ArticlePDF Available

Bacterial Community on a Guyot in the Northwest Pacific Ocean Influenced by Physical Dynamics and Environmental Variables


Abstract and Figures

Bacterial communities in sediments of the Caiwei Seamount, a typical guyot located in the northwest Pacific Ocean, were investigated. A total of 727,879 16S ribosomal RNA gene sequences were retrieved from eight sediment samples of the top (mean depth = 1,407 m) and the base (mean depth = 5,525 m) of the guyot through pyrosequencing of V6 hypervariable region and clustered into 32,844 operational taxonomic units. Abundant‐weighted UniFrac metric partitioned bacterial assemblies into two categories (the top community and the base community) by principal coordinates analysis, consisting with the grouping of sampling stations by environmental variables. Differences in depth and physicochemical properties of the surrounding environment (e.g., concentrations of dissolved oxygen and geochemical elements) between the top and the base of the guyot may cause this partition of bacterial communities, whereas the typical fluid flow around the guyot may potentially contribute to the bacterial dispersal and environmental homogeneity along the same layer, resulting in the similarity of bacterial community structure within the same region (the top or the base). The surface sediment on the top of the guyot harbored the bacterial communities with greater diversity and evenness, represented by Gamma‐ and Deltaproteobacteria involved in sulfur cycling. At the base of the guyot, Gammaproteobacteria related to sulfur‐oxidizing and Chloroflexi functioning in the decomposition of refractory organic matter dominated, suggesting that the redox condition at the interface of the sediment and the water can influence bacteria‐mediated elemental cycling, eventually shaping the physicochemical and geological characteristics of a guyot.
This content is subject to copyright. Terms and conditions apply.
Bacterial Community on a Guyot in the Northwest Pacic
Ocean Inuenced by Physical Dynamics and
Environmental Variables
Qian Liu
, YingYi Huo
, YueHong Wu
, Youcheng Bai
, Yeping Yuan
, Min Chen
Dongfeng Xu
, Jun Wang
, ChunSheng Wang
, and XueWei Xu
Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of
Oceanography, Ministry of Natural Resources, Hangzhou, China,
Now at College of Life Sciences, Zhejiang University,
Hangzhou, China,
Ocean College, Zhejiang University, Hangzhou, China,
College of Ocean and Earth Sciences, Xiamen
University, Xiamen, China,
State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of
Oceanography, Ministry of Natural Resources, Hangzhou, China
Abstract Bacterial communities in sediments of the Caiwei Seamount, a typical guyot located in the
northwest Pacic Ocean, were investigated. A total of 727,879 16S ribosomal RNA gene sequences were
retrieved from eight sediment samples of the top (mean depth = 1,407 m) and the base (mean depth = 5,525 m)
of the guyot through pyrosequencing of V6 hypervariable region and clustered into 32,844 operational
taxonomic units. Abundantweighted UniFrac metric partitioned bacterial assemblies into two categories
(the top community and the base community) by principal coordinates analysis, consisting with the
grouping of sampling stations by environmental variables. Differences in depth and physicochemical
properties of the surrounding environment (e.g., concentrations of dissolved oxygen and geochemical
elements) between the top and the base of the guyot may cause this partition of bacterial communities,
whereas the typical uid ow around the guyot may potentially contribute to the bacterial dispersal and
environmental homogeneity along the same layer, resulting in the similarity of bacterial community
structure within the same region (the top or the base). The surface sediment on the top of the guyot
harbored the bacterial communities with greater diversity and evenness, represented by Gammaand
Deltaproteobacteria involved in sulfur cycling. At the base of the guyot, Gammaproteobacteria related to
sulfuroxidizing and Chloroexi functioning in the decomposition of refractory organic matter dominated,
suggesting that the redox condition at the interface of the sediment and the water can inuence
bacteriamediated elemental cycling, eventually shaping the physicochemical and geological characteristics
of a guyot.
Plain Language Summary Seamounts in northwest Pacic Ocean are most abundant in the
world. They have been recognized as important habitats for corals, sh, and etc. The high biodiversity in
seamount regions could be a result of efcient food and energy transfer mediated by microorganisms. In this
study, we investigated bacterial community composition, structure, and potential metabolic characteristics
at different locations of the Caiwei Seamount, a attopped seamount (also called as guyot) in northwest
Pacic Ocean in order to understand the functions of the seamount ecosystem. Our results showed that the
bacterial zonation in the Caiwei Seamount was inuenced by both physicochemical variables and physical
dynamics. Unique circulation of ow currents in seamount region may enhance the homogeneity of
bacterial community at the same depth, while physicochemical variation by depth could be the major factor
partitioning bacterial community vertically. The potential ecological functions of bacterial communities are
strongly associated with the regional environments. They are actively involved in sulfur and nitrogen
cycling, possibly key to energy and substrate productivity.
1. Introduction
Microbial abundance in subseaoor sediment has been estimated to be 2.9×10
, accounting to total prokar-
yotic cell abundance in the water column and in soil (Kallmeyer et al., 2012). They play an important role in
deepocean biogeochemical processes and potentially contribute to high productivity in the deep ocean
(McNichol et al., 2018). Microorganisms have been extensively studied in different environments of
©2019. The Authors.
This is an open access article under the
terms of the Creative Commons
Attribution License, which permits use,
distribution and reproduction in any
medium, provided the original work is
properly cited.
Key Points:
Bacterial community on the guyot is
well partitioned by depth and
physicochemical properties
Uniqueness of physical dynamics
may contribute to the homogeneity
of bacterial community along the
isobath of the guyot
Redox conditions on the guyot are
potentially key to determining
bacterial community composition,
structure, and ecological function
Supporting Information:
Supporting Information S1
Correspondence to:
X.W. Xu,
Received 31 JAN 2019
Accepted 6 JUN 2019
Accepted article online 14 AUG 2019
Author Contributions:
Conceptualization: Qian Liu, YingYi
Huo, YueHong Wu
Data curation: Qian Liu
Formal analysis: Qian Liu, YingYi
Huo, Youcheng Bai, Yeping Yuan, Min
Chen, Dongfeng Xu, Jun Wang
Funding acquisition: ChunSheng
Investigation: YingYi Huo
Methodology: Qian Liu, YingYi Huo,
YueHong Wu, Youcheng Bai, Min
Project administration: ChunSheng
Resources: YingYi Huo
Software: Qian Liu, YingYi Huo
LIU ET AL. 2883
Liu, Q., Huo, Y.Y., Wu, Y.H., Bai, Y.,
Yuan, Y., Chen, M., et al. (2019).
Bacterial community on a guyot in the
northwest Pacic Ocean inuenced by
physical dynamics and environmental
variables. Journal of Geophysical
Research: Biogeosciences,124,
Published online 11 SEP 2019
marine subseaoor, especially in extreme environments (e.g., hydrothermal vent and cold seep), where they
are active and diverse in physiology and metabolism, contributing signicantly to energy ow in deep ocean
(Fullerton et al., 2017; Huber et al., 2007; LópezGarcía et al., 2003; Meyers et al., 2014; Moyer et al., 1995;
Scott et al., 2017; Sogin et al., 2006; Teske et al., 2002).
Seamounts are the unique environment widely distributed in deepocean subseaoor (Wessel & Kroenke,
1997). They are the important habitats for marine organisms (Clark et al., 2010). The topographic
induced turbulent mixing at seamounts may potentially cause high primary productivity in the upper
water column (Boehlert & Genin, 1987; Polzin et al., 1997), beneting the sh and benthic communities
in seamount areas (Clark et al., 2010; Richer de Forges et al., 2000). Most of seamounts discovered in the
world are located in the west Pacic (Kim & Wessel, 2011). Flattopped seamounts, also called as guyots,
are the major types in the west Pacic. The at top is a result of coral reef growth and erosion as their
conical tops reached the sea surface during evolutionary processes (Stanley, 2005). Thus, the top of a
guyot is covered by carbonate rock with shallowwater coral and bivalve reefs formed millions of years
ago. At the base of a guyot, it is majorly composed of manganese crust or ironmanganese (FeMn) coat-
ing precipitating from cold water (Asavin et al., 2008). The varied compositions of sediments at different
regions of a guyot provide diverse biological habitats, indicating potential importance of guyots to the
deepsea ecosystem. Currently, there are a few studies on microbial communities in guyot environments,
which mostly focus on the communities associated with ferromanganese crust and potentially function-
ing in metal precipitation (Kato et al., 2018; Nitahara et al., 2011, 2017); however, the patterns of micro-
bial distribution and their relationship with guyot environment on guyots are less understood.
The Caiwei Seamount is a deepsea guyot located in the northeast of the eastern Marianas Basin of the
west Pacic Ocean at a latitude and longitude of 15.016.2°N and 154.6155.8°E (Figure 1). The depth
of the top is between 1,500 and 1,600 m and that of the base is approximately 5,500 m. The Caiwei
Seamount is covered by cobaltrich crusts, the density of which increases with depth. Other mineral
resources, such as nickel, copper, iron, and manganese are also rich on the seamount (Wang et al.,
2016). The Caiwei Seamount has been extensively surveyed by the China Ocean Mineral Resources
R&D Association (COMRA) for mineral resources and megafaunal community (Wang et al., 2016; Xu
et al., 2016); however, the microorganisms that are potentially important in food web and energy transfer
in seamount ecosystem have not been investigated yet. In this study, bacterial community structure in
sediment samples of the Caiwei Seamount were studied for enhancing our understanding in (1) diversity
and genetic ngerprinting of guyot bacterial community, (2) interaction between bacterial community
structure and guyot environments, and (3) potential roles of bacteria in biogeochemical processes of
the Caiwei Seamount that could be extremely important in food and energy transfer, shaping the ecolo-
gical function of the guyot ecosystem.
2. Materials and Methods
2.1. Sample Collection and environmental Variables
Sediment samples were collected from the Caiwei Seamount located in the west Pacic Seamount Province
during the DY27 cruise of the R/V Haiyang Liu Hao in July, 2012. Using multiple corer (surface area =
0.00785 m
, height = 0.6 m) as well as box corer (surface area = 0.25 m
) systems, four sediment samples
were obtained at the at top of the seamount (1,3621,500 m in depth; MAMC01, MAMC02, MAMC03,
and MAMC04) and four were collected at the base of the seamount (5,2695,920 m in depth; MABC02,
MAMC06, MABC06, and MAMC08; Figure 1 and Table S1). Box corer samples were immediately sub-
sampled using push corers. The top 5 cm of sediment were collected in all sediment cores and stored at
20°C until analysis in the laboratory for subsequently microbiological and geochemical experiments.
