| 1. |
- Andersson, Agneta, et al.
(författare)
-
DNA-streckkodning av marina växtplankton : Ett nytt verktyg i miljöövervakningen
- 2024
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Växtplankton utgör grunden i den marina näringsväven och används världen över för att bestämma miljöstatus i hav och sjöar. De ingår exempelvis som en kvalitetsfaktor i EU:s vattendirektiv och havsmiljödirektiv. Det finns långa tidsserier av växtplanktonövervakning där analyserna utförts med mikroskopi. Det sker nu en snabb internationell utveckling av DNA-metoder för att övervaka växtplankton. Målsättningen med detta projekt var att utveckla en praktisk och robust DNA analysmetod som kan implementeras i svensk marin miljöövervakning. Vårt tillvägagångssätt var att följa med på ordinarie marina miljöövervakningsexpeditioner under ett års tid (2019–2020) och ta parallella havsvattenprov för så kallad DNA-streckkodning av växtplankton. Sammanlagt tog vi prov vid 19 övervakningsstationer som var spridda från Bottenviken i norr till Skagerrak i söder. Provtagningsfrekvensen var cirka 1 gång per månad. Praktiska metoder utarbetades för fältprovtagning, DNA-extraktion, sekvensering, bioinformatisk analys och taxonomisk annotering. Vi har även tagit fram system för datahantering hos nationell datavärd och gett förslag på en ny datatyp för nationellt datavärdskap för marinbiologi och oceanografi vid Svenskt Oceanografiskt Datacentrum (https://sharkweb. smhi.se/hamta-data/). En viktig del har varit att jämföra resultaten av DNA-streckkodning och mikroskopi. Resultaten visar att DNA-streckkodning ger ungefär dubbelt så högt biodiversitetsmått än mikroskopering, även om det skiljer sig åt mellan olika grupper av växtplankton. För att undersöka om DNA-streckkodning kan användas för kvantitativ analys tillsatte vi en intern standard till proverna bestående av syntetiskt DNA, men eftersom resultatet varierade så behöver man arbeta vidare med detta. Den relativa fördelningen av vanliga eukaryota växtplanktongrupper visade sig ha relativt bra överensstämmelse mellan DNA-streckkodning och mikroskopimåttet kolbiomassa, medan biovolym och abundans skiljde sig åt mer. DNA-streckkodning visade sig ge detaljerade utbredningsmönster av skadliga alger, till exempel för släktet Prymnesium bland häftalgerna (Coccolithophyceae). Vi har inom projektet kunnat utvärdera ekologiska drivkrafter för växtplanktonsamhällets diversitet och artsammansättning, genom att miljöövervakningen mäter många fysikalisk-kemiska parametrar. Både salthalt och närsalter visade sig ha stor inverkan på växtplanktonsamhällets sammansättning och diversitet. Sammanfattningsvis ser vi att den framtagna DNA-streckkodningsmetoden skulle vara ett bra komplement till den etablerade växtplanktonövervakningen.
|
|
| 2. |
- Grujčić, Vesna, 1988-, et al.
(författare)
-
Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton
- 2024
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 19:1 January
-
Tidskriftsartikel (refereegranskat)abstract
- Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter”, although further optimizations are necessary to increase the signal-to-noise ratio.
|
|
| 3. |
- Lankinen, Åsa, et al.
(författare)
-
Challenges and opportunities for increasing the use of low-risk plant protection products in sustainable production. A review
- 2024
-
Ingår i: Agronomy for Sustainable Development. - : Springer. - 1774-0746 .- 1773-0155. ; 44:2
-
Forskningsöversikt (refereegranskat)abstract
- Plant production systems worldwide are struggling to meet the diverse and increasing needs of humankind while also facing challenges such as climate change and biodiversity loss. This, combined with the desirable transition from the use of conventional pesticides to more sustainable plant protection solutions, has led to an urgent, and increasing, need for low-risk plant protection products (PPPs) to be developed, applied, and integrated into management practices across all types of plant production systems. Despite a high demand from end users and consumers together with joint political goals at the EU level to replace conventional pesticides, the number of low-risk PPPs on the European market remains low, in comparison to synthetic agrochemicals. In this review, we summarize knowledge about the policy, technical, and administrative issues hampering the process of bringing new low-risk PPPs to the European market. We present an overview of the challenges in using the low-risk PPPs that are currently available within the EU agricultural, horticultural, and forestry sectors. We describe the variation in modes of action and the limitations associated with different application techniques and give concrete examples of problems and solutions from Swedish plant production sectors, in contrast to global perspectives as demonstrated by examples from African agriculture. Finally, we conclude that trans-sectoral, multi-actor approaches are required and provide suggestions on how to address the remaining knowledge gaps related to efficiency, application, and economics of low-risk PPP use in Integrated Pest Management (IPM) solutions for plant protection to improve future food security in Europe.
|
|
| 4. |
- Latz, Meike, et al.
(författare)
-
A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea
- 2024
-
Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- The Baltic Sea is one of the largest brackish water environments on earth and is characterised by pronounced physicochemical gradients and seasonal dynamics. Although the Baltic Sea has a long history of microscopy-based plankton monitoring, DNA-based metabarcoding has so far mainly been limited to individual transect cruises or time-series of single stations. Here we report a dataset covering spatiotemporal variation in prokaryotic and eukaryotic microbial communities and physicochemical parameters. Within 13-months between January 2019 and February 2020, 341 water samples were collected at 22 stations during monthly cruises along the salinity gradient. Both salinity and seasonality are strongly reflected in the data. Since the dataset was generated with both metabarcoding and microscopy-based methods, it provides unique opportunities for both technical and ecological analyses, and is a valuable biodiversity reference for future studies, in the prospect of climate change.
|
|
| 5. |
- Latz, Meike, et al.
(författare)
-
Short- and long-read metabarcoding of the eukaryotic rRNA operon : Evaluation of primers and comparison to shotgun metagenomics sequencing
- 2022
-
Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 22:6, s. 2304-2318
-
Tidskriftsartikel (refereegranskat)abstract
- High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics data sets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.
|
|
| 6. |
- Rojas, Edward C., et al.
(författare)
-
The Fungal Endophyte Penicillium olsonii ML37 Reduces Fusarium Head Blight by Local Induced Resistance in Wheat Spikes
- 2022
-
Ingår i: Journal of Fungi. - : MDPI AG. - 2309-608X. ; 8:4
-
Tidskriftsartikel (refereegranskat)abstract
- The fungal endophyte Penicillium olsonii ML37 is a biocontrol agent of Fusarium head blight in wheat (caused by Fusarium graminearum), which has shown a limited direct inhibition of fungal growth in vitro. We used RNA-seq and LC-MS/MS analyses to elucidate metabolic interactions of the three-way system Penicillium-wheat-Fusarium in greenhouse experiments. We demonstrated that P. olsonii ML37 colonises wheat spikes and transiently activates plant defence mechanisms, as pretreated spikes show a faster and stronger expression of the defence metabolism during the first 24 h after pathogen inoculation. This effect was transient and the expression of the same genes was lower in the pathogen-infected spikes than in those infected by P. olsonii alone. This response to the endophyte includes the transcriptional activation of several WRKY transcription factors. This early activation is associated with a reduction in FHB symptoms and significantly lower levels of the F. graminearum metabolites 15-acetyl-DON and culmorin. An increase in the Penicillium-associated metabolite asperphanamate confirms colonisation by the endophyte. Our results suggest that the mode of action used by P. olsonii ML37 is via a local defence activation in wheat spikes, and that this fungus has potential as a novel biological alternative in wheat disease control.
|
|
