Review Article | Published:

Microbial seed banks: the ecological and evolutionary implications of dormancy

Nature Reviews Microbiology volume 9, pages 119130 (2011) | Download Citation

Abstract

Dormancy is a bet-hedging strategy used by a wide range of taxa, including microorganisms. It refers to an organism's ability to enter a reversible state of low metabolic activity when faced with unfavourable environmental conditions. Dormant microorganisms generate a seed bank, which comprises individuals that are capable of being resuscitated following environmental change. In this Review, we highlight mechanisms that have evolved in microorganisms to allow them to successfully enter and exit a dormant state, and discuss the implications of microbial seed banks for evolutionary dynamics, population persistence, maintenance of biodiversity, and the stability of ecosystem processes.

Key points

  • Dormancy is a bet-hedging strategy used by a wide range of taxa, including microorganisms. It refers to an organism's ability to enter a reversible state of low metabolic activity when faced with unfavourable environmental conditions.

  • Dormant microorganisms generate a seed bank, which consists of individuals that are capable of being resuscitated following environmental change. Seed banks can prolong the persistence of genotypes and populations, and also have important consequences for community- and ecosystem-level processes.

  • A review of the literature demonstrates that dormancy is common and phylogenetically widespread. However, microorganisms have evolved diverse genetic and cellular mechanisms for entering and exiting dormancy.

  • Dormancy may help explain various ecological and evolutionary phenomena in microbial systems, including: patterns of biogeography; outbreaks, blooms and successional dynamics; the maintenance of rare taxa; the inability of microbiologists to culture most microorganisms; and the inherent stability of ecosystem services.

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References

  1. 1.

    & Metabolic depression in animals: physiological perspectives and biochemical generalizations. Biol. Rev. Camb. Philos. Soc. 74, 1–40 (1999).

  2. 2.

    , & Fitness consequences of hibernal diapause in the pitcher-plant mosquito, Wyeomyia smithii. Ecology 79, 1458–1462 (1998).

  3. 3.

    Microbial maintenance: a critical review on its quantification. Microb. Ecol. 53, 513–523 (2007).

  4. 4.

    Evolutionary ecology of seed dormancy and seed size. Phil. Trans. R. Soc. B 351, 1299–1308 (1996).

  5. 5.

    & How long to rest: the ecology of optimal dormancy and environmental constraint. Ecology 84, 1189–1198 (2003).

  6. 6.

    & Variability in diapause duration in the chestnut weevil: mixed ESS, genetic polymorphism or bet-hedging? Oikos 100, 574–580 (2003).

  7. 7.

    , & Dormancy in non-sporulating bacteria. FEMS Microbiol. Rev. 10, 271–285 (1993).

  8. 8.

    , , & Halophilic Archaea cultured from ancient halite, Death Valley, California. Environ. Microbiol. 12, 440–454 (2010).

  9. 9.

    et al. Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia. BMC Genomics 9, 417 (2008).

  10. 10.

    & Environmental variability promotes coexistence in lottery competitive systems. Am. Nat. 117, 923–943 (1981). The theoretical development of the storage effect and how it can influence biodiversity.

  11. 11.

    & The role of the seed bank in gap regeneration in a calcareous grassland community. Ecology 83, 1017–1025 (2002).

  12. 12.

    Aquatic microbiology for ecosystem scientists: new and recycled paradigms in ecological microbiology. Ecosystems 2, 215–225 (1999).

  13. 13.

    (ed.) Dormancy and Low-Growth States in Microbial Disease. (Cambridge Univ. Press, Cambridge, UK, 2003).

  14. 14.

    & Dormancy in microbial spores. Ann. Rev. Plant Physiol. 24, 311–352 (1973).

  15. 15.

    & in Microbial Ecology of the Oceans (ed. D. L. Kirchman) 243–298 (Wiley & Sons, 2008). A comprehensive review of the major concepts and techniques used to evaluate single-cell physiologicalstructure.

  16. 16.

    A case for bacterial dormancy in aquatic systems. Microb. Ecol. 4, 127–133 (1977). A classic paper proposing the importance of dormancy in natural ecosystems.

  17. 17.

    & Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39, 321–346 (1985).

  18. 18.

    et al. Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb. Ecol. 8, 313–323 (1982).

  19. 19.

    & Increase in the proportion of metabolically active bacteria along gradients of enrichment in freshwater and marine plankton: implications for estimates of bacterial growth and production rates. J. Plankton Res. 17, 1905–1924 (1995).

  20. 20.

    , , & Temporal changes in bacterial rRNA and rRNA genes in Delaware (USA) coastal waters. Aquat. Microb. Ecol. 57, 123–135 (2009).

  21. 21.

    , & Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons. ISME J. 4, 498–508 (2010).

  22. 22.

    & Dormancy contributes to the maintenance of microbial diversity. Proc. Natl Acad. Sci. USA 107, 5881–5886 (2010).

  23. 23.

    & Species sorting affects bacterioplankton community composition as determined by 16S rDNA and 16S rRNA fingerprints. ISME J. 4, 728–738 (2010).

  24. 24.

    et al. Gene expression profile of Vibrio cholerae in the cold stress-induced viable but non-culturable state. Environ. Microbiol. 9, 869–879 (2007).

  25. 25.

    et al. Proteomic analysis of stationary phase in the marine bacterium “Candidatus Pelagibacter ubique”. Appl. Environ. Microbiol. 74, 4091–4100 (2008).

  26. 26.

    Intramembrane-sensing histidine kinases: a new family of cell envelope stress sensors in Firmicutes bacteria. FEMS Microbiol. Lett. 264, 133–144 (2006).

  27. 27.

    , , & Proteins of Mycobacterium bovis BCG induced in the Wayne dormancy model. J. Bacteriol. 183, 2672–2676 (2001).

  28. 28.

    & Sporulation of Bacillus subtilis. Curr. Opin. Microbiol. 7, 579–586 (2004).

  29. 29.

    & Stress and how bacteria cope with death and survival. Crit. Rev. Microbiol. 30, 263–273 (2004).

  30. 30.

    , , & The asgE locus is required for cell–cell signalling during Myxococcus xanthus development. Mol. Microbiol. 35, 812–824 (2000).

  31. 31.

    , , , & New horizons for (p)ppGpp in bacterial and plant physiology. Trends Microbiol. 14, 45–54 (2006). A thorough review of the mechanisms by which ppGpp and pppGpp influence cell physiology.

  32. 32.

    & Phenotypic diversity, population growth, and information in fluctuating environments. Science 309, 2075–2078 (2005). A theoretical analysis of the conditions that select for responsive versus spontaneous initiation of dormancy.

  33. 33.

    Treatment of staphylococcal infections with penicillin by intermittent sterilisation. Lancet 2, 497–500 (1944).

  34. 34.

    Persister cells, dormancy, and infectious disease. Nature Rev. Microbiol. 5, 48–56 (2007). A review on the biology of persister cells, including the genetic mechanisms regulating this form of dormancy.

  35. 35.

    , , , & Bacterial persistence as a phenotypic switch. Science 305, 1622–1625 (2004).

  36. 36.

    Microbial cell individuality and the underlying sources of heterogeneity. Nature Rev. Microbiol. 4, 577–587 (2006).

  37. 37.

    , & Is bacterial persistence a social trait? PLoS ONE 2, e752 (2007).

  38. 38.

    , , & The transient phase between growth and nongrowth of heterotrophic bacteria, with emphasis on the marine environment. Annu. Rev. Microbiol. 41, 25–49 (1987).

  39. 39.

    , & Content of carbon, nitrogen, oxygen, sulfur, and phosphorus in native aquatic and cultured bacteria. Aquat. Microb. Ecol. 10, 15–27 (1996).

  40. 40.

    et al. Comparative study of the elemental composition of vegetative and resting microbial cells. Microbiology 71, 31–40 (2002).

  41. 41.

    & Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere. (Princeton Univ. Press, Princeton, 2002).

  42. 42.

    Mechanisms for the prevention of damage to DNA in spores of Bacillus species. Annu. Rev. Microbiol. 49, 29–54 (1995).

  43. 43.

