Microbiome influence on host community dynamics: Conceptual integration of microbiome feedback with classical host-microbe theory

Symbiotic microbial population composition of Apolygus lucorum under temperature and pesticide pressures

Insect population control using pesticides faces new challenges as global temperatures change. Symbiotic bacteria of insects play a key role in insect resistance to pesticides, and these symbiotic bacteria themselves are sensitive to the effects of temperature changes. Apolygus lucorum, a sucking pest, survives in a wide range of temperatures (15°C-35°C), and is presently controlled predominantly using the pesticide imidacloprid. Here, we investigated the effects of temperature and imidacloprid on A. lucorum microbial population composition using 16S rRNA sequencing. We found that the application of imidacloprid in high-temperature environments led to an increase in the species diversity of bacteria in the body of A. lucorum. High temperatures may disrupt the symbiotic relationship between certain bacteria and A. lucorum, such as Cedecea neteri. High temperatures led to a decrease in the abundance of Cedecea neteri. Agathobaculum butyriciproducens, Advenella migardefenensis, and Akkermansia muciniphila were very sensitive to temperature and were strongly affected by temperature changes. Microorganisms that were greatly affected by the concentration of imidacloprid in the community include Aeromonas caviae and Akkermansia muciniphila. The aim of this study is to reveal the dynamics and diversity of symbiotic bacteria of A. lucorum treated with imidacloprid at a range of temperatures. These results provide insight into new strategies for pest control in a changing climate.

Arbuscular mycorrhizal fungi equalize differences in plant fitness and facilitate plant species coexistence through niche differentiation

Mycorrhizal fungi are essential to the establishment of the vast majority of plant species but are often conceptualized with contradictory roles in plant community assembly. On the one hand, host-specific mycorrhizal fungi may allow a plant to be competitively dominant by enhancing growth. On the other hand, host-specific mycorrhizal fungi with different functional capabilities may increase nutrient niche partitioning, allowing plant species to coexist. Here, to resolve the balance of these two contradictory forces, we used a controlled greenhouse study to manipulate the presence of two main types of mycorrhizal fungus, ectomycorrhizal fungi and arbuscular mycorrhizal fungi, and used a range of conspecific and heterospecific competitor densities to investigate the role of mycorrhizal fungi in plant competition and coexistence. We find that the presence of arbuscular mycorrhizal fungi equalizes fitness differences between plants and stabilizes competition to create conditions for host species coexistence. Our results show how below-ground mutualisms can shift outcomes of plant competition and that a holistic view of plant communities that incorporates their mycorrhizal partners is important in predicting plant community dynamics.

Mechanisms of synthetic bacterial flora YJ-1 to enhance cucumber resistance under combined phthalate-disease stresses

Biotic and abiotic stresses have emerged as major constraints to agricultural production, causing irreversible adverse impacts on agricultural production systems and thus posing a threat to food security. In this study, a new strain of Bacillus subtilis DNYB-S1 was isolated from soil contaminated with Fusarium wilt. It was found that artificially synthetic flora (YJ-1) [Enterobacter sp. DNB-S2 and Rhodococcus pyridinovorans DNHP-S2, DNYB-S1] could effectively mitigate both biotic (Fusarium wilt) and abiotic (phthalates) sources of stresses, with the inhibition rate of YJ-1 resistant to wilt being 71.25% and synergistic degradation of 500 mg/L PAEs was 91.23%. The adaptive difference of YJ-1 was 0.59 and the ecological niche overlap value was -0.05 as determined by Lotka-Volterra modeling. These results indicate that YJ-1 has good ecological stability. The major degradation intermediates included 2-ethylhexyl benzoate (EHBA), phthalic acid (PA), diisobutyl phthalate (DIBP), and butyl benzoate, suggesting that YJ-1 can provide a more efficient pathway for PAEs degradation. In addition, there was metabolic mutualism among the strains that will selectively utilize the provided carbon source (some metabolites of PAEs) for growth. The pot experiment showed that YJ-1 with cucumber reduced the incidence of cucumber wilt by 45.31%. YJ-1 could reduce the concentration of PAEs (DBP: DEHP = 1:1) in soil species from 30 mg/kg to 4.26 mg/kg within 35 d, with a degradation efficiency of 85.81%. Meanwhile, the concentration of PAEs in cucumber was reduced to 0.01 mg/kg, indicating that YJ-1 is directly involved in the degradation of soil PAEs and the enhancement of plant immunity. In conclusion, this study provides a new perspective for the development of customized microbiomes for phytoremediation under combined biotic-abiotic stresses in agricultural production processes.

Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana

In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.

Time-dependent interaction modification generated from plant-soil feedback

Pairwise interactions between species can be modified by other community members, leading to emergent dynamics contingent on community composition. Despite the prevalence of such higher-order interactions, little is known about how they are linked to the timing and order of species' arrival. We generate population dynamics from a mechanistic plant-soil feedback model, then apply a general theoretical framework to show that the modification of a pairwise interaction by a third plant depends on its germination phenology. These time-dependent interaction modifications emerge from concurrent changes in plant and microbe populations and are strengthened by higher overlap between plants' associated microbiomes. The interaction between this overlap and the specificity of microbiomes further determines plant coexistence. Our framework is widely applicable to mechanisms in other systems from which similar time-dependent interaction modifications can emerge, highlighting the need to integrate temporal shifts of species interactions to predict the emergent dynamics of natural communities.

Quantifying soil microbial effects on plant species coexistence: A conceptual synthesis

Soil microorganisms play a critical role in shaping the biodiversity dynamics of plant communities. These microbial effects can arise through direct mediation of plant fitness by pathogens and mutualists, and over the past two decades, numerous studies have shined a spotlight on the role of dynamic feedbacks between plants and soil microorganisms as key determinants of plant species coexistence. Such feedbacks occur when plants modify the composition of the soil community, which in turn affects plant performance. Stimulated by a theoretical model developed in the 1990s, a bulk of the empirical evidence for microbial controls over plant coexistence comes from experiments that quantify plant growth in soil communities that were previously conditioned by conspecific or heterospecific plants. These studies have revealed that soil microbes can generate strong negative to positive frequency-dependent dynamics among plants. Even as soil microbes have become recognized as a key player in determining plant coexistence outcomes, the past few years have seen a renewed interest in expanding the conceptual foundations of this field. New results include re-interpretations of key metrics from classic two-species models, extensions of plant-soil feedback theory to multispecies communities, and frameworks to integrate plant-soil feedbacks with processes like intra- and interspecific competition. Here, I review the implications of theoretical developments for interpreting existing empirical results and highlight proposed analyses and designs for future experiments that can enable a more complete understanding of microbial regulation of plant community dynamics.

Fungal community dissimilarity predicts plant-soil feedback strength in a lowland tropical forest

Soil microbes impact plant community structure and diversity through plant-soil feedbacks. However, linking the relative abundance of plant pathogens and mutualists to differential plant recruitment remains challenging. Here, we tested for microbial mediation of pairwise feedback using a reciprocal transplant experiment in a lowland tropical forest in Panama paired with amplicon sequencing of soil and roots. We found evidence that plant species identity alters the microbial community, and these changes in microbial composition alter subsequent growth and survival of conspecific plants. We also found that greater community dissimilarity between species in their arbuscular mycorrhizal and nonpathogenic fungi predicted increased positive feedback. Finally, we identified specific microbial taxa across our target functional groups that differentially accumulated under conspecific settings. Collectively, these findings clarify how soil pathogens and mutualists mediate net feedback effects on plant recruitment, with implications for management and restoration.

