Advertisement

The Evolution of Living Beings Started with Prokaryotes and in Interaction with Prokaryotes

  • Télesphore Sime-NgandoEmail author
  • Jean-Claude Bertrand
  • Didier Bogusz
  • Jean-François Brugère
  • Claudine Franche
  • Marie-Laure Fardeau
  • Emilie Froussart
  • Anne Geiger
  • Maria Soledad Goñi-Urriza
  • Bernard Ollivier
  • Paul W. O’Toole
Chapter

Abstract

In natural world, no organism exists in absolute isolation, and thus every organism must interact with the environment and other organisms. Next-generation sequencing technologies are increasingly revealing that most of the cells in the environment resist cultivation in the laboratory and several prokaryotic divisions have no known cultivated representatives. Based on this, we hypothesize that species that live together in the same ecosystem are more or less dependent upon each other and are very large in diversity and number, outnumbering those that can be isolated in single-strain laboratory culture. In natural environments, bacteria and archaea interact with other organisms (viruses, protists, fungi, animals, plants, and human) in complex ecological networks, resulting in positive, negative, or no effect on one or another of the interacting partners. These interactions are sources of ecological forces such as competitive exclusion, niche partitioning, ecological adaptation, or horizontal gene transfers, which shape the biological evolution. In this chapter, we review the biological interactions involving prokaryotes in natural ecosystems, including plant, animal, and human microbiota, and give an overview of the insights into the evolution of living beings. We conclude that studies of biological interactions, including multipartite interactions, are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, the evolution of the cellular world, and the ecosystem services to the living beings.

Keywords

Prokaryotes Viruses Protists Fungi Plants Animals Human Microbial mats Biotic interactions Evolution 

Notes

Acknowledgments

The authors thank the “Institut de Recherche pour le Développement,” the International Atomic Energy Agency (IAEA), and “France Génomique” for their support. This project has received funding from the French ANR under grant agreement ANR-12-BSV7-0019. The initial figures were improved by M. A. Galeron; thanks to our co-author B.O. for the payment of the associated costs.

References

  1. Abramowicz DA (1990) Aerobic and anaerobic biodegradation of PCBs: a review. Crit Rev Biotechnol 10:241–151CrossRefGoogle Scholar
  2. Ackermann HW (1999) Tailed bacteriophages : the order Caudovirales. AdvVirus Res 51(135):201.  https://doi.org/10.1016/S0065-3527(08)60785-X CrossRefGoogle Scholar
  3. Akman L, Rio RV, Beard CB, Aksoy S (2001) Genome size determination and coding capacity of Sodalis glossinidius, an enteric symbiont of tsetse flies, as revealed by hybridization to Escherichia coli gene arrays. J Bacteriol 183:4517–4525PubMedPubMedCentralCrossRefGoogle Scholar
  4. Akman L, Yamashita A, Watanabe H, Oshima K, Shiba T, Hattori M, Aksoy S (2002) Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat Genet 32:402–407PubMedCrossRefPubMedCentralGoogle Scholar
  5. Aksoy S (2000) Tsetse - a haven for microorganisms. Parasitol Today 16:114–118PubMedCrossRefPubMedCentralGoogle Scholar
  6. Aksoy S, Pourhosseini AA, Chow A (1995) Mycetome endosymbionts of tsetse flies constitute a distinct lineage related to Enterobacteriaceae. Insect Mol Biol 4:15–22PubMedCrossRefPubMedCentralGoogle Scholar
  7. Aksoy E, Telleria EL, Echodu R, Wu Y, Okedi LM, Weiss BL, Aksoy S, Caccone A (2014) Analysis of multiple tsetse fly populations in Uganda reveals limited diversity and species-specific gut microbiota. Appl Environ Microbiol 80:4301–4312PubMedPubMedCentralCrossRefGoogle Scholar
  8. Alam U, Medlock J, Brelsfoard C, Pais R, Lohs C, Balmand S, Carnogursky J, Heddi A, Takac P, Galvani A, Aksoy S (2011) Wolbachia symbiont infections induce strong cytoplasmic incompatibility in the tsetse fly Glossina morsitans. PLoS Pathog 7:e1002415PubMedPubMedCentralCrossRefGoogle Scholar
  9. Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1):143–169PubMedPubMedCentralGoogle Scholar
  10. Anderson D.M., Cembella A.D., and G. M. Hallegraeff (ed.) (1998). Physiological ecology of harmful algal blooms, vol. G 41. Springer, Berlin, GermanyGoogle Scholar
  11. Aoki S, Ito M, Iwasaki W (2013) From β- to α-Proteobacteria: the origin and evolution of Rhizobial nodulation genes nodIJ. Mol Biol Evol 30:2494–2508.  https://doi.org/10.1093/molbev/mst153 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Arakaki N, Miyoshi T, Noda H (2001) Wolbachia-mediated parthenogenesis in the predatory thrips Franklinothrips vespiformis (Thysanoptera: Insecta). Proc R Soc London Ser B 268:1011–1016CrossRefGoogle Scholar
  13. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Dore J, Antolin M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Merieux A, Melo Minardi R, M’Rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P (2011) Enterotypes of the human gut microbiome. Nature 473(7346):174–180.  https://doi.org/10.1038/nature09944 PubMedPubMedCentralCrossRefGoogle Scholar
  14. Azambuja P, Garcia ES, Ratcliffe NA (2005) Gut microbiota and parasite transmission by insect vectors. Trends Parasitol 21:568–572PubMedCrossRefPubMedCentralGoogle Scholar
  15. Baena S, Fardeau ML, Labat M, Ollivier B, Thomas P, Garcia JL, Patel BK (1998) Aminobacterium colombiense gen. Nov., sp. nov., an amino acid-degrading anaerobe isolated from anaerobic sludge. Anaerobe 4:241–250PubMedCrossRefPubMedCentralGoogle Scholar
  16. Baena S, Fardeau ML, Ollivier B, Labat M, Thomas P, Garcia JL, Patel BK (1999) Aminomonas paucivorans gen. Nov., sp. nov., a mesophilic, anaerobic, amino-acid-utilizing bacterium. Int J Syst Bacteriol 49:975–982PubMedCrossRefPubMedCentralGoogle Scholar
  17. Baena S, Fardeau ML, Labat M, Ollivier B, Garcia JL, Patel BK (2000) Aminobacterium mobile sp. nov., a new anaerobic amino-acid-degrading bacterium. Int J Syst Evol Microbiol 50:259–264PubMedCrossRefPubMedCentralGoogle Scholar
  18. Balmand S, Lohs C, Aksoy S, Heddi A (2013) Tissue distribution and transmission routes for the tsetse fly endosymbionts. J Invertebr Pathol 112(Suppl):S116–S122PubMedCrossRefPubMedCentralGoogle Scholar
  19. Bandi C, Trees AJ, Brattig NW (2001) Wolbachia in filarial nematodes: evolutionary aspects and implications for the pathogenesis and treatment of filarial diseases. Vet Parasitol 98:215–238PubMedCrossRefPubMedCentralGoogle Scholar
  20. Barile D, Rastall RA (2013) Human milk and related oligosaccharides as prebiotics. Curr Opin Biotechnol 24(2):214–219.  https://doi.org/10.1016/j.copbio.2013.01.008 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Beam HW, Perry JJ (1974) Microbial degradation of cycloparaffinic hydrocarbons via co-metabolism and commensalism. J Gen Microbiol 82:163–169CrossRefGoogle Scholar
  22. Beard CB, Durvasula RV, Richards FF (1998) Bacterial symbiosis in arthropods and the control of disease transmission. Emerg Infect Dis 4:581–591PubMedPubMedCentralCrossRefGoogle Scholar
  23. Beatty JT, Overmann J, Lince MT, Manske AK, Lang AS, Blankenship RE, Van Dover CL, Martinson TA, Plumley FG (2005) An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent. Proc Natl Acad Sci U S A 102(26):9306–9310PubMedPubMedCentralCrossRefGoogle Scholar
  24. Becking JH (1992) The rhizobium symbiosis of the non-legume Parasponia. In: Stacey G, Burris RH, Evans HJ (eds) Biological nitrogen fixation: achievements and objectives. Chapman & Hall, New York, pp 497–559Google Scholar
  25. Bergthorsson U, Ochman H (1998) Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol Biol Evol 15:6–16PubMedCrossRefPubMedCentralGoogle Scholar
  26. Berleman JE et al (2014) The lethal cargo of Myxococcus xanthus outer membrane vesicles. Front Microbiol 5:474.  https://doi.org/10.3389/fmicb.2014.00474 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Bertrand J-C, Rambeloarisoa E, Rontani J-F, Guisti G, Mattei G (1983) Microbial degradation of crude oil in sea water and continuous culture. Biotechnol Lett 5:567–572CrossRefGoogle Scholar
  28. Bertrand J-C, Bonin P, Caumette P, Gattuso J-P, Grégori G, Guyoneaud LRX, Matheron R, Poly F (2015a) Biogeochemical cycles. In: Bertrand JC, Caumette P, Lebaron P, Matheron R, Normand P, Sime-Ngando T (eds) Environmental microbiology: fundamentals and aplications. Springer, Dordrecht/Heidelberg/New York/London, pp 511–617Google Scholar
  29. Bertrand J-C, Doumenq P, Guyoneaud R, Marrot B, Martin-Laurent F, Matheron R, Moulin P, Soulas G (2015b) Applied microbial ecology and bioremediation. Microorganisms as major actors of pollution elimination in the environment. In: Bertrand JC, Caumette P, Lebaron P, Matheron R, Normand P, Sime-Ngando T (eds) Environmental microbiology: fundamentals and aplications. Springer, Dordrecht/Heidelberg/New York/London, pp 659–753Google Scholar
  30. Boller EF, Russ K, Vallo V, Bush GL (1976) Incompatible races of European cherry fruit fly, Rhagoletis cerasi (Diptera, Tephritidae), their origin and potential use in biological control. Entomol Exp Appl 20:237–247CrossRefGoogle Scholar
  31. Bonaldi K, Gourion B, Fardoux J, Hannibal L, Cartieaux F, Boursot M, Vallenet D, Chaintreuil C, Prin Y, Nouwen N, Giraud E (2010) Large-scale transposon mutagenesis of photosynthetic Bradyrhizobium sp. strain ORS278 reveals new genetic loci putatively important for nod-independent symbiosis with Aeschynomene indica. Mol Plant-Microbe Interact 23:760–770.  https://doi.org/10.1094/MPMI-23-6-0760 CrossRefPubMedPubMedCentralGoogle Scholar
  32. Bontemps C, Elliott GN, Simon MF, Dos Reis Júnior FB, Gross E, Lawton RC, Neto NE, De Fatima Loureiro M, De Faria SM, Sprent JI, James EK, Young JP (2010) Burkholderia species are ancient symbionts of legumes. Mol Ecol 19:44–52.  https://doi.org/10.1111/j.1365-294X.2009.04458.x CrossRefPubMedPubMedCentralGoogle Scholar
  33. Bordenave S, Goñi-Urriza MS, Caumette P, Duran R. 2007. Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl Environ Microbiol Oct;73(19):6089–6097. Epub 2007 Aug 17PubMedPubMedCentralCrossRefGoogle Scholar
  34. Bordenstein SR, Fitch DHA, Werren JH (2003) Absence of Wolbachia in nonfilariid nematodes. J Nematol 35:266–270PubMedPubMedCentralGoogle Scholar
  35. Borrel G, Parisot N, Harris HM, Peyretaillade E, Gaci N, Tottey W, Bardot O, Raymann K, Gribaldo S, Peyret P, O’Toole PW, Brugere JF (2014) Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 15:679.  https://doi.org/10.1186/1471-2164-15-679 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Borrel G, McCann A, Deane J, Neto MC, Lynch DB, Brugere JF, O’Toole PW (2017) Genomics and metagenomics of trimethylamine-utilizing archaea in the human gut microbiome. ISME J 11(9):2059–2074.  https://doi.org/10.1038/ismej.2017.72 CrossRefPubMedPubMedCentralGoogle Scholar
  37. Bressac C, Rousset F (1993) The reproductive incompatibility system in Drosophila simulans: DAPI-staining analysis of the Wolbachia symbionts in sperm cysts. J Invertebr Pathol 61:226–230PubMedCrossRefPubMedCentralGoogle Scholar
  38. Bronstein JL (1994) Conditional outcomes in mutualistic interactions. Trends Ecol Evol 9:214–217PubMedCrossRefPubMedCentralGoogle Scholar
  39. Browne HP, Neville BA, Forster SC, Lawley TD (2017) Transmission of the gut microbiota: spreading of health. Nat Rev Microbiol 15(9):531–543.  https://doi.org/10.1038/nrmicro.2017.50 CrossRefPubMedPubMedCentralGoogle Scholar
  40. Brownlie JC, Cass BN, Riegler M, Witsenburg JJ, Iturbe-Ormaetxe I, McGraw EA, O’Neill SL (2009) Evidence for metabolic provisioning by a common invertebrate endosymbiont, Wolbachia pipientis, during periods of nutritional stress. PLoS Pathog 5:e1000368PubMedPubMedCentralCrossRefGoogle Scholar
  41. Brüssow H, Hendrix RW (2002) Phagegenomics : small is beautiful. Cell 108:13–16.  https://doi.org/10.1016/S0092-8674(01)00637-7 CrossRefPubMedPubMedCentralGoogle Scholar
  42. Bryant MP, Wolin EA, Wolin MJ, Wolfe RS (1967) Methanobacillus omelianskii, a symbiotic association of two species of bacteria. Arch Microbiol 59:20–31Google Scholar
