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  • 1.
    Backman, Agneta
    et al.
    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.
    Degradation of 4-chlorophenol at low temperature and during extreme temperature fluctuations by Arthrobacter chlorophenolicus A62004In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 48, no 2, p. 246-253Article in journal (Refereed)
    Abstract [en]

    Low average temperatures and temperature fluctuations in temperate soils challenge the efficacy of microbial strains used for clean up of pollutants. In this study, we investigated the cold tolerance of Arthrobacter chlorophenolicus A6, a microorganism previously shown to degrade high concentrations of 4-chlorophenol at 28degreesC. Luciferase activity from a luc-tagged derivative of the strain (A6L) was used to monitor the metabolic status of the population during 4-chlorophenol degradation. The A6L strain could degrade 200-300 mug mL(-1) 4-chlorophenol in pure cultures incubated at 5degreesC, although rates of degradation, growth and the metabolic status of the cells were lower at 5degreesC compared to 28degreesC. When subjected to temperature fluctuations between 5 and 28degreesC, A6L continued to degrade 4-chlorophenol and remained active. In soil microcosm experiments, the degradation rates were significantly faster the first week at 28degreesC, compared to 5degreesC. However, this difference was no longer seen after 7 days, and equally low 4-chlorophenol concentrations were reached after 17 days at both temperatures. During 4-chlorophenol degradation in soil, CFU and luciferase activity values remained constant at both 5 and 28degreesC. However, once most of the 4-chlorophenol was degraded, both values decreased by 1-1.5 logarithmic values at 28degreesC, whereas they remained constant at 5degreesC, indicating a high survival of the cells at low temperatures. Because of the ability of A. chlorophenolicus A6 to degrade high concentrations of 4-chlorophenol at 5degreesC, together with its tolerance to temperature fluctuations and stress conditions found in soil, this strain is a promising candidate for bioaugmentation of chlorophenol-contaminated soil in temperate climates.

  • 2.
    Backman, Agneta
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Maraha, Ninwe
    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.
    Impact of temperature on the physiological status of a potential bioremediation inoculant, Arthrobacter chlorophenolicus A62004In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 70, no 5, p. 2952-2958Article in journal (Refereed)
    Abstract [en]

    Arthrobacter chlorophenolicus A6 (A6) can degrade large amounts of 4-chlorophenol in soil at 5 and 28degreesC. In this study, we investigated the effects of temperature on the physiological status of this bacterium in pure culture and in soil. A derivative of A6 tagged with the gfp gene (encoding green fluorescent protein [GFP]) was used to specifically quantify A6 cells in soil. In addition, cyano-ditolyl-tetrazoliumchloride was used to stain GFP-fluorescent cells with an active electron transfer system ("viable cellis") whereas propidium iodide (PI) was used to stain cells with damaged membranes ("dead cells"). Another derivative of the strain (tagged with the firefly luciferase gene [luc]) was used to monitor the metabolic activity of the cell population, since the bioluminescence phenotype is dependent on cellular energy reserves. When the cells were incubated in soil at 28degreesC, the majority were stained with PI, indicating that they had lost their cell integrity. In addition, there was a corresponding decline in metabolic activity and in the ability to be grown in cultures on agar plates after incubation in soil at 28degreesC, indicating that the cells were dying under those conditions. When the cells were incubated in soil at 5degreesC, by contrast, the majority of the cells remained intact and a large fraction of the population remained metabolically active. A similar trend towards better cell survival at lower temperatures was found in pure-culture experiments. These results make A. chlorophenolicus A6 a good candidate for the treatment of chlorophenol-contaminated soil in cold climates.

  • 3.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences. SLU.
    Hårdeman, Fredrik
    Södertörn University, School of Life Sciences. Karolinska institutet.
    Jansson, Janet K.
    SLU / Lawrence Berkeley National Laboratory, Berkeley, USA.
    Sjöling, Sara
    Södertörn University, School of Life Sciences.
    Active bacterial community structure along vertical redox gradients in Baltic Sea sediment2008In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 10, no 8, p. 2051-2063Article in journal (Refereed)
    Abstract [en]

    Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, -64 and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.

