Experimental Quantification of Pollen with DNA Metabarcoding Using
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DNA Metabarcoding of Microbial Communities for Healthcare I
Reviews ISSN 1993-6842 (on-line); ISSN 0233-7657 (print) Biopolymers and Cell. 2016. Vol. 32. N 1. P 3–8 doi: http://dx.doi.org/10.7124/bc.000906 UDC 577.25 + 579.61 DNA metabarcoding of microbial communities for healthcare I. Ye. Zaets1, O. V. Podolich1, O. N. Reva2, N. O. Kozyrovska1 1 Institute of Molecular Biology and Genetics, NAS of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680 2 Department of Biochemistry, Bioinformatics and Computational Biology Unit, University of Pretoria Lynnwood road, Hillcrest, Pretoria, South Africa, 0002 [email protected], [email protected], [email protected] High-throughput sequencing allows obtaining DNA barcodes of multiple species of microorganisms from a single environmental sample. Next Generation Sequencing (NGS)-based profiling provides new opportunities to evaluate the human health effect of microbial community members affiliated to probiotics. DNA metabar- coding may serve as a quality control of microbial communities, comprising complex probiotics and other fermented foods. A detailed inventory of complex communities is a pre-requisite of understanding their func- tionality as whole entities that makes it possible to design more effective bio-products by precise replacement of one community member by others. The present paper illustrates how the NGS-based DNA metabarcoding allows profiling of both wild and hybrid multi-microbial communities with the example of a kombucha probi- otic beverage fermented by yeast-bacterial partners. Keywords: DNA metabarcoding, microbial communities, healthcare, -
Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens
microorganisms Review Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens Edoardo Piombo 1,2 , Ahmed Abdelfattah 3,4 , Samir Droby 5, Michael Wisniewski 6,7, Davide Spadaro 1,8,* and Leonardo Schena 9 1 Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, 10095 Grugliasco, Italy; [email protected] 2 Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala, Sweden 3 Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria; [email protected] 4 Department of Ecology, Environment and Plant Sciences, University of Stockholm, Svante Arrhenius väg 20A, 11418 Stockholm, Sweden 5 Department of Postharvest Science, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7505101, Israel; [email protected] 6 U.S. Department of Agriculture—Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430, USA; [email protected] 7 Department of Biological Sciences, Virginia Technical University, Blacksburg, VA 24061, USA 8 AGROINNOVA—Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, 10095 Grugliasco, Italy 9 Department of Agriculture, Università Mediterranea, 89122 Reggio Calabria, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-0116708942 Abstract: Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegeta- bles, with a corresponding increase in economic losses caused by the introduction of transboundary Citation: Piombo, E.; Abdelfattah, A.; plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance Droby, S.; Wisniewski, M.; Spadaro, protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding D.; Schena, L. -
Studies on Authentication of True Source of Honey Using Pollen DNA
Journal of Entomology and Zoology Studies 2018; 6(3): 255-261 E-ISSN: 2320-7078 P-ISSN: 2349-6800 Studies on authentication of true source of honey JEZS 2018; 6(3): 255-261 © 2018 JEZS using pollen DNA barcoding Received: 09-03-2018 Accepted: 10-04-2018 Praghadeesh Manivanan Praghadeesh Manivanan, Srinivasan Madapuji Rajagopalan and Department of Plant Mohankumar Subbarayalu Biotechnology, Centre for Plant Molecular Biology& Biotechnology, Tamil Nadu Abstract Agricultural University, Plant pollen DNA comprising unique barcode signatures– serve as a highly resilient biomarker to Coimbatore, Tamil Nadu, India establish its true biological origin. Over a decade, DNA barcoding of plants has evolved as an effective tool to identify its origin down to species level that promptedits practical applications in various fields of Srinivasan Madapuji Rajagopalan applied biology. Premium unifloral honey, due to its economic value as a medicinal product is vulnerable Department of Agricultural to intentional mislabelling and adulteration to fetch higher price. Melissopalynological and Entomology, Tamil Nadu physiochemical based approaches to ascertain the true source of honey is not yet available on commercial Agricultural University, scale. DNA barcoding of pollen trapped in honey can be effectively used to identify the true source of Coimbatore, Tamil Nadu, India honey with high feasibility across labs at cheaper price. The current study was carried out to standardise Mohankumar Subbarayalu an efficient pollen DNA isolation protocol and to assess the efficiency of two barcode (rbcL and matK Professor and Head, Department gene) combinations in identifying the botanical origin of pollen and to ascertain its true source. Six honey of Plant Biotechnology, Centre samples with diverse characteristics were used in the study. -
