Skip to main content
SpringerLink
Log in

Role of Microorganisms in Adaptation, Development, and Evolution of Animals and Plants: The Hologenome Concept

  • Reference work entry
The Prokaryotes

Abstract

Eukaryotes evolved from prokaryotes and have remained in close association with them. All animals and plants establish symbiotic relationships with microorganisms; often the combined genetic information of the diverse microbiota exceeds that of the host. How the genetic wealth of the microbiota affects all aspects of the holobiont’s (host plus all of its associated microorganisms) fitness (adaptation, survival, development, growth, and reproduction) and evolution is reviewed, using selected invertebrate, vertebrate, plant, and insect published experimental results. The data are discussed within the framework of the hologenome concept of evolution, which demonstrates that changes in environmental parameters, for example, diet, can cause rapid changes in the diverse microbiota, which not only can benefit the holobiont in the short term but also can be transmitted to offspring and lead to long-lasting cooperations. During periods of rapid changes in the environment, the diverse microbial symbiont community can assist the holobiont in surviving, multiplying, and buying the time necessary for the host genome to evolve. The potential application of the hologenome concept can be seen in the fields of prebiotics and probiotics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 699.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 549.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abbas Hilmi HT, Surakka A, Apajalahti J, Saris PE (2007) Identification of the most abundant Lactobacillus species in the crop of 1- and 5-week-old broiler chickens. Appl Environ Microbiol 73:7867–7873

    PubMed  Google Scholar 

  • Abe T, Bignell DE, Higashi M (eds) (2000) Termites: evolution, sociality, symbioses, ecology. Kluwer, Dordrecht

    Google Scholar 

  • Abrams GD, Bishop JE (1967) Effect of normal microbial flora on gastrointestinal motility. Proc Soc Exp Biol Med 126:301–304

    PubMed  CAS  Google Scholar 

  • Abu-Shanab A, Eamonn MM, Quigley EMM (2010) The role of the gut microbiota in nonalcoholic fatty liver disease. Nat Rev Gastro Hepatol 7:691–701

    Google Scholar 

  • Akman LA, Yamashita H, Watanabe A et al (2002) Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glosssinidia. Nat Genet 32:402–407

    PubMed  CAS  Google Scholar 

  • Andersson SGE, Zomorodipour A, Andersson JO (1998) The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133–143

    PubMed  CAS  Google Scholar 

  • Barbieri E, Paster BJ, Hughes D, Zurek L, Moser DP, Teske A, Sogin ML (2001) Phylogenetic characterization of epibiotic bacteria in the accessory nidamental gland and egg capsules of the squid Loligo pealei (Cephalopoda: Loliginidae). Environ Microbiol 3:151–167

    PubMed  CAS  Google Scholar 

  • Bäckhed F, Manchester JK, Semenkovich CF, Gordon JI (2007) Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci USA 104:979–984

    PubMed  Google Scholar 

  • Baumann P, Moran NA, Baumann L (2006) Bacteriocyte-associated endosymbionts of insects. In: Dworkin M, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes, vol 1. Springer, New York, pp 403–438

    Google Scholar 

  • Bednarek P, Kwon C, Schulze-Lefert P (2010) Not a peripheral issue: secretion in plant–microbe interactions. Curr Opin Plant Biol 13:378–387

    PubMed  CAS  Google Scholar 

  • Belden LK, Harris RN (2007) Infectious diseases in wildlife: the community ecology context. Front Ecol Environ 5(10):533–539

    Google Scholar 

  • Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1–13

    PubMed  CAS  Google Scholar 

  • Blaser MJ, Falkow S (2009) What are the consequences of the disappearing human microbiota? Nature Rev Microbiol 7:887–894

    CAS  Google Scholar 

  • Breibart M, Hewson I, Felts B et al (2003) Metagenomic analysis of an uncultured viral community from human feces. J Bacteriol 185:6220–6223

