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diversity; 454 tag sequencing. in the microbial community composition. At the local scale, most vents host a
distinct population of Epsilonproteobacteria, regardless of seamount location. This
suggests that there may be barriers to exchange and dispersal for these vent
endemic microorganisms at hydrothermal seamounts of the Mariana Arc.
c 2010 Federation of European Microbiological Societies FEMS Microbiol Ecol 73 (2010) 538–549
Published by Blackwell Publishing Ltd. All rights reserved
Epsilonproteobacteria in vents of the Mariana Arc 539
multiple samples from within a seamount fell into more also collected and analyzed according to Butterfield et al.
than one cluster, highlighting the heterogeneity of the (2004). Fluid samples were preserved for cell enumeration
microbial mats and hydrothermal systems they sampled using epifluorescence microscopy with DAPI as described
(Davis & Moyer, 2008). They concluded that arc and backarc previously (Huber et al., 2002), as well as cultivation of
hydrothermal systems may represent bacterial hotspots of anaerobic thermophiles and hyperthermophiles.
diversity in the ocean.
Here, we focus on volcanoes of the Mariana Arc using Quantitative PCR (qPCR)
venting fluids as an access point to the subseafloor microbial
communities of seamounts (Schrenk et al., 2010). Our qPCR TaqMan assays described previously by Nadkarni et al.
previous work in diffuse vents from mid-ocean ridges (2002) and Takai & Horikoshi (2000) were used to deter-
showed remarkable microbial diversity (based on 16S rRNA mine the relative abundance of bacterial and archaeal 16S
24°N
500
Nikko Pacific
Plate
22°N
Seamount
Daikoku
Province
20°N
Central
Seamount
Province
18°N
900
0
–1000
–2000 16°N
Southern
–3000 Seamount
–4000 Province
Depth (m)
–5000
Phillipine NW Rota-1
–6000
Plate
–7000 14°N
Forecast
–11000
forward primer or a recognizable match to the reverse database (https://vamps.mbl.edu) and the National Center
primer sequence (including rare variants) at either end, for Biotechnology Information Sequence Read Archive
reads covering only a portion of the variable region, and (SRA) under the accession number SRA012278.
reads that could not be assigned unambiguously to a sample A variety of analyses were then carried out using internal
were discarded. The resulting datasets contained 229 913 V6 SQL database queries, SLP PWAL (Huse et al., 2010), MOTHUR
tags. Sequences were assigned taxonomy using the global (Schloss et al., 2009), and PRIMER-E (Clarke & Gorley, 2006).
alignment for sequence taxonomy (GAST) process (Huse All Epsilonproteobacteria sequences from each sample were
et al., 2008), which incorporates the RDP II taxonomy (Cole pooled and operational taxonomic units (OTUs) were
et al., 2007). Seventy-four thousand seven hundred and calculated via SLP PWAL and MOTHUR. To reduce the residual
sixty-seven tag sequences mapped to the Epsilonproteo- effects of sequencing error and noise, SLP PWAL uses pairwise
bacteria. Sequences have been deposited in the VAMPS alignments of the V6 tags based on the Needleman–Wunsch
c 2010 Federation of European Microbiological Societies FEMS Microbiol Ecol 73 (2010) 538–549
Published by Blackwell Publishing Ltd. All rights reserved
Epsilonproteobacteria in vents of the Mariana Arc 541
No data
sequence in the final clustering step, which uses the ESPRIT
pairwise alignment distances and the average-linkage meth-
od of MOTHUR. The resulting matrix of OTUs shared between
samples was normalized to total and transformed via square
Volume (mL)
Results
13.395
13.395
14.601
14.601
14.601
14.601
14.601
21.487
21.487
21.325
21.325
23.081
23.079
23.08
Site descriptions
The Mariana Arc is located in the western Pacific from about
6.56
6.23
1.64
3.75
2.62
5.25
5.09
5.26
5.28
5.89
3.36
5.54
5.05
6.21
1612
1578
560
534
521
584
568
438
414
458
445
413
Alka Seltzer
Snail Scrum
Sulfur Flow
Cliff House
North Vent
Brimstone
Top Vent
Iceberg
NW Rota-1
NW Rota-1
NW Rota-1
NW Rota-1
NW Rota-1
NW Eifuku
NW Eifuku
Daikoku
Daikoku
Forecast
Forecast
Both of these vents had relatively high pH values (Table 1) 3.36) with relatively low gas and iron concentrations (M.
