Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase

Abstract

The actinobacterial acI lineage is among the most successful and ubiquitous freshwater bacterioplankton found on all continents, often representing more than half of all microbial cells in the lacustrine environment and constituting multiple ecotypes. However, stably growing pure cultures of the acI lineage have not been established despite various cultivation efforts based on ecological and genomic studies on the lineage, which is in contrast to the ocean from which abundant microorganisms such as Prochlorococcus, Pelagibacter, and Nitrosopumilus have been isolated. Here, we report the first two pure cultures of the acI lineage successfully maintained by supplementing the growth media with catalase. Catalase was critical for stabilizing the growth of acI strains irrespective of the genomic presence of the catalase-peroxidase (katG) gene. The two strains, representing two novel species, displayed differential phenotypes and distinct preferences for reduced sulfurs and carbohydrates, some of which were difficult to predict based on genomic information. Our results suggest that culture of previously uncultured freshwater bacteria can be facilitated by a simple catalase-supplement method and indicate that genome-based metabolic prediction can be complemented by physiological analyses.

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Data availability

The complete genome sequences of strains IMCC25003 and IMCC26103 obtained from cell pellets using the Illumina MiSeq platform have been deposited in GenBank with the accession numbers CP029557 for IMCC25003 and CP029558 for IMCC26103.

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Acknowledgements

The authors are grateful to Dr. Sung-Keun Rhee and Dr. Jong-Geol Kim for their help in measuring H2O2 concentration. This study was supported by the Mid-Career Research Program (to J-CC, No. NRF-2016R1A2B2015142) and Science Research Center grant (to J-CC, No. NRF-2018R1A5A1025077) through the National Research Foundation (NRF) funded by the Ministry of Sciences and ICT, and by the Basic Science Research Program funded by the Ministry of Education, Republic of Korea (to IK, No. NRF-2016R1A6A3A11934789; to J-HS, No. NRF-2016R1A6A3A11935361).

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Kim, S., Kang, I., Seo, J. et al. Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase. ISME J 13, 2252–2263 (2019). https://doi.org/10.1038/s41396-019-0432-x

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