uu.seUppsala University Publications
Change search
Refine search result
1 - 30 of 30
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Anderson, Jennifer L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nieuwenhuis, Bart P. S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Division of Evolutionary Biology, Faculty of Biology, Ludwig- Maximilians-Universität München.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Asexual reproduction and growth rate: independent and plastic lifehistory traits in Neurospora crassa2019In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 13, no 3, p. 780-788Article in journal (Refereed)
  • 2.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, 40 Lai St, EE-50411 Tartu, Estonia.
    Kohout, Petr
    Anslan, Sten
    Harend, Helery
    Abarenkov, Kessy
    Tedersoo, Leho
    Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, p. 885-896Article in journal (Refereed)
    Abstract [en]

    A central challenge in ecology is to understand the relative importance of processes that shape diversity patterns. Compared with aboveground biota, little is known about spatial patterns and processes in soil organisms. Here we examine the spatial structure of communities of small soil eukaryotes to elucidate the underlying stochastic and deterministic processes in the absence of environmental gradients at a local scale. Specifically, we focus on the fine-scale spatial autocorrelation of prominent taxonomic and functional groups of eukaryotic microbes. We collected 123 soil samples in a nested design at distances ranging from 0.01 to 64 m from three boreal forest sites and used 454 pyrosequencing analysis of Internal Transcribed Spacer for detecting Operational Taxonomic Units of major eukaryotic groups simultaneously. Among the main taxonomic groups, we found significant but weak spatial variability only in the communities of Fungi and Rhizaria. Within Fungi, ectomycorrhizas and pathogens exhibited stronger spatial structure compared with saprotrophs and corresponded to vegetation. For the groups with significant spatial structure, autocorrelation occurred at a very fine scale (<2 m). Both dispersal limitation and environmental selection had a weak effect on communities as reflected in negative or null deviation of communities, which was also supported by multivariate analysis, that is, environment, spatial processes and their shared effects explained on average <10% of variance. Taken together, these results indicate a random distribution of soil eukaryotes with respect to space and environment in the absence of environmental gradients at the local scale, reflecting the dominant role of drift and homogenizing dispersal.

  • 3. Bendall, Matthew L
    et al.
    Stevens, Sarah LR
    Chan, Leong-Keat
    Malfatti, Stephanie
    Schwientek, Patrick
    Tremblay, Julien
    Schackwitz, Wendy
    Martin, Joel
    Pati, Amrita
    Bushnell, Brian
    Froula, Jeff
    Kang, Dongwan
    Tringe, Susannah G
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Moran, Mary A
    Shade, Ashley
    Newton, Ryan J
    McMahon, Katherine D
    Malmstrom, Rex R
    Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 7, p. 1589-1601Article in journal (Refereed)
    Abstract [en]

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005-2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the /`ecotype model/' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.

  • 4.
    Bravo, Andrea Garcia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Zopfi, J
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Xu, J
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Schaefer, J. K.
    Poté, J.
    Cosio, C.
    Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by wastewater releasesIn: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370Article in journal (Refereed)
  • 5.
    Bravo, Andrea Garcia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zopfi, Jakob
    Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel CH-4056, Switzerland.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jingying, Xu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Schaefer, Jeffra K.
    Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA.
    Poté, John
    Environmental Biogeochemistry and Ecotoxicology, University of Geneva, Geneva CH-1205, Switzerland.
    Cosio, Claudia
    Environmental Biogeochemistry and Ecotoxicology, University of Geneva, Geneva CH-1205, Switzerland.;Unité Stress Environnementaux et BIOSurveillance des Milieux Aquatiques UMR-I 02 (SEBIO), Université de Reims Champagne Ardenne, Reims F-51687, France.
    Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, p. 802-812Article in journal (Refereed)
    Abstract [en]

