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  • 1. Abrahamsson, T. R.
    et al.
    Jakobsson, H. E.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Björkstén, B.
    Engstrand, Lars
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Jenmalm, M. C.
    Low gut microbiota diversity in early infancy precedes asthma at school age2014In: Clinical and Experimental Allergy, ISSN 0954-7894, E-ISSN 1365-2222, Vol. 44, no 6, p. 842-850Article in journal (Refereed)
    Abstract [en]

    Background Low total diversity of the gut microbiota during the first year of life is associated with allergic diseases in infancy, but little is known how early microbial diversity is related to allergic disease later in school age. Objective To assess microbial diversity and characterize the dominant bacteria in stool during the first year of life in relation to the prevalence of different allergic diseases in school age, such as asthma, allergic rhinoconjunctivitis (ARC) and eczema. Methods The microbial diversity and composition was analysed with barcoded 16S rDNA 454 pyrosequencing in stool samples at 1week, 1month and 12months of age in 47 infants which were subsequently assessed for allergic disease and skin prick test reactivity at 7years of age (ClinicalTrials.gov ID NCT01285830). Results Children developing asthma (n=8) had a lower diversity of the total microbiota than non-asthmatic children at 1week (P=0.04) and 1month (P=0.003) of age, whereas allergic rhinoconjunctivitis (n=13), eczema (n=12) and positive skin prick reactivity (n=14) at 7years of age did not associate with the gut microbiota diversity. Neither was asthma associated with the microbiota composition later in infancy (at 12months). Children having IgE-associated eczema in infancy and subsequently developing asthma had lower microbial diversity than those that did not. There were no significant differences, however, in relative abundance of bacterial phyla and genera between children with or without allergic disease. Conclusion and Clinical Relevance Low total diversity of the gut microbiota during the first month of life was associated with asthma but not ARC in children at 7years of age. Measures affecting microbial colonization of the infant during the first month of life may impact asthma development in childhood.

  • 2. Abrahamsson, Thomas R.
    et al.
    Jakobsson, Hedvig E.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Björksten, Bengt
    Engstrand, Lars
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Jenmalm, Maria C.
    Gut microbiota diversity and atopic disease: Does breast-feeding play a role? Reply2013In: Journal of Allergy and Clinical Immunology, ISSN 0091-6749, E-ISSN 1097-6825, Vol. 131, no 1, p. 248-249Article in journal (Other academic)
  • 3. Abrahamsson, Thomas R.
    et al.
    Jakobsson, Hedvig E.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Björkstén, Bengt
    Engstrand, Lars
    Jenmalm, Maria C.
    Low diversity of the gut microbiota in infants with atopic eczema2012In: Journal of Allergy and Clinical Immunology, ISSN 0091-6749, E-ISSN 1097-6825, Vol. 129, no 2, p. 434-U244Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: It is debated whether a low total diversity of the gut microbiota in early childhood is more important than an altered prevalence of particular bacterial species for the increasing incidence of allergic disease. The advent of powerful, cultivation-free molecular methods makes it possible to characterize the total microbiome down to the genus level in large cohorts. OBJECTIVE: We sought to assess microbial diversity and characterize the dominant bacteria in stool during the first year of life in relation to atopic eczema development. METHODS: Microbial diversity and composition were analyzed with barcoded 16S rDNA 454-pyrosequencing in stool samples at 1 week, 1 month, and 12 months of age in 20 infants with IgE-associated eczema and 20 infants without any allergic manifestation until 2 years of age (ClinicalTrials.gov ID NCT01285830). RESULTS: Infants with IgE-associated eczema had a lower diversity of the total microbiota at 1 month (P= .004) and a lower diversity of the bacterial phylum Bacteroidetes and the genus Bacteroides at 1 month (P= .02 and P= .01) and the phylum Proteobacteria at 12 months of age (P= .02). The microbiota was less uniform at 1 month than at 12 months of age, with a high interindividual variability. At 12 months, when the microbiota had stabilized, Proteobacteria, comprising gram-negative organisms, were more abundant in infants without allergic manifestation (Empirical Analysis of Digital Gene Expression in R edgeR test: P= .008, q= 0.02). CONCLUSION: Low intestinal microbial diversity during the first month of life was associated with subsequent atopic eczema.

  • 4. Ahmed, Engy
    et al.
    Hugerth, Luisa W.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Logue, Jürg Brendan
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bruchert, Volker
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Holmström, Sara J. M.
    Mineral Type Structures Soil Microbial Communities2017In: Geomicrobiology Journal, ISSN 0149-0451, E-ISSN 1521-0529, Vol. 34, no 6, p. 538-545Article in journal (Refereed)
    Abstract [en]

    Soil microorganisms living in close contact with minerals play key roles in the biogeochemical cycling of elements, soil formation, and plant nutrition. Yet, the composition of microbial communities inhabiting the mineralosphere (i.e., the soil surrounding minerals) is poorly understood. Here, we explored the composition of soil microbial communities associated with different types of minerals in various soil horizons. To this effect, a field experiment was set up in which mineral specimens of apatite, biotite, and oligoclase were buried in the organic, eluvial, and upper illuvial horizons of a podzol soil. After an incubation period of two years, the soil attached to the mineral surfaces was collected, and microbial communities were analyzed by means of Illumina MiSeq sequencing of the 16S (prokaryotic) and 18S (eukaryotic) ribosomal RNA genes. We found that both composition and diversity of bacterial, archaeal, and fungal communities varied across the different mineral surfaces, and that mineral type had a greater influence on structuring microbial assemblages than soil horizon. Thus, our findings emphasize the importance of mineral surfaces as ecological niches in soils.

  • 5.
    Alneberg, Johannes
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Bennke, Christin
    Leibniz Inst Balt Sea Res, Warnemunde, Germany..
    Beier, Sara
    Leibniz Inst Balt Sea Res, Warnemunde, Germany.;Sorbonne Univ, CNRS, Lab Oceanog Microbienne, LOMIC, Banyuls Sur Mer, France..
    Bunse, Carina
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.;Carl von Ossietzky Univ Oldenburg, HIFMB, Oldenburg, Germany.;Helmholtz Zentrum Polar & Meeresforsch, Alfred Wegener Inst, Bremerhaven, Germany..
    Quince, Christopher
    Univ Warwick, Warwick Med Sch, Coventry, W Midlands, England..
    Ininbergs, Karolina
    Stockholm Univ, Dept Ecol Environm & Plant Sci, Stockholm, Sweden.;Karolinska Inst, Dept Lab Med, Stockholm, Sweden..
    Riemann, Lasse
    Univ Copenhagen, Marine Biol Sect, Dept Biol, Helsingor, Denmark..
    Ekman, Martin
    Stockholm Univ, Dept Ecol Environm & Plant Sci, Stockholm, Sweden..
    Juergens, Klaus
    Leibniz Inst Balt Sea Res, Warnemunde, Germany..
    Labrenz, Matthias
    Leibniz Inst Balt Sea Res, Warnemunde, Germany..
    Pinhassi, Jarone
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden..
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes2020In: Communications Biology, E-ISSN 2399-3642, Vol. 3, no 1, article id 119Article in journal (Refereed)
    Abstract [en]

    Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes. The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.

