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inorganic fertilizers on soil microbial community structure and function: a field study with sweet
corn. Biol Fertil Soils 49:723–733
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for
RNA-seq data with DESeq2. Genome Biol 15:550
Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial
communities. Appl Environ Microbiol 71:8228–8235
Mas-Carrió E, Dini-Andreote F, Brossi MJ, Salles J, Olff H (2018) Organic amendment under
increasing agricultural intensification: effects on soil bacterial communities and plant productivity. Front Microbiol 9:2612
Medina-Sauza RM, Álvarez-Jiménez M, Delhal A, Reverchon F, Blouin M, Guerrero-Analco JA,
Cerdán CR, Guevara R, Villain L, Barois I (2019) Earthworms building up soil microbiota, a
review. Front Environ Sci 7:81
Price MN, Dehal PS, Arkin AP (2010) FastTree 2—approximately maximum-likelihood trees for
large alignments. PLoS One 5:e9490
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2013) The
SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Nucleic Acids Res 41:D590–D596
Sánchez-Hernández JC, Domínguez J (2019) Dual role of vermicomposting in relation to environmental pollution: detoxification and bioremediation. In: Sánchez-Hernández J
(ed) Bioremediation of agricultural soils. CRC Press, Boca Raton, pp 217–230
Shade A, Handelsman J (2012) Beyond the venn diagram: the hunt for a core microbiome. Environ
Microbiol 14:4–12
Song X, Liu M, Wu D, Griffiths BS, Jiao J, Li H, Hu F (2015) Interaction matters: synergy between
vermicompost and PGPR agents improves soil quality, crop quality and crop yield in the field.
Appl Soil Ecol 89:25–34
Tilman D (1999) The ecological consequences of changes in biodiversity: a search for general
principles. Ecology 80:1455–1474
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of
rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267
Yang W, Yang Z, Guan Y, Zhai C, Shi D, Chen J, Wang T, Gu S (2019) Dose-dependent effect of
compost amendment on soil bacterial community composition and co-occurrence network
patterns in soybean agroecosystem. Arch Agron Soil Sci. https://doi.org/10.1080/03650340.
2019.1651450
Yakushev AV, Bubnov IA, Semenov AM (2011) Estimation of the effects of earthworms and initial
substrates on the bacterial community in vermicomposts. Eurasian Soil Sci 44:1117–1124
140
M. Gómez-Brandón et al.
inorganic fertilizers on soil microbial community structure and function: a field study with sweet
corn. Biol Fertil Soils 49:723–733
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for
RNA-seq data with DESeq2. Genome Biol 15:550
Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial
communities. Appl Environ Microbiol 71:8228–8235
Mas-Carrió E, Dini-Andreote F, Brossi MJ, Salles J, Olff H (2018) Organic amendment under
increasing agricultural intensification: effects on soil bacterial communities and plant productivity. Front Microbiol 9:2612
Medina-Sauza RM, Álvarez-Jiménez M, Delhal A, Reverchon F, Blouin M, Guerrero-Analco JA,
Cerdán CR, Guevara R, Villain L, Barois I (2019) Earthworms building up soil microbiota, a
review. Front Environ Sci 7:81
Price MN, Dehal PS, Arkin AP (2010) FastTree 2—approximately maximum-likelihood trees for
large alignments. PLoS One 5:e9490
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO (2013) The
SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Nucleic Acids Res 41:D590–D596
Sánchez-Hernández JC, Domínguez J (2019) Dual role of vermicomposting in relation to environmental pollution: detoxification and bioremediation. In: Sánchez-Hernández J
(ed) Bioremediation of agricultural soils. CRC Press, Boca Raton, pp 217–230
Shade A, Handelsman J (2012) Beyond the venn diagram: the hunt for a core microbiome. Environ
Microbiol 14:4–12
Song X, Liu M, Wu D, Griffiths BS, Jiao J, Li H, Hu F (2015) Interaction matters: synergy between
vermicompost and PGPR agents improves soil quality, crop quality and crop yield in the field.
Appl Soil Ecol 89:25–34
Tilman D (1999) The ecological consequences of changes in biodiversity: a search for general
principles. Ecology 80:1455–1474
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of
rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267
Yang W, Yang Z, Guan Y, Zhai C, Shi D, Chen J, Wang T, Gu S (2019) Dose-dependent effect of
compost amendment on soil bacterial community composition and co-occurrence network
patterns in soybean agroecosystem. Arch Agron Soil Sci. https://doi.org/10.1080/03650340.
2019.1651450
Yakushev AV, Bubnov IA, Semenov AM (2011) Estimation of the effects of earthworms and initial
substrates on the bacterial community in vermicomposts. Eurasian Soil Sci 44:1117–1124
140
M. Gómez-Brandón et al.