代谢互养关系在维持微生物物种多样性中的作用

互养关系（cross-feeding）是微生物物种之间普遍存在的一种相互关系,其中物种利用环境中其他成员的代谢产物以促进自身生长的情形称为代谢互养关系,这种关系对物种间的竞争结果往往有很大影响,甚至会改变种群结构。为了研究代谢互养关系在维持微生物物种多样性中的作用,构建包含不同代谢互养关系的资源竞争模型,这些模型既体现了微生物物种竞争资源时种群密度及资源量的动态,也展示了物种利用其他竞争者的代谢资源对自身生存状况的影响。数值模拟结果显示：（1）考虑微生物中不同的代谢互养关系结构：两物种间单向互养、双向互养以及多物种间的互养,不同的互养关系都可以促进竞争物种稳定共存,竞争中处于劣势的物种通过利用其他竞争成员的代谢产物,打破外界资源量对其生长的限制,改变原本消亡的命运;而处于优势的物种则通过利用其他竞争成员的代谢产物,增大种群密度。（2）多物种竞争同一种有限资源时,不是所有物种都能共存,在四物种模拟中,原本处于最劣势的物种灭绝,其余三者共存。物种产生代谢资源对其本身是"不利"的,如果在模拟中物种利用代谢资源的能力相同,那么物种竞争外界资源的劣势就很可能无法被抵消。通过改变资源利用率发现只有互养关系中代谢资源的利用可以弥补劣势种在竞争外界资源时的不足,多物种才可以全部共存。（3）验证数值模拟结果的普遍性,分析参数变化对共存的影响,结果表明代谢互养关系促进的共存对代谢资源相关参数不敏感,参数的改变只影响平衡态时物种的种群密度。所以,代谢互养关系可以促进相互竞争的微生物物种共存,即微生物之间的互养关系很可能是维持物种多样性的一种机制。     

Influence of substrate composition and flow rate on growth of Azospirillum brasilense Cd in a co-culture with 3 sorghum rhizobacteria

The ability of Azospirillum brasilense Cd to colonize the niche occupied by 3 bacterial strains previously isolated from sorghum rhizosphere was studied by means of the Biolog system. The isolates were identified by different methods as strains belonging to Pseudomonas putida, Stenotrophomonas maltophilia, and Klebsiella terrigena species. Several C sources, also chosen among the constituents of sorghum root exudates, were used to evaluate the metabolic profiles of Azospirillum and the sorghum rhizobacteria. Azospirillum brasilense Cd exploited the same class of C compounds as the sorghum rhizobacteria and overlapped in their niche requirements. Since structure and functioning of a microbial community are largely affected by the flow rate of nutrient supply, the competitive behavior of A. brasilense Cd was studied in a chemostat mixed culture under C-limited conditions using disodium succinate as C source. Only at high growth rates, i.e., when the C source was highly supplied, A. brasilense Cd appeared to be a good competitor and it became the dominant species, whereas at low growth rates, it was outnumbered by the other species. However, the coexistence of all the strains was always maintained, thus suggesting that interactions other than competition or a potential cross-feeding might occur within the mixed culture.     

Evolutionary coexistence in a fluctuating environment by specialization on resource level

Microbial communities in fluctuating environments, such as oceans or the human gut, contain a wealth of diversity. This diversity contributes to the stability of communities and the functions they have in their hosts and ecosystems. To improve stability and increase production of beneficial compounds, we need to understand the underlying mechanisms causing this diversity. When nutrient levels fluctuate over time, one possibly relevant mechanism is coexistence between specialists on low and specialists on high nutrient levels. The relevance of this process is supported by the observations of coexistence in the laboratory, and by simple models, which show that negative frequency dependence of two such specialists can stabilize coexistence. However, as microbial populations are often large and fast growing, they evolve rapidly. Our aim is to determine what happens when species can evolve; whether evolutionary branching can create diversity or whether evolution will destabilize coexistence. We derive an analytical expression of the invasion fitness in fluctuating environments and use adaptive dynamics techniques to find that evolutionarily stable coexistence requires a special type of trade-off between growth at low and high nutrients. We do not find support for the necessary evolutionary trade-off in data available for the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae on glucose. However, this type of data is scarce and might exist for other species or in different conditions. Moreover, we do find evidence for evolutionarily stable coexistence of the two species together. Since we find this coexistence in the scarce data that are available, we predict that specialization on resource level is a relevant mechanism for species diversity in microbial communities in fluctuating environments in natural settings.     