  43. Byndloss MX, Olsan EE, Rivera-Chavez F, Tiffany CR, Cevallos SA, Lokken KL, Torres TP, Byndloss AJ, Faber F, Gao Y, Litvak Y, Lopez CA, Xu G, Napoli E, Giulivi C, Tsolis RM, Revzin A, Lebrilla CB, Baumler AJ (2017) Microbiota-activated PPAR-gamma signaling inhibits dysbiotic Enterobacteriaceae expansion. Science 357(6351):570–575.  https://doi.org/10.1126/science.aam9949 CrossRefPubMedPubMedCentralGoogle Scholar
  44. Cannon SB, McKain MR, Harkess A, Nelson MN, Dash S, Deyholos MK, Peng Y, Joyce B, Stewart CN, Rolf M et al (2014) Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes. Mol Biol Evol 32:193–210.  https://doi.org/10.1093/molbev/msu296 CrossRefPubMedPubMedCentralGoogle Scholar
  45. Cario E (2010) Toll-like receptors in inflammatory bowel diseases: a decade later. Inflamm Bowel Dis 16(9):1583–1597.  https://doi.org/10.1002/ibd.21282 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Caron DA, Goldman JC, Dennett MR (1988) Experimental demonstration of the roles of bacteria and bacterivorous protozoa in plankton nutrient cycles. Hydrobiologia 159:27–40CrossRefGoogle Scholar
  47. Casiraghi M, Anderson TJ, Bandi C, Bazzocchi C, Genchi C (2001) A phylogenetic analysis of filarial nematodes: comparison with the phylogeny of Wolbachia endosymbionts. Parasitology 122:93–103PubMedCrossRefPubMedCentralGoogle Scholar
  48. Cavalier-Smith T (2002) The phagotrophic origin of eukaryotes and phylogenetic classification of protozoa. Int J Syst Evol Microbiol 52:297–354PubMedCrossRefPubMedCentralGoogle Scholar
  49. Cérémonie H, Debellé F, Fernandez MP (1999) Structural and functional comparison of Frankia root hair deforming factor and rhizobia nod factor. Can J Bot 77:1293–1301.  https://doi.org/10.1139/b99-060 CrossRefGoogle Scholar
  50. Cerqueda-García D, Martínez-Castilla LP, Falcón LI, Delaye L (2014) Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in ‘Chlorochromatium aggregatum. ISME J 8:991–998PubMedCrossRefPubMedCentralGoogle Scholar
  51. Chabaud M, Gherbi H, Pirolles E, Vaissayre V, Fournier J, Moukouanga D, Franche C, Bogusz D, Tisa LS, Barker DG, Svistoonoff S (2016) Chitinase-resistant hydrophilic symbiotic factors secreted by Frankia activate both Ca2+ spiking and NIN gene expression in the actinorhizal plant Casuarina glauca. New Phytol.  https://doi.org/10.1111/nph.13732 PubMedCrossRefPubMedCentralGoogle Scholar
  52. Charlat S, Hornett EA, Dyson EA, Ho PP, Loc NT, Schilthuizen M, Davies N, Roderick GK, Hurst GD (2005) Prevalence and penetrance variation of male-killing Wolbachia across indo-Pacific populations of the butterfly Hypolimnas bolina. Mol Ecol 14:3525–3530PubMedCrossRefPubMedCentralGoogle Scholar
  53. Charlat S, Hornett EA, Fullard JH, Davies N, Roderick GK, Wedell N, Hurst GD (2007) Extraordinary flux in sex ratio. Science 317:214PubMedCrossRefPubMedCentralGoogle Scholar
  54. Chen X, Li S, Aksoy S (1999) Concordant evolution of a symbiont with its host insect species: molecular phylogeny of genus Glossina and its bacteriome-associated endosymbiont, Wigglesworthia glossinidia. J Mol Evol 48:49–58PubMedCrossRefPubMedCentralGoogle Scholar
  55. Cheng TC (1991) Is parasitism symbiosis ? A definition of terms and the evolution of concepts. In: Toft CA, Aeschlimann A, Bolis L (eds) Parasite-host associations, coexistence or conflict? Oxford University Press, New York, pp 15–36Google Scholar
  56. Cheng Q, Aksoy S (1999) Tissue tropism, transmission and expression of foreign genes in vivo in midgut symbionts of tsetse flies. Insect Mol Biol 8:125–132PubMedCrossRefPubMedCentralGoogle Scholar
  57. Cheng Q, Ruel TD, Zhou W, Moloo SK, Majiwa P, O’Neill SL, Aksoy S (2000) Tissue distribution and prevalence of Wolbachia infections in tsetse flies, Glossina spp. Med Vet Entomol 14:44–50PubMedCrossRefPubMedCentralGoogle Scholar
  58. Chivian D, Brodie EL, Alm EJ, Culler DE, Dehal PS, Desantis TZ, GihringI TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, Andersen GL, Hazen TC, Brockman FJ, Adam P, Arkin AP, Onstott TC (2008) Environmental genomics reveals a single-species ecosystem deep within earth. Science 322(5899):275–278.  https://doi.org/10.1126/science.1155495 CrossRefPubMedPubMedCentralGoogle Scholar
  59. Cirimotich CM, Dong Y, Clayton AM, Sandiford SL, Souza-Neto JA, Mulenga M, Dimopoulos G (2011) Natural microbe-mediated refractoriness to Plasmodium infection in Anopheles gambiae. Science 332:855–858PubMedPubMedCentralCrossRefGoogle Scholar
  60. Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, Harris HM, Coakley M, Lakshminarayanan B, O’Sullivan O, Fitzgerald GF, Deane J, O’Connor M, Harnedy N, O’Connor K, O’Mahony D, van Sinderen D, Wallace M, Brennan L, Stanton C, Marchesi JR, Fitzgerald AP, Shanahan F, Hill C, Ross RP, O’Toole PW (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488(7410):178–184.  https://doi.org/10.1038/nature11319 CrossRefPubMedPubMedCentralGoogle Scholar
  61. Claesson MJ, Clooney AG, O’Toole PW (2017) A clinician’s guide to microbiome analysis. Nat Rev Gastroenterol Hepatol 14(10):585–595.  https://doi.org/10.1038/nrgastro.2017.97 CrossRefPubMedPubMedCentralGoogle Scholar
  62. Clark EL, Karley AJ, Hubbard SF (2010) Insect endosymbionts: manipulators of insect herbivore trophic interactions. Protoplasma 244:25–51PubMedCrossRefPubMedCentralGoogle Scholar
  63. Clavijo F, Diedhou I, Vaissayre V, Brottier L, Ascolate J, Moukouanga D, Crabos A, Auguy F, Franche C, Gherbi H, Champion A, Hocher V, Barker D, Bogusz D, Tisa L, Svistoonoff S (2015) The Casuarina NIN gene is transcriptionally activated throughout Frankia root infection as well as in response to bacterial diffusible signals. New Phytol 208:887–903.  https://doi.org/10.1111/nph.13506 CrossRefPubMedPubMedCentralGoogle Scholar
  64. Clerissi C, Desdevises Y, Grimsley N (2012) Prasinoviruses of the marine green alga Ostreococcus tauri : are mainly species specific. J Virology 86:4611–4619PubMedCrossRefPubMedCentralGoogle Scholar
  65. Coburn PS, Gilmore MS (2003) The Enterococcus faecalis cytolysin: a novel toxin active against eukaryotic and prokaryotic cells. Cell Microbiol 5:661–669PubMedCrossRefPubMedCentralGoogle Scholar
  66. Cornelis GR (2000) Type III secretion: a bacterial device for close combat with cells of their eukaryotic host. Philos Trans R Soc Lond Ser B Biol Sci 355:681–693CrossRefGoogle Scholar
  67. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2009) Bacterial community variation in human body habitats across space and time. Science 326(5960):1694–1697.  https://doi.org/10.1126/science.1177486 CrossRefPubMedPubMedCentralGoogle Scholar
  68. Cotter PD, Ross RP, Hill C (2013) Bacteriocins - a viable alternative to antibiotics? Nat Rev Microbiol 11(2):95–105.  https://doi.org/10.1038/nrmicro2937 CrossRefPubMedPubMedCentralGoogle Scholar
  69. Dale C, Maudlin I (1999) Sodalis gen. Nov. and Sodalis glossinidius sp. nov., a microaerophilic secondary endosymbiont of the tsetse fly Glossina morsitans morsitans. Int J Syst Bacteriol 1:267–275CrossRefGoogle Scholar
  70. Darby AC, Lagnel J, Matthew CZ, Bourtzis K, Maudlin I, Welburn SC (2005) Extrachromosomal DNA of the symbiont Sodalis glossinidius. J Bacteriol 187:5003–5007PubMedPubMedCentralCrossRefGoogle Scholar
  71. Davidov Y, Jurkevitch E (2009) Predation between prokaryotes and the origin of eukaryotes. BioEssays 31:748–757.  https://doi.org/10.1002/bies.200900018 CrossRefPubMedPubMedCentralGoogle Scholar
  72. Dawson JO (2007) Ecology of Actinorhizal plants. In: Pawlowski K, Newton WE (eds) Nitrogen-fixing Actinorhizal symbioses. Nitrogen fixation: origins, applications, and research Progress, vol 6. Springer, DordrechtGoogle Scholar
  73. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107(33):14691–14696.  https://doi.org/10.1073/pnas.1005963107 CrossRefPubMedPubMedCentralGoogle Scholar
  74. De León, K.B., Zane, G.M., Trotter, V.V., Krantz, G.P., Arkin, A.P., Butland, G.P., Walian, P.J., Fields, M.W., Wall, J.D. (2017). Unintended laboratory-driven evolution reveals genetic requirements for biofilm formation by desulfovibrio vulgaris Hildenborough (2017) MBio, 8 (5), art. no. e01696–17Google Scholar
  75. De Vooght L, Caljon G, Stijlemans B, De Baetselier P, Coosemans M, Van den Abbeele J (2012) Expression and extracellular release of a functional anti-trypanosome Nanobody® in Sodalis glossinidius, a bacterial symbiont of the tsetse fly. Microb Cell Factories 11:23CrossRefGoogle Scholar
  76. De Vooght L, Caljon G, De Ridder K, Van Den Abbeele J. 2014. Delivery of a functional anti-trypanosome Nanobody in different tsetse fly tissues via a bacterial symbiont, Sodalis glossinidius. Microb Cell Fact. 13:156PubMedPubMedCentralCrossRefGoogle Scholar
  77. De Vooght L, Caljon G, Van Hees J, Van Den Abbeele J (2015) Paternal transmission of a secondary Symbiont during mating in the viviparous tsetse Fly. Mol Biol Evol 32:1977–1980PubMedPubMedCentralCrossRefGoogle Scholar
  78. Dedeine F, Vavre F, Fleury F, Loppin B, Hochberg ME, Bouletreau M (2001) Removing symbiotic Wolbachia bacteria specifically inhibits oogenesis in a parasitic wasp. Proc Natl Acad Sci U S A 98:6247–6252PubMedPubMedCentralCrossRefGoogle Scholar
  79. Dedeine F, Vavre F, Shoemaker DD, Bouletreau M (2004) Intra-individual coexistence of a Wolbachia strain required for host oogenesis with two strains inducing cytoplasmic incompatibility in the wasp Asobara tabida. Evolution 58:2167–2174PubMedCrossRefPubMedCentralGoogle Scholar
  80. Degnan PH, Moran NA (2008a) Evolutionary genetics of a defensive facultative symbiont of insects: exchange of toxin-encoding bacteriophage. Mol Ecol 17:916–929PubMedCrossRefPubMedCentralGoogle Scholar
  81. Degnan PH, Moran NA (2008b) Diverse phage-encoded toxins in a protective insect endosymbiont. Appl Environ Microbiol 74:6782–6791PubMedPubMedCentralCrossRefGoogle Scholar
  82. Degnan PH, Yu Y, Sisneros N, Wing RA, Moran NA (2009) Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proc Natl Acad Sci U S A 106:9063–9068PubMedPubMedCentralCrossRefGoogle Scholar
  83. Diagne N, Diouf D, Svistoonoff S, Kane A, Noba K, Franche C et al (2013) Casuarina in Africa: distribution, role and importance of arbuscular mycorrhizal, ectomycorrhizal fungi and Frankia on plant development. J Environ Manag 128:204–209.  https://doi.org/10.1016/j.jenvman.2013.05.009 CrossRefGoogle Scholar
  84. Diédhiou I, Tromas A, Cissoko M, Gray K, Parizot B, Crabos A, Alloisio N, Fournier P, Carro L, Svistoonoff S, Gherbi H, Hocher V, Diouf D, Laplaze L, Champion A (2014) Identification of potential transcriptional regulators of actinorhizal symbioses in Casuarina glauca and Alnus glutinosa. BMC Plant Biol 14:342.  https://doi.org/10.1186/s12870-014-0342-z CrossRefPubMedPubMedCentralGoogle Scholar
  85. Dobson SL (2003) Reversing Wolbachia-based population replacement. Trends Parasitol 19:128–133PubMedCrossRefPubMedCentralGoogle Scholar
  86. Dobson SL, Bourtzis K, Braig HR, Jones BF, Zhou W, Rousset F, O’Neill SL (1999) Wolbachia infections are distributed throughout insect somatic and germ line tissues. Insect Biochem Mol Biol 29:153–160PubMedCrossRefPubMedCentralGoogle Scholar
  87. Dobson SL, Marsland EJ, Rattanadechakul W (2002) Mutualistic Wolbachia infection in Aedes albopictus: accelerating cytoplasmic drive. Genetics 160:1087–1094PubMedPubMedCentralGoogle Scholar
  88. Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC (2016) Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med 22(3):250–253.  https://doi.org/10.1038/nm.4039 CrossRefPubMedPubMedCentralGoogle Scholar
  89. Donaldson GP, Lee SM, Mazmanian SK (2016) Gut biogeography of the bacterial microbiota. Nat Rev Microbiol 14(1):20–32.  https://doi.org/10.1038/nrmicro3552 CrossRefPubMedPubMedCentralGoogle Scholar
  90. Dong Y, Manfredini F, Dimopoulos G (2009) Implication of the mosquito midgut microbiota in the defense against malaria parasites. PLoS Pathog 5:e1000423PubMedPubMedCentralCrossRefGoogle Scholar
  91. Doudoumis V, Tsiamis G, Wamwiri F, Brelsfoard C, Alam U, Aksoy E, Dalaperas S, Abd-Alla A, Ouma J, Takac P, Aksoy S, Bourtzis K (2012) Detection and characterization of Wolbachia infections in laboratory and natural populations of different species of tsetse flies (genus Glossina). BMC Microbiol 12 Suppl 1:S3PubMedPubMedCentralCrossRefGoogle Scholar
