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  • 1.
    Edlund, Anna
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Microbial diversity in Baltic Sea sediments2007Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    This thesis focuses on microbial community structures and their functions in Baltic Sea sediments. First we investigated the distribution of archaea and bacteria in Baltic Sea sediments along a eutrophication gradient. Community profile analysis of 16S rRNA genes using terminal restriction length polymorphism (T-RFLP) indicated that archaeal and bacterial communities were spatially heterogeneous. By employing statistical ordination methods we observed that archaea and bacteria were structured and impacted differently by environmental parameters that were significantly linked to eutrophication. In a separate study, we analyzed bacterial communities at a different site in the Baltic Sea that was heavily contaminated with polyaromatic hydrocarbons (PAHs) and several other pollutants. Sediment samples were collected before and after remediation by dredging in two consecutive years. A polyphasic experimental approach was used to assess growing bacteria and degradation genes in the sediments. The bacterial communities were significantly different before and after dredging of the sediment. Several isolates collected from contaminated sediments showed an intrinsic capacity for degradation of phenanthrene (a PAH model compound). Quantititative real-time PCR was used to monitor the abundance of degradation genes in sediment microcosms spiked with phenanthrene. Although both xylE and phnAc genes increased in abundance in the microcosms, the isolates only carried phnAc genes. Isolates with closest 16S rRNA gene sequence matches to Exigobacterium oxidotolerans, a Pseudomonas sp. and a Gammaproteobacterium were identified by all approaches used as growing bacteria that are capable of phenanthrene degradation. These isolates were assigned species and strain designations as follows: Exiguobacterium oxidotolerans AE3, Pseudomonas fluorescens AE1 and Pseudomonas migulae AE2. We also identified and studied the distribution of actively growing bacteria along red-ox profiles in Baltic Sea sediments. Community structures were found to be significantly different at different red-ox depths. Also, according to multivariate statistical ordination analysis organic carbon, nitrogen, and red-ox potential were crucial parameters for structuring the bacterial communities on a vertical scale. Novel lineages of bacteria were obtained by sequencing 16S rRNA genes from different red-ox depths and sampling stations indicating that bacterial diversity in Baltic Sea sediments is largely unexplored.

  • 2.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Hårdeman, Fredrik
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska institutet.
    Jansson, Janet K.
    SLU / Lawrence Berkeley National Laboratory, Berkeley, USA.
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Active bacterial community structure along vertical redox gradients in Baltic Sea sediment2008Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 10, nr 8, s. 2051-2063Artikel i tidskrift (Refereegranskat)
    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.

  • 3.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Jansson, Janet K.
    SLU.
    Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments2006Ingår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 72, nr 10, s. 6800-6807Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Bacteria residing in sediments have key functions in the marine food web. However, it has been difficult to correlate the identity and activity of bacteria in sediments due to lack of appropriate methods beyond cultivation-based techniques. Our aim was to use a combination of molecular approaches, bromodeoxyuridine incorporation and immunocapture, terminal restriction fragment length polymorphism, and cloning and sequencing of 16S rRNA genes to assess the composition of growing bacteria in Baltic Sea sediments. The study site was a highly polluted area off the Swedish coast. The sediments were sampled in two consecutive years, before and after remediation, by dredging of the top sediments. Levels of polyaromatic hydrocarbons (PAHs), mercury, and polychlorinated biphenyls were dramatically reduced as a result of the cleanup project. The compositions of growing members of the communities were significantly different at the two sampling periods. In particular, members from the class Deltaproteobacteria and genus Spirochaeta were more dominant before dredging, but members of the classes Gammaproteobacteria and the Flavobacteria represented the most dominant growing populations after dredging. We also cultivated isolates from the polluted sediments that could transform the model PAH compound, phenanthrene. Some of these isolates were confirmed as dominant growing populations by the molecular methods as well. This suite of methods enabled us to link the identity and activity of the members of the sediment communities.

  • 4.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Jansson, Janet K.
    SLU.
    Identification of metabolically active phenanthrene transforming bacteria in polluted Baltic Sea sedimentsManuskript (preprint) (Övrigt vetenskapligt)
  • 5.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper.
    Jansson, Janet K.
    Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments2008Ingår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 65, nr 3, s. 513-525Artikel i tidskrift (Refereegranskat)
    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.

  • 6.
    Edlund, Anna
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. SLU.
    Soule, T
    Sjöling, Sara
    Södertörns högskola, Institutionen för livsvetenskaper.
    Jansson, J K
    Microbial community structure in polluted Baltic Sea sediments2006Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 8, nr 2, s. 223-232Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Nearly half the seabed of the Baltic Proper is incapable of supporting life of higher organisms as a consequence of oxygen depletion resulting from eutrophication. However, these areas are actually teeming with microbial life. Here we used terminal-restriction fragment length polymorphism (T-RFLP) to investigate the dominant archaeal and bacterial groups, with respect to community structure, in surface layers of bottom sediments of the Baltic Sea along a coastal pollution gradient. Both archaeal and bacterial communities formed distinct clusters along the pollution gradient and the community compositions were different at the polluted sites compared with the relatively clean reference sites. The structures of the bacterial communities were most strongly correlated to water depth, followed by organic carbon, oxygen, salinity and silicate levels. In contrast, the structures of the archaeal communities were most strongly correlated to oxygen, salinity, organic carbon, silicate and nitrate levels. Some members of the microbial communities were identified using a combination of traditional and molecular approaches. Isolates obtained on different culture media were identified by partial sequencing of their 16S rRNA genes and some novel species were found. In addition, we developed a computer program, APLAUS, to elucidate the putative identities of the most dominant community members by T-RFLP.

  • 7. Gorokhova, Elena
    et al.
    Edlund, Anna
    Södertörns högskola, Institutionen för livsvetenskaper.
    Hajdu, Susanna
    Zhivotova, Elena N.
    Nucleic acid levels in copepods: dynamic response to phytoplankton blooms in the northern Baltic proper2007Ingår i: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 349, s. 213-225Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We examined changes in nucleic acids and concomitant population development of the copepods Acartia bifilosa and Eurytemora affinis in relation to the progress of the phytoplankton spring bloom in the northern Baltic proper. Individual RNA and DNA concentrations and their ratios in female copepods as well as copepod abundance and population structure were analyzed in 2 coastal areas that differed in the degree of eutrophication and phytoplankton development. During the study period (February to June 2002), bloom conditions were evident, with chlorophyll (chl) a values being 42% higher in the eutrophic area than in the reference area. In both areas, diatoms dominated; in the reference area, they were replaced by dinoflagellates toward the end of the bloom. Copepod RNA-DNA concentrations increased rapidly at the onset of the bloom and gradually decreased thereafter. Moreover, in the eutrophic area, both copepods had higher RNA content and RNA:DNA ratios throughout the study period, suggesting higher productivity in this area. In both species, we found positive correlations between RNA-based indices and chl a. Thus, as suggested by RNA dynamics, growth rates of A. bifilosa and E. affinis appear to respond rapidly to both temporal variation in spring phytoplankton stock and spatial variation due to the magnitude of the bloom. In addition, we found that species-specific RNA dynamics and RNA-chl a relationships differed between species, indicating possible differences in feeding preferences and growth potential.

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