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VIRAL,
ARCHAEAL
AND
BACTERIAL
COLONIZATION
OF
NATIVE
MARINE
ROCK
SUBSTRATA
by
Anand
Patel
_____________________________________________________________________
A
Dissertation
Presented
to
the
FACULTY
OF
THE
USC
GRADUATE
SCHOOL
UNIVERSITY
OF
SOUTHERN
CALIFORNIA
In
Partial
Fulfillment
of
the
Requirements
for
the
Degree
DOCTOR
OF
PHILOSOPHY
(BIOLOGY)
December
2010
Copyright
2010
Anand
Patel
Object Description
| Title | Viral, archaeal and bacterial colonization of native marine rock substrata |
| Author | Patel, Anand |
| Author email | aylanand@gmail.com; anandp@usc.edu |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Biology |
| School | College of Letters, Arts and Sciences |
| Date submitted | 2010 |
| Restricted until | Restricted until 08 Nov. 2011. |
| Date published | 2011-11-08 |
| Advisor (committee chair) | Fuhrman, Jed A. |
| Advisor (committee member) |
Edwards, Katrina J. Nealson, Kenneth Ziebis, Wiebke Goodman, Steven |
| Abstract | A biofilm is a microbially dominated, mucus-laden coating. Almost all submerged or even moist solid surfaces are enveloped in a bacterial and archaeal biofilm. In anthropogenic settings, many biofilms are a nuisance and a major source of bacterial infections. But in the marine environment, biofilms occur naturally everywhere at any liquid and solid interface, from microscopic floating particles in the coastal water column to the expansive rock surfaces that exist throughout the global network of mid-oceanic seafloor ridges. The strong forcing that drives bacteria and archaea to colonize a surface has created a global biofilm ecosystem that likely contains the largest fraction of earth's biomass.; Over the last three decades an immense body of knowledge from laboratory based research is uncovering critical information on bioflm formation, development and dispersal. Environmental biofilms are typically complex, species rich and cellularly dense, which poses difficulty in unraveling both the diversity and mechanisms of colonization and growth. The body of work presented within reveals information pertaining to the dominant microbial colonizers of native rock substrata at a shallow coastal site (Santa Catalina Island, California). Specifically, we present some novel data on the archaeal and viral microbial constituents of marine biofilms.; Our principle findings suggest bacterial colonizers of rocks are taxonomically distinct to those colonizing synthetic surfaces. The bacteria settling on the two surfaces may be phylogenetically related at the family taxonomic hierarchical designation, but at the genera (or better) level of resolution microbial communities on native surfaces are clearly unique, revealing a greater taxonomic richness and consistency over communities in synthetic biofilms. The latter are typically less diverse and show considerable variation in dominance by any particular bacterial taxa. Evidence of colonization by members of the other prokaryotic domain, the Archaea, is typically seen over the first twelve days of biofilm development at our field site and their presence withers as the microbial community undergoes a successional shift as it matures. The archaea present in these early biofilms are almost exclusively members of the mesophilic Crenarchaeota division and seem to possess autotrophic ammonia oxidative capabilities. Finally, a super-family of T4-like viruses belonging to the Myoviridae, and closely related to the well-described E.coli T4 bacteriophage, exists as a truly cosmopolitan group across all oceanic and terrestrial environments. Viral members of this super-family appear to also colonize both coastal and deep-sea native rock surfaces. More interestingly, the T4-like phage sequences obtained from rock biofilm samples and originating from the two field locations, separated by considerable physical distance, appear to be evolutionarily more closely linked to each other then to their planktonic water column cousins. This phenomenon is indicative of a possible biofilm-specific ecotype within the T4-like bacteriophage superfamily.; In conclusion, microbes dominating a biofilm microbial community are distinct from the abundant groups in the overlying free-living planktonic medium. Substratum type can shape the microbes that gather to a surface and trigger the attachment phase of biofilm growth. Biofilm dispersal processes in adjacent sediments and suspended aggregates likely serve as the recruitment reservoir for microbiota poised to take advantage of a newly exposed rock surface. As the biofilm matures over time, multiple shifts can occur in the taxonomic composition of the microbial community held within its slimey layers. Species belonging to both the family Rhodobacteraceae (phylum Alphaproteobacteria) and the proposed new phylum Thaumarchaeota (previously mesophilic Crenarchaeota), plus a subset of T4-like viruses (family Myoviridae) together appear to play founding roles as biological colonizers of coastal rock surfaces in the marine environment. |
| Keyword | archaea; bacteria; biofilm; phage; rock; virus |
| Geographic subject | islands: Santa Catalina Island |
| Geographic subject (state) | California |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m3522 |
| Rights | Patel, Anand |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | http://www.usc.edu/isd/libraries/services/ask_a_librarian/email/ |
| Filename | etd-Patel-3502 |
| Archival file | uscthesesreloadpub_Volume26/etd-Patel-3502.pdf |
Description
| Title | Page 1 |
| Full text | VIRAL, ARCHAEAL AND BACTERIAL COLONIZATION OF NATIVE MARINE ROCK SUBSTRATA by Anand Patel _____________________________________________________________________ A Dissertation Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (BIOLOGY) December 2010 Copyright 2010 Anand Patel |
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