48 results on '"Eiler, Alexander"'
Search Results
2. Bacterial bioindicators enable biological status classification along the continental Danube river.
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Fontaine, Laurent, Pin, Lorenzo, Savio, Domenico, Friberg, Nikolai, Kirschner, Alexander K. T., Farnleitner, Andreas H., and Eiler, Alexander
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BIOLOGICAL classification ,BIOINDICATORS ,WATERSHEDS ,BACTERIAL communities ,MICROBIAL communities ,MACHINE learning - Abstract
Despite the importance of bacteria in aquatic ecosystems and their predictable diversity patterns across space and time, biomonitoring tools for status assessment relying on these organisms are widely lacking. This is partly due to insufficient data and models to identify reliable microbial predictors. Here, we show metabarcoding in combination with multivariate statistics and machine learning allows to identify bacterial bioindicators for existing biological status classification systems. Bacterial beta-diversity dynamics follow environmental gradients and the observed associations highlight potential bioindicators for ecological outcomes. Spatio-temporal links spanning the microbial communities along the river allow accurate prediction of downstream biological status from upstream information. Network analysis on amplicon sequence veariants identify as good indicators genera Fluviicola, Acinetobacter, Flavobacterium, and Rhodoluna, and reveal informational redundancy among taxa, which coincides with taxonomic relatedness. The redundancy among bacterial bioindicators reveals mutually exclusive taxa, which allow accurate biological status modeling using as few as 2–3 amplicon sequence variants. As such our models show that using a few bacterial amplicon sequence variants from globally distributed genera allows for biological status assessment along river systems. Bacterial communities sampled over 2,600 km of the River Danube revealed the predictability of downstream river conditions from upstream microbiota, with variance and prevalence of dominant taxa linked to environmental gradients, unveiling potential bioindicators. [ABSTRACT FROM AUTHOR] more...
- Published
- 2023
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3. Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat.
- Author
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Wei, Jing, Fontaine, Laurent, Valiente, Nicolas, Dörsch, Peter, Hessen, Dag O., and Eiler, Alexander
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GLOBAL warming ,MICROBIAL genomics ,NITROGEN cycle ,GREENHOUSE gases ,FRESH water ,SOIL heating - Abstract
Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming. Diverse microbial trajectories in carbon and nitrogen cycle processes represent a positive feedback loop of deglaciation on climate warming. [ABSTRACT FROM AUTHOR] more...
- Published
- 2023
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4. Drivers and variability of CO2:O2 saturation along a gradient from boreal to Arctic lakes.
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Allesson, Lina, Valiente, Nicolas, Dörsch, Peter, Andersen, Tom, Eiler, Alexander, and Hessen, Dag O.
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DISSOLVED organic matter ,LAKES ,LATITUDE ,BEDROCK ,WATER chemistry ,HETEROTROPHIC respiration ,SOIL respiration - Abstract
Lakes are significant players for the global climate since they sequester terrestrially derived dissolved organic carbon (DOC), and emit greenhouse gases like CO
2 to the atmosphere. However, the differences in environmental drivers of CO2 concentrations are not well constrained along latitudinal and thus climate gradients. Our aim here is to provide a better understanding of net heterotrophy and gas balance at the catchment scale in a set of boreal, sub-Arctic and high-Arctic lakes. We assessed water chemistry and concentrations of dissolved O2 and CO2 , as well as the CO2 :O2 ratio in three groups of lakes separated by steps of approximately 10 degrees latitude in South-Eastern Norway (near 60° N), sub-Arctic lakes in the northernmost part of the Norwegian mainland (near 70° N) and high-Arctic lakes on Svalbard (near 80° N). Across all regions, CO2 saturation levels varied more (6–1374%) than O2 saturation levels (85–148%) and hence CO2 saturation governed the CO2 :O2 ratio. The boreal lakes were generally undersaturated with O2 , while the sub-Arctic and high-Arctic lakes ranged from O2 saturated to oversaturated. Regardless of location, the majority of the lakes were CO2 supersaturated. In the boreal lakes the CO2 :O2 ratio was mainly related to DOC concentration, in contrast to the sub-Arctic and high-Arctic localities, where conductivity was the major statistical determinant. While the southern part is dominated by granitic and metamorphic bedrock, the sub-Arctic sites are scattered across a range of granitic to sedimentary bed rocks, and the majority of the high-Arctic lakes are situated on limestone, resulting in contrasting lake alkalinities between the regions. DOC dependency of the CO2 :O2 ratio in the boreal region together with low alkalinity suggests that in-lake heterotrophic respiration was a major source of lake CO2 . Contrastingly, the conductivity dependency indicates that CO2 saturation in the sub-Arctic and high-Arctic lakes was to a large part explained by DIC input from catchment respiration and carbonate weathering. [ABSTRACT FROM AUTHOR] more...- Published
- 2022
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5. Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.
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Suarez, Carolina, Sedlacek, Christopher J., Gustavsson, David J. I., Eiler, Alexander, Modin, Oskar, Hermansson, Malte, and Persson, Frank
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- 2022
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6. National eDNA-based monitoring of Batrachochytrium dendrobatidis and amphibian species in Norway.
