Open access
Environmental Microbiology
Announcement
17 February 2022

Complete Genome Sequence of Luteitalea sp. Strain TBR-22

ABSTRACT

We report a complete genome sequence of a novel bacterial isolate, strain TBR-22, belonging to the class Vicinamibacteria of the phylum Acidobacteria, which was isolated from duckweed fronds. The genome expands our knowledge of the lifestyle of this abundant but rarely characterized phylum.

ANNOUNCEMENT

Duckweeds are commonly observed freshwater aquatic plants and have been shown to harbor unique microbial communities on their body surface (1, 2). With efforts to isolate novel bacterial lineages from a duckweed-associated microbial community, we successfully isolated a bacterial strain, TBR-22, belonging to the phylum Acidobacteria (3). Briefly, isolation was performed with wild duckweeds (Lemnoideae spp.) collected from rice paddies located in Ibaraki Prefecture, Japan. Duckweeds were washed and then sonicated with sterile distilled water (SDW), followed by serial dilution with SDW and inoculation on 2.0% (wt/vol) agar plates of diluted tryptic soy broth supplemented with phosphate buffer, vitamin mixture, and basal salt solution (modified diluted tryptic soy broth [mDTS]). The phylum Acidobacteria is known to be one of the most abundant bacterial lineages in soils and is also found in various natural environments, including terrestrial freshwater, sediments, and terrestrial plants (4, 5). Despite its wide distribution in natural environments, physiological and ecological characterizations of Acidobacteria have not been extensively performed due to its fastidious and difficult-to-culture nature, as only 61 species in this phylum have been validly described to date (4, 5).
Genomic DNA was extracted from cells grown in mDTS at 30°C under static conditions by chemical and enzymatic procedures, as described previously (6), or by using the MagAttract high-molecular-weight (HMW) DNA kit (Qiagen). Library preparation and sequencing were performed by using commercial kits according to the manufacturers’ instructions (Table 1). A total of 1.53 million paired-end reads and 6.32 million mate-pair reads were obtained with the Illumina MiSeq system, and 15 thousand single long reads (mean length, 11,446 bp) were obtained with the Oxford Nanopore Technologies MinION system. Read quality control was performed by FastQC version 0.11.5 (7). Hybrid genome assembly was performed by hybridSPAdes version 3.13.0 (8) in KBase (9) with default settings, and a single scaffold was obtained. Closing of two assembly gaps and genome circularization were performed by Sanger sequencing. The DDBJ Fast Annotation and Submission Tool (DFAST) pipeline version 1.2.13 (10) was used for structural annotation of the TBR-22 genome with following programs: MetaGeneAnnotator version 2008/08/19 (11) for coding sequences, Barrnap version 0.8 (12) for rRNAs, ARAGORN version 1.2.38 (13) for tRNAs, and CRT version 1.2 (14) for CRISPRs.
TABLE 1
TABLE 1 Library preparation kits and sequencing platforms
Sequencing typeLibrary prepn kit(s)Sequencing platform
Illumina short-read sequencingKAPA HyperPrep kit (for Illumina) (Kapa Biosciences) and Illumina Nextera mate-pair library prepn kit (Illumina)aIllumina MiSeq system (paired-end 2 × 300 bp)
MinION long-read sequencingRapid sequencing kit (Oxford Nanopore Technologies)MinION system (R9.4 flow cell)
a
Insert lengths for mate-pair libraries were 3 kb and 8 kb.
The complete genome of TBR-22 consists of a 6,468,984-bp-long chromosome, with a G+C content of 70.5%; 5,364 predicted protein-coding DNA sequences, 55 tRNAs, a single set of 5S/165S/23S rRNAs, and no CRISPRs were identified. Genome completeness was estimated with CheckM version 1.1.3 (15), and the genome was determined to be 96.56% complete and 6.64% redundant and to have 4.55% strain heterogeneity. Taxonomic assignment by the Genome Taxonomy Database Toolkit (GTDB-Tk) version 0.1.4 (16) placed TBR-22 within the genus Luteitalea in the phylum Acidobacteriota (Acidobacteria), but it was not assigned a species. The genome obtained can largely contribute to understanding of the ecophysiology of Acidobacteria, especially in interactions with aquatic plants, which have been less well investigated than those with terrestrial plants.