    Microbial mercury (Hg) methylation in sediments can result in bioaccumulation of the neurotoxin methylmercury (MMHg) in aquatic food webs. Recently, the discovery of the gene hgcA, required for Hg methylation, revealed that the diversity of Hg methylators is much broader than previously thought. However, little is known about the identity of Hg-methylating microbial organisms and the environmental factors controlling their activity and distribution in lakes. Here, we combined high-throughput sequencing of 16S rRNA and hgcA genes with the chemical characterization of sediments impacted by a waste water treatment plant that releases significant amounts of organic matter and iron. Our results highlight that the ferruginous geochemical conditions prevailing at 1–2 cm depth are conducive to MMHg formation and that the Hgmethylating guild is composed of iron and sulfur-transforming bacteria, syntrophs, and methanogens. Deltaproteobacteria, notably Geobacteraceae, dominated the hgcA carrying communities, while sulfate reducers constituted only a minor component, despite being considered the main Hg methylators in many anoxic aquatic environments. Because iron is widely applied in waste water treatment, the importance of Geobacteraceae for Hg methylation and the complexity of Hgmethylating communities reported here are likely to occur worldwide in sediments impacted by waste water treatment plant discharges and in iron-rich sediments in general.

  • 6.
    Comte, Jerome
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Can marine bacteria be recruited from freshwater sources and the air?2014In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 8, no 12, p. 2423-2430Article in journal (Refereed)
    Abstract [en]

    There is now clear evidence that microorganisms present biogeographic patterns, yet the processes that create and maintain them are still not well understood. In particular, the contribution of dispersal and its exact impact on local community composition is still unclear. For example, dispersing cells may not thrive in recipient environments, but may still remain part of the local species pool. Here, we experimentally tested if marine bacteria can be retrieved from freshwater communities (pelagic and sediment) and the atmosphere by exposing bacteria from three lakes, that differ in their proximity to the Norwegian Sea, to marine conditions. We found that the percentage of freshwater taxa decreased with increasing salinities, whereas marine taxa increased along the same gradient. Our results further showed that this increase was stronger for lake and sediment compared with air communities. Further, significant increases in the average niche breadth of taxa were found for all sources, and in particular lake water and sediment communities, at higher salinities. Our results therefore suggests that marine taxa can readily grow from freshwater sources, but that the response was likely driven by the growth of habitat generalists that are typically found in marine systems. Finally, there was a greater proportion of marine taxa found in communities originating from the lake closest to the Norwegian Sea. In summary, this study shows that the interplay between bacterial dispersal limitation and dispersal from internal and external sources may have an important role for community recovery in response to environmental change.

  • 7.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mondav, Rhiannon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sinclair, Lucas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Fernandez-Vidal, Leyden
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schwientek, Patrick
    Martinez-Garcia, Manuel
    Torrents, David
    McMahon, Katherine D.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stepanauskas, Ramunas
    Woyke, Tanja
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 8, p. 1902-1914Article in journal (Refereed)
  • 8. Farnelid, Hanna
    et al.
    Bentzon-Tilia, Mikkel
    Andersson, Anders F.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    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.

  • 9.
    Fortunato, Caroline S.
    et al.
    University of Maryland Center for Environmental Science.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Herfort, Lydie
    Oregon Health & Sciences University.
    Needoba, Joseph A.
    Oregon Health & Sciences University.
    Peterson, Tawnya D.
    Oregon Health & Sciences University.
    Crump, Byron C.
    University of Maryland Center for Environmental Science.
    Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 10, p. 1899-1911Article in journal (Refereed)
    Abstract [en]

    Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=−0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, andProchlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.

  • 10.
    Garcia, Sarahi L
    et al.
    Jena School for Microbial Communication (JSMC) and Microbial Ecology Group at Friedrich Schiller University Jena, Jena, Germany.
    McMahon, Katherine D
    Martinez-Garcia, Manuel
    Srivastava, Abhishek
    Sczyrba, Alexander
    Stepanauskas, Ramunas
    Grossart, Hans-Peter
    Woyke, Tanja
    Warnecke, Falk
    Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 1, p. 137-147Article in journal (Refereed)
    Abstract [en]

    Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (~42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (~15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an actinorhodopsin gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria.