Seawaters were also collected from the surface to the depths close to the seaoor near stations MAMC02
and MAMC04 at the top of the seamount (MACTD01 and MACTD04) and stations MABC02, MABC06
and MAMC08 at the base of the seamount (MACTD07, MACTD08, and MACTD06) using 8 L Niskin bottles
mounted on a rosette frame equipped with a SBE917 CTD system (SeaBird Electronics, Inc.; Figure 1 and
Table S1).
Concentrations of dissolved oxygen (DO) in seawaters were measured following the Winkler method
(Winkler, 1888). For nutrient measurements, seawater samples were collected into 500ml highdensity
Journal of Geophysical Research: Biogeosciences
Supervision: YueHong Wu, Chun
Sheng Wang
Validation: Qian Liu
Visualization: Qian Liu, Yeping Yuan
Writing original draft: Qian Liu,
YingYi Huo, Yeping Yuan
Writing review & editing: Qian Liu,
YingYi Huo, YueHong Wu, Yeping
Yuan, Min Chen, Dongfeng Xu, Chun
Sheng Wang
polyethylene bottles and ltered onto cellulose acetate lters (47mm diameter and 0.45μm pore size).
Concentrations of ammonia, nitrite, and phosphate were determined using a standard colorimetric
method (Grasshoff et al., 1999), and nitrate concentrations were measured using a cadmiumreduction
method coupled with diazotization (Grasshoff et al., 1999). Elemental analysis of sedimentary
concentrations of total organic carbon (TOC) and nitrogen (TON) were performed using an Elementar
Vario Micro Cube (Elementar, Germany). Elemental contents of P, S, Si, B, Ca, Na, Al, Fe, K, Mg, Zn, Cu,
Mn, Ba, Ni, Cr, Co, Li, Sr, V, and Pb were determined using inductively coupled plasma optical emission
spectrometer (ICPOES, Optima 8000DV, PerkinElmer, USA).
2.2. DNA Extraction, Polymerase Chain Reaction Amplication, and Sequencing
DNA was extracted from the sediment samples (0.5 g of each sample) using the FastDNA® Spin kit for soil
(MP Biomedicals, USA). The environmental DNA was then used as polymerase chain reaction (PCR) tem-
plate, and bacterial 16S rRNA genes were amplied using primers 967F (5′‐CAACGCGAAGAACCTTACC
3) and 1046R (5′‐CGACAGCCATGCANCACCT3) targeting at the V6 hypervariable region (Sogin et al.,
2006). PCR amplication was performed in 50μl reaction volume containing 5 μl of 10 × reaction buffer,
1.5 μl of 10 mM dNTP, 1 μlof10μM each primer, 2 μl of template, and 1 μlof5U/μlPfx50
DNA polymer-
ase (Invitrogen, USA), supplemented with doubledistilled water. Thirty cycles of amplication were carried
Figure 1. (a) Location of the Caiwei Seamount in the northwest Pacic Ocean; (b) sampling stations at the top and the
base of the Caiwei Seamount: water samples were collected at stations MACTD1 and MACTD4 on the top and
MACTD6, MACTD7, and MACTD8 on the base; sediment samples were collected at stations MAMC01, MAMC02,
MAMC03, and MAMC04 on the top and MAMC06, MABC06, MABC02, and MAMC08 on the base.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2885
out under the following conditions: denaturation at 94°C for 15 s, annealing at 57°C for 30 s, and elongation
at 68°C for 30 s. The quality and quantity of the genomic DNA were determined by 2% agarose gel
electrophoresis with DL2000 DNA marker (TaKaRa, China) and by a Qubit® uorometer (Invitrogen,
USA) with Qubit dsDNA BR Assay kit (Invitrogen, USA). The barcoding, sequencing, and quality assurance
processes of PCR products were performed at the Beijing Genome Institute (BGI, Shenzhen). The sequen-
cing was performed using Solexa pairedend sequencing technology (HiSeq2000 system, Illumina, USA).
The sequencing data have been deposited at NCBI Sequence Read Archive under accession
number SRR7888608SRR7888615.
2.3. Sequence and Statistical Analysis
Sequences analysis was performed by QIIME v1.8.0 software package (Caporaso, Kuczynski, et al., 2010).
Sequences were clustered into operational taxonomic units (OTUs) at 97% sequence identity with uclust
Figure 2. Concentrations of geochemical elements measured in sediment samples collected from the top and the base of
the Caiwei Seamount. The differences in concentration between the top and the base are all signicant (pvalues0.05; t
test). The error bar represents standard deviation.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2886
v1.2.22q (Edgar, 2010). OTUs were aligned to fulllength 16S rDNA sequences with PyNAST (Caporaso,
Bittinger, et al., 2010) and assigned taxonomy with uclust (Edgar, 2010). Species diversity, richness, and rar-
efaction curves were conducted with a step size of 500 and 10 repetitions at each step. Beta diversity was ana-
lyzed with 90,330 sequences per sample, which is the smallest library.
The weighted UniFrac metric was computed to quantify the relatedness of OTUs retrieved from the top and
the base of the seamount, and the results were displayed by the principal coordinate analysis (Lozupone
et al., 2006). The similarity percentage (SIMPER, Primer 6) analysis was used to determine the sequences
that mostly contributed to community dissimilarity between top and base samples of the seamount
(Hamdan et al., 2013). Individual ttest run in R (R Development Core Team, 2011) was used to test the sta-
tistical signicance of spatial differences in geochemical measurements and bacterial abundances between
top and base samples of the seamount. Principal component analysis (PCA) and redundancy analysis
(RDA) were applied to detect the similarity of environmental conditions among stations and correlations
between bacterial distribution and environmental variables, respectively (Canoco 5.1; Ter Braak &
Šmilauer, 2012).
3. Results
3.1. Physical and Geochemical Characteristics in Seawaters and Sediments
The hydrochemical characteristics in surrounding seawaters of the top and the base of the seamount were
similar (i.e., salinity, pH, and concentrations of ammonia, nitrite, nitrate, and phosphate) except tempera-
ture and DO (Table S2). Temperature was higher in seawater overlying the top of the seamount, while
DO concentrations were in an opposite trend (Table S2). Concentrations of the major geochemical elements
were in a similar range in samples collected from the same region (top or base of the Caiwei Seamount), but
signicantly different between samples collected from two regions (ttest, p< 0.01; Figure 2). The sediments
from the base contained higher concentrations of metal elements (i.e., Fe, Mn, Al, and Mg) but lower in Si,
Sr, and Ca (Figure 2). TIC and TIN were the major components of TC (99.80 ± 0.38%) and TN (95.40 ± 1.77%)
in sediments at the top, respectively, while TOC and TON occupied greater proportions of TC (75.40 ±
3.69%) and TN (92.30 ± 5.92%) at the base, respectively. Samples were well explained by variations in phy-
sicochemical parameters of the sediment (Figure 3a) as well as the seawater listed in Table S2 (Figure 3b) by
PCA analysis.
3.2. Bacterial Diversity
A total of 727,879 sequences were retrieved from eight samples and clustered into 32,844 OTUs (0.03 cut-
off). The number of sequences of each station (90,985 ± 629) was similar, but that of OTUs ranged from
6,000 to 10,859 (Table 1). According to rarefaction analysis and Chao 1 statistic often used to estimate the
depth of coverage by sequencing, bacteria communities were under sequenced by 4164% in samples
(Figure 4 and Table 1). The Chao 1 indices were not statistically different between top and base stations
(ttest, p= 0.71), but two top stations MAMC02 and MAMC03 as well as one base station MAMC06,
located at the northern and eastern sides of the seamount, had relatively higher Chao 1 indices in
comparison to those in sedimentary samples collected from the southern part of the seamount
(MAMC01 and MABC02; Table 1). It indicated that the northern part of the seamount potentially har-
bored more OTUs than the south. Shannon and Simpson indices were averagely greater in samples from
the top of the seamount (ttest, p< 0.01; Table 1), suggesting higher bacterial diversity and evenness in
sediments from the top of the seamount.
3.3. Phylogenetic Composition
Of total obtained bacterial sequences, Proteobacteria dominated the bacterial communities in all sediment
samples (top: 57.4 ± 1.1%, base: 54.3 ± 2.7%) followed by Acidobacteria (top: 11.5 ± 0.6%, base: 7.7 ± 0.4%)
and Gemmatimonadetes (top: 7.2 ± 0.5%, base: 9.4 ± 0.4%) in top and base sediments, respectively. The phy-
lum Chloroexi also occupied a greater proportion in base sediments (9.1 ± 1.7%) than in the top (2.9 ± 0.4%;
ttest, p= 0.001; Figure 5 and Table 2). The rest of phylotypes were scattering over a broad taxonomic distri-
bution including Planctomycetes,Nitrospirae,Actinobacteria, the division NC10, and Bacteroidetes (>1% at
least at one location). All these dominating bacterial groups occupied approximately 96.7% and 94.8% of total
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2887
retrieved bacterial sequences from the top and base sediments, respectively (Figure 5). Other phyla, which
are more than 0.1% but less than 1% of total retrieved bacterial sequences, are listed in Table S3.
Gammaproteobacteria were the dominant taxa within the phylum of Proteobacteria in all samples (top: 26.0
± 1.2%, base: 28.9 ± 1.5%; ttest, p= 0.04) and were mostly represented by the order Thiotrichales constituting
11.3 ± 0.5% and 19.2 ± 1.2% of total sequences in top and base sediments, respectively (ttest, p< 0.001;
Table 2). More than 98% of the sequences of Thiotrichales were classied into the Piscirickettsiaceae family,
which includes several genera of Soxidizing chemolithoautotrophs (Barco et al., 2017; Zhang et al., 2017).
The order Chromatiales, also called the purple sulfur bacteria capable of photosynthesis using sulde, thio-
sulfate, H
, etc. as the electron donor under anaerobic or microaerophilic conditions (Hunter et al.,
2009), was the secondly most abundant group of Gammaproteobacteria and represented 6.5 ± 0.8% and 3.1 ±
0.3% of the retrieved sequences at the top and the base, respectively (ttest, p< 0.001; Table 2).
