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EISSN 2602-473X
AQUATIC SCIENCES AND ENGINEERING
Aquat Sci Eng 2020; 35(2): 52-56 • DOI: https://doi.org/10.26650/ASE2020652073 Research Article
Bacterial Community Composition of Sapanca Lake During a Cyanobacterial
Bloom
E. Gözde Özbayram1 , Latife Köker1 , Reyhan Akçaalan1 , Orhan İnce2 , Meriç Albay1
Cite this article as: Özbayram, E. G., Köker, L., Akçaalan, R., İnce, O., Albay, M. (2020). Bacterial community composition of sapanca lake during a
cyanobacterial bloom. Aquatic Sciences and Engineering, 35(2), 52–56.
ORCID IDs of the authors:
E.G.O. 0000-0002-5416-0611;
L.K. 0000-0002-9134-2801;
R.A. 0000-0002-0756-8972;
O.I. 0000-0001-5028-8872;
M.A. 0000-0001-9726-945X
1Istanbul University, Faculty of
Aquatic Sciences, Department of
Marine and Freshwater Resources
Management, Istanbul, Turkey
2Istanbul Technical University,
Faculty of Civil Engineering,
Department of Environmental
Engineering, Istanbul, Turkey
Submitted:
28.11.2019
Revision Requested:
17.01.2020
Last Revision Received:
20.01.2020
Accepted:
21.01.2020
Correspondence:
E. Gözde Özbayram
E-mail:
gozde.ozbayram@istanbul.edu.tr
©Copyright 2020 by Aquatic
Sciences and Engineering
Available online at
https://dergipark.org.tr/ase
ABSTRACT
Microbial community compositions and functions of freshwater ecosystems vary due to the envi-
ronmental parameters and water chemistry. Transient bloom events play a crucial role on the
community profiles. In this study, a specific focus was set to provide a snapshot of the bacterial
community composition in Lake Sapanca, associated with cyanobacterial bloom by high through-
put sequencing method. For this purpose, a sample was collected in the shore of Lake Sapanca
during a cyanobacterial bloom, and the bacterial community profile was examined by 16S rRNA
amplicon sequencing using the Illumina MiSeq platform. Cyanobacteria represented 94% of the all
reads. The bacterial community was re-calculated to evaluate the bacterial diversity in detail by
filtering cyanobacterial sequences. The community was dominated by Proteobacteria (44%) and
Bacteroidetes (33%) species which are abundant in freshwater ecosystems having an ability to de-
grade complex organics. Among the classified genera, Flavobacterium and Rheinheimera domi-
nated the bacterial community suggesting a strong link between those species and the cyanobac-
terial bloom. The experimental work presented here provides one of the first investigations of total
bacterial communities in Lake Sapanca by the high throughput sequencing method. Further work
is needed with more sampling points and time series to fully understand the bacterial diversity and
dynamics.
Keywords: Bacterial community, cyanobacterial bloom, illumina miseq, Sapanca lake, 16S rRNA
INTRODUCTION
Freshwater habitats have a vital role in global
biogeochemical cycles. However, cyanobacteri-
al blooms are getting more widespread in
freshwater lakes due to nutrient runoff and cli-
mate change, and have become a serious risk
on the sustainability of these ecosystems (Cai
et al., 2014; Liu et al., 2019) which cause difficul-
ties to secure and maintain ecosystem health
(Woodhouse et al., 2016).
Microorganisms drive crucial functions in the
freshwater ecosystems and have a role in the
degradation of organic materials, energy con-
version and nutrient recycling, overall contrib-
ute to the ecosystem balance (Su et al., 2017a;
Zhu et al., 2019). Microbial community compo-
sitions and functions vary due to the water
chemistry, nutrient concentrations, hydrody-
namic stability and climate (Steffen et al., 2012),
and they respond to environmental alterations
quickly being critical indicators (Su et al.,
2017b). Furthermore, community structures are
highly dependent on transient bloom events
which affect the abundance and activity of
these communities (Eiler & Bertilsson, 2004).