  92. Douglas AE (1998) Nutritional interactions in insect-microbial symbioses: aphids and their symbiotic bacteria Buchnera. Annu Rev Entomol 43:17–37PubMedCrossRefPubMedCentralGoogle Scholar
  93. Downie JA (2014) Legume nodulation. Curr Biol 24:184–190.  https://doi.org/10.1016/j.cub.2014.01.028 CrossRefGoogle Scholar
  94. Doyle JJ (1998) Phylogenetic perspectives on nodulation: an evolving views of plants and symbiotic bacteria. Trends Plant Sci 3:473–478.  https://doi.org/10.1016/S1360-1385(98)01340-5 CrossRefGoogle Scholar
  95. Doyle JJ (2011) Phylogenetic perspectives on the origins of nodulation. Mol Plant-Microbe Interact 24:1289–1295PubMedCrossRefPubMedCentralGoogle Scholar
  96. Doyle JJ, Luckow MA (2003) The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol 131:900–910.  https://doi.org/10.1104/pp.102.018150 CrossRefPubMedPubMedCentralGoogle Scholar
  97. Dragoš A, Lakshmanan N, Martin M, Horváth B, Maróti G, Falcón García C, Lieleg O, Kovács ÁT (2018) Evolution of exploitative interactions during diversification in Bacillus subtilis biofilms. FEMS Microbiol Ecol 94(1)Google Scholar
  98. Dubey GP, Ben-Yehuda S (2011) Intercellular nanotubes mediate bacterial communication. Cell 144:590–600PubMedCrossRefPubMedCentralGoogle Scholar
  99. Duron O (2014) Arsenophonus insect symbionts are commonly infected with APSE, a bacteriophage involved in protective symbiosis. FEMS Microbiol Ecol 90:184–194PubMedCrossRefPubMedCentralGoogle Scholar
  100. Duron O, Bouchon D, Boutin S, Bellamy L, Zhou L, Engelstädter J, Hurst GD (2008) The diversity of reproductive parasites among arthropods: Wolbachia do not walk alone. BMC Biol 6:27PubMedPubMedCentralCrossRefGoogle Scholar
  101. Dyer KA, Jaenike J (2004) Evolutionarily stable infection by a male-killing endosymbiont in Drosophila innubila: molecular evidence from the host and parasite genomes. Genetics 168:1443–1455PubMedPubMedCentralCrossRefGoogle Scholar
  102. Dyer KA, Minhas MS, Jaenike J (2005) Expression and modulation of embryonic male killing in Drosophila innubila: opportunities for multilevel selection. Evolution 59:838–848PubMedCrossRefPubMedCentralGoogle Scholar
  103. Ebert D, Herre EA (1996) The evolution of parasitic diseases. Parasitol Today 12:96–101PubMedCrossRefGoogle Scholar
  104. Echaubard P, Duron O, Agnew P, Sidobre C, Noël V, Weill M, Michalakis Y (2010) Rapid evolution of Wolbachia density in insecticide resistant Culex pipiens. Heredity 104:15–19PubMedCrossRefGoogle Scholar
  105. Eloe-Fadrosh EA, Ivanova NN, Woyke T, Kyrpides NC (2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nature Microbiol, 15032, doi: https://doi.org/10.1038/nmicrobiol.2015.32 PubMedCrossRefGoogle Scholar
  106. El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N (2005) Comparative genomics of trypanosomatid parasitic protozoa. Science 309:404–409PubMedCrossRefGoogle Scholar
  107. Engelstadter J, Hurst GDD (2009) The ecology and evolution of microbes that manipulate host reproduction. Annual Review of Ecology. Evol Syst 40:127–149CrossRefGoogle Scholar
  108. Engelstadter J, Telschow A (2009) Cytoplasmic incompatibility and host population structure. Heredity 103:196–207PubMedCrossRefGoogle Scholar
  109. Fadhlaoui K, Ben-Hania W, Armougom F, Bartoli M, Fardeau ML, Erauso G, Brasseur G, Aubert C, Hamdi M, Brochier-Armanet C, Dolla A, Ollivier B (2018) Obligate sugar oxidation in Mesotoga spp., phylum Thermotogae, in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor. Environ Microbiol 20:281–292PubMedCrossRefPubMedCentralGoogle Scholar
  110. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D’Hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J (2016) Population-level analysis of gut microbiome variation. Science 352(6285):560–564.  https://doi.org/10.1126/science.aad3503 CrossRefPubMedGoogle Scholar
  111. Farikou O, Njiokou F, Mbida Mbida JA, Njitchouang GR, Djeunga HN, Asonganyi T, Simarro PP, Cuny G, Geiger A (2010) Tripartite interactions between tsetse flies, Sodalis glossinidius and trypanosomes--an epidemiological approach in two historical human African trypanosomiasis foci in Cameroon. Infect Genet Evol 10:115–121PubMedCrossRefGoogle Scholar
  112. Farikou O, Thevenon S, Njiokou F, Allal F, Cuny G, Geiger A (2011) Genetic diversity and population structure of the secondary symbiont of tsetse flies, Sodalis glossinidius, in sleeping sickness foci in Cameroon. PLoS Negl Trop Dis 5:e1281PubMedPubMedCentralCrossRefGoogle Scholar
  113. Faust K, Raes J (2012) Microbial interactions: from networks to models. Nat Rev Microbiol 10:538–550PubMedCrossRefPubMedCentralGoogle Scholar
  114. Fay P (1992) Oxygen relations of nitrogen fixation in cyanobacteria. Microbiol Rev 56:340–373PubMedPubMedCentralGoogle Scholar
  115. Fazli M, Almblad H, Rybtke ML, Givskov M, Eberl L, Tolker-Nielsen T (2014) Regulation of biofilm formation in Pseudomonas and Burkholderia species. Environ Microbiol 16(7):1961–1981PubMedCrossRefPubMedCentralGoogle Scholar
  116. Fialho RF, Stevens L (2000) Male-killing Wolbachia in a flour beetle. Proc R Soc B Biol Sci 267:1469–1473CrossRefGoogle Scholar
  117. Flemer B, Gaci N, Borrel G, Sanderson IR, Chaudhary PP, Tottey W, O’Toole PW, Brugere JF (2017) Fecal microbiota variation across the lifespan of the healthy laboratory rat. Gut Microbes 8(5):428–439.  https://doi.org/10.1080/19490976.2017.1334033 CrossRefPubMedPubMedCentralGoogle Scholar
  118. Fourçans A, Ranchou-Peyruse A, Caumette P, Duran R (2008) Molecular analysis of the spatio-temporal distribution of sulfate-reducing bacteria (SRB) in Camargue (France) hypersaline microbial mat. Microb Ecol 56(1):90–100PubMedCrossRefPubMedCentralGoogle Scholar
  119. Franche C, Lindstrom K, Elmerich C (2009) Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants. Plant Soil 321:35–59.  https://doi.org/10.1007/s11104-008-9833-8 CrossRefGoogle Scholar
  120. Frank SA (1996) Host control of symbiont transmission. The separation of symbionts into germ and soma. Am Nat 148:1113–1124CrossRefGoogle Scholar
  121. Frimmer U, Widdel F (1989) Oxidation of ethanol by methanogenic bacteria. Arch Microbiol 152:479–483CrossRefGoogle Scholar
  122. Fröstl MJ, Overmann J (1998) Physiology and tactic response of the phototrophic consortium chlorochromatium aggregatum. Arch Microbiol 169:129–135PubMedCrossRefPubMedCentralGoogle Scholar
  123. Froussart E, Bonneau J, Franche C, Bogusz D (2016) Recent advances in actinorhizal symbiosis signaling. Plant Mol Biol.  https://doi.org/10.1007/s11104-016-0450-2
  124. Fry AJ, Palmer MR, Rand DM (2004) Variable fitness effects of Wolbachia infection in Drosophila melanogaster. Heredity 93:379–389PubMedCrossRefPubMedCentralGoogle Scholar
  125. Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399:541–548PubMedCrossRefPubMedCentralGoogle Scholar
  126. Fuhrman JA, Noble RT (1995) Viruses and protists cause similar bacterial mortality in coastal water. Limnol Oceanogr 40:1236–1242CrossRefGoogle Scholar
  127. Fukatsu T, Nikoh N, Kawai R, Koga R (2000) The secondary endosymbiotic bacterium of the pea aphid Acyrthosiphon pisum (Insecta: Homoptera). Appl Environ Microbiol 66:2748–2758PubMedPubMedCentralCrossRefGoogle Scholar
  128. Garcia JL, Patel BKC, Ollivier B (2000) Phylogenetic and ecological diversity of methanogenic archaea. Anaerobe 6:205–226PubMedCrossRefPubMedCentralGoogle Scholar
  129. Gause GF (1935) Vérifications expérimentales de la théorie mathématique de la lutte pour la vie. Actual Scient ind 277:1–63Google Scholar
  130. Geiger A, Cuny G, Frutos R (2005) Two tsetse fly species, Glossina palpalis gambiensis and Glossina morsitans morsitans, carry genetically distinct populations of the secondary symbiont Sodalis glossinidius. Appl Environ Microbiol 71:8941–8943PubMedPubMedCentralCrossRefGoogle Scholar
  131. Geiger A, Ravel S, Mateille T, Janelle J, Patrel D, Cuny G, Frutos R (2007) Vector competence of Glossina palpalis gambiensis for Trypanosoma brucei s.l. and genetic diversity of the symbiont Sodalis glossinidius. Mol Biol Evol 24:102–109PubMedCrossRefPubMedCentralGoogle Scholar
  132. Geiger A, Fardeau ML, Grebaut P, Vatunga G, Josénando T, Herder S, Cuny G, Truc P, Ollivier B (2009) First isolation of Enterobacter, Enterococcus, and Acinetobacter spp. as inhabitants of the tsetse fly (Glossina palpalis palpalis) midgut. Infect Genet Evol 9:1364–1370PubMedCrossRefPubMedCentralGoogle Scholar
  133. Geiger A, Fardeau ML, Falsen E, Ollivier B, Cuny G (2010) Serratia glossinae sp. nov., isolated from the midgut of the tsetse fly Glossina palpalis gambiensis. Int J Syst Evol Microbiol 60:1261–1265PubMedCrossRefGoogle Scholar
  134. Geiger A, Fardeau ML, Njiokou F, Joseph M, Asonganyi T, Ollivier B, Cuny G (2011) Bacterial diversity associated with populations of Glossina spp. from Cameroon and distribution within the campo sleeping sickness focus. Microb Ecol 62:632–643PubMedCrossRefGoogle Scholar
  135. Gemerden V (1993) Microbial mats: a joint venture. Mar Geol 113:3–25CrossRefGoogle Scholar
  136. Genre A, Chabaud M, Balzergue C, Puech-Pagès V, Novero M, Rey T, Fournier J, Rochange S, Bécard G, Bonfante P, Barker DG (2013) Short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear Ca2+ spiking in Medicago truncatula roots and their production is enhanced by strigolactone. New Phytol 198:190–202.  https://doi.org/10.1111/nph.12146 CrossRefPubMedGoogle Scholar
  137. Gensollen T, Iyer SS, Kasper DL, Blumberg RS (2016) How colonization by microbiota in early life shapes the immune system. Science 352(6285):539–544.  https://doi.org/10.1126/science.aad9378 CrossRefPubMedPubMedCentralGoogle Scholar
  138. Gherbi H, Markmann K, Svistoonoff S, Estevan J, Autran D, Giczey G, Auguy F, Péret B, Laplaze L, Franche C, Parniske M, Bogusz D (2008) SymRK defines a common genetic basis for plant root endosymbioses with arbuscular mycorrhiza fungi, rhizobia, and Frankia bacteria. Proc Natl Acad Sci U S A 105:4928–4932.  https://doi.org/10.1073/pnas.0710618105 CrossRefPubMedPubMedCentralGoogle Scholar
  139. Giannone RJ, Huber H, Karpinets T, Heimerl T, Küper U, Rachel R, Keller M, Hettich RL, Podar M (2011) Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans-Ignicoccus hospitalis relationship. PLoS One 6(8):e22942.  https://doi.org/10.1371/journal.pone.0022942 CrossRefPubMedPubMedCentralGoogle Scholar
  140. Giannone RJ, Wurch LL, Heimerl T, Martin S, Yang Z, Huber H, Rachel R, Hettich RL, Podar M (2015) Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans. ISME J 9:101–114PubMedCrossRefGoogle Scholar
  141. Gilboa-Garber N (1972) Purification and properties of hemagglutinin from Pseudomonas aeruginosa and its reaction with human blood cells. Biochim Biophys Acta 273:165–173PubMedCrossRefPubMedCentralGoogle Scholar
  142. Giraud E, Moulin L, Vallenet D, Barbe V, Cytryn E, Avarre JC et al (2007) Legumes symbioses: absence of nod genes in photosynthetic bradyrhizobia. Science 316:1307–1312.  https://doi.org/10.1126/science.1139548 CrossRefPubMedPubMedCentralGoogle Scholar
  143. Gjermansen M, Nilsson M, Yang L, Tolker-Nielsen T (2010) Characterization of starvation-induced dispersion in Pseudomonas putida biofilms: genetic elements and molecular mechanisms. Mol Microbiol 75:815–826PubMedCrossRefPubMedCentralGoogle Scholar
  144. Glaser RL, Meola MA (2010) The native Wolbachia endosymbionts of Drosophila melanogaster and Culex quinquefasciatus increase host resistance to West Nile virus infection. PLoS One 5:e11977PubMedPubMedCentralCrossRefGoogle Scholar
  145. Godfroy O, Debellé F, Timmers T, Rosenberg C (2006) A rice calcium- and calmodulin-dependent protein kinase restores nodulation to a legume mutant. Mol Plant-Microbe Interact 19:495–501.  https://doi.org/10.1094/MPMI-19-0495 CrossRefPubMedPubMedCentralGoogle Scholar
  146. Gomez de Aguero M, Ganal-Vonarburg SC, Fuhrer T, Rupp S, Uchimura Y, Li H, Steinert A, Heikenwalder M, Hapfelmeier S, Sauer U, McCoy KD, Macpherson AJ (2016) The maternal microbiota drives early postnatal innate immune development. Science 351(6279):1296–1302.  https://doi.org/10.1126/science.aad2571 CrossRefPubMedPubMedCentralGoogle Scholar
  147. González JM, Sherr EB, Sherr BF (1990) Size selective grazing on bacteria by natural assemblages of estuarine flagellates and ciliates. Appl Environ Microbiol 56:583–589PubMedPubMedCentralGoogle Scholar
