85
He Z, Piceno Y, Deng Y, Xu M, Lu Z, DeSantis T, Andersen G, Sarah E, Hobbie SE, Reich PB,
Zhou J (2012) The phylogenetic composition and structure of soil microbial communities shifts
in response to elevated carbon dioxide. ISME J 6:259–272
Henson J, Tischler G, Ning Z (2012) Next-generation sequencing and large genome assemblies.
Pharmacogenomics 13:901–915
Hernández-León R, Rojas-Solís D, Contreras-Pérez M, Orozco-Mosqueda MC, Macías-Rodríguez
LI, Reyes-de la Cruz H, Valencia-Cantero E, Santoyo G (2015) Characterization of the antifungal and plant growth-promoting effects of diffusible and volatile organic compounds produced
by Pseudomonas fluorescensstrains. Biol Control 81:83–92
Hettich RL, Chourey K, Jansson J, VerBerkmoes N, Shah M, Chavarria KL, Tom LM, Brodie EL
(2010) Direct cellular Lysis/protein extraction protocol for soil metaproteomics. J Proteome
Res 9:6615–6622
Hettich RL, Pan C, Chourey K, Giannone RJ (2013) Metaproteomics: harnessing the power of
high performance mass spectrometry to identify the suite of proteins that control metabolic
activities in microbial communities. Anal Chem 85:4203–4214
Hewson I, Fuhrman JA (2004) Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl Environ Microbiol 70:3425–3433
Higashi S, Barreto AMS, Cantão ME, Vasconcelos ATR (2012) Analysis of composition-based
metagenomic classification. BMC Genomics 13:S1
Higuchi R, Dollinger G, Walsh PS, Griffith R (1992) Simultaneous amplification and detection of
specific DNA sequences. Nat Biotechnol 10:413–417
Hoff KJ, Lingner T, Meinicke P, Tech M (2009) Orphelia: predicting genes in metagenomic
sequencing reads. Nucleic Acids Res 37:W101–W105
Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC (2010) Estimating DNA
coverage and abundance in metagenomes using a gamma approximation. Bioinformatics
26:295–301
Horton M, Bodenhausen N, Bergelson J (2010) MARTA: a suite of Java-based tools for assigning
taxonomic status to DNA sequences. Bioinformatics 26:568–569
Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, Wu H (2012) Single-cell exome sequencing and
monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 148(5):873–885
Hou J, Liu W, Wang B, Wang Q, Luo Y, Franks AE (2015) PGPR enhanced phytoremediation of
petroleum contaminated soil and rhizosphere microbial community response. Chemosphere
138:592–598
Huang XD, El-Alawi Y, Penrose DM, Glick BR, Greenberg BM (2004) Responses of three grass
species to creosote during phytoremediation. Environ Pollut 130:453–463
Huang CJ, Tsay JF, Chang SY, Yang HP, Wu WS, Chen CY (2012) Dimethyl disulfide is an induced
systemic resistance elicitor produced by Bacillus cereus C1L. Pest Manag Sci 68:1306–1310
Huang XF, Chaparro JM, Reardon KF, Zhang R, Shen Q, Vivanco JM (2014) Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 92:267–275
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R,
McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan
R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA
(2014a) metagenomics-a new resource for the analysis and archiving of metagenomic data.
Nucleic Acids Res 42:D600–D606
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R,
McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan
R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA
(2014b) EBI metagenomics-a new resource for the analysis and archiving of metagenomic
data. Nucleic Acids Res 42:D600–D606
Huse SM, Mark Welch DB, Voorhis A, Shipunova A, Morrison HG, Eren AM, Sogin ML (2014)
VAMPS: a website for visualization and analysis of microbial population structures. BMC
Bioinform 15:41
Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome
Res 17:377–386
References
He Z, Piceno Y, Deng Y, Xu M, Lu Z, DeSantis T, Andersen G, Sarah E, Hobbie SE, Reich PB,
Zhou J (2012) The phylogenetic composition and structure of soil microbial communities shifts
in response to elevated carbon dioxide. ISME J 6:259–272
Henson J, Tischler G, Ning Z (2012) Next-generation sequencing and large genome assemblies.
Pharmacogenomics 13:901–915
Hernández-León R, Rojas-Solís D, Contreras-Pérez M, Orozco-Mosqueda MC, Macías-Rodríguez
LI, Reyes-de la Cruz H, Valencia-Cantero E, Santoyo G (2015) Characterization of the antifungal and plant growth-promoting effects of diffusible and volatile organic compounds produced
by Pseudomonas fluorescensstrains. Biol Control 81:83–92
Hettich RL, Chourey K, Jansson J, VerBerkmoes N, Shah M, Chavarria KL, Tom LM, Brodie EL
(2010) Direct cellular Lysis/protein extraction protocol for soil metaproteomics. J Proteome
Res 9:6615–6622
Hettich RL, Pan C, Chourey K, Giannone RJ (2013) Metaproteomics: harnessing the power of
high performance mass spectrometry to identify the suite of proteins that control metabolic
activities in microbial communities. Anal Chem 85:4203–4214
Hewson I, Fuhrman JA (2004) Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Appl Environ Microbiol 70:3425–3433
Higashi S, Barreto AMS, Cantão ME, Vasconcelos ATR (2012) Analysis of composition-based
metagenomic classification. BMC Genomics 13:S1
Higuchi R, Dollinger G, Walsh PS, Griffith R (1992) Simultaneous amplification and detection of
specific DNA sequences. Nat Biotechnol 10:413–417
Hoff KJ, Lingner T, Meinicke P, Tech M (2009) Orphelia: predicting genes in metagenomic
sequencing reads. Nucleic Acids Res 37:W101–W105
Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC (2010) Estimating DNA
coverage and abundance in metagenomes using a gamma approximation. Bioinformatics
26:295–301
Horton M, Bodenhausen N, Bergelson J (2010) MARTA: a suite of Java-based tools for assigning
taxonomic status to DNA sequences. Bioinformatics 26:568–569
Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, Wu H (2012) Single-cell exome sequencing and
monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 148(5):873–885
Hou J, Liu W, Wang B, Wang Q, Luo Y, Franks AE (2015) PGPR enhanced phytoremediation of
petroleum contaminated soil and rhizosphere microbial community response. Chemosphere
138:592–598
Huang XD, El-Alawi Y, Penrose DM, Glick BR, Greenberg BM (2004) Responses of three grass
species to creosote during phytoremediation. Environ Pollut 130:453–463
Huang CJ, Tsay JF, Chang SY, Yang HP, Wu WS, Chen CY (2012) Dimethyl disulfide is an induced
systemic resistance elicitor produced by Bacillus cereus C1L. Pest Manag Sci 68:1306–1310
Huang XF, Chaparro JM, Reardon KF, Zhang R, Shen Q, Vivanco JM (2014) Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 92:267–275
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R,
McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan
R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA
(2014a) metagenomics-a new resource for the analysis and archiving of metagenomic data.
Nucleic Acids Res 42:D600–D606
Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R,
McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan
R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA
(2014b) EBI metagenomics-a new resource for the analysis and archiving of metagenomic
data. Nucleic Acids Res 42:D600–D606
Huse SM, Mark Welch DB, Voorhis A, Shipunova A, Morrison HG, Eren AM, Sogin ML (2014)
VAMPS: a website for visualization and analysis of microbial population structures. BMC
Bioinform 15:41
Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome
Res 17:377–386
References