Complex species interactions and the dynamics of ecological systems: long-term experiments

Dysbiosis linking periodontal disease and oral squamous cell carcinoma-A brief narrative review

An association between periodontal disease and oral squamous cell carcinoma (OSCC) has been recognized. However, there is no causal relationship between the two. The polymicrobial etiology of periodontal disease is confirmed, and so are the proven etiological factors for OSCC. Inflammation lies at the core of periodontal pathogenesis induced by the putative microbes. OSCC has inflammatory overtures in its pathobiology. Bacterial species involved in periodontal disease have been extensively documented and validated. The microbial profile in OSCC has been explored with no specific conclusions. The scientific reasoning to link a common microbial signature that connects periodontal disease to OSCC has led to many studies but has not provided conclusive evidence. Therefore, it would be beneficial to know the status of any plausible microbiota having a similarity in periodontal disease and OSCC. This brief review attempted to clarify the existence of a dysbiotic "fingerprint" that may link these two diseases. The review examined the literature with a focused objective of identifying periodontal microbial profiles in OSCC that could provide insights into pathogen commonality. The review concluded that there is great diversity in microbial association, but important bacterial species that correlate with periodontal disease and OSCC are forthcoming.

Impact of aridity rise and arid lands expansion on carbon-storing capacity, biodiversity loss, and ecosystem services

Drylands, comprising semi-arid, arid, and hyperarid regions, cover approximately 41% of the Earth's land surface and have expanded considerably in recent decades. Even under more optimistic scenarios, such as limiting global temperature rise to 1.5°C by 2100, semi-arid lands may increase by up to 38%. This study provides an overview of the state-of-the-art regarding changing aridity in arid regions, with a specific focus on its effects on the accumulation and availability of carbon (C), nitrogen (N), and phosphorus (P) in plant-soil systems. Additionally, we summarized the impacts of rising aridity on biodiversity, service provisioning, and feedback effects on climate change across scales. The expansion of arid ecosystems is linked to a decline in C and nutrient stocks, plant community biomass and diversity, thereby diminishing the capacity for recovery and maintaining adequate water-use efficiency by plants and microbes. Prolonged drought led to a -3.3% reduction in soil organic carbon (SOC) content (based on 148 drought-manipulation studies), a -8.7% decrease in plant litter input, a -13.0% decline in absolute litter decomposition, and a -5.7% decrease in litter decomposition rate. Moreover, a substantial positive feedback loop with global warming exists, primarily due to increased albedo. The loss of critical ecosystem services, including food production capacity and water resources, poses a severe challenge to the inhabitants of these regions. Increased aridity reduces SOC, nutrient, and water content. Aridity expansion and intensification exacerbate socio-economic disparities between economically rich and least developed countries, with significant opportunities for improvement through substantial investments in infrastructure and technology. By 2100, half the world's landmass may become dryland, characterized by severe conditions marked by limited C, N, and P resources, water scarcity, and substantial loss of native species biodiversity. These conditions pose formidable challenges for maintaining essential services, impacting human well-being and raising complex global and regional socio-political challenges.

Salivary microbiomes vary among orthodontic appliances and associate with clinical periodontal parameters

OBJECTIVE

To investigate the salivary bacterial communities during the first 6-month orthodontic treatment with Clear Aligners (CA) and Fixed Appliances (FA), and its correlation with clinical periodontal parameters.

MATERIALS AND METHODS

Saliva and periodontal parameters were sampled from individuals wearing CA or FA before treatment (T0), and after 3- (T3) and 6-month (T6) treatments. Salivary bacterial communities characterized based on the 16S rRNA V3-V4 region were compared between FA and CA and correlated with clinical periodontal parameters.

RESULTS

Probing Depth (PD) significantly increased at T6 in the FA group versus T0, whereas it remained stable in the CA group. The Shannon and Pielou indices were significantly higher in the FA group and significantly positively correlated with periodontal inflammation parameters. β-diversity analysis revealed distinct communities between the FA group and CA group at T6. The relative abundances of 3 genera and 15 species were significantly higher in the FA group. Among the above appliance-type related taxa, bacterial genera Selenomonas, Stomatobaculum, Olsenella and Faecalicoccus and bacterial species Selenomonas_sputigena, Dialister_invisus, Olsenella_profus, Prevotella_buccae, Cryptobacterium_curtum and Clostridium_spiroforme were significantly positively associated with periodontal parameters.

CONCLUSIONS

Orthodontic treatments trigger appliance-related salivary bacterial communities, highlighting the importance of developing appliance-orientated periodontal strategies during orthodontic treatments. Salivary bacterial communities harboured by patients wearing FA possess higher bacterial parameters which were associated with increasing PD, PI and Gingival Index.

How collectively integrated are ecological communities?

Beyond abiotic conditions, do population dynamics mostly depend on a species' direct predators, preys and conspecifics? Or can indirect feedback that ripples across the whole community be equally important? Determining where ecological communities sit on the spectrum between these two characterizations requires a metric able to capture the difference between them. Here we show that the spectral radius of a community's interaction matrix provides such a metric, thus a measure of ecological collectivity, which is accessible from imperfect knowledge of biotic interactions and related to observable signatures. This measure of collectivity integrates existing approaches to complexity, interaction structure and indirect interactions. Our work thus provides an original perspective on the question of to what degree communities are more than loose collections of species or simple interaction motifs and explains when pragmatic reductionist approaches ought to suffice or fail when applied to ecological communities.