  • 4.
    Edlund, Anna
    et al.
    Södertörn University, School of Life Sciences. SLU.
    Jansson, Janet K.
    SLU.
    Identification of metabolically active phenanthrene transforming bacteria in polluted Baltic Sea sedimentsManuscript (preprint) (Other academic)
  • 5.
    Elväng, Annelie M.
    et al.
    Stockholms universitet.
    Westerberg, Karolina
    Stockholms universitet.
    Jernberg, Cecilia
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Jansson, Janet K
    Södertörn University, Avdelning Naturvetenskap.
    Use of green fluorescent protein and luciferase biomarkers to monitor survival and activity of Arthrobacter chlorophenolicus A6 cells during degradation of 4-chlorophenol in soil2001In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 3, no 1, p. 32-42Article in journal (Refereed)
    Abstract [en]

    The recently isolated novel species Arthrobacter chlorophenolicus A6 is capable of growth on and degradation of high concentrations of 4-chlorophenol (up to 350 mug ml(-1)) as the sole carbon and energy source, This strain shows promise for bioremediation of environmental sites contaminated with high levels of chlorophenols. In this study, green fluorescent protein (gfp) or luciferase (luc) genes were used as biomarkers for monitoring cell number and activity, respectively, during degradation of 4-chlorophenol by A. chlorophenolicus cells. The individual marked strains, Arthrobacter chlorophenolicus A6L (luc-tagged) and Arthrobacter chlorophenolicus A6G (gfp-tagged), were monitored during degradation of 250 mug ml(-1) 4-chlorophenol in pure culture and 175 mug g(-1) 4-chlorophenol in soil microcosms. Both gene-tagged strains were capable of cleaning up the contaminated soil during 9 d incubation. During the bioremediation experiments, the luc-tagged cells were monitored using luminometry and the gfp tagged cells using flow cytometry, in addition to selective plate counting for both strains. The cells remained at high population levels in the soil (evidenced by GFP-fluorescent cell counts) and the A. chlorophenolicus A6L population was metabolically active (evidenced by luciferase activity measurements). These results demonstrate that the Arthrobacter chlorophenolicus A6 inoculum is effective for cleaning-up soil containing high concentrations of 4-chlorophenol.

  • 6.
    Espínola, Fernando
    et al.
    Centro Nacional Patagónico, Puerto Madryn, Argentina.
    Dionisi, Hebe M
    Centro Nacional Patagónico, Puerto Madryn, Argentina.
    Borglin, Sharon
    Lawrence Berkeley National Laboratory, Berkeley, USA.
    Brislawn, Colin J
    Pacific Northwest National Laboratory, Richland, USA.
    Jansson, Janet K.
    Pacific Northwest National Laboratory, Richland, USA.
    Mac Cormack, Walter P
    Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina / Instituto Antártico Argentino, Buenos Aires, Argentina.
    Carroll, JoLynn
    UiT The Arctic University of Norway, Tromsø, Norway.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Lozada, Mariana
    Centro Nacional Patagónico, Puerto Madryn, Argentina.
    Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes2018In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, no 1, p. 123-139Article in journal (Refereed)
    Abstract [en]

    In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

  • 7.
    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.

  • 8.
    Jakobsson, Hedvig
    et al.
    Swedish Institute for Infectious Disease Control.
    Jernberg, Cecilia
    Karolinska Institute.
    Sjölund, Maria
    Central Hospital, Växjö.
    Jansson, Janet
    Swedish University of Agricultural Sciences.
    Engstrand, Lars
    Swedish Institute for Infectious Disease Control.
    Molecular analysis of ecological changes in the human normal microflora after treatment with clarithromycin and metronidazoleManuscript (preprint) (Other academic)
  • 9.
    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.

  • 10.
    Jernberg, Cecilia
    et al.
    Karolinska Institutet.
    Löfmark, Sonja
    Karolinska Institutet.
    Edlund, Charlotta
    Karolinska Institutet / Medical Products Agency.
    Jansson, Janet K.
    Swedish University of Agricultural Sciences.
    Long-term ecological impacts of antibiotic administration on the human intestinal microbiota2007In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 1, no 1, p. 56-66Article in journal (Refereed)
    Abstract [en]

