Strain RR4-40, a novel bacterium within the family Flavo- bacteriaceae was isolated from a biofilter of seawater re- circulating aquaculture system (RAS) in Busan, South Korea.
Its complete genome was obtained using PacBio RS II platform and was 3,386,965 bp in size with 37.4% G + C content. The genome annotation presented that the genome comprises a total of 3,018 genes, 2,973 CDSs, 6 rRNAs, 35 tRNAs, and 4 ncRNAs. Genes related to osmotic regulation, peptidoglycan degradation, protein hydrolysis, and antibacterial peptides were detected in the genome. The genome analysis showed that strain RR4-40 might be associated with biodegradation of waste materials and antimicrobial activity in the RAS.
Keywords: Flavobacteriaceae, complete genome, recirculating aquaculture system
Recirculating aquaculture system (RAS) is a closed aqua- culture system where rearing water circulates through rearing tank and biofilters. Biofilters remove the waste materials such as toxic nitrogen compounds, feed debris, fish feces, and other organic compounds which are harmful to cultured animals (Zhang et al., 2011). A study reported that Flavobacteriaceae
on biofilter might be involved in rearing water purification in RAS (Chen et al., 2019). Flavobacteriaceae family is one of major bacterial groups within the phylum Bacteroidetes and comprises over 90 genera currently. Bacteria belonging to this family have been found in various environments including freshwater, soil, and aquatic habitats (Bernardet, 2002; Zhang et al., 2016).
A yellow pigmented, Gram-negative, and aerobic bacterium, strain RR4-40 was isolated from the biofilm on the surface of RAS mesh biofilter by the serial dilution method using phosphate buffered saline solution. The 16S rRNA gene sequence of strain RR4-40 shared low sequence similarity with Marinirhabdus gelatinilytica NH83
T(94.73%), Marinirhabdus citrea MEBiC09412
T(94.53%), and Ulvibacter antarcticus DSM 23424
T(93.97%) that are belonging to the family Flavobacteriaceae. In this study, the complete genome of the strain RR4-40 will contribute to understand the characteristics of the novel strain within the Flavobacteriaceae family.
Genomic DNA of strain RR4-40 was extracted using Genomic DNA Prep Kit (BIOFACT) according to the manufacturer’s instruction and subjected to the library construction and single-molecule real-time (SMRT) sequencing (Macrogen) using PacBio RS II platform. SMRT yielded a total of 164,805 subreads (1,391,678,734 subread bases; N50, 12,346 bp; mean
Korean Journal of Microbiology (2020) Vol. 56, No. 2, pp. 183-185 pISSN 0440-2413
DOI https://doi.org/10.7845/kjm.2020.0045 eISSN 2383-9902
Copyright ⓒ 2020, The Microbiological Society of Korea
Whole genome of strain RR4-40, novel bacterium in the family Flavobacteriaceae
Young-Sam Kim
1†, Seong-Jin Kim
1†, and Kyoung-Ho Kim
1,2*
1
Department of Microbiology, Pukyong National University, Busan 48513, Republic of Korea
2
School of Marine and Fisheries Life Science, Pukyong National University, Busan 48513, Republic of Korea
Flavobacteriaceae 과의 신균인 RR4-40의 전장 유전체 분석
김영삼
1†･ 김성진
1†･ 김경호
1,2*
1
부경대학교 미생물학과,
2부경대학교 해양수산생명과학부
(Received May 12, 2020; Revised June 3, 2020; Accepted June 4, 2020)
†
The authors equally contributed to this work
*For correspondence. E-mail: [email protected];
Tel.: +82-51-629-5611; Fax: +82-51-629-5619
184 ∙ Kim et al.
미생물학회지 제56권 제2호
subread length, 8,444 bp) and de novo assembly using Hierarchical Genome Assembly Process [HGAP, Version 3.0;
Chin et al. (2013)] generated a single closed genome sequence which is 3,388,965 bp in size with G + C content of 37.4%. The complete genome sequence of strain RR4-40 was annotated by NCBI Prokaryotic Genome Annotation Pipeline [PGAP;
Tatusova et al. (2016)] and a total of 3,018 genes, 2,973 CDSs, 6 rRNAs, 35 tRNAs, and 4 ncRNAs were confirmed (Table 1).
