C. J. Marx and . Microbiology, Getting in touch with your friends, Science, vol.324, pp.1150-1151, 2009.

J. A. Fuhrman, Microbial community structure and its functional implications, Nature, vol.459, pp.193-202, 2009.

S. Freilich, A. Kreimer, I. Meilijson, U. Gophna, R. Sharan et al., The largescale organization of the bacterial network of ecological co-occurrence interactions, Nucleic Acids Res, vol.38, pp.3857-68, 2010.

S. Freilich, R. Zarecki, O. Eilam, E. S. Segal, C. S. Henry et al., Competitive and cooperative metabolic interactions in bacterial communities, Nat Commun, vol.2, pp.589-95, 2011.

N. Klitgord and D. Segrè, Environments that induce synthetic microbial ecosystems, PLoS Comput Biol, vol.6, pp.1-17, 2010.

N. Klitgord and D. Segrè, Ecosystems biology of microbial metabolism, Curr Opin Biotechnol, vol.22, pp.541-547, 2011.

T. Großkopf and O. S. Soyer, Synthetic microbial communities, Curr Opin Microbiol, vol.18, pp.72-79, 2014.

R. Levy and E. Borenstein, Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules, Proc Natl Acad Sci, vol.110, pp.12804-12813, 2013.

I. Zilber-rosenberg and E. Rosenberg, Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution, FEMS Microbiol Rev, vol.32, pp.723-758, 2008.

A. Moya, J. Peretó, R. Gil, and A. Latorre, Learning how to live together: genomic insights into prokaryote-animal symbioses, Nat Rev Genet, vol.9, pp.218-247, 2008.

P. Buchner, Endosymbiosis of animals with plant microorganisms, 1965.

P. Baumann, Biology bacteriocyte-associated endosymbionts of plant sapsucking insects, Annu Rev Microbiol, vol.59, pp.155-89, 2005.

N. A. Moran, Symbiosis as an adaptive process and source of phenotypic complexity, Proc Natl Acad Sci, vol.104, pp.8627-8660, 2007.

E. Zchori-fein and B. Kostas, Manipulative Tenants: Bacteria assosiated with arthropods, 2011.

G. Gueguen, F. Vavre, O. Gnankine, M. Peterschmitt, D. Charif et al., Endosymbiont metacommunities, mtDNA diversity and the evolution of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex, Mol Ecol, vol.19, pp.4365-78, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00746855

J. Jaenike, Population genetics of beneficial heritable symbionts, Trends Ecol. Evol, vol.27, pp.226-232, 2012.

L. M. Henry, J. Peccoud, J. C. Simon, J. D. Hadfield, M. Maiden et al., Horizontally transmitted symbionts and host colonization of ecological niches, Curr Biol, vol.23, pp.1713-1720, 2013.

G. M. Bennett and N. A. Moran, Heritable symbiosis: the advantages and perils of an evolutionary rabbit hole, Proc Natl Acad Sci, vol.112, pp.10169-76, 2015.

S. J. Macdonald, G. H. Thomas, and A. E. Douglas, Genetic and metabolic determinants of nutritional phenotype in an insect-bacterial symbiosis, Mol Ecol, vol.20, pp.2073-84, 2011.

J. P. Mccutcheon, V. Dohlen, and C. D. , An interdependent metabolic patchwork in the nested symbiosis of mealybugs, Curr Biol, vol.21, pp.1366-72, 2011.

Q. Rao, P. A. Rollat-farnier, D. T. Zhu, D. Santos-garcia, F. J. Silva et al., Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci, BMC Genomics, vol.16, pp.226-264, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01139508

S. Stolyar, S. Van-dien, K. L. Hillesland, N. Pinel, T. J. Lie et al., Metabolic modeling of a mutualistic microbial community, Mol Syst Biol, vol.3, pp.92-104, 2007.

