Forest gene diversity is correlated with the composition and function of soil microbial communities

Biodiversity within phytoplankton-associated microbiomes regulates host physiology, host community ecology, and nutrient cycling

Biological diversity is declining across the tree of life, including among prokaryotes. With the increasing awareness of host-associated microbes as potential regulators of eukaryotic host physiology, behavior, and ecology, it is important to understand the implications of declining diversity within host microbiomes on host fitness, ecology, and ecosystem function. We used phytoplankton and their associated environmental microbiomes as model systems to test the independent and interactive effects of declining microbiome diversity with and without other stressors often caused by human activity-elevated temperature and altered nutrient availability. We found effects of low microbiome diversity on host physiology, phytoplankton community dynamics, and nutrient cycling. Low microbiome diversity caused greater host cellular stress, as indicated by elevated δ13C and δ15N. Microbiome diversity also significantly affected host cell morphological metrics, likely as a consequence of this effect on cell stress. Despite causing greater host cellular stress, the effects of low microbiome diversity on host community ecology included elevated phytoplankton community diversity and biomass. The diversity of these host-associated microbes also had cascading implications on ecosystem nutrient cycling, where lower microbiome diversity caused a depletion of total dissolved N and P in the environment. The magnitude of these effects, caused by microbiome diversity, was greatest among nutrient-depleted environments and at elevated temperatures. Our results emphasize the widespread implications of declining host-associated microbial diversity from host cellular physiology to ecosystem nutrient cycling. These demonstrated effects of declining microbiome diversity are likely to be amplified in ecosystems experiencing multiple stressors caused by anthropogenic activities.

IMPORTANCE

As evidence is emerging of the key roles that host-associated microbiomes often play in regulating the physiology, fitness, and ecology of their eukaryotic hosts, human activities are causing declines in biological diversity, including within the microbial world. Here, we use a multifactorial manipulative experiment to test the effects of declining diversity within host microbiomes both alone and in tandem with the effects of emerging global changes, including climate warming and shifts in nutrient bioavailability, which are inflicting increasing abiotic stress on host organisms. Using single-celled eukaryotic phytoplankton that harbor an external microbiome as a model system, we demonstrate that diversity within host-associated microbiomes impacts multiple tiers of biological organization, including host physiology, the host population and community ecology, and ecosystem nutrient cycling. Notably, these microbiome diversity-driven effects became magnified in abiotically stressful environments, suggesting that the importance of microbiome diversity may have increased over time during the Anthropocene.

Complex eco-evolutionary responses of a foundational coastal marsh plant to global change

Predicting the fate of coastal marshes requires understanding how plants respond to rapid environmental change. Environmental change can elicit shifts in trait variation attributable to phenotypic plasticity and act as selective agents to shift trait means, resulting in rapid evolution. Comparably, less is known about the potential for responses to reflect the evolution of trait plasticity. Here, we assessed the relative magnitude of eco-evolutionary responses to interacting global change factors using a multifactorial experiment. We exposed replicates of 32 Schoenoplectus americanus genotypes 'resurrected' from century-long, soil-stored seed banks to ambient or elevated CO2 , varying levels of inundation, and the presence of a competing marsh grass, across two sites with different salinities. Comparisons of responses to global change factors among age cohorts and across provenances indicated that plasticity has evolved in five of the seven traits measured. Accounting for evolutionary factors (i.e. evolution and sources of heritable variation) in statistical models explained an additional 9-31% of trait variation. Our findings indicate that evolutionary factors mediate ecological responses to environmental change. The magnitude of evolutionary change in plant traits over the last century suggests that evolution could play a role in pacing future ecosystem response to environmental change.

