| 1. |
- Sundelöf, Andreas, et al.
(författare)
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Fisk- och skaldjursbestånd i hav och sötvatten 2021 : Resursöversikt
- 2022
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- I rapporten kan du ta del av bedömningen som görs av situationen för bestånd som regleras inom ramen för EU:s gemensamma fiskeripolitik (GFP). Bedömningarna baseras på det forskningssamarbete och den rådgivning som sker inom det Internationella Havsforskningsrådet (ICES). Sammantaget redovisas tillståndet för 107 bestånd av 48 fisk- och skaldjursarter.De bestånd som förvaltas nationellt baseras på de biologiska underlagen, och rådgivningen i huvudsak på den forskning och övervakning samt analys som bedrivs av Institutionen för akvatiska resurser vid Sveriges lantbruksuniversitet (SLU Aqua) samt yrkesfiskets rapportering.Rapporten är en beställning från Havs- och vattenmyndigheten (HaV) till Sveriges lantbruksuniversitet (SLU) och utgör ett viktigt kunskapsunderlag till myndighetens arbete. Den uppfyller de krav som finns inom EU:s gemensamma fiskeripolitik om att basera förvaltningen på bästa tillgängliga vetenskap. Denna rapport är också ett stöd till det arbete som beskrivs närmare i strategin för framtidens fiske och tillhörande handlingsplaner för vattenbruk, yrkes- och fritidsfiske som HaV och Jordbruksverket har tagit fram i dialog med fiskets och vattenbrukets intressenter.
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| 2. |
- Adill, Anders, et al.
(författare)
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Biologisk recipientkontroll vid Forsmarks kärnkraftverk : årsrapport för 2022
- 2023
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Forsmarks kärnkraftverk är Sveriges största elproducent. På grund av intag och utsläpp av kylvatten från havet som kyler processen i verket sker en påverkan på den omgivande kustvattenmiljön. Denna påverkan övervakas och analyseras i det pågående biologiska recipientkontrollprogrammet. Föreliggande årsrapport presenterar resultat i undersökningarna inom kontrollprogrammet för 2022 med fokus på samhällena av fisk, bentisk fauna (bottenlevande djur) och sjöfågel. Under 2022 producerade Forsmarks kärnkraftverk 25,5 terawattimmar (TWh) el i sina anläggningar, vilket var samma som föregående års produktionsrekord av elektricitet. Den rekordstora produktionen kan härledas till de senaste åren moderniseringar och livstidsförlängande åtgärder i anläggningarna, vilket resultaterat i effekthöjningar i kraftverket. Den höga produktionen under 2022 medförde därmed en hög omsättning på kylvatten. Utsläppsområdet för kylvatten, Biotestsjön, hade vattentemperaturer över 25ºC i 29 dagar under sommarperioden. På grund av revisionsarbeten på F2 under juli månad förekom inga extrema temperaturer över 29ºC i Biotestsjön, något som vanligtvis brukar förekomma under högsommaren. I utsläppsområdet för F3 noterades vattentemperaturer över 30°C under endast ett dygn och med högsta notering 30,1°C i mitten av augusti. Förlusterna av fisk i silstationerna vid kylvattenintaget utgjordes som tidigare år av främst småväxta fiskarter och årsyngel. Totalt fastnade cirka 37,5 miljoner individer i silstationerna under provtagningsperioderna under 2022, närmare 20 miljoner färre jämfört med 57 miljoner individer som fastnade 2021. Det lägre antalet beror på att det fastnade färre årsyngel under hösten, som kan vara ett tecken på att det har varit sämre fiskreproduktion i närområdet under 2022, vilket också återspeglades i yngelundersökningarna i Forsmarksskärgård. Likt föregående år var storspigg den dominerande arten i provtagningarna och omfattade cirka 85 % av förlusterna under året. Resultatet för storspigg speglar sannolikt artens stora förekomst i omgivande kust- och havsområden. Antalet ålar som fastnade i silstationen var relativt litet. Till skillnad från tidigare år var förlusterna av ål högre under våren än på hösten, med fler småväxta individer. Genom framtagen metodik kunde totalt fem ålar tas hand om och återutsättas till havet levande. Under de senaste åren har varmvattenarterna mört, björkna och sutare blivit allt vanligare i silstationerna, sannolikt en effekt av de gynnsamma förhållandena i Biotestsjön för lek hos dessa arter. Undersökningarna i Biotestsjön under våren visade att tätheterna av fisk var de absolut största som någonsin observerats. De arter som förekommer i störst omfattning var likt föregående år mört, björkna, abborre och sarv. Likt tidigare fanns tydliga tecken på att stora mängder fisk lockas till Biotestsjöns varma vatten för lek. Förutom stora mängder lekmogen mört och abborre förekom höga tätheter av björkna under våren. Under senare år förefaller även tätheterna av gädda och sutare ha ökat i området. För ålen däremot är utvecklingen den motsatta och förekomsten av arten är låg i jämförelse med tidigare år. Till skillnad från nätprovfiskena i Forsmarks skärgård påträffas inga så kallade kallvattenarter i Biotestsjön, såsom strömming, nors, sik och tånglake. För varmvattenarter som mört och abborre visade resultaten att förhållandena i Biotestsjön var goda under 2022, då både tillväxt och kondition låg på goda nivåer. Under hösten 2022 noterades flera äldre individer av abborre vid provfiskena i Biotestsjön; 7 % av undersökta abborrar var fyra år eller äldre. Tidigare år har nästintill samtliga abborrar varit tre år eller yngre. I Forsmarks skärgård visade undersökningarna att tätheterna av fisk var höga om än något lägre jämfört med rekordfångsterna 2021. Fångsterna för de flesta arterna var något lägre än föregående år, men de mindre totala fångsterna var till stor del ett resultat av de förhållandevis låga antalet fångade mörtar i Forsmark. Förekomsten av mört i undersökningsområdet har under nästintill hela provfiskeperioden uppvisat en negativ utveckling, men har med de stora fångsterna under de senaste tre åren visat på en möjlig återhämtning. Det Sammanfattning låga antalet mörtar i årets provfisken i kombination med den förhållandevis låga förekomsten i silstationen skulle kunna tyda på en generell minskning av mört i Forsmarks skärgård. Ett fåtal individer registrerades av sutare och vimma, två karpfiskar (Cyprinidae) som vanligtvis inte förekommer i provfisket, men som de senaste åren blivit alltmer vanliga i fisket. Under 2022 års undersökningar av mjukbottenfauna registrerades totalt tio arter i Forsmark och femton arter i referensområdet Finbofjärden. Likt tidigare år var arttätheten högre i referensområdet än i Forsmark på både djupa och medeldjupa bottnar. Förekomsten av nyckelarten vitmärla var lägre än föregående år på samtliga stationer både i Finbofjärden och Forsmarks skärgård. Alla hårdbottenstationer frånsett Borgarna hade ett högre artantal än föregående år, men på alla stationer utom Plymen var individtätheten lägre. I Biotestsjön hade individtätheten mer än halverats jämfört med senaste året. Förändringen beror främst på den ovanligt låga förekomsten av tångmärla. Den låga förekomsten kan troligtvis kopplas till de stora mängderna röd pungräka som tillkommit på lokalen. Den röda pungräkan hittades för första gången under 2021 då en enda individ registrerades, medan under 2022 hittades nästan 280 individer per artificiellt substrat. Antalet sjöfåglar i inventeringsområdet var fortsatt hög under 2022. De höga förekomsterna kan förklaras med att antalet mellanskarv i undersökningsområdet dubblerades jämfört med 2021. Den största mängden mellanskarv observerades i Biotestsjön och likt tidigare år noterades misslyckade häckningsförsök. Biotestsjön är det enskilt viktigaste området för sjöfågel i Forsmarks skärgård följt av Asphällafjärden utanför intagskanalen. Utsläppet av varmt kylvatten från kärnkraftverket in i Biotestsjön ger bra förutsättningar till hög produktion av vegetation, bottenlevande djur och fisk samt en isfri yta under vintern. Detta ger gynnsamma förhållanden för sjöfågel under hela året men särskilt under häckningstiden och vinter. Antalet viggar i Forsmarks skärgård var lägre under 2022 jämfört med föregående år, trots detta var viggen tillsammans med mellanskarven de mest vanliga förekommande arterna. Förekomsterna av knölsvan var fortsatt hög i Forsmarks skärgård, trots att antalet var något lägre än föregående år. Det finns skillnader för vilka funktionella grupper som nyttjar de olika områdena i inventeringsområdet. Fisk- och växtätande fåglar föredrar Biotestsjön året om medan bottendjursätande fåglar visar skillnader säsongsvis med en täthetstopp i Biotestsjön under hösten och i Asphällafjärden under vintern.