Since microbial communities are key players on
biogeochemical cycles, there is still limited in-
formation on the characterization and function
of bacterial communities inhabiting freshwater
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Aquat Sci Eng 2020; 35(2): 52-56
Özbayram, Köker, Akçaalan, İnce and Albay. Snapshot of Bacterial Diversity in Sapanca Lake
ecosystems, especially during bloom events (Eiler & Bertilsson,
2004; Steffen et al., 2012).
Recent developments in advanced molecular genetic technolo-
gies enable us to have deep information about microbial diversi-
ty and interactions between the community structure and their
environment (Nakatsu, Byappanahalli, & Nevers, 2019). Since the
16S rRNA gene is considered as a molecular marker of prokary-
otes and used to investigate microbial communities in a wide va-
riety of habitats, it has also been used to asses microbial commu-
nity dynamics during cyanobacterial blooms (Nakatsu et al.,
2019; Zhu et al., 2019).
Lake Sapanca, a freshwater lake, is located in the northeast of the
Marmara Region of Turkey. It is a source for drinking water for the
cities of Sakarya and Kocaeli, as well as for industrial usage
(Akçaalan et al., 2014; Leroy & Albay, 2010), and has been moni-
tored according to the presence of cyanobacteria and cyanotox-
in for years to indicate the ecological status of the lake, and it has
now a well-established cyanobacteria diversity (Akçaalan et al.,
2007; Akçaalan et al., 2014). Moreover, there are some studies in
the literature on Lake Sapanca which evaluated the total bacteri-
al counts, pathogenic bacteria and petroleum-resistant bacteria
presence by a culture dependent technique (Altuğ et al. 2006;
Çiftçi Türetken et al., 2018), and seasonal dynamics of pathogens
by the microarray method (Akçaalan et al., 2018). So far, there
have been no attempts to examine the total bacterial communi-
ty structure in Lake Sapanca, and it has remained unclear. This
study, therefore, sets out to assess the bacterial community com-
position in Lake Sapanca during a cyanobacterial bloom by the
high throughput sequencing method. The experimental work
presented here provides one of the first investigations into the
bacterial community profile of Lake Sapanca by a next genera-
tion sequencing platform.
MATERIALS AND METHODS
Physico-chemical characterization
A surface cyanobacterial bloom occurred in Lake Sapanca on 8
April, 2019 and the sample was collected during the bloom event
in the shore. pH, temperature and dissolved oxygen were mea-
sured with a portable multiparameter (6600, YSI, USA) on the
sampling date.
DNA extraction and amplicon sequencing
First, 10 mL the sample was filtered with a 0.22 µm filter, and to-
tal DNA was extracted from that filter paper using a MoBio Pow-
erWater® DNA Isolation Kit (MoBio Laboratories, Inc., CA, USA)
according to the manufacturer’s protocol. The DNA quantifica-
tion was performed by NanoDrop 1000 (Thermo Fisher Scientific,
Inc., DE, USA), and the extracted DNA was stored at -20°C for
further analysis.
The bacterial community composition of the sample was ana-
lyzed with the ZymoBIOMICS™ Service - Targeted Amplicon Se-
quencing (Zymo Research, Irvine, CA). 16S ribosomal RNA gene
targeted sequencing was performed using the Quick-16S™ NGS
Library Preparation Kit (Zymo Research, Irvine, CA). Shortly, the
16S primers used amplified the V3-V4 region of the 16S rRNA
gene (341f-CCTACGGGNGGCWGCAG and 805r-GACTACHVG-
GGTATCTAATCC). The PCR products were quantified with qPCR
fluorescence readings, and pooled together based on equal mo-
larity. The final pooled library was cleaned up with Select-a-Size
DNA Clean & Concentrator™ (Zymo Research, Irvine, CA), then
quantified with TapeStation® and Qubit®. The final library was
sequenced on Illumina® MiSeq™ with a v3 reagent kit (600 cy-
cles). The sequencing was performed with >10% PhiX mix and in
paired-end mode.