Competition-cooperation mechanism between Escherichia coli and Staphylococcus aureus based on systems mapping

Introduction

Interspecies interactions are a crucial driving force of species evolution. The genes of each coexisting species play a pivotal role in shaping the structure and function within the community, but how to identify them at the genome-wide level has always been challenging.

Methods

In this study, we embed the Lotka-Volterra ordinary differential equations in the theory of community ecology into the systems mapping model, so that this model can not only describe how the quantitative trait loci (QTL) of a species directly affects its own phenotype, but also describe the QTL of the species how to indirectly affect the phenotype of its interacting species, and how QTL from different species affects community behavior through epistatic interactions.

Results

By designing and implementing a co-culture experiment for 100 pairs of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), we mapped 244 significant QTL combinations in the interaction process of the two bacteria using this model, including 69 QTLs from E. coli and 59 QTLs from S. aureus, respectively. Through gene annotation, we obtained 57 genes in E. coli, among which the genes with higher frequency were ypdC, nrfC, yphH, acrE, dcuS, rpnE, and ptsA, while we obtained 43 genes in S. aureus, among which the genes with higher frequency were ebh, SAOUHSC_00172, capF, gdpP, orfX, bsaA, and phnE1.

Discussion

By dividing the overall growth into independent growth and interactive growth, we could estimate how QTLs modulate interspecific competition and cooperation. Based on the quantitative genetic model, we can obtain the direct genetic effect, indirect genetic effect, and genome-genome epistatic effect related to interspecific interaction genes, and then further mine the hub genes in the QTL networks, which will be particularly useful for inferring and predicting the genetic mechanisms of community dynamics and evolution. Systems mapping can provide a tool for studying the mechanism of competition and cooperation among bacteria in co-culture, and this framework can lay the foundation for a more comprehensive and systematic study of species interactions.

Changing climate and reorganized species interactions modify community responses to climate variability

While an array of ecological mechanisms has been shown to stabilize natural community dynamics, how the effectiveness of these mechanisms-including both their direction (stabilizing vs. destabilizing) and strength-shifts under a changing climate remains unknown. Using a 35-y dataset (1985 to 2019) from a desert stream in central Arizona (USA), we found that as annual mean air temperature rose 1°C and annual mean precipitation reduced by 40% over the last two decades, macroinvertebrate communities experienced dramatic changes, from relatively stable states during the first 15 y of this study to wildly fluctuating states highly sensitive to climate variability in the last 10 y. Asynchronous species responses to climatic variability, the primary mechanism historically undergirding community stability, greatly weakened. The emerging climate regime-specifically, concurrent warming and prolonged multiyear drought-resulted in community-wide synchronous responses and reduced taxa richness. Diversity loss and new establishment of competitors reorganized species interactions. Unlike manipulative experiments that often suggest stabilizing roles of species interactions, we found that reorganized species interactions switched from stabilizing to destabilizing influences, further amplifying community fluctuations. Our study provides evidence of climate change-induced modifications of mechanisms underpinning long-term community stability, resulting in an overall destabilizing effect.

Climatic and Non-Climatic Drivers of Plant Diversity along an Altitudinal Gradient in the Taihang Mountains of Northern China

Climate is critical for plant altitudinal distribution patterns. Non-climatic factors also have important effects on vegetation altitudinal distribution in mountain regions. The purpose of this study was to explore the current distribution of plant diversity along the altitudinal gradient in the Taihang Mountain range of northern China and to estimate the effects of climatic and non-climatic factors on the elevational pattern. Through a field survey, a total of 480 sampling plots were established in the central Taihang Mountain range. Alpha diversities (the Shannon–Weiner index and Simpson index) and beta diversities (the Jaccard index and Cody index) were measured based on the survey data. Plant community structure change based on the altitudinal gradient was explored by measuring the diversity indices. Canonical correspondence analysis was carried out to determine the factors influencing plant altitudinal distribution. The contributions of climatic and non-climatic factors on plant distribution were determined by partial methods. The results showed that the plant diversity of the elevational gradient complied with a “hump-shaped” pattern, in which communities in the medium altitude area with higher plant diversity had a higher species turnover rate, and non-climatic factors, particularly the anthropogenic factors, had an important influence on the plant altitudinal pattern. In conclusion, climatic and non-climatic factors both had important effects on the plant altitudinal pattern. It is strongly recommended to reduce human interference in mountain vegetation protection and management.

Arbuscular mycorrhizal fungi influence host infection during epidemics in a wild plant pathosystem

While pathogenic and mutualistic microbes are ubiquitous across ecosystems and often co-occur within hosts, how they interact to determine patterns of disease in genetically diverse wild populations is unknown. To test whether microbial mutualists provide protection against pathogens, and whether this varies among host genotypes, we conducted a field experiment in three naturally occurring epidemics of a fungal pathogen, Podosphaera plantaginis, infecting a host plant, Plantago lanceolata, in the Åland Islands, Finland. In each population, we collected epidemiological data on experimental plants from six allopatric populations that had been inoculated with a mixture of mutualistic arbuscular mycorrhizal fungi or a nonmycorrhizal control. Inoculation with arbuscular mycorrhizal fungi increased growth in plants from every population, but also increased host infection rate. Mycorrhizal effects on disease severity varied among host genotypes and strengthened over time during the epidemic. Host genotypes that were more susceptible to the pathogen received stronger protective effects from inoculation. Our results show that arbuscular mycorrhizal fungi introduce both benefits and risks to host plants, and shift patterns of infection in host populations under pathogen attack. Understanding how mutualists alter host susceptibility to disease will be important for predicting infection outcomes in ecological communities and in agriculture.