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| 3. |
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| 4. |
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| 5. |
- Bagatini, Inessa Lacativa, et al.
(författare)
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Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton
- 2014
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:1, s. e85950-
-
Tidskriftsartikel (refereegranskat)abstract
- Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways.
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| 6. |
- Bertilsson, Stefan, et al.
(författare)
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Links between bacterial production, amino acid utilization and community composition in productive lakes
- 2007
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 1:6, s. 532-544
-
Tidskriftsartikel (refereegranskat)abstract
- Influence of distribution and abundance of bacterial taxa on ecosystem function are poorly understood for natural microbial communities. We related 16S rRNA-based terminal restriction fragment length polymorphism to bacterial production and arginine uptake kinetics to test if functional features of bacterioplankton in four lakes could be predicted from community composition. Maximum arginine uptake rate (arginine Vmax) ranged from 10% to 100% of bacterial production. Owing to high growth efficiencies on arginine (63–77%), the bacterial community could potentially saturate its carbon demand using this single organic substrate, for example, during sudden surges of free amino acids. However, due to low in situ concentrations of arginine in these lakes (<0.9 g l-1), actual uptake rates at ambient concentrations rarely exceeded 10% of Vmax. Bacterial production and arginine Vmax could be predicted from a subset of bacterial ribotypes, tentatively affiliated with several bacterial divisions (Cyanobacteria, Actinobacteria, Bacteroidetes and Proteobacteria). Multivariate statistical analysis indicates that there were both highly important and less important ribotypes for the prediction of bacterial production and arginine Vmax. These populations were either negatively or positively related to the respective functional feature, indicating contrasting ecological roles. Our study provides a statistically robust demonstration that, apart from environmental conditions, patterns in bacterial community composition can also be used to predict lake ecosystem function.
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| 7. |
- Bryhn, Andreas, et al.
(författare)
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Fisk- och skaldjursbestånd i hav och sötvatten 2020 : Resursöversikt
- 2021
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- I rapporten kan du ta del av bedömningen som görs av situationen för bestånd som regleras inom ramen för EU:s gemensamma fiskeripolitik (GFP). Bedömningarna baseras på det forskningssamarbete och den rådgivning som sker inom det Internationella Havsforskningsrådet (ICES). Totalt redovisas underlag och råd för 48 fisk- och skaldjursarter.De bestånd som förvaltas nationellt baseras på de biologiska underlagen, och rådgivningen i huvudsak på den forskning och övervakning samt analys som bedrivs av Institutionen för akvatiska resurser vid Sveriges lantbruksuniversitet (SLU Aqua) samt yrkesfiskets rapportering.
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| 8. |
- Denfeld, Blaize A., et al.
(författare)
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Constraints on methane oxidation in ice-covered boreal lakes
- 2016
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Ingår i: Journal of Geophysical Research - Biogeosciences. - : AMER GEOPHYSICAL UNION. - 2169-8953 .- 2169-8961. ; 121:7, s. 1924-1933
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Tidskriftsartikel (refereegranskat)abstract
- Boreal lakes can be ice covered for a substantial portion of the year at which time methane (CH4) can accumulate below ice. The amount of CH4 emitted at ice melt is partially determined by the interplay between CH4 production and CH4 oxidation, performed by methane-oxidizing bacteria (MOB). Yet the balance between oxidation and emission and the potential for CH4 oxidation in various lakes during winter is largely unknown. To address this, we performed incubations at 2 degrees C to screen for wintertime CH4 oxidation potential in seven lakes. Results showed that CH4 oxidation was restricted to three lakes, where the phosphate concentrations were highest. Molecular analyses revealed that MOB were initially detected in all lakes, although an increase in type I MOB only occurred in the three lake water incubations where oxidation could be observed. Accordingly, the increase in CO2 was on average 5 times higher in these three lake water incubations. For one lake where no oxidation was measured, we tested if temperature and CH4 availability could trigger CH4 oxidation. However, regardless of incubation temperatures and CH4 concentrations, ranging from 2 to 20 degrees C and 1-500M, respectively, no oxidation was observed. Our study indicates that some lakes with active wintertime CH4 oxidation may have low emissions during ice melt, while other and particularly nutrient poor lakes may accumulate large amounts of CH4 below ice that, in the absence of CH4 oxidation, will be emitted following ice melt. This variability in CH4 oxidation rates between lakes needs to be accounted for in large-scale CH4 emission estimates.
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| 9. |
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| 10. |
- Eiler, Alexander, et al.
(författare)
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Coherent dynamics and association networks among lake bacterioplankton taxa
- 2012
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Ingår i: The ISME Journal: multidisciplinary journal of microbial ecology. - : Springer Science and Business Media LLC. - 1751-7362. ; 6:2, s. 330-342
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Tidskriftsartikel (refereegranskat)abstract
- Bacteria have important roles in freshwater food webs and in the cycling of elements in the ecosystem. Yet specific ecological features of individual phylogenetic groups and interactions among these are largely unknown. We used 454 pyrosequencing of 16S rRNA genes to study associations of different bacterioplankton groups to environmental characteristics and their co-occurrence patterns over an annual cycle in a dimictic lake. Clear seasonal succession of the bacterioplankton community was observed. After binning of sequences into previously described and highly resolved phylogenetic groups (tribes), their temporal dynamics revealed extensive synchrony and associations with seasonal events such as ice coverage, ice-off, mixing and phytoplankton blooms. Coupling between closely and distantly related tribes was resolved by time-dependent rank correlations, suggesting ecological coherence that was often dependent on taxonomic relatedness. Association networks with the abundant freshwater Actinobacteria and Proteobacteria in focus revealed complex interdependencies within bacterioplankton communities and contrasting linkages to environmental conditions. Accordingly, unique ecological features can be inferred for each tribe and reveal the natural history of abundant cultured and uncultured freshwater bacteria.
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| 11. |
- Eiler, Alexander, et al.
