Investigating the diversity of pseudomonas spp. in soil using culture dependent and independent techniques

Current Microbiology

Volumn 67, Issue 4, 2013, Pages 423-430

  Li, Lili ^a   Abu Al Soud, Waleed ^a   Bergmark, Lasse ^a   Riber, Leise ^a   Hansen, Lars H ^a   Magid, Jakob ^b   Sørensen, Søren J ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FERTILIZER; NITROGEN; RNA 16S;

AMPLICON; ARTICLE; BACTERIAL COUNT; BACTERIUM COLONY; BACTERIUM CULTURE; BACTERIUM ISOLATION; CATTLE; COLONY FORMING UNIT; CONTROLLED STUDY; CULTURE MEDIUM; DNA EXTRACTION; GENE DOSAGE; MANURE; MICROBIAL COMMUNITY; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSEUDOMONAS; PYROSEQUENCING; QUANTITATIVE ANALYSIS; SENSITIVITY AND SPECIFICITY; SLUDGE; SOIL MICROFLORA; SPECIES DIVERSITY; URBAN AREA;

BACTERIA (MICROORGANISMS); BOS; PSEUDOMONAS;

EID: 84883231380     PISSN: 03438651     EISSN: 14320991     Source Type: Journal    
DOI: 10.1007/s00284-013-0382-x     Document Type: Article

References (36)

1. Aagot N, Nybroe O, Nielsen P, Johnsen K (2001) An altered Pseudomonas diversity is recovered from soil by using nutrient-poor Pseudomonas-selective soil extract media. Appl Environ Microbiol 67:5233-5239
2. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
3. Bergmark L, Poulsen PHB, Al-Soud WA, Norman A, Hansen LH, Sørensen SJ (2012) Assessment of the specificity of Burkholderia and Pseudomonas qPCR assays for detection of these genera in soil using 454 pyrosequencing. FEMS Microbiol Lett 333:77-84
4. Bodilis J, Nsigue-Meilo S, Besaury L, Quillet L (2012) Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in Pseudomonas. PLoS ONE 7:e35647
5. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266-267
6. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335-336
7. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33:D294-D296
8. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461
9. Evans FF, Seldin L, Sebastian GV, Kjelleberg S, Holmstrom C, Rosado AS (2004) Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. in soil microcosms as evaluated by 16S rRNA based-PCR and DGGE. Lett Appl Microbiol 38:93-98
10. Fava F, Armenante PM, Kafkewitz D (1995) Aerobic degradation and dechlorination of 2-chlorophenol, 3-chlorophenol and 4-chlorophenol by a Pseudomonas pickettii strain. Lett Appl Microbiol 21:307-312
11. Goebel BM, Stackebrandt E (1994) Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl Environ Microbiol 60:1614-1621
12. Gould WD, Hagedorn C, Bardinelli TR, Zablotowicz RM (1985) New selective media for enumeration and recovery of fluorescent pseudomonads from various habitats. Appl Environ Microbiol 49:28-32
13. Hill GA, Robinson CW (1975) Substrate inhibition kinetics - phenol degradation by Pseudomonas putida. Biotechnol Bioeng 17:1599-1615
14. Johnsen K, Nielsen P (1999) Diversity of Pseudomonas strains isolated with King's B and Gould's S1 agar determined by repetitive extragenic palindromic polymerase chain reaction, 16S rDNA sequencing and Fourier transform infrared spectroscopy characterisation. FEMS Microbiol Lett 173:155-162
15. Johnson JK, Arduino SM, Stine OC, Johnson JA, Harris AD (2007) Multilocus sequence typing compared to pulsed-field gel electrophoresis for molecular typing of Pseudomonas aeruginosa. J Clin Microbiol 45:3707-3712
16. Kim M, Morrison M, Yu ZT (2011) Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J Microbiol Methods 84:81-87
17. King EO, Ward MK, Raney DE (1954) Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 44:301-307
18. Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 29:181-184
19. Kragelund L, Leopold K, Nybroe O (1996) Outer membrane protein heterogeneity within Pseudomonas fluorescens and P. putida and use of an OprF antibody as a probe for rRNA homology group I pseudomonads. Appl Environ Microbiol 62:480-485
20. Lloyd-Jones G, Laurie AD, Tizzard AC (2005) Quantification of the Pseudomonas population in New Zealand soils by fluorogenic PCR assay and culturing techniques. J Microbiol Methods 60:217-224
21. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228-8235
22. Magid J, Luxhøi J, Jensen LS, Møller J, Bruun S (2006) Establishment of a long-term field trial with urban fertilizers - is recycling of nutrients from urban areas to peri-urban organic farms feasible? In: Raupp J, Pekrun C, Oltmanns M, Köpke U (eds) Long-term field experiments in organic farming. Society of Organic Agriculture Research (ISOFAR). Verlag Dr. Köster, Berlin, pp 59-78
23. Masoud W, Takamiya M, Vogensen FK, Lillevang S, Abu Al-Soud W, Sorensen SJ, Jakobsen M (2011) Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing. Int Dairy J 21:142-148
24. Masuda N, Sakagawa E, Ohya S, Gotoh N, Tsujimoto H, Nishino T (2000) Substrate specificities of MexAB-OprM, MexCD-OprJ, and MexXY-OprM efflux pumps in Pseudomonas aeruginosa. Antimicrob Agents Chemother 44:3322-3327
25. Peix A, Ramirez-Bahena MH, Velazquez E (2009) Historical evolution and current status of the taxonomy of genus Pseudomonas. Infect Genet Evol 9:1132-1147
26. Poole K (2001) Multidrug efflux pumps and antimicrobial resistance in Pseudomonas aeruginosa and related organisms. J Mol Microbiol Biotechnol 3:255-264
27. Poulsen PHB, Al-Soud WA, Bergmark L, Magid J, Hansen LH, Sørensen SJ (2013) Effects of fertilization with urban and agricultural organic wastes in a field trial - Prokaryotic diversity investigated by pyrosequencing. Soil Biol Biochem 57:784-793
28. Quince C, Curtis TP, Sloan WT (2008) The rational exploration of microbial diversity. ISME J 2:997-1006
29. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283-290
30. Ross IL, Alami Y, Harvey PR, Achouak W, Ryder MH (2000) Genetic diversity and biological control activity of novel species of closely related pseudomonads isolated from wheat field soils in South Australia. Appl Environ Microbiol 66:1609-1616
31. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 103:12115-12120
32. Spasenovski T, Carroll MP, Payne MS, Bruce KD (2009) Molecular analysis of diversity within the genus Pseudomonas in the lungs of cystic fibrosis patients. Diagn Microbiol Infect Dis 63:261-267
33. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FSL, Hufnagle WO, Kowalik DJ, Lagrou M et al (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406:959-964
34. Tarnawski S, Hamelin J, Locatelli L, Aragno M, Fromin N (2003) Examination of Gould's modified S1 (mS1) selective medium and Angle's non-selective medium for describing the diversity of Pseudomonas spp. in soil and root environments. FEMS Microbiol Ecol 45:97-104
35. Widmer F, Seidler RJ, Gillevet PM, Watrud LS, Di Giovanni GD (1998) A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl Environ Microbiol 64:2545-2553
36. Yao JDC, Moellering RC Jr (1999) Antibacterial agents. In: Murrary PR (ed) Manual of clinical microbiology, 7th edn. American Society for Microbiology, Washington DC, pp 1474-1504