Spatiotemporal Analysis of Bacterial Diversity in Sediments

ENVIRONMENTAL MICROBIOLOGY
Spatiotemporal Analysis of Bacterial Diversity in Sediments
of Sundarbans Using Parallel 16S rRNA Gene Tag Sequencing
Pijush Basak & Niladri Shekhar Majumder & Sudip Nag & Anish Bhattacharyya &
Debojyoti Roy & Arpita Chakraborty & Sohan SenGupta & Arunava Roy &
Arghya Mukherjee & Rudradip Pattanayak & Abhrajyoti Ghosh &
Dhrubajyoti Chattopadhyay & Maitree Bhattacharyya
Received: 26 March 2014 /Accepted: 10 September 2014
# Springer Science+Business Media New York 2014
Abstract The influence of temporal and spatial variations on
the microbial community composition was assessed in the
unique coastal mangrove of Sundarbans using parallel 16S
rRNA gene pyrosequencing. The total sediment DNA was
extracted and subjected to the 16S rRNA gene pyrosequenc-
ing, which resulted in 117 Mbp of data from three experimen-
tal stations. The taxonomic analysis of the pyrosequencing
data was grouped into 24 different phyla. In general,
Proteobacteria were the most dominant phyla with predomi-
nance of Deltaproteobacteria, Alphaproteobacteria, and
Gammaproteobacteria within the sediments. Besides
Proteobacteria, there are a number of sequences affiliated to
the following major phyla detected in all three stations in both
the sampling seasons: Actinobacteria, Bacteroidetes,
Planctomycetes, Acidobacteria, Chloroflexi, Cyanobacteria,
Nitrospira, and Firmicutes. Further taxonomic analysis re-
vealed abundance of micro-aerophilic and anaerobic microbi-
al population in the surface layers, suggesting anaerobic na-
ture of the sediments in Sundarbans. The results of this study
add valuable information about the composition of microbial
communities in Sundarbans mangrove and shed light on pos-
sible transformations promoted by bacterial communities in
the sediments.
Keywords Sundarbans . Microbial diversity .
454-amplicon sequencing . 16S rRNA gene
Introduction
Recent advancement in high-throughput sequencing, popular-
ly known as next-generation sequencing technology, has im-
mensely contributed in global increase in microbial diversity
and ecology studies employing samples from different envi-
ronments, e.g., soil or sediment, marine or freshwater, animal,
or insect gut. Precise description of microbial diversity and
abundance has recently been achieved using high-throughput
sequencing platforms and explored results clearly account
over 100 times more depth in the microbial diversity assess-
ment in comparison to previous reports using the traditional
culture-dependent methods [1–3]. Mangroves are among the
world’s most productive ecosystems, and microbes play a key
role in maintaining this productivity [4]. In effect, they also
constitute the largest and most diverse pool of metabolic
pathways on Earth [5] with potential biotechnological and
environmental implications [6]. It is estimated that about three
fourth of the world’s tropical and subtropical coastlines are
Electronic supplementary material The online version of this article
(doi:10.1007/s00248-014-0498-y) contains supplementary material,
which is available to authorized users.
P. Basak :S. Nag :A. Bhattacharyya :D. Roy :A. Chakraborty :
S. SenGupta :R. Pattanayak :D. Chattopadhyay (*) :
M. Bhattacharyya (*)
Department of Biochemistry, University College of Science,
University of Calcutta, 35, Ballygunge Circular Road,
Calcutta 700019, India
e-mail: djcbcg@caluniv.ac.in
e-mail: bmaitree@gmail.com
N. S. Majumder
Roche Diagnostics India Pvt. Ltd., 4C, Akash Tower, 781
Anandapur, Calcutta 700 107, India
A. Roy :A. Mukherjee :D. Chattopadhyay
Department of Biotechnology, University College of Science,
University of Calcutta, 35, Ballygunge Circular Road,
Calcutta 700019, India
A. Ghosh (*)
Department of Biochemistry, Bose Institute, Centenary Campus, P
1/12, C. I. T. Road, Scheme, VIIM, Calcutta 700054, West Bengal,
India
e-mail: abhrajyoti.ghosh@jcbose.ac.in
Microb Ecol
DOI 10.1007/s00248-014-0498-y

covered by mangrove biome. These ecosystems play numer-
ous important roles in maintaining and sustaining the environ-
ment. They also act as buffer zones between the land and sea
and are thus essential for maintenance of sea level and for
protection of the coast [7]. Moreover, these ecosystems often
serve as terminal basins for inland wastes and nutrient-rich
sediments. The unique mangrove ecosystem serves to absorb
these excess nutrients without suffering any major structural
or functional disturbance [8] and, therefore, is capable of
reducing eutrophication in adjacent coastal waters [8].
Mangroves are a complex and dynamic microbial ecosys-
tem. Periodic tidal flooding, high rainfall, and humidity, to-
gether with extremely variable environmental factors such as
salinity, light, temperature, and nutrient availability [5, 6] give
rise to a highly diverse and adaptive microbial community in
mangrove ecosystems [6, 9]. Knowledge of the microbial
diversity and the activities of microorganisms in mangrove
sediments are thus important for understanding how the man-
grove ecosystems function. This is in turn necessary to formu-
late effective management and conservation strategies [6] as
mangroves are already critically endangered or approaching
extinction in 26 out of the 120 countries having mangroves [7].
Until recently, only a limited number of studies have
attempted to analyze the microbial diversity of mangroves.
