The cryptic role of biodiversity in the emergence of host-microbial mutualisms

Metamicrobiome diversity promotes the evolution of host-microbial mutualisms

Ecological theory suggests that a host organism's internal spatial structure can promote the persistence of mutualistic microbes by allowing for the turnover of tissue occupied by non-beneficial or cheating microbes. This type of regulation, whereby a host preferentially rewards tissue occupied by beneficial members of its microbiome but sanctions tissue occupied by non-beneficial cheaters, is expected to generate a competition-extinction trade-off by allowing beneficial microbes to experience a lower extinction rate than competitively dominant cheaters. Using an adaptive dynamics approach, we demonstrate that although ecologically stable, microbial regulation via sanctioning is not stable in any evolutionary sense, as each individual host will be under pressure to reduce the costs incurred from cheater suppression in order to maximize its own fitness at the expense of the rest of the host population. However, increasing the diversity of non-beneficial cheaters in the host population metamicrobiome can lead to an increase in the relative fitness of hosts that actively sanction non-performing tissue, thus facilitating the evolutionary emergence and persistence of such strategies in host-microbial systems. These counter-intuitive results demonstrate how diversity at multiple levels of biological organization and spatiotemporal scales can interact to facilitate the establishment and maintenance of mutualistic relationships.

Ecological Dynamics and Microbial Treatments against Oomycete Plant Pathogens

In this review, we explore how ecological concepts may help assist with applying microbial biocontrol agents to oomycete pathogens. Oomycetes cause a variety of agricultural diseases, including potato late blight, apple replant diseases, and downy mildew of grapevine, which also can lead to significant economic damage in their respective crops. The use of microbial biocontrol agents is increasingly gaining interest due to pressure from governments and society to reduce chemical plant protection products. The success of a biocontrol agent is dependent on many ecological processes, including the establishment on the host, persistence in the environment, and expression of traits that may be dependent on the microbiome. This review examines recent literature and trends in research that incorporate ecological aspects, especially microbiome, host, and environmental interactions, into biological control development and applications. We explore ecological factors that may influence microbial biocontrol agents’ efficacy and discuss key research avenues forward.

Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth

As natural selection acts on individual organisms the evolution of costly cooperation between microorganisms is an intriguing phenomenon. Introduction of spatial structure to privatize exchanged molecules can explain the evolution of cooperation. However, in many natural systems cells can also grow to low cell concentrations in the absence of these exchanged molecules, thus showing "cooperation-independent background growth". We here serially propagated a synthetic cross-feeding consortium of lactococci in the droplets of a water-in-oil emulsion, essentially mimicking group selection with varying founder population sizes. The results show that when the growth of cheaters completely depends on cooperators, cooperators outcompete cheaters. However, cheaters outcompete cooperators when they can independently grow to only ten percent of the consortium carrying capacity. This result is the consequence of a probabilistic effect, as low founder population sizes in droplets decrease the frequency of cooperator co-localization. Cooperator-enrichment can be recovered by increasing the founder population size in droplets to intermediate values. Together with mathematical modelling our results suggest that co-localization probabilities in a spatially structured environment leave a small window of opportunity for the evolution of cooperation between organisms that do not benefit from their cooperative trait when in isolation or form multispecies aggregates.

Interactions among interactions: The dynamical consequences of antagonism between mutualists

Species often interact with multiple mutualistic partners that provide functionally different benefits and/or that interact with different life-history stages. These functionally different partners, however, may also interact directly with one another in other ways, indirectly altering net outcomes and persistence of the mutualistic system as a whole. We present a population dynamical model of a three-species system involving antagonism between species sharing a mutualist partner species with two explicit life stages. We find that, regardless of whether the antagonism is predatory or non-consumptive, persistence of the shared mutualist is possible only under a restrictive set of conditions. As the rate of antagonism between the species sharing the mutualist increases, indirect rather than direct interactions increasingly determine species' densities and sometimes result in complex, oscillatory dynamics for all species. Surprisingly, persistence of the mutualistic system is particularly dependent upon the degree to which each of the two mutualistic interactions is specialized. Our work investigates a novel mechanism by which changing ecological conditions can lead to extinction of mutualist partners and provides testable predictions regarding the interactive roles of mutualism and antagonism in net outcomes for species' densities.

Station and train surface microbiomes of Mexico City's metro (subway/underground)

The metro is one of the more representative urban transportation systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the exchange of microbes between humans. In this study, we determined the bacterial diversity profile of the Mexico City metro by massive sequencing of the 16S rRNA gene. We identified a total of 50,174 operational taxonomic units (OTUs) and 1058 genera. The metro microbiome was dominated by the phylum Actinobacteria and by the genera Cutibacterium (15%) (C. acnes 13%), Corynebacterium (13%), Streptococcus (9%), and Staphylococcus (5%) (S. epidermidis; 4%), reflecting the microbe composition of healthy human skin. The metro likely microbial sources were skin, dust, saliva, and vaginal, with no fecal contribution detected. A total of 420 bacterial genera were universal to the twelve metro lines tested, and those genera contributed to 99.10% of the abundance. The annual 1.6 billion ridership makes this public transport a main hub for microbe-host-environment interactions. Finally, this study shows that the microbial composition of the Mexico City metro comes from a mixture of environmental and human sources and that commuters are exposed to healthy composition of the human microbiota.