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Osman, Omneya Ahmed, Andersson, Johan, Martin-Sanchez, Pedro M., and Eiler, Alexander
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FRESH water ,BATRACHOCHYTRIUM dendrobatidis ,AMPHIBIANS ,DNA ,POLYMERASE chain reaction - Abstract
Freshwaters represent the most threatened environments with regard to biodiversity loss and, therefore, there is a need for national monitoring programs to effectively document species distribution and evaluate potential risks for vulnerable species. The monitoring of species for effective management practices is, however, challenged by insufficient data acquisition when using traditional methods. Here we present the application of environmental DNA (eDNA) metabarcoding of amphibians in combination with quantitative PCR (qPCR) assays for an invasive pathogenic chytrid species (Batrachochytrium dendrobatidis -Bd), a potential threat to endemic and endangered amphibian species. Statistical comparison of amphibian species detection using either traditional or eDNA-based approaches showed weak correspondence. By tracking the distribution of Bd over three years, we concluded that the risk for amphibian extinction is low since Bd was only detected at five sites where multiple amphibians were present over the sampled years. Our results show that eDNA-based detection can be used for simultaneous monitoring of amphibian diversity and the presence of amphibian pathogens at the national level in order to assess potential species extinction risks and establish effective management practices. As such our study represents suggestions for a national monitoring program based on eDNA. [ABSTRACT FROM AUTHOR] more...
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- 2022
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7. Two different approaches of microbial community structure characterization in riverine epilithic biofilms under multiple stressors conditions: Developing molecular indicators.
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Pin, Lorenzo, Eiler, Alexander, Fazi, Stefano, and Friberg, Nikolai
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BIOINDICATORS ,FLUORESCENCE in situ hybridization ,WATERSHEDS ,MICROBIAL communities ,BIOFILMS ,GENETIC barcoding ,REGIONAL differences - Abstract
Microbial communities are major players in the biogeochemical processes and ecosystem functioning of river networks. Despite their importance in the ecosystem, biomonitoring tools relying on prokaryotes are still lacking. Only a few studies have employed both metabarcoding and quantitative techniques such as catalysed reported deposition fluorescence in situ hybridization (CARD‐FISH) to analyse prokaryotic communities of epilithic biofilms in river ecosystems. We intended to investigate the efficacy of both techniques in detecting changes in microbial community structure associated with environmental drivers. We report a significant correlation between the prokaryotic community composition and pH in rivers from two different geographical areas in Norway. Both CARD‐FISH and metabarcoding data were following the pattern of the environmental variables, but the main feature distinguishing the community composition was the regional difference itself. Beta‐dispersion analyses on both CARD‐FISH abundance and metabarcoding data revealed higher accuracy of metabarcoding to differentiate regions and river systems. The CARD‐FISH results showed high variability, even for samples within the same river, probably due to some unmeasured microscale ecological variability which we could not resolve. We also present a statistical method, which uses variation coefficient and overall prevalence of taxonomic groups, to detect possible biological indicators among prokaryotes using metabarcoding data. The development of new prokaryotic bioindicators would benefit from both techniques used in this study, but metabarcoding seems to be faster and more reliable than CARD‐FISH for large scale bio‐assessment. [ABSTRACT FROM AUTHOR] more...
- Published
- 2021
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8. Phosphorus Availability Promotes Bacterial DOC-Mineralization, but Not Cumulative CO2-Production.
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Allesson, Lina, Andersen, Tom, Dörsch, Peter, Eiler, Alexander, Wei, Jing, and Hessen, Dag O.
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DISSOLVED organic matter ,MICROBIAL respiration ,HETEROTROPHIC bacteria ,ATMOSPHERIC carbon dioxide ,BACTERIAL growth ,PHOSPHORUS ,RESPIRATION ,RESPIRATION in plants - Abstract
The current trend of increasing input of terrestrially derived dissolved organic carbon (DOC) to boreal freshwater systems is causing increased levels of carbon dioxide (CO
2 ) supersaturation and degassing. Phosphorus (P) is often the most limiting nutrient for bacterial growth and would thus be expected to increase overall mineralization rates and CO2 production. However, high carbon (C) to P ratios of terrestrially derived DOC could also cause elevated cell-specific respiration of the excess C in heterotrophic bacteria. Using data from a survey of 75 Scandinavian lakes along an ecosystem gradient of DOC, we estimated in situ CO2 production rates. These rates showed a unimodal response with DOC-specific CO2 production negatively related to DOC:total phosphorus (TP) ratio, and a turning point at 5 mg C L−1 , indicating higher DOC turnover rates in productive than in unproductive lakes. To further assess the dependency of bacterial respiration (BR) on DOC and P, we monitored CO2 production in incubations of water with a gradient of DOC crossed with two levels of inorganic P. Finally, we crossed DOC and P with a temperature gradient to test the temperature dependency of respiration rates [as oxygen (O2 ) consumption]. While total CO2 production seemed to be unaffected by P additions, respiration rates, and growth yields, as estimated by ribosomal gene copy numbers, suggest increased bacterial growth and decreased cell-specific respiration under non-limited P conditions. Respiration rates showed a sigmoid response to increasing DOC availability reaching a plateau at about 20 mg C L−1 of initial DOC concentrations. In addition to these P and DOC level effects, respiration rates responded in a non-monotonic fashion to temperature with an increase in respiration rates by a factor of 2.6 (±0.2) from 15 to 25°C and a decrease above 30°C. The combined results from the survey and experiments highlight DOC as the major determinant of CO2 production in boreal lakes, with P and temperature as significant modulators of respiration kinetics. [ABSTRACT FROM AUTHOR] more...- Published
- 2020
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9. Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.