  • 11.
    Garcia, Sarahi L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab. University of Wisconsin-Madison, Madison, USA.
    Stevens, Sarah L R
    University of Wisconsin-Madison, Madison, USA.
    Crary, Benjamin
    University of Wisconsin-Madison, Madison, USA.
    Martinez-Garcia, Manuel
    University of Alicante, Alicante, Spain.
    Stepanauskas, Ramunas
    Bigelow Laboratory for Ocean Sciences, East Boothbay, USA.
    Woyke, Tanja
    DOE Joint Genome Institute, Walnut Creek, USA.
    Tringe, Susannah G
    DOE Joint Genome Institute, Walnut Creek, USA.
    Andersson, Siv G E
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Malmstrom, Rex R
    DOE Joint Genome Institute, Walnut Creek, USA.
    McMahon, Katherine D
    University of Wisconsin-Madison, Madison, USA.
    Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, no 3, p. 742-755Article in journal (Refereed)
    Abstract [en]

    To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.

  • 12. Ghylin, Trevor W
    et al.
    Garcia, Sarahi L
    Moya, Francisco
    Oyserman, Ben O
    Schwientek, Patrick
    Forest, Katrina T
    Mutschler, James
    Dwulit-Smith, Jeffrey
    Chan, Leong-Keat
    Martinez-Garcia, Manuel
    Sczyrba, Alexander
    Stepanauskas, Ramunas
    Grossart, Hans-Peter
    Woyke, Tanja
    Warnecke, Falk
    Malmstrom, Rex
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    McMahon, Katherine D
    Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage2014In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 8, no 12, p. 2503-2516Article in journal (Refereed)
    Abstract [en]

    Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.

  • 13.
    Guy, Lionel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Saw, Jimmy Hser Wah
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum2014In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 8, no 7, p. 1353-1357Article in journal (Other academic)
  • 14.
    Hubalek, Valerie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Wu, Xiaofen
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Buck, Moritz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Heim, Christine
    Univ Gottingen, GZG Geobiol, Gottingen, Germany.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMiS, Kalmar, Sweden.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ionescu, Danny
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Neuglobsow, Germany.
    Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 10, p. 2447-2458Article in journal (Refereed)
    Abstract [en]

    Little research has been conducted on microbial diversity deep under the Earth/'s surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

  • 15.
    Langenheder, Silke
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Berga, Mercé
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Östman, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Székely, Anna J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Temporal variation of beta-diversity and assembly mechanisms in a bacterial metacommunity2012In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 6, no 6, p. 1107-1114Article in journal (Refereed)
    Abstract [en]

    The turnover of community composition across space, beta-diversity, is influenced by different assembly mechanisms, which place varying weight on local habitat factors, such as environmental conditions and species interactions, and regional factors such as dispersal and history. Several assembly mechanisms may function simultaneously; however, little is known about how their importance changes over time and why. Here, we implemented a field survey where we sampled a bacterial metacommunity consisting of 17 rock pools located at the Swedish Baltic Sea coast at 11 occasions during 1 year. We determined to which extent communities were structured by different assembly mechanisms using variation partitioning and studied changes in beta-diversity across environmental gradients over time. beta-Diversity was highest at times of high overall productivity and environmental heterogeneity in the metacommunity, at least partly due to species sorting, that is, selection of taxa by the prevailing environmental conditions. In contrast, dispersal-driven assembly mechanisms were primarily detected at times when beta-diversity was relatively low. There were no indications for strong and persistent differences in community composition or beta-diversity between permanent and temporary pools, indicating that the physical disturbance regime is of relatively minor importance. In summary, our study clearly suggests that there are temporal differences in the relative importance of different assembly mechanisms related to abiotic factors and shows that the temporal variability of those factors is important for a more complete understanding of bacterial metacommunity dynamics.

  • 16.
    Lind, Anders E.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lewis, William H
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Guy, Lionel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Embley, T Martin
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle.2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, no 11, p. 2655-2667Article in journal (Refereed)
    Abstract [en]

    Endosymbiosis is a widespread phenomenon in the microbial world and can be based on diverse interactions between endosymbiont and host cell. The vast majority of the known endosymbiotic interactions involve bacteria that have invaded eukaryotic host cells. However, methanogenic archaea have been found to thrive in anaerobic, hydrogenosome-containing protists and it was suggested that this symbiosis is based on the transfer of hydrogen. Here, we used culture-independent genomics approaches to sequence the genomes of two distantly related methanogenic endosymbionts that have been acquired in two independent events by closely related anaerobic ciliate hosts Nyctotherus ovalis and Metopus contortus, respectively. The sequences obtained were then validated as originating from the ciliate endosymbionts by in situ probing experiments. Comparative analyses of these genomes and their closest free-living counterparts reveal that the genomes of both endosymbionts are in an early stage of adaptation towards endosymbiosis as evidenced by the large number of genes undergoing pseudogenization. For instance, the observed loss of genes involved in amino acid biosynthesis in both endosymbiont genomes indicates that the endosymbionts rely on their hosts for obtaining several essential nutrients. Furthermore, the endosymbionts appear to have gained significant amounts of genes of potentially secreted proteins, providing targets for future studies aiming to elucidate possible mechanisms underpinning host-interactions. Altogether, our results provide the first genomic insights into prokaryotic endosymbioses from the archaeal domain of life.

  • 17.
    Logares, Ramiro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Logue, Jürg Brendan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Paterson, Harriet
    Laybourn-Parry, Johanna
    Rengefors, Karin
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Biogeography of bacterial communities exposed to progressive long-term environmental change2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 5, p. 937-948Article in journal (Refereed)
    Abstract [en]

    The response of microbial communities to long-term environmental change is poorly understood. Here, we study bacterioplankton communities in a unique system of coastal Antarctic lakes that were exposed to progressive long-term environmental change, using 454 pyrosequencing of the 16S rDNA gene (V3-V4 regions). At the time of formation, most of the studied lakes harbored marine-coastal microbial communities, as they were connected to the sea. During the past 20 000 years, most lakes isolated from the sea, and subsequently they experienced a gradual, but strong, salinity change that eventually developed into a gradient ranging from freshwater (salinity 0) to hypersaline (salinity 100). Our results indicated that present bacterioplankton community composition was strongly correlated with salinity and weakly correlated with geographical distance between lakes. A few abundant taxa were shared between some lakes and coastal marine communities. Nevertheless, lakes contained a large number of taxa that were not detected in the adjacent sea. Abundant and rare taxa within saline communities presented similar biogeography, suggesting that these groups have comparable environmental sensitivity. Habitat specialists and generalists were detected among abundant and rare taxa, with specialists being relatively more abundant at the extremes of the salinity gradient. Altogether, progressive long-term salinity change appears to have promoted the diversification of bacterioplankton communities by modifying the composition of ancestral communities and by allowing the establishment of new taxa. The ISME Journal (2013) 7, 937-948; doi:10.1038/ismej.2012.168; published online 20 December 2012

  • 18.
    Logue, Jurg B.
    et al.
    Lund Univ, Dept Biol Aquat Ecol, Solvegatan 37, S-22362 Lund, Sweden.;Sci Life Lab, Solna, Sweden..
    Stedmon, Colin A.
    Tech Univ Denmark, Natl Inst Aquat Resources, Charlottenlund, Denmark..
    Kellerman, Anne M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Nielsen, Nikoline J.
    Univ Copenhagen, Dept Plant & Environm Sci, Copenhagen, Denmark..
    Andersson, Anders F.
    KTH Royal Inst Technol, Sch Biotechnol, Sci Life Lab, Div Gene Technol, Solna, Sweden..
    Laudon, Hjalmar
    Swedish Univ Agr Sci, Dept Forest Ecol & Management, S-90183 Umea, Sweden..
    Lindstrom, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Kritzberg, Emma S.
    Lund Univ, Dept Biol Aquat Ecol, Solvegatan 37, S-22362 Lund, Sweden..
    Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 3, p. 533-545Article in journal (Refereed)
    Abstract [en]

    Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low-or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance.

