Contributions of Descriptive and Functional Genomics to Microbial Ecology

  • Philippe N. Bertin
  • Valérie Michotey
  • Philippe Normand


Originally, “genomics” was used only to describe a scientific discipline which consisted in mapping, sequencing, and analyzing genomes. Nowadays, this term is widely used by a growing number of people in a broader sense to describe global techniques for studying genomes including from a functional point of view. These include the analysis of messenger RNAs (transcriptomics), protein contents (proteomics), and metabolites (metabolomics). At a higher level of complexity, it also describes the so-called “meta” approaches that allow to investigate the ecology of microbial communities, including uncultured microorganisms. Based on the use of recent technological developments, the numerous examples provide an integrated view of how microorganisms adapt to particular ecological niches and participate in the dynamics of ecosystems.


Bacterial artificial chromosome (BAC) Cloning Cosmid Cultured and uncultured strains DNA chips Genomics High-performance liquid chromatography or high-pressure liquid chromatography (HPLC) High-resolution liquid chromatography (HRLC) Isoelectric focusing (IEF) Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) Metabolomics Metagenomics Plasmid Proteomics Pyrosequencing Sequencing Shotgun Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) Synteny Transcriptomics 


  1. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198–207PubMedCrossRefGoogle Scholar
  2. Alloisio N et al (2010) The Frankia alni symbiotic transcriptome. Mol Plant Microbe Interact 23:593–607PubMedCrossRefGoogle Scholar
  3. Arsène-Ploetze F et al (2010) Structure, function and evolution of Thiomonas spp. inferred from genome sequencing and comparative genomic analysis. PLoS Genet 6:e1000859PubMedCentralPubMedCrossRefGoogle Scholar
  4. Arsène-Ploetze F, Carapito C, Plewniak F, Bertin PN (2012) Proteomics as a tool for the characterization of microbial isolates and complex communities. In: Heazlewood J, Petzold CJ (eds) Proteomic applications in biology. InTech, Croatia, pp 69–92Google Scholar
  5. Bailly X, Olivieri I, De Mita S, Cleyet-Marel JC, Bena G (2006) Recombination and selection shape the molecular diversity pattern of nitrogen-fixing Sinorhizobium sp. associated to Medicago. Mol Ecol 15:2719–2734PubMedCrossRefGoogle Scholar
  6. Beja O et al (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 5486:1902–1906CrossRefGoogle Scholar
  7. Beliaev AS et al (2005) Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors. J Bacteriol 20:7138–7145CrossRefGoogle Scholar
  8. Bentley SD et al (2003) Sequencing and analysis of the genome of the Whipple’s disease bacterium Tropheryma whipplei. Lancet 361:637–644PubMedCrossRefGoogle Scholar
  9. Bertin PN, Médigue C, Normand P (2008) Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems. Microbiology 154:347–359PubMedCrossRefGoogle Scholar
  10. Bertin PN et al (2011) Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics. ISME J 5:1735–1747PubMedCentralPubMedCrossRefGoogle Scholar
  11. Bestel-Corre G, Dumas-Gaudot E, Gianinazzi S (2004) Proteomics as a tool to monitor plant-microbe endosymbiosis in the rhizosphere. Mycorrhiza 14:1–10PubMedCrossRefGoogle Scholar
  12. Blattner FR et al (1997) The complete genome sequence of Escherichia coli K-12. Science 5:1453–1474CrossRefGoogle Scholar
  13. Bru C, Courcelle E, Carrere S, Beausse Y, Dalmar S, Kahn D (2005) The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res 3(Database issue):D212–D215Google Scholar
  14. Carapito C et al (2006) Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome. Biochimie 88:595–606PubMedCrossRefGoogle Scholar
  15. Chain P et al (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol 185:2759–2773PubMedCentralPubMedCrossRefGoogle Scholar
  16. Chen Z, Terai M, Fu L, Herrero R, DeSalle R, Burk RD (2005) Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses. J Virol 79:7014–7023PubMedCentralPubMedCrossRefGoogle Scholar
  17. Cleiss-Arnold J et al (2010) Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans. BMC Genomics 11:709PubMedCentralPubMedCrossRefGoogle Scholar
