Fundamental Ecological Concepts Research Articles

Composition, divergence and variability: A comprehensive analysis of fish trait responses to connectivity

Connectivity, a fundamental concept in ecology, refers to the extent to which different habitats or ecosystems are interconnected through the movement of organisms, nutrients, and energy. Lateral hydrological connectivity (LHC) plays an especially critical role in shaping aquatic community organization in river-floodplain systems. However, a comprehensive understanding of various trait responses to LHC remains elusive. We characterized how attributes of fish community traits, specifically composition, divergence, and temporal variability respond to LHC in the Austrian-Hungarian floodplains of the Danube River using environmental DNA (eDNA) metabarcoding. Trait composition was quantified by community-level weighted means (CWM) as the degree of changes in trait responses along the LHC gradient from isolated oxbows to the main river. Divergence was measured using Rao’s quadratic functional diversity index and a null model approach to calculate standardized effect sizes (SES), with larger SES values indicating greater divergence and smaller values indicating convergence. Temporal variability, representing the degree of instability in community traits over time, was calculated using a functional beta diversity measure for multiple communities. Our findings revealed apparent compositional changes for many trait variables, highlighting the significance of LHC in shaping community functional diversity. Divergence patterns indicated that isolated habitats foster trait convergence presumably due to habitat filtering, whereas more connected areas promote trait divergence due to higher species richness and habitat availability. Temporal variability of traits associated with flow preference exhibited a hump-shaped relationship with LHC, suggesting intermediate connectivity zones are hotspots of ecological dynamism. The study suggests that examining composition, divergence, and temporal variability together provides a more complete understanding of trait responses to connectivity, stressing the importance of maintaining diverse connectivity levels in river-floodplain systems for effective conservation and ecosystem management.

Harnessing open science practices to teach ecology and evolutionary biology using interactive tutorials.

Open science skills are increasingly important for a career in ecology and evolutionary biology (EEB) as efforts to make data and analyses publicly available continue to become more commonplace. While learning core concepts in EEB, students are also expected to gain skills in conducting open science to prepare for future careers. Core open science skills like programming, data sharing, and practices that promote reproducibility can be taught to undergraduate students alongside core concepts in EEB. Yet, these skills are not always taught in biology undergraduate programs, and a major challenge in developing open science skills and learning EEB concepts simultaneously is the high cognitive load associated with learning multiple disparate concepts at the same time. One solution is to provide students with easily digestible, scaffolded, pre-formatted code in the form of vignettes and interactive tutorials. Here, we present six open source teaching tutorials for undergraduate students in EEB. These tutorials teach fundamental ecological concepts, data literacy, programming (using R software), and analysis skills using publicly available datasets while introducing students to open science concepts and tools. Spanning a variety of EEB topics and skill levels, these tutorials serve as examples and resources for educators to integrate open science tools, programming, and data literacy into teaching EEB at the undergraduate level.

Investigation into Eco-Architecture at Pulisan Beach Coastal Area

Coastal regions represent transitional zones between terrestrial and marine ecosystems, rendering them particularly susceptible to changes. For tourism development to be viewed as a comprehensive and holistic endeavor, it must prioritize local ecology, especially amidst heightened productivity and activity. The distinctive ecological attributes of Pulisan Beach underscore the strategy to draw diverse tourists to North Sulawesi. The research methodology adopts a qualitative descriptive approach, entailing studies and analyses of environmental potentials through field observations. This survey type seeks factual information and employs Ecological Architecture theory for analysis. Identification and analysis of the coastal tourist area of Pulisan Beach are conducted using fundamental concepts and principles of Ecological Architecture. These principles emphasize holistic unity, drawing upon human experiences and interactions with the natural environment, viewing development as an ongoing process rather than a static reality, and advocating for cooperation between humans and nature to ensure mutual safety. The study on the developmental status of Pulisan Beach tourism area, utilizing an Eco-Architecture framework, concludes that it adheres to fundamental ecological concepts and principles. It yields insights into organizing the beach area as a sustainable tourism destination, emphasizing ecological preservation. The arrangement prioritizes principles of Eco-Architecture that are environmentally conscious, aiming to conserve the surrounding environment.

