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  • 1.
    Urbina, Hector
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Purdue Univ, Dept Bot & Plant Pathol, 915 W State St, W Lafayette, IN 47907 USA.
    Breed, Martin F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Adelaide, Sch Biol Sci, North Terrace, SA 5005, Australia;Univ Adelaide, Environm Inst, North Terrace, SA 5005, Australia.
    Zhao, Weizhou
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Gurrala, Kanaka Lakshmi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Andersson, Siv G.E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere2018In: Fungal Biology, ISSN 1878-6146, E-ISSN 1878-6162, Vol. 122, no 4, p. 231-240Article in journal (Refereed)
    Abstract [en]

    Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endo-sphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.

  • 2.
    Zaremba-Niedzwiedzka, Katarzyna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Viklund, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Zhao, Weizhou
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ast, Jennifer
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Scandinavian Languages.
    Sczyrba, Alexander
    Woyke, Tanja
    McMahon, Katherina
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Stepanauskas, Ramunas
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade2013In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 14, no 11, article id R130Article in journal (Refereed)
    Abstract [en]

    Background: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt-and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. Results: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. Conclusions: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.

  • 3.
    Zhao, Weizhou
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Evolution of streamlined genomes in ultra-small aquatic bacteria2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis investigates the evolutionary processes of streamlined genomes from aquatic bacteria adapting to different salinities, using two groups of ultra-small aquatic bacteria (LD12 Alphaproteobacteria and acI Actinobacteria). Due to difficulties in obtaining pure cultures of these bacteria, culture-free approaches (single-cell genomics and metagenomics) were used to construct and compare genomes, and to study the mechanisms and selective forces of adaptation to freshwater, brackish, and marine ecosystems.

    A study of single-cell amplified genomes (SAGs) from freshwater LD12 Alphaproteobacteria revealed that LD12 forms a clade embedded within the globally dominant marine Alphaproteobacteria SAR11, and subclades were organized into distinct microclusters. LD12 genomes had a very low ratio of recombination to point mutations, in contrast to their marine relatives which had a very high ratio of recombination to mutation. We suggested that the transition from marine to freshwater was a bottleneck event, resulting in reduced opportunities for recombination.

    In a separate study, we analyzed complete genomes and SAGs from acI Actinobacteria abundant in freshwater ecosystems, and found overall low rates of sequence divergence with however a dramatic acceleration near genomic island 1 (GI-1). We also identified a type IV topoisomerase, the delta subunit of DNA polymerase, and an RNA polymerase sigma factor near GI-1. Based on these results, we proposed a model for the evolution and expression of novel genes in these genomes.

    We also isolated and analyzed the genomes of single cells from a marine Actinobacteria (subclass Candidatus Actinomarinidae). These were not related to acI, but to Acidimicrobiia, which suggested salinity barriers have been crossed several times by Actinobacteria.

    To further understand the transition to different salinities, we obtained acI SAGs from three different intermediate-salinity Baltic Sea locations. We took sequence reads from 21 metagenomes taken along the salinity gradient, and recruited these fragments to both the freshwater and brackish acI reference genomes. These results indicated that transitions between fresh and brackish waters have occurred multiple times in acI Actinobacteria and some of these strains are globally present in coastal waters.

    List of papers
    1. Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade
    Open this publication in new window or tab >>Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade
    Show others...
    2013 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 14, no 11, article id R130Article in journal (Refereed) Published
    Abstract [en]

    Background: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt-and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. Results: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. Conclusions: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.

    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-206203 (URN)10.1186/gb-2013-14-11-r130 (DOI)000330616200009 ()24286338 (PubMedID)
    Funder
    Swedish Research Council, 349-2007-831 621-2008-3259 621-2011-4669-4669 2009-3784 2008-1923 2012-3892EU, European Research CouncilGöran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyKnut and Alice Wallenberg Foundation, KAW-2011.0148 KAW-2012.0075Swedish National Infrastructure for Computing (SNIC), p2006019 p2009043
    Available from: 2013-09-03 Created: 2013-08-29 Last updated: 2019-09-20Bibliographically approved
    2. Rapid diversification of functional homologs in replacement genomic islands of freshwater Actinobacteria
    Open this publication in new window or tab >>Rapid diversification of functional homologs in replacement genomic islands of freshwater Actinobacteria
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-393357 (URN)
    Available from: 2019-09-19 Created: 2019-09-19 Last updated: 2019-09-26
    3. Evolution of subclass Candidatus Actinomarinidae inferred from single-cell amplified genomes of saltwater Actinobacteria
    Open this publication in new window or tab >>Evolution of subclass Candidatus Actinomarinidae inferred from single-cell amplified genomes of saltwater Actinobacteria
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-393359 (URN)
    Available from: 2019-09-19 Created: 2019-09-19 Last updated: 2019-09-23
    4. A phylometagenomic study based on single-cell amplified genomes from Actinobacteria in the brackish waters of the Baltic Sea
    Open this publication in new window or tab >>A phylometagenomic study based on single-cell amplified genomes from Actinobacteria in the brackish waters of the Baltic Sea
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-393361 (URN)
    Available from: 2019-09-19 Created: 2019-09-19 Last updated: 2019-09-26
  • 4.
    Zhao, Weizhou
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Single cell genomics of deep ocean bacteria2014In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 22, no 5, p. 233-234Article in journal (Other academic)
    Abstract [en]

    SAR11 is one of the most abundant bacterioplanktons in the upper surface waters of the oceans. In a recent issue of The ISME Journal, Thrash and colleagues present the genomes of four single SAR11 cells isolated from the deep oceans that are enriched in genes for membrane biosynthetic functions.

  • 5.
    Zhao, Weizhou
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Garcia, Sarahi L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Siv G.E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rapid diversification of functional homologs in replacement genomic islands of freshwater ActinobacteriaManuscript (preprint) (Other academic)
  • 6.
    Zhao, Weizhou
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Garcia, Sarahi L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Evolution of subclass Candidatus Actinomarinidae inferred from single-cell amplified genomes of saltwater ActinobacteriaManuscript (preprint) (Other academic)
  • 7.
    Zhao, Weizhou
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Garcia, Sarahi L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Grossart, Hans-Peter
    Leibniz Institute for Freshwater Ecology and Inland Fisheries.
    Wannicke, Nicola
    Leib­niz In­sti­tu­te for Plas­ma Sci­ence and Tech­no­lo­gy.
    McMahon, Katherine D
    Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin, Madison.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    A phylometagenomic study based on single-cell amplified genomes from Actinobacteria in the brackish waters of the Baltic SeaManuscript (preprint) (Other academic)
1 - 7 of 7
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