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Juottonen, Heli, Fontaine, Laurent, Wurzbacher, Christian, Drakare, Stina, Peura, Sari, and Eiler, Alexander
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ARCHAEBACTERIA ,LAKES ,BIOGEOCHEMICAL cycles ,DETERMINISTIC processes ,COMMUNITIES - Abstract
Summary: Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high‐resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large‐scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea‐specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co‐occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake‐specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia‐oxidizing archaea were frequently detected across the lakes. Archaea‐specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes. [ABSTRACT FROM AUTHOR] more...
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- 2020
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10. Diazotroph Genomes and Their Seasonal Dynamics in a Stratified Humic Bog Lake.
- Author
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Fernandez, Leyden, Peura, Sari, Eiler, Alexander, Linz, Alexandra M., McMahon, Katherine D., and Bertilsson, Stefan
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Aquatic N-fixation is generally associated with the growth and mass development of Cyanobacteria in 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 and nif gene clusters analysis. Groups with diazotrophic operons were functionally divergent and included Cholorobi , Geobacter , Desulfobacterales , Methylococcales , and Acidobacteria. In addition to nifH (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 the Chlorobi population, 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 of rnf genes (related to the expression of H
+ /Na+ -translocating ferredoxin: NAD+ oxidoreductase) in Methylococcales and Desulfobacterales suggests 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. [ABSTRACT FROM AUTHOR] more...- Published
- 2020
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11. Ontogenic succession of thermokarst thaw ponds is linked to dissolved organic matter quality and microbial degradation potential.
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Peura, Sari, Wauthy, Maxime, Simone, Domenico, Eiler, Alexander, Einarsdóttir, Karólína, Rautio, Milla, and Bertilsson, Stefan
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DISSOLVED organic matter ,PONDS ,TUNDRAS ,FROZEN ground ,CARBON cycle ,MICROBIAL communities - 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. [ABSTRACT FROM AUTHOR] more...
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- 2020
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12. Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.
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Garcia, Sarahi L., Buck, Moritz, Hamilton, Joshua J., Wurzbacher, Christian, Grossart, Hans-Peter, McMahon, Katherine D., and Eiler, Alexander
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- 2018
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13. Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors.
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Ricão Canelhas, Monica, Andersson, Martin, Eiler, Alexander, Lindström, Eva S., and Bertilsson, Stefan
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FRESHWATER bacteria ,BACTERIAL communities ,BIOREACTORS ,AQUATIC ecology ,BIOCHEMICAL substrates - 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. [ABSTRACT FROM AUTHOR] more...
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- 2017
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14. Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing.
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Corcoll, Natàlia, Österlund, Tobias, Sinclair, Lucas, Eiler, Alexander, Kristiansson, Erik, Backhaus, Thomas, and Eriksson, K. Martin
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GENETICS of bacterial diversity ,RIBOSOMAL RNA ,BIOFILMS - Abstract
High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterisation of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol® Reagent (PlantDNAzol) and the FastDNA® SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77
-1 30 μg g wet wt-1 ). Lower amounts of DNA were obtained (<37 μg g wet wt-1 ) with the Power Plant® Pro DNA Isolation Kit (PowerPlant) and the Power Biofilm® DNA Isolation Kit (PowerBiofilm) methods, but integrity and purity of the extracted DNA were higher. Results from 16S rRNA amplicon sequencing demonstrate that the choice of a DNA extraction method significantly influences the bacterial community profiles generated. A higher number of bacterial OTUs were detected when DNA was extracted with the PowerBiofilm and the PlantDNAzol methods. Overall, this study demonstrates the potential bias in metagenomic diversity estimates associated with different DNA extraction methods. [ABSTRACT FROM AUTHOR] more...- Published
- 2017
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15. Lake bacterioplankton dynamics over diurnal timescales.
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Grubisic, Lorena M., Bertilsson, Stefan, Eiler, Alexander, Heinrich, Friederike, Brutemark, Andreas, Alonso‐Sáez, Laura, Andersson, Anders F., Gantner, Stephan, Riemann, Lasse, and Beier, Sara
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BACTERIOPLANKTON ,FOOD chains ,BROMODEOXYURIDINE ,PLANKTON ,FLAVOBACTERIUM - 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. [ABSTRACT FROM AUTHOR] more...
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- 2017
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16. Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.
- Author
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Hubalek, Valerie, Wu, Xiaofen, Eiler, Alexander, Buck, Moritz, Heim, Christine, Dopson, Mark, Bertilsson, Stefan, and Ionescu, Danny
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- 2016
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17. Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria.
