1. Amann RI, Ludwig W, Schleifer K-H. 1995. Phylogenetic Identification and In Situ
Detection of Individual Microbial Cells without Cultivation. MICROBIOL REV
59:33.
2. Staley JT, Konopka A. 1985. MEASUREMENT OF IN SITU ACTIVITIES OF
NONPHOTOSYNTHETIC MICROORGANISMS IN AQUATIC AND
TERRESTRIAL HABITATS. Annu Rev Microbiol 39:321–346.
3. Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ,
Wrighton KC, Williams KH, Banfield JF. 2015. Unusual biology across a group
comprising more than 15% of domain Bacteria. Nature 523:208–211.
4. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield
CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM,
Amundson R, Thomas BC, Banfield JF. 2016. A new view of the tree of life. Nat
Microbiol 1:16048.
5. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden
MCJ, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC,
Whitman WB. 2002. Report of the ad hoc committee for the re-evaluation of the
species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047.
6. Lloyd KG, Steen AD, Ladau J, Yin J, Crosby L. 2018. Phylogenetically Novel
Uncultured Microbial Cells Dominate Earth Microbiomes 3:12.
7. Dance A. 2020. The search for microbial dark matter. Nature 582:301–303.
8. Naveed M, Chaudhry Z, Ali Z, Amjad M, Zulfiqar F, Numan A. 2018. Annotation
and curation of hypothetical proteins: prioritizing targets for experimental study 5:15.
9. Davis KER, Sangwan P, Janssen PH. 2011. Acidobacteria, Rubrobacteridae and
71
Chloroflexi are abundant among very slow-growing and mini-colony-forming soil
bacteria: Slow-growing and mini-colony-forming soil bacteria. Environ Microbiol
13:798–805.
10. Song J, Oh H-M, Cho J-C. 2009. Improved culturability of SAR11 strains in
dilution-to-extinction culturing from the East Sea, West Pacific Ocean. FEMS
Microbiol Lett 295:141–147.
11. D’Onofrio A, Crawford JM, Stewart EJ, Witt K, Gavrish E, Epstein S, Clardy J,
Lewis K. 2010. Siderophores from Neighboring Organisms Promote the Growth of
Uncultured Bacteria. Chem Biol 17:254–264.
12. Tanaka Y, Benno Y. 2015. Application of a single-colony coculture technique to the
isolation of hitherto unculturable gut bacteria: Isolation of uncultured gut bacteria.
Microbiol Immunol 59:63–70.
13. Murugkar PP, Collins AJ, Chen T, Dewhirst FE. 2020. Isolation and cultivation of
candidate phyla radiation Saccharibacteria (TM7) bacteria in coculture with bacterial
hosts. J Oral Microbiol 12:1814666.
14. Chaudhary DK, Khulan A, Kim J. 2019. Development of a novel cultivation
technique for uncultured soil bacteria. Sci Rep 9:6666.
15. Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A, Belanger A, Kanigan
T, Lewis K, Epstein SS. 2010. Use of Ichip for High-Throughput In Situ Cultivation
of “Uncultivable” Microbial Species. Appl Environ Microbiol 76:2445–2450.
16. Ohta H, Hattori T. 1980. Bacteria sensitive to nutrient broth medium in terrestrial
environments. Soil Sci Plant Nutr 26:99–107.
17. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M. 2002. Improved
Culturability of Soil Bacteria and Isolation in Pure Culture of Novel Members of the
72
Divisions Acidobacteria , Actinobacteria , Proteobacteria , and Verrucomicrobia.
Appl Environ Microbiol 68:2391–2396.
18. Bartelme RP, Custer JM, Dupont CL, Espinoza JL, Torralba M, Khalili B, Carini P.
2020. Influence of Substrate Concentration on the Culturability of Heterotrophic Soil
Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation. mSphere
5:e00024-20.
19. Gutleben J, Loureiro C, Ramírez Romero LA, Shetty S, Wijffels RH, Smidt H,
Sipkema D. 2020. Cultivation of Bacteria From Aplysina aerophoba: Effects of
Oxygen and Nutrient Gradients. Front Microbiol 11:175.