Most of these studies have concentrated on the South Amer-
ican mangroves, which contribute to about 11 % of the total
mangrove vegetation [10]. Early studies relied mostly on
culture-dependent techniques, fingerprinting methods, and
use of clone libraries to analyze phylogenetic and functional
genes [11–16]. As a result, these studies were limited to only a
small population size and did not represent the total microbial
diversity. Some studies focused on the effects of pollution, oil
spills, or anthropogenic stress factors on the mangrove micro-
bial community [6, 17–21]. However, a complete snapshot of
the total microbial diversity of a pristine mangrove ecosystem
is presently sparse. Recently, Andreote et al. have reported a
comprehensive metagenomic analysis of the Brazilian man-
groves [22]. Such metagenomic studies using next-generation
high-throughput sequencing techniques have the potential of
providing the widest, unbiased view of the microbial diversity
present in the environment [22, 23]. In addition to taxonomy
and diversity, metagenomic approaches can provide a view of
the potential metabolic pathways and community structures
present in the environment.
The Sundarbans is the largest single block of tidal halo-
phytic mangrove ecosystem in the world with 20,400 km2
(7900 sq mi) of area covered and has been recognized as a
UNESCO World Heritage site. Situated in the Ganges-
Brahmaputra river delta on the Bay of Bengal, it is shared
between West Bengal, India, and Bangladesh. Home to a wide
variety of endangered species including the Bengal tiger, the
Sundarbans play a pivotal role in protecting the coastline and
averting natural calamities. However, to our knowledge, only
two studies have attempted to investigate the biodiversity of
this vital and fragile ecosystem. Manna et al. attempted to
correlate the different components of Sundarbans ecosystem
[24], while both Ghosh et al. [12] and Chakraborty et al.
[communicated] carried out small scale studies on the micro-
bial diversity using cultivation-independent molecular ap-
proaches. Therefore, a comprehensive study of the vast mi-
crobial diversity of this unique mangrove biome is severely
lacking.
In this study, we present the first detailed description of the
microbes found at the surface and subsurface sediment layers
in three different mangrove areas in the Indian Sundarbans.
These descriptions are based on sequences of the V1–V3
region of the 16S rRNA gene as determined by 454 amplicon
sequencing (pyrosequencing). Furthermore, we examined
temporal changes in the microbial diversity of the sampling
stations during the post-monsoon (December 2011) and mon-
soon (July 2012) seasons mainly to understand the role of
climate and other parameters in shaping the sediment micro-
bial communities in Sundarbans.
Materials and Methods
Study Area and Soil Sampling
Samples were taken in triplicate from surface (2 cm) and
subsurface (16 cm) sediments of the Sundarbans mangrove
wetland, which is located on the northeastern coast of India
(Fig. 1). The samples were collected during two different
seasons (post-monsoon, December 2011, and monsoon, July
2012) from three different stations, i.e., Jharkhali (station A),
Sahidnagar (station B), and Godkhali (station C) along the
tidal gradient in close proximity of each other (Fig. 1). The
stations are representatives of different anthropogenic influ-
ences described previously. Samples were collected in tripli-
cate from each station, and individual collection was then
mixed to homogeneity to generate a representative composite
sample for further analysis. Samples were brought to the
laboratory in sealed sterile container, flash frozen in liquid
nitrogen, and stored at −80 °C.
Soil Analyses and Site Climate
Microbiological and biochemical analyses were performed
with the field moist soils. Physical and chemical analyses
were carried out with air-dried soil samples. The soil pH was
measured in 1:2.5 soil/water suspensions and found to be
alkaline (Table 1). The total organic carbon (TOC) was mea-
sured by the methods described previously [25, 26]. Briefly,
TOC in a sample was determined by combusting the air-dried
sediment sample catalytically in oxygen atmosphere into in-
strument chamber at 500–900 °C, and the resulting carbon
P. Basak et al.

dioxide gas was detected by a non-dispersive infrared (NDIR)
detector in an Aurora TOC Analyzer (O I Analytical, College
station, TX, USA) that was calibrated to directly display the
detected carbon dioxide mass. This mass was proportional to
the TOC mass in the sediment sample and calculated as total
mass of carbon per unit of sediment sample.
Conductivity and salinity were measured in situ with Hach
Portable Meters (HQ40d) (Hach Company, Loveland, CO,
USA). Measured salinity was expressed in parts per thousand
(ppt) or grams per kilogram, as described previously [27].
Nutrients like inorganic nitrogen (ammonia, nitrite, and nitrate),
soluble phosphate, and reactive silicate were measured after
quantitative extraction in respective buffering conditions follow-
ing standard methodologies [28]. Briefly, nitrite was measured
after complexing with sulfanilamide followed by a coupling
reaction with n(1-napthyl)-ethylene diaminedihydrochloride,
Fig. 1 Geographical location of the sampling stations (Jharkhali—A, Sahidnagar—B, and Godkhali—C) in Indian Sundarbans. Coordinates of the
sampling points and description of the stations are presented in the “Materials and Methods”
Table 1 Physicochemical parameters of the post-monsoon samples (December 2011) and the monsoon samples (July 2012)
Physicochemical parameters Station A (Jharkhali) Station B (Sahidnagar) Station C (Godkhali)
Post-monsoon samples
pH 7.5±0.2 7.4±0.1 7.2±0.2
Salinity (PSU) 15–18 15–17 14–16
Conductivity (ms/cm) 30–36 30–34 28–32
Temperature (°C) 24±0.5 25±0.4 26±0.5
Total organic carbon (TOC) (mg/L) AS, 8.5; A6, 8.5 BS, 5.8; B6, 12.0 CS, 2.0; C6, 7.5
Total nitrogen (N) (mg/L) AS, 1.6; A6, 0.63 BS, 1.3; B6, 1.3 CS, 1.2; C6, 1.01
Total bacterial count (cells/g) AS, 3×106
; A6, 7×106
BS, 3.5×106
; B6, 8.4×106
CS, 8.8×106
; C6, 9.6×106
Monsoon samples
pH 7.3±0.2 7.3±0.1 7.6±0.2
Salinity (PSU) 9–11 10–12 8–10
Conductivity (ms/cm) 18–22 20–24 16–20
Temperature (°C) 29±0.5 30±0.4 31±0.5
Total organic carbon (TOC) (mg/L) AS, 7.2; A6, 8.8 BS, 4.9; B6, 9.0 CS, 1.5; C6, 6.2
Total nitrogen (N) (mg/L) AS, 1.9; A6, 0.74 BS, 1.52; B6, 1.34 CS, 1.4; C6, 1.21
Total bacterial count (cells/g) AS, 2.8×106
; A6, 8×106
BS, 3.6×106
; B6, 10×106
CS, 7.2×106
; C6, 1.04×107
PSU practical salinity unit
Spatiotemporal Analysis of Bacterial Diversity

which forms an azo dye upon coupling. The resulting azo dye
was measured spectrophotometrically at 543 nm. The nitrate, in
contrary, was quantitatively reduced to nitrite using cadmium
(Cd) granules prior to measurement. The total nitrite was then
measured spectrophotometrically as described earlier, and fur-
ther subtraction of the measured value of free nitrite in the
sediment resulted in determination of nitrate in the sample.
