80
Brady A, Salzberg S (2011) PhymmBL expanded: confidence scores, custom databases,
parallelization and more. Nat Methods 8(5):367. https://doi.org/10.1038/nmeth0511-367
Braud A, Jézéquel K, Bazot S, Lebeau T (2009) Enhanced phytoextraction of an agricultural
Cr-and Pb-contaminated soil by bioaugmentation with siderophore-producing bacteria.
Chemosphere 74:280–286
Brown MV, Fuhrman JA (2005) Marine bacterial microdiversity as revealed by internal transcribed
spacer analysis. Aquat Microb Ecol 41:15–23
Bulgarelli D et al (2013) Structure and functions of the bacterial micro biota of plants. Annu Rev
Plant Biol 64:807–838
Burd GI, Dixon DG, Glick BR (2000) Plant growth-promoting bacteria that decrease heavy metal
toxicity in plants. Can J Microbiol 46:237–245
Butterly CR, Phillips LA, Wiltshire JL, Franksc AE, Armstronga RD, Chene D, Melea PM,
Tanga C (2016) Long-term effects of elevated CO2 on carbon and nitrogen functional capacity of microbial communities in three contrasting soils. Soil Biol Biochem 97:157–167
Calderon FJ, Nielsen ID, Acosta-Martinez V, Vigil MF, Lyon D (2016) Cover crop and irrigation
effects on soil microbial communities and enzymes in semiarid agroecosystems of the central
Great Plains of North America. Pedosphere 26:192–205
Canfield DE, Glazer AN, Falkowski PG (2010) The evolution and future of Earth’s nitrogen cycle.
Science 330:192–196
Caracciolo AB, Bottoni P, Grenni P (2010) Fluorescence in situ hybridization in soil and water
ecosystems: a useful method for studying the effect of xenobiotics on bacterial community
structure. Toxicol Environ Chem 92:567–579
Carr R, Borenstein E (2014) Comparative analysis of functional metagenomic annotation and the
mappability of short reads. PLoS One 9:e105776
Carvalhais LC, Dennis PG, Tyson GW, Schenk PM (2012) Application of metatranscriptomics to
soil environments. J Microbiol Methods 91:246–251
Chang P, Gerhardt KE, Huang XD, Yu XM, Glick BR, Gerwing PD, Greenberg BM (2014)
Plant growth-promoting bacteria facilitate the growth of barley and oats in salt-impacted
soil: implications for phytoremediation of saline soils. Int J Phytoremediation 16:1133–1147
Charuvaka A, Rangwala H (2011) Evaluation of short read metagenomic assembly. BMC
Genomics 12:S8
Chaudhari NM, Gupta VK, Dutta C (2016) BPGA-an ultra-fast pan-genome analysis pipeline.
Sci Rep. https://doi.org/10.1038/srep24373
Chauhan A, Smartt A, Wang J, Utturkar S, Frank A, Bi M, Arreaza A (2014) Integrated metagenomics and metatranscriptomics analyses of root-associated soil from transgenic switchgrass.
Genome Announc 2(4):e00777–e00714. https://doi.org/10.1128/genomeA.00777-14
Chen Y, Murrell JC (2010) When metagenomics meets stable-isotope probing: progress and
perspectives. Trends Microbiol 18:157–163
Chen Y, Dumont MG, McNamara NP, Chamberlain PM, Bodrossy L, Pavese NS, Murrell JC
(2008) Diversity of the active methanotrophic community in acidic peatlands as assessed by
mRNA and SIP-PLFA analyses. Environ Microbiol 110:446–459
Chen LX, Hu M, Huang LN, Hua ZS, Kuang JL, Li SJ, Shu WS (2015) Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.
ISME J 9(7):1579–1592
Chen IMA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, Ratner A, Huang J,
Andersen E, Huntemann M, Varghese N, Hadjithomas M, Tennessen K, Nielsen T,
Ivanova NN, Kyrpides NC (2017) IMG/M: integrated genome and metagenome comparative
data analysis system. Nucleic Acids Res 4:D507–D516
Choksawangkarn W, Edwards N, Wang Y, Gutierrez P, Fenselau C (2012) Comparative study of
workflows optimized for in-gel, in-solution, and on-filter proteolysis in the analysis of plasma
membrane proteins. J Proteome Res 11:3030–3034
Chourey K, Jansson J, VerBerkmoes N, Shah M, Chavarria KL, Tom LM, Brodie EL, Hettich RL
(2010) Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome
Res 9:6615–6622
References
Brady A, Salzberg S (2011) PhymmBL expanded: confidence scores, custom databases,
parallelization and more. Nat Methods 8(5):367. https://doi.org/10.1038/nmeth0511-367
Braud A, Jézéquel K, Bazot S, Lebeau T (2009) Enhanced phytoextraction of an agricultural
Cr-and Pb-contaminated soil by bioaugmentation with siderophore-producing bacteria.
