1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 1

sp. nov., a novel type II methanotrophic bacterium isolated from landfill cover soil No Access

Abstract

A bacterial strain, designated NLS-7, was isolated through enrichment of landfill cover soil in methane-oxidizing conditions. Strain NLS-7 is a Gram-stain negative, non-motile rod, approximately 0.8 µm wide by 1.3 µm long. Phylogenetic analysis based on 16S rRNA gene sequencing places it within the genus , with its closest relatives being , and , with 99.9, 99.7 and 99.6 % sequence similarity respectively. However, average nucleotide identity and average amino acid identity values below the 95 % threshold compared to all the close relatives and digital DNA–DNA hybridization values between 20.9 and 54.1 % demonstrate that strain NLS-7 represents a novel species. Genome sequencing generated 4.31 million reads and genome assembly resulted in the generation of 244 contigs with a total assembly length of 3 820 957 bp (N50, 37 735 bp; L50, 34). Genome completeness is 99.5 % with 3.98 % contamination. It is capable of growth on methane and methanol. It grows optimally at 30 °C between pH 6.5 and 7.0. Strain NLS-7 is capable of atmospheric dinitrogen fixation and can use ammonium (as NHCl), -aspartate, -arginine, yeast extract, nitrate, -leucine, -proline, -methionine, -lysine and -alanine as nitrogen sources. The major fatty acids are C ω8 and C ω7. Based upon this polyphasic taxonomic study, strain NLS-7 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NLS-7 (=ATCC TSD-256=DSM 112294). The 16S rRNA gene and genome sequences of strain NLS-7 have been deposited in GenBank under accession numbers ON715489 and GCA_024448135.1, respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): landfill , methanotroph , methanotroph genomics and methylocystis
Funding
This study was supported by the:
  • National Science Foundation (Award 1736255)
    • Principle Award Recipient: LeeR. Krumholz
© 2024 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006239
2024-01-23
2024-05-14
Loading full text...

Full text loading...