The effect of interspecific and intraspecific diversity on microplastic ingestion in two co-occurring mussel species in South Africa

Interspecific and intraspecific diversity are essential components of biodiversity with far-reaching implications for ecosystem function and service provision. Importantly, genotypic and phenotypic variation within a species can affect responses to anthropogenic pressures more than interspecific diversity. We investigated the effects of interspecific and intraspecific diversity on microplastic ingestion by two coexisting mussel species in South Africa, Mytilus galloprovincialis and Perna perna, the latter occurring as two genetic lineages. We found significantly higher microplastic abundance in M. galloprovincialis (0.54 ± 0.56 MP items g-1WW) than P. perna (0.16 ± 0.21 MP items g-1WW), but no difference between P. perna lineages. Microbeads were the predominant microplastic (76 % in P. perna, 99 % in M. galloprovincialis) and polyethylene the prevalent polymer. Interspecific differences in microplastic abundance varied across locations, suggesting diverse sources of contamination. We suggest that microplastic ingestion can be species-specific even in organisms that coexist and play similar functional roles within ecosystems.

Fine-scale genetic structure in rhizosphere microbial communities associated with Chamaecrista fasciculata (Fabaceae)

Soil microbiota of the rhizosphere are an important extension of the plant phenotype because they impact the health and fitness of host plants. The composition of these communities is expected to differ among host plants due to influence by host genotype. Given that many plant populations exhibit fine-scale genetic structure (SGS), associated microbial communities may also exhibit SGS. In this study, we tested this hypothesis using Chamaecrista fasciculata, a legume species that has previously been determined to have significant SGS. We collected genetic data from prokaryotic and fungal rhizosphere communities in association with 70 plants in an area of ~400 square meters to investigate the presence of SGS in microbial communities. Bacteria of Acidobacteria, Protobacteria, and Bacteroidetes and fungi of Basidiomycota, Ascomycota, and Mortierellomycota were dominant members of the rhizosphere. Although microbial alpha diversity did not differ significantly among plants hosts, we detected significant compositional differences among the microbial communities as well as isolation by distance. The strongest factor associated with microbial distance was genetic distance of the other microbial community, followed by geographic distance, but there was not a significant association with plant genetic distance for either microbial community. This study further demonstrates the strong potential for spatial structuring of soil microbial communities at the smallest spatial scales and provides further insight into the complexity of factors that influence microbial composition in soils and in association with host plants.

Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.

Transcriptome Analysis and Intraspecific Variation in Spanish Fir (Abies pinsapo Boiss.)

Spanish fir (Abies pinsapo Boiss.) is an endemic, endangered tree that has been scarcely investigated at the molecular level. In this work, the transcriptome of Spanish fir was assembled, providing a large catalog of expressed genes (22,769), within which a high proportion were full-length transcripts (12,545). This resource is valuable for functional genomics studies and genome annotation in this relict conifer species. Two intraspecific variations of A. pinsapo can be found within its largest population at the Sierra de las Nieves National Park: one with standard green needles and another with bluish-green needles. To elucidate the causes of both phenotypes, we studied different physiological and molecular markers and transcriptome profiles in the needles. "Green" trees showed higher electron transport efficiency and enhanced levels of chlorophyll, protein, and total nitrogen in the needles. In contrast, needles from "bluish" trees exhibited higher contents of carotenoids and cellulose. These results agreed with the differential transcriptomic profiles, suggesting an imbalance in the nitrogen status of "bluish" trees. Additionally, gene expression analyses suggested that these differences could be associated with different epigenomic profiles. Taken together, the reported data provide new transcriptome resources and a better understanding of the natural variation in this tree species, which can help improve guidelines for its conservation and the implementation of adaptive management strategies under climatic change.

