Applied Microbiology and Biotechnology

, Volume 100, Issue 8, pp 3433–3449 | Cite as

Application of compost for effective bioremediation of organic contaminants and pollutants in soil

Mini-Review

Abstract

Soils contaminated with hazardous chemicals worldwide are awaiting remediation activities; bioremediation is often considered as a cost-effective remediation approach. Potential bioapproaches are biostimulation, e.g. by addition of nutrients, fertiliser and organic substrates, and bioaugmentation by addition of compound-degrading microbes or of organic amendments containing active microorganisms, e.g. activated sludge or compost. In most contaminated soils, the abundance of the intrinsic metabolic potential is too low to be improved by biostimulation alone, since the physical and chemical conditions in these soils are not conducive to biodegradation. In the last few decades, compost or farmyard manure addition as well as composting with various organic supplements have been found to be very efficient for soil bioremediation. In the present minireview, we provide an overview of the composting and compost addition approaches as ‘stimulants’ of natural attenuation. Laboratory degradation experiments are often biased either by not considering the abiotic factors or by focusing solely on the elimination of the chemicals without taking the biotic factors and processes into account. Therefore, we first systemise the concepts of composting and compost addition, then summarise the relevant physical, chemical and biotic factors and mechanisms for improved contaminant degradation triggered by compost addition. These factors and mechanisms are of particular interest, since they are more relevant and easier to determine than the composition of the degrading community, which is also addressed in this review. Due to the mostly empirical knowledge and the nonstandardised biowaste or compost materials, the field use of these approaches is highly challenging, but also promising. Based on the huge metabolic diversity of microorganisms developing during the composting processes, a highly complex metabolic diversity is established as a ‘metabolic memory’ within developing and mature compost materials. Compost addition can thus be considered as a ‘super-bioaugmentation’ with a complex natural mixture of degrading microorganisms, combined with a ‘biostimulation’ by nutrient containing readily to hardly degradable organic substrates. It also improves the abiotic soil conditions, thus enhancing microbial activity in general. Finally, this minireview also aims at guiding potential users towards full exploitation of the potentials of this approach.

Keywords

Soil amendment Composting Biodegradation Organic contaminants Microbial communities Bioremediation processes Fate of pollutants Residual concentrations Metabolic cooperation Functional redundancy 

References

  1. Abdelhafid R, Houot S, Barriuso E (2000) Dependence of atrazine degradation on C and N availability in adapted and non-adapted soils. Soil Biol Biochem 32:389–401CrossRefGoogle Scholar
  2. Abraham WR, Nogales B, Golyshin PN, Pieper DH, Timmis KN (2002) Polychlorinated biphenyl-degrading microbial communities and sediments. Curr Opin Microbiol 5:246–253PubMedCrossRefGoogle Scholar
  3. Adam IKU, Miltner A, Kästner M (2015) Degradation of 13C-labelled pyrene degradation in soil-compost mixtures and fertilized soil. Appl Microbiol Biotechnol 99:9813–9824PubMedCrossRefGoogle Scholar
  4. Adam IKU, Rein A, Miltner A, da Costa Fulgêncio AC, Trapp S, Kästner M (2014) Experimental results and integrated modeling of bacterial growth on an insoluble hydrophobic substrate (phenanthrene). Environ Sci Technol 48:8717–8726PubMedCrossRefGoogle Scholar
  5. Ahlawat OP, Gupta P, Kumar S, Sharma DK, Ahlawat K (2010) Bioremediation of fungicides by spent mushroom substrate and its associated microflora. Ind J Microbiol 50:390–395CrossRefGoogle Scholar
