All together now: experimental multispecies biofilm model systems

Studies of microorganisms have traditionally focused on single species populations, which have greatly facilitated our understanding of the genetics and physiology that underpin microbial growth, adaptation and biofilm development. However, given that most microorganisms exist as multispecies consortia, the field is increasingly exploring microbial communities using a range of technologies traditionally limited to populations, including meta‐omics based approaches and high resolution imaging. The experimental communities currently being explored range from relatively low diversity, for example, two to four species, to significantly more complex systems, comprised of several hundred species. Results from both defined and undefined communities have revealed a number of emergent properties, including improved stress tolerance, increased biomass production, community level signalling and metabolic cooperation. Based on results published to date, we submit that community‐based studies are timely and increasingly reveal new properties associated with multispecies consortia that could not be predicted by studies of the individual component species. Here, we review a range of defined and undefined experimental systems used to study microbial community interactions.     

New approaches in bioprocess‐control: Consortium guidance by synthetic cell‐cell communication based on fungal pheromones

Bioconversions in industrial processes are currently dominated by single‐strain approaches. With the growing complexity of tasks to be carried out, microbial consortia become increasingly advantageous and eventually may outperform single‐strain fermentations. Consortium approaches benefit from the combined metabolic capabilities of highly specialized strains and species, and the inherent division of labor reduces the metabolic burden for each strain while increasing product yields and reaction specificities. However, consortium‐based designs still suffer from a lack of available tools to control the behavior and performance of the individual subpopulations and of the entire consortium. Here, we propose to implement novel control elements for microbial consortia based on artificial cell–cell communication via fungal mating pheromones. Coupling to the desired output is mediated by pheromone‐responsive gene expression, thereby creating pheromone‐dependent communication channels between different subpopulations of the consortia. We highlight the benefits of artificial communication to specifically target individual subpopulations of microbial consortia and to control e.g. their metabolic profile or proliferation rate in a predefined and customized manner. Due to the steadily increasing knowledge of sexual cycles of industrially relevant fungi, a growing number of strains and species can be integrated into pheromone‐controlled sensor‐actor systems, exploiting their unique metabolic properties for microbial consortia approaches.     

Environments that induce synthetic microbial ecosystems

Interactions between microbial species are sometimes mediated by the exchange of small molecules, secreted by one species and metabolized by another. Both one-way (commensal) and two-way (mutualistic) interactions may contribute to complex networks of interdependencies. Understanding these interactions constitutes an open challenge in microbial ecology, with applications ranging from the human microbiome to environmental sustainability. In parallel to natural communities, it is possible to explore interactions in artificial microbial ecosystems, e.g. pairs of genetically engineered mutualistic strains. Here we computationally generate artificial microbial ecosystems without re-engineering the microbes themselves, but rather by predicting their growth on appropriately designed media. We use genome-scale stoichiometric models of metabolism to identify media that can sustain growth for a pair of species, but fail to do so for one or both individual species, thereby inducing putative symbiotic interactions. We first tested our approach on two previously studied mutualistic pairs, and on a pair of highly curated model organisms, showing that our algorithms successfully recapitulate known interactions, robustly predict new ones, and provide novel insight on exchanged molecules. We then applied our method to all possible pairs of seven microbial species, and found that it is always possible to identify putative media that induce commensalism or mutualism. Our analysis also suggests that symbiotic interactions may arise more readily through environmental fluctuations than genetic modifications. We envision that our approach will help generate microbe-microbe interaction maps useful for understanding microbial consortia dynamics and evolution, and for exploring the full potential of natural metabolic pathways for metabolic engineering applications.     

Deciphering microbial interactions in synthetic human gut microbiome communities

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model‐guided framework to predict higher‐dimensional consortia from time‐resolved measurements of lower‐order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi‐species community dynamics, as opposed to higher‐order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history‐dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human‐associated intestinal species and illuminated design principles of microbial communities.     