(författare)
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Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes
- 2004
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 6, s. 1228-1243
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Tidskriftsartikel (refereegranskat)abstract
- The diversity of freshwater bacterioplankton communities has not been extensively studied despite their key role in foodwebs and the cycling of carbon and associated major elements. In order to explore and characterize the composition of bacterioplankton associated with cyanobacterial blooms, large 16S rRNA clone libraries from four lakes experiencing such blooms were analysed. The four libraries contained 1461 clones, of which 559 were prokaryotic sequences of non-cyanobacterial origin. These clones were classified into 158 operational taxonomic units affiliated mainly with bacterial divisions commonly found in freshwater systems, e.g. Proteobacteria, Bacteriodetes, Actinobacteria, Verrucomicrobia and Planctomycetes. Richness and evenness of non-cyanobacterial clones were similar to other clone libraries obtained for freshwater bacterioplankton, suggesting that bacterial communities accompanying cyanobacterial blooms are as diverse as non-bloom communities. Many of the identified operational taxonomic units grouped with known freshwater clusters but the libraries also contained novel clusters of bacterial sequences that may be characteristic for cyanobacterial blooms. About 25% of the operational taxonomic units were detected in more than one lake. Even so, 16S rRNA heterogeneity analysis demonstrated large differences in community composition between lakes regardless of their similar characteristics and close proximity. Hence even the similar environmental conditions created by different cyanobacterial blooms may foster very dissimilar bacterial communities, which could indicate that the genetic diversity in lake bacteria have been underestimated in the past.
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| 12. |
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| 13. |
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| 14. |
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| 15. |
- Eiler, Alexander, et al.
(författare)
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Environmental influences on Vibrio populations in northern temperate and boreal coastal waters (Baltic and Skagerrak Seas)
- 2006
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 72:9, s. 6004-6011
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Tidskriftsartikel (refereegranskat)abstract
- Even if many Vibrio spp. are endemic to coastal waters, their distribution in northern temperate and boreal waters is poorly studied. To identify environmental factors regulating Vibrio populations in a salinity gradient along the Swedish coastline, we combined Vibrio-specific quantitative competitive PCR with denaturant gradient gel electrophoresis-based genotyping. The total Vibrio abundance ranged from 4 X 10(3) to 9.6 X 10(4) cells liter(-1), with the highest abundances in the more saline waters of the Skagerrak Sea. Several Vibrio populations were present throughout the salinity gradient, with abundances of single populations ranging from 5 X 10(4) to 7 X 10(4) cells liter(-1). Clear differences were observed along the salinity gradient, where three populations dominated the more saline waters of the Skagerrak Sea and two populations containing mainly representatives of V anguillarum and V. aestuarianus genotypes were abundant in the brackish waters of the Baltic Sea. Our results suggest that this apparent niche separation within the genus Vibrio may also be influenced by alternate factors such as nutrient levels and high abundances of dinoflagellates. A V. choleraelV. mimicus population was detected in more than 50% of the samples, with abundances exceeding 10(3) cells liter(-1), even in the cold (annual average water temperature of around 5 degrees C) and low-salinity (2 to 4 parts per thousand) samples from the Bothnian Bay (latitude, 65 degrees N). The unsuspected and widespread occurrence of this population in temperate and boreal coastal waters suggests that potential Vibrio pathogens may also be endemic to cold and brackish waters and hence may represent a previously overlooked health hazard.
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| 16. |
- Eiler, Alexander, et al.
(författare)
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Flavobacteria blooms in four eutrophic lakes : Linking population dynamics of freshwater bacterioplankton to resource availability
- 2007
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 73:11, s. 3511-3518
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Tidskriftsartikel (refereegranskat)abstract
- Heterotrophic bacteria are major contributors to biogeochemical cycles and influence water quality. Still, the lack of representative isolates and the few quantitative surveys leave the ecological role and significance of single bacterial populations to be revealed. Here we analyzed the diversity and dynamics of freshwater Flavobacteria populations in four eutrophic temperate lakes. From each lake, clone libraries were constructed using primers specific for either the class Flavobacteria or Bacteria. Sequencing of 194 Flavobacteria clones from 8 libraries revealed a diverse freshwater Flavobacteria community and distinct differences among lakes. Abundance and seasonal dynamics of Flavobacteria were assessed by quantitative PCR with class-specific primers. In parallel, the dynamics of individual populations within the Flavobacteria community were assessed with terminal restriction fragment length polymorphism analysis using identical primers. The contribution of Flavobacteria to the total bacterioplankton community ranged from 0.4 to almost 100% (average, 24%). Blooms where Flavobacteria represented more than 30% of the bacterioplankton were observed at different times in the four lakes. In general, high proportions of Flavobacteria appeared during episodes of high bacterial production. Phylogenetic analyses combined with Flavobacteria community fingerprints suggested dominance of two Flavobacteria lineages. Both drastic alterations in total Flavobacteria and in community composition of this class significantly correlated with bacterial production, emphasizing that resource availability is an important driver of heterotrophic bacterial succession in eutrophic lakes.
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| 17. |
- Eiler, Alexander, et al.
(författare)
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Growth response of Vibrio cholerae and other Vibrio spp. to cyanobacterial dissolved organic matter and temperature in Brackish Water
- 2007
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 60:3, s. 411-418
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Tidskriftsartikel (refereegranskat)abstract
- Environmental control of growth and persistence of vibrios in aquatic environments is poorly understood even though members of the genus Vibrio are globally important pathogens. To study how algal-derived organic matter and temperature influenced the abundance of different Vibrio spp., Baltic Sea microcosms inoculated with Vibrio cholerae, Vibrio vulnificus, Vibrio parahaemolyticus, Vibrio alginolyticus and native bacterioplankton, were exposed to different temperatures (12–25°C) and amended with dissolved organic matter from Nodularia spumigena (0–4.2 mg C L−1). Vibrio abundance was monitored by culture-dependent and molecular methods. Results suggested that Vibrio populations entered a viable but nonculturable state during the incubations. Abundance of Vibrio spp. and total bacterioplankton were orders of magnitude higher in microcosms amended with organic matter compared with reference microcosms. Vibrio cholerae abundances ranged from 0.9 to 1.9 × 105 cells mL−1 in treatments amended with 4.2 mg C L−1. Vibrio cholerae abundance relative to total bacterioplankton and other Vibrio spp. also increased >10-fold. In addition, V. vulnificus abundance increased in mesocosms with the highest organic matter addition (0.9–1.8 × 104 cells mL−1). Temperature alone did not significantly affect abundances of total bacterioplankton, total Vibrio spp. or individual Vibrio populations. By contrast, cyanobacterial-derived organic matter represented an important factor regulating growth and abundance of V. cholerae and V. vulnificus in brackish waters.
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| 18. |
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| 19. |
- Eiler, Alexander, et al.
(författare)
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High Ratio of Bacteriochlorophyll Biosynthesis Genes to Chlorophyll Biosynthesis Genes in Bacteria of Humic Lakes
- 2009
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 75:22, s. 7221-7228
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies highlight the diversity and significance of marinephototrophic microorganisms such as picocyanobacteria, phototrophicpicoeukaryotes, and bacteriochlorophyll- and rhodopsin-holdingphototrophic bacteria. To assess if freshwater ecosystems alsoharbor similar phototroph diversity, genes involved in the biosynthesisof bacteriochlorophyll and chlorophyll were targeted to exploreoxygenic and aerobic anoxygenic phototroph composition in awide range of lakes. Partial dark-operative protochlorophyllideoxidoreductase (DPOR) and chlorophyllide oxidoreductase (COR)genes in bacteria of seven lakes with contrasting trophic statuseswere PCR amplified, cloned, and sequenced. Out of 61 sequencesencoding the L subunit of DPOR (L-DPOR), 22 clustered with aerobicanoxygenic photosynthetic bacteria, whereas 39 L-DPOR sequencesrelated to oxygenic phototrophs, like cyanobacteria, were observed.Phylogenetic analysis revealed clear separation of these freshwaterL-DPOR genes as well as 11 COR gene sequences from their marinecounterparts. Terminal restriction fragment length analysisof L-DPOR genes was used to characterize oxygenic aerobic andanoxygenic photosynthesizing populations in 20 lakes differingin physical and chemical characteristics. Significant differencesin L-DPOR community composition were observed between dystrophiclakes and all other systems, where a higher proportion of genesaffiliated with aerobic anoxygenic photosynthetic bacteria wasobserved than in other systems. Our results reveal a significantdiversity of phototrophic microorganisms in lakes and suggestniche partitioning of oxygenic and aerobic anoxygenic phototrophsin these systems in response to trophic status and coupled differencesin light regime.