S. Ofaim, M. Ofek-lalzar, N. Sela, J. Jinag, Y. Kashi et al., Analysis of microbial functions in the rhizosphere using a metabolic-network based framework for metagenomics interpretation, Front Microbiol, 2017.

O. Ebenhöh, T. Handorf, and R. Heinrich, Structural analysis of expanding metabolic networks, Genome Inform, vol.15, pp.35-45, 2004.

A. Kreimer, A. Doron-faigenboim, E. Borenstein, and S. Freilich, NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species, Bioinformatics, vol.28, pp.2195-2202, 2012.

G. Duan, N. Christian, J. Schwachtje, D. Walther, and O. Ebenhöh, The metabolic interplay between plants and phytopathogens, Meta, vol.3, pp.1-23, 2013.

A. Zelezniak, S. Andrejev, O. Ponomarova, D. R. Mende, P. Bork et al., Metabolic dependencies drive species co-occurrence in diverse microbial communities, Proc Natl Acad Sci USA, vol.112, pp.6449-54, 2015.
DOI : 10.1073/pnas.1421834112
URL : http://www.pnas.org/content/112/20/6449.full.pdf

P. A. Stansly and S. E. Naranjo, Bemisia: bionomics and management of a global pest, 2010.

D. Barro, P. J. Liu, S. Boykin, L. Dinsdale, and A. B. , Bemisia tabaci : a statement of species status, Annu Rev Entomol, vol.56, pp.1-19, 2011.

J. Hu, Z. Jiang, F. Nardi, Y. Liu, X. Luo et al., Members of Bemisia tabaci (Hemiptera: Aleyrodidae ) cryptic species and the status of two invasive alien species in the Yunnan province ( China ), J Insect Sci, vol.6, pp.1-8, 2014.

M. L. Thao and P. Baumann, Evolutionary relationships of primary prokaryotic endosymbionts of whiteflies and their hosts, Appl Environ Microbiol, vol.70, pp.3401-3407, 2004.

D. Santos-garcia, P. Farnier, F. Beitia, E. Zchori-fein, F. Vavre et al., Complete genome sequence of "Candidatus Portiera aleyrodidarum" BTQVLC , an obligate symbiont that supplies amino acids and carotenoids to Bemisia tabaci, J Bacteriol, vol.194, pp.6654-6659, 2012.
DOI : 10.1128/jb.01793-12
URL : https://hal.archives-ouvertes.fr/hal-00763436

D. B. Sloan and N. A. Moran, Endosymbiotic bacteria as a source of carotenoids in whiteflies, Biol Lett, vol.8, pp.986-995, 2012.

E. Zchori-fein, T. Lahav, and S. Freilich, Variations in the identity and complexity of endosymbiont combinations in whitefly hosts, Front Ecol Environ, vol.5, pp.1-8, 2014.

Y. Gottlieb, M. Ghanim, G. Gueguen, S. Kontsedalov, F. Vavre et al., Inherited intracellular ecosystem: symbiotic bacteria share bacteriocytes in whiteflies, FASEB J, vol.22, pp.2591-2600, 2008.
DOI : 10.1096/fj.07-101162
URL : https://hal.archives-ouvertes.fr/hal-00428116

X. L. Bing, J. Yang, E. Zchori-fein, X. W. Wang, and S. S. Liu, Characterization of a newly discovered symbiont of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae), Appl Environ Microbial, vol.79, pp.569-75, 2013.

K. D. Everett, M. Thao, M. Horn, G. E. Dyszynski, and P. Baumann, Novel chlamydiae in whiteflies and scale insects: endosymbionts 'Candidatus Fritschea bemisiae' strain Falk and 'Candidatus Fritschea eriococci' strain elm, Int. J. Syst. Evol. Microbiol, vol.55, pp.1581-1588, 2005.
DOI : 10.1099/ijs.0.63454-0

A. G. Himler, T. Adachi-hagimori, J. E. Bergen, A. Kozuch, S. E. Kelly et al., Rapid spread of a bacterial symbiont in an invasive whitefly is driven by fitness benefits and female bias, Science, vol.332, pp.254-260, 2011.