20. Bruns A, Cypionka H, Overmann J. 2002. Cyclic AMP and Acyl Homoserine
Lactones Increase the Cultivation Efficiency of Heterotrophic Bacteria from the
Central Baltic Sea. Appl Environ Microbiol 68:3978–3987.
21. Selvin J, Gandhimathi R, Kiran GS, Priya SS, Ravji TR, Hema TA. 2009.
Culturable heterotrophic bacteria from the marine sponge Dendrilla nigra: isolation
and phylogenetic diversity of actinobacteria. Helgol Mar Res 63:239–247.
22. Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M,
Kamagata Y. 2005. Comparative Analysis of Bacterial Diversity in Freshwater
Sediment of a Shallow Eutrophic Lake by Molecular and Improved CultivationBased Techniques. Appl Environ Microbiol 71:2162–2169.
23. Tamaki H, Hanada S, Sekiguchi Y, Tanaka Y, Kamagata Y. 2009. Effect of gelling
agent on colony formation in solid cultivation of microbial community in lake
sediment. Environ Microbiol 11:1827–1834.
24. Tanaka T, Kawasaki K, Daimon S, Kitagawa W, Yamamoto K, Tamaki H, Tanaka
M, Nakatsu CH, Kamagata Y. 2014. A Hidden Pitfall in the Preparation of Agar
73
Media Undermines Microorganism Cultivability. Appl Environ Microbiol 80:7659–
7666.
25. Kawasaki K, Kamagata Y. 2017. Phosphate-Catalyzed Hydrogen Peroxide
Formation from Agar, Gellan, and κ-Carrageenan and Recovery of Microbial
Cultivability via Catalase and Pyruvate. Appl Environ Microbiol 83:e01366-17.
26. Park S, You X, Imlay JA. 2005. Substantial DNA damage from submicromolar
intracellular hydrogen peroxide detected in Hpx - mutants of Escherichia coli. Proc
Natl Acad Sci 102:9317–9322.
27. Sen A, Imlay JA. 2021. How Microbes Defend Themselves From Incoming
Hydrogen Peroxide. Front Immunol 12:667343.
28. Mishra S, Imlay J. 2012. Why do bacteria use so many enzymes to scavenge
hydrogen peroxide? Arch Biochem Biophys 525:145–160.
29. Kato S, Yamagishi A, Daimon S, Kawasaki K, Tamaki H, Kitagawa W, Abe A,
Tanaka M, Sone T, Asano K, Kamagata Y. 2018. Isolation of Previously Uncultured
Slow-Growing Bacteria by Using a Simple Modification in the Preparation of Agar
Media. Appl Environ Microbiol 84:e00807-18.
30. Kato S, Terashima M, Yama A, Sato M, Kitagawa W, Kawasaki K, Kamagata Y.
2020. Improved Isolation of Uncultured Anaerobic Bacteria using Medium Prepared
with Separate Sterilization of Agar and Phosphate. Microbes Environ 35:n/a.
31. Brandi G, Sestili P, Pedrini MA, Salvaggio L, Cattabeni F, Cantoni O. 1987. The
effect of temperature or anoxia on Escherichia coli killing induced by hydrogen
peroxide. Mutat Res Lett 190:237–240.
32. Panek HR, O’Brian MR. 2004. KatG Is the Primary Detoxifier of Hydrogen
Peroxide Produced by Aerobic Metabolism in Bradyrhizobium japonicum. J Bacteriol
74
186:7874–7880.
33. Bakshi CS, Malik M, Regan K, Melendez JA, Metzger DW, Pavlov VM, Sellati TJ.
2006. Superoxide Dismutase B Gene ( sodB )-Deficient Mutants of Francisella
tularensis Demonstrate Hypersensitivity to Oxidative Stress and Attenuated
Virulence. J Bacteriol 188:6443–6448.
34. Verneuil N, Rincé A, Sanguinetti M, Posteraro B, Fadda G, Auffray Y, Hartke A,
Giard J-C. 2005. Contribution of a PerR-like regulator to the oxidative-stress
response and virulence of Enterococcus faecalis. Microbiology 151:3997–4004.
