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Applied and Environmental Microbiology, February 2000, p. 651-658, Vol. 66, No. 2
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Genetic Variation among Endosymbionts of Widely
Distributed Vestimentiferan Tubeworms
Carol A.
Di Meo,1
Ami E.
Wilbur,2
William E.
Holben,3
Robert A.
Feldman,4
Robert C.
Vrijenhoek,5,
and
S.
Craig
Cary1,*
Graduate College of Marine Studies, University of Delaware,
Lewes, Delaware 199581; Florida Marine
Research Institute, St. Petersburg, Florida
337012; Division of Biological Sciences,
The University of Montana, Missoula, Montana
59812-10023; Molecular Dynamics,
Sunnyvale, California 94086-45204; and
Center for Theoretical and Applied Genetics, Cook College,
Rutgers University, New Brunswick, New Jersey
08903-02315
Received 29 July 1999/Accepted 30 November 1999
 |
ABSTRACT |
Vestimentiferan tubeworms thriving in sulfidic deep-sea
hydrothermal vents and cold seeps are constrained by their nutritional reliance on chemoautotrophic endosymbionts. In a recent phylogenetic study using 16S ribosomal DNA, we found that endosymbionts from vent
and seep habitats form two distinct clades with little variation within
each clade. In the present study, we used two different approaches to
assess the genetic variation among biogeographically distinct
vestimentiferan symbionts. DNA sequences were obtained for the
noncoding, internal transcribed spacer (ITS) regions of the rRNA
operons of symbionts associated with six different genera of
vestimentiferan tubeworms. ITS sequences from endosymbionts of host
genera collected from different habitats and widely distributed vent
sites were surprisingly conserved. Because the ITS region was not
sufficient for distinguishing endosymbionts from different habitats or
locations, we used a DNA fingerprinting technique, repetitive-extragenic-palindrome PCR (REP-PCR), to reveal differences in the distribution of repetitive sequences in the genomes of the
bacterial endosymbionts. Most of the endosymbionts displayed unique
REP-PCR patterns. A cladogram generated from these fingerprints reflected relationships that may be influenced by a variety of factors,
including host genera, geographic location, and bottom type.
 |
INTRODUCTION |
Invertebrates that are endemic to
the highly sulfidic, reducing environments at deep-sea hydrothermal
vents and cold seeps are commonly associated with chemosynthetic
endosymbiotic bacteria (7, 18, 19). These bacteria oxidize
the reduced sulfur compounds that are abundant in hydrothermal fluid
(8, 36, 46). The resultant energy produced by the
endosymbiont is coupled to the production of carbon sources that
support the growth and maintenance of the invertebrate hosts (6,
8, 37, 48). The metabolic link between the invertebrate hosts and
their endosymbionts has obvious implications for the dispersal and
colonization strategies employed by the host organisms.
Vent endemic host organisms may employ one of three different
mechanisms for transmission of their endosymbionts to the next generation. Previous studies have shown that the Vesicomyid bivalves form species-specific associations with endosymbiotic bacteria (12, 13, 16). Host specificity is maintained in these
associations by vertical transmission of the bacteria through the egg
from the parent to the offspring (3, 35). The endosymbiont
and host phylogenies are congruent, which is consistent with a vertical mode of symbiont transmission (3, 4, 12, 35). In contrast, results from several studies suggest that endosymbiont transmission in
vestimentiferan tubeworms occurs horizontally (5, 17), possibly through ingestion of bacteria upon larval settlement (28,
42). It is also possible that horizontal transmission in
vestimentiferan-bacterial symbioses could occur through infection of
new recruits with bacteria previously associated with established congeners (20), although potential mechanisms for this
transfer have not been determined. If horizontal transmission is indeed the mechanism for bacterial acquisition in vestimentiferans, we expect
that biogeographic variation would exist among symbionts acquired from
the same host species collected in geographically isolated vent and
seep sites. Conversely, if vestimentiferan larvae settle in the same
locations where their symbionts are acquired, we expect that
vestimentiferans living at the same site would harbor identical symbionts.
In a recent study, genetic variation in vestimentiferan endosymbionts
was investigated by comparing sequences of the 16S rRNA genes of
bacteria collected from various species of hydrothermal vent and cold
seep tubeworms (20). The results showed a marked phylogenetic distinction between vestimentiferan endosymbionts collected from hydrothermal vents and soft-bottom, cold seep
environments. This study suggested that vestimentiferans acquire one of
two distinct species of free-living bacteria depending on whether they
settle on basaltic, hydrothermal vent sites or sedimented, cold seep
sites. A third, unique bacterial species was discovered in a tubeworm
that inhabited a sedimented whale fall. Significant genetic variation
was not found among symbionts found within each of the habitat types.
