Fur seal microbiota are shaped by the social and physical environment,show mother–offspring similarities and are associated with host genetic quality

Despite an increasing appreciation of the importance of host–microbe interactions in ecological and evolutionary processes, the factors shaping microbial communities in wild populations remain poorly understood. We therefore exploited a natural experiment provided by two adjacent Antarctic fur seal (Arctocephalus gazella) colonies of high and low social density and combined 16S rRNA metabarcoding with microsatellite profiling of mother–offspring pairs to investigate environmental and genetic influences on skin microbial communities. Seal‐associated bacterial communities differed profoundly between the two colonies, despite the host populations themselves being genetically undifferentiated. Consistent with the hypothesis that social stress depresses bacterial diversity, we found that microbial alpha diversity was significantly lower in the high‐density colony. Seals from one of the colonies that contained a stream also carried a subset of freshwater‐associated bacteria, indicative of an influence of the physical environment. Furthermore, mothers and their offspring shared similar microbial communities, in support of the notion that microbes may facilitate mother–offspring recognition. Finally, a significant negative association was found between bacterial diversity and heterozygosity, a measure of host genetic quality. Our study thus reveals a complex interplay between environmental and host genetic effects, while also providing empirical support for the leash model of host control, which posits that bacterial communities are driven not only by bottom‐up species interactions, but also by top‐down host regulation. Taken together, our findings have broad implications for understanding host–microbe interactions as well as prokaryotic diversity in general.     

High-throughput DNA barcoding for ecological network studies

The network theoretical framework of ecological community studies is expected to promote not only the basic understanding of ecological and coevolutionary dynamics but also the application of those scientific insights into ecosystem management. However, our knowledge of ecological network architecture in the wild largely stems from empirical studies on macro-organismal systems such as those of plant–pollinator, plant–seed disperser, and prey–predator interactions. In this sense, we have remained ignorant of the diversity of ecological network architecture, its underlying assembly processes, and its consequences on ecological and coevolutionary dynamics. In this paper, I discuss how the high-throughput DNA barcoding of microbes, especially that based on next-generation sequencing, potentially expands the target of ecological network studies. I review the methodological platforms of next-generation sequencing-based analyses of microbe–host animal/plant networks and then introduce some case studies on the networks of plants and their hyper-diverse fungal symbionts. As those preliminary studies are uncovering the unexpected diversity of ecological network architecture, further application of such next-generation sequencing-based analyses to a diverse array of microbial systems will significantly improve our views on community ecological and coevolutionary processes.     

Reflections on,and visions for,the changing field of pollination ecology

Since the launch of Ecology Letters in 1998, the field of Pollination Ecology has changed considerably in its focus. In this review, we discuss the major discoveries across the past two decades. We quantitatively synthesise the frequency by which different concepts and topics appeared in the peer‐reviewed literature, as well as the connections between these topics. We then look forward to identify pressing research frontiers and opportunities for additional integration in the future. We find that there has been a shift towards viewing plant–pollinator interactions as networks and towards understanding how global drivers influence the plants, pollinators and the ecosystem service of pollination. Future frontiers include moving towards a macroecological view of plant–pollinator interactions, understanding how ecological intensification and urbanisation will influence pollination, considering other interactions, such as plant–microbe–pollinator networks, and understanding the causes and consequences of extinctions. Pollination Ecology is poised to advance our basic understanding of the ecological and evolutionary factors that shape plant–animal interactions and to create applied knowledge that informs conservation decision making.     

More than words: the chemistry behind the interactions in the plant holobiont

Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant-associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant–microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant–microbe and microbe–microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe–microbe and microbe–plant communication pathways during plant development and on different plant organs.     

Plant scent and plant–insect interactions—Review and outlook from a macroevolutionary perspective

The astonishing diversity of plants and insects and their entangled interactions are cornerstones in terrestrial ecosystems. Co-occurring with species diversity is the diversity of plant secondary metabolites (PSMs). So far, their estimated number is more than 200 000 compounds, which are not directly involved in plant growth and development but play important roles in helping plants handle their environment including the mediation of plant–insect interactions. Here, we use plant volatile organic compounds (VOCs), a key olfactory communication channel that mediates plant–insect interactions, as a showcase of PSMs. In spite of the cumulative knowledge of the functional, ecological, and microevolutionary roles of VOCs, we still lack a macroevolutionary understanding of how they evolved with plant–insect interactions and contributed to species diversity throughout the long coevolutionary history of plants and insects. We first review the literature to summarize the current state-of-the-art research on this topic. We then present various relevant types of phylogenetic methods suitable to answer macroevolutionary questions on plant VOCs and suggest future directions for employing phylogenetic approaches in studying plant VOCs and plant–insect interactions. Overall, we found that current studies in this field are still very limited in their macroevolutionary perspective. Nevertheless, with the fast-growing development of metabolome analysis techniques and phylogenetic methods, it is becoming increasingly feasible to integrate the advances of these two areas. We highlight promising approaches to generate new testable hypotheses and gain a mechanistic understanding of the macroevolutionary roles of chemical communication in plant–insect interactions.     