A shared limiting resource leads to competitive exclusion in a cross-feeding system

Species interactions and coexistence are often dependent upon environmental conditions. When two cross-feeding bacteria exchange essential nutrients, the addition of a cross-fed nutrient to the environment can release one species from its dependence on the other. Previous studies suggest that continued coexistence depends on relative growth rates: coexistence is maintained if the slower-growing species is released from its dependence on the other, but if the faster-growing species is released, the slower-growing species will be lost (a hypothesis that we call ‘feed the faster grower’ or FFG). Using invasion-from-rare experiments with two reciprocally cross-feeding bacteria, genome-scale metabolic modelling and classical ecological models, we explored the potential for coexistence when one cross-feeder became independent. We found that whether nutrient addition shifted an interaction from mutualism to commensalism or parasitism depended on whether the nutrient that limited total growth was required by one or both species. Parasitism resulted when both species required the growth-limiting resource. Importantly, coexistence was only lost when the interaction became parasitism, and the obligate species had a slower growth rate. Under these restricted conditions, the FFG hypothesis applied. Our results contribute to a mechanistic understanding of how resources can be manipulated to alter interactions and coexistence in microbial communities.     

Parabiotic ants: the costs and benefits of symbiosis

1. Mutualisms are important drivers of co‐evolution and speciation. However, they typically imply costs for one or both partners. Each partner consequently tries to maximise benefits and minimise costs. Mutualisms can therefore develop towards commensalism or parasitism if one partner fails to provide sufficient benefits. This is particularly likely in diffuse interactions, where multiple species can associate with each other. If costs and benefits of a species vary with the identity of the partner species, this may result in a geographical mosaic of co‐evolution. 2. In the present study, inter‐specific interactions in two parabiotic associations of ants were studied (Hymenoptera: Formicidae). One Crematogaster species was associated with one of two closely related Camponotus species. We assessed cost and benefits by studying behavioural interactions, foraging behaviour, and nest defence in the associations. 3. While parabioses had been shown to be mutualistic, evidence was found for exploitation and aggressive competition between species. In spite of apparent costs of being exploited, we found no benefits for one partner (Crematogaster). The magnitude of potential costs to Crematogaster varied between the two Camponotus species. 4. We conclude that the cost/benefit ratio for Crematogaster varies between the two Camponotus partners, and between environmental conditions. Parabiosis can thus fluctuate between mutualism, commensalism, and parasitism, with Crematogaster being the species that may have higher costs than benefits. 5. We suggest that geneflow in the Crematogaster population hinders local adaptation to the resulting mosaic of locally varying selection pressures. This study demonstrates how diffuse interactions and environmental variation can result in a complex of local selection pressures.     

Evolution of dispersal in metacommunities of interacting species

Theoretical studies on the evolution of dispersal in metacommunities are rare despite empirical evidence suggesting that interspecific interactions can modify dispersal behaviour of organisms. To understand the role of species interactions for dispersal evolution, we utilize an individual‐based model of a metacommunity where local population dynamics follows a stochastic version of the Nicholson–Bailey model and dispersal probability is an evolving trait. Our results show that in comparison with a neutral system (commensalism), parasitism promotes dispersal of hosts and parasites, while mutualism tends to reduce dispersal in both partners. Search efficiency of guests (only in the case of parasitism), dispersal mortality and external extinction risk can influence the evolution of dispersal of all partners. In systems composed of two host and two guest species, lower dispersal probabilities evolve under parasitism as well as mutualism than in one host and one guest species systems. This is because of frequency‐dependent modulations of dispersal benefits emerging in such systems for all partners.     

Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea

Nanoarchaeum equitans and Ignicoccus hospitalis represent a unique, intimate association of two archaea. Both form a stable coculture which is mandatory for N. equitans but not for the host I. hospitalis. Here, we investigated interactions and mutual influence between these microorganisms. Fermentation studies revealed that during exponential growth only about 25% of I. hospitalis cells are occupied by N. equitans cells (one to three cells). The latter strongly proliferate in the stationary phase of I. hospitalis, until 80 to 90% of the I. hospitalis cells carry around 10 N. equitans cells. Furthermore, the expulsion of H2S, the major metabolic end product of I. hospitalis, by strong gas stripping yields huge amounts of free N. equitans cells. N. equitans had no influence on the doubling times, final cell concentrations, and growth temperature, pH, or salt concentration ranges or optima of I. hospitalis. However, isolation studies using optical tweezers revealed that infection with N. equitans inhibited the proliferation of individual I. hospitalis cells. This inhibition might be caused by deprivation of the host of cell components like amino acids, as demonstrated by 13C-labeling studies. The strong dependence of N. equitans on I. hospitalis was affirmed by live-dead staining and electron microscopic analyses, which indicated a tight physiological and structural connection between the two microorganisms. No alternative hosts, including other Ignicoccus species, were accepted by N. equitans. In summary, the data show a highly specialized association of N. equitans and I. hospitalis which so far cannot be assigned to a classical symbiosis, commensalism, or parasitism.     

Evolutionary responses to climate change in parasitic systems

Species may respond to climate change in many ecological and evolutionary ways. In this simulation study, we focus on the concurrent evolution of three traits in response to climate change, namely dispersal probability, temperature tolerance (or niche width), and temperature preference (optimal habitat). More specifically, we consider evolutionary responses in host species involved in different types of interaction, that is parasitism or commensalism, and for low or high costs of a temperature tolerance–fertility trade‐off (cost of generalization). We find that host species potentially evolve all three traits simultaneously in response to increasing temperature but that the evolutionary response interacts and may be compensatory depending on the conditions. The evolutionary adjustment of temperature preference is slower in the parasitism than in commensalism scenario. Parasitism, in turn, selects for higher temperature tolerance and increased dispersal. High costs for temperature tolerance (i.e. generalization) restrict evolution of tolerance and thus lead to a faster response in temperature preference than that observed under low costs. These results emphasize the possible role of biotic interactions and the importance of ‘multidimensional’ evolutionary responses to climate change.     

Metabolomic profiling elucidates community dynamics of the Ketogulonicigenium vulgare–Bacillus megaterium consortium

Many microbial consortia are established upon metabolic interactions. Elucidating such interactions is a priority in understanding the population dynamics of these microbial consortia. In this study, we investigated the interaction dynamics of the vitamin C biosynthesis consortium comprising of Ketogulonicigenium vulgare and Bacillus megaterium. We systematically quantified the dynamic evolution of the ecosystem??s population and metabolism in response to a wide range of seeding concentrations and compositions of the two microorganisms. The consortium population dynamics was determined by quantitative PCR. The metabolomic profile of the community was systematically investigated by gas chromatography coupled with time-of-flight mass spectrometry. Our results showed that B. megaterium was responsible for initiating the reproduction of K. vulgare, meanwhile, K. vulgare could promote the growth of B. megaterium. Principal component analysis of the metabolomic profiling elucidated variations of intermediates in central carbon metabolism, nucleotide and amino acids metabolism in this microbial consortium. These findings provided new insights into the characterization of the community dynamics and the optimization of co-culture fermentation for vitamin C biosynthesis.     

Parasitism,the diversity of life,and paleoparasitology

The parasite-host-environment system is dynamic, with several points of equilibrium. This makes it difficult to trace the thresholds between benefit and damage, and therefore, the definitions of commensalism, mutualism, and symbiosis become worthless. Therefore, the same concept of parasitism may encompass commensalism, mutualism, and symbiosis. Parasitism is essential for life. Life emerged as a consequence of parasitism at the molecular level, and intracellular parasitism created evolutive events that allowed species to diversify. An ecological and evolutive approach to the study of parasitism is presented here. Studies of the origin and evolution of parasitism have new perspectives with the development of molecular paleoparasitology, by which ancient parasite and host genomes can be recovered from disappeared populations. Molecular paleoparasitology points to host-parasite co-evolutive mechanisms of evolution traceable through genome retrospective studies.     