A direct comparison of the effects and mechanisms between species richness and genotype richness in a dominant species on multiple ecosystem functions

Both species (interspecific) richness and genotype (intraspecific) richness of dominant species have significant effects on ecosystem functioning directly or indirectly by regulating plant community functional structure. However, the similarities and differences of the effects between inter- and intraspecific levels are poorly understood. In this study, we selected the main species in the semi-arid Eurasian typical steppe as study objects and simultaneously carried out a species richness experiment and a genotype richness experiment of Stipa grandis which is one of the dominant species in this region. We investigated how plants at each of the two richness levels affected multiple ecosystem functions (biomass, soil C, N and P cycles) directly and indirectly by regulating community functional structure, including community-weighted mean trait values (CWM) and functional dispersion (FDis). Both species richness and genotype richness showed significant direct effects on soil P cycle, and FDis significantly mediated the responses of aboveground biomass and soil N cycle to the changes of species richness and the response of belowground biomass to the changes of genotype richness in S. grandis. CWM showed significant effects on biomass in the species richness experiment and soil nutrient cycles in the genotype richness experiment, independently of the levels of plant richness. These findings provide experimental insights of intraspecific richness effects into the relationships between biodiversity and ecosystem functioning, and highlight the importance of conserving the intraspecific diversity of dominant species in the semi-arid steppe regions.

Site-Dependent Relationships Between Fungal Community Composition, Plant Genotypic Diversity and Environmental Drivers in a Salix Biomass System

Soil fungi are strongly affected by plant species or genotypes since plants modify their surrounding environment, but the effects of plant genotype diversity on fungal diversity and function have not been extensively studied. The interactive responses of fungal community composition to plant genotypic diversity and environmental drivers were investigated in Salix biomass systems, posing questions about: (1) How fungal diversity varies as a function of plant genotype diversity; (2) If plant genotype identity is a strong driver of fungal community composition also in plant mixtures; (3) How the fungal communities change through time (seasonally and interannually)?; and (4) Will the proportion of ECM fungi increase over the rotation? Soil samples were collected over 4 years, starting preplanting from two Salix field trials, including four genotypes with contrasting phenology and functional traits, and genotypes were grown in all possible combinations (four genotypes in Uppsala, Sweden, two in Rostock, Germany). Fungal communities were identified, using Pacific Biosciences sequencing of fungal ITS2 amplicons. We found some site-dependent relationships between fungal community composition and genotype or diversity level, and site accounted for the largest part of the variation in fungal community composition. Rostock had a more homogenous community structure, with significant effects of genotype, diversity level, and the presence of one genotype ("Loden") on fungal community composition. Soil properties and plant and litter traits contributed to explaining the variation in fungal species composition. The within-season variation in composition was of a similar magnitude to the year-to-year variation. The proportion of ECM fungi increased over time irrespective of plant genotype diversity, and, in Uppsala, the 4-mixture showed a weaker response than other combinations. Species richness was generally higher in Uppsala compared with that in Rostock and increased over time, but did not increase with plant genotype diversity. This significant site-specificity underlines the need for consideration of diverse sites to draw general conclusions of temporal variations and functioning of fungal communities. A significant increase in ECM colonization of soil under the pioneer tree Salix on agricultural soils was evident and points to changed litter decomposition and soil carbon dynamics during Salix growth.

Plant genotypic diversity effects on soil nematodes vary with trophic level

At local spatial scales, loss of genetic diversity within species can lead to species loss. Few studies, however, have examined plant genotypic diversity effects across trophic levels. We investigated genotypic diversity effects of Phragmites australis on belowground biomass and soil nematode communities. Our results revealed that belowground plant biomass and nematode abundance responses to plant genotypic diversity were uncoupled. Decreasing plant genotypic diversity decreased the abundance of lower, but not higher trophic level nematodes. Low plant genotypic diversity also decreased the structural footprint and functional indices of nematodes, indicating lowered metabolic functioning of higher trophic level nematodes and decreased soil food web stability. Our study suggests that plant genotypic diversity effects differ across trophic levels, taxonomic groups and ecosystem functions and that decreasing plant genotypic diversity could destabilise belowground food webs. This highlights the importance of conserving intraspecific plant diversity.

Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: A field-based experiment

Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting, we found that bacterial community composition differed among R. mangle maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of R. mangle. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.