Phage cocktail strategies for the suppression of a pathogen in a cross-feeding coculture

Cocktail combinations of bacteria-infecting viruses (bacteriophages) can suppress pathogenic bacterial growth. However, predicting how phage cocktails influence microbial communities with complex ecological interactions, specifically cross-feeding interactions in which bacteria exchange nutrients, remains challenging. Here, we used experiments and mathematical simulations to determine how to best suppress a model pathogen, E. coli, when obligately cross-feeding with S. enterica. We tested whether the duration of pathogen suppression caused by a two-lytic phage cocktail was maximized when both phages targeted E. coli, or when one phage targeted E. coli and the other its cross-feeding partner, S. enterica. Experimentally, we observed that cocktails targeting both cross-feeders suppressed E. coli growth longer than cocktails targeting only E. coli. Two non-mutually exclusive mechanisms could explain these results: (i) we found that treatment with two E. coli phage led to the evolution of a mucoid phenotype that provided cross-resistance against both phages, and (ii) S. enterica set the growth rate of the coculture, and therefore, targeting S. enterica had a stronger effect on pathogen suppression. Simulations suggested that cross-resistance and the relative growth rates of cross-feeders modulated the duration of E. coli suppression. More broadly, we describe a novel bacteriophage cocktail strategy for pathogens that cross-feed.     

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR− and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.Subject terms: Microbial ecology, Population genetics, Symbiosis, Population dynamics, Molecular evolution     

Spatial aggregation across ephemeral resource patches in insect communities: an adaptive response to natural enemies?

Although an increase in competition is a common cost associated with intraspecific crowding, spatial aggregation across food-limited resource patches is a widespread phenomenon in many insect communities. Because intraspecific aggregation of competing insect larvae across, e.g. fruits, dung, mushrooms etc., is an important means by which many species can coexist (aggregation model of species coexistence), there is a strong need to explore the mechanisms that contribute to the maintenance of this kind of spatial resource exploitation. In the present study, by using Drosophila-parasitoid interactions as a model system, we tested the hypothesis whether intraspecific aggregation reflects an adaptive response to natural enemies. Most of the studies that have hitherto been carried out on Drosophila-parasitoid interactions used an almost two-dimensional artificial host environment, where host larvae could not escape from parasitoid attacks, and have demonstrated positive density-dependent parasitism risk. To test whether these studies captured the essence of such interactions, we used natural breeding substrates (decaying fruits). In a first step, we analysed the parasitism risk of Drosophila larvae on a three-dimensional substrate in natural fly communities in the field, and found that the risk of parasitism decreased with increasing host larval density (inverse density dependence). In a second step, we analysed the parasitism risk of Drosophila subobscura larvae on three breeding substrate types exposed to the larval parasitoids Asobara tabida and Leptopilina heterotoma. We found direct density-dependent parasitism on decaying sloes, inverse density dependence on plums, and a hump-shaped relationship between fly larval density and parasitism risk on crab apples. On crab apples and plums, fly larvae benefited from a density-dependent refuge against the parasitoids. While the proportion of larvae feeding within the fruit tissues increased with larval density, larvae within the fruit tissues were increasingly less likely to become victims of parasitoids than those exposed at the fruit surface. This suggests a facilitating effect of group-feeding larvae on reaching the spatial refuge. We conclude that spatial aggregation in Drosophila communities can at least in part be explained as a predator avoidance strategy, whereby natural enemies act as selective agents maintaining spatial patterns of resource utilisation in their host communities.     

Stabilizing factors interact in promoting host-parasite coexistence

Understanding the mechanisms that promote coexistence among species is a fundamental problem in evolutionary ecology. Such mechanisms include environmental noise, spatial population structure, density dependence, and genetic variation. In natural populations such factors may exert combined effects on coexistence. Thus, to disentangle the contribution of several factors to coexistence, their effects have to be considered simultaneously. Here we investigate the effects of Ricker-type density dependence, genetic variation, and the frequency of sex on host-parasite coexistence, using Nicholson-Bailey models with and without host density dependence. Interestingly, a low frequency of sex (and the genetic variation induced by sex) is the most important factor in explaining the stability of the host-parasite interaction. However, the carrying capacity K and the frequency of sex interact in affecting coexistence. If K is low (strong density regulation), coexistence is easily attained in the density-dependent model, independently of the frequency of sex. In contrast, for high values of K (weak density regulation), low frequencies of sex considerably improve coexistence. Thus, our results suggest that coexistence among species may strongly depend on interactions among several stabilizing factors. These results seem to be robust since they remain qualitatively unchanged if one assumes (1) Beverton-Holt-type or genotype-specific rather than Ricker-type density dependence in the host, or (2) different genotype-specific susceptibilities of hosts to their parasites, or if one adds (3) moderate levels of environmental stochasticity.     

