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Palovaara, Joakim
Publications (10 of 14) Show all publications
Baltar, F., Palovaara, J., Unrein, F., Catala, P., Hornak, K., Simek, K., . . . Pinhassi, J. (2016). Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions. The ISME Journal, 10(3), 568-581
Open this publication in new window or tab >>Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions
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2016 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 3, p. 568-581Article in journal (Refereed) Published
Abstract [en]

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.

National Category
Ecology
Research subject
Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-51064 (URN)10.1038/ismej.2015.135 (DOI)000370472500004 ()26262814 (PubMedID)2-s2.0-84939141929 (Scopus ID)
Available from: 2016-03-18 Created: 2016-03-18 Last updated: 2018-11-15Bibliographically approved
Bunse, C., Lundin, D., Karlsson, C. M. G., Akram, N., Vila-Costa, M., Palovaara, J., . . . Pinhassi, J. (2016). Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2. Nature Climate Change, 6(5), 483-487
Open this publication in new window or tab >>Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2
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2016 (English)In: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 6, no 5, p. 483-487Article in journal (Refereed) Published
Abstract [en]

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.

National Category
Microbiology Ecology Climate Research
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-49969 (URN)10.1038/nclimate2914 (DOI)000375125200015 ()2-s2.0-84964949342 (Scopus ID)
Projects
EcoChange
Available from: 2016-02-29 Created: 2016-02-29 Last updated: 2018-10-24Bibliographically approved
Baltar, F., Palovaara, J., Vila-Costa, M., Salazar, G., Calvo, E., Pelejero, C., . . . Pinhassi, J. (2015). Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site. FEMS Microbiology Ecology, 91(6), Article ID UNSP fiv058.
Open this publication in new window or tab >>Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site
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2015 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 91, no 6, article id UNSP fiv058Article in journal (Refereed) Published
Abstract [en]

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.

National Category
Microbiology Ecology
Research subject
Natural Science, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-43485 (URN)10.1093/femsec/fiv058 (DOI)000359690000012 ()2-s2.0-84944171729 (Scopus ID)
Available from: 2015-05-29 Created: 2015-05-29 Last updated: 2017-12-04Bibliographically approved
Palovaara, J., Akram, N., Baltar, F., Bunse, C., Forsberg, J., Pedrós-Alió, C., . . . Pinhassi, J. (2014). Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria. Proceedings of the National Academy of Sciences of the United States of America, 111(35), E3650-E3658
Open this publication in new window or tab >>Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria
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2014 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 35, p. E3650-E3658Article in journal (Refereed) Published
Abstract [en]

Proteorhodopsin (PR) is present in half of surface ocean bacterioplankton, where its light-driven proton pumping provides energy to cells. Indeed, PR promotes growth or survival in different bacteria. However, the metabolic pathways mediating the light responses remain unknown. We analyzed growth of the PR-containing Dokdonia sp. MED134 (where light-stimulated growth had been found) in seawater with low concentrations of mixed [yeast extract and peptone (YEP)] or single (alanine, Ala) carbon compounds as models for rich and poor environments. We discovered changes in gene expression revealing a tightly regulated shift in central metabolic pathways between light and dark conditions. Bacteria showed relatively stronger light responses in Ala compared with YEP. Notably, carbon acquisition pathways shifted toward anaplerotic CO2 fixation in the light, contributing 31 +/- 8% and 24 +/- 6% of the carbon incorporated into biomass in Ala and YEP, respectively. Thus, MED134 was a facultative double mixotroph, i.e., photo- and chemotrophic for its energy source and using both bicarbonate and organic matter as carbon sources. Unexpectedly, relative expression of the glyoxylate shunt genes (isocitrate lyase and malate synthase) was >300-fold higher in the light-but only in Ala-contributing a more efficient use of carbon from organic compounds. We explored these findings in metagenomes and metatranscriptomes and observed similar prevalence of the glyoxylate shunt compared with PR genes and highest expression of the isocitrate lyase gene coinciding with highest solar irradiance. Thus, regulatory interactions between dissolved organic carbon quality and central metabolic pathways critically determine the fitness of surface ocean bacteria engaging in PR phototrophy.