  • 19.
    Martijn, Joran
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Schulz, Frederik
    Zaremba-Niedzwiedzka, Katarzyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Viklund, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stepanauskas, Ramunas
    Andersson, Siv G E
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Horn, Matthias
    Guy, Lionel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J G
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution2015In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 9, no 11, p. 2373-2385Article in journal (Refereed)
    Abstract [en]

    The bacterial family Rickettsiaceae includes a group of well-known etiological agents of many human and vertebrate diseases, including epidemic typhus-causing pathogen Rickettsia prowazekii. Owing to their medical relevance, rickettsiae have attracted a great deal of attention and their host-pathogen interactions have been thoroughly investigated. All known members display obligate intracellular lifestyles, and the best-studied genera, Rickettsia and Orientia, include species that are hosted by terrestrial arthropods. Their obligate intracellular lifestyle and host adaptation is reflected in the small size of their genomes, a general feature shared with all other families of the Rickettsiales. Yet, despite that the Rickettsiaceae and other Rickettsiales families have been extensively studied for decades, many details of the origin and evolution of their obligate host-association remain elusive. Here we report the discovery and single-cell sequencing of 'Candidatus Arcanobacter lacustris', a rare environmental alphaproteobacterium that was sampled from Damariscotta Lake that represents a deeply rooting sister lineage of the Rickettsiaceae. Intriguingly, phylogenomic and comparative analysis of the partial 'Candidatus Arcanobacter lacustris' genome revealed the presence chemotaxis genes and vertically inherited flagellar genes, a novelty in sequenced Rickettsiaceae, as well as several host-associated features. This finding suggests that the ancestor of the Rickettsiaceae might have had a facultative intracellular lifestyle. Our study underlines the efficacy of single-cell genomics for studying microbial diversity and evolution in general, and for rare microbial cells in particular.

  • 20. Mukherjee, Shinjini
    et al.
    Juottonen, Heli
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Siivonen, Pauli
    Quesada, Cosme Lloret
    Tuom, Pirjo
    Pulkkine, Pertti
    Yrjälä, Kim
    Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site2014In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 8, no 11, p. 2131-2142Article in journal (Refereed)
    Abstract [en]

    Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.

  • 21.
    Peura, Sari
    et al.
    Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Nykanen, Hannu
    Univ Jyvaskyla, Dept Biol & Environm Sci, Jyvaskyla 40014, Finland.
    Tiirola, Marja
    Univ Jyvaskyla, Dept Biol & Environm Sci, Jyvaskyla 40014, Finland.
    Jones, Roger I.
    Univ Jyvaskyla, Dept Biol & Environm Sci, Jyvaskyla 40014, Finland.
    Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD12012In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 6, no 9, p. 1640-1652Article in journal (Refereed)
    Abstract [en]

    Lakes have a central role in the carbon cycle of the boreal landscape. These systems typically stratify in summer and their hypolimnetic microbial communities influence burial of biogenic organic matter in sediments. The composition of bacterial communities in these suboxic habitats was studied by pyrosequencing of 16S rRNA amplicons from five lakes with variable dissolved organic carbon (DOC) concentrations. Bacterioplankton communities in the hypolimnetic waters were clearly different from the surface layer with candidate division OD1, Chlorobi and Bacteroidetes as dominant community members. Several operational taxonomic units (OTUs) affiliated with candidate division OD1 were abundant and consistently present in the suboxic hypolimnion in these boreal lakes. The overall representation of this group was positively correlated with DOC and methane concentrations. Network analysis of time-series data revealed contrasting temporal patterns but suggested similar ecological roles among the abundant OTUs affiliated with candidate division OD1. Together, stable isotope data and taxonomic classification point to methane oxidation and autotrophic denitrification as important processes in the suboxic zone of boreal lakes. Our data revealed that while hypolimnetic bacterial communities are less dynamic, they appear to be more diverse than communities from the oxic surface layer. An appreciable proportion of the hypolimnetic bacteria belong to poorly described phyla.

  • 22.
    Rubin-Blum, Maxim
    et al.
    Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany;Israel Limnol & Oceanog Res, Tel Shikmona, IL-3108000 Haifa, Israel.
    Antony, Chakkiath Paul
    Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.
    Sayavedra, Lizbeth
    Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany;Quadram Inst Biosci, Norwich Res Pk, Norwich, Norfolk, England.
    Martinez-Perez, Clara
    Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany.
    Birgel, Daniel
    Univ Hamburg, Ctr Earth Syst Res & Sustainabil, Inst Geol, D-20146 Hamburg, Germany.
    Peckmann, Jörn
    Univ Hamburg, Ctr Earth Syst Res & Sustainabil, Inst Geol, D-20146 Hamburg, Germany.
    Wu, Yu-Chen
    Univ Kiel, RD3 Marine Microbiol & Christian Albrechts, GEOMAR Helmholtz Ctr Ocean Res, Dustembrooker Weg 20, D-24105 Kiel, Germany.
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    MacDonald, Ian
    Florida State Univ, POB 3064326, Tallahassee, FL 32306 USA.
    Marcon, Yann
    Helmholtz Ctr Polar & Marine Res, Wegener Inst, HGF MPG Grp Deep Sea Ecol & Technol, Handelshafen 12, D-27570 Bremerhaven, Germany.
    Sahling, Heiko
    Univ Bremen, Ctr Marine Environm Sci, MARUM, D-28359 Bremen, Germany.
    Hentschel, Ute
    Univ Kiel, RD3 Marine Microbiol & Christian Albrechts, GEOMAR Helmholtz Ctr Ocean Res, Dustembrooker Weg 20, D-24105 Kiel, Germany.
    Dubilier, Nicole
    Max Planck Inst Marine Microbiol, Celsiusstr 1, D-28359 Bremen, Germany;Univ Bremen, Ctr Marine Environm Sci, MARUM, D-28359 Bremen, Germany.
    Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts2019In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 13, no 5, p. 1209-1225Article in journal (Refereed)
    Abstract [en]

    Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 Glade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host-symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.

  • 23.
    Schwank, Katrin
    et al.
    Univ Duisburg Essen, Biofilm Ctr, Dept Chem, GAME, Duisburg, Germany.
    Bornemann, Till L., V
    Univ Duisburg Essen, Biofilm Ctr, Dept Chem, GAME, Duisburg, Germany.
    Dombrowski, Nina
    Univ Utrecht, Royal Netherlands Inst Sea Res NIOZ, Dept Marine Microbiol & Biogeochem MMB, Den Burg, Netherlands.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Utrecht, Royal Netherlands Inst Sea Res NIOZ, Dept Marine Microbiol & Biogeochem MMB, Den Burg, Netherlands.
    Banfield, Jillian F.
    Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA.
    Probst, Alexander J.
    Univ Duisburg Essen, Biofilm Ctr, Dept Chem, GAME, Duisburg, Germany.
    An archaeal symbiont-host association from the deep terrestrial subsurface2019In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 13, no 8, p. 2135-2139Article in journal (Refereed)
    Abstract [en]

    DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal hostsymbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.

  • 24. Sentchilo, Vladimir
    et al.
    Mayer, Antonia P.
    Guy, Lionel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Miyazaki, Ryo
    Tringe, Susannah Green
    Barry, Kerrie
    Malfatti, Stephanie
    Goessmann, Alexander
    Robinson-Rechavi, Marc
    van der Meer, Jan R.
    Community-wide plasmid gene mobilization and selection2013In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 7, no 6, p. 1173-1186Article in journal (Refereed)
    Abstract [en]

    Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions.