Integrative Approaches to Understanding Organismal Responses to Aquatic Deoxygenation

AbstractOxygen bioavailability is declining in aquatic systems worldwide as a result of climate change and other anthropogenic stressors. For aquatic organisms, the consequences are poorly known but are likely to reflect both direct effects of declining oxygen bioavailability and interactions between oxygen and other stressors, including two-warming and acidification-that have received substantial attention in recent decades and that typically accompany oxygen changes. Drawing on the collected papers in this symposium volume ("An Oxygen Perspective on Climate Change"), we outline the causes and consequences of declining oxygen bioavailability. First, we discuss the scope of natural and predicted anthropogenic changes in aquatic oxygen levels. Although modern organisms are the result of long evolutionary histories during which they were exposed to natural oxygen regimes, anthropogenic change is now exposing them to more extreme conditions and novel combinations of low oxygen with other stressors. Second, we identify behavioral and physiological mechanisms that underlie the interactive effects of oxygen with other stressors, and we assess the range of potential organismal responses to oxygen limitation that occur across levels of biological organization and over multiple timescales. We argue that metabolism and energetics provide a powerful and unifying framework for understanding organism-oxygen interactions. Third, we conclude by outlining a set of approaches for maximizing the effectiveness of future work, including focusing on long-term experiments using biologically realistic variation in experimental factors and taking truly cross-disciplinary and integrative approaches to understanding and predicting future effects.

Oscillatory periodic pattern dynamics in hyperbolic reaction-advection-diffusion models

In this work we consider a quite general class of two-species hyperbolic reaction-advection-diffusion system with the main aim of elucidating the role played by inertial effects in the dynamics of oscillatory periodic patterns. To this aim, first, we use linear stability analysis techniques to deduce the conditions under which wave (or oscillatory Turing) instability takes place. Then, we apply multiple-scale weakly nonlinear analysis to determine the equation which rules the spatiotemporal evolution of pattern amplitude close to criticality. This investigation leads to a cubic complex Ginzburg-Landau (CCGL) equation which, owing to the functional dependence of the coefficients here involved on the inertial times, reveals some intriguing consequences. To show in detail the richness of such a scenario, we present, as an illustrative example, the pattern dynamics occurring in the hyperbolic generalization of the extended Klausmeier model. This is a simple two-species model used to describe the migration of vegetation stripes along the hillslope of semiarid environments. By means of a thorough comparison between analytical predictions and numerical simulations, we show that inertia, apart from enlarging the region of the parameter plane where wave instability occurs, may also modulate the key features of the coherent structures, solution of the CCGL equation. In particular, it is proven that inertial effects play a role, not only during transient regime from the spatially-homogeneous steady state toward the patterned state, but also in altering the amplitude, the wavelength, the angular frequency, and even the stability of the phase-winding solutions.

Habitat Specificity Modulates the Response of Small Mammals to Habitat Fragmentation, Loss, and Quality in a Neotropical Savanna

Landscape conversion of natural environments into agriculture and pasture are driving a marked biodiversity decline in the tropics. Consequences of fragmentation might depend upon habitat amount in the landscape, while the quality of remnants can also affect some species. These factors have been poorly studied in relation to different spatial scales. Furthermore, the impacts of these human-driven alterations may go beyond species loss, possibly causing a loss of ecosystem function and services. In this study, we investigated how changes in landscape configuration (patch size and isolation), habitat loss (considering a landscape gradient of 10, 25, and 40% of remnant forest cover), and habitat quality (forest structure) affect small mammal abundance, richness, taxonomic/functional diversity, and species composition in fragmented landscapes of semideciduous forests in the Brazilian Cerrado. Analyses were performed separately for habitat generalists and forest specialists. We live-trapped small mammals and measured habitat quality descriptors four times in 36 forest patches over the years 2018 and 2019, encompassing both rainy and dry seasons, with a total capture effort of 45,120 trap-nights. Regression analyses indicated that the effect of landscape configuration was not dependent on the proportion of habitat amount in the landscape to determine small mammal assemblages. However, both patch size and habitat loss impacted different aspects of the assemblages in distinct ways. Smaller patches were mainly linked to an overall increase in small mammal abundance, while the abundance of habitat generalists was also negatively affected by habitat amount. Generalist species richness was determined by the proportion of habitat amount in the landscape. Specialist richness was influenced by patch forest quality only, suggesting that species with more demanding habitat requirements might respond to fragmentation and habitat loss at finer scales. Taxonomic or functional diversity were not influenced by landscape structure or habitat quality. However, patch size and habitat amount in the landscape were the major drivers of change in small mammal species composition in semideciduous forests in the Brazilian savanna.