Ammonia was measured in a reaction with hypochlorite under
alkaline condition, which results in formation of
monochloramine. In a successive reaction with phenol and
nitroprusside, monochloramine was converted into indophenol
blue, which was measured spectrophotometrically at 630 nm.
The soluble phosphate was measured using acidified molybdate
reagent, which yields phosphomolybdate complex upon reac-
tion with soluble phosphate. This complex has further reduced
into molybdenum blue and measured spectrophotometrically at
880 nm. The reactive silicate was measured using the formation
of yellow silicomolybdic acid in the presence of molybdate
under acidic condition (Figure S1).
Soil DNA Isolation
Soil DNA was extracted from 0.5 g soil subsamples using the
MoBio DNA Power Soil kit (MoBio Laboratories, Carlsbad,
CA). A NanoDrop (Thermo Scientific, Wilmington, DE,
USA) spectrophotometer was used to obtain an accurate
quantification of the extracted DNA and to measure other
important parameters for DNA quality, such as the ratio of
absorbance at 260:280 nm and 260:230 nm. Isolated soil
DNA with a ratio of absorbance at 260:280 nm and 260:230
of 1.8 and 2.0, respectively, was used to initiate amplicon
sequencing analysis.
PCR Amplification of Bacterial 16S rRNA Gene
Amplification of the V1–V3 region of the 16S rRNA gene
was performed in a 25-μl reaction mixture containing 17.50 μl
of water (Invitrogen, USA), 2.5 μl Fast Start buffer (10×),
0.5 μl dNTP (10 mM), 1.0 μl Fusion Forward Primer
(10 μM), 1.0 μl Fusion Reverse Primer (10 μM), 0.5 μl fast
start enzyme (5 U/μl fast start high PCR system, Roche), and
2 μl extracted soil DNA. The fusion primers consisted of a
template-specific sequence and a fixed sequence, as recom-
mended by the “Sequencing Technical Bulletin No. 013-
2009” (454 Life Sciences, USA). In the 5′–3′ direction, for-
ward primers contained a Roche A sequencing adaptor
(CCATCTCATCCCTGCGTGTCTCCGAC), a key sequence
(TCAG), a 10-bp Multiplex Identifier (MID) sequence, and a
template specific sequence GAGTTTGATCCTGGCTCAG.
Reverse primers contained a Roche B sequencing adaptor
(CCTATCCCCTGTGTGCCTTGGCAGTC), a key sequence
(TCAG), and a template-specific sequence ATTACCGCGG
CTGCTGG. The PCR reactions were run on a Veriti Thermal
Cycler (Applied Biosystem) under the following conditions:
initial denaturation at 94 °C for 3 min, followed by 25 cycles
of denaturation at 94 °C for 15 s, annealing at 58 °C for 45 s,
elongation at 72 °C for 1 min, and a final elongation at 72 °C
for 10 min. Samples were held at 4 °C.
Library Preparation
PCR amplicons were evaluated by electrophoresis on a 1.5 %
agarose gel. The amplicon library was purified with Agencourt
AMPure XP beads (Beckman Coulter Inc., Canada) and quan-
tified by fluorometry using the Quant-iT™
PicoGreen dsDNA
Assay Kit (Invitrogen, Burlington, ON) according to the Roche
454 “Amplicon Library Preparation Method Manual” of the
GS Junior Titanium Series (454 Life Sciences, USA). Pooled
amplicons were diluted as recommended and amplified by
emulsion PCR on a Thermal Cycler 9700 (Applied
Biosystems) according to the Roche 454 “em-PCR Amplifi-
cation Method Manual–Lib L” (454 Life Sciences, USA).
Pyrosequencing was performed for 200 cycles on a Roche
454 GS-Junior sequencing instrument according to the manu-
facturer’s protocol (454 Life Sciences, USA). All reads were
filtered using the standard read rejecting filters of the GS Junior
sequencer, namely key pass filters, dot and mixed filters, signal
intensity filters, and primer filters (454 Sequencing System
software Manual, V 2.5.3, 454 Life Sciences, USA).
454 Data Processing and Analysis
Analysis of the pyrosequence data was carried out using a
combination of mothur (software version 1.33.0) and Ribo-
somal Database Project (RDP-II). The raw data were subject-
ed to initial quality trimming using the mothur software [29],
and all reads having an average quality value of <20 were
discarded. Then, we removed the number of chimeric se-
quence by using UCHIME algorithm. Then, the chimeric free
reads were further screened for the presence of ambiguous
bases, and any reads which have a length <200 were discarded
and forward primer sequence was removed from the final
dataset. The obtained processed reads were then de-
multiplexed to separate sample based on the 10-bp MID
sequence, and any reads which do not match to the MID were
discarded. The high-quality reads were then aligned to bacterial
16S rRNA gene sequence, and clustering was performed at
97 % similarity using the RDP pipeline; a representative se-
quence from each cluster was selected based on abundance
using the sequence selection tool. The representative sequences
obtained from each cluster were then classified using the naive
Bayesian Classifier (Ribosomal Data Project, release 10) at a
bootstrap confidence of 80.
