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Genome Announc. 2017 August; 5(33): e00526-17.
Published online 2017 August 17. doi:  10.1128/genomeA.00526-17
PMCID: PMC5604758

Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems

ABSTRACT

The genomes of the aerobic methanotrophs “Methyloterricola oryzae” strain 73aT and Methylomagnum ishizawai strain 175 were sequenced. Both strains were isolated from rice plants. Methyloterricola oryzae strain 73aT represents the first isolate of rice paddy cluster I, and strain 175 is the second representative of the recently described genus Methylomagnum.

GENOME ANNOUNCEMENT

Aerobic methanotrophic bacteria play a key role in controlling global climate by reducing the emission of the greenhouse gas methane in ecosystems such as paddy fields (1). Gammaproteobacterial methanotrophs are common inhabitants of rice fields (2, 3). We sequenced the genomes of two gammaproteobacterial isolates from rice plants (4). “Methyloterricola oryzae” strain 73aT (=LMG 29185=VKM-B-2986) is currently the only cultivated representative of rice paddy cluster I (3, 5), and Methylomagnum ishizawai strain 175 (= LMG 28717=VKM-B-2989) is the second representative of the genus (6).

Genomic DNA was extracted from bacterial cultures using a phenol-chloroform method (7), and draft genome sequences were generated at the DOE Joint Genome Institute. The genome of strain 73aT was sequenced using an Illumina HiSeq 2000, which generated 11,844,428 reads (1.79 Gb). The Pacific Biosciences RS was used for strain 175, and 230,505 filtered subreads (0.73 Gb) were generated. Sequence filtering, genome assembly, and gene annotation were performed as described earlier (8, 9). The final draft of strain 73aT had 302.0× read coverage, contained 74 contigs in 73 scaffolds, was 4.9 Mb in size, and had an average GC content of 61.1%. The draft of strain 175 had 140.8× read coverage, contained 8 contigs in 8 scaffolds, was 5.5 Mb in size, and had an average GC content of 63.0%.

Both strains encode metabolic inventory typical for type I methanotrophs (10). They harbor genes encoding a particulate methane monooxygenase (pmoCAB) and a methane/ammonia monooxygenase-related protein (pxmABC) (11). Additionally, the genome of strain 175 encodes a soluble methane monooxygenase (mmoXYBZDCGR). Gene clusters for PQQ-dependent methanol dehydrogenases and PQQ biosynthesis were found in both strains (mxaFJGIRSACKLD, xoxFJ, pqqABCDE, and pqqFG). Formaldehyde oxidation is predicted to proceed via the tetrahydromethanopterin (H4MPT) pathway (presence of fae, mtdB, mch, fhcABCD, and H4MPT biosynthesis genes) (12). Additionally, both strains contained genes encoding the tetrahydrofolate-dependent pathway (presence of mtdA, fchA, fhs, and, additionally, a folD gene in strain 73aT). Formate can potentially be oxidized via one (strain 175) or two (strain 73aT) types of formate dehydrogenase.

Both strains may assimilate formaldehyde via the ribulose monophosphate pathway. The cleavage cascade can be realized via fructose-1,6-bisphosphate, and in strain 73aT additionally via 2-keto-3-deoxy-6-phosphogluconate. Rearrangement of ribulose-5-phosphate can occur by transketolase and transaldolase reactions. A complete serine cycle is unlikely to be present. Both strains have the genes necessary for operational oxidative pentose phosphate and TCA cycle pathways, whereas a complete glycolysis cascade is encoded only in strain 73aT. RubisCO genes are present (cbbL and cbbS in strain 175; cbbM in strain 73aT), as well as genes for a complete Calvin-Benson-Bassham cycle.

For nitrogen acquisition, both strains possessed genes encoding ammonium (amtB), nitrate (nasA), and urea (urtABCDE) transporters, as well as urease genes (ureABCDEFG). Moreover, nif genes were present, suggesting the potential for dinitrogen fixation. The strains may form polyphosphate (ppk) and glycogen (glgAB, glgC, glgP, glgX, malQ, and pgm) as storage compounds. Strain 175, in addition, can potentially produce polyhydroxybutyrate (phbAB and phbC), a characteristic not yet known for type I methanotrophs (13).