    Google Scholar 

  • Breznak JA, Brune A (1994) Role of microorganisms in the digestion of lignocellulose by termites. Ann Rev Entomol 39:453–487

    CAS  Google Scholar 

  • Brooks SPJ, McAllister M, Sandoz M, Kalmokoff ML (2003) Culture-independent phylogenetic analysis of the faecal flora of the rat. Can J Microbiol 49:589–601

    PubMed  CAS  Google Scholar 

  • Broz AK, Manter DK, Vivanco JM (2007) Soil fungal abundance and diversity: another victim of the invasive plant Centaurea maculosa. ISMEJ 1:763–765

    CAS  Google Scholar 

  • Bucher M, Wegmüller S, Drissner D (2009) Chasing the structures of small molecules in arbuscular mycorrhizal signaling. Curr Opin Plant Biol 12:500–507

    PubMed  CAS  Google Scholar 

  • Buddemeier RW, Baker AC, Fautin DG, Jacobs JR (2004) The adaptive hypothesis of bleaching. In: Rosenberg E, Loya Y (eds) Coral health and disease. Springer, New York, pp 427–444

    Google Scholar 

  • Caesar R, Fåk F, Bäckhed F (2010) Effects of gut microbiota on obesity and atherosclerosis via modulation of inflammation and lipid metabolism. J Intern Med 268:320–328

    PubMed  CAS  Google Scholar 

  • Cani PD, Delzenne NM (2009) The role of the gut microbiota in energy metabolism and metabolic disease. Curr Pharm Des 15:1546–1558

    PubMed  CAS  Google Scholar 

  • Cankar K, Kraigher H, Ravnikar M, Rupnik M (2005) Bacterial endophytes from seeds of Norway spruce (Picea abies L. Karst). FEMS Microbiol Lett 244:341–345

    PubMed  CAS  Google Scholar 

  • Chelius MK, Triplett EW (2001) The diversity of Archaea and bacteria in association with the roots of Zea mays. Microb Ecol 41:252–263

    PubMed  CAS  Google Scholar 

  • Costerton JW, Lewandowski Z, Caldwell DE, Korber DR, Lappin-Scott HM (1995) Microbial biofilms. Annu Rev Microbiol 49:711–745

    PubMed  CAS  Google Scholar 

  • Coyne JA (1992) Genetics and speciation. Nature 355:511–515

    PubMed  CAS  Google Scholar 

  • Currie CR, Poulsen M, Mendenhall J et al (2006) Coevolved crypts and exocrine glands support mutualistic bacteria in fungus-growing ants. Science 311:81–83

    PubMed  CAS  Google Scholar 

  • Davidov Y, Jurkevitch E (2009) Predation between prokaryotes and the origin of eukaryotes. Bioessays 31:748–757

    PubMed  CAS  Google Scholar 

  • Dedeine F, Vavre F, Fleury F et al (2001) Removing symbiotic Wolbachia bacteria specifically inhibits oogenesis in a parasitic wasp. Proc Natl Acad Sci USA 98:6247–6252

    PubMed  CAS  Google Scholar 

  • Dehority BA (2003) Rumen microbiology. Nottingham University Press, Nottingham

    Google Scholar 

  • de la Cruz F, Davies J (2005) Industrial revolution and microbial evolution. In: McFall-Ngai MJ, Henderson B, Ruby EG (eds) (2005) The influence of cooperative bacteria on animal host biology. Cambridge University Press, New York, pp 73–82

    Google Scholar 

  • Delmotte N, Knief C, Chaffron S et al (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci USA 106:16428–16433

    PubMed  CAS  Google Scholar 

  • Dethlefsen L, Eckburg PB, Bik EM, Relman DA (2006) Assembly of the human intestinal microbiota. Trends Ecol Evol 21:517–523

    PubMed  Google Scholar 

  • Devi SM, Ahmed I, Khan AA et al (2006) Genomes of Helicobacter pylori from native Peruvians suggest a mixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island. BMC Genomics 7:191