  6. Ahmad R, Jilani G, Arshad M, Zahi ZA, Khalid A (2007) Bio-conversion of organic wastes for their recycling in agriculture: an overview of perspectives and prospects. Ann Microbiol 57:471–479CrossRefGoogle Scholar
  7. Aitken MD, Stringfellow WT, Nagel RD, Kazunga C, Chen SH (1998) Characteristics of phenanthrene-degrading bacteria isolated from soils contaminated with polycyclic aromatic hydrocarbons. Can J Microbiol 44(8):743–752. doi:10.1139/cjm-44-8-743 PubMedCrossRefGoogle Scholar
  8. Alburquerque JA, de la Fuente C, Bernal MP (2011) Improvement of soil quality after “alperujo” compost application to two contaminated soils characterised by differing heavy metal solubility. J Environ Manag 92:733–741CrossRefGoogle Scholar
  9. Alburquerque JA, Gonzalve J, Tortosa G, Baddi GA, Cegarra J (2009) Evaluation of “alperujo” composting based on organic matter degradation, humification and compost quality. Biodegradation 20:257–270PubMedCrossRefGoogle Scholar
  10. Al-Daher R, Al-Ahwadi N, Yateem A, Balba MT (2001) Compost Soil piles for treatment of oil contaminated Soil. Soil Sed Contam 10(2):197–209CrossRefGoogle Scholar
  11. Allison SD, Martiny JBH (2008) Resistance, resilience, and redundancy in microbial communities. P Natl Acad Sci 105:11512–11519CrossRefGoogle Scholar
  12. Alvey S, Crowley DE (1995) Influence of organic amendments on biodegradation of atrazine as a nitrogen source. J Environ Qual 24:1156–1162CrossRefGoogle Scholar
  13. Antizar-Ladislao B, Lopez-Real JM, Beck AJ (2004) Bioremediation of polycyclic aromatic hydrocarbons (PAH)-contaminated waste using Composting strategies. Crit Rev Environ Sci Technol 34:249–289CrossRefGoogle Scholar
  14. Bamforth SM, Singleton I (2005) Bioremediation of polycyclic aromatic hydrocarbons: current knowledge and future directions. J Chem Technol Biotechnol 80(7):723–736. doi:10.1002/jctb.1276 CrossRefGoogle Scholar
  15. Barriuso E, Houot S, Serra-Wittling C (1997) Influence of compost addition to Soil on the behaviour of herbicides. Pest Sci 49:65–75CrossRefGoogle Scholar
  16. Bastida F, Jemlich N, Lima K, Morris BEL, Richnow HH, Hernandez T, von Bergen M, Garcia C (2015) The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment. J Proteomics. doi:10.1016/j.jprot.2015.07.023 PubMedGoogle Scholar
  17. Benoit P, Barriuso E, Calvet R (1998) Biosorption characterization of herbicides, 2,4,-D and atrazine, and two chlorophenols on fungal mycelium. Chemosphere 37(7):1271–1282CrossRefGoogle Scholar
  18. von Bergen M, Jehmlich N, Taubert M, Vogt C, Bastida F, Herbst FA, Schmidt F, Richnow HH, Seifert J (2013) Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology. ISME J 7:1877–1885CrossRefGoogle Scholar
  19. Boschker HTS, Middelburg JJ (2002) Stable isotopes and biomarkers in microbial ecology. FEMS Microbiol Ecol 40:85–95PubMedCrossRefGoogle Scholar
  20. Bosma TNP, Middeldorp PJM, Schraa G, Zehnder AJB (1997) Mass transfer limitation of biotransformation: quantifying bioavailability. Environ Sci Technol 31(1):248–252. doi:10.1021/Es960383u CrossRefGoogle Scholar
  21. Breitung J, Bruns-Nagel D, Steinbach K, Kaminski L, Gemsa D, von Löw E (1996) Bioremediation of 2,4,6-trinitrotoluene-contaminated soils by two different aerated compost systems. Appl Microbiol Biotechnol 44:795–800PubMedCrossRefGoogle Scholar
  22. Bruns-Nagel D, Dryzyzga O, Steinbach K, Schmidt TC, von Löw E, Gorontzy T, Blotevogel K-H, Gemsa D (1998) Anaerobic/aerobic composting of 2,4,6-trinitrotoluene-contaminated soil in a reactor system. Environ Sci Technol 32:1676–1679CrossRefGoogle Scholar
  23. Cerniglia CE (1984) Microbial metabolism of polycyclic aromatic hydrocarbons. Adv Appl Microbiol 30:31–71. doi:10.1016/S0065-2164(08)70052-2 PubMedCrossRefGoogle Scholar
  24. Cerniglia CE (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3:351–368CrossRefGoogle Scholar
  25. Cerniglia CE, Heitkamp MA (1989) Microbial metabolism of polycyclic aromatic hydrocarbons (PAH) in the aquatic environment. In: Varanasi U (ed) Metabolism of polycyclic aromatic hydrocarbons in the aquatic environment. CRC Press, Boca Raton, pp. 41–68Google Scholar