    Starvation-survival of heterotrophs in the marine environment. Adv. Microb. Ecol. 6, 171–178 (1982).

  44. 44.

    & Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. Proc. Natl Acad. Sci. USA 101, 4631–4636 (2004).

  45. 45.

    et al. Ancient bacteria show evidence of DNA repair. Proc. Natl Acad. Sci. USA 104, 14401–14405 (2007). Strong empirical evidence for ancient (0.5 million years old) and viable bacteria in permafrost samples.

  46. 46.

    , & Cannibalism by sporulating bacteria. Science 301, 510–513 (2003).

  47. 47.

    , , , & The proton motive force is required for maintaining ATP homeostasis and viability of hypoxic, nonreplicating Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 105, 11945–11950 (2008).

  48. 48.

    , , & Ecological and agricultural significance of bacterial polyhdroxyalkanoates. Crit. Rev. Microbiol. 43, 93–100 (2005).

  49. 49.

    The viable but nonculturable state in bacteria. J. Microbiol. 43, 93–100 (2005).

  50. 50.

    & Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber. Science 268, 1060–1064 (1995).

  51. 51.

    & Dormant bacteria in lake sediments as paleoecological indicators. J. Paleolimnol. 7, 127–135 (1992).

  52. 52.

    et al. Buried in time: culturable fungi in a deep-sea sediment core from the Chagos Trench, Indian Ocean. Deep Sea Res. Part I Oceanogr. Res. Pap. 51, 1759–1768 (2004).

  53. 53.

    , & Isolation of 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature 407, 897–900 (2000).

  54. 54.

    & Life in extreme environments. Nature 409, 1092–1101 (2001).

  55. 55.

    et al. Genetic analyses from ancient DNA. Annu. Rev. Gen. 38, 645–679 (2004).

  56. 56.

    , & Geologically ancient DNA: fact or artefact? Trends Microbiol. 13, 212–220 (2005).

  57. 57.

    & Exit from dormancy in microbial organisms. Nature Rev. Microbiol. 8, 890–896 (2010).

  58. 58.

    Spore germination. Curr. Opin. Microbiol. 6, 550–556 (2003).

  59. 59.

    & Resuscitation of Vibrio vulnificus from the viable but nonculturable state. Appl. Environ. Microbiol. 63, 1002–1005 (1997).

  60. 60.

    & A matter of bacterial life and death. EMBO Rep. 2, 770–774 (2001).

  61. 61.

    , , , & Are the actively respiring cells (CTC+) those responsible for bacterial production in aquatic environments? FEMS Microbiol. Ecol. 35, 171–179 (2001).

  62. 62.

    , & Estimation of dormant Micrococcus luteus cells by penicillin lysis and by resuscitation in cell-free spent culture medium at high dilution. FEMS Microbiol. Lett. 115, 347–352 (1994).

  63. 63.

    , , & On resuscitation from the dormant state of Micrococcus luteus. Antonie Van Leeuwenhoek 73, 237–243 (1998).

  64. 64.

    , , , & A bacterial cytokine. Proc. Natl Acad. Sci. USA 95, 8916–8921 (1998). This article describes the isolation of a quorum sensing protein that is responsible for resuscitating dormant bacteria.

  65. 65.

    , , & Wake up! Peptidoglycan lysis and bacterial non-growth states. Trends Microbiol. 14, 271–276 (2006).

  66. 66.

    , & A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement. BMC Genomics 6, 39 (2005).

  67. 67.

    Microbial awakenings. Nature 457, 1083 (2009).

  68. 68.

    et al. The role of ecological theory in microbial ecology. Nature Rev. Microbiol. 5, 384–392 (2007).

  69. 69.

    & The Theory of Island Biogeography. (Princeton Univ. Press, Princeton, 1967).

  70. 70.

    , & Biogeography. 3rd edn (Sinauer Associates, Sunderland, Massachusetts, 2006).

  71. 71.

    et al. Microbial biogeography: putting microorganisms on the map. Nature Rev. Microbiol. 4, 102–112 (2006).

  72. 72.

    Geobiologie of Inleiding Tot de Milleukeunde (Van Stockum & Zoon, 1934) (in Dutch).

