Short-term dynamics of culturable bacteria in a soil amended with biotransformed dry olive residue

Systematic and Applied Microbiology

Volumn 37, Issue 2, 2014, Pages 113-120

  Siles, J A ^a   Pascual, J ^b   Gonzalez Menendez V ^b   Sampedro, I ^a,c   Garcia Romera I ^a   Bills, G F ^b,d  

^a CSIC   (Spain)

^b Fundación MEDINA Centro de Excelencia en Investigaciovn de Medicamentos Innovadores en Andalucía   (Spain)

^c University of Vermont ^*  (United States)

^d UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

Bioremediation; Culturable bacteria; Dry olive residue; Granada soil; Organic amendments and fertilizers; Soil bacteria

Indexed keywords

FATTY ACID ESTER; OLIVE OIL; RNA 16S;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARTICLE; BACILLI; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM ISOLATION; BETAPROTEOBACTERIA; BIOTRANSFORMATION; CELL PHAGOCYTOSIS; COLONY FORMING UNIT; DRY OLIVE RESIDUE; GAMMAPROTEOBACTERIA; MICROBIAL DIVERSITY; NONHUMAN; OLIVE; ORGANIC WASTE; PRIORITY JOURNAL; SOIL AMENDMENT; SOIL MICROFLORA; SPHINGOBACTERIA;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; BACILLI (CLASS); BACTERIA (MICROORGANISMS); BASIDIOMYCOTA; BETAPROTEOBACTERIA; CORIOLOPSIS FLOCCOSA; GAMMAPROTEOBACTERIA; SPHINGOBACTERIA;

BIOREMEDIATION; CULTURABLE BACTERIA; DRY OLIVE RESIDUE; GRANADA SOIL; ORGANIC AMENDMENTS AND FERTILIZERS; SOIL BACTERIA;

BACTERIA; BACTERIAL LOAD; BIOTA; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; MICROBIAL VIABILITY; MOLECULAR SEQUENCE DATA; OLEA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SPAIN;

EID: 84896734493     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2013.08.005     Document Type: Article

References (52)

1. Alburquerque J.A., Gonzálvez J., Tortosa G., Baddi G.A., Cegarra J. Evaluation of alperujo composting based on organic matter degradation, humification and compost quality. Biodegradation 2009, 20:257-270.
2. Aranda E., Sampedro I., Ocampo J.A., García-Romera I. Phenolic removal of olive-mill dry residue by laccase activity of white rot fungi and its impact on tomato plant growth. Int. Biodeterior. Biodegradation 2006, 58:176-179.
3. Blanco E.M., Little C.R., Davelos Baines A.L. Variation in antibiotic inhibitory abilities among streptomycetes from south Texas agricultural soils. Soil Biol. Biochem. 2007, 39:268-275.
4. Benitez E., Melgar R., Nogales R. Estimating soil resilience to a toxic organic waste by measuring enzyme activities. Soil Biol. Biochem. 2004, 36:1615-1623.
5. Blagodatskaya E., Kuzyakov Y. Mechanisms of real and apparent priming effects and their dependence on soil microbial biomass and community structure: critical review. Biol. Fert. Soils 2008, 45:115-131.
6. Böhme L., Böhme F. Soil microbiological and biochemical properties affected by plant growth and different long-term fertilization. Eur. J. Soil. Biol. 2006, 42:1-12.
7. Bulgarelli D., Rott M., Schlaeppi K., Ver Loren van Themaat E., Ahmadinejad N., Assenza F., Rauf P., Huettel B., Reinhardt R., Schmelzer E., Peplies J., Gloeckner F.O., Amann R., Eickhorst T., Schulze-Lefert P. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 2012, 487:91-95.
8. Çakmakçi R., Dönmez M.F., Ertürk Y., Erat M., Haznedar A., Sekban R. Diversity and metabolic potential of culturable bacteria from the rhizosphere of Turkish tea grown in acidic soils. Plant Soil 2010, 332:299-318.
9. Casa R., D'Annibale A., Pieruccetti F., Stazi S.R., Sermanni G.G., Lo Cascio B. Reduction of the phenolic components in olive-mill wastewater by an enzymatic treatment and its impact on durum wheat (Triticum durum Desf.) germinability. Chemosphere 2003, 50:959-966.
10. Cayuela M.L., Sánchez-Monedero M.A., Roig A. Two-phase olive mill waste composting: enhancement of the composting rate and compost quality by grape stalks addition. Biodegradation 2010, 21:465-473.
11. Chaudhry V., Rehman A., Mishra A., Chauhan P.S., Nautiyal C.S. Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microb. Ecol. 2012, 64:450-460.
12. Danellakis D., Ntaikou I., Kornaros M., Dailianis S. Olive oil mill wastewater toxicity in the marine environment: alterations of stress indices in tissues of mussel Mytilus galloprovincialis. Aquat. Toxicol. 2011, 101:358-366.
13. Fierer N., Jackson R.B. The diversity and biogeography of soil bacteria communities. Proc. Natl. Acad. Sci. Bio. 2006, 103:626-631.
14. Gans J., Wolinsky M., Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 2005, 309:1387-1390.
15. Gigliotti G., Proietti P., Said-Pullicino D., Nasini L., Pezzolla D., Rosati L., Porceddu P.R. Co-composting of olive husks with high moisture contents: organic matter dynamics and compost quality. Int. Biodeterior. Biodegradation 2012, 67:8-14.
16. Giuntini E., Bazzicalupo M., Castaldini M., Fabiani A., Miclaus N., Piccolo R., Ranalli G., Santomassimo F., Zanobini S., Mengoni A. Genetic diversity of dinitrogen-fixing bacterial communities in soil amended with olive husks. Ann. Microbiol. 2006, 56:83-88.
17. Haack S.K., Garchow H., Odelson D.A., Forney L.J., Klug M.J. Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities. Appl. Environ. Microbiol. 1994, 60:2483-2493.
18. Hammer Ø., Harper D.A.T., Ryan P.D. PAST: paleontological statistics software package for education and data analysis. Paleontol. Electron. 2001, 4:9-17.
19. He J.Z., Zheng Y., Chen C.R., He Y.Q., Zhang L.M. Microbial composition and diversity of an upland red soil under long term fertilization treatments as revealed by culture-dependent and culture-independent approaches. J. Soils Sediments 2008, 8:349-358.
20. Heyrman J., Mergaert J., Denys R., Swings J. The use of fatty acid methyl ester analysis (FAME) for the identification of heterotrophic bacteria present on three mural paintings showing severe damage by microorganisms. FEMS Microbiol. Lett. 1999, 181:55-62.
21. Justino C.I.L., Pereira R., Freitas A.C., Rocha-Santos T.A.P., Panteleitchouk T.S.L., Duarte A.C. Olive oil mill wastewaters before and after treatment: a critical review from the ecotoxicological point of view. Ecotoxicology 2012, 21:615-629.
22. Karpouzas D.G., Ntougiasb S., Iskidoua E., Rousidou C., Papadopouloua K.K., Zervakisb G.I., Ehaliotis C. Olive mill wastewater affects the structure of soil bacterial communities. Appl. Soil Ecol. 2010, 45:101-111.
23. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H., Yi H., Won S., Chun J. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 2012, 62:716-721.
24. Kirk J.L., Beaudette L.A., Hart M., Moutoglis P., Klironomos J.N., Lee H., Trevors J.T. Methods of studying soil microbial diversity. J. Microbiol. Meth. 2004, 58:169-188.
25. Kotsou M., Mari I., Lasaridi K., Chatzipavlidis I., Balis C., Kyriacou A. The effect of olive oil mill wastewater (OMW) on soil microbial communities and suppressiveness against Rhizoctonia solani. Appl. Soil Ecol. 2004, 26:113-121.
26. Lambshead P.J.F. Numerical biodiversity analysis with the natural history museum and Scottish Association for Marine Sciences BioDiversity Professional PC package. Oceanis 1998, 24:375-391.
27. Magurran A. Ecological diversity and its measurement 1988, Princeton University Press, Princeton.
28. Mechri B., Echbili A., Issaoui M., Braham M., Elhadj S.B., Hammami M. Short-term effects in soil microbial community following agronomic application of olive mill waste waters in a field of olive trees. Appl. Soil Ecol. 2007, 36:216-223.
29. Medina E., Romero C., de los Santos B., de Castro A., García A., Romero F., Brenes M. Antimicrobial activity of olive solutions from stored alpeorujo against plant pathogenic microorganisms. J. Agric. Food Chem. 2011, 59:6927-6932.
30. Mekki A., Dhouib A., Sayadi S. Changes in microbial and soil properties following amendment with treated and untreated olive mill wastewater. Microbiol. Res. 2006, 161:93-101.
31. Mergaert J., Verhelst A., Cnockaert M.C., Tan T.L., Swings J. Characterization of facultative oligotrophic bacteria from polar seas by analysis of their fatty acids and 16S rDNA sequences. Syst. Appl. Microbiol. 2001, 24:98-107.
32. Miransari M. Soil microbes and plant fertilization. Appl. Microbiol. Biotechnol. 2011, 92:875-885.
33. Nannipieri P., Ascher J., Ceccherini T., Landi L., Pietramellara G., Renella G. Microbial diversity and soil functions. Eur. J. Soil Sci. 2003, 54:665-670.
34. Pepi M., Altieri R., Esposito A., Lobianco A., Borghini F., Stendardi A., Gasperini S., Focardi S. Effects of amendment with olive mill by-products on soils revealed by nitrifying bacteria. Chem. Ecol. 2009, 25:293-303.
35. Pham V.H.T., Kim J. Cultivation of unculturable soil bacteria. Trends Biotechnol. 2012, 30:475-484.
36. Rousidou C., Papadopoulou K., Zervakis G., Singh B.K., Ehaliotis C., Karpouzas D.G. Repeated application of diluted olive mill wastewater induces changes in the structure of the soil microbial community. Eur. J. Soil Biol. 2010, 46:34-40.
37. Sait M., Davis K.E.R., Janssen P.H. Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl. Environ. Microbiol. 2006, 72:1852-1857.
38. Sampedro I., Aranda E., Rodríguez-Gutiérrez G., Lama-Muñoz A., Ocampo J.A., Fernández-Bolaños J., García-Romera I. Effect of a new thermal treatment in combination with saprobic fungal incubation on the phytotoxicity level of alpeorujo. J. Agric. Food Chem. 2011, 59:3239-3245.
39. Sampedro I., D'Annibale.A., Ocampo J.A., Stazi S.R., García-Romera I. Bioconversion of olive-mill dry residue by Fusarium lateritium and subsequent impact on its phytotoxicity. Chemosphere 2005, 60:1393-1400.
40. Sampedro I., Giubilei M.A., Cajthaml T., Federici E., Federici F., Petruccioli M., D'Annibale A. Short-term impact of dry olive mill residue addition to soil on the resident microbiota. Bioresource Technol. 2009, 100:6098-6106.
41. Sampedro I., Marinari S., D'Annibale A., Grego S., Ocampo J.A., García-Romera I. Organic matter evolution and partial detoxification in two-phase olive mill waste colonized by white-rot fungi. Int. Biodet. Biodegrad. 2007, 60:116-125.
42. Sampedro I., Marinari S., Grego S., Petruccioli M., Federici F., D'Annibale A. Immobilized inocula of white-rot fungi accelerate both detoxification and organic matter transformation in two-phase dry olive-mill residue. J. Agric. Food Chem. 2009, 57:5452-5460.
43. Sánchez-Hidalgo M., Pascual J., de la Cruz M., Martín J., Kath G.S., Sigmung J.M., Masurekar P., Vicente F., Genilloud O., Bills G.F. Prescreening bacterial colonies for bioactive molecules with Janus plates, a SBS standard double-faced microbial culturing system. A. van Leeuw. J. Microb. 2012, 102:361-374.
44. Saparrat M.C.N., Jurado M., Diaz R., García-Romera I., Martínez M.J. Transformation of the water soluble fraction from alpeorujo by Coriolopsis rigida: the role of laccase in the process and its impact on Azospirillum brasiliense survival. Chemosphere 2010, 78:72-76.
45. Schlatter D., Fubuh A., Xiao K., Hernandez D., Hobbie S., Kinkel L. Resource amendments influence density and competitive phenotypes of Streptomyces in soil. Microb. Ecol. 2009, 57:414-420.
46. Schloss P.D., Handelsman J. Status of the microbial census. Microbiol. Mol. Biol. Rev. 2004, 68:686-691.
47. Shade A., Hogan C.S., Klimowicz A.K., Linske M., McManus P.S., Handelsman J. Culturing captures members of the soil rare biosphere. Environ. Microbiol. 2012, 14:2247-2252.
48. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
49. Torsvik V.L., Ovreas L., Thingstad T.F. Prokaryotic diversity-magnitude, dynamics and controlling factors. Science 2002, 296:1064-1066.
50. Tortosa G., Alburquerque J.A., Ait-Baddi G., Cegarra J. The production of commercial organic amendments and fertilizers by composting of two-phase olive mill waste (alpeorujo). J. Cleaner Prod. 2012, 26:48-55.
51. van Trappen S., Mergaert J., Van Eygen S., Dawyndt P., Cnockaert M.C., Swings J. Diversity of 746 heterotrophic bacteria isolated from microbial mats from ten Antarctic lakes. Syst. Appl. Microbiol. 2002, 25:603-610.
52. Zhang L., Xu Z., Patel B. Culture-dependent and culture-independent microbial investigation of pine litters and soil in subtropical Australia. J. Soils Sediments 2009, 9:148-160.