Culture-dependent and culture-independent microbial investigation of pine litters and soil in subtropical Australia

Journal of Soils and Sediments

Volumn 9, Issue 2, 2009, Pages 148-160

  Zhang, Li ^a   Xu, Zhihong ^a   Patel, Bharat ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

16S rRNA gene libraries; Bacterial community; Isolation; Phylogeny; Pine forest leaf litters and soil

Indexed keywords

BACTERIUM; CONIFEROUS TREE; ECOSYSTEM FUNCTION; LITTER; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; PLANTATION; REFORESTATION; SOIL MICROORGANISM; SOIL QUALITY; SPECIES DIVERSITY; SUBTROPICAL REGION;

ACIDOBACTERIUM; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); FIRMICUTES; PINUS ELLIOTTII; PLANCTOMYCETES; PROTEOBACTERIA; UNCLASSIFIED BACTERIA; VERRUCOMICROBIALES;

EID: 63149088178     PISSN: 14390108     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11368-009-0059-z     Document Type: Article

References (63)

1. SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller DJ Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402
2. KT Andrews BKC Patel 1996 Fervidobacterium gondwanense sp nov, a new thermophilic anaerobic bacterium isolated from nonvolcanically heated geothermal waters of the Great Artesian Basin of Australia Int J Syst Evol Bacteriol 46 265 269
3. PE Axelrood ML Chow CC Radomski JM McDermott J Davies 2002 Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance Can J Microbiol 48 655 674
4. GM Balestra IJ Misaghi 1997 Increasing the efficiency of the plate counting method for estimating bacterial diversity J Microbiol Methods 30 111 117
5. J Bengtsson H Lundkvist P Saetre B Sohlenius B Solbreck 1998 Effects of organic matter removal on the soil food web: Forestry practices meet ecological theory Appl Soil Ecol 9 137 143
6. L Bragazza C Siffi P Iacumin R Gerdol 2007 Mass loss and nutrient release during litter decay in peatland: the role of microbial adaptability to litter chemistry Soil Biol Biochem 39 257 267
7. CR Chen ZH Xu 2005 Soil carbon and nitrogen pools and microbial properties in a 6-year-old slash pine plantation of subtropical Australia: impacts of harvest residue management For Ecol Manage 206 237 247
8. CR Chen ZH Xu P Keay SL Zhang 2005 Total soluble nitrogen in forest soils as determined by persulfate oxidation and by high temperature catalytic oxidation Aust J Soil Res 43 515 523
9. O Dilly J Bloem A Vos JC Munch 2004 Bacterial diversity in agricultural soils during litter decomposition Appl Environ Microbiol 70 468 474
10. J Dunbar S Takala SM Barns JA Davis CR Kuske 1999 Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning Appl Environ Microbiol 65 1662 1669
11. J Felsenstein 1985 Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 783 791
12. A Felske A Wolterink R Van Lis WM De Vos AD Akkermans 2000 Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes Appl Environ Microbiol 66 3998 4003
13. MJ Ferris AL Ruff-Roberts ED Kopczynski MM Bateson DM Ward 1996 Enrichment culture and microscopy conceal diverse thermophilic Synechococcus populations in a single hot spring microbial mat habitat Appl Environ Microbiol 62 1045 1050
14. JS Garland CP Alex KJ Henrickson TL McAuliffe DG Maki 2005 A vancomycin-heparin lock solution for prevention of nosocomial bloodstream infection in critically ill neonates with peripherally inserted central venous catheters: a prospective, randomized trial Pediatrics 116 E198 E205
15. Y Ge JZ He YG Zhu JB Zhang ZH Xu LM Zhang YM Zheng 2008 Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies? ISME J 2 254 264
16. Y Ge JB Zhang LM Zhang M Yang JZ He 2008 Long-term fertilization regimes and diversity of an agricultural affect bacterial community structure soil in northern China J Soils Sediments 8 43 50
17. R Großkropf PH Janssen W Liesack 1998 Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval Appl Environ Microbiol 64 960 969
18. E Hackl S Zechmeister-Boltenstern L Bodrossy A Sessitsch 2004 Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils Appl Environ Microbiol 70 5057 5065
19. E Hackl M Pfeffer C Donat G Bachmann S Zechmeister-Boltenstern 2005 Composition of the microbial communities in the mineral soil under different types of natural forest Soil Biol Biochem 37 661 671
20. L Hall-Stoodley P Stoodley 2005 Biofilm formation and dispersal and the transmission of human pathogens Trends Microbiol 13 300 301
21. H Hayashidani Y Ohtomo Y Toyokawa M Saito K Kaneko J Kosuge M Kato M Ogawa G Kapperud 1995 Sources of sporadic human infection with Yersinia enterocolitica serovar O:8 in Aomori Prefecture, Japan Contrib Microbiol Immunol 13 29 32
22. JZ He ZH Xu J Hughes 2006 Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia FEMS Microbiol Ecol 55 38 47
23. B Hoorens R Aerts M Stroetenga 2003 Does initial litter chemistry explain litter mixture effects on decomposition? Oecologia 137 578 586
24. RA Hurt XY Qiu LY Wu Y Roh AV Palumbo JM Tiedje JH Zhou 2001 Simultaneous recovery of RNA and DNA from soils and sediments Appl Environ Microbiol 67 4495 4503
25. H Jin R Zhou MS Kang R Luo XW Cai HC Chen 2006 Biofilm formation by field isolates and reference strains of Haemophilus parasuis Veterin Microbiol 118 117 123
26. SJ Joseph P Hugenholtz P Sangwan CA Osborne PH Janssen 2003 Laboratory cultivation of widespread and previously uncultured soil bacteria Appl Environ Microbiol 69 7210 7215
27. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic, New York, USA, pp 21-32
28. O Kaiser A Puhler W Selbitschka 2001 Phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches Microb Ecol 42 136 149
29. P Kampfer FA Rainey MA Andersson ELN Lassila U Ulrych HJ Busse N Weiss R Mikkola M Salkinoja-Salonen 2000 Frigoribacterium faeni gen. nov., sp nov., a novel psychrophilic genus of the family Microbacteriaceae Int J Syst Evol Microbiol 50 355 363
30. JL Kirk LA Beaudette M Hart P Moutoglis JN Klironomos H Lee JT Trevors 2004 Methods of studying soil microbial diversity J Microbiol Methods 58 169 188
31. N Kishimoto T Tano 1987 Acidophilic heterotrophic bacteria isolated from acidic mine drainage, sewage and soils J Gen Appl Microbiol 33 11 25
32. CR Kuske SM Barns JD Busch 1997 Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions Appl Environ Microbiol 63 3614 3621
33. AM Laverman M Braster WFM Roling HW van Verseveld 2005 Bacterial community structure and metabolic profiles in a forest soil exhibiting spatially variable net nitrate production Soil Biol Biochem 37 1581 1588
34. SE Leckie 2005 Methods of microbial community profiling and their application to forest soils For Ecol Manage 220 88 106
35. 2 efflux and fungal and bacterial biomass in a plantation and a secondary forest in wet tropics in Puerto Rico Plant Soil 268 151 160
36. W Liesack E Stackebrandt 1992 Occurrence of novel groups of the domain bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment J Bacteriol 174 5072 5078
37. Liesack W, Janssen PH, Rainey FA, Ward-Rainey NL, Stackenbrandt E (1997) Microbial diversity in soil: the need for a combined approach using molecular and cultivation techniques. In: van Elsas JD, Trevors JT, Wellington EMH (eds) Modern soil microbiology. Marcel Dekker, New York, NY, pp 375-439
38. BL Maidak GJ Olsen N Larsen R Overbeek MJ McCaughey CR Woese 1997 The RDP (Ribosomal Database Project) Nucleic Acids Res 25 109 110
39. PE Maloney AHC van Bruggen S Hu 1997 Bacterial community structure in relation to the carbon environments in lettuce and tomato rhizospheres and in bulk soil Microb Ecol 34 109 117
40. MK Mannisto P Schumann FA Rainey P Kampfer K Tsitko MA Tiirola MS Salkinoja-Salonen 2000 Subtercola boreus gen. nov., sp. nov and Subtercola frigoramans sp nov., two new psychrophilic actinobacteria isolated from boreal groundwater Int J Syst Evol Microbiol 50 1731 1739