  73. 73.

    et al. A constant flux of diverse thermophilic bacteria into the cold Arctic seabed. Science 325, 1541–1544 (2009).

  74. 74.

    Synthesizing traditional biogeography with microbial ecology: the importance of dormancy. J. Biogeogr. 37, 1835–1841 (2010).

  75. 75.

    , , & A taxa–area relationship for bacteria. Nature 432, 750–753 (2004). This article provides empirical evidence demonstrating that bacterial populations have biogeographical distributions.

  76. 76.

    Predation on prokaryotes in the water column and its ecological implications. Nature Rev. Microbiol. 3, 537–546 (2005).

  77. 77.

    , , & Bacterial competition: surviving and thriving in the microbial jungle. Nature Rev. Microbiol. 8, 15–25 (2010).

  78. 78.

    et al. Alexandrium fundyense cyst dynamics in the Gulf of Maine. Deep Sea Res. Part II Top. Stud. Oceanogr. 52, 2522–2542 (2005).

  79. 79.

    Physiological ecology of plant succession. Annu. Rev. Ecol. Syst. 10, 351–371 (1979).

  80. 80.

    , , & Changes through time: integrating microorganisms into the study of succession. Res. Microbiol. 161, 635–642 (2010).

  81. 81.

    The role of seed banks in vegetation dynamics and restoration of dry tropical ecosystems. J. Veg. Sci. 3, 357–360 (1992).

  82. 82.

    et al. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl Acad. Sci. USA 103, 13104–13109 (2006).

  83. 83.

    , , , & Typhoons initiate predictable change in aquatic bacterial communities. Limnol. Oceanogr. 53, 1319–1326 (2008).

  84. 84.

    & Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13, 278–284 (2005).

  85. 85.

    et al. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl Acad. Sci. USA 103, 12115–12120 (2006).

  86. 86.

    , , & Ecology of the rare microbial biosphere of the Arctic Ocean. Proc. Natl Acad. Sci. USA 106, 22427–22432 (2009).

  87. 87.

    , , , & Large-scale paterns in biodiversity of microbial eukaryotes from the abyssal sea floor. Proc. Natl Acad. Sci. USA 107, 115–120 (2010).

  88. 88.

    , & Population dynamic principles (and discussion). Phil. Trans. R. Soc. B 344, 61–68 (1994).

  89. 89.

    Marine microbial diversity: can it be determined? Trends Microbiol. 14, 257–263 (2006).

  90. 90.

    & Microbial diversity and the genetic nature of microbial species. Nature Rev. Microbiol. 6, 431–440 (2008).

  91. 91.

    Central role of the cell in microbial ecology. Microbiol. Mol. Biol. Rev. 73, 712–729 (2009).

  92. 92.

    & Physiological and ecological adaptations of slow-growing, heterotrophic microbes and consequences for cultivation. Microbiol. Monogr. 10, 101–120 (2009).

  93. 93.

    , & Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 296, 1127–1129 (2002).

  94. 94.

    , , , & New strategies for cultivation and detection of previously uncultured microbes. Appl. Environ. Microbiol. 70, 4748–4755 (2004).

  95. 95.

    , , , & The viable but non-culturable phenomenon explained? Microbiology 144, 1–3 (1998).

  96. 96.

    & Cryptic freshwater ciliates in a hypersaline lagoon. Protist 154, 411–418 (2003).

  97. 97.

    , & Cyclic AMP and acyl homoserine lactons increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl. Environ. Microbiol. 68, 3978–3987 (2002).

  98. 98.

    , , , & The contribution of species richness and composition to bacterial services. Nature 436, 1157–1160 (2005).

  99. 99.

    et al. Diversity predicts stability and resource use efficiency in natural phytoplankton communities. Proc. Natl Acad. Sci. USA 105, 5134–5138 (2008).

  100. 100.

    , , & Biodiversity in microbial communities: system scale patterns and mechanisms. Mol. Ecol. 18, 1455–1462 (2009).

  101. 101.

    et al. Initial community evenness favours functionality under selective stress. Nature 458, 623–626 (2009).

  102. 102.