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Eiler, Alexander, Mondav, Rhiannon, Sinclair, Lucas, Fernandez-Vidal, Leyden, Scofield, Douglas G, Schwientek, Patrick, Martinez-Garcia, Manuel, Torrents, David, McMahon, Katherine D, Andersson, Siv GE, Stepanauskas, Ramunas, Woyke, Tanja, and Bertilsson, Stefan more...
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- 2016
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18. Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin.
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Langenheder, Silke, Comte, Jérôme, Zha, Yinghua, Samad, Md Sainur, Sinclair, Lucas, Eiler, Alexander, and Lindström, Eva S.
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SEDIMENT microbiology ,BACTERIA ,RIBOSOMAL RNA ,BACTERIAL communities ,MARINE ecology - Abstract
Some bacteria can be preserved over time in deep sediments where they persist either in dormant or slow-growing vegetative stages. Here, we hypothesized that such cells can be revived when exposed to environmental conditions similar to those before they were buried in the sediments. To test this hypothesis, we collected bacteria from sediment samples of different ages (140-8500 calibrated years before present, cal BP) from three lakes that differed in the timing of their physical isolation from the Baltic Sea following postglacial uplift. After these bacterial communities were grown in sterile water from the Baltic Sea, we determined the proportion of 16S rRNA sequence reads associated with marine habitats by extracting the environment descriptive terms of homologous sequences retrieved from public databases. We found that the proportion of reads associated with marine descriptive term was significantly higher in cultures inoculated with sediment layers formed under Baltic conditions and where salinities were expected to be similar to current levels. Moreover, a similar pattern was found in the original sediment layers. Our study, therefore, suggests that remnants of marine bacterial communities can be preserved in sediments over thousands of years and can be revived from deep sediments in lakes of marine origin. [ABSTRACT FROM AUTHOR] more...
- Published
- 2016
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19. Constraints on methane oxidation in ice-covered boreal lakes.
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Denfeld, Blaize A., Ricão Canelhas, Monica, Weyhenmeyer, Gesa A., Bertilsson, Stefan, Eiler, Alexander, and Bastviken, David
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- 2016
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20. Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?
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Ricão Canelhas, Monica, Eiler, Alexander, and Bertilsson, Stefan
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BACTERIOPLANKTON ,AMINO acids ,CARBON compounds ,BACTERIAL diversity ,MARINE ecology - 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. [ABSTRACT FROM AUTHOR] more...
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- 2016
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21. Bacterial diversity along a 2600 km river continuum.
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Savio, Domenico, Sinclair, Lucas, Ijaz, Umer Z., Parajka, Juraj, Reischer, Georg H., Stadler, Philipp, Blaschke, Alfred P., Blöschl, Günter, Mach, Robert L., Kirschner, Alexander K. T., Farnleitner, Andreas H., and Eiler, Alexander more...
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BACTERIOPLANKTON ,BACTERIAL diversity ,PLANKTON diversity ,RIBOSOMAL RNA ,BIODIVERSITY ,NUCLEOTIDE sequence - Abstract
The bacterioplankton diversity in large rivers has thus far been under-sampled despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA-gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free-living and particle-associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the Polynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and ground water affiliated bacteria. Based on views of the meta community and River Continuum Concept, we interpret the observed taxonomic patterns and accompanying changes in alpha and beta diversity with the intention of laying the foundation for a unified concept for river bacterioplankton diversity. [ABSTRACT FROM AUTHOR] more...
- Published
- 2015
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22. A network-based approach to disturbance transmission through microbial interactions.
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Hunt, Dana E., Ward, Christopher S., Fouilland, Eric, and Eiler, Alexander
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AQUATIC microbiology ,ECOLOGICAL disturbances ,BIOGEOCHEMISTRY - Abstract
Microbes numerically dominate aquatic ecosystems and play key roles in the biogeochemistry and the health of these environments. Due to their short generations times and high diversity, microbial communities are among the first responders to environmental changes, including natural and anthropogenic disturbances such as storms, pollutant releases, and upwelling. These disturbances affect members of the microbial communities both directly and indirectly through interactions with impacted community members. Thus, interactions can influence disturbance propagation through the microbial community by either expanding the range of organisms affected or buffering the influence of disturbance. For example, interactions may expand the number of disturbance-affected taxa by favoring a competitor or buffer the impacts of disturbance when a potentially disturbance-responsive clade's growth is limited by an essential microbial partner. Here, we discuss the potential to use inferred ecological association networks to examine how disturbances propagate through microbial communities focusing on a case study of a coastal community's response to a storm. This approach will offer greater insight into how disturbances can produce community-wide impacts on aquatic environments following transient changes in environmental parameters. [ABSTRACT FROM AUTHOR] more...
- Published
- 2015
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23. Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community.
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Garcia, Sarahi L., Buck, Moritz, McMahon, Katherine D., Grossart, Hans‐Peter, Eiler, Alexander, and Warnecke, Falk
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BACTERIAL cultures ,AUXOTROPHY ,METAGENOMICS ,VITAMIN B12 ,CRENARCHAEOTA ,FRESHWATER microbiology ,BACTERIAL metabolism - Abstract
Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes ( MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to 'social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring 'interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature. [ABSTRACT FROM AUTHOR] more...