and low gas (H2, H2S, and CH4) concentrations (M. Lilley, Lilley, unpublished data). The final site was NW Eifuku, the
unpublished data). The second site sampled was NW Rota- deepest of the sites, with venting fluids rich in both liquid
1, an actively erupting volcano with abundant diffuse and gas CO2, as well as large mussel beds and dense
venting (Embley et al., 2006; Chadwick et al., 2008). We microbial mats (Lupton et al., 2006; Embley et al., 2007;
sampled the eruptive Brimstone Pit (FS445) during a quiet Tunnicliffe et al., 2009). Both samples of sites here, Sulfur
period, as well as four diffuse vents (FS446–FS449) trending Flow (FS467) and Cliff House (FS468), were taken near
east and downslope from the eruptive area, many of which areas where liquid CO2 droplets were venting with high
had abundant white microbial mat, as well as shrimp concentrations of CO2 and H2S as well as minor CH4 and H2
present. The lowest pH values were found both at the (Lupton et al., 2006). The gas data (CO2, H2S, H2, CH4) are
eruptive pit (pH 1.64) and at nearby diffuse vents Sandy presented in Lupton et al. (2006) and further discussed in
c 2010 Federation of European Microbiological Societies FEMS Microbiol Ecol 73 (2010) 538–549
Published by Blackwell Publishing Ltd. All rights reserved
Epsilonproteobacteria in vents of the Mariana Arc 543
100%
Percent of Epsilonproteobacteria
75%
V6 tag sequences
50%
Fig. 2. Taxonomic breakdown and relative
abundance at the genus level for the individual
tag sequences of Epsilonproteobacteria in each 25%
vent fluid sample. Only those genera that
occurred 4 1000 times across all datasets are
0%
labeled. All others are lumped into ‘Other.’
100
Taxonomy and total diversity of
Epsilonproteobacteria
The taxonomic breakdown at the genera level for each sample 50
is shown in Fig. 2. Dominant genera included Thioreductor,
Lebetimonas, Caminibacter, Sulfurovum, Sulfurimonas, and
0
Arcobacter. Sequences that were found o 1000 times across 0 2000 4000 6000 8000
all samples were binned into ‘Other’ and included Nautilia, Number of Epsilonproteobacteria tags sampled
Sulfuricurvum, Hydrogenimons, Nitratifractor, and Sulfuro- Fig. 3. Rarefaction curves at the 3% difference level for each of the vent
spirillum. Because sites were unequally sampled, rarefaction fluid samples.
was used to compare sampling effort and richness across all
sites at the 3% difference level (Fig. 3). Results indicate that
eight of the 14 sites cluster together, whereas the two vents
from Forecast have the highest richness (FS431 and FS432)
structure differences among the individual samples
and two of the vents from NW Rota-1 along with Alka
(p = 6.23, P value o 0.001). At the 3% difference level,
Seltzer from Daikoku have the lowest richness (FS445,
nMDS and cluster analysis yielded the pattern seen in Fig.
FS446, and FS475). It is only in these latter three sites that
4. The two vents from Forecast (FS431 and FS432) group
sampling of Epsilonproteobacteria appears to be near com-
together, the five vents from NW Rota-1 group together
plete. Vents from Forecast had the highest pH and samples
(FS445–FS449), and the vents from Nikko, Daikoku, and
FS445, FS446, and FS475 had among the lowest with respect
Eifuku group together. One-way ANOSIM test using the
to pH values (Table 1).
distance matrix and seamount resulted in a global R value
of 0.667 (P o 0.0002), indicating that the groupings by
Patterns of Epsilonproteobacteria distribution
seamount are significant. Pairwise R values indicate that
All sequences were pooled together to generate OTUs, the major differences are found between the two southern
resulting in 739 OTUs at the 3% difference level. Only five seamounts (Forecast and NW Rota-1) and the southern
OTUs occurred in all 14 datasets, compromising o 0.7% seamounts as compared with all of the northern sea-
of the total OTUs, but over 10% of the total sequences. mounts (NW Eifuku, Daikoku, and Nikko, Table 3).
Approximately 40% of the OTUs were found in 2–13 Nikko is the only seamount that has a significant overlap
samples, comprising 88% of sequences. Over half of the with the other two northern seamounts, with North Vent
OTUs (59%, representing about 0.6% of the total se- and Tubeworm Hangover (FS479 and FS480) clustering
quences) were only found in one sample. SIMPROF test of with Daikoku and Top Vent (FS481) clustering with NW
the data indicated that there were significant community Eifuku (Fig. 4).
NW Eifuku
40
Similarity
NW Rota-1
60
FS446
FS448
FS449
FS445
FS447
FS480
FS475
FS479
FS473
FS467
FS468
FS481
(b) finding that Forecast and NW Rota-1 are distinct from one
another and from the northern seamounts. No significant
groupings or correlations were found based on chemical
parameters, including temperature, pH, gas (H2S, H2, CH4),
Na, Li, Fe, Mn, and Si (data not shown).
Considerable concern has been raised recently over pyr-
osequencing errors and their contribution to diversity
estimates (Quince et al., 2009; Reeder & Knight, 2009; Kunin
et al., 2010). In order to account for potential errors, all
samples were run on the same sequencing platform (GS20)
within a few weeks of one another, and all samples were
treated identically from DNA extraction all the way through
to sequence analysis. We used stringent quality control
measures based on our knowledge of known GS20 sequen-
Fig. 4. (a) Cluster diagram and (b) nMDS 2D similarity plot comparing
cing errors (Huse et al., 2007). In addition, here, we report
vent samples at the 3% difference level of Epsilonproteobacteria, with the most conservative methodology to date for reporting
each sample labeled according to seamount. The circles represent OTUs via the SLP PWAL pipeline (Huse et al., 2010). The SLP
similarity boundaries from the cluster diagram. PWAL approach is thought to more accurately predict ex-
pected OTUs than multiple alignment and complete-linkage
clustering methods and reduces the number of OTUs almost
by half compared with the multiple alignment complete-
Table 3. Pairwise R values from the ANOSIM test between groupings and
linkage clustering methods (Huse et al., 2010). We also
seamounts
repeated all analyses with singletons removed to insure that
Forecast NW Rota-1 NW Eifuku Daikoku Nikko potentially erroneous singletons were not skewing commu-
Forecast nity patterns.
NW Rota-1 0.95
NW Eifuku 1 0.64
Daikoku 1 0.73 0.5 Discussion
Nikko 0.67 0.82 0.08 0.33
In this study, we used 454 tag sequencing of the V6 bacterial
region to determine the diversity and distribution of
Epsilonproteobacteria in rock-hosted diffuse vent fluids from
Sequences from each seamount were pooled and analysis five hydrothermally active seamounts along the Mariana
was repeated with grouping by seamount rather than Arc. While universal bacterial primers were used and a large
individual vent site. A UPGMA tree calculated from Mor- taxonomic diversity of bacteria was detected, we chose to
isita–Horn distances between datasets (Fig. 5) supports the only analyze a subset of the sequences that were classified to
c 2010 Federation of European Microbiological Societies FEMS Microbiol Ecol 73 (2010) 538–549
Published by Blackwell Publishing Ltd. All rights reserved
Epsilonproteobacteria in vents of the Mariana Arc 545
Epsilonproteobacteria. Diffuse vents represent a mixture of into an unresolved group within the Nautiliaceae (accession
seawater and vent fluids that mix in the crust before venting number EU574679, IBB_14). The taxonomic breadth found
on the seafloor (Butterfield et al., 2004). We sampled vent in the vent fluids also included rare members that occurred
fluids from a large range of depths and locations less than a total of 1000 times across the datasets, such as
(400–1600 m), and we did not want background seawater Nautilia, Sulfuricurvum, Hydrogenimons, Nitratifractor, and
organisms from different regions and depths complicating Sulfurospirillum.
the interpretation of vent-specific patterns. Epsilonproteo- Because samples were unequally sampled, we used rar-
bacteria are rarely detected in nonplume, nonvent back- efaction analysis rather than absolute OTU numbers or
ground oxygenated seawater and are considered endemic to nonparametric estimators to compare richness and sam-
sulfidic environments such as deep-sea hydrothermal vents pling effort among samples. As illustrated in Fig. 3, we
(Campbell et al., 2006). found that the Epsilonproteobacteria in three of the samples
Papke & Ward, 2004; Whitaker, 2006; Green et al., 2008 for Along the Mariana Arc, it is possible that the central
reviews). In the marine hydrothermal environment, there is province is a geographical barrier to distribution and
also some evidence of geographic isolation of microbial exchange between the northern and the southern provinces.
communities. For example, recent work at Axial Seamount The central province is mostly subaerial, with little submar-
found that individual vents within the caldera maintain a ine volcanism found (Embley et al., 2007). However, the two
distinct composition over time (Opatkiewicz et al., 2009), seamounts in the southern province (Forecast and NW
and no correlation was found between total bacterial or Rota-1) were as different from one another as they were
archaeal community structure and geochemical parameters. from seamounts to the north. Similarly, NW Eifuku and
However, the authors did find trends in Epsilonproteobacter- Daikoku have different community compositions, despite
ia community composition that were linked to changes in the fact that they are located closer together than any of the
hydrogen, sulfur, and iron chemistry. Similarly, Huber et al. other seamounts. Clearly, distance is not the distinguishing
c 2010 Federation of European Microbiological Societies FEMS Microbiol Ecol 73 (2010) 538–549
Published by Blackwell Publishing Ltd. All rights reserved
Epsilonproteobacteria in vents of the Mariana Arc 547
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