Survival of a novel endophytic fungus Phomopsis liquidambari B3 in the indole-contaminated soil detected by real-time PCR and its effects on the indigenous microbial community

Microbiological Research

Volumn 169, Issue 12, 2014, Pages 881-887

  Wang, Hong Wei ^a   Dai, Chuan Chao ^a   Zhu, Hong ^a   Wang, Xing Xiang ^b  

^a NANJING NORMAL UNIVERSITY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

DGGE; Endophyte; Internal standard; Phomopsis liquidambari; Real time PCR

Indexed keywords

BIOREMEDIATION; BIOTECHNOLOGY; ELECTROPHORESIS; MICROORGANISMS; POLYCYCLIC AROMATIC HYDROCARBONS; POLYMERASE CHAIN REACTION; RISK ASSESSMENT; SOILS;

DGGE; ENDOPHYTE; INTERNAL STANDARDS; PHOMOPSIS; REAL-TIME PCR;

SOIL POLLUTION;

AROMATIC HYDROCARBON; BIOREMEDIATION; ENDOPHYTE; FUNGUS; MICROBIAL COMMUNITY; REAL TIME; SOIL ECOSYSTEM; SOIL MICROORGANISM; SOIL POLLUTION; SURVIVAL;

FUNGI; PHOMOPSIS LIQUIDAMBARI;

INDOLE; INDOLE DERIVATIVE; SOIL POLLUTANT;

ASCOMYCETES; BIOMASS; BIOREMEDIATION; DENATURING GRADIENT GEL ELECTROPHORESIS; ENDOPHYTE; ISOLATION AND PURIFICATION; METABOLISM; MICROBIAL VIABILITY; MICROBIOLOGY; MICROFLORA; PHYSIOLOGY; REAL TIME POLYMERASE CHAIN REACTION; SOIL POLLUTANT;

ASCOMYCOTA; BIODEGRADATION, ENVIRONMENTAL; BIOMASS; DENATURING GRADIENT GEL ELECTROPHORESIS; ENDOPHYTES; INDOLES; MICROBIAL VIABILITY; MICROBIOTA; REAL-TIME POLYMERASE CHAIN REACTION; SOIL MICROBIOLOGY; SOIL POLLUTANTS;

EID: 85050298072     PISSN: 09445013     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.micres.2014.05.006     Document Type: Article

References (39)

