| 1. |
- Akram, Neelam, et al.
(författare)
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Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp AND4
- 2013
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 15:5, s. 1400-1415
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Tidskriftsartikel (refereegranskat)abstract
- Proteorhodopsin (PR), a ubiquitous membrane photoprotein in marine environments, acts as a light-driven proton pump and can provide energy for bacterial cellular metabolism. However, knowledge of factors that regulate PR gene expression in different bacteria remains strongly limited. Here, experiments with Vibrio sp. AND4 showed that PR phototrophy promoted survival only in cells from stationary phase and not in actively growing cells. PR gene expression was tightly regulated, with very low values in exponential phase, a pronounced peak at the exponential/stationary phase intersection, and a marked decline in stationary phase. Thus, PR gene expression at the entry into stationary phase preceded, and could therefore largely explain, the stationary phase light-induced survival response in AND4. Further experiments revealed nutrient limitation, not light exposure, regulated this differential PR expression. Screening of available marine vibrios showed that the PR gene, and thus the potential for PR phototrophy, is found in at least three different clusters in the genus Vibrio. In an ecological context, our findings suggest that some PR-containing bacteria adapted to the exploitation of nutrient-rich micro-environments rely on a phase of relatively slowly declining resources to mount a cellular response preparing them for adverse conditions dispersed in the water column.
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| 2. |
- Baltar, Federico, et al.
(författare)
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Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions
- 2016
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 10:3, s. 568-581
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Tidskriftsartikel (refereegranskat)abstract
- To test whether protist grazing selectively affects the composition of aquatic bacterial communities, we combined high-throughput sequencing to determine bacterial community composition with analyses of grazing rates, protist and bacterial abundances and bacterial cell sizes and physiological states in a mesocosm experiment in which nutrients were added to stimulate a phytoplankton bloom. A large variability was observed in the abundances of bacteria (from 0.7 to 2.4 x 10(6) cells per ml), heterotrophic nanoflagellates (from 0.063 to 2.7 x 10(4) cells per ml) and ciliates (from 100 to 3000 cells per l) during the experiment (similar to 3-, 45- and 30-fold, respectively), as well as in bulk grazing rates (from 1 to 13 x 10(6) bacteria per ml per day) and bacterial production (from 3 to 379 mu g per Cl per day) (1 and 2 orders of magnitude, respectively). However, these strong changes in predation pressure did not induce comparable responses in bacterial community composition, indicating that bacterial community structure was resilient to changes in protist predation pressure. Overall, our results indicate that peaks in protist predation (at least those associated with phytoplankton blooms) do not necessarily trigger substantial changes in the composition of coastal marine bacterioplankton communities.
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| 3. |
- Baltar, Federico, et al.
(författare)
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Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic
- 2016
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.
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| 4. |
- Baltar, Federico, et al.
(författare)
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Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site
- 2015
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 91:6
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Tidskriftsartikel (refereegranskat)abstract
- Bacterioplankton communities are made up of a small set of abundant taxa and a large number of low-abundant organisms (i.e. 'rare biosphere'). Despite the critical role played by bacteria in marine ecosystems, it remains unknown how this large diversity of organisms are affected by human-induced perturbations, or what controls the responsiveness of rare compared to abundant bacteria. We studied the response of a Mediterranean bacterioplankton community to two anthropogenic perturbations (i.e. nutrient enrichment and/or acidification) in two mesocosm experiments (in winter and summer). Nutrient enrichment increased the relative abundance of some operational taxonomic units (OTUs), e.g. Polaribacter, Tenacibaculum, Rhodobacteraceae and caused a relative decrease in others (e.g. Croceibacter). Interestingly, a synergistic effect of acidification and nutrient enrichment was observed on specific OTUs (e.g. SAR86). We analyzed the OTUs that became abundant at the end of the experiments and whether they belonged to the rare (<0.1% of relative abundance), the common (0.1-1.0% of relative abundance) or the abundant (>1% relative abundance) fractions. Most of the abundant OTUs at the end of the experiments were abundant, or at least common, in the original community of both experiments, suggesting that ecosystem alterations do not necessarily call for rare members to grow.
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| 5. |
- Bunse, Carina, et al.