Tree genotypes affect rock lichens and understory plants: examples of trophic-independent interactions

Genetic variation in foundation tree species can strongly influence communities of trophic‐dependent organisms, such as herbivorous insects, pollinators, and mycorrhizal fungi. However, the extent and manner in which this variation results in unexpected interactions that reach trophic‐independent organisms remains poorly understood, even though these interactions are essential to understanding complex ecosystems. In pinyon–juniper woodland at Sunset Crater (Arizona, USA), we studied pinyon (Pinus edulis) that were either resistant or susceptible to stem‐boring moths (Dioryctria albovittella). Moth herbivory alters the architecture of susceptible trees, thereby modifying the microhabitat beneath their crowns. We tested the hypothesis that this interaction between herbivore and tree genotype extends to affect trophic‐independent communities of saxicolous (i.e., growing on rocks) lichens and bryophytes and vascular plants beneath their crowns. Under 30 pairs of moth‐resistant and moth‐susceptible trees, we estimated percent cover of lichens, bryophytes, and vascular plants. We also quantified the cover of leaf litter and rocks as well as light availability. Four major findings emerged. (1) Compared to moth‐resistant trees, which exhibited monopodial architecture, the microhabitat under the shrub‐like susceptible trees was 60% darker and had 21% more litter resulting in 68% less rock exposure. (2) Susceptible trees had 56% and 87% less cover, 42% and 80% less richness, and 38% and 92% less diversity of saxicolous and plant communities, respectively, compared to resistant trees. (3) Both saxicolous and plant species accumulated at a slower rate beneath susceptible trees, suggesting an environment that might inhibit colonization and/or growth. (4) Both saxicolous and plant communities were negatively affected by the habitat provided by susceptible trees. The results suggest that herbivory of moth‐susceptible trees generated litter at high enough rates to reduce rock substrate availability, thereby suppressing the saxicolous communities. However, our results did not provide a causal pathway explaining the suppression of vascular plants. Nonetheless, the cascading effects of genetic variation in pinyon appear to extend beyond trophic‐dependent moths to include trophic‐independent saxicolous and vascular plant communities that are affected by specific tree–herbivore interactions that modify the local environment. We suggest that such genetically based interactions are common in nature and contribute to the evolution of complex communities.

Disturbance and the (surprising?) role of ecosystem engineering in explaining spatial patterns of non-native plant establishment

Different conceptions of disturbance differ in the degree to which they appeal to mechanisms that are general and equivalent, or species-, functional group-, or interaction-specific. Some concepts of disturbance, for example, predict that soil disturbances and herbivory have identical impacts on species richness via identical mechanisms (reduction in biomass and in competition). An alternative hypothesis is that the specific traits of disturbance agents (small mammals) and plants differentially affect the richness or abundance of different plant groups. We tested these hypotheses on a degu (Octodon degus) colony in central Chile. We ask whether native and non-native forbs respond differently to degu bioturbation on runways versus herbivory on grazing lawns. We ask whether this can explain the increase in non-native plants on degu colonies. We found that biopedturbation did not explain the locations of non-native plants. We did not find direct evidence of grazing increasing non-native herbs either, but a grazing effect appears to be mediated by grass, which is the dominant cover. Further, we provide supplementary evidence to support our interpretation that a key mechanism of non-native spread is the formation of dry soil conditions on grazing lawns. Thus, ecosystem engineering (alteration of soil qualities) may be an outcome of disturbances, in which each interacts with specific plant traits, to create the observed pattern of non-native spread in the colony. Based on these results, we propose to extend Jentsch and White (Ecology, 100, 2019, e02734) concept of combined pulse/ disturbance events to the long-term process duality of ecosystem engineering/ disturbance.

Declines in rodent abundance and diversity track regional climate variability in North American drylands

Regional long-term monitoring can enhance the detection of biodiversity declines associated with climate change, improving future projections by reducing reliance on space-for-time substitution and increasing scalability. Rodents are diverse and important consumers in drylands, regions defined by the scarcity of water that cover 45% of Earth's land surface and face increasingly drier and more variable climates. We analyzed abundance data for 22 rodent species across grassland, shrubland, ecotone, and woodland ecosystems in the southwestern USA. Two time series (1995-2006 and 2004-2013) coincided with phases of the Pacific Decadal Oscillation (PDO), which influences drought in southwestern North America. Regionally, rodent species diversity declined 20%-35%, with greater losses during the later time period. Abundance also declined regionally, but only during 2004-2013, with losses of 5% of animals captured. During the first time series (wetter climate), plant productivity outranked climate variables as the best regional predictor of rodent abundance for 70% of taxa, whereas during the second period (drier climate), climate best explained variation in abundance for 60% of taxa. Temporal dynamics in diversity and abundance differed spatially among ecosystems, with the largest declines in woodlands and shrublands of central New Mexico and Colorado. Which species were winners or losers under increasing drought and amplified interannual variability in drought depended on ecosystem type and the phase of the PDO. Fewer taxa were significant winners (18%) than losers (30%) under drought, but the identities of winners and losers differed among ecosystems for 70% of taxa. Our results suggest that the sensitivities of rodent species to climate contributed to regional declines in diversity and abundance during 1995-2013. Whether these changes portend future declines in drought-sensitive consumers in the southwestern USA will depend on the climate during the next major PDO cycle.

Expansion of intertidal mussel beds following disease-driven reduction of a keystone predator

Disease shapes community composition by removing species with strong interactions. To test whether the absence of keystone predation due to disease produced changes to the species composition of rocky intertidal communities, we leverage a natural experiment involving mass mortality of the keystone predator Pisaster ochraceus from Sea Star Wasting Syndrome. Over four years, we measured dimensions of mussel beds, sizes of Mytilus californianus, mussel recruitment, and species composition on vertical rock walls at six rocky intertidal sites on the central California coast. We also assessed the relationship between changes in mussel cover and changes in sea star density across 33 sites along the North American Pacific coast using data from long-term monitoring. After four years, the lower boundary of the central California mussel beds shifted downward toward the water 18.7 ± 15.8 cm (SD) on the rock and 11.7 ± 11.0 cm in elevation, while the upper boundary remained unchanged. In central California, downward expansion and total area of the mussel bed were positively correlated with mussel recruitment but were not correlated with pre-disease sea star density or biomass. At a multi-region scale, changes in mussel percent cover were positively correlated with pre-disease sea star densities but not change in densities. Species composition of primary substrate holders and epibionts below the mussel bed remained similar across years. Extirpation of the community below the bed did not occur. Instead, this community became limited to a smaller spatial extent while the mussel bed expanded.