Q. Rao, S. Wang, D. T. Zhu, X. W. Wang, and S. S. Liu, Draft genome sequence of Rickettsia sp. strain MEAM1, isolated from the whitefly Bemisia tabaci, J Bacteriol, vol.194, pp.4741-4743, 2012.
DOI : 10.1128/jb.00909-12
URL : https://jb.asm.org/content/194/17/4741.full.pdf

D. Santos-garcia, P. A. Rollat-farnier, F. Beitia, E. Zchori-fein, F. Vavre et al., The genome of Cardinium cBtQ1 provides insights into genome reduction, symbiont motility, and its settlement in Bemisia tabaci, Genome Biol Evol, vol.6, pp.1013-1043, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01092610

D. Santos-garcia, C. Vargas-chavez, A. Moya, A. Latorre, and F. J. Silva, Genome evolution in the primary endosymbiont of whiteflies sheds light on their divergence, Genome Biol Evol, vol.7, pp.873-88, 2015.

J. B. Luan, W. Chen, D. K. Hasegawa, A. M. Simmons, W. M. Wintermantel et al., Metabolic coevolution in the bacterial symbiosis of whiteflies and related plant sap-feeding insects, Genome Biol Evol, vol.7, pp.2635-2682, 2015.

P. A. Rollat-farnier, D. Santos-garcia, Q. Rao, M. F. Sagot, F. J. Silva et al., Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts, Genome Biol Evol, vol.7, pp.839-55, 2015.
DOI : 10.1093/gbe/evv030
URL : https://hal.archives-ouvertes.fr/hal-01139507

N. Ankrah, J. Luan, and A. E. Douglas, Cooperative metabolism in a three-partner insect-bacterial symbiosis revealed by metabolic modeling, J Bacteriol, 2017.
DOI : 10.1128/jb.00872-16
URL : http://jb.asm.org/content/199/15/e00872-16.full.pdf

,

D. H. Parks, M. Imelfort, C. T. Skennerton, P. Hugenholtz, and G. W. Tyson, CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes, Genome Res, vol.25, pp.1043-55, 2015.

V. M. Markowitz, I. Chen, K. Palaniappan, K. Chu, E. Szeto et al., IMG 4 version of the integrated microbial genomes comparative analysis system, Nucleic Acids Res, vol.42, pp.560-567, 2014.

F. Meyer, D. Paarmann, D. 'souza, M. Olson, R. Glass et al., The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinformatics, vol.9, pp.386-390, 2008.

A. Pati, N. N. Ivanova, N. Mikhailova, G. Ovchinnikova, S. D. Hooper et al., GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes, Nat Methods, vol.7, pp.455-462, 2010.

M. H. Zimmermann, Phloem Transport MJA. Transp. Plants I, 1975.

S. K. Upadhyay, S. Sharma, H. Singh, S. Dixit, J. Kumar et al., Whitefly genome expression reveals host-symbiont interaction in amino acid biosynthesis, PLoS One, vol.10, pp.1-16, 2015.

. R-core-team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, R Foundation for Statistical Computing, 2012.

R. Carr and E. Borenstein, NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment, Bioinformatics, vol.28, issue.5, p.734, 2012.

Z. Jiang, F. Xia, K. W. Johnson, C. D. Brown, E. Bartom et al., Comparison of the genome sequences of "Candidatus Portiera aleyrodidarum" primary endosymbionts of the whitefly Bemisia tabaci B and Q biotypes, Appl Environ Microbiol, vol.79, pp.1757-1766, 2013.

