Classical Ecological Theory Research Articles

The development of ecological systems along paths of least resistance

A long-standing question in biology is whether there are common principles that characterize the development of ecological systems (the appearance of a group of taxa), regardless of organismal diversity and environmental context.1,2,3,4,5,6,7,8,9,10,11 Classic ecological theory holds that these systems develop following a sequenced, orderly process that generally proceeds from fast-growing to slow-growing taxa and depends on life-history trade-offs.2,12,13 However, it is also possible that this developmental order is simply the path with the least environmental resistance for survival of the component species and hence favored by probability alone. Here, we use theory and data to show that the order from fast- to slow-growing taxa is the most likely developmental path for diverse systems when local taxon interactions self-organize in light of environmental resistance. First, we demonstrate theoretically that a sequenced development is more likely than a simultaneous one, at least until the number of iterations becomes so large as to be ecologically implausible. We then show that greater diversity of taxa and life histories improves the likelihood of a sequenced order from fast- to slow-growing taxa. Using data from bacterial and metazoan systems,14,15,16,17,18,19 we present empirical evidence that the developmental order of ecological systems moves along the paths of least environmental resistance. The capacity of simple principles to explain the trend in the developmental order of diverse ecological systems paves the way to an enhanced understanding of collective features of life.

Lysogeny destabilizes computationally simulated microbiomes.

Microbiomes are ecosystems, and their stability can impact the health of their hosts. Theory predicts that predators influence ecosystem stability. Phages are key predators of bacteria in microbiomes, but phages are unusual predators because many have lysogenic life cycles. It has been hypothesized that lysogeny can destabilize microbiomes, but lysogeny has no direct analog in classical ecological theory, and no formal theory exists. We studied the stability of computationally simulated microbiomes with different numbers of temperate (lysogenic) and virulent (obligate lytic) phage species. Bacterial populations were more likely to fluctuate over time when there were more temperate phages species. After disturbances, bacterial populations returned to their pre-disturbance densities more slowly when there were more temperate phage species, but cycles engendered by disturbances dampened more slowly when there were more virulent phage species. Our work offers the first formal theory linking lysogeny to microbiome stability.

Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes

BackgroundMetagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists’ (Linnaeus & Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies—amplicon sequencing and whole-genome (shotgun sequencing)—respectively generate two contrastingly different categories of metagenomic reads (data)—OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.ResultsThe ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan’s near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.ConclusionsAll of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.

Ecosystem functions and functional traits for the study of phytophagous scarab beetles (Coleoptera: Scarabaeidae)

Abstract Owing to the rapid and ongoing anthropogenic changes impacting ecosystem functions and their interplay with biodiversity, there is a growing focus on assessing insect functional diversity. This emphasis helps to unravel key roles of insects on ecosystem processes and to identify the assembly mechanisms that regulate species coexistence. The ecological functions of phytophagous scarab beetles (Scarabaeidae) have been relatively unexplored, and potential functional traits are scattered throughout the literature. Species within this group exhibit diverse lifestyles, forms and sizes. They exploit various resources such as decomposing wood, foliage, roots and flowers, with a small subset identified as predators. Although many of their representatives are significant agricultural pests, information on their contributions in natural ecosystems has not been consolidated. This study reviews the ecological functions potentially carried out by phytophagous scarab beetles and proposes functional traits to be incorporated into studies of functional diversity. Through this, the goal is to integrate the scattered information, stimulate the generation of questions that go beyond classical ecological theory and contribute to advancing our knowledge of their ecosystem functions, as well as the foundations for understanding community structure. We propose to use trophic groups to define functions such as bioturbation, organic matter decomposition, biological control and potential pollination. A simplified list of functional traits was obtained by conducting correlation analyses using a trait matrix from a region in northern Colombia. This represents a significant advance for the study of traits within the framework of functional ecology, applicable to territorial planning and biodiversity conservation.