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| 20. |
- Eiler, Alexander, et al.
(författare)
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Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
- 2014
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 16:9, s. 2682-2698
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Tidskriftsartikel (refereegranskat)abstract
- Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared to freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.
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| 21. |
- Eiler, Alexander, 1976-
(författare)
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The Niches of Bacterial Populations in Productive Waters : Examples from Coastal Waters and Four Eutrophic Lakes
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Recent research in microbial ecology has focused on how aquatic bacterial communities are assembled. Only a few of these studies follow a “Gleasonian” approach where the roles of single bacterial populations are in focus. In this thesis, novel molecular tools were used to describe the distribution and evolutionary relationships of microbes in productive aquatic environments. Many new phylogenetic groups of bacteria were identified, likely representing bacterial populations restricted to productive freshwaters. I also addressed the dynamics and functional role of individual bacterial populations in eutrophic lakes and brackish environments with a focus on either biogeochemically significant or potentially pathogenic representatives. Flavobacteria blooms were observed, on occasions characterized by high heterotrophic production. In addition to high temporal dynamics microbial community composition and function differed on the spatial scale, as exemplified by free-living and Cyanobacteria-associated habitats. At the community scale, microbial processes, such as biomass production and substrate uptake could be predicted from the presence and absence of individual bacterial populations. I also studied the niches of potentially pathogenic Vibrio populations in various coastal waters. Using a novel culture-independent method, a V. cholerae population was detected along the entire Swedish coastline. Results from an environmental survey and a laboratory mesocosm experiment reveal that phytoplankton-derived dissolved organic matter enhance the growth of V. cholerae and other Vibrio spp. and hence create a largely overlooked niche for these heterotrophic bacteria. This thesis and future work on the role of individual bacterial populations will facilitate predictions of biogeochemical cycles and the distribution of bacteria in the context of global climate change and local eutrophication.
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| 22. |
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| 23. |
- Eiler, Alexander, et al.
(författare)
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Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach
- 2013
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:1, s. e53516-
-
Tidskriftsartikel (refereegranskat)abstract
- The recognition and discrimination of phytoplankton species is one of the foundations of freshwater biodiversity research and environmental monitoring. This step is frequently a bottleneck in the analytical chain from sampling to data analysis and subsequent environmental status evaluation. Here we present phytoplankton diversity data from 49 lakes including three seasonal surveys assessed by next generation sequencing (NGS) of 16S ribosomal RNA chloroplast and cyanobacterial gene amplicons and also compare part of these datasets with identification based on morphology. Direct comparison of NGS to microscopic data from three time-series showed that NGS was able to capture the seasonality in phytoplankton succession as observed by microscopy. Still, the PCR-based approach was only semi-quantitative, and detailed NGS and microscopy taxa lists had only low taxonomic correspondence. This is probably due to, both, methodological constraints and current discrepancies in taxonomic frameworks. Discrepancies included Euglenophyta and Heterokonta that were scarce in the NGS but frequently detected by microscopy and Cyanobacteria that were in general more abundant and classified with high resolution by NGS. A deep-branching taxonomically unclassified cluster was frequently detected by NGS but could not be linked to any group identified by microscopy. NGS derived phytoplankton composition differed significantly among lakes with different trophic status, showing that our approach can resolve phytoplankton communities at a level relevant for ecosystem management. The high reproducibility and potential for standardization and parallelization makes our NGS approach an excellent candidate for simultaneous monitoring of prokaryotic and eukaryotic phytoplankton in inland waters.
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| 24. |
- Falk, Alexandra, et al.
(författare)
-
Faktablad – Resultat från övervakningen av kustfisk : Barsebäck (Öresund) 1999–2019 och 2021– 2022
- 2023
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- • Provfisket i Barsebäck har utförts med ryssjor i augusti varje år sedan 1977, förutom 2020. Från och med 2021 utförs fisket med reviderat provfiskemetod. Fisket var ursprungligen en del av kontrollprogrammet för kärnkraftverket. I detta faktablad presenteras resultat från år 1999 och framåt, eftersom effekten från de numera stängda reaktorerna varit obetydlig från det året. • Omgivningsfaktorerna temperatur, salthalt och siktdjup vid fiske har fluktuerat under åren 1999–2022 utan att några trender kan urskiljas. • Resultaten visar att det kustnära fisksamhället i Barsebäck har förändrats sedan 1999 där antalet mesopredatorer (icke-rovfisk) har ökat. • Stor fisk i fångsten har oftast varit ål eller torsk. Ål har bortsett från 2005 och 2010 varit talrikast i fångsten sett till individer över MRB (minsta referensstorlek för bevarande). • Det totala antalet fiskar i fångsten har ökat under perioden 1999–2019. Detta förklaras av att flera arter som skrubbskädda, abborre och tånglake visar en ökande trend. • Den vanligaste arten i fångsten, med avseende på antal, har varit strandkrabba som i snitt svarat för 75 procent av fångsten. Den vanligaste fiskarten till antalet har varit ål (gulål och blankål) tätt följt av tånglake, skrubbskädda och torsk som vardera stått för 3–4 procent av fångsten. • Fyra arter som har förekommit i fångsten återfinns på ArtDatabankens rödlista (version 2020): torsk, lyrtorsk, vitling och ål. • Under provfisket 2021 och 2022, som utfördes enligt den reviderade provfiskemetoden, har ansträngningen minskat och fler djupstrata tillkommit. Shannon-Wieners diversitetsindex låg 2021-2022 på liknande nivå som provfisket enligt den äldre fiskemetoden 1999-2019. • Den invasiva främmande arten svartmunnad smörbult fångades för första gången i Barsebäck 2021 och återfanns i fångsten 2022.
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| 25. |
- Fernandez-Vidal, Leyden, et al.
(författare)
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Diazotroph genomes and their seasonal dynamics in a stratified humic bog lake
- 2020
-
Ingår i: Frontiers in Microbiology. - : FRONTIERS MEDIA SA. - 1664-302X. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- Aquatic N-fixation is generally associated with the growth and mass development ofCyanobacteriain nitrogen-deprived photic zones. However, sequenced genomes and environmental surveys suggest active aquatic N-fixation also by many non-cyanobacterial groups. Here, we revealed the seasonal variation and genomic diversity of potential N-fixers in a humic bog lake using metagenomic data andnifgene clusters analysis. Groups with diazotrophic operons were functionally divergent and includedCholorobi,Geobacter,Desulfobacterales,Methylococcales, andAcidobacteria. In addition tonifH(a gene that encodes the dinitrogenase reductase component of the molybdenum nitrogenase), we also identified sequences corresponding to vanadium and iron-only nitrogenase genes. Within theChlorobipopulation, the nitrogenase (nifH) cluster was included in a well-structured retrotransposon. Furthermore, the presence of light-harvesting photosynthesis genes implies that anoxygenic photosynthesis may fuel nitrogen fixation under the prevailing low-irradiance conditions. The presence ofrnfgenes (related to the expression of H+/Na+-translocating ferredoxin: NAD+ oxidoreductase) inMethylococcalesandDesulfobacteralessuggests that other energy-generating processes may drive the costly N-fixation in the absence of photosynthesis. The highly reducing environment of the anoxic bottom layer of Trout Bog Lake may thus also provide a suitable niche for active N-fixers and primary producers. While future studies on the activity of these potential N-fixers are needed to clarify their role in freshwater nitrogen cycling, the metagenomic data presented here enabled an initial characterization of previously overlooked diazotrophs in freshwater biomes.