Chemosphere 74:280–286
Brown MV, Fuhrman JA (2005) Marine bacterial microdiversity as revealed by internal transcribed
spacer analysis. Aquat Microb Ecol 41:15–23
Bulgarelli D et al (2013) Structure and functions of the bacterial micro biota of plants. Annu Rev
Plant Biol 64:807–838
Burd GI, Dixon DG, Glick BR (2000) Plant growth-promoting bacteria that decrease heavy metal
toxicity in plants. Can J Microbiol 46:237–245
Butterly CR, Phillips LA, Wiltshire JL, Franksc AE, Armstronga RD, Chene D, Melea PM,
Tanga C (2016) Long-term effects of elevated CO2 on carbon and nitrogen functional capacity of microbial communities in three contrasting soils. Soil Biol Biochem 97:157–167
Calderon FJ, Nielsen ID, Acosta-Martinez V, Vigil MF, Lyon D (2016) Cover crop and irrigation
effects on soil microbial communities and enzymes in semiarid agroecosystems of the central
Great Plains of North America. Pedosphere 26:192–205
Canfield DE, Glazer AN, Falkowski PG (2010) The evolution and future of Earth’s nitrogen cycle.
Science 330:192–196
Caracciolo AB, Bottoni P, Grenni P (2010) Fluorescence in situ hybridization in soil and water
ecosystems: a useful method for studying the effect of xenobiotics on bacterial community
structure. Toxicol Environ Chem 92:567–579
Carr R, Borenstein E (2014) Comparative analysis of functional metagenomic annotation and the
mappability of short reads. PLoS One 9:e105776
Carvalhais LC, Dennis PG, Tyson GW, Schenk PM (2012) Application of metatranscriptomics to
soil environments. J Microbiol Methods 91:246–251
Chang P, Gerhardt KE, Huang XD, Yu XM, Glick BR, Gerwing PD, Greenberg BM (2014)
Plant growth-promoting bacteria facilitate the growth of barley and oats in salt-impacted
soil: implications for phytoremediation of saline soils. Int J Phytoremediation 16:1133–1147
Charuvaka A, Rangwala H (2011) Evaluation of short read metagenomic assembly. BMC
Genomics 12:S8
Chaudhari NM, Gupta VK, Dutta C (2016) BPGA-an ultra-fast pan-genome analysis pipeline.
Sci Rep. https://doi.org/10.1038/srep24373
Chauhan A, Smartt A, Wang J, Utturkar S, Frank A, Bi M, Arreaza A (2014) Integrated metagenomics and metatranscriptomics analyses of root-associated soil from transgenic switchgrass.
Genome Announc 2(4):e00777–e00714. https://doi.org/10.1128/genomeA.00777-14
Chen Y, Murrell JC (2010) When metagenomics meets stable-isotope probing: progress and
perspectives. Trends Microbiol 18:157–163
Chen Y, Dumont MG, McNamara NP, Chamberlain PM, Bodrossy L, Pavese NS, Murrell JC
(2008) Diversity of the active methanotrophic community in acidic peatlands as assessed by
mRNA and SIP-PLFA analyses. Environ Microbiol 110:446–459
Chen LX, Hu M, Huang LN, Hua ZS, Kuang JL, Li SJ, Shu WS (2015) Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.
ISME J 9(7):1579–1592
Chen IMA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, Ratner A, Huang J,
Andersen E, Huntemann M, Varghese N, Hadjithomas M, Tennessen K, Nielsen T,
Ivanova NN, Kyrpides NC (2017) IMG/M: integrated genome and metagenome comparative
data analysis system. Nucleic Acids Res 4:D507–D516
Choksawangkarn W, Edwards N, Wang Y, Gutierrez P, Fenselau C (2012) Comparative study of
workflows optimized for in-gel, in-solution, and on-filter proteolysis in the analysis of plasma
membrane proteins. J Proteome Res 11:3030–3034
Chourey K, Jansson J, VerBerkmoes N, Shah M, Chavarria KL, Tom LM, Brodie EL, Hettich RL
(2010) Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome
Res 9:6615–6622
References