    PubMed  Google Scholar 

  • Dewhirst FE, Chen T, Izard J et al (2010) The human oral microbiome. J Bacteriol 192:341–345

    Google Scholar 

  • Dodd DMB (1989) Reproductive isolation as a consequence of adaptive divergence in Drosophila pseudoobscura. Evolution 43:1308–1311

    Google Scholar 

  • Douglas AE (1998) Nutritional interactions in insect-microbial symbioses: aphids and their symbiotic bacteria Buchnera. Annu Rev Entomol 43:17–37

    PubMed  CAS  Google Scholar 

  • Ducklow HW, Mitchel R (1979) Bacterial populations and adaptations in the mucus layers on living corals. Limnol Oceanogr 24:715–725

    Google Scholar 

  • Edwards JE, McEwan NR, Travis AJ, Wallace RJ (2004) 16S rDNA library-based analysis of ruminal bacterial diversity. Anton Van Leeuw 86:263–281

    CAS  Google Scholar 

  • Ercolani GL (1991) Distribution of epiphytic bacteria on olive leaves and the influence of leaf age and sampling time. Microb Ecol 21:35–48

    Google Scholar 

  • Falcon L, Magallon S, Castillo A (2010) Dating the cyanobacterial ancestor of the chloroplast. ISME J 4:777–783

    PubMed  CAS  Google Scholar 

  • Fine M, Loya Y (2002) Endolithic algae: an alternative source of photoassimilates during coral bleaching. Proc R Soc Lond B 269:1205–1210

    Google Scholar 

  • Fraune S, Bosch TCH (2007) Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra. Proc Natl Acad Sci USA 104:13146–13151

    PubMed  CAS  Google Scholar 

  • Frey JC, Rothman JM, Pell AN et al (2006) Fecal bacterial diversity in a wild gorilla. Appl Environ Microbiol 72:3788–3792

    PubMed  CAS  Google Scholar 

  • Gibson GR, Probert HM, Van Loo J, Rastall RA, Roberfroid MB (2004) Dietary modulation of the human colonic microbiota: updating the concept of prebiotics. Nutr Res Rev 17(2):259–275

    PubMed  CAS  Google Scholar 

  • Gilbert SF, McDonald E, Boyle N et al (2010) Symbiosis as a source of selectable epigenetic variation: taking the heat for the big guy. Philos Trans R Soc Lond B 365:671–678

    Google Scholar 

  • Golichenkov MV, Kostina NV, Ul’yanova TA et al (2002) Specific features of nitrogen fixation and denitrification in termites Neotermes castaneus, Zootermopsis angusticollis, and Reticulitermes lucifugus. Biol Bull 29:172–175

    CAS  Google Scholar 

  • Grice EA, Kong HH, Contan S et al (2009) Topographical and temporal diversity of the human skin microbiome. Science 324:1190–1192

    PubMed  CAS  Google Scholar 

  • Hapfelmeier S, Lawson MAE, Slack E et al (2010) Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses. Science 328:1705–1709

    PubMed  CAS  Google Scholar 

  • Hardison RC (1996) A brief history of hemoglobins: plant, animal, protist, and bacteria. Proc Natl Acad Sci USA 93:5675–5679

    PubMed  CAS  Google Scholar 

  • Herwig RP, Staley JT, Nerini MK, Braham HW (1984) Baleen whales: preliminary evidence for forestomach microbial fermentation. Appl Environ Microbiol 47:421–423

    PubMed  CAS  Google Scholar 

  • Hickman CS (2005) How have bacteria contributed to the evolution of multicellular animals? In: McFall-Ngai MJ, Henderson B, Ruby EG (eds) The influence of cooperative bacteria on animal host biology. Cambridge University Press, New York, pp 3–33

    Google Scholar 

  • Hoffman FA, Heimbach JT, Sanders ME, Hibberd PL (2008) Executive Summary: Scientific and regulatory challenges of development of probiotics as food and drugs. Clinical Infect Dis 46:S53–S57