- Published
- 2015
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24. Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform.
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Sinclair, Lucas, Osman, Omneya Ahmed, Bertilsson, Stefan, and Eiler, Alexander
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BIODIVERSITY ,MICROBIAL ecology ,RIBOSOMAL RNA ,POLYMERASE chain reaction ,BIOTIC communities ,SEQUENCE alignment - 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. [ABSTRACT FROM AUTHOR] more...
- Published
- 2015
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25. Can marine bacteria be recruited from freshwater sources and the air?
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Comte, Jérôme, Lindström, Eva S, Eiler, Alexander, and Langenheder, Silke
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MARINE bacteria ,FRESHWATER bacteria ,LIFE zones ,SEDIMENTATION & deposition ,HABITATS ,MARINE ecology - Abstract
There is now clear evidence that microorganisms present biogeographic patterns, yet the processes that create and maintain them are still not well understood. In particular, the contribution of dispersal and its exact impact on local community composition is still unclear. For example, dispersing cells may not thrive in recipient environments, but may still remain part of the local species pool. Here, we experimentally tested if marine bacteria can be retrieved from freshwater communities (pelagic and sediment) and the atmosphere by exposing bacteria from three lakes, that differ in their proximity to the Norwegian Sea, to marine conditions. We found that the percentage of freshwater taxa decreased with increasing salinities, whereas marine taxa increased along the same gradient. Our results further showed that this increase was stronger for lake and sediment compared with air communities. Further, significant increases in the average niche breadth of taxa were found for all sources, and in particular lake water and sediment communities, at higher salinities. Our results therefore suggests that marine taxa can readily grow from freshwater sources, but that the response was likely driven by the growth of habitat generalists that are typically found in marine systems. Finally, there was a greater proportion of marine taxa found in communities originating from the lake closest to the Norwegian Sea. In summary, this study shows that the interplay between bacterial dispersal limitation and dispersal from internal and external sources may have an important role for community recovery in response to environmental change. [ABSTRACT FROM AUTHOR] more...
- Published
- 2014
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26. Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics.
- Author
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Eiler, Alexander, Zaremba ‐ Niedzwiedzka, Katarzyna, Martínez ‐ García, Manuel, McMahon, Katherine D., Stepanauskas, Ramunas, Andersson, Siv G. E., and Bertilsson, Stefan
- Subjects
FRESHWATER microbiology ,METAGENOMICS ,PLANKTON ,SALINITY ,MICROBIAL diversity ,BIOTIC communities ,PHYSIOLOGY - 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 with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities. [ABSTRACT FROM AUTHOR] more...
- Published
- 2014
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27. Enhanced greenhouse gas emissions and changes in plankton communities following an experimental increase in organic carbon loading to a humic lake.
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Peura, Sari, Nykänen, Hannu, Kankaala, Paula, Eiler, Alexander, Tiirola, Marja, and Jones, Roger
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GREENHOUSE gas mitigation ,PLANKTON ,AQUATIC organisms ,CARBON content of water ,SUGAR ,CARBON monoxide ,ORGANIC compounds - Abstract
Organic carbon concentrations in the surface waters of the boreal region have increased during the past two decades. We investigated the impact of elevated dissolved organic carbon (DOC) loading to a humic lake by a whole-lake experiment in which DOC in the form of cane sugar was added monthly during the ice-free period over two consecutive years. The sugar addition represented an increased concentration of 2 mg l of DOC in the epilimnion and led to an increase in CO emission and also an apparent increase in CH emission to the atmosphere from the lake surface. The composition of the bacterial, phytoplankton and zooplankton communities altered during the study period and the bacterial abundance in the metalimnion and hypolimnion of the lake decreased. No changes were detected in epilimnetic primary production or respiration, but there was an increase in bacterial production in the epilimnion. The nutrient and particulate organic carbon concentrations also suggested possible changes in the activity of heterotrophic bacteria in the metalimnion. Carbon stable isotope analyses indicated transfer of some added sugar carbon through the food web to zooplankton consumers. Overall the results suggest that future increases in organic carbon loading to boreal lakes will increase greenhouse gas emissions, although the magnitude of any change is likely to depend on the availability of nutrients like phosphorus and nitrogen which influence organic matter processing and the development of plankton communities. [ABSTRACT FROM AUTHOR] more...
- Published
- 2014
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28. Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton.
- Author
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Bagatini, Inessa Lacativa, Eiler, Alexander, Bertilsson, Stefan, Klaveness, Dag, Tessarolli, Letícia Piton, and Vieira, Armando Augusto Henriques
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FRESHWATER phytoplankton ,HOST specificity (Biology) ,WATER quality ,AQUATIC organisms ,HETEROTROPHIC bacteria ,PLANT species ,CYANOBACTERIA - 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. [ABSTRACT FROM AUTHOR] more...
- Published
- 2014
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29. Disturbance induced decoupling between host genetics and composition of the associated microbiome.
