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Complete genome of Microcystis aeruginosa FBCC-A68 isolated from wetland, South Korea
Korean J. Microbiol. 2024;60(2):95-97
Published online June 30, 2024
© 2024 The Microbiological Society of Korea.

So-Jeong Kim1, Hyeonjung Yu1, Jungho Ryu1, Bok Yeon Jo2, Seung Won Nam2*, and In-Hyun Nam1*

1Mineral Resources Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Republic of Korea
2Bio-resources Bank Division, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
Correspondence to: *(S.W. Nam) E-mail:;
Tel.: +82-54-530-0892; Fax: +82-54-530-0889 /
(I.H. Nam) E-mail:;
Tel.: +82-42-868-3164; Fax: +82-42-868-3418
Received April 11, 2024; Revised April 15, 2024; Accepted April 16, 2024.
Here, we reported a complete genome of a new strain of Microcystis aeruginosa, the most representative cyanobacteria that forms toxic blooms. Strain FBCC-A68 was isolated from wetland, Republic of Korea. The genome is approximately 5.8 Mb, consisting of 5,241 protein-coding genes including genes related to synthesis for gas vesicle and microcystin. This strain might have an advantage in competition at low CO2 levels by having a high affinity-bicarbonate transporter (SbtA). Identifying the characteristics of the M. aeruginosa genome of the new strain can help us understand harmful blooms in the environment.
Keywords : Microcystis, bloom, microcystin, wetland

Microcystis is a common harmful cyanobacterium, widespread and dense-bloom-forming in freshwater around the world. It threatens water supplies and human and animal health because many strains can produce the toxin, microcystin (Merder et al., 2023). According to drinking water health advisories for cyanotoxins by Environmental Protection Agency (EPA), microcystin was set at less than 0.3 µg/L for infants (US EPA, 2015).

Due to its complex and controversial taxonomy, analysis of the genome of Microcystis was important for classification. Furthermore, the high genomic plasticity of Microcystis aeruginosa was predicted to be a strategy for adaptation to various environments (Cai et al., 2023). In this study, we aim to expand the genome information of Microcystis by providing new genome information of M. aeruginosa isolated from a wetland, Republic of Korea.

A xenic culture of M. aeruginosa FBCC-A68 (relative abundance was over 40% based on 16S rRNA gene using microbial community analysis) was obtained from the Freshwater Bioresources Culture Collection (FBCC), Republic of Korea ( Cells were routinely cultured in BG11 medium (sigma) at 25°C under a day-night cycle (16 h-8 h) and bubbled with air. The cultures of 10 ml for DNA extraction were collected by centrifugation and DNA was extracted using CTAB buffer method (Hurt et al., 2001). The obtained DNA was sequenced by Pacbio Sequel II and Illumina HiSeq at Macrogen Inc. Each library was constructed by [3.0] PacBio Microbial library kit and TruSeq Nano DNA library kit, respectively. De novo assembly was performed with HiFi Reads by SMRT Link v11 and then, errors were corrected by HiSeq reads. Among assembled scaffolds, one contig was assigned as M. aeruginosa. The selected contig was annotated using NCBI Prokaryotic Genome Annotation Pipeline (Tatusova et al., 2016). Average nucleotide identity (ANI) and average amino acid identity (AAI) between type strain and FBCC-A68 were calculated by ANI Calculator (Yoon et al., 2017) and CompareM (, respectively. The genome of strain FBCC-A68 is 5,868,208 bp and is composed to have 5,241 protein-coding genes, 6 rRNAs and 42 tRNAs with 42.7% G + C content (Table 1). Compared to the genome of type strain NIES-843, the genome of strain FBCC-A68 is 25kb longer (Kaneko et al., 2007). The values of ANI and AAI were 96.9% and 97.1%, respectively. It showed that FBCC-A68 was a new strain of M. aeruginosa.

