81
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell
DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved
alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145
Collins G, Kavanagh S, Mchugh S, Connaughton S, Kearney A, Rice O, Carrigg C, Scully C,
Bhreathnach N, Mahony T, Madden P, Enright AM, Flaherty V (2006) Accessing the black box
of microbial diversity and ecophysiology: recent advances through polyphasic experiments.
J Environ Sci Health A 41:897–922
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal
tool for annotation, visualization and analysis in functional genomics research. Bioinformatics
21:3674–3676
Cong J, Yang Y, Liu X, Lu H, Liu X, Zhou J, Li D, Yin H, Ding J, Zhang Y (2015) Analyses of
soil microbial community compositions and functional genes reveal potential consequences of
natural forest succession. Sci Rep-UK 5:10007
Costa R, Götz M, Mrotzek N, Lottmann J, Berg G, Smalla K (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of different microbial guilds. FEMS Microbiol Ecol 56:236–249
Couillerot O, Ramírez-Trujillo A, Walker V, von Felten A, Jansa J, Maurhofer M, Moënne-Loccoz
Y (2013) Comparison of prominent Azospirillum strains in Azospirillum-PseudomonasGlomus consortia for promotion of maize growth. Appl Microbiol Biotechnol 97:4639–4649
Creer S, Deiner K, Frey S, Porazinska D, Taberlet P, Thomas WK, Potter C, Bik HM (2016)
The ecologist’s field guide to sequence-based identification of biodiversity. Methods Ecol Evol
7:1008–1018
Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, Fraissinet-Tachet L, Marmeisse R
(2012) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest
soils. PLoS One 7(1):e28967. https://doi.org/10.1371/journal.pone.0028967
Dang QL, Shin TS, Park MS, Choi YH, Choi GJ, Jang KS, Kim IS, Kim J-C (2014) Antimicrobial
activities of novel mannosyl lipids isolated from the biocontrol fungus Simplicillium lamellicolaBCP against Phytopathogenic Bacteria. J Agric Food Chem 62:3363–3370
Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA (2014) Phylogenetic analysis of
genomes and metagenomes. PeerJ 2:e243
De Bourcy CF, De Vlaminck I, Kanbar JN, Wang J, Gawad C, Quake SR (2014) A quantitative comparison of singlecell whole genome amplification methods. PLoS One 9(8):e105585.
https://doi.org/10.1371/journal.pone.0105585
de la Luz Mora M, Demaneta R, Acunaa JJ, Viscardia S, Jorqueraa M, Rengelb Z, Duran P (2017)
Aluminium-tolerant bacteria improve the plant growth and phosphorus content in ryegrass
grown in a volcanic soil amended with cattle dung manure. Appl Soil Ecol 115:19–26
de-Bashan LE, Hernandez JP, Bashan Y (2012) The potential contribution of plant growth-promoting bacteria to reduce environmental degradation – a comprehensive evaluation. Appl Soil
Ecol 61:171–189
Degefu Y, Somervuo P, Aittamaa M, Virtanen E, Valkonen JPT (2016) Evaluation of a diagnostic microarray for the detection of major bacterial pathogens of potato from tuber samples.
Bull OEPP 46:103–111
Delahunty CM, Yates JR (2007) MudPIT: multidimensional protein identification technology.
BioTechniques 43:563–567
Deleye L, Tilleman L, Vander Plaetsen AS, Cornelis S, Deforce D, Van Nieuwerburgh F (2017)
Performance of four modern whole genome amplification methods for copy number variant
detection in single cells. Sci Rep 7(1):3422
DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for
the identification of single cells. Science 243:1360–1363
Deng Z, Zhang R, Shi Y, Tan H, Cao L (2014) Characterization of Cd-, Pb-, Zn-resistant endophytic Lasiodiplodia sp. MXSF31 from metal accumulating Portulaca oleracea and its potential in promoting the growth of rape in metal-contaminated soils. Environ Sci Pollut Res
21:2346–2357
References
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell
DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved
alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145
Collins G, Kavanagh S, Mchugh S, Connaughton S, Kearney A, Rice O, Carrigg C, Scully C,
Bhreathnach N, Mahony T, Madden P, Enright AM, Flaherty V (2006) Accessing the black box
of microbial diversity and ecophysiology: recent advances through polyphasic experiments.
