| 1. |
- Krause, Sascha, et al.
(författare)
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Trait-based approaches for understanding microbial biodiversity and ecosystem functioning
- 2014
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 5, s. 251-
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Forskningsöversikt (refereegranskat)abstract
- In ecology, biodiversity-ecosystem functioning (BEE) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEE of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEE using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEE studies are often inadequate to unravel BEE relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEE relationships and thus generating systematic principles in microbial ecology and more generally ecology.
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| 2. |
- Brothers, Soren, et al.
(författare)
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A feedback loop links brownification and anoxia in a temperate, shallow lake
- 2014
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 59:4, s. 1388-1398
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Tidskriftsartikel (refereegranskat)abstract
- This study examines a natural, rapid, fivefold increase in dissolved organic carbon (DOC) concentrations in a temperate shallow lake, describing the processes by which increased DOC resulted in anoxic conditions and altered existing carbon cycling pathways. High precipitation for two consecutive years led to rising water levels and the flooding of adjacent degraded peatlands. Leaching from the flooded soils provided an initial increase in DOC concentrations (from a 2010 mean of 12 ± 1 mg L−1 to a maximum concentration of 53 mg L−1 by June 2012). Increasing water levels, DOC, and phytoplankton concentrations reduced light reaching the sediment surface, eliminating most benthic primary production and promoting anoxia in the hypolimnion. From January to June 2012 there was a sudden increase in total phosphorus (from 57 µg L−1 to 216 µg L−1), DOC (from 24.6 mg L−1 to 53 mg L−1), and iron (from 0.12 mg L−1 to 1.07 mg L−1) concentrations, without any further large fluxes in water levels. We suggest that anoxic conditions at the sediment surface and flooded soils produced a dramatic release of these chemicals that exacerbated brownification and eutrophication, creating anoxic conditions that persisted roughly 6 months below a water depth of 1 m and extended periodically to the water surface. This brownification-anoxia feedback loop resulted in a near-complete loss of macroinvertebrate and fish populations, and increased surface carbon dioxide (CO2) emissions by an order of magnitude relative to previous years.
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| 3. |
- Brothers, Soren M, et al.
(författare)
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A regime shift from macrophyte to phytoplankton dominance enhances carbon burial in a shallow, eutrophic lake
- 2013
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Ingår i: Ecosphere. - 2150-8925 .- 2150-8925. ; 4:11
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Tidskriftsartikel (refereegranskat)abstract
- Ecological regime shifts and carbon cycling in aquatic systems have both been subject to increasing attention in recent years, yet the direct connection between these topics has remained poorly understood. A four-fold increase in sedimentation rates was observed within the past 50 years in a shallow eutrophic lake with no surface in- or outflows. This change coincided with an ecological regime shift involving the complete loss of submerged macrophytes, leading to a more turbid, phytoplankton-dominated state. To determine whether the increase in carbon (C) burial resulted from a comprehensive transformation of C cycling pathways in parallel to this regime shift, we compared the annual C balances (mass balance and ecosystem budget) of this turbid lake to a similar nearby lake with submerged macrophytes, a higher transparency, and similar nutrient concentrations. C balances indicated that roughly 80% of the C input was permanently buried in the turbid lake sediments, compared to 40% in the clearer macrophyte-dominated lake. This was due to a higher measured C burial efficiency in the turbid lake, which could be explained by lower benthic C mineralization rates. These lower mineralization rates were associated with a decrease in benthic oxygen availability coinciding with the loss of submerged macrophytes. In contrast to previous assumptions that a regime shift to phytoplankton dominance decreases lake heterotrophy by boosting whole-lake primary production, our results suggest that an equivalent net metabolic shift may also result from lower C mineralization rates in a shallow, turbid lake. The widespread occurrence of such shifts may thus fundamentally alter the role of shallow lakes in the global C cycle, away from channeling terrestrial C to the atmosphere and towards burying an increasing amount of C.
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| 4. |
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| 5. |
- Garcia, Sarahi L, et al.
(författare)
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Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton
- 2013
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 7:1, s. 137-147
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Tidskriftsartikel (refereegranskat)abstract
- Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (~42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (~15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an actinorhodopsin gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria.
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| 6. |
- Garcia, Sarahi L, et al.
(författare)
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Successful enrichment of the ubiquitous freshwater acI Actinobacteria
- 2014
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229 .- 1758-2229. ; 6:1, s. 21-27
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Tidskriftsartikel (refereegranskat)abstract
- Actinobacteriaof the acI lineage are often thenumerically dominant bacterial phylum in surfacefreshwaters, where they can account for>50% oftotal bacteria. Despite their abundance, there are nodescribed isolates. In an effort to obtain enrichmentof these ubiquitous freshwaterActinobacteria, dilutedfreshwater samples from Lake Grosse Fuchskuhle,Germany, were incubated in 96-well culture plates.With this method, a successful enrichment containinghigh abundances of a member of the lineage acI wasestablished. Phylogenetic classification showed thatthe acIActinobacteriaof the enrichment belonged tothe acI-B2 tribe, which seems to prefer acidic lakes.This enrichment grows to low cell densities and thusthe oligotrophic nature of acI-B2 was confirmed.
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| 7. |
- Ghylin, Trevor W, et al.
