Search

Fecal microbiota transplantation (FMT) is a procedure used to treat diseases related to microbiome imbalances. We discuss how ecological principles can inform the design of FMT clinical trials and contribute to data interpretation. This effort will promote a better understanding of microbiome engraftment and assist the development of clinical protocols. [ABSTRACT FROM AUTHOR]

Terrestrial plants can affect the growth and health of adjacent plants via interspecific interaction. Here, we studied the mechanism by which plant root exudates affect the recruitment of the rhizosphere microbiome in adjacent plants—with implications for plant protection—using a tomato (Solanum lycopersicum)–potatoonion (Allium cepa var. agrogatum) intercropping system. First, we showed that the intercropping system results in a disease-suppressive rhizosphere microbiome that protects tomato plants against Verticillium wilt disease caused by the soilborne pathogen Verticillium dahliae. Second, 16S rRNA gene sequencing revealed that intercropping with potatoonion altered the composition of the tomato rhizosphere microbiome by promoting the colonization of specific Bacillus sp. This taxon was isolated and shown to inhibit V. dahliae growth and induce systemic resistance in tomato plants. Third, a belowground segregation experiment found that root exudates mediated the interspecific interaction between potatoonion and tomato. Moreover, experiments using split-root tomato plants found that root exudates from potatoonion, especially taxifolin—a flavonoid compound—stimulate tomato plants to recruit plant-beneficial bacteria, such as Bacillus sp. Lastly, ultra-high-pressure liquid chromatography–mass spectrometry analysis found that taxifolin alters tomato root exudate chemistry; thus, this compound acts indirectly in modulating root colonization by Bacillus sp. Our results revealed that this intercropping system can improve tomato plant fitness by changing rhizosphere microbiome recruitment via the use of signaling chemicals released by root exudates of potatoonion. This study revealed a novel mechanism by which interspecific plant interaction modulates the establishment of a disease-suppressive microbiome, thus opening up new avenues of research for precision plant microbiome manipulations. Intercropping with potatoonions can enhance tomato resistance to Verticillium wilt disease by changing rhizosphere microbiome recruitment via root-exudate-mediated belowground interspecific plant interaction. Experiments suggest that root exudates from potatoonions, especially taxifolin—a flavonoid compound—alter tomato root exudate chemistry and recruit plant-beneficial bacteria, such as Bacillus sp. [ABSTRACT FROM AUTHOR]

Dispersal is simply defined as the movement of species across space and time. Despite this terse definition, dispersal is an essential process with direct ecological and evolutionary implications that modulate community assembly and turnover. Seminal ecological studies have shown that environmental context (e.g., local edaphic properties, resident community), dispersal timing and frequency, and species traits, collectively account for patterns of species distribution resulting in either their persistence or unsuccessful establishment within local communities. Despite the key importance of this process, relatively little is known about how dispersal operates in microbiomes across divergent systems and community types. Here, we discuss parallels of macro- and micro-organismal ecology with a focus on idiosyncrasies that may lead to novel mechanisms by which dispersal affects the structure and function of microbiomes. Within the context of ecological implications, we revise the importance of short- and long-distance microbial dispersal through active and passive mechanisms, species traits, and community coalescence, and how these align with recent advances in metacommunity theory. Conversely, we enumerate how microbial dispersal can affect diversification rates of species by promoting gene influxes within local communities and/or shifting genes and allele frequencies via migration or de novo changes (e.g., horizontal gene transfer). Finally, we synthesize how observed microbial assemblages are the dynamic outcome of both successful and unsuccessful dispersal events of taxa and discuss these concepts in line with the literature, thus enabling a richer appreciation of this process in microbiome research. [ABSTRACT FROM AUTHOR]

Plant hormones have been recently shown to exert an indirect influence on the recruitment of plant-associated microbiomes. However, it remains unclear the extent to which the disruption of the ethylene (ET) signaling pathway affects the assembly and functioning of plant-root microbiomes. In this study, the Never-ripe tomato mutant (Nr) was profiled for differences compared to the wild type (control). Tomato plants were subjected to root exudate profiling and the characterization of bacterial and fungal communities. Compared to the control, Nr revealed differences in the composition of root exudates, including lower amounts of esculetin, gallic acid, L-fucose, eicosapentaenoic acid, and higher amounts of β-aldehyde. Interestingly, Nr significantly differed in the composition and functioning of the rhizosphere bacterial community. We also identified the taxa that occurred at relatively higher abundances in Nr, including the genus Lysobacter, which displayed a significant negative correlation with changes in eicosapentaenoic acid and esculetin, and a significant positive correlation with changes in β-aldehyde. Taken together, our study provides evidence that a mutation in the ET receptor exerts predictable changes in the root-associated microbial taxa of tomato plants. These indirect effects can potentially be explored towards new strategies to engineer beneficial plant microbiomes via targeted changes in plant genetics and physiology. [ABSTRACT FROM AUTHOR]

Microorganisms in association with roots can protect plants against soil-borne diseases. A recent study mechanistically revealed how root endophytes act as a second microbiological layer of plant defense. Integrating ecological concepts with principles of plant pathology provides an innovative way to manipulate and engineer beneficial plant microbiomes. [ABSTRACT FROM AUTHOR]

Community coalescence is defined as the mixing of intact ecological communities and their environments. It is a common phenomenon in microbial systems with implications for biodiversity, ecosystem functioning, and human health. Research on community coalescence has recently surged, spanning various fields from clinical settings to natural and engineered microbial (eco)systems. We provide a synthesis that integrates an existing framework for invasion biology with commonalities and idiosyncrasies of community coalescence. Embracing the complexity of community coalescence in microbial systems and advancing the study of the ecological processes determining microbial engraftment is of paramount importance to better inform and predict the outcomes of microbiome manipulation across divergent systems. Community coalescence is defined as the mixing of intact ecological communities. From river confluences to fecal microbiota transplantation, community coalescence constitutes a common ecological occurrence affecting natural and engineered microbial systems. In this opinion article, we propose an integrative framework for microbial community coalescence to guide advances in our understanding of this important – yet underexplored – ecological phenomenon. We start by aligning community coalescence with the unified framework of biological invasion and enumerate commonalities and idiosyncrasies between these two analogous processes. Then, we discuss how organismal interactions and cohesive establishment affect coalescence outcomes with direct implications for community functioning. Last, we propose the use of ecological null modeling to study the interplay of ecological processes structuring community reassembly following coalescence. [ABSTRACT FROM AUTHOR]

In Drosophila, diet is considered a prominent factor shaping the associated bacterial community. However, the host population background (e.g. genotype, geographical origin and founder effects) is a factor that may also exert a significant influence and is often overlooked. To test for population background effects, we characterized the bacterial communities in larvae of six genetically differentiated and geographically distant D. melanogaster lines collected from natural populations across Europe. The diet for these six lines had been identical for ca. 50 generations, thus any differences in the composition of the microbiome originates from the host populations. We also investigated whether induced shifts in the microbiome—in this case by controlled antibiotic administration—alters the hosts’ resistance to parasitism. Our data revealed a clear signature of population background on the diversity and composition of D. melanogaster microbiome that differed across lines, even after hosts had been maintained at the same diet and laboratory conditions for over 4 years. In particular, the number of bacterial OTUs per line ranged from 8 to 39 OTUs. Each line harboured 2 to 28 unique OTUs, and OTUs that were highly abundant in some lines were entirely missing in others. Moreover, we found that the response to antibiotic treatment differed among the lines and significantly altered the host resistance to the parasitoid Asobara tabida in one of the six lines. Wolbachia, a widespread intracellular endosymbiont associated with parasitoid resistance, was lacking in this line, suggesting that other components of the Drosophila microbiome caused a change in host resistance. Collectively, our results revealed that lines that originate from different population backgrounds show significant differences in the established Drosophila microbiome, outpacing the long-term effect of diet. Perturbations on these naturally assembled microbiomes to some degree influenced the hosts’ resistance against natural parasites. [ABSTRACT FROM AUTHOR]

The poultry industry is evolving towards antibiotic-free production to meet market demands and decelerate the increasing spread of the antimicrobial resistance. The growing need for antibiotic free products has challenged producers to decrease or completely stop using antimicrobials as feed supplements in broiler diet to improve feed efficiency, growth rate, and intestinal health. Natural feed additives (e.g., probiotics and phytobiotics) are promising alternatives to substitute antimicrobial growth promoters. The goal of our study was to characterize the effects of a Probiotic and an Essential Oils blend on broilers' performance and perform a time-series analysis to describe their excreta microbiome. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 d in 32 randomly allocated cages. Treatments consisted of 4 experimental diets: a basal diet, and a basal diet mixed with an Antibiotic (bacitracin methylene disalicylate), an essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Body weight (on 1, 10, and 21d), and feed intake (10d and 21d) were recorded and feed conversion ratio was calculated. Droppings were collected daily (1–21d) to characterize broilers' excreta microbiota by targeted sequencing of the bacterial 16S rRNA gene. The Probiotic significantly improved feed conversion ratio for starter phase 1 to 10d (P = 0.03), grower phase 10 to 21d (P = 0.05), and total period 1 to 21d (P = 0.01) compared to the Antibiotic. Feed supplements did not affect alpha diversity but did impact microbial beta diversity (P < 0.01). Age also impacted microbiome turnover as differences in alpha and beta diversity were detected. Furthermore, when compared to the basal diet, the probiotic and antibiotic significantly impacted relative abundance of Bifidobacterium (log2 fold change −1.44, P = 0.03), Intestinimonas (log2 fold change 0.560, P < 0.01) and Ligilactobacillus (log2 fold change −1.600, P < 0.01). Overall, Probiotic supplementation but not essential oils supplementation positively impacted broilers' growth performance by directly causing directional shifts in broilers' excreta microbiota structure. [ABSTRACT FROM AUTHOR]