Data availability.

The genome and raw sequences have been deposited in DDBJ/ENA/GenBank under accession number AP024452 and in the DDBJ Sequence Read Archive (DRA) under accession numbers DRA011791 and DRA013041, respectively.

ACKNOWLEDGMENTS

This work was supported by the Advanced Low Carbon Technology Research and Development Program (ALCA) of the Japan Science and Technology Agency (JST) (grant JPMJAL1108). This work was also partly supported by JST ERATO grant JPMJER1502 and by a Grant-in-Aid for Scientific Research on Innovative Areas Post-Koch Ecology (grant JP19H05683), Japan.

REFERENCES

1.
Tanaka Y, Tamaki H, Matsuzawa H, Nigaya M, Mori K, Kamagata Y. 2012. Microbial community analysis in the roots of aquatic plants and isolation of novel microbes including an organism of the candidate phylum OP10. Microbes Environ 27:149–157.
2.
Tanaka Y, Matsuzawa H, Tamaki H, Tagawa M, Toyama T, Kamagata Y, Mori K. 2017. Isolation of novel bacteria including rarely cultivated phyla, Acidobacteria and Verrucomicrobia, from the roots of emergent plants by simple culturing method. Microbes Environ 32:288–292.
3.
Yoneda Y, Yamamoto K, Makino A, Tanaka Y, Meng X-Y, Hashimoto J, Shin-Ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. 2021. Novel plant-associated Acidobacteria promotes growth of common floating aquatic plants, duckweeds. Microoganisms 9:1133.
4.
Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. 2016. The ecology of Acidobacteria: moving beyond genes and genomes. Front Microbiol 7:744.
5.
Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, Suriani NL. 2020. Recent understanding of soil acidobacteria and their ecological significance: a critical review. Front Microbiol 11:580024.
6.
Komatsu M, Komatsu K, Koiwai H, Yamada Y, Kozone I, Izumikawa M, Hashimoto J, Takagi M, Omura S, Shin-Ya K, Cane DE, Ikeda H. 2013. Engineered Streptomyces avermitilis host for heterologous expression of biosynthetic gene cluster for secondary metabolites. ACS Synth Biol 2:384–396.
7.
Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
8.
Antipov D, Korobeynikov A, McLean J, Pevzner P. 2016. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics 32:1009–1015.
9.
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia J-M, Chia J-M, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D. 2018. KBase: the United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 36:566–569.
10.
Tanizawa Y, Fujisawa T, Nakamura Y. 2018. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34:1037–1039.
11.
Noguchi H, Taniguchi T, Itoh T. 2008. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 15:387–396.
12.
Seemann T. 2013. Barrnap 0.7: rapid ribosomal RNA prediction. https://github.com/tseemann/barrnap.
13.
Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16.
14.
Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. 2007. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8:209.
15.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055.
16.
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. 2019. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36:1925–1927.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 11Number 217 February 2022
eLocator: e00455-21
Editor: Irene L. G. Newton, Indiana University, Bloomington
PubMed: 35175120

History

Received: 6 May 2021
Accepted: 28 January 2022
Published online: 17 February 2022

Contributors

Authors

Kyosuke Yamamoto
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Hokkaido, Japan
Yasuko Yoneda
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
Ayaka Makino
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
Yasuhiro Tanaka
Department of Environmental Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi, Japan
Xian-Ying Meng
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
Junko Hashimoto
Japan Biological Informatics Consortium, Tokyo, Japan
Kazuo Shin-ya
Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
Noriyuki Satoh
Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
Manabu Fujie
Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
Tadashi Toyama
Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi, Kofu, Yamanashi, Japan
Kazuhiro Mori
Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi, Kofu, Yamanashi, Japan
Michihiko Ike
Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita, Japan
Masaaki Morikawa
Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
Yoichi Kamagata
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki, Japan
Biotechnology Research Center, The University of Tokyo, Tokyo, Japan

Editor

Irene L. G. Newton
Editor
Indiana University, Bloomington

Notes

The authors declare no conflict of interest.

Metrics & Citations

Metrics

Note:

  • For recently published articles, the TOTAL download count will appear as zero until a new month starts.
  • There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.
  • Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy