Change search
Refine search result
1 - 22 of 22
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • 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. Alneberg, Johannes
    et al.
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Bennke, Christin
    Beier, Sara
    Lundin, Daniel
    Hugerth, Luisa W.
    Pinhassi, Jarone
    Kisand, Veljo
    Riemann, Lasse
    Jürgens, Klaus
    Labrenz, Matthias
    Andersson, Anders F.
    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. [GRAPHICS] .

  • 2.
    Asplund-Samuelsson, Johannes
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Larsson, John
    Stockholm University, Faculty of Science, Department of Botany.
    Prokaryotic Caspase Homologs: Phylogenetic Patterns and Functional Characteristics Reveal Considerable Diversity2012In: PLOS ONE, E-ISSN 1932-6203, Vol. 7, no 11, p. e49888-Article in journal (Refereed)
    Abstract [en]

    Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18%) were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota). Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse subgroups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.

  • 3.
    Bergman, Birgitta
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Sandh, Gustaf
    Stockholm University, Faculty of Science, Department of Botany.
    Lin, Senjie
    Larsson, John
    Stockholm University, Faculty of Science, Department of Botany.
    Carpenter, Edward J.
    Trichodesmium - a widespread marine cyanobacterium with unusual nitrogen fixation properties2013In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 37, no 3, p. 286-302Article, review/survey (Refereed)
    Abstract [en]

    The last several decades have witnessed dramatic advances in unfolding the diversity and commonality of oceanic diazotrophs and their N2-fixing potential. More recently, substantial progress in diazotrophic cell biology has provided a wealth of information on processes and mechanisms involved. The substantial contribution by the diazotrophic cyanobacterial genus Trichodesmium to the nitrogen influx of the global marine ecosystem is by now undisputable and of paramount ecological importance, while the underlying cellular and molecular regulatory physiology has only recently started to unfold. Here, we explore and summarize current knowledge, related to the optimization of its diazotrophic capacity, from genomics to ecophysiological processes, via, for example, cellular differentiation (diazocytes) and temporal regulations, and suggest cellular research avenues that now ought to be explored.

  • 4. Dupont, Chris L.
    et al.
    Larsson, John
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Yooseph, Shibu
    Ininbergs, Karolina
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Goll, Johannes
    Asplund-Samuelsson, Johannes
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    McCrow, John P.
    Celepli, Narin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Allen, Lisa Zeigler
    Ekman, Martin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Lucas, Andrew J.
    Hagström, Åke
    Thiagarajan, Mathangi
    Brindefalk, Björn
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Richter, Alexander R.
    Andersson, Anders F.
    Tenney, Aaron
    Lundin, Daniel
    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
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    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.

  • 5.
    Grujčić, Vesna
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Saarenpää, Sami
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Sennblad, Bengt
    Norgren, Benjamin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Latz, Meike
    Giacomello, Stefania
    Foster, Rachel Ann
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Andersson, Anders F.
    Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton2024In: PLOS ONE, E-ISSN 1932-6203, Vol. 19, no 1, 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.

  • 6. Hagström, Åke
    et al.
    Zweifel, Ulla Li
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Osbeck, Christofer M. G.
    Bunse, Carina
    Sjöstedt, Johanna
    Müller-Karulis, Bärbel
    Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Pinhassi, Jarone
    Composition and Seasonality of Membrane Transporters in Marine Picoplankton2021In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 12, article id 714732Article in journal (Refereed)
    Abstract [en]

    In this study, we examined transporter genes in metagenomic and metatranscriptomic data from a time-series survey in the temperate marine environment of the Baltic Sea. We analyzed the abundance and taxonomic distribution of transporters in the 3μm–0.2μm size fraction comprising prokaryotes and some picoeukaryotes. The presence of specific transporter traits was shown to be guiding the succession of these microorganisms. A limited number of taxa were associated with the dominant transporter proteins that were identified for the nine key substrate categories for microbial growth. Throughout the year, the microbial taxa at the level of order showed highly similar patterns in terms of transporter traits. The distribution of transporters stayed the same, irrespective of the abundance of each taxon. This would suggest that the distribution pattern of transporters depends on the bacterial groups being dominant at a given time of the year. Also, we find notable numbers of secretion proteins that may allow marine bacteria to infect and kill prey organisms thus releasing nutrients. Finally, we demonstrate that transporter proteins may provide clues to the relative importance of biogeochemical processes, and we suggest that virtual transporter functionalities may become important components in future population dynamics models.