    Antibiotic administration is known to cause short-term disturbances in the microbiota of the human gastrointestinal tract, but the potential long-term consequences have not been well studied. The aims of this study were to analyse the long-term impact of a 7-day clindamycin treatment on the faecal microbiota and to simultaneously monitor the ecological stability of the microbiota in a control group as a baseline for reference. Faecal samples from four clindamycin-exposed and four control subjects were collected at nine different time points over 2 years. Using a polyphasic approach, we observed highly significant disturbances in the bacterial community that persisted throughout the sampling period. In particular, a sharp decline in the clonal diversity of Bacteroides isolates, as assessed by repetitive sequence-based PCR (rep-PCR) and long-term persistence of highly resistant clones were found as a direct response to the antibiotic exposure. The Bacteroides community never returned to its original composition during the study period as assessed using the molecular fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP). Furthermore, using real-time PCR we found a dramatic and persistent increase in levels of specific resistance genes in DNA extracted from the faeces after clindamycin administration. The temporal variations in the microbiota of the control group were minor compared to the large and persistent shift seen in the exposed group. These results demonstrate that long after the selection pressure from a short antibiotic exposure has been removed, there are still persistent long term impacts on the human intestinal microbiota that remain for up to 2 years post-treatment.

  • 11.
    Jernberg, Cecilia
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Sullivan, A
    Karolinska Institute.
    Edlund, Charlotta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Jansson, J K
    Swedish University of Agricultural Sciences.
    Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism2005In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, no 1, p. 501-506Article in journal (Refereed)
    Abstract [en]

    Terminal restriction fragment length polymorphism (T-RFLP) was investigated as a tool for monitoring the human intestinal microflora during antibiotic treatment and during ingestion of a probiotic product. Fecal samples from eight healthy volunteers were taken before, during, and after administration of clindamycin. During treatment, four subjects were given a probiotic, and four subjects were given a placebo. Changes in the microbial intestinal community composition and relative abundance of specific microbial populations in each subject were monitored by using viable counts and T-RFLP fingerprints. T-RFLP was also used to monitor specific bacterial populations that were either positively or negatively affected by clindamycin. Some dominant bacterial groups, such as Eubacterium spp., were easily monitored by T-RFLP, while they were hard to recover by cultivation. Furthermore, the two probiotic Lactobacillus strains were easily tracked by T-RFLP and were shown to be the dominant Lactobacillus community members in the intestinal microflora of subjects who received the probiotic.

  • 12.
    Lowder, M
    et al.
    University of North Carolina at Charlotte, Charlotte, USA.
    Unge, A
    Stockholms universitet.
    Maraha, Ninwe
    Södertörn University, Avdelning Naturvetenskap.
    Jansson, Janet K
    Södertörn University, Avdelning Naturvetenskap. Stockholms universitet.
    Swiggett, J
    Carolinas Medical Center, Charlotte, USA.
    Oliver, J D
    University of North Carolina at Charlotte, Charlotte, USA.
    Effect of starvation and the viable-but-nonculturable state on green fluorescent protein (GFP) fluorescence in GFP-tagged Pseudomonas fluorescens A5062000In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 66, no 8, p. 3160-3165Article in journal (Refereed)
    Abstract [en]

    The green fluorescent protein (GFP) gene, gfp, of the jellyfish Aequorea victoria is being used as a reporter system for gene expression and as a marker for tracking prokaryotes and eukaryotes. Cells that have been genetically altered with the gfp gene produce a protein that fluoresces when it is excited by UV light. This unique phenotype allows gth-tagged cells to be specifically monitored by nondestructive means, In this study we determined whether a gfp-tagged strain of Pseudomonas fluorescens continued to fluoresce under conditions under which the cells were starved, viable but nonculturable (VBNC), or dead. Epifluorescent microscopy, flow cytometry, and spectrofluorometry were used to measure fluorescence intensity in starved, VBNC, and dead or dying cells. Results obtained by using how cytometry indicated that microcosms containing VBNC cells, which were obtained by incubation under stress conditions (starvation at 37.5 degrees C), fluoresced at an intensity that mas at least 80% of the intensity of nonstressed cultures, Similarly, microcosms containing starved cells incubated at 5 and 30 degrees C had fluorescence intensities that were 90 to 110% of the intensity of nonstressed cells. VBNC cells remained fluorescent during the entire 6-month incubation period. in addition, cells starved at 5 or 30 degrees C remained fluorescent for at least 11 months. Treatment of the cells with UV light or incubation at 39 or 50 degrees C resulted in a loss of GFP from the cells. There was a strong correlation between cell death and leakage of GFP from the cells, although the extent of leakage varied depending on the treatment, Most dead cells were not GFP fluorescent, but a small proportion of the dead cells retained some GFP at a lower concentration than the concentration in live cells, Our results suggest that gfp-tagged cells remain fluorescent following starvation and entry into the VBNC state but that fluorescence is lost when the cells die, presumably because membrane integrity is lost.

