M. Aira, F. Monroy, and J. Domínguez, Eisenia fetida (Oligochaeta: Lumbricidae) Modifies the Structure and Physiological Capabilities of Microbial Communities Improving Carbon Mineralization During Vermicomposting of Pig Manure, Microbial Ecology, vol.78, issue.4
DOI : 10.1007/s00248-007-9223-4

M. Aira and J. Domínguez, Optimizing vermicomposting of animal wastes: Effects of rate of manure application on carbon loss and microbial stabilization, Journal of Environmental Management, vol.88, issue.4, pp.1525-1529, 2008.
DOI : 10.1016/j.jenvman.2007.07.030

M. Aira and J. Domí?nguez, Microbial and nutrient stabilization of two animal manures after the transit through the gut of the earthworm Eisenia fetida (Savigny, 1826), Journal of Hazardous Materials, vol.161, issue.2-3, pp.1234-1238, 2009.
DOI : 10.1016/j.jhazmat.2008.04.073

J. Amossé, Y. Bettarel, C. Bouvier, T. Bouvier, T. D. Tran et al., The flows of nitrogen, bacteria and viruses from the soil to water compartments are influenced by earthworm activity and organic fertilization (compost vs. vermicompost), Soil Biology and Biochemistry, vol.66, 2013.
DOI : 10.1016/j.soilbio.2013.07.007

A. Anastasi, G. C. Varese, and V. F. Marchisio, Isolation and identification of fungal communities in compost and vermicompost, Mycologia, vol.97, issue.1, pp.33-44, 2005.
DOI : 10.1080/15572536.2006.11832836

N. Q. Arancon, C. A. Edwards, R. Dick, and L. Dick, Vermicompost tea production and plant growth impacts, pp.51-52, 2007.

R. M. Atiyeh, C. A. Edwards, S. Subler, and J. D. Metzger, Pig manure vermicompost as a component of a horticultural bedding plant medium: effects on physicochemical properties and plant growth, Bioresource Technology, vol.78, issue.1, pp.78-89, 2001.
DOI : 10.1016/S0960-8524(00)00172-3

K. Bailey, G. Lazarovits, and G. , Suppressing soil-borne diseases with residue management and organic amendments, Soil and Tillage Research, vol.72, issue.2, pp.169-180, 2003.
DOI : 10.1016/S0167-1987(03)00086-2

. Blanchart, Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil, The ISME J, vol.6, pp.213-222, 2012.

N. Bottinelli, T. Henry-des-tureaux, V. Hallaire, Y. Benard, J. Mathieu et al., Earthworms accelerate soil porosity turnover under watering conditions, Geoderma, vol.156, issue.1-2, pp.43-47, 2010.
DOI : 10.1016/j.geoderma.2010.01.006

URL : https://hal.archives-ouvertes.fr/hal-01460935

G. Brown, B. Pashanasi, C. Villenave, J. C. Patron, B. K. Senapati et al., Effects of earthworms on plant production in the tropics Earthworm Management in Tropical Agroecosystems, pp.87-137, 1999.

L. R. Bulluck, M. Brosius, G. K. Evanylo, and J. B. Ristaino, Organic and synthetic fertility amendments influence soil microbial, physical and chemical properties on organic and conventional farms, Applied Soil Ecology, vol.19, issue.2, pp.147-160, 2002.
DOI : 10.1016/S0929-1393(01)00187-1

B. A. Byzov, N. V. Khomyakov, S. A. Kharin, and A. V. Kurakov, Fate of soil bacteria and fungi in the gut of earthworms, European Journal of Soil Biology, vol.43, pp.43-149, 2007.
DOI : 10.1016/j.ejsobi.2007.08.012

K. H. Choi and F. C. Dobbs, Comparison of two kinds of Biolog microplates (GN and ECO) in their ability to distinguish among aquatic microbial communities, Journal of Microbiological Methods, vol.36, issue.3
DOI : 10.1016/S0167-7012(99)00034-2

J. P. Curry and O. Schmidt, The feeding ecology of earthworms ??? A review, Pedobiologia, vol.50, issue.6, pp.463-477, 2007.
DOI : 10.1016/j.pedobi.2006.09.001

M. Diacono and F. Montemurro, Long-Term Effects of Organic Amendments on Soil Fertility, A review Agro. Sustain. Dev, vol.30, pp.401-422, 2010.
DOI : 10.1007/978-94-007-0394-0_34

URL : https://hal.archives-ouvertes.fr/hal-00886539

T. T. Doan, T. P. Ngo, C. Rumpel, V. B. Nguyen, and P. Jouquet, Interaction between compost, vermicompost and earthworm activity. A one year greenhouse experiment, Sci. Hort, pp.160-148, 2012.

H. L. Drake and M. A. Horn, As the Worm Turns: The Earthworm Gut as a Transient Habitat for Soil Microbial Biomes, Annual Review of Microbiology, vol.61, issue.1, pp.61-169, 2007.
DOI : 10.1146/annurev.micro.61.080706.093139

C. A. Edwards and N. Q. Arancon, The use of earthworms in the breakdown of organic wastes to produce vermicomposts and animal feed protein

C. A. Edwards, J. Dominguez, and Q. A. Norman, The influence of vermicomposts on plant growth and pest incidence, Soil Zoology for Sustainable Development in the 21st Century

C. A. Eicherner, R. W. Erb, K. N. Timmis, and I. Wagner-dobler, Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shock in the activated sludge microbial community, Appl. Environ. Microbiol, pp.65-102, 1999.

. Fao, Soil map of the world revised legend, World Soil Resources Rept, vol.60, 1988.

R. García-ruiz, V. Ochoa, M. B. Hinojosa, and J. A. Carreira, Suitability of enzyme activities for the monitoring of soil quality improvement in organic agricultural systems, Soil Biology and Biochemistry, vol.40, issue.9, pp.40-2137, 2008.
DOI : 10.1016/j.soilbio.2008.03.023

J. L. Garland and A. L. Mills, Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level-sole carbonsource-utilization, Appl. Environ. Microb, vol.57, pp.2351-2359, 1991.

F. Gil-sotres, C. Trasar-cepeda, M. C. Leirós, and S. Seoane, Different approaches to evaluating soil quality using biochemical properties, Soil Biology and Biochemistry, vol.37, issue.5, pp.877-887, 2005.
DOI : 10.1016/j.soilbio.2004.10.003

E. Gomez, L. Ferreras, and S. Toresani, Soil bacterial functional diversity as influenced by organic amendment application, Bioresource Technology, vol.97, issue.13, pp.1484-1489, 2006.
DOI : 10.1016/j.biortech.2005.06.021

T. Gomiero, M. G. Paoletti, and D. Pimentel, Energy and Environmental Issues in Organic and Conventional Agriculture, Critical Reviews in Plant Sciences, vol.10, issue.4, pp.239-254, 2008.
DOI : 10.1016/j.cropro.2005.08.008

M. Gonzalez, E. Gomez, R. Comese, M. Quesada, and M. Conti, Influence of organic amendments on soil quality potential indicators in an urban horticultural system, Bioresource Technology, vol.101, issue.22, pp.8897-8901, 2010.
DOI : 10.1016/j.biortech.2010.06.095

S. Haruyama, H. T. Dinh, and V. T. Le, Problem Soils of the Paddy Fields in the Eastern Coastal Plain of the Red River Delta, Vietnam, Journal of Geography (Chigaku Zasshi), vol.115, issue.6, pp.737-749, 2006.
DOI : 10.5026/jgeography.115.6_737

S. Hueso, C. García, and T. Hernández, Severe drought conditions modify the microbial community structure, size and activity in amended and unamended soils, Soil Biology and Biochemistry, vol.50, pp.50-167, 2012.
DOI : 10.1016/j.soilbio.2012.03.026

P. Jouquet, J. Dauber, J. Lagerlöf, P. Lavelle, and M. Lepage, Soil invertebrates as ecosystem engineers: Intended and accidental effects on soil and feedback loops, Applied Soil Ecology, vol.32, issue.2, pp.153-164, 2006.
DOI : 10.1016/j.apsoil.2005.07.004

URL : https://hal.archives-ouvertes.fr/bioemco-00139210

P. Jouquet, T. Plumere, T. D. Thu, C. Rumpel, T. T. Duc et al., The rehabilitation of tropical soils using compost and vermicompost is affected by the presence of endogeic earthworms, Applied Soil Ecology, vol.46, issue.1, pp.125-133, 2010.
DOI : 10.1016/j.apsoil.2010.07.002