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Wegner, Karl Mathias, Volkenborn, Nils, Peter, Hannes, and Eiler, Alexander
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PATHOGENIC microorganisms ,MICROORGANISMS ,BACTERIAL diversity ,NUCLEOTIDE sequence ,PACIFIC oysters - Abstract
Background Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host. Results While the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains. Conclusion The decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations. [ABSTRACT FROM AUTHOR] more...
- Published
- 2013
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30. Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.
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Fortunato, Caroline S, Eiler, Alexander, Herfort, Lydie, Needoba, Joseph A, Peterson, Tawnya D, and Crump, Byron C
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BIOINDICATORS ,SPATIAL behavior in animals ,SPECIES diversity ,ENVIRONMENTAL impact analysis ,ACTINOBACTERIA - Abstract
Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=−0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments. [ABSTRACT FROM AUTHOR] more...
- Published
- 2013
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31. Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance.
- Author
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Yeo, Sara K., Huggett, Megan J., Eiler, Alexander, and Rappé, Michael S.
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BACTERIOPLANKTON ,MICROBIAL population genetics ,RIBOSOMAL RNA ,COASTAL ecology ,MICROBIAL ecology ,MARINE ecology ,POPULATION biology ,POPULATION dynamics ,OCEANOGRAPHY - Abstract
In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition. [ABSTRACT FROM AUTHOR] more...
- Published
- 2013
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32. Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach.
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Eiler, Alexander, Drakare, Stina, Bertilsson, Stefan, Pernthaler, Jakob, Peura, Sari, Rofner, Carina, Simek, Karel, Yang Yang, Znachor, Petr, and Lindström, Eva S.
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PHYTOPLANKTON ,FRESHWATER biodiversity ,NUCLEOTIDE sequence ,PROKARYOTIC genomes ,ENVIRONMENTAL monitoring ,APPLIED ecology - 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. [ABSTRACT FROM AUTHOR] more...
- Published
- 2013
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33. Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1.
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Peura, Sari, Eiler, Alexander, Bertilsson, Stefan, Nykänen, Hannu, Tiirola, Marja, and Jones, Roger I
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BIOTIC communities ,LAKES ,LANDSCAPES ,ORGANIC compounds ,RIBOSOMAL RNA ,DATA analysis - 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. [ABSTRACT FROM AUTHOR] more...
- Published
- 2012
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34. Bacterial and Phytoplankton Responses to Nutrient Amendments in a Boreal Lake Differ According to Season and to Taxonomic Resolution.
- Author
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Peura, Sari, Eiler, Alexander, Hiltunen, Minna, Nykänen, Hannu, Tiirola, Marja, and Jones, Roger I.
- Subjects
PHYTOPLANKTON ,BIOLOGICAL classification ,BACTERIOPLANKTON ,PHYLOGENY ,NITROGEN - Abstract
Nutrient limitation and resource competition in bacterial and phytoplankton communities may appear different when considering different levels of taxonomic resolution. Nutrient amendment experiments conducted in a boreal lake on three occasions during one open water season revealed complex responses in overall bacterioplankton and phytoplankton abundance and biovolume. In general, bacteria were dominant in spring, while phytoplankton was clearly the predominant group in autumn. Seasonal differences in the community composition of bacteria and phytoplankton were mainly related to changes in observed taxa, while the differences across nutrient treatments within an experiment were due to changes in relative contributions of certain higher- and lower-level phylogenetic groups. Of the main bacterioplankton phyla, only Actinobacteria had a treatment response that was visible even at the phylum level throughout the season. With increasing resolution (from 75 to 99% sequence similarity) major responses to nutrient amendments appeared using 454 pyrosequencing data of 16S rRNA amplicons. This further revealed that OTUs (defined by 97% sequence similarity) annotated to the same highly resolved freshwater groups appeared to occur during different seasons and were showing treatment-dependent differentiation, indicating that OTUs within these groups were not ecologically coherent. Similarly, phytoplankton species from the same genera responded differently to nutrient amendments even though biovolumes of the majority of taxa increased when both nitrogen and phosphorus were added simultaneously. The bacterioplankton and phytoplankton community compositions showed concurrent trajectories that could be seen in synchronous succession patterns over the season. Overall, our data revealed that the response of both communities to nutrient changes was highly dependent on season and that contradictory results may be obtained when using different taxonomic resolutions. [ABSTRACT FROM AUTHOR] more...
- Published
- 2012
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35. Coherent dynamics and association networks among lake bacterioplankton taxa.
- Author
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Eiler, Alexander, Heinrich, Friederike, and Bertilsson, Stefan
- Subjects
BACTERIOPLANKTON ,BIOTIC communities ,MICROBIAL ecology ,PHYLOGENY ,NUCLEOTIDE sequence ,RIBOSOMAL RNA ,ALGAL blooms ,MARINE microbiology - 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. [ABSTRACT FROM AUTHOR] more...
- Published
- 2012
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36. Dynamics of the SAR11 bacterioplankton lineage in relation to environmental conditions in the oligotrophic North Pacific subtropical gyre.
- Author
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Eiler, Alexander, Hayakawa, Darin H., Church, Matthew J., Karl, David M., and Rappé, Michael S.