(författare)
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Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage
- 2014
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 8:12, s. 2503-2516
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Tidskriftsartikel (refereegranskat)abstract
- Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.
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| 8. |
- Glaeser, Stefanie P., et al.
(författare)
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Contrasting Effects of Singlet Oxygen and Hydrogen Peroxide on Bacterial Community Composition in a Humic Lake
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:3, s. e92518-
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Tidskriftsartikel (refereegranskat)abstract
- Light excitation of humic matter generates reactive oxygen species (ROS) in surface waters of aquatic ecosystems. Abundant ROS generated in humic matter rich lakes include singlet oxygen (O-1(2)) and hydrogen peroxide (H2O2). Because these ROS differ in half-life time and toxicity, we compared their effects on microbial activity (C-14-Leucine incorporation) and bacterial community composition (BCC) in surface waters of humic Lake Grosse Fuchskuhle (North-eastern Germany). For this purpose, experiments with water samples collected from the lake were conducted in July 2006, September 2008 and August 2009. Artificially increased O-1(2) and H2O2 concentrations inhibited microbial activity in water samples to a similar extent, but the effect of the respective ROS on BCC varied strongly. BCC analysis by 16S rRNA gene clone libraries and RT-PCR DGGE revealed ROS specific changes in relative abundance and activity of major bacterial groups and composition of dominating phylotypes. These changes were consistent in the three experiments performed in different years. The relative abundance of Polynucleobacter necessarius, Limnohabitans-related phylotypes (Betaproteobacteria), and Novosphingobium acidiphilum (Alphaproteobacteria) increased or was not affected by photo-sensitized O-1(2) exposure, but decreased after H2O2 exposure. The opposite pattern was found for Actinobacteria of the freshwater AcI-B cluster which were highly sensitive to O-1(2) but not to H2O2 exposure. Furthermore, group-specific RT-PCR DGGE analysis revealed that particle-attached P. necessarius and Limnohabitans-related phylotypes exhibit higher resistance to O-1(2) exposure compared to free-living populations. These results imply that O-1(2) acts as a factor in niche separation of closely affiliated Polynucleobacter and Limnohabitans-related phylotypes. Consequently, oxidative stress caused by photochemical ROS generation should be regarded as an environmental variable determining abundance, activity, and phylotype composition of environmentally relevant bacterial groups, in particular in illuminated and humic matter rich waters.
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| 9. |
- Salka, Ivette, et al.
(författare)
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Distribution of acI-Actinorhodopsin genes in Baltic Sea salinity gradients indicates adaptation of facultative freshwater photoheterotrophs to brackish waters
- 2014
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 16:2, s. 586-597
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge onActinobacteriarhodopsin gene (actR)diversity and spatial distribution is scarce. The BalticSea is characterized by strong salinity gradientsleading to the coexistence of marine and freshwaterbacteria and hence is an ideal study area to elucidatethe dispersion and phylogenetic affiliation ofactRindependence on salinity. ActRDGGE fingerprints insummer 2008 revealed between 3 and 19 distinctbands within a salinity range of 2.4–27 PSU. Environ-mentalactRclone sequences were obtained from sta-tions distributed along the whole salinity gradient.Overall, 20 differentactRsequence groups (opera-tional taxonomic units) were found, with up to 11different ones per station. Phylogenetically, theactRsequences were predominantly (80%) affiliated with freshwater acI-Actinobacteriawhose 16S rRNA geneaccounted for 2–33% of total 16S rRNA genes in both the Bothnian Sea and central Baltic Sea. However, atsalinities above 14 PSU, acI-16S rRNA gene accounted for less than 1%. In contrast, the diversity of actRremained high. Changes in actRgene diversity were significantly correlated with salinity, oxygen, silica orabundance of Synechococcussp. Our results demonstrate a wide distribution of freshwater actRalong theBaltic Sea salinity gradient indicating that some fresh-water Actinobacteriamight have adapted to higher salinities.
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| 10. |
- Tang, Kam W., et al.
(författare)
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Paradox reconsidered : Methane oversaturation in well-oxygenated lake waters
- 2014
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 59:1, s. 275-284
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Tidskriftsartikel (refereegranskat)abstract
- The widely reported paradox of methane oversaturation in oxygenated water challenges the prevailing paradigm that microbial methanogenesis only occurs under anoxic conditions. Using a combination of field sampling, incubation experiments, and modeling, we show that the recurring mid-water methane peak in Lake Stechlin, northeast Germany, was not dependent on methane input from the littoral zone or bottom sediment or on the presence of known micro-anoxic zones. The methane peak repeatedly overlapped with oxygen oversaturation in the seasonal thermocline. Incubation experiments and isotope analysis indicated active methane production, which was likely linked to photosynthesis and/or nitrogen fixation within the oxygenated water, whereas lessening of methane oxidation by light allowed accumulation of methane in the oxygen-rich upper layer. Estimated methane efflux from the surface water was up to 5 mmol m(-2) d(-1). Mid-water methane oversaturation was also observed in nine other lakes that collectively showed a strongly negative gradient of methane concentration within 0-20% dissolved oxygen (DO) in the bottom water, and a positive gradient within >= 20% DO in the upper water column. Further investigation into the responsible organisms and biochemical pathways will help improve our understanding of the global methane cycle.
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