Abstract (Chap.13)
To date, we know of two types of cellular organisms: prokaryotes (Bacteria and Archaea) and eukaryotes (protists, fungi, plants and animals). How are, or were, they evolutionarily related? Contemporary eukaryotes are defined as chimeras integrated by at least two types of cells: an ancient bacterium transformed into mitochondria and the host cell, probably from an archaeal lineage known as ‘Asgard’ archaea. Most known prokaryotes have been found to exist in association with eukaryotes. Thus, what was formerly considered an individual “organism”, such as a given plant or animal, is in fact a set of many different organisms living and evolving together, a complex co-evolving assemblage known as a “holobiont”. The concept of holobiont is an essential life-changing force that has resulted in a complex coordinated coevolution of life forms.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Berkermer SJ, McGlynn AE (2020) A new analysis of archaea-bacteria domain separation: variable phylogenetic distance and the tempo of early evolution. Mol Biol Evol:1–16. https://doi.org/10.1093/molbev/mst012
Berlanga M (2015) Functional symbiosis and communication in microbial exosystems. The case of wood-eating termites and cockroaches. Int Microbiol 18:159–169. https://doi.org/10.2436/20.1501.01.246
Berlanga M, Guerrero R (2016a) Living together in biofilms: the microbial cell factory and its biotechnological implications. Microb Cell Factories 15:165. https://doi.org/10.1186/s12934-016-0569-5
Berlanga M, Guerrero R (2016b) The holobiont concept: the case of xylophagous termites and cockroaches. Symbiosis 68:49–60. https://doi.org/10.1007/s13199-016-0388-9
Berlanga M, Paster BJ, Guerrero R (2009) The taxophysiological paradox: changes in the intestinal microbiota of the xylophagous cockroach Cryptocercus punctulatus depending on the physiological state of the host. Int Microbiol 12:227–236. https://doi.org/10.2436/20.1501.01.102
Berlanga M, Palau M, Guerrero R (2018) Gut microbiota dynamics and functionality in Reticulitermes grassei after a 7-day dietery shift and ciprofloxacin treatment. PLoS One 13(12):e0209789. https://doi.org/10.1371/journal.pone.0209789
Bhadra U, Thakkar N, Das P, Bhadra MP (2017) Evolution of circadian rhythms: from bacteria to human. Sleep Med 35:49–61. https://doi.org/10.1016/j.sleep.2017.04.008
Boedeker C, Schüler M, Reintjes G, Jeske O, van Teeseling MCF, Jogler M et al (2017) Determining the bacterial cell biology of Planctomycetes. Nat Commun 8:14853. https://doi.org/10.1038/ncomms14853
Brown K, Wolf JM, Prados-Rosles R, Casadevall A (2015) Through the wall: extracellular vesicles in Gram-positive bacteria, mycobacteria and fungi. Nat Rev Microbiol 13:620–630. https://doi.org/10.1038/nrmicro3480
Cabeen MT, Jacobs-Wagner C (2010) The bacterial cytoskeleton. Annu Rev Genet 44:356–392. https://doi.org/10.1146/annurev-genet-102108-134845
Caforio A, Siliakus MF, Exterkate M, Jain S, Jumde VR, Andringa RLH et al (2018) Converting Escherichia coli into an archaeobacterium with a hybrid heterochiral membrane. Proc Natl Acad Sci U S A 115:3704–3709. https://doi.org/10.1073/pnas.1721604115
Cohen SE, Golden SS (2015) Circadian rhythms in cyanobacteria. Microbiol Mol Biol Rev 79:373–385. https://doi.org/10.1128/MMBR.00036-15
Cornish-Bowden A, Cárdenas ML (2017) Life before LUCA. J Theor Biol 434:68–74. https://doi.org/10.1016/j.jtbi.2017.05.023
Dean SN, Rimmer MA, Turner KB, Phillips DA, Caruana JC, Hervey WJ IV et al (2020) Lactobacillus acidophilus membrane vesicles as a vehicle of bacteriocin delivery. Front Microbiol. https://doi.org/10.3389/fmicb.2020.00710
Doolittle WF (2017) Darwinizing Gaia. J Theor Biol 434:11–19. https://doi.org/10.1016/j.jtbi.2017.02.015
Eldredge N, Gould SJ (1977) Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology 3:115–151