  26. Cerniglia CE, Sutherland JB (2010) Degradation of polycyclic aromatic hydrocarbons by fungi. In: McGenity T, van der Meer JR, de Lorenzo V (eds) Timmis KN. Springer, Handbook of Hydrocarbon and Lipid Microbiology, pp. 2079–2110Google Scholar
  27. Certini G, Scalenghe R, Woods WI (2013) The impact of warfare on the soil environment. Earth Sci Rev 127:1–15CrossRefGoogle Scholar
  28. Chefetz B, Xing B (2009) Relative role of aliphatic and aromatic moieties as sorption domains for organic compounds: a review. Environ Sci Technol 43:1680–1688PubMedCrossRefGoogle Scholar
  29. Chen M, Xua P, Zeng G, Yang C, Huang D, Zhang J (2015) Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavymetals by composting: applications, microbes and future research needs. Biotechnol Adv. doi:10.1016/j.biotechadv.2015.05.003 Google Scholar
  30. Covino S, Fabianova T, Kresinova Z, Cvancarova M, Burianova E, Filipova A, Voriskova J, Baldrian P, Cajthaml T (2015) Polycyclic aromatic hyrdrocarbons degradation and microbial community shifts during composting of creosote-treated wood. J Haz Mat. doi:10.1016/j.jhazmat.2015.08.023 Google Scholar
  31. Crocker F, Indest K, Fredrickson H (2006) Biodegradation of the cyclic nitramine explosives RDX, HMX, and CL-20. Appl Microbiol Biotechnol 73:274–290PubMedCrossRefGoogle Scholar
  32. De Gannes V, Eudoxie G, Hickey WJ (2013a) Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing. Biores Technol 133:573–580CrossRefGoogle Scholar
  33. De Gannes V, Eudoxie G, Hickey WJ (2013b) Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety. Front Microbiol 4:164PubMedPubMedCentralGoogle Scholar
  34. Dees PM, Ghiorse WC (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 35:207–216PubMedCrossRefGoogle Scholar
  35. Dickerson GW (2001) Vermicomposting: guide H-164 (PDF). New Mexico State UniversityGoogle Scholar
  36. Ding GC, Pronk GJ, Babin D, Heuer H, Heister K, Kögel-Knabner I, Smalla K (2013) Mineral composition and charcoal determine the bacterial community structure in artificial soils. FEMS Microbiol Ecol 86:15–25PubMedCrossRefGoogle Scholar
  37. Dumont MG, Murrell JC (2005) Innovation: stable isotope probing — linking microbial identity to function. Nat Rev Microbiol 3:499–504PubMedCrossRefGoogle Scholar
  38. Eberhardt C, Grathwohl P (2002) Time scales of organic contaminant dissolution from complex source zones: coal tar vs. blobs. J Contam Hydrol 59:45–66PubMedCrossRefGoogle Scholar
  39. EC (1999) The council of the European Union, COUNCIL DIRECTIVE 1999/31/EC of 26 April 1999 on the landfill of waste.Google Scholar
  40. EC (2006) Regulation (EC) No 1907/2006 of the European Parliament and the council of 18 December 2006 concerning Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH).Google Scholar
  41. Eggen T (1999) Application of fungal substrate from commercial mushroomproduction - Pleuorotus ostreatus - for bioremediation of creosote contaminated soil. Int Biodet Biodeg 44:117–126CrossRefGoogle Scholar
  42. Esteve-Nunez A, Caballero A, Ramos JL (2001) Biological degradation of 2,4,6-trinitrotoluene. Microbiol Mol Biol Rev 65:335–352PubMedPubMedCentralCrossRefGoogle Scholar
  43. Farrell M, Jones DL (2010) Use of composts in the remediation of heavy metal contaminated soil. J Haz Mat 175:575–582CrossRefGoogle Scholar
  44. Fogarty AM, Tuovinen OH (1991) Microbiological degradation of pesticides in yard waste composting. Microb Rev 55:225–233Google Scholar
  45. Freilich S, Zarecki R, Eilam O, Segal ES, Henry CS, Kupiec M, Gophna U, Sharan R, Ruppin E (2011) Competitive and cooperative metabolic interactions in bacterial communities. Nat Comm. doi:10.1038/ncomms1597 Google Scholar
  46. Gandolfi I, Sicolo M, Franzetti A, Fontanarosa E, Santagostino A, Bestetti G (2010) Influence of compost amendment on microbial community and ecotoxicity of hydrocarbon-contaminated soils. Biores Technol 101:568–575CrossRefGoogle Scholar
