Microbial community composition of lake sediment in the High Arctic

Title:
Microbial community composition of lake sediment in the High Arctic
Creator:
Berdy, Brittany M. (Author)
Contributor:
Epstein, Slava (Advisor)
Godoy-Carter, Veronica (Committee member)
Lewis, Kim (Committee member)
Chai, Yunrong (Committee member)
Nelson, Karen E. (Committee member)
Language:
English
Publisher:
Boston, Massachusetts : Northeastern University, 2017
Date Accepted:
April 2017
Date Awarded:
May 2017
Type of resource:
Text
Genre:
Dissertations
Format:
electronic
Digital origin:
born digital
Abstract/Description:
The holy grail of microbial ecology would be to know what species are present and active in a community, what functions they are performing, and at what point in time. In recent years it has become clear that environmental meta-omic approaches are essential to gain insight into microbial communities; however the importance of cultivation cannot be overlooked. High quality reference genomes are necessary for the interpretation of meta-omic data, and these can only come from pure cultures. In order to contribute to the ever-growing body of work investigating microbial ecology, and to assess current methods commonly used, we studied the composition of a microbial community within lake sediment in the High Arctic (Thule, Greenland) using a multi-faceted approach. My specific aims were to:

1. Utilize cultivation-independent molecular approaches to define microbial community structure and identify potentially active organisms

2. Utilize culture-dependent approaches to create a comprehensive culture collection

3. Analyze and synthesize the data obtained from Aims 1 and 2 and assess the biological relevance of cultured organisms

The community appeared relatively rich and stable over time based upon a 16S rRNA gene survey. However, analysis of the expressed 16S rRNA genes indicated that activity of operational taxonomic units (OTUs) within the sediment community was dynamic, even across very small distances. Additionally, the most active members were not represented in any database to date.

Despite increasing advancements in microbial cultivation, our results emphasize the need to develop new tools and techniques. A total of 1173 strains were cultivated, but only a small fraction was detected as active (<7%), or even present in the community (<12%) based on 16S gene surveys. We conclude that the variation in OTU activity between replicate samples, and the low abundance and activity of OTUs cultured, are a result of microheterogeneity in spatial distribution within microbial communities. Thus, samples taken even millimeters apart were actually from potentially different communities. The results of this dissertation highlight the increasing need to study microbial communities on a scale relevant to microbial life.
Subjects and keywords:
activity
community
cultivation
extreme
microbial
uncultivated
DOI:
https://doi.org/10.17760/D20248636
Permanent Link:
http://hdl.handle.net/2047/D20248636
Use and reproduction:
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