Harnessing trophic cascades to improve foundation species restoration: A meta‐analysis

AbstractGlobal declines in foundation species and associated losses of biodiversity and ecosystem services have made restoration of foundation species and the habitats they create a top priority. Because restoration success has been highly variable, the field is increasingly using both experimentation and ecological theory to augment success. We conducted a meta‐analysis of studies (18) in estuarine and marine systems, which increased the abundance of top predators as a restoration approach, thus improving biogenic habitat‐forming foundation species recovery by reducing consumers. Beyond testing the general idea of whether top predator addition enhances foundation species restoration, we examined whether the degree of restoration success could be explained by classic predictors of top‐down strength, such as taxonomic identity of the foundation species and top predators, direct and indirect effects of top predators, and the latitude and duration of the study. Top predators successfully elicited a trophic cascade by decreasing consumer abundances (direct effect) and increasing foundation species recovery (indirect effect) when compared with control restoration projects without top predators. Direct effects are expected to be stronger than indirect effects, in accordance with classic ecological theory. We found no evidence of magnitude differences between direct and indirect effects of top predator addition. Increasing invertebrate top predators produced a 3.5× greater increase in the basal trophic level than adding vertebrate top predators. Despite the strong effect of predator type, the log response ratio of all foundation species types (algae, animal, and plant) increased 10‐fold in top predator addition treatments. We found diminishing effects of top predator addition as study duration increased, which supports recent developments that the positive effects of marine protected area designation decline over time. Our results highlight the promise of harnessing top‐down control via top predator addition as a mechanism to aid foundation species recovery.

Plant economic strategies in two contrasting forests

BackgroundPredicting relationships between plant functional traits and environmental effects in their habitats is a central issue in terms of classic ecological theories. Yet, only weak correlation with functional trait composition of local plant communities may occur, implying that some essential information might be ignored. In this study, to address this uncertainty, the objective of the study is to test whether and how the consistency of trait relationships occurs by analyzing broad variation in eight traits related to leaf morphological structure, nutrition status and physiological activity, within a large number of plant species in two distinctive but comparable harsh habitats (high-cold alpine fir forest vs. north-cold boreal coniferous forest).ResultsThe contrasting and/or consistent relationships between leaf functional traits in the two distinctive climate regions were observed. Higher specific leaf area, photosynthetic rate, and photosynthetic nitrogen use efficiency (PNUE) with lower N concentration occurred in north-cold boreal forest rather than in high-cold alpine forest, indicating the acquisitive vs. conservative resource utilizing strategies in both habitats. The principal component analysis illuminated the divergent distributions of herb and xylophyta groups at both sites. Herbs tend to have a resource acquisition strategy, particularly in boreal forest. The structural equation modeling revealed that leaf density had an indirect effect on PNUE, primarily mediated by leaf structure and photosynthesis. Most of the traits were strongly correlated with each other, highlighting the coordination and/or trade-offs.ConclusionsWe can conclude that the variations in leaf functional traits in north-cold boreal forest were largely distributed in the resource-acquisitive strategy spectrum, a quick investment-return behavior; while those in the high-cold alpine forest tended to be mainly placed at the resource-conservative strategy end. The habitat specificity for the relationships between key functional traits could be a critical determinant of local plant communities. Therefore, elucidating plant economic spectrum derived from variation in major functional traits can provide a fundamental insight into how plants cope with ecological adaptation and evolutionary strategies under environmental changes, particularly in these specific habitats.

Harmonizing spatial scales and ecological theories to predict avian richness and functional diversity within forest ecosystems.

Classic ecological theory has proven that temperature, precipitation and productivity organize ecosystems at broad scales and are generalized drivers of biodiversity within different biomes. At local scales, the strength of these predictors is not consistent across different biomes. To better translate these theories to localized scales, it is essential to determine the links between drivers of biodiversity. Here we harmonize existing ecological theories to increase the predictive power for species richness and functional diversity. We test the relative importance of three-dimensional habitat structure as a link between local and broad-scale patterns of avian richness and functional diversity. Our results indicate that habitat structure is more important than precipitation, temperature and elevation gradients for predicting avian species richness and functional diversity across different forest ecosystems in North America. We conclude that forest structure, influenced by climatic drivers, is essential for predicting the response of biodiversity with future shifts in climatic regimes.

A latitudinal gradient of deep-sea invasions for marine fishes

Although the tropics harbor the greatest species richness globally, recent work has demonstrated that, for many taxa, speciation rates are faster at higher latitudes. Here, we explore lability in oceanic depth as a potential mechanism for this pattern in the most biodiverse vertebrates – fishes. We demonstrate that clades with the highest speciation rates also diversify more rapidly along the depth gradient, drawing a fundamental link between evolutionary and ecological processes on a global scale. Crucially, these same clades also inhabit higher latitudes, creating a prevailing latitudinal gradient of deep-sea invasions concentrated in poleward regions. We interpret these findings in the light of classic ecological theory, unifying the latitudinal variation of oceanic features and the physiological tolerances of the species living there. This work advances the understanding of how niche lability sculpts global patterns of species distributions and underscores the vulnerability of polar ecosystems to changing environmental conditions.