  • 6.
    Alneberg, Johannes
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Bennke, Christin
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Beier, Sara
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Pinhassi, Jarone
    Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Jürgens, Klaus
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Ekman, Martin
    Department of Ecology, Environment and Plant Sciences, Stockholm University Science for Life Laboratory, Solna, Sweden.
    Ininbergs, Karolina
    Department of Ecology, Environment and Plant Sciences, Stockholm University Science for Life Laboratory, Solna, Sweden.
    Labrenz, Matthias
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binningManuscript (preprint) (Other academic)
    Abstract [en]

    Aquatic microorganism are key drivers of global biogeochemical cycles and form the basis of aquatic food webs. However, there is still much left to be learned about these organisms and their interaction within specific environments, such as the Baltic Sea. Crucial information for such an understanding can be found within the genome sequences of organisms within the microbial community.

    In this study, the previous set of Baltic Sea clusters, constructed by Hugert et al., is greatly expanded using a large set of metagenomic samples, spanning the environmental gradients of the Baltic Sea. In total, 124 samples were individually assembled and binned to obtain 2,032 Metagenome Assembled Genomes (MAGs), clustered into 353 prokaryotic and 14 eukaryotic species- level clusters. The prokaryotic genomes were widely distributed over the prokaryotic tree of life, representing 20 different phyla, while the eukaryotic genomes were mostly limited to the division of Chlorophyta. The large number of reconstructed genomes allowed us to identify key factors determining the quality of the genome reconstructions.

    The Baltic Sea is heavily influenced of human activities of which we might not see the full implications. The genomes reported within this study will greatly aid further studies in our strive for an understanding of the Baltic Sea microbial ecosystem.

  • 7.
    Alneberg, Johannes
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bjarnason, Brynjar Smári
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    de Bruijn, Ino
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Bioinformatics Infrastructure for Life Sciences (BILS), Sweden.
    Schirmer, Melanie
    Quick, Joshua
    Ijaz, Umer Z.
    Lahti, Leo
    Loman, Nicholas J.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Quince, Christopher
    Binning metagenomic contigs by coverage and composition2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 11, p. 1144-1146Article in journal (Refereed)
    Abstract [en]

    Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets.

  • 8.
    Alneberg, Johannes
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Karlsson, Christofer M. G.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden..
    Divne, Anna-Maria
    Uppsala Univ, Dept Cell & Mol Biol, SciLifeLab, Uppsala, Sweden..
    Bergin, Claudia
    Uppsala Univ, Dept Cell & Mol Biol, SciLifeLab, Uppsala, Sweden..
    Homa, Felix
    Uppsala Univ, Dept Cell & Mol Biol, SciLifeLab, Uppsala, Sweden..
    Lindh, Markus V.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden.;Lund Univ, Dept Biol, Lund, Sweden..
    Hugerth, Luisa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala Univ, Dept Cell & Mol Biol, SciLifeLab, Uppsala, Sweden..
    Bertilsson, Stefan
    Uppsala Univ, Dept Ecol & Genet, Sci Life Lab, Limnol, Uppsala, Sweden..
    Andersson, Anders F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pinhassi, Jarone
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden..
    Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes2018In: Microbiome, E-ISSN 2049-2618, Vol. 6, article id 173Article in journal (Refereed)
    Abstract [en]

    Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

  • 9.
    Alneberg, Johannes
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Karlsson, Christofer M.G.
    Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 391 82 Kalmar, Sweden.
    Divne, Anna-Maria
    Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden .
    Bergin, Claudia
    Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden .
    Homa, Felix
    Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden .
    Lindh, Markus V.
    Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 391 82 Kalmar, Sweden.
    Hugerth, Luisa W.
    Karolinska Institutet, Science for Life Laboratory, Department of Molecular, Tumour and Cell Biology, Centre for Translational Microbiome Research, Solna, Sweden.
    Ettema, Thijs JG
    Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden.
    Bertilsson, Stefan
    Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Pinhassi, Jarone
    Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Barlastgatan 11, 391 82 Kalmar, Sweden.
    Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomesManuscript (preprint) (Other academic)
    Abstract [en]

    Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.

    Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (>98.7% identity) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs; the metagenome assembly was found to cause incompleteness to a higher degree than the binning procedure.

    Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

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  • 10.
    Alneberg, Johannes
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sundh, John
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
    Bennke, Christin
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Beier, Sara
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Lundin, Daniel
    Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Hugerth, Luisa
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Pinhassi, Jarone
    Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Kisand, Veljo
    University of Tartu, Institute of Technology, Tartu, Estonia.
    Riemann, Lasse
    Section for Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
    Jürgens, Klaus
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Labrenz, Matthias
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Andersson, Anders F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic SeaManuscript (preprint) (Other academic)
    Abstract [en]

    The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within microbial ecosystems, but are computationally heavy to perform. We here present the BAltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

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  • 11.
    Alneberg, Johannes
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sundh, John
    Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, S-17165 Solna, Sweden..
    Bennke, Christin
    Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany..
    Beier, Sara
    Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany..
    Lundin, Daniel
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, S-39182 Kalmar, Sweden..
    Hugerth, Luisa W.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska Inst, Dept Mol Tumor & Cell Biol, Ctr Translat Microbiome Res, Sci Life Lab, S-17165 Solna, Sweden..
    Pinhassi, Jarone
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, S-39182 Kalmar, Sweden..
    Kisand, Veljo
    Univ Tartu, Inst Technol, EE-50411 Tartu, Estonia..
    Riemann, Lasse
    Univ Copenhagen, Sect Marine Biol Sect, Dept Biol, DK-3000 Helsingor, Denmark..
    Juergens, Klaus
    Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany..
    Labrenz, Matthias
    Leibniz Inst Balt Sea Res Warnemunde, D-18119 Rostock, Germany..
    Andersson, Anders F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180146Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

  • 12.
    Alonso-Sáez, Laura
    et al.
    Department of Ecology and Genetics, Limnology. Uppsala University. Norbyvägen 18D, SE-75236 Uppsala, Sweden..
    Andersson, Anders
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Ecology and Genetics, Limnology. Uppsala University. Norbyvägen 18D, SE-75236 Uppsala, Sweden..
    Heinrich, Friederike
    Department of Ecology and Genetics, Limnology. Uppsala University. Norbyvägen 18D, SE-75236 Uppsala, Sweden..
    Bertilsson, Stefan
    Department of Ecology and Genetics, Limnology. Uppsala University. Norbyvägen 18D, SE-75236 Uppsala, Sweden..
    High archaeal diversity in Antarctic circumpolar deep waters2011In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 3, no 6, p. 689-697Article in journal (Refereed)
    Abstract [en]

    Archaea are abundant in polar oceans but important ecological aspects of this group remain enigmatic, such as patterns of diversity and biogeography. Here, we provide the first high-throughput sequencing population study of Antarctic archaea based on 198 bp fragments of the 16S rRNA gene, targeting different water masses across the Amundsen and Ross Seas. Our results suggest that archaeal commu- nity composition is strongly shaped by hydrography and significantly influenced by environmental param- eters. Archaeal communities from cold continental shelf waters (SW) of the Ross Sea were similar over depth with a single thaumarchaeal phylotype domi- nating Antarctic surface waters (AASW) and deeper SW (contributing up to 80% of reads). However, this phylotype contributed less than 8% of reads in cir- cumpolar deep waters (CDW). A related thaumar- chaeon (98% identity) was almost absent in AASW, but contributed up to 30% of reads in CDW, suggest- ing ecological differentiation of closely related phylo- types. Significantly higher archaeal richness and evenness were observed in CDW, with Shannon indices (c. 2.5) twice as high as for AASW, and high contributions of Group II Euryarchaeota. Based on these results, we suggest that CDW is a hotspot of archaeal diversity and may play an important role in the dispersal of archaeal phylotypes to other oceanic water masses.