Symbionts from three different host genera collected from five
different hydrothermal vent sites along the East Pacific Rise (EPR) had
identical 16S rRNA gene sequences.
The observation of so little sequence variation among
endosymbiont 16S rRNA genes suggests that all tubeworm
endosymbionts may belong to a single species. However, the
conservative nature of the 16S rRNA gene often renders it
inadequate for distinguishing among conspecific strains of bacteria
(50). Therefore, it is not surprising that Feldman et al.
(20) did not find significant genetic variation within the
habitat clades. It is possible that significant genetic variation
exists between endosymbionts of geographically distributed
vestimentiferan hosts but that these species- or strain-level
differences have not been detected by approaches that have been
employed to date.
The goal of our study was to resolve the question of genetic variation
among widely distributed vestimentiferan endosymbionts by utilizing two
molecular techniques that have historically proven useful for comparing
closely related strains of bacteria. Our first approach entailed
sequencing of the internal transcribed spacer (ITS) region, a noncoding
region within the rRNA that often contains genetic variation sufficient
for differentiating species of prokaryotes (2). Our second
approach involved using a DNA fingerprinting technique that utilizes
repetitive extragenic palindromes (REPs) as priming sites to generate
diagnostic banding patterns from prokaryotic genomic DNA (25,
45). The REP-PCR technique is particularly useful for
investigations of bacterial symbiosis because REP sequences have been
found only in bacterial DNA; phage and eukaryotes do not contain REP
elements (25). By virtue of these repetitive elements,
symbiont DNA can be selectively amplified from a mixed population of
symbiont and host DNA to allow analysis of bacterial population
diversity. Our results provide information on the extent of genetic
variation among the symbionts, as well as further evidence to support a
horizontal mode of symbiont acquisition among the vestimentiferan tubeworms.
 |
MATERIALS AND METHODS |
Sample collection.
Vestimentiferans were collected with the
aid of submersibles from several locations, including two sites in the
Western Pacific Ocean, four sites along the EPR, two sites in the
Pacific Northwest, one site along the Galapagos Rift (GR), two sites
along the western coast of California and Mexico, and two locations in
the Gulf of Mexico (GOM) (Table 1).
Samples included in this study were chosen to represent the entire
range of host vestimentiferan distribution. Habitat types included
hydrothermal vent sites with a basaltic substrate, cold seep habitats
with a sedimented bottom, and one sedimented site associated with a
whale carcass (Table 1). All samples were carried to the surface in
chilled seawater (0.5 to 2°C).
DNA extraction.
The symbiont-containing trophosome tissue
from each vestimentiferan host was aseptically removed, and a small
portion of it was homogenized in 5 M guanidinium isothiocyanate. Prior
to DNA extraction, 25 µl of a 20% Chelex 100 (47)
solution was added to the homogenate and incubated for 1 h at
4°C. The samples were briefly spun to remove the Chelex 100. Total
bacterial DNA was extracted from 100 µl of guanidinium isothiocyanate
homogenate using the IsoQuick DNA purification kit (Orca, Bothell,
Wash.) according to the manufacturer's instructions and quantified
spectrophotometrically. In addition to symbiont DNA, host DNA from
three different genera was extracted from vestimentum tissue
(non-symbiont-containing tissue) using the same extraction protocol to
serve as controls. A number of the DNA samples used in this study
(e.g., 18°S Riftia pachyptila, Guaymas Vent and Seep
[GY-V and GY-S, respectively] Escarpia spicata, whale
E. spicata, Gorda Lamellibrachia sp., 21°N
Oasisia alvinae, and GY-V R. pachyptila) were
prepared separately at Rutgers University according to previously
published protocols (20).
16S rRNA gene characterization.
The methods used to PCR
amplify, purify, and sequence the 16S rRNA symbiont genes were as
described in the work of Feldman et al. (20). DNA sequence
alignments were initially constructed using PileUp and then optimized
(minimizing overall alignment differences) by eye in the SeqLab
environment (Genetics Computing Group). Insertions and deletions were
eliminated from the alignment before phylogenetic trees were
determined. Phylogenetic trees for the symbiont 16S rRNA genes were
computed using fastDNAml and bootstrapped 100 times using fastDNAml
boot (21, 34). For the maximum likelihood analyses,
operational taxonomic unit input order was randomized and global
rearrangements were performed at each bootstrap replication.
