The Relevance and Challenges of Studying Microbial Evolution

  • Pabulo Henrique RampelottoEmail author
Part of the Grand Challenges in Biology and Biotechnology book series (GCBB)


The evolution of microbes had been underway for about 3 billion years, covering much of the earlier evolutionary history of life. Many of the genes, molecular machines, regulatory, metabolic, and synthetic pathways found in all living organisms today evolved first in microorganisms. Even now, most of the biodiversity of life on Earth is microbial. The great diversity of microbes allows them to synthesize or break down a vast range of chemical substrates and govern biogeochemical cycles that make Earth a habitable planet. As such, microbes are essential to Earth’s functioning at every scale, and understanding them is essential for a complete understanding of life. As a brief introduction to this book, herein I highlight some of the reasons why understanding how microbes evolve is important to science and society and how challenging is to study microbial evolution.


  1. Adams J, Rosenzweig F (2014) Experimental microbial evolution: history and conceptual underpinnings. Genomics 104(6 Pt A):393–398CrossRefGoogle Scholar
  2. Alegado RA, King N (2014) Bacterial influences on animal origins. Cold Spring Harb Perspect Biol 6(11):a016162CrossRefGoogle Scholar
  3. Alkım C, Turanlı-Yıldız B, Cakar ZP (2014) Evolutionary engineering of yeast. Methods Mol Biol 1152:169–183CrossRefGoogle Scholar
  4. Arora T, Bäckhed F (2016) The gut microbiota and metabolic disease: current understanding and future perspectives. J Intern Med 280(4):339–349CrossRefGoogle Scholar
  5. Bakermans C (2015) Microbial evolution under extreme conditions. Walter de Gruyter, BerlinCrossRefGoogle Scholar
  6. Bardgett RD, Freeman C, Ostle NJ (2008) Microbial contributions to climate change through carbon cycle feedbacks. ISME J 2(8):805–814CrossRefGoogle Scholar
  7. Bentley SD, Parkhill J (2015) Genomic perspectives on the evolution and spread of bacterial pathogens. Proc Biol Sci 282(1821):20150488CrossRefGoogle Scholar
  8. Bosch TCG, Miller DJ (2016) The holobiont imperative: perspectives from early emerging animals. Springer, LondonCrossRefGoogle Scholar
  9. Britton T, House T, Lloyd AL, Mollison D, Riley S, Trapman P (2015) Five challenges for stochastic epidemic models involving global transmission. Epidemics 10:54–57CrossRefGoogle Scholar
  10. Cakar ZP, Turanli-Yildiz B, Alkim C, Yilmaz U (2012) Evolutionary engineering of Saccharomyces cerevisiae for improved industrially important properties. FEMS Yeast Res 12(2):171–182CrossRefGoogle Scholar
  11. Elena SF, Lenski RE (2003) Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4(6):457–469CrossRefGoogle Scholar
  12. EPA (2018) Inventory of U.S. greenhouse gas. Emissions and sinks: 1990–2016. U.S. Environmental Protection Agency, WashingtonGoogle Scholar
  13. Foster JA, Lyte M, Meyer E, Cryan JF (2016) Gut microbiota and brain function: an evolving field in neuroscience. Int J Neuropsychopharmacol 19(5):pyv114CrossRefGoogle Scholar
  14. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R (2018) Current understanding of the human microbiome. Nat Med 24(4):392–400CrossRefGoogle Scholar
  15. Goodman B, Gardner H (2018) The microbiome and cancer. J Pathol 244(5):667–676CrossRefGoogle Scholar
  16. Hamilton TL, Bryant DA, Macalady JL (2016) The role of biology in planetary evolution: cyanobacterial primary production in low-oxygen Proterozoic oceans. Environ Microbiol 18(2):325–340CrossRefGoogle Scholar
  17. Jackson RW, Johnson LJ, Clarke SR, Arnold DL (2012) Bacterial pathogen evolution: breaking news. Trends Genet 27(1):32–40CrossRefGoogle Scholar
  18. Kashyap PC, Chia N, Nelson H, Segal E, Elinav E (2017) Microbiome at the frontier of personalized medicine. Mayo Clin Proc 92(12):1855–1864CrossRefGoogle Scholar
  19. Koonin EV, Wolf YI (2012) Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol 2:119CrossRefGoogle Scholar
  20. Ladau J, Shi Y, Jing X, He J-S, Chen L, Lin X, Fierer N, Gilbert JA, Pollard KS, Chu H (2018) Climate change will lead to pronounced shifts in the diversity of soil microbial communities. bioRxiv 180174.
  21. Lloyd-Smith JO, Funk S, McLean AR, Riley S, Wood JL (2015) Nine challenges in modelling the emergence of novel pathogens. Epidemics 10:35–39CrossRefGoogle Scholar