Climate-driven reduction of genetic variation in plant phenology alters soil communities and nutrient pools

We examined the hypothesis that climate-driven evolution of plant traits will influence associated soil microbiomes and ecosystem function across the landscape. Using a foundation tree species, Populus angustifolia, observational and common garden approaches, and a base population genetic collection that spans 17 river systems in the western United States, from AZ to MT, we show that (a) as mean annual temperature (MAT) increases, genetic and phenotypic variation for bud break phenology decline; (b) soil microbiomes, soil nitrogen (N), and soil carbon (C) vary in response to MAT and conditioning by trees; and (c) with losses of genetic variation due to warming, population-level regulation of community and ecosystem functions strengthen. These results demonstrate a relationship between the potential evolutionary response of populations and subsequent shifts in ecosystem function along a large temperature gradient.

Strong associations between plant genotypes and bacterial communities in a natural salt marsh

Although microbial communities have been shown to vary among plant genotypes in a number of experiments in terrestrial ecosystems, relatively little is known about this relationship under natural conditions and outside of select model systems. We reasoned that a salt marsh ecosystem, which is characterized by twice‐daily flooding by tides, would serve as a particularly conservative test of the strength of plant–microbial associations, given the high degree of abiotic regulation of microbial community assembly resulting from alternating periods of inundation and exposure. Within a salt marsh in the northeastern United States, we characterized genotypes of the foundational plant Spartina alterniflora using microsatellite markers, and bacterial metagenomes within marsh soil based on pyrosequencing. We found significant differences in bacterial community composition and diversity between bulk and rhizosphere soil, and that the structure of rhizosphere communities varied depending on the growth form of, and genetic variation within, the foundational plant S. alterniflora. Our results indicate that there are strong plant–microbial associations within a natural salt marsh, thereby contributing to a growing body of evidence for a relationship between plant genotypes and microbial communities from terrestrial ecosystems and suggest that principles of community genetics apply to this wetland type.

The ecological importance of intraspecific variation

Human activity is causing wild populations to experience rapid trait change and local extirpation. The resulting effects on intraspecific variation could have substantial consequences for ecological processes and ecosystem services. Although researchers have long acknowledged that variation among species influences the surrounding environment, only recently has evidence accumulated for the ecological importance of variation within species. We conducted a meta-analysis comparing the ecological effects of variation within a species (intraspecific effects) with the effects of replacement or removal of that species (species effects). We evaluated direct and indirect ecological responses, including changes in abundance (or biomass), rates of ecological processes and changes in community composition. Our results show that intraspecific effects are often comparable to, and sometimes stronger than, species effects. Species effects tend to be larger for direct ecological responses (for example, through consumption), whereas intraspecific effects and species effects tend to be similar for indirect responses (for example, through trophic cascades). Intraspecific effects are especially strong when indirect interactions alter community composition. Our results summarize data from the first generation of studies examining the relative ecological effects of intraspecific variation. Our conclusions can help inform the design of future experiments and the formulation of strategies to quantify and conserve biodiversity.

Arthropod communities on hybrid and parental cottonwoods are phylogenetically structured by tree type: Implications for conservation of biodiversity in plant hybrid zones

Although hybridization in plants has been recognized as an important pathway in plant speciation, it may also affect the ecology and evolution of associated communities. Cottonwood species (Populus angustifolia and P. fremontii) and their naturally occurring hybrids are known to support different plant, animal, and microbial communities, but no studies have examined community structure within the context of phylogenetic history. Using a community composed of 199 arthropod species, we tested for differences in arthropod phylogenetic patterns within and among hybrid and parental tree types in a common garden. Three major patterns emerged. (1) Phylogenetic diversity (PD) was significantly different between arthropod communities on hybrids and Fremont cottonwood when pooled by tree type. (2) Mean phylogenetic distance (MPD) and net relatedness index (NRI) indicated that communities on hybrid trees were significantly more phylogenetically overdispersed than communities on either parental tree type. (3) Community distance (D_pw) indicated that communities on hybrids were significantly different than parental species. Our results show that arthropod communities on parental and hybrid cottonwoods exhibit significantly different patterns of phylogenetic structure. This suggests that arthropod community assembly is driven, in part, by plant-arthropod interactions at the level of cottonwood tree type. We discuss potential hypotheses to explain the effect of plant genetic dissimilarity on arthropod phylogenetic community structure, including the role of competition and environmental filtering. Our findings suggest that cottonwood species and their hybrids function as evolutionarily significant units (ESUs) that affect the assembly and composition of associated arthropod communities and deserve high priority for conservation.