ITS region characterization.
PCRs amplified the ITS region
of the symbiont ribosomal DNA (rDNA) using two ITS-specific primers,
ITS16F-G1 (5'-GAAGTCGTAACAAGG-3') (27) and
ITS23R-L1 (5'-CAAGGCATCCACCGT-3') (27). ITS16F-G1 is nested about 30 to 40 nucleotides upstream from the spacer boundary
in the 3' end of the 16S rRNA gene (positions 1491 to 1505, Escherichia coli 16S rRNA gene). ITS23R-L1 is nested in the
5' end of the 23S rRNA gene, approximately 20 bases downstream from the
spacer boundary (positions 21 to 35, E. coli 23S rRNA gene).
PCR mixtures (50-µl total volume) contained final concentrations of
the following: 50 ng of symbiont DNA, 1× PCR buffer, 0.2 mM (each)
deoxynucleoside triphosphates, 10 pmol of each primer, 1.5 mM
MgCl2, 5% (vol/vol) acetamide, and 1.25 U of
Taq polymerase (Promega). PCR conditions were as follows: 35 cycles, each consisting of denaturation at 92°C for 1 min,
hybridization at 55°C for 2 min, and elongation at 72°C for 2 min
with 5 s added to each extension per cycle. A hot start
(9) with denaturation at 95°C for 2 min was used at the
beginning of the reaction to heighten reaction specificity. In
addition, acetamide was added to the PCR to encourage more efficient
amplification of GC-rich templates (38). All PCRs were
performed on an MJ-Minicycler (MJ Research, Inc., Watertown, Mass.).
Because our attempts to directly sequence the smaller ITS PCR amplicon
yielded poor results, amplified ITS regions were cloned
to facilitate
sequencing. Amplification products were pooled from
three separate PCRs
and cloned directly using the TA cloning kit
with the pCR-II or the
pCR-2.1-TOPO cloning vectors (Invitrogen,
San Diego, Calif.) according
to the manufacturer's instructions.
Plasmid preparations were made
using a standard alkaline-lysis
preparation (
39). The sizes
of the inserts were verified before
sequencing by restriction analysis.
The plasmid DNA was further
purified for sequencing using the Plasmid
MiniKit (Qiagen, Inc.,
Valencia, Calif.) according to the
manufacturer's instructions.
Two clones from each amplified ITS region
were cycle sequenced
using the Perkin-Elmer (Foster City, Calif.) ABI
BigDye dye termination
cycle sequencing ready reaction kit with Ampli
Taq DNA polymerase
FS according to the manufacturer's
instructions. Sequencing was
performed on an ABI PRISM 310 genetic
analyzer.
The ITS regions were bidirectionally sequenced and confirmed prior to
their alignment using the Sequence Navigator and AutoAssembler
programs
(Applied Biosystems, Inc.). Only sequences that overlapped
with 0%
ambiguity were included in the analysis. Final alignments
were
generated in the Genetic Data Environment, version 3.2. Phylogenetic
relationships were determined from these aligned sequences using
PHYLIP
version 3.572 (
22). A Kimura two-parameter distance matrix
was constructed, from which neighbor-joining trees with 100 bootstrap
replications were generated. A second distance matrix, based on
pairwise differences in the geographic distribution between samples,
was generated from latitude-longitude information for each sample
site
using GeoDist version 3.01e, R package (
32). A third
distance
matrix, based on pairwise comparisons of the sample habitat
types,
was created by assigning "0" values to pairs of samples that
were
taken from similar habitat types (both vent or both seep) and
"1" values to pairs of samples that were taken from different
habitat types. Mantel correlation tests were performed to compare
ITS
sequence distance with geographic and habitat distance (
14,
33). Two- and three-way Mantel tests were performed using
different
combinations of the three distance matrices to assess whether
ITS genetic distance significantly correlates with the geographic
distances between endosymbiont collection sites or their habitat
types
(
41). These Mantel tests were performed using the R package
(
32).
REP elements.
REP sequences were amplified from each of the
vestimentiferan symbionts with PCR using two universal REP primers,
REPIR-I (5'-IIIICGICGICATCIGGC-3') (45) and REP2-I
(5'-ICGICTTATCIGGCCTAC-3') (44). Each 25-µl REP-PCR
mixture contained 50 ng of symbiont or host DNA and final
concentrations of 1× Gitschier buffer [16.6 mM
(NH4)2SO4, 67 mM Tris-HCl, 6.7 mM
MgCl2, 6.7 µM EDTA, 30 mM
-mercaptoethanol
(29)], 160 µg of DNA-grade bovine serum albumin per ml,
10% dimethyl sulfoxide, 1.25 mM (each) four deoxynucleoside triphosphates, 10 pmol of each REP primer, and 2 U of Taq
polymerase (Gibco). One cycle of 95°C for 7 min was performed to
denature the genomic DNA, followed by 30 cycles of 94°C for 1 min,
44°C for 1 min, and 65°C for 8 min, and a final extension at 65°C
for 15 min. PCRs were performed with an MJ-Minicycler (MJ Research, Inc.). Reaction products (7.5 µl) were analyzed via agarose gel electrophoresis.
A digital image of each gel was captured and stored using the Alpha
Imager 2000 Documentation and Analysis System (AlphaInnotech
Corp., San
Leandro, Calif.). Each gel image was analyzed using
the software
package GelCompar (version 4; Applied Maths, Kortrijk,
Belgium). This
software was used to normalize the molecular weight
of each of the
bands in each gel to all of the others based on
the inclusion of the
same set of molecular weight markers on each
gel. Once normalized, all
of the fingerprints in the database
were compared to each other using
an unweighted-pair-group-method-with-averages
clustering algorithm and
Jaccard
coefficient.
Nucleotide sequence accession numbers.
GenBank accession
numbers for the new ITS sequences reported in this paper are as
follows: AF076795, Ridgeia piscesae endosymbiont, Juan de
Fuca Ridge (JDF); AF076796, Escarpia laminata endosymbiont, West Florida Escarpment (WFE); AF076797, Lamellibrachia sp. endosymbiont, GOM-10; AF076798, E. spicata endosymbiont,
GY-S; AF076799, R. pachyptila endosymbiont, GY-V; AF076800,
Tevnia jerichonana endosymbiont, 9N; AF076801, R. pachyptila endosymbiont, 9N; AF076802, T. jerichonana
endosymbiont, 13N; AF076803, R. pachyptila endosymbiont,
13N; AF076804, Lamellibrachia sp. endosymbiont, Gorda;
AF076805, R. pachyptila endosymbiont, GR; AF076806, R. pachyptila endosymbiont, 18S; AF076807, O. alvinae
endosymbiont, 21N; AF076808, E. spicata endosymbiont, whale;
AF076809, undescribed species endosymbiont, Nikko Seamount; AF076810,
L. columna endosymbiont, Lau-Fiji; AF076811,
Lamellibrachia sp. endosymbiont, GOM-12; AF076812, E. spicata endosymbiont, GY-V; AF076813, Lucina floridana
endosymbiont. Accession numbers for the three 16S rRNA sequences
generated for this study are as follows: AF165909, E. spicata endosymbiont, GY-V; AF165907, undescribed species
endosymbiont, Nikko Seamount; and AF165908, E. spicata
endosymbiont, GY-S.
 |
RESULTS AND DISCUSSION |
16S rDNA sequence variation among vestimentiferan
endosymbionts.
In order to maintain a comparable data set, many of
the endosymbiont DNA samples used in our ITS and REP-PCR analyses are the same DNA samples used in the previous 16S rDNA study of
geographically distinct endosymbionts (20). Our study also
includes additional samples to expand the representation of symbiont
distribution. In concordance with our expanded data set, a new 16S rDNA
phylogenetic tree was generated to include three of the endosymbionts
that were added: GY-V E. spicata, GY-S E. spicata, and the undescribed species from the Nikko Seamount (Fig.
1A). In this new analysis of 16S rDNA
sequences, the symbionts continue to cluster into two main groups:
group I includes all of the symbionts from seep- or sediment-dwelling
host organisms, while group II includes all of the symbionts from
vent-dwelling host fauna. These relationships are in accordance with
our previous findings (20). Interestingly, the difference
between vent and seep symbionts is maintained between symbionts from
the same host, E. spicata, collected from vent (GY-V) and
seep (GY-S) habitats at a single site in Guaymas Basin. Likewise,
symbionts from two different vestimentiferan hosts are closely related
when collected from the same habitat type (e.g., 9N R. pachyptila and T. jerichonana symbionts, both from vent habitats).

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FIG. 1.
(A) Dendrogram based on 16S rDNA sequences of
vestimentiferan symbionts. Phylogenetic relationships were computed
using fastDNAml and bootstrapped 100 times using fastDNAml boot
(21, 34). For the maximum likelihood analyses, operational
taxonomic unit input order was randomized and global rearrangements
were performed at each bootstrap replication. Two major groups of
endosymbionts are indicated. Scale bar represents 10% sequence
dissimilarity. Reference sequences used in this 16S study were obtained
from the GenBank database and include the following accession numbers:
L25712, Codakia costata symbiont; L25711, Anodontia
phillipiana symbiont; M99446, Calyptogena magnifica
symbiont; L25710, Calyptogena pacifica symbiont; L25718 and
L25719, Calyptogena elongata symbiont; M90662,
Thiobacillus hydrothermalis; V00348, E. coli;
U77478, 9N and 18S R. pachyptila endosymbiont and 9N
T. jerichonana endosymbiont; U77479, GOM
Lamellibrachia sp. endosymbiont and WFE E. laminata endosymbiont; U77480, JDF Ridgeia piscesae
endosymbiont and GY-V and GR R. pachyptila endosymbiont;
U77481, Lau-Fiji L. columna endosymbiont; U77482, whale
E. spicata endosymbiont. (B) Dendrogram showing the
relationships of vestimentiferan symbionts based on ITS sequences. The
tree was rooted with the symbiont from a marine bivalve, L. floridana, as an outgroup. The tree was constructed using the
neighbor-joining method with 100 bootstrap replicates. Each number on a
branch indicates the number of times (out of 100) that the node was
supported by the bootstrap analysis. Only bootstrap values of 50%
are reported. Two major clusters of endosymbionts are indicated. Scale
bar represents 10% sequence dissimilarity.
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ITS sequence variation among vestimentiferan symbionts.
ITS
amplifications of vestimentiferan symbionts were generally 550 bp in
length, although some individuals yielded a second, larger PCR product
of roughly 800 bp in length (data not shown). The larger amplicon did
not match any ITS sequences in the database, and we found that its
intensity in the total PCR product was reduced by the use of higher
annealing temperatures. For these reasons, we believe that the larger
product represented an artifact of the PCR rather than rRNA operon
heterogeneity. To separate these two distinct amplicons, we cloned the
ITS PCR amplification products and used only the smaller amplicon from
each symbiont for sequence analysis. As in many bacteria, all of the
endosymbiont ITS regions contained putative sequences for the tRNA
genes for alanine and isoleucine (Fig.
2). Five of the symbionts contained
prominent insertion sequences (approximately base position 312 in ITS
region) that totaled approximately 50 bp (Fig. 2).

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FIG. 2.
Alignment of a portion of the ITS region (bp 240 to
480). Putative sequences for the tRNA genes for alanine and isoleucine
are indicated by the boxes. A 50-bp insertion that is present in five
of the sequences is highlighted by boldface. Identical bases are
indicated by dots, while gaps in the sequence alignment corresponding
to insertions or deletions are indicated with dashes.
Lamell., Lamellibrachia.
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ITS sequences of endosymbionts collected from several vestimentiferan
host genera were compared phylogenetically using the
corresponding ITS
sequence of the symbiont of the lucinid bivalve
L. floridana
as an outgroup. A similarity matrix of ITS sequences
was constructed
based upon a Kimura two-parameter distance estimate.
Genetic distances
were calculated based on 500 bp of aligned sequences
after the
nucleotide insertions and deletions were removed. The
sequences were
surprisingly conserved overall, with percent sequence
similarity
ranging from 87.0 to 100% (data not shown). The symbionts
from
R. pachyptila hosts collected from Guaymas Basin, 9°N, and
18°S displayed 100% sequence
similarity.
Symbiont relationships were depicted as a cladogram based upon ITS
sequence diversity (Fig.
1B). Because of the high similarity
among the
ITS sequences, many of the bootstrap values at branch
points in the
neighbor-joining analysis were low or insignificant.
Only bootstrap
values of

50% were reported. The ITS cladogram
showed a prominent
break within the symbionts: group I included
the symbionts of
E. spicata from the whale carcass,
L. columna from the
Lau-Fiji basin, the undescribed species from a vent site
at the Nikko
Seamount, one of the two
Lamellibrachia spp. collected
from
a seep site in the GOM (GOM-12), and
E. laminata from the
seep site at Guaymas Basin; group II included the rest of the
symbionts
(Fig.
1B). Apart from differing in sequence from the
members of group
II, the symbionts in group I contained prominent
insertion sequences
that totaled approximately 50 bp (Fig.
2).
The sequences of these
insertions were nearly identical in all
of the symbionts in which they
were found. Groups I and II in
the 16S rDNA cladogram (Fig.
1A)
correlate well with groups I
and II in the ITS cladogram (Fig.
1B),
with one exception:
E. laminata symbiont, WFE, appears in
group I according to its 16S
rDNA sequence and in group II according to
its ITS sequence (Fig.
1).
To determine if there was a significant correlation between ITS
sequence diversity and either geography or habitat type, we
performed
two- and three-way Mantel tests to compare distance
matrices generated
from pairwise differences between ITS sequences,
geographic distances,
or habitat types. The results of these Mantel
tests are shown in Table
2. Despite the remarkable similarity
among the ITS sequences, the genetic distances among ITS regions
correlate significantly with geographic distances. Although none
of the
correlations were particularly strong (
r

0.334 for
all
tests),
P values from two different Mantel tests
indicated that
ITS sequence similarity and geography were significantly
correlated
(
P = 0.0349, test 3;
P = 0.0480, test 4). In contrast,
P values
for a two-way
Mantel test of ITS sequence similarity versus habitat
type alone (test
1) or a three-way test versus habitat type with
geography factored out
(test 5) were not statistically significant
(
P = 0.146
and 0.102, respectively). Thus, ITS sequence similarity
was
significantly correlated with broad-scale endosymbiont geography
(
P 
0.05) but not significantly correlated with
habitat type.
In light of the fact that the ITS sequences for 9°N,
18°S, and
Guaymas
R. pachyptila were identical, our
results suggest that
the ITS region is variable enough to show
broad-scale biogeographic
variation but is not variable enough to
distinguish among symbionts
located along the same ridge axis. These
results are in contrast
to the results of Feldman et al.
(
20) and the new analysis of
16S rDNA relationships
presented in this study, which suggest
that symbiont sequence distances
correlate with habitat type (basaltic,
vent versus sedimented, seep
substrates). Although our data suggest
that the geographic distribution
of the hosts may be a dominant
influence in determining genetic
variation of the endosymbionts,
it is clear that several factors affect
endosymbiont diversity.
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TABLE 2.
Mantel tests of correlation among geographic, habitat,
and ITS sequence similarity matrices for
vestimentiferan symbiontsa
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Historically, the ITS region has been useful for discriminating among
strains of several bacterial species, including a hyperthermophilic
archaeon (
11),
Rhizobium sp. (
30),
Bifidobacterium sp. (
31),
infectious
Pseudomonas sp. (
43), and
Trichodesmium sp. (
49).
In the present study, we
found that the ITS region was much more
conserved than expected.
Although the ITS region is usually very
informative at the subspecies
and/or strain level (
11,
30,
31,
49), it has been unreliable
in some cases. In studies
of the
Mycobacterium tuberculosis
complex (
23) and with several
Listeria isolates
(
15), the ITS region failed to differentiate
between species
and/or
strains.
REP-PCR fingerprints of the vestimentiferan symbionts.
The
REP-PCR technique is particularly well suited for investigations of
bacterial symbiosis, in that it allows investigators to survey the
symbiont genome in the presence of host DNA because the REP priming
sites are exclusively bacterial (25). To confirm that REP
sequences were not present in the genomes of the vestimentiferan hosts,
we performed REP-PCR amplifications on DNA that was aseptically acquired from vestimentum (non-symbiont-containing) tissue from three
different host genera (Escarpia, Riftia, and
Tevnia). Most of these samples failed to amplify at all
(data not shown). The exception was E. laminata, which
produced a single band that did not correspond with any of the bands
seen in the REP fingerprint of its endosymbiont.
Fingerprint patterns of the vestimentiferan endosymbiont DNA displayed
remarkable variation (Fig.
3).
Relationships based
upon the number of shared bands among the
fingerprint patterns
were compared using GelCompar software and
depicted as a cladogram
with a corresponding, computer-generated gel
image (Fig.
4). All
of the symbionts
included in the REP analysis displayed unique
fingerprints, with the
exception of 9°N
R. pachyptila, and GR
R. pachyptila, which exhibited indistinguishable patterns (Fig.
3 and
4). The REP analysis seems to divide the symbionts into
four distinct
groups, or clades (Fig.
4). Group I includes both
Lamellibrachia symbionts from the GOM and the symbiont from
Ridgeia piscesae from the JDF. Group II includes the
R. pachyptila symbionts
and the symbiont from
T. jerichonana. Group III includes all of
the
Escarpia
symbionts, from both
E. spicata and
E. laminata.
Group IV includes the endosymbionts from the undescribed species
at
Nikko Seamount and
L. columna from the Lau-Fiji Basin, two
distantly located sites in the western Pacific Ocean.

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FIG. 3.
Digital image of the REP-PCR fingerprint patterns of the
vestimentiferan symbionts. Shown are the REP-PCR products generated by
using chromosomal DNA of endosymbionts extracted from the following
vestimentiferans: R. pachyptila, GY-V (lane 1); R. pachyptila, 9N (lane 2); R. pachyptila, GR (lane 3);
R. pachyptila, 18S (lane 4); Ridgeia piscesae,
JDF (lane 5); T. jerichonana, 9N (lane 6); undescribed sp.,
Nikko Seamount (lane 7); L. columna, Lau-Fiji (lane 8);
E. spicata, whale (lane 9); E. spicata, GY-V
(lane 10); E. spicata, GY-S (lane 11);
Lamellibrachia sp., GOM-10 (lane 12); E. laminata, WFE (lane 13); Lamellibrachia sp., GOM-11
(lane 14). Lanes H, Hi Low DNA marker; lane M, 1-kb DNA ladder.
Molecular sizes (base pairs) of selected bands in the DNA markers are
indicated. The photo represents a composite of a larger gel that was
altered in Adobe Photoshop version 5.0 to include only the individuals
presented in this study.
|
|

View larger version (32K):
[in this window]
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|
FIG. 4.
Cladogram depicting relationships of vestimentiferan
endosymbionts based upon their REP-PCR fingerprints. The degree of
genetic similarity is indicated above the cladogram in percentage
units. To facilitate visual comparison, a computer-generated gel that
depicts the lanes reloaded according to their relationships in the
dendrogram has been included. The symbionts separated into four groups
based upon the percent similarity (measured as number of shared bands)
among their REP fingerprint patterns. Group I, GOM
Lamellibrachia sp. symbionts and JDF Ridgeia
piscesae symbiont; group II, R. pachyptila and T. jerichonana symbionts; group III, Escarpia spp.
symbionts; group IV, Nikko Seamount and Lau-Fiji Basin L. columna symbionts. Slight visual differences from the original gel
lane images in Fig. 3 result from the normalization and analysis
process of the GelCompar software.
|
|
Upon closer examination, the REP analysis seems to reflect three
different influences on endosymbiont differentiation: host
genus,
bottom or substrate type, and geography. Host genus seems
to be the
primary source of differentiation, as most of the clades
break up into
distinct groupings of congeners. The only clade
where this breaks down
is group II, which includes symbionts from
Riftia and
Tevnia host genera. This clade, however, supports previous
studies using DNA-DNA hybridization and in situ hybridization
that
suggest that the endosymbionts of
Riftia and
Tevnia are closely
related (
5,
17).
The secondary influences for symbiont genetic differentiation seem to
be geographic location and substrate type. Within clades
of congeners,
it appears that symbionts differ based upon where
they are collected
and/or the habitat type (basaltic or sedimented).
In group II, all of
the
R. pachyptila symbionts collected from
the hosts at
northern EPR sites (i.e. GY-V, 9N, and GR) are less
closely related to
the
R. pachyptila symbiont collected from a
site 18°S
along the southern EPR. Within the
Escarpia symbiont
clade
(group III), both geographic location and substrate type
seem to be at
work: symbionts collected from hosts at the whale
fall in the Santa
Catalina Basin (whale), Guaymas Basin seep (GY-S),
and WFE, all
soft-bottom substrate types, clade together and group
away from the
symbionts collected from the Guaymas Basin vent
(GY-V). Within the
soft-bottom grouping of
Escarpia symbionts,
it appears that
the symbionts from California and Guaymas (both
on the western coast of
North America) group away from the symbiont
from Florida (on the
eastern coast). The symbionts from the Nikko
Seamount and Lau-Fiji
Basin are clearly different from the rest
of the symbionts, presumably
because they are so geographically
removed from the rest of the
collection
sites.
REP-PCR has been useful for genomic fingerprinting of various strains
of bacteria, including
Actinobacillus (
1),
Rhizobium (
10,
30),
Legionella
(
24),
Streptococcus (
44),
Bacillus (
26), and
Citrobacter
diversus (
51) strains. In the present
study, we found
that the REP-PCR fingerprint analysis was sufficiently
fine-scaled to
reveal some interesting strain-level genetic variation
among
vestimentiferan symbionts. Presumably, this is because the
REP analysis
targets the whole genome, rather than a specific,
relatively
conservative region of the DNA. This physically maximizes
the
probability of finding strain-level variation. It should be
noted that
the symbiont of
O. alvinae was not included in the
REP
analysis, because a reliable REP-PCR amplification and subsequent
fingerprint pattern were not obtainable with this DNA. When the
DNA was
run on an agarose gel, it appeared sheared, and although
it was
sufficiently large enough for performance of the 550-bp
ITS
amplification, there was insufficient high-molecular-weight
genomic DNA
to support the REP
analysis.
