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  • 1.
    Degerholm, Jenny
    et al.
    Stockholm University.
    Gundersen, Kjell
    Stockholm University.
    Bergman, Birgitta
    Stockholm University.
    Söderbäck, Erik
    Stockholm University.
    Phosphorus-limited growth dynamics in two Baltic Sea cyanobacteria, Nodularia sp and Aphanizomenon sp.2006In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 58, no 3, p. 323-332Article in journal (Refereed)
    Abstract [en]

    Rates of carbon (C) specific growth and nitrogen (N(2)) fixation were monitored in cultures of Baltic Sea Nodularia and Aphanizomenon exposed to gradual limitation by inorganic phosphorus (P). Both cyanobacteria responded by decreased cellular P content followed by lowered rates of growth and N(2) fixation. C-specific growth and cellular N content changed faster in Aphanizomenon both when inorganic P was lowered as well as during reintroduction of P. Aphanizomenon also showed a more rapid increase in N-specific N(2) fixation associated with increased C-specific growth. When ambient concentrations of inorganic P declined, both cyanobacteria displayed higher rates of alkaline phosphatase (APase) activity. Lower substrate half-saturation constants (K(M)) and higher V(max) : K(M) ratio of the APase enzyme associated with Nodularia suggest a higher affinity for dissolved organic P (DOP) substrate than Aphanizomenon. Aphanizomenon, which appears more sensitive to changes in ambient dissolved inorganic P, may be adapted to environments with elevated concentrations of P or repeated intrusions of nutrient-rich water. Nodularia on the other hand, with its higher tolerance to increased P starvation may have an ecological advantage in stratified surface waters of the Baltic Sea during periods of low P availability.

  • 2.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences.
    Jansson, Janet K.
    Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments2008In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 65, no 3, p. 513-525Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to enrich and identify psychrotolerant phenanthrene-degrading bacteria from polluted Baltic Sea sediments. Polyaromatic hydrocarbon (PAH)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the DNA of replicating cells. The bromodeoxyuridine-incorporated DNA was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16S rRNA gene cloning and sequencing to identify bacterial populations that were growing. In addition, degradation genes were quantified in the bromodeoxyuridine-incorporated DNA by real-time PCR. Phenanthrene concentrations decreased after 2 months of incubation in the phenanthrene-enriched sediments and this reduction correlated to increases in copy numbers of xylE and phnAc dioxygenase genes. Representatives of Exiguobacterium, Schewanella, Methylomonas, Pseudomonas, Bacteroides and an uncultured Deltaproteobacterium and a Gammaproteobacterium dominated the growing community in the phenanthrene-spiked sediments. Isolates that were closely related to three of these bacteria (two pseudomonads and an Exiguobacterium sp.) could reduce phenanthrene concentrations in pure cultures and they all harbored phnAc dioxygenase genes. These results confirm that this combination of culture-based and molecular approaches was useful for identification of actively growing bacterial species with a high potential for phenanthrene degradation.

  • 3.
    Hjort, Karin
    et al.
    Södertörn University, School of Life Sciences, Molecular biology.
    Bergström, Maria
    Adesina, Modupe F.
    Jansson, Janet K.
    Smalla, Kornelia
    Sjöling, Sara
    Södertörn University, School of Life Sciences, Environmental science. Södertörn University, School of Life Sciences, Molecular biology.
    Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil2010In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 71, no 2, p. 197-207Article in journal (Refereed)
    Abstract [en]

    Soil that is suppressive to disease caused by fungal pathogens is an interesting source to target for novel chitinases that might be contributing towards disease suppression. In this study, we screened for chitinase genes, in a phytopathogen-suppressive soil in three ways: (1) from a metagenomic library constructed from microbial cells extracted from soil, (2) from directly extracted DNA and (3) from bacterial isolates with antifungal and chitinase activities. Terminal restriction fragment length polymorphism (T-RFLP) of chitinase genes revealed differences in amplified chitinase genes from the metagenomic library and the directly extracted DNA, but approximately 40% of the identified chitinase terminal restriction fragments (TRFs) were found in both sources. All of the chitinase TRFs from the isolates were matched to TRFs in the directly extracted DNA and the metagenomic library. The most abundant chitinase TRF in the soil DNA and the metagenomic library corresponded to the TRF103 of the isolate Streptomyces mutomycini and/or Streptomyces clavifer. There were good matches between T-RFLP profiles of chitinase gene fragments obtained from different sources of DNA. However, there were also differences in both the chitinase and the 16S rRNA gene T-RFLP patterns depending on the source of DNA, emphasizing the lack of complete coverage of the gene diversity by any of the approaches used.

  • 4.
    Hårdeman, Fredrik
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Sjöling, Sara
    Södertörn University, School of Life Sciences.
    Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment2007In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 59, no 2, p. 524-534Article in journal (Refereed)
    Abstract [en]

    A novel lipase was isolated from a metagenomic library of Baltic Sea sediment bacteria. Prokaryotic DNA was extracted and cloned into a copy control fosmid vector (pCC1FOS) generating a library of > 7000 clones with inserts of 24-39 kb. Screening for clones expressing lipolytic activity based on the hydrolysis of tributyrin and p-nitrophenyl esters, identified 1% of the fosmids as positive. An insert of 29 kb was fragmented and subcloned. Subclones with lipolytic activity were sequenced and an open reading frame of 978 bp encoding a 35.4-kDa putative lipase/esterase h1Lip1 (DQ118648) with 54% amino acid similarity to a Pseudomomas putida esterase (BAD07370) was identified. Conserved regions, including the putative active site, GDSAG, a catalytic triad (Ser148, Glu242 and His272) and a HGG motif, were identified. The h1Lip1 lipase was over expressed, (pGEX-6P-3 vector), purified and shown to hydrolyse p-nitrophenyl esters of fatty acids with chain lengths up to C-14. Hydrolysis of the triglyceride derivative 1,2-di-O-lauryl-rac-glycero-3-glutaric acid 6'-methylresorufin ester (DGGR) confirmed that h1Lip1 was a lipase. The apparent optimal temperature for h1Lip1, by hydrolysis of p-nitrophenyl butyrate, was 35 degrees C. Thermal stability analysis showed that h1Lip1 was unstable at 25 degrees C and inactivated at 40 degrees C with t(1/2) < 5 min.

  • 5.
    Jernberg, Cecilia
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Jansson, Janet K
    Södertörn University, Avdelning Naturvetenskap.
    Impact of 4-chlorophenol contamination and/or inoculation with the 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L, on soil bacterial community structure2002In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 42, no 3, p. 387-97Article in journal (Refereed)
    Abstract [en]

    The 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L (chromosomally tagged with the firefly luciferase gene, luc) was inoculated into 4-chlorophenol-contaminated soil to assess the impact of bioaugmentation with a biodegrading strain on the indigenous microbiota. Simultaneously, the impact of 4-chlorophenol alone, or inoculation with A. chlorophenolicus into non-contaminated soil, was addressed. Using terminal restriction fragment length polymorphism (T-RFLP) several significant changes were detected in community fingerprint patterns obtained from soil microcosms treated under the different conditions. The relative abundances of some populations, as judged by the relative intensity of terminal restriction fragments, were significantly impacted by either 4-chlorophenol, A. chlorophenolicus inoculation, or by a combination of both inoculation and 4-chlorophenol contamination. Some populations were significantly stimulated and others were significantly repressed when compared to control soil with no additions. For several peaks, the positive or negative impact imposed by the treatments increased over the 13-day incubation period. Some members of the bacterial community were specifically sensitive to A. chlorophenolicus inoculation or to 4-chlorophenol contamination, whereas other populations remained relatively unaffected by any of the treatments. The A. chlorophenolicus inoculum was also monitored by T-RFLP and was found to have a significantly higher relative abundance in soil contaminated with 4-chlorophenol. These results were substantiated by a high correlation to luciferase activity measurements and the number of colony forming units of the inoculum. Therefore, the A. chlorophenolicus A6L population was positively stimulated by the presence of the 4-chlorophenol substrate (180 microg g(-1) soil) that it catabolized during the first 8 days of the incubation period as a carbon and energy source. Together, these results demonstrate that specific populations in the soil bacterial community rapidly fluctuated in response to specific disturbances and the resulting shifts in the community may therefore represent an adjustment in community structure favoring those populations best capable of responding to novel stress scenarios.

