To hunt or to rest: prey depletion induces a novel starvation survival strategy in bacterial predators

Abstract

The small size of bacterial cells necessitates rapid adaption to sudden environmental changes. In Bdellovibrio bacteriovorus, an obligate predator of bacteria common in oligotrophic environments, the non-replicative, highly motile attack phase (AP) cell must invade a prey to ensure replication. AP cells swim fast and respire at high rates, rapidly consuming their own contents. How the predator survives in the absence of prey is unknown. We show that starvation for prey significantly alters swimming patterns and causes exponential decay in prey-searching cells over hours, until population-wide swim-arrest. Swim-arrest is accompanied by changes in energy metabolism, enabling rapid swim-reactivation upon introduction of prey or nutrients, and a sweeping change in gene expression and gene regulation that largely differs from those of the paradigmatic stationary phase. Swim-arrest is costly as it imposes a fitness penalty in the form of delayed growth. We track the control of the swim arrest-reactivation process to cyclic-di-GMP (CdG) effectors, including two motility brakes. CRISPRi transcriptional inactivation, and in situ localization of the brakes to the cell pole, demonstrated their essential role for effective survival under prey-induced starvation. Thus, obligate predators evolved a unique CdG-controlled survival strategy, enabling them to sustain their uncommon lifestyle under fluctuating prey supply.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Changes in motility of B. bacteriovorus with time under starvation, and after adding prey.
Fig. 2: Changes in the motility of B. bacteriovorus HD100 aAP2 cells exposed to various elicitors.
Fig. 3: Comparative transcriptomic analysis of B. bacteriovorus HD100 motility-arrested attack phase cells (aAP2) and fresh attack phase cells (AP1).
Fig. 4: Changes in expression levels of cyclic-di-GMP (CdG) signaling-related genes in B. bacteriovorus HD100.
Fig. 5: Changes in motility and predation dynamics in B. bacteriovorus HD100 silenced for break proteins expression.
Fig. 6: Transcriptional changes in sigma factors in B. bacteriovorus HD100 motility-arrested attack phase cells (aAP2) compared to fresh attack phase cells (AP1).
Fig. 7: The life cycle of the periplasmic predator Bdellovibrio bacteriovorus (left).

References

  1. 1.

    Ho A, Di Lonardo DP, Bodelier PLE. Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiol Ecol. 2017;93:fix006.

    Google Scholar 

  2. 2.

    Poindexter JS. Oligotrophy. In: Alexander M, editor. Advances in microbial ecology. Springer US, Boston, MA: Springer US; 1981. pp. 63–89.

  3. 3.

    Madigan MT, Bender KS, Buckley DH, Sattley WM, Stahl DA. Brock Biology of Microorganisms, 15th Global edition. Boston, US: Benjamin Cummins. 2018.

  4. 4.

    Navarro Llorens JM, Tormo A, Martínez-García E. Stationary phase in gram-negative bacteria. FEMS Microbiol Rev. 2010;34:476–95.

    PubMed  Google Scholar 

  5. 5.

    Wood TK, Knabel SJ, Kwan BW. Bacterial persister cell formation and dormancy. Appl Environ Microbiol. 2013;79:7116–21.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Klotz A, Georg J, Bučinská L, Watanabe S, Reimann V, Januszewski W, et al. Awakening of a dormant cyanobacterium from nitrogen chlorosis reveals a genetically determined program. Curr Biol. 2016;26:2862–72.

    CAS  PubMed  Google Scholar 

  7. 7.

    Setlow P, Wang S, Li Y-Q. Germination of spores of the orders Bacillales and Clostridiales. Annu Rev Microbiol. 2017;71:459–77.

    CAS  PubMed  Google Scholar 

  8. 8.

    Song S, Wood TK. ppGpp ribosome dimerization model for bacterial persister formation and resuscitation. bioRxiv. 2019. https://doi.org/10.1101/663658.

  9. 9.