    Google Scholar 

  • Hongoh Y, Deevong P, Inoue T et al (2005) Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host. Appl Environ Microbiol 71:6590–6599

    PubMed  CAS  Google Scholar 

  • Hooper LV, Gordon JI (2001) Commensal host-bacterial relationships in the gut. Science 292:1115–1118

    PubMed  CAS  Google Scholar 

  • Hurek T, Reinhold-Hurek B (2003) Azoarcus sp. strain BH72 as a model for nitrogen-fixing grass endophytes. J Biotechnol 106:169–178

    PubMed  CAS  Google Scholar 

  • Innes L, Hobbs PJ, Bardgett RD (2004) The impacts of individual plant species on rhizosphere microbial communities in soils of different fertility. Biol Fertil Soils 40:7–13

    Google Scholar 

  • Ivanov II, Littman DR (2011) Modulation of immune homeostasis by commensal bacteria. Curr Opin Microbiol 14:106–114

    PubMed  CAS  Google Scholar 

  • Iwanaga S, Lee BL (2005) Recent advances in the innate immunity of invertebrate animals. J Biochem Mol Biol 38:128–150

    PubMed  CAS  Google Scholar 

  • Jones KM, Kobayashi H, Davies BW, Taga ME, Walker GC (2007) How rhizobial symbionts invade plants: the Sinorhizobium medicago model. Nat Rev Microbiol 5:619–633

    PubMed  CAS  Google Scholar 

  • Kaufman MR, Ikeda Y, Patton C, Van Dykhuizen G, Epel D (1998) Bacterial symbionts colonize the accessory nidamental gland of the squid Loligo opalescens via horizontal transmission. Bio Bull 194:36–43

    Google Scholar 

  • Kikuchi Y, Hosokawa T, Fukatsu T (2007) Insect–microbe mutualism without vertical transmission: a stinkbug acquires a beneficial gut symbiont from the environment every generation. Appl Environ Microbiol 73:4308–4316

    PubMed  CAS  Google Scholar 

  • Komai M, Shirakawa H, Kimura S (1988) Newly developed model for vitamin K deficiency in germfree mice. Int J Vitam Nutr Res 58(1):55–59

    PubMed  CAS  Google Scholar 

  • Koren O, Rosenberg E (2006) Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter. Appl Environ Microbiol 72:5254–5259

    PubMed  CAS  Google Scholar 

  • Lambais MR, Crowley DE, Cury JC, Büll RC, Rodrigues RR (2006) Bacterial diversity in tree canopies of the Atlantic Forest. Science 312:1917

    PubMed  CAS  Google Scholar 

  • Leser TD, Amenuvor JZ, Jensen TK et al (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68:673–690

    PubMed  CAS  Google Scholar 

  • Ley RE, Bäckhed F, Turnbaugh P et al (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102:11070–11075

    PubMed  CAS  Google Scholar 

  • Ley RE, Peterson DA, Gordon JI (2006a) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:837–848

    PubMed  CAS  Google Scholar 

  • Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006b) Human gut microbes associated with obesity. Nature 444:1022–1023

    PubMed  CAS  Google Scholar 

  • Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nature Rev Microbiol 6:776–788

    CAS  Google Scholar 

  • Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69:1875–1883

    PubMed  CAS  Google Scholar 

  • Lugtenberg B, Kamilova F (2009) Plant-growth-promoting Rhizobacteria. Annu Rev Microbiol 63:541–556

    PubMed  CAS  Google Scholar 

  • Luoto R, Laitinen K, Nermes M, Isolauri E (2010a) Impact of maternal probiotic-supplemented dietary counseling on pregnancy outcome and prenatal and postnatal growth: a double-blind, placebo-controlled study. Br J Nutr 103:1792–1799

    PubMed  CAS  Google Scholar 

  • Luoto R, Kalliomaki M, Laitinen K, Isolalauri E (2010b) The impact of perinatal intervention on the development of overweight and obesity: follow-up study from birth to 10 years. Int J Obes 34:1531–1537

