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Complete genome of Aquidulcibacter sp. strain 19MK03-0.1R-21, isolated from the Nakdong River, associated with cyanobacterial algal blooms
Korean J. Microbiol. 2024;60(2):104-106
Published online June 30, 2024
© 2024 The Microbiological Society of Korea.

Ahyoung Choi* , Kiwoon Baek, and Jaeduk Goh

Biological Resources Research Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Republic of Korea
Correspondence to: *E-mail:;
Tel.: +82-54-530-0841; Fax: +82-54-530-0849
Received April 19, 2024; Revised May 13, 2024; Accepted May 13, 2024.
Aquidulcibacter sp. strain 19MK03-0.1R-21, isolated from the Nakdong River during a cyanobacterial outbreak, underwent comprehensive genome analysis. The analysis revealed a single circular chromosome comprising 3,097,386 base pairs with a GC content of 67.9%, encompassing 3,008 protein- coding genes, 43 tRNA genes, and 3 rRNA genes. The genome of this strain contains genes for the uptake and transport of nitrogen (N), phosphorus (P), and sulfur (S), essential for cyanobacterial growth and establishment. The whole genome sequence obtained will contribute to a better understanding of the relationship between heterotrophic bacteria and cyanobacteria, as well as the resolution of issues associated with bacterial growth.
Keywords : Amycolatopsis sp., complete genome, cyanobacterial algal blooms

The type species, Aquidulcibacter paucihalophilus, belonging to the genus Aquidulcibacter within the class Alphaproteobacteria, was originally isolated from cyanobacterial aggregates in a eutrophic lake (Cai et al., 2017). Aquidulcibacter paucihalophilus is a Gram-negative, slightly curved, and rod-shaped bacterium. Members of the genus Aquidulcibacter have previously been associated with cyanobacteria culture. The heterotrophic bacterium Aquidulcibacter sp. strain 19MK03-0.1R-21 was isolated from cyanobacterial aggregates in the Nakdong River. The complete genome of Aquidulcibacter sp. strain 19MK03-0.1R-21 was obtained to enhance our understanding of heterotrophic bacterium-cyanobacterium associations.

Cyanobacterial aggregate samples were collected from the lower reaches of the eutrophic Nakdong River in South Korea in March 2019 (coordinates: 35° 18' 8.73'' N, 128° 58' 45.8'' E). Aquidulcibacter sp. strain 19MK03-0.1R-21 was isolated using a standard dilution plating method on 1/10-diluted R2A agar (BD Difco) after 2 weeks of incubation at 20°C. Colonies grown on R2A agar are convex, smooth, and beige-colored after incubation for 4 days at 25°C (Cho et al., 2020). The primary objective of this study was to sequence the genome of strain 19MK03-0.1R-21 to elucidate its metabolic potential and determine its taxonomic position.

To achieve high-quality genome sequencing, the genomic DNA of strain 19MK03-0.1R-21 was extracted and purified from a pure culture isolated on R2A agar using the DNeasy Blood and Tissue Kit (Qiagen) and the Wizard Genomic DNA Purification Kit (Promega). The complete genome was sequenced at Macrogen, Inc. using a Pacific Biosciences (PacBio) RS II platform. For PacBio sequencing, DNA was fragmented to 20 kbp using a g-TUBE (Covaris), and a DNA library was constructed using a SMRTbell template prep kit (Pacific Biosciences). High-quality de novo assembly was performed using Canu v1.7 (Koren et al., 2017). Overall, 152,805 subreads (1,550,527,214 bp, mean subread length: 10,147 bp) were produced before quality filtering (minimum polymerase read quality 0.80; minimum polymerase read length 100 bp) and adapter trimming using the Hierarchical Genome Assembly Process 3 (HGAP3) within PacBio SMRT analysis 2.3.0 (Chin et al., 2013). The resulting complete genome sequence was annotated by the NCBI Prokaryotic Genome Annotation Pipeline v6.5 (PGAP) (Tatusova et al., 2016). Default parameters were used for all software unless otherwise specified.

Consequently, the complete genome of strain 19MK03-0.1R-21 contains one circular chromosome of 3,097,386 bp, with a G + C content of 67.9%. Annotation of the genome revealed 3,008 protein-coding sequences, 43 tRNA, and 3 rRNA genes. The genome statistics are further provided in Table 1. The 16S rRNA gene sequence was compared to sequences in the EzBioCloud database (Yoon et al., 2017), revealing that strain 19MK03-0.1R-21 was most closely related to Aquidulcibacter paucihalophilus TH1-2T (99.8% similarity, Accession no. NCSQ01000081). The OrthoANI value between strain 19MK03-0.1R-21 and A. paucihalophilus is 67.0% (Lee et al., 2016). These values fall below the standard cutoff criteria for identifying new bacterial species (Richter and Rosselló-Móra 2009; Jain et al., 2018).

General genomic features of the strain 19MK03-0.1R-21

Features Value
Genome size (bp) 3,097,386
GC content (mol%) 67.9
No. of contigs 1
Genes (total) 3,070
CDSs (total) 3,020
Genes (coding) 3,008
No. of rRNA genes (5S, 16S, 23S) 3 (1, 1, 1)
No. of tRNA genes 43
No. of ncNA genes 4
No. of pseudo genes 12

Nitrogen and sulfur are vital nutrients for cyanobacteria blooms (Vahtera et al., 2007; Roth-Rosenberg et al., 2020). The annotated genome of strain 19MK03-0.1R-21 contains genes encoding nitrogen regulation proteins (NtrX and NtrY) and enzymes involved in sulfur metabolism (SufA, SufB, SufC, SufD, SufE, and SufS). Additionally, the genome harbors genes encoding PstABC phosphate transporters, which facilitate phosphate uptake and transport. The whole genome sequence we obtained should be useful for better understanding the association between heterotrophic bacteria and cyanobacteria, as well as elucidating issues regarding bacterial growth.

Strain and nucleotide sequence accession numbers

Strain 19MK03-0.1R-21 has been deposited at the Nakdonggang National Institute of Biological Resources (NNIBR) under the accession number NNIBR2019643BA7. The GenBank/EMBL/DDBJ accession number for the complete genome sequence of strain 19MK03-0.1R-21 is CP127384. The associated BioProject and BioSample accession numbers are PRJNA721829 and SAMN18739954, respectively.

적 요

이 연구에서는 남조류의 대발생 시점에 낙동강 하구에서 분리된 Aquidulcibacter sp. 19MK03-0.1R-21 균주의 전장 유전체에 대해 분석하였다. 해당 균주는 원형의 완성된 하나의 염색체를 갖고 있으며, 전체 3,097,386 bp 크기와 67.9%의 GC함량을 나타낸다. 총 3,008개의 protein-coding 유전자, 43개의 tRNA, 3개의 rRNA 유전자로 구성되어 있다. 이 균주의 게놈에는 시아노박테리아의 성장과 정착에 필수적인 질소(N), 인(P) 및 황(S)의 흡수 및 수송을 위한 유전자가 포함되어 있다. 획득된 전체 게놈 서열은 종속영양세균과 시아노박테리아 사이의 관계를 더 잘 이해하고 박테리아 성장과 관련된 문제를 해결하는 데 도움이 될 것이다.


This study was supported by a grant from the Nakdonggang National Institute of Biological Resources (NNIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NNIBR20241103), and by the Korea Environment Industry & Technology Institute (KEITI) through a project to make multi-ministerial national bio-logical research resources more advanced, funded by the Korea Ministry of Environment (MOE) (2021003420003).

Conflict of Interest

The authors declare no conflict of interest.

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