A comprehensive framework for vegetation succession

AbstractSuccession is defined as a directional change in species populations, the community, and the ecosystem at a site following a disturbance. Succession is a fundamental concept in ecology as it links different disciplines. An improved understanding of succession is urgently needed in the Anthropocene to predict the widespread effects of global change on succession and ecosystem recovery, but a comprehensive successional framework (CSF) is lacking. A CSF is needed to synthesize results, draw generalizations, advance successional theory, and make improved decisions for ecosystem restoration. We first show that succession is an integral part of socio‐ecological system dynamics and that it is driven by social and ecological factors operating at different spatial scales, ranging from the patch to the globe. We then present a CSF at the local scale (patch and landscape) at which succession takes place and explain the underlying successional processes and mechanisms operating at that scale. The CSF reflects the increasingly broader perspective on succession and includes recent theoretical advances by not only focusing on species replacement but also on ecosystem development, considering succession as part of a socio‐ecological system, and taking the effect of past and current land use, the landscape context, biotic interactions, and feedback loops into account. We discuss how the CSF can be used to integrate and synthesize successional studies, and its implications for ecosystem restoration.

Predicting niche overlap with model‐based ordination

The ecological niche is a fundamental concept in ecology that can be used in order better understand species relationships. The overlap in species niches provides a measure of the likelihood for species to co‐occur. Most approaches that quantify niche overlap have been based on distance and similarity indices, for pairwise combinations of species. In this paper, we suggest that niche overlap can be calculated from the predictions of a model. Using a statistical model to predict niche overlap provides various benefits, includes the possibility to adjust the model to properties of the data. We demonstrate this using an example dataset of an ecological community of Foraminifera species, to which we fit a generalized linear latent variable model (GLLVM). GLLVMs are a flexible class of models that allow to estimate the distribution of species using both measured environmental predictors and residual covariation between species. We demonstrate how to calculate niche overlap from GLLVMs for any combination of species, and separately for different environments. Predicting niche overlap from a model further expands the toolset available to ecologists for the exploration of species co‐occurrence patterns.

Seasonally mediated niche partitioning in a vertically compressed pelagic predator guild.

Niche partitioning among closely related, sympatric species is a fundamental concept in ecology, and its mechanisms are of broad interest for understanding ecosystem functioning and predicting the impacts of human-driven environmental change. However, identifying mechanisms by which top marine predators partition available resources has been especially challenging given the difficulty of quantifying resource use of large pelagic animals. In the eastern tropical Pacific (ETP), three large, highly mobile and ecologically similar pelagic predators (blue marlin (Makaira nigricans), black marlin (Istiompax indica) and sailfish (Istiophorus platypterus)) coexist in a vertically compressed habitat. To evaluate each species' ecological niche, we leveraged a decade of recreational fisheries data, multi-year satellite tracking with high-resolution dive data, and stable isotope analysis. Fishery interaction and telemetry-based three-dimensional seasonal utilization distributions suggested high spatial and temporal overlap among species; however, seasonal and diel variability in diving behaviour produced spatial partitioning, leading to low trophic overlap among species. Expanding oxygen minimum zones will reduce the available vertical habitat within predator guilds, likely leading to increases in interspecific competition. Thus, understanding the mechanisms of habitat partitioning among predators in the vertically compressed ETP can provide insight into how predators in other ocean regions may respond to vertically limited habitats.

Successional theories.

