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Active bacterial community structure along vertical redox gradients in Baltic Sea sediment
Södertörn University, School of Life Sciences. SLU.
Södertörn University, School of Life Sciences. Karolinska institutet.
SLU / Lawrence Berkeley National Laboratory, Berkeley, USA.
Södertörn University, School of Life Sciences.ORCID iD: 0000-0002-5802-5126
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. Vol. 10, no 8, 2051-2063 p.
Keyword [en]
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: urn:nbn:se:sh:diva-6181DOI: 10.1111/j.1462-2920.2008.01624.xISI: 000257715500012PubMedID: 18452546ScopusID: 2-s2.0-49249138150OAI: oai:DiVA.org:sh-6181DiVA: diva2:397066
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2011-02-11 Created: 2011-02-11 Last updated: 2016-12-29Bibliographically approved
In thesis
1. Microbial diversity in Baltic Sea sediments
Open this publication in new window or tab >>Microbial diversity in Baltic Sea sediments
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
Havsbottnen, Mikroorganismer
National Category
Biological Sciences
Research subject
Baltic and East European studies
Identifiers
urn:nbn:se:sh:diva-31261 (URN)91-576-7325-X (ISBN)
Supervisors
Available from: 2016-12-01 Created: 2016-12-01 Last updated: 2016-12-01Bibliographically approved
2. Exploring the metagenome of the Baltic Sea sediment
Open this publication in new window or tab >>Exploring the metagenome of the Baltic Sea sediment
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Environmental microorganisms are fundamental to ecosystem function, acting as drivers in processes such as primary production, organic matter remineralisation, pollution remediation and global biogeochemical cycling. However, the study of the bacterial communities requires the application of advanced culture-independent methods considering that only a small fraction of the community is otherwise accessed. The goal of this thesis was to investigate the bacterial community structures and functions of Baltic Sea coastal sediments. To assess the distribution and identity of metabolically active bacteria along a vertical redox gradient, a polyphasic method was applied including: reverse transcriptase-PCR (transcription) and bromodeoxyuridine immunocapture (replication) for 16S rRNA gene analyses through both clone library sequence analysis and terminal restriction fragment length polymorphism (T-RFLP). It was demonstrated that the bacterial communities were highly diverse and significantly different at different redox layers. Phylogenetic analysis identified several novel bacterial groups, some with potentially important ecological roles, notably the first genetic evidence of active anammox bacteria, demonstrating that the bacterial community of the Baltic Sea sediment includes several largely unexplored groups. A metagenomic approach was used to access the bacterial diversity. Considering that the Baltic Sea sediment contained a diverse and largely unexplored bacterial community and also represent a permanently cold environment. This community is likely to harbor bacteria with enzymes adapted to low temperatures that would have a potential biotechnological value. The capacity of functional metagenomics for bioprospecting was demonstrated though the construction of a fosmid library of the prokaryotic genomic pool and expression screening, which enabled the identification of several novel lipolytical enzymes. A novel lipase, h1Lip1 (DQ118648) was isolated, overexpressed, purified and characterized for catalytic activity, substrate specificity, apparent temperature optimum and thermo-stability, demonstrating that the enzyme was low temperature active. 3D protein structure modelling of the lipase supported the presence of an alpha/beta-hydrolase fold, a catalytic triad and a lid structure, covering the active site. Comparative structure analyses and site directed-mutagenesis further showed the importance of a region within the N-terminal and lid for substrate affinity and thermal stability. In conclusion, these targeted molecular strategies demonstrate that the Baltic Sea sediments contain a highly diverse and unique bacterial community that also represents a useful source of biotechnologically interesting molecules.

Place, publisher, year, edition, pages
Stockholm: Karolinska institutet, 2008. 47 p.
Keyword
Maringeologi, Bakterier
National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-31555 (URN)978-91-7357-386-3 (ISBN)
Public defence
2008-05-30, MA624, Huddinge, 10:00 (English)
Opponent
Supervisors
Available from: 2016-12-29 Created: 2016-12-29 Last updated: 2016-12-29Bibliographically approved

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