Deltaproteobacteria,Alphaproteobacteria, and Betaproteobacteria in the phylum Proteobacteria were also
relatively abundant (>1% of total sequences), but only Deltaproteobacteria showed a greater proportion on
the top (16.44 ± 1.10%; ttest, p< 0.001) and were mostly related to the candidate division NB1j and the
order Syntrophobacterales (Table 2). Deltaproteobacteria are usually related to sulfate reduction in anoxic
environments (LópezGarcía et al., 2003; Ye et al., 2016). The order Rhodospirillales, almost 100% composed
of the family Rhodospirillacea, occurred abundantly at both locations, amounting to more than half abun-
dance of Alphaproteobacteria (Table 2). Rhodospirillacea has also been reported to function as a sulfur
oxidizer (Zhang et al., 2017). The proportion of Betaproteobacteria was relatively minor compared to
Gammabacteria, Deltabacteria, and Alphaproteobacteria, of which the order Burkholderiales were the major
members in sediments from top stations (>1%; Table 2). Although numbers of Nitrosomonadales in the class
Betaproteobacteria were in a small proportion (<1%), the family Nitrosomonadaceae recognized as major
ammonia oxidizers was found to be one of important identied family members at the base (Purkhold
et al., 2003; 0.99 ± 0.07%; ttest, p< 0.001). The nitriteoxidizing Nitrospiraceae in the order Nitrospirales
represented almost all generated Nitrospira sequences and became a major group in sediments from the
top (1.67 ± 0.23%; ttest, p< 0.001). With the cutoff of 0.1, only 2.6% and 2.3% of total sequences on average
were grouped to known genera on the top and the base, respectively.
Figure 3. Principal component analysis for samples collected from sediments (a) and seawaters (b) with geochemical data
shown in Figure 2 and listed in Table S2, respectively.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2888
3.4. Bacterial Community Structure
The abundanceweighted UniFrac analysis using the principal coordinate analysis separated samples into
two distinct communities with the bacterial groups from the same region (top or base) clustering together
on the axis of PC1 (76.7%; Figure 6). Proportions of OTUs shared by top and base stations (26.6 ± 4.4%) of
the seamount were lower than those of unique OTUs they owned, while samples collected at the same region
tent to share more OTUs (top 45.6 ± 8.1%, base 40.3 ± 3.7%; Table 3). Permutational multivariate analysis of
variance analysis showed that bacterial community composition was signicantly different between top and
base regions at OTU level (p= 0.036, r
= 0.739)
SIMPER analysis revealed that major bacterial groups (% of total reads > 1%) had different contributions to
the dissimilarity of the bacterial community structure between top and base stations if considering their
abundances and compositions (Table S4). Three OTUs belonging to the family Piscirickettsiaceae of the order
Thiotrichales (denovo28753, denovo16605, and denovo4356) and one OTU classied into the order
Chromatiales of Gammaproteobacteria (denovo16603) contributed to a total of 11.4% of the dissimilarity,
in which the formers had greater abundances in samples from the base while the latter had a higher number
of sequences in samples from the top sediments (Table S4). Two OTUs belong to the family Rhodospirillaceae
in the order Rhodospirillales of Alphaproteobacteria (denovo20286 and denovo17655), one OTU identied to
the family Syntrophobacteraceae in the order Syntrophobacterales of Deltaproteobacteria (denovo12887), and
two OTUs from Acidobacteria (denovo2989 and denovo6417) added the total contribution up to ~20% of the
dissimilarity subsequently (Table S4).
3.5. Correlations Between Bacterial Community and Environmental Variables
The RDA analysis showed that the bacterial groups were well divided into two clusters (top and base) by
environmental factors on the axis of RDA 1, which explained 79.2% of variations. The axis of RDA 2 increased
the explained variation to 90.7% (Figure 7). BPC015 and Sva0725 in Acidobacteria, CL50015 in
Planctomycetes,Chromatiales in Gammaproteobacteria,Syntrophobacterales and NB1jin
Deltaproteobacteria, and Nitrospirales in Nitrospirae were intensely associated with TIC (%) and concentra-
tions of Ca and Si (mg/g). Similarly, the bacterial groups with higher weights at the base of the seamount,
including Thiotrichales in Gammaproteobacteria, Sva0853 in Deltaproteobacteria,Rhodobacterales in
Alphaproteobacteria, B110 in Acidobacteria, CCM11a in Planctomycetes,Acidimicrobiales in Actinobacteria,
and SAR202 in Chloroexi, were clustered with depth and the environmental factors that were greater at
the base (e.g., TOC, TON, Fe, Mn, S, and P; Figure 7). Other metal or ions (e.g., Cu, Zn, Mg, and Na) were
strongly correlated with the selected factors, thus were not included in the analysis. Variabilities in
Pseudomonadales in Gammaproteobacteria,Burkholderiales in Betaproteobacteria, and Rhodospirillales in
Alphaproteobacteria among stations were not signicantly explained by environmental variables, the propor-
tions of which were consistent in samples collected from the top and the base of the seamount.
Table 1
The Total Number of Bacterial Sequences and OTUs as Well as Indices of Biodiversity and Richness at Each Station
Sampling Station No. of Sequences No. of OTUs Chao 1 Shannon Index (H) Simpson Index
MAMC01 90,330 6,168 10,410 9.170 0.992
MAMC02 90,439 10,859 27,211 9.828 0.993
MAMC03 90,583 9,222 23,355 9.386 0.991
MAMC04 91,129 7,499 16,014 9.186 0.991
Mean ± SD 90,620 ± 307 8,437 ± 1,769 19,248 ± 6,497 9.393 ± 0.265 0.992 ± 0.001
MABC02 91,649 6,000 12,464 8.202 0.982
MAMC06 90,660 7,999 22,274 8.542 0.986
MABC06 92,279 6,688 16,417 8.126 0.982
MAMC08 90,810 7,345 19,208 8.344 0.984
Mean ± SD 91,350 ± 656 7,008 ± 744 17,591 ± 3,613 8.304 ± 0.158 0.984 ± 0.002
pvalue 0.132 0.245 0.713 0.001 <0.001
Note. The pvalues were calculated by ttest.
Abbreviation: SD, standard deviation.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2889
4. Discussions
4.1. Factors Inuencing Patterns of Bacterial Community Composition and Structure
Increasing studies have shown that microbial community composition and structure can be relatively con-
sistent in similar marine environments even though the distance was thousands of kilometers away or het-
erogeneous in environments with different characteristics but only in a few tens of kilometers (Agogué et al.,
2011; Hewson et al., 2007; Inagaki et al., 2006; Walsh et al., 2015). In this study, PCA analysis showed that
sampling stations were highly divided into two categories (top and base) by environmental variables col-
lected from surrounding waters and sediments (Figure 3), indicating environmental homogeneity at the
top or the base but great varieties between two regions. Consistently, bacterial community structure showed
similar pattern (Figures 5 and 6), supporting a tight association between bacterial community and
environmental variation.
Besides the effect of physiochemical characteristics, patterns of bacterial community composition and struc-
ture in sediments could also be inuenced by fast bacteria dispersal near seaoor, which transit through
Figure 4. Rarefaction analyses of observed operational taxonomic units in sediments collected from the top (MAMC01
MAMC04) and the base (MABC02, MAMC06, MABC06, and MAMC08).
Figure 5. Bacterial community composition identied with uclust (Edgar, 2010) in samples collected from the top and the
base of the Caiwei Seamount.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2890
water along the route of the uid ow, contributing to the similarity of bacterial community composition
and structure within the same region (Hamdan et al., 2013; Schauer et al., 2010). In an idealized model,
the incoming ow over the seamount is separated, creating a circulation around the seamount and forming
eddies or wakes at the lee side in a stratied ocean (Chapman & Haidvogel, 1992). The dynamics is even
more complex when the incoming ow is oscillating (i.e., tidal current). The interaction between internal
wave and bathymetry will potentially cause the reection of internal waves or the generation of the internal
tide (Gilbert & Garrett, 1989), companied by strong turbulent mixing. Measurements of turbulent kinetic
energy near a shallow seamount show 100 to 10,000 times larger than regions far away from seamount areas
(Lueck & Mudge, 1997). Nevertheless, majority of the ow near seamounts tends to follow the isobath
despite of localized enhanced turbulent mixing regions. At the region of the Caiwei Seamount, the
Table 2
Proportions of Phylogenetic Groups in Sediment Samples Collected From the Top and the Base of the Caiwei Seamount
Taxonomy Top Mean ± SD Base Mean ± SD pvalue
Gammaproteobacteria 26.0 ± 1.18 28.9 ± 1.48 0.041
Thiotrichales 11.3 ± 0.50 19.2 ± 1.23 0.000
Chromatiales 6.52 ± 0.81 3.07 ± 0.27 0.000
Pseudomonadales 1.28 ± 0.98 1.00 ± 0.47 0.676
Deltaproteobacteria 16.4 ± 1.06 10.4 ± 0.96 0.000
NB1j7.64 ± 0.45 3.89 ± 0.10 0.000
Syntrophobacterales 6.33 ± 1.09 3.13 ± 0.73 0.005
Sva0853 0.47 ± 0.07 1.50 ± 0.21 0.000
Alphaproteobacteria 12.4 ± 1.70 13.7 ± 2.6 0.493
Rhodospirillales 6.24 ± 1.62 8.28 ± 2.25 0.250
Rhodobacterales 0.85 ± 0.08 1.46 ± 0.36 0.028
Betaproteobacteria 2.14 ± 0.88 1.21 ± 0.08 0.122
Burkholderiales 1.14 ± 0.97 0.18 ± 0.07 0.139
Acidobacteria 11.5 ± 0.58 7.66 ± 0.41 0.000
Acidobacteria62.65 ± 0.08 1.12 ± 0.11 0.000
BPC015 1.66 ± 0.13 0.66 ± 0.07 0.000
RB25 2.34 ± 0.20 0.83 ± 0.06 0.000
Sva0725 2.26 ± 0.44 0.37 ± 0.10 0.000
Sva0725 2.26 ± 0.44 0.37 ± 0.10 0.000
BPC102 1.42 ± 0.19 2.26 ± 0.45 0.025
B110 1.42 ± 0.19 2.26 ± 0.45 0.024
Solibacteres 1.03 ± 0.27 0.23 ± 0.07 0.003
Gemmatimonadetes 7.22 ± 0.49 9.44 ± 0.44 0.001
Gemm2 4.09 ± 0.39 3.71 ± 0.27 0.213
Gemm1 1.95 ± 0.08 4.60 ± 0.47 0.000
Chloroexi 2.92 ± 0.36 9.12 ± 1.72 0.001
SAR202 2.06 ± 0.26 4.63 ± 1.20 0.011
S085 0.26 ± 0.05 3.87 ± 1.12 0.001
Planctomycetes 3.37 ± 0.37 3.16 ± 0.19 0.399
OM190 1.62 ± 0.21 0.71 ± 0.15 0.001
CL50015 1.06 ± 0.13 0.51 ± 0.13 0.002
Phycisphaerae 0.69 ± 0.16 2.01 ± 0.15 0.000
CCM11a 0.42 ± 0.09 1.11 ± 0.08 0.000
Nitrospirae 1.69 ± 0.22 0.59 ± 0.09 0.000
Nitrospira 1.69 ± 0.22 0.59 ± 0.09 0.000
Nitrospirales 1.69 ± 0.22 0.59 ± 0.09 0.000
Actinobacteria 1.40 ± 0.33 1.83 ± 0.31 0.146
Acidimicrobiia 1.05 ± 0.32 1.55 ± 0.30 0.095
Acidimicrobiales 1.05 ± 0.32 1.55 ± 0.30 0.095
NC10 1.27 ± 0.29 0.13 ± 0.03 0.001
wb1A12 1.27 ± 0.29 0.13 ± 0.03 0.001
Bacteroidetes 1.00 ± 0.31 1.64 ± 0.18 0.023
Note. The mean was calculated by averaging data from four stations on the top and the base, respectively. The pvalues
were calculated by ttest. Higher values are in bold.