URL : https://hal.archives-ouvertes.fr/bioemco-00575425

P. Jouquet, E. Bloquel, T. T. Doan, M. Ricoy, D. Orange et al., Do Compost and Vermicompost Improve Macronutrient Retention and Plant Growth in Degraded Tropical Soils?, Compost Science & Utilization, vol.63, issue.1, pp.15-24, 2011.
DOI : 10.1080/1065657X.2011.10736972

P. Jouquet, G. Huchet, N. Bottinelli, and D. T. Thu, What are the limits of the drilosphere? An incubation experiment using Metaphire posthuma, Pedobiologia, vol.54, pp.113-117, 2011.
DOI : 10.1016/j.pedobi.2011.07.013

P. Jouquet, G. Huchet, N. Bottinelli, D. T. Thu, and T. D. Tran, Does the influence of earthworms on water infiltration, nitrogen leaching and soil respiration depend on the initial soil bulk density? A mesocosm experiment with the endogeic species Metaphire posthuma, Biology and Fertility of Soils, vol.365, issue.5, pp.561-567, 2012.
DOI : 10.1007/s00374-011-0652-3

E. P. Kandeler, M. Stemmer, and M. Gerzabek, Tillage changes microbial biomass and enzyme activities in particle-size fractions of a Haplic Chernozem, Soil Biology and Biochemistry, vol.31, issue.9, pp.31-1253, 1999.
DOI : 10.1016/S0038-0717(99)00041-3

D. J. Lane, S. Stackebrandt, E. Goodfellow, and M. , Nucleic acid techniques in bacterial systematics, pp.115-175, 1991.

P. Lavelle, D. Bignell, and M. Lepage, Soil function in a changing world: the role of invertebrate ecosystem engineers, Eur. Soil Biol, vol.33, pp.159-193, 1997.

Y. J. Liu, A. Zaprasis, S. J. Liu, H. L. Drake, and M. A. Horn, The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders, The ISME Journal, vol.169, issue.3, pp.473-485, 2011.
DOI : 10.1007/BF00361617

C. Macci, S. Doni, E. Peruzzi, G. Masciandaro, C. Mennone et al., Almond tree and organic fertilization for soil quality improvement in southern Italy, Journal of Environmental Management, vol.95
DOI : 10.1016/j.jenvman.2010.10.050

S. Marhan, E. Kandeler, and S. Scheu, Phospholipid fatty acid profiles and xylanase activity in particle size fractions of forest soil and casts of Lumbricus terrestris L. (Oligochaeta, Lumbricidae), Applied Soil Ecology, vol.35, issue.2, pp.412-422, 2007.
DOI : 10.1016/j.apsoil.2006.06.003

S. Marinari, G. Masciandaro, B. Ceccanti, and S. Grego, Influence of organic and mineral fertilisers on soil biological and physical properties, Bioresource Technology, vol.72, issue.1, pp.9-17, 2000.
DOI : 10.1016/S0960-8524(99)00094-2

B. Moeskops, D. Buchan, S. Van-beneden, V. Fievez, S. Sleutel et al., The impact of exogenous organic matter on SOM contents and microbial soil quality, Pedobiologia, vol.55, issue.3, pp.55-175, 2012.
DOI : 10.1016/j.pedobi.2012.03.001

P. Mora, E. Miambi, J. J. Jiménez, T. Decaëns, and C. Rouland, Functional complement of biogenic structures produced by earthworms, termites and ants in the neotropical savannas, Soil Biology and Biochemistry, vol.37, issue.6, pp.37-1043, 2005.
DOI : 10.1016/j.soilbio.2004.10.019

D. L. Mummey, M. C. Rillig, and J. Six, Endogeic earthworms differentially influence bacterial communities associated with different soil aggregate size fractions, Soil Biology and Biochemistry, vol.38, issue.7
DOI : 10.1016/j.soilbio.2005.11.014

G. Muyzer, E. C. De-waal, and A. G. Uitterlinden, Profiling of complex microbial population by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA, Appl. Environ. Microb, pp.59-695, 1993.

