98
Trivedi P, Anderson IC, Singh BK (2013) Microbial modulators of soil carbon storage: integrating
genomic and metabolic knowledge for global prediction. Trends Microbiol 21:641–651
Troutt AB, McHeyzer-Williams MG, Pulendran B, Nossal GJ (1992) Ligation-anchored PCR:
a simple amplification technique with single-sided specificity. Proc Natl Acad Sci U S A
89:9823–9825
Tseng CH, Tang SL (2014) Marine microbial metagenomics: from individual to the environment.
Int J Mol Sci 15:8878–8892
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human
microbiome project. Nature 449(7164):804–810. https://doi.org/10.1038/nature06244
Tveit AT, Urich T, Svenning MM (2014) Metatranscriptomic analysis of arctic peat soil
microbiota. Appl Environ Microbiol 80:5761–5772
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV,
Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through
reconstruction of microbial genomes from the environment. Nature 428:37–43
Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for
detecting changes in protein extracts. Electrophoresis 18:2071–2077
van der Heijden MGA, Bardgett RD, van Straalen NM (2008) The unseen majority: soil microbes
as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I,
Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O,
Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO
(2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74
Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG,
Apajalahti J, Tysk C, Hettich RL, Jansson JK (2009) Shotgun metaproteomics of the human
distal gut microbiota. ISME J 3:179–189
von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev
21:213–229
Walker A, Parkhill J (2008) Single-cell genomics. Nat Rev Microbiol 6:176–177
Wang Z, Chen Y, Li Y (2004) A brief review of computational gene prediction methods. Genomics
Proteomics Bioinformatics 2:216–221
Wang W, Vignani R, Scali M, Cresti M (2006) A universal and rapid protocol for protein extraction
from recalcitrant plant tissues for proteomic analysis. Electrophoresis 27:2782–2786
Wang L, Feng Z, Wang X, Wang X, Zhang X (2009) DEGseq: an R package for identifying
differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138
Wang Y, Leung HC, Yiu SM, Chin FY (2012) MetaCluster 4.0: a novel binning algorithm for NGS
reads and huge number of species. J Comput Biol 19:241–249
Wang C, Dong D, Wang H, Müller K, Qin Y, Wang H, Wu W (2016) Metagenomic analysis of
microbial consortia enriched from compost: new insights into the role of Actinobacteria in
lignocellulose decomposition. Biotechnol Biofuels 9:22
Wang B, Wang Q, Liu W, Liu X, Hou J, Teng Y, Christie P (2017) Biosurfactant-producing microorganism Pseudomonas sp. SB assists the phytoremediation of DDT-contaminated soil by two
grass species. Chemosphere 182:137–142
Wang M, Liu P, Xiong W, Zhou Q, Wangxiao J, Zeng Z, Sun Y (2018) Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated
manure-soil microcosms. Ecotoxicol Environ Saf 147:817–823
White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M (2010) Alignment and clustering of phylogenetic markers – implications for microbial diversity studies. BMC Bioinform
11:152
White AK et al (2011) High-throughput microfluidic singlecell RT-qPCR. Proc Natl Acad Sci
U S A 108:13999–14004
Widjojoatmodjo MN, Fluit AC, Verhoef J (1995) Molecular identification of bacteria by
fluorescence- based PCR–single-strand conformation polymorphism analysis of the 16S rRNA
gene. J Clin Microbiol 33:2601–2606
References
Trivedi P, Anderson IC, Singh BK (2013) Microbial modulators of soil carbon storage: integrating
genomic and metabolic knowledge for global prediction. Trends Microbiol 21:641–651
Troutt AB, McHeyzer-Williams MG, Pulendran B, Nossal GJ (1992) Ligation-anchored PCR:
a simple amplification technique with single-sided specificity. Proc Natl Acad Sci U S A
89:9823–9825
Tseng CH, Tang SL (2014) Marine microbial metagenomics: from individual to the environment.
Int J Mol Sci 15:8878–8892
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human
microbiome project. Nature 449(7164):804–810. https://doi.org/10.1038/nature06244
Tveit AT, Urich T, Svenning MM (2014) Metatranscriptomic analysis of arctic peat soil
microbiota. Appl Environ Microbiol 80:5761–5772
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV,
Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through
reconstruction of microbial genomes from the environment. Nature 428:37–43
Unlu M, Morgan ME, Minden JS (1997) Difference gel electrophoresis: a single gel method for
detecting changes in protein extracts. Electrophoresis 18:2071–2077
van der Heijden MGA, Bardgett RD, van Straalen NM (2008) The unseen majority: soil microbes
as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I,
Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O,
Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO
(2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74
Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG,
Apajalahti J, Tysk C, Hettich RL, Jansson JK (2009) Shotgun metaproteomics of the human
distal gut microbiota. ISME J 3:179–189
von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev
21:213–229
Walker A, Parkhill J (2008) Single-cell genomics. Nat Rev Microbiol 6:176–177
Wang Z, Chen Y, Li Y (2004) A brief review of computational gene prediction methods. Genomics
Proteomics Bioinformatics 2:216–221
Wang W, Vignani R, Scali M, Cresti M (2006) A universal and rapid protocol for protein extraction
from recalcitrant plant tissues for proteomic analysis. Electrophoresis 27:2782–2786
Wang L, Feng Z, Wang X, Wang X, Zhang X (2009) DEGseq: an R package for identifying
differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138
Wang Y, Leung HC, Yiu SM, Chin FY (2012) MetaCluster 4.0: a novel binning algorithm for NGS
reads and huge number of species. J Comput Biol 19:241–249
Wang C, Dong D, Wang H, Müller K, Qin Y, Wang H, Wu W (2016) Metagenomic analysis of
microbial consortia enriched from compost: new insights into the role of Actinobacteria in
lignocellulose decomposition. Biotechnol Biofuels 9:22
Wang B, Wang Q, Liu W, Liu X, Hou J, Teng Y, Christie P (2017) Biosurfactant-producing microorganism Pseudomonas sp. SB assists the phytoremediation of DDT-contaminated soil by two
grass species. Chemosphere 182:137–142
Wang M, Liu P, Xiong W, Zhou Q, Wangxiao J, Zeng Z, Sun Y (2018) Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated
manure-soil microcosms. Ecotoxicol Environ Saf 147:817–823
White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M (2010) Alignment and clustering of phylogenetic markers – implications for microbial diversity studies. BMC Bioinform
11:152
White AK et al (2011) High-throughput microfluidic singlecell RT-qPCR. Proc Natl Acad Sci
U S A 108:13999–14004
Widjojoatmodjo MN, Fluit AC, Verhoef J (1995) Molecular identification of bacteria by
fluorescence- based PCR–single-strand conformation polymorphism analysis of the 16S rRNA
gene. J Clin Microbiol 33:2601–2606
References