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Oligotrophic Growth of Rhodococcus

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Biology of Rhodococcus

Part of the book series: Microbiology Monographs ((MICROMONO,volume 16))

Abstract

We can relatively easily isolate “super” oligotrophs from various environments, which can grow on minimal medium without additional carbon and energy sources. The super oligotrophs isolated to date have all belonged to the genera Rhodococcus and Streptomyces. This chapter primarily describes the genetics and biochemistry of one of the super oligotrophs, R. erythropolis N9T-4, which was isolated from crude oil. It is suggested that C2 metabolism starting from acetaldehyde is the key to oligotrophic carbon metabolism of N9T-4. Intriguingly, this bacterium is also oligotrophic for nitrogen and sulfur sources. The most unequivocal evidence for the oligotrophy of N9T-4 relates to the utilization of nitrogen, in which ammonium transporter is involved in the incorporation of atmospheric ammonia under oligotrophic conditions. A unique intracellular structure found in the oligotrophically grown super oligotroph is also introduced.

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References

  • Adroer N, Casas C, de Mas C, Solà C (1990) Mechanism of formaldehyde biodegradation by Pseudomonas putida. Appl Microbiol Biotechnol 33:217–220

    Article  CAS  Google Scholar 

  • Al-Haideri H, White MA, Kelly DJ (2016) Major contribution of the type II beta carbonic anhydrase CanB (Cj0237) to the capnophilic growth phenotype of Campylobacter jejuni. Environ Microbiol 18:721–735

    Article  CAS  Google Scholar 

  • Berg IA (2011) Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl Environ Microbiol 77:1925–1936

    Article  CAS  Google Scholar 

  • Bonilla-Rosso G, Peimbert M, Alcaraz LD, Hernández I, Eguiarte LE, Olmedo-Alvarez G, Souza V (2012) Comparative metagenomics of two microbial mats at Cuatro Ciénegas Basin II: community structure and composition in oligotrophic environments. Astrobiology 12:659–673

    Article  CAS  Google Scholar 

  • Bury-Moné S, Mendz GL, Ball GE, Thibonnier M, Stingl K, Ecobichon C, Avé P, Huerre M, Labigne A, Thiberge JM, De Reuse H (2008) Roles of alpha and beta carbonic anhydrases of Helicobacter pylori in the urease-dependent response to acidity and in colonization of the murine gastric mucosa. Infect Immun 76:497–509

    Article  Google Scholar 

  • Bystrykh LV, Vonck J, van Bruggen EF, van Beeumen J, Samyn B, Govorukhina NI, Arfman N, Duine JA, Dijkhuizen L (1993) Electron microscopic analysis and structural characterization of novel NADP(H)-containing methanol: N,N′-dimethyl-4-nitrosoaniline oxidoreductases from the gram-positive methylotrophic bacteria Amycolatopsis methanolica and Mycobacterium gastri MB19. J Bacteriol 175:1814–1822

    Article  CAS  Google Scholar 

  • Castro AR, Rocha I, Alves MM, Pereira MA (2016) Rhodococcus opacus B4: a promising bacterium for production of biofuels and biobased chemicals. AMB Express 6:35

    Article  Google Scholar 

  • Constant P, Chowdhury SP, Pratscher J, Conrad R (2010) Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase. Environ Microbiol 12:821–829

    Article  CAS  Google Scholar 

  • Docampo R, de Souza W, Miranda K, Rohloff P, Moreno SN (2005) Acidocalcisomes—conserved from bacteria to man. Nat Rev Microbiol 3:251–261

    Article  CAS  Google Scholar 

  • Figueroa IA, Barnum TP, Somasekhar PY, Carlström CI, Engelbrektson AL, Coates JD (2018) Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway. Proc Natl Acad Sci U S A 115:E92–E101

    Article  CAS  Google Scholar 

  • Greening C, Berney M, Hards K, Cook GM, Conrad R (2014) A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases. Proc Natl Acad Sci U S A 111:4257–4261

    Article  CAS  Google Scholar 

  • Ishige T, Tani A, Takabe K, Kawasaki K, Sakai Y, Kato N (2002) Wax ester production of n-alkanes by Acinetobacter sp. strain M-1: ultrastructure of cellular inclusions and role of acyl coenzyme A reductase. Appl Environ Microbiol 68:1192–1195