  • 13.
    Andersson, Anders
    KTH, School of Biotechnology (BIO).
    Microarray-based investigation of genome and transcriptome organisation in the archaeon sulfolobus2005Doctoral thesis, comprehensive summary (Other scientific)
  • 14.
    Andersson, Anders
    et al.
    Departments of Earth and Planetary Science and Environmental Science, Policy, and Management, University of California, Berkeley.
    Banfield, J. F.
    Virus population dynamics and acquired virus resistance in natural microbial communities2008In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 320, no 5879, p. 1047-1050Article in journal (Refereed)
    Abstract [en]

    Viruses shape microbial community structure and function by altering the fitness of their hosts and by promoting genetic exchange. The complexity of most natural ecosystems has precluded detailed studies of virus-host interactions. We reconstructed virus and host bacterial and archaeal genome sequences from community genomic data from two natural acidophilic biofilms. Viruses were matched to their hosts by analyzing spacer sequences that occur among clustered regularly interspaced short palindromic repeats (CRISPRs) that are a hallmark of virus resistance. Virus population genomic analyses provided evidence that extensive recombination shuffles sequence motifs sufficiently to evade CRISPR spacers. Only the most recently acquired spacers match coexisting viruses, which suggests that community stability is achieved by rapid but compensatory shifts in host resistance levels and virus population structure.

  • 15.
    Andersson, Anders
    et al.
    KTH, School of Biotechnology (BIO).
    Bernander, R.
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO).
    Dual-genome primer design for construction of DNA microarrays2005In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, no 3, p. 325-332Article in journal (Refereed)
    Abstract [en]

    Motivation: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information. Results: We have developed a method, implemented in the software DualPrime, that reduces the number of primers required to amplify the genes of two different genomes. The software identifies regions of high sequence similarity, and from these regions selects PCR primers shared between the genomes, such that either one or, preferentially, both primers in a given PCR can be used for amplification from both genomes. To assure high microarray probe specificity, the software selects primer pairs that generate products of low sequence similarity to other genes within the same genome. We used the software to design PCR primers for 2182 and 1960 genes from the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. Primer pairs were shared among 705 pairs of genes, and single primers were shared among 1184 pairs of genes, resulting in a saving of 31% compared to using only unique primers. We also present an alternative primer design method, in which each gene shares primers with two different genes of the other genome, enabling further savings.

  • 16.
    Andersson, Anders
    et al.
    KTH, School of Biotechnology (BIO).
    Eriksson, S.
    Nilsson, P.
    Bernander, R.
    Early replicating ridge-like domains in archaeal chromosomesManuscript (preprint) (Other academic)
  • 17.
    Andersson, Anders
    et al.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Keskitalo, J.
    Sjödin, A.
    Bhalerao, Rupali
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Sterky, Fredrik
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Wissel, K.
    Tandre, K.
    Aspeborg, Henrik
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Moyle, R.
    Ohmiya, Y.
    Brunner, A.
    Gustafsson, P.
    Karlsson, J.
    Lundeberg, Joakim
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Nilsson, O.
    Sandberg, G.
    Strauss, S.
    Sundberg, B.
    Uhlén, Mathias
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Jansson, S.
    Nilsson, Peter
    KTH, Superseded Departments (pre-2005), Biotechnology.
    A transcriptional timetable of autumn senescence2004In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 5, no 4, p. R24-Article in journal (Refereed)
    Abstract [en]

    Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

  • 18.
    Andersson, Anders
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lundgren, Magnus
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Eriksson, Stefan
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Rosenlund, Magnus
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.).
    Bernander, Rolf
    Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Global analysis of mRNA stability in the archaeon Sulfolobus2006In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 7, no 10, p. R99-Article in journal (Refereed)
    Abstract [en]

    Background: Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determine the stability of a transcript. To address these issues, genome-wide mRNA decay studies have been conducted in eukaryotes and bacteria. In contrast, relatively little is known about RNA stability in the third domain of life, Archaea. Here, we present a microarray-based analysis of mRNA half-lives in the hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, constituting the first genome-wide study of RNA decay in archaea. Results: The two transcriptomes displayed similar half-life distributions, with medians of about five minutes. Growth-related genes, such as those involved in transcription, translation and energy production, were over-represented among unstable transcripts, whereas uncharacterized genes were over-represented among the most stable. Half-life was negatively correlated with transcript abundance and, unlike the situation in other organisms, also negatively correlated with transcript length. Conclusion: The mRNA half-life distribution of Sulfolobus species is similar to those of much faster growing bacteria, contrasting with the earlier observation that median mRNA half-life is proportional to the minimal length of the cell cycle. Instead, short half-lives may be a general feature of prokaryotic transcriptomes, possibly related to the absence of a nucleus and/or more limited post-transcriptional regulatory mechanisms. The pattern of growth-related transcripts being among the least stable in Sulfolobus may also indicate that the short half-lives reflect a necessity to rapidly reprogram gene expression upon sudden changes in environmental conditions.

  • 19.
    Andersson, Anders
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Pelve, Erik A.
    Lindeberg, Stefan
    Lundgren, Magnus
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Bernander, Rolf
    Replication-biased genome organisation in the crenarchaeon Sulfolobus2010In: BMC Genomics, E-ISSN 1471-2164, Vol. 11, p. 454-Article in journal (Refereed)
    Abstract [en]

    Background: Species of the crenarchaeon Sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. Results: We demonstrate that global gene expression in two Sulfolobus species is highly biased, such that early replicating genome regions are more highly expressed at all three origins. The bias by far exceeds what would be anticipated by gene dosage effects alone. In addition, early replicating regions are denser in archaeal core genes (enriched in essential functions), display lower intergenic distances, and are devoid of mobile genetic elements. Conclusion: The strong replication-biased structuring of the Sulfolobus chromosome implies that the multiple replication origins serve purposes other than simply shortening the time required for replication. The higher-level chromosomal organisation could be of importance for minimizing the impact of DNA damage, and may also be linked to transcriptional regulation.

  • 20.
    Andersson, Anders
    et al.
    Limnology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala. Department of Bacteriology, Swedish Institute for Infectious Disease Control, Solna, Sweden.
    Riemann, L.
    Bertilsson, S
    Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities2010In: ISME JOURNAL, ISSN 1751-7362, Vol. 4, no 2, p. 171-181Article in journal (Refereed)
    Abstract [en]

    Variation in traits causes bacterial populations to respond in contrasting ways to environmental drivers. Learning about this will help us understand the ecology of individual populations in complex ecosystems. We used 454 pyrosequencing of the hypervariable region V6 of the 16S rRNA gene to study seasonal dynamics in Baltic Sea bacterioplankton communities, and link community and population changes to biological and chemical factors. Surface samples were collected from May to October 2003 and in May 2004 at the Landsort Deep in the central Baltic Sea Proper. The analysis rendered, on average, 20 200 sequence reads for each of the eight samples analyzed, providing the first detailed description of Baltic Sea bacterial communities. Community composition varied dramatically over time, supporting the idea of strong temporal shifts in bacterioplankton assemblages, and clustered according to season (including two May samples from consecutive years), suggesting repeatable seasonal succession. Overall, community change was most highly correlated with change in phosphorus concentration and temperature. Individual bacterial populations were also identified that tightly co-varied with different Cyanobacteria populations. Comparing the abundance profiles of operational taxonomic units at different phylogenetic distances revealed a weak but significant negative correlation between abundance profile similarity and genetic distance, potentially reflecting habitat filtering of evolutionarily conserved functional traits in the studied bacterioplankton.