Sandy beach ecology in the Anthropocene: Ghost shrimp (Crustacea: Callianassidae) as a study model

The close relationship between biotic systems and physical conditions determines the classic ecological hypotheses and theories of sandy beaches. Accordingly, the Habitat Harshness Hypothesis (HHH) predicts that macroinvertebrates inhabiting beaches with less hydrodynamic severity have larger body size, higher fecundity and thrive more abundant populations than harsher beaches. The current omnipresence of human impacts on beaches demands that ecological studies take on a holistic approach, including the interaction between physical factors and variables that represent these disturbances as regulators in diversity patterns. Here we tested the classic HHH, using the ghost shrimp Callichirus major (Crustacea: Callianassidae) as a study model. Considering this species as a habitat specialist, we predicted that the ghost shrimp would respond mainly to sedimentological changes, used as a proxy for the physical harshness of the habitat. Eleven sectors were sampled along two extensive beach arcs in southeastern Brazil, including counting burrows to estimate abundance metrics and collecting individuals to measure individual attributes, such as body size and fecundity. Abundance and body size were greater in beaches with smaller sediment particles size and well-sorted sediments, confirming the typical predictions of HHH. Moreover, larger individuals were found in beaches that were closer to major rivers, probably due to greater trophic subsidies. The urbanization indicator imposed negative effects on body size and fecundity, though with lower predictive power than sediment features and distance to rivers. Our results are useful for modelling coastal impacts, guiding monitoring, conservation and restoration planning, and offer a better understanding of the ecology of ghost shrimp.

Disease‐mediated nutrient dynamics: Coupling host–pathogen interactions with ecosystem elements and energy

AbstractAutotrophs play an essential role in the cycling of carbon and nutrients, yet disease‐ecosystem relationships are often overlooked in these dynamics. Importantly, the availability of elemental nutrients like nitrogen and phosphorus impacts infectious disease in autotrophs, and disease can induce reciprocal effects on ecosystem nutrient dynamics. Relationships linking infectious disease with ecosystem nutrient dynamics are bidirectional, though the interdependence of these processes has received little attention. We introduce disease‐mediated nutrient dynamics (DND) as a framework to describe the multiple, concurrent pathways linking elemental cycles with infectious disease. We illustrate the impact of disease–ecosystem feedback loops on both disease and ecosystem nutrient dynamics using a simple mathematical model, combining approaches from classical ecological (logistic and Droop growth) and epidemiological (susceptible and infected compartments) theory. Our model incorporates the effects of nutrient availability on the growth rates of susceptible and infected autotroph hosts and tracks the return of nutrients to the environment following host death. While focused on autotroph hosts here, the DND framework is generalizable to higher trophic levels. Our results illustrate the surprisingly complex dynamics of host populations, infection patterns, and ecosystem nutrient cycling that can arise from even a relatively simple feedback between disease and nutrients. Feedback loops in disease‐mediated nutrient dynamics arise via effects of infection and nutrient supply on host stoichiometry and population size. Our model illustrates how host growth rate, defense, and tissue chemistry can impact the dynamics of disease–ecosystem relationships. We use the model to motivate a review of empirical examples from autotroph–pathogen systems in aquatic and terrestrial environments, demonstrating the key role of nutrient–disease and disease–nutrient relationships in real systems. By assessing existing evidence and uncovering data gaps and apparent mismatches between model predictions and the dynamics of empirical systems, we highlight priorities for future research intended to narrow the persistent disciplinary gap between disease and ecosystem ecology. Future empirical and theoretical work explicitly examining the dynamic linkages between disease and ecosystem ecology will inform fundamental understanding for each discipline and will better position the field of ecology to predict the dynamics of disease and elemental cycles in the context of global change.

Microbiome influence on host community dynamics: Conceptual integration of microbiome feedback with classical host-microbe theory.