    Article  CAS  Google Scholar 

  • Jaureguibeitia A, Saá L, Llama MJ, Serra JL (2007) Purification, characterization and cloning of aldehyde dehydrogenase from Rhodococcus erythropolis UPV-1. Appl Microbiol Biotechnol 73:1073–1086

    Article  CAS  Google Scholar 

  • Kato N, Yamagami T, Shimao M, Sakazawa C (1986) Formaldehyde dismutase, a novel NAD-binding oxidoreductase from Pseudomonas putida F61. Eur J Biochem 156:59–64

    Article  CAS  Google Scholar 

  • Kim D, Choi KY, Yoo M, Zylstra GJ, Kim E (2018) Biotechnological potential of Rhodococcus biodegradative pathways. J Microbiol Biotechnol 28:1037–1051

    CAS  PubMed  Google Scholar 

  • Kuroda A, Nomura K, Ohtomo R et al (2001) Role of inorganic polyphosphate in promoting ribosomal protein degradation by the lon protease in E. coli. Science 293:705–708

    Article  CAS  Google Scholar 

  • Kuznetsov S, Dubinina G, Lapteva N (1979) Biology of oligotrophic bacteria. Annu Rev Microbiol 33:377–387

    Article  CAS  Google Scholar 

  • Matsumoto M, Ueda N, Ono N (1998) Precise measurements of acidic and alkaline gaseous and particulate species in the atmosphere using annular denuder system. Annual Report of Nara Prefectural Institute of Public Health 32:39–46

    Google Scholar 

  • Matsuoka T, Yoshida N (2018) Establishment of an effective oligotrophic cultivation system for Rhodococcus erythropolis N9T-4. Biosci Biotechnol Biochem 82:1652–1655

    Article  CAS  Google Scholar 

  • Meyer A (1904) Orientirende Untersuchungen uber Verbreitung, Morphologie und chemie des volutins. Botanische Zeitung 7:113–152

    Google Scholar 

  • Mitsui R, Sakai Y, Yasueda H, Kato N (2000) A novel operon encoding formaldehyde fixation: the ribulose monophosphate pathway in the gram-positive facultative methylotrophic bacterium Mycobacterium gastri MB19. J Bacteriol 182:944–948

    Article  CAS  Google Scholar 

  • Nagy I, Verheijen S, De Schrijver A, Van Damme J, Proost P, Schoofs G, Vanderleyden J, De Mot R (1995) Characterization of the Rhodococcus sp. NI86/21 gene encoding alcohol: N,N′-dimethyl-4-nitrosoaniline oxidoreductase inducible by atrazine and thiocarbamate herbicides. Arch Microbiol 163:439–446

    Article  CAS  Google Scholar 

  • Ohhata N, Yoshida N, Egami H, Katsuragi T, Tani Y, Takagi H (2007) An extremely oligotrophic bacterium, Rhodococcus erythropolis N9T-4, isolated from crude oil. J Bacteriol 189:6824–6831

    Article  CAS  Google Scholar 

  • Sahuquillo-Arce JM, Chouman-Arcas R, Molina-Moreno JM, Hernández-Cabezas A, Frasquet-Artés J, López-Hontangas JL (2017) Capnophilic Enterobacteriaceae. Diagn Microbiol Infect Dis 87:318–319

    Article  CAS  Google Scholar 

  • Siering P, Wolfe G, Wilson M, Yip A, Carey C, Wardman C, Shapiro R, Stedman K, Kyle J, Yuan T (2013) Microbial biogeochemistry of boiling springs lake: a physically dynamic, oligotrophic, low-pH geothermal ecosystem. Geobiology 11:356–376

    Article  CAS  Google Scholar 

  • Soleimani M, Bassi A, Margaritis A (2007) Biodesulfurization of refractory organic sulfur compounds in fossil fuels. Biotechnol Adv 25:570–596

    Article  CAS  Google Scholar 

  • Steinhauser D, Fernie AR, Araújo WL (2012) Unusual cyanobacterial TCA cycles: not broken just different. Trends Plant Sci 17:503–509

    Article  CAS  Google Scholar 

  • Tajparast M, Frigon D (2015) Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition. BMC Syst Biol 9:43