- Subjects
PLANKTON ,POLYMERASE chain reaction ,GENES ,GENETICS - Abstract
A quantitative PCR assay for the SAR11 clade of marine Alphaproteobacteria was applied to nucleic acids extracted from monthly depth profiles sampled over a 3-year period (2004–2007) at the open-ocean Station ALOHA (A Long-term Oligotrophic Habitat Assessment; 22°45′N, 158°00′W) in the oligotrophic North Pacific Ocean. This analysis revealed a high contribution (averaging 36% of 16S rRNA gene copies) of SAR11 to the total detected 16S rRNA gene copies over depths ranging from the surface layer to 4000 m, and revealed consistent spatial and temporal variation in the relative abundance of SAR11 16S rRNA gene copies. On average, a higher proportion of SAR11 rRNA gene copies were detected in the photic zone (< 175 m depth; mean = 38%) compared with aphotic (> 175 m depth; mean = 30%), and in the winter months compared with the summer (mean = 44% versus 33%, integrated over 175 m depth). Partial least square to latent structure projections identified environmental variables that correlate with variation in the absolute abundance of SAR11, and provided tools for developing a predictive model to explain time and depth-dependent variations in SAR11. Moreover, this information was used to hindcast temporal dynamics of the SAR11 clade between 1997 and 2006 using the existing HOT data set, which suggested that interannual variations in upper ocean SAR11 abundances were related to ocean-climate variability such as the El Niño Southern Oscillation. [ABSTRACT FROM AUTHOR] more...
- Published
- 2009
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37. Sequential colonization by river periphyton analysed by microscopy and molecular fingerprinting.
- Author
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Szabó, Katalin É., Makk, Judit, Kiss, Keve Tihamér, Eiler, Alexander, Ács, Éva, Tóth, Bence, Kiss, Áron Keve, and Bertilsson, Stefan
- Subjects
PERIPHYTON ,MICROSCOPY ,HUMAN fingerprints ,MOLECULAR models ,COLONIZATION (Ecology) ,DIATOMS ,MICROALGAE - Abstract
1. An artificial glass substratum was incubated in the River Danube for a period of 28 days in order to detect the sequential colonization of microorganisms. 2. Light and fluorescent microscopy showed that microalgae and the picoalgal fraction on the slides increased rapidly over the first 2 weeks of colonization. Diatoms were numerically the most abundant component of the periphyton and their species richness and diversity increased rapidly in the early phase of colonization whereas diversity subsequently increased moderately. 3. Evenness of the diatom community was initially high, lower in the intermediate phase and again higher later on. Succession involving early, intermediate and late colonizer species was observed. Community composition during the first 5 days of colonization was very different from later stages whereas there were only minor changes subsequently. 4. Molecular community analysis by means of terminal restriction fragment length polymorphism analysis of PCR amplified 16S rRNA and 18S rRNA genes pointed to even larger differences between the composition of samples obtained early and late in the period. 5. The number of 18S rRNA and 16S rRNA terminal restriction fragments (T-RF-s) was variable over the colonization period and the fragment patterns of both the bacterial and eukaryotic portion of the microbial community were variable, with most T-RF-s unique to a single sample, suggesting a wide diversity and dynamic properties of periphytic organisms. [ABSTRACT FROM AUTHOR] more...
- Published
- 2008
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38. Links between bacterial production, amino-acid utilization and community composition in productive lakes.
- Author
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Bertilsson, Stefan, Eiler, Alexander, Nordqvist, Anneli, and Jørgensen, Niels Ole Gerslev
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AMINO acids ,MICROBIAL ecology ,BIOTIC communities ,POLYMORPHISM (Crystallography) ,ARGININE - 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 V
max ) 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 μg 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.The ISME Journal (2007) 1, 532–544; doi:10.1038/ismej.2007.64; published online 2 August 2007 [ABSTRACT FROM AUTHOR] more...- Published
- 2007
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39. Growth response of Vibrio cholerae and other Vibrio spp. to cyanobacterial dissolved organic matter and temperature in brackish water.
- Author
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Eiler, Alexander, Gonzalez-Rey, Carlos, Allen, Sophie, and Bertilsson, Stefan
- Subjects
VIBRIO cholerae ,CYANOBACTERIA ,ORGANIC compounds ,BRACKISH waters ,PLANKTON - 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. [ABSTRACT FROM AUTHOR] more...- Published
- 2007
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40. Corrigendum: Phosphorus Availability Promotes Bacterial DOC-Mineralization, but Not Cumulative CO2-Production.
- Author
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Allesson, Lina, Andersen, Tom, Dörsch, Peter, Eiler, Alexander, Wei, Jing, and Hessen, Dag O.
- Subjects
PHOSPHORUS ,AQUATIC microbiology - Abstract
Keywords: dissolved organic carbon-mineralization; lake metabolism; response curves; phosphorus addition; stoichiometry EN dissolved organic carbon-mineralization lake metabolism response curves phosphorus addition stoichiometry N.PAG N.PAG 2 11/27/20 20201123 NES 201123 In the original article, there was a mistake in Figure 2 as published. Dissolved organic carbon-mineralization, lake metabolism, response curves, phosphorus addition, stoichiometry. [Extracted from the article] more...