Dilution of specialist pathogens drives productivity benefits from diversity in plant mixtures

Productivity benefits from diversity can arise when compatible pathogen hosts are buffered by unrelated neighbors, diluting pathogen impacts. However, the generality of pathogen dilution has been controversial and rarely tested within biodiversity manipulations. Here, we test whether soil pathogen dilution generates diversity- productivity relationships using a field biodiversity-manipulation experiment, greenhouse assays, and feedback modeling. We find that the accumulation of specialist pathogens in monocultures decreases host plant yields and that pathogen dilution predicts plant productivity gains derived from diversity. Pathogen specialization predicts the strength of the negative feedback between plant species in greenhouse assays. These feedbacks significantly predict the overyielding measured in the field the following year. This relationship strengthens when accounting for the expected dilution of pathogens in mixtures. Using a feedback model, we corroborate that pathogen dilution drives overyielding. Combined empirical and theoretical evidence indicate that specialist pathogen dilution generates overyielding and suggests that the risk of losing productivity benefits from diversity may be highest where environmental change decouples plant-microbe interactions.

Are Plant-Soil Feedbacks Caused by Many Weak Microbial Interactions?

We used high-throughput sequencing and multivariate analyses to describe soil microbial community composition in two four-year field plant-soil feedback (PSF) experiments in Minnesota, USA and Jena, Germany. In descending order of variation explained, microbial community composition differed between the two study sites, among years, between bulk and rhizosphere soils, and among rhizosphere soils cultivated by different plant species. To try to identify soil organisms or communities that may cause PSF, we correlated plant growth responses with the microbial community composition associated with different plants. We found that plant biomass was correlated with values on two multivariate axes. These multivariate axes weighted dozens of soil organisms, suggesting that PSF was not caused by individual pathogens or symbionts but instead was caused by 'many weak' plant-microbe interactions. Taken together, the results suggest that PSFs result from complex interactions that occur within the context of a much larger soil microbial community whose composition is determined by factors associated with 'site' or year, such as soil pH, soil type, and weather. The results suggest that PSFs may be highly variable and difficult to reproduce because they result from complex interactions that occur in the context of a larger soil microbial community.

Rapid differentiation of soil and root microbiomes in response to plant composition and biodiversity in the field

Research suggests that microbiomes play a major role in structuring plant communities and influencing ecosystem processes, however, the relative roles and strength of change of microbial components have not been identified. We measured the response of fungal, arbuscular mycorrhizal fungal (AMF), bacteria, and oomycete composition 4 months after planting of field plots that varied in plant composition and diversity. Plots were planted using 18 prairie plant species from three plant families (Poaceae, Fabaceae, and Asteraceae) in monoculture, 2, 3, or 6 species richness mixtures and either species within multiple families or one family. Soil cores were collected and homogenized per plot and DNA were extracted from soil and roots of each plot. We found that all microbial groups responded to the planting design, indicating rapid microbiome response to plant composition. Fungal pathogen communities were strongly affected by plant diversity. We identified OTUs from genera of putatively pathogenic fungi that increased with plant family, indicating likely pathogen specificity. Bacteria were strongly differentiated by plant family in roots but not soil. Fungal pathogen diversity increased with planted species richness, while oomycete diversity, as well as bacterial diversity in roots, decreased. AMF differentiation in roots was detected with individual plant species, but not plant family or richness. Fungal saprotroph composition differentiated between plant family composition in plots, providing evidence for decomposer home-field advantage. The observed patterns are consistent with rapid microbiome differentiation with plant composition, which could generate rapid feedbacks on plant growth in the field, thereby potentially influencing plant community structure, and influence ecosystem processes. These findings highlight the importance of native microbial inoculation in restoration.

Towards defining the core Saccharum microbiome: input from five genotypes

Background

Plant microbiome and its manipulation inaugurate a new era for plant biotechnology with the potential to benefit sustainable crop production. Here, we used the large-scale 16S rDNA sequencing analysis to unravel the dynamic, structure, and composition of exophytic and endophytic microbial communities in two hybrid commercial cultivars of sugarcane (R570 and SP80–3280), two cultivated genotypes (Saccharum officinarum and Saccharum barberi) and one wild species (Saccharum spontaneum).