Succession is a fundamental concept in ecology because it indicates how species populations, communities, and ecosystems change over time on new substrate or after a disturbance. A mechanistic understanding of succession is needed to predict how ecosystems will respond to land-use change and to design effective ecosystem restoration strategies. Yet, despite a century of conceptual advances a comprehensive successional theory is lacking. Here we provide an overview of 19 successional theories ('models') and their key points, group them based on conceptual similarity, explain conceptual development in successional ideas and provide suggestions how to move forward. Four groups of models can be recognised. The first group (patch & plants) focuses on plants at the patch level and consists of three subgroups that originated in the early 20th century. One subgroup focuses on the processes (dispersal, establishment, and performance) that operate sequentially during succession. Another subgroup emphasises individualistic species responses during succession, and how this is driven by species traits. A last subgroup focuses on how vegetation structure and underlying demographic processes change during succession. A second group of models (ecosystems) provides a more holistic view of succession by considering the ecosystem, its biota, interactions, diversity, and ecosystem structure and processes. The third group (landscape) considers a larger spatial scale and includes the effect of the surrounding landscape matrix on succession as the distance to neighbouring vegetation patches determines the potential for seed dispersal, and the quality of the neighbouring patches determines the abundance and composition of seed sources and biotic dispersal vectors. A fourth group (socio-ecological systems) includes the human component by focusing on socio-ecological systems where management practices have long-lasting legacies on successional pathways and where regrowing vegetations deliver a range of ecosystem services to local and global stakeholders. The four groups of models differ in spatial scale (patch, landscape) or organisational level (plant species, ecosystem, socio-ecological system), increase in scale and scope, and reflect the increasingly broader perspective on succession over time. They coincide approximately with four periods that reflect the prevailing view of succession of that time, although all views still coexist. The four successional views are: succession of plants (from 1910 onwards) where succession was seen through the lens of species replacement; succession of communities and ecosystems (from 1965 onwards) when there was a more holistic view of succession; succession in landscapes (from 2000 onwards) when it was realised that the structure and composition of landscapes strongly impact successional pathways, and increased remote-sensing technology allowed for a better quantification of the landscape context; and succession with people (from 2015 onwards) when it was realised that people and societal drivers have strong effects on successional pathways, that ecosystem processes and services are important for human well-being, and that restoration is most successful when it is done by and for local people. Our review suggests that the hierarchical successional framework of Pickett is the best starting point to move forward as this framework already includes several factors, and because it is flexible, enabling application to different systems. The framework focuses mainly on species replacement and could be improved by focusing on succession occurring at different hierarchical scales (population, community, ecosystem, socio-ecological system), and by integrating it with more recent developments and other successional models: by considering different spatial scales (landscape, region), temporal scales (ecosystem processes occurring over centuries, and evolution), and by taking the effects of the surrounding landscape (landscape integrity and composition, the disperser community) and societal factors (previous and current land-use intensity) into account. Such a new, comprehensive framework could be tested using a combination of empirical research, experiments, process-based modelling and novel tools. Applying the framework to seres across broadscale environmental and disturbance gradients allows a better insight into what successional processes matter and under what conditions.

Assessment of Habitat Selection by Invasive Plants and Conditions with the Best Performance of Invasiveness Traits

Habitat selection is one of the fundamental concepts in ecology and means that each organism should choose the habitat that will maximize its success. Invaders may be an underestimated object in research on habitat selection. Invasive plants experience enormous propagule pressure and bear the costs of spreading in disturbed anthropogenic habitats. It means that they do not necessarily achieve maximum invasiveness traits in such habitats, which they selected to colonize. This study aimed to assess habitats where invaders are likely to occur from the set of all available ones in the landscape and the habitats with the best performed traits of invaders. The research was conducted on 52 and 112 plots in 2019 and 2021, respectively, in South-Eastern Poland, and the invasive plants were Caucasian hogweeds Heracleum sp. In the first year, the circle plots had a 50 m radius and were to measure habitat areas and traits of hogweeds (height, number of individuals in the plot, cover, and number of flowering specimens). Detrimental correspondence analysis and linear mixed model investigated that hogweeds achieved the best performance reflected by traits in continuous habitats—meadows and forests. In the second year, the plots to measure habitats had a 100 m radius. The reference plots were far from the invasion exposure, and the paired control vs. Heracleum ones had the same habitats with the potential to be invaded. The generalized linear mixed model showed that the probability of the hogweeds occurrence was higher when the habitat was overgrowing with a simultaneous decrease in open areas and in the increasing ruderal area with a decrease in bushes. The impact of the invader’s habitat on the invasion performance depended on the purpose of habitat selection. When invaders spread and increased invasive extent or appeared in habitat edges, they did not reach the highest traits, the best performing in continuous habitats. The specificity of habitat selection of invaders is another aspect that distinguishes invasion science from classic ecology.

Inconsistent relationships between area, heterogeneity and plant species richness in temperate farmed landscapes

Relationships between area, heterogeneity and species richness are fundamental concepts in ecology yet questions remain about how area and heterogeneity tradeoff (AHTO) to constrain biodiversity. Although there is growing evidence for unimodal heterogeneity diversity relationships (HDR's) and an AHTO, tests of the concept and consequences for species richness across a landscape‐scale gradient of human‐modified ecosystems are rare. Using data from a national (Wales) field survey we analysed relationships between environmental heterogeneity and plant species richness (α and γ). We used ordination to produce a composite metric of heterogeneity and compared this to commonly used metrics. We used niche hypervolumes to categorise the breadth of plant species' ecological preferences and analysed relationships between species richness, niche width and heterogeneity. The HDR was unimodal with α diversity at the smallest scale and positive with α and γ diversity (non‐linear) at the 1 km scale although in low intensity landscapes the HDR with γ diversity was unimodal. There was a unimodal relationship between habitat diversity and γ diversity. Land use intensity was unimodally related to diversity. There were significant interactions between niche width and heterogeneity. Richness of broad niche species increased with heterogeneity with flattening of the curve at higher levels. Narrow niche species were rare and mostly unresponsive. The expected decline in narrow niche species with increasing heterogeneity was not found although they did decline with land‐use intensity. Using a unique dataset, an analysis of a large‐scale mosaic of ecosystems found that the shape of the HDR varies with land use intensity, the heterogeneity metric, spatial scale, diversity type and niche width. Although heterogeneity can increase species richness, there may be tradeoffs at higher heterogeneity. A fundamental constraint on realising the benefit of heterogeneity is the low availability of narrower niche species in local species pools in modified landscapes.