Indirect interaction between butterfly species mediated by a shared pupal parasitoid

Indirect interactions among species can greatly affect their abundances and the structure of the community they live in. Using a field experiment, we tested the hypothesis that congeneric butterfly species interact indirectly through a shared pupal parasitoid. We predicted that symmetrical apparent competition would lead to high parasitism of both species, and the effect would increase with regional butterfly abundance. Instead, parasitism of one host, Melitaea cinxia, was reduced in the presence of the second host, M. athalia. Parasitism of M. athalia did not differ whether or not M. cinxia was present. This pattern did not vary with regional butterfly abundance, though overall rate of parasitism did. Details of the experiment suggest that the apparent commensalism occurred because M. cinxia pupae are protected by silk tents whereas M. athalia are exposed, causing locally foraging parasitoids to favour the more accessible host where the two are present together. The local short-term apparent commensalism favouring M. cinxia opposes the landscape scale trend, in which parasitism increases where butterfly density is high. The outcome of this study illustrates short-term apparent commensalism, that host suitability can depend on relative accessibility, and that indirect interactions occurring at different scales may be in opposition.     

Rapid evolution destabilizes species interactions in a fluctuating environment

Positive species interactions underlie the functioning of ecosystems. Given their importance, it is crucial to understand the stability of positive interactions over evolutionary timescales, in both constant and fluctuating environments; e.g., environments interrupted with periods of competition. We addressed this question using a two-species microbial system in which we modulated interactions according to the nutrient provided. We evolved in parallel four experimental replicates of species growing in isolation or together in consortia for 200 generations in both a constant and fluctuating environment with daily changes between commensalism and competition. We sequenced full genomes of single clones isolated at different time points during the experiment. We found that the two species coexisted over 200 generations in the constant commensal environment. In contrast, in the fluctuating environment, coexistence broke down when one of the species went extinct in two out of four cases. We showed that extinction was highly deterministic: when we replayed the evolution experiment from an intermediate time point we repeatably reproduced species extinction. We further show that these dynamics were driven by adaptive mutations in a small set of genes. In conclusion, in a fluctuating environment, rapid evolution destabilizes the long-term stability of positive pairwise interactions.Subject terms: Microbial ecology, Bacterial genetics, Population genetics     

Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics

Human gut microbiome is a diversified, resilient, immuno-stabilized, metabolically active and physiologically essential component of the human body. Scientific explorations have been made to seek in-depth information about human gut microbiome establishment, microbiome functioning, microbiome succession, factors influencing microbial community dynamics and the role of gut microbiome in health and diseases. Extensive investigations have proposed the microbiome therapeutics as a futuristic medicine for various physiological and metabolic disorders. A comprehensive outlook of microbial colonization, host–microbe interactions, microbial adaptation, commensal selection and immuno-survivability is still required to catalogue the essential genetic and physiological features for the commensal engagement. Evolution of a structured human gut microbiome relies on the microbial flexibility towards genetic, immunological and physiological adaptation in the human gut. Key features for commensalism could be utilized in developing tailor-made microbiome-based therapy to overcome various physiological and metabolic disorders. This review describes the key genetics and physiological traits required for host–microbe interaction and successful commensalism to institute a human gut microbiome.     

甘油歧化生产1,3-丙二醇过程的代谢和基因调控机理研究进展

用生物转化法将可再生资源(如淀粉、纤维素等)转化为重要的化工原料是目前生物技术领域的一个重要课题。本文以甘油生物转化为1,3丙二醇过程为考察对象,系统综述了该过程代谢和基因调控的研究现状,并对今后的研究提出了一些建议。     

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, “omics” approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.     

Reactions of Peroxynitrite with Uric Acid: Formation of Reactive Intermediates,Alkylated Products and Triuret,and In Vivo Production of Triuret Under Conditions of Oxidative Stress