1. Aly A.H., Debbab A., Kjer J., Proksch P. Fungal endophytes from higher plants: a prolific source of phytochemicals and other bioactive natural products. Fungal Divers 2010, 41(1):1-16.
2. Andreoni V., Cavalca L., Rao M., Nocerino G., Bernasconi S., Dell'Amico E., et al. Bacterial communities and enzyme activities of PAHs polluted soils. Chemosphere 2004, 57(5):401-412.
3. Avrahami S., Bohannan B.J. Response of Nitrosospira sp. strain AF-like ammonia oxidizers to changes in temperature, soil moisture content, and fertilizer concentration. Appl Environ Microbiol 2007, 73(4):1166-1173.
4. Borges W.S., Borges K.B., Bonato P.S., Said S., Pupo M.T. Endophytic fungi: natural products, enzymes and biotransformation reactions. Curr Org Chem 2009, 13(12):1137-1163.
5. Bossio J.P., Harry J., Kinney C.A. Application of ultrasonic assisted extraction of chemically diverse organic compounds from soils and sediments. Chemosphere 2008, 70(5):858-864.
6. Brookes P., Landman A., Pruden G., Jenkinson D. Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol Biochem 1985, 17(6):837-842.
7. Carlson J., Yokoyama M., Dickinson E. Induction of pulmonary edema and emphysema in cattle and goats with 3-methylindole. Science 1972, 176(4032):298-299.
8. Chen Y., Peng Y., Dai C.C., Ju Q. Biodegradation of 4-hydroxybenzoic acid by Phomopsis liquidambari. Appl Soil Ecol 2011, 51(8):102-110.
9. Chen Y., Ren C.G., Yang B., Peng Y., Dai C.C. Priming effects of the endophytic fungus Phomopsis liquidambari on soil mineral N transformations. Microb Ecol 2013, 65(1):161-170.
10. Chen Y., Xie X.G., Ren C.G., Dai C.C. Degradation of N-heterocyclic indole by a novel endophytic fungus Phomopsis liquidambari. Bioresour Technol 2013, 129(4):568-574.
11. Chimerel C., Field C.M., Piñero-Fernandez S., Keyser U.F., Summers D.K. Indole prevents Escherichia coli cell division by modulating membrane potential. Biochim Biophys Acta - Biomembr. 2012, 1818(7):1590-1594.
12. Daniell T., Davidson J., Alexander C., Caul S., Roberts D. Improved real-time PCR estimation of gene copy number in soil extracts using an artificial reference. J Microbiol Methods 2012, 91(1):38-44.
13. D'Annibale A., Rosetto F., Leonardi V., Federici F., Petruccioli M. Role of autochthonous filamentous fungi in bioremediation of a soil historically contaminated with aromatic hydrocarbons. Appl Environ Microbiol 2006, 72(1):28-36.
14. Dejonghe W., Boon N., Seghers D., Top E.M., Verstraete W. Bioaugmentation of soils by increasing microbial richness: missing links. Environ Microbiol 2001, 3(10):649-657.
15. Duarte S., Pascoal C., Alves A., Correia A., Cássio F. Assessing the dynamic of microbial communities during leaf decomposition in a low-order stream by microscopic and molecular techniques. Microbiol Res 2010, 165(5):351-362.
16. Gobbin D., Rezzonico F., Gessler C. Quantification of the biocontrol agent Pseudomonas fluorescens Pf153 in soil using a quantitative competitive PCR assay unaffected by variability in cell lysis-and DNA-extraction efficiency. Soil Biol Biochem 2007, 39(7):1609-1619.
17. Hammond A., Carlson J., Breeze R. Indole toxicity in cattle. Vet Rec 1980, 107(15):344-346.
18. Hong X., Zhang X., Liu B., Mao Y., Liu Y., Zhao L. Structural differentiation of bacterial communities in indole-degrading bioreactors under denitrifying and sulfate-reducing conditions. Res Microbiol 2010, 161(8):687-693.
19. Jiménez-Fernández D., Montes-Borrego M., Navas-Cortés J.A., Jiménez-Díaz R.M., Landa B.B. Identification and quantification of Fusarium oxysporum in planta and soil by means of an improved specific and quantitative PCR assay. Appl Soil Ecol 2010, 46(3):372-382.
20. Kamath A.V., Vaidyanathan C. New pathway for the biodegradation of indole in Aspergillus niger. Appl Environ Microbiol 1990, 56(1):275-280.
21. Kim J., Hong H., Heo A., Park W. Indole toxicity involves the inhibition of adenosine triphosphate production and protein folding in Pseudomonas putida. FEMS Microbiol Lett 2013, 343(1):89-99.
22. Liu S., Jones W., Rogers J. Influence of redox potential on the anaerobic biotransformation of nitrogen-heterocyclic compounds in anoxic freshwater sediments. Appl Microbiol Biotechnol 1994, 41(6):717-724.
23. Longa C., Savazzini F., Tosi S., Elad Y., Pertot I. Evaluating the survival and environmental fate of the biocontrol agent Trichoderma atroviride SC1 in vineyards in northern Italy. J Appl Microbiol 2009, 106(5):1549-1557.
24. Luo Y., Gao W., Doster M., Michailides T. Quantification of conidial density of Aspergillus flavus and A. parasiticus in soil from almond orchards using real-time PCR. J Appl Microbiol 2009, 106(5):1649-1660.
25. Madsen E., Francis A., Bollag J. Environmental factors affecting indole metabolism under anaerobic conditions. Appl Environ Microbiol 1988, 54(1):74-78.
26. Mayer A.M., Staples R.C. Laccase: new functions for an old enzyme. Phytochemistry 2002, 60(6):551-565.
27. Moreno J.L., Aliaga A., Navarro S., Hernández T., García C. Effects of atrazine on microbial activity in semiarid soil. Appl Soil Ecol 2007, 35(1):120-127.
28. Mrozik A., Piotrowska-Seget Z. Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiol Res 2010, 165(5):363-375.
29. Orr K.A., Knudsen G.R. Use of green fluorescent protein and image analysis to quantify proliferation of Trichoderma harzianum in nonsterile soil. Phytopathology 2004, 94(12):1383-1389.
30. Park J.W., Crowley D.E. Normalization of soil DNA extraction for accurate quantification of target genes by real-time PCR and DGGE. Biotechniques 2005, 38(4):579-586.
31. Pujol M., Badosa E., Manceau C., Montesinos E. Assessment of the environmental fate of the biological control agent of fire blight, Pseudomonas fluorescens EPS62e, on apple by culture and real-time PCR methods. Appl Environ Microbiol 2006, 72(4):2421-2427.
32. Russell J.R., Huang J., Anand P., Kucera K., Sandoval A.G., Dantzler K.W., et al. Biodegradation of polyester polyurethane by endophytic fungi. Appl Environ Microbiol 2011, 77(17):6076-6084.
33. Singh J., Singh D.K. Dehydrogenase and phosphomonoesterase activities in groundnut (Arachis hypogaea L.) field after diazinon, imidacloprid and lindane treatments. Chemosphere 2005, 60(1):32-42.
34. Teng Y., Luo Y., Sun M., Liu Z., Li Z., Christie P. Effect of bioaugmentation by Paracoccus sp. strain HPD-2 on the soil microbial community and removal of polycyclic aromatic hydrocarbons from an aged contaminated soil. Bioresour Technol 2010, 101(10):3437-3443.
35. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25(24):4876-4882.
36. Tyagi M., da Fonseca M.M.R., de Carvalho C.C. Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes. Biodegradation 2011, 22(2):231-241.
37. Vance E., Brookes P., Jenkinson D. An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 1987, 19(6):703-707.
38. Wang H.W., Zhu H., Liang X.F., Du W., Dai C.C. Molecular cloning and expression of a novel laccase showing thermo-and acid-stability from the endophytic fungus Phomopsis liquidambari and its potential for growth promotion of plants. Biotechnol Lett 2014, 36(1):167-173.
39. Yin B., Gu J.D., Wan N. Degradation of indole by enrichment culture and Pseudomonas aeruginosa Gs isolated from mangrove sediment. Int Biodeterior Biodegrad 2005, 56(4):243-248.