(författare)
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Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2
- 2016
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Ingår i: Nature Climate Change. - : Macmillan Publishers Ltd.. - 1758-678X .- 1758-6798. ; 6:5, s. 483-487
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Tidskriftsartikel (refereegranskat)abstract
- Human-induced ocean acidification impacts marine life. Marine bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes1; hence, understanding their performance under projected climate change scenarios is crucial for assessing ecosystem functioning. Whereas genetic and physiological responses of phytoplankton to ocean acidification are being disentangled2, 3, 4, corresponding functional responses of bacterioplankton to pH reduction from elevated CO2 are essentially unknown. Here we show, from metatranscriptome analyses of a phytoplankton bloom mesocosm experiment, that marine bacteria responded to lowered pH by enhancing the expression of genes encoding proton pumps, such as respiration complexes, proteorhodopsin and membrane transporters. Moreover, taxonomic transcript analysis showed that distinct bacterial groups expressed different pH homeostasis genes in response to elevated CO2. These responses were substantial for numerous pH homeostasis genes under low-chlorophyll conditions (chlorophyll a <2.5 μg l−1); however, the changes in gene expression under high-chlorophyll conditions (chlorophyll a >20 μg l−1) were low. Given that proton expulsion through pH homeostasis mechanisms is energetically costly, these findings suggest that bacterioplankton adaptation to ocean acidification could have long-term effects on the economy of ocean ecosystems.
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| 6. |
- Hakman, Inger, et al.
(författare)
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The polar auxin transport inhibitor NPA impairs embryo morphology and increases the expression of an auxin efflux facilitator protein PIN during Picea abies somatic embryo development
- 2009
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Ingår i: Tree Physiology. - : Oxford University Press. - 0829-318X .- 1758-4469. ; 29:4, s. 483-496
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Tidskriftsartikel (refereegranskat)abstract
- Auxin and polar auxin transport have been implicated in controlling embryo patterning and development in angiosperms but less is known from the gymnosperms. The aims of this study were to determine at what stages of conifer embryo development auxin and polar auxin transport are the most important for normal development and to analyze the changes in embryos after treatment with the polar auxin inhibitor N-1-naphthylphthalamic acid (NPA). For these studies, somatic embryos of Norway spruce (Picea abies L. Karst) were used. Growth on medium containing NPA leads to the formation of embryos with poor shoot apical meristem (SAM) and fused cotyledons, and to a pin-formed phenotype of the regenerated plantlets. The effect of NPA on embryo morphology was most severe if embryos were transferred to NPA-containing medium immediately before cotyledon initiation and SAM specification. Indole-3-acetic acid (IAA) was identified by immunolocalization in developing embryos. The highest staining intensity was seen in early staged embryos and then decreased as the embryos matured. No clear IAA-maxima was seen, although the apical parts of embryos, particularly the protoderm, and the suspensor cells appear to accumulate more IAA, as reflected by the staining pattern. The NPA treatment also caused expanded procambium and a broader root apical meristem in embryos, and a significant increase in the expression of a PIN1-like gene. Taken together, our results show that, for proper cotyledon initiation, correct auxin transport is needed only during a short period at the transition stage of embryo development, probably involving PIN efflux proteins and that a common mechanism is behind proper cotyledon formation within the species of angiosperms and conifers, despite their cotyledon number which normally differs.
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| 7. |
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| 8. |
- Palovaara, Joakim, 1978-, et al.
(författare)
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Comparative expression pattern analysis of WUSCHEL-related homeobox 2 (WOX2) and WOX8⁄9 in developing seeds and somatic embryos of the gymnosperm Picea abies
- 2010
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 188:1, s. 122-135
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Tidskriftsartikel (refereegranskat)abstract
- In seed plants, current knowledge concerning embryonic pattern formation by polar auxin transport (PAT) and WUSCHEL-related homeobox (WOX) gene activity is primarily derived from studies on angiosperms, while less is known about these processes in gymnosperms. In view of the differences in their embryogeny, and the fact that somatic embryogenesis is used for mass propagation of conifers, a better understanding of embryo development is vital.The expression patterns of PaWOX2 and PaWOX8/9 were followed with quantitative reverse transcription–polymerase chain reaction (qRT-PCR) and in situ hybridization (ISH) during seed and somatic embryo development in Norway spruce (Picea abies), and in somatic embryos treated with the PAT inhibitor N-1-naphthylphthalamic acid (NPA).Both PaWOX2 and PaWOX8/9 were highly expressed at the early growth stages of zygotic and somatic embryos, and shared a similar expression pattern over the entire embryo. At later embryo stages, high expression of PaWOX8/9 became restricted to cotyledon primordia, epidermis, procambium and root apical meristem (RAM), which became most evident in NPA-treated somatic embryos, while expression of PaWOX2 was much lower.Our results suggest an ancestral role of WOX in seed plant embryo development, and strengthen the proposed connection between PAT, PIN-FORMED (PIN) and WOX in the regulation of embryo patterning in seed plants.
