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Metabarcoding vs Microscopy - comparison of methods to monitor phytoplankton communities
Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. (EcoChange; UMFpub)ORCID iD: 0000-0001-7819-9038
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).ORCID iD: 0000-0002-1298-3839
Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Marine Sciences Centre (UMF).
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2023 (English)In: ACS - ES & T Water, E-ISSN 2690-0637, Vol. 3, no 8, p. 2671-2680Article in journal (Other academic) Published
Abstract [en]

Phytoplankton are used worldwide to monitor environmental status in aquatic systems. Long-time series of microscopy-analyzed phytoplankton are available from many monitoring stations. The microscopy-method is however time consuming and has short-comings. DNA metabarcoding has been suggested as an alternative method, but the consistency between different methods need further investigation. We performed a comparative study of microscopy and metabarcoding analyzing micro- and nanophytoplankton. For metabarcoding, 25-1000 ml seawater were filtered, DNA extracted and the 18S and 16S rRNA gene amplicons sequenced. For microscopy, based on the Utermöhl method we evaluated the use of three metrics: abundance, biovolume and carbon biomass. At the genus, species, and unidentified taxa level, metabarcoding generally showed higher taxonomic diversity than microscopy, and diversity was already captured at the lowest filtration volume tested, 25 ml. Metabarcoding and microscopy displayed relatively similar distribution pattern at the group level. The results showed that the relative abundances of the 18S rRNA amplicon at the group level best fitted the microscopy carbon biomass metric. The results are promising for implementing DNA metabarcoding as a complement to microscopy in phytoplankton monitoring, especially if databases would be improved and group level indexes could be applied to classify the environmental state of water bodies.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023. Vol. 3, no 8, p. 2671-2680
Keywords [en]
Sampling volume, diversity, carbon biomass, gene abundance, group/class-level consistency
National Category
Oceanography, Hydrology and Water Resources
Identifiers
URN: urn:nbn:se:umu:diva-207745DOI: 10.1021/acsestwater.3c00176ISI: 001033834200001Scopus ID: 2-s2.0-85166755712OAI: oai:DiVA.org:umu-207745DiVA, id: diva2:1753979
Note

Originally included in thesis in manuscript form. 

Available from: 2023-05-02 Created: 2023-05-02 Last updated: 2023-12-11Bibliographically approved
In thesis
1. Microbial communities: descriptors of environmental change in marine ecosystems
Open this publication in new window or tab >>Microbial communities: descriptors of environmental change in marine ecosystems
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Mikrobiella samhällen : indikatorer på miljöförändringar i marina ekosystem
Abstract [en]

In northern marginal seas, like the northern Baltic Sea, climate change will lead to many alterations, for example increased inflows of nutrients and dissolved organic matter (DOM). Nutrients and DOM are fundamental drivers shaping marine microbial communities, including both bacterial and phytoplankton populations. Potentially microbial communities and their functions can be used as descriptors of environmental change in marine systems. 

Changed nutrient availability will affect the phytoplankton communities, which is widely used as descriptor of environmental state in aquatic systems. Traditionally phytoplankton is analyzed using microscopy in monitoring, while molecular methods holds a great potential for future development. I performed a comparative study between metabarcoding and microscopy. Metabarcoding and microscopy displayed relatively similar distribution pattern at the group level. The results showed that the relative abundances of the 18S rRNA amplicon at the group level best fitted the microscopy carbon biomass metric. The results are promising for implementing DNA metabarcoding as a complement to microscopy in phytoplankton monitoring, especially if databases would be improved and group level indexes could be applied to classify environmental state of water bodies.

Bacterioplankton are the main DOM processors in the marine food web. A shift in the quality and quantity of the DOM pool could affect the microbial community structure and alter their functioning. Presently it is poorly known how coastal bacteria respond compositionally and functionally to quality and quantity changes in DOM supply. To comprehensively address this question, there is a critical need for microcosm experimental studies as well as field studies. Thus, I used approaches from single species laboratory experiment to community levels in situ incubation experiments and community levels spatiotemporal field surveys to evaluate the impacts of climate shifts on microbial community. Intricate relationships between environmental factors and microbial communities, for example, links between key microbial functional genes and DOM conditions were identified. Results showed that bacteria isolated from coastal area harbor genes for the sequestration of autochthonously produced carbon substrates, while bacteria isolated from a river contained genes for the degradation of relatively refractive terrestrial organic matter. A field experiment showed that Gammaproteobacteria was promoted by plankton extract addition and the genes for chitin and cellulose catabolism are enriched by addition of autochthonous carbon sources. The field survey with comprehensive metagenomic investigation of microbial community composition indicated that the temporal variation is larger compare to spatial changes. Bacteroidia, Actinomycetia, Gammaproteobacteria, Acidimicrobiia, and Alphaproteobacteria were the dominant bacterial classes, with Bacteroidia being more abundant in inshore stations compared to offshore locations. The seasonal shift in the relative abundance of these bacterial classes suggests that environmental factors and ecological processes drive changes in the abundance of different bacterial classes over time. Overall, these studies strengthen our understanding of the relationships between microbial composition and biogeochemical processes in coastal areas.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2023. p. 23
National Category
Oceanography, Hydrology and Water Resources
Identifiers
urn:nbn:se:umu:diva-207755 (URN)978-91-8070-087-0 (ISBN)978-91-8070-088-7 (ISBN)
Public defence
2023-05-26, KB.E3.01, KBC-huset, Umeå, 09:00 (English)
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Supervisors
Available from: 2023-05-05 Created: 2023-05-02 Last updated: 2023-08-14Bibliographically approved

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Andersson, AgnetaZhao, LiBrugel, SoniaFigueroa, DanielaHuseby, Siv

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