35. Park B, Nizet V, Liu GY. 2008. Role of Staphylococcus aureus Catalase in Niche
Competition against Streptococcus pneumoniae. J Bacteriol 190:2275–2278.
36. Saumaa S, Tover A, Tark M, Tegova R, Kivisaar M. 2007. Oxidative DNA Damage
Defense Systems in Avoidance of Stationary-Phase Mutagenesis in Pseudomonas
putida. J Bacteriol 189:5504–5514.
37. Xue X, Tomasch J, Sztajer H, Wagner-Döbler I. 2010. The Delta Subunit of RNA
Polymerase, RpoE, Is a Global Modulator of Streptococcus mutans Environmental
Adaptation. J Bacteriol 192:5081–5092.
38. Reder A, Höper D, Gerth U, Hecker M. 2012. Contributions of Individual σ B Dependent General Stress Genes to Oxidative Stress Resistance of Bacillus subtilis. J
Bacteriol 194:3601–3610.
39. Jiang Y, Dong Y, Luo Q, Li N, Wu G, Gao H. 2014. Protection from Oxidative
Stress Relies Mainly on Derepression of OxyR-Dependent KatB and Dps in
Shewanella oneidensis. J Bacteriol 196:445–458.
40. Farizano JV, Torres MA, Pescaretti M de las M, Delgado MA. 2014. The RcsCDB
regulatory system plays a crucial role in the protection of Salmonella enterica serovar
75
Typhimurium against oxidative stress. Microbiology 160:2190–2199.
41. Zhang L, Alfano JR, Becker DF. 2015. Proline Metabolism Increases katG
Expression and Oxidative Stress Resistance in Escherichia coli. J Bacteriol 197:431–
440.
42. Karas VO, Westerlaken I, Meyer AS. 2015. The DNA-Binding Protein from
Starved Cells (Dps) Utilizes Dual Functions To Defend Cells against Multiple
Stresses. J Bacteriol 197:3206–3215.
43. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naïve Bayesian Classifier for
Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl
Environ Microbiol 73:5261–5267.
44. Jiang Z-Y, Woollard ACS, Wolff SP. 1990. Hydrogen peroxide production during
experimental protein glycation. FEBS Lett 268:69–71.
45. Wilson CL, Hinman NW, Cooper WJ, Brown CF. 2000. Hydrogen Peroxide
Cycling in Surface Geothermal Waters of Yellowstone National Park. Environ Sci
Technol 34:2655–2662.
46. Flowers RS, Martin SE, Brewer DG, Ordal ZJ. 1977. Catalase and enumeration of
stressed Staphylococcus aureus cells. Appl Environ Microbiol 33:1112–1117.
47. Harmon SM, Kautter DA. 1976. Beneficial effect of catalase treatment on growth of
Clostridium perfringens. Appl Environ Microbiol 32:409–416.
48. Imazaki I, Kobori Y. 2010. Improving the culturability of freshwater bacteria using
FW70, a low-nutrient solid medium amended with sodium pyruvate. Can J Microbiol
56:333–341.
49. Norrod EP, Morse SA. 1982. Presence of hydrogen peroxide in media used for
cultivation of Neisseria gonorrhoeae. J Clin Microbiol 15:103–108.
76
50. Watanabe M, Igarashi K, Kato S, Kamagata Y, Kitagawa W. 2022. Critical Effect of
H 2 O 2 in the Agar Plate on the Growth of Laboratory and Environmental Strains.
Microbiol Spectr 10:e03336-22.
51. Seaver LC, Imlay JA. 2001. Hydrogen Peroxide Fluxes and Compartmentalization
inside Growing Escherichia coli. J Bacteriol 183:7182–7189.
52. Imlay JA. 2019. Where in the world do bacteria experience oxidative stress?:
Oxidative stress in natural environments. Environ Microbiol 21:521–530.
53. Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G. 2001. DNA
Microarray-Mediated Transcriptional Profiling of the Escherichia coli Response to
Hydrogen Peroxide. J Bacteriol 183:4562–4570.
54. Sambrook J, Russell D. 2001. Molecular cloning: a laboratory manual, 3rd ed, vol 1.
Cold Spring Harbor Laboratory Press, NY.
55. Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ
preprocessor. Bioinformatics 34:i884–i890.
56. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for
Illumina sequence data. Bioinformatics 30:2114–2120.
57. Tange O. GNU Parallel 20210622 ('Protasevich’).
58. De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. 2018.
NanoPack: visualizing and processing long-read sequencing data. Bioinformatics
34:2666–2669.
59. Antipov D, Korobeynikov A, McLean JS, Pevzner PA. 2016. hybridSPAdes: an
algorithm for hybrid assembly of short and long reads. Bioinformatics 32:1009–1015.
60. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. 2020. Using
SPAdes De Novo Assembler. Curr Protoc Bioinforma 70:e102.
77
61. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics
30:2068–2069.
62. Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J, Edbali O, Madhusoodanan N,
Kolesnikov A, Lopez R. 2022. Search and sequence analysis tools services from
EMBL-EBI in 2022. Nucleic Acids Res 50:W276–W279.
63. Watanabe M, Igarashi K, Kato S, Kamagata Y, Kitagawa W. Genome sequences of
Comamonadaceae bacterium OS-1 and OS-4, two H2O2 highly sensitive strains
isolated from pond water. Microbiol Resour Annoucement. [under peer review]
64. Schmid M, Frei D, Patrignani A, Schlapbach R, Frey JE, Remus-Emsermann MNP,
Ahrens CH. 2018. Pushing the limits of de novo genome assembly for complex
prokaryotic genomes harboring very long, near identical repeats. Nucleic Acids Res
46:8953–8965.
65. Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A,
Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D.
2019. Tandem repeats lead to sequence assembly errors and impose multi-level
challenges for genome and protein databases. Nucleic Acids Res 47:10994–11006.
66. Seaver LC, Imlay JA. 2001. Alkyl Hydroperoxide Reductase Is the Primary
Scavenger of Endogenous Hydrogen Peroxide in Escherichia coli. J Bacteriol
183:7173–7181.
67. Yuan F, Yin S, Xu Y, Xiang L, Wang H, Li Z, Fan K, Pan G. 2021. The Richness
and Diversity of Catalases in Bacteria. Front Microbiol 12:645477.
68. Ezraty B, Henry C, Hérisse M, Denamur E, Barras F. 2014. Commercial Lysogeny
Broth culture media and oxidative stress: A cautious tale. Free Radic Biol Med
74:245–251.
78
69. Shi M, Wan F, Mao Y, Gao H. 2015. Unraveling the Mechanism for the Viability
Deficiency of Shewanella oneidensis oxyR Null Mutant. J Bacteriol 197:2179–2189.
70. Wan F, Shi M, Gao H. 2017. Loss of OxyR reduces efficacy of oxygen respiration
in Shewanella oneidensis. Sci Rep 7:42609.
71. Li X, Imlay JA. 2018. Improved measurements of scant hydrogen peroxide enable
experiments that define its threshold of toxicity for Escherichia coli. Free Radic Biol
Med 120:217–227.
72. Wan F, Feng X, Yin J, Gao H. 2021. Distinct H2O2-Scavenging System in Yersinia
pseudotuberculosis: KatG and AhpC Act Together to Scavenge Endogenous
Hydrogen Peroxide. Front Microbiol 12:626874.
73. Lee J-S, Heo Y-J, Lee JK, Cho Y-H. 2005. KatA, the Major Catalase, Is Critical for
Osmoprotection and Virulence in Pseudomonas aeruginosa PA14. Infect Immun
73:4399–4403.
74. Parales RE, Harwood CS. 1993. Construction and use of a new broad-host-range
lacZ transcriptional fusion vector, pHRP309, for gram- bacteria. Gene 133:23–30.
75. Loewen PC, Switala J, von Ossowski I, Hillar A, Christie A, Tattrie B, Nicholls P.
1993. Catalase HPII of Escherichia coli catalyzes the conversion of protoheme to cisheme d. Biochemistry 32:10159–10164.
76. Singh R, Wiseman B, Deemagarn T, Jha V, Switala J, Loewen PC. 2008.
Comparative study of catalase-peroxidases (KatGs). Arch Biochem Biophys
471:207–214.