    CAS  Google Scholar 

  • Mai V, Ukhanova M, Baer DJ (2010) Understanding the extent and sources of variation in gut microbiota studies; a prerequisite for establishing associations with disease. Diversity 2:1085–1096

    Google Scholar 

  • Margulis L (1993) Symbiosis in cell evolution: microbial communities in the Archean and Proterozoic eons, 2nd edn. Freeman, New York

    Google Scholar 

  • Margulis L, Sagan D (2001) Marvellous microbes. Resurgence 206:10–12

    Google Scholar 

  • Mart´ınez-Garc´ıa M, D´ıaz-Vald´ez M,Wanner G et al (2007) Microbial community associated with the colonial ascidian Cyctodytes dellechiajei. Environ Microbiol 9:521–534

    Google Scholar 

  • Mateos M, Castrezana SJ, Nankivell BJ, Estes AM, Markow TA, Moran NA (2006) Heritable endosymbionts of Drosophila. Genetics 174:363–376

    PubMed  CAS  Google Scholar 

  • McFall-Ngai MJ (1999) Consequences of evolving with bacterial symbionts: insights from the squid–Vibrio association. Ann Rev Ecol Syst 30:235–256

    Google Scholar 

  • Micallef SA, Shiaris MP, Colon-Carmona A (2009) Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation. J Exp Bot 60:1729–1742

    PubMed  CAS  Google Scholar 

  • Minkley N, Fujita A, Brune A, Kirchner WH (2006) Nest specificity of the bacterial community in termite guts (Hodotermes mossambicus). Insect Soc 53:339–344

    Google Scholar 

  • Montgomery MK, McFall-Ngai M (1994) Bacterial symbionts induce host organ morphogenesis during early postembryonic development of the squid Euprymna scolopes. Development 120:1719–1729

    PubMed  CAS  Google Scholar 

  • Mueller S, Saunier K, Hanisch C et al (2006) Differences in fecal microbiota in different European study populations in relation to age, gender and country: a cross-sectional study. Appl Environ Microbiol 72:1027–1033

    PubMed  CAS  Google Scholar 

  • Nissimov J, Rosenberg E, Munn C (2009) Antimicrobial properties of resident coral mucus bacteria of Oculina patagonica. FEMS Microb Lett 292:210–215

    CAS  Google Scholar 

  • Nyholm SV, McFall-Ngai M (2004) The winnowing: establishing the squid vibrio symbiosis. Nat Rev Microbiol 2:632–642

    PubMed  CAS  Google Scholar 

  • Ochman HM, Worobey CH, Kuo JB et al (2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol 8:e1000546. online

    Google Scholar 

  • O’Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7:688–693

    PubMed  Google Scholar 

  • Olsen MA, Aagnes TH, Mathiesen SD (1994) Digestion of herring by indigenous bacteria in the minke whale forestomach. Appl Environ Microbiol 60:4445–4455

    PubMed  CAS  Google Scholar 

  • Ott T, Sullivan J, James EK et al (2009) Absence of symbiotic leghemoglobins alters bacteroid and plant cell differentiation during development of Lotus japonicus root nodules. Mol Plant Microbe Interact 22:800–808

    PubMed  CAS  Google Scholar 

  • Pennisi E (2004) Evolutionary biology. The birth of the nucleus. Science 305:766–768

    PubMed  CAS  Google Scholar 

  • Portier P (1918) Les symbiotes. Masson, Paris

    Google Scholar 

  • Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65

    PubMed  CAS  Google Scholar 

  • Redford AJ, Fierer N (2009) Bacterial succession on the leaf surface: a novel system for studying successional dynamics. Microb Ecol 58:189–198

    PubMed  Google Scholar 

  • Redford AJ, Bowers RM, Knight R et al (2010) The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 12:2885–2893

