Evidence of variability in the structure and recruitment of rhizospheric and endophytic bacterial communities associated with arable sweet sorghum (Sorghum bicolor (L) Moench)

Plant and Soil

Volumn 372, Issue 1-2, 2013, Pages 265-278

  Ramond, Jean Baptiste ^a,b   Tshabuse, Freedom ^a   Bopda, Cyprien W ^a   Cowan, Don A ^a,b   Tuffin, Marla I ^a  

^a UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^b UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

Bacteria recruitment; Molecular fingerprinting (T RFLP DGGE); Plant microbe interactions; Sorghum bicolor

Indexed keywords

AGRICULTURAL PRACTICE; AGRICULTURAL TECHNOLOGY; BACTERIUM; BIOTECHNOLOGY; COMMUNITY DYNAMICS; ENDOPHYTE; ENVIRONMENTAL FACTOR; NITRATE; RHIZOSPHERE; SOIL PROFILE; SOIL STRUCTURE; SORGHUM;

SOUTH AFRICA;

BACTERIA (MICROORGANISMS); SORGHUM BICOLOR;

EID: 84886307930     PISSN: 0032079X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11104-013-1737-6     Document Type: Article

References (60)

1. Adams DG, Duggan PS (2012) Signaling in cyanobacteria-plant symbioses. In: Perotto S, Baluška F (eds) Signaling and communication in plant symbiosis. Springer, Berlin Heidelberg, pp 93-121.
2. Bai Y, Aoust FD, Smith DL, Driscoll BT (2002) Isolation of plant growth promoting Bacillus strains from soybean root nodules. Can J Microbiol 48: 230-238.
3. Berg G (2009) Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84: 11-18.
4. Blackwood CB, Hudleston D, Zak DR, Buyer JS (2007) Interpreting ecological diversity indices applied to terminal restriction fragment length polymorphism data: insights from simulated microbial communities. Appl Environ Microbiol 73: 5276-5283.
5. Budi SW, van Tuinen D, Martinotti G, Gianinazzi S (1999) Isolation from the Sorghum bicolor mycorrhizosphere of a bacterium compatible with arbuscular mycorrhiza development and antagonistic towards soilborne fungal pathogens. Appl Environ Microbiol 65: 5148-5150.
6. Carson JK, Rooney D, Gleeson DB, Clipson N (2007) Altering the mineral composition of soil causes a shift in microbial community structure. FEMS Microbiol Ecol 61: 414-423.
7. Clarke K (1993) Non-parametric multivariate analysis of changes in community structure. Aust J Ecol 18: 117-143.
8. Clarke KR, Gorley RN (2006) PRIMER v6: user manual. Plymouth Marine Laboratory, Plymouth.
9. Cocking EC (2003) Endophytic colonization of plant roots by nitrogen-fixing bacteria. Plant Soil 252: 169-175.
10. Coelho MRR, de Vos M, Carneiro NP, Marriel IE, Paiva E, Seldi L (2008) Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer. FEMS Microbiol Lett 279: 15-22.
11. Coelho MRR, Carneiro NP, Marriel IE, Seldin L (2009) Molecular detection of nifH gene-containing Paenibacillus in the rhizosphere of sorghum (Sorghum bicolor) sown in Cerrado soil. Lett Appl Microbiol 48: 611-617.
12. Compant S, Duffy B, Nowak J, Clemet C, Barka EA (2005) Use of plant-growth promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 71: 4951-4959.
13. Culman SW, Bukowski R, Gauch HG, Cadillo-Quiroz H, Buckley DH (2009) T-REX: software for the processing and analysis of T-RFLP data. BMC Bioinforma 10: 171.
14. Dicko MH, Gruppen H, Traore AS, Voragen AGJ, van Berkel WJH (2006) Sorghum grain as human food in Africa: relevance of content of starch and amylase activities. Afr J Biotechnol 5: 384-395.
15. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
16. Fierer N, Jackson RB (2005) The diversity and biogeography of soil bacterial communities. PNAS 103: 626-631.
17. Food and Agricultural Organization (FAO) (1995) FAO food and nutrition series, no. 27 Sorghum and millet in human nutrition. http://www. fao. org/docrep/T0818E/T0818E00. htm.
18. Food and Agricultural Organization/World Food Production (FAO/WFP) (2010) Crop and food security assessment mission to Mozambique. http://www. fao. org/docrep/012/ak350e/ak350e00. htm.
19. Franche C, Lindström K, Elmerich C (2009) Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants. Plant Soil 321: 35-59.
20. Funnel-Harris DL, Sattler SE, Pedersen JF (2013) Characterization of fluorescent Pseudomonas spp. Associated with roots and soil of two sorghum genotypes. Eur J Plant Pathol. doi: 10. 1007/s10658-013-0179-6.
21. Girvan MS, Bullimore J, Pretty JN, Osborn MA, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69: 1800-1809.
22. Gottel NR, Castro HF, Kerley M et al (2011) Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77: 5934-5944.
23. Hafeez FY, Yasmin S, Ariani D, Mehboob-ur-Rahman Zafar Y, Malik KA (2006) Plant growth-promoting bacteria as biofertilizer. Agron Sustain Dev 26: 143-150.
24. Hardoim PR, van Overbeek LS, van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16: 463-471.
25. Hartmann A, Schimd M, van Tuinen D, Berg G (2009) Plant-driven selection of microbes. Plant Soil 321: 235-257.
26. Hinsinger P, Bengough AG, Vetterlein D, Young IM (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil 321: 117-152.
27. Hirel B, Le Gouis J, Ney B, Gallais A (2007) The challenge of improving nitrogen use efficiency in crop plants: towards a more central role for genetic variability and quantitative genetics within integrated approaches. J Exp Bot 58: 2369-2387.
28. Kevin Vessey J (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255: 571-586.
29. Lauber C, Knight R, Hamady M, Fierer N (2009) Soil pH as a predictor of soil bacterial community structure at the continental scale: a pyrosequencing-based assessment. Appl Environ Microbiol 75: 5111-5120.
30. Loiret F, Ortega E, Kleiner D, Ortega-Rodes P, Rodes R, Dong Z (2004) A putative new endophytic nitrogen-fixing bacterium Pantoea sp. from sugarcane. J Appl Microbiol 97: 504-511.
31. Lugtenberg B, De Weger L, Bennett J (1991) Microbial stimulation of plant growth and protection from disease. Curr Opin Biotechnol 2: 457-464.
32. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG (1998) Design and evaluation of useful bacterial primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 795-799.
33. Martiny JBH, Bohannan BJM, Brown JH et al (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev 4: 102-112.
34. Mendes R, Pizzirani-Kleiner A, Araujo W, Raaijmarkers J (2007) Diversity of cultivated endophytic bacteria from sugarcane: genetic and biochemical characterization of Burkholderia cepacia complex isolates. Appl Environ Microbiol 73: 7259-7267.
35. Morgan JAW, White PJ (2005) Biological costs and benefits to plant-microbe interactions in the rhizosphere. J Exp Bot 56: 1729-1739.
36. Murray M, Thompson W (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8: 4321-4325.
37. Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
38. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York.
39. Nijland R, Burgess JG, Errington J, Veening J-W (2010) Transformation of environmental Bacillus subtilis isolates by transiently inducing genetic competence. PLoS One 5: e9724. doi: 10. 1371/journal. pone. 0009724.
40. Nocker A, Burr M, Camper AK (2007) Genotypic microbial community profiling: a critical technical review. Microb Ecol 54: 276-289.
