99
Wilke A, Bischof J, Gerlach W, Glass E, Harrison T, Keegan KP, Paczian T, Trimble WL, Bagchi
S, Grama A, Chaterji S, Meyer F (2016) The MG-RAST metagenomics database and portal in
2015. Nucleic Acids Res 4:44
Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams
KL (1995) Progress with proteome projects: why all proteins expressed by a genome should
be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50
Wilkinson SC, Anderson JM, Scardelis SP, Tisiafouli M, Taylor A, Wolters V (2002) PLFA profiles
of microbial communities in decomposing conifer litters subject to moisture stress. Soil Biol
Biochem 34:189–200
Williams MA, Taylor EB (2010) Microbial protein in soil: influence of extraction method and C
amendment on extraction and recovery. Microb Ecol 59:390–399
Wilmes P, Bond PL (2004) The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ
Microbiol 6:911–920
Wiśniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for
proteome analysis. Nat Methods 6:359–362
Witters N, Mendelsohn RO, Van Slyckenc S, Weyens N, Schreurs E, Meers E, Tack F, Carleer R,
Vangronsveld J (2012) Phytoremediation, a sustainable remediation technology? Conclusions
from a case study. I: energy production and carbon dioxide abatement. Biomass Bioenergy
39:454–469
Wooley JC, Ye Y (2009) Metagenomics: facts and artifacts, and computational challenges.
J Comput Sci Technol 25:71–81
Woyke T, Jarett J (2015) Function-driven single-cell genomics. Microb Biotechnol 8:38–39
Wu M, Eisen JA (2008) A simple, fast, and accurate method of phylogenomic inference. Genome
Biol. https://doi.org/10.1186/gb-2008-9-10-r151
Wu M, Scott AJ (2012) Phylogenomic analysis of bacterial and archaeal sequences with
AMPHORA2. Bioinformatics 28:1033–1034
Wu G, Feng B, Xu J, Zhu XT, Li YC, Zeng NK, Yang ZL (2014) Molecular phylogenetic analyses
redefine seven major clades and reveal 22 new generic clades in the fungal family Boletaceae.
Fungal Divers 69(1):93–115
Wu C, Wang W, Wang K, Li X, Qiu W, Li W (2016) Phospholipids fatty acids analysis of microbial
communities in sewage sludge composting with inorganic bulking agent. Desalin Water Treat
57:27181–27190
Xie X, Liao M, Yang J, Chai J, Fang S, Wang R (2012) Influence of root-exudates concentration on pyrene degradation and soil microbial characteristics in pyrene contaminated soil.
Chemosphere 88:1190–1195
Xue K, Wu L, Deng Y, He Z, Nostrand JV, Robertson PG, Schmidt TM, Zhou J (2013) Functional
gene differences in soil microbial communities from conventional, low-input, and organic
farmlands. Appl Environ Microbiol 79:1284–1292
Xun F, Xie B, Liu S, Guo C (2015) Effect of plant growth-promoting bacteria (PGPR) and
arbuscular mycorrhizal fungi (AMF) inoculation on oats in saline-alkali soil contaminated by
petroleum to enhance phytoremediation. Environ Sci Pollut Res 22:598–608
Yang M-M, Wen S-S, Mavrodi DV, Mavrodi OV, von Wettstein D, Thomashow LS, Guo J-H,
Weller DM (2014) Biological control of wheat root diseases by the CLP-producing strain
Pseudomonas fluorescens HC1-07. Phytopathology 104:248–256
Yates JR (2004) Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct
33:297–316
Yates JR, Speicher S, Griffin PR, Hunkapiller T (1993) Peptide mass maps: a highly informative
approach to protein identification. Anal Biochem 214:397–408
Ye Y, Tang H (2009) An ORFome assembly approach to metagenomics sequences analysis.
