90
NC (2012) IMG/M: the integrated metagenome data management and comparative analysis
system. Nucleic Acids Res 40:D123–D129
Maron PA, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53:486–493
Martin HG, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He SM,
Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I,
Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P (2006) Metagenomic analysis of
two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol
24:1263–1269
Martínez-García M, Santos F, Moreno-Paz M, Parro V, Antón J (2014) Unveiling viral-host
interactions within the ‘microbial dark matter’. Nat Commun 5:4542
Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001)
DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl
Environ Microbiol 67:2354–2359
Mathé C, Sagot MF, Schiex T, Rouzé P (2002) Survey and summary: current methods of gene
prediction, their strengths and weaknesses. Nucleic Acids Res 30:4103–4117
McElroy KE, Luciani F, Thomas T (2012) GemSIM: general, error-model based simulator of
next- generation sequencing data. BMC Genomics 13:74
McGenity TJ, Crombie AT, Murrell JC (2018) Microbial cycling of isoprene, the most abundantly
produced biological volatile organic compound on Earth. ISME J 12:931–941
McGrath KC, Mondav R, Sintrajaya R, Slattery B, Schmidt S, Schenk PM (2010) Development
of an environmental functional gene microarray for soil microbial communities. Appl Environ
Microbiol 76:7161–7170
McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I (2007) Accurate phylogenetic
classification of variable-length DNA fragments. Nat Methods 4(63–72):10
McKenney DW, Yemshanov D, Fraleigh S, Allen D, Preto F (2011) An economic assessment of the
use of short-rotation coppice woody biomass to heat greenhouses in southern Canada. Biomass
Bioenergy 35:374–384
Meers E, Van Slyckena S, Adriaensenb K, Ruttensb A, Vangronsveld J, Du Laing G, Witters
N, Thewysb T, Tack FM (2010) The use of bio-energy crops (Zea mays) for ‘phytoattenuation’ of heavy metals on moderately contaminated soils: a field experiment. Chemosphere
78:35–41
Melcher U, Verma R, Schneider WL (2014) Metagenomic search strategies for interactions among
plants and multiple microbes. Front Plant Sci 5:268
Mendoza MLZ, Sicheritz-Pontén T, Gilbert MTP (2015) Environmental genes and genomes:
understanding the differences and challenges in the approaches and software for their analyses.
Brief Bioinform 16:745–758
Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A,
Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server –
a public resource for the automatic phylogenetic and functional analysis of metagenomes.
BMC Bioinform 9:386
Mijangos I, Becerril JM, Albizu I, Epelde L, Garbisu C (2009) Effects of glyphosate on rhizosphere
soil microbial communities under two different plant compositions by cultivation-dependent
and independent methodologies. Soil Biol Biochem 41:505–513
Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data.
Genomics 95:315–327
Mocali S, Benedetti A (2010) Exploring research frontiers in microbiology: the challenge of
metagenomics in soil microbiology. Res Microbiol 161:497–505
Mohammed MH, Ghosh TS, Reddy RM, Reddy CV, Singh NK, Mande SS (2011) INDUS – a
composition-based approach for rapid and accurate taxonomic classification of metagenomic
sequences. BMC Genomics 3:S4
References
NC (2012) IMG/M: the integrated metagenome data management and comparative analysis
system. Nucleic Acids Res 40:D123–D129
Maron PA, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53:486–493
Martin HG, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He SM,
Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I,
Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P (2006) Metagenomic analysis of
two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol
24:1263–1269
Martínez-García M, Santos F, Moreno-Paz M, Parro V, Antón J (2014) Unveiling viral-host
interactions within the ‘microbial dark matter’. Nat Commun 5:4542
Martin-Laurent F, Philippot L, Hallet S, Chaussod R, Germon JC, Soulas G, Catroux G (2001)
DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl
Environ Microbiol 67:2354–2359
Mathé C, Sagot MF, Schiex T, Rouzé P (2002) Survey and summary: current methods of gene
prediction, their strengths and weaknesses. Nucleic Acids Res 30:4103–4117
McElroy KE, Luciani F, Thomas T (2012) GemSIM: general, error-model based simulator of
next- generation sequencing data. BMC Genomics 13:74
McGenity TJ, Crombie AT, Murrell JC (2018) Microbial cycling of isoprene, the most abundantly
produced biological volatile organic compound on Earth. ISME J 12:931–941
McGrath KC, Mondav R, Sintrajaya R, Slattery B, Schmidt S, Schenk PM (2010) Development
of an environmental functional gene microarray for soil microbial communities. Appl Environ
Microbiol 76:7161–7170
McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I (2007) Accurate phylogenetic
classification of variable-length DNA fragments. Nat Methods 4(63–72):10
McKenney DW, Yemshanov D, Fraleigh S, Allen D, Preto F (2011) An economic assessment of the
use of short-rotation coppice woody biomass to heat greenhouses in southern Canada. Biomass
Bioenergy 35:374–384
Meers E, Van Slyckena S, Adriaensenb K, Ruttensb A, Vangronsveld J, Du Laing G, Witters
N, Thewysb T, Tack FM (2010) The use of bio-energy crops (Zea mays) for ‘phytoattenuation’ of heavy metals on moderately contaminated soils: a field experiment. Chemosphere
78:35–41
Melcher U, Verma R, Schneider WL (2014) Metagenomic search strategies for interactions among
plants and multiple microbes. Front Plant Sci 5:268
Mendoza MLZ, Sicheritz-Pontén T, Gilbert MTP (2015) Environmental genes and genomes:
understanding the differences and challenges in the approaches and software for their analyses.
Brief Bioinform 16:745–758
Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A,
Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server –
a public resource for the automatic phylogenetic and functional analysis of metagenomes.
BMC Bioinform 9:386
Mijangos I, Becerril JM, Albizu I, Epelde L, Garbisu C (2009) Effects of glyphosate on rhizosphere
soil microbial communities under two different plant compositions by cultivation-dependent
and independent methodologies. Soil Biol Biochem 41:505–513
Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data.
Genomics 95:315–327
Mocali S, Benedetti A (2010) Exploring research frontiers in microbiology: the challenge of
metagenomics in soil microbiology. Res Microbiol 161:497–505
Mohammed MH, Ghosh TS, Reddy RM, Reddy CV, Singh NK, Mande SS (2011) INDUS – a
composition-based approach for rapid and accurate taxonomic classification of metagenomic
sequences. BMC Genomics 3:S4
References