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| 9. |
- Palovaara, Joakim, 1978-
(författare)
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Conifer embryology : a study of polar auxin transport and WOX transcription factors
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plants, like animals, use endogenous signaling molecules to coordinate their own physiology and development. One such molecule in plants is the hormone auxin and recent research has implicated auxin and its polar transport, together with the WOX transcription factors, in regulating embryo patterning and development in angiosperms (flowering plants), the most diverse group of land plants. No extensive investigation of this has been carried out on the more evolutionary distant gymnosperms, the other major taxa of seed plants. Thus, in this thesis I, together with my co-authors, have analyzed the regulation of embryonic pattern formation in the coniferous gymnosperm Picea abies (Norway spruce) using seed and somatic embryos. Conifers are important forestry species and knowledge of their embryology is vital for reforestration programs, where the method of somatic embryogenesis is employed for mass propagation as well as it is used as a model system for embryo development.Mature spruce embryos display a basic body plan and contain a shoot apical meristem (SAM), cotyledons, hypocotyl, embryonic root and a root apical meristem (RAM), with the meristems generating differentiated cells for organ formation. Treatment of embryos with a polar auxin transport (PAT) inhibitor produce embryos with poor SAM and, in some cases, fused cotyledons. Thus, PAT is essential for the correct patterning of conifer embryos. In angiosperms, PAT is mainly established and maintained by members of the auxin efflux facilitator PIN-FORMED (PIN) family. I isolated a PIN homologue (PaPIN1), of high abundance in conifer tissues, that is localized, together with auxin, to the epidermis of precotyledonary spruce embryos and upregulated as well as delocalized from the epidermis in early PAT inhibited embryos. Since also auxin concentration seems to decrease in the epidermis of these embryos, my data indicate that local auxin accumulation in the epidermis is mediated by PIN-dependent auxin transport.Further, I investigated WOX genes in conifers and isolated two homologues, PaWOX2 and PaWOX8/9, that are expressed throughout spruce embryo development. Their expression profile suggests involvement in cell proliferation and specification, and, indeed, they both serve as markers for conifer somatic embryogenesis. The expression of PaWOX2 and PaWOX8/9 overlap with PaPIN1 in differentiating vascular tissue (procambium) of spruce embryos and is also upregulated in early PAT inhibited embryos. Thus, PaWOX2, PaWOX8/9, and PaPIN1 may all act together in procambium differentiation. With this, I conclude that a common mechanism, involving PAT and WOX, regulate embryo pattern formation in seed plants. Results in post-embryonic tissue imply a common mechanism regulating pattern formation also here.
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| 10. |
- Palovaara, Joakim, 1978-, et al.
(författare)
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Conifer WOX-related homedomain transcription factors, developmental considerations and expression dynamic of WOX2 during Picea abies somatic embryogenesis
- 2008
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Ingår i: Plant Molecular Biology. - : Springer. - 0167-4412 .- 1573-5028. ; 66:5, s. 533-549
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Tidskriftsartikel (refereegranskat)abstract
- In angiosperms, the WOX family of transcription factors has important functions in meristem regulation and in control of the partitioning of developing embryos into functional domains. In this study, a putative WOX2 homologous gene was isolated from Picea abies, and its expression pattern during somatic embryo development was followed using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). We used strategies of both absolute and relative quantification of gene expression, and benefits and disadvantages of the two methods are presented and discussed. During embryogenesis, PaWOX2 expression was highest at the earliest stages of development, but low levels were also detected in seedling tissues. No PaWOX2expression was detected in a non-embryogenic cell culture, indicating thatPaWOX2 plays a fundamental role during early somatic embryo development, and can be used as a possible marker for embryogenic potential. Additional results show that conifers, like angiosperms, contain a large number of WOX-related genes, many of them expressed during embryo development. In phylogenetic analysis based on the deduced homeodomain of retrieved pine and spruce EST sequences, no conifer WUS homolog was found. Neither did we find any homeodomain to cluster with WOX5. Interestingly, a clade including only conifer sequences derived from various tissues was resolved as sister to a PhyscomitrellaWOX-like gene, suggestive of the early origin of this gene family. Our results thus provide basic information for further studies of the evolution of this gene family and of their function in relation to meristem dynamics and specification of stem cells in gymnosperms.
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