    PubMed  Google Scholar 

  • Reichenbach H (1984) Myxobacteria: a most peculiar group of social prokaryotes. In: Rosenberg E (ed) Myxobacteria: development and cell interactions. Springer, New York, pp 1–50

    Google Scholar 

  • Reid G, Younes JA, Van der Mei HC et al (2011) Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat Rev Microbiol 9:27–38

    PubMed  CAS  Google Scholar 

  • Reitner J, Schumann-Kindel G (1997) Pyrite in mineralized sponge tissue-product of sulfate reducing sponge related bacteria. Facies 36:272–276

    Google Scholar 

  • Ritchie KB (2006) Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar Ecol Prog Ser 322:1–14

    CAS  Google Scholar 

  • Rohwer F, Seguritan V, Azam F, Knowlton N (2002) Diversity and distribution of coral-associated bacteria. Mar Ecol Prog Ser 243:1–10

    Google Scholar 

  • Rosenberg E, Falkovitz L (2004) The Vibrio shiloi/Oculina patagonica model system of coral bleaching. Ann Rev Microbiol 58:143–159

    CAS  Google Scholar 

  • Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I (2007) The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol 5:355–362

    PubMed  CAS  Google Scholar 

  • Ruby EG (1996) Lessons from a cooperative bacterial-animal association: the Vibrio fischeri-Euprymna scolopes light organ symbiosis. Annu Rev Microbiol 50:591–624

    PubMed  CAS  Google Scholar 

  • Russell JB, Rychlik JL (2001) Factors that alter rumen ecology. Science 292:1119–1122

    PubMed  CAS  Google Scholar 

  • Russell JA, Latorre A, Sabater-Muñoz B, Moya A, Moran NA (2003) Side-stepping secondary symbionts: widespread horizontal transfer across and beyond the Aphidoidea. Mol Ecol 12:1061–1075

    PubMed  CAS  Google Scholar 

  • Sandström JP, Russel JA, White JP, Moran NA (2001) Independent origins and horizontal transfer of bacterial symbionts of aphids. Mol Ecol 10:217–228

    PubMed  Google Scholar 

  • Savage DC, Siegel JD, Snellen JE, Whitt DD (1981) Transit time of epithelial cells in the small intestines of germfree mice and ex-germfree mice associated with indigenous microorganisms. Appl Environ Microbiol 42:996–1001

    PubMed  CAS  Google Scholar 

  • Schluter D (2009) Evidence for ecological speciation and its alternative. Science 323:737–741

    PubMed  CAS  Google Scholar 

  • Schmitt-Wagner D, Friedrich MW, Wagner B, Brune A (2003) Phylogenetic diversity, abundance, and axial distribution of bacteria in the intestinal tract of two soil-feeding termites. Appl Environ Microbiol 69:6007–6017

    PubMed  CAS  Google Scholar 

  • Schopf JW (1993) Microfossils of the early Archean Apex chert: new evidence of the antiquity of life. Science 260:640–646

    PubMed  CAS  Google Scholar 

  • Sharon G, Segal D, Ringo JM, Zilber-Rosenberg I, Rosenberg E (2010) Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proc Natl Acad Sci USA 107:20051–20056

    PubMed  CAS  Google Scholar 

  • Sharp KH, Eam B, Faulkner DJ, Haygood MG (2007) Vertical transmission of diverse microbes in the tropical sponge Corticium sp. Appl Environ Microbiol 73:622–629

    PubMed  CAS  Google Scholar 

  • Shashar N, Cohen Y, Loya Y, Sar N (1994) Nitrogen fixation (acetylene reduction) in stony corals: evidence for coral–bacteria interactions. Mar Ecol Prog Ser 111:259–264

    CAS  Google Scholar 

  • She X, Jiang Z, Clark RA, Liu G et al (2004) Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431:927–930

    PubMed  CAS  Google Scholar 

  • Shnit-Orland M, Kushmaro A (2009) Coral mucus-associated bacteria: a possible first line of defense. FEMS Microbiol Ecol 67:371–380

