Research ArticleECOLOGY

Transient invaders can induce shifts between alternative stable states of microbial communities

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Science Advances  19 Feb 2020:
Vol. 6, no. 8, eaay8676
DOI: 10.1126/sciadv.aay8676
  • Fig. 1 Transient invaders can induce shifts between alternative stable states in a laboratory ecosystem.

    (A) We exposed cocultures of Lp and Ca to a serial dilution protocol that includes daily migration of fresh cells from both species. (B) Average fraction (three replicates, SE smaller than linewidth) of Lp cells in the community at the end of each dilution cycle, as described in (A). Depending on the initial species fraction, cocultures reach a different outcome in which either species grows to dominate the system. The inset cartoon shows a mechanical analog of the ecosystem: Each of the two basins of attraction can keep the marble (the community) in an alternative stable state. (C) We explored the effects of invasions into this bistable ecosystem. The cartoon shows an unsuccessful invasion by Pc that nevertheless induced a shift toward an alternative stable state. (D) Time series for the cell densities during an unsuccessful invasion by Pc (bars show the SE of three replicates). The inset cartoon depicts this invasion event as a perturbation that drives the system toward an alternative basin of stability, where it remains after the perturbation is gone.

  • Fig. 2 Feedback loops between microbial growth and pH can determine the community impact of transient invaders.

    (A) Observed shift in pH after a Pc invasion into the stable state governed by Lp. The solid line stands for the pH at the end of each daily cycle. During each cycle, microbes induce changes in the pH of the fresh medium (dashed line) in which they were diluted into. (B) pH range in which Lp (in orange), Pc (purple), and Ca (green) exhibit growth, indicated by the fold growth in OD after monocultures spent 24 hours in highly (100 mM phosphate) buffered media. Arrows indicate how each species modifies the pH in standard (10 mM phosphate) buffer conditions. The head of the arrow points toward the pH value reached after a 24-hour culture that started at pH 6.5. (C) A temporary shock in which cells were transferred to alkaline medium during a single daily cycle (gray area) induced a transition from the Lp state to the Ca state (orange), while cocultures in the Ca state (green) remained unaltered. (D) Three main features observed in species that can act as transient invaders, as predicted by a minimal model that considers feedbacks between microbial growth and pH. (E) Fold growth in highly buffered media for monocultures from six different species, and pH modification induced by those species in standard buffer conditions (arrows). (F) Ticks and crosses indicate which species acted as transient invaders inducing community switches: Pa and Pc induced switches toward the alkaline state, and Sm was able to cause a switch toward the acidic state. Data in (B) and (D) correspond to average from four replicates (fold growth SE ≤ 2, pH modification SE ≤ 0.1).

  • Fig. 3 Transient invaders can drive transitions between stable states of a community isolated from the soil.

    (A) Time series for the pH of 39 replicates of a soil community exposed to serial dilutions. At the end of nine cycles, these replicates showed signs of pH stabilization (fig. S8). The colored (blue and cream) lines correspond to two cultures in which the community composition was also stable. 16S sequencing revealed that the community in cream was highly dominated by a Pantoea genus, while the one in blue was governed by Bacillus (blue). (B) Time series for the pH as the Pantoea and Bacillus communities were exposed to migration from each other. Measures for six replicates for each stable community are shown. (C) Time series for the community composition during an invasion by Pc into the Bacillus community as revealed by 16S amplicon sequencing. The Bacillus community was exposed to a daily dilution protocol including migration from the Pantoea community as in (B). (D) Time series for the pH during the same invasion presented in (C), along with three additional replicates. For reference, shaded areas indicate the observed pH range for each community in the presence of migration [as in (B)].

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/6/8/eaay8676/DC1

    Fig. S1. Number of cells transferred to fresh media during daily dilution and migration steps.

    Fig. S2. Successful invasion by Bc.

    Fig. S3. Six different species performed unsuccessful invasions into the Ca and Lp ecosystem.

    Fig. S4. The invader Pc thrives and decays within the 24 hours following inoculation into the Lp stable state.

    Fig. S5. Temporary perturbations in pH induce shifts between the Lp and Ca states.

    Fig. S6. Minimal model incorporating feedbacks between microbial growth and pH predicts a minimum inoculum size for the invasions to induce community shifts.

    Fig. S7. The invader Sm can induce transitions from the alkaline (Ca) to the acidic (Lp) stable state.

    Fig. S8. Early dynamics of soil communities in laboratory environments.

    Fig. S9. Mutual resilience against migration between the Bacillus and Pantoea soil communities.

    Fig. S10. Different behavior in laboratory microcosms for three genetically similar soil isolates.

    Fig. S11. Both Pc and Pa can induce transitions from the Bacillus to the Pantoea stable states.

    Reference (44)

  • Supplementary Materials

    This PDF file includes:

    • Fig. S1. Number of cells transferred to fresh media during daily dilution and migration steps.
    • Fig. S2. Successful invasion by Bc.
    • Fig. S3. Six different species performed unsuccessful invasions into the Ca and Lp ecosystem.
    • Fig. S4. The invader Pc thrives and decays within the 24 hours following inoculation into the Lp stable state.
    • Fig. S5. Temporary perturbations in pH induce shifts between the Lp and Ca states.
    • Fig. S6. Minimal model incorporating feedbacks between microbial growth and pH predicts a minimum inoculum size for the invasions to induce community shifts.
    • Fig. S7. The invader Sm can induce transitions from the alkaline (Ca) to the acidic (Lp) stable state.
    • Fig. S8. Early dynamics of soil communities in laboratory environments.
    • Fig. S9. Mutual resilience against migration between the Bacillus and Pantoea soil communities.
    • Fig. S10. Different behavior in laboratory microcosms for three genetically similar soil isolates.
    • Fig. S11. Both Pc and Pa can induce transitions from the Bacillus to the Pantoea stable states.
    • Reference (44)

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