  • 25.
    Strassert, Jürgen F H
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
    Karnkowska, Anna
    Hehenberger, Elisabeth
    del Campo, Javier
    Kolisko, Martin
    Okamot, Noriko
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
    Janouškovec, Jan
    Poirier, Camille
    Leonard, Guy
    Hallam, Steven J
    Richards, Thomas A
    Worden, Alexandra Z
    Santoro, Alyson E
    Keeling, Patrick J
    Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, p. 304-308Article in journal (Refereed)
    Abstract [en]

    Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.

  • 26.
    Svoboda, Pavel
    et al.
    Charles Univ Prague, Fac Sci, Dept Bot, Prague 2, Czech Republic..
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Osman, Omneya Ahmed
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Dispersal timing determines the importance of priority effects in bacterial communities2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, no 2, p. 644-646Article in journal (Refereed)
    Abstract [en]

    The order and timing of species arrival during community assembly can have long term effects on community structure due to priority effects. The importance of such processes in complex bacterial communities where dispersal involves mixing of entire communities is currently not known. Here we used a transplant experiment with two bacterioplankton communities of different origin (freshwater and brackish). Sterile medium of each origin was initially inoculated with a bacterial community of different ('alien') origin, followed by dispersal of the respective 'home' community at different time points after initial inoculation. We found that the later the dispersal with the 'home' community occurred the smaller the effect on the final community composition. This suggests that priority effects by the initially inoculated community reduce the establishment success of taxa from the later arriving community and that this effect depends on dispersal timing.

  • 27.
    Szekely, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Effects of drought-rewetting cycles on the diversity and functioning of bacterial metacommunities2017In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370Article in journal (Refereed)
  • 28.
    Székely, Anna J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Langenheder, Silke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Dispersal timing and drought history influence the response of bacterioplankton to drying–rewetting stress2017In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 11, no 8, p. 1764-1776Article in journal (Refereed)
    Abstract [en]

    The extent and frequency of drought episodes is expected to increase in the following decades making it a crucial stress factor for smaller water bodies. However, very little is known about how bacterioplankton is affected by increased evaporation and how these communities reassemble after rewetting. Here, we present results from a microcosm experiment that assessed the effect of drying–rewetting stress on bacterioplankton in the light of the stress history and the rate and timing of dispersal after the rewetting. We found that the drying phase resulted mainly in a change of function, whereas the complete desiccation and rewetting processes strongly affected both composition and function, which were, however, influenced by the initial conditions and stress history of the communities. Effects of dispersal were generally stronger when it occurred at an early stage after the rewetting. At this stage, selective establishment of dispersed bacteria coupled with enhanced compositional and functional recovery was found, whereas effects of dispersal were neutral, that is, predictable by dispersal rates, at later stages. Our studies therefore show that both the stress history and the timing of dispersal are important factors that influence the response of bacterial communities to environmental change and stress events.

  • 29. Wu, Xiaofen
    et al.
    Holmfeldt, Karin
    Hubalek, Valerie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lundin, Daniel
    Åström, Mats
    Bertilsson, Stefan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Dopson, Mark
    Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 5, p. 1192-1203Article in journal (Refereed)
    Abstract [en]

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 mu m filter. Such cells of <0.22 mu m would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 mu m populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

  • 30.
    Wurzbacher, Christian
    et al.
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Gothenburg, Sweden..
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Gothenburg, Sweden..
    Rautio, Milla
    Univ Quebec Chicoutimi, Dept Sci Fondamentales, Chicoutimi, PQ, Canada.;Univ Quebec Chicoutimi, Ctr Northern Studies CEN, Chicoutimi, PQ, Canada..
    Peura, Sari
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular epidemiology. Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Sci Life Lab, Uppsala, Sweden..
    Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds2017In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 11, no 8, p. 1938-1941Article in journal (Refereed)
    Abstract [en]

    In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.

1 - 30 of 30
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf