Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

Abstract

Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting.

Figure 1. Fitness of locally adapted SBW25.

Mean (±s.e.m.) selection coefficient of evolved SBW25 (after 48 days cultivation in sterile compost at 26 °C) determined by competing against its ancestor for 5 days in both sterile and unsterile compost. Note that selection coefficient (S) was calculated here by the difference between the estimated Malthusian parameter of the locally adapted SBW25 population (m_LA) and the ancestral SBW25-lacZ strain (m_Anct), where a value of zero indicates equal fitness.

Figure 2. Bacterial population densities in the natural microbial community.

(a) Mean densities (±s.e.m.) of the six replicates of ancestral (white square) and locally adapted (black square) P. fluorescens SBW25 (CFUs g⁻¹ soil) in the presence of the natural microbial community (solid line) and the presence of phages (dash line). (b) Mean densities (±s.e.m.) of phage SBW25φ2 (plaque-forming units (PFUs)  g⁻¹ soil) populations. (c) Mean densities (±s.e.m.) of the six replicates of the culturable bacteria (CFUs g⁻¹ soil) in the natural microbial community with no SBW25 (grey diamond), ancestral SBW25 (white circle, white triangle) and locally adapted SBW25 (black circle, black triangle) in the absence (solid line) and presence (dashed line) of phages.

Figure 3. Changes in community composition.

(a) Principal Coordinate Analysis (PCoA) plot of communities based on UniFrac distances. The percentage of variation explained is shown on each axis (calculated from the relevant eigenvalues). Replicates within treatments and time points have similar community compositions, while there are notable differences between treatments and time points. (b) Points show mean (95%±confidence intervals (CIs)) distances between treatment centroids at 30 and 60 days in the absence (open circles) and presence (closed circles) of phages. These centroids are the mean position of all the points in all coordinate directions from the PCoA plot, and their differences reflect the effect of adaptation and species presence on community change. The difference between ancestral and locally adapted treatments shows the magnitude of the effect of adaptation, while difference between presence and absence of SBW25 shows the magnitude of effect of species presence. (c) Points show mean (95%±CIs) distances between treatment centroids to show how phages (+φ2) affect community structure in the presence of either ancestral or evolved SBW25. (d) Common bacterial orders across treatments (>5% in at least one treatment–time point combination). Note consistently high frequency of Bacillales (Bac) across time in evolved SBW25 treatment. Act, Actinomycetales; Bur, Burkholderiales; Cau, Caulobacterales; Fla, Flavobacteriales; Oce, Oceanospirillales; Pse, Pseudomonadales; Rhi, Rhizobiales; Sap, Saprospirales; Sph, Sphingobacteriales; Xan, Xanthomonadales. Square represents day 0, circle represents day 30, triangle represents day 60; black represents No SBW25; blue represents locally adapted (LA), red represents ancestral (Anct); open symbols indicate no phage, closed symbols indicate with phage (+φ).

Figure 4. Differences in community composition.

Principal Coordinate Analysis (PCoA) based on Bray–Curtis dissimilarity of bacterial orders between communities. PCA loadings for orders playing key roles in determining community differences are shown for comparison as arrows: Bac, Bacillales; Pse, Pseudomonadales; Sap, Saprospirales; Sph, Sphingobacteriales; Xan, Xanthomonadales. Square represents day 0, circle represents day 30, triangle represents day 60; black represents No SBW25; blue represents locally adapted (LA), red represents ancestral (Anc); open symbols indicate no phage, closed symbols indicate with phage (φ2).

Figure 5. Beta diversity.

Box plot representation of the values of the distances to centroid for treatment–time point combinations; No SBW25, ancestral (Anct) and locally adapted (LA) treatments at 30 and 60 days in the absence and presence of phages, based on UniFrac distances. The box plots show medians (horizontal line in box), 25 and 75% quartiles, and max/min values, outliers marked as circles.

Figure 6. Shannon diversity index.

Representation of the within-population diversity values of the community from No SBW25, ancestral and locally adapted treatments at 30 and 60 days in the absence and presence of phages. Square represents day 0, circle represents day 30, triangle represents day 60; black represents No SBW25; red represents ancestral (Anct); blue represents locally adapted (LA); open symbols indicate no phage, closed symbols indicate with phage (+φ).