  148. Good AG, Beatty PH (2011) Fertilizing nature: a tragedy of excess in the commons. PLoS Biol 9:e1001124. doi:10.1371/journal.pbio.1001124CrossRefGoogle Scholar
  149. Gorby YA, Yanina S, McLean JS, Rosso KM, Moyles D, Dohnalkova A, Beveridge TJ, Chang IS, Kim BH, Kim KS, Culley DE, Reed SB, Romine MF, Saffarini DA, Hill EA, Shi L, Elias DA, Kennedy DW, Pinchuk G, Watanabe K, Ishii S, Logan B, Nealson KH, Fredrickson JK (2006) Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. Proc Natl Acad Sci U S A 103:11358–11363PubMedPubMedCentralCrossRefGoogle Scholar
  150. Gotoh T, Sugasawa J, Noda H, Kitashima Y (2007) Wolbachia-induced cytoplasmic incompatibility in Japanese populations of Tetranychus urticae (Acari: Tetranychidae). Exp Appl Acarol 42:1–16PubMedCrossRefPubMedCentralGoogle Scholar
  151. Gould SB, Waller RF, McFadden GI (2008) Plastid evolution. Annu Rev Plant Biol 59:491–517PubMedCrossRefPubMedCentralGoogle Scholar
  152. Graham PH, Vance CP (2000) Nitrogen fixation in perspective: an overview of research and extension needs. Field Crops Res 65:93–106.  https://doi.org/10.1016/S0378-4290(99)00080-5 CrossRefGoogle Scholar
  153. Gray MW, Lang BF, Burger G (2004) Mitochondria of protists. Annu Rev Genet 38:477–524PubMedCrossRefPubMedCentralGoogle Scholar
  154. Guerrero R, Pedrós-Alió C, Esteves I, Mas J, Chase D, Margulis L (1986) Predatoryprokaryotes: predation and primary consumption evolved in bacteria. Proc Natl Acad Sci U S A 83:2138–2142PubMedPubMedCentralCrossRefGoogle Scholar
  155. Gupta V, Smemo KA, Yavitt J, Fowle DA, Branfireun BA, Basiliko N (2013) Stable isotopes reveal widespread anaerobic methane oxidation across latitude and peatland type. Environ Sci Technol 47:8273–8279PubMedGoogle Scholar
  156. Gutjahr C, Parniske M (2013) Cell and developmental biology of arbuscular mycorrhiza symbiosis. Annu Rev Cell Dev Biol 29:593–617.  https://doi.org/10.1146/annurev-cellbio-101512-122413 CrossRefPubMedGoogle Scholar
  157. Hahn D (2008) Polyphasic taxonomy of the genus Frankia. In: Pawlowski K, Newton WE (eds) Nitrogen –fixing actinorhizal symbioses. Springer, New York, pp 25–45.  https://doi.org/10.1007/978-1-4020-3547-0-2 CrossRefGoogle Scholar
  158. Hamerly T, Tripet BP, Tigges M, Giannone RJ, Wurch L, Hettich RL, Podar M, Copie V, Bothner B (2015) Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis. Metabolomics 11:895–907.  https://doi.org/10.1007/s11306-014-0747-6 CrossRefPubMedGoogle Scholar
  159. Hamidou Soumana I, Berthier D, Tchicaya B, Thevenon S, Njiokou F, Cuny G, Geiger A (2013) Population dynamics of Glossina palpalis gambiensis symbionts, Sodalis glossinidius, and Wigglesworthia glossinidia, throughout host-fly development. Infect Genet Evol 13:41–48PubMedCrossRefGoogle Scholar
  160. Hamidou Soumana I, Loriod B, Ravel S, Tchicaya B, Simo G, Rihet P, Geiger A (2014a) The transcriptional signatures of Sodalis glossinidius in the Glossina palpalis gambiensis flies negative for Trypanosoma brucei gambiense contrast with those of this symbiont in tsetse flies positive for the parasite: possible involvement of a Sodalis-hosted prophage in fly Trypanosoma refractoriness? Infect Genet Evol 24:41–56PubMedCrossRefGoogle Scholar
  161. Hamidou Soumana I, Tchicaya B, Loriod B, Rihet P, Geiger A (2014b) Identification of overexpressed genes in Sodalis glossinidius inhabiting trypanosome-infected self-cured tsetse flies. Front Microbiol 5:255PubMedPubMedCentralGoogle Scholar
  162. Hamidou Soumana I, Tchicaya B, Simo G, Geiger A (2014c) Comparative gene expression of Wigglesworthia inhabiting non-infected and Trypanosoma brucei gambiense-infected Glossina palpalis gambiensis flies. Front Microbiol 5:620PubMedPubMedCentralGoogle Scholar
  163. Hamidou Soumana I, Klopp C, Ravel S, Nabihoudine I, Tchicaya B, Parrinello H, Abate L, Rialle S, Geiger A. 2015. RNA-seq de novo assembly reveals differential gene expression in Glossina palpalis gambiensis infected with Trypanosoma brucei gambiense vs. non-infected and self-cured flies. Front Microbiol. 6:1259Google Scholar
  164. Hamidou Soumana I, Tchicaya B, Rialle S, Parrinello H, Geiger A (2017) Comparative genomics of Glossina palpalis gambiensis and G. morsitans morsitans to reveal gene orthologs involved in infection by Trypanosoma brucei gambiense. Frontiers Microbiol in pressGoogle Scholar
  165. Hamilton JJ, Contreras M, Reed JL (2015) Thermodynamics and H2 transfer in a methanogenic community. PLoS Comput Biol 11(7):e1004364.  https://doi.org/10.1371/journal.pcbi.1004364 CrossRefPubMedPubMedCentralGoogle Scholar
  166. Hansen SR, Hubbel SP (1980) Single-nutrient microbial competition : qualitative agreement between experimental and theoretically forecast outcomes. Science 207:1491–1493PubMedCrossRefGoogle Scholar
  167. Hansen SK, Rainey PB, Haagensen JAJ, Molin S (2007) Evolution of species interactions in a biofilm community. Nature 445.  https://doi.org/10.1038/nature05514 PubMedCrossRefPubMedCentralGoogle Scholar
  168. Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Rev:439–471Google Scholar
  169. Haroon MF, Hu SH, Shi Y, Imelfort M, Keller J, Hugenholtz P, Yuan Z, Tyson GW (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500:567–570CrossRefGoogle Scholar
  170. Hedges LM, Brownlie JC, O’Neill SL, Johnson KN (2008) Wolbachia and virus protection in insects. Science 322:702–702PubMedCrossRefPubMedCentralGoogle Scholar
  171. Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D (2009) Germ warfare in a microbial mat Community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLoS One 4(1):e4169PubMedPubMedCentralCrossRefGoogle Scholar
  172. Hendrix R (1999) The long evolutionary reach of viruses. Curr Biol 9:9914–9917CrossRefGoogle Scholar
  173. Hertig M (1936) The rickettsia, Wolbachia pipientis (gen. Et sp. n.) and associated inclusions of the mosquito Culex pipiens. Parasitology 28:454–486CrossRefGoogle Scholar
  174. Hertig M, Wolbach SB (1924) Studies on rickettsia-like microorganisms in insects. J Med Res 44:329–374PubMedPubMedCentralGoogle Scholar
  175. Hertle R, Hilger M, Weingardt-Kocher S, Walev I (1999) Cytotoxic action of Serratia marcescens hemolysin on human epithelial cells. Infect Immun 67:817–825PubMedPubMedCentralGoogle Scholar
  176. Hilgenboecker K, Hammerstein P, Schlattmann P, Telschow A, Werren JH (2008) How many species are infected with Wolbachia?--a statistical analysis of current data. FEMS Microbiol Lett 281:215–220PubMedPubMedCentralCrossRefGoogle Scholar
  177. Hiroki M, Kato Y, Kamito T, Miura K (2002) Feminization of genetic males by a symbiotic bacterium in a butterfly, Eurema hecabe (Lepidoptera: Pieridae). Naturwissenschaften 89:167–170PubMedCrossRefPubMedCentralGoogle Scholar
  178. Hoffmann AA, Turelli M, Simmons GM (1986) Unidirectional incompatibility between populations of Drosophila simulans. Evolution 40:692–701PubMedCrossRefPubMedCentralGoogle Scholar
  179. Hoffmann AA, Turelli M, Harshman LG (1990) Factors affecting the distribution of cytoplasmic incompatibility in Drosophila simulans. Genetics 126:933–948PubMedPubMedCentralGoogle Scholar
  180. Hornett EA, Charlat S, Duplouy AM, Davies N, Roderick GK, Wedell N, Hurst GD (2006) Evolution of male-killer suppression in a natural population. PLoS Biol 4:e283PubMedPubMedCentralCrossRefGoogle Scholar
  181. Hosokawa T, Koga R, Kikuchi Y, Meng XY, Fukatsu T (2010) Wolbachia as a bacteriocyte associated nutritional mutualist. Proc Natl Acad Sci U S A 107:769–774PubMedCrossRefPubMedCentralGoogle Scholar
  182. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67PubMedCrossRefPubMedCentralGoogle Scholar
  183. Huber H, Küper U, Daxer S, Rachel R (2012) The unusual cell biology of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis. Antonie Van Leeuwenhoek 102:203–219.  https://doi.org/10.1007/s10482-012-9748-5 CrossRefPubMedPubMedCentralGoogle Scholar
  184. Human Microbiome Project (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214.  https://doi.org/10.1038/nature11234 CrossRefGoogle Scholar
  185. Imachi H, Sekiguchi Y, Kamagata Y, Loy A, Qiu YL, Hugenholtz P, Kimura N, Wagner M, Ohashi A, Harada H (2006) Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl Environ Microbiol 72:2080–2091PubMedPubMedCentralCrossRefGoogle Scholar
  186. International Glossina Genome Initiative (2014) Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science 344:380–386PubMedCentralCrossRefGoogle Scholar
  187. Jackson BE, Bhupathiraju VK, Tanner RS, Woese CR, McInerney MJ (1999) Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms. Arch Microbiol 171:107–114PubMedCrossRefPubMedCentralGoogle Scholar
  188. Jackson AP, Sanders M, Berry A, McQuillan J, Aslett MA, Quail MA, Chukualim B, Capewell P, MacLeod A, Melville SE, Gibson W, Barry JD, Berriman M, Hertz-Fowler C (2010) The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis. PLoS Negl Trop Dis 4:e658PubMedPubMedCentralCrossRefGoogle Scholar
  189. Jaenike J, Brekke TD (2011) Defensive endosymbionts: a cryptic trophic level in community ecology. Ecol Lett 14:150–155PubMedCrossRefPubMedCentralGoogle Scholar
  190. Jaenike J, Dyer KA (2008) No resistance to male-killing Wolbachia after thousands of years of infection. J Evol Biol 21:1570–1577PubMedCrossRefPubMedCentralGoogle Scholar
  191. Jaenike J, Unckless R, Cockburn SN, Boelio LM, Perlman SJ (2010) Adaptation via symbiosis: recent spread of a Drosophila defensive symbiont. Science 329:212–215PubMedCrossRefPubMedCentralGoogle Scholar
  192. Jahn U, Gallenberger M, Paper W, Junglas B, Eisenreich W, Stetter KO, Rachel R, Huber H (2008) Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea. J Bacteriol 190(5):1743–1750.  https://doi.org/10.1128/JB.01731-07 CrossRefPubMedPubMedCentralGoogle Scholar
  193. Jasti S, Sieracki ME, Poulton NJ, Giewat MW, Rooney-Varga JN (2005) Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton. Appl Environ Microbiol 71:3483–3494PubMedPubMedCentralCrossRefGoogle Scholar
  194. Jeffery IB, Claesson MJ, O’Toole PW, Shanahan F (2012) Categorization of the gut microbiota: enterotypes or gradients? Nat Rev Microbiol 10(9):591–592PubMedCrossRefPubMedCentralGoogle Scholar
  195. Jeyaprakash A, Hoy MA (2000) Long PCR improves Wolbachia DNA amplification: wsp sequences found in 76% of sixty-three arthropod species. Insect Mol Biol 9:393–405PubMedCrossRefPubMedCentralGoogle Scholar
  196. Jiang SC, Paul JH (1998) Significance of lysogeny in the marine environments: studies with isolates and a model of lysogenic phage-production. Microb Ecol 35:235–243PubMedCrossRefPubMedCentralGoogle Scholar
  197. Jiggins FM, Hurst GD, Schulenburg JH, Majerus ME (2001) Two male-killing Wolbachia strains coexist within a population of the butterfly Acraea encedon. Heredity 86:161–166PubMedCrossRefPubMedCentralGoogle Scholar
  198. Jimenez E, Marin ML, Martin R, Odriozola JM, Olivares M, Xaus J, Fernandez L, Rodriguez JM (2008) Is meconium from healthy newborns actually sterile? Res Microbiol 159(3):187–193.  https://doi.org/10.1016/j.resmic.2007.12.007 CrossRefPubMedPubMedCentralGoogle Scholar
  199. Jones EO, White A, Boots M (2007) Interference and the persistence of vertically transmitted parasites. J Theor Biol 246:10–17PubMedCrossRefPubMedCentralGoogle Scholar
  200. Joyce SA, MacSharry J, Casey PG, Kinsella M, Murphy EF, Shanahan F, Hill C, Gahan CG (2014) Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut. Proc Natl Acad Sci U S A 111(20):7421–7426.  https://doi.org/10.1073/pnas.1323599111 CrossRefPubMedPubMedCentralGoogle Scholar
  201. Kadouri DE, To K, Shanks RMQ, Doi Y (2013) Predatory bacteria: a potential ally against multidrug-resistant gram-negative pathogens. PLoS One 8(5):e63397PubMedPubMedCentralCrossRefGoogle Scholar
  202. Kageyama D, Nishimura G, Hoshizaki S, Ishikawa Y (2002) Feminizing Wolbachia in an insect, Ostrinia furnacalis (Lepidoptera: Crambidae). Heredity 88:444–449PubMedCrossRefPubMedCentralGoogle Scholar
  203. Kamada N, Seo SU, Chen GY, Nunez G (2013) Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol 13(5):321–335.  https://doi.org/10.1038/nri3430 CrossRefPubMedPubMedCentralGoogle Scholar
  204. Kambris Z, Cook PE, Phuc HK, Sinkins SP (2009) Immune activation by life-shortening Wolbachia and reduced filarial competence in mosquitoes. Science 326:134–136PubMedPubMedCentralCrossRefGoogle Scholar