  47. García-Delgado C, D’Annibale A, Pesciaroli L, Yunta F, Crognale S, Petruccioli M, Eymar E (2015) Implications of polluted soil biostimulation and bioaugmentation with spent mushroom substrate (Agaricus bisporus) on themicrobial community and polycyclic aromatic hydrocarbons biodegradation. Sci Tot Environ 508:20–28CrossRefGoogle Scholar
  48. Geng C, Haudin C-S, Zhang Y, Lashermes G, Houot S, Garnier P (2015) Modeling the release of organic contaminants during compost decomposition in soil. Chemosphere 119:423–431PubMedCrossRefGoogle Scholar
  49. Ghoshal S, Ramaswami A, Luthy RG (1996) Biodegradation of naphthalene from coal tar and heptamethylnonane in mixed batch systems. Environ Sci Technol 30:1282–1291CrossRefGoogle Scholar
  50. Grotenhuis T, Field J, Wasseveld R, Rulkens W (1999) Biodegradation of polyaromatic hydrocarbons (PAH) in polluted soil by the white-rot fungus Bjerkandera. J Chem Technol Biotechnol 71:359–360CrossRefGoogle Scholar
  51. Haderlein A, Legros R, Ramsay B (2001) Enhancing pyrene mineralization in contaminated soil by the addition of humic acids or composted contaminated soil. Appl Microbiol Biotechnol 56:555–559PubMedCrossRefGoogle Scholar
  52. Häggblom M, Valo RJ (1985) Bioremediation of chlorophenol wastes. In: Young LY, Cerniglia CE (eds) Microbial transformation and degradation of Toxic Organic Chemicals. John Wiley & Sons, New York, pp. 389–434Google Scholar
  53. Harms H, Schlosser D, Wick LY (2011) Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nat Rev Microbiol 9:177–191PubMedCrossRefGoogle Scholar
  54. Hatzinger PB, Alexander M (1995) Effect of aging of Chemicals In Soil on their biodegradability and extractability. Environ Sci Technol 29(2):537–545PubMedCrossRefGoogle Scholar
  55. Hawari J, Beaudet S, Halasz A, Thiboutot S, Ampleman G (2000) Microbial degradation of explosives: biotransformation versus mineralization. Appl Microbiol Biotechnol 54:605–618PubMedCrossRefGoogle Scholar
  56. Hernandez T, Garcia E, Garcia C (2015) A strategy for marginal semiarid degraded soil restoration: A sole addition of compost at a high rate. A Five-Year Field Experiment. Soil Biol Biochem 89:61–71CrossRefGoogle Scholar
  57. van Herwijnen R, Hutchings TR, Al-Tabbaa A, Moffat AJ, Johns ML, Ouki SK (2007) Remediation of metal contaminated soil with mineral-amended composts. Environ Poll 150:347–354CrossRefGoogle Scholar
  58. Hofrichter M (2002) Review: lignin conversion by manganese peroxidase (MnP). Enz Microbiol Technol 30:454–466CrossRefGoogle Scholar
  59. Jaspers CJ, Ewbank G, McCarthy AJ, Penninckx MJ (2002) Successive rapid reductive dehalogenation and mineralization of pentachlorophenol by the indigenous microflora of farmyard manure compost. J Appl Microbiol 92:127–133PubMedCrossRefGoogle Scholar
  60. Johnsen AR, Wick LY, Harms H (2005) Principles of microbial PAH-degradation in soil. Environ Poll 133:71–84CrossRefGoogle Scholar
  61. Jones MD, Crandell DW, Singleton DR, Aitken MD (2011) Stable-isotope probing of the polycyclic aromatic hydrocarbon-degrading bacterial guild in a contaminated soil. Environ Microbiol 13(10):2623–2632PubMedPubMedCentralCrossRefGoogle Scholar
  62. Juhasz AL, Naidu R (2000) Bioremediation of high molecular weight polycyclic aromatic hydrocarbons: a review of the microbial degradation of benzo[a] pyrene. Int Biodet Biodeg 45(1–2):57–88CrossRefGoogle Scholar
  63. Kanaly RA, Harayama S (2010) Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria. Microb Biotechnol 3(2):136–164PubMedPubMedCentralCrossRefGoogle Scholar
  64. Kästner M (2000) Degradation of aromatic and polyaromatic compounds. In: Rehm H-J, Reed G, Pühler A, Stadler P (eds) Biotechnology, 2nd edition, vol 11b. Weinheim, Environmental Processes. Wiley-VCH, pp. 211–239Google Scholar
  65. Kästner M, Mahro B (1996) Microbial degradation of polycyclic aromatic hydrocarbons in soils affected by the organic matrix of compost. Appl Microbiol Biotechnol 44(5):668–675PubMedCrossRefGoogle Scholar