  • 7. Jonsson, Hans
    et al.
    Hugerth, Luisa W.
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Lundin, Eva
    Andersson, Anders F.
    Genome sequence of segmented filamentous bacteria present in the human intestine2020In: Communications biology, E-ISSN 2399-3642, Vol. 3, no 1, article id 485Article in journal (Refereed)
    Abstract [en]

    Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host's intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65-71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment. Hans Jonsson et al. report the metagenomic reconstruction of the genome of a potentially immune modulatory segmented filamentous bacteria (SFB) from a human ileostomy sample. They demonstrate that the genome clusters closely with SFB genomes from other species. They also detect the unique SFB variant in human faecal metagenomics datasets.

  • 8. Kasmaei, Kamyar Mogodiniyai
    et al.
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning2019In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 10, article id 2673Article in journal (Refereed)
    Abstract [en]

    Feruloyl esterases (FAEs) can reduce the recalcitrance of lignocellulosic biomass to enzymatic hydrolysis, thereby enhancing biorefinery potentials or animal feeding values of the biomass. In addition, ferulic acid, a product of FAE activity, has applications in pharmaceutical and food/beverage industries. It is therefore of great interest to identify new FAEs to enhance understanding about this enzyme family. For this purpose, we used whole-genome shotgun metagenomics and genome binning to explore rumens of dairy cows, large intestines of horses, sediments of freshwater and forest topsoils to identify novel prokaryotic FAEs and trace the responsible microorganisms. A number of prokaryotic genomes were recovered of which, genomes of Clostridiales order and Candidatus Rhabdochlamydia genus showed FAE coding capacities. In total, five sequences were deemed as putative FAE. The BLASTP search against non-redundant protein database of NCBI indicated that these putative FAEs represented novel sequences within this enzyme family. The phylogenetic analysis showed that at least three putative sequences shared evolutionary lineage with FAEs of type A and thus could possess specific activities similar to this type of FAEs, something that is not previously found outside fungal kingdom. We nominate Candidatus Rhabdochlamydia genus as a novel FAE producing taxonomic unit.

  • 9.
    Larsson, John
    Stockholm University, Faculty of Science, Department of Botany.
    Cyanobacterial genome evolution subsequent to domestication by a plant (Azolla)2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cyanobacteria are an ancient and globally distributed group of photosynthetic prokaryotes including species capable of fixing atmospheric dinitrogen (N2) into biologically available ammonia via the enzyme complex nitrogenase. The ability to form symbiotic interactions with eukaryotic hosts is a notable feature of cyanobacteria and one which, via an ancient endosymbiotic event, led to the evolution of chloroplasts and eventually to the plant dominated biosphere of the globe. Some cyanobacteria are still symbiotically competent and form symbiotic associations with eukaryotes ranging from unicellular organisms to complex plants. Among contemporary plant-cyanobacteria associations, the symbiosis formed between the small fast-growing aquatic fern Azolla and its cyanobacterial symbiont (cyanobiont), harboured in specialized cavities in each Azolla leaf, is the only one which is perpetual and in which the cyanobiont has lost its free-living capacity, suggesting a long-lasting co-evolution between the two partners. In this study, the genome of the cyanobiont in Azolla filiculoides was sequenced to completion and analysed. The results revealed that the genome is in an eroding state, evidenced by a high proportion of pseudogenes and transposable elements. Loss of function was most predominant in genetic categories related to uptake and metabolism of nutrients, response to environmental stimuli and in the DNA maintenance machinery. Conversely, function was retained in key symbiotic processes such as nitrogen-fixation and cell differentiation. A comparative analysis shows that the size of the cyanobiont genome has remained relatively stable, and that few genes have been completely eliminated, since the symbiotic establishment. Indications of genes acquired via horizontal gene transfer were discovered in thec yanobiont genome, some of which may have originated from the bacterial community in the Azolla leaf-cavities. It is concluded that the perpetual nature of the Azolla symbiosis has resulted in pronounced ongoing streamlining of the cyanobiont genome around core symbiotic functions, a process not described previously for complex cyanobacteria or for any bacterial plant symbiont. Further, the status of the genome indicates that the cyanobiont is at an early stage of adapting to its host-restricted environment and continued co-evolution with the plant may result in additional genome reductions. However, although a vertical transmission process is already established, the unusual extracellular location of the cyanobiont and the intricate nature of the symbiosis, may still impose restrictions on such a reductive process.