  • 13.
    Lu, Zexun
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Tombolini, R
    Woo, S
    Zeilinger, S
    Lorito, M
    Jansson, Janet K
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. SLU.
    In vivo study of Trichoderma-pathogen-plant interactions, using constitutive and inducible green fluorescent protein reporter systems2004In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 70, no 5, p. 3073-3081Article in journal (Refereed)
    Abstract [en]

    Plant tissue colonization by Trichoderma atroviride plays a critical role in the reduction of diseases caused by phytopathogenic fungi, but this process has not been thoroughly studied in situ. We monitored in Situ interactions between gfp-tagged biocontrol strains of T. atroviride and soilborne plant pathogens that were grown in cocultures and on cucumber seeds by confocal scanning laser microscopy and fluorescence stereomicroscopy. Spores of T. atroviride adhered to Pythium ultimum mycelia in coculture experiments. In mycoparasitic interactions of T. atroviride with P. ultimum or Rhizoctonia solani, the mycoparasitic hyphae grew alongside the pathogen mycelia, and this was followed by coiling and formation of specialized structures similar to hooks, appressoria, and papillae. The morphological changes observed depended on the pathogen tested. Branching of T. atroviride mycelium appeared to be an active response to the presence of the pathogenic host. Mycoparasitism of P. ultimum by T. atroviride occurred on cucumber seed surfaces while the seeds were germinating. The interaction of these fungi on the cucumber seeds was similar to the interaction observed in coculture experiments. Green fluorescent protein expression under the control of host-inducible promoters was also studied. The induction of specific Trichoderma genes was monitored visually in cocultures, on plant surfaces, and in soil in the presence of colloidal chitin or Rhizoctonia by confocal microscopy and fluorescence stereomicroscopy. These tools allowed initiation of the mycoparasitic gene expression cascade to be monitored in vivo.

  • 14.
    Löfmark, Sonja
    et al.
    Karolinska Institute.
    Jernberg, Cecilia
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Jansson, Janet K.
    Swedish University of Agricultural Sciences.
    Edlund, Charlotta
    Karolinska Institute / Medical Products Agency.
    Clindamycin-induced enrichment and long-term persistence of resistant Bacteroides spp. and resistance genes2006In: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 58, no 6, p. 1160-1167Article in journal (Refereed)
    Abstract [en]

    Objectives: The aim was to study the long-term consequences of 1 week clindamycin administration regarding selection and persistence of resistance, resistance determinants and diversity of the Bacteroides spp. in the intestinal microflora. Methods: A total of 1306 Bacteroides isolates were collected from constitutively cultured faecal samples during a 2 year period from eight healthy volunteers. The strains were identified by biochemical and genotyping methods. MIC values were determined by the agar dilution method and presence of resistance genes was screened by real-time PCR. Results: Ecological changes in the intestinal microflora persisting up to 24 months were recorded after a 7 day clindamycin administration to four healthy volunteers. Compared to a control group, not exposed to clindamycin, an enrichment and stabilization of resistant Bacteroides strains and resistance determinants were discovered up to 2 years after clindamycin exposure. Conclusions: The results indicate that even a short-term antibiotic administration can cause long-term alterations in the commensal microbiota of individual subjects, detectable 2 years after dosing. The recorded selection and persistence of resistant strains and resistance genes, illustrates the importance of increasing our knowledge of the role of the abundant intestinal microbial community as a reservoir for spread of resistance.

  • 15.
    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.

  • 16.
    Maraha, Ninwe
    et al.
    Södertörn University, School of Life Sciences. Karolinska Institutet.
    VerBerkmoes, Nathan
    Oak Ridge National Laboratory, Oak Ridge, USA.
    Spiers, Andrew
    CEH-Oxford, Oxford, England.
    Shah, Manesh
    Oak Ridge National Laboratory, Oak Ridge, USA.
    Timms-Wilson, Tracey
    CEH-Oxford, Oxford, England.
    Goodall, Tim
    CEH-Oxford, Oxford, England.
    Bailey, Mark
    CEH-Oxford, Oxford, England.
    Jansson, Janet K.
    SLU.
    Use of proteomics to study impact of nutrient status on Pseudomonas fluorescens SBW25Manuscript (preprint) (Other academic)
  • 17.
    Matos, Marina N
    et al.
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Lozada, Mariana
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Anselmino, Luciano E
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Musumeci, Matías A
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Henrissat, Bernard
    Aix-Marseille Université, Marseille, France / INRA, Marseille, France / King Abdulaziz University, Jeddah, Saudi Arabia.
    Jansson, Janet K.
    Pacific Northwest National Laboratory, Richland, USA.
    Mac Cormack, Walter P
    Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, Argentina / Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
    Carroll, JoLynn
    High North Research Centre for Climate and the Environment, Tromsø, Norway / UiT The Arctic University of Norway, Tromsø, Norway.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Biology.
    Lundgren, Leif
    Stockholm University.
    Dionisi, Hebe M
    Centro para el Estudio de Sistemas Marinos, Puerto Madryn, Argentina.
    Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4471-4484Article in journal (Refereed)
    Abstract [en]

    Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.

  • 18.
    Musumeci, Matías A
    et al.
    Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Argentina.
    Lozada, Mariana
    Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Argentina.
    Rial, Daniela V
    Universidad Nacional de Rosario, CONICET, Rosario, Argentina.
    Mac Cormack, Walter P
    Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, Argentina / CONICET—Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
    Jansson, Janet K.
    Pacific Northwest National Laboratory, Richland, USA.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Carroll, JoLynn
    Fram—High North Research Centre for Climate and the Environment, Tromsø, Norway / UiT The Arctic University of Norway, Tromsø, Norway.
    Dionisi, Hebe M
    Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Argentina.
    Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach2017In: Marine Drugs, ISSN 1660-3397, E-ISSN 1660-3397, Vol. 15, no 4, article id 114Article in journal (Refereed)
    Abstract [en]

    The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. This work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments.

  • 19.
    Nordin, Karolina
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Unell, M
    Jansson, Janet K
    Södertörn University, School of Life Sciences. SLU.
    Novel 4-chlorophenol degradation gene cluster and degradation route via hydroxyquinol in Arthrobacter chlorophenolicus A62005In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 71, no 11, p. 6538-6544Article in journal (Refereed)
    Abstract [en]

    Arthrobacter chlorophenolicus A6, a previously described 4-chlorophenol-degrading strain, was found to degrade 4-chlorophenol via hydroxyquinol, which is a novel route for aerobic microbial degradation of this compound. In addition, 10 open reading frames exhibiting sequence similarity to genes encoding enzymes involved in chlorophenol degradation were cloned and designated part of a chlorophenol degradation gene cluster (cph genes). Several of the open reading frames appeared to encode enzymes with similar functions; these open reading frames included two genes, cphA-I and cphA-H, which were shown to encode functional hydroxyquinol 1,2-dioxygenases. Disruption of the cphA-I gene yielded a mutant that exhibited negligible growth on 4-chlorophenol, thereby linking the cph gene cluster to functional catabolism of 4-chlorophenol in A. chlorophenolicus A6. The presence of a resolvase pseudogene in the cph gene cluster together with analyses of the G+C content and codon bias of flanking genes suggested that horizontal gene transfer was involved in assembly of the gene cluster during evolution of the ability of the strain to grow on 4-chlorophenol.

  • 20. 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.

  • 21. Unge, A
    et al.
    Jansson, Janet
    Södertörn University, Avdelning Naturvetenskap.
    Monitoring population size, activity, and distribution of gfp-luxAB-tagged Pseudomonas fluorescens SBW25 during colonization of wheat2001In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 41, no 4, p. 290-300Article in journal (Refereed)
    Abstract [en]

    Increasingly, focus has been directed towards the use of microorganisms as biological control agents to combat fungal disease, as an alternative to chemical fungicides. Pseudomonas fluorescens SBW25 is one bacterial strain that has been demonstrated to promote plant growth by biocontrol of pathogenic fungi. To understand the mode of action of this bacterium, information regarding its localization and metabolic activity on plants is important. In this study, a gfp/luxAB-tagged derivative of P. fluorescens SBW25, expressing the green fluorescent protein (GFP) and bacterial luciferase, was monitored during colonization of wheat starting from seed inoculation. Since bacterial luciferase is dependent on cellular energy reserves for phenotypic expression, metabolically active cells were detected using this marker. In contrast, the stable GFP fluorescence phenotype was used to detect the cells independently of their metabolic status. The combination of these two markers enabled P. fluorescens SBW25 cells to be monitored on wheat plants to determine their specific location and metabolic activity. Studies on homogenized wheat plant parts demonstrated that the seed was the preferred location of P. fluorescens SBW25 during the 65-day time period studied, but the leaves and roots were also colonized. Interestingly, the bacteria were also found to be metabolically active on all plant parts examined. In situ localization of P. fluorescens SBW25 using a combination of different microscopic techniques confirmed the preference for the cells to colonize specific regions of the seed. We speculate that the colonization pattern of P. fluorescens SBW25 can be linked to the mechanism of protection of plants from fungal infection.

