of Oceanography, National Institute of Oceanography and Applied Geophysics, via Piccard 54, 34151, Trieste, Italy
| | - Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy
| | - David Stanković
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy.,Marine Biology Station, National Institute of Biology, Fornače 41, Piran, Slovenia
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy.,Division of Oceanography, National Institute of Oceanography and Applied Geophysics, via Piccard 54, 34151, Trieste, Italy.,Department of Biology and Evoliution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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32
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Unnikrishnan R, Dev SA, Jayaraj R. Pitfalls and promises of raw drug identification techniques in the ayurvedic industry: an overview. 3 Biotech 2020; 10:497. [PMID: 33150123 DOI: 10.1007/s13205-020-02482-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/13/2020] [Indexed: 11/26/2022] Open
Abstract
India, with a rich heritage of floral diversity, is well-known for its medicinal plant wealth and is the largest producer of medicinal herbs in the world. Ethnobiological Survey of Ministry of Environment and Forests (MOEF) could identify 8000 plant species utilized in various systems of medicine with approximately 25,000 effective herbal formulations. The extensive consumption to meet demand-supply ratio exerts a heavy strain on the existing resources. This subsequently led to the adulteration and substitution of medicinal plants with look-alike species. The consumer's faith on herbal medicine is in the phase of decline due to the extremities in adulteration/substitution and ensuing consequences. It is imperative to bring forth universally acceptable standard tools to authenticate raw drugs before being processed further into formulations. A vast array of techniques such as physical, chemical (analytical), biochemical, anatomical, organoleptic, and recently emerged DNA based molecular methods are widely used for plant species authentication. In recent years, DNA barcoding has made remarkable progress in the field of medicinal plants research. DNA metabarcoding is the latest development for qualitative evaluation of the herbal formulations, whereas for quantitative analysis, combination of pharmacognostic, pharmacovigilance and analytical methods are inevitable for authentication. This review addresses the overall strengths and shortcomings of the existing as well as recently emerged techniques in authenticating ayurvedic raw drugs.
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Affiliation(s)
- Remya Unnikrishnan
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala India
- Cochin University of Science & Technology, Kochi, Kerala India
| | - Suma Arun Dev
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala India
| | - R Jayaraj
- Forest Ecology and Biodiversity Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala India
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33
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Wildlife forensics: A boon for species identification and conservation implications. Forensic Sci Int 2020; 317:110530. [PMID: 33096398 DOI: 10.1016/j.forsciint.2020.110530] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/03/2020] [Accepted: 09/26/2020] [Indexed: 01/05/2023]
Abstract
Wildlife trade and fraudulence in food, artefacts and cosmetic industries had raised serious concern in protection of the wild faunal diversity. Lack of proper tools and molecular based techniques for identification of wild species are some of the major constrains faced by the judiciary and law enforcement agencies while framing charges against poachers and illicit agitator. The emergence of wildlife forensics serves as a boon in solving long pending cases of wildlife crimes. Wildlife forensics have proven to be fast, accurate and reliable criminal investigation processes with comprehensive coverage and easy accessibility. It has also helped resolving taxonomic disputes, determining spatiotemporal genetic divergence, evolutionary history, origins and even endemism. Collaboration among inter-disciplinary fields has even led to engineered signature markers and phylogenetics for several species. Development in fields of genetics, molecular and evolutionary biology and other omics techniques have further contributed in accurate identification of species. Wildlife forensics, with the support of proper international mega database units for population reference, will be fundamental in wildlife investigations through its unlimited information sharing ability. The efficient conservation of species will, however, require a collaborative approach consisting of national policy makers, local stakeholders and implementation agencies in addition to experts from the scientific communities.