The effect of top-predator presence and phenotype on aquatic microbial communities

The presence of predators can impact a variety of organisms within the ecosystem, including microorganisms. Because the effects of fish predators and their phenotypic differences on microbial communities have not received much attention, we tested how the presence/absence, genotype, and plasticity of the predatory three‐spine stickleback (Gasterosteus aculeatus) influence aquatic microbes in outdoor mesocosms. We reared lake and stream stickleback genotypes on contrasting food resources to adulthood, and then added them to aquatic mesocosm ecosystems to assess their impact on the planktonic bacterial community. We also investigated whether the effects of fish persisted following the removal of adults, and the subsequent addition of a homogenous juvenile fish population. The presence of adult stickleback increased the number of bacterial OTUs and altered the size structure of the microbial community, whereas their phenotype affected bacterial community composition. Some of these effects were detectable after adult fish were removed from the mesocosms, and after juvenile fish were placed in the tanks, most of these effects disappeared. Our results suggest that fish can have strong short‐term effects on microbial communities that are partially mediated by phenotypic variation of fish.

A community genetics perspective: opportunities for the coming decade

Community genetics was originally proposed as a novel approach to identifying links between genes and ecosystems, and merging ecological and evolutional perspectives. The dozen years since the birth of community genetics have seen many empirical studies and common garden experiments, as well as the rise of eco-evolutionary dynamics research and a general shift in ecology to incorporate intraspecific variation. So what have we learned from community genetics? Can individual genes affect entire ecosystems? Are there interesting questions left to be answered, or has community genetics run its course? This perspective makes a series of key points about the general patterns that have emerged and calls attention to gaps in our understanding to be addressed in the coming years.

Root-associated fungi of Vaccinium carlesii in subtropical forests of China: intra- and inter-annual variability and impacts of human disturbances

Ericoid mycorrhiza (ERM) are expected to facilitate establishment of ericaceous plants in harsh habitats. However, diversity and driving factors of the root-associated fungi of ericaceous plants are poorly understood. In this study, hair-root samples of Vaccinium carlesii were taken from four forest types: old growth forests (OGF), secondary forests with once or twice cutting (SEC I and SEC II), and Cunninghamia lanceolata plantation (PLF). Fungal communities were determined using high-throughput sequencing, and impacts of human disturbances and the intra- and inter-annual variability of root-associated fungal community were evaluated. Diverse fungal taxa were observed and our results showed that (1) Intra- and inter-annual changes in root-associated fungal community were found, and the Basidiomycota to Ascomycota ratio was related to mean temperature of the sampling month; (2) Human disturbances significantly affected structure of root-associated fungal community of V. carlesii, and two secondary forest types were similar in root-associated fungal community and were closer to that of the old growth forest; (3) Plant community composition, edaphic parameters, and geographic factors significantly affected root-associated fungal communities of V. carlesii. These results may be helpful in better understanding the maintenance mechanisms of fungal diversity associated with hair roots of ERM plants under human disturbances.