  18. Cole ST et al (2001) Massive gene decay in the leprosy bacillus. Nature 409:1007–1011PubMedCrossRefGoogle Scholar
  19. Coppée JY (2008) Do DNA microarrays have their future behind them? Microbes Infect 10:1067–1071PubMedCrossRefGoogle Scholar
  20. Croucher NJ, Thomson NR (2010) Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol 13:619–624. PMCID: PMC3025319PubMedCentralPubMedCrossRefGoogle Scholar
  21. Daubin V, Ochman H (2004a) Recognizing lateral gene transfer by quartet mapping. Mol Biol Evol 21:48–51Google Scholar
  22. Daubin V, Ochman H (2004b) Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res 14:1036–1042PubMedCentralPubMedCrossRefGoogle Scholar
  23. Daubin V, Lerat E, Perriere G (2003) The source of laterally transferred genes in bacterial genomes. Genome Biol 21:48–51Google Scholar
  24. Demirjian DC, Moris-Varas F, Cassidy CS (2001) Enzymes from extremophiles. Curr Opin Chem Biol 5:144–151PubMedCrossRefGoogle Scholar
  25. De-Vriendt K, Sandra K, Desmet T, Nerinckx W, Van Beeumen J, Devreese B (2004) Evaluation of automated nano-electrospray mass spectrometry in the determination of non-covalent protein-ligand complexes. Rapid Commun Mass Spectrom 18:3061–3067PubMedCrossRefGoogle Scholar
  26. Dougherty MJ, D’haeseleer P, Simmons BA, Adams PD, Hadi MZ (2012) Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization. BMC Biotechnol 12:38PubMedCentralPubMedCrossRefGoogle Scholar
  27. Eberly JO, Ely RL (2008) Thermotolerant hydrogenases: biological diversity, properties, and biotechnological applications. Crit Rev Microbiol 34:117–130PubMedCrossRefGoogle Scholar
  28. Faust K, Raes J (2012) Microbial interactions: from networks to models. Nat Rev Microbiol 10:538–550PubMedCrossRefGoogle Scholar
  29. Fleischmann RD et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae. Science 269:496–512PubMedCrossRefGoogle Scholar
  30. Gil R, Sabater-Munoz B, Latorre A, Silva FJ, Moya A (2002) Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life. Proc Natl Acad Sci U S A 99:4454–4458PubMedCentralPubMedCrossRefGoogle Scholar
  31. Giovannoni SJ et al (2005) Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438:82–85PubMedCrossRefGoogle Scholar
  32. Gomez-Consarnau L et al (2010) Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol 8:e1000358PubMedCentralPubMedCrossRefGoogle Scholar
  33. Halter D et al (2012) In situ proteo-metabolomics revealed metabolite secretion by the acid mine drainage bioindicator, Euglena mutabilis. ISME J 6:1391–1402PubMedCentralPubMedCrossRefGoogle Scholar
  34. Hecker M, Volker U (2004) Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics. Proteomics 4:3727–3750PubMedCrossRefGoogle Scholar
  35. Hocher V et al (2011) Transcriptomics of actinorhizal symbioses reveals homologs of the whole common symbiotic signaling cascade. Plant Physiol 156:700–711PubMedCentralPubMedCrossRefGoogle Scholar
  36. Holt JG, Krieg NR, Sneath PH, Staley JT, Williams ST (eds) (1994) Bergey’s manual of determinative bacteriology. Williams & Wilkins, BaltimoreGoogle Scholar
  37. Hou S et al (2004) Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci U S A 101:18036–18041PubMedCentralPubMedCrossRefGoogle Scholar
  38. Jenner RG, Young RA (2005) Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol 3:281–294PubMedCrossRefGoogle Scholar
  39. Johnson E, Baron D, Naranjo B, Bond D, Schmidt-Dannert C, Gralnick J (2010) Enhancement of survival and electricity production in an engineered bacterium by light-driven proton pumping. Appl Environ Microbiol 76:4123–4129PubMedCentralPubMedCrossRefGoogle Scholar
  40. Jungblut PR (2001) Proteome analysis of bacterial pathogens. Microbes Infect 3:831–840PubMedCrossRefGoogle Scholar
  41. Kahn P (1995) From genome to proteome: looking at a cell’s proteins. Science 270:369–370PubMedCrossRefGoogle Scholar
  42. Kim ST et al (2004) Proteomic analysis of pathogen-responsive proteins from rice leaves induced by rice blast fungus, Magnaporthe grisea. Proteomics 4:3569–3578PubMedCrossRefGoogle Scholar
  43. Kimura M (1968) Evolutionary rate at the molecular level. Nature 217:624–626PubMedCrossRefGoogle Scholar