To assess the dissimilarities between the bacterial commu-
nities in the given surface and subsurface sediment samples in
two seasons, non-metric multidimensional scaling (NMDS)
P. Basak et al.

was performed. NMDS plots for communities using Jaccard
and Sorenson similarity indices (jclass and sorclass) were
created using the NMDS algorithm in mothur [29].
In addition, sample dispersion based on various environ-
mental parameters was evaluated through principal component
analysis (PCA) using Past v 2.17c software [30]. Prior to the
multivariate analysis, standardization of the entire dataset was
carried out by subtracting the mean from each observation and
divided by the corresponding standard deviation. The stan-
dardized dataset was also used to generate a cluster of the
samples according to the environmental variables using Eu-
clidean distance as the measure of similarity between samples.
Nucleotide Sequence Accession Numbers
All 454-GS Junior sequence data from this study were submit-
ted to the NCBI Sequence Read Archive (SRA) under acces-
sion numbers: SRR1032105 (ASurface_Dec11), SRR1221694
(BSurface_Dec11), SRR1231523 (CSurface_Dec11),
SRR1060346 (AS u b s u r f a c e _Dec11), SRR1224602
(BSubsurface_Dec11), SRR1231530 (CSubsurface_Dec11),
SRR1523729 (AS u r f a c e _July12), SRR1224601
(BSurface_July12), SRR1231528 (CSurface_July12),
SRR1060363 (ASu bsu rface_July12), SRR1224603
(BSubsurface_July12), and SRR1231524 (CSubsurface_July12).
Result and Discussion
Description of Sampling Sites
The Sundarbans mangrove along the Bay of Bengal has
evolved as deltaic formations through natural deposition of
upstream sediments by three major rivers: Ganges, Brahma-
putra, and Meghna and their tributaries. Other major rivers
flowing through this ecosystem are Saptamukhi, Thakuran,
Vidyadhari, Matla, and Goasaba. The geosystem in
Sundarbans is dominated by deltaic formations that are made
up of a mosaic of low-lying “islands” intersected by a com-
plex network of tidal waterways, estuaries, creeks, and mud-
flats. The Sundarbans floor varies from 0.9 to 2.11 m above
sea level. The average temperature ranges between 20 and
40 °C, with average high during May–June and low in De-
cember–January, respectively. Rainfall is heavy with humidity
as high as 80 % as it is close to the Bay of Bengal. The
subtropical monsoon lasts from June to September with an
average rainfall of 125.5–221.07 mm/month during the mon-
soon period. Samples were collected in December 2011 (with
an average rainfall of 5.4 mm/month) and July 2012 (with an
average rainfall of 293.6 mm/month). The pH was found
comparable in both the sampling seasons. Previous studies
have shown that the salinity in Sundarbans gradually
increased from post-monsoon (17.3 PSU) to pre-monsoon
periods (24.5 PSU) and reached its lowest value during the
monsoon (12.6 PSU) season. Within the water column, dis-
solved oxygen (DO) concentration was found to be high
during post-monsoon period and low in monsoon season [24].
In the present study, two sampling stations are located in
Jharkhali Island (Fig. 1). This island is surrounded on the three
sides by the Matla and the Vidyadhari rivers and by a creek,
Boro Herobhanga Khal, joining these two river flow. This
creek remains flooded by water coming from both rivers
particularly during high tide and monsoon season. The area
is dominated by typical mangrove habitat. Station A
(Jharkhali jetty; 22° 01′ 07.6139″ N, 88° 40′ 56.1910″ E) is
located in the subtidal area at the southern part of the Jharkhali
island and on the bank of Boro Herobhanga creek. This station
is inundated by sea water throughout the year. This station
consists of low-density mangrove vegetation mostly dominat-
ed by Hental Palm (Phoenix paludosa). Due to the presence of
the jetty in this sampling station, the area is under anthropo-
genic pressure mainly due to oil leakage and agri-waste dis-
posal from the inhabited area within the island. Station B
(Sahid Nagar; 22° 00′ 25.5999″ N, 88° 42′ 13.9438″ E) is
located near the subtidal preserved area on the southeastern
side of the Jharkhali Island and at the junction of Vidyadhari
river and Boro Herobhanga creek. This area is in the process
of eco-restoration because of the large-scale successful affor-
estation program. This area is densely vegetated with man-
grove plant species like Hental Palm (P. paludosa), Sundari
(Heritiera fomes), Gewa (Excoecaria agallocha), Goran
(Ceriops decandra), and Keora (Sonneratia apetala). Little
anthropogenic influences are present in station B, mainly due
to human activities and sedimentation events and could be
considered as nearly pristine mangrove sediment in the pres-
ent study. Station C (Godkhali; 22° 06′ 32.57″ N, 88° 46′
22.22″ E) is located on opposite side of the Gosaba Island
(Fig. 1), which is the last inhabited island towards the
Sajnekhali Wildlife sanctuary and Sundarbans Tiger project
area of Sundarbans reserve forest (UNESCO World Heritage
site: 1989). This station is situated in an intertidal zone with
high anthropogenic influences mainly due to the addition of
industrial effluents and oil leakage. The Commercial and
touristic use of the Jetty situated near this station further
influence the flora and fauna in the neighborhood. Mangrove
plants are scarce in this area, and non-mangrove plant species
dominate the floral counterpart indicating that the typical
mangrove ecosystem has been altered in this area.