Eme L, Sharpe SC, Brown MW, Roger AJ (2014) On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. Cold Spring Harb Perspect Biol 6:a016139. https://doi.org/10.1101/cshperspect.a016139
Eme L, Spang A, Lombard J, Stairs CW, Ettema TJ (2017) Archaea and the origin of eukaryotes. Nat Rev Microbiol 15:711–723. https://doi.org/10.1038/nrmicro.2017.133
Falkowski P, Fenchel T, Delong EF (2008) The microbial engines that drive earth’s biogeochemical cycles. Science 320:1034–1039. https://doi.org/10.1126/science.1153213
Faust K, Lahti L, Gonze D, de Vos WM, Raes J (2015) Metagenomics meets time series analysis: unraveling microbial community dynamics. Curr Opin Microbiol 25:56–66. https://doi.org/10.1016/j.mib.2015.04.004
Flint HJ, Scott KP, Louis P, Duncan SH (2012) The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 9:577–589. https://doi.org/10.1038/nrgastro.2012.156
Friedman JR, Nunnari J (2014) Mitochondrial form and function. Nature 505:335–343. https://doi.org/10.1038/nature12985
Giacomello M, Pyakurel A, Glytsou C, Scorrano L (2020) The cell biology of mitochondrial membrane dynamics. Nat Rev Mol Cell Biol 21:204–224. https://doi.org/10.1038/s41580-020-0210-7
Gould AL, Zhang V, Lamberti L, Jones EW, Obadia B, Korasidis N et al (2018) Microbiome interactions shape host fitness. Proc Natl Acad Sci U S A 115:E11951–E11960. https://doi.org/10.1073/pnas.1809349115
Govindarajan S, Amster-Choder O (2016) Where are things inside a bacterial cell? Curr Opin Microbiol 33:83–90. https://doi.org/10.1016/j.mib.2016.07.003
Guerrero R (1998) Crucial crises in biology: life in the deep biosphere. Int Microbiol 1:285–294
Guerrero R, Berlanga M (2006) Life’s unity and flexibility: the ecological link. Int Microbiol 9:225–235
Guerrero R, Berlanga M (2007) The hidden side of the prokaryotic cell: rediscovering the microbial world. Int Microbiol 10:157–168. https://doi.org/10.2436/20.1501.01.23
Guerrero R, Berlanga M (2016) From the cell to the ecosystem: the physiological evolution of simbiosis. Evol Biol 43:543–552. https://doi.org/10.1007/s11692-015-9360-5
Guerrero R, Piqueras M, Berlanga M (2002) Microbial mats and the search for minimal ecosystems. Int Microbiol 5:177–188
Guerrero R, Margulis L, Berlanga M (2013) Symbiogenesis: the holobiont as a unit of evolution. Int Microbiol 16:133–143. https://doi.org/10.2436/20.1501.01.188
Häcker G (2013) Is there, and should there be, apoptosis in bacteria? Microbes Infect 15:640–644. https://doi.org/10.1016/j.micinf.2013.05.005
Holland HD (2006) The oxygenation of the atmosphere and oceans. Philos Trans R Soc B 361:903–915
Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki T et al (2020) Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577:519. https://doi.org/10.1038/s41586-019-1916-6
Jarett JK, Nayfach S, Podar M, Inskeep W, Ivanova NN, Munson-McGee J et al (2018) Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis. Microbiome 6:161. https://doi.org/10.1186/s40168-018-0539-8
Kluyver AJ, van Niel CB (1956) The microbe’s contribution to biology. Harvard University Press, Cambridge, MA
Koonin EV, Zhang F (2016) Coupling immunity and programmed cell suicide in prokayotes: life-or-death choices. Bioessays 39:1–9. https://doi.org/10.1002/bies.201600186
Lederberg J (2006) The microbe’s contribution to biology—50 years after. Int Microbiol 9:155–156
Lederberg J, McCray AT (2001) ‘Ome sweet’ omics—a genealogical treasury of words. Scientist 15:8
Lewis K (2000) Programmed death in bacteria. Microbiol Mol Biol Rev 64:503–514
Liang X, FitzGerald GA (2017) Timing the microbes: the circadian rhythm of the gut microbiome. J Biol Rhythm 32(6):505–515. https://doi.org/10.1177/0748730417729066
Lin Z, Nei M, Ma H (2007) The origins and early evolution of DNA mismatch repair genes–multiple horizontal gene transfers and co-evolution. Nucleic Acids Res 35:7591–7603. https://doi.org/10.1093/nar/gkm921