The influence of varying spatial heterogeneity on the refuge model for coexistence of specialist parasitoid assemblages

Models of host–parasitoid dynamics often assume constant levels of spatial heterogeneity in parasitoid attack rate, which tends to stabilize the interactions. Recently, authors have questioned this assumption and shown that outcomes of simple host–parasitoid models change if spatial heterogeneity is allowed to vary with parasitoid density. Here, we allow spatial heterogeneity to vary with either parasitoid density or percent parasitism in a model designed to explain specialist parasitoid coexistence on insect hosts with various levels of refuge. By examining this model we can evaluate the effect of varying spatial heterogeneity on a more complex model in which spatial heterogeneity is not considered the primary determinant of persistence. By modeling communities with one host and two parasitoid species, we show that the probability of species persistence for the competitively inferior parasitoid depends on the assumed relationship between spatial heterogeneity and both parasitoid density and percent parasitism. The probability of parasitoid coexistence is generally lower when spatial heterogeneity varies with parasitoid demographics. We conclude that the conditions for which host refuge promote specialist parasitoid coexistence are less common that proposed by the original model. Finally, we compared a model in which spatial heterogeneity varies with percent parasitism to data from laboratory trials and find a reasonable fit. We conclude that the change in spatial heterogeneity strongly influenced the outcome of the laboratory trials, and we suggest more research is necessary before researchers can assume constant spatial heterogeneity in future models.     

Signs of stabilisation and stable coexistence

Many empirical studies motivated by an interest in stable coexistence have quantified negative density dependence, negative frequency dependence, or negative plant–soil feedback, but the links between these empirical results and ecological theory are not straightforward. Here, we relate these analyses to theoretical conditions for stabilisation and stable coexistence in classical competition models. By stabilisation, we mean an excess of intraspecific competition relative to interspecific competition that inherently slows or even prevents competitive exclusion. We show that most, though not all, tests demonstrating negative density dependence, negative frequency dependence, and negative plant–soil feedback constitute sufficient conditions for stabilisation of two‐species interactions if applied to data for per capita population growth rates of pairs of species, but none are necessary or sufficient conditions for stable coexistence of two species. Potential inferences are even more limited when communities involve more than two species, and when performance is measured at a single life stage or vital rate. We then discuss two approaches that enable stronger tests for stable coexistence‐invasibility experiments and model parameterisation. The model parameterisation approach can be applied to typical density‐dependence, frequency‐dependence, and plant–soil feedback data sets, and generally enables better links with mechanisms and greater insights, as demonstrated by recent studies.     

A keystone effect for parasites in intraguild predation?

Intraguild predation (IGP) is common in communities, yet theory suggests it should not often persist and coexistence of participating species should be rare. As parasitism can play keystone roles in interactions between competitors, and between predators and prey, here we examine the role of parasites in maintaining IGP. We used numerical exploration of population dynamic equations to determine coexistence and exclusion zones for two species engaged in IGP with shared parasitism. We demonstrate that parasitism increases the range of conditions leading to coexistence when the parasite exerts a greater deleterious effect on the 'stronger' species in terms of the combined effects of competition and predation. Such a parasite can enable an inferior competitor that is also the less predatory to persist, and may actually lead to numerical dominance of this species.     

Positive interactions among competitors can produce species-rich communities

Although positive interactions between species are well documented, most ecological theory for investigating multispecies coexistence remains rooted in antagonistic interactions such as competition and predation. Standard resource-competition models from this theory predict that the number of coexisting species should not exceed the number of factors that limit population growth. Here I show that positive interactions among resource competitors can produce species-rich model communities supported by a single limiting resource. Simulations show that when resource competitors reduce each others' per capita mortality rate (e.g. by ameliorating an abiotic stress), stable multispecies coexistence with a single resource may be common, even while the net interspecific interaction remains negative. These results demonstrate that positive interactions may provide an important mechanism for generating species-rich communities in nature. They also show that focusing on the net interaction between species may conceal important coexistence mechanisms when species simultaneously engage in both antagonistic and positive interactions.     