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| 26. |
- Grubisic, Lorena M., et al.
(författare)
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Lake bacterioplankton dynamics over diurnal timescales
- 2017
-
Ingår i: Freshwater Biology. - : Blackwell Publishing. - 0046-5070 .- 1365-2427. ; 62:1, s. 191-204
-
Tidskriftsartikel (refereegranskat)abstract
- 1. Planktonic bacterial community dynamics over short timescales can be of great importance for food webs and ecosystem functioning but are rarely described when microbial community and composition are assessed. To study the significance of such dynamics we sampled the surface water at the deepest point of a mesotrophic lake (Lake Erken, Sweden) every third hour over two days. 2. By combining 454 pyrosequencing of 16S rRNA genes with bromodeoxyuridine immunocapturing of DNA, replicating populations were identified and compared to the community retrieved from total DNA samples. This comparison revealed a significant difference between the actively replicating and total community. 3. The high-frequency diurnal sampling was compared to a year-long survey conducted in the same lake in order to compare the diurnal and seasonal variation in bacterioplankton community composition. At the diurnal-scale, the variation was significantly higher in the replicating than in the total community. However, variation in both active and total diurnal community was significantly lower than the variation in the seasonal total community. 4. Our analysis revealed pronounced short-term dynamics of individual bacterial populations uncoupled from the diurnal light cycle. For example, the proliferating fraction of the most abundant bacterial tribe (LD12) followed a cyclic pattern that covaried with viral abundance. This implies that environmental factors other than light may act as important drivers of microbial community composition, at least in mesotrophic Lake Erken.
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| 27. |
- Heinrich, Friederike, 1979-
(författare)
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Drivers of Population Dynamics in Bacterioplankton : Spotlight on Alphaproteobacteria and its dominant SAR11 Lineage
- 2015
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Bacteria are mediators of biogeochemical cycles and are in this way vital for maintaining life on earth. Their distribution, abundance and functioning are driven by environmental heterogeneity and dynamic change in abiotic and biotic factors. Both, freshwater lakes and oceans play central roles in the global carbon cycle and bacteria in these systems perform many services for the ecosystems, such as the transfer of organic carbon from primary producers to higher trophic levels. With estimated relative abundances up to 50% of the total bacterioplankton, the Alphaproteobacteria lineage SAR11 is the most abundant group of aquatic bacteria. It is globally distributed and can be partitioned into multiple sub-clades, one of which is exclusive to freshwaters. Until recently, the distribution, abundance and ecological role of this freshwater SAR11 named LD12 was unknown. The aim of the thesis was to study the drivers and mechanisms that influence the dynamics of aquatic bacterial communities in general and the SAR11 and LD12 groups in particular. The thesis consists of environmental surveys of a mesotrophic Lake Erken and the western Southern Ocean, an experiment and a data-mining exercise to reveal the phylogenetic structure of the SAR11 lineage on various temporal and spatial scales. The analysis of a long-term bacterioplankton community survey in lake Erken provided insights about the dynamics of the entire bacterial community and the LD12 population over an annual cycle. The results demonstrate that LD12 can be an equally abundant member of freshwater communities as marine SAR11 in oceans. LD12 featured strong seasonality and was positively coupled to environmental conditions indicative for an oligotrophic lifestyle. LD12 as well as other dominant lake bacterioplankton also maintained stable populations throughout spatial and temporal varying environments, but at high phylogenetic resolution, habitat preferences were revealed, particularly in response to oxygen concentrations. The later was not the case in LD12 as a single ribotype dominated. This is in stark contrast to the habitat partitioning with light availability, depth and water masses observed for marine SAR11 subclades in the Southern Ocean. The global data-mining corroborated that LD12 as a group was much less diverse than SAR11 furthermore, suggesting that the marine-freshwater barrier acted as a population bottleneck. My work shows that bacterial populations can respond in very different ways to environmental drivers, highlight the importance of highly resolved temporal and spatial scales as well as the need for high phylogenetic resolutions to target ecologically coherent populations.
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| 28. |
- Heinrich, Friederike, et al.
(författare)
-
Seasonality and environmental control of freshwater SAR11 (LD12) in a temperate lake (Lake Erken, Sweden)
- 2013
-
Ingår i: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 70:1, s. 33-44
-
Tidskriftsartikel (refereegranskat)abstract
- THE SAR11 clade is ubiquitous and abundant in planktonic environments. In freshwater lakes, the clade is represented by tribe LD12 which is phylogenetically distinct from the marine SAR11. We studied the ecology of LD12 in a temperate dimictic lake (Lake Erken, Sweden), by analyzing its seasonal dynamics with quantitative PCR, CARD-FISH and 454 pyrosequencing of the 16S rRNA gene. Results showed that LD12 can be as numerous in freshwater bacterioplankton as their marine SAR11 siblings. They exhibited strong seasonality and made up from 1.8 to 40% of the total bacterial 16S rRNA pool (mean 14%) with pronounced peaks in summer and late fall. Except in spring, LD12 was the dominant Alphaproteobacteria, contributing on average 72% of the 16S rRNA within this class. The LD12 population was dominated by a single persistent ribotype, suggesting low local divergence, at least at the phylogenetic resolution accessed with rRNA genes. The relative abundance of LD12 was positively correlated to nutrient concentrations (phosphate, ammonia, nitrate, and silica) and water transparency whereas the relative abundance was lower during periods characterized by high phytoplankton biomass. Based on these observations we propose that LD12 are poor competitors during periods of high phytoplankton productivity and associated release of labile organic compounds, but thrive when availability of inorganic nutrients is high. Similar to the marine SAR11 sibling group, local LD12 populations appear to respond in contrasting ways to nutrient availability in different lakes, pointing to either ecological divergence within the tribe or variations in the interplay between environmental driver variables.
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| 29. |
- Holliland, Per, et al.
(författare)
-
Bulleröfjärden (Egentliga Östersjön) 2021
- 2022
-
Ingår i: Faktablad: resultat från övervakningen av kustfisk.
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Provfisket genomfördes 2021 som del av arbetet i Nationalparksbildningen av Nämdöskärgård.Totalt 19 arter fångades under provfisket och Bullerfjärden har högre diversitet än närliggande provfiskeområden.Artsammansättningen är präglat av att provfiskeområdet ligger i ytterskärgården, med ett stort inslag av marina arter.Mesopredatorerna strömming och löja dominerade fångsterna. Abborre var tredje vanligaste i fångsterna och utgjorde över 99 procent av rovfiskefångsten.Den trofiska medelnivån är lägre än i närliggande provfiskeområden och beror till stor del på den höga förekomsten av mesopredatorer.Abborrarna i området har snabb tillväxt och är stora vid given ålder. De senaste årens varma somrar samt god födotillgång i området har sannolikt bidragit till detta.L90 för abborre (storleken på individen vid den 90:de percentilen i längdfördelningen) ligger på 27 centimeter, vilket är högt jämfört med andra provfiskeområden vid östkusten. Det tyder på att det finns gott om stora abborrar i området.
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| 30. |
- Holliland, Per, et al.
(författare)
-
Lagnö (Egentliga Östersjön) 2002–2020
- 2021
-
Ingår i: Faktablad: resultat från övervakningen av kustfisk.