A stable home: Autocorrelated Kernel Density Estimated home ranges of the critically endangered Elongated tortoise

Home range analysis is a standard and fundamental concept in ecology used to describe animal space use over their lifetimes. Connecting home range sizes with animal characteristics, location, and habitat can be used to inform conservation decisions. Reptiles are frequently lacking robust estimates of space use, particularly reptiles in tropical regions. Here we analyse a publicly available dataset, collected by the authors of this study, describing the movements of Critically Endangered Elongated tortoises Indotestudo elongata. The tortoise data included the locations of 17 tortoises (12 females, 5 males) collected on average once every three days for an average duration of 353.76 SE ± 33.10 days. We use these data to estimate the home range of Elongated tortoise, and explore how tortoise size and sex influences home range size. To mitigate issues resulting from low effective sample sizes and low temporal resolution of the data, we used a modern home range estimation method – Autocorrelated Kernel Density Estimators (AKDE). We found 14 of 17 individuals appear to be occupying a stable home range (using variograms to determine range residency). The average AKDE home range for all 14 individuals with range residency was 44.81 ± 10.44 ha. Bayesian Regression Models suggest comparable size estimates between male and female home ranges, despite males being physically larger than females in both mass and carapace length. These AKDE home range estimates have the added utility of being more comparable with other studies, less susceptible to errors from a suboptimal tracking regime, and are well positioned for inclusion in future meta-analyses. Keywords: testudine, autocorrelated kernel density estimator, spatial ecology, space use, Thailand, Indotestudo elongata

Bridging the scale gap: Predicting large‐scale population dynamics from small‐scale variation in strongly heterogeneous landscapes

Abstract Often, ecologists are challenged with a mismatch of scales: how do we upscale from local variation and available data to landscape‐level models and predictions? We present a general recipe for coarse‐graining from local‐ to landscape‐scale reaction–diffusion equations when spatial heterogeneity is small in extent compared to dispersal of organisms. Our homogenization approach uses the fundamental ecological concepts of Turchin's residence index and Skellam's dynamic level. Our approach opens avenues to new ecological theory that connects different scales, which we illustrate using predator–prey interactions. It also presents opportunities for using the increasingly available small‐scale data for landscape‐level predictions, such as range expansion rates. We find several unexpected nonlinear relationships between the movement behaviour on the local level and the spatially implicit and explicit outcomes at the landscape level, for example, predator spread rate may increase or decrease when predators move faster locally. Our method provides a mechanistic link for population dynamics and data integration across spatial and temporal scales, addressing a fundamental goal of landscape ecology.

Ecological awareness among secondary school pupils

This paper presents the results of quantitative research to survey ecological awareness among pupils in terms of three interlinked components: knowledge, attitudes and behavior. The survey participants were 529 secondary school pupils from the city of Zagreb, and the instrument used was a survey questionnaire. The analysis of the results shows that Zagreb secondary school pupils are environmentally aware to some extent but that there is room for improvement in regard to their familiarity with certain concepts in the area of ecology and changing behavior related to environmental protection. The survey identified statistically significant differences in pro-environmental behavior among respondents based on gender and class year in a number of situations. The results indicate the need to continually work on raising awareness of ecological issues and environmental protection, especially in terms of familiarising pupils with fundamental ecological concepts and pro-environmental behavior.

Ecological niche differentiation among six annual Lythrum species in Mediterranean temporary pools.