J Environ Sci Health A 41:897–922
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal
tool for annotation, visualization and analysis in functional genomics research. Bioinformatics
21:3674–3676
Cong J, Yang Y, Liu X, Lu H, Liu X, Zhou J, Li D, Yin H, Ding J, Zhang Y (2015) Analyses of
soil microbial community compositions and functional genes reveal potential consequences of
natural forest succession. Sci Rep-UK 5:10007
Costa R, Götz M, Mrotzek N, Lottmann J, Berg G, Smalla K (2006) Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of different microbial guilds. FEMS Microbiol Ecol 56:236–249
Couillerot O, Ramírez-Trujillo A, Walker V, von Felten A, Jansa J, Maurhofer M, Moënne-Loccoz
Y (2013) Comparison of prominent Azospirillum strains in Azospirillum-PseudomonasGlomus consortia for promotion of maize growth. Appl Microbiol Biotechnol 97:4639–4649
Creer S, Deiner K, Frey S, Porazinska D, Taberlet P, Thomas WK, Potter C, Bik HM (2016)
The ecologist’s field guide to sequence-based identification of biodiversity. Methods Ecol Evol
7:1008–1018
Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, Fraissinet-Tachet L, Marmeisse R
(2012) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest
soils. PLoS One 7(1):e28967. https://doi.org/10.1371/journal.pone.0028967
Dang QL, Shin TS, Park MS, Choi YH, Choi GJ, Jang KS, Kim IS, Kim J-C (2014) Antimicrobial
activities of novel mannosyl lipids isolated from the biocontrol fungus Simplicillium lamellicolaBCP against Phytopathogenic Bacteria. J Agric Food Chem 62:3363–3370
Darling AE, Jospin G, Lowe E, Matsen FA, Bik HM, Eisen JA (2014) Phylogenetic analysis of
genomes and metagenomes. PeerJ 2:e243
De Bourcy CF, De Vlaminck I, Kanbar JN, Wang J, Gawad C, Quake SR (2014) A quantitative comparison of singlecell whole genome amplification methods. PLoS One 9(8):e105585.
https://doi.org/10.1371/journal.pone.0105585
de la Luz Mora M, Demaneta R, Acunaa JJ, Viscardia S, Jorqueraa M, Rengelb Z, Duran P (2017)
Aluminium-tolerant bacteria improve the plant growth and phosphorus content in ryegrass
grown in a volcanic soil amended with cattle dung manure. Appl Soil Ecol 115:19–26
de-Bashan LE, Hernandez JP, Bashan Y (2012) The potential contribution of plant growth-promoting bacteria to reduce environmental degradation – a comprehensive evaluation. Appl Soil
Ecol 61:171–189
Degefu Y, Somervuo P, Aittamaa M, Virtanen E, Valkonen JPT (2016) Evaluation of a diagnostic microarray for the detection of major bacterial pathogens of potato from tuber samples.
Bull OEPP 46:103–111
Delahunty CM, Yates JR (2007) MudPIT: multidimensional protein identification technology.
BioTechniques 43:563–567
Deleye L, Tilleman L, Vander Plaetsen AS, Cornelis S, Deforce D, Van Nieuwerburgh F (2017)
Performance of four modern whole genome amplification methods for copy number variant
detection in single cells. Sci Rep 7(1):3422
DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for
the identification of single cells. Science 243:1360–1363
Deng Z, Zhang R, Shi Y, Tan H, Cao L (2014) Characterization of Cd-, Pb-, Zn-resistant endophytic Lasiodiplodia sp. MXSF31 from metal accumulating Portulaca oleracea and its potential in promoting the growth of rape in metal-contaminated soils. Environ Sci Pollut Res
21:2346–2357
References