General Statistics
To our knowledge, this is the first report of the microbial
diversity analysis in the Sundarbans sediment using pyrose-
quencing. We analyzed bacterial 16S rRNA gene (SSU)
amplicons prepared from 12 sediment samples originated

from three sampling stations at two different depths and
sampled in two seasons, i.e., post-monsoon (December
2011) and monsoon (July 2012) respectively. We generated
a pyrosequencing dataset containing 2,24,413 sequences with
an average length ranges between 494 and 530 bases, which
add up to a total of 116.98 Mb (Table S1).
Estimation of Richness and Diversity
The maximum operational taxonomic units (OTUs) detected
across the sampling stations according to the observed clusters
(sorbs) at 3 % dissimilarity was 8766 (Table 2) in the subsur-
face sample from station A, Jharkhali, during the post-
monsoon season (December 2011). The maximum amount
of OTUs observed is also reflected in the Chao values pre-
dicted for the sample (Table 2). Though the higher values of
OTUs corroborated well with the estimated Chao index, the
richness values were not necessarily followed similar trends.
In general, for the surface samples collected during the sam-
pling seasons (December 2011 and July 2012), Chao and
Shannon indices showed marginal differences. However, for
subsurface samples, the species richness decreased from De-
cember 2011 to July 2012. The rarefaction curves indicated
similar profiles of all samples (Fig. 2). We also normalized the
data considering the same number of sequences to all samples
(Table 2), and we observed clear seasonal differences between
the subsurface samples collected from three stations. To this
end, our diversity analysis revealed that despite of several
changes in the physico-chemical parameters (salinity, conduc-
tivity, and water level) during the monsoon season compared
to previous post-monsoon season, little changes appeared in
the microbial diversity and richness at the surface levels in all
three sampling stations. However, a continuous decrease in
both microbial diversity and richness at the subsurface sam-
ples during the seasonal shift from post-monsoon to monsoon
possibly exemplifies the attainment of continuous anaerobic
environment at the subsurface sediment levels during the
monsoon season.
Further, we have performed NMDS to compare the com-
munity composition using presence/absence data. NMDS em-
ploys an iterative algorithm that optimizes the position of
samples into a low-dimensional space minimizing the differ-
ence between rank-order of multivariate ecological dissimilar-
ity and distances in NMDS space (Fig. 3). From the figure, it is
easily observed that despite the low temporal variation in the
relative abundance of different phyla, surface and subsurface
communities from different sampling stations were more
closely related to each other during a season (monsoon/
post-monsoon), with only exception of Cs_July11 sample
[Godkhali (C)], than to samples from surface and subsurface
levels of a station in either of the seasons or between surface
and subsurface samples from two seasons.
In order to examine the temporal variations of the environ-
mental parameters in the sampling stations, we performed a
principal component analysis (PCA) on all environmental data
using PAST. Environmental parameters assessed for each
composite sample representing either the surface or subsur-
face origin has been summarized in Table 1. The PCA biplot
analysis reveals a distinctive pattern of the environmental
parameters recorded in the present analysis (Figure S2). Sa-
linity, conductivity, total organic carbon (TOC), and tempera-
ture are distributed along the PC1 axis (54.06 %) whereas pH
and total nitrogen (TN) are predominantly dispersed along the
PC2 axis (16.29 %) (Figure S2).
Bacterial Diversity in Mangroves Based on SSU rRNA Genes
(Taxonomic Description and Inventory)
A total of 2,24,413 representative sequences for SSU rRNA
were present in the dataset, with the values of 38,968, 77,836,
Table 2 Estimated OTU richness and diversity indices for 16S rRNA
libraries of sediment of mangrove samples
Sample ID Number Cluster Chao index Shannon index
ASurface_Dec11 11,544 2959 5711.98 6.90
BSurface_Dec11 10,303 4037 11,945.09 7.56
CSurface_Dec11 12,186 3411 6444.97 7.13
ASubsurface_Dec11 22,607 8766 22059.0 8.11
BSubsurface_Dec11 18,491 5103 12019.89 7.30
CSubsurface_Dec11 31,208 7388 15510.24 7.74
ASurface_July12 21,543 4622 9236.25 6.83
BSurface_July12 20,793 6081 13727.18 7.46
CSurface_July12 16,183 3870 7070.82 7.21
ASubsurface_July12 8248 901 1047.63 5.86
BSubsurface_July12 8712 1202 1538.12 6.10
CSubsurface_July12 7295 945 1149.29 6.25
Fig. 2 Rarefaction curves of partial sequences of 16S rDNA
P. Basak et al.

67,397, and 40,212 for Surface_Dec 2011, Subsurface_Dec
2011, Surface_July 2012, and Subsuface_July 2012, respec-
tively (Table S1). The analysis of the sediment samples from
all three stations in two seasons using pyrosequencing
grouped the sequences into 24 different phyla. In general,
Proteobacteria were the most dominant phyla that account
for about 57–72.4 % in December 2011 and 49–79 % in July
2012 samples, respectively, of the total number of phyla
detected in all three stations (Fig. 4, Table S2). In the man-
groves, higher abundance of Proteobacteria has been reported
using different molecular approaches previously [18, 22].