  • 21. Bagnoud, Alexandre
    et al.
    de Bruijn, Ino
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Diomidis, Nikitas
    Leupin, Olivier X.
    Schwyn, Bernhard
    Bernier-Latmani, Rizlan
    A minimalistic microbial food web in an excavated deep subsurface clay rock2016In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 92, no 1, article id UNSP fiv138Article in journal (Refereed)
    Abstract [en]

    Clay rocks are being considered for radioactive waste disposal, but relatively little is known about the impact of microbes on the long-term safety of geological repositories. Thus, a more complete understanding of microbial community structure and function in these environments would provide further detail for the evaluation of the safety of geological disposal of radioactive waste in clay rocks. It would also provide a unique glimpse into a poorly studied deep subsurface microbial ecosystem. Previous studies concluded that microorganisms were present in pristine Opalinus Clay, but inactive. In this work, we describe the microbial community and assess the metabolic activities taking place within borehole water. Metagenomic sequencing and genome-binning of a porewater sample containing suspended clay particles revealed a remarkably simple heterotrophic microbial community, fueled by sedimentary organic carbon, mainly composed of two organisms: a Pseudomonas sp. fermenting bacterium growing on organic macromolecules and releasing organic acids and H-2, and a sulfate-reducing Peptococcaceae able to oxidize organic molecules to CO2. In Opalinus Clay, this microbial system likely thrives where pore space allows it. In a repository, this may occur where the clay rock has been locally damaged by excavation or in engineered backfills.

  • 22. Beier, S.
    et al.
    Andersson, Anders
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Galand, P. E.
    Hochart, C.
    Logue, J. B.
    McMahon, K.
    Bertilsson, S.
    The environment drives microbial trait variability in aquatic habitats2020In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArticle in journal (Refereed)
    Abstract [en]

    A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage–prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.

  • 23. Bell, E.
    et al.
    Lamminmäki, T.
    Alneberg, Johannes
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Qian, C.
    Xiong, W.
    Hettich, R. L.
    Balmer, L.
    Frutschi, M.
    Sommer, G.
    Bernier-Latmani, R.
    Biogeochemical cycling by a low-diversity microbial community in deep groundwater2018In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 9, no SEP, article id 2129Article in journal (Refereed)
    Abstract [en]

    Olkiluoto, an island on the south-west coast of Finland, will host a deep geological repository for the storage of spent nuclear fuel. Microbially induced corrosion from the generation of sulphide is therefore a concern as it could potentially compromise the longevity of the copper waste canisters. Groundwater at Olkiluoto is geochemically stratified with depth and elevated concentrations of sulphide are observed when sulphate-rich and methane-rich groundwaters mix. Particularly high sulphide is observed in methane-rich groundwater from a fracture at 530.6 mbsl, where mixing with sulphate-rich groundwater occurred as the result of an open drill hole connecting two different fractures at different depths. To determine the electron donors fuelling sulphidogenesis, we combined geochemical, isotopic, metagenomic and metaproteomic analyses. This revealed a low diversity microbial community fuelled by hydrogen and organic carbon. Sulphur and carbon isotopes of sulphate and dissolved inorganic carbon, respectively, confirmed that sulphate reduction was ongoing and that CO2 came from the degradation of organic matter. The results demonstrate the impact of introducing sulphate to a methane-rich groundwater with limited electron acceptors and provide insight into extant metabolisms in the terrestrial subsurface. 

  • 24. Bell, E.
    et al.
    Lamminmäki, T.
    Alneberg, Johannes
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Qian, C.
    Xiong, W.
    Hettich, R. L.
    Frutschi, M.
    Bernier-Latmani, R.
    Active sulfur cycling in the terrestrial deep subsurface2020In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 14, no 5, p. 1260-1272Article in journal (Refereed)
    Abstract [en]

    The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. We investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.

  • 25.
    Borgström, Erik
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Redin, David
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundin, Sverker
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Berglund, Emelie
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Phasing of single DNA molecules by massively parallel barcoding2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, article id 7173Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.

  • 26. Brouns, Stan J. J.
    et al.
    Walther, Jasper
    Snijders, Ambrosius P. L.
    de Werken, Harmen J. G. van
    Willemen, Hanneke L. D. M.
    Worm, Petra
    de Vos, Marjon G. J.
    Andersson, Anders
    KTH, School of Biotechnology (BIO), Gene Technology.
    Lundgren, Magnus
    Mazon, Hortense F. M.
    van den Heuvel, Robert H. H.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Salmon, Laurent
    de Vos, Willem M.
    Wright, Phillip C.
    Bernander, Rolf
    van der Oost, John
    Identification of the missing links in prokaryotic pentose oxidation pathways - Evidence for enzyme recruitment2006In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 281, no 37, p. 27378-27388Article in journal (Refereed)
    Abstract [en]

    The pentose metabolism of Archaea is largely unknown. Here, we have employed an integrated genomics approach including DNA microarray and proteomics analyses to elucidate the catabolic pathway for D-arabinose in Sulfolobus solfataricus. During growth on this sugar, a small set of genes appeared to be differentially expressed compared with growth on D-glucose. These genes were heterologously overexpressed in Escherichia coli, and the recombinant proteins were purified and biochemically studied. This showed that D-arabinose is oxidized to 2-oxoglutarate by the consecutive action of a number of previously uncharacterized enzymes, including a D-arabinose dehydrogenase, a D-arabinonate dehydratase, a novel 2-keto-3-deoxy-D-arabinonate dehydratase, and a 2,5-dioxopentanoate dehydrogenase. Promoter analysis of these genes revealed a palindromic sequence upstream of the TATA box, which is likely to be involved in their concerted transcriptional control. Integration of the obtained biochemical data with genomic context analysis strongly suggests the occurrence of pentose oxidation pathways in both Archaea and Bacteria, and predicts the involvement of additional enzyme components. Moreover, it revealed striking genetic similarities between the catabolic pathways for pentoses, hexaric acids, and hydroxyproline degradation, which support the theory of metabolic pathway genesis by enzyme recruitment.

  • 27.
    Capo, Eric
    et al.
    Umeå Univ, Dept Chem, Umeå, Sweden.;Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden..
    Bravo, Andrea G.
    Inst Ciencies Mar ICM CSIC, Barcelona, Spain..
    Soerensen, Anne L.
    Swedish Museum Nat Hist, Dept Environm Res & Monitoring, Stockholm, Sweden..
    Bertilsson, Stefan
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden..
    Pinhassi, Jarone
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden..
    Feng, Caiyan
    Umeå Univ, Dept Chem, Umeå, Sweden..
    Andersson, Anders F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Buck, Moritz
    Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden..
    Björn, Erik
    Umeå Univ, Dept Chem, Umeå, Sweden..
    Deltaproteobacteria and Spirochaetes-Like Bacteria Are Abundant Putative Mercury Methylators in Oxygen-Deficient Water and Marine Particles in the Baltic Sea2020In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 11, article id 574080Article in journal (Refereed)
    Abstract [en]

    Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the composition and distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this knowledge gap, we used the Baltic Sea Reference Metagenome (BARM) dataset to study the abundance and distribution of the genes involved in Hg methylation (thehgcABgene cluster). We determined the relative abundance of thehgcABgenes and their taxonomic identity in 81 brackish metagenomes that cover spatial, seasonal and redox variability in the Baltic Sea water column. ThehgcABgenes were predominantly detected in anoxic water, but somehgcABgenes were also detected in hypoxic and normoxic waters. Phylogenetic analysis identified putative Hg methylators within Deltaproteobacteria, in oxygen-deficient water layers, but also Spirochaetes-like and Kiritimatiellaeota-like bacteria. Higher relative quantities ofhgcABgenes were found in metagenomes from marine particles compared to free-living communities in anoxic water, suggesting that such particles are hotspot habitats for Hg methylators in oxygen-depleted seawater. Altogether, our work unveils the diversity of the microorganisms with the potential to mediate MeHg production in the Baltic Sea and pinpoint the important ecological niches for these microorganisms within the marine water column.

