| 1. |
- Aguilera, Anabella, et al.
(author)
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Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria
- 2023
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In: Environmental Microbiology. - Chichester : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 25:9, s. 1674-1695
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Journal article (peer-reviewed)abstract
- Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcBandcpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10–30°C), light(10–190 μmol photons m-2s-1), and salinity (2–14 PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.
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| 2. |
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| 3. |
- Churakova, Yelena, et al.
(author)
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Biogenic silica accumulation in picoeukaryotes : Novel players in the marine silica cycle
- 2023
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In: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229 .- 1758-2229. ; 15:4, s. 282-290
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Journal article (peer-reviewed)abstract
- It is well known that the biological control of oceanic silica cycling is dominated by diatoms, with sponges and radiolarians playing additional roles. Recent studies have revealed that some smaller marine organisms (e.g. the picocyanobacterium Synechococcus) also take up silicic acid (dissolved silica, dSi) and accumulate silica, despite not exhibiting silicon dependent cellular structures. Here, we show biogenic silica (bSi) accumulation in five strains of picoeukaryotes (<2-3 mu m), including three novel isolates from the Baltic Sea, and two marine species (Ostreococcus tauri and Micromonas commoda), in cultures grown with added dSi (100 mu M). Average bSi accumulation in these novel biosilicifiers was between 30 and 92 amol Si cell(-1). Growth rate and cell size of the picoeukaryotes were not affected by dSi addition. Still, the purpose of bSi accumulation in these smaller eukaryotic organisms lacking silicon dependent structures remains unclear. In line with the increasing recognition of picoeukaryotes in biogeochemical cycling, our findings suggest that they can also play a significant role in silica cycling.
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| 4. |
- Laber, Christien P., et al.
(author)
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Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak
- 2022
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In: Frontiers in Microbiology. - Lausanne : Frontiers Media S.A.. - 1664-302X. ; 13
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Journal article (peer-reviewed)abstract
- The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3-V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 x 10(4) cells ml(-1). This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.
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| 5. |
- Martínez-García, Sandra, et al.
(author)
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Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent
- 2022
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In: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 13
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Journal article (peer-reviewed)abstract
- Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 mu m) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05-0.27) of FL bacteria (defined as the size-fraction <3.0 mu m) indicated the magnitude of seasonal variability of ecological settings bacteria experience. Accordingly, 16S rRNA gene analyses of bacterial community composition uncovered distinct correlations between taxa, environmental variables and metabolisms, including Firmicutes associated with elevated hydrolytic enzyme activity in winter and Verrucomicrobia with utilization of algal-derived substrates during summer. Further, our results suggested a substrate-controlled succession in the PA fraction, from Bacteroidetes using polymers to Actinobacteria and Betaproteobacteria using monomers across the spring to autumn phytoplankton bloom transition. Collectively, our findings emphasize pronounced seasonal changes in both the composition of the bacterial community in the PA and FL size-fractions and their contribution to organic matter utilization and carbon cycling. This is important for interpreting microbial ecosystem function-responses to natural and human-induced environmental changes.
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| 6. |
- Shu, Rui, 1990-, et al.
(author)
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Influence of Metal Substitution and Ion Energy on Microstructure Evolution of High-Entropy Nitride (TiZrTaMe)N1-x (Me = Hf, Nb, Mo, or Cr) Films
- 2021
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In: ACS APPLIED ELECTRONIC MATERIALS. - : American Chemical Society (ACS). - 2637-6113. ; 3:6, s. 2748-2756
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Journal article (peer-reviewed)abstract
- Multicomponent or high-entropy ceramics show unique combinations of mechanical, electrical, and chemical properties of importance in coating applications. However, generalizing controllable thin-film processes for these complex materials remains a challenge. Here, understoichiometric (TiZrTaMe)N1-x (Me = Hf, Nb, Mo, or Cr, 0.12 <= x <= 0.30) films were deposited on Si(100) substrates at 400 degrees C by reactive magnetron sputtering using single elemental targets. The influence of ion energy during film growth was investigated by varying the negative substrate bias voltage from similar to 10 V (floating potential) to 130 V. The nitrogen content for the samples determined by elastic recoil detection analysis varied from 34.9 to 43.8 at. % (0.12 <= x <= 0.30), and the metal components were near-equimolar and not affected by the bias voltage. On increasing the substrate bias, the phase structures of (TiZrTaMe)N1-x (Me = Hf, Nb, or Mo) films evolved from a polycrystalline fcc phase to a (002) preferred orientation along with a change in surface morphology from faceted triangular features to a dense and smooth structure with nodular mounds. All the four series of (TiZrTaMe)N1-x (Me = Hf, Nb, Mo, or Cr) films exhibited increasing intrinsic stress with increasing negative bias. The maximum compressive stress reached similar to 3.1 GPa in Hf- and Cr-containing films deposited at -130 V. The hardness reached a maximum value of 28.0 +/- 1.0 GPa at a negative bias >= 100 V for all the four series of films. The effect of bias on the mechanical properties of (TiNbZrMe)N1-x films can thus guide the design of protective high-entropy nitride films.
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| 7. |
- Alneberg, Johannes, et al.
(author)
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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
- 2018
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In: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 5
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Journal article (peer-reviewed)abstract
- The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .
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| 8. |
- Amnebrink, Dennis
(author)
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Seasonality influences gene expression in Baltic Sea microbial communities
- 2024
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Doctoral thesis (other academic/artistic)abstract
- Prokaryotes are the most abundant living organisms in the marine environment. They contribute to primary production and the recycling of its products. Collectively they influence the marine element cycles of carbon along with elements like nitrogen and sulfur. However, much remains to learn of the functional characteristics of microbial communities carrying out these processes, and how different communities respond to changing environmental conditions in space and time.The composition of marine prokaryotic communities is known to change in a seasonal manner, but how seasonality influences their gene expression or “activity” remains largely unknown. In this thesis I investigate the relationship between prokaryotic activity, relative gene expression, and seasonality using time series field data on gene expression combined with reference genomes of prokaryotic populations (metagenome assembled genomes, MAGs). This revealed pronounced seasonal succession in overall transcriptional dynamics. Importantly, roughly half of the 50 populations with highest relative abundance in transcription altered their transcriptional profiles across seasons. Thus, changes in relative gene expression on the annual scale is explained by community turnover and modulation of activity within populations. Characterization of a MAG representative of the filamentous cyanobacterial genus Aphanizomenon that forms summer blooms in the Baltic Proper, highlighted seasonal patterns in transcription of genes underlying key prokaryotic activities. This included genes related to photosynthesis (different genes expressed in different seasons), nitrogen- fixation (expression peaking in summer) and oxidative stress (peaking in winter). A mesocosm study in the Bothnian Sea using temperature and nutrient manipulations simulating the winter to summer transition showed lower growth efficiency and higher maintenance respiration in winter conditions, implying larger relative losses of CO2 through respiration in winter. Additionally, temperature, nutrients, and their combination, caused separation in both prokaryotic taxonomy and transcription of metabolic pathways. Key features included archaeal transcription of ammonium oxidation in winter conditions, and Oceanospirillales central metabolisms in summer. Taken together, these results highlight the pronounced effect of seasonality on prokaryotic community gene expression and the capability of prokaryotic populations to alter their expressed genetic repertoire. This emphasizes the importance of the temporal perspective when considering how prokaryotic communities will respond to changes in environmental conditions.
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| 9. |
- Amnebrink, Dennis, et al.
(author)
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Structuring of marine prokaryotic gene expression by temperature and dissolved organic matter
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Other publication (other academic/artistic)abstract
- Temperature and dissolved organic matter (DOM) are important drivers of marine microbial activity, but their effects, alone or in combination, on the physiological responses of sub-arctic prokaryotic assemblages remain poorly understood. In a one-month mesocosm experiment initiated in early March in the northern Baltic Sea, we thus exposed a coastal microbial community to temperature and nutrient regimes representative of winter and early summer (i.e., 1°C and 10°C, with and without DOM additions) in a 2x2 factorial design. Prokaryotic abundance and heterotrophic production increased until around day 17 in the 10°C mesocosms. Yet, mid through the experiment (days 10 and 17, when samples for metatranscriptomics analyses were analyzed), estimates of growth rates were highest for the 10°C plus DOM treatment (TN; ~2.5 day-1), comparable for the 1°C plus DOM (N) and the 10°C treatments (T; ~1.0 day-1), and low for the control (C; 0.2 day-1). PCA analysis showed that samples for prokaryotic transcription in the 1°C plus DOM and the 10°C treatments clustered in different directions from the control, and the combined 10°C plus DOM treatment triggered even further changes. Taxonomic analysis of the transcripts uncovered broad treatment specific responses. This included a dominance of Nitrosopumilus (Archaea) in the 1°C mesocosms (with and without DOM), an increase in the relative expression of Alphaproteobacteria (both Rhodobacterales and SAR11) in the 10°C mesocosms without DOM addition, and an increase in Oceanospirillales in the 10°C plus DOM treatment. Burkholderiales (Betaproteobacteria) maintained a high relative expression (up to 25%) in all mesocosms. A PERMANOVA on the total of 182,618 transcribed genes revealed statistically significant effects of both temperature and DOM, and also a significant interaction effect between the two factors. EdgeR analysis identified significant differential transcription for up to 10% of the genes in each of the tested contrasts. Prominent features among the significant genes included Nitrosopumilus genes for ammonium uptake and ammonia oxidation in the 1°C mesocosms (C, N), membrane transporters for small organic acids in the N-treatment, genes for N and P assimilation along with molecular chaperones in the T-treatment, and dominance of Oceanospirillales genes for energy and growth metabolism in the TN treatment. These metatranscriptomics responses were associated with changes in ecologically important characteristics of the prokaryotic communities, such as growth rates and growth efficiency, providing clues to how successional changes in community composition and metabolism are induced by environmental conditions linked with seasonality.
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| 10. |
- Antunes, V. G., et al.
(author)
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Influence of the magnetic field on the extension of the ionization region in high power impulse magnetron sputtering discharges
- 2023
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In: Plasma sources science & technology. - : IOP Publishing. - 0963-0252 .- 1361-6595. ; 32:7
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Journal article (peer-reviewed)abstract
- The high power impulse magnetron sputtering (HiPIMS) discharge brings about increased ionization of the sputtered atoms due to an increased electron density and efficient electron energization during the active period of the pulse. The ionization is effective mainly within the electron trapping zone, an ionization region (IR), defined by the magnet configuration. Here, the average extension and the volume of the IR are determined based on measuring the optical emission from an excited level of the argon working gas atoms. For particular HiPIMS conditions, argon species ionization and excitation processes are assumed to be proportional. Hence, the light emission from certain excited atoms is assumed to reflect the IR extension. The light emission was recorded above a 100 mm diameter titanium target through a 763 nm bandpass filter using a gated camera. The recorded images directly indicate the effect of the magnet configuration on the average IR size. It is observed that the shape of the IR matches the shape of the magnetic field lines rather well. The IR is found to expand from 10 and 17 mm from the target surface when the parallel magnetic field strength 11 mm above the racetrack is lowered from 24 to 12 mT at a constant peak discharge current.
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