    Download full text (pdf)
    FULLTEXT01
  • 10.
    Larsson, John
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Celepli, Narin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Ininbergs, Karolina
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Dupont, Christopher L.
    Yooseph, Shibu
    Bergman, Bigitta
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Ekman, Martin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea2014In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 8, no 9, p. 1892-1903Article in journal (Refereed)
    Abstract [en]

    Photoautotrophic picocyanobacteria harvest light via phycobilisomes (PBS) consisting of the pigments phycocyanin (PC) and phycoerythrin (PE), encoded by genes in conserved gene clusters. The presence and arrangement of these gene clusters give picocyanobacteria characteristic light absorption properties and allow the colonization of specific ecological niches. To date, a full understanding of the evolution and distribution of the PBS gene cluster in picocyanobacteria has been hampered by the scarcity of genome sequences from fresh-and brackish water-adapted strains. To remediate this, we analysed genomes assembled from metagenomic samples collected along a natural salinity gradient, and over the course of a growth season, in the Baltic Sea. We found that while PBS gene clusters in picocyanobacteria sampled in marine habitats were highly similar to known references, brackish-adapted genotypes harboured a novel type not seen in previously sequenced genomes. Phylogenetic analyses showed that the novel gene cluster belonged to a clade of uncultivated picocyanobacteria that dominate the brackish Baltic Sea throughout the summer season, but are uncommon in other examined aquatic ecosystems. Further, our data suggest that the PE genes were lost in the ancestor of PC-containing coastal picocyanobacteria and that multiple horizontal gene transfer events have re-introduced PE genes into brackish-adapted strains, including the novel clade discovered here.

  • 11.
    Larsson, John
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Nylander, Johan A. A.
    Stockholm University, Faculty of Science, Department of Botany.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits2011In: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 11, p. 187-Article in journal (Refereed)
    Abstract [en]

    Background: Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. Results: A total of 404 protein families, present in all cyanobacterial genomes, were identified. Two of these are unique to the phylum, corresponding to an AbrB family transcriptional regulator and a gene that escapes functional annotation although its genomic neighbourhood is conserved among the organisms examined. The evolution of cyanobacterial genome sizes involves a mix of gains and losses in the clade encompassing complex cyanobacteria, while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. Orthologs unique to cyanobacteria exhibiting specific characteristics, such as filament formation, heterocyst differentiation, diazotrophy and symbiotic competence, were also identified. An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genes, 4%-6% of which are unique to cyanobacteria today. Conclusions: The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the history of cyanobacteria. The expansion strategy is driven by gene-family enlargment and generates a broad adaptive potential; while the genome streamlining strategy imposes adaptations to highly specific niches, also reflected in their different functional capacities. A few genomes display extreme proliferation of non-coding nucleotides which is likely to be the result of initial expansion of genomes/gene copy number to gain adaptive potential, followed by a shift to a life-style in a highly specific niche (e. g. symbiosis). This transition results in redundancy of genes and gene families, leading to an increase in junk DNA and eventually to gene loss. A few orthologs can be correlated with specific phenotypes in cyanobacteria, such as filament formation and symbiotic competence; these constitute exciting exploratory targets.