    Fenton AK, Kanna M, Woods R, Aizawa S, Sockett RE. Shadowing the actions of a predator: Backlit fluorescent microscopy reveals synchronous nonbinary septation of predatory Bdellovibrio inside prey and exit through discrete bdelloplast pores. J Bacteriol. 2010;192:6329–35.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Makowski Ł, Donczew R, Weigel C, Zawilak-Pawlik A, Zakrzewska-Czerwinska J. Initiation of chromosomal replication in predatory bacterium Bdellovibrio bacteriovorus. Front Microbiol. 2016;7.

  11. 11.

    Rotem O, Pasternak Z, Jurkevitch E. The genus Bdellovibrio and like organisms. The prokaryotes: deltaproteobacteria and epsilonproteobacteria. 2014. pp. 3–17.

  12. 12.

    Lambert C, Evans KJ, Till R, Hobley L, Capeness M, Rendulic S, et al. Characterizing the flagellar filament and the role of motility in bacterial prey-penetration by Bdellovibrio bacteriovorus. Mol Microbiol. 2006;60:274–86.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Thomashow LS, Rittenberg SC. Waveform analysis and structure of flagella and basal complexes from Bdellovibrio bacteriovorus 109J. J Bacteriol. 1985;163:1038–46.

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Hespell RB, Rosson RA, Thomashow MF, Rittenberg SC.  Respiration of Bdellovibrio bacteriovorus strain 109J and its energy substrates for intraperiplasmic growth. J Bacteriol. 1973;113:1280–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Hespell RB, Thomashow MF, Rittenberg SC. Changes in cell composition and viability of Bdellovibrio bacteriovorus during starvation. Arch Microbiol. 1974;97:313–27.

    CAS  PubMed  Google Scholar 

  16. 16.

    Paix B, Ezzedine JA, Jacquet S. Diversity, dynamics, and distribution of Bdellovibrio and like organisms in perialpine lakes. Appl Environ Microbiol. 2019;85.

  17. 17.

    Varon M, Fine M, Stein A. The maintenance of Bdellovibrio at low prey density. Microb Ecol. 1984;10:95–8.

    CAS  PubMed  Google Scholar 

  18. 18.

    Varon M, Zeigler BP. Bacterial predator-prey interaction at low prey density. Appl Environ Microbiol. 1978;36:11–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Chen H, Young S, Berhane TK, Williams HN. Predatory Bacteriovorax communities ordered by various prey species. PLoS ONE. 2012;7.

  20. 20.

    Rogosky AM, Moak PL, Emmert EAB. Differential predation by Bdellovibrio bacteriovorus 109J. Curr Microbiol. 2006;52:81–5.

    CAS  PubMed  Google Scholar 

  21. 21.

    Jurkevitch E, Minz D, Ramati B, Barel G. Prey range characterization, ribotyping, and diversity of soil and rhizosphere Bdellovibrio spp. isolated on phytopathogenic bacteria. Appl Environ Microbiol. 2000;66:2365–71.

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Kandel PP, Pasternak Z, van Rijn J, Nahum O, Jurkevitch E. Abundance, diversity and seasonal dynamics of predatory bacteria in aquaculture zero discharge systems. FEMS Microbiol Ecol. 2014;89:149–61.

    CAS  PubMed  Google Scholar 

  23. 23.

    Pineiro SA, Williams HN, Stine OC, Piñeiro SA, Williams HN, Stine OC. Phylogenetic relationships amongst the saltwater members of the genus Bacteriovorax using rpoB sequences and reclassification of Bacteriovorax stolpii as Bacteriolyticum stolpii gen. nov., comb. nov. Int J Syst Evol Microbiol. 2008;58:1203–9.

    CAS  PubMed  Google Scholar 

  24. 24.

    Chen H, Athar R, Zheng G, Williams HN. Prey bacteria shape the community structure of their predators. ISME J. 2011;5:1314–22.

    PubMed  PubMed Central  Google Scholar 

  25. 25.

    Shatzkes K, Connell ND, Kadouri DE. Predatory bacteria: a new therapeutic approach for a post-antibiotic era. Future Microbiol. 2017;12:469–72.