General features of genome sequence of M. aeruginosa FBCC-A68

Features FBCC-A68
Length 5,868,208 bp
G + C 42.7
Total genes 5,785
Total coding genes 5,241
rRNAs 2, 2, 2 (5S, 16S, 23S)
tRNAs 42
Accession number CP136248

The genome of strain FBCC-A68 had the multiple uptake systems for inorganic carbon (Ci): high-affinity ATP-dependent HCO3- transporter (BCT1, RVR34_02250-02265) and high-affinity Na+-dependent HCO3- transporter (SbtA, RVR34_19325) but fragmented low-affinity Na+-dependent HCO3- transporter (BicA, RVR34_19320). Therefore, strain FBCC-A68 was belonging to bicA lacked group (genotype II) like type strain NIES-843 (Sandrini et al., 2015). In the previous study showed that specialist with only sbtA was advantageous in the competition at low CO2 levels (Sandrini et al., 2014). Through the mentioned transporters the accumulated inorganic carbon is transferred to the carboxysome and carbon fixation occurs (Price, 2011). Genes encoding carboxysome for CO2 concentrating mechanism (CCM) and RuBisCO for carbon fixation were clustered in the genome of FBCC-A68 (CcmK2KLMN and rbcLXS, respectively, RVR34_03405-RVR34_03440).

The gas vesicles (GVs) provide buoyancy, allowing Microcystis cells to float at the surface of various water environments, position them under the advantage of the surrounding light and nutrient conditions (Mlouka et al., 2004). GVs are an important factor triggering the Microcystis blooms (Wu et al., 2023). Eleven of these are organized in one operon, gvpAIAIICNJXKFGVW (RVR34_14005-14055). The amino acid sequence of GvpA, a small hydrophobic protein, is known to be highly conserved (Kaneko et al., 2007), and the sequences of this strain and NIES-843 are actually identical (100% identity). However, FBCC-A68 had two genes for GvpA (AIAII) and NIES-843 had three genes for GvpA (AI-AIII).

Genes coding for microcystin synthesis are located with one transposase in between mcyCBA (RVR34_14465-14475) and mcyDEFGHIJ (RVR34_14485-14515). The discovery of the transposase in the mcy gene cluster was known to result from instability and genetic diversity of mcy genes in natural populations (Kaneko et al., 2007). In addition to toxin production, this strain can also affect arsenic transformation. The genome included gene coding for arsenite methyltransferase (RVR34_21790), to catalyze the formation of methylated arsenite from As (III). Genes related to heavy metal detoxification were also detected: chromate efflux transporter (RVR34_18905) and mercury reductase (RVR34_09530).

The genomic flexibility Microcystis is known to important to maintain blooms in the environment (Meyer et al., 2017), the new genome information of Microcystis might be help to understand harmful blooms.

Nucleotide sequence accession numbers

The sequence of M. aeruginosa FBCC-A68 has been deposited in GenBank under accession number CP136248. Cells of strain FBCC-A68 is available from the collection of FBCC.

적 요

본 연구에서 유해 녹조를 일으키는 대표적 남세균인 Microcystis aeruginosa의 새로운 균주의 유전체 정보를 보고한다. FBCC-A68균주는 한국의 습지에서 분리되었다. 유전체는 약 5.8 Mb이며, 기낭 및 마이크로시스틴 합성에 관련된 유전자를 포함하여 5,241개의 단백질 코딩 유전자로 구성된다. 이 균주는 높은 친화성 중탄산염 수송체(SbtA)를 가짐으로써 낮은 CO2 수준에서 경쟁 시 이점을 가질 수 있을 것이다. 새로운 M. aeruginosa 균주의 유전체 정보의 특성 분석은 환경에서 유해 녹조 발생의 이해에 도움이 될 수 있을 것이다.


This work was supported by the Korea Environment Industry & Technology Institute (KEITI) through a project to Aquatic Ecosystem Conservation Research Program, funded by the Korea Ministry of Environment (MOE) RS-2022-KE002133 (2022003040001).

Conflict of Interest

So-Jeong Kim is Editor of KJM. Dr. Kim was not involved in the review process of this article. Also, authors have no conflicts of interest to report.

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