Advertisement

Antonie van Leeuwenhoek

, Volume 108, Issue 6, pp 1457–1468 | Cite as

Taxonomic characterisation of Proteus terrae sp. nov., a N2O-producing, nitrate-ammonifying soil bacterium

  • Undine BehrendtEmail author
  • Jürgen Augustin
  • Cathrin Spröer
  • Jörg Gelbrecht
  • Peter Schumann
  • Andreas Ulrich
Original Paper

Abstract

In the context of studying the influence of N-fertilization on N2 and N2O flux rates in relation to the soil bacterial community composition in fen peat grassland, a group of bacterial strains was isolated that performed dissimilatory nitrate reduction to ammonium and concomitantly produced N2O. The amount of nitrous oxide produced was influenced by the C/N ratio of the medium. The potential to generate nitrous oxide was increased by higher availability of nitrate-N. Phylogenetic analysis based on the 16S rRNA and the rpoB gene sequences demonstrated that the investigated isolates belong to the genus Proteus, showing high similarity with the respective type strains of Proteus vulgaris and Proteus penneri. DNA–DNA hybridization studies revealed differences at the species level. These differences were substantiated by MALDI-TOF MS analysis and several distinct physiological characteristics. On the basis of these results, it was concluded that the soil isolates represent a novel species for which the name Proteus terrae sp. nov. (type strain N5/687T =DSM 29910T =LMG 28659T) is proposed.

Keywords

Proteus terrae sp. nov. Phylogenetic characterization Phenotypic characterisation Dissimilatory nitrate reduction to ammonium Nitrous oxide production C/N ratio Fen peat soil 

Notes

Acknowledgments

We wish to thank Mrs. B. Selch, Mrs. S. Weinert, Mr. B. Gusovius (ZALF-Müncheberg), Mrs. A. Wasner, Mrs. B. Sträubler and Mrs. G. Pötter (DSMZ-Braunschweig), and Mr. Th. Rossoll (IGB-Berlin) for their excellent technical assistance.

Supplementary material

10482_2015_601_MOESM1_ESM.eps (891 kb)
Fig. S1 Neighbour joining tree of the 16S rRNA gene showing the relationships between strain N5/687T and type strains of the species of the genus Proteus and related genera. Filled circles indicate branches of the tree that were also obtained using the maximum likelihood method. The sequence of Yersinia kristensenii ATCC 33638T (GenBank accession no. AF366381) was used as an outgroup (not shown). Numbers at the nodes indicate bootstrap support of more than 70 % (based on 1000 resampled datasets). Bar 0.01 changes per nucleotide position. Supplementary material 1 (EPS 890 kb)
10482_2015_601_MOESM2_ESM.eps (770 kb)
Fig. S2 Neighbour joining tree of the rpoB gene showing the relationships between strain N5/687T and type strains of the species of the genus Proteus and related genera. Filled circles indicate branches of the tree that were also obtained using the maximum likelihood method. The sequence of Yersinia kristensenii CCUG 11294T (GenBank accession no. EF1755969) was used as an outgroup (not shown). Numbers at the nodes indicate bootstrap support of more than 70 % (based on 1000 resampled datasets). Bar 0.01 changes per nucleotide position. Supplementary material 2 (EPS 769 kb)
10482_2015_601_MOESM3_ESM.eps (823 kb)
Fig. S3 Consensus tree showing the molecular evolutionary relationships of the 16S rRNA and rpoB genes. The sequences of Yersinia kristensenii ATCC 33638T (GenBank accession no. AF366381 and EF1755969) was used as an outgroup (not shown). Bar, 0.01 changes per nucleotide position. Supplementary material 3 (EPS 822 kb)
10482_2015_601_MOESM4_ESM.docx (36 kb)
Supplementary material 4 (DOCX 35 kb)
10482_2015_601_MOESM5_ESM.docx (16 kb)
Supplementary material 5 (DOCX 16 kb)
10482_2015_601_MOESM6_ESM.docx (19 kb)
Supplementary material 6 (DOCX 19 kb)

