Microbial diversity determines the invasion of soil by a bacterial pathogen

Abstract

Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity-function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invader's fate in soil was determined in the presence of (i) differentially constructed culturable bacterial communities, and (ii) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.

Fig. 1.

E. coli strain T population dynamics (log cfu g⁻¹ soil) over a 60-d period in soil with differently established diversities of culturable bacteria from the assembly experiment. ▲, control, no strains added; *, 5 strains; ■, 20 strains; ●,100 strains. Each symbol represents the mean value of three replicates. Bars represent SDs of the mean. E. coli strain T population dynamics in natural soil is not shown, because it would seriously mask the differences between the established communities; it was characterized by a near-linear decline of cfu numbers by approximately 6 log units, from approximately 10⁸ cfu g⁻¹ soil to 10² cfu g⁻¹ dry soil, within 60 d after release.

Fig. 2.

Relationship between E. coli strain T population dynamics (log cfu g⁻¹ soil) and the relative richness (Sr) of bacterial species from the assembly experiment, as estimated from bacterial PCR-DGGE assessments (number of bands) over a 60-d period, at days 3 (R² = 0.407; Survival = −0.21* ln (Sr) + 8.36), 30 (R² = 0.387; Survival = −0.20* ln (Sr) + 8.08), and 60 (R² = 0.767; Survival = −0.42* ln (Sr) + 8.54) after strain T introduction. At all time points, a logarithmic decay curve [Survival = −0.27* ln (Sr) + 8.35; ANOVA F_(1,58) = 36.7, P = 0.0001] fitted the data points best and better (higher R²) than a linear one. The differences in the initial slopes were significant between d60 and d3/d30 (P < 0.05). Open circles, day 3; open triangles, day 30; open squares, day 60.

Fig. 3.

E. coli strain T population dynamics (log cfu g⁻¹ soil) over a 60-d period in soil with differently established microbial diversities using a dilution-to-extinction approach. ▲, 10⁶ treatment (number indicates the dilution factor of the sample microbial community; *, 10³; ●, 10¹; ■, 10¹-F (F indicates sequential filtering over membrane filters to remove higher organisms, including protozoa); ◆, natural soil. Each symbol represents the mean value of three replicates. Bars represent SDs of the mean.

Fig. 4.

Relationship between E. coli strain T population dynamics (log cfu g⁻¹ soil) and the global richness indicator (GRI) at different times after introduction of the invader. The GRI (34) was derived from the sum of five richness values (number of bands on DGGE gels) obtained from the following microbial groups: total bacteria, total fungi, pseudomonads, actinobacteria, and bacilli, each normalized per group, and divided by 5. Linear correlations between E. coli survival and GRI increased over time (R² = 0.34, R² = 0.654, and R² = 0.846 for 3, 30, and 60 d after pathogen inoculation, respectively). Open circles, day 3; open triangles, day 30; open squares, day 60.

Fig. 5.

Relationship between manipulated species richness and the competitive ability of E. coli strain T. The competitive abilities are expressed both in relation to the amount of resources consumed (A) and their rate of consumption (B) and represent the dissimilarity in resource utilization patterns, obtained by pairwise comparisons of bacterial communities of increasing richness (1, 5, 10, and 20 species), in the presence and absence of strain T. Each circle represents a pairwise comparison. Resource utilization patterns correspond to the average in the amount (A, R² = 0.46, P = 0.0001) or in the rate of consumption (B, R² = 0.33, P = 0.0001) of 31 carbon sources present in the Biolog Ecoplate. Similar data were obtained when only the 10 carbon sources used by E. coli strain T were analyzed (R² = 0.47, P < 0.0001 and R² = 0.43, P < 0.0001, for amount and rate of consumption, respectively).