  • 12.
    Larsson, John
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Nylander, Johan
    Natural History Museum, University of Oslo.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traitsIn: BMC Evolutionary Biology, E-ISSN 1471-2148Article in journal (Refereed)
  • 13.
    Larsson, John
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Nylander, Johan
    Natural History Museum, University of Oslo.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Horizontally transferred genes in a cyanobacterial plant symbiont suggest roles in symbiosis maintenanceManuscript (preprint) (Other academic)
  • 14. Law, Simon R.
    et al.
    Serrano, Alonso R.
    Daguerre, Yohann
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Schneider, Andreas N.
    Stangl, Zsofia R.
    Castro, David
    Grabherr, Manfred
    Näsholm, Torgny
    Street, Nathaniel R.
    Hurry, Vaughan
    Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests2022In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 119, no 26, article id e2118852119Article in journal (Refereed)
    Abstract [en]

    Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions. 

  • 15. Mehrshad, Maliheh
    et al.
    Lopez-Fernandez, Margarita
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Bell, Emma
    Simone, Domenico
    Buck, Moritz
    Bernier-Latmani, Rizlan
    Bertilsson, Stefan
    Dopson, Mark
    Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 4253Article in journal (Refereed)
    Abstract [en]

    While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome. Ecological constraints on microbial niches in oligotrophic deep groundwaters remain elusive. This study provides support for the existence of a common core microbiome in two deep groundwater biomes of the Fennoscandian Shield using a genome-resolved, integrated omics analysis.

  • 16. Paerl, Ryan W.
    et al.
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
    Tan, Demeng
    Svenningsen, Sine L.
    Hylander, Samuel
    Pinhassi, Jarone
    Andersson, Anders F.
    Riemann, Lasse
    Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 44, p. E10447-E10456Article in journal (Refereed)
    Abstract [en]

    Vitamin B1 (B1 herein) is a vital enzyme cofactor required by virtually all cells, including bacterioplankton, which strongly influence aquatic biogeochemistry and productivity and modulate climate on Earth. Intriguingly, bacterioplankton can be de novo B1 synthesizers or B1 auxotrophs, which cannot synthesize B1 de novo and require exogenous B1 or B1 precursors to survive. Recent isolate-based work suggests select abundant bacterioplankton are B1 auxotrophs, but direct evidence of B1 auxotrophy among natural communities is scant. In addition, it is entirely unknown if bulk bacterioplankton growth is ever B1-limited. We show by surveying for B1-related genes in estuarine, marine, and freshwater metagenomes and metagenome-assembled genomes (MAGs) that most naturally occurring bacterioplankton are B1 auxotrophs. Pyrimidine B1-auxotrophic bacterioplankton numerically dominated metagenomes, but multiple other B1-auxotrophic types and distinct uptake and B1-salvaging strategies were also identified, including dual (pyrimidine and thiazole) and intact B1 auxotrophs that have received little prior consideration. Time-series metagenomes from the Baltic Sea revealed pronounced shifts in the prevalence of multiple B1-auxotrophic types and in the B1-uptake and B1salvaging strategies over time. Complementarily, we documented B1/precursor limitation of bacterioplankton production in three of five nutrient-amendment experiments at the same time-series station, specifically when intact B1 concentrations were <= 3.7 pM, based on bioassays with a genetically engineered Vibrio anguillarum B1-auxotrophic strain. Collectively, the data presented highlight the prevalent reliance of bacterioplankton on exogenous B1/precursors and on the bioavailability of the micronutrients as an overlooked factor that could influence bacterioplankton growth and succession and thereby the cycling of nutrients and energy in aquatic systems.

  • 17. Plominsky, Álvaro M.
    et al.
    Larsson, John
    Stockholm University, Faculty of Science, Department of Botany.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Delherbe, Nathalie
    Osses, Igor
    Vásquez, Mónica
    Dinitrogen Fixation Is Restricted to the Terminal Heterocysts in the Invasive Cyanobacterium Cylindrospermopsis raciborskii CS-5052013In: PLOS ONE, E-ISSN 1932-6203, Vol. 8, no 2, article id e51682Article in journal (Refereed)
    Abstract [en]