Abbreviation: SD, standard deviation.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2891
northeast trade winds drive the westward surface current all year round from surface to 4,000 m. According
to the data collected with current meter (Seaguard RCM) and ADCP (WHLR75kHz) deployed at nine sites
surrounding the seamount, a huge anticyclonic eddy cycling around the seamount was detected
(Figure 8). The anticyclonic eddy was averagely stronger at the depth of approximately 1,000 m, right
Figure 6. Weighted UniFrac distances for sediment operational taxonomic units data retrieved from the top (blue dot)
and the base (red square) of the Caiwei Seamount. The results are displayed by the principal coordinate analysis
(Lozupone et al., 2006).
Table 3
Numbers of OTUs Shared Within the Sediment Samples Collected From Top and Base Stations of the Caiwei Seamount
Top Base
MAMC01 6,168 (100) 3,544 (33) 3,326 (36) 3,305 (44) 1,829 (31) 1,803 (23) 1,560 (23) 1,810 (25)
MAMC02 3,544 (58) 10,895 (100) 4,250 (46) 3,943 (53) 2,292 (38) 2,465 (31) 2,017 (30) 2,401 (33)
MAMC03 3,326 (54) 4,250 (39) 9,222 (100) 3,978 (53) 2,095 (35) 2,148 (27) 1,838 (28) 2,153 (29)
MAMC04 3,305 (54) 3,943 (36) 3,978 (43) 7,499 (100) 2,002 (33) 1,967 (25) 1,709 (26) 1,969 (27)
MABC02 1,829 (30) 2,292 (21) 2,095 (23) 2,002 (27) 6,000 (100) 2,852 (36) 2,549 (38) 2,737 (37)
MAMC06 1,803 (29) 2,465 (23) 2,148 (23) 1,967 (26) 2,852 (48) 7,999 (100) 2,818 (42) 3,125 (43)
MABC06 1,560 (25) 2,017 (19) 1,838 (20) 1,709 (23) 2,549 (43) 2,818 (35) 6,688 (100) 2,728 (37)
MAMC08 1,810 (29) 2,401 (22) 2,153 (23) 1,969 (26) 2,737 (46) 3,125 (39) 2,728 (41) 7,345 (100)
Note. Numbers in the brackets are the percentages (%) of shared OTUs in total numbers of OTUs in samplesof the stations on the toprow. The grayshaded areas
are the comparisons between the same sample, used for differentiating from those between different samples.
Abbreviation: OTUs, operational taxonomic units.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2892
above the top layer of the seamount, driving the clockwise current transport on the top of the seamount
(average current velocity: 7.710.1 cm/s; Figure 8). It may potentially enhance the bacterial transit and
sinking. Similarly, at the base of the seamount, although the seamount seems acting as a barrier
among stations, the clockwise ow cycled around the seamount (average current velocity: 2.85.0 cm/s;
Figure 8), still being able to drive bacterial dispersal and potentially contributing to the similarity of
Figure 7. Correlations between bacterial groups and environmental factors in samples collected from sediments of the top
and the base of the Caiwei Seamount by redundancy analysis (RDA).
Figure 8. The timeaveraged observed bottom current vector of the Caiwei Seamount by nine bottom mounted mooring
stations (15 m above the bottom). An anticyclonic circulation around the seamount was detected.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2893
bacterial community composition and structure along the circulation of the seamount. Overall, it is con-
cluded that the bacterial community composition and structure in a guyot may be coinuenced by physico-
chemical variables and unique physical dynamics.
4.2. Interaction Between Bacterial Community and Environmental Gradients
Although the richness of bacterial communities was similar in two regions, the signicant difference in
diversity and evenness indicated the compositional and physiological heterogeneity between the top and
the base of the seamount (Dang & Lovell, 2016; Kato et al., 2018). Based on the assigned taxonomy of the
bacterial community by 16S rRNA genes in this study, the potential physiological and metabolic features
of bacteria were found relating to environmental gradients in the Caiwei Seamount.
The abundance and metabolic features of bacteria in marine sediments are related to the organic contents
and oxidationreduction potentials (Zobell, 1955). Usually, oxygen in the sediment is depleted rapidly from
the surface. Zonation of microbial community and activity rely on the type and the availability of electron
donors and acceptors, which have been intensely studied in dark environments (Orcutt et al., 2011). In
the Caiwei Seamount, oxygen and nutrient concentrations were measured through the water column of
the guyot (Figure S1). The oxygen concentration was found lowest at ~1,000 m, above the top of the sea-
mount (Figures S1a, S1c, and S1e). The cooccurrence of the phosphate peak and lowest pH at the same depth
suggests a rapid degradation of organic matter by microbes (Figure S1). Consequently, the reduced gradient
of oxygen in seawater near the top inhibits the diffusion of oxygen from the sediment surface to the deeper
depth and a relatively reduced environment is formed in a shallower depth of the sediment. Other electron
acceptors, such as NO
, and SO
, may be subsequently reduced and play more important roles
in the acquisition of carbon and energy by microorganisms (Reimers et al., 2013). Moreover, a greater pro-
portion of Deltaproteobacteria related to sulfate reduction (e.g., NB1j) and syntrophic sulfate reduction
(Syntrophobacteales) were detected at the same layer, an indicator of low or depleted oxygen in the sediment
(Baumgartner et al., 2006; Orcutt et al., 2011).
In comparison, at the base of the Caiwei Seamount, DO concentrations in surrounding seawater were almost
2 times greater than those measured near the top of the seamount (Table S2), possibly a result of slow decom-
position of recalcitrant organic matter accumulated on the base after a long sinking process (Kallmeyer et al.,
2012). The elevated oxygen gradients enhanced the diffusion of oxygen to the deeper depth of the sediment
and affected the microniches in the sediments (D'Hondt et al., 2009). Oxidized forms of Fe and Mn were
much more abundant at the base (Figure 2), which can be formed by abiotic kinetics under aerobic condi-
tions or by microbial oxidation of reduced iron and manganese compounds (Emerson & Moyer, 2002;
Orcutt et al., 2011; Schippers & Jørgensen, 2002). However, in the sediment collected from the top 5cm
layer, bacteria reported that were mostly afliated to iron oxidation in marine environments were not
detected, such as Mariprofundus ferrooxydans in Zetaproteobacteria (Emerson et al., 2007) and Leptothrix
spp. in Betaproteobacteria (Hedrich et al., 2011). This could be the bias of sampling depth. Decreased propor-
tion of sulfatereducing Deltaproteobacteria and increased Soxidizing Gammaproteobacteria both reected
the reduction of the redox potentials as a result of increased oxygen. The presence of the phylum
Chloroexi related to the decomposition of the refractory organic compounds is an evidence of greater pro-
portions of recalcitrant organic matter (Landry et al., 2017), reducing decomposition rate and oxygen con-
sumption. Substrates for Soxidizing bacteria at the base of the seamount may be from a variety of
sources, such as elemental S (S
), organosulfur, pyrite (FeS
), and Chalcopyrite (CuS). The SAR202 cluster
belonging to this phylum has been recently found metabolizing several organosulfur compounds, being a
sulteoxidizer and important in sulfur turnover in the dark ocean (Mehrshad et al., 2017). Due to the accu-
mulation of complex and refractory organic matter that may reduce the efciency of energy acquisition by
bacteria in base sediments of the seamount, and considering similar bacterial richness between the top
and the base of the seamount, there must be energy sources to compensate. Nitahara et al. (2011) has
reported that chemoautotrophs are the major energy sources for sustaining the microbial ecosystem on
the Mn crust, where both degradation of organic compounds by anaerobes and fermenters would be limited.
Soxidizing bacteria have been recognized as one group of major primary producers in benthic environ-
ments, supporting heterotrophic bacteria and benthic organisms (Ye et al., 2016). Moreover, OTUs classied
as ammoniaoxidizing chemolithoautotrophic bacterium Nitrosospira in the Betaproteobacteria were also
ndetected within sediment samples from the base of the seamount. Although ammoniaoxidizing
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2894
Thaumarchaeota were not analyzed in this study, they have been reported as the major group of chemoau-
throphs in sediments of similar guyot environment in northwest Pacic Ocean (Kato et al., 2018; Nitahara
et al., 2011, 2017). Therefore, the domination of sulfuroxidizing bacteria and ammoniaoxidizing microbes
at the base of the seamount may play vital roles in food and energy supply.
4.3. Comparison of Bacterial Community on Guyots to Other Seaoor Environments
The bacterial community composition in sediments of the Caiwei Seamount is similar to that in abyssal
environment enriched with polymetallic nodules and other guyots that have been explored in Pacic
Ocean (Kato et al., 2018; Liao et al., 2011; Lindh et al., 2017; Nitahara et al., 2011, 2017; Shulse et al.,
2016), but had key difference from active seamount environments (LópezGarcía et al., 2003; Moyer et al.,
1995; Scott et al., 2017; Teske et al., 2002). The family Piscirickettsiaceae and the order Chromatiales in
Gammaproteobacteria, the family Rhodospirillales in Alphaproteobacteria,Chlorexi and
Deltaproteobacteria found in the Caiwei Seamount are also the common groups in deepsea surface sediment
as well as at seaoor with polymetallic nodule, even with similar relative abundances in the samples
(Shulse et al., 2016). Although we did not sequence archaeal 16S rRNA in this study, as removing sequence
contamination from total bacterial sequences, we found that about 75% of detected archaeal sequences were
identied to be Thaumarchaeota (data not shown), similar to results from the seaoor and seamount in
Pacic Ocean (Kato et al., 2018; Nitahara et al., 2011, 2017; Zinke et al., 2018). It is believed that
Thaumarchaeota could be the key group in the Caiwei Seamount and play an important role in guyot
ecosystem. It needs to be investigated in future studies.
Two ubiquitous groups Zetaproteobacteria and Epsiloproteobacteria in hydrothermal vents were not
retrieved from any sequence pool of the Caiwei Seamount in this study. Ironoxidizing bacteria
Zetaproteobacteria have been mostly described as gradient organismsbecause they tend to colonize at
the interface between aerobic and anoxic zones (Hedrich et al., 2011). Thus, the nondetection of
Zetaproteobacteria in the Caiwei Seamount could be due to lower surrounding temperature and chemical
gradient at the interface between sediment and water column (Scott et al., 2017). The presence of
Epsiloproteobacteria usually related to the oxidation of hydrogen sulde in deepsea sediments where vents
surround and the hydrogen sulde is abundantly supplied (LópezGarcía et al., 2003). In sediment environ-
ments of the Caiwei Seamount, the redox potentials may not be low to the level with rapid and plenty supply
of hydrogen sulde by sulfatereducers as the sources to support the growth of Epsiloproteobacteria.
Different from hydrothermal system, bacterial communities in the Caiwei Seamount are dominated by
the sulfurcycle associated groups commonly existing on the surface of oligotrophic oceanic sediments.
5. Conclusions
Currently, there are only a few studies on microbial community in seamounts located in the northwest
Pacic Ocean, but most focused on communities in niches associated with FeMn crusts. In this study, we
investigated bacterial community compositions and structures from locations featured by different environ-
mental characteristics in order to understand the diversity of microniches, microorganisms, and metabolic
potentials in a guyot ecosystem. Our results indicate that the bacterial community structures and composi-
tions are similar in sediments from the same region (top or base of the seamount) but different between two
regions, highly associated with the depth and environmental variables, such as DO concentrations, elemen-
tal densities, and availabilities of organic matter. The homogeneity of microniches and bacterial commu-
nities at the same depth of the Caiwei Seamount suggests a key effect of physical dynamics on guyot
environment and biological community, while heterogeneous patterns vertically emphasize the important
of physicochemical characteristics on the formation of bacterial niches. Bacterial metabolic potentials
inferred from bacterial community compositions also suggest a strong interaction between microbial mod-
ication and environmental impact.
More than 90% of OTUs were not assigned to genus level, indicating that a large proportion of unknown spe-
cies, diversity, and hidden functions in guyot ecosystem need to be explored in future. As we are working on
isolating new species through culture methods, we will apply metagenomic analysis on guyot samples to
reveal unknown genetic diversity and functions, increasing sequencing resolution to identify key species
as well as their spatiotemporal variations in guyot ecosystem.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2895
Agogué, H., Lamy, D., Neal, P. R., Sogin, M. L., & Herdnel, G. J. (2011). Water massspecicity of bacterial communities in the North
Atlantic revealed by massively parallel sequencing. Molecular Ecology,20(2), 258274. https:/ /
Asavin, A. M., Anikeeva, L. I., Kazakova, V. A., Andreev, S. I., Sapozhnikov, D. A., Roshchina, I. A., & Kogarko, L. N. (2008). Trac e element
and PGE distribution in layered ferromanganese crusts. Geochemistry International,46(12), 11791205.
Barco, R. A., Hoffman, C. L., Ramírez, G. A., Toner, B. M., Edwards, K. J., & Sylvan, J. B. (2017). Insitu incubation of ironsulfur mineral
reveals a diverse chemolithoautotrophic community and a new biogeochemical role for Thiomicrospira.Environmental Microbiology,
19(3), 13221337.
Baumgartner, L. K., Reid, R. R., Dupraz, C., Decho, A. W., Buckley, D. H., Spear, J. R., et al. (2006). Sulfate reducing bacteria in microbial
mats: Changing paradigms, new discoveries. Sedimentary Geology,185(34), 131145.
Boehlert, G. W., & Genin, A. (1987). A review of the effects of seamounts on biological processes. Seamounts, Islands and Atolls,43, 319334
Caporaso, J. G., Bittinger, K., Bushman, F. D., DeSantis, T. Z., Andersen, G. L., & Knight, R. (2010). PyNAST: a exible tool for aligning
sequences to a template alignment. Bioinformatics,26(2), 266267.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010). QIIME allows analysis of high
throughput community sequencing data. Nature Methods,7(5), 335336.
Chapman, D. C., & Haidvogel, D. B. (1992). Formation of Taylor caps over a tall isolated seamount in a stratied ocean. Geophysical and
Astrophysical Fluid Dynamics,64(14), 3165.
Clark, M. R., Rowden, A. A., Schlacher, T., Williams, A., Consalvey, M., Stocks, K. I., et al. (2010). The ecology of seamounts: structure,
function, and human impacts. Annual Review of Marine Science,2(1), 253278.
Dang, H., & Lovell, C. R. (2016). Microbial surface colonization and biolm development in marine environments. Microbiology and
Molecular Biology Reviews,80,1.
D'Hondt, S., Splvack, A. J., Pockalny, R., Ferdelman, T. G., Fischer, J. P., Kallmeyer, J., et al. (2009). Subseaoor sedimentary life in the
South Pacic Gyre. PNAS,106(28), 11,65111,656.
Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics,26(19), 24602461.
Emerson, D., & Moyer, C. (2002). Neutrophilic Feoxidizing bacteria are abundant at the Loihi seamount hydrothermal vents and play a
major role in Fe oxide deposition. Applied and Environmental Microbiology,68(6), 30853093.
Emerson, D., Rentz, J. A., Lilburn, T. G., David, R. E., Aldrich, H., Chan, C., & Moyer, C. L. (2007). A novel lineage of proteobacteria
involved in formation of marine Feoxidizing microbial mat communities. PLoS ONE,2(8), e667.
Fullerton, H., Hager, K. W., McAllister, S. M., & Moyer, C. L. (2017). Hidden diversity revealed by genomeresolved metagenomics of iron
oxidizing microbial mats from Lo'ihi Seamount, Hawai'i. The ISME Journal,11(8), 19001914.
Gilbert, D., & Garrett, C. (1989). Implications for ocean mixing of internal wave scattering off irregular topography. Journal of Physical
Oceanography,19(11), 17161729.<1716:IFOMOI>2.0.CO;2
Grasshoff, K., Kremling, K., & Erhardt, M. (1999). Methods of seawater analysis, (3rd ed., Vol. 1999). Verlag GmbH: WileyVCH. ISBN 3
Hamdan, L. J., Cofn, R. B., Sikaroodi, M., Greinert, J., Treude, T., & Gillevet, P. M. (2013). Ocean currents shape the microbiome of Arctic
marine sediments. The ISME Journal,7(4), 685696.
Hedrich, S., Schlömann, M., & Johnson, D. B. (2011). The ironoxidizing proteobacteria. Microbiology,157(6), 15511564.
Hewson, I., Jacobson/Meyers, M. E., & Fuhrman, J. A. (2007). Diversity and biogeography of bacterial assemblages in surface sediments
across the San Pedro Basin, Southern California Borderlands. Environmental Microbiology,9(4), 923933. https://doi .org/10.1111/j.1462
Huber, J. A., Mark Welch, D. B., Morrison, H. G., Huse, S. M., Neal, P. R., Buttereld, D. A., & Sogin, M. L. (2007). Microbial population
structures in the deep marine biosphere. Science,318(5847), 97100.
Hunter, C. N., Daldal, F., Thurnauer, M. C., & Beatty, J. T. (2009). The purple phototrophic bacteria. Dordrecht: Springer.
Inagaki, F., Nunoura, T., Nakagawa, S., Teske, A., Lever, M., Lauer, A., et al. (2006). Biogeogr aphical distribution and diversity of microbes
in methane hydratebearing deep marine sediments on the Pacic Ocean Margin. PNAS,103(8), 28152820.
Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., & D'Hondt, S. (2012). Global distribution of microbial abundance and biomass in
subseaoor sediment. PNAS,109(40), 16,21316,216.
Kato, S., Okumura, T., Uematsu, K., Hirai, M., Iijima, K., Usui, A., & Suzuki, K. (2018). Heterogeneity of microbial communities on deep
sea ferromanganese crusts in the TakuyoDaigo Seamount. Microbes and Environments,33(4), 366377.
Kim, S.S., & Wessel, P. (2011). New global seamount census from altimetryderived gravity data. Geophysical Journal Internationa l,186(2),
Landry, Z., Swan, B. K., Herndl, G. J., Stepanauskas, R., & Giovannoni, S. J. (2017). SAR202 genomes from the dark ocean predict pathway s
for the oxidation of recalcitrant dissolved organic matter. MBio,8(2), e0041317).
Liao, L., Xu, X.W., Jiang, X.W., Wang, C.S., Zhang, D.S., Ni, J.Y., & Wu, M. (2011). Microbial diversity in deepsea sediment from the
cobaltrich crust deposit region in the Pacic Ocean. FEMS Microbiology Ecology,78(3), 565585.
Lindh, M. V., Maillot, B. M., Shulse, C. N., Gooday, A. J., Amon, D. J., Smith, C. R., & Church, M. J. (2017). From the surface to the deepsea:
Bacterial Distributions across polymetallic nodule elds in the ClarionClipperton Zone of the Pacic Ocean. Frontiers in Microbiology,
8, 1696.
LópezGarcía, P., Duperron, S., Philippot, P., Foriel, J., Susini, J., & Moreira, D. (2003). Bacterial diversity in hydrothermal sediment and
epsilonproteobacterial dominance in experimental microcolonizers at the MidAtlantic Ridge. Environmental Microbiology,5(10),
Journal of Geophysical Research: Biogeosciences
We would like to thank the crew of R/V
Haiyang Liu Hao and the scientists who
joint the cruise and helped with
samplings. We thank Dr. Hong Cheng
for assisting with the submission of
sequencing data to NCBI, as well as
Dr. Changming Dong and Mr.
Xingliang Jiang from Nanjing
University of Information Science and
Technology for providing the vector
diagram of Figure 1. The research was
funded by grants from China Ocean
Mineral Resources R & D Association
(COMRA) Special Foundation (grants
No.DY135E2205 and No. DY135E2
202), Scientic Research Fund of
Second Institute of Oceanography,
MNR (grant No. JB1703) and the
National Natural Science Foundation of
China (grants No. 41706150 and No.
41876182).Complying with AGU's data
policy, the sequencing data can be
accessed at NCBI Sequence Read
Archive under accession number
SRR7888608SRR7888615, and others
can be accessed from the text and sup-
porting information.