  • 28.
    Charvet, Sophie
    et al.
    IOW Leibniz Inst Balt Sea Res, Warnemunde, Germany..
    Riemann, Lasse
    Univ Copenhagen, Marine Biol Sect, Dept Biol, Copenhagen, Denmark..
    Alneberg, Johannes
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    von Borries, Julian
    HYDRO BIOS Apparatebau GmbH, Altenholz, Germany..
    Fischer, Uwe
    HYDRO BIOS Apparatebau GmbH, Altenholz, Germany..
    Labrenz, Matthias
    IOW Leibniz Inst Balt Sea Res, Warnemunde, Germany..
    AFISsys - An autonomous instrument for the preservation of brackish water samples for microbial metatranscriptome analysis2019In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 149, p. 351-361Article in journal (Refereed)
    Abstract [en]

    Microbial communities are the main drivers of biogeochemical cycling of multiple elements sustaining life in the ocean. The rapidity of their response to stressors and abrupt environmental changes implies that even fast and infrequent events can affect local transformations of organic matter and nutrients. Modern molecular techniques now allow for monitoring of microbial activities and functions in the environment through the analysis of genes and expressed genes contained in natural microbial assemblages. However, messenger RNA turnover in cells can be as short as 30 seconds and stability varies greatly between transcripts. Sampling of in situ communities involves an inevitable delay between the collection of seawater and the extraction of its RNA, leaving the bacterial communities plenty of time to alter their gene expression. The characteristics of microbial RNA turnover make time-series very difficult because samples need to be processed immediately to limit alterations to the metatranscriptomes. To address these challenges we designed an autonomous in situ fixation multi-sampler (AFISsys) for the reliable sampling of microbial metatranscriptomes at frequent intervals, for refined temporal resolution. To advance the development of this instrument, we examined the minimal seawater volume necessary for adequate coverage of community gene expression, and the suitability of phenol/ethanol fixation for immediate and long-term preservation of transcripts from a microbial community. We then evaluated the field eligibility of the instrument itself, with two case studies in a brackish system. AFISsys is able to collect, fix, and store water samples independently at a predefined temporal resolution. Phenol/ethanol fixation can conserve metatranscriptomes directly in the environment for up to a week, for later analysis in the laboratory. Thus, the AFISsys constitutes an invaluable tool for the integration of molecular functional analyses in environmental monitoring in brackish waters and in aquatic environments in general. 

  • 29.
    Delgado, Luis F.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Evaluating metagenomic assembly approaches for biome-specific gene catalogues2022In: Microbiome, E-ISSN 2049-2618, Vol. 10, no 1, article id 72Article in journal (Refereed)
    Abstract [en]

    Background: For many environments, biome-specific microbial gene catalogues are being recovered using shotgun metagenomics followed by assembly and gene calling on the assembled contigs. The assembly is typically conducted either by individually assembling each sample or by co-assembling reads from all the samples. The co-assembly approach can potentially recover genes that display too low abundance to be assembled from individual samples. On the other hand, combining samples increases the risk of mixing data from closely related strains, which can hamper the assembly process. In this respect, assembly on individual samples followed by clustering of (near) identical genes is preferable. Thus, both approaches have potential pros and cons, but it remains to be evaluated which assembly strategy is most effective. Here, we have evaluated three assembly strategies for generating gene catalogues from metagenomes using a dataset of 124 samples from the Baltic Sea: (1) assembly on individual samples followed by clustering of the resulting genes, (2) co-assembly on all samples, and (3) mix assembly, combining individual and co-assembly. Results: The mix-assembly approach resulted in a more extensive nonredundant gene set than the other approaches and with more genes predicted to be complete and that could be functionally annotated.The mix assembly consists of 67 million genes (Baltic Sea gene set, BAGS) that have been functionally and taxonomically annotated. The majority of the BAGS genes are dissimilar (< 95% amino acid identity) to the Tara Oceans gene dataset, and hence, BAGS represents a valuable resource for brackish water research. Conclusion: The mix-assembly approach represents a feasible approach to increase the information obtained from metagenomic samples.

  • 30. Dick, G J
    et al.
    Andersson, Anders
    KTH, School of Biotechnology (BIO), Gene Technology.
    Baker, B J
    Simmons, S L
    Thomas, B C
    Yelton, A P
    Banfield, J F
    Community-wide analysis of microbial genome sequence signatures2009In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 10, no 8, p. R85-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them. RESULTS: We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low-abundance organisms. Genome signatures, in the form of tetranucleotide frequencies analyzed by emergent self-organizing maps, segregated sequences from all known populations sharing < 50 to 60% average amino acid identity and revealed previously unknown genomic clusters corresponding to low-abundance organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters were resolved because intra-genome differences resulting from translational selection or protein adaptation to the intracellular (pH approximately 5) versus extracellular (pH approximately 1) environment were small relative to inter-genome differences. We found that these genome signatures stem from multiple influences but are primarily manifested through codon composition, which we propose is the result of genome-specific mutational biases. CONCLUSIONS: An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities.

  • 31. Dupont, Chris L.
    et al.
    Larsson, John
    Yooseph, Shibu
    Ininbergs, Karolina
    Goll, Johannes
    Asplund-Samuelsson, Johannes
    McCrow, John P.
    Celepli, Narin
    Allen, Lisa Zeigler
    Ekman, Martin
    Lucas, Andrew J.
    Hagström, Åke
    Thiagarajan, Mathangi
    Brindefalk, Björn
    Richter, Alexander R.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Tenney, Aaron
    Lundin, Daniel
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Tovchigrechko, Andrey
    Nylander, Johan A. A.
    Brami, Daniel
    Badger, Jonathan H.
    Allen, Andrew E.
    Rusch, Douglas B.
    Hoffman, Jeff
    Norrby, Erling
    Friedman, Robert
    Pinhassi, Jarone
    Venter, J. Craig
    Bergman, Birgitta
    Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition2014In: PLOS ONE, E-ISSN 1932-6203, Vol. 9, no 2, p. e89549-Article in journal (Refereed)
    Abstract [en]

    Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

  • 32. Edberg, F.
    et al.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Holmström, S. J. M.
    Bacterial Community Composition in the Water Column of a Lake Formed by a Former Uranium Open Pit Mine2012In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 64, no 4, p. 870-880Article in journal (Refereed)
    Abstract [en]

    Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.