    The toxin producing nitrogen-fixing heterocystous freshwater cyanobacterium Cylindrospermopsis raciborskii recently radiated from its endemic tropical environment into sub-tropical and temperate regions, a radiation likely to be favored by its ability to fix dinitrogen (diazotrophy). Although most heterocystous cyanobacteria differentiate regularly spaced intercalary heterocysts along their trichomes when combined nitrogen sources are depleted, C. raciborskii differentiates only two terminal heterocysts (one at each trichome end) that can reach >100 vegetative cells each. Here we investigated whether these terminal heterocysts are the exclusive sites for dinitrogen fixation in C. raciborskii. The highest nitrogenase activity and NifH biosynthesis (western-blot) were restricted to the light phase of a 12/12 light/dark cycle. Separation of heterocysts and vegetative cells (sonication and two-phase aqueous polymer partitioning) demonstrated that the terminal heterocysts are the sole sites for nifH expression (RT-PCR) and NifH biosynthesis. The latter finding was verified by the exclusive localization of nitrogenase in the terminal heterocysts of intact trichomes (immunogold-transmission electron microscopy and in situ immunofluorescence-light microscopy). These results suggest that the terminal heterocysts provide the combined nitrogen required by the often long trichomes (>100 vegetative cells). Our data also suggests that the terminal-heterocyst phenotype in C. raciborskii may be explained by the lack of a patL ortholog. These data help identify mechanisms by which C. raciborskii and other terminal heterocyst-forming cyanobacteria successfully inhabit environments depleted in combined nitrogen.

  • 18.
    Ran, Liang
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Larsson, John
    Stockholm University, Faculty of Science, Department of Botany.
    Vigil-Stenman, Theoden
    Stockholm University, Faculty of Science, Department of Botany.
    Nylander, Johan A. A.
    Stockholm University, Faculty of Science, Department of Botany.
    Ininbergs, Karolina
    Stockholm University, Faculty of Science, Department of Botany.
    Zheng, Wei-Wen
    Lapidus, Alla
    Lowry, Stephen
    Haselkorn, Robert
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium2010In: PLOS ONE, E-ISSN 1932-6203, Vol. 5, no 7, article id e11486Article in journal (Refereed)
    Abstract [en]

    Background: An ancient cyanobacterial incorporation into a eukaryotic organism led to the evolution of plastids (chloroplasts) and subsequently to the origin of the plant kingdom. The underlying mechanism and the identities of the partners in this monophyletic event remain elusive.

    Methodology/Principal Findings: To shed light on this evolutionary process, we sequenced the genome of a cyanobacterium residing extracellularly in an endosymbiosis with a plant, the water-fern Azolla filiculoides Lam. This symbiosis was selected as it has characters which make it unique among extant cyanobacterial plant symbioses: the cyanobacterium lacks autonomous growth and is vertically transmitted between plant generations. Our results reveal features of evolutionary significance. The genome is in an eroding state, evidenced by a large proportion of pseudogenes (31.2%) and a high frequency of transposable elements (,600) scattered throughout the genome. Pseudogenization is found in genes such as the replication initiator dnaA and DNA repair genes, considered essential to free-living cyanobacteria. For some functional categories of genes pseudogenes are more prevalent than functional genes. Loss of function is apparent even within the ‘core’ gene categories of bacteria, such as genes involved in glycolysis and nutrient uptake. In contrast, serving as a critical source of nitrogen for the host, genes related to metabolic processes such as cell differentiation and nitrogen-fixation are well preserved.

    Conclusions/Significance: This is the first finding of genome degradation in a plant symbiont and phenotypically complex cyanobacterium and one of only a few extracellular endosymbionts described showing signs of reductive genome evolution. Our findings suggest an ongoing selective streamlining of this cyanobacterial genome which has resulted in an organism devoted to nitrogen fixation and devoid of autonomous growth. The cyanobacterial symbiont of Azolla can thus be considered at the initial phase of a transition from free-living organism to a nitrogen-fixing plant entity, a transition process which may mimic what drove the evolution of chloroplasts from a cyanobacterial ancestor.

    Download full text (pdf)
    fulltext
  • 19. Schneider, Andreas N.
    et al.
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Sundström, Görel
    Richau, Kerstin
    Delhomme, Nicolas
    Grabherr, Manfred
    Hurry, Vaughan
    Street, Nathaniel R.
    Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce2021In: mSystems, E-ISSN 2379-5077, Vol. 6, no 1, article id e00884-20Article in journal (Refereed)
    Abstract [en]

    The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius.

    IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.

  • 20. Steffen, Karin
    et al.
    Proux-Wéra, Estelle
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Soler, Lucile
    Churcher, Allison
    Sundh, John
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Cárdenas, Paco
    Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae) 2023In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 13, no 10Article in journal (Refereed)
    Abstract [en]

    Sponges are among the earliest branching extant animals. As such, genetic data from this group are valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence, and hence, genomic data are scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high microbial abundance species Geodia barretti, from a single individual collected on the West Coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mb; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein-coding genes. 

  • 21.
    Vigil-Stenman, Theoden
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Ekman, Martin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Larsson, John
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    High transcriptional activity of insertion sequences in Baltic Sea microorganismsManuscript (preprint) (Other academic)
    Abstract [en]

    Insertion sequences (ISs) are mobile genetic elements found in almost all prokaryotic genomes. They consist of a gene encoding a transposase, surrounded by inverted repeats. The transposase has the ability to excise the IS and insert it elsewhere in the genome, a process referred to as transposition. ISs have high copy numbers in prokaryotes inhabiting “extreme” environments, and it is proposed that their activity facilitates adaptation to environmental changes and subsequent adaptive evolution. The initial step in the transposition of an IS is the transcription of the open reading frame encoding the transposase. In an effort to evaluate the presence, activity and role of ISs in microbes of a temperate water body offering steep changes in salinity and nutrient conditions, the metatranscriptomes and metagenomes of ten water samples from the brackish water Baltic Sea were examined. ISs in the limnic Lake Torne Träsk, the marine waters off the Swedish west coast and off the coast of California were included to get perspective. The results reveal that insertion sequences make up a considerably higher fraction of the metatranscriptomes of brackish waters (0.3-1.8%) than of marine waters (0.0005-0.2%), and that the IS fraction of the metatranscriptome is commonly double that of the IS fraction of the metagenome. From these data it is concluded that ISs occupy a significant part of Baltic Sea bacterial transcription activity, in line with their proposed function as facilitators of adaptive change to changing and stressful environments.

  • 22. Zheng, Weiwen
    et al.
    Rasmussen, Ulla
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Zheng, Siping
    Bao, Xiaodong
    Chen, Bin
    Gao, Yuan
    Guan, Xiong
    Larsson, John
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Multiple Modes of Cell Death Discovered in a Prokaryotic (Cyanobacterial) Endosymbiont2013In: PLOS ONE, E-ISSN 1932-6203, Vol. 8, no 6, p. e66147-Article in journal (Refereed)
    Abstract [en]

    Programmed cell death (PCD) is a genetically-based cell death mechanism with vital roles in eukaryotes. Although there is limited consensus on similar death mode programs in prokaryotes, emerging evidence suggest that PCD events are operative. Here we present cell death events in a cyanobacterium living endophytically in the fern Azolla microphylla, suggestive of PCD. This symbiosis is characterized by some unique traits such as a synchronized development, a vertical transfer of the cyanobacterium between plant generations, and a highly eroding cyanobacterial genome. A combination of methods was used to identify cell death modes in the cyanobacterium. Light- and electron microscopy analyses showed that the proportion of cells undergoing cell death peaked at 53.6% (average 20%) of the total cell population, depending on the cell type and host developmental stage. Biochemical markers used for early and late programmed cell death events related to apoptosis (Annexin V-EGFP and TUNEL staining assays), together with visualization of cytoskeleton alterations (FITC-phalloidin staining), showed that all cyanobacterial cell categories were affected by cell death. Transmission electron microscopy revealed four modes of cell death: apoptotic-like, autophagic-like, necrotic-like and autolytic-like. Abiotic stresses further enhanced cell death in a dose and time dependent manner. The data also suggest that dynamic changes in the peptidoglycan cell wall layer and in the cytoskeleton distribution patterns may act as markers for the various cell death modes. The presence of a metacaspase homolog (domain p20) further suggests that the death modes are genetically programmed. It is therefore concluded that multiple, likely genetically programmed, cell death modes exist in cyanobacteria, a finding that may be connected with the evolution of cell death in the plant kingdom.

1 - 22 of 22
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • 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