    PubMed  CAS  Google Scholar 

  • Silva AM, Barbosa FH, Duarte R et al (2004) Effect of Bifidobacterium longum ingestion on experimental salmonellosis in mice. J Appl Microbiol 97:29–37

    PubMed  CAS  Google Scholar 

  • Singh BK, Millard P, Whiteley AS, Murrell JC (2004) Unravelling rhizosphere–microbial interactions: opportunities and limitations. Trends Microbiol 12:386–393

    PubMed  CAS  Google Scholar 

  • Smith KP, Handelsman J, Goodman RM (1999) Genetic basis in plants for interactions with disease-suppressive bacteria. Proc Natl Acad Sci USA 96:4786–4790

    PubMed  CAS  Google Scholar 

  • Somers E, Vanderleyden J, Srinivasan M (2004) Rhizosphere bacterial signalling: a love parade beneath our feet. Crit Rev Microbiol 30:205–240

    PubMed  CAS  Google Scholar 

  • Stappenbeck TS, Hooper LV, Gordon JI (2002) Developmental regulation of intestinal angiogenesis by Peneth cells. Proc Natl Acad Sci USA 99:15451–15455

    PubMed  CAS  Google Scholar 

  • Stecher B, Hardt WD (2008) The role of microbiota in infectious disease. Trends Microbiol 16:107–114

    PubMed  CAS  Google Scholar 

  • Stougaard J (2000) Regulators and regulation of legume root nodule development. Plant Physiol 124:531–540

    PubMed  CAS  Google Scholar 

  • Stow A, Beattie A (2008) Chemical and genetic defenses against disease in insect societies. Brain Behav Immun 22:1009–1013

    PubMed  CAS  Google Scholar 

  • Sundset MA, Praesteng KE, Cann IK, Mathiesen SD, Mackie RI (2007) Novel rumen bacterial diversity in two geographically separated sub-species of reindeer. Microb Ecol 54:424–438

    PubMed  Google Scholar 

  • Tannock G (1995) Normal microflora. Chapman & Hall, London

    Google Scholar 

  • Taylor MW, Radax R, Steger D, Wagner M (2007) Sponge associated microorganisms: evolution, ecology and biotechnological potentials. Microbiol Mol Biol Rev 71:295–347

    PubMed  CAS  Google Scholar 

  • Thingstad TF, Lignell R (1997) Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat Microb Ecol 13:19–27

    Google Scholar 

  • Turnbaugh PJ, Ley RE, Mahowald MA et al (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031

    PubMed  Google Scholar 

  • van der Heijden MGA, Bardgett RD, van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310

    PubMed  Google Scholar 

  • Veneti ZL, Reuter M, Montenegro H et al (2005) Interactions between inherited bacteria and their hosts: the Wolbachia paradigm. In: McFall Ngai MJ, Henderson B, Ruby EG (eds) The influence of cooperative bacteria on animal host biology. Cambridge University Press, New York, pp 119–141

    Google Scholar 

  • Visick KL, Foster J, Doino J, McFall-Ngai MJ, Ruby EG (2000) Vibrio fischeri lux genes play an important role in colonization and development of the host light organ. J Bact 182:4578–4586

    PubMed  CAS  Google Scholar 

  • Wallace RJ (2004) Antimicrobial properties of plant secondary metabolites. Proc Nutr Soc 63:621–629

    PubMed  CAS  Google Scholar 

  • Warnecke F, Luginbu P, Ivanova N et al (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560–565

    PubMed  CAS  Google Scholar 

  • Watanabe H, Tokuda G (2010) Cellulolytic systems in insects. Annu Rev Entomol 55:609–632

    PubMed  CAS  Google Scholar 

  • Webster NS, Wilson KJ, Blackall LL, Hill RT (2001) Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile. Appl Environ Microbiol 67:434–444