  • 33.
    Eriksson, Kaja
    et al.
    Karolinska Inst, Dept Dent Med, Div Periodontol, S-14104 Huddinge, Sweden..
    Fei, Guozhong
    Acad Specialist Ctr, Ctr Rheumatol, Stockholm Hlth Serv, S-10235 Stockholm, Sweden..
    Lundmark, Anna
    Karolinska Inst, Dept Dent Med, Div Periodontol, S-14104 Huddinge, Sweden..
    Benchimol, Daniel
    Karolinska Inst, Dept Dent Med, Div Orofacial Diagnost & Surg Image & Funct Odont, S-14104 Huddinge, Sweden..
    Lee, Linkiat
    Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, 14104, Sweden.
    Hu, Yue O. O.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Kats, Anna
    Karolinska Inst, Dept Dent Med, Div Periodontol, S-14104 Huddinge, Sweden..
    Saevarsdottir, Saedis
    Karolinska Univ Hosp, Dept Med, Rheumatol Unit, S-17176 Stockholm, Sweden..
    Catrina, Anca Irinel
    Karolinska Univ Hosp, Dept Med, Rheumatol Unit, S-17176 Stockholm, Sweden..
    Klinge, Bjorn
    Karolinska Inst, Dept Dent Med, Div Periodontol, S-14104 Huddinge, Sweden.;Malmö Univ, Fac Odontol, Dept Periodontol, S-20506 Malmö, Sweden..
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Klareskog, Lars
    Karolinska Univ Hosp, Dept Med, Rheumatol Unit, S-17176 Stockholm, Sweden..
    Lundberg, Karin
    Karolinska Univ Hosp, Dept Med, Rheumatol Unit, S-17176 Stockholm, Sweden..
    Jansson, Leif
    Karolinska Inst, Dept Dent Med, Div Periodontol, S-14104 Huddinge, Sweden.;Stockholm Cty Council, Eastmaninst, Dept Periodontol, S-11382 Stockholm, Sweden..
    Yucel-Lindberg, Tulay
    Karolinska Inst, Dept Dent Med, Div Periodontol, S-14104 Huddinge, Sweden..
    Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis2019In: Journal of Clinical Medicine, E-ISSN 2077-0383, Vol. 8, no 5, article id 630Article in journal (Refereed)
    Abstract [en]

    This study aimed to investigate the periodontal health of patients with established rheumatoid arthritis (RA) in relation to oral microbiota, systemic and oral inflammatory mediators, and RA disease activity. Forty patients underwent full-mouth dental/periodontal and rheumatological examination, including collection of blood, saliva, gingival crevicular fluid (GCF) and subgingival plaque. Composition of plaque and saliva microbiota were analysed using 16S rRNA sequencing and levels of inflammatory mediators by multiplex-immunoassay. The majority of the patients (75%) had moderate or severe periodontitis and the rest had no/mild periodontitis. Anti-citrullinated protein antibody (ACPA) positivity was significantly more frequent in the moderate/severe periodontitis (86%) compared to the no/mild group (50%). No significance between groups was observed for RA disease duration or activity, or type of medication. Levels of sCD30/TNFRSF8, IFN-2, IL-19, IL-26, MMP-1, gp130/sIL-6R ss, and sTNF-R1 were significantly higher in serum or GCF, and April/TNFSF13 was significantly higher in serum and saliva samples in moderate/severe periodontitis. The microbial composition in plaque also differed significantly between the two groups. In conclusion, the majority of RA patients had moderate/severe periodontitis and that this severe form of the disease was significantly associated with ACPA positivity, an altered subgingival microbial profile, and increased levels of systemic and oral inflammatory mediators.

  • 34.
    Eriksson, Kaja
    et al.
    Karolinska Inst, Dept Dent Med, Div Pediat Dent, Huddinge, Sweden..
    Lundmark, Anna
    Karolinska Inst, Dept Dent Med, Div Pediat Dent, Huddinge, Sweden..
    Delgado, Luis F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. lfdz@kth.se.
    Hu, Yue O. O.
    Karolinska Inst, Ctr Translat Microbiome Res, Dept Microbiol Tumor & Cell Biol, Stockholm, Sweden..
    Fei, Guozhong
    Stockholm Hlth Reg, Acad Specialist Ctr, Ctr Rheumatol, Stockholm, Sweden..
    Lee, Linkiat
    Karolinska Inst, Dept Dent Med, Div Pediat Dent, Huddinge, Sweden..
    Fei, Carina
    Karolinska Inst, Dept Dent Med, Div Pediat Dent, Huddinge, Sweden..
    Catrina, Anca I.
    Karolinska Univ Hosp, Rheumatol Clin, Stockholm, Sweden..
    Jansson, Leif
    Karolinska Inst, Dept Dent Med, Div Periodontol, Huddinge, Sweden.;Folktandvarden Eastmaninst, Folktandvarden Stockholms lan AB, Dept Periodontol, Stockholm, Sweden..
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Yucel-Lindberg, Tuelay
    Karolinska Inst, Dept Dent Med, Div Pediat Dent, Huddinge, Sweden..
    Salivary Microbiota and Host-Inflammatory Responses in Periodontitis Affected Individuals With and Without Rheumatoid Arthritis2022In: Frontiers in Cellular and Infection Microbiology, E-ISSN 2235-2988, Vol. 12, article id 841139Article in journal (Refereed)
    Abstract [en]

    ObjectivesPeriodontitis and rheumatoid arthritis (RA) are two widespread chronic inflammatory diseases with a previously suggested association. The objective of the current study was to compare the oral microbial composition and host ' s inflammatory mediator profile of saliva samples obtained from subjects with periodontitis, with and without RA, as well as to predict biomarkers, of bacterial pathogens and/or inflammatory mediators, for classification of samples associated with periodontitis and RA. MethodsSalivary samples were obtained from 53 patients with periodontitis and RA and 48 non-RA with chronic periodontitis. The microbial composition was identified using 16S rRNA gene sequencing and compared across periodontitis patients with and without RA. Levels of inflammatory mediators were determined using a multiplex bead assay, compared between the groups and correlated to the microbial profile. The achieved data was analysed using PCoA, DESeq2 and two machine learning algorithms, OPLS-DA and sPLS-DA. ResultsDifferential abundance DESeq2 analyses showed that the four most highly enriched (log2 FC >20) amplicon sequence variants (ASVs) in the non-RA periodontitis group included Alloprevotella sp., Prevotella sp., Haemophilus sp., and Actinomyces sp. whereas Granulicatella sp., Veillonella sp., Megasphaera sp., and Fusobacterium nucleatum were the most highly enriched ASVs (log2 FC >20) in the RA group. OPLS-DA with log2 FC analyses demonstrated that the top ASVs with the highest importance included Vampirovibrio sp. having a positive correlation with non-RA group, and seven ASVs belonging to Sphingomonas insulae, Sphingobium sp., Novosphingobium aromaticivorans, Delftia acidovorans, Aquabacterium spp. and Sphingomonas echinoides with a positive correlation with RA group. Among the detected inflammatory mediators in saliva samples, TWEAK/TNFSF12, IL-35, IFN-alpha 2, pentraxin-3, gp130/sIL6Rb, sIL-6Ra, IL-19 and sTNF-R1 were found to be significantly increased in patients with periodontitis and RA compared to non-RA group with periodontitis. Moreover, correlations between ASVs and inflammatory mediators using sPLS-DA analysis revealed that TWEAK/TNFSF12, pentraxin-3 and IL-19 were positively correlated with the ASVs Sphingobium sp., Acidovorax delafieldii, Novosphingobium sp., and Aquabacterium sp. ConclusionOur results suggest that the combination of microbes and host inflammatory mediators could be more efficient to be used as a predictable biomarker associated with periodontitis and RA, as compared to microbes and inflammatory mediators alone.