  44. Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 7058:543–546CrossRefGoogle Scholar
  45. Kunst F et al (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 20:249–256CrossRefGoogle Scholar
  46. Lander ES et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921PubMedCrossRefGoogle Scholar
  47. Liedert C et al (2010) Two-dimensional proteome reference map for the radiation-resistant bacterium Deinococcus geothermalis. Proteomics 10:555–563PubMedCrossRefGoogle Scholar
  48. Liu Z et al (2005) Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans. Mol Biol Evol 22:659–672PubMedCrossRefGoogle Scholar
  49. Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3:510–516PubMedCrossRefGoogle Scholar
  50. Matsumoto N, Yoshinaga H, Ohmura N, Ando A, Saiki H (2000) High density cultivation of two strains of iron-oxidizing bacteria through reduction of ferric iron by intermittent electrolysis. Biotechnol Bioeng 70:464–466PubMedCrossRefGoogle Scholar
  51. Matsuzaki M et al (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428:653–657PubMedCrossRefGoogle Scholar
  52. Médigue C et al (2005) Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. 1. Genome Res 15:1325–1335PubMedCentralPubMedCrossRefGoogle Scholar
  53. Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11:31–46PubMedCrossRefGoogle Scholar
  54. Moretti M et al (2010) A proteomics approach to study synergistic and antagonistic interactions of the fungal-bacterial consortium Fusarium oxysporum wild-type MSA 35. Proteomics 10:3292–3320PubMedCrossRefGoogle Scholar
  55. Mulder NJ et al (2005) InterPro, progress and status in 2005. Nucleic Acids Res 33(Database issue):D201–D205PubMedCentralPubMedCrossRefGoogle Scholar
  56. Muller D et al (2007) A tale of two oxydation states: bacterial colonization of arsenic-rich environments. PLoS Genet 3:e53PubMedCentralPubMedCrossRefGoogle Scholar
  57. Nadon R, Shoemaker J (2002) Statistical issues with microarrays: processing and analysis. Trends Genet 18:265–271PubMedCrossRefGoogle Scholar
  58. Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M (2006) The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314:267PubMedCrossRefGoogle Scholar
  59. Narasingarao P et al (2012) De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6:81–93PubMedCentralPubMedCrossRefGoogle Scholar
  60. Noel-Georis I et al (2004) Global analysis of the Ralstonia metallidurans proteome: prelude for the large-scale study of heavy metal response. Proteomics 4:151–179PubMedCrossRefGoogle Scholar
  61. Normand P et al (2007) Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 17:7–15PubMedCentralPubMedCrossRefGoogle Scholar
  62. Ou K et al (2005) Integrative genomic, transcriptional, and proteomic diversity in natural isolates of the human pathogen Burkholderia pseudomallei. J Bacteriol 187:4276–4285PubMedCentralPubMedCrossRefGoogle Scholar
  63. Parales RE, Ditty JL (2005) Laboratory evolution of catabolic enzymes and pathways. Curr Opin Biotechnol 16:315–325PubMedCrossRefGoogle Scholar
  64. Pradella S, Hans A, Sproer C, Reichenbach H, Gerth K, Beyer S (2002) Characterisation, genome size and genetic manipulation of the myxobacterium Sorangium cellulosum So ce56. Arch Microbiol 178:484–492PubMedCrossRefGoogle Scholar
  65. Pühler A, Ariat M, Becker A, Göttfert M, Morrissey JP, O’Gara F (2004) What can bacterial genome research teach us about bacteria-plant interaction? Curr Opin Plant Biol 7:137–147PubMedCrossRefGoogle Scholar
  66. Rabilloud T (2002) Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2:3–10PubMedCrossRefGoogle Scholar
  67. Rhodius VA, LaRossa RA (2003) Uses and pitfalls of microarrays for studying transcriptional regulation. Curr Opin Microbiol 6:114–119PubMedCrossRefGoogle Scholar
  68. Ronaghi M (2001) Pyrosequencing sheds light on DNA sequencing. Genome Res 11:3–11PubMedCrossRefGoogle Scholar
  69. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467PubMedCentralPubMedCrossRefGoogle Scholar
  70. Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, Cavicchioli R (2005) Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii. J Proteome Res 4:464–472PubMedCrossRefGoogle Scholar