Results

Our analysis identified 1372 amplicon sequence variants (ASVs). The microbial communities’ profiles are grouped by two, root and bulk soils and stem and leave when these four components are compared. However, PCoA-based data supports that endophytes and epiphytes communities form distinct groups, revealing an active host-derived mechanism to select the resident microbiota. A strong genotype-influence on the assembly of microbial communities in Saccharum ssp. is documented. A total of 220 ASVs persisted across plant cultivars and species. The ubiquitous bacteria are two potential beneficial bacteria, Acinetobacter ssp., and Serratia symbiotica.

Conclusions

The results presented support the existence of common and cultivar-specific ASVs in two commercial hybrids, two cultivated canes and one species of Saccharum across tissues (leaves, stems, and roots). Also, evidence is provided that under the experimental conditions described here, each genotype bears its microbial community with little impact from the soil conditions, except in the root system. It remains to be demonstrated which aspect, genotype, environment or both, has the most significant impact on the microbial selection in sugarcane fields.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02598-8.

A strategic model of a host–microbe–microbe system reveals the importance of a joint host–microbe immune response to combat stress-induced gut dysbiosis

Microbiomes provide key ecological functions to their host; however, most host-associated microbiomes are too complicated to allow a model of essential host–microbe–microbe interactions. The intestinal microbiota of salmonids may offer a solution since few dominating species often characterize it. Healthy fish coexist with a mutualistic Mycoplasma sp. species, while stress allows the spread of pathogenic strains, such as Aliivibrio sp. Even after a skin infection, the Mycoplasma does not recover; Aliivibrio sp. often remains the dominant species, or Mycoplasma–Aliivibrio coexistence was occasionally observed. We devised a model involving interactions among the host immune system, Mycoplasma sp. plus a toxin-producing pathogen. Our model embraces a complete microbiota community and is in harmony with experimental results that host–Mycoplasma mutualism prevents the spread of pathogens. Contrary, stress suppresses the host immune system allowing dominance of pathogens, and Mycoplasma does not recover after stress disappears.

A quantitative synthesis of soil microbial effects on plant species coexistence

SignificanceUnderstanding the processes that maintain plant diversity is a key goal in ecology. Many previous studies have shown that soil microbes can generate stabilizing or destabilizing feedback loops that drive either plant species coexistence or monodominance. However, theory shows that microbial controls over plant coexistence also arise through microbially mediated competitive imbalances, which have been largely neglected. Using data from 50 studies, we found that soil microbes affect plant dynamics primarily by generating competitive fitness differences rather than stabilizing or destabilizing feedbacks. Consequently, in the absence of other competitive asymmetries among plants, soil microbes are predicted to drive species exclusion more than coexistence. These results underscore the need for measuring competitive fitness differences when evaluating microbial controls over plant coexistence.

No robust multispecies coexistence in a canonical model of plant-soil feedbacks

Plant–soil feedbacks (PSFs) are considered a key mechanism generating frequency‐dependent dynamics in plant communities. Negative feedbacks, in particular, are often invoked to explain coexistence and the maintenance of diversity in species‐rich communities. However, the primary modelling framework used to study PSFs considers only two plant species, and we lack clear theoretical expectations for how these complex interactions play out in communities with natural levels of diversity. Here, we extend this canonical model of PSFs to include an arbitrary number of plant species and analyse the dynamics. Surprisingly, we find that coexistence of more than two species is virtually impossible, suggesting that alternative theoretical frameworks are needed to describe feedbacks observed in diverse natural communities. Drawing on our analysis, we discuss future directions for PSF models and implications for experimental study of PSF‐mediated coexistence in the field.