The ecological niche defines the favourable range of a species in a multidimensional space of ecological factors that determine the presence and function of individuals. This fundamental concept in ecology is widely used to understand plant species coexistence and segregation. In this study, we test for ecological differentiation among six annual Lythrum species that are characteristic of temporary pools in the South of France, where they either coexist or occur separately. We first analysed the co-occurrence of species at two different geographical scales: cluster analyses of species presence in 10km grid cells and coexistence in 0.25 m2 quadrats within populations of each species. Second, for three to nine populations of each species, we quantified a range of biotic and abiotic parameters using point contacts and soil measurements in five 0.25 m2 quadrats per population. We performed PCA on all variables and analysed each variable separately to compare the ecological niche features of the six species. A phenological index was assessed for the plant community of each site. We detected highly localized niche differentiation in terms of soil pH (all species) and for a range of variables among pairs of species. The six species also showed marked differences in the flowering period relative to the mean and variability of flowering time in their local community. These fine-scaled niche differences are associated with phylogenetic distances among species and may contribute to species' coexistence. These results are integrated in a conservation management plan for the habitat of the rarest species in this group.

Niche partitioning among dead wood-dependent beetles

Niche partitioning among species with virtually the same requirements is a fundamental concept in ecology. Nevertheless, some authors suggest that niches have little involvement in structuring communities. This study was done in the Pardubice Region (Czech Republic) on saproxylic beetles with morphologically similar larvae and very specific requirements, which are related to their obligatory dependence on dead wood material: Cucujus cinnaberinus, Pyrochroa coccinea, and Schizotus pectinicornis. This work was performed on 232 dead wood pieces at the landscape scale over six years. Based on the factors studied, the relationships among these species indicated that their co-occurrence based on species presence and absence was low, which indicated niche partitioning. However, based on analyses of habitat requirements and species composition using observed species abundances, there was no strong evidence for niche partitioning at either studied habitat levels, the tree and the microhabitat. The most likely reasons for the lack of strong niche partitioning were that dead wood is a rich resource and co-occurrence of saproxylic community was not driven by resource competition. This might be consistent with the theory that biodiversity could be controlled by the neutral drift of species abundance. Nevertheless, niche partitioning could be ongoing, meaning that the expanding C. cinnaberinus may have an advantage over the pyrochroids and could dominate in the long term.

Leveraging public data to offer online inquiry opportunities.

Inquiry activities have become increasingly common in Ecology and Evolution courses, but the rapid shift to remote instruction for many faculty members in response to the COVID‐19 pandemic has created new challenges for maintaining these student‐centered activities in a distance learning format. Moving forward, many instructors will be asked to create flexible course structures that allow for a mix of different teaching modalities and will be looking for resources to support student inquiry in both online and in‐person settings. Here, we propose the use of data‐driven inquiry activities as a flexible option for offering students experiences to build career‐relevant skills and learn fundamental ecological concepts. We share lessons learned from our experiences teaching a two‐semester course‐based research experience in global change ecology that leverages publicly available datasets to engage students in broadly relevant scientific inquiry.

MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data.

Niche is a fundamental concept in ecology. It integrates the sum of biotic and abiotic environmental requirements that determines a taxon's distribution. Microbiologists currently lack quantitative approaches to address niche-related hypotheses. We tested four approaches for the quantification of niche breadth and overlap of taxa in amplicon sequencing datasets, with the goal of determining generalists, specialists and environmental-dependent distributions of community members. We applied these indices to in silico training datasets first, and then to real human gut and desert biological soil crust (biocrust) case studies, assessing the agreement of the indices with previous findings. Implementation of each approach successfully identified a priori conditions within in silico training data, and we found that by including a limit of quantification based on species rank, one could identify taxa falsely classified as specialists because of their low, sparse counts. Analysis of the human gut study offered quantitative support for Bacilli, Gammaproteobacteria and Fusobacteria specialists enriched after bariatric surgery. We could quantitatively characterise differential niche distributions of cyanobacterial taxa with respect to precipitation gradients in biocrusts. We conclude that these approaches, made publicly available as an R package (MicroNiche), represent useful tools to assess microbial environment-taxon and taxon-taxon relationships in a quantitative manner.

Long-term cyclic persistence in an experimental predator-prey system.