References

  1. Hanson RS, Hanson TE. Methanotrophic bacteria. Microbiol Rev 1996; 60:439–471 [View Article] [PubMed]
     [Google Scholar]
  2. Milich L. The role of methane in global warming: where might mitigation strategies be focused?. Global Environmental Change 1999; 9:179–201 [View Article]
     [Google Scholar]
  3. Oremland RS, Culbertson CW. Importance of methane-oxidizing bacteria in the methane budget as revealed by the use of a specific inhibitor. Nature 1992; 356:421–423 [View Article]
     [Google Scholar]
  4. Henneberger R, Lüke C, Mosberger L, Schroth MH. Structure and function of methanotrophic communities in a landfill-cover soil. FEMS Microbiol Ecol 2012; 81:52–65 [View Article] [PubMed]
     [Google Scholar]
  5. Knief C. Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker. Front Microbiol 2015; 6:1346 [View Article] [PubMed]
     [Google Scholar]
  6. Bowman JP, Sly LI, Nichols PD, Hayward AC. Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, Validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int J Syst Evol Microbiol 1993; 43:735–753 [View Article]
     [Google Scholar]
  7. Wartiainen I, Hestnes AG, McDonald IR, Svenning MM. Methylocystis rosea sp. nov., a novel methanotrophic bacterium from Arctic wetland soil, Svalbard, Norway (78 degrees N). Int J Syst Evol Microbiol 2006; 56:541–547 [View Article] [PubMed]
     [Google Scholar]
  8. Lindner AS, Pacheco A, Aldrich HC, Costello Staniec A, Uz I et al. Methylocystis hirsuta sp. nov., a novel methanotroph isolated from a groundwater aquifer. Int J Syst Evol Microbiol 2007; 57:1891–1900 [View Article] [PubMed]
     [Google Scholar]
  9. Dedysh SN, Belova SE, Bodelier PLE, Smirnova KV, Khmelenina VN et al. Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing “signature” fatty acids of type I methanotrophs. Int J Syst Evol Microbiol 2007; 57:472–479 [View Article] [PubMed]
     [Google Scholar]
  10. Belova SE, Kulichevskaya IS, Bodelier PLE, Dedysh SN. Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993. Int J Syst Evol Microbiol 2013; 63:1096–1104 [View Article] [PubMed]
     [Google Scholar]
  11. Tikhonova EN, Grouzdev DS, Avtukh AN, Kravchenko IK. Methylocystis silviterrae sp.nov., a high-affinity methanotrophic bacterium isolated from the boreal forest soil. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  12. Kaise H, Sawadogo JB, Alam MS, Ueno C, Dianou D et al. Methylocystis iwaonis sp. nov., a type II methane-oxidizing bacterium from surface soil of a rice paddy field in Japan, and emended description of the genus Methylocystis (Ex Whittenbury et al. 1970) Bowman et al. 1993. Int J Syst Evol Microbiol 2023; 73:005925
     [Google Scholar]
  13. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article] [PubMed]
     [Google Scholar]
  14. Souvorov A, Agarwala R, Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol 2018; 19:153 [View Article] [PubMed]
     [Google Scholar]
  15. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  16. O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 2016; 44:D733–D745 [View Article] [PubMed]
     [Google Scholar]
  17. Sayers EW, Beck J, Brister JR, Bolton EE, Canese K et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2020; 48:D9–D16 [View Article] [PubMed]
     [Google Scholar]
  18. Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 2021; 49:9077–9096 [View Article] [PubMed]
     [Google Scholar]
  19. Kanehisa M. Toward understanding the origin and evolution of cellular organisms. Protein Sci 2019; 28:1947–1951 [View Article] [PubMed]
     [Google Scholar]
  20. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
     [Google Scholar]
  21. Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 2020; 36:2251–2252 [View Article] [PubMed]
     [Google Scholar]
  22. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4:e1900v1 [View Article]
     [Google Scholar]
  23. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  24. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  25. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:113 [View Article] [PubMed]
     [Google Scholar]
  26. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  27. Lane DJ. 16S/23S rRNA Sequencing. In Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp 115–175
     [Google Scholar]
  28. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  29. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article] [PubMed]
     [Google Scholar]
  30. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  31. Li C, Hambright KD, Bowen HG, Trammell MA, Grossart H-P et al. Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates. Environ Microbiol 2021; 23:6503–6519 [View Article] [PubMed]
     [Google Scholar]
  32. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  33. Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
     [Google Scholar]
  34. Fotedar R, Sankaranarayanan K, Caldwell ME, Zeyara A, Al Malki A et al. Reclassification of Facklamia ignava, Facklamia sourekii and Facklamia tabacinasalis as Falseniella ignava gen. nov., comb. nov., Hutsoniella sourekii gen. nov., comb. nov., and Ruoffia tabacinasalis gen. nov., comb. nov., and description of Ruoffia halotolerans sp. nov., isolated from hypersaline Inland Sea of Qatar. Antonie van Leeuwenhoek 2021; 114:1181–1193 [View Article] [PubMed]
     [Google Scholar]
  35. Fotedar R, Caldwell ME, Sankaranarayanan K, Al-Zeyara A, Al-Malki A et al. Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf. Int J Syst Evol Microbiol 2020; 70:4130–4138 [View Article] [PubMed]
     [Google Scholar]
  36. Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE et al. Community-led, integrated, reproducible multi-omics with Anvi’o. Nat Microbiol 2021; 6:3–6 [View Article] [PubMed]
     [Google Scholar]
  37. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  38. van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. Methods Mol Biol 2012; 804:281–295 [View Article] [PubMed]
     [Google Scholar]
  39. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–D269 [View Article] [PubMed]
     [Google Scholar]
  40. Hobbie JE, Daley RJ, Jasper S. Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 1977; 33:1225–1228 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006239
Loading
Methylocystis suflitae sp. nov., a novel type II methanotrophic bacterium isolated from landfill cover soil
Int J Syst Evol Microbiol 74, 006239 (2024); https://doi.org/10.1099/ijsem.0.006239
/content/journal/ijsem/10.1099/ijsem.0.006239
/content/journal/ijsem/10.1099/ijsem.0.006239
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error