References

  1. Appleyard RK (1954) Segregation of new lysogenic types during growth of a doubly lysogenic strain derived from Escherichia coli K12. Genetics 39:440–452PubMedPubMedCentralGoogle Scholar
  2. Behrendt U, Ulrich A, Schumann P, Erler W, Burghardt J, Seyfarth W (1999) A taxonomic study of bacteria isolated from grasses: a proposed new species Pseudomonas graminis sp. nov. Int J Syst Bacteriol 49:297–308. doi: 10.1099/00207713-49-1-297 CrossRefPubMedGoogle Scholar
  3. Behrendt U, Ulrich A, Schumann P (2003) Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov. Int J Syst Evol Microbiol 53:1461–1469. doi: 10.1099/ijs.0.02567-0 CrossRefPubMedGoogle Scholar
  4. Behrendt U, Ulrich A, Schumann P (2008) Chryseobacterium gregarium sp. nov., isolated from decaying plant material. Int J Syst Evol Microbiol 58:1069–1074. doi: 10.1099/ijs.0.65544-0 CrossRefPubMedGoogle Scholar
  5. Behrendt U, Schumann P, Stieglmeier M, Pukall R, Augustin J, Spröer C, Schwendner P, Moissl-Eichinger C, Ulrich A (2010) Characterization of heterotrophic nitrifying bacteria with respiratory ammonification and denitrification activity - description of Paenibacillus uliginis sp. nov., an inhabitant of fen peat soil and Paenibacillus purispatii sp. nov., isolated from a spacecraft assembly clean room. Syst Appl Microbiol 33:328–336. doi: 10.1016/j.syapm.2010.07.004 CrossRefPubMedGoogle Scholar
  6. Bleakley BH, Tiedje JM (1982) Nitrous oxide production by organisms other than nitrifiers or denitrifiers. Appl Environ Microbiol 44:1342–1348PubMedPubMedCentralGoogle Scholar
  7. Cashion P, Holder-Franklin MA, McCully J, Franklin M (1977) A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81:461–466CrossRefPubMedGoogle Scholar
  8. De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142CrossRefPubMedGoogle Scholar
  9. Fazzolari E, Mariotti A, Germon JC (1990) Nitrate reduction to ammonia: a dissimilatory process in Enterobacter amnigenus. Can J Microbiol 36:779–785. doi: 10.1139/m90-134 CrossRefPubMedGoogle Scholar
  10. Fazzolari E, Nicolardo B, Germon JC (1998) Simultaneous effects of increasing levels of glucose and oxygen partial pressures on denitrification and dissimilatory nitrate reduction to ammonium in repacked soil cores. Eur J Soil Biol 34:47–52CrossRefGoogle Scholar
  11. Felsenstein J (1981) Evolutionary tree from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  12. Felsenstein J (1993) PHYLIP (phylogeny interference package), 3.6a edn. University of Washington, SeattleGoogle Scholar
  13. Giammanco GM, Grimont PAD, Grimont F, Lefevre M, Giammanco G, Pignato S (2011) Phylogenetic analysis of the genera Proteus, Morganella and Providencia by comparison of rpoB gene sequences of type and clinical strains suggests the reclassification of Proteus myxofaciens in a new genus, Cosenzaea gen. nov., as Cosenzaea myxofaciens comb. nov. Int J Syst Evol Microbiol 61:1638–1644. doi: 10.1099/ijs.0.021964-0 CrossRefPubMedGoogle Scholar
  14. He Y, Li H, Lu X, Stratton CW, Tang Y-W (2010) Mass spectrometry biotyper system identifies enteric bacterial pathogens directly from colonies grown on selective stool culture media. J Clin Microbiol 48:3888–3892. doi: 10.1128/jcm.01290-10 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Hickman FW, Steigerwalt AG, Farmer JJ, Brenner DJ (1982) Identification of Proteus penneri sp. nov., formerly known as Proteus vulgaris indole negative or as Proteus vulgaris biogroup 1. J Clin Microbiol 15:1097–1102PubMedPubMedCentralGoogle Scholar
  16. Huss VAR, Festl H, Schleifer KH (1983) Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192. doi: 10.1016/S0723-2020(83)80048-4 CrossRefPubMedGoogle Scholar
  17. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press Inc, New York, pp 21–132CrossRefGoogle Scholar
  18. Kämpfer P, Meyer S, Müller HE (1997) Characterization of Buttiauxella and Kluyvera species by analysis of whole cell fatty acid patterns. Syst Appl Microbiol 20:566–571. doi: 10.1016/S0723-2020(97)80028-8 CrossRefGoogle Scholar
  19. Manos J, Belas R (2006) The Genera Proteus, Providencia, and Morganella. In: Dworkin M, Falkow S, Rosenber E, Schleifer KH, Stackebrandt E (eds) Prokaryotes, vol 6, 3rd edn. Springer, New York, pp 245–269CrossRefGoogle Scholar
  20. Martin K, Schumann P, Rainey FA, Schuetze B, Groth I (1997) Janibacter limosus gen. nov., sp. nov., a new actinomycete with meso-diaminopimelic acid in the cell wall. Int J Syst Bacteriol 47:529–534CrossRefPubMedGoogle Scholar
  21. Mohan SB, Cole JA (2007) The dissimilatory reduction of nitrate to ammonia by anaerobic bacteria. In: Bothe H, Ferguson S, Newton WE (eds) Biology of the nitrogen cycle. Elsevier, Amsterdam, pp 93–106CrossRefGoogle Scholar
  22. Mohan SB, Schmid M, Jetten M, Cole J (2004) Detection and widespread distribution of the nrfA gene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification. FEMS Microbiol Ecol 49:433–443. doi: 10.1016/j.femsec.2004.04.012 CrossRefPubMedGoogle Scholar