Roles of plant volatiles in defence against microbial pathogens and microbial exploitation of volatiles

Plants emit a large variety of volatile organic compounds during infection by pathogenic microbes, including terpenes, aromatics, nitrogen‐containing compounds, and fatty acid derivatives, as well as the volatile plant hormones, methyl jasmonate, and methyl salicylate. Given the general antimicrobial activity of plant volatiles and the timing of emission following infection, these compounds have often been assumed to function in defence against pathogens without much solid evidence. In this review, we critically evaluate current knowledge on the toxicity of volatiles to fungi, bacteria, and viruses and their role in plant resistance as well as how they act to induce systemic resistance in uninfected parts of the plant and in neighbouring plants. We also discuss how microbes can detoxify plant volatiles and exploit them as nutrients, attractants for insect vectors, and inducers of volatile emissions, which stimulate immune responses that make plants more susceptible to infection. Although much more is known about plant volatile–herbivore interactions, knowledge of volatile–microbe interactions is growing and it may eventually be possible to harness plant volatiles to reduce disease in agriculture and forestry. Future research in this field can be facilitated by making use of the analytical and molecular tools generated by the prolific research on plant–herbivore interactions.     

Measurement of the Girth of Coniferous Trees at Braemar in 1894

ABSTRACT

Background: Plant communities are usually characterised by species composition and abundance, but also underlie a multitude of complex interactions that we have only recently started unveiling. Yet, we are still far from understanding ecological and evolutionary processes shaping the network-level organisation of plant diversity, and to what extent these processes are specific to certain spatial scales or environments.

Aims: Understanding the systemic mechanisms of plant–plant network assembly and their consequences for diversity patterns.

Methods: We review recent methods and results of plant–plant networks.

Results: We synthetize how plant–plant networks can help us to: (a) assess how competition and facilitation may balance each other through the network; (b) analyse the role of plant–plant interactions beyond pairwise competition in structuring plant communities, and (c) forecast the ecological implications of complex species dependencies. We discuss pros and cons, assumptions and limitations of different approaches used for inferring plant–plant networks.

Conclusions: We propose novel opportunities for advancing plant ecology by using ecological networks that encompass different ecological levels and spatio-temporal scales, and incorporate more biological information. Embracing networks of interactions among plants can shed new light on mechanisms driving evolution and ecosystem functioning, helping us to mitigate diversity loss.     

Winning and losing with microbes: how microbially mediated fitness differences influence plant diversity

Interactions between plants and soil microbes can strongly influence plant diversity and community dynamics. Soil microbes may promote plant diversity by driving negative frequency‐dependent plant population dynamics, or may favor species exclusion by providing one species an average fitness advantage over others. However, past empirical research has focused overwhelmingly on the consequences of frequency‐dependent feedbacks for plant species coexistence and has generally neglected the consequences of microbially mediated average fitness differences. Here we use theory to develop metrics that quantify microbially mediated plant fitness differences, and show that accounting for these effects can profoundly change our understanding of how microbes influence plant diversity. We show that soil microbes can generate fitness differences that favour plant species exclusion when they disproportionately harm (or favour) one plant species over another, but these fitness differences may also favor coexistence if they trade off with competition for other resources or generate intransitive dominance hierarchies among plants. We also show how the metrics we present can quantify microbially mediated fitness differences in empirical studies, and explore how microbial control over coexistence varies along productivity gradients. In all, our analysis provides a more complete theoretical foundation for understanding how plant–microbe interactions influence plant diversity.     

Temporal and geographic variation in parasitoid attack with no evidence for ant protection of the Melissa blue butterfly,Lycaeides melissa

相似文献   

Interdomain ecological networks between plants and microbes

While macroscopic interkingdom relationships have been intensively investigated in various ecosystems, the above–belowground ecology in natural ecosystems has been poorly understood, especially for the plant–microbe associations at a regional scale. In this study, we proposed a workflow to construct interdomain ecological networks (IDEN) between multiple plants and various microbes (bacteria and archaea in this study). Across 30 latitudinal forests in China, the regional IDEN showed particular topological features, including high connectance, nested structure, asymmetric specialization and modularity. Also, plant species exhibited strong preference to specific microbial groups, and the observed network was significantly different from randomly rewired networks. Network module analysis indicated that a majority of microbes associated with plants within modules rather than across modules, suggesting specialized associations between plants and microorganisms. Consistent plant–microbe associations were captured via IDENs constructed within individual forest locations, which reinforced the validity of IDEN analysis. In addition, the plant–forest link distribution showed the geographical distribution of plants had higher endemicity than that of microorganisms. With cautious experimental design and data processing, this study shows interdomain species associations between plants and microbes in natural forest ecosystems and provides new insights into our understanding of meta‐communities across different domain species.     