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34
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Young JM, Linacre A. Massively parallel sequencing is unlocking the potential of environmental trace evidence. Forensic Sci Int Genet 2020; 50:102393. [PMID: 33157385 DOI: 10.1016/j.fsigen.2020.102393] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 01/16/2023]
Abstract
Massively parallel sequencing (MPS) has revolutionised the field of genomics enabling substantial advances in human DNA profiling. Further, the advent of MPS now allows biological signatures to be obtained from complex DNA mixtures and trace amounts of low biomass samples. Environmental samples serve as ideal forms of contact trace evidence as detection at a scene can establish a link between a suspect, location and victim. Many studies have applied MPS technology to characterise the biodiversity within high biomass environmental samples (such as soil and water) to address questions related to ecology, conservation, climate change and human health. However, translation of these tools to forensic science remains in its infancy, due in part to the merging of traditional forensic ecology practices with unfamiliar DNA technologies and complex datasets. In addition, people and objects also carry low biomass environmental signals which have recently been shown to reflect a specific individual or location. The sensitivity, and reducing cost, of MPS is now unlocking the power of both high and low biomass environmental DNA (eDNA) samples as useful sources of genetic information in forensic science. This paper discusses the potential of eDNA to forensic science by reviewing the most explored applications that are leading the integration of this technology into the field. We introduce novel areas of forensic ecology that could also benefit from these tools with a focus on linking a suspect to a scene or establishing provenance of an unknown sample and discuss the current limitations and validation recommendations to achieve translation of eDNA into casework.
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Affiliation(s)
- J M Young
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.
| | - A Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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Alsos IG, Lavergne S, Merkel MKF, Boleda M, Lammers Y, Alberti A, Pouchon C, Denoeud F, Pitelkova I, Pușcaș M, Roquet C, Hurdu BI, Thuiller W, Zimmermann NE, Hollingsworth PM, Coissac E. The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material. PLANTS (BASEL, SWITZERLAND) 2020; 9:E432. [PMID: 32244605 PMCID: PMC7238428 DOI: 10.3390/plants9040432] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
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Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Sebastien Lavergne
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | - Marti Boleda
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - Youri Lammers
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Charles Pouchon
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; (A.A.); (F.D.)
| | - Iva Pitelkova
- Tromsø Museum, UiT—The Arctic University of Norway, N-9037 Tromsø, Norway; (M.K.F.M.); (Y.L.); (I.P.)
| | - Mihai Pușcaș
- A. Borza Botanical Garden and Faculty of Biology and Geology, Babeș-Bolyai University, 400015 Cluj-Napoca, Romania;
| | - Cristina Roquet
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, ES-08193 Bellaterra, Spain
| | - Bogdan-Iuliu Hurdu
- Institute of Biological Research, National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015 Cluj-Napoca, Romania;
| | - Wilfried Thuiller
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
| | | | | | - Eric Coissac
- LECA, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000 Grenoble, France; (S.L.); (M.B.); (C.P.); (C.R.); (W.T.)
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van der Heyde M, Bunce M, Wardell-Johnson G, Fernandes K, White NE, Nevill P. Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding. Mol Ecol Resour 2020; 20. [PMID: 32065512 DOI: 10.1111/1755-0998.13148] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/30/2019] [Accepted: 02/10/2020] [Indexed: 11/26/2022]
Abstract
Biological surveys based on visual identification of the biota are challenging, expensive and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims to test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap. Samples (n = 200) were collected in the Pilbara (hot desert climate) and Swan Coastal Plain (hot Mediterranean climate) regions of Western Australia. Soil samples yielded little plant or animal DNA, especially in the Pilbara, probably due to conditions not conducive to long-term preservation. In contrast, scat samples contained the highest overall diversity with 131 plant, vertebrate and invertebrate families detected. Invertebrate and plant sequences were detected in the plant (86 families), pitfall (127 families) and vane trap (126 families) samples. In total, 278 families were recovered from the survey, 217 in the Swan Coastal Plain and 156 in the Pilbara. Aside from soil, 22%-43% of the families detected were unique to the particular substrate, and community composition varied significantly between substrates. These results demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys. If the aim is to broadly capture all biota then multiple substrates will be required.