  • 22. van Elsas, Jan Dirk
    et al.
    Costal, Rodrigo
    Jansson, Janet
    Sjöling, Sara
    Södertörn University, School of Life Sciences.
    Bailey, Mark
    Nalin, Renaud
    Vogel, Timothy M.
    van Overbeek, Leo
    The metagenomics of disease-suppressive soils - experiences from the METACONTROL project2008In: Trends in Biotechnology, ISSN 0167-7799, E-ISSN 1879-3096, Vol. 26, no 11, p. 591-601Article, review/survey (Refereed)
    Abstract [en]

    Soil teems with microbial genetic information that can be exploited for biotechnological innovation. Because only a fraction of the soil microbiota is cultivable, our ability to unlock this genetic complement has been hampered. Recently developed molecular tools, which make it possible to utilize genomic DNA from soil, can bypass cultivation and provide information on the collective soil metagenome with the aim to explore genes that encode functions of key interest to biotechnology. The metagenome of disease-suppressive soils is of particular interest given the expected prevalence of antibiotic biosynthetic clusters. However, owing to the complexity of soil microbial communities, deciphering this key genetic information is challenging. Here, we examine crucial issues and challenges that so far have hindered the metagenomic exploration of soil by drawing on experience from a trans-European project on disease-suppressive soils denoted METACONTROL.

  • 23.
    von der Weid, Irene
    et al.
    Södertörn University, School of Life Sciences. Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
    Artursson, V
    Seldin, L
    Jansson, Janet K
    Södertörn University, School of Life Sciences. SLU.
    Antifungal and root surface colonization properties of GFP-tagged Paenibacillus brasilensis PB1772005In: World Journal of Microbiology & Biotechnology, ISSN 0959-3993, E-ISSN 1573-0972, Vol. 21, no 8-9, p. 1591-1597Article in journal (Refereed)
    Abstract [en]

    This study evaluates the potential of Paenibacillus brasilensis strain PB177 to inhibit phytopathogenic fungi commonly causing maize diseases and to colonize maize plants. In vitro assays demonstrated antagonistic activity against the fungal pathogens, Fusarium moniliforme and Diplodia macrospora. The PB177 strain was tagged with the gfp gene, encoding the green fluorescent protein (GFP) and GFP-tagged bacteria were detected attached to maize roots by stereo- and confocal microscopy. The GFP-tagged bacteria were also used to treat maize seeds before challenging the seeds with two phytopathogenic fungi. The results demonstrated that the bacterial cells are mobilized to the maize roots in the presence of the fungal pathogens. The ability of P. brasilensis PB177 to inhibit fungal growth in vitro and its capability of colonization of maize roots in vivo suggest a potential application of this strain as a biological control agent. This is the first report on the successful introduction of the GFP marker gene into a P. brasilensis strain, enabling the direct observation of these promising plant growth promoting bacteria on maize roots in situ.

  • 24.
    Westerberg, Karolina
    et al.
    Stockholm University.
    Elväng, Annelie M
    Stockholm Unversity.
    Stackebrandt, E
    DSMZ–Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Germany.
    Jansson, Janet K
    Södertörn University, Avdelning Naturvetenskap.
    Arthrobacter chlorophenolicus sp nov., a new species capable of degrading high concentrations of 4-chlorophenol2000In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 50, p. 2083-2092Article in journal (Refereed)
    Abstract [en]

    A micro-organism was isolated from soil which could grow on high concentrations [up to 350 p.p.m. (2.7 mM)] of 4-chlorophenol (4-CP). The isolate, designated strain A6(T), was obtained from a soil suspension that had been selectively enriched with gradually increasing concentrations of 4-CP. Strain A6T could also grow on several other para-substituted phenols. Characterization of strain A6T with respect to chemical, biochemical and morphological properties, 16S rDNA sequencing and DNA-DNA hybridization indicated that the isolate is a novel species within the genus Arthrobacter for which the name Arthrobacter chlorophenolicus sp. nov. is proposed. The type strain is DSM 12829(T).

1 - 24 of 24
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