1887

Abstract

Two anaerobic, Fe(III)-reducing and Gram-stain-negative strains, designated SG12 and SG195, were isolated from paddy soils in Fujian Province, PR China. Phylogenetic trees based on 16S rRNA genes and conserved core genes from genomes indicated that strains SG12 and SG195 clustered with members of the genus The two strains showed the highest 16S rRNA sequences similarities to the type strains of ‘’ SG184 (98.4–99.6 %), ‘’ SG263 (98.4–99.6 %) and DSM 14018 (98.2–98.8 %). The average nucleotide identity and digital DNA–DNA hybridization values between the two strains and the closely related species were 85.1–93.5 % and 29.8–52.9 %, respectively, lower than the cut-off level for prokaryotic species delineation. The menaquinone was MK-8 in both strains. The major fatty acids were iso-C, anteiso-C and C. Additionally, the two strains possessed iron reduction ability and could utilize organics such as benzene and benzoic acid as electron donors to reduce ferric citrate to ferrous iron. Based on the morphological, biochemical, chemotaxonomic and genome data, the two isolated strains represent two novel species of the genus , for which the names sp. nov. and sp. nov. are proposed. The type strains are SG12 (=GDMCC 1.3407=JCM 39330) and SG195 (= GDMCC 1.3308=JCM 39327), respectively.

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2023-05-26
2024-03-03
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References

  1. Li Y, Gong X. Effects of dissolved organic matter on the bioavailability of heavy metals during microbial dissimilatory iron reduction: a review. Rev Environ Contam Toxicol 2021; 257:69–92 [View Article] [PubMed]
    [Google Scholar]
  2. Cummings DE, March AW, Bostick B, Spring S, Caccavo F et al. Evidence for microbial Fe(III) reduction in anoxic, mining-impacted lake sediments (Lake Coeur d’Alene, Idaho). Appl Environ Microbiol 2000; 66:154–162 [View Article] [PubMed]
    [Google Scholar]
  3. Achtnich C, Bak F, Conrad R. Competition for electron donors among nitrate reducers, ferric iron reducers, sulfate reducers, and methanogens in anoxic paddy soil. Biol Fertil Soils 1995; 19:65–72 [View Article]
    [Google Scholar]
  4. Nealson KH, Saffarini D. Iron and manganese in anaerobic respiration: environmental significance, physiology, and regulation. Annu Rev Microbiol 1994; 48:311–343 [View Article] [PubMed]
    [Google Scholar]
  5. Hu A, Ye J, Ren GP, Qi YP, Chen YP et al. Metal-free semiconductor-based bio-nano hybrids for sustainable CO2-to-CH4 conversion with high quantum yield. Angewandte Chemie 2022; 34:
    [Google Scholar]
  6. Coates JD, Ellis DJ, Gaw CV, Lovley DR. Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. Int J Syst Bacteriol 1999; 49:1615–1622 [View Article] [PubMed]
    [Google Scholar]
  7. Han S, Tang R, Yang S, Xie CJ, Narsing Rao MP et al. Two ferric-reducing bacteria Geothrix terrae sp. nov. and Geothrix alkalitolerans sp. nov., isolated from paddy soil. Arch Microbiol 2022; 204:699 [View Article] [PubMed]
    [Google Scholar]
  8. Liu GH, Yang S, Tang R, Xie CJ, Zhou SG. Genome analysis and description of three novel diazotrophs Geomonas species isolated from paddy soils. Front Microbiol 2021; 12:801462 [View Article] [PubMed]
    [Google Scholar]
  9. Dong ZY, Narsing Rao MP, Wang HF, Fang BZ, Liu YH et al. Transcriptomic analysis of two endophytes involved in enhancing salt stress ability of Arabidopsis thaliana. Sci Total Environ 2019; 686:107–117 [View Article] [PubMed]
    [Google Scholar]
  10. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  14. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  16. Kumar S, Stecher G, Li M, Knyaz C, Tamura K et al. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
    [Google Scholar]
  17. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article]
    [Google Scholar]
  18. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
    [Google Scholar]
  19. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article] [PubMed]
    [Google Scholar]
  20. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:277D–280 [View Article]
    [Google Scholar]
  21. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006; 34:D354–7 [View Article] [PubMed]
    [Google Scholar]
  22. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
    [Google Scholar]
  23. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  24. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article]
    [Google Scholar]
  25. Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
  26. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  27. 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]
  28. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  29. Itoh H, Xu Z, Masuda Y, Ushijima N, Hayakawa C et al. Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas. Int J Syst Evol Microbiol 2021; 71: [View Article]
    [Google Scholar]
  30. Pitts KE, Dobbin PS, Reyes-Ramirez F, Thomson AJ, Richardson DJ et al. Characterization of the Shewanella oneidensis MR-1 decaheme cytochrome MtrA: expression in Escherichia coli confers the ability to reduce soluble Fe(III) chelates. J Biol Chem 2003; 278:27758–27765 [View Article] [PubMed]
    [Google Scholar]
  31. Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS et al. FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genome and metagenome assemblies. Front Microbiol 2020; 11:37 [View Article] [PubMed]
    [Google Scholar]
  32. Campeciño J, Lagishetty S, Wawrzak Z, Sosa Alfaro V, Lehnert N et al. Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass. J Biol Chemist 2020; 295:11455–11465 [View Article]
    [Google Scholar]
  33. Braker G, Tiedje JM. Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Appl Environ Microbiol 2003; 69:3476–3483 [View Article] [PubMed]
    [Google Scholar]
  34. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
    [Google Scholar]
  35. Chen YG, Cui XL, Pukall R, Li HM, Yang YL et al. Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China. Int J Syst Evol Microbiol 2007; 57:2327–2332 [View Article] [PubMed]
    [Google Scholar]
  36. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article] [PubMed]
    [Google Scholar]
  37. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
    [Google Scholar]
  38. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using Reverse Phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  39. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News 1990; 20:16
    [Google Scholar]
  40. Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJ et al. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol 1993; 159:336–344 [View Article] [PubMed]
    [Google Scholar]
  41. Onley JR, Ahsan S, Sanford RA, Löffler FE. Denitrification by Anaeromyxobacter dehalogenans, a common soil bacterium lacking the nitrite reductase genes nirS and nirK. Appl Environ Microbiol 2018; 84:e1985–e1917 [View Article] [PubMed]
    [Google Scholar]
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