Furthermore, capillary sequencing-based molecular studies
in Sundarbans mangrove revealed the dominance of
Proteobacteria within the sediment bacterial community
[12]. Besides Proteobacteria, there are a number of sequences
affiliated to the following major phyla detected in all three
stations in both the sampling seasons: Actinobacteria [1.57–
3.12 % in December 2011 and 1.9–23.2 % in July 2012],
Bacteroidetes [4.23–14.26 % in December 2011 and 4.27–
15.62 % in July 2012], Planctomycetes [2.06–6.08 % in
December 2011 and 2.43–5.46 % in July 2012],
Acidobacteria [5.45–9.91 % in December 2011 and 3.41–
7.07 % in July 2012], Chloroflexi [2.53–8.10 % in December
2011 and 1.48–5.42 % in July 2012], Cyanobacteria [0.09–
4.01 % in December 2011 and 0.10–0.97 % in July 2012],
Nitrospira [0.32–3.11 % in December 2011 and 0.71–1.75 %
in July 2012], and Firmicutes [0.06–1.06 % in December
2011 and 2.30–7.96 % in July 2012] (Figure 4a, b;
Table S2). Among the distinct sediment samples collected in
two seasons (post-monsoon, December 2011, and monsoon,
July 2012), the following differences were observed: Higher
abundance of Proteobacteria was evident in the surface com-
munities in monsoon season and subsurface samples in post-
monsoon season in all the three stations; higher abundance of
Bacteroidetes in the surface communities was evident in all
three stations in both the season; Firmicutes were more abun-
dant in these stations in monsoon samples with comparatively
higher in numbers in the subsurface samples; Actinobacteria
were higher in numbers in the subsurface samples collected
from these stations in monsoon and finally a comparable abun-
dance of Cyanobacteria, Acidobacteria, Planctomycetes,
Chloroflexi, and Nitrospira was evident in three stations in both
the seasons (Fig. 4a, b). Candidate phyla Gemmatimonadetes,
Chlorobi, Spirochaetes, Verrucomicrobia, Fusobacteria,
Deferribacteres, Armatimonadetes, Tenericutes, Deinococcus-
Thermus, Lentisphaerae, TM7, OD1, OP11, BRC1, and WS3
were represented by comparatively less number of sequences
detected in the sediment samples. A full list of bacterial taxo-
nomic data can be found in the supplementary table S2. The
taxonomic groups found and their relative level of occurrence
found comparable to the data obtained by Andreote et al. [22]
and Dos Santos et al. [18], who assessed the diversity of
bacteria in the tropical mangrove sediments of Brazil.
Phylogenetic analysis of the identified proteobacterial se-
quences revealed a common distribution pattern of the classes
in all three stations in the present study. The most frequent
classes detected were Deltaproteobacteria (except for station
B), followed by Gammaproteobacteria, Alphaproteobacteria,
Betaproteobacteria, and Epsilonproteobacteria (Fig. 4c). In
both prestine mangrove sediments and mangroves under an-
thropogenic influences, dominance of the classes
Deltaproteobacteria and Gammaproteobacteria was recorded
previously using 16S rRNA gene tag sequencing technique
and metagenomics [18, 22]. In the tropical mangrove sedi-
ments located on the coast of Sao Paulo state of Brazil,
Andreote et al. [22] have performed metagenomic analysis
Fig. 3 Non-metric
multidimensional scaling plot of
all samples studied (surface and
subsurface samples of three
sampling stations, e.g., A, B, and
C in December 2011 and July
2012, respectively). Pairwise
abundance-based Jaccard indices
were used to construct the plot

where they detected higher abundance of the classes
Deltaproteobacteria and Gammaproteobacteria. Further-
more, Dos Santos et al. [18] have used pyrosequencing of
16S rDNA tags to show dominance of these group of
proteobacterial classes in the sediments of “Restinga da
Marambaia” mangrove in Rio de Janeiro, Brazil, under natural
conditions and after simulated oil spills. Taken together, bac-
terial community analysis of the tropical mangrove sediments
revealed a universal dominance of the proteobacterial classes
Deltaproteobacteria and Gammaproteobacteria both under
pristine conditions and under anthropogenic interference.
The higher abundance of Deltaproteobacteria in sea water
and in marine sediments has been proposed to be similar to the
mangrove ecosystems, where frequent anaerobic conditions
facilitate in selection of microaerophilic/anaerobic sulfate-
reducing organisms belonging to deltaproteobacterial class
[20]. In general, oxygen penetration in the sediment remains
limited to the upper few centimeters, and the subsurface
sediment beneath the surface is shown to be anaerobic in
nature. Predominance of Deltaproteobacteria at the surface
and subsurface sediment samples collected in the present
study clearly demonstrates the anaerobic nature of the sedi-
ments both at the subtidal and intertidal regions of Sundarbans
especially during the monsoon season.
The Deltaproteobacteria were dominated by orders
Desulfobacterales, Desulfuromonadales, Myxococcales, and
Bdellovibrionales. Abundance of Desulfobacterales,
Desulfuromonadales, and Bdellovibrionales in the sediment
samples collected from three stations in general indicates
anaerobic nature of the sediment. Previous studies have shown
that the Deltaproteobacteria were dominant due to anaerobic
condition of the mangrove sediment that drives selection of
specific microbial groups such as sulfur/sulfate-reducing bac-
teria belonging to phylum Deltaproteobacteria [20]. In the
present study, the Myxococcales, representing the only aerobic
deltaproteobacterial order, found mostly abundant in the
surface-derived samples from station B in both the seasons
indicates comparatively less anaerobic nature of the samples
Fig. 4 Composition of different phyla based on the classification of
partial rRNA gene sequences of bacteria from Sundarbans sediments
using RDPII classifier (v 2.2). a Distribution of phyla in post-monsoon
(December 2011) sediments, b Distribution of phyla in monsoon (July
2012) sediments. c Differential proportion of sequences assigned within
the phylum Proteobacteria
P. Basak et al.

collected from this station. To this end, we believe that the
station B (Sahidnagar), which is under eco-restoration, has
sufficient mangrove vegetation that further influenced the
microbial abundance and diversity, as evident from the present
dataset. It has been proposed that the activities of the man-
grove roots provide a source of oxygen and interfere directly
to the redox potential of the mangrove sediment [31]. Due to
eco-restoration, station B might receive more available oxy-
gen compared to other two stations. In contrary, in both
stations A (Jharkhali) and C (Godkhali), vegetation has been
heavily affected due to anthropogenic influences, such as oil
leakage and addition of agri-industrial wastes, which ultimate-
ly reduced the number of mangrove trees and most importantly
not all the mangrove plant species are present in these stations.