The Dada2 pipeline was used to infer the amplicon sequences
from raw reads (Callahan et al., 2016). The raw sequence reads
were trimmed with Trimmomatic-0.33 (Bolger, Lohse, & Usadel,
2014). Whereas, SeqPrep were used to assemble the two paired-
end reads to have a complete amplicon sequence with (https://
github.com/jstjohn/SeqPrep). Usearch (v. 6.1) was used to check
and remove chimeric amplicon sequences (Edgar, 2010) in ref
mode against a curated database (http://drive5.com/uchime/
rdp_gold.fa). Amplicon sequences smaller than 320 bp were re-
moved. For each sample, up to 40,000 sequences were randomly
sampled to reduce the potential bias caused by uneven sam-
pling. These amplicon sequences were compiled, clustered and
analyzed with Qiime 1.9.1 (Caporaso et al., 2010). OTUs were
picked by the workflow of pick_open_reference_otus.py using
the GreenGene database (gg_13_8) as reference database. Sin-
gleton OTUs were removed. Taxonomy assignment was per-
formed with Qiime v.1.9.1 (Caporaso et al., 2010). The microbial
community structures were shown by Krona graphs (Ondov,
Bergman, & Phillippy, 2011; Ozbayram et al., 2017).
RESULTS AND DISCUSSION
The physical properties of Lake Sapanca during the bloom are
depicted in Table 1. The water was slightly alkaline and the char-
acteristics of the lake matched those observed in early studies
(Akçaalan et al., 2007, 2014) showing a typical O2 saturation level
during the bloom event with high dissolved oxygen.
The number of raw reads and after filtration were 78,735 and
65,748, respectively and the rarefaction curve reached a plateau.
The microbial community composition of the bloom sample was
presented at multiple taxonomic levels by a Krona chart in Figure
1. The microbial community comprised 7 phyla, however, the mi-
crobial community was dominated by Cyanobacteria members,
representing 94% of all sequences as it was expected. At the ge-
nus level, all of the Cyanobacteria reads belonged to Planktothrix.
The results are in keeping with previous observational studies,
Table 1. Physical properties of Lake Sapanca during the
cyanobacterial bloom
Parameter Lake Sapanca
Temperature (°C) 15.9
pH 8.51
Conductivity (uS/cm) 215.6
Dissolved Oxygen (mg/L) 13.57
O2 Saturation (%) 130.3
54
Aquat Sci Eng 2020; 35(2): 52-56
Özbayram, Köker, Akçaalan, İnce and Albay. Snapshot of Bacterial Diversity in Sapanca Lake
which showed that the cyanobacterial bloom was mainly caused
by Planktothrix rubescens in Lake Sapanca (Akçaalan et al., 2007,
2014). Proteobacteria and Bacteroidetes were the following phyla,
representing 5% of the microbial community. The results are in
agreement with those of previous studies, indicating that the bac-
terial community was dominated by Proteobacteria, Actinobacte-
ria, and Bacteriodetes during the phytoplankton bloom (Berg et
al., 2009; Eiler, Bertilsson, & Centre, 2007; Zhu et al., 2019).
To understand the microbial community diversity better, the bac-
terial reads were evaluated excluding Cyanobacterial sequenc-
es, and re-calculated relative abundances of the bacterial com-
munity are depicted in Figure 2. As it is clear from the chart, more
than half of the reads were represented by Proteobacteria (44%)
and Bacteroidetes (33%). Actinobacteria was the third dominant
phylum, representing only 5% of the bacterial community, fol-
lowed by Planctomycetes (5.3%), Verrucomicrobia (5%) and Gem-
matimonadetes. Proteobacteria and Bacteroidetes have the abil-
ity to become abundant in the presence of bioavailable organic
material, and dominate the community (Eiler et al., 2007). The
members are known to be able to decompose complex organic
materials, and the peptides of the organic carbon plays a crucial
role with their ABC membrane transporters which may support
toxin degradation (Lezcano et al., 2017).