Implications for symbiont relatedness and acquisition.
Previous studies have suggested that vestimentiferans acquire their
symbionts through ingestion of free-living bacteria upon larval
settlement (28, 42). If this mechanism alone is employed, one would expect that symbionts from two different vestimentiferan host
species living at the same location would be identical or related more
closely to each other than they are to other endosymbionts collected
from distant vent sites. This, in fact, was not the case, as symbionts
from 9°N T. jerichonana and 9°N R. pachyptila (both collected from the same rock) did not display identical ITS
sequences or REP-PCR fingerprints. Instead, the symbionts grouped
according to their respective host species as revealed through
comparisons of shared bands in their REP-PCR fingerprints.
One explanation for this is that larvae could acquire their symbionts
prior to attachment, either from a different substrate
than where they
eventually colonize or from the water column.
This could enable two
vestimentiferans that reside in the same
site to harbor different
symbionts. Alternatively, symbiont acquisition
may be related to
ecological succession.
T. jerichonana is the
first colonizer
of new hydrothermal vent fields, in areas of the
most intense diffuse
flow (
40). Presumably, this is because
T. jerichonana is more tolerant (than
R. pachyptila) of
the high
temperatures and elevated concentrations of H
2S
that are present
in newly formed vent sites. It is only after
T. jerichonana has
become established and the
levels of reduced chemicals have attenuated
that
R. pachyptila begins to colonize a new hydrothermal vent
site
(
40). The
T. jerichonana and
R. pachyptila hosts may simply
acquire a different subset of a
free-living chemoautotrophic community
due to temporal and/or
spatial consequences of ecological
succession.
Specific host recognition mechanisms may exist that allow certain
strains of endosymbiont bacteria to survive in specific
vestimentiferan
hosts. Although these mechanisms have not been
demonstrated in
vestimentiferans, they could explain how two different
hosts living on
the same rock could harbor different symbionts.
Alternatively, the
larvae may acquire bacteria that have been
released from congeners
residing at the site of larval settlement,
potentially through host
decomposition. These mechanisms might
yield REP-PCR fingerprint
patterns that imply close relationships
between endosymbionts of the
same host genus. Because only one
individual from each vestimentiferan
genus was sampled from most
of the locations, we cannot determine the
extent of ITS sequence
variation among endosymbionts at each
site.
The extent of vestimentiferan symbiont relatedness and the host
transmission mechanisms used to maintain these symbioses have
remained
ongoing questions. The results presented here demonstrate
the existence
of significant strain-level variation between endosymbionts
of
different vestimentiferan hosts collected from geographically
separated
areas. Further work to pinpoint the stage during vestimentiferan
development when the symbiosis is first established will shed
light on
symbiont transmission and help to explain the genetic
diversity among
symbiont
populations.
 |
ACKNOWLEDGMENTS |
We thank the crews and pilots of the R/V Atlantis II
and the deep-submergence vehicle Alvin, the
Nautile, and the U.S. Navy Advanced Tethered Vehicle for
their assistance in sample collection. Samples of L. columna
from the Lau-Fiji Basin were generously provided by A. M. Alayse.
Samples of Lamellibrachia sp. from Green Canyon, GOM, were
graciously supplied by Craig Young and Adele Pile. ITS primers and
sequences for 13°N Tevnia and Riftia, Gorda Lamellibrachia, and Galapagos Riftia were
contributed by Jeff Stein. We thank Barbara Campbell for assistance
with REP-PCR fingerprinting and Kathy Coyne for critically reviewing
the manuscript. We also thank Ken Halanych for thoughtful discussion.
The manuscript was greatly improved by the helpful comments of two
anonymous reviewers.
This work was supported by two NSF grants to S.C.C. (OCE-9314595 and
OCE-9596082). The whale carcass E. spicata sample was collected on a cruise led by Craig Smith and funded by an NSF grant to
R.C.V. (OCE-9633131).
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Graduate College
of Marine Studies, University of Delaware, Cannon Lab, 700 Pilottown Rd., Lewes, DE 19958. Phone: (302) 645-4078. Fax: (302) 645-4007. E-mail: caryc{at}udel.edu.
Present address: Monterey Bay Aquarium Research Institute, Moss
Landing, CA 95039-0628.
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