Accession number(s).

The genome sequences have been deposited in GenBank under the accession numbers JYNS00000000, for Methyloterricola oryzae strain 73aT, and FXAM00000000, for Methylomagnum ishizawai strain 175.

ACKNOWLEDGMENTS

We thank all members of the Organization for Methanotroph Genome Analysis (OMeGA) and Genoscope (France) for access to its MicroScope platform for comparative genome analysis (http://www.genoscope.cns.fr/agc/microscope/home). The work conducted by the DOE Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.

Footnotes

This is contribution 13 from the Organization for Methanotroph Genome Analysis (OMeGA).

REFERENCES

1. Conrad R. 2009. The global methane cycle: recent advances in understanding the microbial processes involved. Environ Microbiol Rep 1:285–292. doi:.10.1111/j.1758-2229.2009.00038.x [PubMed] [Cross Ref]
2. Conrad R. 2007. Microbial ecology of methanogens and methanotrophs. Adv Agron 96:1–63. doi:.10.1016/S0065-2113(07)96005-8 [Cross Ref]
3. Knief C. 2015. Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker. Front Microbiol 6:1346. doi:.10.3389/fmicb.2015.01346 [PMC free article] [PubMed] [Cross Ref]
4. Frindte K, Maarastawi SA, Lipski A, Hamacher J, Knief C 2017. Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and extended description of Methylomagnum ishizawai. Int J Syst Evol Microbiol, in press.
5. Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E, Frenzel P 2010. Biogeography of wetland rice methanotrophs. Environ Microbiol 12:862–872. doi:.10.1111/j.1462-2920.2009.02131.x [PubMed] [Cross Ref]
6. Khalifa A, Lee CG, Ogiso T, Ueno C, Dianou D, Demachi T, Katayama A, Asakawa S 2015. Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere. Int J Syst Evol Microbiol 65:3527–3534. doi:.10.1099/ijsem.0.000451 [PubMed] [Cross Ref]
7. Sambrook J, Fritsch EF, Maniatis T 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
8. Hamilton R, Kits KD, Ramonovskaya VA, Rozova ON, Yurimoto H, Iguchi H, Khmelenina VN, Sakai Y, Dunfield PF, Klotz MG, Knief C, Op den Camp HJ, Jetten MS, Bringel F, Vuilleumier S, Svenning MM, Shapiro N, Woyke T, Trotsenko YA, Stein LY, Kalyuzhnaya MG 2015. Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc 3(3):e00515-15. doi:.10.1128/genomeA.00515-15 [PMC free article] [PubMed] [Cross Ref]
9. Kalyuzhnaya MG, Lamb AE, McTaggart TL, Oshkin IY, Shapiro N, Woyke T, Chistoserdova L 2015. Draft genome sequences of gammaproteobacterial methanotrophs isolated from Lake Washington sediment. Genome Announc 3(2):e00103-15. doi:.10.1128/genomeA.00103-15 [PMC free article] [PubMed] [Cross Ref]
10. Trotsenko YA, Murrell JC 2008. Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 63:183–229. doi:.10.1016/S0065-2164(07)00005-6 [PubMed] [Cross Ref]
11. Tavormina PL, Orphan VJ, Kalyuzhnaya MG, Jetten MS, Klotz MG 2011. A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs. Environ Microbiol Rep 3:91–100. doi:.10.1111/j.1758-2229.2010.00192.x [PubMed] [Cross Ref]
12. Vorholt JA. 2002. Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Arch Microbiol 178:239–249. doi:.10.1007/s00203-002-0450-2 [PubMed] [Cross Ref]
13. Pieja AJ, Sundstrom ER, Criddle CS 2012. Cyclic, alternating methane and nitrogen limitation increases PHB production in a methanotrophic community. Bioresour Technol 107:385–392. doi:.10.1016/j.biortech.2011.12.044 [PubMed] [Cross Ref]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)