  66. Kästner M, B-J M, Mahro B (1998) PAH degradation and survival of degrading bacteria introduced into soil. Appl Environ Microbiol 64:359–362PubMedPubMedCentralGoogle Scholar
  67. Kästner M, Nowak KM, Miltner A, Trapp S, Schäffer A (2014) Classification and modelling of non-extractable residue (NER) formation of xenobiotics in soil - a synthesis. Crit Rev Environ Sci Technol 44:2107–2171CrossRefGoogle Scholar
  68. Kirchmann H, Ewnetu W (1998) Biodegradation of petroleum-based oil waste through composting. Biodegradation 9:151–156PubMedCrossRefGoogle Scholar
  69. Kues U (2015) Fungal enzymes for environmental management. Curr Op Biotechnol 33:268–278CrossRefGoogle Scholar
  70. Kuzyakov Y, Friedel JK, Stahr K (2000) Review of mechanisms and quantification of priming effects. Soil Biol Biochem 32:1485–1498CrossRefGoogle Scholar
  71. Laine MM, Jörgensen KS (1997a) Effective and safe composting of chlorophenol-contaminated soil in pilot scale. Environ Sci Technol 31:371–378CrossRefGoogle Scholar
  72. Laine MM, Ahtiainen J, Wagman N, Öberg LG, Jörgensen KS (1997b) Fate and toxicity of chlorophenols, polychlorinated dibenzo-p-dioxins and dibenzofurans during composting of contaminated sawmill soil. Environ Sci Technol 31:3224–3250Google Scholar
  73. Lazcano C, Gómez-Brandón M, Domínguez J (2008) Comparison of the effectiveness of composting and vermicomposting for the biological stabilization of cattle manure. Chemosphere 72:1013–1019PubMedCrossRefGoogle Scholar
  74. Lee LS, Rao PSC, Okuda I (1992) Equilibirum partitioning of polycyclic aromatic hydrocarbons from coal tar into water. Environ Sci Technol 26:2110–2115CrossRefGoogle Scholar
  75. Li X, Lin X, Zhang J, Wu Y, Yin R, Feng Y, Wang Y (2010) Degradation of polycyclic aromatic hydrocarbons by crude extracts from spent mushroom substrate and its possible mechanisms. Curr Microbiol 60:336–342PubMedCrossRefGoogle Scholar
  76. Li Z, Lu H, Ren L, He L (2013) Experimental and modeling approaches for food waste composting: A review. Chemosphere 93:1247–1257PubMedCrossRefGoogle Scholar
  77. Loick N, Hobbs PJ, Hale MCD, Jones DL (2012) Bioremediation of poly-aromatic hyrdocarbon (PAH)-contaminated Soil by Composting. Crit Rev Environ Sci Technol 39(4):271–332CrossRefGoogle Scholar
  78. Lu X-Y, Zhang T, Fang HH-P (2011) Bacteria-mediated PAH degradation in soil and sediment. Appl Microbiol Biotechnol 89:1357–1371PubMedCrossRefGoogle Scholar
  79. Luthy RG, Dzombak DA, Peters CA, Roy SB, Ramaswami A, Nakles DV, Nott BR (1994) Remediating tar-contaminated soils At Manufactured Gas Plant sites. Environ Sci Technol 28(6):266–276CrossRefGoogle Scholar
  80. Luthy RG, Ramaswami A, Ghoshal S (1993) Interfacial films in coal tar nonaqueous-phase liquid-water systems. Environ Sci Technol 27:2914–2918CrossRefGoogle Scholar
  81. Madsen T, Kristensen P (1997) Effects of bacterial inoculation and nonionic surfactants on degradation of polycyclic aromatic hydrocarbons in soil. Environ Toxicol Cheml 16:631–637CrossRefGoogle Scholar
  82. Marchal G, Smith KEC, Rein A, Winding A, de Jonge LW, Trapp S, Karlson UG (2013a) Impact of activated carbon, biochar and compost on the desorption and mineralization of phenenthrene in soil. Environ Poll 181:200–210CrossRefGoogle Scholar
  83. Marchal G, Smith KEC, Rein A, Winding A, Trapp S, Karlson UG (2013b) Comparing the desorption and biodegradation of low concentrations of phenanthrene sorbed to activated carbon, biochar and compost. Chemosphere 90(6):1767–1778. doi:10.1016/j.chemosphere.2012.07.048 PubMedCrossRefGoogle Scholar
  84. Mayer P, Fernqvist MM, Christensen PS, Karlson U, Trapp S (2007) Enhanced diffusion of polycyclic aromatic hydrocarhons in artificial and natural aqueous solutions. Environ Sci Technol 41(17):6148–6155. doi:10.1021/Es070495t PubMedCrossRefGoogle Scholar
  85. Mayer P, Karlson U, Christensen P, Johnsen A, Trapp S (2005) Quantifying the effect of medium composition on the diffusive mass transfer of Hydrophobic Organic Chemicals through unstirred boundary layers. Environ Sci Technol 39:6123–6129PubMedCrossRefGoogle Scholar