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Affiliation(s)
- Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.,Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
| | - Grant Wardell-Johnson
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Kristen Fernandes
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.,Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
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Janik P, Ronikier M, Ronikier A. New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes. PeerJ 2020; 8:e8406. [PMID: 32002333 PMCID: PMC6984339 DOI: 10.7717/peerj.8406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/16/2019] [Indexed: 11/23/2022] Open
Abstract
Herbarium collections provide an essential basis for a wide array of biological research and, with development of DNA-based methods, they have become an invaluable material for genetic analyses. Yet, the use of such material is hindered by technical limitations related to DNA degradation and to quantity of biological material. The latter is inherent for some biological groups, as best exemplified by myxomycetes which form minute sporophores. It is estimated that ca. two-thirds of myxomycete taxa are represented by extremely scanty material. As DNA isolation methods applied so far in myxomycete studies require destructive sampling of many sporophores, a large part of described diversity of the group remains unavailable for phylogenetic studies or barcoding. Here, we tested several procedures of DNA isolation and amplification to seek for an efficient and possibly non-destructive method of sampling. Tests were based on herbarium specimens of 19 species representing different taxonomic orders. We assayed several variants of isolation based on silica gel membrane columns, and a newly designed procedure using highly reduced amount of biological material (small portion of spores), based on fine disruption of spores and direct PCR. While the most frequently used column-based method led to PCR success in 89.5% of samples when a large amount of material was used, its performance dropped to 52% when based on single sporophores. Single sporophores provided amplicons in 89.5% of samples when using a kit dedicated to low-amount DNA samples. Our new procedure appeared the most effective (94.7%) while it used only a small fraction of spores, being nearly non-destructive; it was also the most cost-effective. We thus demonstrate that combination of adequate handling of spore micro-disruption coupled with application of direct PCR can be an efficient way to circumvent technical limitations for genetic studies in myxomycetes and thus can substantially improve taxon sampling for phylogeny and barcoding. Additionally, this approach gives a unique possibility to apply both molecular and morphological assays to the same structure (sporophore), which then can be further stored as documentation.
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Affiliation(s)
- Paulina Janik
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Michał Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Anna Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
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Nevill PG, Zhong X, Tonti-Filippini J, Byrne M, Hislop M, Thiele K, van Leeuwen S, Boykin LM, Small I. Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics. PLANT METHODS 2020; 16:1. [PMID: 31911810 PMCID: PMC6942304 DOI: 10.1186/s13007-019-0534-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/27/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Herbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant identification and phylogenomics, we sequenced 672 samples covering 21 families, 142 genera and 530 named and proposed named species. We explored the impact of parameters such as sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error. We also tested the efficacy of DNA sequence information for identifying plant samples using 45 specimens recently collected in the Pilbara. RESULTS Genome skimming was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples. We were able to extract sequences for the core DNA barcode regions rbcL and matK from 96 to 93.3% of samples, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content (Goodenia, Scaevola, Cyperus, Bulbostylis, Fimbristylis) suggesting biological rather than technical explanations. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the order cpDNA >> rDNA > matK >> rbcL. CONCLUSIONS We showed that a large-scale approach to genome sequencing using herbarium specimens produces high-quality complete cpDNA and rDNA sequences as a source of data for DNA barcoding and phylogenomics.
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Affiliation(s)
- Paul G. Nevill
- Australian Research Council Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6102 Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009 Australia
- Kings Park and Botanic Garden, Fraser Ave, Kings Park, WA 6005 Australia
| | - Xiao Zhong
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009 Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
| | - Julian Tonti-Filippini
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009 Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
| | - Margaret Byrne
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009 Australia
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983 Australia
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6102 Australia
| | - Michael Hislop
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983 Australia
| | - Kevin Thiele
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009 Australia
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983 Australia
| | - Stephen van Leeuwen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983 Australia
| | - Laura M. Boykin
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009 Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009 Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
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Bell KL, Batchelor KL, Bradford M, McKeown A, Macdonald SL, Westcott D. Optimisation of a pollen DNA metabarcoding method for diet analysis of flying-foxes (Pteropus spp.). AUST J ZOOL 2020. [DOI: 10.1071/zo20085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Determining the diet of flying-foxes can increase understanding of how they function as pollinators and seed dispersers, as well as managing any negative impacts of large roosts. Traditional methods for diet analysis are time consuming, and not feasible to conduct for hundreds of animals. In this study, we optimised a method for diet analysis, based on DNA metabarcoding of environmental DNA (eDNA) from pollen and other plant parts in the faeces. We found that existing eDNA metabarcoding protocols are suitable, with the most useful results being obtained using a commercial food DNA extraction kit, and sequencing 350–450 base pairs of a DNA barcode from the internally transcribed spacer region (ITS2), with ~550 base pairs of the chloroplast rubisco large subunit (rbcL) as a secondary DNA barcode. A list of forage plants was generated for the little red flying-fox (Pteropus scapulatus), the black flying-fox (Pteropus alecto) and the spectacled flying-fox (Pteropus conspicillatus) from our collection sites across Queensland. The diets were determined to comprise predominantly Myrtaceae species, particularly those in the genera Eucalyptus, Melaleuca and Corymbia. With more plant genomes becoming publicly available in the future, there are likely to be further applications of eDNA methods in understanding the role of flying-foxes as pollinators and seed dispersers.
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