P. T. Ngo, C. Rumpel, M. F. Dignac, D. Billou, T. T. Duc et al., Transformation of buffalo manure by composting or vermicomposting to rehabilitate degraded tropical soils, Ecological Engineering, vol.37, issue.2, pp.37-269, 2011.
DOI : 10.1016/j.ecoleng.2010.11.011

URL : https://hal.archives-ouvertes.fr/bioemco-00575967

P. T. Ngo, C. Rumpel, T. T. Doan, and P. Jouquet, The effect of earthworms on carbon storage and soil organic matter composition in tropical soil amended with compost and vermicompost, Soil Biology and Biochemistry, vol.50, pp.50-214, 2012.
DOI : 10.1016/j.soilbio.2012.02.037

K. P. Pramanik, G. K. Ghosh, P. K. Ghosal, and K. P. Bani, and Enzyme Activities in Vermicompost of Biodegradable Organic Wastes under Liming and Microbial Inoculants, Biores. Technol, vol.13, 2007.

R. Development and C. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2008.

N. Ruiz, J. Mathieu, L. Célini, C. Rollard, G. Hommay et al., IBQS: A synthetic index of soil quality based on soil macro-invertebrate communities
URL : https://hal.archives-ouvertes.fr/bioemco-00881416

M. Sebastiana, C. Juan, P. Ruiz, F. H. Juan, and M. Engracia, Chemical and biochemical properties in a silty loam soil under conventional and organic management, Soil Till. Res, vol.1, pp.162-170, 2006.

V. C. Sheffield, J. S. Beck, E. M. Stone, and R. M. Myers, A simple and efficient method for 632 attachment of a 40base pair, GC rich sequence to PCR amplified DNA, BioTechn, pp.12-386, 1992.

B. Sen and T. S. Chandra, Do earthworms affect dynamics of functional response and genetic structure of microbial community in a lab-scale composting system?, Bioresource Technology, vol.100, issue.2, pp.804-811, 2009.
DOI : 10.1016/j.biortech.2008.07.047

C. Stark, L. M. Condron, A. Stewart, H. J. Di, and M. O. Callaghan, Influence of organic and mineral amendments on microbial soil properties and processes, Applied Soil Ecology, vol.35, issue.1, pp.79-93, 2007.
DOI : 10.1016/j.apsoil.2006.05.001

M. Tejada, J. González, A. M. García-martínez, and J. Parrado, Application of a green manure and green manure composted with beet vinasse on soil restoration: Effects on soil properties, Bioresource Technology, vol.99, issue.11, pp.99-4949, 2008.
DOI : 10.1016/j.biortech.2007.09.026

A. V. Tiunov and S. Scheu, Carbon availability controls the growth of detritivores (Lumbricidae) and their effect on nitrogen mineralization, Oecologia, vol.138, issue.1, pp.83-90, 2004.
DOI : 10.1007/s00442-003-1391-4

A. Vivas, B. Moreno, S. Garcia-rodriguez, and E. Benitez, Assessing the impact of composting and vermicomposting on bacterial community size and structure, and microbial functional diversity of an olive-mill waste, Bioresource Technology, vol.100, issue.3, pp.1319-1326, 2009.
DOI : 10.1016/j.biortech.2008.08.014

A. Yajima, P. Jouquet, D. Do-trung, T. D. Thi-cam, D. Orange et al., High latrine coverage is not reducing the prevalence of soil-transmitted helminthiasis in Hoa Binh province, Vietnam, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.103, issue.3, pp.237-241, 2009.
DOI : 10.1016/j.trstmh.2008.08.012

URL : https://hal.archives-ouvertes.fr/bioemco-00396245

A. V. Yakushev, S. A. Blagodatsky, and B. A. Byzov, The effect of earthworms on the physiological state of the microbial community at vermicomposting. Microbiol, pp.78-510, 2009.

A. V. Yakushev, I. A. Bubnov, and A. M. Semenov, Estimation of the effects of earthworms and initial substrates on the bacterial community in vermicomposts, Eurasian Soil Science, vol.44, issue.10
DOI : 10.1134/S1064229311100164

M. Yasir, Z. Aslam, S. W. Kim, S. W. Lee, C. O. Jeon et al., Bacterial community composition and chitinase gene diversity of vermicompost with antifungal activity, Bioresource Technology, vol.100, issue.19, pp.4396-4403, 2009.
DOI : 10.1016/j.biortech.2009.04.015

J. C. Zak, M. Willig, D. L. Moorhead, and H. G. Wildman, 72) a 14, ) c nd nd Compost EW- 2.13 (0.16) a 2.46 (0.08) c 42.41, 1994.