Functional relationship between woody plants and insect communities in response to Bursaphelenchus xylophilus infestation in the Three Gorges Reservoir region

To study the effect of the invasion of Bursaphelenchus xylophilus on the functional relationship between woody plants and insect communities, the populations of tree species and insect communities were investigative in the Masson pine forests with different infestation durations of B. xylophilus. In this study, the number of Pinus massoniana began to decrease sharply, whereas the total number of other tree species in the arboreal layer increased gradually with the infestation duration of B. xylophilus. The principal component analysis ordination biplot shows that there was a significant change in the spatial distribution of woody plant species in different Masson pine forest stands. Additionally, a total of 7,188 insect specimens were obtained. The insect population showed an upward trend in stand types with the increase of pine wilt disease infection periods, which demonstrated that the insect community had been significantly affected by the invasion of B. xylophilus. However, the insect diversity indexes were not significantly different among Masson pine forest stands. The structure of insect functional groups changed from herbivorous (He) > omnivorous (Om) > predatory (Pr) > parasitic (Pa) > detritivorous (De) in the control stand to He > Pa > Om, De > Pr after B. xylophilus infestation in the forests. The results showed that the populations of He, Pa, and De increased after the invasion of B. xylophilus, but the populations of Pr decreased. Moreover, the redundancy analysis ordination biplots reflected the complicated functional relationship between woody plant communities and insects after the invasion of B. xylophilus. The present study provides insights into the changes in the community structure of woody plants and insects, as well as the functional relationship between woody plant communities and insect communities after invasion of B. xylophilus.

Some species flourish when many do not: a pattern in data on ecological communities

Patterns in species × sample tables of communities depend above all on the organisms of the data sets and the conditions involved. Patterns that surpass individual sets are of special interest. Our question, looking for a shared pattern in 12 sets, is if relative abundances among species are independent of the sample, or formulated alternatively, if species have abundances that are correlated with total abundances over samples. For exploration we study the overdispersion/aggregation of the data. A relatively high variation in the total abundances of samples is noticed, indicating an effect of environmental variation. Overdispersion imposes constraints on the accommodation of relatively high abundance values to samples with a relatively low total abundance. The null hypothesis of ‘no association’ is modelled by permutation/resampling of the data at the level of the individual. A correlation study of actual and permuted sets is performed. All actual sets contain a significant number of species that defy our question. These species flourish when many do not. The relation of our question with issues in theoretical ecology, such as the assumption of a neutral effect of environmental conditions and/or of neutral characteristics of species, is discussed.

Microbial signatures of health, gingivitis, and periodontitis

The subgingival crevice harbors diverse microbial communities. Shifts in the composition of these communities occur with the development of gingivitis and periodontitis, which are considered as successive stages of periodontal health deterioration. It is not clear, however, to what extent health- and gingivitis-associated microbiota are protective, or whether these communities facilitate the successive growth of periodontitis-associated taxa. To further our understanding of the dynamics of the microbial stimuli that trigger disruptions in periodontal homeostasis, we reviewed the available literature with the aim of defining specific microbial signatures associated with different stages of periodontal dysbiosis. Although several studies have evaluated the subgingival communities present in different periodontal conditions, we found limited evidence for the direct comparison of communities in health, gingivitis, and periodontitis. Therefore, we aimed to better define subgingival microbiome shifts by merging and reanalyzing, using unified bioinformatic processing strategies, publicly available 16S ribosomal RNA gene amplicon datasets of periodontal health, gingivitis, and periodontitis. Despite inherent methodological differences across studies, distinct community structures were found for health, gingivitis, and periodontitis, demonstrating the specific associations between gingival tissue status and the subgingival microbiome. Consistent with the concept that periodontal dysbiosis is the result of a process of microbial succession without replacement, more species were detected in disease than in health. However, gingivitis-associated communities were more diverse than those from subjects with periodontitis, suggesting that certain species ultimately become dominant as dysbiosis progresses. We identified the bacterial species associated with each periodontal condition and prevalent species that do not change in abundance from one state to another (core species), and we also outlined species co-occurrence patterns via network analysis. Most periodontitis-associated species were rarely detected in health but were frequently detected, albeit in low abundance, in gingivitis, which suggests that gingivitis and periodontitis are a continuum. Overall, we provide a framework of subgingival microbiome shifts, which can be used to generate hypotheses with respect to community assembly processes and the emergence of periodontal dysbiosis.

A network-based approach to deciphering a dynamic microbiome's response to a subtle perturbation

Over the past decades, one main issue that has emerged in ecological and environmental research is how losses in biodiversity influence ecosystem dynamics and functioning, and consequently human society. Although biodiversity is a common indicator of ecosystem functioning, it is difficult to measure biodiversity in microbial communities exposed to subtle or chronic environmental perturbations. Consequently, there is a need for alternative bioindicators to detect, measure, and monitor gradual changes in microbial communities against these slight, chronic, and continuous perturbations. In this study, microbial networks before and after subtle perturbations by adding S. acidaminiphila showed diverse topological niches and 4-node motifs in which microbes with co-occurrence patterns played the central roles in regulating and adjusting the intertwined relationships among microorganisms in response to the subtle environmental changes. This study demonstrates that microbial networks are a good bioindicator for chronic perturbation and should be applied in a variety of ecological investigations.

