Staff View
Experimental studies on fermentative firmicutes from anoxic environments

Descriptive

TitleInfo
Title
Experimental studies on fermentative firmicutes from anoxic environments
SubTitle
isolation, evolution, and their geochemical impacts
Name (type = personal)
NamePart (type = family)
Choi
NamePart (type = given)
Jessica
NamePart (type = date)
1990-
DisplayForm
Jessica Choi
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Yee
NamePart (type = given)
Nathan
DisplayForm
Nathan Yee
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = personal)
NamePart (type = family)
Young
NamePart (type = given)
Lily
DisplayForm
Lily Young
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Vetriani
NamePart (type = given)
Costantino
DisplayForm
Costantino Vetriani
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Dawson
NamePart (type = given)
Katherine
DisplayForm
Katherine Dawson
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
outside member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
School of Graduate Studies
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (qualifier = exact)
2017
DateOther (qualifier = exact); (type = degree)
2017-10
CopyrightDate (encoding = w3cdtf); (qualifier = exact)
2017
Place
PlaceTerm (type = code)
xx
Language
LanguageTerm (authority = ISO639-2b); (type = code)
eng
Abstract (type = abstract)
Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated further. We studied three clostridial organisms, Clostridium sp. FGH that was previously enriched from Oak Ridge, TN; Clostridium beijerinckii; and Clostridium acetobutylicum to determine how Fe(III) oxide reduction occurs. The results indicate that Fe(III) oxide reduction by fermentative clostridial species does not require direct cell-to-mineral contact, meaning that it is an extracellular process mediated by a soluble molecule. Fermentation oft leads to the accumulation of acidic by-products, which can act as Fe(III)-chelating ligands. But during glucose fermentation, soluble Fe(III) accumulation did not occur, nor did supplementation of organic acids to fermenting cultures stimulate either the rate or extent of Fe(III) reduction even though rapid Fe(III) solubilization was observed. This extracellular process may be mediated by flavins, and supplementation of flavin adenine dinucleotide (FAD), a flavin molecule that serves as an electron carrier intracellularly, stimulated Fe(III) oxide reduction. These results indicate the potential for Clostridium species to perform Fe(III) reduction in contaminated environments and may be relevant towards bioremediation. Clostridum sp. FGH was enriched as a co-culture with another spore-forming Firmicutes organism that we isolated and named Anaerosporomusa subterranea strain RU4. This organism is likewise an obligate fermenter but with a very narrow metabolic niche. Surprisingly, this organism in pure culture showed no ability to reduce Fe(III), despite the fact that it was isolated from an Fe(III)-reducing enrichment culture. Furthermore, the addition of typical terminal electron acceptors were not utilized by A. subterranea. However, this organism was interesting because it was a Gram-negative (or didermic, since they have two membranes in their cell wall structure) organism within a phylum that was previously thought to be only Gram-positive (or monodermic, since these microorganisms have only one membrane as part of their cell wall). We investigated how this organism could have evolved through comparative phylogenomics of outer membrane biosynthesis genes. We identified 46 potential protein sequences involved in lipopolysaccharide and outer membrane biosynthesis in the genome of A. subterranea. Specifically out of these proteins, we focused on the proteins LptACD that are responsible for transporting mature lipopolysaccharide from the inner membrane, across the periplasmic space, and to the outer membrane. This is because most Gram-negative or didermic bacteria require these proteins to synthesize an outer membrane. Our results demonstrated that A. subterranea shared approximately 50% sequence similarity for the LptACD proteins with other Negativicutes. When the alignment was expanded to other Gram-negative or didermic bacterial clades, on average 25% similarity was reported. This suggested significant homology within the Negativicutes and with other microorganisms, such that these genes in A. subterranea were ancestrally derived. Furthermore, phylogenetic comparisons using the LptACD protein sequences showed comparable tree topology to the widely-accepted 16S phylogenetic tree, illustrating vertical gene transfer and that recent horizontal gene transfer did not occur. In conclusion, our data suggests that the ancestor to the Firmicutes phylum was originally didermic and that A. subterranea may represent an ancestral lineage.
Subject (authority = RUETD)
Topic
Microbial Biology
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_8500
PhysicalDescription
Form (authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
1 online resource (xiii, 124 p. : ill.)
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references
Subject (authority = ETD-LCSH)
Topic
Geomicrobiology
Note (type = statement of responsibility)
by Jessica Kee Eun Choi
RelatedItem (type = host)
TitleInfo
Title
School of Graduate Studies Electronic Theses and Dissertations
Identifier (type = local)
rucore10001600001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/T31G0QCV
Genre (authority = ExL-Esploro)
ETD doctoral
Back to the top

Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Choi
GivenName
Jessica
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2017-10-03 08:12:43
AssociatedEntity
Name
Jessica Choi
Role
Copyright holder
Affiliation
Rutgers University. School of Graduate Studies
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
Back to the top

Technical

RULTechMD (ID = TECHNICAL1)
ContentModel
ETD
OperatingSystem (VERSION = 5.1)
windows xp
CreatingApplication
Version
1.5
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2017-10-03T08:02:15
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2017-10-03T08:02:15
ApplicationName
Microsoft® Word 2013
Back to the top
Version 8.4.8
Rutgers University Libraries - Copyright ©2022