Lozupone, C., Hamady, M., & Knight, R. (2006). UniFracAn online tool for comparing microbial community diversity in a phylogenetic
context. BMC Bioinformatics,7(1), 371.
Lueck, R. G., & Mudge, T. D. (1997). Topographically induced mixing around a shallow seamount. Science,276(5320), 18311833. https://
McNichol, J., Stryhanyuk, H., Sylva, S. P., Thomas, F., Musat, N., Seewald, J. S., & Sievert, S. M. (2018). Primary productivity below the
seaoor at deepsea hot springs. PNAS,115(26), 67566761.
Mehrshad, M., RodriguezValera, F., Amoozegar, M. A., LópezGarcía, P., & Ghai, R. (2017). The enigmatic SAR202 cluster up close:
shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. The ISME Journal,12, 655668.
Meyers, M. E. J., Sylvan, J. B., & Edwards, K. J. (2014). Extracellular enzyme activity and microbial diversity measured on seaoor exposed
basalts from Loihi Seamount indicate the importance of basalts to global biogeochemical cycling. Applied and Environmental
Microbiology,80(16), 48544864.
Moyer, C. L., Dobbs, F. C., & Karl, D. M. (1995). Phylogenetic diversity of the bacterial community from a microbial mat at an active,
hydrothermal vent system, Loihi Seamount, Hawaii. Applied and Environmental Microbiology,61, 15551562.
Nitahara, S., Kato, S., Urabe, T., Usui, A., & Yamagishi, A. (2011). Molecular characterization of the microbial community in hydrogenetic
ferromanganese crusts of the TakuyoDaigo Seamount, northwest Pacic. FEMS Microbiology Ecology,321(2), 121129.
Nitahara, S., Kato, S., Usui, A., Urabe, T., Suzuki, K., & Yamagishi, A. (2017). Archaeal and bacterial communities in deepsea hydrogene tic
ferromanganese crusts on old seamounts of the northwestern Pacic. PLoS ONE,12(2), e0173071.
Orcutt, B. N., Sylvan, J. B., Knab, N. J., & Edwards, K. (2011). Microbial Ecology of the Dark Ocean above, at, and below the seaoor.
Microbiology and Molecular Biology Reviews,75(2), 361422.
Polzin, K. L., Toole, M., Ledwell, J. R., & Schmitt, R. W. (1997). Spatial variability of turbulent mixing in the abyssal ocean. Science,
276(5309), 9396.
Purkhold, U., Wagner, M., Timmermann, G., PommereningRoser, A., & Koops, H. P. (2003). 16S rRNA and amoAbased phylogeny of 12
novel betaproteobacterial ammoniaoxidizing isolates, extension of the dataset and proposal of a new lineage within the Nitrosomonads.
International Journal of Systematic and Evolutionary Microbiology,53(5), 14851494.
R Development Core Team (2011). A language and environment for statistical computing. Vienna: R Development Core Team.
Reimers, C. E., Alleau, Y., Bauer, J. E., Delaney, J., Girguis, P. R., Schrader, P. S., & Stecher, H. A. III (2013). Redox effects on the microbial
degradation of refractory organic matter in marine sediments. Geochimica et Cosmochimica Acta,121, 582598.
Richer de Forges, B., Koslow, J. A., & Poore, G. C. B. (2000). Diversity and endemism of the benthic seamount fauna in the southwest
Pacic. Nature,405, 744947.
Schauer, R., Bienhold, C., Ramette, A., & Harder, J. (2010). Bacterial divers ity and biogeography in deepsea surface sediments of the South
Atlantic Ocean. The ISME Journal,4(2), 159170.
Schippers, A., & Jørgensen, B. B. (2002). Biogeochemistry of pyrite and iron sulde oxidation in marine sediments. Geochimica et
Cosmochimica Acta,66(1), 8592.
Scott, J. J., Glazer, B. T., & Emerson, D. (2017). Bringing microbial divers ity into focus: Highresolution analysis of iron mats from the Lo'ihi
seamount. Environmental Microbiology,19(1), 301316.
Shulse, C. N., Maillot, B., Smith, C. R., & Church, M. J. (2016). Polymetallic nodules, sediments, and deep waters in the equatorial North
Pacic exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities. MicrobiologyOpen,6, e428.
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse, S. M., Neal, P. R., et al. (2006). Microbial diversity in the deep sea and the
underexplored rare biosphere.Proceedings of the National Academy of Sciences,103(32), 12,11512,120.
Stanley, S. M. (2005). Earth system history. New York: Freeman, W. H. & Company.
Ter Braak, C. J. F., & Šmilauer, P. (2012). Canoco reference manual and user's guide: software for ordination, version 5.0. Microcomputer
Power, Ithaca, USA, 496 pp.
Teske, A., Hinrichs, K.U., Edgcomb, V., Gomez, A. V., Kysela, D., Sylva, S. P., et al. (2002). Microbial diversity of hydrothermal sediments
in the Guaymas Basin: Evidence for anaerobic methanotrophic communities. Applied and Environmental Microbiology,68(4),
Walsh, E. A., Smith, D. C., Sogin, M. L., & D'Hondt, S. L. (2015). Bacterial and archaeal biogeography of the deep chlorophyll maximum in
the South Pacic Gyre. Aquatic Microbial Ecology,75(1), 113.
Wang, Y., Zhang, H., Liu, J., Zhang, X., & Zhu, B. (2016). Abundances and spatial distributions of associated useful elements in corich
crusts from Caiwei Seamount in Magellan Seamounts [J]. Marine Geology & Quaternary Geology, 02
Wessel, P., & Kroenke, L. W. (1997). A geometric technique for relocating hotspots and rening absolute plate motions. Nature,387(6631),
Winkler, L. (1888). Die bestimmung des in Wasser Gelösten Sauerstoffes. Berichte der Deutschen Chemischen Gesellschaft,21(2), 28432854.
Xu, P., Liu, F., Ding, Z., & Wang, C. (2016). A new species of the thorid genus Paralebbeus Bruce & Chace, 1986 (Crustacea: Decapoda:
Caridea) from the deep sea of the Northwestern Pacic Ocean. Zootaxa,4085(1), 119126.
Ye, Q., Wu, Y., Zhu, Z., Wang, X., Li, Z., & Zhang, J. (2016). Bacterial diversity in the surface sediments of the hypoxic zone near the
Changjiang Estuary and in the East China Sea. MicrobiologyOpen,5(2), 323339.
Zhang, Y., Wang, X., Zhen, Y., Mi, T., He, H., & Yu, Z. (2017). Microbial diversity and community structure of sulfatereducing and sulfur
oxidizing bacteria in sediment cores from the East China Sea. Frontiers in Microbiology,8, 2133.
Zinke, L. A., Reese, B. K., McManus, J., Wheat, C. G., Orcutt, B. N., & Amend, J. P. (2018). Sediment microbial communities inuenced by
cool hydrothermal uid migration. Frontiers in Microbiology,9, 1249.
Zobell, C. E. (1955). Occurrence and activity of bacteria in marine sediment. Special Publications of The Society of Economic
Paleontologists and Mineralogists (SEPM). Recent Marine Sediments,416427.
Journal of Geophysical Research: Biogeosciences
LIU ET AL. 2897
... Besides, microorganisms are essential contributors to marine biogeochemical cycles and possibly supply high productivity found in seamounts (Leitner et al., 2020;Morato et al., 2010;Rowden et al., 2010). Bacteria and Archaea have been studied in the deep ocean, where they are diverse and possibly supply the energy flow in the Pacific and Atlantic seamounts (Bergo et al., 2021;Fullerton et al., 2017;Liu et al., 2019;Orcutt et al., 2020). ...
... Most efforts to study Atlantic seamounts with Fe-Mn deposits have been to assessed mineral resources and their megafaunal community Montserrat et al., 2019;Perez et al., 2018;Ramiro-Sánchez et al., 2019;Yeo et al., 2018). Previous studies on the diversity, taxonomy, and functions of microbial communities of seamount with Fe-Mn deposits have mainly focused on the Pacific Ocean (Kato et al., 2018;Kato et al., 2019;Liu et al., 2019;Nitahara et al., 2017). ...
... Previous studies have shown that microbial community structure can be relatively similar in analogous marine environments even though distancing thousands of kilometers away (Agogué et al., 2011;Walsh et al., 2015). However, microbial communities can also be variable over only a few tens of kilometers away within heterogeneous environments (Hewson et al., 2007;Kato et al., 2018;Liu et al., 2019). Our PCA analysis showed that microbial communities in Fe-Mn crusts, nodules, and associated sediment are grouped by ocean and sampling areas. ...
Mining of deep-sea Fe-Mn deposits will remove crusts and nodules from the seafloor. The growth of these minerals takes millions of years, yet little is known about their microbiome. Besides being key elements of the biogeochemical cycles and essential links of food and energy to deep-sea, microbes have been identified to affect manganese oxide formation. In this study, we determined the composition and diversity of Bacteria and Archaea in deep-sea Fe-Mn crusts, nodules, and associated sediments from two areas in the Atlantic Ocean, the Tropic Seamount and the Rio Grande Rise. Samples were collected using ROV and dredge in 2016 and 2018 oceanographic campaigns, and the 16S rRNA gene was sequenced using Illumina platform. Additionally, we compared our results with microbiome data of Fe-Mn crusts, nodules, and sediments from Clarion-Clipperton Zone and Takuyo-Daigo Seamount in the Pacific Ocean. We found that Atlantic seamounts harbor an unusual and unknown Fe-Mn deposit microbiome with lower diversity and richness compared to Pacific areas. Crusts and nodules from Atlantic seamounts have unique taxa (Alteromonadales, Nitrospira, and Magnetospiraceae) and a higher abundance of potential metal-cycling bacteria, such as Betaproteobacteriales and Pseudomonadales. The microbial beta-diversity from Atlantic seamounts was clearly grouped into microhabitats according to sediments, crusts, nodules, and geochemistry. Despite the time scale of million years for these deposits to grow, a combination of environmental settings played a significant role in shaping the microbiome of crusts and nodules. Our results suggest that microbes of Fe-Mn deposits are key in biogeochemical reactions in deep-sea ecosystems. These findings demonstrate the importance of microbial community analysis in environmental baseline studies for areas within the potential of deep-sea mining.
... The sediments on the guyot are mainly cobaltrich crusts, carbonate rocks, and/or calcareous pelagic deposits [13][14][15]. The Caiwei Guyot has been extensively surveyed in terms of mineral resources and megafaunal community [16,17] and microorganisms [18][19][20]. For example, cobalt-rich crusts on the guyot were found in the northeast [13]; furthermore, organic matters were supposed to be the main controlling factor in bioturbation around the guyot [19]. ...