National Category
Ecology
Research subject
Natural Science, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-37306 (URN)10.1073/pnas.1402617111 (DOI)000341230800012 ()2-s2.0-84907227908 (Scopus ID)
Available from: 2014-09-27 Created: 2014-09-27 Last updated: 2017-12-11Bibliographically approved
Akram, N., Palovaara, J., Forsberg, J., Lindh, M. V., Milton, D. L., Luo, H., . . . Pinhassi, J. (2013). Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp AND4. Environmental Microbiology, 15(5), 1400-1415
Open this publication in new window or tab >>Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp AND4
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2013 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 15, no 5, p. 1400-1415Article in journal (Refereed) Published
Abstract [en]

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.

National Category
Ecology
Research subject
Natural Science, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-26291 (URN)10.1111/1462-2920.12085 (DOI)000318041800012 ()2-s2.0-84876480250 (Scopus ID)
Available from: 2013-06-11 Created: 2013-06-11 Last updated: 2017-12-06Bibliographically approved
Hallberg, H., Palovaara, J. & Hakman, I. (2010). Auxin polar transport and PIN localization pattern during conifer embryo development. Paper presented at FESPB 2010 Spain.
Open this publication in new window or tab >>Auxin polar transport and PIN localization pattern during conifer embryo development
2010 (English)Conference paper, Published paper (Other academic)
National Category
Botany
Research subject
Natural Science, Cell and Organism Biology
Identifiers
urn:nbn:se:lnu:diva-6084 (URN)
Conference
FESPB 2010 Spain
Available from: 2010-06-12 Created: 2010-06-12 Last updated: 2011-06-13Bibliographically approved
Palovaara, J., Hallberg, H., Stasolla, C. & Hakman, I. (2010). Comparative expression pattern analysis of WUSCHEL-related homeobox 2 (WOX2) and WOX8⁄9 in developing seeds and somatic embryos of the gymnosperm Picea abies. New Phytologist, 188(1), 122-135
Open this publication in new window or tab >>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 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 188, no 1, p. 122-135Article in journal (Refereed) Published
Abstract [en]

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.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Keywords
archegonia, conifer, in situ hybridization, N-1-naphthylphthalamic acid (NPA), PCR, polar auxin transport (PAT), rocambium, transcription factor
National Category
Botany
Research subject
Natural Science, Cell and Organism Biology
Identifiers
urn:nbn:se:hik:diva-2929 (URN)10.1111/j.1469-8137.2010.03336.x (DOI)2-s2.0-77956295063 (Scopus ID)
Available from: 2010-03-01 Created: 2010-03-01 Last updated: 2017-12-12Bibliographically approved
Palovaara, J. (2010). Conifer embryology: a study of polar auxin transport and WOX transcription factors. (Doctoral dissertation). Kalmar/Växjö: Linnaeus University Press
Open this publication in new window or tab >>Conifer embryology: a study of polar auxin transport and WOX transcription factors
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Place, publisher, year, edition, pages
Kalmar/Växjö: Linnaeus University Press, 2010
Series
Linnaeus University Dissertations ; 10/2010
National Category
Botany
Research subject
Natural Science, Cell and Organism Biology
Identifiers
urn:nbn:se:hik:diva-2932 (URN)978-91-86491-12-3 (ISBN)
Public defence
2010-04-16, Hörsalen Fullrigaren, Landgången 4, Kalmar, 09:30 (English)
Opponent
Supervisors
Available from: 2010-04-09 Created: 2010-03-01 Last updated: 2014-05-12Bibliographically approved
Palovaara, J., Hallberg, H., Stasolla, C., Luit, B. & Hakman, I. (2010). Expression of a gymnosperm PIN homologous gene correlates with auxin immunolocalization pattern at cotyledon formation and in demarcation of the procambium during Picea abies somatic embryo development and in seedling tissues. Tree Physiology, 30(4), 479-489
Open this publication in new window or tab >>Expression of a gymnosperm PIN homologous gene correlates with auxin immunolocalization pattern at cotyledon formation and in demarcation of the procambium during Picea abies somatic embryo development and in seedling tissues
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2010 (English)In: Tree Physiology, ISSN 0829-318X, E-ISSN 1758-4469, Vol. 30, no 4, p. 479-489Article in journal (Refereed) Published
Abstract [en]