  205. Kambris Z, Blagborough AM, Pinto SB, Blagrove MS, Godfray HC, Sinden RE, Sinkins SP (2010) Wolbachia stimulates immune gene expression and inhibits plasmodium development in Anopheles gambiae. PLoS Pathog 6:e1001143PubMedPubMedCentralCrossRefGoogle Scholar
  206. Kanzler BE, Pfanes KR, Vogl K, Overmann J (2005) Molecular characterization of the nonphotosynthetic partner bacterium in the consortium ‘Chlorochromatium aggregatum. Appl Environ Microb 71:7434–7441CrossRefGoogle Scholar
  207. Keane R, Berleman J (2016) The predatory life cycle of Myxococcus xanthus. Microbiology 162:1–11.  https://doi.org/10.1099/mic.0.00020 CrossRefPubMedPubMedCentralGoogle Scholar
  208. Keller GP, Windsor DM, Saucedo JM, Werren JH (2004) Reproductive effects and geographical distributions of two Wolbachia strains infecting the Neotropical beetle, Chelymorpha alternans Boh. (Chrysomelidae, Cassidinae). Mol Ecol 13:2405–2420PubMedCrossRefPubMedCentralGoogle Scholar
  209. Kolev NG, Franklin JB, Carmi S, Shi H, Michaeli S, Tschudi C (2010) The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog 6:e1001090PubMedPubMedCentralCrossRefGoogle Scholar
  210. Kosuta S, Chabaud M, Lougnon G, Gough C, Dénarié J, Barker DG, Bécard G (2003) A diffusible factor from arbuscular mycorrhizal fungi induces symbiosis-specific MtENOD11 expression in roots of Medicago truncatula. Plant Physiol 131:952–962.  https://doi.org/10.1104/pp.011882 CrossRefPubMedPubMedCentralGoogle Scholar
  211. Krumholz LR, Bryant MP (1986) Syntrophococcus sucromutans sp. nov. gen. Nov. uses carbohydrates as electron donors and formate, methoxymonobenzenoids or Methanobrevibacter as electron acceptor systems. Arch Microbiol 143:313–318CrossRefGoogle Scholar
  212. Lavin M, Herendeen PS, Wojciechowski MF (2005) Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst Biol 54:575–594.  https://doi.org/10.1080/10635150590947131 CrossRefPubMedPubMedCentralGoogle Scholar
  213. Lawrence JG, Hatfull GF, Hendrix RW (2002) Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 184:4891–4905PubMedPubMedCentralCrossRefGoogle Scholar
  214. Lazaro JE, Nitcheu J, Predicala RZ, Mangalindan GC, Nesslany F, Marzin D, Concepcion GP, Diquet B (2002) Heptyl prodigiosin, a bacterial metabolite is antimalarial in vivo and non-mutagenic in vitro. J NatToxins 11:367–377Google Scholar
  215. Leadbetter ER, Foster JW (1958) Studies on some methane-utilizing bacteria. Archiv Mikrobio 30:91–118CrossRefGoogle Scholar
  216. Lebba V et al (2014) Bdellovibrio bacteriovorus directly attacks Pseudomonas aeruginosa and Staphylococcus aureus cystic fibrosis isolates. Front Microbiol 5:1–9., article 280.  https://doi.org/10.3389/fmicb.2014.00280 CrossRefGoogle Scholar
  217. LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M (2013) Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol 24(2):160–168.  https://doi.org/10.1016/j.copbio.2012.08.005 CrossRefPubMedPubMedCentralGoogle Scholar
  218. Levin BR, Bull JJ (2004) Population and evolutionary dynamics of phage therapy. Nat Rev Microb 2:166–173CrossRefGoogle Scholar
  219. Lewis G, Schrire B, Mackind B, Lock M (2005) Legumes of the world. Royal Botanic Gardens, Kew, UKGoogle Scholar
  220. Li H-L, Wang W, Mortimer PE et al (2015) Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change. Sci Rep 5:14023.  https://doi.org/10.1038/srep14023 CrossRefPubMedPubMedCentralGoogle Scholar
  221. Lidicker WZA (1979) Clarification of interactions in ecological systems. Bioscience 29:475–477CrossRefGoogle Scholar
  222. Lill R, Kispal G (2000) Maturation of cellular Fe-S proteins: an essential function of mitochondria. Trends Biochem Sci 25:352–356PubMedCrossRefPubMedCentralGoogle Scholar
  223. Lindh JM, Lehane MJ (2011) The tsetse fly Glossina fuscipes fuscipes (Diptera: Glossina) harbours a surprising diversity of bacteria other than symbionts. Antonie Van Leeuwenhoek 99:711–720PubMedCrossRefGoogle Scholar
  224. Liu Z et al (2013) Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium “Chlorochromatium aggregatum”. Genome Biol 14:R127.  https://doi.org/10.1186/gb-2013-14-11-r127 CrossRefPubMedPubMedCentralGoogle Scholar
  225. Liu Z, Niu H, Wu S, Huang R (2014) CsgD regulatory network in a bacterial trait-altering biofilm formation. Emerg Microbes Infect 3:e1.  https://doi.org/10.1038/emi.2014.1 CrossRefPubMedPubMedCentralGoogle Scholar
  226. Lively CM, Clay K, Wade MJ, Fuqua C (2005) Competitive co-existence of vertically and horizontally transmitted parasites. Evol Ecol Res 7:1183–1190Google Scholar
  227. Lloyd-Price J, Abu-Ali G, Huttenhower C (2016) The healthy human microbiome. Genome Med 8(1):51.  https://doi.org/10.1186/s13073-016-0307-y CrossRefPubMedPubMedCentralGoogle Scholar
  228. Lønborg C, Middelboe M, Brussaard CP (2013) Viral lysis of Micromonas pusilla: impacts on dissolved organic matter production and composition. Biogeochemistry 116:231–240CrossRefGoogle Scholar
  229. Long SR (1996) Rhizobium symbiosis: nod factors in perspective. Plant Cell 8:1885–1898.  https://doi.org/10.1105/tpc.8.10.1885 CrossRefPubMedPubMedCentralGoogle Scholar
  230. Mackinder LCM, Worthy C, Biggi G, Hall M, Ryan KP, Varsani A et al (2009) A unicellular algal virus, Emiliania huxleyi virus 86, exploits an animal-like infection strategy. J Gen Virol 90:2306–2316PubMedCrossRefGoogle Scholar
  231. Mackowiak PA (2013) Recycling metchnikoff: probiotics, the intestinal microbiome and the quest for long life. Front Public Health 1:52.  https://doi.org/10.3389/fpubh.2013.00052 CrossRefPubMedPubMedCentralGoogle Scholar
  232. Madigan MT, Martinko JM, Bender KS, Buckley DH, Stahl DA, Brock T (2015) Brock Biology of Microorganisms (14th Edition) Pearson EducationGoogle Scholar
  233. Maeda H, Morihara K (1995) Serralysin and related bacterial proteinases. Methods Enzymol 248:395–413PubMedCrossRefPubMedCentralGoogle Scholar
  234. Maillet F, Poinsot V, André O, Puech-Pagés V, Haout A, Gueunier M, Cromer L, Giraudet D, Formey D, Niebel A, Martinez EA, Driguez H, Bécard G, Dénarié J (2011) Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza. Nature 469:58–63.  https://doi.org/10.1038/nature09622 CrossRefPubMedPubMedCentralGoogle Scholar
  235. Malele I, Nyingilili H, Lyaruu E, Tauzin M, Ollivier B, Fardeau M-L, Geiger A Bacterial diversity in the gut of G. pallidipes population from a non sleeping sickness focus in Tanzania and its implication for species’ vectorial capacity. BMC Microbiol in submissionGoogle Scholar
  236. Malkin SY, Meysman FJR (2015) Rapid redox signal transmission by “cable Bacteria” beneath a photosynthetic biofilm. Appl Environ Microbial 81(3):948–956CrossRefGoogle Scholar
  237. Malvankar NS, Lovley DR (2014) Microbial nanowires for bioenergy applications. Curr Opin Biotechnol 27:88–95PubMedCrossRefPubMedCentralGoogle Scholar
  238. Mao X, Jiang R, Xiao W, Yu J (2015) Use of surfactants for the remediation of contaminated soils: a review. J Hazard Mater 285:419–435PubMedCrossRefPubMedCentralGoogle Scholar
  239. Margulis L (1981) Symbiosis in cell evolution. W. H. Freeman and Co, San FranciscoGoogle Scholar
  240. Margulis L (1993) Symbiosis in cell evolution. Microbial communities in the Archaean and Proterozoic eons. W. H. Freeman and Co, New YorkGoogle Scholar
  241. Markmann K, Parniske M (2009) Evolution of root endosymbiosis with bacteria: how novel are nodules? Trends Plant Sci 14:77–86.  https://doi.org/10.1016/j.tplants.2008.11.009 CrossRefPubMedPubMedCentralGoogle Scholar
  242. Markmann K, Giczey G, Parniske M (2008) Functional adaptation of a plant receptor- kinase paved the way for the evolution of intracellular root symbioses with Bacteria. PLoS Biol 6:e68.  https://doi.org/10.1371/journal.pbio.0060068 CrossRefPubMedPubMedCentralGoogle Scholar
  243. Marsh JF, Rakocevic A, Mitra RM, Brocard L, Eschstruth A, Long SR, Schultze M, Ratet P, Oldroyd GE (2007) Medicago truncatula NIN is essential for rhizobial-independent nodule organogenesis induced by autoactive calcium/calmodulin-dependent protein kinase. Plant Physiol 144:324–335.  https://doi.org/10.1104/pp.106.093021 CrossRefPubMedPubMedCentralGoogle Scholar
  244. Martin MO (2002) Predatory prokaryotes: an emerging research opportunity. J Mol Microbiol Biotechnol 4(5):467–477PubMedPubMedCentralGoogle Scholar
  245. Mashburn-Warren LM, Whiteley M (2006) Special delivery: vesicle trafficking in prokaryotes. Mol Microbiol 61(4):839–846.  https://doi.org/10.1111/j.1365-2958.2006.05272.x CrossRefPubMedPubMedCentralGoogle Scholar
  246. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122(1):107–118.  https://doi.org/10.1016/j.cell.2005.05.007 CrossRefPubMedPubMedCentralGoogle Scholar
  247. Mbewe NJ, Mweempwa C, Guya S, Wamwiri FN (2015) Microbiome frequency and their association with trypanosome infection in male Glossina morsitans centralis of Western Zambia. Vet Parasitol 211:93–98PubMedCrossRefPubMedCentralGoogle Scholar
  248. McCutcheon JP, Moran NA (2007) Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. Proc Natl Acad Sci U S A 104:19392–19397PubMedPubMedCentralCrossRefGoogle Scholar
  249. McGenity TJ, Folwell BD, McKew BA, Sanni GO (2012) Marine crude-oil biodegradation : a central role for interspecies interactions. Aquat Biosyst 8(10).  https://doi.org/10.1186/2046-9063-8-10 PubMedPubMedCentralCrossRefGoogle Scholar
  250. McInerney JO, O’Connell MJ, Pisani D (2014) The hybrid nature of the Eukaryota and a consilient view of life on earth. Nat Rev Microbiol 12:449–455PubMedCrossRefPubMedCentralGoogle Scholar
  251. McInnerney MJ, Sieber JR, Gunsalus RP (2009) Syntrophy in anaerobic global carbon cycles. Curr Opin Biotechnol 20:623–632CrossRefGoogle Scholar
  252. Medina-Sanchez JM, Villar-Argaiz M, Carrillo P (2004) Neither with nor without you: a complex algal control on bacterioplankton in a high mountain lake. Limnol Oceanogr 49:1722–1733CrossRefGoogle Scholar
  253. Mercado TI, Colon-Whitt A (1982) Lysis of Trypanosoma cruzi by Pseudomonas fluorescens. AntimicrobAgents Chemother 22:1051–1057CrossRefGoogle Scholar
  254. Milucka J, Ferdelman TG, Polerecky L, Franzke D, Wegener G et al (2012) Zero-valent Sulphur is a key intermediate in marine methane oxidation. Nature 491:541–546CrossRefGoogle Scholar
  255. Min KT, Benzer S (1997) Wolbachia, normally a symbiont of Drosophila, can be virulent, causing degeneration and early death. Proc Natl Acad Sci U S A 94:10792–10796PubMedPubMedCentralCrossRefGoogle Scholar
  256. Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, Oldroyd GED, Long SR (2004) A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: gene identification by transcript-based cloning. Proc Natl Acad Sci U S A 101:4701–4705.  https://doi.org/10.1073/pnas.0400595101 CrossRefPubMedPubMedCentralGoogle Scholar
  257. Miwa H, Sun J, Oldroyd GED, Downie JA (2006) Analysis of nod-factor-induced calcium signaling in root hairs of symbiotically defective mutants of Lotus japonicus. Mol Plant-Microbe Interact 19:914–923.  https://doi.org/10.1094/MPMI-19-0914 CrossRefPubMedGoogle Scholar
  258. Moissl-Eichinger C, Hubert H (2011) Archaeal symbionts and parasites. Curr Opin Microbiol 14:364–370PubMedCrossRefGoogle Scholar
  259. Mondot S, Lepage P (2016) The human gut microbiome and its dysfunctions through the meta-omics prism. Ann N Y Acad Sci 1372(1):9–19.  https://doi.org/10.1111/nyas.13033 CrossRefPubMedGoogle Scholar
  260. Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3:371–394CrossRefGoogle Scholar
  261. Moore RL (1981) The biology of Hyphomicrobium and other prosthecate, budding bacteria. Annu Rev Microbiol 35:567–594PubMedCrossRefGoogle Scholar
  262. Moran NA (1996) Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A 93:2873–2878PubMedPubMedCentralCrossRefGoogle Scholar
  263. Moran NA, Munson MA, Baumann P, Ishikawa H (1993) A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts. Proc R Soc London Ser B 253:167–171CrossRefGoogle Scholar
  264. Moran NA, McCutcheon JP, Nakabachi A (2008) Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 42:165–190PubMedCrossRefPubMedCentralGoogle Scholar