    Species redundancy and ecosystem reliability. Conserv. Biol. 12, 39–45 (1998).

  103. 103.

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

  104. 104.

    , & Biodiversity may regulate the temporal variability of ecological systems. Ecol. Lett. 4, 72–85 (2001).

  105. 105.

    et al. The dual nature of community variability. Oikos 85, 161–169 (1999).

  106. 106.

    & Resistance, resilience, and redundancy in microbial communities. Proc. Natl Acad. Sci. USA 105, 11512–11519 (2008).

  107. 107.

    & Demography of an age-structred annual: resampled projection matrices, elasticity analyses, and seed bank effects. Ecology 73, 1082–1093 (1992).

  108. 108.

    & The causes and consequences of compensatory dynamics in ecological communities. Annu. Rev. Ecol. Evol. Syst. 40, 393–414 (2009).

  109. 109.

    , & Synchrony and stability of food webs in metacommunities. Am. Nat. 175, E16–E34 (2010).

  110. 110.

    & Does dormancy increase fitness of bacterial populations in time-varying environments? Bull. Math. Biol. 70, 1140–1162 (2008).

  111. 111.

    & Prey-size selection by freshwater flagellated protozoa. Limnology 35, 1429–1436 (1990).

  112. 112.

    , , , & Nongenetic individuality in the host–phage interaction. PLoS Biol. 6, e120 (2008).

  113. 113.

    et al. Metagenomic analysis of apple orchard soil reveals antibiotic resistance genes encoding predicted bifunctional proteins. Appl. Environ. Microbiol. 76, 4396–4401 (2010).

  114. 114.

    et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450, 560–565 (2007).

  115. 115.

    et al. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotech. 24, 1263–1269 (2006).

  116. 116.

    & Resuscitation-promoting factors as lytic enzymes for bacterial growth and signaling. FEMS Immunol. Med. Microbiol. 58, 39–50 (2010).

  117. 117.

    Phenotypic plasticity in life-history traits: demographic effects and evolutionary consequences. Am. Zool. 23, 35–46 (1983).

  118. 118.

    Rates of molecular evolution in bacteria are relatively constant despite spore dormancy. Evolution 61, 280–288 (2007).

  119. 119.

    , & Adaptation, plasticity, and extinction in a changing environment: towards a predictive theory. PLoS Biol. 8, e1000357 (2010).

  120. 120.

    , & Coevolution and maladaptation. Integr. Comp. Biol. 42, 381–387 (2002).

  121. 121.

    , , , & Toward a population genetic framework of developmental evolution: the costs, limits, and consequences of phenotypic plasticity. Bioessays 32, 71–81 (2010).

  122. 122.

    , & The loss of adaptive plasticity during long periods of environmental stasis. Am. Nat. 169, 38–46 (2007).

  123. 123.

    et al. The timescale of phenotypic plasticity and its impact on competition in fluctuating environments. Am. Nat. 172, e169–e185 (2008).

  124. 124.

    , & Transcriptome divergence and the loss of plasticity in Bacillus subtilis after 6,000 generations of evolution under relaxed selection for sporulation. J. Bacteriol. 191, 428–433 (2009).

  125. 125.

    , , & Nonuniform spatial patterns of respiratory activity within biofilms during disinfection. Appl. Environ. Microbiol. 61, 2252–2256 (1995).

  126. 126.

    , , & Brock Biology of Microorganisms 12th edn (Pearson Bejamin-Cummings, San Francisco, 2009).

  127. 127.

    & Morphological characterization of small cells resulting from nutrient starvation of a psychrophilic marine Vibrio. Appl. Environ. Microbiol. 32, 617–622 (1976).

  128. 128.

    & Isolation and characterization of ultra-microbacteria from a Gulf-Coast estuary. Appl. Environmen. Microbiol. 43, 566–571 (1982).

  129. 129.

    , & Relation between presence absence of a visible nucleoid and metabolic activity in bacterioplankton cells. Limnol. Oceanogr. 41, 1161–1168 (1996).

  130. 130.

    , , , & Does the high nucleic acid content of individual bacterial cells allow us to discriminate between active cells and inactive cells in aquatic systems? Appl. Environ.Microbiol. 67, 1775–1782 (2001).

