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Karlsson, Christofer M. G.
Publications (8 of 8) Show all publications
Karlsson, C. M. G., Cerro-Galvez, E., Lundin, D., Karlsson, C., Vila-Costa, M. & Pinhassi, J. (2019). Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341. Microbial Biotechnology, 12(5), 892-906
Open this publication in new window or tab >>Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341
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2019 (English)In: Microbial Biotechnology, ISSN 1751-7907, E-ISSN 1751-7915, Vol. 12, no 5, p. 892-906Article in journal (Refereed) Published
Abstract [en]

Organic pollutants (OPs) are critically toxic, bioaccumulative and globally widespread. Moreover, several OPs negatively influence aquatic wildlife. Although bacteria are major drivers of the ocean carbon cycle and the turnover of vital elements, there is limited knowledge of OP effects on heterotrophic bacterioplankton. We therefore investigated growth and gene expression responses of the Baltic Sea model bacterium Rheinheimera sp. BAL341 to environmentally relevant concentrations of distinct classes of OPs in 2-h incubation experiments. During exponential growth, exposure to a mix of polycyclic aromatic hydrocarbons, alkanes and organophosphate esters (denoted MIX) resulted in a significant decrease (between 9% and 18%) in bacterial abundance and production compared with controls. In contrast, combined exposure to perfluorooctanesulfonic acids and perfluorooctanoic acids (denoted PFAS) had no significant effect on growth. Nevertheless, MIX and PFAS exposures both induced significant shifts in gene expression profiles compared with controls in exponential growth. This involved several functional metabolism categories (e.g. stress response and fatty acids metabolism), some of which were pollutant-specific (e.g. phosphate acquisition and alkane-1 monooxygenase genes). In stationary phase, only two genes in the MIX treatment were significantly differentially expressed. The substantial direct influence of OPs on metabolism during bacterial growth suggests that widespread OPs could severely alter biogeochemical processes governed by bacterioplankton.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-86985 (URN)10.1111/1751-7915.13441 (DOI)000474143400001 ()31270938 (PubMedID)2-s2.0-85068617751 (Scopus ID)
Available from: 2019-07-25 Created: 2019-07-25 Last updated: 2019-11-25Bibliographically approved
Nilsson, E., Li, K., Fridlund, J., Sulcius, S., Bunse, C., Karlsson, C. M. G., . . . Holmfeldt, K. (2019). Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341. Applied and Environmental Microbiology, 85(18), 1-19, Article ID e01003-19.
Open this publication in new window or tab >>Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341
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2019 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 85, no 18, p. 1-19, article id e01003-19Article in journal (Refereed) Published
Abstract [en]

Knowledge in aquatic virology has been greatly improved by culture-independent methods, yet there is still a critical need for isolating novel phages to identify the large proportion of "unknowns" that dominate metagenomes and for detailed analyses of phage-host interactions. Here, 54 phages infecting Rheinheimem sp. strain BAL341 (Gammaproteobacteria) were isolated from Baltic Sea seawater and characterized through genome content analysis and comparative genomics. The phages showed a myovirus-like morphology and belonged to a novel genus, for which we propose the name Barbavirus. All phages had similar genome sizes and numbers of genes (80 to 84 kb; 134 to 145 genes), and based on average nucleotide identity and genome BLAST distance phylogeny, the phages were divided into five species. The phages possessed several genes involved in metabolic processes and host signaling, such as genes encoding ribonucleotide reductase and thymidylate synthase, phoH, and rnazG. One species had additional metabolic genes involved in pyridine nucleotide salvage, possibly providing a fitness advantage by further increasing the phages' replication efficiency. Recruitment of viral metagenomic reads (25 Baltic Sea viral metagenomes from 2012 to 2015) to the phage genomes showed pronounced seasonal variations, with increased relative abundances of barba phages in August and September synchronized with peaks in host abundances, as shown by 16S rRNA gene amplicon sequencing. Overall, this study provides detailed information regarding genetic diversity, phage-host interactions, and temporal dynamics of an ecologically important aquatic phage-host system. IMPORTANCE Phages are important in aquatic ecosystems as they influence their microbial hosts through lysis, gene transfer, transcriptional regulation, and expression of phage metabolic genes. Still, there is limited knowledge of how phages interact with their hosts, especially at fine scales. Here, a Rheinheimera phage-host system constituting highly similar phages infecting one host strain is presented. This relatively limited diversity has previously been seen only when smaller numbers of phages have been isolated and points toward ecological constraints affecting the Rheinheimera phage diversity. The variation of metabolic genes among the species points toward various fitness advantages, opening up possibilities for future hypothesis testing. Phage-host dynamics monitored over several years point toward recurring "kill-the-winner" oscillations and an ecological niche fulfilled by this system in the Baltic Sea. Identifying and quantifying ecological dynamics of such phage-host model systems in situ allow us to understand and study the influence of phages on aquatic ecosystems.