Using RNA-Seq to Characterize Pollen–Stigma Interactions for Pollination
www.nature.com/scientificreports OPEN Using RNA‑seq to characterize pollen–stigma interactions for pollination studies Juan Lobaton1,3*, Rose Andrew1, Jorge Duitama2, Lindsey Kirkland1, Sarina Macfadyen3 & Romina Rader1 Insects are essential for the reproduction of pollinator‑dependent crops and contribute to the pollination of 87% of wild plants and 75% of the world’s food crops. Understanding pollen fow dynamics between plants and pollinators is thus essential to manage and conserve wild plants and ensure yields are maximized in food crops. However, the determination of pollen transfer in the feld is complex and laborious. We developed a feld experiment in a pollinator‑dependent crop and used high throughput RNA sequencing (RNA‑seq) to quantify pollen fow by measuring changes in gene expression between pollination treatments across diferent apple (Malus domestica Borkh.) cultivars. We tested three potential molecular indicators of successful pollination and validated these results with feld data by observing single and multiple visits by honey bees (Apis mellifera) to apple fowers and measured fruit set in a commercial apple orchard. The frst indicator of successful outcrossing was revealed via diferential gene expression in the cross‑pollination treatments after 6 h. The second indicator of successful outcrossing was revealed by the expression of specifc genes related to pollen tube formation and defense response at three diferent time intervals in the stigma and the style following cross‑pollination (i.e. after 6, 24, and 48 h). Finally, genotyping variants specifc to donor pollen could be detected in cross‑pollination treatments, providing a third indicator of successful outcrossing. Field data indicated that one or fve fower visits by honey bees were insufcient and at least 10 honey bee fower visits were required to achieve a 25% probability of fruit set under orchard conditions. -
Cristescu TREE 2014.Pdf
TREE-1853; No. of Pages 6 Opinion From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity Melania E. Cristescu Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada DNA-based species identification, known as barcoding, introduced by Arnot et al. [6] and was firmly advanced transformed the traditional approach to the study of and standardized by Hebert et al. [7]. The simple idea of biodiversity science. The field is transitioning from bar- using a short DNA fragment as a barcode (see Glossary) for coding individuals to metabarcoding communities. This identifying species across the Metazoa has been both revolution involves new sequencing technologies, bio- strongly embraced and vigorously scrutinized over the past informatics pipelines, computational infrastructure, and decade [8,9]. Nevertheless, the efforts led by Paul Hebert, experimental designs. In this dynamic genomics land- and supported by the Consortium for the Barcode of Life scape, metabarcoding studies remain insular and biodi- (CBoL; http://www.barcodeoflife.org/) resulted in a global versity estimates depend on the particular methods enterprise that combined molecular tools with valuable but used. In this opinion article, I discuss the need for a scarce taxonomic expertise [10,11]. Today, DNA barcodes coordinated advancement of DNA-based species identi- are being used commonly to identify specimens and the fication that integrates taxonomic and barcoding infor- approach has wide applications in biodiversity conserva- mation. Such an approach would facilitate access to tion, environmental management, invasion biology, the almost 3 centuries of taxonomic knowledge and 1 de- study of trophic interactions, and food safety [12–14]. -
Edna in a Bottleneck: Obstacles to Fish Metabarcoding Studies in Megadiverse Freshwater 3 Systems 4 5 Authors: 6 Jake M