J Bioinforma Comput Biol 7:455–471
Yooseph S, Sutton G, Rusch DB et al (2007) The sorcerer II global ocean sampling expedition:
expanding the universe of protein families. PLoS Biol 5:e16
References
Wilke A, Bischof J, Gerlach W, Glass E, Harrison T, Keegan KP, Paczian T, Trimble WL, Bagchi
S, Grama A, Chaterji S, Meyer F (2016) The MG-RAST metagenomics database and portal in
2015. Nucleic Acids Res 4:44
Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams
KL (1995) Progress with proteome projects: why all proteins expressed by a genome should
be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50
Wilkinson SC, Anderson JM, Scardelis SP, Tisiafouli M, Taylor A, Wolters V (2002) PLFA profiles
of microbial communities in decomposing conifer litters subject to moisture stress. Soil Biol
Biochem 34:189–200
Williams MA, Taylor EB (2010) Microbial protein in soil: influence of extraction method and C
amendment on extraction and recovery. Microb Ecol 59:390–399
Wilmes P, Bond PL (2004) The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ
Microbiol 6:911–920
Wiśniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for
proteome analysis. Nat Methods 6:359–362
Witters N, Mendelsohn RO, Van Slyckenc S, Weyens N, Schreurs E, Meers E, Tack F, Carleer R,
Vangronsveld J (2012) Phytoremediation, a sustainable remediation technology? Conclusions
from a case study. I: energy production and carbon dioxide abatement. Biomass Bioenergy
39:454–469
Wooley JC, Ye Y (2009) Metagenomics: facts and artifacts, and computational challenges.
J Comput Sci Technol 25:71–81
Woyke T, Jarett J (2015) Function-driven single-cell genomics. Microb Biotechnol 8:38–39
Wu M, Eisen JA (2008) A simple, fast, and accurate method of phylogenomic inference. Genome
Biol. https://doi.org/10.1186/gb-2008-9-10-r151
Wu M, Scott AJ (2012) Phylogenomic analysis of bacterial and archaeal sequences with
AMPHORA2. Bioinformatics 28:1033–1034
Wu G, Feng B, Xu J, Zhu XT, Li YC, Zeng NK, Yang ZL (2014) Molecular phylogenetic analyses
redefine seven major clades and reveal 22 new generic clades in the fungal family Boletaceae.
Fungal Divers 69(1):93–115
Wu C, Wang W, Wang K, Li X, Qiu W, Li W (2016) Phospholipids fatty acids analysis of microbial
communities in sewage sludge composting with inorganic bulking agent. Desalin Water Treat
57:27181–27190
Xie X, Liao M, Yang J, Chai J, Fang S, Wang R (2012) Influence of root-exudates concentration on pyrene degradation and soil microbial characteristics in pyrene contaminated soil.
Chemosphere 88:1190–1195
Xue K, Wu L, Deng Y, He Z, Nostrand JV, Robertson PG, Schmidt TM, Zhou J (2013) Functional
gene differences in soil microbial communities from conventional, low-input, and organic
farmlands. Appl Environ Microbiol 79:1284–1292
Xun F, Xie B, Liu S, Guo C (2015) Effect of plant growth-promoting bacteria (PGPR) and
arbuscular mycorrhizal fungi (AMF) inoculation on oats in saline-alkali soil contaminated by
petroleum to enhance phytoremediation. Environ Sci Pollut Res 22:598–608
Yang M-M, Wen S-S, Mavrodi DV, Mavrodi OV, von Wettstein D, Thomashow LS, Guo J-H,
Weller DM (2014) Biological control of wheat root diseases by the CLP-producing strain
Pseudomonas fluorescens HC1-07. Phytopathology 104:248–256
Yates JR (2004) Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct
33:297–316
Yates JR, Speicher S, Griffin PR, Hunkapiller T (1993) Peptide mass maps: a highly informative
approach to protein identification. Anal Biochem 214:397–408
Ye Y, Tang H (2009) An ORFome assembly approach to metagenomics sequences analysis.
J Bioinforma Comput Biol 7:455–471
Yooseph S, Sutton G, Rusch DB et al (2007) The sorcerer II global ocean sampling expedition:
expanding the universe of protein families. PLoS Biol 5:e16
References