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Sedan provfiskets start 2002, med undantag för 2015–2017 då mört dominerade, har fångsten i Lagnö dominerats av abborre, följt av mört, strömming, nors och gärs.Under 2018 års provfiske utgjorde abborre 61 procent av fångsten och den stora fångsten bröt en tidigare nedåtgående trend för arten. Även under 2020 års provfiske var fångsten av abborre relativt stor. På grund av ökande fångster av mört och abborre har den totala mängden fisk som fångats också ökat över tid.Mört, strömming, nors, löja, sarv och tånglake har ökat i fångsten medan gädda och gös har minskat. Totala antalet fångade individer för löja, sarv, tånglake, gädda och gös är dock liten så att trenduppskattningar ska tolkas med försiktighet.Fångsten av karpfiskar har ökat över tid. Detta beror främst på att fångsten av mört, den vanligaste karpfisken i provfiskefångsten, har ökat. Även fångsten av karpfiskarna löja och sarv har ökat, medan id och vimma inte har påträffats under de senaste årens provfisken.Antalet fångade arter per år har minskat över tid. Exempel på arter som tidigare fångats men som inte förekommit under senare år är gädda, id, vimma, braxen och gös.Fångsten av stora individer har minskat sedan provfiskets start, generellt för alla arter (> 30 centimeter) och specifikt för abborre (> 25 centimeter). Även indikatorn L90 för abborre (storleken på individen vid den 90:de percentilen i längdfördelningen) har minskat över tid. Möjliga förklaringar kan vara ett ökat fisketryck eller en ökad predation.Den trofiska medelnivån har minskat över tid. Detta beror på att det i början av provfiskeperioden fanns större andel rovfiskar (främst abborre) med högre trofisk nivå och färre karpfiskar (främst mört) med lägre trofisk nivå i fångsten jämfört med i slutet av provfiskeperioden.Abborrens tillväxt har inte förändrats över tid. Det antyder att den minskade förekomsten av stor abborre i fångsten inte kan förklaras av en långsammare tillväxthastighet.Sikens tillväxt har inte förändrats över tid. Sikens tillväxt i Lagnö stannar av vid 4 års ålder, då är sikarna runt 35 cm. Att tillväxten stannar av tyder på att siken blir könsmogen.
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| 31. |
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| 32. |
- Hubalek, Valerie, et al.
(författare)
-
Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield
- 2016
-
Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 10:10, s. 2447-2458
-
Tidskriftsartikel (refereegranskat)abstract
- Little research has been conducted on microbial diversity deep under the Earth/'s surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.
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| 33. |
- Hubalek, Valerie, 1981-
(författare)
-
Exposing the Dark Microbial Biosphere
- 2015
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Dark biosphere research has been widely neglected, although by volume this biome comprises the lion’s share of habitats on our planet. In these systems the main metabolic strategies are of chemotrophic nature, leading to gradual depletion of redox gradients essential for sustaining life. Thus these environments are regarded more or less close to chemical equilibrium.Here, we use sequence data of whole community metagenomes and taxonomic marker approaches to study the ecology of environments close to the thermodynamic limit: deep terrestrial aquifers and aphotic systems impacted by petroleum- derived products. We show that these systems select for individuals with reduced genomes and cell sizes, likely as a mode to save energy. Due to genome reduction, these so called “streamlined” cells are reduced in the number of genes and metabolic pathways. This loss has led to community members sharing the metabolic burden of synthesizing in particular energy costly metabolites, creating tight interdependencies between the community members, as a consequence. In addition, we propose that cells scavenging anabolic products derived from detrital biomass and intermediate fermentation products are equally important in these systems. Hence, life at the thermodynamic limit involves a much more complex biological system than previously shown, that goes beyond traditionally described electron- and intermediate metabolite-transfer dependencies.This thesis furthermore includes ecological implications, demonstrating how species diversity and community metabolism are shaped by redox gradients and dispersal potential in the deep biosphere and contaminated sediments. This research is also relevant from a practical point of view, as it pinpoints new opportunities for enhanced bioremediation through metabolite additions in order to raise the efficiency of degradation processes.
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| 34. |
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| 35. |
- Hubalek, Valerie, 1981-, et al.
(författare)
-
Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions
- 2017
-
Ingår i: mSystems. - 2379-5077. ; 2:5
-
Tidskriftsartikel (refereegranskat)abstract
- Syntrophy among Archaea and Bacteria facilitates the anaerobic degra- dation of organic compounds to CH4 and CO2 . Particularly during aliphatic and aro- matic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutu- alistic microbial partners are of central importance. Using micromanipulation com- bined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methano- genic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermenta- tion of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and inter- mediate fermentation products derived from detrital biomass was a common fea- ture. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2 -producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocar- bon transformation. IMPORTANCE
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| 36. |
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| 37. |
- Johansson, Mona, et al.
(författare)
-
Distribution of the Dinoflagellate parasite Parvilucifera infectans (Parkinsozoa) along the Swedish coast
- 2006
-
Ingår i: Aquatic Microbial Ecology. - 0948-3055 .- 1616-1564. ; 43:3, s. 289-302
-
Tidskriftsartikel (refereegranskat)abstract
- Dinoflagellate parasites, e.g. Parvilucifera infectans Noren et Moestrup, 1996 can potentially control dinoflagellate blooms and thereby modify plankton communities and nutrient fluxes. Parvilucifera infectans has been detected in Swedish waters, but its distribution is largely unknown. Based on 18S rRNA sequences of 2 P. infectans isolates of different geographic origin (Sweden and Tasmania), we designed 2 primer pairs for specific PCR amplification of rRNA fragments from these parasites. We screened for presence of F infectans in a salinity gradient along the Swedish coastline (2 to 30 parts per thousand, 13 stations) from June to August 2004. Parasites were only detected in July and August at 3 stations in the region with highest salinity (Skagerrak). Presence of parasites was correlated with high abundances of dinoflagellate hosts (Prorocentrum spp., Ceratium spp.) but was also restricted to warm and saline waters. In addition, these stations were characterized by low bacterial abundances, low chl a and low nutrient levels. Parasites were not detected in this region in June, when temperatures were lower (< 15 degrees C) and microzooplankton predators were most abundant. Hence, our study reveals both temporal and spatial patchiness of P. infectans in coastal waters.
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| 38. |
- Käll, Filip, et al.
(författare)
-
Lagnö (Egentliga Östersjön) 2002–2021
- 2022
-
Ingår i: Faktablad: resultat från övervakningen av kustfisk.
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- • Sedan provfiskets start 2002, med undantag för 2015–2017 då mört dominerade, har fångsten vid Lagnö dominerats av abborre, följt av mört, strömming, gärs och nors.• Den totala fångsten av fisk har ökat sedan provfiskets start 2002. Detta beror till stor del på den stora andelen av abborre och mört som också har ökat över tid. Under 2021 så utgjorde abborre och mört 39, respektive 37 procent av den totala fångsten. Den största totala fångsten av fisk noterades under 2020. Mört, strömming, löja, sarv och sutare har ökat i fångsten medan gädda har minskat. Totala antalet fångade individer av löja, sarv, och gädda är dock liten så att trenduppskattningar ska tolkas med försiktighet.• Fångsten av karpfiskar har ökat över tid. Detta beror främst på att fångsten av mört, den vanligaste karpfisken i provfiskefångsten, har ökat. Även fångsten av karpfiskarna löja och sarv har ökat.• Antalet fångade fiskarter per år har varierat mellan åren och det går inte att se någon trend som visar på förändrat artantal. Det finns några arter som tidigare fångats, men som inte förekommit under senare åren, som till exempel gädda, id, vimma, braxen och gös. Ruda fångades dock för första gången i provfisket och id fångades för första gången sedan 2003.• Fångsten av stora individer har minskat sedan provfiskets start, generellt för alla arter (> 30 centimeter) och specifikt för abborre (> 25 centimeter). Även indikatorn L90 för abborre (storleken på individen vid den 90:de percentilen i längdfördelningen) har minskat över tid. Möjliga förklaringar kan vara ett ökat fisketryck eller en ökad predation.• Den trofiska medelnivån har minskat över tid. Detta beror på att det i början av provfiskeperioden fanns större andel rovfiskar (främst abborre) med högre trofisk nivå och färre karpfiskar (främst mört) med lägre trofisk nivå i fångsten jämfört med i slutet av provfiskeperioden.• Åldersanalys av abborrhonor visar att medellängden för ett till femåriga individer har ökat sedan provfiskets början. Detta beror dock huvudsakligen på en stor ökning sedan 2018. Detta antyder att den minskade förekomsten av stor abborre i fångsten inte kan förklaras av en långsammare tillväxthastighet.• Ingen individprovtagning och åldersanalys gjordes på sik under 2021.