  23. Mollet C, Drancourt M, Raoult D (1997) rpoB sequence analysis as a novel basis for bacterial identification. Mol Microbiol 26:1005–1011CrossRefPubMedGoogle Scholar
  24. O’Hara CM, Brenner FW, Miller JM (2000a) Classification, identification, and clinical significance of Proteus, Providencia, and Morganella. Clin Microbiol Rev 13:534–546. doi: 10.1128/cmr.13.4.534-546.2000 CrossRefPubMedPubMedCentralGoogle Scholar
  25. O’Hara CM et al (2000b) Classification of Proteus vulgaris biogroup 3 with recognition of Proteus hauseri sp. nov., nom. rev. and unnamed Proteus genomospecies 4, 5 and 6. Int J Syst Evol Microbiol 50:1869–1875. doi: 10.1099/00207713-50-5-1869 CrossRefPubMedGoogle Scholar
  26. Pavlovic M, Konrad R, Iwobi AN, Sing A, Busch U, Huber I (2012) A dual approach employing MALDI-TOF MS and real-time PCR for fast species identification within the Enterobacter cloacae complex. FEMS Microbiol Lett 328:46–53. doi: 10.1111/j.1574-6968.2011.02479.x CrossRefPubMedGoogle Scholar
  27. Philippot L (2005) Tracking nitrate reducers and denitrifiers in the environment. Biochem Soc Trans 33:200–204. doi: 10.1042/BST0330200 CrossRefPubMedGoogle Scholar
  28. Richard C, Kiredjian M (1995) Laboratory methods for the identification of strictly aerobic gram-negative bacilli. Institut Pasteur, ParisGoogle Scholar
  29. Rózalski A, Sidorczyk Z, Kotełko K (1997) Potential virulence factors of Proteus bacilli. Microbiol Mol Biol Rev 61:65–89PubMedPubMedCentralGoogle Scholar
  30. Rütting T, Boeckx P, Müller C, Klemedtsson L (2011) Assessment of the importance of dissimilatory nitrate reduction to ammonium for the terrestrial nitrogen cycle. Biogeosci 8:1169–1196. doi: 10.5194/bg-8-1779-2011 CrossRefGoogle Scholar
  31. Ryu E (1938) On the Gram-differentiation of bacteria by the simplest method. J Jap Soc Vet Sci 17:58–63CrossRefGoogle Scholar
  32. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  33. Schreiber F, Wunderlin P, Udert KM, Wells GF (2012) Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies. Front Microbiol 3:1–24. doi: 10.3389/fmicb.2012.00372 CrossRefGoogle Scholar
  34. Simon J (2002) Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev 26:285–309CrossRefPubMedGoogle Scholar
  35. Simon J (2011) Organization of respiratory electron transport chains in nitrate-reducing and nitrifying bacteria. In: Moir JWB (ed) Nitrogen cycling in bacteria: molecular analysis. Caister Academic Press, Norfolk, pp 39–58Google Scholar
  36. Simon J, Klotz MG (2013) Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations. Biochim Biophys Acta 1827:114–135. doi: 10.1016/j.bbabio.2012.07.005 CrossRefPubMedGoogle Scholar
  37. Simon J, Kern M, Hermann B, Einsle O, Butt JN (2011) Physiological function and catalytic versatility of bacterial multihaem cytochromes c involved in nitrogen and sulfur cycling. Biochem Soc Trans 39:1864–1870. doi: 10.1042/BST20110713 CrossRefPubMedGoogle Scholar
  38. Smith MS, Zimmermann K (1981) Nitrous oxide production by nondenitrifying soil nitrate reducers. Soil Sci Soc Am J 45:865–871. doi: 10.2136/sssaj1981.03615995004500050008x CrossRefGoogle Scholar
  39. Stein LY (2011) Surveying N2O-producing pathways in bacteria. In: Klotz MG (ed) Methods in Enzymology, vol 486. Academic Press, Burlington, pp 131–152Google Scholar
  40. Stewart V (1994) Regulation of nitrate and nitrite reductase synthesis in enterobacteria. Antonie Van Leeuwenhoek 66:37–45. doi: 10.1007/BF00871631 CrossRefPubMedGoogle Scholar
  41. Stremińska MA, Felgate H, Rowley G, Richardson DJ, Baggs EM (2012) Nitrous oxide production in soil isolates of nitrate-ammonifying bacteria. Env Microbiol Rep 4:66–71. doi: 10.1111/j.1758-2229.2011.00302.x CrossRefGoogle Scholar
  42. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  43. Ulrich K, Ulrich A, Ewald D (2008) Diversity of endophytic bacterial communities in poplar grown under field conditions. FEMS Microbiol Ecol 63:169–180. doi: 10.1111/j.1574-6941.2007.00419.x CrossRefPubMedGoogle Scholar
  44. Wayne LG et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464. doi: 10.1099/00207713-37-4-463 CrossRefGoogle Scholar
  45. Welsh A, Chee-Sanford JC, Connor LM, Loffler FE, Sanford RA (2014) Refined NrfA phylogeny improves PCR-based nrfA gene detection. Appl Environ Microbiol 80:2110–2119. doi: 10.1128/AEM.03443-13 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Leibniz Centre for Agricultural Landscape Research (ZALF)Institute for Landscape BiogeochemistryMünchebergGermany
  2. 2.Leibniz-Institute of Freshwater Ecology and Inland FisheriesCentral Chemical LaboratoryBerlinGermany
  3. 3.Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell CulturesBraunschweigGermany

Personalised recommendations