Liu Z, Müller J, Li T, Alvey RM, Vogl K, Frigaard NU et al (2013) Genomic analysis reveals key aspects of prokaryotic simbiosis in the phototrophic consortium “Chlorochromatium aggegatum”. Genome Biol 14:R127. https://doi.org/10.1186/gb-2013-14-11-r127
López-García P, Moreira D (2015) Open questions on the origin of eukaryotes. Trends Ecol Evol 30:697–708. https://doi.org/10.1016/j.tree.2015.09.005
López-García P, Eme L, Moreira D (2017) Symbiosis in eukaryotic evolution. J Theor Biol 434:20–33. https://doi.org/10.1016/j.jtbi.2017.02.031
Lovelock J (2019) Novacene. The coming age of hyperintelligence. Penguin Random House, London
Lyons TW, Reinhard CT, Planavsky NJ (2014) The rise of oxygen in Earth’s early ocean and atmosphere. Nature 506:307–315. https://doi.org/10.1038/nature13068
Margulis L (1998) Symbiotic planet: a new look at evolution. Basic Books, New York
Margulis L, Dolan MF, Guerrero R (2000) The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists. Proc Natl Acad Sci U S A 97:6954–6959
McFall-Ngai MJ (2002) Unseen forces: the influence of bacteria on animal development. Dev Biol 242:1–14
McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N et al (2011) Planctomycetes and eukaryotes: a case of analogy not homology. BioEssays 33:810–817. https://doi.org/10.1002/bies.201100045
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 12:449–455. https://doi.org/10.1038/nrmicro3271
Munson-McGee JH, Field EK, Batenson M, Rooney C, Stepanauskas R, Young MJ (2015) Nanoarchaeota, their Sulfolobales host, and Nanoarchaeota virus distribution across Yellowstone National Park hot springs. Appl Environ Microbiol 81:7860–7868. https://doi.org/10.1128/AEM.01539-15
Nadell CD, Xavier JB, Foster KR (2008) The sociobiology of biofilms. FEMS Microbiol Rev 33:206–224. https://doi.org/10.1111/j.1574-6976.2008.00150.x
Nakamura Y, Yamamoto N, Kino Y, Yamamoto N, Kamai S et al (2016) Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities. Appl Microbiol Biotechnol 100:7263–7279. https://doi.org/10.1007/s00253-016-7532-6
Nikolic N (2019) Autoregulation of bacterial gene expression: lessons from the MazEF toxin-antitoxin system. Curr Genet 65:133–138. https://doi.org/10.1007/s00294-018-0879-8
Oshiki M, Satoh H, Okabe S (2016) Ecology and physiology of anaerobic ammonium oxidizing bacteria. Environ Microbiol 18:2784–2796. https://doi.org/10.1111/1462-2920.13134
Parkar SG, Kalsbeek A, Cheeseman JE (2019) Potential role for the gut microbiota in modulating host circadian rhytms and metabolic health. Microorganisms 7:41. https://doi.org/10.3390/microorganisms7020041
Pathirana RD, Kaparakis-Liaskos M (2016) Bacterial membrane vesicles: biogenesis, immune regulation and pathogenesis. Cell Microbiol 18:1518–1524. https://doi.org/10.1111/cmi.12658
Paulose JK, Wright JM, Patel AG, Cassine VM (2016) Human gut bacteria are sensitive to melatonin and express endogenous circadian rhythmicity. PLoS One 11(1):e0146643. https://doi.org/10.1371/journal.pone.0146643
Pérez-Cruz C, Delgado L, López-Iglesias C, Mercade E (2015) Outer-inner membrane vesicles naturally secretes by Gram-negative pathogenic bacteria. PLoS One 10(1):e0116896. https://doi.org/10.1371/journal.pone.0116896
Pilhofer M, Jensen GJ (2013) The bacterial cytoskeleton: more than twisted filaments. Curr Opin Cell Biol 25:125–133. https://doi.org/10.1016/j.ceb.2012.10.019
Quispel A (1998) Lourens G.M. Baas Becking (1895–1963), inspirator for many (micro)biologists. Int Microbiol 1:69–72
Rivera MC, Jain R, Moore JE, Lake JA (1998) Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci U S A 95:6239–6244. https://doi.org/10.1073/pnas.95.11.6239
Sachs JL, Hollowed AC (2012) The origins of cooperative bacterial communities. mBio. https://doi.org/10.1128/mBio.000099-12
Sagan L (1967) On the origin of mitosing cells. J Theor Biol 14:255–274