Co-dynamics of Symbiodiniaceae and bacterial populations during the first year of symbiosis with Acropora tenuis juveniles

Interactions between corals and their associated microbial communities (Symbiodiniaceae and prokaryotes) are key to understanding corals' potential for and rate of acclimatory and adaptive responses. However, the establishment of microalgal and bacterial communities is poorly understood during coral ontogeny in the wild. We examined the establishment and co-occurrence between multiple microbial communities using 16S rRNA (bacterial) and ITS2 rDNA (Symbiodiniaceae) gene amplicon sequencing in juveniles of the common coral, Acropora tenuis, across the first year of development. Symbiodiniaceae communities in juveniles were dominated by Durusdinium trenchii and glynnii (D1 and D1a), with lower abundances of Cladocopium (C1, C1d, C50, and Cspc). Bacterial communities were more diverse and dominated by taxa within Proteobacteria, Cyanobacteria, and Planctomycetes. Both communities were characterized by significant changes in relative abundance and diversity of taxa throughout the year. D1, D1a, and C1 were significantly correlated with multiple bacterial taxa, including Alpha-, Deltra-, and Gammaproteobacteria, Planctomycetacia, Oxyphotobacteria, Phycisphaerae, and Rhizobiales. Specifically, D1a tended to associate with Oxyphotobacteria and D1 with Alphaproteobacteria, although these associations may represent correlational and not causal relationships. Bioenergetic modeling combined with physiological measurements of coral juveniles (surface area and Symbiodiniaceae cell densities) identified key periods of carbon limitation and nitrogen assimilation, potentially coinciding with shifts in microbial community composition. These results demonstrate that Symbiodiniaceae and bacterial communities are dynamic throughout the first year of ontology and may vary in tandem, with important fitness effects on host juveniles.

Costs and benefits of alternative food handling tactics help explain facultative exploitation of pollination mutualisms

Many mutualisms are taken advantage of by organisms that take rewards from their partners but provide no benefit in return. In the absence of traits that limit exploitation, facultative exploiters (partners that can either exploit or cooperate) are widely predicted by mutualism theory to choose an exploitative strategy, potentially threatening mutualism stability. However, it is unknown whether facultative exploiters choose to exploit, and, if so, make this choice because it is the most beneficial strategy for them. We explored these questions in a subalpine plant-insect community in which individuals of several bumble bee species visit flowers both "legitimately" (entering via the flower opening, picking up and depositing pollen, and hence behaving mutualistically) and via nectar robbing (creating holes through corollas or using an existing hole, bypassing stigmas and anthers). We applied foraging theory to (1) quantify handling costs, benefits and foraging efficiencies incurred by three bumble bee species as they visited flowers legitimately or robbed nectar in cage experiments, and (2) determine whether these efficiencies matched the food handling tactics these bee species employed in the field. Relative efficiencies of legitimate and robbing tactics depended on the combination of bee and plant species. In some cases (Bombus mixtus visiting Corydalis caseana or Mertensia ciliata), the robbing tactic permitted more efficient nectar removal. As both mutualism and foraging theory would predict, in the field, B. mixtus visiting C. caseana were observed more frequently robbing than foraging legitimately. However, for Bombus flavifrons visiting M. ciliata, the expectation from mutualism theory did not hold: legitimate visitation was the more efficient tactic. Legitimate visitation to M. ciliata was in fact more frequently observed in free-flying B. flavifrons. Free-flying B. mixtus also frequently visited M. ciliata flowers legitimately. This may reflect lower nectar volumes in robbed than unrobbed flowers in the field. These results suggest that a foraging ecology perspective is informative to the choice of tactics facultative exploiters make. In contrast, the simple expectation that exploiters should always have an advantage, and hence could threaten mutualism persistence unless they are deterred or punished, may not be broadly applicable.

Biological invasions increase the richness of arbuscular mycorrhizal fungi from a Hawaiian subtropical ecosystem

Biological invasions can have various impacts on the diversity of important microbial mutualists such as mycorrhizal fungi, but few studies have tested whether the effects of invasions on mycorrhizal diversity are consistent across spatial gradients. Furthermore, few of these studies have taken place in tropical ecosystems that experience an inordinate rate of invasions into native habitats. Here, we examined the effects of plant invasions dominated by non-native tree species on the diversity of arbuscular mycorrhizal (AM) fungi in Hawaii. To test the hypothesis that invasions result in consistent changes in AM fungal diversity across spatial gradients relative to native forest habitats, we sampled soil in paired native and invaded sites from three watersheds and used amplicon sequencing to characterize AM fungal communities. Whether our analyses considered phylogenetic relatedness or not, we found that invasions consistently increased the richness of AM fungi. However, AM fungal species composition was not related to invasion status of the vegetation nor local environment, but stratified by watershed. Our results suggest that while invasions can lead to an overall increase in the diversity of microbial mutualists, the effects of plant host identity or geographic structuring potentially outweigh those of invasive species in determining the community membership of AM fungi. Thus, host specificity and spatial factors such as dispersal need to be taken into consideration when examining the effects of biological invasions on symbiotic microbes.

Mutualisms Are Not on the Verge of Breakdown

Mutualisms teeter on a knife-edge between conflict and cooperation, or so the conventional wisdom goes. The costs and benefits of mutualism often depend on the abiotic or biotic context in which an interaction occurs, and experimental manipulations can induce shifts in interaction outcomes from mutualism all the way to parasitism. Yet, research suggests that mutualisms rarely turn parasitic in nature. Similarly, despite the potential for 'cheating' to undermine mutualism evolution, empirical evidence for fitness conflicts between partners and, thus, selection for cheating in mutualisms is scant. Furthermore, mutualism seldom leads to parasitism at macroevolutionary timescales. Thus, I argue here that mutualisms do not deserve their reputation for ecological and evolutionary instability, and are not on the verge of breakdown.

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.