79
Bashan LE, Hernandez JP, Bashan Y (2012) The potential contribution of plant growth-promoting
bacteria to reduce environmental degradation – a comprehensive evaluation. Appl Soil Ecol
61:171–189
Bashiardes S, Shapiro H, Rozin S, Shibolet O, Elinav E (2016a) Non-alcoholic fatty liver and the
gut microbiota. Mol Metab 5:782–794
Bashiardes S, Zilberman-Schapira G, Elinav E (2016b) Use of metatranscriptomics in microbiome research. Bioinform Biol Insights 10:BBI-S34610. https://doi.org/10.4137/BBI.S34610.
eCollection 2016
Bashir Y, Singh SP, Konwar BK (2014) Metagenomics: an application based perspective. Chin
J Biol. https://doi.org/10.1155/2014/146030
Bastida F, Moreno JL, Nicolas C, Hernandez T, Garcia C (2009) Soil metaproteomics: a review
of an emerging environmental science. significance, methodology and perspectives. Eur J Soil
Sci 60:845–859
Beauregard PB, Chai Y, Vlamakis H, Losick R, Kolter R (2013) Bacillus subtilis biofilm induction
by plant polysaccharides. Proc Natl Acad Sci U S A 110:E1621–E1630
Becker JM, Parkin T, Nakatsu CH, Wilbur JD, Konopka A (2006) Bacterial activity, community
structure and centimeter-scale spatial heterogeneity in contaminated soils. Microbiol Ecol
51:220–231
Begum MM, Sariah M, Puteh B, Zainal Abidin M, Rahman M, Siddiqui Y (2010) Field performance of bio-primed seeds to suppress Colletotrichum truncatum causing damping-off and
seedling stand of soybean. Biol Control 53:18–23
Ben-David EA, Holden PJ, Stone DJ, Harch BD, Foster LJ (2004) The use of phospholipid fatty
acid analysis to measure impact of acid rock drainage on microbial communities in sediments. Microb Ecol 48:300–315
Ben-David EA, Zaady E, Sher Y, Nejidat A (2011) Assessment of the spatial distribution of soil
microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using
combined PLFA and DGGE analyses. FEMS Microbiol Ecol 76:492–450
Benndorf D, Balcke GU, Harms H, von Bergen M (2007) Functional metaproteome analysis of
protein extracts from contaminated soil and groundwater. ISME J 1:224–234
Bentley S (2009) Sequencing the species pan-genome. https://doi.org/10.1038/nrmicro2123
Berendsen R, Pieterse C, Bakker P (2012) The rhizosphere microbiome and plant health. Trends
Plant Sci 17:478–486
Berg G, Raaijmakers JM (2018) Saving seed microbiomes. ISME J 12:1167–1170
Berger SA, Stamatakis A (2011) Aligning short reads to reference alignments and trees.
Bioinformatics 27:2068–2075
Berta G, Copetta A, Gamalero E, Bona E, Cesaro P, Scarafoni A, D’Agostino G (2014) Maize
development and grain quality are differentially affected by mycorrhizal fungi and a growthpromoting pseudomonad in the field. Mycorrhiza 24:161–170
Bertani I, Abbruscato P, Piffanelli P, Subramoni S, Venturi V (2016) Rice bacterial endophytes:
isolation of a collection, identification of beneficial strains and microbiome analysis. https://
doi.org/10.1111/1758-2229.12403
Beverley SM et al (2002) Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling. Philos Trans R Soc Lond B 357:47–53
Blainey PC (2012) The future is now: single-cell genomics of bacteria and archaea. https://doi.