  • 6.
    López, J L
    et al.
    Universidad de Buenos Aires, Argentina.
    Golemba, M
    Hospital de Pediatría "Juan P. Garrahan", Argentina.
    Hernández, E
    UNSAM Campus Miguelete, Argentina / Universidad de Buenos Aires, Argentina.
    Lozada, M
    Centro Nacional Patagónico-CONICET, Argentina.
    Dionisi, H M
    Centro Nacional Patagónico-CONICET, Argentina.
    Jansson, J
    Pacific Northwest National Laboratory, Richland, WA, USA.
    Carroll, J
    UiT The Arctic University of Norway, Tromsø, Norway / Fram - High North Research Centre for Climate and the Environment, Tromsø, Norway.
    Lundgren, L
    Stockholm University.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Cormack, W P Mac
    UNSAM Campus Miguelete, Argentina / Universidad de Buenos Aires, Argentina.
    Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions.2017In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 93, no 1, article id fiw216Article in journal (Refereed)
    Abstract [en]

    Rhodopsins are broadly distributed. In this work we analyzed 23 metagenomes corresponding to marine sediment samples from four regions which share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral-rodopsins, an initial set of 6224 bacterial rhodopsins sequences according COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment 123 viral (51) and non-viral (72) sequences (>50 aminoacids) were finally included in further analysis. Viral rhodopsin genes were homologues of Phaeocystis globosa virus and Organic lake Phycodnavirus Non-viral microbial rhodopsin genes were ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus as well as Cryptophyta and Fungi. A re-screening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 aminoacids). Phylogeographic analysis revealed a geographycal clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsins (PAVR) genes related to Actinobacteria and Chloroflexi This is the first report about the existence of a phylogeographic association of the viral rhodopsins sequences from marine sediments.

  • 7.
    Ma, Shiyu
    et al.
    Ghent University, Gontrode, Belgium.
    De Frenne, Pieter
    Ghent University, Gontrode, Belgium.
    Boon, Nico
    Ghent University, Ghent, Belgium.
    Brunet, Jörg
    Swedish University of Agricultural Sciences.
    Cousins, Sara A O
    Stockholm University.
    Decocq, Guillaume
    University of Picardy Jules Verne, Amiens, France.
    Kolb, Annette
    University of Bremen, Bremen, Germany.
    Lemke, Isa
    University of Bremen, Bremen, Germany.
    Liira, Jaan
    University of Tartu, Tartu, Estonia.
    Naaf, Tobias
    Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.
    Orczewska, Anna
    University of Silesia, Katowice, Poland.
    Plue, Jan
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science. Stockholm University.
    Wulf, Monika
    Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.
    Verheyen, Kris
    Ghent University, Gontrode, Belgium.
    Plant species identity and soil characteristics determine rhizosphere soil bacteria community composition in European temperate forests2019In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 95, no 6, article id fiz063Article in journal (Refereed)
    Abstract [en]

    Soil bacteria and understorey plants interact and drive forest ecosystem functioning. Yet, knowledge about biotic and abiotic factors that affect the composition of the bacterial community in the rhizosphere of understorey plants is largely lacking. Here, we assessed the effects of plant species identity (Milium effusum vs Stachys sylvatica), rhizospheric soil characteristics, large-scale environmental conditions (temperature, precipitation and nitrogen (N) deposition), and land-use history (ancient vs recent forests) on bacterial community composition in rhizosphere soil in temperate forests along a 1700 km latitudinal gradient in Europe. The dominant bacterial phyla in the rhizosphere soil of both plant species were Acidobacteria, Actinobacteria and Proteobacteria. Bacterial community composition differed significantly between the two plant species. Within plant species, soil chemistry was the most important factor determining soil bacterial community composition. More precisely, soil acidity correlated with the presence of multiple phyla, e.g. Acidobacteria (negatively), Chlamydiae (negatively) and Nitrospirae (positively), in both plant species. Large-scale environmental conditions were only important in S. sylvatica and land-use history was not important in either of the plant species. The observed role of understorey plant species identity and rhizosphere soil characteristics in determining soil bacterial community composition extends our understanding of plant-soil bacteria interactions in forest ecosystem functioning.

  • 8.
    Maraha, Ninwe
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Backman, Agneta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Jansson, Janet K
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. SLU.
    Monitoring physiological status of GFP-tagged Pseudomonas fluorescens SBW25 under different nutrient conditions and in soil by flow cytometry2004In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 51, no 1, p. 123-132Article in journal (Refereed)
    Abstract [en]