Microbiomes have profound effects on host fitness, yet we struggle to understand the implications for host ecology. Microbiome influence on host ecology has been investigated using two independent frameworks. Classical ecological theory powerfully represents mechanistic interactions predicting environmental dependence of microbiome effects on host ecology, but these models are notoriously difficult to evaluate empirically. Alternatively, host–microbiome feedback theory represents impacts of microbiome dynamics on host fitness as simple net effects that are easily amenable to experimental evaluation. The feedback framework enabled rapid progress in understanding microbiomes’ impacts on plant ecology, and can also be applied to animal hosts. We conceptually integrate these two frameworks by deriving expressions for net feedback in terms of mechanistic model parameters. This generates a precise mapping between net feedback theory and classic population modelling, thereby merging mechanistic understanding with experimental tractability, a necessary step for building a predictive understanding of microbiome influence on host ecology.

On tree longevity.

Large, majestic trees are iconic symbols of great age among living organisms. Published evidence suggests that trees do not die because of genetically programmed senescence in their meristems, but rather are killed by an external agent or a disturbance event. Long tree lifespans are therefore allowed by specific combinations of life history traits within realized niches that support resistance to, or avoidance of, extrinsic mortality. Another requirement for trees to achieve their maximum longevity is either sustained growth over extended periods of time or at least the capacity to increase their growth rates when conditions allow it. The growth plasticity and modularity of trees can then be viewed as an evolutionary advantage that allows them to survive and reproduce for centuries and millennia. As more and more scientific information is systematically collected on tree ages under various ecological settings, it is becoming clear that tree longevity is a key trait for global syntheses of life history strategies, especially in connection with disturbance regimes and their possible future modifications. In addition, we challenge the long-held notion that shade-tolerant, late-successional species have longer lifespans than early-successional species by pointing out that tree species with extreme longevity do not fit this paradigm. Identifying extremely old trees is therefore the groundwork not only for protecting and/or restoring entire landscapes, but also to revisit and update classic ecological theories that shape our understanding of environmental change.

Ontogenetic development underlies population response to mortality

Understanding demographic responses to mortality is crucial to predictive ecology. While classic ecological theory posits reductions in population biomass in response to extrinsic mortality, models containing realistic developmental change predict the potential for counterintuitive increase in stage‐specific biomass, i.e. biomass overcompensation. Patterns of biomass overcompensation should be predictable based on differences in the relative energetic efficiencies of juvenile maturation and adult reproduction. Specifically, in populations where reproduction is the limiting process, adult‐specific mortality should enhance total reproduction and thus juvenile biomass. We tested this prediction by inducing an array of stage‐specific harvesting treatments across replicate populations of Daphnia pulex. In accordance with reproductive regulation, the greatest biomass response occurred in the juvenile Daphnia stage and this response occurred most strongly in response to adult mortality. Nevertheless, we failed to detect significant biomass overcompensation and instead report largely compensatory effects. In total, our work demonstrates that knowledge of population structure is necessary to accurately predict population dynamics, but cautions that further research is needed to illuminate the factors generating over‐compensatory versus compensatory responses across natural populations.

Microbiome and environment explain the absence of correlations between consumers and their diet in Bornean microsnails.

Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co‐occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other layers in the food web, or by the environment. Here we show, by studying the relationship between communities of consumers (land snails) and individual diets (from seed plants), that there is in fact no direct, or at most a weak but negative, relationship. However, we found that the diversity of the individual microbiome positively correlates with both consumer community diversity and individual diet diversity in three target species. Moreover, these correlations were affected by various environmental variables, such as anthropogenic activity, habitat island size, and a possibly important nutrient source, guano runoff from nearby caves. Our results suggest that the microbiome and the environment explain the absence of correlations between diet and consumer community diversity. Hence, we advocate that microbiome inventories are routinely added to any community dietary analysis, which our study shows can be done with relatively little extra effort. Our approach presents the tools to quickly obtain an overview of the relationships between consumers and their resources. We anticipate our approach to be useful for ecologists and environmentalists studying different communities in a local food web.

Predicting the Outbreak Risks and Inflection Points of COVID-19 Pandemic with Classic Ecological Theories.