    Article  Google Scholar 

  • Tian J, Bryk R, Itoh M, Suematsu M, Nathan C (2005a) Variant tricarboxylic acid cycle in Mycobacterium tuberculosis: identification of α-ketoglutarate decarboxylase. Proc Natl Acad Sci U S A 102:10670–10675

    Article  CAS  Google Scholar 

  • Tian J, Bryk R, Shi S, Erdjument-Bromage H, Tempst P, Nathan C (2005b) Mycobacterium tuberculosis appears to lack α-ketoglutarate dehydrogenase and encodes pyruvate dehydrogenase in widely separated genes. Mol Microbiol 57:859–868

    Article  CAS  Google Scholar 

  • Vorholt JA (2002) Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Arch Microbiol 178:239–249

    Article  CAS  Google Scholar 

  • Yamada H, Kobayashi M (1996) Nitrile hydratase and its application to industrial production of acrylamide. Biosci Biotechnol Biochem 60:1391–1400

    Article  CAS  Google Scholar 

  • Yano T, Yoshida N, Takagi H (2012) Carbon monoxide utilization of an extremely oligotrophic bacterium, Rhodococcus erythropolis N9T-4. J Biosci Bioeng 114:53–55

    Article  CAS  Google Scholar 

  • Yano T, Yoshida N, Yu F, Wakamatsu M, Takagi H (2015) The glyoxylate shunt is essential for CO2-requiring oligotrophic growth of Rhodococcus erythropolis N9T-4. Appl Microbiol Biotechnol 99:5627–5637

    Article  CAS  Google Scholar 

  • Yano T, Funamizu Y, Yoshida N (2016) Intracellular accumulation of trehalose and glycogen in an extreme oligotroph, Rhodococcus erythropolis N9T-4. Biosci Biotechnol Biochem 80:610–613

    Article  CAS  Google Scholar 

  • Yonemitsu H, Kikuchi Y (2018) Biodegradation of high concentrations of formaldehyde using Escherichia coli expressing the formaldehyde dismutase gene of Methylobacterium sp. FD1. Biosci Biotechnol Biochem 82:49–56

    Article  CAS  Google Scholar 

  • Yoshida N, Ohhata N, Yoshino Y, Katsuragi T, Tani Y, Takagi H (2007) Screening of carbon dioxide-requiring extreme oligotrophs from soil. Biosci Biotechnol Biochem 71:2830–2832

    Article  CAS  Google Scholar 

  • Yoshida N, Hayasaki T, Takagi H (2011) Gene expression analysis of methylotrophic oxidoreductases involved in the oligotrophic growth of Rhodococcus erythropolis N9T-4. Biosci Biotechnol Biochem 75:123–127

    Article  CAS  Google Scholar 

  • Yoshida N, Inaba S, Takagi H (2014) Utilization of atmospheric ammonia by an extremely oligotrophic bacterium, Rhodococcus erythropolis N9T-4. J Biosci Bioeng 117:28–32

    Article  CAS  Google Scholar 

  • Yoshida N, Yano T, Kedo K, Fujiyoshi T, Nagai R, Iwano M, Taguchi E, Nishida T, Takagi H (2017) A unique intracellular compartment formed during the oligotrophic growth of Rhodococcus erythropolis N9T-4. Appl Microbiol Biotechnol 101:331–340

    Article  CAS  Google Scholar 

  • Zhang H, Ishige K, Kornberg A (2002) A polyphosphate kinase (PPK2) widely conserved in bacteria. Proc Natl Acad Sci U S A 99:16678–16683

    Article  CAS  Google Scholar 

Download references

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Authors and Affiliations

  1. Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu, Japan

    Nobuyuki Yoshida

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  1. Nobuyuki Yoshida
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Correspondence to Nobuyuki Yoshida .

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Editors and Affiliations

  1. INBIOP, Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB) and CONICET, Comodoro Rivadavia, Chubut, Argentina

    Héctor M. Alvarez

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Yoshida, N. (2019). Oligotrophic Growth of Rhodococcus. In: Alvarez, H. (eds) Biology of Rhodococcus. Microbiology Monographs, vol 16. Springer, Cham. https://doi.org/10.1007/978-3-030-11461-9_4

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