86
Hussa EA, Goodrich-Blair H (2013) It takes a village: ecological and fitness impacts of multipartite mutualism. Annu Rev Microbiol 67:161–178
Huyghe A, Francois P, Schrenzel J (2009) Characterization of microbial pathogens by DNA microarrays. Infect Genet Evol 9:987–995
Hyland C, Pinney JW, McConkey GA, Westhead DR (2006) metaSHARK: a WWW plateform for
interactive exploration of metabolic networks. Nucleic Acids Res 34:W725–W728
Ishii K, Mußmann M, MacGregor BJ, Amann R (2004) An improved fluorescence in situ
hybridization protocol for the identification of bacteria and archaea in marine sediments.
FEMS Microbiol Ecol 50:203–212
Iwasaki Y, Abe T, Wada K, Wada Y, Ikemura T (2013) A novel bioinformatics strategy to analyze
microbial big sequence data for efficient knowledge discovery: batch-learning self-organizing
map (BLSOM). Microorganisms 1:137–157
Janczyk P, Pieper R, Smidt H, Wolfgang B (2010) Souffrant effect of alginate and inulin on
intestinal microbial ecology of weanling pigs reared under different husbandry conditions.
FEMS Microbiol Ecol 72:132–142
Jansson J (2011) Soil microbes: metagenomic approaches. https://eesa.lbl.gov/soil-microbesmetagenomic-approaches/2011
Jansson JK (2013) The life beneath our feet. Nature 494:40
Ji SH, Gururani MA, Chun SC (2014) Isolation and characterization of plant growth promoting
endophytic diazotrophic bacteria from Korean rice cultivars. Microbiol Res 169:83–98
Jiang L, He L, Fountoulakis M (2004) Comparison of protein precipitation methods for sample
preparation prior to proteomic analysis. J Chromatogr A 1023:317–320
Jousset A, Lara E, Nikolausz M, Harms H, Chatzinotas A (2010) Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate
communities in soil. Sci Total Environ 408:1221–1225
Kakar KU, Duan Y-P, Nawaz Z, Sun G, Almoneafy AA, Hassan MA, Elshakh A, Li B, Xie G-L
(2014) A novel rhizobacterium Bk7 for biological control of brown sheath rot of rice caused by
Pseudomonas fuscovaginaeand its mode of action. Eur J Plant Pathol 138:819–834
Kalisky T, Blainey P, Quake SR (2011) Genomic analysis at the single-cell level. Annu Rev Genet
45:431–445
Kamke J, Bayer K, Woyke T, Hentschel U (2012) Exploring symbioses by single-cell genomics.
Biol Bull 223:30–43
Kan J, Hanson TE, Ginter JM, Wang K, Chen F (2005) Metaproteomic analysis of Chesapeake
Bay microbial communities. Saline Syst 1:7–10
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids
Res 28:27–30
Kaur A, Chaudhary A, Kaur A, Choudhary R, Kaushik R (2005) Phospholipid fatty acid – a bioindicator of environment monitoring assessment in soil ecosystem. Curr Sci 89:1103–1112
Keegan KP, Glass EM, Meyer F (2016) MG-RAST, a metagenomics service for analysis of microbial community structure and function. Methods Mol Biol 1399:207–233
Keiblinger KM, Wilhartitz IC, Schneider T, Roschitzki B, Schmid E, Eberl L, Riedel K,
Zechmeister-Boltenstern S (2012) Soil metaproteomicse comparative evaluation of protein
extraction protocols. Soil Biol Biochem 54:14–24
Kembel SW, Eisen JA, Pollard KS, Green JL (2011) The phylogenetic diversity of metagenomes.
PLoS One 6:e23214
Khaksar G, Treesubsuntorn C, Thiravetyan P (2016) Effect of endophytic Bacillus cereus ERBP
inoculation into non-native host: potentials and challenges for airborne formaldehyde removal.