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.05.425493; this version posted January 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Title: 2 eDNA in a bottleneck: obstacles to fish metabarcoding studies in megadiverse freshwater 3 systems 4 5 Authors: 6 Jake M. Jackman1, Chiara Benvenuto1, Ilaria Coscia1, Cintia Oliveira Carvalho2, Jonathan S. 7 Ready2, Jean P. Boubli1, William E. Magnusson3, Allan D. McDevitt1* and Naiara Guimarães 8 Sales1,4* 9 10 Addresses: 11 1Environment and Ecosystem Research Centre, School of Science, Engineering and Environment, 12 University of Salford, Salford, M5 4WT, UK 13 2Centro de Estudos Avançados de Biodiversidade, Instituto de Ciências Biológicas, Universidade 14 Federal do Pará, Belém, Brazil 15 3Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, 16 Amazonas, Brazil 17 4CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, 18 Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal 19 20 *Corresponding authors: 21 Naiara Guimarães Sales, [email protected] 22 Allan McDevitt, [email protected] 23 24 Running title: Obstacles to eDNA surveys in megadiverse systems 25 26 Keywords: Amazon, barcoding gap, freshwater, MiFish, Neotropics, reference database, 27 taxonomic resolution 28 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.05.425493; this version posted January 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Metabarcoding in the Abyss: Uncovering Deep-Sea Biodiversity Through Environmental
Metabarcoding in the abyss : uncovering deep-sea biodiversity through environmental DNA Miriam Isabelle Brandt To cite this version: Miriam Isabelle Brandt. Metabarcoding in the abyss : uncovering deep-sea biodiversity through environmental DNA. Agricultural sciences. Université Montpellier, 2020. English. NNT : 2020MONTG033. tel-03197842 HAL Id: tel-03197842 https://tel.archives-ouvertes.fr/tel-03197842 Submitted on 14 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En Sciences de l'Évolution et de la Biodiversité École doctorale GAIA Unité mixte de recherche MARBEC Pourquoi Pas les Abysses ? L’ADN environnemental pour l’étude de la biodiversité des grands fonds marins Metabarcoding in the abyss: uncovering deep - sea biodiversity through environmental DNA Présentée par Miriam Isabelle BRANDT Le 10 juillet 2020 Sous la direction de Sophie ARNAUD-HAOND et Daniela ZEPPILLI Devant le jury composé de Sofie DERYCKE, Senior researcher/Professeur rang A, ILVO, Belgique Rapporteur -
Fungal Genomes Tell a Story of Ecological Adaptations
Folia Biologica et Oecologica 10: 9–17 (2014) Acta Universitatis Lodziensis Fungal genomes tell a story of ecological adaptations ANNA MUSZEWSKA Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland E-mail: [email protected] ABSTRACT One genome enables a fungus to have various lifestyles and strategies depending on environmental conditions and in the presence of specific counterparts. The nature of their interactions with other living and abiotic elements is a consequence of their osmotrophism. The ability to degrade complex compounds and especially plant biomass makes them a key component of the global carbon circulation cycle. Since the first fungal genomic sequence was published in 1996 mycology has benefited from the technolgical progress. The available data create an unprecedented opportunity to perform massive comparative studies with complex study design variants targeted at all cellular processes. KEY WORDS: fungal genomics, osmotroph, pathogenic fungi, mycorrhiza, symbiotic fungi, HGT Fungal ecology is a consequence of osmotrophy Fungi play a pivotal role both in encountered as leaf endosymbionts industry and human health (Fisher et al. (Spatafora et al. 2007). Since fungi are 2012). They are involved in biomass involved in complex relationships with degradation, plant and animal infections, other organisms, their ecological fermentation and chemical industry etc. repertoire is reflected in their genomes. They can be present in the form of The nature of their interactions with other resting spores, motile spores, amebae (in organisms and environment is defined by Cryptomycota, Blastocladiomycota, their osmotrophic lifestyle. Nutrient Chytrydiomycota), hyphae or fruiting acquisition and communication with bodies. The same fungal species symbionts and hosts are mediated by depending on environmental conditions secreted molecules. -
1 Molecular Analysis of Honey Bee Foraging Ecology Dissertation
Molecular analysis of honey bee foraging ecology Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Rodney Trey Richardson Graduate Program in Entomology The Ohio State University 2018 Dissertation Committee Professor Reed Johnson, Advisor Professor Mary Gardiner Professor John Christman Professor Roman Lanno 1 Copyrighted by Rodney Trey Richardson 2018 2 Abstract While numerous factors currently impact the health of honey bees and other pollinating Hymenoptera, poor floral resource availability due to habitat loss and land conversion is thought to be important. This issue is particularly salient in the upper Midwest, a location which harbors approximately 60 percent of the US honey bee colonies each summer for honey production. This region has experienced a dramatic expansion in the area devoted to crop production over the past decade. Consequently, understanding how changes to landscape composition affect the diversity, quality and quantity of available floral resources has become an important research goal. Here, I developed molecular methods for the identification of bee-collected pollen by adapting and improving upon the existing amplicon sequencing infrastructure used for microbial community ecology. In thoroughly benchmarking our procedures, I show that a simple and cost-effective three-step PCR-based library preparation protocol in combination with Metaxa2-based hierarchical classification yields an accurate and highly quantitative pollen metabarcoding approach when applied across multiple plant markers. In Chapter 1, I conducted one of the first ever proof-of-concept studies applying amplicon sequencing, or metabarcoding, to the identification of bee-collected pollen. -
Characterization of Bacterial Communities Associated
www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5. -
Introduction to Bioinformatics Analysis of Metabarcoding Data
Introduction to Bioinformatics analysis of Metabarcoding data Theoretical part Alvaro Sebastián Yagüe www.sixthresearcher.com @SixthResearcher • Experimental design • Sampling • Sample processing • Sequencing • Sequence processing www.sixthresearcher.com @SixthResearcher • Experimental design • Sampling • Sample processing • Sequencing • Sequence processing www.sixthresearcher.com @SixthResearcher What do we want to sequence? Whole genome sequencing (WGS) ChIP-seq Amplicon sequencing (AS) Whole exome sequencing (WES) RNA-seq Mass spectrometry www.sixthresearcher.com @SixthResearcher How do we want to sequence? Green,E.D. (2001) Strategies for the systematic sequencing of complex www.sixthresearcher.com genomes. Nat. Rev. Genet., 2, 573–583. @SixthResearcher Metagenomics - Shotgun sequencing www.sixthresearcher.com @SixthResearcher Metagenomics - High-throughput sequencing DNA extraction DNA fragmentation and sequencing Read mapping to reference genome De novo assembly Chimeras! www.sixthresearcher.com @SixthResearcher Metabarcoding - Amplicon sequencing 1. PCR amplification and sample tagging Barcode 1 Barcode 2 Barcode 3 2. Sequencing of PCR products 3. De-multiplexing of reads Samples 1 2 3 4 5 6 Barcode 1 Barcode 2 Barcode 3 www.sixthresearcher.com @SixthResearcher Metabarcoding vs Metagenomics Kress, W. J., & Erickson, D. L. (2008). DNA barcodes: genes, genomics, and bioinformatics. Proceedings of the National Academy of Sciences of the United States of America, 105(8), 2761–2. www.sixthresearcher.com @SixthResearcher Metabarcoding vs Metagenomics http://luckylion.de/2015/10/11/dna-metabarcoding-vs-metagenomics/ www.sixthresearcher.com @SixthResearcher • Experimental design • Sampling • Sample processing • Sequencing • Sequence processing www.sixthresearcher.com @SixthResearcher ➢ Where? Variability in abundance within soil and plant. Consider vertical and horizontal distribution of fungi. ➢ When? Temporal dynamics over short and long term. For complete community census, sample across multiple seasons. -
Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.01.322941; this version posted October 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae Emily Jacobs-Palmer1, Ramón Gallego1,2, Kelly Cribari1, Abigail Keller1, Ryan P. Kelly1 1University of Washington School of Marine and Environmental Affairs 2NRC Research Associateship Program, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration. Abstract Harmful algae can have profound economic, environmental, and social consequences. As the timing, frequency, and severity of harmful algal blooms (HABs) change alongside global climate, efficient tools to monitor and understand the current ecological context of these taxa are increasingly important. Here we employ environmental DNA metabarcoding to identify patterns in a wide variety of harmful algae and associated ecological communities in the Hood Canal of Puget Sound in Washington State, USA. We track trends of presence and abundance in a series of water samples across nearly two years. We find putative harmful algal sequences in a majority of samples, suggesting that these groups are routinely present in local waters. We report patterns in variants of the economically important genus Pseudo-nitzschia (family Bacillariaceae), as well as multiple harmful algal taxa previously unknown or poorly documented in the region, including a cold-water variant from the saxitoxin-producing genus Alexandrium (family Gonyaulacaceae), two variants from the karlotoxin-producing genus Karlodinium (family Kareniaceae), and one variant from the parasitic genus Hematodinium (family Syndiniaceae).