    Pseudomonas fluorescens SBW25, a plant growth promoting bacterium. has been widely studied due to its potential as an inoculum for improving crop yields. Environmental inoculants are usually applied oil seeds or directly to soil and to effectively promote plant growth they need to be viable and active. However, it is difficult to study the physiological status of specific microorganisms in complex environments, such as soil. In this study, our aim was to use molecular tools to specifically monitor the physiological status of P. fluorescens SBW25 in soil and ill pure cultures incubated under different nutritional conditions. The cells were previously tagged with marker genes (encoding green fluorescent protein and bacterial luciferase) to specifically track the cells in environmental samples. The physiological status of the cells was determined using the viability stains 5-cyano-2,3-ditolyl-tetrazolium chloride (CTC) and propidium iodide (PI), which stain active and dead cells, respectively. Luciferase activity was used to monitor the metabolic activity of the population. Most of the cells died after incubation for nine days in nutrient rich medium. By contrast when incubated under starvation conditions, most of the population was not stained with CTC or PI (i.e. intact but inactive cells), indicating that most of the cells were presumably dormant. In soil, a large fraction of the SBW25 cell population became inactive and died, as determined by a decline in luciferase activity and CTC-stained cells, an increase in PI-stained cells, and an inability of the cells to be cultured oil agar medium. However, approximately 60% of the population was unstained, presumably indicating that the cells entered a state of dormancy in soil similar to that observed under starvation conditions in pure cultures. These results demonstrate the applicability of this approach for monitoring the physiological status of specific cells under stress conditions, such as those experienced by environmental inoculants in soil.

  • 9.
    Mhatre, Snehit S
    et al.
    Aarhus University, Aarhus, Denmark / University of Southern Denmark, Odense, Denmark.
    Kaufmann, Stefan
    Aarhus University, Aarhus, Denmark.
    Marshall, Ian P G
    Aarhus University, Aarhus, Denmark.
    Obrochta, Stephen
    Akita University, Akita City, Japan.
    Andrén, Thomas
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Jørgensen, Bo Barker
    Aarhus University, Aarhus, Denmark.
    Lomstein, Bente Aa
    Aarhus University, Aarhus, Denmark.
    Microbial biomass turnover times and clues to cellular protein repair in energy-limited deep Baltic Sea sediments2019In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 95, no 6, article id fiz068Article in journal (Refereed)
    Abstract [en]

    The discovery of active microbial life deeply buried beneath the seafloor has opened important questions: how do microorganisms cope with extreme energy limitation, what is their metabolic activity, and how do they repair damages to essential biomolecules? We used a D:L-amino acid model to calculate microbial biomass turnover times. We used a metagenome and metatranscriptome analysis to investigate the distribution of the gene that encodes Protein-L-iso aspartate(D-aspartate) O-methyltransferase (PCMT), an enzyme which recognizes damaged L-isoapartyl and D-aspartyl residues in proteins and catalyzes their repair. Sediment was retrieved during the Integrated Ocean Drilling Program (IODP) Expedition 347 from Landsort Deep and the Little Belt in the Baltic Sea. The study covers the period from the Baltic Ice Lake ca. 13 000 years ago to the present. Our results provide new knowledge on microbial biomass turnover times and protein repair in relation to different regimes of organic matter input. For the first time, we show that the PCMT gene was widely distributed and expressed among phylogenetically diverse groups of microorganisms. Our findings suggest that microbial communities are capable of repairing D-amino acids within proteins using energy obtained from the degradation of a mixture of labile compounds in microbial necromass and more recalcitrant organic matter.

  • 10. Räsänen, L A
    et al.
    Elväng, A M
    Jansson, Janet
    Södertörn University, Avdelning Naturvetenskap.
    Lindström, K
    Effect of heat stress on cell activity and cell morphology of the tropical rhizobium, Sinorhizobium arboris2001In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 34, no 3, p. 267-278Article in journal (Refereed)
    Abstract [en]

    The effect of heat stress oil the growth, physiological state, cell activity and cell morphology of the tropical Sinorhizobium ariboris strain HAMBI 2190 was studied. The cells were chromosomally tagged with the firefly luciferase gene, luc. Since the bioluminescence phenotype is dependent on cellular energy reserves it was used as an indicator of the metabolic status of the cell population under various heat conditions. Variations in the numbers and lengths of growth phases between individual cultures indicated that the growth pattern at 40 degreesC was disturbed compared to growth at 37 or 28 degreesC. In addition, the cell morphology was changed radically. The number of culturable cells and the luciferase activity declined when the cultures were incubated at 40 degreesC. By contrast, under all conditions studied, the cells could be stained with 5-(and 6-)sulfofluorescein diacetate, indicating esterase activity. This demonstrated that although the culturability and cellular energy reserves decreased considerably during heat stress, a majority of the of S. arboris cell population maintained basal enzyme activity.

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