Change search
Link to record
Permanent link

Direct link
Bergman, Birgitta
Publications (10 of 65) Show all publications
Berg, C., Dupont, C. L., Asplund-Samuelsson, J., Celepli, N. A., Eiler, A., Allen, A. E., . . . Ininbergs, K. (2018). Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics. Frontiers in Marine Science, Article ID UNSP 55.
Open this publication in new window or tab >>Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics
Show others...
2018 (English)In: Frontiers in Marine Science, E-ISSN 2296-7745, article id UNSP 55Article in journal (Refereed) Published
Abstract [en]

Marine and brackish surface waters are highly dynamic habitats that undergo repeated seasonal variations in microbial community composition and function throughout time. While succession of the various microbial groups has been well investigated, little is known about the underlying gene-expression of the microbial community. We investigated microbial interactions via metatranscriptomics over a spring to fall seasonal cycle in the brackish Baltic Sea surface waters, a temperate brackish water ecosystem periodically promoting massive cyanobacterial blooms, which have implications for primary production, nutrient cycling, and expansion of hypoxic zones. Network analysis of the gene expression of all microbes from 0.22 to 200 mu m in size and of the major taxonomic groups dissected the seasonal cycle into four components that comprised genes peaking during different periods of the bloom. Photoautotrophic nitrogen-fixing Cyanobacteria displayed the highest connectivity among the microbes, in contrast to chemoautotrophic ammonia-oxidizing Thaumarchaeota, while heterotrophs dominated connectivity among pre- and post-bloom peaking genes. The network was also composed of distinct functional connectivities, with an early season balance between carbon metabolism and ATP synthesis shifting to a dominance of ATP synthesis during the bloom, while carbon degradation, specifically through the glyoxylate shunt, characterized the post-bloom period, driven by Alphaproteobacteria as well as by Gammaproteobacteria of the SAR86 and SAR92 clusters. Our study stresses the exceptionally strong biotic driving force executed by cyanobacterial blooms on associated microbial communities in the Baltic Sea and highlights the impact cyanobacterial blooms have on functional microbial community composition.

Keywords
cyanobacteria, Baltic Sea, metatranscriptomics, WGCNA, glyoxylate shunt, autotrophy, nifH, amoA
National Category
Earth and Related Environmental Sciences Biological Sciences
Identifiers
urn:nbn:se:su:diva-166875 (URN)10.3389/fmars.2018.00055 (DOI)000456927900001 ()
Available from: 2019-03-06 Created: 2019-03-06 Last updated: 2022-03-23Bibliographically approved
Vigil-Stenman, T., Ininbergs, K., Bergman, B. & Ekman, M. (2017). High abundance and expression of transposases in bacteria from the Baltic Sea. The ISME Journal, 11(11), 2611-2623
Open this publication in new window or tab >>High abundance and expression of transposases in bacteria from the Baltic Sea
2017 (English)In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 11, no 11, p. 2611-2623Article in journal (Refereed) Published
Abstract [en]

Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200 mu m) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments. Large variations in expression were found between transposase families and groups of bacteria, with a two-fold higher transcription in Cyanobacteria than in any other phylum. The community-level results were corroborated at the genus level by Synechococcus transposases reaching up to 5.2% of genes and 6.9% of transcripts, which is in contrast to marine Synechococcus that largely lack these genes. Levels peaked in Synechococcus from the largest size fraction, suggesting high frequencies of lateral gene transfer and high genome plasticity in colony-forming picocyanobacteria. Together, the results support an elevated rate of transposition-based genome change and adaptation in bacterial populations of the Baltic Sea, and possibly also of other highly dynamic estuarine waters.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-148964 (URN)10.1038/ismej.2017.114 (DOI)000413240100016 ()28731472 (PubMedID)
Available from: 2017-12-08 Created: 2017-12-08 Last updated: 2022-03-23Bibliographically approved
Celepli, N., Sundh, J., Ekman, M., Dupont, C. L., Yooseph, S., Bergman, B. & Ininbergs, K. (2017). Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation. Environmental Microbiology, 19(2), 673-686
Open this publication in new window or tab >>Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation
Show others...
2017 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 2, p. 673-686Article in journal (Refereed) Published
Abstract [en]

Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradients in salinity and nutrient concentrations. Here, we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa. Cyanobacteria in the Baltic Sea differed genetically from those in adjacent limnic and marine waters as well as from cultivated and sequenced picocyanobacterial strains. Diversity peaked at brackish salinities 3.5-16psu, with low N:P ratios. A shift in community composition from brackish to marine strains was accompanied by a change in the repertoire and expression of genes involved in salt acclimation. Overall, the pre-bloom cyanobacterial population was more genetically diverse, widespread and abundant than previously documented, with unicellular picocyanobacteria being the most abundant clade along the entire Baltic Sea salinity gradient.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-142535 (URN)10.1111/1462-2920.13592 (DOI)000394973000025 ()27871145 (PubMedID)
Available from: 2017-05-08 Created: 2017-05-08 Last updated: 2022-03-23Bibliographically approved
Alcamán, M. E., Alcorta, J., Bergman, B., Vásquez, M., Polz, M. & Díez, B. (2017). Physiological and gene expression responses to nitrogen regimes and temperatures in Mastigocladus sp strain CHP1, a predominant thermotolerant cyanobacterium of hot springs. Systematic and Applied Microbiology, 40(2), 102-113
Open this publication in new window or tab >>Physiological and gene expression responses to nitrogen regimes and temperatures in Mastigocladus sp strain CHP1, a predominant thermotolerant cyanobacterium of hot springs
Show others...
2017 (English)In: Systematic and Applied Microbiology, ISSN 0723-2020, E-ISSN 1618-0984, Vol. 40, no 2, p. 102-113Article in journal (Refereed) Published
Abstract [en]

Cyanobacteria are widely distributed primary producers with significant implications for the global biogeochemical cycles of carbon and nitrogen. Diazotrophic cyanobacteria of subsection V (Order Stigonematales) are particularly ubiquitous in photoautotrophic microbial mats of hot springs. The Stigonematal cyanobacterium strain CHPI isolated from the Porcelana hot spring (Chile) was one of the major contributors of the new nitrogen through nitrogen fixation. Further morphological and genetic characterization verified that the strain CHP1 belongs to Stigonematales, and it formed a separate Glade together with other thermophiles of the genera Fischerella and Mastigocladus. Strain CHP1 fixed maximum N-2 in the light, independent of the temperature range. At 50 degrees C niJH gene transcripts showed high expression during the light period, whereas the nifH gene expression at 45 degrees C was arrhythmic. The strain displayed a high affinity for nitrate and a low tolerance for high ammonium concentrations, whereas the narB and glnA genes showed higher expression in light and at the beginning of the dark phase. It is proposed that Mastigocladus sp. strain CHPI would represent a good model for the study of subsection V thermophilic cyanobacteria, and for understanding the adaptations of these photoautotrophic organisms inhabiting microbial mats in hot springs globally.

Keywords
Gene expression, Mastigocladus sp., Nitrate/ammonium preference, Thermotolerance
National Category
Environmental Biotechnology Biological Sciences
Identifiers
urn:nbn:se:su:diva-142478 (URN)10.1016/j.syapm.2016.11.007 (DOI)000395610300005 ()28081924 (PubMedID)
Available from: 2017-05-17 Created: 2017-05-17 Last updated: 2022-02-28Bibliographically approved
Hamisi, M. I., Lugomela, C., Lyimo, T. J., Bergman, B. & Díez, B. (2017). Plankton composition, biomass, phylogeny and toxin genes in Lake Big Momela, Tanzania. African Journal of Aquatic Science, 42(2), 109-121
Open this publication in new window or tab >>Plankton composition, biomass, phylogeny and toxin genes in Lake Big Momela, Tanzania
Show others...
2017 (English)In: African Journal of Aquatic Science, ISSN 1608-5914, E-ISSN 1727-9364, Vol. 42, no 2, p. 109-121Article in journal (Refereed) Published
Abstract [en]

