| 1. |
- Andersson, Agneta, et al.
(författare)
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DNA-streckkodning av marina växtplankton : Ett nytt verktyg i miljöövervakningen
- 2024
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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.
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| 2. |
- Latz, Meike, et al.
(författare)
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A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea
- 2024
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 11:1
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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.
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| 3. |
- Latz, Meike, et al.
(författare)
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Short- and long-read metabarcoding of the eukaryotic rRNA operon : Evaluation of primers and comparison to shotgun metagenomics sequencing
- 2022
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 22:6, s. 2304-2318
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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.
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| 4. |
- Ademuyiwa, Adesoji O., et al.
(författare)
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Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
- 2016
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Ingår i: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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| 5. |
- Andersson, Agneta, et al.
(författare)
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Influence of allochthonous dissolved organic matter on pelagic basal production in a northerly estuary
- 2018
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Ingår i: Estuarine, Coastal and Shelf Science. - : Elsevier. - 0272-7714 .- 1096-0015. ; 204, s. 225-235
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Tidskriftsartikel (refereegranskat)abstract
- Phytoplankton and heterotrophic bacteria are key groups at the base of aquatic food webs. In estuaries receiving riverine water with a high content of coloured allochthonous dissolved organic matter (ADOM), phytoplankton primary production may be reduced, while bacterial production is favoured. We tested this hypothesis by performing a field study in a northerly estuary receiving nutrient-poor, ADOM-rich riverine water, and analyzing results using multivariate statistics. Throughout the productive season, and especially during the spring river flush, the production and growth rate of heterotrophic bacteria were stimulated by the riverine inflow of dissolved organic carbon (DOC). In contrast, primary production and photosynthetic efficiency (i.e. phytoplankton growth rate) were negatively affected by DOC. Primary production related positively to phosphorus, which is the limiting nutrient in the area. In the upper estuary where DOC concentrations were the highest, the heterotrophic bacterial production constituted almost 100% of the basal production (sum of primary and bacterial production) during spring, while during summer the primary and bacterial production were approximately equal. Our study shows that riverine DOC had a strong negative influence on coastal phytoplankton production, likely due to light attenuation. On the other hand DOC showed a positive influence on bacterial production since it represents a supplementary food source. Thus, in boreal regions where climate change will cause increased river inflow to coastal waters, the balance between phytoplankton and bacterial production is likely to be changed, favouring bacteria. The pelagic food web structure and overall productivity will in turn be altered. (C) 2018 The Authors. Published by Elsevier Ltd.
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| 6. |
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| 7. |
- Andersson, Agneta, et al.
(författare)
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Metabarcoding vs Microscopy - comparison of methods to monitor phytoplankton communities
- 2023
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Ingår i: ACS - ES & T Water. - : American Chemical Society (ACS). - 2690-0637. ; 3:8, s. 2671-2680
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 8. |
- Andersson, Agneta, et al.
(författare)
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Microbial food web changes induced by terrestrial organic matter and elevated temperature in the coastal northern Baltic Sea
- 2023
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Ingår i: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Climate change has been projected to cause increased temperature and amplified inflows of terrestrial organic matter to coastal areas in northern Europe. Consequently, changes at the base of the food web favoring heterotrophic bacteria over phytoplankton are expected, affecting the food web structure. We tested this hypothesis using an outdoor shallow mesocosm system in the northern Baltic Sea in early summer, where the effects of increased temperature (+ 3°C) and terrestrial matter inputs were studied following the system dynamics and conducting grazing experiments. Juvenile perch constituted the highest trophic level in the system, which exerted strong predation on the zooplankton community. Perch subsequently released the microbial food web from heavy grazing by mesozooplankton. Addition of terrestrial matter had a stronger effect on the microbial food web than the temperature increase, because terrestrial organic matter and accompanying nutrients promoted both heterotrophic bacterial production and phytoplankton primary production. Moreover, due to the shallow water column in the experiment, terrestrial matter addition did not reduce the light below the photosynthesis saturation level, and in these conditions, the net-autotrophy was strengthened by terrestrial matter enrichment. In combination with elevated temperature, the terrestrial matter addition effects were intensified, further shifting the size distribution of the microbial food web base from picoplankton to microphytoplankton. These changes up the food web led to increase in the biomass and proportion of large-sized ciliates (>60 µm) and rotifers. Despite the shifts in the microbial food web size structure, grazing experiments suggested that the pathway from picoplankton to nano- and microzooplankton constituted the major energy flow in all treatments. The study implies that the microbial food web compartments in shallow coastal waters will adjust to climate induced increased inputs of terrestrial matter and elevated temperature, and that the major energy path will flow from picoplankton to large-sized ciliates during the summer period.
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| 9. |
- Ask, Jenny, et al.
(författare)
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Importance of coastal primary production in the northern Baltic Sea
- 2016
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Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 45:6, s. 635-648
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we measured depth-dependent benthic microalgal primary production in a Bothnian Bay estuary to estimate the benthic contribution to total primary production. In addition, we compiled data on benthic microalgal primary production in the entire Baltic Sea. In the estuary, the benthic habitat contributed 17 % to the total annual primary production, and when upscaling our data to the entire Bothnian Bay, the corresponding value was 31 %. This estimated benthic share (31 %) is three times higher compared to past estimates of 10 %. The main reason for this discrepancy is the lack of data regarding benthic primary production in the northern Baltic Sea, but also that past studies overestimated the importance of pelagic primary production by not correcting for system-specific bathymetric variation. Our study thus highlights the importance of benthic communities for the northern Baltic Sea ecosystem in general and for future management strategies and ecosystem studies in particular.
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| 10. |
- Bandara, Tharindu, et al.
(författare)
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Retention of essential fatty acids in fish differs by species, habitat use and nutritional quality of prey
- 2023
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 13:6
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Tidskriftsartikel (refereegranskat)abstract
- Algae-produced long-chain polyunsaturated fatty acids (LC-PUFA; with ≥20 carbon atoms) are key biomolecules for consumer production and animal health. They are transferred to higher trophic levels and accumulated in food chains. However, LC-PUFA accumulation in consumers and their trophic transfer vary with the diet quality and the physiological demand for LC-PUFA of consumers. The goal of this study was to investigate spatial and taxonomic differences in LC-PUFA retention of coastal fish predators that potentially differ in their habitat use (benthic versus pelagic) and prey quality. We analyzed the fatty acid (FA) composition of common fish species, namely roach and European perch, as well as their potential prey from benthic and pelagic habitats in three bays of the northern Baltic Sea. We then assessed whether the fish LC-PUFA retention differed between species and among the study bays with different diet quality, that is, LC-PUFA availability. Our data indicated taxon-specific differences in the retention of LC-PUFA and their precursor FA in fish (i.e., short-chain PUFA with <20 carbon atoms). Perch did not show any spatial variation in the retention of all these FA, while roach showed spatial differences in the retention of docosahexaenoic acid (DHA) and their precursor FA, but not eicosapentaenoic acid (EPA). Data suggest that diet quality and trophic reliance on benthic prey underlay the DHA retention differences in roach. Although the PUFA supply might differ among sites, the low spatial variation in LC-PUFA content of perch and roach indicates that both fishes were able to selectively retain dietary LC-PUFA. Climate change together with other existing human-caused environmental stressors are expected to alter the algal assemblages and lower their LC-PUFA supply for aquatic food webs. Our findings imply that these stressors will pose heterogeneous impacts on different fish predators. We advocate further investigations on how environmental changes would affect the nutritional quality of the basal trophic level, and their subsequent impacts on LC-PUFA retention, trophic ecology, and performance of individual fish species.
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