  • 35. Ettema, Thijs J. G.
    et al.
    Lindas, Ann-Christin
    Hjort, Karin
    Poplawski, Andrzej B.
    Kaessmann, Henrik
    Grogan, Dennis W.
    Kelman, Zvi
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pelve, Erik
    Lundgren, Magnus
    Svard, Staffan G.
    Rolf Bernander (1956-2014): pioneer of the archaeal cell cycle (vol 92, pg 903, 2014)2014In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 93, no 3, p. 582-582Article in journal (Refereed)
  • 36. Ettema, Thijs J. G.
    et al.
    Lindås, Ann-Christin
    Hjort, Karin
    Poplawski, Andrzej B.
    Kaessmann, Henrik
    Grogan, Dennis W.
    Kelman, Zvi
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Pelve, Erik A.
    Lundgren, Magnus
    Svard, Staffan G.
    Rolf Bernander (1956-2014): pioneer of the archaeal cell cycle Obituary2014In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 92, no 5, p. 903-909Article in journal (Refereed)
    Abstract [en]

    On 19 January 2014 Rolf (Roffe') Bernander passed away unexpectedly. Rolf was a dedicated scientist; his research aimed at unravelling the cell biology of the archaeal domain of life, especially cell cycle-related questions, but he also made important contributions in other areas of microbiology. Rolf had a professor position in the Molecular Evolution programme at Uppsala University, Sweden for about 8 years, and in January 2013 he became chair professor at the Department of Molecular Biosciences, The Wenner-Gren Institute at Stockholm University in Sweden. Rolf was an exceptional colleague and will be deeply missed by his family and friends, and the colleagues and co-workers that he leaves behind in the scientific community. He will be remembered for his endless enthusiasm for science, his analytical mind, and his quirky sense of humour.

  • 37. Farnelid, Hanna
    et al.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Abu Al-Soud, Waleed
    Hansen, Lars H.
    Sørensen, Søren
    Steward, Grieg F.
    Hagstöom, Åke
    Riemann, Lasse
    Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria2011In: PLOS ONE, ISSN 1932-6203, Vol. 6, no 4, p. e19223-Article in journal (Refereed)
    Abstract [en]

    Cyanobacteria are thought to be the main N-2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations worldwide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N-2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.

  • 38. Farnelid, Hanna
    et al.
    Bentzon-Tilia, Mikkel
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Jost, Guenter
    Labrenz, Matthias
    Juergens, Klaus
    Riemann, Lasse
    Active nitrogen-fixing heterotrophic bacteria at and below the chemocline of the central Baltic Sea2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 7, p. 1413-1423Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea receives large nitrogen inputs by diazotrophic (N-2-fixing) heterocystous cyanobacteria but the significance of heterotrophic N-2 fixation has not been studied. Here, the diversity, abundance and transcription of the nifH fragment of the nitrogenase enzyme in two basins of the Baltic Sea proper was examined. N-2 fixation was measured at the surface (5 m) and in anoxic water (200 m). Vertical sampling profiles of >10 and <10 mu m size fractions were collected in 2007, 2008 and 2011 at the Gotland Deep and in 2011 in the Bornholm Basin. Both of these stations are characterized by permanently anoxic bottom water. The 454-pyrosequencing nifH analysis revealed a diverse assemblage of nifH genes related to alpha-, beta- and gammaproteobacteria (nifH cluster I) and anaerobic bacteria (nifH cluster III) at and below the chemocline. Abundances of genes and transcripts of seven diazotrophic phylotypes were investigated using quantitative polymerase chain reaction revealing abundances of heterotrophic nifH phylotypes of up to 2.1 x 10(7) nifH copies l(-1). Abundant nifH transcripts (up to 3.2 x 10(4) transcripts l(-1)) within nifH cluster III and co-occurring N-2 fixation (0.44 +/- 0.26 nmol l(-1) day(-1)) in deep water suggests that heterotrophic diazotrophs are fixing N2 in anoxic ammonium-rich waters. Our results reveal that N-2 fixation in the Baltic Sea is not limited to illuminated N-deplete surface waters and suggest that N-2 fixation could also be of importance in other suboxic regions of the world's oceans.

  • 39.
    Ferro, Lorenza
    et al.
    Umeå Univ, Dept Chem, S-90187 Umeå, Sweden..
    Hu, Yue O. O.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. Karolinska Inst, Dept Microbiol Tumor & Cell Biol, Stockholm, Sweden..
    Gentili, Francesco G.
    Swedish Univ Agr Sci, Dept Forest Biomat & Technol, S-90183 Umeå, Sweden..
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Funk, Christiane
    Umeå Univ, Dept Chem, S-90187 Umeå, Sweden..
    DNA metabarcoding reveals microbial community dynamics in a microalgae-based municipal wastewater treatment open photobioreactor2020In: Algal Research, ISSN 2211-9264, Vol. 51, article id 102043Article in journal (Refereed)
    Abstract [en]

    Controlling the growth of desired algal strains in microalgal-based wastewater treatment systems is challenging, and understanding the dynamics and interactions in the system is vital for proper management. A pilot-scale open photobioreactor located in Northern Sweden, was inoculated with the culture collection strain Scenedesmus dimorphus UTEX 417, which had been grown in Nordic climate for 8 years. The microbial diversity of eukaryotic and prokaryotic communities and their seasonal dynamics were revealed throughout the growth period by high-throughput sequencing of 18S and 16S rRNA genes and correlated with various environmental factors. S. dimorphus was stable in batch culture, but other microalgae appeared during semi-batch mode and co-dominated the system as a consequence of predation by zooplankton. Desmodesmus, Pseudocharaciopsis, Chlorella, Characium and Oocystis were the main microalgal species co-occurring in the system, with Characium and Chlorella acting as main competitors to Scenedesmus. Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundant bacterial phyla, some of which showing significant positive or negative influence on Scenedesmus growth over time. Light, temperature, dissolved oxygen, pH and nutrients concentrations were found to have significant influence on the bacterial and/or zooplanktonic community changes.

  • 40. Gantner, S
    et al.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Alonso-Saez, L
    Bertilsson, S
    Novel primers for 16S rRNA-based archaeal community analyses in environmental samples2011In: Journal of Microbiological Methods, ISSN 0167-7012, E-ISSN 1872-8359, Vol. 84, no 1, p. 12-18Article in journal (Refereed)
    Abstract [en]

    Next generation sequencing technologies for in depth analyses of complex microbial communities rely on rational primer design based on up-to-date reference databases. Most of the 16S rRNA-gene based analyses of environmental Archaea community composition use PCR primers developed from small data sets several years ago, making an update long overdue. Here we present a new set of archaeal primers targeting the 16S rRNA gene designed from 8500 aligned archaeal sequences in the SILVA database. The primers 340F-1000R showed a high archaeal specificity (<1% bacteria amplification) covering 93 and 97% of available sequences for Crenarchaeota and Euryarchaeota respectively. In silico tests of the primers revealed at least 38% higher coverage for Archaea compared to other commonly used primers. Empirical tests with clone libraries confirmed the high specificity of the primer pair to Archaea in three biomes: surface waters in the Arctic Ocean, the pelagic zone of a temperate lake and a methanogenic bioreactor. The clone libraries featured both Euryarchaeota and Crenarchaeota in variable proportions and revealed dramatic differences in the archaeal community composition and minimal phylogenetic overlap between samples.

  • 41.
    Gharizadeh, Baback
    et al.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Käller, Max
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Nyrén, Pål
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Andersson,, Anders F.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Uhlén, Mathias
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Ahmadian, Afshin
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays2003In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 31, no 22, p. e146-Article in journal (Refereed)
    Abstract [en]

     Detection and identification of microbial pathogens are important for disease diagnosis, treatment and prophylaxis measurements. By introducing an innovative technique, we show a robust, reliable and accurate microarray-based method for identification of microbial pathogens. The technique utilizes a unique combination of multiplex competitive hybridization, which enhances hybridization accuracy of oligonucleotides to the specific target, and apyrase-mediated allele-specific extension, which improves specific extension. As a model system, different clinically relevant human papillomaviruses were selected for this study. The method generated accurate results and proves to be promising for specific and correct microbial and viral typing.