41. Non-Affiliated Soil Analysis Work Committee (1990) Handbook of standard soil testing methods for advisory purposes, vol 160. Soil Science Society of South Africa, Pretoria.
42. Panchal H, Ingle S (2011) Isolation and characterization of endophytes from the root of the medicinal plant Chlorophytum borivilianum (Safed musli). J Adv Dev Res 2: 205-209.
43. Pedersen WL, Chakrabarty K, Klucas RV, Vidave AK (1978) Nitrogen fixation (acetylene reduction) associated with roots of winter wheat and sorghum in Nebraska. Appl Environ Microbiol 35: 129-135.
44. Reysenbach A-L, Pace NR (1995) In: Robb FT, Place AR (eds) Archaea: a laboratory. Manual - thermophiles. Cold Spring Harbour Laboratory Press, New York, pp 101-107.
45. Rodriguez-Caballero A, Ramond J-B, Welz PJ, Cowan DA, Odlare M, Burton SG (2012) Treatment of high ethanol concentration wastewater by biological sand filters: enhanced COD removal and bacterial community dynamics. J Environ Manag 109: 54-60.
46. Roesch LFW, Camargo FAO, Bento FM, Triplett EW (2008) Biodiversity of diazotrophic bacteria within the soil, root and stem of field-grown maize. Plant Soil 302: 91-104.
47. Rosenblueth M, Martinez-Romero E (2006) A review. Bacterial endophytes and their interactions with hosts. Mol Plant Microbe Interact 19: 827-837.
48. Rout ME, Chrzanowski TH (2009) The invasive Sorghum halepense harbors endophytic N2-fixing bacteria and alters soil biogeochemistry. Plant Soil 315: 163-172.
49. Saharan BS, Nehra V (2011) Plant growth promoting rhizobacteria: a critical review. Life Sci Med Res 21: 1-30.
50. Saito A, Ikeda S, Ezura H, Minamisawa K (2007) A minireview. Microbial community analysis of the phytosphere using culture-independent methodologies. Microbes Environ 22: 93-105.
51. Schenk PM, Carvalhais LC, Kazan K (2012) Unraveling plant-microbe interactions: Can multi-species transcriptomics help? Trends Biotechnol 30: 177-184.
52. Seghers D, Wittebolle L, Top EM, Verstraete W, Siciliano SD (2004) Impact of agricultural practices on the Zea mays L. endophytic community. Appl Environ Microbiol 70: 1475-1482.
53. Sercu B, van de Werfhorst LC, Murray JLS, Holden PA (2011) Cultivation-independent analysis of bacteria in IDEXX quanti-tray/2000 fecal indicator assays. Appl Environ Microbiol 77: 627-633.
54. Shyu C, Soule T, Bent SJ, Foster JA, Forney LJ (2007) MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. J Microb Ecol 53: 562-570.
55. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
56. Taylor JRN (2003) Overview: importance of sorghum in Africa. http://www. afripro. org. uk/papers/Paper01Taylor. pdf.
57. Terakado-Tonooka J, Ohwaki Y, Yamakawa H, Tanaka F, Yoneyama T, Fujihara S (2008) Expressed nifH genes of endophytic bacteria detected in field-grown sweet patatoes (Ipoema batatas L.). Microbes Environ 23: 89-93.
58. Tyson GW, Baker BJ, Alle EE, Hugenholtz P, Banfield JF (2005) Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidic microbial community. Appl Environ Microbiol 71: 6319-6324.
59. van Felten A, Meyer JB, Défago G, Maurhofer M (2011) Novel T-RFLP method to investigate six main groups of 2, 4-diacetylphloroglucinol-producing pseudomonads in environmental samples. J Microbiol Methods 84: 379-387.
60. Zinniel DK, Lambrecht P, Beth Harris N, Feng Z, Kuczmarski D, Higley P, Ishimaru CA, Arunakumari A, Barletta RG, Vidaver AK (2002) Isolation and characterization of endophytic colonizing bacteria from agronomic crops and prairie plants. Appl Environ Microbiol 68: 2198-2208.