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts

This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.

While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera “Candidatus Planktophila” (acI-A) and “Candidatus Nanopelagicus” (acI-B) and the proteobacterial genus “Candidatus Fonsibacter” (LD12). While “Ca. Planktophila” and “Ca. Fonsibacter” had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which “Ca. Planktophila” is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain “Ca. Planktophila” population abundance, the success of “Ca. Nanopelagicus” and “Ca. Fonsibacter” is better explained as a community by-product. Ecotype differentiation of “Ca. Fonsibacter” as a means of escaping predation was supported but not for overcoming auxotrophies.

IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.

Harmony on the prairie? Grassland plant and animal community responses to variation in climate across land-use gradients

Human induced climate and land-use change are severely impacting global biodiversity, but how community composition and richness of multiple taxonomic groups change in response to local drivers and whether these responses are synchronous remains unclear. We used long-term community-level data from an experimentally manipulated grassland to assess the relative influence of climate and land use as drivers of community structure of four taxonomic groups: birds, mammals, grasshoppers, and plants. We also quantified the synchrony of responses among taxonomic groups across land-use gradients and compared climatic drivers of community structure across groups. All four taxonomic groups responded strongly to land use (fire frequency and grazing), while responses to climate variability were more pronounced in grasshoppers and small mammals. Animal groups exhibited asynchronous responses across all land-use treatments, but plant and animal groups, especially birds, exhibited synchronous responses in composition. Asynchrony was attributed to taxonomic groups responding to different components of climate variability, including both current climate conditions and lagged effects from the previous year. Data-driven land management strategies are crucial for sustaining native biodiversity in grassland systems, but asynchronous responses of taxonomic groups to climate variability across land-use gradients highlight a need to incorporate response heterogeneity into management planning.

What Drives Declining Support for Long-Term Ecological Research?

Several recent papers have reinvigorated a chronic concern about the need for ecological science to focus more on long-term research. For a few decades, significant voices among ecologists have been assembling elements of a case in favor of long-term ecological research. In this article and for the first time, we synthesize the elements of this case and present it in succinct form. We also argue that this case is unlikely to result in more long-term research. Finally, we present ideas that, if implemented, are more likely to result in appropriate levels of investment in long-term research in ecological science. The article comes at an important time, because the US National Science Foundation is currently undertaking a 40-year review of its Long-Term Ecological Research Network.

Shrub facilitation of tree establishment varies with ontogenetic stage across environmental gradients

Plant-plant interactions are important drivers of ecosystem structure and function, yet predicting interaction outcomes across environmental gradients remains challenging. Understanding how interactions are affected by ontogenetic shifts in plant characteristics can provide insight into the drivers of interactions and improve our ability to anticipate ecosystem responses to environmental change. We developed a conceptual framework of nurse shrub facilitation of tree establishment. We used a combination of field experiments and environmental measurements to test the framework with a shrub (Artemisia tridentata) and a tree (Pinus monophylla), two foundation species in a semiarid environment. Shrub microsites allowed trees to overcome an early population bottleneck and successfully establish in areas without tree cover. Shrubs facilitated trees at multiple ontogenetic stages, but the net outcome of the interaction shifted from strongly positive to neutral after the transition of P. monophylla from juvenile to adult foliage. Microhabitat conditions varied across a broad elevational gradient, but interaction outcomes were not strongly related to elevation. Favorable microsites provided by A. tridentata cover are crucial for P. monophylla recovery after stand-replacing disturbance. Models of vegetation response to rapid global environmental change should incorporate the critically important role of nurse shrub interactions for ameliorating population bottlenecks in tree establishment.

Male social plasticity influences transient dynamics in the emergence of alternative mating systems in water striders

Animal mating systems are often studied with the goal of understanding why species, populations, or groups vary from one another in the system they display. Although these differences are often treated as basically stable, it is also known that mating systems may shift over time (e.g., from one breeding season to the next). There has been some study of how ecological factors correlate with these changes; however, few, if any, studies have investigated how the phenotypic composition of a group governs the timing and probability of these mating system transitions. Groups of stream water striders (Aquarius remigis) can experience rapid changes in mating system dynamics, with small groups often transitioning into a system in which a single, large male monopolizes mating opportunities. We asked if variation in individual- and group-level traits associated with morphology and behavior (e.g., size of the largest individual, average activity behavioral type in the group) could partially explain the variability in how rapidly groups make this transition, if they make it at all. We show that groups with males that exhibit higher social plasticity tended to take longer to transition to a mating system dominated by a single male. Our results, therefore, suggest that groups in identical ecological conditions can diverge in their mating systems based on how much individuals in the group change their behavior in response to the behavior of other members of the group.

Constructing Causal Understanding in Complex Systems: Epistemic Strategies Used by Ecosystem Scientists

Moving from a correlational to a causal account involves epistemological assumptions in any discipline. It presents particular challenges when phenomena involve multiple causes, time lags, feedback loops, or thresholds, as is the case in ecosystem science. Although reductionist approaches may contribute to explanatory efforts, investigation in ecosystems science requires a systems perspective. Understanding how ecosystem scientists arrive at causal accounts—and importantly, that they do—is critical to public understanding of science. Interviews with ten ecosystem scientists revealed the strategies and habits of mind that ecosystem scientists bring to examining complex systems. The scientists described challenges in conducting experiments at relevant scales and the epistemic strategies employed in response. The themes included constructing a body of evidence using multiple approaches, integrating results through statistical and process-based models, measuring and describing variability, conducting experiments in context, thinking across levels, considering the limits to generalizability, and exercising epistemic fluency. We discuss implications for K–20 education.