    CAS  PubMed  Google Scholar 

  26. 26.

    Guo Y, Yan L, Cai J. Effects of Bdellovibrio and like organisms on survival and growth performance of juvenile turbot, scophthalmus maximus. J World Aquac Soc. 2016;47:633–45.

    Google Scholar 

  27. 27.

    Youdkes D, Helman Y, Burdman S, Matan O, Jurkevitch E. Potential control of potato soft rot disease by the obligate predators Bdellovibrio and like organisms. Appl Environ Microbiol. 2020;86.

  28. 28.

    Sathyamoorthy R, Maoz A, Pasternak Z, Im H, Huppert A, Kadouri D, et al. Bacterial predation under changing viscosities. Environ Microbiol. 2019;21:2997–3010.

    CAS  PubMed  Google Scholar 

  29. 29.

    Hobley L, Fung RKY, Lambert C, Harris MATS, Dabhi JM, King SS, et al. Discrete cyclic di-GMP-dependent control of bacterial predation versus axenic growth in Bdellovibrio bacteriovorus. PLoS Pathog. 2012;8.

  30. 30.

    Karunker I, Rotem O, Dori-Bachash M, Jurkevitch E, Sorek R. A global transcriptional switch between the attack and growth forms of Bdellovibrio bacteriovorus. PLoS ONE. 2013;8.

  31. 31.

    Amikam D, Galperin MY. PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics. 2006;22:3–6.

    CAS  PubMed  Google Scholar 

  32. 32.

    Ko J, Ryu K-S, Kim H, Shin J-S, Lee J-O, Cheong C, et al. Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by PilZ domain proteins. J Mol Biol. 2010;398:97–110.

    CAS  PubMed  Google Scholar 

  33. 33.

    Wirebrand L, Österberg S, López-Sánchez A, Govantes F, Shingler V. PP4397/FlgZ provides the link between PP2258 c-di-GMP signalling and altered motility in Pseudomonas putida. Sci Rep. 2018;8:1–10.

    CAS  Google Scholar 

  34. 34.

    Shanks RMQ, Davra VR, Romanowski EG, Brothers KM, Stella NA, Godboley D, et al. An eye to a kill: using predatory bacteria to control gram-negative pathogens associated with ocular infections. PLOS ONE. 2013;8:e66723.

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35.

    Wurtzel O, Dori-Bachash M, Pietrokovski S, Jurkevitch E, Sorek R. Mutation detection with next-generation resequencing through a mediator genome. PLoS ONE. 2010;5.

  36. 36.

    Pasternak Z, Njagi M, Shani Y, Chanyi R, Rotem O, Lurie-Weinberger MN, et al. In and out: an analysis of epibiotic vs periplasmic bacterial predators. ISME J. 2014;8:625–35.

    CAS  PubMed  Google Scholar 

  37. 37.

    Pletnev P, Osterman I, Sergiev P, Bogdanov A, Dontsova O. Survival guide: Escherichia coli in the stationary phase. Acta Nat. 2015;7:22–33.

    CAS  Google Scholar 

  38. 38.

    Kazmierczak MJ, Wiedmann M, Boor KJ. Alternative sigma factors and their roles in bacterial virulence. Microbiol Mol Biol Rev. 2005;69:527–43.

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Paget MS. Bacterial sigma factors and anti-sigma factors: structure, function and distribution. Biomolecules. 2015;5:1245–65.

    CAS  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Avidan O, Petrenko M, Becker R, Beck S, Linscheid M, Pietrokovski S, et al. Identification and characterization of differentially-regulated type IVb pilin genes necessary for predation in obligate bacterial predators. Sci Rep. 2017;7:1–12.

  41. 41.

    Barembruch C, Hengge R. Cellular levels and activity of the flagellar sigma factor FliA of Escherichia coli are controlled by FlgM-modulated proteolysis. Mol Microbiol. 2007;65:76–89.

    CAS  PubMed  Google Scholar 

  42. 42.

    Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C, Lanz C, et al. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science. 2004;303:689–92.

    CAS  PubMed  Google Scholar 

  43. 43.

    Nyström T. Stationary-phase physiology. Annu Rev Microbiol. 2004;58:161–81.

    PubMed  Google Scholar 

  44. 44.

    Browning AP, Sharp JA, Mapder T, Baker CM, Burrage K, Simpson MJ. Persistence is an optimal hedging strategy for bacteria in volatile environments. bioRxiv. 2019. https://doi.org/10.1101/2019.12.19.883645.

  45. 45.

    Ratcliff WC, Denison RF. Individual-level bet hedging in the bacterium Sinorhizobium meliloti. Curr Biol. 2010;20:1740–4.

    CAS  PubMed  Google Scholar 

  46. 46.

    Zhang X-X, Rainey PB. Bet hedging in the underworld. Genome Biol. 2010;11:137.

    PubMed  PubMed Central  Google Scholar 

  47. 47.

    Franklin RB, Mills AL. Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiol Ecol. 2003;44:335–46.

    CAS  PubMed  Google Scholar 

  48. 48.

    Manderscheid B, Matzner E. Spatial heterogeneity of soil solution chemistry in a mature Norway spruce (Picea abies (L.) Karst.) stand. Water Air Soil Pollut. 1995;85:1185–90.

    CAS  Google Scholar 

  49. 49.

    Ranjard L, Lejon DPH, Mougel C, Schehrer L, Merdinoglu D, Chaussod R. Sampling strategy in molecular microbial ecology: Influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ Microbiol. 2003;5:1111–20.

    CAS  PubMed  Google Scholar 

  50. 50.

    Jenal U, Reinders A, Lori C. Cyclic di-GMP: second messenger extraordinaire. Nat Rev Microbiol. 2017;15:271–84.

    CAS  PubMed  Google Scholar 

  51. 51.

    Boehm A, Kaiser M, Li H, Spangler C, Kasper CA, Ackermann M, et al. Second messenger-mediated adjustment of bacterial swimming velocity. Cell. 2010;141:107–16.

    CAS  PubMed  Google Scholar 

  52. 52.

    Paul K, Nieto V, Carlquist WC, Blair DF, Harshey RM. The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a ‘Backstop Brake’ mechanism. Mol Cell. 2010;38:128–39.

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Dattner I, Miller E, Petrenko M, Kadouri DE, Jurkevitch E, Huppert A. Modelling and parameter inference of predator–prey dynamics in heterogeneous environments using the direct integral approach. J R Soc Interface. 2017;14:20160525.

    PubMed  PubMed Central  Google Scholar 

  54. 54.

    Hol FJH, Rotem O, Jurkevitch E, Dekker C, Koster DA. Bacterial predator–prey dynamics in microscale patchy landscapes. Proc R Soc B Biol Sci. 2016;283:20152154.

    Google Scholar 

  55. 55.

    Gabel CV, Berg HC. The speed of the flagellar rotary motor of Escherichia coli varies linearly with protonmotive force. Proc Natl Acad Sci USA. 2003;100:8748–51.

    CAS  PubMed  Google Scholar 

  56. 56.

    Gadkari D, Stolp H. Energy metabolism of Bdellovibrio bacteriovorus. I. Energy production, ATP pool, energy charge. Arch Microbiol. 1975;102:179–85.

    CAS  PubMed  Google Scholar 

  57. 57.

    Shioi JI, Galloway RJ, Niwano M, Chinnock RE, Taylor BL. Requirement of ATP in bacterial chemotaxis. J Biol Chem. 1982;257:7969–75.

  58. 58.

    Fang X, Gomelsky M. A post-translational, c-di-GMP-dependent mechanism regulating flagellar motility. Mol Microbiol. 2010;76:1295–305.

    CAS  PubMed  Google Scholar 

  59. 59.

    Varon M. Interaction of Bdellovibrio with its prey in mixed microbial populations. Microb Ecol. 1981;7:97–105.

    CAS  PubMed  Google Scholar 

  60. 60.

    Kessel M, Shilo M. Relationship of Bdellovibrio elongation and fission to host cell size. J Bacteriol. 1976;128:477–80.

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61.

    LaMarre AG, Straley SC, Conti SF. Chemotaxis toward amino acids by Bdellovibrio bacteriovorus. J Bacteriol. 1977;131:201–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  62. 62.

    Chauhan A, Williams HN. Response of Bdellovibrio and like organisms (BALOs) to the migration of naturally occurring bacteria to chemoattractants. Curr Microbiol. 2006;53:516–22.

    CAS  PubMed  Google Scholar 

  63. 63.

    Feng S, Tan CH, Constancias F, Kohli GS, Cohen Y, Rice SA. Predation by Bdellovibrio bacteriovorus significantly reduces viability and alters the microbial community composition of activated sludge flocs and granules. FEMS Microbiol Ecol. 2017;93.

  64. 64.

    Kadouri DE, O’Toole GA. Susceptibility of biofilms to Bdellovibrio bacteriovorus attack. Appl Environ Microbiol. 2005;71:4044–51.

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 65.

    Szabó E, Liébana R, Hermansson M, Modin O, Persson F, Wilén B-MB-MB-M, et al. Comparison of the bacterial community composition in the granular and the suspended phase of sequencing batch reactors. AMB Express. 2017;7:168.

    PubMed  PubMed Central  Google Scholar 

  66. 66.

    Lambert C, Smith MCM, Sockett RE. A novel assay to monitor predator-prey interactions for Bdellovibrio bacteriovorus 109 J reveals a role for methyl-accepting chemotaxis proteins in predation. Environ Microbiol. 2003;5:127–32.

    CAS  PubMed  Google Scholar 

  67. 67.

    Petrenko M, Friedman SP, Fluss R, Pasternak Z, Huppert A, Jurkevitch E. Spatial heterogeneity stabilizes predator–prey interactions at the microscale while patch connectivity controls their outcome. Environ Microbiol. 2019;22:694–704.

  68. 68.

    Mukherjee S, Brothers KM, Shanks RMQQ, Kadouri DE. Visualizing Bdellovibrio bacteriovorus by using the tdTomato fluorescent protein. Appl Environ Microbiol. 2015;82:1653–61.

    PubMed  Google Scholar 

  69. 69.

    Jurkevitch E. Isolation and classification of Bdellovibrio and like organisms. Curr Protoc Microbiol. 2012;Chapter 7:Unit 7B.1.

    Google Scholar 

  70. 70.

    Peters JM, Koo B-M, Patino R, Heussler GE, Hearne CC, Qu J, et al. Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi. Nat Microbiol. 2019;4:244–50.

    CAS  PubMed  PubMed Central  Google Scholar 

  71. 71.

    Copeland MF, Weibel DB. Bacterial swarming: a model system for studying dynamic self-assembly. Soft Matter. 2009;5:1174–87.

    CAS  PubMed  PubMed Central  Google Scholar 

  72. 72.

    Rotem O, Pasternak Z, Shimoni E, Belausov E, Porat Z, Pietrokovski S, et al. Cell-cycle progress in obligate predatory bacteria is dependent upon sequential sensing of prey recognition and prey quality cues. Proc Natl Acad Sci. 2015;112:E6028–37.

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This research was supported by the Korea–Israel Cooperative Scientific Research, budget number 3-14168, and by the U.S. Army Research Office and the Defense Advanced Research Projects Agency and was accomplished under Cooperative Agreement Number W911NF-15-2-0036 to DEK, EJ, and AH. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office, DARPA, or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation hereon. We would like to thank Menyat Elsayed for her help with the paper.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Edouard Jurkevitch.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Sathyamoorthy, R., Kushmaro, Y., Rotem, O. et al. To hunt or to rest: prey depletion induces a novel starvation survival strategy in bacterial predators. ISME J (2020). https://doi.org/10.1038/s41396-020-00764-2

Download citation

Search