Lake Big Momela, one of the East African soda lakes in Northern Tanzania characterised by highly saline-alkaline conditions, making them inhospitable to a range of organisms, although supporting massive growths of some adapted planktonic microorganisms that serve as food for birds, such as Lesser Flamingo. The temporal dynamics of plankton, with an emphasis on cyanobacteria, were examined in 2007 using morphological traits and ribosomal genetic markers (16S and 18S rRNA). Cyanobacterial genes encoding for hepatotoxins (mcyE and ndaF) were also screened. Rotifers and copepods dominated the zooplankton, whereas cyanobacteria, such as Anabaenopsis elenkinii and Arthrospira fusiformis dominated the phytoplankton community, and these being related to representatives in other East African soda lakes. The cyanobacteria community also showed distinct seasonal patterns influenced by environmental parameters, mainly salinity, pH and nitrate. Significant positive correlations were found between phytoplankton abundance and nitrate concentrations (r = 0.617, p = 0.033). No signals of the hepatotoxin synthetase genes mcyE and ndaF were retrieved from cyanobacteria during the whole year. In general, our data illustrate the presence of rich planktonic communities, including some unique and potentially endemic cyanobacteria.

Keywords
cyanotoxin, limnology, plankton diversity, soda lakes
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-148106 (URN)10.2989/16085914.2017.1334621 (DOI)000410575700003 ()
Available from: 2017-10-18 Created: 2017-10-18 Last updated: 2022-02-28Bibliographically approved
Allen, L. Z., McCrow, J. P., Ininbergs, K., Dupont, C. L., Badger, J. H., Hoffman, J. M., . . . Venter, J. C. (2017). The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses. mSystems, 2(1), Article ID UNSP e00125-16.
Open this publication in new window or tab >>The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
Show others...
2017 (English)In: mSystems, E-ISSN 2379-5077, Vol. 2, no 1, article id UNSP e00125-16Article in journal (Refereed) Published
Abstract [en]

Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Tornetrask in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Tornetrask. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.

Keywords
marine microbiology, viral ecology, viral metagenomics, viral metatranscriptomics, viral/host inference
National Category
Environmental Sciences Ecology
Identifiers
urn:nbn:se:su:diva-147242 (URN)10.1128/mSystems.00125-16 (DOI)000408193500005 ()
Available from: 2017-09-20 Created: 2017-09-20 Last updated: 2022-03-23Bibliographically approved
Brindefalk, B., Ekman, M., Ininbergs, K., Dupont, C. L., Yooseph, S., Pinhassi, J. & Bergman, B. (2016). Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters. Environmental Microbiology, 18(12), 4442-4455
Open this publication in new window or tab >>Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters
Show others...
2016 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4442-4455Article in journal (Refereed) Published
Abstract [en]

Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from similar to 0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 mu m), relative to the medium (0.8-3.0 mu m) and large (> 3.0 mu m) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-140253 (URN)10.1111/1462-2920.13407 (DOI)000392946900012 ()27306515 (PubMedID)
Available from: 2017-03-15 Created: 2017-03-15 Last updated: 2022-03-23Bibliographically approved
Díez, B., Nylander, J. A. A., Ininbergs, K., Dupont, C. L., Allen, A. E., Yooseph, S., . . . Bergman, B. (2016). Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution. PLOS ONE, 11(5), Article ID e0155757.
Open this publication in new window or tab >>Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution
Show others...
2016 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 5, article id e0155757Article in journal (Refereed) Published
Abstract [en]

Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 mu m to 20 mu m and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial lightharvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.

National Category
Microbiology
Identifiers
urn:nbn:se:su:diva-132074 (URN)10.1371/journal.pone.0155757 (DOI)000376291100096 ()27196065 (PubMedID)2-s2.0-84973636378 (Scopus ID)
Available from: 2016-07-06 Created: 2016-07-06 Last updated: 2022-06-21Bibliographically approved
Berntzon, L., Ronnevi, L. O., Bergman, B. & Eriksson, J. (2015). DETECTION OF BMAA IN THE HUMAN CENTRAL NERVOUS SYSTEM. Neuroscience, 292, 137-147
Open this publication in new window or tab >>DETECTION OF BMAA IN THE HUMAN CENTRAL NERVOUS SYSTEM
2015 (English)In: Neuroscience, ISSN 0306-4522, E-ISSN 1873-7544, Vol. 292, p. 137-147Article in journal (Refereed) Published
Abstract [en]