  86. Megharaj M, Ramakrishnan B, Venkateswarlu K, Sethunathan N, Naidu R (2011) Bioremediation approaches for organic pollutants: A critical perspective. Environ Intern 37:1362–1375CrossRefGoogle Scholar
  87. Megharaj M, Wittich RW, Blanco E, Pieper DH, Timmis KN (2002) Superior survival and degradation of dibenzo-p-dioxin and dibenzofuran in soil by soil-adapted Sphingomonas sp. strain RW1. Appl Microbiol Biotechnol 48:109–114CrossRefGoogle Scholar
  88. Michels J, Track T, Gehrke U, Sell D (2000) Leitfaden - biologische verfahren zur bodensanierung. Veröffentlichungen des BMBF (Grün-Weiße-Reihe), Umweltbundesamt, BerlinGoogle Scholar
  89. Miltner A, Bombach P, Schmidt-Brücken B, Kästner M (2012) SOM genesis: microbial biomass a significant source. Biogeochemistry 111:41–55CrossRefGoogle Scholar
  90. Monroy F, Aira M, Domínguez J (2008) Changes in density of nematodes, protozoa and total coliforms after transit through the gut of four epigeic earthworms (Oligochaeta). Appl Soil Ecol 39:127–132CrossRefGoogle Scholar
  91. Moorman TB, Cowan JK, Arthur EL, Coats JR (2001) Organic amendments to enhance herbicide biodegradation in contaminated soils. Biol Fert Soil 33:541–545CrossRefGoogle Scholar
  92. Morimoto K, Tatsumi K (1997) Effect of humic substances on the enzymatic formation of OCDD from PCP. Chemosphere 34:1277–1283CrossRefGoogle Scholar
  93. Neher DA, Weicht TR, Bates ST, Leff JW, Fierer N (2013) Changes in bacterial and fungal communities across compost recipes, preparation methods, and Composting Times. PLoS one 8(11):e79512. doi:10.1371/journal.pone.0079512 PubMedPubMedCentralCrossRefGoogle Scholar
  94. Neufeld JD, Dumont MG, Vohra J, Murrell JC (2007) Methodological considerations for the use of stable isotope probing in microbial ecology. Microb Ecol 53(3):435–442PubMedCrossRefGoogle Scholar
  95. Öberg LG, Glas B, Swanson SE, Rappe C, Paul KG (1990) Peroxidase-catalyzed oxidation of chlorophenols to polychlorinated dibenzo-p-dioxins and dibenzofurans. Arch Environ Contam Toxicol 19:930–938PubMedCrossRefGoogle Scholar
  96. Ortega-Calvo JJ, Saiz-Jimenez C (1998) Effect of humic fractions and clay on biodegradation of phenanthrene by a Pseudomonas fluorescens strain isolated from Soil. Appl Environ Microbiol 64(8):3123–3126PubMedPubMedCentralGoogle Scholar
  97. Palatinszky M, Herbold C, Jehmlich N, Pogoda M, Han P, von Bergen M, Lagkouvardos I, Karst SM, Galushko A, Koch H, Berry D, Daims H, Wagner M (2015) Cyanate as an energy source for nitrifiers. Nature 524:105–108PubMedPubMedCentralCrossRefGoogle Scholar
  98. Pande S, Merker H, Bohl K, Reichelt M, Schuster S, de Figueiredo L, Kaleta C, Kost C (2014) Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria. ISME J 8:953–962PubMedPubMedCentralCrossRefGoogle Scholar
  99. Peng J, Zhang Y, Su J, Qiu Q, Jia Z, Zhu YG (2013) Bacterial communities predominant in the degradation of 13C4-4,5,9,10-pyrene during composting. Biores Technol 143:608–614CrossRefGoogle Scholar
  100. Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, Tian YS, Yao QH (2008) Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol Rev 32(6):927–955. doi:10.1111/j.1574-6976.2008.00127.x PubMedCrossRefGoogle Scholar
  101. Pérez DV, Alcantara S, Ribeiro CC, Pereira R, Fontes GC, Wasserman M, Venezuelad TC, Meneguellia NA, de Macedoa JR, Barradase CAA (2007) Composted municipal waste effects on chemical properties of a Brazilian soil. Biores Technol 98:525–533CrossRefGoogle Scholar
  102. Phan CW, Sabaratnam V (2012) Potential uses of spent mushroom substrate and its associated lignocellulosic enzymes. Appl Microbiol Biotechnol 96:863–873PubMedCrossRefGoogle Scholar
  103. Pignatello JJ, Xing BS (1996) Mechanisms of slow sorption of organic chemicals to natural particles. Environ Sci Technol 30(1):1–11. doi:10.1021/Es940683g CrossRefGoogle Scholar