Within Proteobacteria, Betaproteobacteria was the dominant
class, representing almost half of the total reads in Proteobacte-
ria, followed by Gammaproteobacteria and Alphaproteobacte-
ria. Betaproteobacteria was found as abundant in freshwater
ecosystems (Zhu et al., 2019). Flavobacteriia (29%) was the domi-
nant class within Bacteroidetes, and showed a relatively high
abundance compared to Sphingobacteriia (2%) and Cytophagia
(2%). Most of the Flavobacteriia members are chemoorgano-
trophs, and are able to use complex organic materials as a car-
bon source (Parulekar et al., 2017). In terms of family level, 25% of
the bacterial community was represented by Flavobacteriaceae
(phylum: Bacteroidetes), which was by far the most abundant
among all the families. Comamonadaceae (phylum: Proteobac-
teria) was the second most abundant family, representing 14% of
the total reads. Moreover, 9% of the bacterial community was as-
signed to Chromatiaceae (phylum: Proteobacteria). The families
Burkholderiaceae, Sphingomonadaceae, Pseudomonadaceae,
Cryomorphaceae and Phycisphaeraceae together represented
18% of the bacterial community.
The overgrowth of Cyanobacterial species causes bacterial com-
munity changes with an increasing abundances of the members
which have an ability to decompose organic matter and toxic
compounds (Lezcano et al., 2017; Su et al., 2017b). Thus, it is ex-
pected to observe Bacteroidetes members in high abundance
during the phytoplankton blooms (Eiler et al., 2007). Among the
classified genera, Flavobacterium (phylum: Bacteroidetes) domi-
nated the bacterial community, accounting for 25% of the total
sequences (Figure 3). The high abundance suggests that a strong
link may exist between the bloom and Flavobacterium species
which can degrade various biomacromolecules and carbohy-
drates. The members can react to transient nutrient loads imme-
diately, which is a result of phytoplankton blooms (Buchan, Le-
Cleir, Gulvik, & González, 2014). Whereas some of Flavobacteri-
um species have a potential to degrade cyanotoxin, some of
them are reported to have a role in denitrification (Parulekar et
al., 2017). Rheinheimera was the second most dominant genus,
representing 9% of the bacterial community. Rheinheimera has
also higher abundances in the aquatic environments and can hy-
Figure 1. Krona chart illustrating the microbial community
composition.
Figure 2. Krona chart illustrating the bacterial community
composition (excluding Cyanobacteria).
55
Aquat Sci Eng 2020; 35(2): 52-56
Özbayram, Köker, Akçaalan, İnce and Albay. Snapshot of Bacterial Diversity in Sapanca Lake
drolyze organic materials. It is speculated that, Rheinheimera
species can regulate phosphate exchange in the cyanobacterial
mucilage capsule resulting in the enhancement of Microcystis
growth (Parulekar et al., 2017).
CONCLUSION
The present research explores, for the first time, the bacterial
communities associated with cyanobacterial blooms in Lake Sa-
panca by 16S rRNA targeted amplicon sequencing. This study
has shown that the bacterial community was dominated by
bloom-associated phyla, Proteobacteria and Bacteroidetes, hav-
ing the ability to grow on complex organic materials.
These findings provide a snapshot of the bacterial communities
in Lake Sapanca during the cyanobacterial bloom. Further work
is needed, with more sampling, to fully understand the bacterial
diversity and dynamics.
Conflict of Interest: The author has no conflicts of interest to de-
clare.
Ethics Committee Approval: Ethics committee approval is not
required.
Financial Disclosure: The authors declared that this study re-
ceived no financial support.
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