E. H. Wintermute and P. A. Silver, Emergent cooperation in microbial metabolism, Mol Syst Biol, vol.6, pp.407-420, 2010.

P. J. Boer, The present status of the competitive exclusion principle, Trends Ecol Evol, vol.1, pp.25-33, 1986.

J. Calle-espinosa, M. Ponce-de-leon, D. Santos-garcia, F. J. Silva, F. Montero et al., Nature lessons: the whitefly bacterial endosymbiont is a minimal amino acid factory with unusual energetics, J Theor Biol, vol.407, pp.303-320, 2016.

C. W. Russell, A. Poliakov, M. Haribal, G. Jander, K. J. Van-wijk et al., Matching the supply of bacterial nutrients to the nutritional demand of the animal host, Proc R Soc B Biol Sci, vol.281, p.20141163, 2014.

G. Blanc, H. Ogata, C. Robert, S. Audic, K. Suhre et al., Reductive genome evolution from the mother of Rickettsia, PLoS Genet, vol.3, pp.103-117, 2007.

L. A. Weinert, J. H. Werren, A. Aebi, G. N. Stone, and F. M. Jiggins, Evolution and diversity of Rickettsia bacteria, BMC Biol, vol.7, p.6, 2009.

A. Osterman and R. Overbeek, Missing genes in metabolic pathways: a comparative genomics approach, Curr Opin Chem Biol, vol.7, pp.238-51, 2003.

P. D. Leroy, A. Sabri, S. Heuskin, P. Thonart, G. Lognay et al., Microorganisms from aphid honeydew attract and enhance the efficacy of natural enemies, Nat Commun, 2011.

K. M. Oliver, K. Noge, E. M. Huang, J. M. Campos, J. X. Becerra et al., Parasitic wasp responses to symbiont-based defense in aphids, BMC Biol, vol.10, pp.11-21, 2012.

S. Vandermoten, M. C. Mescher, F. Francis, E. Haubruge, and F. J. Verheggen, Aphid alarm pheromone: an overview of current knowledge on biosynthesis and functions, Insect Biochem Mol Biol, vol.42, pp.155-63, 2012.

E. R. Vimr, K. A. Kalivoda, E. L. Deszo, and S. M. Steenbergen, Diversity of microbial sialic acid metabolism, Microbiol Mol Biol Rev, vol.68, pp.132-53, 2004.

B. Py and F. Barras, Building Fe-S proteins: bacterial strategies, Nat Rev Microbiol, vol.8, pp.436-482, 2010.
DOI : 10.1038/nrmicro2356

K. M. Ellegaard, L. Klasson, K. Näslund, K. Bourtzis, and S. Andersson, Comparative genomics of Wolbachia and the bacterial species concept, PLoS Genet, 2013.

N. Paczia, A. Nilgen, T. Lehmann, J. Gätgens, W. Wiechert et al., Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms, Microb Cell Factories, vol.11, pp.122-157, 2012.
DOI : 10.1186/1475-2859-11-122
URL : https://microbialcellfactories.biomedcentral.com/track/pdf/10.1186/1475-2859-11-122

S. K. Hansen, P. B. Rainey, J. A. Haagensen, and S. Molin, Evolution of species interactions in a biofilm community, Nature, vol.445, pp.533-539, 2007.

R. Zindel, Y. Gottlieb, and A. Aebi, Arthropod symbioses: a neglected parameter in pest-and disease-control programmes, J Appl Ecol, vol.48, pp.864-72, 2011.

M. Gebiola, J. A. White, B. N. Cass, A. Kozuch, L. R. Harris et al., Cryptic diversity, reproductive isolation and cytoplasmic incompatibility in a classic biological control success story, Linn Soc London, vol.117, pp.217-247, 2016.
DOI : 10.1111/bij.12648
URL : https://academic.oup.com/biolinnean/article-pdf/117/2/217/16710414/bij12648.pdf

W. Chen, D. K. Hasegawa, N. Kaur, A. Kliot, P. V. Pinheiro et al., The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance, BMC Biol, 2016.