Effects of biodiversity in agricultural landscapes on the protective microbiome of insects – a review

Symbiotic bacteria in herbivorous insects can have strong beneficial impacts on their host's survival, including conferring resistance to natural enemies such as parasitoid wasps or pathogens, while also imposing energetic costs on the host, resulting in cost‐benefit trade‐offs. Whether these trade‐offs favour the hosting of symbionts depends on the growth environment of the herbivore. Long‐term experimental grassland studies have shown that increasing plant species richness leads to an increased diversity of associated herbivores and their natural enemies. Such a change in natural enemy diversity, related to changes in plant diversity, could also drive changes in the community of symbionts hosted by the herbivorous insects. Aphids are one model system for studying symbionts in insects, and effects of host‐plant species and diversity on aphid‐symbiont interactions have been documented. Yet, we still understand little of the mechanisms underlying such effects. We review the current state of knowledge of how biodiversity can impact aphid‐symbiont communities and the underlying drivers. Then, we discuss this in the framework of sustainable agriculture, where increased plant biodiversity, in the form of wildflower strips, is used to recruit natural enemies to crop fields for their pest control services. Although aphid symbionts have the potential to reduce biological control effectiveness through conferring protection for the host insect, we discuss how increasing plant and natural enemy biodiversity can mitigate these effects and identify future research opportunities. Understanding how to promote beneficial interactions in ecological systems can help in the development of more sustainable agricultural management strategies.     

Evolutionary “Experiments” in Symbiosis: The Study of Model Animals Provides Insights into the Mechanisms Underlying the Diversity of Host–Microbe Interactions

Current work in experimental biology revolves around a handful of animal species. Studying only a few organisms limits science to the answers that those organisms can provide. Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host–microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of the mechanisms that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host–microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease.     

A review of the role of parasites in the ecology of reptiles and amphibians

A great diversity of parasites, from viruses and bacteria to a range of remarkable eukaryotic organisms, exploit reptile and amphibian hosts. Recent increases in the emergence of infectious disease have revealed the importance of understanding the effects of interactions between hosts and their parasites. Here we review the effects of parasite infection on a range of demographic, behavioural, genomic and physiological factors in reptile and amphibian species. Reviewing these parasite roles collectively, and prioritising areas for research, advances our ecological understanding and guides direction for conservation in a time of rapid species decline. Poorly resolved systems include Gymnophionan amphibians and Crocodilian hosts, in addition to viral and bacterial parasites. Future research should seek to understand processes enabling population recovery and examining synergistic interactions of parasites with fragmentation, climate change and other processes that threaten species persistence.     

Generalising indirect defence and resistance of plants

Indirect defence, the adaptive top‐down control of herbivores by plant traits that enhance predation, is a central component of plant–herbivore interactions. However, the scope of interactions that comprise indirect defence and associated ecological and evolutionary processes has not been clearly defined. We argue that the range of plant traits that mediate indirect defence is much greater than previously thought, and we further organise major concepts surrounding their ecological functioning. Despite the wide range of plant traits and interacting organisms involved, indirect defences show commonalities when grouped. These categories are based on whether indirect defences boost natural enemy abundance via food or shelter resources, or, alternatively, increase natural enemy foraging efficiency via information or alteration of habitat complexity. The benefits of indirect defences to natural enemies should be further explored to establish the conditions in which indirect defence generates a plant–natural enemy mutualism. By considering the broader scope of plant–herbivore–natural enemy interactions that comprise indirect defence, we can better understand plant‐based food webs, as well as the evolutionary processes that have shaped them.     