Evolution of cooperative cross-feeding could be less challenging than originally thought

The act of cross-feeding whereby unrelated species exchange nutrients is a common feature of microbial interactions and could be considered a form of reciprocal altruism or reciprocal cooperation. Past theoretical work suggests that the evolution of cooperative cross-feeding in nature may be more challenging than for other types of cooperation. Here we re-evaluate a mathematical model used previously to study persistence of cross-feeding and conclude that the maintenance of cross-feeding interactions could be favoured for a larger parameter ranges than formerly observed. Strikingly, we also find that large populations of cross-feeders are not necessarily vulnerable to extinction from an initially small number of cheats who receive the benefit of cross-feeding but do not reciprocate in this cooperative interaction. This could explain the widespread cooperative cross-feeding observed in natural populations.     

Nitrogen and Phosphorus Release from Mixed Litter Layers is Lower than Predicted from Single Species Decay

Ecosystem-level nutrient dynamics during decomposition are often estimated from litter monocultures. If species effects are additive, we can statistically predict nutrient dynamics in multi-species systems from monoculture work, and potential consequences of species loss. However, if species effects are dependent on interactions with other litter species (that is, non-additive), predictions based on monoculture data will likely be inaccurate. We conducted a 3-year, full-factorial, mixed-litter decomposition study of four dominant tree species in a temperate forest and measured nitrogen and phosphorus dynamics to explore whether nutrient dynamics in mixtures were additive or non-additive. Following common approaches, we used litterfall data to predict nutrient dynamics at the ecosystem-level. In mixtures, we observed non-additive effects of litter mixing on nutrient dynamics: the presence of nutrient-rich species in mixture facilitated nutrient release, whereas nutrient-poor species facilitated nutrient retention. Fewer nutrients were released from mixtures containing high-quality litter, and more immobilized from mixtures containing low-quality litter, than predicted from monocultures, creating a difference in overall nutrient release between predicted and actual dynamics in litter mixtures. Nutrient release at the ecosystem-level was greatly overestimated when based on monocultures because the effect of species interactions on nutrient immobilization was not accounted for. Our data illustrate that the identity of species in mixtures is key to their role in non-additive interactions, with repercussions for mineral nutrient availability and storage. These results suggest that predictions of ecosystem-level nutrient dynamics using litter monoculture data likely do not accurately represent actual dynamics because the effects of litter species interactions are not incorporated. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Modelling parasitism and predation of mosquitoes by water mites

Parasitism and predation are two ecological interactions that can occur simultaneously between two species. This is the case of Culicidae (Insecta: Diptera) and water mites (Acari: Hydrachnidia). The larva mites are~parasites of aquatic and semiaquatic insects, and deutonymphs and adults are predators of insect larvae and eggs. Since several families of water mites are associated with mosquitoes there is an interest in the potential use of these mites as biological control agents. The aim of this paper is to use mathematical modelling and analysis to assess the impact of predation and parasitism in the mosquito population. We propose a system of ordinary differential equations to model the interactions among the larval and adult stages of mosquitoes and water mites. The model exhibits three equilibria: the first equilibrium point corresponds to the state where the two species are absent, the second one to the state where only mosquitoes are present (water mites need insects to complete their life cycle), and the third one is the coexistence equilibrium. We analyze conditions for the asymptotic stability of equilibria, supported by analytical and numerical methods. We discuss the different scenarios that appear when we change the parasitism and predation parameters. High rates of parasitism and moderate predation can drive two species to a stable coexistence.     

Role of toxin and nutrient for the occurrence and termination of plankton bloom--results drawn from field observations and a mathematical model

The termination of harmful algal blooms (HABs) and coexistence of phytoplankton-zooplankton populations are of great importance to human health, ecosystem, environment, tourism and fisheries. In this paper we propose a three-component model consisting of dissolved limiting nutrients (N) supplied at constant rate and partially recycled after the death of plankton by bacterial decomposition, phytoplankton (P) and zooplankton (Z), where the growth of zooplankton species reduce due to toxic chemicals released by phytoplankton species. Our analysis leads to different thresholds which are expressible in terms of model parameters and determine the existence and stability of various states of the system. We observe that phytoplankton-zooplankton persist if the maximal zooplankton ingestion rate exceeds a lower threshold value. It is shown that the coexistence equilibrium loses its stability when the dilution rate of the nutrient concentration passes through a critical value and Hopf bifurcation occurs that induces oscillations of the population. Our results indicate that the occurrence of bloom increases when the nutrient concentration is very high, and in that case toxin produced by the phytoplankton plays a very crucial role towards the termination of the planktonic bloom.     