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| 39. |
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| 40. |
- Nagler, Christina, et al.
(författare)
-
Examination of functional morphology of dajiid isopods using Arthrophryxus sp. parasitising a mysid shrimp as an example
- 2020
-
Ingår i: Acta Zoologica. - : Wiley. - 0001-7272 .- 1463-6395. ; 101:4, s. 339-352
-
Tidskriftsartikel (refereegranskat)abstract
- Parasitic isopods have become specialised to many different host species and therefore show a wide variety of attachment and feeding specialisations. Often such structures are difficult to examine due to their small sizes which makes a more complete understanding of their functional morphology difficult. Here we present a new report and a first time high-resolution, non-SEM documentation of a parasitic epicaridean isopod, a female of the dajiid Arthrophryxus sp. from the Sea of Okhotsk. It was found during the SokhoBio 2015 on its host, a mysid shrimp (Holmsiella sp.). Arthrophryxus has only one formally described species, Arthrophryxus beringanus Richardson, 1908. With high-resolution documentation methods, we reveal new details of the morphological structures of mouthparts and thoracopods of this dajiid. Furthermore, we discuss the functional morphology of attachment to the host and feeding according to our new findings. We suggest that the thoracopods are involved in the attachment process even more than formerly assumed for different dajiids. The piercing-sucking mouthparts and the additional attachment mechanisms strongly indicate a permanent parasitism of the dajiid isopod. Permanent parasites affect the fitness of their hosts; therefore, deep-sea forms of dajiid isopods have direct impact on the deep-sea crustacean communities.
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| 41. |
- Newton, Ryan J., et al.
(författare)
-
A Guide to the Natural History of Freshwater Lake Bacteria
- 2011
-
Ingår i: Microbiology and molecular biology reviews. - 1092-2172 .- 1098-5557. ; 75:1, s. 14-49
-
Forskningsöversikt (refereegranskat)abstract
- Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.
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| 42. |
- Peura, Sari, et al.
(författare)
-
Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1
- 2012
-
Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 6:9, s. 1640-1652
-
Tidskriftsartikel (refereegranskat)abstract
- Lakes have a central role in the carbon cycle of the boreal landscape. These systems typically stratify in summer and their hypolimnetic microbial communities influence burial of biogenic organic matter in sediments. The composition of bacterial communities in these suboxic habitats was studied by pyrosequencing of 16S rRNA amplicons from five lakes with variable dissolved organic carbon (DOC) concentrations. Bacterioplankton communities in the hypolimnetic waters were clearly different from the surface layer with candidate division OD1, Chlorobi and Bacteroidetes as dominant community members. Several operational taxonomic units (OTUs) affiliated with candidate division OD1 were abundant and consistently present in the suboxic hypolimnion in these boreal lakes. The overall representation of this group was positively correlated with DOC and methane concentrations. Network analysis of time-series data revealed contrasting temporal patterns but suggested similar ecological roles among the abundant OTUs affiliated with candidate division OD1. Together, stable isotope data and taxonomic classification point to methane oxidation and autotrophic denitrification as important processes in the suboxic zone of boreal lakes. Our data revealed that while hypolimnetic bacterial communities are less dynamic, they appear to be more diverse than communities from the oxic surface layer. An appreciable proportion of the hypolimnetic bacteria belong to poorly described phyla.
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| 43. |
- Peura, Sari, et al.
(författare)
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Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Thousands of net-heterotrophic and strongly stratifying lakes dominate the boreal landscape. Besides their central role as emitters of greenhouse gases, we have only recently begun to understand the microbial systems driving the metabolic processes and elemental cycles in these lakes. Using shotgun metagenomics, we show that the functional potential differs among lake types, with humic lakes being particularly enriched in carbon degradation genes. Most of the metabolic pathways exhibit oxygen- and temperature-dependent stratification over depth, coinciding with shifts in bacterial community composition, implying that stratification is a major factor controlling lake metabolism. In the bottom waters, rare and poorly characterized taxa, such as epsilon-Proteobacteria, but also autotrophs, such as photolithotrophic Chlorobia were abundant. These oxygen-depleted layers exhibited high genetic potential for mineralization, but also for fixation of carbon and nitrogen, and genetic markers for both methane production and oxidation were present. Our study provides a first glimpse of the genetic versatility of freshwater anoxic zones, and demonstrates the potential for complete turnover of carbon compounds within the water column.
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| 44. |
- Peura, Sari, et al.
(författare)
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Ontogenic succession of thermokarst thaw ponds is linked to dissolved organic matter quality and microbial degradation potential
- 2020
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Ingår i: Limnology and Oceanography. - : WILEY. - 0024-3590 .- 1939-5590. ; 65:SI, s. S248-S263
-
Tidskriftsartikel (refereegranskat)abstract
- Warming climate is thawing the permafrost in arctic and subarctic regions, leading to formation of thermokarst ponds. During the formation and geomorphological succession of these ponds, carbon that has been trapped in frozen soils for thousands of years is hydrologically mobilized and returned to the active carbon cycle. We sampled 12 thermokarst ponds representing three different stages of pond succession to study the potential of microbial communities to metabolize the organic carbon in the water. We investigated the quality of the dissolved organic carbon (DOC) in the water column based on the spectrophotometric and fluorometric properties of the chromophoric dissolved organic matter combined with parallel factor analysis and the potential of the microbial community for degrading these carbon compounds based on genetic markers related to carbon degradation. Our analysis showed a clear difference in the DOC quality across the different developmental stages. In the younger ponds, organic matter quality suggested that it was originating from the degrading permafrost and in the metagenomes collected from these ponds, the normalized abundance of genes related to degradation of carbon compounds was higher. There was also a shift in the degradation potential in the water column of the ponds, with higher potential for organic matter degradation in deeper, anoxic layers. In conclusion, our results show that the DOC quality and the genetic potential of the microbial community for carbon cycling change across the pond ontogeny, suggesting a capacity of the microbial communities to adapt to changing environmental conditions.
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| 45. |
- Peura, Sari, et al.
(författare)
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Resistant Microbial Cooccurrence Patterns Inferred by Network Topology
- 2015
-
Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 81:6, s. 2090-2097
-
Tidskriftsartikel (refereegranskat)abstract
- Although complex cooccurrence patterns have been described for microbes in natural communities, these patterns have scarcely been interpreted in the context of ecosystem functioning and stability. Here we constructed networks from species cooccurrences between pairs of microorganisms which were extracted from five individual aquatic time series, including a dystrophic and a eutrophic lake as well as an open ocean site. The resulting networks exhibited higher clustering coefficients, shorter path lengths, and higher average node degrees and levels of betweenness than those of random networks. Moreover, simulations demonstrated that taxa with a large number of cooccurrences and placement at convergence positions in the network, so-called "hubs" and "bottlenecks," confer resistance against random removal of "taxa." Accordingly, we refer to cooccurrences at convergence positions as system-relevant interdependencies, as they, like hubs and bottlenecks, determine network topology. These topology features of the cooccurrence networks point toward microbial community dynamics being resistant over time and thus could provide indicators for the state of ecosystem stability.