Predator-prey cycles rank among the most fundamental concepts in ecology, are predicted by the simplest ecological models and enable, theoretically, the indefinite persistence of predator and prey1-4. However, it remains an open question for how long cyclic dynamics can be self-sustained in real communities. Field observations have been restricted to a few cycle periods5-8 and experimental studies indicate that oscillations may be short-lived without external stabilizing factors9-19. Here we performed microcosm experiments with a planktonic predator-prey system and repeatedly observed oscillatory time series of unprecedented length that persisted for up to around 50 cycles or approximately 300 predator generations. The dominant type of dynamics was characterized by regular, coherent oscillations with a nearly constant predator-prey phase difference. Despite constant experimental conditions, we also observed shorter episodes of irregular, non-coherent oscillations without any significant phase relationship. However, the predator-prey system showed a strong tendency to return to the dominant dynamical regime with a defined phase relationship. A mathematical model suggests that stochasticity is probably responsible for the reversible shift from coherent to non-coherent oscillations, a notion that was supported by experiments with external forcing by pulsed nutrient supply. Our findings empirically demonstrate the potential for infinite persistence of predator and prey populations in a cyclic dynamic regime that shows resilience in the presence of stochastic events.

Habitat selection and potential fitness consequences of two early-successional species with differing life-history strategies.

Habitat selection and its relationship to fitness is a fundamental concept in ecology, but the mechanisms driving this connection are complex and difficult to detect. Despite the difficulties in understanding such intricate relationships, it is imperative that we study habitat selection and its relationship with fitness. We compared habitat selection of least terns (Sternula antillarum) and piping plovers (Charadrius melodus) on the Missouri River (2012–2014) to examine the consequences of those choices on nest and chick survival. We hypothesized that plovers and terns would select habitat that minimized the chance of flooding and predation of eggs, chicks, and adults, but that plovers would also select habitat that would provide foraging habitat for their chicks. We developed an integrated habitat selection model that assessed selection across multiple scales (sandbar and nest scales) and directly modeled the effect of selection on nest and chick survival. In general, the species selected habitat in keeping with our hypotheses, such that predation and flooding, in particular, may have been reduced. Sandbar selection had either a negative or no appreciable effect on nest survival for both species across years. Nest‐site selection in 2012 had a generally positive effect on nest survival and chick survival for both terns and plovers, and this trended toward a negative effect by 2014. This result suggested that early selection decisions appeared to be adaptive, but we speculate that relatively high site fidelity and habitat degradation led to reduced benefit over time. Our results highlight the complex nature of habitat selection and its relationship to fitness.

Coming to Common Ground: The Challenges of Applying Ecological Theory Developed Aboveground to Rhizosphere Interactions

Accumulating evidence supports the importance of belowground interactions for plant performance, ecosystem functioning, and conservation biology. However, studying species interactions belowground has unique challenges relative to the aboveground realm. The structure of the media and spatial scale are among the key aspects that seem to strongly influence belowground interactions. As a consequence, our understanding of species interactions belowground is limited, at least compared to what is known about interactions aboveground. Here we address the general question: Do the ecological concepts that have been developed largely in aboveground systems apply to understanding species interactions in the rhizosphere? We first explore to what extent ecological concepts related to species interactions are considered in rhizosphere studies across various subdisciplines. Next, we explore differences and similarities above- and belowground for fundamental concepts in ecology, choosing topics that are underrepresented in rhizosphere studies but represent a swath of concepts: species diversity, island biogeography, self-organization and ecosystem engineering, trophic cascades, and chemical communication. Finally, we highlight to overcome major challenges of current methodologies to study rhizosphere interactions in order to advance the understanding of belowground interactions in an ecological context. By synthesizing literature related to rhizosphere interactions, we reveal similarities, as well as key differences, in how fundamental ecological concepts are used and tested in above- and belowground studies. Closing the knowledge gaps identified in our synthesis will promote a deeper understanding of the differences above- and belowground and ultimately lead to integration of these concepts.

Metaproteomic analysis adds a functional glimpse into host-microbe succession in an infant's GI.

Succession is a fundamental concept in ecology, describing the process by which pioneering species colonize a new environmental niche, paving the way for increasingly complex, yet stable ecosystems. The human gut-among the most complex ecosystems known-develops from a nearly sterile state as newborns to a thriving functional network of trillions of organisms living in concert with the host. Recent microbiome analyses have begun to characterize the identities of the microbes during this period of colonization. However, the biochemical processes that govern the stages of interorganism succession remains a poorly understood, yet exciting frontier. Toward the goal of learning how host-microbe symbiosis arises and is maintained, Young etal. (Proteomics 2015, 15, 3463-3473) present a longitudinal metaproteomic case study of an infant during her second and third weeks of life. In the first such analysis of its kind, Young etal. portray overlapping stages of protein production by both the microbiota and the host consistent with their increasing complexity, and deepening interactions.