Place, publisher, year, edition, pages
American Society for Microbiology, 2019
Keywords
Baltic Sea, bacteriophage, genomics, temporal variation
National Category
Ecology Microbiology
Research subject
Ecology, Microbiology; Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-89282 (URN)10.1128/AEM.01003-19 (DOI)000483596700008 ()31324626 (PubMedID)
Available from: 2019-09-25 Created: 2019-09-25 Last updated: 2019-10-01Bibliographically approved
Alneberg, J., Karlsson, C. M. G., Divne, A.-M., Bergin, C., Homa, F., Lindh, M. V., . . . Pinhassi, J. (2018). Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. Microbiome, 6, Article ID 173.
Open this publication in new window or tab >>Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
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2018 (English)In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 6, article id 173Article in journal (Refereed) Published
Abstract [en]

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

Place, publisher, year, edition, pages
BioMed Central, 2018
Keywords
Single-amplified genomes, Metagenome-assembled genomes, Metagenomics, Binning, Single-cell genomics
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-78465 (URN)10.1186/s40168-018-0550-0 (DOI)000446307400001 ()30266101 (PubMedID)2-s2.0-85054254141 (Scopus ID)
Available from: 2018-10-24 Created: 2018-10-24 Last updated: 2019-11-25Bibliographically approved
Sjöstedt, J., Langenheder, S., Kritzberg, E., Karlsson, C. M. G. & Lindström, E. S. (2018). Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community. Environmental Microbiology Reports, 10(4), 493-500
Open this publication in new window or tab >>Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community
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2018 (English)In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, no 4, p. 493-500Article in journal (Refereed) Published
Abstract [en]

Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2018
National Category
Microbiology Ecology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-77730 (URN)10.1111/1758-2229.12656 (DOI)000442577600011 ()29733107 (PubMedID)2-s2.0-85050464256 (Scopus ID)
Available from: 2018-09-13 Created: 2018-09-13 Last updated: 2019-08-29Bibliographically approved
Bunse, C., Lundin, D., Karlsson, C. M. G., Akram, N., Vila-Costa, M., Palovaara, J., . . . Pinhassi, J. (2016). Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2. Nature Climate Change, 6(5), 483-487
Open this publication in new window or tab >>Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2
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2016 (English)In: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 6, no 5, p. 483-487Article in journal (Refereed) Published
Abstract [en]

Human-induced ocean acidification impacts marine life. Marine bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes1; hence, understanding their performance under projected climate change scenarios is crucial for assessing ecosystem functioning. Whereas genetic and physiological responses of phytoplankton to ocean acidification are being disentangled2, 3, 4, corresponding functional responses of bacterioplankton to pH reduction from elevated CO2 are essentially unknown. Here we show, from metatranscriptome analyses of a phytoplankton bloom mesocosm experiment, that marine bacteria responded to lowered pH by enhancing the expression of genes encoding proton pumps, such as respiration complexes, proteorhodopsin and membrane transporters. Moreover, taxonomic transcript analysis showed that distinct bacterial groups expressed different pH homeostasis genes in response to elevated CO2. These responses were substantial for numerous pH homeostasis genes under low-chlorophyll conditions (chlorophyll a <2.5 μg l−1); however, the changes in gene expression under high-chlorophyll conditions (chlorophyll a >20 μg l−1) were low. Given that proton expulsion through pH homeostasis mechanisms is energetically costly, these findings suggest that bacterioplankton adaptation to ocean acidification could have long-term effects on the economy of ocean ecosystems.