  22. Long PE, Williams KH, Hubbard SS, Banfield JF (2016) Microbial metagenomics reveals climate-relevant subsurface biogeochemical processes. Trends Microbiol 24(8):600–610CrossRefGoogle Scholar
  23. Martínez JL (2013) Bacterial pathogens: from natural ecosystems to human hosts. Environ Microbiol 15(2):325–333CrossRefGoogle Scholar
  24. McFall-Ngai M, Hadfield MG, Bosch TC et al (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci USA 110(9):3229–3236CrossRefGoogle Scholar
  25. Nazaries L, Pan Y, Bodrossy L, Baggs EM, Millard P, Murrell JC, Singh BK (2013) Evidence of microbial regulation of biogeochemical cycles from a study on methane flux and land use change. Appl Environ Microbiol 79(13):4031–4040CrossRefGoogle Scholar
  26. Nuccio SP, Bäumler AJ (2015) Reconstructing pathogen evolution from the ruins. Proc Natl Acad Sci USA 112(3):647–648CrossRefGoogle Scholar
  27. O’Malley MA (2018) The experimental study of bacterial evolution and its implications for the modern synthesis of evolutionary biology. J Hist Biol 51(2):319–354. CrossRefPubMedGoogle Scholar
  28. Paun A, Yau C, Danska JS (2017) The influence of the microbiome on type 1 diabetes. J Immunol 198(2):590–595CrossRefGoogle Scholar
  29. Petrosino JF (2018) The microbiome in precision medicine: the way forward. Genome Med 10(1):12CrossRefGoogle Scholar
  30. Rampelotto PH (2010) Resistance of microorganisms to extreme environmental conditions and its contribution to astrobiology. Sustainability 2(6):1602–1623CrossRefGoogle Scholar
  31. Rampelotto PH (2013) Extremophiles and extreme environments. Life 3(3):482–485CrossRefGoogle Scholar
  32. Rosenberg E, Zilber-Rosenberg I (2016) Microbes drive evolution of animals and plants: the hologenome concept. MBio 7(2):e01395CrossRefGoogle Scholar
  33. Rothman DH, Fournier GP, French KL, Alm EJ, Boyle EA, Cao C, Summons RE (2014) Methanogenic burst in the end-Permian carbon cycle. Proc Natl Acad Sci USA 111(15):5462–5467CrossRefGoogle Scholar
  34. Rousk J, Bååth E (2011) Growth of saprotrophic fungi and bacteria in soil. FEMS Microbiol Ecol 78:17–30CrossRefGoogle Scholar
  35. Rousk J, Bengtson P (2014) Microbial regulation of global biogeochemical cycles. Front Microbiol 5:103CrossRefGoogle Scholar
  36. Sahney S, Benton MJ (2008) Recovery from the most profound mass extinction of all time. Proc R Soc Lond B 275(1636):759–765CrossRefGoogle Scholar
  37. Schirrmeister BE, de Vos JM, Antonelli A, Bagheri HC (2013) Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. Proc Natl Acad Sci USA 110(5):1791–1796CrossRefGoogle Scholar
  38. Schirrmeister BE, Gugger M, Donoghue PC (2015) Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils. Palaeontology 58(5):769–785CrossRefGoogle Scholar
  39. Schuur EA, McGuire AD, Schädel C et al (2015) Climate change and the permafrost carbon feedback. Nature 520(7546):171–179CrossRefGoogle Scholar
  40. Singh BK, Bardgett RD, Smith P, Reay DS (2010) Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat Rev Microbiol 8(11):779–790CrossRefGoogle Scholar
  41. Soo RM, Hemp J, Parks DH, Fischer WW, Hugenholtz P (2017) On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science 355(6332):1436–1440CrossRefGoogle Scholar
  42. Szukics U, Abell GCJ, Hödl V et al (2010) Nitrifiers and denitrifiers respond rapidly to changed moisture and increasing temperature in a pristine forest soil. FEMS Microbiol Ecol 72:395–406CrossRefGoogle Scholar
  43. Tian H, Lu C, Ciais P et al (2016) The terrestrial biosphere as a net source of greenhouse gases to the atmosphere. Nature 531(7593):225–228CrossRefGoogle Scholar
  44. Tibayrenc M (2017) Genetics and evolution of infectious diseases. Elsevier, LondonGoogle Scholar
  45. Treseder KK, Balser TC, Bradford MA et al (2012) Integrating microbial ecology into ecosystem models: challenges and priorities. Biogeochemistry 109(1–3):7–18CrossRefGoogle Scholar
  46. Vuong HE, Yano JM, Fung TC, Hsiao EY (2017) The microbiome and host behavior. Annu Rev Neurosci 40:21–49CrossRefGoogle Scholar
  47. Ward CP, Nalven SG, Crump BC, Kling GW, Cory RM (2017) Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration. Nat Commun 8(1):772CrossRefGoogle Scholar
  48. Winkler JD, Kao KC (2014) Recent advances in the evolutionary engineering of industrial biocatalysts. Genomics 104(6 Pt A):406–411CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Center of Biotechnology and PPGBCMFederal University of Rio Grande do SulPorto AlegreBrazil

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