  • 42. Grubisic, Lorena M.
    et al.
    Bertilsson, Stefan
    Eiler, Alexander
    Heinrich, Friederike
    Brutemark, Andreas
    Alonso-Saez, Laura
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Gantner, Stephan
    Riemann, Lasse
    Beier, Sara
    Lake bacterioplankton dynamics over diurnal timescales2017In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 62, no 1, p. 191-204Article in journal (Refereed)
    Abstract [en]

    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.

  • 43.
    Grujčić, Vesna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden,.
    Saarenpää, Sami
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sundh, John
    Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Solna, Sweden,.
    Sennblad, Bengt
    Science for Life Laboratory, Dept of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden.
    Norgren, Benjamin
    Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden,.
    Latz, Meike
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Giacomello, Stefania
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Foster, Rachel A.
    Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden,.
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton2024In: PLOS ONE, E-ISSN 1932-6203, Vol. 19, no 1 January, article id e0296672Article in journal (Refereed)
    Abstract [en]

    Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter”, although further optimizations are necessary to increase the signal-to-noise ratio.

  • 44. Happel, E. M.
    et al.
    Markussen, T.
    Teikari, J. E.
    Huchaiah, V.
    Alneberg, Johannes
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sivonen, K.
    Middelboe, M.
    Kisand, V.
    Riemann, L.
    Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites2019In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 95, no 9, article id fiz123Article in journal (Refereed)
    Abstract [en]

    Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.

  • 45.
    Herlemann, D. P. R.
    et al.
    Leibniz Inst Baltic Sea Res Warnemunde, Rostock, Germany.;Estonian Univ Life Sci, Ctr Limnol, Elva Parish, Tartu County, Estonia..
    Markert, S.
    Ernst Moritz Arndt Univ Greifswald, Inst Pharm, Dept Pharmaceut Biotechnol, Greifswald, Germany.;Inst Marine Biotechnol eV, Greifswald, Germany..
    Meeske, C.
    Leibniz Inst Baltic Sea Res Warnemunde, Rostock, Germany..
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    de Bruijn, Ino
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hentschker, C.
    Ernst Moritz Arndt Univ Greifswald, Dept Microbial Prote, Inst Microbiol, Greifswald, Germany..
    Unfried, F.
    Ernst Moritz Arndt Univ Greifswald, Inst Pharm, Dept Pharmaceut Biotechnol, Greifswald, Germany.;Inst Marine Biotechnol eV, Greifswald, Germany..
    Becher, D.
    Ernst Moritz Arndt Univ Greifswald, Dept Microbial Prote, Inst Microbiol, Greifswald, Germany..
    Juergens, K.
    Leibniz Inst Baltic Sea Res Warnemunde, Rostock, Germany..
    Schweder, T.
    Ernst Moritz Arndt Univ Greifswald, Inst Pharm, Dept Pharmaceut Biotechnol, Greifswald, Germany.;Inst Marine Biotechnol eV, Greifswald, Germany..
    Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations2019In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 85, no 15, article id UNSP e00825-19Article in journal (Refereed)
    Abstract [en]

    Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter. In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures. IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects ("bottle effect") may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called "bottle effect," which is well known to occur during enclosure experiments.

  • 46. Herlemann, Daniel P. R.
    et al.
    Labrenz, Matthias
    Juergens, Klaus
    Bertilsson, Stefan
    Waniek, Joanna J.
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea2011In: ISME JOURNAL, ISSN 1751-7362, Vol. 5, no 10, p. 1571-1579Article in journal (Refereed)
    Abstract [en]

    Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater-freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche.

  • 47. Herlemann, Daniel P. R.
    et al.
    Lundin, Daniel
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Labrenz, Matthias
    Juergens, Klaus
    Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea2016In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 7, article id 1883Article in journal (Refereed)
    Abstract [en]

    Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity.

  • 48. Herlemann, Daniel P. R.
    et al.
    Lundin, Daniel
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Labrenz, Matthias
    Jürgens, Klaus
    Zheng, Zongli
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO), Glycoscience.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria2013In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 4, no 3, p. e00569-12-Article in journal (Refereed)
    Abstract [en]

    The verrucomicrobial subdivision 2 class Spartobacteria is one of the most abundant bacterial lineages in soil and has recently also been found to be ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of the Spartobacteria is one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within the Spartobacteria exists. Since no aquatic representative from the Spartobacteria has been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic Sea Spartobacteria phylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near-complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates, like cellulose, mannan, xylan, chitin, and starch, as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype's distribution within the Baltic Sea indicate a connection to Cyanobacteria that may be the main source of the polysaccharide substrates. IMPORTANCE The ecosystem roles of many phylogenetic lineages are not yet well understood. One such lineage is the class Spartobacteria within the Verrucomicrobia that, despite being abundant in soil and aquatic systems, is relatively poorly studied. Here we circumvented the difficulties of growing aquatic Verrucomicrobia by applying shotgun metagenomic sequencing on a water sample from the Baltic Sea. By using a method based on sequence signatures, we were able to in silico isolate genome fragments belonging to a phylotype of the Spartobacteria. The genome, which represents the first aquatic representative of this clade, encodes a diversity of glycoside hydrolases that likely allow degradation of various complex carbohydrates. Since the phylotype cooccurs with Cyanobacteria, these may be the primary producers of the carbohydrate substrates. The phylotype, which is highly abundant in the Baltic Sea during summer, may thus play an important role in the carbon cycle of this ecosystem.

  • 49.
    Holmfeldt, Karin
    et al.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden..
    Nilsson, Emelie
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden..
    Simone, Domenico
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.;Swedish Univ Agr Sci, Dept Plant Biol, Uppsala, Sweden.;Swedish Univ Agr Sci, SLU Bioinformat Infrastruct, Uppsala, Sweden..
    Lopez-Fernandez, Margarita
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.;Helmholtz Zentrum Dresden Rossendorf eV, Inst Resource Ecol, Dresden, Germany..
    Wu, Xiaofen
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.;Univ Tennessee, Ctr Environm Biotechnol, Knoxville, TN 37932 USA..
    de Bruijn, Ino
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. Mem Sloan Kettering Canc Ctr, 1275 York Ave, New York, NY 10021 USA..
    Lundin, Daniel
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden..
    Andersson, Anders F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Bertilsson, Stefan
    Uppsala Univ, Dept Ecol & Genet, Limnol & Sci Life Lab, Uppsala, Sweden.;Swedish Univ Agr Sci, Dept Aquat Sci & Assessment, Uppsala, Sweden..
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden..
    The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles2021In: Communications Biology, E-ISSN 2399-3642, Vol. 4, no 1, article id 307Article in journal (Refereed)
    Abstract [en]

    The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in 'metabolic standby'. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of 'kill-the-winner' oscillations creating slow motion 'boom and burst' cycles. Karin Holmfeldt et al. sequence metagenomes and metatranscriptomes of viruses in deep groundwaters down to 448m below the surface. The results reveal ecological dynamics of viruses including slow motion 'boom and burst' cycles and a 'kill the winner' model potentially driven by viral predation.

  • 50.
    Hu, Yue O. O.
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
    Karlson, Bengt
    Charvet, Sophie
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea2016In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 7, article id 679Article in journal (Refereed)
    Abstract [en]

    Microbial plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities sampled in summer along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. In contrast, no clear trends in alpha-diversity for bacterial or eukaryotic communities could be detected along the transect. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but groups novel to the Baltic Sea were also identified, such as relatives to the coccolithophore Erniliana huxleyi detected in the northern Baltic Sea. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.

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