This scenario might have led to higher abundance of anaerobic
sulfur-reducing bacteria such as Desulfobacterales,
Desulfuromonadales, and Bdellovibrionales in stations A and
C, respectively.
After Deltaproteobacteria, Gammaproteobacteria were
the most abundant proteobacterial class in all the three stations
in post-monsoon samples (Fig. 4c). However, in monsoon
samples, Gammaproteobacteria and Alphaproteobacteria
both shared equal abundance after Deltaproteobacteria in
these stations (Fig. 5a). Neither depth dependent (spatial)
nor any seasonal differentiation was observed with respect to
the abundance of Gammaproteobacteria in the sampling sta-
tions. Within our dataset, the Gammaproteobacteria were
dominated by the orders Chromatiales, Legionellales, and
Xanthomonadales (Fig. 5c). Chromatiales includes a group
of anaerobic bacteria, commonly known as purple sulfur
bacteria, which are capable of photosynthesis by oxidizing
hydrogen sulfide to sulfide and sulfate. Chromatiales are
commonly reported in anoxic lake sediments and in other
aquatic habitats including mangrove sediments and anoxic
conditions are primary pre-requisites for their sulfur-
photolithoautotrophy [32]. In contrary, members of the order
Legionellales are not commonly encountered in mangrove
sediments and they comprised two families, Legionella and
Coxiella, both are involved in human disease [33]. Abundance
of Legionellales in Sundarbans sediments clearly indicates
human intervention in this ecosystem. Besides these orders
of Gammaproteobacteria, a number of sequences affiliated to
the orders Pseudomonadales, Enterobacteriales,
Methylococcales, Alteromonadales, Oceanospirillales, and
Thiotrichales were identified within the present dataset. In
their study on Brazilian mangrove sediments, Dos Santos
et al. [18] have shown that several orders within the
Gammaproteobacteria show major shift after oil contamina-
tion. Especially, the order Chromatiales was shown to be
sensitive as it was dominant before oil contamination and
decreased significantly after oil contamination. Within
Sundarbans sediments, however, we could see a constant
dominance of the order Chromatiales in all three sampling
stations with different history of anthropogenic activities
Fig. 5 Composition of different classes based on the classification of partial 16S rRNA sequences of Proteobacteria from Sundarbans sediment using
RDPII classifier (v 2.2). Deltaproteobacterial orders (a), Alphaproteobacterial orders (b), and Gammaproteobacteria orders (c)

possibly confirming the fact that although oil and hydrocarbon
contaminations are evident in Sundarbans, especially in sta-
tions A and C, alteration of the abundance of an order requires
considerable concentration of those contaminants to be added
into the Sundarbans mangrove sediment systems. Besides, no
representatives of the orders Alteromonadales and
Oceanospirillales were detected in the present study. These
gammaproteobacterial orders were shown by Dos Santos et al.
[18] to be dominant after oil contamination in the Brazilian
mangrove sediment.
Alphaproteobacteria were dominated by the orders
Rhodospirillales, Rhodobacterales, Rhizobiales, and
Sphingomonadales (Fig. 5b). Among the alphaproteobacterial
orders, Rhodospirillales was the most abundant and recorded
to be maximum in the monsoon dataset from stations A
(71.7 %) and B (63.1 %). In general, the order
Rhodospirillales is represented by two families, e.g., photo-
synthetic non-sulfur Rhodospirillaceae and heterotrophic
acetic acid synthesizer, Acetobacteraceae. Besides
Rhodospirillales, Rhizobiales representing nitrogen fixing
and symbiotic bacteria, Rhodobacterales representing primary
colonizer on the temperate ocean sediments and coastal water
columns [34], and Sphingomonadales representing the aro-
matic hydrocarbon-degrading bacteria [35] were the dominant
alphaproteobacterial orders detected in all three stations in
both the seasons. Besides the dominant alphaproteobacterial
orders, a number of sequences affiliated to the orders
Caulobacterales, Kordiimonadales, Rickettsiales,
Sneathiellales, and Kiloniellales were detected within the
present dataset.
Betaproteobacterial sequences were dominated by the or-
ders Burkholderiales and Rhodocyclales. In Sundarbans sedi-
ment, members of the order Burkholderiales with diverse
functional attributes have been reported previously [12, 36].
Most of the identified members of Rhodocyclales order include
organisms that reside in aquatic habitat and prefer oligotrophic
conditions. Besides these orders, Nitrosomonadales,
Hydrogenophilales, Methylophilales, and Neisseriales were
also detected with the dataset.
Actinobacterial sequences were detected in all the three
stations in both the seasons under study. Interestingly,
actinobacterial sequences are more abundant in the subsurface
samples in monsoon samples. This might be due to the ad-
sorption of Actinobacteria to the mineral particle surface, and
the salinity in such micro-niches was lower than what was
measured for the subsurface sediment samples. However, the
diversity was found lower at the surface confirming the eco-
logical principle that more extreme environment, e.g., salinity
in this case, affects the diversity of Actinobacteria. Further-
more, during the monsoon season, an increased addition of the
freshwater/rain water through the major rivers in this area
further reduces the local salinity in these sampling stations
(approx. 12 PSU). The phylum Actinobacteria was dominated
by orders Actinomycetales and Acidimicrobiales. Besides,
members of the following orders were also detected in limited
number with the sediment: Solirubrobacterales,
Rubrobacterales, Nitriliruptorales, Coriobacterales,
Euzebyales, and Spaerobacterales. Actinomycetales was
found highly abundant at the subsurface samples in the mon-
soon season. Previous analyses on diversity of Actinobacteria
in saline sediments revealed detection of Acidimicrobiales in
low-salinity sediments and absence in higher salinity sediment
samples [37]. In Sundarbans sediment, the observed salinity
remained in the lower side (12–20 PSU) possibly due to the
addition of continuous freshwater and this has further sug-
gested the reason for domination of halo-tolerant
Acidimicrobiales in this sediment. Previous culture-
dependent analyses in Indian Sundarbans mangrove have
identified and characterized several salt-tolerant antibacterial
Streptomyces spp. [38].