The nutrient-load hypothesis: patterns of resource limitation and community structure driven by competition for nutrients and light

Resource competition theory predicts that the outcome of competition for two nutrients depends on the ratio at which these nutrients are supplied. Yet there is considerable debate whether nutrient ratios or absolute nutrient loads determine the species composition of phytoplankton and plant communities. Here we extend the classical resource competition model for two nutrients by including light as additional resource. Our results suggest the nutrient-load hypothesis, which predicts that nutrient ratios determine the species composition in oligotrophic environments, whereas nutrient loads are decisive in eutrophic environments. The underlying mechanism is that nutrient enrichment shifts the species interactions from competition for nutrients to competition for light, which favors the dominance of superior light competitors overshadowing all other species. Intermediate nutrient loads can generate high biodiversity through a fine-grained patchwork of two-species and three-species coexistence equilibria. Depending on the species traits, however, competition for nutrients and light may also produce multiple alternative stable states, suppressing the predictability of the species composition. The nutrient-load hypothesis offers a solution for several discrepancies between classical resource competition theory and field observations, explains why eutrophication often leads to diversity loss, and provides a simple conceptual framework for patterns of biodiversity and community structure observed in nature.     

Parasitism levels in Orgyia leucostigma feeding on two tree species: implications for the slow-growth- high-mortality hypothesis

The slow‐growth‐high‐mortality hypothesis proposes that increased development time in arthropods feeding on suboptimal food may result in an increased vulnerability to natural enemies. We measured the development time of the forest caterpillar Orgyia leucostigma J.E. Smith (Lepidoptera: Lymantriidae: Orgyiini) on two of its host plants and used a 7‐year database on parasitism of this species to test the slow‐growth‐high‐mortality hypothesis. We found that female O. leucostigma developed faster when fed on willow (Salix nigra Marsh) than when fed on box elder (Acer negundo L.). However, only one of the parasitoids of the parasitoid community that attack these larvae followed the prediction of the slow‐growth‐high‐mortality hypothesis. Overall parasitism of O. leucostigma on willow was greater than in box elder, contradicting the slow‐growth‐high‐mortality hypothesis prediction. This is the first test of the hypothesis to consider parasitism by several species in the parasitoid community attacking a free‐feeding herbivore on two distantly related plant species.     

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

Cross-feeding interactions, in which bacterial cells exchange costly metabolites to the benefit of both interacting partners, are very common in the microbial world. However, it generally remains unclear what maintains this type of interaction in the presence of non-cooperating types. We investigate this problem using synthetic cross-feeding interactions: by simply deleting two metabolic genes from the genome of Escherichia coli, we generated genotypes that require amino acids to grow and release other amino acids into the environment. Surprisingly, in a vast majority of cases, cocultures of two cross-feeding strains showed an increased Darwinian fitness (that is, rate of growth) relative to prototrophic wild type cells—even in direct competition. This unexpected growth advantage was due to a division of metabolic labour: the fitness cost of overproducing amino acids was less than the benefit of not having to produce others when they were provided by their partner. Moreover, frequency-dependent selection maintained cross-feeding consortia and limited exploitation by non-cooperating competitors. Together, our synthetic study approach reveals ecological principles that can help explain the widespread occurrence of obligate metabolic cross-feeding interactions in nature.     

The effect of recycling on plant competitive hierarchies

Evidence from field studies suggests that some plant species enhance their persistence by reinforcing patterns of N availability through differences in litter quality. Using mathematical models of nutrient flow, we explore whether and how recycling affects plant growth, competition, and coexistence and whether it leads to positive feedbacks. Two mechanisms are considered: the ability of plants to access two forms of soil N, complex (e.g., organic) and simple (e.g., nitrate), and the effect of density-dependent limitation of growth. Except in the trivial case of limitation by N in one form without density dependence, differences in litter quality can prevent the establishment of competitors. Feedback can, conversely, facilitate the invasion of competitors. At equilibrium, the rate of decomposition does not affect the outcome of competition. Species affect their long-term persistence if they alter the fraction of nitrogen that is returned to the soil and becomes available for plant uptake. Increasing the fraction of N that is recycled favors specialists in complex nitrogen and species that suppress the growth of others at high nitrogen availability. Increasing the rate of microbial decomposition of complex nitrogen favors specialists in simple nitrogen.