  104. Pignatello JJ, Kwon S, Lu Y (2006) Effect of natural organic substances on the surface and adsorptive properties of environmental black carbon (char): attenuation of surface activity by humic and fulvic acids. Environ Sci Technol 40:7757–7763PubMedCrossRefGoogle Scholar
  105. Potts M (1994) Desiccation tolerance of prokaryotes. Microb Rev 58(4):755–805Google Scholar
  106. Pronk GJ, Heister K, Kögel-Knabner I (2013) Is turnover and development of organic matter controlled by mineral composition? Soil Biol Biochem 67:235–244CrossRefGoogle Scholar
  107. Prosser J (2015) Dispersing misconceptions and identifying opportunities for the use of ‘omics’ in soil microbial ecology. Nat Rev Microbiol 13:439–446PubMedCrossRefGoogle Scholar
  108. Puglisi E, Cappa F, Fragoulis G, Trevisan M, Del Re AAM (2007) Bioavailability and degradation of phenanthrene in compost amended soils. Chemosphere 67:548–556PubMedCrossRefGoogle Scholar
  109. Purnomo AS, Mori T, Kamei I, Nishii T, Kondo R (2010) Application of mushroom waste medium from Pleurotus ostreatusfor bioremediation of DDT-contaminated soil. Int Biodet Biodeg 64:397–402Google Scholar
  110. Rein A, Adam IKU, Miltner A, Brumme K, Kästner M, Trapp S (2015) Simulations and impact of bacterial activity on the turnover of insoluble hydrophobic substrates (phenanthrene and pyrene). J Haz Mat submittedGoogle Scholar
  111. Rodriguez E, Garcia-Encina PA, Stams AJM, Maphosa F, Sousa DZ (2015) Meta-omics approaches to understand and improve wastewater treatment systems. Rev Environ Sci Bio/Technol 14:385–406CrossRefGoogle Scholar
  112. Ros M, Rodríguez I, Hernández CGT (2010) Microbial communities involved in the bioremediation of an aged recalcitrant hydrocarbon polluted soil by using organic amendments. Biores Technol 101:6916–6923CrossRefGoogle Scholar
  113. Ryckeboer J, Mergaert J, Coosemans J, Deprins K, Swings J (2003) Microbiological aspects of biowaste during composting in a monitored compost bin. J Appl Microbiol 94:127–137PubMedCrossRefGoogle Scholar
  114. Sasek V, Bhatt M, Cajthaml T, Malachova K, Lednicha D (2003) Compost-mediated removal of polycyclic aromatic hydrocarbons from contaminated soil. Arch Environ Contam Toxicol 44:336–342PubMedCrossRefGoogle Scholar
  115. Scelza R, Rao MA, Gianfreda L (2008) Response of an agricultural soil to pentachlorophenol (PCP) contamination and the addition of compost or dissolved organic matter. Soil Biol Biochem 40:2162–2169CrossRefGoogle Scholar
  116. Schloss PD, Hay AG, Wilson DB, Walker LP (2003) Tracking temporal changes of bacterial community fingerprints during the initial stages of composting. FEMS Microbiol Ecol 46:1–9PubMedCrossRefGoogle Scholar
  117. Seifert J, Herbst F-A, Nielsen PH, Planes FJ, Ferrer M, von Bergen M (2013) Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities. Proteomics 13:2786–2804PubMedGoogle Scholar
  118. Semple KT, Reid BJ, Fermor TR (2001) Impact of composting strategies on the treatment of soils contaminated with organic pollutants. Environ Poll 112:269–283CrossRefGoogle Scholar
  119. Smith KEC, Thullner M, Wick LY, Harms H (2009) Sorption to humic acids enhances polycyclic aromatic hydrocarbon biodegradation. Environ Sci Technol 43:7205–7211PubMedCrossRefGoogle Scholar
  120. Smith KEC, Thullner M, Wick LY, Harms H (2011) Dissolved organic carbon enhances the mass transfer of Hydrophobic organic compounds from nonaqueous phase liquids (NAPLs) into the aqueous phase. Environ Sci Technol 45:8741–8747PubMedCrossRefGoogle Scholar
  121. Steffen KT, Hatakka A, Hofrichter M (2002) Removal and mineralization of polycyclic aromatic hydrocarbons by litter-decomposing basidiomycetous fungi. Appl Microbiol Biotechnol 60:212–217PubMedCrossRefGoogle Scholar
  122. Steger K, Elind Y, Olsson J, Sundh I (2005) Microbial community growth and utilization of carbon constituents during thermophilic composting at different oxygen levels. Microb Ecol 50:163–170PubMedCrossRefGoogle Scholar
