87
Kim HJ, Choi HS, Yang SY, Kim IS, Yamaguchi T, Sohng JK, Park SK, Kim JC, Lee CH,
Gardener BM et al (2014) Both extracellular chitinase and a new cyclic lipopeptide, chromobactomycin, contribute to the biocontrol activity of Chromobacterium sp. C61. Mol Plant
Pathol 15:122–132
Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries SS et al (2013) Single-cell dynamics of
genome-nuclear lamina interactions. Cell 153:178–192
Klose J (1975) Protein mapping by combined isoelectric focusing and electrophoresis of mouse
tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik
26:231–243
Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Melnik AV (2018) Best
practices for analysing microbiomes. Nat Rev Microbiol 16:410–422
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight
R, Kelley ST (2011) Bayesian community-wide culture-independent microbial source tracking. Nat Methods 8:761–763
Ko CH, Yu FC, Chang FC, Yang BY, Chen WH, Hwang WS, Tu TC (2017) Bioethanol production
from recovered napier grass with heavy metals. J Environ Manag 203:1005–1010
Köcher T, Pichler P, Swart R, Mechtler K (2012) Analysis of protein mixtures from whole-cell
extracts by single-run nanoLC-MS/MS using ultralong gradients. Nat Protoc 7:882–890
Kohler J, Caravaca F, Azcon R, Diaz G, Roldan A (2016) Suitability of the microbial community
composition and function in a semiarid mine soil for assessing phytomanagement practices
based on mycorrhizal inoculation and amendment addition. J Environ Manag 169:236–246
Kolmeder CA, de Been M, Nikkilä J, Ritamo I, Mättö J, Valmu L, Salojärvi J, Palva A, Salonen
A, de Vos WM (2012) Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One
7:e29913–e29910
Korf BR, Rehm HL (2013) New approaches to molecular diagnosis. JAMA 309:1511–1521
Kovacs A, Yacoby K, Gophna U (2010a) A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Res. Microbiology
161:192–197
Kovacs A et al (2010b) Genotype is a stronger determinant than sex of the mouse gut microbiota.
Microbial Ecol 1:6
Krey T, Vassilev N, Baum C, Eichler-Löbermann B (2013) Effects of long-term phosphorus application and plant-growth promoting rhizobacteria on maize phosphorus nutrition under field
conditions. Eur J Soil Biol 55:124–130
Kristiansson E, Hugenholtz P, Dalevi D (2009) ShotgunFunctionalizeR: an R-package for
functional comparison of metagenomes. Bioinformatics 25:2737–2738
Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J,
Wang J, Bork P (2012) MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS
One 7:e47656
Kumar KV, Singh N, Behl HM, Srivastava S (2008) Influence of plant growth promoting bacteria
and its mutant on heavy metal toxicity in Brassica juncea grown in fly ash amended soil.
Chemosphere 72:678–683
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide
to metagenomics. Microbiol Mol Biol Rev 72:557–578
Lacerda CMR, Choe LH, Reardon KF (2007) Metaproteomic analysis of a bacterial community
response to cadmium exposure. J Proteome Res 6:1145–1152
Landry ZC, Giovanonni SJ, Quake SR, Blainey PC (2013) Optofluidic cell selection from complex
microbial communities for single-genome analysis. Methods Enzymol 531:61–90
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie2. Nat Methods
9:357–359
Lapidot D, Dror R, Vered E, Mishli O, Levy D, Helman Y (2014) Disease protection and growth
promotion of potatoes (Solanum tuberosum L.) by Paenibacillus dendritiformis. Plant Pathol.
https://doi.org/10.1111/ppa.1228
References
Kim HJ, Choi HS, Yang SY, Kim IS, Yamaguchi T, Sohng JK, Park SK, Kim JC, Lee CH,
Gardener BM et al (2014) Both extracellular chitinase and a new cyclic lipopeptide, chromobactomycin, contribute to the biocontrol activity of Chromobacterium sp. C61. Mol Plant
Pathol 15:122–132
Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries SS et al (2013) Single-cell dynamics of
genome-nuclear lamina interactions. Cell 153:178–192
Klose J (1975) Protein mapping by combined isoelectric focusing and electrophoresis of mouse
tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik
26:231–243
Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Melnik AV (2018) Best
practices for analysing microbiomes. Nat Rev Microbiol 16:410–422
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight
R, Kelley ST (2011) Bayesian community-wide culture-independent microbial source tracking. Nat Methods 8:761–763
Ko CH, Yu FC, Chang FC, Yang BY, Chen WH, Hwang WS, Tu TC (2017) Bioethanol production
from recovered napier grass with heavy metals. J Environ Manag 203:1005–1010
Köcher T, Pichler P, Swart R, Mechtler K (2012) Analysis of protein mixtures from whole-cell
extracts by single-run nanoLC-MS/MS using ultralong gradients. Nat Protoc 7:882–890
Kohler J, Caravaca F, Azcon R, Diaz G, Roldan A (2016) Suitability of the microbial community
composition and function in a semiarid mine soil for assessing phytomanagement practices
based on mycorrhizal inoculation and amendment addition. J Environ Manag 169:236–246
Kolmeder CA, de Been M, Nikkilä J, Ritamo I, Mättö J, Valmu L, Salojärvi J, Palva A, Salonen
A, de Vos WM (2012) Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One
7:e29913–e29910
Korf BR, Rehm HL (2013) New approaches to molecular diagnosis. JAMA 309:1511–1521
Kovacs A, Yacoby K, Gophna U (2010a) A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Res. Microbiology
161:192–197
Kovacs A et al (2010b) Genotype is a stronger determinant than sex of the mouse gut microbiota.
Microbial Ecol 1:6
Krey T, Vassilev N, Baum C, Eichler-Löbermann B (2013) Effects of long-term phosphorus application and plant-growth promoting rhizobacteria on maize phosphorus nutrition under field
conditions. Eur J Soil Biol 55:124–130
Kristiansson E, Hugenholtz P, Dalevi D (2009) ShotgunFunctionalizeR: an R-package for
functional comparison of metagenomes. Bioinformatics 25:2737–2738
Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J,
Wang J, Bork P (2012) MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS
One 7:e47656
Kumar KV, Singh N, Behl HM, Srivastava S (2008) Influence of plant growth promoting bacteria
and its mutant on heavy metal toxicity in Brassica juncea grown in fly ash amended soil.
Chemosphere 72:678–683
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide
to metagenomics. Microbiol Mol Biol Rev 72:557–578
Lacerda CMR, Choe LH, Reardon KF (2007) Metaproteomic analysis of a bacterial community
response to cadmium exposure. J Proteome Res 6:1145–1152
Landry ZC, Giovanonni SJ, Quake SR, Blainey PC (2013) Optofluidic cell selection from complex
microbial communities for single-genome analysis. Methods Enzymol 531:61–90
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie2. Nat Methods
9:357–359
Lapidot D, Dror R, Vered E, Mishli O, Levy D, Helman Y (2014) Disease protection and growth
promotion of potatoes (Solanum tuberosum L.) by Paenibacillus dendritiformis. Plant Pathol.
https://doi.org/10.1111/ppa.1228
References