  265. Moreira LA, Iturbe-Ormaetxe I, Jeffery JA, Lu G, Pyke AT, Hedges LM, Rocha BC, Hall-Mendelin S, Day A, Riegler M, Hugo LE, Johnson KN, Kay BH, McGraw EA, van den Hurk AF, Ryan PA, O’Neill SL (2009) A Wolbachia symbiont in Aedes aegypti limits infection with dengue, Chikungunya, and Plasmodium. Cell 139:1268–1278PubMedCrossRefPubMedCentralGoogle Scholar
  266. Moret Y, Juchault P, Rigaud T (2001) Wolbachia endosymbiont responsible for cytoplasmic incompatibility in a terrestrial crustacean: effects in natural and foreign hosts. Heredity 86:325–332PubMedCrossRefPubMedCentralGoogle Scholar
  267. Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C (2013) Microbial syntrophy: interaction for the common good. FEMS Microbiol Rev 37:384–406.  https://doi.org/10.1111/1574-6976.12019 CrossRefPubMedPubMedCentralGoogle Scholar
  268. Moss M (2002) Bacterial pigments. Microbiologist 3:10–12Google Scholar
  269. Mouton L, Dedeine F, Henri H, Boulétreau M, Profizi N, Vavre F (2004) Virulence, multiple infections and regulation of symbiotic population in the Wolbachia/Asobara tabida symbiosis. Genetics 168:181–189PubMedPubMedCentralCrossRefGoogle Scholar
  270. Mueller N, Griffin BM, Stingl U, Schink B (2008) Dominant sugar utilizers in sediment of Lake Constance depend on syntrophic cooperation with methanogenic partner organisms. Environ Microbiol 10:1501–1511CrossRefGoogle Scholar
  271. Müller J, Overmann J (2011) Close interspecies interactions between prokaryotes from sulfureous environments. Front Microbiol 2:146.  https://doi.org/10.3389/fmicb.2011.0014 CrossRefPubMedPubMedCentralGoogle Scholar
  272. Mus F, Crook MB, Garcia K, Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu M-H, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané J-M, Peters JW (2016) Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Appl Environ Microbiol 82:3698–3710.  https://doi.org/10.1128/AEM.01055-16 CrossRefPubMedPubMedCentralGoogle Scholar
  273. 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 314:267–267PubMedCrossRefPubMedCentralGoogle Scholar
  274. Nakagawa T, Imaizumi-Anraku H (2015) Rice arbuscular mycorrhiza as a tool to study the molecular mechanisms of fungal symbiosis and a potential target to increase productivity. Rice 8:32.  https://doi.org/10.1186/s12284-015-0067-0 CrossRefPubMedPubMedCentralGoogle Scholar
  275. Negri I, Pellecchia M, Mazzoglio PJ, Patetta A, Alma A (2006) Feminizing Wolbachia in Zyginidia pullula (Insecta, Hemiptera), a leafhopper with an XX/X0 sex-determination system. Proc R Soc London Ser B 273:2409–2416CrossRefGoogle Scholar
  276. Nielsen LP, Risgaard-Petersen N, Fossing H, Christensen PB, Sayama M (2010) Electric currents couple spatially separated biogeochemical processes in marine sediment. Nature 463:1071–1074.  https://doi.org/10.1038/nature08790 CrossRefPubMedGoogle Scholar
  277. Nogge G (1982) Significance of symbionts for the maintenance of an optional nutritional state for successful reproduction in hematophagous arthropods. Parasitology 82:299–304Google Scholar
  278. Normand P, Orso S, Cournoyer B, Jeannin P, Chapelon C, Dawson J, Evtushenko L, Misra AK (1996) Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int J Syst Bacteriol 46:1–9.  https://doi.org/10.1099/00207713-46-1-1 CrossRefPubMedGoogle Scholar
  279. Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR (2007) Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 17:7–15.  https://doi.org/10.1101/gr.5798407 CrossRefPubMedPubMedCentralGoogle Scholar
  280. Nowack EC, Melkonian M, Glockner G (2008) Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes. Curr Biol 18:410–418PubMedCrossRefGoogle Scholar
  281. Nzila A (2013) Update on the cometabolism of organic pollutants by bacteria. Environ Poll 178:474–482CrossRefGoogle Scholar
  282. O’Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7:688–693PubMedPubMedCentralCrossRefGoogle Scholar
  283. O’Neill SL, Gooding RH, Aksoy S (1993) Phylogenetically distant symbiotic microorganisms reside in Glossina midgut and ovary tissues. Med Vet Entomol 7:377–383PubMedCrossRefGoogle Scholar
  284. O’Toole PW, Jeffery IB (2015) Gut microbiota and aging. Science 350(6265):1214–1215.  https://doi.org/10.1126/science.aac8469 CrossRefPubMedGoogle Scholar
  285. Okazaki S, Noisangiam R, Okubo T, Kaneko T, Oshima K, Hattori M, Teamtisong K, Songwattana P, Tittabutr P, Boonkerd N, Saeki K, Sato S, Uchiumi T, Minamisawa K, Teaumroong N (2015) Genome analysis of a novel Bradyrhizobium sp. DOA9 carrying a symbiotic plasmid. PLoS One 10:e0117392. doi:10.1371/journal.pone.0117392Google Scholar
  286. Oldroyd GE (2013) Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants. Nature Rev. Microbiol. 11:252–263.  https://doi.org/10.1038/nrmicro2990 CrossRefGoogle Scholar
  287. Oldroyd GE, Murray JD, Poole PS, Downie JA (2011) The rules of engagement in the legume-rhizobial symbiosis. Annu Rev Genet 45:119–144.  https://doi.org/10.1146/annurev-genet-110410-132549 CrossRefPubMedGoogle Scholar
  288. Oliver KM, Russell JA, Moran NA, Hunter MS (2003) Facultative bacterial symbionts in aphids confer resistance to parasitic wasps. Proc Natl Acad Sci U S A 100:1803–1807PubMedPubMedCentralCrossRefGoogle Scholar
  289. Oliver KM, Campos J, Moran NA, Hunter MS (2008) Population dynamics of defensive symbionts in aphids. Proc R Soc B Biol Sci 275:293–299CrossRefGoogle Scholar
  290. Oliver KM, Degnan PH, Hunter MS, Moran NA (2009) Bacteriophages encode factors required for protection in a symbiotic mutualism. Science 325:992–994PubMedPubMedCentralCrossRefGoogle Scholar
  291. Op den Camp, R.H. (2012). Evolution of rhizobium symbiosis. Thesis, Wageningen University, ISBN 978-94-6137-198-2Google Scholar
  292. Op den Camp R, Streng A, De Mita S, Cao Q, Polone E et al (2011) LysM-type mycorrhizal receptor recruited for rhizobium symbiosis in nonlegume Parasponia. Science 331:909–912.  https://doi.org/10.1126/science.1198181 CrossRefPubMedPubMedCentralGoogle Scholar
  293. Op den Camp RH, Polone E, Fedorova E et al (2012) Nonlegume Parasponia andersonii deploys a broad rhizobium host range strategy resulting in largely variable symbiotic effectiveness. Mol Plant-Microbe Interact 25:954–963PubMedCrossRefGoogle Scholar
  294. Ostaff MJ, Stange EF, Wehkamp J (2013) Antimicrobial peptides and gut microbiota in homeostasis and pathology. EMBO Mol Med 5(10):1465–1483.  https://doi.org/10.1002/emmm.201201773 CrossRefPubMedPubMedCentralGoogle Scholar
  295. Overmann J, Schubert K (2002) Phototrophic consortia: model systems for symbiotic interrelations between prokaryotes. Arch Microbiol 177:201–208PubMedCrossRefGoogle Scholar
  296. Paerl H, Pinckney J (1996) A mini-review of microbial consortia: their roles in aquatic production and biogeochemical cycling. Microb Ecol 31:225–247PubMedCrossRefGoogle Scholar
  297. Pagé A, Tivey MK, Stakes DS, Reysenbach AL (2008) Temporal and spatial archaeal colonization of hydrothermal vent deposits. Environ Microbiol 10(4):874–884PubMedCrossRefGoogle Scholar
  298. Pais R, Lohs C, Wu YN, Wang JW, Aksoy S (2008) The obligate mutualist Wigglesworthia glossinidia influences reproduction, digestion, and immunity processes of its host, the tsetse fly. Appl Environ Microbiol 74:5965–5974PubMedPubMedCentralCrossRefGoogle Scholar
  299. Palesse S. (2014) Déterminisme de la Decision lysogénique au sein des communautés virales aquatiques: importance des fluctuations physiologiques et métaboliques. PhD Thesis, Université Clermont Auvergne, 165 pp.Google Scholar
  300. Pamp SJ, Gjermansen M, Tolker-Nielsen T (2007) The biofilm matrix: a sticky framework. In the biofilm mode of life: mechanisms and adaptations. Kjelleberg, S., and Givskov, M. (eds). Norfolk, UK: horizon. Bioscience:37–69Google Scholar
  301. Pasternak Z et al (2014) In and out: an analysis of epibiotic vs periplasmic bacterial predators. ISME J 8:625–635PubMedCrossRefPubMedCentralGoogle Scholar
  302. Pawlowski K, Bisseling T (1996) Rhizobial and Actinorhizal symbioses: what are the shared features? Plant Cell 8:1899–1913PubMedPubMedCentralCrossRefGoogle Scholar
  303. Pérez J, Moraleda-Muñoz A, Marcos-Torres FJ, Muñoz-Dorado J (2016) Bacterial predation: 75 years and counting! Environ Microbiol 18(3):766–779PubMedCrossRefPubMedCentralGoogle Scholar
  304. Pernthaler J (2005) Predation on prokaryotes in the water column and its ecological implications. Nature Review Microbiol 3:537–546CrossRefGoogle Scholar
  305. Persson T, Benson DR, Normand P, Vanden Heuvel B, Pujic P, Chertkov O, Teshima H, Bruce DC, Detter C, Tapia R, Han S, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Ivanova N, Pati A, Land ML, Pawlowski K, Berry AM (2011) Genome sequence of “Candidatus Frankia datiscae” Dg1, the uncultured microsymbiont from nitrogen-fixing root nodules of the dicot Datisca glomerata. J Bacteriol 193:7017–7018.  https://doi.org/10.1128/JB.06208-11 CrossRefPubMedPubMedCentralGoogle Scholar
  306. Persson T, Battenberg K, Demina IV, Vigil-Stenman T, Vanden Heuvel B, Pujic P, Facciotti MT, Wilbanks EG, O'Brien A, Fournier P, Cruz Hernandez MA, Mendoza Herrera A, Médigue C, Normand P, Pawlowski K, Berry AM (2015) Candidatus Frankia Datiscae Dg1, the actinobacterial microsymbiont of Datisca glomerata, expresses the canonical nod genes nodABC in symbiosis with its host plant. PLoS One e0127630:10.  https://doi.org/10.1371/journal.pone.0127630 CrossRefGoogle Scholar
  307. Pfennig N, Biebl H (1976) “Desulfuromonas acetoxidans” gen. Nov. and sp. nov., a new anaerobic, sulfur-reducing, acetate-oxidizing bacterium. Arch Microbiol 110:3–12PubMedCrossRefPubMedCentralGoogle Scholar
  308. Pradeep Ram AS, Sime-Ngando T (2010) Resources drive trade-off between viral lifestyles in the plankton: evidence from freshwater microbial microcosms. Environ Microbiol 12:467–479PubMedCrossRefPubMedCentralGoogle Scholar
  309. Pradeep Ram AS, Boucher D, Sime-Ngando T, Debroas D, Romagoux JC (2005) Phage bacteriolysis, protistan bacterivory potential, and bacterial production in a freshwater reservoir: coupling with temperature. Microb Ecol 50:64–72PubMedCrossRefPubMedCentralGoogle Scholar
  310. Prangishvili D, Forterre P, Garrett RA (2006) Viruses of the archaea: a unifying view. Nature Rev. Microbiol. 4:837–848CrossRefGoogle Scholar
  311. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium BP, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65PubMedPubMedCentralCrossRefGoogle Scholar
  312. Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394.  https://doi.org/10.1146/annurev.micro.57.030502.090759 CrossRefPubMedPubMedCentralGoogle Scholar
  313. Ravel S, Grébaut P, Cuisance D, Cuny G (2003) Monitoring the developmental status of Trypanosoma brucei gambiense in the tsetse fly by means of PCR analysis of anal and saliva drops. Acta Trop 88:161–165PubMedCrossRefPubMedCentralGoogle Scholar
  314. Raven JA (1997) Phagotrophy in phototrophs. Limnol Oceanogr 42:198–205CrossRefGoogle Scholar
  315. Reeburgh WS (1976) Methane consumption in Cariaco trench waters and sediments. Earth Planet Sci Lett 28:337–344CrossRefGoogle Scholar
  316. Reguera G, McCarthy KD, Metha T, Nicoli JS, Teominen MT, Loveley DR (2005) Extracellular electron transfer via microbial nanowires. Nature 435:1098–1101PubMedCrossRefPubMedCentralGoogle Scholar
  317. Reichert AS, Neupert W (2004) Mitochondriomics or what makes us breathe. Trends Genet 20:555–562PubMedCrossRefPubMedCentralGoogle Scholar
  318. Remigi P, Zhu J, Young JPW, Masson-Boivin C (2016) Symbiosis within Symbiosis: evolving nitrogen-fixing legume Symbionts. Trends Microbiol 24:63–75.  https://doi.org/10.1016/j.tim.2015.10.007 CrossRefPubMedGoogle Scholar
  319. Remy W, Taylor TN, Hass H, Kerp H (1994) Four hundred-million-year-old vesicular arbuscular mycorrhizae. Proc Natl Acad Sci U S A 91:11841–11843PubMedPubMedCentralCrossRefGoogle Scholar
  320. Reyes-Prieto A, Weber AP, Bhattacharya D (2007) The origin and establishment of the plastid in algae and plants. Annu Rev Genet 41:147–168PubMedCrossRefPubMedCentralGoogle Scholar
  321. Reynolds KT, Thomson LJ, Hoffmann AA (2003) The effects of host age, host nuclear background and temperature on phenotypic effects of the virulent Wolbachia strain popcorn in Drosophila melanogaster. Genetics 164:1027–1034PubMedPubMedCentralGoogle Scholar