Hyperuricemia is associated with hypertension, metabolic syndrome, preeclampsia, cardio-vascular disease and renal disease, all conditions associated with oxidative stress. We hypothesized that uric acid, a known antioxidant, might become prooxidative following its reaction with oxidants; and, thereby contribute to the pathogenesis of these diseases. Uric acid and 1,3-¹⁵N₂-uric acid were reacted with peroxynitrite in different buffers and in the presence of alcohols, antioxidants and in human plasma. The reaction products were identified using liquid chromatography-mass spectrometry (LC-MS) analyses. The reactions generate reactive intermediates that yielded triuret as their final product. We also found that the antioxidant, ascorbate, could partially prevent this reaction. Whereas triuret was preferentially generated by the reactions in aqueous buffers, when uric acid or 1,3-¹⁵N₂-uric acid was reacted with peroxynitrite in the presence of alcohols, it yielded alkylated alcohols as the final product. By extension, this reaction can alkylate other biomolecules containing OH groups and others containing labile hydrogens. Triuret was also found to be elevated in the urine of subjects with preeclampsia, a pregnancy-specific hypertensive syndrome that is associated with oxidative stress, whereas very little triuret is produced in normal healthy volunteers. We conclude that under conditions of oxidative stress, uric acid can form reactive intermediates, including potential alkylating species, by reacting with peroxynitrite. These reactive intermediates could possibly explain how uric acid contributes to the pathogenesis of diseases such as the metabolic syndrome and hypertension.     

Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis

Anaerobic digestion is a key biological process for renewable energy, yet the mechanistic knowledge on its hidden microbial dynamics is still limited. The present work charted the interaction network in the anaerobic digestion microbiome via the full characterization of pairwise interactions and the associated metabolite exchanges. To this goal, a novel collection of 836 genome-scale metabolic models was built to represent the functional capabilities of bacteria and archaea species derived from genome-centric metagenomics. Dominant microbes were shown to prefer mutualistic, parasitic and commensalistic interactions over neutralism, amensalism and competition, and are more likely to behave as metabolite importers and profiteers of the coexistence. Additionally, external hydrogen injection positively influences microbiome dynamics by promoting commensalism over amensalism. Finally, exchanges of glucogenic amino acids were shown to overcome auxotrophies caused by an incomplete tricarboxylic acid cycle. Our novel strategy predicted the most favourable growth conditions for the microbes, overall suggesting strategies to increasing the biogas production efficiency. In principle, this approach could also be applied to microbial populations of biomedical importance, such as the gut microbiome, to allow a broad inspection of the microbial interplays.     

Interspecific interactions affect species and community responses to climate shifts

The response of individual species to climate change may alter the composition and dynamics of communities. Here, we show that the impacts of environmental change on communities can depend on the nature of the interspecific interactions: mutualistic communities typically respond differently than commensalistic or parasitic communities. We model and analyse the geographic range shifting of metapopulations of two interacting species – a host and an obligate species. Different types of interspecific interactions are implemented by modifying local extinction rates according to the presence/absence of the other species. We distinguish and compare three fundamentally different community types: mutualism, commensalism and parasitism. We find that community dynamics during geographic range shifting critically depends on the type of interspecific interactions. Parasitic interactions exacerbate the negative effect of environmental change whereas mutualistic interactions only partly compensate it. Commensalistic interactions exhibit an intermediate response. Based on these model outcomes, we predict that parasitic species interactions may be more vulnerable to geographic range shifting than commensalistic or mutualistic ones. However, we observe that when climate stabilises following a period of change, the rate of community recovery is largely independent of the type of interspecific interactions. These results emphasize that communities respond delicately to environmental change, and that local interspecific interactions can affect range shifting communities at large spatial scales.     

Parasitoids, polydnaviruses and endosymbiosis

Symbiotic associations traditionally have been treated as evolutionary curios rather than as a major source of evolutionary innovation. Recent research on a wide variety of organisms is changing this view and is breaking down the barriers between the traditional categories of parasitism, commensalism and mutualism, to produce a more flexible view of multispecific interactions. An especially abundant, but little discussed, mutualism exists between parasitoid wasps in the superfamily Ichneumonoidea and a novel form of DNA viruses known as polydnaviruses. Mutualisms between viruses and eukaryotes are not often reported, although as many as 100 000 species of organisms may exhibit this unusual association. In this review Jim Whitfield considers what is known about the parasitoid-polydnavirus relationship and how (and from what) it might have arisen.