  131. 131.

    , , , & Nucleic acid (DNA, RNA) quantification and RNA/DNA ratio determination in marine sediments: comparison of spectrophotometric, fluorometric, and high-performance liquid chromotography methods and estimation of detrital DNA. Appl. Environ. Microbiol. 64, 3238–3245 (1998).

  132. 132.

    et al. Ultrastructure of resting cells of some non-spore-forming bacteria. Microbiology 73, 435–447 (2004).

  133. 133.

    , , , & Survival and phospholipid fatty acid profiles of surface and subsurface bacteria in natural sediment microcosms. Appl. Environ. Microbiol. 63, 1531–1542 (1997).

  134. 134.

    & Membrane fatty-acid and virulence changes in the viable but nonculturable state of Vibrio vulnificus. Appl.Environ. Microbiol. 55, 2837–2842 (1989).

  135. 135.

    , & Mycobacterium avium enters a state of metabolic dormancy in response to starvation. Tuberculosis 85, 147–158 (2005).

  136. 136.

    & Aerobic and anaerobic starvation metabolism in methanotrophic bacteria. Appl. Environ. Microbiol. 61, 1563–1570 (1995).

  137. 137.

    , , , & Ultrastructure of coccoid viable but non-culturable Vibrio cholerae. Environ. Microbiol. 9, 393–402 (2007).

  138. 138.

    & Screening of soil bacteria for poly-β-hydroxybutyric acid production and its role in the survival of starvation. Microb. Ecol. 35, 94–101 (1998).

  139. 139.

    & Use of adenylate energy charge ratio to measure growth state of natural microbial communities. Proc. Natl Acad. Sci. USA 72, 2112–2115 (1975).

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Acknowledgements

We acknowledge K. Bird, K. Locey, M. Larsen, J. Palange and three anonymous reviewers for critical feedback on this manuscript. We thank B. Lehmkuhl for technical assistance, and the National Science Foundation (DEB-0842441 and OCE- 0851113) and the US Department of Agriculture National Institute of Food and Agriculture (2008-35107-04481) for financial support. This is Kellogg Biological Station (KBS) contribution number 1559.

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Author notes

    • Stuart E. Jones

    Present address: Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA.

Affiliations

  1. W.K. Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, Michigan 49060, USA.

    • Jay T. Lennon
    •  & Stuart E. Jones
  2. Department of Microbiology and Molecular Genetics, Michigan State University.

    • Jay T. Lennon

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The authors declare no competing financial interests.

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Correspondence to Jay T. Lennon.

Supplementary information

Glossary

Storage effect

An ecological hypothesis stating that environmental fluctuations drive temporal variations in population growth that produce long-lived individual organisms, thus promoting multispecies coexistence.

Metacommunity

A collection of local communities within a heterogeneous landscape that are connected through the dispersal of potentially interacting species.

Histidine kinase sensor

A transmembrane protein that senses external stimuli and conveys signals that lead to changes in cell function.

Stringent response

The microbial stress response to starvation, leading to the reallocation of resources from growth to survival.

Quorum sensing

A process whereby gene expression in and/or growth of microorganisms are coordinated through the production and interpretation of signalling molecules.

Kin selection

Evolutionary selection that occurs when a non-adaptive strategy of an individual improves the fitness of genetically related individuals.

Succession

An ecological phenomenon characterized by predictable changes in community composition over time owing to variation in the colonization potentials and competitive abilities of species and in their responses to disturbances.

Rare biosphere

A concept describing the observation that a very large proportion of the taxa in microbial communities are extremely uncommon.

The Great Plate Count Anomaly

The name given to the underestimation of microbial abundance and diversity, owing to the inability of microorganisms from environmental samples to form colonies on agar media under laboratory conditions.

Stability

In an ecological context: the extent to which populations, communities and ecosystems respond to natural and anthropogenic variability.

Compensatory dynamics

A process whereby a decrease in the abundance of one species results in the increase in the abundance of another species; this balancing can be due to competition or to differences in environmental optima, and can stabilize the functions of ecological communities.

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