  123. Stringfellow WT, Alvarez-Cohen L (1999) Evaluating the relationship between the sorption of PAHs to bacterial biomass and biodegradation. Water Res 33(11):2535–2544CrossRefGoogle Scholar
  124. Takaku H, Kodaira S, Kimoto A, Nashimoto M, Takagi M (2006) Microbial communities in the garbage composting with rice Hull as an amendment revealed by culture-dependent and independent approaches. J Biosci Bioeng 101:42–50PubMedCrossRefGoogle Scholar
  125. Thummes K, Kämpfer P, Jäckel U (2007) Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material. Sys Appl Microbiol 30(5):418–429CrossRefGoogle Scholar
  126. Trellu C, Mousset E, Pechaud Y, Huguenot E, van Hullebusch ED, Esposito G, Oturan MA (2016) Removal of hydrophobic organic pollutants from soil washing/flushing solutions: A critical review. J Haz Mat 306:149–174CrossRefGoogle Scholar
  127. Vacca DJ, Bleam WF, Hickey WJ (2005) Isolation of Soil bacteria adapted to degrade humic acid-sorbed phenanthrene. Appl Environ Microbiol 71(7):3797–3805PubMedPubMedCentralCrossRefGoogle Scholar
  128. Valo R, Salkinoja-Salonen M (1986) Bioreclamation of chlorophenol-contaminated soil by composting. Appl Microbiol Biotechnol 25:68–75Google Scholar
  129. Vila J, Tauler M, Grifoll M (2015) Bacterial PAH degradation in marine and terrestrial habitats. Curr Op Biotechnol 33:95–102CrossRefGoogle Scholar
  130. Volkering F, Breure AM, Sterkenburg A, Vanandel JG (1992) Microbial degradation of polycyclic aromatic hydrocarbons - effect of substrate availability on bacterial growth kinetics. Appl Microbiol Biotechnol 36(4):548–552CrossRefGoogle Scholar
  131. Wang C, Guo XH, Deng H, Dong D, Tu QP, Wu WX (2014) New insights into the structure and dynamics of actinomycetal community during manure composting. Appl Microbiol Biotechnol 98:3327–3337PubMedCrossRefGoogle Scholar
  132. Wang X, Cui H, Shi J, Zhao X, Zhao Y, Wei Z (2015) Relationship between bacterial diversity and environmental parameters during composting of different raw materials. Biores Technol 198:395–402CrossRefGoogle Scholar
  133. Wehrer M, Rennert T, Totsche K-U (2013) Kinetic control of contaminant release from NAPLs - experimental evidence. Environ Poll 179:315–325CrossRefGoogle Scholar
  134. Weiss M, Geyer R, Gunther T, Kaestner M (2004b) Fate and stability of 14C-labeled 2,4,6-trinitrotoluene in contaminated soil following microbial bioremediation processes. Environ Toxicol Chem 23(9):2049–2060PubMedCrossRefGoogle Scholar
  135. Weiss M, Geyer R, Russow R, Richnow HH, Kastner M (2004a) Fate and metabolism of [15N]2,4,6-trinitrotoluene in soil. Environ Toxicol Chem 23(8):1852–1860PubMedCrossRefGoogle Scholar
  136. Wick LY, Colangelo T, Harms H (2001) Kinetics of mass transfer-limited bacterial growth on solid PAHs. Environ Sci Technol 35(2):354–361. doi:10.1021/Es001384w PubMedCrossRefGoogle Scholar
  137. Wiesmann U (1994) Der Steinkohleteer und seine Destillationsprodukte - Ein Beitrag zur Geschichte der Technik und der Bodenverschmutzung. In: Wiegert B (ed) Biologischer Abbau von polyzyklichen aromatischen Kohlenwasserstoffen. Schriftenreihe Bologische Abwasserreinigung. SFB 193, TU Berlin, Berlin, pp. 3–18Google Scholar
  138. Williams RT, Ziegenfuss PS, Sisk WE (1992) Composting of explosives and propellant contaminated soils under thermophilic and mesophilic conditions. J Ind Microbiol 9:137–144CrossRefGoogle Scholar
  139. Xu F, Webb JP (2015) Tianjin clean-up after explosion. Can Med Assoc J 187:E404CrossRefGoogle Scholar
  140. Zhang Y, Lashermes G, Houot S, Zhu Y-G, Barriuso E, Garnier P (2014) COP-compost: a sofware to study the degradation of organic pollutants in composts. Environ Sci Poll Res 21(4):2761–2776CrossRefGoogle Scholar
  141. Zhang Y, Zhu Y-G, Houot S, Qiao M, Nunan N, Garnier P (2011) Remediation of polycyclic aromatic hydrocarbon (PAH) contaminated soil through composting with fresh organic wastes. Environ Sci Poll Res 18:1574–1584CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research – UFZLeipzigGermany

Personalised recommendations