41. AE McCaig LA Glover JI Prosser 1999 Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures Appl Environ Microbiol 65 1721 1730
42. B Nogales ER Moore WR Abraham KN Timmis 1999 Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil Environ Microbiol 1 199 212
43. NR Pace 1997 A molecular view of microbial diversity and the biosphere Science 276 734 740
44. LA Proteous JL Armstrong 1991 Recovery of bulk DNA from soil by a rapid, small-scale extraction method Curr Microbiol 22 345 348
45. MR Rondon RM Goodman J Handelsman 1999 The Earth's bounty: assessing and accessing soil microbial diversity Trends Biotechnol 17 403 409
46. MR Rondon PR August AD Bettermann SF Brady TH Grossman MR Liles KA Loiacono BA Lynch IA MacNeil C Minor CL Tiong M Gilman MS Osburne J Clardy J Handelsman RM Goodman 2000 Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms Appl Environ Microbiol 66 2541 2547
47. P Rosenbrock F Buscot JC Munch 1995 Fungal succession and changes in the fungal degradation potential during the initial-stage of litter decomposition in a black-alder forest [Alnus glutinosa (L) Gaertn] Eur J Soil Biol 31 1 11
48. M Sait P Hugenholtz PH Janssen 2002 Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys Environ Microbiol 4 654 666
49. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
50. P Sangwan S Kovac KE Davis M Sait PH Janssen 2005 Detection and cultivation of soil verrucomicrobia Appl Environ Microbiol 71 8402 8410
51. E Stackebrandt W Liesack BM Goebel 1993 Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis FASEB J 7 232 236
52. YL Tsai BH Olson 1992 Detection of low numbers of bacterial cells in soil and sediments by polymerase chain reaction Appl Environ Microbiol 58 754 757
53. T Tsuchida K Makimoto M Toki K Sakai E Onaka Y Otani 2007 The effectiveness of a nurse-initiated intervention to reduce catheter-associated bloodstream infections in an urban acute hospital: An intervention study with before and after comparison Int J Nurs Stud 44 1324 1333
54. Y Van de Peer J Jansen P De Rijk P De Wachter 1997 Database on the structure of small ribosomal subunit RNA Nucleic Acids Res 25 111 116
55. FV Wintzingerode UB Gobel E Staackebrandt 1997 Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis FEMS Microbiol Rev 21 213 229
56. CR Woese 1987 Bacterial evolution Microbiol Rev 51 221 271
57. AKC Wong M You 1985 Entropy and distance of random graphs with application to structural pattern-recognition IEEE Trans Pattern Anal Machine Intel 7 599 609
58. ZH Xu JA Simpson DO Osborne 1995 Mineral-nutrition of slash pine in subtropical Australia. 1. Stand growth-response to fertilization Fertil Res 41 93 100
59. ZH Xu PG Saffigna GD Farquhar JA Simpson RJ Haines S Walker DO Osborne D Guinto 2000 Carbon isotope discrimination and oxygen isotope composition in clones of the F-1 hybrid between slash pine and Caribbean pine in relation to tree growth, water-use efficiency and foliar nutrient concentration Tree Physiol 20 1209 1217
60. QF Xu PK Jiang ZH Xu 2008 Soil microbial functional diversity under intensively managed bamboo plantations in southern China J Soils Sediments 8 177 183
61. ZH Xu S Ward CR Chen T Blumfield N Prasolova JX Liu 2008 Soil carbon and nutrient pools, microbial properties and gross nitrogen transformations in adjacent natural forest and hoop pine plantations of subtropical Australia J Soils Sediments 8 99 105
62. DR Zak D Tilman RR Parmenter CW Rice FM Fisher J Vose D Milchunas CW Martin 1994 Plant-production and soil-microorganisms in late-successional ecosystems-a continental-scale study Ecology 75 2333 2347
63. JK Zimmerman WM Pulliam DJ Lodge V Quinonesorfila N Fetcher S Guzmangrajales JA Parrotta CE Asbury LR Walker RB Waide 1995 Nitrogen immobilization by decomposing woody debris and the recovery of tropical wet forest from hurricane damage Oikos 72 314 322