National Category
Microbiology Ecology Climate Research
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-49969 (URN)10.1038/nclimate2914 (DOI)000375125200015 ()2-s2.0-84964949342 (Scopus ID)
Projects
EcoChange
Available from: 2016-02-29 Created: 2016-02-29 Last updated: 2019-11-25Bibliographically approved
Karlsson, C. M. G., Lundin, D., Karlsson, C., Teikari, J. E., Moran, M. A. & Pinhassi, J.Different gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter.
Open this publication in new window or tab >>Different gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Phytoplankton release massive amounts of dissolved organic matter (DOM) into the water column during recurring blooms in coastal waters and inland seas. The released DOM includes dissolved organic carbon, nitrogen and phosphorus, in a complex mixture of both known and unknown compounds, and is a rich nutrient source for heterotrophic bacteria. The metabolic activity of heterotrophic bacteria during and after phytoplankton blooms can hence be expected to reflect the characteristics of the released DOM. With this in mind, we wanted to investigate if bacterioplankton could be used as “living sensors” of phytoplankton DOM quantity and quality, and to trace the flow of nutrients in the ecosystem. We used transcriptional activity from Baltic Sea bacterial isolates (Polaribacter sp. BAL334 (Flavobacteriia) and Brevundimonas sp. BAL450 (Alphaproteobacteria)) exposed to DOM derived from the dinoflagellate Prorocentrum minimum in exponential and stationary growth phases respectively. We observed strong responses both in terms of physiology – bacterial abundance – and the expressed metabolic pathways – e.g. Membrane Transport, Fatty Acids, Lipids and Isoprenoids – of the populations in samples exposed to dinoflagellate DOM compared with controls. Particularly striking was the increased expression of Ton and Tol transport systems, commonly associated with uptake of complex molecules, in both isolates. Equally important were the differences in metabolic responses between the two isolates, caused by differences in gene repertoire between them, emphasizing the importance of separating the responses of different taxa in analyses of community sequence data. Differences in response to DOM sourced from exponentially and stationary growing dinoflagellates were less pronounced, although not absent, than differences between the bacterial isolates. This suggests that shifts in metabolism during the different phases of a phytoplankton bloom might be detectable in individual bacterial populations. To conclude, our work opened a door to the future use of bacterioplankton as living sensors of environmental status, particularly with respect to phytoplankton blooms.

Keywords
Alphaproteobacteria, Brevundimonas sp., Flavobacteria, mRNA, phytoplankton exudation, Polaribacter sp., Prorocentrum minimum
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-90255 (URN)
Available from: 2019-11-25 Created: 2019-11-25 Last updated: 2019-11-29Bibliographically approved
Karlsson, C. M. G., Pontiller, B., Teikari, J. E., Traving, S. J., Happel, E. M., Henke, B., . . . Pinhassi, J.Metatranscriptomic analysis uncovers divergent responses of Baltic Sea bacteria to forest and agriculture river loadings.
Open this publication in new window or tab >>Metatranscriptomic analysis uncovers divergent responses of Baltic Sea bacteria to forest and agriculture river loadings
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Climate change is predicted to induce substantial changes in precipitation patterns across the globe. In Northern Europe, precipitation is expected to increase more than the global average (particularly in northern Scandinavia), causing increased river runoff. The Baltic Sea is one of the largest brackish environments on earth with a catchment area that spans 14 countries, encompassing primarily forested areas and agricultural landscapes. Despite the acknowledged role of marine bacteria in nutrient cycling, there is a lack of knowledge in their metabolic responses to inorganic and organic nutrient loading from riverine runoff. We investigated the bacterial growth and gene expression responses in a mesocosm experiment in which river water from boreal forest- (enriched in humic substances) or agriculture- influenced catchment areas were added to Baltic Sea Proper water. The riverine nutrient input triggered extensive phytoplankton blooms and bacterial growth, most notably in the agriculture river treatment. Interestingly, bacterial gene expression analysis (metatranscriptomics) showed similar responses to agriculture and humic river inputs at the start of the experiment (before the phytoplankton bloom), but expression patterns diverged significantly upon bloom senescence.Notably, transcripts associated with phosphate metabolism were significantly enriched , whereas transcripts related to nitrogen metabolism were significantly lower in the agriculture river treatment compared to the boreal forest river treatment. The opposite pattern was observed in the boreal forest river water treatment. Overall, our results showed that interactions between river nutrient loading and phytoplankton organic matter are important in regulating bacterial activities and responses at the molecular level. This suggests that bacterial transformations of organic matter and nutrient cycling in coastal waters and estuarine environments are sensitive to changes in precipitation patterns in a catchment area-dependent manner.

Keywords
Marine bacteria, nutrient loading, dissolved organic carbon, dissolved organic nitrogen, phytoplankton bloom, humic substances
National Category
Biological Sciences
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-90254 (URN)
Available from: 2019-11-25 Created: 2019-11-25 Last updated: 2019-11-29Bibliographically approved
Bunse, C., Lundin, D., Lindh, M. V., Sjöstedt, J., Israelsson, S., Martínez-García, S., . . . Pinhassi, J.Seasonality and co-occurrences of free-living Baltic Sea bacterioplankton.
Open this publication in new window or tab >>Seasonality and co-occurrences of free-living Baltic Sea bacterioplankton
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(English)Manuscript (preprint) (Other academic)
Keywords
seasonal succession, marine bacteria, amplicon 16S rRNA, microbial time series, highfrequency sampling
National Category
Environmental Sciences Microbiology Oceanography, Hydrology and Water Resources
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-69150 (URN)
Available from: 2017-12-11 Created: 2017-12-11 Last updated: 2019-02-27Bibliographically approved
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