Sánchez-Romero MA, Casadesús J (2020) The bacterial epigenome. Nat Rev Microbiol 18:7–20. https://doi.org/10.1038/s41579-019-0286-2
Schaechter M (2006) From physiology to systems biology. Int Microbiol 9:157–161
Schwechheimer C, Kuehn M (2015) Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions. Nat Rev Microbiol 13:605–619
Sieber JR, Mclnemey MJ, Gunsalus RP (2012) Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation. Annu Rev Microbiol 66:429–452. https://doi.org/10.1146/annurev-micro-090110-102844
Sousa FL, Nelson-Sathi S, Martin WF (2016) One step beyond a ribosome: the ancient anaerobic core. Biochim Biophys Acta 1857:1027–1038. https://doi.org/10.1016/j.bbabio.2016.04.284
Spang A, Saw JH, Jorgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE et al (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–179. https://doi.org/10.1038/nature14447
Thiergart T, Landan G, Schenk M, Dagan T, Martin WF (2012) An evolutionary network of genes present in the Eukaryote Common Ancestors polls genomes on eukaryotic and microchondrial origin. Genome Biol Evol 4:466–485. https://doi.org/10.1093/gbe/evs018
Timmers PHA, Gieteling J, Widjaja-Greefkes A, Plugge CM, Stams AJM, Lens PNL et al (2015) Growth of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a high-pressure membrane capsule bioreactor. Appl Environ Microbiol 81:1286–1296. https://doi.org/10.1128/AEM.03255-14
Updegrove TB, Ramamurthi KS (2017) Geometric protein localization cues in bacterial cells. Curr Opin Microbiol 36:7–13. https://doi.org/10.1016/j.mib.2016.12.001
Ward LM, Kirschvink JL, Fischer WW (2016) Timescales of oxygenation following the evolution of oxygenic photosynthesis. Orig Life Evol Biosph 46:51–65. https://doi.org/10.1007/s11084-015-9460-3
Wein T, Romero-Picazo D, Blow F, Whoehle C, Jami E, Reusch TBH et al (2019) Currency, exchange, and inheritance in the evolution of symbiosis. Trends Microbiol 27:836–849. https://doi.org/10.1016/j.tim.2019.05.010
Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF (2016) The physiology and habitat of the last universal common ancestor. Nat Microbiol 1(9):16116. https://doi.org/10.1038/NMICROBIOL.2016.116
Welte CU, Rasigraf O, Vaksmaa A, Op den Camp HJM, Jetten MSM, Üke LC et al (2016) Nitrate- and nitrite-depenent anaerobic oxidation of methane. Environ Microbiol Rep 8:941–955. https://doi.org/10.1111/1758-2229.12487
Wiegand S, Jogler M, Jogler C (2018) On the maverick Planctomycetes. FEMS Microbiol Rev 42:739–760. https://doi.org/10.1093/femsre/fuy029
Williams TA, Foster PG, Cox CJ, Embley TM (2013) An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504:231–236. https://doi.org/10.1038/nature12779
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87:4576–4579
Yu Y-J, Wang X-H, Fan G-C (2018) Versatile effects of bacterium-releases membrane vesicles on mammalian cells and infectious/inflammatory diseases. Acta Pharmacol Sin 39:514–533. https://doi.org/10.1038/aps.2017.82
Yun JH, Roh SW, Whon TW, Jung MJ, Kim MS, Park DS et al (2014) Insect gut bacterial diversity determined by environmental habitat, diet, developmental stage, and phylogeny of host. Appl Environ Microbiol 80:5254–5264. https://doi.org/10.1128/AEM.01226-14
Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Backstrom D, Juzokaite L, Vancaester E et al (2017) Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541:353–358. https://doi.org/10.1038/nature21031
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Berlanga, M., Viñas, M., Guerrero, R. (2021). Prokaryotic Basis of Eukaryotic Eco-Evo Development. In: Villa, T.G., de Miguel Bouzas, T. (eds) Developmental Biology in Prokaryotes and Lower Eukaryotes. Springer, Cham. https://doi.org/10.1007/978-3-030-77595-7_13
Download citation
DOI: https://doi.org/10.1007/978-3-030-77595-7_13
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-77594-0
Online ISBN: 978-3-030-77595-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)