- Published
- 2020
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41. Diurnal variations in the auto- and heterotrophic activity of cyanobacterial phycospheres ( Gloeotrichia echinulata) and the identity of attached bacteria.
- Author
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Eiler, Alexander, Olsson, Jan A., and Bertilsson, Stefan
- Subjects
PRIMARY productivity (Biology) ,CYANOBACTERIA ,BACTERIAL physiology ,AQUATIC microbiology ,CARBON ,BACTERIA ,CARBON dioxide ,AUTOTROPHIC bacteria ,HETEROTROPHIC bacteria ,LAKES - Abstract
1. We assessed the role of cyanobacterial–bacterial consortia ( Gloeotrichia echinulata phycospheres) for net changes in inorganic carbon, primary production (PP) and secondary production in Lake Erken (Sweden). 2. At the time of sampling, large colonies of G. echinulata formed a massive bloom with abundances ranging from 102 colonies L
−1 in the pelagic zone to 5000 colonies L−1 in shallow bays. These colonies and their surrounding phycospheres contributed between 17 and 92% of total PP, and phycosphere-associated bacteria contributed between 8.5 and 82% of total bacterial secondary production. PP followed a diurnal cycle, whereas bacterial production showed no such pattern. Over a 24 h period, carbon dioxide measurements showed that the phycospheres were net autotrophic in the top layer of the water column, whereas they were net heterotrophic below 2 m depth. 3. Sequencing and phylogenetic analysis of 16S rRNA genes of attached bacteria revealed a diverse bacterial community that included populations affiliated with Proteobacteria, Bacteriodetes, Acidobacteria, Fusobacteria, Firmicutes, Verrucomicrobia, and other Cyanobacteria. 4. Compared with their planktonic counterparts, bacteria associated with cyanobacterial phycospheres had lower affinity for arginine, used as a model compound to assess uptake of organic compounds. 5. Extrapolation of our data to the water column of lake Erken suggests that microorganisms that were not associated with cyanobacteria dominated CO2 production at the ecosystem scale during our experiments, as CO2 fixation balanced CO2 production in the cyanobacterial phycospheres. [ABSTRACT FROM AUTHOR] more...- Published
- 2006
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42. Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes.
- Author
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Eiler, Alexander and Bertilsson, Stefan
- Subjects
CYANOBACTERIAL blooms ,RNA ,CYANOBACTERIA ,FRESHWATER biodiversity ,PROKARYOTES ,CARBON cycle ,BACTERIA - 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. [ABSTRACT FROM AUTHOR] more...
- Published
- 2004
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43. Inorganic and organic carbon biogeochemistry in the Gautami Godavari estuary (Andhra Pradesh, India) during pre-monsoon: The local impact of extensive mangrove forests.
- Author
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Bouillon, Steven, Frankignoulle, Michel, Dehairs, Frank, Velimirov, Branko, Eiler, Alexander, Abril, Gwenaël, Etcheber, Henri, and Borges, Alberto Vieira
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- 2003
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44. Effects of predation stress and food ration on perch gut microbiota.
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Zha, Yinghua, Eiler, Alexander, Johansson, Frank, and Svanbäck, Richard
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- 2018
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45. Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.
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Hubalek, Valerie, Wu, Xiaofen, Eiler, Alexander, Buck, Moritz, Heim, Christine, Dopson, Mark, Bertilsson, Stefan, and Ionescu, Danny
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- 2016
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46. DOES ECOSYSTEM SIZE DETERMINE AQUATIC BACTERIAL RICHNESS? COMMENT.
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Eva S. Lindström, Eiler, Alexander, Langenheder, Silke, Bertilsson, Stefan, Drakare, Stina, Ragnarsson, Henrik, and Tranvik, Lars J.
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BIOTIC communities ,LAKES ,BIOGEOGRAPHY ,HABITATS ,AQUATIC organisms ,ISLANDS ,SPECIES ,ECOLOGY ,GEOGRAPHY - Abstract
The article comments of the study entitled "Does ecosystem size determine aquatic bacterial richness?" according to the author, a significant correlation between lake surface area and lake bacterial operational taxonomic unit richness in 32 lakes was observed in the study. It was cited that the relationship affirms one prediction of the island-biogeography theory that larger islands support more species than smaller islands. On the other hand, it was also showed that the study does not provide bacterial richness and habitat size due to inadequate methods used. more...
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- 2007
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47. Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes.
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Peura, Sari, Sinclair, Lucas, Bertilsson, Stefan, and Eiler, Alexander
- Subjects
ANTIMETABOLITES ,GENOMES ,OXYGEN ,METABOLISM ,DNA metabolism - 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 ε-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. [ABSTRACT FROM AUTHOR] more...
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- 2015
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48. Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes.
- Author
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Eiler, Alexander and Bertilsson, Stefan
- Subjects
CYANOBACTERIAL blooms - Abstract
A correction to the article "Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes" published in a previous issue of the periodical is presented. more...
- Published
- 2007
- Full Text
- View/download PDF
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