77. Takeda K, Nojima H, Kuwahara K, Chidya RC, Adesina AO, Sakugawa H. 2018.
Nanomolar Determination of Hydrogen Peroxide in Coastal Seawater Based on the
Fenton Reaction with Terephthalate. Anal Sci 34:459–464.
79
78. Garcia PE, Gerea M, Diéguez MC. 2020. Natural levels of hydrogen peroxide
(H2O2) in deep clear South temperate lakes: Field and laboratory evidence of photoand biotic production. Sci Total Environ 727:138641.
79. Olson JB, Lord CC, McCarthy PJ. 2000. Improved Recoverability of Microbial
Colonies from Marine Sponge Samples. Microb Ecol 40:139–147.
80. Adam D, Maciejewska M, Naômé A, Martinet L, Coppieters W, Karim L, Baurain
D, Rigali S. 2018. Isolation, Characterization, and Antibacterial Activity of Hard-toCulture Actinobacteria from Cave Moonmilk Deposits. Antibiotics 7:28.
80
Acknowledgements
I would like to express my deep gratitude to my supervisor Dr. Wataru Kitagawa,
without his support, my research would have not proceeded to this point. Whose expertise,
patience and generous support made everything possible during my study in the graduate
school. I learned a lot through these five years with him, not only the experimental
techniques, but also the techniques on logical thinking, critical thinking, and “scientific”
presentation. His taught will surely be my treasure for the rest of my life, no matter what
kind of career I would choose in the future. I can’t thank him enough for all his efforts
and hard works which made my academic career to be exiting and meaningful.
I appreciate Dr. Yoichi Kamagata for his supports. He was the motivation for me to
study in the graduate school of Agriculture in Hokkaido university and to work on the
cultivation of uncultured microbes. For these years, no matter how busy he was, he always
cared about me and my experiments, which was the strongest mental support. It was my
pleasure to be the student of the greatest microbiologist, and I would be pleased if my
works would be his aid in the future.
Dr. Yoshitomo Kikuchi and Dr. Souichiro Kato had helped me a lot on my studies.
Although our researching themes were slightly different, they always treated my
problems as theirs and gave me valuable suggestions. They also kindly welcomed me to
their fields, and they always gave me opportunities to talk with their co-workers. Which
had widened my perspectives and helped me to gain wide variety of knowledges.
The days I spent in the Hokkaido center of National Institute of Advanced Industrial
Science and Technology (AIST Hokkaido) were always exiting because of the people I
met there. I was always surrounded by the talented scientists with different expertise,
81
which was the biggest advantage that I got. They were always friendly and patient,
wishing my success on my study in the graduate school. I really appreciate every staff
who supported my career, especially, I really appreciate Dr. Kensuke Igarashi, Dr.
Ryosuke Nakai, and Dr. Shusei Kanie for their supports. I also feel many thanks to Ms.
Miyako Hata, who supported me a lot in the laboratory. She was the most patient teacher
on the operation of the laboratory equipment and without her, I wasn’t able to complete
the identification of more than 1,200 bacterial colonies, which was one of the biggest
experiments in my life.
I appreciate Prof. Teruo Sone for his warm supports. Although I had no opportunity to
work on his topics, he always kindly welcomed me to his field of study, letting me to
participate in his students’ seminars and journal clubs. With him and his students, my
days were always brilliant. Current and former students in the laboratory of Applied
Molecular Microbiology (also known as oukin laboratory), were always supportive and
the days I spent with them were the precious experiences.
My appreciation also extends to Dr. Seonghan Jang, who was the most respectful
“senpai” that I had met in my life. We discussed a lot on our experiments inside and
outside of the laboratory, and his attitudes toward his career had always motivated me to
do better. I will never forget the days we spent with our common friend Mr. Kota Ishigami.
Last but not the least, my deep appreciation goes to my family members. My life
wouldn’t have been this complete without their understanding and supports. My gratitude
extends to my deceased grandfather Akiyoshi Sano, who gave me opportunities for
education and to be like him is my lifelong goal.
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