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FlexTaxD: flexible modification of taxonomy databases for improved sequence classification
CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden.ORCID iD: 0000-0002-6269-0217
CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden.
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden;Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.ORCID iD: 0000-0002-4476-9255
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. CBRN Security and Defence, FOI, Swedish Defence Research Agency, Umeå, Sweden;Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.
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2021 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 37, no 21, p. 3932-3933Article in journal (Refereed) Published
Abstract [en]

The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads.

Place, publisher, year, edition, pages
Oxford University Press, 2021. Vol. 37, no 21, p. 3932-3933
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-189091DOI: 10.1093/bioinformatics/btab621ISI: 000733832700036Scopus ID: 2-s2.0-85126297774OAI: oai:DiVA.org:umu-189091DiVA, id: diva2:1608608
Available from: 2021-11-04 Created: 2021-11-04 Last updated: 2023-09-05Bibliographically approved
In thesis
1. Using airborne eDNA to study ecosystem dynamics
Open this publication in new window or tab >>Using airborne eDNA to study ecosystem dynamics
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this era of global biodiversity crisis, the need to monitor ecological communities over space and time is more pressing than ever to effectively direct biodiversity conservation and management efforts. To understand the natural dynamics of an ecosystem, and the impact of anthropogenic activities related to environmental and climate change, long time series are needed to accurately link such processes to ecosystem change. This thesis uses a unique resource of archived air filters collected in Sweden originally intended for radioactive particle measurements to reconstruct historical eDNA abundance in the most extensive time-series of airborne eDNA abundance to date - spanning across four decades. By using metabarcoding and metagenomic analysis, it is evident that airborne eDNA from a very large diversity of species is present in air, representing all major branches of the tree of life, including bacteria, fungi, plants, metazoans, and viruses, from a wide range of terrestrial and aquatic sources. These have seasonal as well as long term trends that in part can be explained by temporal variation in climate and regional differences. The data generated in this thesis comprise an extensive resource for analysis of trends related to climate and environmental change and will also allow deeper studies on phenology, phenological change, functional genomics, and potentially antibiotic resistance. The results presented here show the potential of using airborne eDNA to monitor species in the local ecosystem over time and the methods provides an efficient tool for assessment of broad scale biodiversity, in a non-invasive and cost-effective way.

Place, publisher, year, edition, pages
Umeå: Umeå Universitet, 2021. p. 34
National Category
Biochemistry and Molecular Biology Ecology Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-189117 (URN)978-91-7855-698-4 (ISBN)978-91-7855-697-7 (ISBN)
Public defence
2021-12-03, Betula, Norrlands Universitetssjukhus, Umeå, 10:00 (English)
Opponent
Supervisors
Available from: 2021-11-12 Created: 2021-11-04 Last updated: 2021-11-09Bibliographically approved

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Svensson, DanielKarlsson, EdvinStenberg, Per

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