Amyotrophic lateral sclerosis (ALS) is an extremely devastating neurodegenerative disease with an obscure etiology. The amino acid beta-N-methyl-L-alanine (BMAA) produced by globally widespread phytoplankton has been implicated in the etiology of human motor neuron diseases. BMAA was recently proven to be present in Baltic Sea food webs, ranging from plankton to larger Baltic Sea organisms, some serving as important food items (fish) for humans. To test whether exposure to BMAA in a Baltic Sea setting is reflected in humans, blood and cerebrospinal fluid (CSF) from individuals suffering from ALS were analyzed, together with sex- and age-matched individuals not inflicted with ALS. Ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) and multiple reaction monitoring (MRM), in conjunction with diagnostic transitions revealed BMAA in three (12%) of the totally 25 Swedish individuals tested, with no preference for those suffering from ALS. The three BMAA-positive samples were all retrieved from the CSF, while BMAA was not detected in the blood. The data show that BMAA, potentially originating from Baltic Sea phytoplankton, may reach the human central nervous system, but does not lend support to the notion that BMAA is resident specifically in ALS-patients. However, while dietary exposure to BMAA may be intermittent and, if so, difficult to detect, our data provide the first demonstration of BMAA in the central nervous system of human individuals ante mortem quantified with UHPLC-MS/MS, and therefore calls for extended research efforts.

Keywords
neurotoxin, BMAA, neurodegeneration, ALS, CSF, blood
National Category
Neurosciences Biological Sciences
Research subject
Plant Physiology
Identifiers
urn:nbn:se:su:diva-116750 (URN)10.1016/j.neuroscience.2015.02.032 (DOI)000351664700013 ()25725357 (PubMedID)
Note

AuthorCount:4;

Available from: 2015-05-12 Created: 2015-04-27 Last updated: 2022-03-23Bibliographically approved
Plominsky, A. M., Delherbe, N., Mandakovic, D., Riquelme, B., Gonzalez, K., Bergman, B., . . . Vasquez, M. (2015). Intercellular transfer along the trichomes of the invasive terminal heterocyst forming cyanobacterium Cylindrospermopsis raciborskii CS-505. FEMS Microbiology Letters, 362(5)
Open this publication in new window or tab >>Intercellular transfer along the trichomes of the invasive terminal heterocyst forming cyanobacterium Cylindrospermopsis raciborskii CS-505
Show others...
2015 (English)In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 362, no 5Article in journal (Refereed) Published
Abstract [en]

Cylindrospermopsis raciborskii CS-505 is an invasive freshwater filamentous cyanobacterium that when grown diazotrophically may develop trichomes of up to 100 vegetative cells while differentiating only two end heterocysts, the sole sites for their N-2-fixation process. We examined the diazotrophic growth and intercellular transfer mechanisms in C. raciborskii CS-505. Subjecting cultures to a combined-nitrogen-free medium to elicit N-2 fixation, the trichome length remained unaffected while growth rates decreased. The structures and proteins for intercellular communication showed that while a continuous periplasmic space was apparent along the trichomes, the putative septal junction sepJ gene is divided into two open reading frames and lacks several transmembrane domains unlike the situation in Anabaena, differentiating a 5-fold higher frequency of heterocysts. FRAP analyses also showed that the dyes calcein and 5-CFDA were taken up by heterocysts and vegetative cells, and that the transfer from heterocysts and 'terminal' vegetative cells showed considerably higher transfer rates than that from vegetative cells located in the middle of the trichomes. The data suggest that C. raciborskii CS-505 compensates its low-frequency heterocyst phenotype by a highly efficient transfer of the fixed nitrogen towards cells in distal parts of the trichomes (growing rapidly) while cells in central parts suffers (slow growth).

Keywords
Cylindrospermopsis raciborskii, intercellular transfer, diazotrophy
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-119010 (URN)10.1093/femsle/fnu009 (DOI)000356885500001 ()
Available from: 2015-07-28 Created: 2015-07-24 Last updated: 2022-02-23Bibliographically approved
Organisations

Search in DiVA

Show all publications