Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions

Abstract

Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context-propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)-is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering.IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).

Keywords: bacterial traits; ecosystem functioning; ecosystem manipulation; fungal traits; invasion biology; microbial composition; microbiome engineering; probiotics.

FIG 1

Experimental setup used to test factors driving composition and functional outcomes of microbial community invasions. In phase I, four microbial suspensions created from soils were used to inoculate microcosms in order to establish many replicates of complex communities in plant litter and R2A agar substrates. In phase II we conducted microbial community invasions, while varying four factors, including dose, frequency, and introduced and resident communities (see Materials and Methods for details).

FIG 2

Histogram of the distribution of ecosystem functioning metrics, CO₂ production (a) and DOC abundance (b), across phase II invaded microcosms (n = 144). Litter environment measures are shown in gold, and medium environment measures are shown in blue. (c) Impact of propagule pressure (dose and frequency) and biotic interactions (resident and introduced composition) in driving ecosystem functioning measured as total CO₂ production and DOC abundance. Estimated variance was computed on reduced ANOVA models. Only significant main factors are shown, and the “other” component is a sum of significant interaction terms. Complete statistics are in Table S1 in the supplemental material.

FIG 3

Impact of propagule pressure (dose and frequency) and biotic factors (resident and invader composition) in driving bacterial and fungal composition and richness in litter and agar environments. Estimated variance was computed on reduced ANOVA and PERMANOVA models. Only significant main factors are shown, and the “other” component is a sum of significant interaction terms. Complete statistics are in Table S1.

FIG 4

Percentage of OTUs that were invaders, resilient, common, noninvasive, or nonresilient across the 12 invasion events. Average OTU distributions for bacteria (a) and fungi (b) across phase I and phase II samples are shown in the Venn diagram circles. For the OTUs in each category, the total relative abundance of OTUs in the phase II invader-resident final communities is shown in parentheses. (c) Distribution of OTUs across categories for each individual invasion event. (Data shown in Table S2.)

FIG 5

Competitor scores for bacterial (a) and fungal (b) families, shown as the square root of the calculated competitor score (see Materials and Methods). Strong competitors are shown in blue (invader, resilient, and invader & resilient), and weak competitors are shown in red (noninvasive, nonresilient, and nonresilient & noninvasive).