Applying population and community ecology theory to advance understanding of belowground biogeochemistry

Approaches to quantifying and predicting soil biogeochemical cycles mostly consider microbial biomass and community composition as products of the abiotic environment. Current numerical approaches then primarily emphasise the importance of microbe–environment interactions and physiology as controls on biogeochemical cycles. Decidedly less attention has been paid to understanding control exerted by community dynamics and biotic interactions. Yet a rich literature of theoretical and empirical contributions highlights the importance of considering how variation in microbial population ecology, especially biotic interactions, is related to variation in key biogeochemical processes like soil carbon formation. We demonstrate how a population and community ecology perspective can be used to (1) understand the impact of microbial communities on biogeochemical cycles and (2) reframe current theory and models to include more detailed microbial ecology. Through a series of simulations we illustrate how density dependence and key biotic interactions, such as competition and predation, can determine the degree to which microbes regulate soil biogeochemical cycles. The ecological perspective and model simulations we present lay the foundation for developing empirical research and complementary models that explore the diversity of ecological mechanisms that operate in microbial communities to regulate biogeochemical processes.     

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria

Identifying the traits that determine spatial distributions can be challenging when studying organisms, like bacteria, for which phenotypic information is limited or non‐existent. However, genomic data provide another means to infer traits and determine the ecological attributes that account for differences in distributions. We determined the spatial distributions of ~124 000 soil bacterial taxa across a 3.41 km² area to determine whether we could use phylogeny and/or genomic traits to explain differences in habitat breadth. We found that occupancy was strongly correlated with environmental range; taxa that were more ubiquitous were found across a broader range of soil conditions. Across the ~500 taxa for which genomic information was available, genomic traits were more useful than phylogeny alone in explaining the variation in habitat breadth; bacteria with larger genomes and more metabolic versatility were more likely to have larger environmental and geographical distributions. Just as trait‐based approaches have proven to be so useful for understanding the distributions of animals and plants, we demonstrate that we can use genomic information to infer microbial traits that are difficult to measure directly and build trait‐based predictions of the biogeographical patterns exhibited by microbes.     

阿米巴-细菌互作：进化、生态与环境效应

阿米巴是原生动物的主要类群,是陆地和水生生态系统的关键组成部分。阿米巴与细菌之间有着密切而复杂的相互作用。一方面,阿米巴通过捕食直接影响细菌群落与多样性,增强细菌活性。另一方面,细菌也进化出抵抗捕食的机制来抵抗甚至感染阿米巴,反向影响阿米巴的生长和多样性。近年来,阿米巴-细菌互作的研究开始受到了广泛关注。本文总结了阿米巴-细菌互作的进化历史、生态关系(捕食、偏利共生、寄生和互利共生)以及其对环境的潜在影响,旨在更好地理解阿米巴-细菌互作这一研究领域,为其他原生动物-微生物之间的研究提供新的思路,也为探究宿主-微生物互作的机制提供参考。     

How do belowground organisms influence plant-pollinator interactions?

Aims The majority of angiosperms are pollinated by animals, and this interaction is of enormous importance in both agricultural and natural systems. Pollinator behavior is influenced by plants' floral traits, and these traits may be modified by interactions with other community members. In recent years, knowledge of ecological linkages between above- and belowground organisms has grown tremendously. Soil communities are extremely diverse, and when their interactions with plants influence floral characteristics, they have the potential to alter pollinator attraction and visitation, but plant–pollinator interactions have been neglected in studies of the direct and indirect effects of soil organism–root interactions. Here, we review these belowground interactions, focusing on the effects of nitrogen-fixing bacteria, arbuscular mycorrhizal fungi and root-feeding herbivores, and their effects on floral traits and pollinators. Further, we identify gaps in our knowledge of these indirect effects and recommend promising directions and topics that should be addressed by future research.Important findings Belowground organisms can influence a wide variety of floral traits that are important mediators of pollinator attraction, including the number and size of flowers and nectar and pollen production. Other traits that are known to influence pollinators in some plant species, such as floral volatiles, color and nectar composition, have rarely or never been examined in the context of belowground plant interactions. Despite clear effects on flowers, relatively few studies have measured pollinator responses to belowground interactions. When these indirect effects have been studied, both arbuscular mycorrhizal fungi and root herbivores were found to shift pollinator visitation patterns. Depending on the interaction, these changes may either increase or decrease pollinator attraction. Finally, we discuss future directions for ecological studies that will more fully integrate belowground ecology with pollination biology. We advocate a multilevel approach to these questions to not only document indirect effect pathways between soil interactions and pollination but also identify the mechanisms driving changes in pollinator impacts and the resultant effects on plant fitness. A more thorough understanding of these indirect interactions will advance ecological theory and may inform management strategies in agriculture and conservation biology.     

Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.

This Essay argues that in order to truly understand how marine hosts benefit from the immense diversity of microbes, we need to expand towards long-term, multi-disciplinary research focussing on few areas of the world’s ocean that we refer to as “natural experiments,” where processes can be studied at scales that far exceed those captured in laboratory experiments.