  71. Scarselli M, Giuliani MM, Adu-Bobie J, Pizza M, Rappuoli R (2005) The impact of genomics on vaccine design. Trends Biotechnol 23:84–91PubMedCrossRefGoogle Scholar
  72. Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3:479–488PubMedCrossRefGoogle Scholar
  73. Schmid MB (2004) Seeing is believing: the impact of structural genomics on antimicrobial drug discovery. Nat Rev Microbiol 2:739–746PubMedCrossRefGoogle Scholar
  74. Schmutz J et al (2004) Quality assessment of the human genome sequence. Nature 429:365–368PubMedCrossRefGoogle Scholar
  75. Siew N, Fischer D (2003) Twenty thousand ORFan microbial protein families for the biologist? Structure 11:7–9PubMedCrossRefGoogle Scholar
  76. Stewart FJ, Dmytrenko O, DeLong EF, Cavanaugh CM (2011) Metatranscriptomic analysis of sulfur oxidation genes in the endosymbiont of Solemya velum. Front Microbiol 2:1–10CrossRefGoogle Scholar
  77. Streit WR, Schmitz RA (2004) Metagenomics – the key to the uncultured microbes. Curr Opin Microbiol 7:492–498PubMedCrossRefGoogle Scholar
  78. Strous M et al (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790–794PubMedCrossRefGoogle Scholar
  79. Tweeddale H, Notley-McRobb L, Ferenci T (1998) Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool (“metabolome”) analysis. J Bacteriol 180:5109–5116PubMedCentralPubMedGoogle Scholar
  80. Tyson GW et al (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43PubMedCrossRefGoogle Scholar
  81. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF (2005) Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol 71:6319–6324PubMedCentralPubMedCrossRefGoogle Scholar
  82. Vallenet D et al (2006) MAGE: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34:53–65PubMedCentralPubMedCrossRefGoogle Scholar
  83. van Ham RC et al (2003) Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A 100:581–586PubMedCentralPubMedCrossRefGoogle Scholar
  84. Velculescu VE et al (1997) Characterization of the yeast transcriptome. Cell 24:243–251CrossRefGoogle Scholar
  85. Venter JC et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74PubMedCrossRefGoogle Scholar
  86. Vezzi A et al (2005) Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307:1459–1461PubMedCrossRefGoogle Scholar
  87. Walter JM, Greenfield D, Bustamante C, Liphardt J (2007) Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci U S A 104:2408–2412PubMedCentralPubMedCrossRefGoogle Scholar
  88. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63PubMedCentralPubMedCrossRefGoogle Scholar
  89. Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 17:737–738CrossRefGoogle Scholar
  90. Weiss S et al (2009) Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data. Biochimie 91:192–203PubMedCrossRefGoogle Scholar
  91. Wilmes P, Bond PL (2004) The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ Microbiol 6:911–920PubMedCrossRefGoogle Scholar
  92. Wishart DS (2005) Metabolomics: the principles and potential applications to transplantation. Am J Transplant 5:2814–2820PubMedCrossRefGoogle Scholar
  93. Woyke T et al (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 7114:950–955CrossRefGoogle Scholar
  94. Yamada T et al (2012) Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Mol Syst Biol 8:581PubMedCentralPubMedCrossRefGoogle Scholar
  95. Yang C et al (2006) Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 40:29872–29885CrossRefGoogle Scholar
  96. Zakrzewski M et al (2012) Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol 158:248–258PubMedCrossRefGoogle Scholar
  97. Zylstra GJ, Kukor JJ (2005) What is environmental biotechnology. Curr Opin Biotechnol 16:243–245CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Philippe N. Bertin
    • 1
  • Valérie Michotey
    • 2
  • Philippe Normand
    • 3
  1. 1.Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR 7156Université de StrasbourgStrasbourg CedexFrance
  2. 2.Institut Méditerranéen d’Océanologie (MIO)UM 110, CNRS 7294 IRD 235, Université de Toulon, Aix-Marseille UniversitéMarseille Cedex 9France
  3. 3.Microbial Ecology CenterUMR CNRS 5557 / USC INRA 1364, Université Lyon 1VilleurbanneFrance

Personalised recommendations