Plant Physiol Biochem 107:326–336
Khan Z, Roman D, Kintz T, delas Alas M, Yap R, Doty S (2014) Degradation, phytoprotection
and phytoremediation of phenanthrene by endophyte Pseudomonas putida, PD1. Environ Sci
Technol 48:12221–12228
Khindaria A, Grover TA, Aust SD (1995) Reductive dehalogenation of aliphatic halocarbons by
lignin peroxidase of Phanerochaete chrysosporium. Environ Sci Technol 29:719–725
References
Hussa EA, Goodrich-Blair H (2013) It takes a village: ecological and fitness impacts of multipartite mutualism. Annu Rev Microbiol 67:161–178
Huyghe A, Francois P, Schrenzel J (2009) Characterization of microbial pathogens by DNA microarrays. Infect Genet Evol 9:987–995
Hyland C, Pinney JW, McConkey GA, Westhead DR (2006) metaSHARK: a WWW plateform for
interactive exploration of metabolic networks. Nucleic Acids Res 34:W725–W728
Ishii K, Mußmann M, MacGregor BJ, Amann R (2004) An improved fluorescence in situ
hybridization protocol for the identification of bacteria and archaea in marine sediments.
FEMS Microbiol Ecol 50:203–212
Iwasaki Y, Abe T, Wada K, Wada Y, Ikemura T (2013) A novel bioinformatics strategy to analyze
microbial big sequence data for efficient knowledge discovery: batch-learning self-organizing
map (BLSOM). Microorganisms 1:137–157
Janczyk P, Pieper R, Smidt H, Wolfgang B (2010) Souffrant effect of alginate and inulin on
intestinal microbial ecology of weanling pigs reared under different husbandry conditions.
FEMS Microbiol Ecol 72:132–142
Jansson J (2011) Soil microbes: metagenomic approaches. https://eesa.lbl.gov/soil-microbesmetagenomic-approaches/2011
Jansson JK (2013) The life beneath our feet. Nature 494:40
Ji SH, Gururani MA, Chun SC (2014) Isolation and characterization of plant growth promoting
endophytic diazotrophic bacteria from Korean rice cultivars. Microbiol Res 169:83–98
Jiang L, He L, Fountoulakis M (2004) Comparison of protein precipitation methods for sample
preparation prior to proteomic analysis. J Chromatogr A 1023:317–320
Jousset A, Lara E, Nikolausz M, Harms H, Chatzinotas A (2010) Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate
communities in soil. Sci Total Environ 408:1221–1225
Kakar KU, Duan Y-P, Nawaz Z, Sun G, Almoneafy AA, Hassan MA, Elshakh A, Li B, Xie G-L
(2014) A novel rhizobacterium Bk7 for biological control of brown sheath rot of rice caused by
Pseudomonas fuscovaginaeand its mode of action. Eur J Plant Pathol 138:819–834
Kalisky T, Blainey P, Quake SR (2011) Genomic analysis at the single-cell level. Annu Rev Genet
45:431–445
Kamke J, Bayer K, Woyke T, Hentschel U (2012) Exploring symbioses by single-cell genomics.
Biol Bull 223:30–43
Kan J, Hanson TE, Ginter JM, Wang K, Chen F (2005) Metaproteomic analysis of Chesapeake
Bay microbial communities. Saline Syst 1:7–10
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids
Res 28:27–30
Kaur A, Chaudhary A, Kaur A, Choudhary R, Kaushik R (2005) Phospholipid fatty acid – a bioindicator of environment monitoring assessment in soil ecosystem. Curr Sci 89:1103–1112
Keegan KP, Glass EM, Meyer F (2016) MG-RAST, a metagenomics service for analysis of microbial community structure and function. Methods Mol Biol 1399:207–233
Keiblinger KM, Wilhartitz IC, Schneider T, Roschitzki B, Schmid E, Eberl L, Riedel K,
Zechmeister-Boltenstern S (2012) Soil metaproteomicse comparative evaluation of protein
extraction protocols. Soil Biol Biochem 54:14–24
Kembel SW, Eisen JA, Pollard KS, Green JL (2011) The phylogenetic diversity of metagenomes.
PLoS One 6:e23214
Khaksar G, Treesubsuntorn C, Thiravetyan P (2016) Effect of endophytic Bacillus cereus ERBP
inoculation into non-native host: potentials and challenges for airborne formaldehyde removal.
Plant Physiol Biochem 107:326–336
Khan Z, Roman D, Kintz T, delas Alas M, Yap R, Doty S (2014) Degradation, phytoprotection
and phytoremediation of phenanthrene by endophyte Pseudomonas putida, PD1. Environ Sci
Technol 48:12221–12228
Khindaria A, Grover TA, Aust SD (1995) Reductive dehalogenation of aliphatic halocarbons by
lignin peroxidase of Phanerochaete chrysosporium. Environ Sci Technol 29:719–725
References