Predicting the outbreak risks and/or the inflection (turning or tipping) points of COVID‐19 can be rather challenging. Here, it is addressed by modeling and simulation approaches guided by classic ecological theories and by treating the COVID‐19 pandemic as a metapopulation dynamics problem. Three classic ecological theories are harnessed, including TPL (Taylor’s power‐law) and Ma’s population aggregation critical density (PACD) for spatiotemporal aggregation/stability scaling, approximating virus metapopulation dynamics with Hubbell’s neutral theory, and Ma’s diversity‐time relationship adapted for the infection−time relationship. Fisher‐Information for detecting critical transitions and tipping points are also attempted. It is discovered that: (i) TPL aggregation/stability scaling parameter (b > 2), being significantly higher than the b‐values of most macrobial and microbial species including SARS, may interpret the chaotic pandemic of COVID‐19. (ii) The infection aggregation critical threshold (M 0) adapted from PACD varies with time (outbreak‐stage), space (region) and public‐health interventions. Exceeding M 0, local contagions may become aggregated and connected regionally, leading to epidemic/pandemic. (iii) The ratio of fundamental dispersal to contagion numbers can gauge the relative importance between local contagions vs. regional migrations in spreading infections. (iv) The inflection (turning) points, pair of maximal infection number and corresponding time, are successfully predicted in more than 80% of Chinese provinces and 68 countries worldwide, with a precision >80% generally.

Assessing and Interpreting the Metagenome Heterogeneity With Power Law.

There are two major sequencing technologies for investigating the microbiome: the amplicon sequencing that generates the OTU (operational taxonomic unit) tables of marker genes (e.g., bacterial 16S-rRNA), and the metagenomic shotgun sequencing that generates metagenomic gene abundance (MGA) tables. The OTU table is the counterpart of species abundance tables in macrobial ecology of plants and animals, and has been the target of numerous ecological and network analyses in recent gold rush for microbiome research and in great efforts for establishing an inclusive theoretical ecology. Nevertheless, MGA analyses have been largely limited to bioinformatics pipelines and ad hoc statistical methods, and systematic approaches to MGAs guided by classic ecological theories are still few. Here, we argue that, the difference between “gene kinds” and “gene species” are nominal, and the metagenome that a microbiota carries is essentially a ‘community’ of metagenomic genes (MGs). Each row of a MGA table represents a metagenome of a microbiota, and the whole MGA table represents a ‘meta-metagenome’ (or an assemblage of metagenomes) of N microbiotas (microbiome samples). Consequently, the same ecological/network analyses used in OTU analyses should be equally applicable to MGA tables. Here we choose to analyze the heterogeneity of metagenome by introducing classic Taylor’s power law (TPL) and its recent extensions in community ecology. Heterogeneity is a fundamental property of metagenome, particularly in the context of human microbiomes. Recent studies have shown that the heterogeneity of human metagenomes is far more significant than that of human genomes. Therefore, without deep understanding of the human metagenome heterogeneity, personalized medicine of the human microbiome-associated diseases is hardly feasible. The TPL extensions have been successfully applied to measure the heterogeneity of human microbiome based on amplicon-sequencing reads of marker genes (e.g., 16s-rRNA). In this article, we demonstrate the analysis of the metagenomic heterogeneity of human gut microbiome at whole metagenome scale (with type-I power law extension) and metagenomic gene scale (type-III), as well as the heterogeneity of gene clusters, respectively. We further examine the influences of obesity, IBD and diabetes on the heterogeneity, which is of important ramifications for the diagnosis and treatment of human microbiome-associated diseases.

Ocean currents and the population genetic signature of fish migrations.

Animal migrations are a fascinating and global phenomenon, yet they are often difficult to study and sometimes poorly understood. Here, we build on classic ecological theory by hypothesizing that some enigmatic spawning migrations across coastal marinehabitats can be inferred from the population genetic signature of larval dispersal by ocean currents. We test this assumption by integrating spatially realistic simulations of alternative spawning migration routes, associated patterns of larval dispersal, and associated variation in the population genetic structure of eastern Australian sea mullet (Mugil cephalus). We then use simulation results to assess the implications of alternative spawning destinations for larval replenishment, and we contrast simulated against measured population genetic variation. Both analyses suggest that the spawning migrations of M.cephalus in eastern Australia are likely to be localized (approximately 100km along the shore), and that spawning is likely to occur in inshore waters. Our conclusions are supported by multiple lines of evidence available through independent studies, but they challenge the more traditional assumption of a single, long-distance migration event with subsequent offshore spawning in the East Australian Current. More generally, our study operationalizes classic theory on the relationship between fish migrations, ocean currents, and reproductive success. However, rather than confirming the traditionally assumed adaptation of migratory behavior to dominant ocean current flow, our findings support the concept of a genetically measurable link between fish migrations and local oceanographic conditions, specifically water temperature and coastal retention of larvae. We believe that future studies using similar approaches for high resolution and spatially realistic ecological-genetic scenario testing can help rapidly advance our understanding of key ecological processes in many other marine species.