... Moreover, since the Caiwei Guyot is located at the main path of the Antarctic bottom water (AABW) and the Lower Circumpolar Deep Water (LCDW) to the north Pacific [21,22], the oceanographic setting is clockwise, and flows around the seamount and a Taylor column phenomenon above the seamount produced by an anti-cyclonic eddy in mesoscale to submesoscales [23,24]. Because of these oceanographic settings, similar hydrochemical properties, such as salinity, pH value, and nitrate, are observed between the top and the base of the seamount [18]. study area and oceanographic setting. ...
... Paleomagnetic samples of core MABC-11 were collected using nonmagnetic plastic U-channels (2 cm × 2 cm × 150 cm). Since the upper part was collected for biological study on board [18] and sediment loss in cutting, 47 cm of sediment (11-58 cm in depth) of the core was sampled for paleomagnetic investigation in this study. All U-channel samples with a 1-cm measuring interval were subjected to stepwise alternating field (AF) demagnetization up to a peak field of 90 mT (13 steps). ...
Full-text available
Seamounts are ubiquitous topographic units in the global ocean, and their effects on local circulation have attracted great research attention in physical oceanography; however, fewer relevant efforts were made on geological timescales in previous studies. The Caiwei (Pako) Guyot in the Magellan Seamounts of the western Pacific is a typical seamount and oceanographic characteristics have been well documented. In this study, we investigate a sediment core by geochronological and geochemical studies to reveal a topography-induce surface-to-bottom linkage. The principal results are as follows: (1) Two magnetozones are recognized in core MABC–11, which can be correlated to the Brunhes and Matuyama chrons; (2) Elements Ca, Si, Cl, K, Mn, Ti, and Fe are seven elements with high intensities by geochemical scanning; (3) Ca intensity can be tuned to global ice volume to refine the age model on glacial-interglacial timescales; (4) The averaged sediment accumulation rate is ~0.73 mm/kyr, agreeing with the estimate of the excess 230Th data in the upper part. Based on these results, a proxy of element Mn is derived, whose variability can be correlated with changes in global ice volume and deep-water masses on glacial-interglacial timescales. This record is also characterized by an evident 23-kyr cycle, highlighting a direct influence of solar insolation on deep-sea sedimentary processes. Overall, sedimentary archives of the Caiwei Guyot not only record an intensified abyssal ventilation during interglaciations in the western Pacific, but also provide a unique window for investigating the topography-induced linkage between the upper and bottom ocean on orbital timescales.
... Microorganisms are suggested to be potentially involved in the elemental transition between seawater and Fe-Mn substrates [16,45], and in the Mn oxidation and precipitation. Microbial diversity and abundance have been studied in the Fe-Mn crusts, and their associated sediment and water of Pacific Ocean seamounts [15,22,30,31]. These studies have detected the potential for microbial chemosynthetic primary production supported by ammonia oxidation [12,15,31]. ...
... Microbial assemblages in samples from the RGR showed the dominance of the classes Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria, as described for others Fe-Mn crusts deposits [21,40,45,49]. However, at higher taxonomic resolution, samples from the RGR showed higher abundance of the orders Steroidobacterales ( f a m i l y W o e s e i a c e a e ) , u n c u l t u r e d M B M P E 2 7 , Methylomirabilales, and Nitrospirales [15,22]. Besides that, SAR11 clade was detected in all samples from the RGR. ...
Full-text available
Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe–Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe–Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe–Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe–Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe–Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe–Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe–Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.
... They can provide denitrification processes and dissimilatory reduction of nitrates to ammonium and be involved in the chain of trophic interactions with anaerobic methanotrophs. Genomic studies of anaerobic enzymatic heterotrophs of the order Woesearchaeales also display their capacity to participate in iron metabolism and methanogenesis processes [109] in consortium with methanogens [30]. Sequences of methylotrophic methanogens of the order Methanomassiliicoccales occurred in three communities (0-1 cm, 9-10 cm and 10-11 cm), but the methane concentrations of sediments did not confirm their activity. ...
Full-text available
Ferromanganese (Fe-Mn) sedimentary layers and nodules occur at different depths within sediments at deep basins and ridges of Lake Baikal. We studied Fe-Mn nodules and host sediments recovered at the slope of Bolshoy Ushkany Island. Layer-by-layer 230Th/U dating analysis determined the initial age of the Fe-Mn nodule formation scattered in the sediments as 96 ± 5–131 ± 8 Ka. The distribution profiles of the main ions in the pore waters of the studied sediment are similar to those observed in the deep-sea areas of Lake Baikal, while the chemical composition of Fe-Mn nodules indicates their diagenetic formation with hydrothermal influence. Among the bacteria in microbial communities of sediments, members of organoheterotrophic Gammaproteobacteria, Chloroflexi, Actinobacteriota, Acidobacteriota, among them Archaea—chemolithoautotrophic ammonia-oxidizing archaea Nitrososphaeria, dominated. About 13% of the bacterial 16S rRNA gene sequences in Fe-Mn layers belonged to Methylomirabilota representatives which use nitrite ions as electron acceptors for the anaerobic oxidation of methane (AOM). Nitrospirota comprised up to 9% of the layers of Bolshoy Ushkany Island. In bacterial communities of Fe-Mn nodule, a large percentage of sequences were attributed to Alphaproteobacteria, Actinobacteriota and Firmicutes, as well as a variety of OTUs with a small number of sequences characteristic of hydrothermal ecosystems. The contribution of representatives of Methylomirabilota and Nitrospirota in communities of Fe-Mn nodule was minor. Our data support the hypothesis that chemolithoautotrophs associated with ammonium-oxidizing archaea and nitrite-oxidizing bacteria can potentially play an important role as primary producers of Fe-Mn substrates in freshwater Lake Baikal.
... The growth process of ferromanganese crusts is related to OMZ on seamounts [12]. The water depth of OMZ in the Caiwei Guyot is less than 1000 m [79]. OMZ can promote the dissolution of Mn in OMZ and ferromanganese crusts with high Mn content form below the OMZ [20,80]. ...
Full-text available
The ferromanganese deposit is a type of marine mineral resource rich in Mn, Fe, Co, Ni, and Cu. Its growth process is generally multi-stage, and the guyot environment and seawater geochemical characteristics have a great impact on the growth process. Here, we use a scanning electron microscope, X-ray diffraction (XRD), inductively coupled plasma optical emission spectrometer (ICP-OES), X-ray fluorescence (XRF), and inductively coupled plasma mass spectrometry (ICP-MS) to test and analyze the texture morphology, microstructure, mineralogical features, geochemical features of ferromanganese crusts deposits at different distribution locations on Caiwei Guyot. The ferromanganese deposits of Caiwei Guyot are ferromanganese nodules on the slope and board ferromanganese crusts on the mountaintop edge, which are both of hydrgenetic origin. Hydrgenetic origin reflects that the metal source is oxic seawater. Global palaeo-ocean events control the geochemistry compositions and growth process of ferromanganese crusts and the nodule. Ferromanganese crusts that formed from the late Cretaceous on the mountaintop edge have a rough surface with black botryoidal shapes, showing an environment with strong hydrodynamic conditions, while the ferromanganese nodule that formed from the Miocene on the slope has an oolitic surface as a result of water depth. What is more, nanoscale or micron-scale diagenesis may occur during the growth process, affecting microstructure, mineralogical and geochemical features.
Full-text available
The Philippine Sea is a typical region of aeolian dust reposition and is located within the Western Pacific Warm Pool. Here, we use the paleomagnetic stratigraphy and the grain‐size distributions of Quaternary abyssal deposits in the Central Philippine Sea to investigate the factors controlling regional sedimentary and paleoenvironmental changes. Our principal results are as follows: (a) A reliable geochronologic framework for Quaternary sediments in the Central Philippine Sea is established. (b) An eastward expansion of the regional depocenter in the Middle Pleistocene is observed. (c) The mean grain size of the abyssal sediments is 7–8 µm, and there are only minor differences between the sites. Comparison of the geochronological framework with various paleoenvironmental events during the Mid‐Pleistocene Transition shows that sedimentary processes can be correlated to a major transition in global climate which affected regions from the Asian interior to the tropical Pacific, and that changes in aeolian sedimentation are likely the predominant factor responsible. A derived grain‐size proxy of the sedimentary dynamics and its comparison with various paleoenvironmental proxies show that the relative contributions are roughly estimated as 23%, 9%, and 68% for aeolian inputs, oceanic circulation, and the tropical Pacific zonal SST gradient, respectively, in the studied region. The relative importance of tropical processes in abyssal sedimentary dynamics highlights the possibility of the long‐term influence of (sub)mesoscale eddies in the upper ocean, via regional upwelling and unique submarine topography, on the deepest part (>5,000 m) of the Central Philippine Sea, from meteorological to geological timescales.
Full-text available
The levels of chlorophyll a and nutrient concentrations in the surface waters of the western subtropical Pacific Ocean are among the lowest globally. In addition, our knowledge of basin-scale diversity and biogeography of microbial communities in this vast extremely oligotrophic environment is still rather limited. Here, high-throughput sequencing was used to examine the biodiversity and biogeography of abundant and rare microbial assemblages throughout the water column from the surface to a depth of 3,000 m across a horizontal distance of 1,100 km in the western Pacific Ocean. Microbial alpha diversity in the 200-m layer was higher than at other depths, with Gammaproteobacteria, Alphaproteobacteria, and Clostridia as the dominant classes in all samples. Distinctly vertical distributions within the microbial communities were revealed, with no difference horizontally. Some microbes exhibited depth stratification. For example, the relative abundances of Cyanobacteria and Alphaproteobacteria decreased with depth, while Nitrososphaeria, Actinobacteria, and Gammaproteobacteria increased with depth in the aphotic layers. Furthermore, we found that environmental (selective process) and spatial (neutral process) factors had different effects on abundant and rare taxa. Geographical distance showed little effect on the dispersal of all and abundant taxa, while statistically significant distance–decay relationships were observed among the rare taxa. Temperature and chlorophyll a were strongly associated with all, abundant, and rare taxa in the photic layers, while total inorganic nitrogen was recognized as the crucial factor in the aphotic layers. Variance partitioning analysis indicated that environmental selection played a relatively important role in shaping all and abundant taxa, while the variation in rare taxa explained by environmental and spatial processes was relatively low, as more than 70% of the variation remained unexplained. This study provides novel knowledge related to microbial community diversity in the western subtropical Pacific Ocean, and the analyzes biogeographical patterns among abundant and rare taxa.