Resource partitioning confirmed by isotopic signatures allows small mammals to share seasonally flooded meadows

Meadows in river deltas are characterized by a high diversity and abundance of small mammals. However, neither their spatial arrangement nor differences in their use of microhabitat can necessarily explain the dense co-occurrence of sympatric species. We investigated how several small mammal species share a seasonally flooded meadow of limited size, testing predictions (P1) that herbivore, granivore, insectivore, and omnivore species are separated in time (dominant in different years), (P2) that sympatric species undergo isotopic partitioning, and (P3) that there are intraspecific differences in diet. Stable carbon and nitrogen isotope signatures in the hair of seven synantropic shrew, vole, and mice species were used as a proxy for their diet. We found that the three most abundant species in eight of the nine years were from different diet groups. However, based on the number of species in the functional groups, the state of small mammal community was considered unfavored in five out of the nine investigation years. In years with the greatest dominance of Apodemus agrarius, the small mammal community was characterized by decreased diversity and Micromys minutus was either in low abundance or absent. In 2014 and 2016, years of low abundance or absence of M. oeconomus, M. agrestis, and M. glareolus were both recorded in high numbers. Differences in the isotopic signatures of the three most abundant small mammal species in the community were clearly expressed and core areas in the isotopic space were separated, showing their dependence on different dietary resources. Intraspecific dietary separation between young and adult animals was observed only in M. oeconomus. Thus, the high species diversity of small mammals and the formation of their community in this investigated flooded meadow are maintained by isotopic partitioning (segregation in dietary space) and by changes in their number over time (shifting dominance).

A triple trophic boost: How carbon emissions indirectly change a marine food chain

The pervasive enrichment of CO₂ in our oceans is a well-documented stressor to marine life. Yet, there is little understanding about how CO₂ affects species indirectly in naturally complex communities. Using natural CO₂ vents, we investigated the indirect effects of CO₂ enrichment through a marine food chain. We show how CO₂ boosted the biomass of three trophic levels: from the primary producers (algae), through to their grazers (gastropods), and finally through to their predators (fish). We also found that consumption by both grazers and predators intensified under CO₂ enrichment, but, ultimately, this top-down control failed to compensate for the boosted biomass of both primary producers and herbivores (bottom-up control). Our study suggests that indirect effects can buffer the ubiquitous and direct, negative effects of CO₂ enrichment by allowing the upward propagation of resources through the food chain. Maintaining the natural complexity of food webs in our ocean communities could, therefore, help minimize the future impacts of CO₂ enrichment.

Long-Term Studies Reveal Differential Responses to Climate Change for Trees Under Soil- or Herbivore-Related Stress

Worldwide, trees are confronting increased temperature and aridity, exacerbating susceptibility to herbivory. Long-term studies comparing patterns of plant performance through drought can help identify variation among and within populations in vulnerability to climate change and herbivory. We use long-term monitoring data to examine our overarching hypothesis that the negative impacts of poor soil and herbivore susceptibility would be compounded by severe drought. We studied pinyon pine, Pinus edulis, a widespread southwestern tree species that has suffered extensive climate-change related mortality. We analyzed data on mortality, growth, male reproduction, and herbivory collected for 14-32 years in three areas with distinct soil-types. We used standardized precipitation-evapotranspiration index (SPEI) as a climate proxy that summarizes the impacts of drought due to precipitation and temperature variation on semi-arid forests. Several key findings emerged: (1) Plant performance measurements did not support our hypothesis that trees growing in stressful, coarse-textured soils would suffer more than trees growing in finer-textured soils. Stem growth at the area with coarse, young cinder soils (area one) responded only weakly to drought, while stem growth on more developed soils with sedimentary (area two) and volcanic (area three) substrates, was strongly negatively affected by drought. Male reproduction declined less with drought at area one and more at areas two and three. Overall mortality was 30% on coarse cinder soils (area one) and averaged 55% on finer soil types (areas two and three). (2) Although moth herbivore susceptible trees were hypothesized to suffer more with drought than moth resistant trees, the opposite occurred. Annual stem growth was negatively affected by drought for moth resistant trees, but much less strongly for moth susceptible trees. (3) In contrast to our hypothesis, moths declined with drought. Overall, chronically water-stressed and herbivore-susceptible trees had smaller declines in performance relative to less-stressed trees during drought years. These long-term findings support the idea that stressed trees might be more resistant to drought since they may have adapted or acclimated to resist drought-related mortality.

Indirect effects of a large mammalian herbivore on small mammal populations: Context-dependent variation across habitat types, mammal species, and seasons

