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Microbial diversity in Baltic Sea sediments
Södertörn University, School of Life Sciences. SLU.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
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.

Place, publisher, year, edition, pages
Uppsala: Sveriges Lantbruksuniversitet, 2007. , 36 p.
Series
Acta Universitatis agriculturae Sueciae, ISSN 1652-6880 ; 2007:6
Keyword [sv]
Havsbottnen, Mikroorganismer
National Category
Biological Sciences
Research subject
Baltic and East European studies
Identifiers
URN: urn:nbn:se:sh:diva-31261ISBN: 91-576-7325-X (print)OAI: oai:DiVA.org:sh-31261DiVA: diva2:1051170
Supervisors
Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2016-12-01Bibliographically approved
List of papers
1. Microbial community structure in polluted Baltic Sea sediments
Open this publication in new window or tab >>Microbial community structure in polluted Baltic Sea sediments
2006 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 8, no 2, 223-232 p.Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
United Kingdom: Wiley-Blackwell Publishing Ltd., 2006
Keyword
RIBOSOMAL-RNA; MARINE BACTERIOPLANKTON; DIVERSITY; EUTROPHICATION; ANTARCTICA; SALINITY; BACTERIAL; DYNAMICS; ARCHAEA; WATERS
National Category
Natural Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-6194 (URN)10.1111/j.1462-2920.2005.00887.x (DOI)000234647600005 ()16423011 (PubMedID)2-s2.0-33644870711 (ScopusID)
Available from: 2011-02-11 Created: 2011-02-11 Last updated: 2016-12-01Bibliographically approved
2. Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments
Open this publication in new window or tab >>Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments
2006 (English)In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 72, no 10, 6800-6807 p.Article in journal (Refereed) Published
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.

National Category
Microbiology
Identifiers
urn:nbn:se:sh:diva-14278 (URN)10.1128/AEM.00971-06 (DOI)000241170300047 ()16950911 (PubMedID)2-s2.0-33750091933 (ScopusID)
Available from: 2011-12-21 Created: 2011-12-20 Last updated: 2016-12-01Bibliographically approved
3. Identification of metabolically active phenanthrene transforming bacteria in polluted Baltic Sea sediments
Open this publication in new window or tab >>Identification of metabolically active phenanthrene transforming bacteria in polluted Baltic Sea sediments
(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Research subject
Baltic and East European studies
Identifiers
urn:nbn:se:sh:diva-31260 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2016-12-01Bibliographically approved
4. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment
Open this publication in new window or tab >>Active bacterial community structure along vertical redox gradients in Baltic Sea sediment
2008 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 10, no 8, 2051-2063 p.Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
United Kingdom: Wiley-Blackwell Publishing Ltd., 2008
Keyword
LENGTH-POLYMORPHISM ANALYSIS; SULFATE-REDUCING BACTERIA; COASTAL MARINE-SEDIMENTS; TIDAL-FLAT SEDIMENTS; MICROBIAL COMMUNITIES; DNA-SEQUENCES; DIVERSITY; DATABASE; DENMARK; CARBON
National Category
Natural Sciences
Research subject
Environmental Studies
Identifiers
urn:nbn:se:sh:diva-6181 (URN)10.1111/j.1462-2920.2008.01624.x (DOI)000257715500012 ()18452546 (PubMedID)2-s2.0-49249138150 (ScopusID)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2011-02-11 Created: 2011-02-11 Last updated: 2016-12-29Bibliographically approved

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