  322. Riedinger N, Formolo MJ, Lyons TW, Henkel S, Beck A, Kasten S (2014) An inorganic geochemical argument for coupled anaerobic oxidation of methane and iron reduction in marine sediments. Geobiology 12:172–181PubMedCrossRefPubMedCentralGoogle Scholar
  323. Rigaud T, Moreau M (2004) A cost of Wolbachia-induced sex reversal and female-biased sex ratios: decrease in female fertility after sperm depletion in a terrestrial isopod. Proc R Soc London Ser B 271:1941–1946CrossRefGoogle Scholar
  324. Rigaud T, Juchault P, Mocquard JP (1997) The evolution of sex determination in isopod crustaceans. BioEssays 19:409–416CrossRefGoogle Scholar
  325. Rinke C et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437.  https://doi.org/10.1038/nature12352 CrossRefPubMedPubMedCentralGoogle Scholar
  326. Rio RV, Lefevre C, Heddi A, Aksoy S (2003) Comparative genomics of insect-symbiotic bacteria: influence of host environment on microbial genome composition. Appl Environ Microbiol 69:6825–6832PubMedPubMedCentralCrossRefGoogle Scholar
  327. Rio RV, Hu Y, Aksoy S (2004) Strategies of the home-team: symbioses exploited for vector-borne disease control. Trends Microbiol 12:325–336PubMedCrossRefPubMedCentralGoogle Scholar
  328. Rio RVM, Symula RE, Wang J, Lohs C, Wu YN, Snyder AK, Bjornson RD, Oshima K, Biehl BS, Perna NT, Hattori M, Aksoy S (2012) Insight into the transmission biology and species-specific functional capabilities of tsetse (Diptera: Glossinidae) obligate symbiont Wigglesworthia. MBio 3:e00240–e00211PubMedPubMedCentralCrossRefGoogle Scholar
  329. Rípodas C, Clúa J, Battaglia M, Baudin M, Niebel A, Zanetti ME, Blanco F (2014) Transcriptional regulators of legume-rhizobia symbiosis: nuclear factors Ys and GRAS are two for tango. Plant Signal Behav 9:e28847.  https://doi.org/10.4161/psb.28847 CrossRefPubMedPubMedCentralGoogle Scholar
  330. Rishiram R, Byung-Hyuk K, Dae-Hyun C, Hee-Mock O, Hee-Sik K (2016) Algae-bacteria interactions: evolution, ecology and emerging applications. Biotechnol Adv 34:14–29CrossRefGoogle Scholar
  331. Rodriguez JM (2014) The origin of human milk bacteria: is there a bacterial entero-mammary pathway during late pregnancy and lactation? Adv Nutrit (Bethesda, Md) 5(6):779–784.  https://doi.org/10.3945/an.114.007229 CrossRefGoogle Scholar
  332. Rohwer F, Thurber RV (2009) Viruses manipulate the marine environment. Nature 459:207–212PubMedCrossRefPubMedCentralGoogle Scholar
  333. Rotaru AE, Shrestha PM, Liu F, Shrestha M, Shrestha D, Embree M, Zengler K, Wardman C, Nevin KP, Loveley DR (2014a) A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane. Ener Environ Sci 7:408–415CrossRefGoogle Scholar
  334. Rotaru AE, Shrestha PM, Liu F, Markovaite B, Chen S, Nevin KP, Loveley DR (2014b) Direct interspecies electron transfer between Geobacter metallireducens and Methanosarcina barkeri. Appl Environ Microbiol 80:4599–4605PubMedPubMedCentralCrossRefGoogle Scholar
  335. Round JL, Mazmanian SK (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9:313–323PubMedPubMedCentralCrossRefGoogle Scholar
  336. Rousset F, Raymond M, Kjellberg F (1991) Cytoplasmic incompatibilities in the mosquito Culex pipiens: how to explain a cytotype polymorphism. J Evol Biol 4:69–81CrossRefGoogle Scholar
  337. Russell JA, Latorre A, Sabater-Munoz B, Moya A, Moran NA (2003) Side-stepping secondary symbionts: widespread horizontal transfer across and beyond the Aphidoidea. Mol Ecol 12:1061–1075PubMedCrossRefPubMedCentralGoogle Scholar
  338. Ruvindy R, White RA 3rd, Neilan BA, Burns BP. 2016 Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics. ISME J 10(1):183–196PubMedPubMedCentralCrossRefGoogle Scholar
  339. Sagan L (1967) On the origin of mitosing cells. J Theor Biol 14:255–274PubMedCrossRefPubMedCentralGoogle Scholar
  340. Samuel BS, Gordon JI (2006) A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A 103(26):10011–10016.  https://doi.org/10.1073/pnas.0602187103 CrossRefPubMedPubMedCentralGoogle Scholar
  341. Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI (2007) Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A 104(25):10643–10648.  https://doi.org/10.1073/pnas.0704189104 CrossRefPubMedPubMedCentralGoogle Scholar
  342. Sandstrom JP, Russell JA, White JP, Moran NA (2001) Independent origins and horizontal transfer of bacterial symbionts of aphids. Mol Ecol 10:217–228PubMedCrossRefPubMedCentralGoogle Scholar
  343. Sanford JA, Gallo RL (2013) Functions of the skin microbiota in health and disease. Semin Immunol 25(5):370–377.  https://doi.org/10.1016/j.smim.2013.09.005 CrossRefPubMedPubMedCentralGoogle Scholar
  344. Sbicego S, Vassella E, Kurath U, Blum B, Roditi I (1999) The use of transgenic Trypanosoma brucei to identify compounds inducing the differentiation of bloodstream forms to procyclic forms. Mol Biochem Parasitol 104:311–322PubMedCrossRefPubMedCentralGoogle Scholar
  345. Scarborough CL, Ferrari J, Godfray HCJ (2005) Aphid protected from pathogen by endosymbiont. Science 310:1781–1781PubMedCrossRefPubMedCentralGoogle Scholar
  346. Schalk IJ, Abdallah MA, Pattus F (2002) Recycling of pyoverdinon the FpvA receptor after ferric pyoverdin uptake and dissociation in Pseudomonas aeruginosa. Biochemistry 41:1663–1671PubMedCrossRefPubMedCentralGoogle Scholar
  347. Schink B (2002) Synergistic interactions in the microbial world. Antonie Van Leeuwenhoek 81:257–261PubMedCrossRefGoogle Scholar
  348. Schwechheimer C, Kuehn MJ (2015) Outer-membrane vesicles from gram-negative bacteria: biogenesis and functions. Nature Rev Microbiol 13:605–619.  https://doi.org/10.1038/nrmicro3525 CrossRefGoogle Scholar
  349. Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp APS. Nature 407:81–86PubMedCrossRefPubMedCentralGoogle Scholar
  350. Shrestha PM, Rotaru AE (2014) Plugging in or going wirelesss: strategies for interspecies electron transfer. Front Microbiol 5:237PubMedPubMedCentralGoogle Scholar
  351. Shrestha PM, Rotaru AE, Aklujkar M, Liu F, Shrestha M, Zarath M, Summers ZM, Malvankar N, Flores DC, Lovley DR (2013) Syntrophic growth with direct interspecies electron transfer as the primary mechanism for energy exchange. Environ Microbiol Rep 5:904–910PubMedCrossRefGoogle Scholar
  352. Sime-Ngando T (2014) Environmental bacteriophages: viruses of microbes in aquatic ecosystems. Frontiers Microbiol 5:355CrossRefGoogle Scholar
  353. Sime-Ngando T, Colombet J (2009) Virus et prophages dans les écosystèmes aquatiques. Can J Microbiol 55:95–109PubMedCrossRefGoogle Scholar
  354. Sime-Ngando T, Niquil N (eds) (2011) Disregarded microbial diversity and ecological potentials in aquatic systems. Springer, New YorkGoogle Scholar
  355. Sime-Ngando T, Lefèvre E, Gleason F (2011) Hidden diversity among aquatic heterotrophic flagellates: ecological potentials of zoosporic fungi. In: Sime-Ngando T, Niquil N (eds) Disregarded microbial diversity and ecological potentials in aquatic systems. Springer, New YorkGoogle Scholar
  356. Sinkins SP, Gould F (2006) Gene drive systems for insect disease vectors. Nat Rev Genet 7:427–435PubMedCrossRefPubMedCentralGoogle Scholar
  357. Sinkins SP, Braig HR, O'Neill SL (1995) Wolbachia pipientis: bacterial density and unidirectional cytoplasmic incompatibility between infected populations of Aedes albopictus. Exp Parasitol 81:284–291PubMedCrossRefPubMedCentralGoogle Scholar
  358. Sinkins SP, Walker T, Lynd AR, Steven AR, Makepeace BL, Godfray HC, Parkhill J (2005) Wolbachia variability and host effects on crossing type in Culex mosquitoes. Nature 436:257–260PubMedCrossRefPubMedCentralGoogle Scholar
  359. Smith JA, Nevin KP, Lovley DR (2015) Syntrophy growth via quinone-mediated interspecies electron transfer. Front Microbiol 6:121PubMedPubMedCentralGoogle Scholar
  360. Snyder AK, Deberry JW, Runyen-Janecky L, Rio RV (2010) Nutrient provisioning facilitates homeostasis between tsetse fly (Diptera: Glossinidae) symbionts. Proc Biol Sci 277:2389–2397PubMedPubMedCentralCrossRefGoogle Scholar
  361. Sockett RE (2009) Predatory lifestyle of Bdellovibrio bacteriovorus. Annu Rev Microbiol 63:523–539.  https://doi.org/10.1146/annurev.micro.091208.073346 CrossRefPubMedPubMedCentralGoogle Scholar
  362. Soltis DE, Soltis PS, Morgan DR, Swensen SM, Mullin BC, Dowd JM, Martin PG (1995) Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms. Proc Natl Acad Sci U S A 92:2647–2651PubMedPubMedCentralCrossRefGoogle Scholar
  363. Spor A, Koren O, Ley R (2011) Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9(4):279–290.  https://doi.org/10.1038/nrmicro2540 CrossRefPubMedPubMedCentralGoogle Scholar
  364. Sprent JI (2001) Nodulation in legumes. Royal Botanical Gardens, Kew, UKGoogle Scholar
  365. Stams AJM, Plugge CM (2009) Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 7:568–577PubMedCrossRefPubMedCentralGoogle Scholar
  366. Stams AJM, Sousa DZ, Kleerebezem R, Plugge CM (2012) Role of syntrophic microbial communities in high-rate methanogenic bioreactors. Water Sci Technol 66:352–362PubMedCrossRefPubMedCentralGoogle Scholar
  367. Stanier RY (1970) Some aspects of the biology of cells and their possible evolutionary significance. Symp Soc Gen Mircrobiol 20:1–38Google Scholar
  368. Starr DJ, Cline TW (2002) A host parasite interaction rescues Drosophila oogenesis defects. Nature 418:76–79PubMedCrossRefPubMedCentralGoogle Scholar
  369. Stewart FM, Levin BR (1984) The population biology of bacterial viruses: why be temperate? Theor. Popul Biol 26:93–117CrossRefGoogle Scholar
  370. Stewart AD, Logsdon JM, Kelley SE (2005) An empirical study of the evolution of virulence under both horizontal and vertical transmission. Evolution 59:730–739PubMedCrossRefPubMedCentralGoogle Scholar
  371. Stouthamer R, Luck RF, Hamilton WD (1990) Antibiotics cause parthenogenetic Trichogramma (Hymenoptera, Trichogrammatidae) to revert to sex. Proc Natl Acad Sci U S A 87:2424–2427PubMedPubMedCentralCrossRefGoogle Scholar
  372. Streng A, Op den Camp R, Bisseling T, Geurts R (2011) Evolutionary origin of rhizobium nod factor signaling. Plant Signal Behav 6:1510–1514.  https://doi.org/10.4161/psb.6.10.17444 CrossRefGoogle Scholar
  373. Summers WC (2001) Bacteriophage therapy. Ann Rev Microbiol 55:437–451CrossRefGoogle Scholar
  374. Summers ZM, Fogarty HE, Leang C, Franks AE, Malvankar NS, Lovley DR (2010) Direct exchange of electrons within aggregates of an evolved syntrophic coculture of anaerobic bacteria. Science 330:1413–1415PubMedCrossRefPubMedCentralGoogle Scholar
  375. Suttle CA (2007) Marine viruses: major players in the global ecosystem. Nature Rev Microbiol 5:801–812CrossRefGoogle Scholar
  376. Svistoonoff S, Benabdoun FM, Nambiar-Veetil M, Imanishi L, Vaissayre V, Cesari S, Diagne N, Hocher V, de Billy F, Bonneau J, Wall L, Ykhlef N, Rosenberg C, Bogusz D, Franche C, Gherbi H (2013) The independent acquisition of plant root nitrogen-fixing symbiosis in Fabids recruited the same genetic pathway for nodule organogenesis. PLoS One 8:e64515.  https://doi.org/10.1371/journal.pone.0064515 CrossRefPubMedPubMedCentralGoogle Scholar
  377. Swensen SM (1996) The evolution of actinorhizal symbioses : evidence for multiple origins of the symbiotic association. Am J Bot 83:1503–1512CrossRefGoogle Scholar
  378. Taylor FJ (1978) Problems in the development of an explicit hypothetical phylogeny of the lower eukaryotes. Biosystems 10:67–89PubMedCrossRefPubMedCentralGoogle Scholar
  379. Teixeira L, Ferreira A, Ashburner M (2008) The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster. PLoS Biol 6:2753–2763CrossRefGoogle Scholar
  380. Teske M, Hinrichs K-U, Edgcomb V, Gomez A d V, Kysela D, Sylva SP, Sogin ML, Jannasch HW (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic Methanotrophic communities. Appl Environ Microbiol 68(4):1994–2007PubMedPubMedCentralCrossRefGoogle Scholar
  381. Thauer RK, Jungermann K, Decker K (1977) Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev 41:100–180PubMedPubMedCentralGoogle Scholar
  382. Thingstad, T..F, and Lignell, R. (1997). Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand, Aquat Microb Ecol 13, 19–27CrossRefGoogle Scholar
  383. Thingstad TF, Havskum H, Garde K, Riemann B (1996) On the strategy of ‘eating your competitor’: a mathematical analysis of algal mixotrophy. Ecology 77:2108–2118CrossRefGoogle Scholar