    PubMed  CAS  Google Scholar 

  • Weimer PJ, Waghorn GC, Odt CL et al (1999) Effect of diet on populations of three species of ruminal cellulolytic bacteria in lactating dairy cows. J Dairy Sci 82:122–134

    PubMed  CAS  Google Scholar 

  • Weisskopf L, Abou-Mansour E, Fromin N et al (2006) White lupin has developed a complex strategy to limit microbial degradation of secreted citrate required for phosphate acquisition. Plant Cell Environ 29:919–927

    PubMed  CAS  Google Scholar 

  • Weitz JS, Hartman H, Levin SA (2005) Coevolutionary arms races between bacteria and bacteriophage. Proc Natl Acad Sci USA 102:9535–9540

    PubMed  CAS  Google Scholar 

  • Whipps JM, Hand P, Pink D, Bending GD (2008) Phyllosphere microbiology with special reference to diversity and plant genotype. J Appl Microbiol 105:1744–1755

    PubMed  CAS  Google Scholar 

  • Wilkinson DM (2001) Mycorrhizal evolution. Trends Ecol Evol 16:64–65

    PubMed  Google Scholar 

  • Wilson EO (1992) The diversity of life. W. W. Norton, New York

    Google Scholar 

  • Wostmann BS (1981) The germ-free animal in nutritional studies. Annu Rev Nutr 1:257–297

    PubMed  CAS  Google Scholar 

  • Wostmann BS, Larkin C, Moriarty A, Bruckner-Kardoss E (1983) Dietary intake, energy metabolism and excretory losses of adult male germfree Wistar rats. Lab Anim Sci 33:46–50

    PubMed  CAS  Google Scholar 

  • Yachi S, Loreau M (1999) Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc Natl Acad Sci USA 96:1463–1468

    PubMed  CAS  Google Scholar 

  • Yang CH, Crowley DE, Borneman J, Keen NT (2001) Microbial phyllosphere populations are more complex than previously realized. Proc Natl Acad Sci USA 98:3889–3894

    PubMed  CAS  Google Scholar 

  • Yen JH, Barr AR (1971) New hypothesis of the cause of cytoplasmic incompatibility in Culex pipens. Nature 232:657–658

    PubMed  CAS  Google Scholar 

  • Zilber-Rosenberg I, Rosenberg E (2008) Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev 32:723–735

    PubMed  CAS  Google Scholar 

  • Zilber-Rosenberg I, Rosenberg E (2011) Prebiotics and probiotics within the framework of the hologenome concept. J Microb Biochem Technol http://dx.doi.org/10.4172/1948-5948.S1-001

  • Zoetendal EG, Akkermans ADL, Akkermans-van Vliet WM et al (2001) A host genotype affects the bacterial community in the human gastrointestinal tract. Microb Ecol Health Dis 13:129–134

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, 69978, Israel

    Dr. Eugene Rosenberg

  2. Independant Scholar, 18 Rachavat Ilan St., Givat Shmuel, Israel

    Ilana Zilber-Rosenberg

Authors
  1. Dr. Eugene Rosenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ilana Zilber-Rosenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Eugene Rosenberg .

Editor information

Editors and Affiliations

  1. Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel

    Eugene Rosenberg

  2. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Edward F. DeLong

  3. Department of Microbiology and Immunology, Harvard Medical School, Boston, MA, USA

    Stephen Lory

  4. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany

    Erko Stackebrandt

  5. Laboratory of Microbiology, Institute of Biology, Center for Health Sciences, Federal University of Rio de Janeiro (UFRJ), Ilha do Fundão, Rio de Janeiro, Brazil

    Fabiano Thompson

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this entry

Cite this entry

Rosenberg, E., Zilber-Rosenberg, I. (2013). Role of Microorganisms in Adaptation, Development, and Evolution of Animals and Plants: The Hologenome Concept. In: Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., Thompson, F. (eds) The Prokaryotes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30194-0_117

Download citation

Publish with us

Policies and ethics

Search

Navigation