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| 46. |
- Ricão Canelhas, Monica, et al.
(författare)
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Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?
- 2016
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 92:2
-
Tidskriftsartikel (refereegranskat)abstract
- A wide range of carbon compounds sustain bacterial activity and growth in freshwater ecosystems and the amount and quality of these substrates influence bacterial diversity and metabolic function. Biologically labile low-molecular-weight compounds, such as dissolved free amino acids, are particularly important substrates and can fuel as much as 20% of the total heterotrophic production. In this study, we show that extensive laboratory incubations with variable amino acids as substrates caused only minimal differences in bacterial growth rate, growth yield, quantitative amino acid usage, community composition and diversity. This was in marked contrast to incubations under dark or light regimes, where significant responses were observed in bacterial community composition and with higher diversity in the dark incubations. While a few individual taxa still responded to amendment with specific amino acids, our results suggest that compositional shifts in the specific supply of amino acids and possibly also other labile organic substrates have a minor impact on heterotrophic bacterioplankton communities, at least in nutrient rich lakes and compared to other prevailing environmental factors.
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| 47. |
- Ricão Canelhas, Monica, et al.
(författare)
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Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors
- 2017
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 19:12, s. 5078-5087
-
Tidskriftsartikel (refereegranskat)abstract
- Aquatic environments are typically not homogenous, but characterized by changing substrate concentration gradients and nutrient patches. This heterogeneity in substrate availability creates a multitude of niches allowing bacteria with different substrate utilization strategies to hypothetically coexist even when competing for the same substrate. To study the impact of heterogeneous distribution of organic substrates on bacterioplankton, bioreactors with freshwater bacterial communities were fed artificial freshwater medium with acetate supplied either continuously or in pulses. After a month-long incubation, bacterial biomass and community-level substrate uptake rates were twice as high in the pulsed treatment compared to the continuously fed reactors even if the same total amount of acetate was supplied to both treatments. The composition of the bacterial communities emerging in the two treatments differed significantly with specific taxa overrepresented in the respective treatments. The higher estimated growth yield in cultures that received pulsed substrate inputs, imply that such conditions enable bacteria to use resources more efficiently for biomass production. This finding agrees with established concepts of basal maintenance energy requirements and high energetic costs to assimilate substrates at low concentration. Our results further imply that degradation of organic matter is influenced by temporal and spatial heterogeneity in substrate availability.
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| 48. |
- Sinclair, Lucas, et al.
(författare)
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Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons : Evaluating the Illumina Platform
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:2
-
Tidskriftsartikel (refereegranskat)abstract
- As new sequencing technologies become cheaper and older ones disappear, laboratories switch vendors and platforms. Validating the new setups is a crucial part of conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates as well as 70 samples from alkaline soda lakes, we evaluated the performance of the method with regards to estimates of alpha and beta diversity. Using different purification and DNA quantification procedures we always found up to 5-fold differences in the yield of sequences between individually barcodes samples. Using either a one-step or a two-step PCR preparation resulted in significantly different estimates in both alpha and beta diversity. Comparing with a previous method based on 454 pyrosequencing, we found that our Illumina protocol performed in a similar manner – with the exception for evenness estimates where correspondence between the methods was low. We further quantified the data loss at every processing step eventually accumulating to 50% of the raw reads. When evaluating different OTU clustering methods, we observed a stark contrast between the results of QIIME with default settings and the more recent UPARSE algorithm when it comes to the number of OTUs generated. Still, overall trends in alpha and beta diversity corresponded highly using both clustering methods. Our procedure performed well considering the precisions of alpha and beta diversity estimates, with insignificant effects of individual barcodes. Comparative analyses suggest that 454 and Illumina sequence data can be combined if the same PCR protocol and bioinformatic workflows are used for describing patterns in richness, beta-diversity and taxonomic composition.
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| 49. |
- Sjöholm, Jonathan, et al.
(författare)
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Faktablad - Resultat från övervakningen av kustfisk : Vaxholm (Egentliga Östersjön) 2016‒2022
- 2023
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Under perioden 2016-2022 som provfisket i Vaxholm har pågått har fångstsammansättningen varit relativt konstant.Totalfångsten har ökat signifikant sedan provfiskets början. Under 2022 fångades i medel 82 fiskar per ansträngning (antal individer per nät och natt) fördelat på 13 arter. Mört var den vanligaste arten i fångsten (47 procent), följt av abborre, strömming, braxen och gärs. Den invasiva arten svartmunnad smörbult fångades i provfisket för första gången 2022.Fångsten av karpfisk i Vaxholm under 2022 uppgick till 44 individer per ansträngning, vilket är något lägre än år 2021 då man uppmätte det högsta antalet per ansträngning sedan provfiskeseriens början. Fångsten av karpfisk har varit hög jämfört med närliggande kustområden. De arter av karpfisk som fångats i Vaxholm är framför allt mört, men även braxen, björkna, löja, id och sutare har förekommit i fångsten.Sedan provfiskets början år 2016 så har det fångats relativt många stora fiskar (>30 cm) och relativt många stora abborrar (>25 cm) i Vaxholm. Av de stora fiskarna har braxen och abborre dominerat, men enstaka individer av gös, sik, mört, id, gädda och sutare över 30 centimeter har också fångats i provfisket.Indikatorn L90 för abborre (storleken vid den 90:e percentilen i längdfördelningen) är ett mått på hur stora de största abborrarna i området har varit. L90 har varit relativt högt i Vaxholm sedan 2016 jämfört med närliggande kustområden, vilket tyder på att abborrarna varit stora i området. Dock så har abborrhanarna i Vaxholm varit relativt små och könskvoten indikerar en något högre andel honor i jämförelse med andra provfiskeområden.I provfiskefångsten år 2022 utgjorde abborre 99,6 % av all rovfisk. Förutom abborre förekom även gös och en öring i fångsten. Både fångsten av abborre och rovfisk har ökat signifikant över tid.Diversitetsindexet och den trofiska medelnivån har varit relativt stabila under perioden 2016‒2022, och är i nivå med närliggande provfiskeområden.Två- till femåriga abborrar samt sjuåriga abborrar har vid given ålder ökat i storlek sedan provfiskets början 2016.Ett lågt siktdjup i kombination med den stora fångsten av karpfisk tyder på att Vaxholm är påverkat av hög näringsbelastning.
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| 50. |
- Sowersby, Will, et al.
(författare)
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Costly sexual ornaments coevolve with fast life-histories in killifishes
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Sexually selected ornaments constitute an important investment into reproduction, increasing current mating success, at a potential cost to survival. Theory suggests that exaggerated sexual ornaments may coevolve with the life-history trade-off between current and future reproduction, however this hypothesis has remained unexplored. Here, we determine how the size of secondary sexual traits coevolves with the pace of life-histories (slow or fast), using a clade of killifishes, where independent adaptations to ephemeral environments have resulted in substantial divergences in life-history strategy. In addition, we assess costs to swimming performance driven by enlarged, ornamental fins. We predict that killifishes with fast life-histories, which inhabit time-limited environments and prioritize current reproduction, will have a greater tendency to evolve enlarged fins, compared to killifishes with slow life-histories. Indeed, we found that species with fast life-histories had more pronounced sexual size dimorphism, with males from these species having exaggerated dorsal and anal fins, compared to species with slow life-histories. Furthermore, males from species with fast life-histories and larger ornaments exhibited lower swimming performances compared to both conspecific females, and individuals from species with slow life-histories. Our results indicate that the trade-off between current and future reproduction, can be an evolutionary driver of costly sexual ornaments.
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