Acidobacteria were found evenly distributed in all three
sampling stations in both seasons. Previous studies have
shown that phylogenetic evenness for Acidobacteria largely
depends on the soil pH [39, 40]. The relative abundance was
shown strongly correlated with the soil pH, with
Acidobacteria representing larger portion of soil bacterial
communities at low pH soils. In Sundarbans sediments,
pH remains nearly neutral and uniform throughout the
year (pH 7.3–7.8). This has further corroborated with
the findings of even distribution of Acidobacteria in
these sampling stations. In marine ecosystems, the abun-
dance of Acidobacteria has been reported previously
[22, 41]. In the Red Sea, for example, Acidobacteria
were reported in the middle and deep layers of coral
reef sands where suboxic and anoxic conditions are
being maintained [41]. Such findings not only supported
acidobacterial distribution in Sundarbans but also corre-
lated well to the findings that the sediments of Sundarbans
are suboxic in nature.
Representative sequences affiliated to candidate phyla
Planctomycetes, Bacteroidetes, Nitrospira, Chloroflexi,
Cyanobacteria, and Firmicutes were ubiquitous in all three
stations both at the surface and at subsurface levels of the
sediments. Planctomycetes sequences were represented by
classes Phycisphaerae and Planctomycetacia. Bacteroidetes
sequences were dominated by the members of the classes
Flavobacteria and Sphingobacteria, which corroborate well
with our previous culture-independent capillary sequencing-
based analysis of the bacterial population in these three sta-
tions [communicated]. Among the Firmicutes, Bacilli, and
Clostridia orders were dominating in all the stations.
Chloroflexi and Nitrospira sequences were dominated by
orders Anaerolineae and Nitrospira, respectively. Only a few
cyanobacterial sequences were detected in each of these sam-
pling stations, and most importantly, we could not assign
cyanobacterial sequences below the phylum level.
P. Basak et al.

The number of sequence reads related to candidate divi-
sions TM7, WS3, OD1, OP11, and BRC1 was detected in the
sediment samples from both seasons. To date, no cultivated
representatives exist representing either TM7, WS3, or OD1
candidate divisions. Thus far, no distinct ecological attribute
has been assigned to members of the candidate division TM7
that are commonly found in a wide range of environments,
including terrestrial (rhizosphere, soils, and peat bog) and
aquatic (groundwater, freshwater, sea water, and deep-sea
sediments) habitats [42]. Members of the candidate division
WS3 were detected only in the methanogenic environments
[43] and OD1 division is widespread in environments domi-
nated by sulfur, such as marine environments and sulfureta
[42]. OP11 division is commonly detected in terrestrial and
marine environments, and recent partial genome sequencing
analysis of one of the members belonging to this division
revealed several eco-physiological aspects in this candidate
division [44, 45]. Candidate division BRC1 was originally
detected in extreme, low-diversity environments, and the eco-
logical role of this candidate division is still yet to be
unraveled [42].
Conclusion
This is the first 16S rRNA gene amplicon sequencing analysis
of microbial diversity of Sundarbans, the unique tiger land
mangrove of the world in the backdrop of climate change. The
massive parallel 454 amplicon sequencing of 12 samples of
the surface and subsurface sediments and data analysis
unraveled the complexity of the bacterial diversity in the
sediment samples. Furthermore, detected diversity of the bac-
terial community composition has clearly provided novel
insights into the ongoing biogeochemical processes associated
with the regular deposition of sediment in this coastal man-
grove. Moreover, this study also unfolds the bacterial com-
munity structure during seasonal changes between permanent-
ly inundated sediments and sediments submitted to seasonal
dewatering. To this end, an increased understanding of micro-
bial community variation with respect to seasonal changes
rather raise the questions of whether this observed composi-
tion changes during monsoon and post-monsoon would con-
fer a better resistance to the subsequent drying stress for
microbial communities in seasonally dewatered sediments or
such changes reflected an alteration of microbial structure
with respect to changes in the biogeochemical cycling of
nutrients. Further analyses, however, are essential for better
understanding of the sediment biogeochemical cycles and
their relationship to the microbial community pattern in the
sediment. This work is also important in building a database
and an understanding of how microbial communities vary
geographically and with anthropogenic intervention.
Acknowledgments The authors would like to acknowledge the instru-
ment facility provided by UGC-CAS, DST–FIST, DBT-IPLS, World
Bank, ICZM project in the Department of Biochemistry, University of
Calcutta, India. We acknowledge Mr. Tapas Paul, World Bank, for his
continuous support and enthusiasm regarding our study in Sundarbans.
The expenditure of this work and the research fellowships of P.B., S.N.,
A.B..., D.R., A.C., and R.P. were supported by the ICZM project, World
Bank. A.G. was supported by Ramanujan Fellowship from the Depart-
ment of Science and Technology, India (SR/S2/RJN-106/2012). The
authors thank Ms. Anwesha Haldar, Department of Geography, Univer-
sity of Calcutta, for making a working map of the study sites in
Sundarbans.
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