Seamounts are ubiquitous topographic units in global oceans, and their influences on local oceanic circulation have attracted great attention in physical oceanography; however, previous efforts were less made in paleoclimatology and paleoceanography. The Caiwei Guyot in the Magellan Seamounts of the western Pacific is a typical seamount, and in this study, we investigate a well-dated sediment core by magnetic properties to reveal the relationship between deep-sea sedimentary processes and global climate changes. The principal results are as follows: (1) the dominant magnetic minerals in the sediments are low-coercivity magnetite in pseudo-single domain range, probably including a biogenic contribution; (2) the variabilities of magnetic parameters can be clustered into two sections at ∼500 ka, and the differences between the two units are evident in amplitudes and means; (3) changes in the grainsize-dependent magnetic parameters can be well correlated to records of global ice volume and atmospheric CO2 in the middle Pleistocene. Based on these results, a close linkage was proposed between deep-sea sedimentary processes in the Caiwei Guyot and global climate changes. This linkage likely involves different roles of biogenic magnetite in the sediments between interglacial and glacial intervals, responding to changes in marine productivity and deep-sea circulation and displaying a major change in the Mid-Brunhes climate event. Therefore, we proposed that the sedimentary archives at the bottom of the Caiwei Guyot record some key signals of global climate changes, providing a unique window to observe interactions between various environmental systems on glacial-interglacial timescales.
Meiofauna particularly marine nematodes around the Caiwei Guyot in the northwest Pacific Ocean and a Polymetallic Nodule Field in the northeast Pacific Ocean were studied. Due to the geographic structure, the Caiwei Guyot and the Polymetallic Nodule Field had different environmental characteristics. Meiofaunal abundances around the Guyot area ranged from 9.18 to 25.59 ind./10 cm², which were much lower than those in the Polymetallic Nodule Field. Marine nematode was the most dominant group. A total of 123 species, belonging to 74 genera and 29 families were found. Xyalidae (21.43%), Cyatholaimidae (9.82%), Linhomoeidae (8.03%) were the dominant families. The values of species number, Margalef's species richness and Shannon-Wiener diversity index ranged from 15 to 62, 4.75 to 12.84 and 2.58 to 3.93, respectively. The combination of water depth, silt-clay content and chlorophyll-a concentration can best explain the differences of nematode community. This study provides a baseline for deep-sea meiofauna distribution.
Full-text available
Rock outcrops of aged deep-sea seamounts are generally covered with Fe and Mn oxides, known as ferromanganese (Fe–Mn) crusts. Although the presence of microorganisms in Fe–Mn crusts has been reported, limited information is currently available on intra- and inter-variations in crust microbial communities. Therefore, we collected several Fe–Mn crusts in bathyal and abyssal zones (water depths of 1,150–5,520 m) in the Takuyo-Daigo Seamount in the northwestern Pacific, and examined microbial communities on the crusts using culture-independent molecular and microscopic analyses. Quantitative PCR showed that microbial cells were abundant (10⁶–10⁸ cells g–1) on Fe–Mn crust surfaces through the water depths. A comparative 16S rRNA gene analysis revealed community differences among Fe–Mn crusts through the water depths, which may have been caused by changes in dissolved oxygen concentrations. Moreover, community differences were observed among positions within each Fe–Mn crust, and potentially depended on the availability of sinking particulate organic matter. Microscopic and elemental analyses of thin Fe–Mn crust sections revealed the accumulation of microbial cells accompanied by the depletion of Mn in valleys of bumpy crust surfaces. Our results suggest that heterogeneous and abundant microbial communities play a role in the biogeochemical cycling of Mn, in addition to C and N, on crusts and contribute to the extremely slow growth of Fe–Mn crusts.
Full-text available
Cool hydrothermal systems (CHSs) are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15°C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I), Alphaproteobacteria (Rhodospirillales), Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation–reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.
Full-text available
Significance The existence of a chemosynthetic subseafloor biosphere was immediately recognized when deep-sea hot springs were discovered in 1977. However, quantifying how much new carbon is fixed in this environment has remained elusive. In this study, we incubated natural subseafloor communities under in situ pressure/temperature and measured their chemosynthetic growth efficiency and metabolic rates. Combining these data with fluid flux and in situ chemical measurements, we derived empirical constraints on chemosynthetic activity in the natural environment. Our study shows subseafloor microorganisms are highly productive (up to 1.4 Tg C produced yearly), fast-growing (turning over every 17–41 hours), and physiologically diverse. These estimates place deep-sea hot springs in a quantitative framework and allow us to assess their importance for global biogeochemical cycles.
Full-text available
The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.
Full-text available
Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99%) and revealed the high diversity, richness, and operational taxonomic unit (OTU) numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB, and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.
Full-text available
Marine bacteria regulate fluxes of matter and energy essential for pelagic and benthic organisms and may also be involved in the formation and maintenance of commercially valuable abyssal polymetallic nodules. Future mining of these nodule fields is predicted to have substantial effects on biodiversity and physicochemical conditions in mined areas. Yet, the identity and distributions of bacterial populations in deep-sea sediments and associated polymetallic nodules has received relatively little attention. We examined bacterial communities using high-throughput sequencing of bacterial 16S rRNA gene fragments from samples collected in the water column, sediment, and polymetallic nodules in the Pacific Ocean (bottom depth ≥4,000 m) in the eastern Clarion-Clipperton Zone. Operational taxonomic units (OTUs; defined at 99% 16S rRNA gene identity) affiliated with JTB255 (Gammaproteobacteria) and Rhodospirillaceae (Alphaproteobacteria) had higher relative abundances in the nodule and sediment habitats compared to the water column. Rhodobiaceae family and Vibrio OTUs had higher relative abundance in nodule samples, but were less abundant in sediment and water column samples. Bacterial communities in sediments and associated with nodules were generally similar; however, 5,861 and 6,827 OTUs found in the water column were retrieved from sediment and nodule habitats, respectively. Cyanobacterial OTUs clustering among Prochlorococcus and Synechococcus were detected in both sediments and nodules, with greater representation among nodule samples. Such results suggest that vertical export of typically abundant photic-zone microbes may be an important process in delivery of water column microorganisms to abyssal habitats, potentially influencing the structure and function of communities in polymetallic nodule fields.
Full-text available
Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist. IMPORTANCE Carbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle.
Full-text available
The Zetaproteobacteria are ubiquitous in marine environments, yet this class of Proteobacteria is only represented by a few closely-related cultured isolates. In high-iron environments, such as diffuse hydrothermal vents, the Zetaproteobacteria are important members of the community driving its structure. Biogeography of Zetaproteobacteria has shown two ubiquitous operational taxonomic units (OTUs), yet much is unknown about their genomic diversity. Genome-resolved metagenomics allows for the specific binning of microbial genomes based on genomic signatures present in composite metagenome assemblies. This resulted in the recovery of 93 genome bins, of which 34 were classified as Zetaproteobacteria. Form II ribulose 1,5-bisphosphate carboxylase genes were recovered from nearly all the Zetaproteobacteria genome bins. In addition, the Zetaproteobacteria genome bins contain genes for uptake and utilization of bioavailable nitrogen, detoxification of arsenic, and a terminal electron acceptor adapted for low oxygen concentration. Our results also support the hypothesis of a Cyc2-like protein as the site for iron oxidation, now detected across a majority of the Zetaproteobacteria genome bins. Whole genome comparisons showed a high genomic diversity across the Zetaproteobacteria OTUs and genome bins that were previously unidentified by SSU rRNA gene analysis. A single lineage of cosmopolitan Zetaproteobacteria (zOTU 2) was found to be monophyletic, based on cluster analysis of average nucleotide identity and average amino acid identity comparisons. From these data, we can begin to pinpoint genomic adaptations of the more ecologically ubiquitous Zetaproteobacteria, and further understand their environmental constraints and metabolic potential.The ISME Journal advance online publication, 31 March 2017; doi:10.1038/ismej.2017.40.
Full-text available
Deep-sea ferromanganese crusts are found ubiquitously on the surface of seamounts of the world’s oceans. Considering the wide distribution of the crusts, archaeal and bacterial communities on these crusts potentially play a significant role in biogeochemical cycling between oceans and seamounts; however little is known about phylogenetic diversity, abundance and function of the crust communities. To this end, we collected the crusts from the northwest Pacific basin and the Philippine Sea. We performed comprehensive analysis of the archaeal and bacterial communities of the collected crust samples by culture-independent molecular techniques. The distance between the sampling points was up to approximately 2,000 km. Surrounding sediments and bottom seawater were also collected as references near the sampling points of the crusts, and analyzed together. 16S rRNA gene analyses showed that the community structure of the crusts was significantly different from that of the seawater. Several members related to ammonia-oxidizers of Thaumarchaeota and Betaproteobacteria were detected in the crusts at most of all regions and depths by analyses of 16S rRNA and amoA genes, suggesting that the ammonia-oxidizing members are commonly present in the crusts. Although members related to the ammonia-oxidizers were also detected in the seawater, they differed from those in the crusts phylogenetically. In addition, members of uncultured groups of Alpha-, Delta- and Gammaproteobacteria were commonly detected in the crusts but not in the seawater. Comparison with previous studies of ferromanganese crusts and nodules suggests that the common members determined in the present study are widely distributed in the crusts and nodules on the vast seafloor. They may be key microbes for sustaining microbial ecosystems there.
The Purple Phototrophic Bacteria is a comprehensive survey of all aspects of these fascinating bacteria, the metabolically most versatile organisms on Earth. This volume is organized into the following sections: Physiology, Evolution and Ecology; Biosynthesis of Pigments, Cofactors and Lipids; Antenna Complexes: Structure, Function and Organization; Reaction Center Structure and Function; Cyclic Electron Transfer Components and Energy Coupling Reactions; Metabolic Processes; Genomics, Regulation and Signaling; and New Applications and Techniques. This book is a compilation of 48 authoritative chapters, written by leading experts who highlight the huge progress made in spectroscopic, structural and genetic studies of these bacteria since 1995, when the last book on this topic was published i.e.Anoxygenic Photosynthetic Bacteria, Volume 2 in the Series, edited by Robert E. Blankenship, Michael T. Madigan and Carl E. Bauer. This new volume is similarly intended to be the definitive text on these bacteria for many years to come, and it will be a valuable resource for experienced researchers, doctoral & masters students, as well as advanced undergraduates in the fields of ecology, microbiology, biochemistry, biophysics, integrative biology, and molecular & cell biology. Scientists interested in future applications of these bacteria which could harness their potential for nanotechnology, solar energy research, bioremediation, or as cell factories, will also find this book useful.