In seed plants, the body organization is established during embryogenesis and is uniform across gymnosperms and angiosperms, despite differences during early embryogeny. Evidence from angiosperms implicates the plant hormone auxin and its polar transport, mainly established by the PIN family of auxin efflux transporters, in the patterning of embryos. Here, PaPIN1 from Norway spruce (Picea abies [L.] Karst.), a gene widely expressed in conifer tissues and organs, was characterized and its expression and localization patterns were determined with reverse transcription polymerase chain reaction and in situ hybridization during somatic embryo development and in seedlings. PaPIN1 shares the predicted structure of other PIN proteins, but its central hydrophilic loop is longer than most PINs. In phylogenetic analyses, PaPIN1 clusters with Arabidopsis thaliana (L.) Heynh. PIN3, PIN4 and PIN7, but its expression pattern also suggests similarity to PIN1. The PaPIN1 expression signal was high in the protoderm of pre-cotyledonary embryos, but not if embryos were pre-treated with the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). This, together with a high auxin immunolocalization signal in this cell layer, suggests a role of PaPIN1 during cotyledon formation. At later stages, high PaPIN1 expression was observed in differentiating procambium, running from the tip of incipient cotyledons down through the embryo axis and to the root apical meristem (RAM), although the mode of RAM specification in conifer embryos differs from that of most angiosperms. Also, the PaPIN1 in situ signal was high in seedling root tips including root cap columella cells. The results thus suggest that PaPIN1 provides an ancient function associated with auxin transport and embryo pattern formation prior to the separation of angiosperms and gymnosperms, in spite of some morphological differences.

Place, publisher, year, edition, pages
Oxford University Press, 2010
Keywords
conifer, embryo patterning, in situ hybridization, meristem, NPA, polar auxin transport (PAT), protoderm, RT-PCR
National Category
Botany
Research subject
Natural Science, Cell and Organism Biology
Identifiers
urn:nbn:se:hik:diva-2928 (URN)10.1093/treephys/tpp126 (DOI)000276305100005 ()2-s2.0-77950538656 (Scopus ID)
Available from: 2010-03-01 Created: 2010-03-01 Last updated: 2017-12-12Bibliographically approved
Palovaara, J., Hallberg, H., Stasolla, C., Luit, B. & Hakman, I. (2009). Expression dynamics of PIN1 and WOX genes during Norway spruce (Picea abies) somatic embryogenesis.. In: . Paper presented at Joint Annual Meetings of the American Society of Plant Biologists and the Phycological Society of America, July 18-22, 2009 Hawaii, USA..
Open this publication in new window or tab >>Expression dynamics of PIN1 and WOX genes during Norway spruce (Picea abies) somatic embryogenesis.
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2009 (English)Conference paper, Published paper (Other academic)
National Category
Biological Sciences
Research subject
Natural Science, Cell and Organism Biology
Identifiers
urn:nbn:se:lnu:diva-5342 (URN)
Conference
Joint Annual Meetings of the American Society of Plant Biologists and the Phycological Society of America, July 18-22, 2009 Hawaii, USA.
Available from: 2010-04-29 Created: 2010-04-29 Last updated: 2012-07-27Bibliographically approved
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