  384. Thomas R, Grimsley N, Escande M-L, Subirana L, Derelle E, Moreau H (2011) Acquisition and maintenance of resistance to viruses in eukaryotic phytoplankton populations. Environ Microbiol 13:1412–1420PubMedCrossRefGoogle Scholar
  385. Thomson NR, Crow MA, McGowan SJ, Cox A, Salmond GPC (2000) Biosynthesis of carbapenem antibiotic and prodigiosin pigment in Serratia is under quorum sensing control. MolMicrobiol 36:539–556Google Scholar
  386. Timmers PHA, Diego A, Suarez-Zuluaga DAS, van Rossem M, Diender M, Stams AJM, Plugge CM (2016) Anaerobic oxidation of methane associated with sulfate reduction in a natural freshwater gas source. ISME J 10:1400–1412PubMedCrossRefPubMedCentralGoogle Scholar
  387. Toft CA, Karter AJ (1990) Parasite-host coevolution. Tren Ecol Evol 5:326–329CrossRefGoogle Scholar
  388. Toh H, Weiss BL, Perkin SA, Yamashita A, Oshima K, Hattori M, Aksoy S (2006) Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res 16:149–156PubMedPubMedCentralCrossRefGoogle Scholar
  389. Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5:240–245PubMedCrossRefPubMedCentralGoogle Scholar
  390. Trinick MJ (1973) Symbiosis between rhizobium and the non-legume, Trema aspera. Nature 244:459–460.  https://doi.org/10.1038/244459a0 CrossRefGoogle Scholar
  391. Trinick MJ (1979) Structure of nitrogen-fixing nodules formed by rhizobium on roots of Parasponia andersonii. Planch Can J Microbiol 25:565–578.  https://doi.org/10.1139/m79-082 CrossRefPubMedPubMedCentralGoogle Scholar
  392. Tsuchida T, Koga R, Horikawa M, Tsunoda T, Maoka T, Matsumoto S, Simon JC, Fukatsu T (2010) Symbiotic bacterium modifies aphid body color. Science 330:1102–1104PubMedCrossRefPubMedCentralGoogle Scholar
  393. Turelli M (1994) Evolution of incompatibility-inducing microbes and their hosts. Evolution 48:1500–1513PubMedCrossRefPubMedCentralGoogle Scholar
  394. Valbuena G, Walker DH (2009) Infection of the endothelium by members of the order Rickettsiales. Thromb Haemost 102:1071–1079PubMedPubMedCentralCrossRefGoogle Scholar
  395. Valen V (1973) A new evolutionary law. Evol Theory 1:1–30Google Scholar
  396. Van den Abbeele J, Claes Y, Bockstaele D, Ray D, Coosemans M (1999) Trypanosoma brucei spp. development in the tsetse fly: characterization of the post-mesocyclic stages in the foregut and proboscis. Parasitology 118:469–478CrossRefGoogle Scholar
  397. van der Giezen M, Tovar J, Clark CG (2005) Mitochondrion-derived organelles in protists and fungi. Int Rev Cytol 244:175–225PubMedCrossRefPubMedCentralGoogle Scholar
  398. Van Essche M, Quirynen M, Sliepen I, Loozen G, Boon N, Van Eldere J, Teughels W (2011) Killing of anaerobic pathogens by predatory bacteria. Mol Oral Biol 26:52–61Google Scholar
  399. Van Nguyen T, Wibberg D, Battenberg K, Blom J, Vanden Heuvel B, Berry AM, Kalinowski J, Pawlowski K (2016) An assemblage of Frankia cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH. BMC Genomics 17:796.  https://doi.org/10.1186/s12864-016-3140-1 CrossRefPubMedPubMedCentralGoogle Scholar
  400. Vernié T, Kim J, Frances L, Ding Y, Sun J, Guan D, Niebel A, Gifford ML, de Carvalho Niebel F, Oldroyd GE (2015) The NIN transcription factor coordinates diverse nodulation programs in different tissues of the Medicago truncatula root. Plant Cell 27:3410–3424.  https://doi.org/10.1105/tpc.15.00461 CrossRefPubMedPubMedCentralGoogle Scholar
  401. Wang J, Aksoy S (2012) PGRP-LB is a maternally transmitted immune milk protein that influences symbiosis and parasitism in tsetse's offspring. Proc Natl Acad Sci U S A 109:10552–10557PubMedPubMedCentralCrossRefGoogle Scholar
  402. Wang F, Zhou H, Meng J, Peng X, Jiang L, Sun P, Zhang C, Van Nostrand JD, Deng Y, He Z, Wu L, Zhou J, Xiao X. 2009a. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca ridge hydrothermal vent. Proc Natl Acad Sci U S A 24;106(12):4840–4845CrossRefGoogle Scholar
  403. Wang J, Wu Y, Yang G, Aksoy S (2009b) Interactions between mutualist Wigglesworthia and tsetse peptidoglycan recognition protein (PGRP-LB) influence trypanosome transmission. Proc Natl Acad Sci U S A 106:12133–12138PubMedPubMedCentralCrossRefGoogle Scholar
  404. Wang H, Moore MJ, Soltis PS, Bell CD, Brockington SF, Alexandre R, Davis CC, Latvis M, Manchester SR, Soltis DE (2009c) Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc Natl Acad Sci U S A 106:3853–3858.  https://doi.org/10.1073/pnas.0813376106 CrossRefPubMedPubMedCentralGoogle Scholar
  405. Wang J, Weiss BL, Aksoy S (2013) Tsetse fly microbiota: form and function. Front Cell Infect Microbiol 3:69PubMedPubMedCentralGoogle Scholar
  406. Wanner G, Vogl K, Overmann J (2008) Ultrastructural characterization of the prokaryotic Symbiosis in “Chlorochromatium aggregatum”. J Bacteriol 190(10):3721.  https://doi.org/10.1128/JB.00027-08 CrossRefPubMedPubMedCentralGoogle Scholar
  407. Warthmann R, Cypionka H, Pfennig N (1992) Photoproduction of H2 from acetate by syntrophic cocultures of green sulfur bacteria and sulfur-reducing bacteria. Arch Microbiol 157:343–348CrossRefGoogle Scholar
  408. Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Jingwei Ni J, Podar M, Richardson T, Granger GG, Simon M, Söll D, Stetter KO, Short JM, Noordewier M (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A 100:12984–12988PubMedPubMedCentralCrossRefGoogle Scholar
  409. Weeks AR, Breeuwer JA (2001) Wolbachia-induced parthenogenesis in a genus of phytophagous mites. Proc R Soc London Ser B 268:2245–2251CrossRefGoogle Scholar
  410. Weeks AR, Turelli M, Harcombe WR, Reynolds KT, Hoffmann AA (2007) From parasite to mutualist: rapid evolution of Wolbachia in natural populations of Drosophila. PLoS Biol 5:e114PubMedPubMedCentralCrossRefGoogle Scholar
  411. Weinbauer MG (2004) Ecology of prokaryotic viruses. FEMS Microbiol Rev 28:127–181PubMedCrossRefPubMedCentralGoogle Scholar
  412. Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Environ Microbiol 4:1–11Google Scholar
  413. Weiss B, Aksoy S (2011) Microbiome influences on insect host vector competence. Trends Parasitol 27:514–522PubMedPubMedCentralCrossRefGoogle Scholar
  414. Weiss BL, Mouchotte R, Rio RV, Wu YN, Wu Z, Heddi A, Aksoy S (2006) Interspecific transfer of bacterial endosymbionts between tsetse fly species: infection establishment and effect on host fitness. Appl Environ Microbiol 72:7013–7021PubMedPubMedCentralCrossRefGoogle Scholar
  415. Weiss BL, Wang J, Aksoy S (2011) Tsetse immune system maturation requires the presence of obligate symbionts in larvae. PLoS Biol 9:e1000619PubMedPubMedCentralCrossRefGoogle Scholar
  416. Weiss BL, Wang J, Maltz MA, Wu Y, Aksoy S (2013) Trypanosome infection establishment in the tsetse fly gut is influenced by microbiome-regulated host immune barriers. PLoS Pathog 9:e1003318PubMedPubMedCentralCrossRefGoogle Scholar
  417. Welburn SC, Arnold K, Maudlin I, Gooday GW (1993) Rickettsia-like organisms and chitinase production in relation to transmission of trypanosomes by tsetse flies. Parasitology 107:141–145PubMedCrossRefPubMedCentralGoogle Scholar
  418. Wernegreen JJ (2002) Genome evolution in bacterial endosymbionts of insects. Nat Rev Genet 3:850–861PubMedCrossRefPubMedCentralGoogle Scholar
  419. Werner GDA, Cornwell WK, Sprent JI, Kattge J, Kiers ET (2014) A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms. Nat Commun 5:4087.  https://doi.org/10.1038/ncomms5087 CrossRefPubMedPubMedCentralGoogle Scholar
  420. Werren JH (1997) Biology of Wolbachia. Annu Rev Entomol 42:587–609PubMedCrossRefPubMedCentralGoogle Scholar
  421. Werren JH, Windsor DM (2000) Wolbachia infection frequencies in insects: evidence of a global equilibrium? Proc R Soc London Ser B 267:1277–1285CrossRefGoogle Scholar
  422. Werren JH, Windsor D, Guo L (1995) Distribution of Wolbachia among neotropical arthropods. Proc R Soc London Ser B 262:197–204CrossRefGoogle Scholar
  423. Werren JH, Baldo L, Clark ME (2008) Wolbachia: master manipulators of invertebrate biology. Nat Rev Microbiol 6:741–751PubMedCrossRefPubMedCentralGoogle Scholar
  424. Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory S, Greenberg EP (2001) Gene expression in Pseudomonas aeruginosa biofilms. Nature 413(6858):860–864PubMedCrossRefPubMedCentralGoogle Scholar
  425. Wieland A, Zopfi J, Benthien M, Kühl M (2005) Biogeochemistry of an iron-rich hypersaline microbial mat (Camargue, France). Microb Ecol 49(1):34–49PubMedCrossRefPubMedCentralGoogle Scholar
  426. Wilhelm SW, Suttle CA (1999) Viruses and nutrient cycles in the sea. Bioscience 49:781–788CrossRefGoogle Scholar
  427. Wilkinson TG, Topiwals H, Hamer G (1974) Interactions in a mixed bacterial population growing on methane in continuous culture. Biotechnol Bioeng 6:41–59CrossRefGoogle Scholar
  428. Windsor DA (1998) Most of the species on earth are parasites. Int J Parasitol 28:1939–1941PubMedCrossRefPubMedCentralGoogle Scholar
  429. Winkel M, de Beer D, Lavik G, Peplies J and Mußmann M. 2014. Close association of active nitrifiers with Beggiatoa mats covering deep-sea hydrothermal sediments. Environ Microbiol 16(6), 1612–1626PubMedCrossRefPubMedCentralGoogle Scholar
  430. Wong JM, de Souza R, Kendall CW, Emam A, Jenkins DJ (2006) Colonic health: fermentation and short chain fatty acids. J Clin Gastroenterol 40(3):235–243PubMedCrossRefPubMedCentralGoogle Scholar
  431. Xie W, Wang F, Guo L, Chen Z, Sievert SM, Meng J, Huang G, Li Y, Yan Q, Wu S, Wang X, Chen S, He G, Xiao X, Xu A (2011) Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries. ISME. J Mar 5(3):414–426Google Scholar
  432. Yamaguchi M et al (2012) Prokaryote or eukaryote? A unique microorganism from the deep sea. J Electron Microsc 61(6):423–431.  https://doi.org/10.1093/jmicro/dfs062 CrossRefGoogle Scholar
  433. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222–227.  https://doi.org/10.1038/nature11053 CrossRefPubMedPubMedCentralGoogle Scholar
  434. Yen JH, Barr AR (1971) New hypothesis of the cause of cytoplasmic incompatibility in Culex pipiens L. Nature 232:657–658PubMedCrossRefGoogle Scholar
  435. Yoshida N, Oeda K, Watanabe E, Mikami T, Fukita Y, Nishimura K, Komai K, Matsuda K (2001) Protein function: chaperonin turned insect toxin. Nature 411:44PubMedCrossRefPubMedCentralGoogle Scholar
  436. Zeh DW, Zeh JA, Bonilla MM (2005) Wolbachia, sex ratio bias and apparent male killing in the harlequin beetle riding pseudoscorpion. Heredity 95:41–49PubMedCrossRefPubMedCentralGoogle Scholar
  437. Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J (2016) Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352(6285):565–569.  https://doi.org/10.1126/science.aad3369 CrossRefPubMedPubMedCentralGoogle Scholar
  438. Zhong C, Zhang Y, Chen Y, Jiang Q, Chen Z, Liang J, Pinyopusarerk K, Franche C, Bogusz D (2010) Casuarina research and applications in China. Symbiosis 50:107–114.  https://doi.org/10.1007/s13199-009-0039-5 CrossRefGoogle Scholar
  439. Zhu H, Riely BK, Burns NJ, Ané JM (2006) Tracing nonlegume orthologs of legume genes required for nodulation and arbuscular mycorrhizal symbioses. Genetics 172:2491–2499.  https://doi.org/10.1534/genetics.105.051185 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Télesphore Sime-Ngando
    • 1
    Email author
  • Jean-Claude Bertrand
    • 2
  • Didier Bogusz
    • 3
  • Jean-François Brugère
    • 4
  • Claudine Franche
    • 3
  • Marie-Laure Fardeau
    • 5
  • Emilie Froussart
    • 3
  • Anne Geiger
    • 6
  • Maria Soledad Goñi-Urriza
    • 7
  • Bernard Ollivier
    • 5
  • Paul W. O’Toole
    • 8
  1. 1.Laboratoire “Microorganismes: Génome et Environnement” (LMGE), CNRS UMR 6023Université Clermont AuvergneClermont-FerrandFrance
  2. 2.Unité Mixte de Service, UMS 3470, OSU PythéasAix Marseille UniversitéMarseille CedexFrance
  3. 3.Équipe Rhizogenèse, UMR DIADE (IRD-UM)Institut de Recherche pour le Développement (IRD)Montpellier, Cedex 5France
  4. 4.Université Clermont AuvergneClermont-FerrandFrance
  5. 5.Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110MarseilleFrance
  6. 6.INTERTRYP, Institut de Recherche pour le DéveloppementUniversity of MontpellierMontpellierFrance
  7. 7.Environmental Microbiology CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnemnet et les Matérieaux, UMR5254Univ. Pau & Pays AdourPauFrance
  8. 8.School of Microbiology and APC Microbiome InstituteUniversity College Cork, Co.CorkIreland

Personalised recommendations