Multiple consumer species frequently co-occur in the same landscape and, through effects on surrounding environments, can interact in direct and indirect ways. These interactions can vary in occurrence and importance, and focusing on this variation is critical for understanding the dynamics of interactions among consumers. Large mammalian herbivores are important engineers of ecosystems worldwide, have substantial impacts on vegetation, and can indirectly affect small-mammal populations. However, the degree to which such indirect effects vary within the same system has received minimal attention. We used a 16-year-old exclosure experiment, stratified across a heterogeneous landscape, to evaluate the importance of context-dependent interactions between tule elk (Cervus canadensis nannodes) and small mammals (deer mice [Peromyscus maniculatus], meadow voles [Microtus californicus], and harvest mice [Reithrodontymys megalotis]) in a coastal grassland in California. Effects of elk on voles varied among habitats and seasons: In open grasslands, elk reduced vole numbers during fall 2013 but not summer 2014; in Lupinus-dominated grasslands, elk reduced vole numbers during summer 2014 but not fall 2013; and in Baccharis-dominated grasslands, elk had no effect on vole numbers in either season. Effects of elk on the two mice species also varied among habitats and seasons, but often in different ways from voles and each other. In fall 2013, elk decreased mice abundances in Lupinus-dominated grasslands, but not in Baccharis-dominated or open grasslands. In summer 2014, elk decreased the abundance of harvest mice consistently across habitat types. In contrast, elk increased deer-mice numbers in open grasslands but not other habitats. Within the same heterogenous study system, the influence of elk on small mammals was strongly context-dependent, varying among habitats, mammal species, and seasons. We hypothesize that such variability is common in nature and that failure to consider it may yield inaccurate findings and limit our understanding of interactions among co-occurring consumers.

A mapping framework of competition-cooperation QTLs that drive community dynamics

Genes have been thought to affect community ecology and evolution, but their identification at the whole-genome level is challenging. Here, we develop a conceptual framework for the genome-wide mapping of quantitative trait loci (QTLs) that govern interspecific competition and cooperation. This framework integrates the community ecology theory into systems mapping, a statistical model for mapping complex traits as a dynamic system. It can characterize not only how QTLs of one species affect its own phenotype directly, but also how QTLs from this species affect the phenotype of its interacting species indirectly and how QTLs from different species interact epistatically to shape community behavior. We validated the utility of the new mapping framework experimentally by culturing and comparing two bacterial species, Escherichia coli and Staphylococcus aureus, in socialized and socially isolated environments, identifying several QTLs from each species that may act as key drivers of microbial community structure and function.

The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression

We found that the cancerous pancreas harbors a markedly more abundant microbiome compared with normal pancreas in both mice and humans, and select bacteria are differentially increased in the tumorous pancreas compared with gut. Ablation of the microbiome protects against preinvasive and invasive pancreatic ductal adenocarcinoma (PDA), whereas transfer of bacteria from PDA-bearing hosts, but not controls, reverses tumor protection. Bacterial ablation was associated with immunogenic reprogramming of the PDA tumor microenvironment, including a reduction in myeloid-derived suppressor cells and an increase in M1 macrophage differentiation, promoting TH1 differentiation of CD4+ T cells and CD8+ T-cell activation. Bacterial ablation also enabled efficacy for checkpoint-targeted immunotherapy by upregulating PD-1 expression. Mechanistically, the PDA microbiome generated a tolerogenic immune program by differentially activating select Toll-like receptors in monocytic cells. These data suggest that endogenous microbiota promote the crippling immune-suppression characteristic of PDA and that the microbiome has potential as a therapeutic target in the modulation of disease progression.Significance: We found that a distinct and abundant microbiome drives suppressive monocytic cellular differentiation in pancreatic cancer via selective Toll-like receptor ligation leading to T-cell anergy. Targeting the microbiome protects against oncogenesis, reverses intratumoral immune tolerance, and enables efficacy for checkpoint-based immunotherapy. These data have implications for understanding immune suppression in pancreatic cancer and its reversal in the clinic. Cancer Discov; 8(4); 403-16. ©2018 AACR.See related commentary by Riquelme et al., p. 386This article is highlighted in the In This Issue feature, p. 371.

Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico

Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall) of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests-upland and lowland (arroyo or riparian) forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian) forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods) and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because of deforestation and the likely impacts of global climate disruption.

Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example

How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively. We identified a large number of SNPs and indels across the genomes (35.69 G clean data of E. coli and 50.41 G of S. aureus). We reported 66 and 111 SNPs that were associated with interaction in E. coli and S. aureus, respectively. 23 out of 66 polymorphic changes resulted in amino acid alterations.12 significant genes, such as murE, treA, argS, and relA, which were also identified in previous evolutionary studies. In S. aureus, 111 SNPs detected in coding sequences could be divided into 35 non-synonymous and 76 synonymous SNPs. Our study illustrated the potential of genome-wide association methods for studying rapidly evolving traits in bacteria. Genetic association study methods will facilitate the identification of genetic elements likely to cause phenotypes of interest and provide targets for further laboratory investigation.

Inconsistent reproductive isolation revealed by interactions between Catostomus fish species

Interactions between species are central to evolution and ecology, but we do not know enough about how outcomes of interactions between species vary across geographic locations, in heterogeneous environments, or over time. Ecological dimensions of interactions between species are known to vary, but evolutionary interactions such as the establishment and maintenance of reproductive isolation are often assumed to be consistent across instances of an interaction between species. Hybridization among Catostomus fish species occurs over a large and heterogeneous geographic area and across taxa with distinct evolutionary histories, which allows us to assess consistency in species interactions. We analyzed hybridization among six Catostomus species across the Upper Colorado River basin (US mountain west) and found extreme variation in hybridization across locations. Different hybrid crosses were present in different locations, despite similar species assemblages. Within hybrid crosses, hybridization varied from only first generation hybrids to extensive hybridization with backcrossing. Variation in hybridization outcomes might result from uneven fitness of hybrids across locations, polymorphism in genetic incompatibilities, chance, unidentified historical contingencies, or some combination thereof. Our results suggest caution in assuming that one or a few instances of hybridization represent all interactions between the focal species, as species interactions vary substantially across locations.