CGView Comparison Tool (Grant et al., 2012) was used to show a genome map showing 1,902 genes assigned to Clusters
of Orthologous Groups (Fig. 1). One candidate CRISPR region was detected by CRISPR finder [http://crispr.i2bc.paris- saclay.fr; Grissa et al. (2007)]. PHAge Search Tool Enhanced Release [PHASTER; http://phaster.ca/; Arndt et al. (2016)]
was not able to detect any prophage. The genome contains genes for six subunits of Na
+-transporting NADH:ubiquinone oxidoreductase (NqrA-NqrF, Genbank locus tag: G5B37_12975, 12980, 12985, 12990, 12995, and 13000) which are related to osmotic regulation and electron transport in marine/halophilic bacteria (Reyes-Prieto et al., 2014). Genes for three murein tripeptide amidase (MpaA, G5B37_02325, 02975, and 14615) and four peptidoglycan/xylan/chitin deacetylase (G5B37_00120, 06610, 11180, and 11255), which are involved in peptidoglycan degradation (https://www.uniprot.org/), were annotated in the genome. G5B37_08780). Five genes (G5B37_00655, G5B37_
07325, G5B37_11480, G5B37_11485, and G5B37_14925) for permease component of ABC-type antimicrobial peptide transport system, which are associated with recognition of the cell wall of Gram-positive bacteria (Gebhard, 2012), are coded in the genome. Rapid Annotations using Subsystems Technology [RAST, https://rast.nmpdr.org/rast.cgi; Aziz et al. (2008)]
Table 1. Genomic features of strain RR4-40
Feature Value
Genome size (bp) 3,388,965
G + C content (%) 37.4
Total gene 3,018
Total CDS 2,973
Genes assigned to COGs 1,902
rRNA (5S, 16S, 23S) 2, 2, 2
tRNA 35
ncRNA 4
Pseudogene 14
Fig. 1. Complete genome map of strain RR4-40. From the center to the outside: genome label, GC skew (green and purple), G + C content (black), CDSs
colored by COG categories on the reverse strand, CDSs including RNAs on the reverse strand, CDSs including RNAs on the forward strand, CDSs colored
by COG categories on the forward strand.
Genome of Flavobacteriaceae strain RR4-40 ∙ 185
Korean Journal of Microbiology, Vol. 56, No. 2 predicted genes related to protein hydrolysis such as dcp
(Dipeptidyl carboxypeptidase, G5B37_12495), pepP (Xaa-Pro aminopeptidase, G5B37_08525), aspX (Isoaspartyl amino- peptidase, G5B37_08710), dacA (D-alanyl-D-alanine carboxy- peptidase, G5B37_13065), mur4pep (Muramoyltetrapeptide carboxypeptidase). The results showed that strain RR4-40 might be involved in biodegradation of waste compounds and antimicrobial activity in the RAS.
Nucleotide sequence accession number
The strain was deposited at the Korean Collection for Type Cultures with accession number KCTC 52650 and the complete genome sequence was deposited in DDBJ/EMBL/NCBI GenBank under accession number CP049057.
적 요
Flavobacteriaceae 과에 속하는 신종 균주 RR4-40는 해수 순환 여과 양식 시스템의 바이오 필터에서 분리되었다. PacBio RS II 분석 기법을 이용하여 획득한 이 균주의 유전체는 총 길 이 3,386,965 bp이며 37.4%의 G + C 함유량을 가진 것으로 분 석되었다. 유전체 분석을 통해 총 3,018개의 유전자와 2,973개 의 CDS, 6개 rRNA, 35개 tRNA, 4개 ncRNA가 확인되었다. 유 전체에서 삼투압 조절, 펩티도글리칸 분해, 단백질 가수분해, 항생활성과 관련된 유전자들이 발견이 되었다. 본 유전체 분 석 결과는 RAS에서 RR4-40 균주가 오염물질의 생분해와 항 생활성과 관련이 있을 가능성을 보여준다.
Acknowledgments
This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2016R1D1A3B 04935909).
References