org/10.1111/1574-6976.12015
Bodrossy L, Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin
Microbiol 7:245–254
Bogan BW, Lamar RT (1996) Polycyclic aromatic hydrocarbon-degrading capabilities of
Phanerochaete laevis HHB-1625 and its extracellular ligninolytic enzymes. Appl Environ
Microbiol 62:1597–1603
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence
data. Bioinformatics 30:2114–2120
Brady A, Salzberg SL (2009) Phymm and Phymm BL: metagenomic phylogenetic classification
with interpolated Markov models. Nat Methods 6:673–676
References
Bashan LE, Hernandez JP, Bashan Y (2012) The potential contribution of plant growth-promoting
bacteria to reduce environmental degradation – a comprehensive evaluation. Appl Soil Ecol
61:171–189
Bashiardes S, Shapiro H, Rozin S, Shibolet O, Elinav E (2016a) Non-alcoholic fatty liver and the
gut microbiota. Mol Metab 5:782–794
Bashiardes S, Zilberman-Schapira G, Elinav E (2016b) Use of metatranscriptomics in microbiome research. Bioinform Biol Insights 10:BBI-S34610. https://doi.org/10.4137/BBI.S34610.
eCollection 2016
Bashir Y, Singh SP, Konwar BK (2014) Metagenomics: an application based perspective. Chin
J Biol. https://doi.org/10.1155/2014/146030
Bastida F, Moreno JL, Nicolas C, Hernandez T, Garcia C (2009) Soil metaproteomics: a review
of an emerging environmental science. significance, methodology and perspectives. Eur J Soil
Sci 60:845–859
Beauregard PB, Chai Y, Vlamakis H, Losick R, Kolter R (2013) Bacillus subtilis biofilm induction
by plant polysaccharides. Proc Natl Acad Sci U S A 110:E1621–E1630
Becker JM, Parkin T, Nakatsu CH, Wilbur JD, Konopka A (2006) Bacterial activity, community
structure and centimeter-scale spatial heterogeneity in contaminated soils. Microbiol Ecol
51:220–231
Begum MM, Sariah M, Puteh B, Zainal Abidin M, Rahman M, Siddiqui Y (2010) Field performance of bio-primed seeds to suppress Colletotrichum truncatum causing damping-off and
seedling stand of soybean. Biol Control 53:18–23
Ben-David EA, Holden PJ, Stone DJ, Harch BD, Foster LJ (2004) The use of phospholipid fatty
acid analysis to measure impact of acid rock drainage on microbial communities in sediments. Microb Ecol 48:300–315
Ben-David EA, Zaady E, Sher Y, Nejidat A (2011) Assessment of the spatial distribution of soil
microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using
combined PLFA and DGGE analyses. FEMS Microbiol Ecol 76:492–450
Benndorf D, Balcke GU, Harms H, von Bergen M (2007) Functional metaproteome analysis of
protein extracts from contaminated soil and groundwater. ISME J 1:224–234
Bentley S (2009) Sequencing the species pan-genome. https://doi.org/10.1038/nrmicro2123
Berendsen R, Pieterse C, Bakker P (2012) The rhizosphere microbiome and plant health. Trends
Plant Sci 17:478–486
Berg G, Raaijmakers JM (2018) Saving seed microbiomes. ISME J 12:1167–1170
Berger SA, Stamatakis A (2011) Aligning short reads to reference alignments and trees.
Bioinformatics 27:2068–2075
Berta G, Copetta A, Gamalero E, Bona E, Cesaro P, Scarafoni A, D’Agostino G (2014) Maize
development and grain quality are differentially affected by mycorrhizal fungi and a growthpromoting pseudomonad in the field. Mycorrhiza 24:161–170
Bertani I, Abbruscato P, Piffanelli P, Subramoni S, Venturi V (2016) Rice bacterial endophytes:
isolation of a collection, identification of beneficial strains and microbiome analysis. https://
doi.org/10.1111/1758-2229.12403
Beverley SM et al (2002) Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling. Philos Trans R Soc Lond B 357:47–53
Blainey PC (2012) The future is now: single-cell genomics of bacteria and archaea. https://doi.
org/10.1111/1574-6976.12015
Bodrossy L, Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin
Microbiol 7:245–254
Bogan BW, Lamar RT (1996) Polycyclic aromatic hydrocarbon-degrading capabilities of
Phanerochaete laevis HHB-1625 and its extracellular ligninolytic enzymes. Appl Environ
Microbiol 62:1597–1603
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence
data. Bioinformatics 30:2114–2120
Brady A, Salzberg SL (2009) Phymm and Phymm BL: metagenomic phylogenetic classification
with interpolated Markov models. Nat Methods 6:673–676
References