An In Vitro Enrichment Strategy for Formulating Synergistic Synbiotics.

Research on the role of diet on gut and systemic health has led to considerable interest toward identifying novel therapeutic modulators of the gut microbiome, including the use of prebiotics and probiotics. However, various host responses have often been reported among many clinical trials. This is in part due to competitive exclusion as a result of the absence of ecological niches as well as host-mediated constraints via colonization resistance. In this research, we developed a novel in vitro enrichment (IVE) method for isolating autochthonous strains that can function as synergistic synbiotics and overcome these constraints. The method relied on stepwise in vitro fecal fermentations to enrich for and isolate Bifidobacterium strains that ferment the prebiotic xylooligosaccharide (XOS). We subsequently isolated Bifidobacterium longum subsp. longum CR15 and then tested its establishment in 20 unique fecal samples with or without XOS. The strain was established in up to 18 samples but only in the presence of XOS. Our findings revealed that the IVE method is suitable for isolating potential synergistic probiotic strains that possess the genetic and biochemical ability to ferment specific prebiotic substrates. The IVE method can be used as an initial high-throughput screen for probiotic selection and isolation prior to further characterization and in vivo tests.IMPORTANCE This study describes an in vitro enrichment method to formulate synergistic synbiotics that have potential for establishing autochthonous strains across multiple individuals. The rationale for this approach-that the chance of survival of a bacterial strain is improved by providing it with its required resources-is based on classic ecological theory. From these experiments, a human-derived strain, Bifidobacterium longum subsp. longum CR15, was identified as a xylooligosaccharide (XOS) fermenter in fecal environments and displayed synergistic effects in vitro The high rate of strain establishment observed in this study provides a basis for using synergistic synbiotics to overcome the responder/nonresponder phenomenon that occurs frequently in clinical trials with probiotic and prebiotic interventions. In addition, this approach can be applied in other protocols that require enrichment of specific bacterial populations prior to strain isolation.

Effect of soil nutrients, neighbor identities and root separation types on intra‐ and interspecific interaction among three clonal plant species

In natural environments, plants frequently interact with both heterospecific and conspecific neighbors. The intensity of belowground plant interaction with neighboring species commonly varies with the availability of soil nutrients in the habitats. According to classical ecological theory, competition between conspecific neighbors may be more severe than competition between unrelated species due to the similar nutrient requirements of close relatives, especially when nutrients are scarce in the habitat. However, many recent studies have shown the opposite pattern, and suggested an alternative mechanism based on species recognition. Taking Zoysia sinica as the focal species, we conducted a controlled experiment to test the results of intraspecific and interspecific interactions among three clonal species Zoysia sinica, Zoysia japonica and Alternanthera philoxeroides, which represent a conspecific, a close relative and a distant relative of the focal species, respectively, and at different root treatments (no separation NS, clone separation CS and ramet separation RS) and two nutrient levels. The results showed that Z. sinica recognized conspecific plants in the NS and CS treatments, and did not show above or belowground competition with these. The performance of the focal plant (Z. sinica) was better when it was grown with a conspecific neighbor as compared to all other types of neighbors. In all root separation treatments, the competition was more intense when Z. sinica grew with a close relative (Z. japonica) than when growing with a distant relative (A. philoxeroides). Generally, competition between plants was more intense at the high nutrient level than at the low nutrient level, suggesting that both soil nutrients and a species recognition mechanism play a significant role for the intra‐ and interspecific interaction and fitness of these three neighboring clonal species.

Microbiomes, Community Ecology, and the Comparative Method.

Microbiomes contain many levels of biological information, and integrating across the levels creates a holistic understanding of host-microbiome interactions. In my research on the evolution and ecology of avian microbiomes, I use two complementary frameworks: the microbiome as a community and the microbiome as a trait of the host. We draw on classic ecological and evolutionary theory and modern statistical models to advance our understanding in each of these frameworks and then integrate what we have learned into a better understanding of host-associated microbiomes, host evolution, and microbial biodiversity. Ecological theories that bear on processes such as community assembly and metacommunities are well suited for application to microbiomes. Phylogenetic comparative methods can quantify the fit of evolutionary models and detect correlations between traits and correlations between traits and the rate of evolution; these methods allow the inference of evolutionary process from contemporary patterns.