Diversity and phylogenetic structure of two complex marine microbial communities
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2004.
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| Format: | Thesis |
| Language: | en_US |
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Massachusetts Institute of Technology
2005
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| Online Access: | http://hdl.handle.net/1721.1/28641 |
| _version_ | 1811095058345099264 |
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| author | Klepac-Ceraj, Vanja, 1976- |
| author2 | Martin F. Polz. |
| author_facet | Martin F. Polz. Klepac-Ceraj, Vanja, 1976- |
| author_sort | Klepac-Ceraj, Vanja, 1976- |
| collection | MIT |
| description | Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2004. |
| first_indexed | 2024-09-23T16:09:51Z |
| format | Thesis |
| id | mit-1721.1/28641 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:09:51Z |
| publishDate | 2005 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/286412019-04-12T11:29:23Z Diversity and phylogenetic structure of two complex marine microbial communities Klepac-Ceraj, Vanja, 1976- Martin F. Polz. Massachusetts Institute of Technology. Dept. of Civil and Environmental Engineering. Massachusetts Institute of Technology. Dept. of Civil and Environmental Engineering. Civil and Environmental Engineering. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2004. Includes bibliographical references (p. 102-103). (cont.) competitive mechanisms are too weak to purge diversity from within them. Molecular surveys have revealed that microbial communities are extraordinarily diverse. Yet, two important questions remain unanswered: how many bacterial types co-exist, and do such types form phylogenetically discrete units of potential ecological relevance? This thesis explores these questions by investigating bacterial diversity in two complex marine communities (coastal bacterioplankton and sediment sulfate-reducing bacteria) by (i) comprehensive analysis of large 16S rRNA clone libraries, and (ii) refinement and application of parametric diversity estimators. Identification and correction of sequence artifacts demonstrated their potentially significant contribution to diversity estimates. Still, hundreds of unique rRNA sequences (ribotypes) were detected in the corrected libraries, and extrapolation to community diversity with commonly used non-parametric diversity estimators suggested at least thousands of co-existing ribotypes in the two communities. However, close inspection revealed that the non-parametric estimators likely lead to underestimation of ribotype diversity in the clone libraries. Thus, an improved parametric method was developed and shown to closely fit the data. The extrapolated total ribotype diversity in the sample by the improved method was up to one order of magnitude higher than estimated with common non-parametric approaches. Most significantly, the compensation for artifacts and improved estimation revealed that the vast majority of ribotypes fall into microdiverse clusters containing <1% sequence divergence. It is proposed that the observed microdiverse clusters form important units of differentiation in microbial communities. They are hypothesized to arise by selective sweeps and contain high diversity because by Vanja Klepac-Ceraj. Ph.D. 2005-09-27T17:28:05Z 2005-09-27T17:28:05Z 2004 2004 Thesis http://hdl.handle.net/1721.1/28641 58918455 en_US M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 106 p. 5426635 bytes 5439562 bytes application/pdf application/pdf application/pdf Massachusetts Institute of Technology |
| spellingShingle | Civil and Environmental Engineering. Klepac-Ceraj, Vanja, 1976- Diversity and phylogenetic structure of two complex marine microbial communities |
| title | Diversity and phylogenetic structure of two complex marine microbial communities |
| title_full | Diversity and phylogenetic structure of two complex marine microbial communities |
| title_fullStr | Diversity and phylogenetic structure of two complex marine microbial communities |
| title_full_unstemmed | Diversity and phylogenetic structure of two complex marine microbial communities |
| title_short | Diversity and phylogenetic structure of two complex marine microbial communities |
| title_sort | diversity and phylogenetic structure of two complex marine microbial communities |
| topic | Civil and Environmental Engineering. |
| url | http://hdl.handle.net/1721.1/28641 |
| work_keys_str_mv | AT klepaccerajvanja1976 diversityandphylogeneticstructureoftwocomplexmarinemicrobialcommunities |