NMR metabolomics for soil analysis provide complementary, orthogonal data to MIR and traditional soil chemistry approaches--a land use study

The present study was designed to analyse soils by different methodologies to determine the range of traits that could be investigated for the study of environmental soil samples. Proton nuclear magnetic resonance spectroscopy ((1) H NMR) was employed for metametabolomic analysis of soils from agricultural systems (managed) or from soils in a native state (remnant). The metabolomic methodologies employed (grinding and extraction with sonication) are capable of breaking up cell walls and so enabled characterisation of both extracellular and intracellular components of soil. Diffuse mid-infrared spectroscopy (MIR) data was obtained for the same sample sets, and in addition, elemental composition was determined by conventional laboratory chemical testing methods. Also investigated was the antibiotic activity of the soil extracts. Resilient or suppressive soils are valued in the agricultural setting as they convey disease resistance (against bacterial and fungal pathogens) to crop plants. In order to test if any such biological activity could be detected in the soils, the extracts were tested against the bacteria Bacillus subtilis. Several extracts showed strong growth inhibition against the bacteria with the most active clustered together in principle component analysis (PCA) of the metabolomic data. The study showed that the NMR metabolomic approach corresponds more accurately to land use and biochemical properties potentially associated with suppression, while MIR data correlated well to inorganic chemical analysis. Thus, the study demonstrates the utility in combining these spectroscopic methods for soil analysis.

Chimaeric load among sympatric social bacteria increases with genotype richness

The total productivity of social groups can be determined by interactions among their constituents. Chimaeric load--the reduction of group productivity caused by antagonistic within-group heterogeneity--may be common in heterogeneous microbial groups due to dysfunctional behavioural interactions between distinct individuals. However, some instances of chimaerism in social microbes can increase group productivity, thus making a general relationship between chimaerism and group-level performance non-obvious. Using genetically similar strains of the soil bacterium Myxococcus xanthus that were isolated from a single centimetre-scale patch of soil, we tested for a relationship between degree of chimaerism (genotype richness) and total group performance at social behaviours displayed by this species. Within-group genotype richness was found to correlate negatively with total group performance at most traits examined, including swarming in both predatory and prey-free environments and spore production during development. These results suggest that interactions between such neighbouring strains in the wild will tend to be mutually antagonistic. Negative correlations between group performance and average genetic distance among group constituents at three known social genes were not found, suggesting that divergence at other loci that govern social interaction phenotypes is responsible for the observed chimaeric load. The potential for chimaeric load to result from co-aggregation among even closely related neighbours may promote the maintenance and strengthening of kin discrimination mechanisms, such as colony-merger incompatibilities observed in M. xanthus. The findings reported here may thus have implications for understanding the evolution and maintenance of diversity in structured populations of soil microbes.

Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful.

Imaging spectroscopy links aspen genotype with below-ground processes at landscape scales

Fine-scale biodiversity is increasingly recognized as important to ecosystem-level processes. Remote sensing technologies have great potential to estimate both biodiversity and ecosystem function over large spatial scales. Here, we demonstrate the capacity of imaging spectroscopy to discriminate among genotypes of Populus tremuloides (trembling aspen), one of the most genetically diverse and widespread forest species in North America. We combine imaging spectroscopy (AVIRIS) data with genetic, phytochemical, microbial and biogeochemical data to determine how intraspecific plant genetic variation influences below-ground processes at landscape scales. We demonstrate that both canopy chemistry and below-ground processes vary over large spatial scales (continental) according to aspen genotype. Imaging spectrometer data distinguish aspen genotypes through variation in canopy spectral signature. In addition, foliar spectral variation correlates well with variation in canopy chemistry, especially condensed tannins. Variation in aspen canopy chemistry, in turn, is correlated with variation in below-ground processes. Variation in spectra also correlates well with variation in soil traits. These findings indicate that forest tree species can create spatial mosaics of ecosystem functioning across large spatial scales and that these patterns can be quantified via remote sensing techniques. Moreover, they demonstrate the utility of using optical properties as proxies for fine-scale measurements of biodiversity over large spatial scales.

Human-aided admixture may fuel ecosystem transformation during biological invasions: theoretical and experimental evidence

Biological invasions can transform our understanding of how the interplay of historical isolation and contemporary (human-aided) dispersal affects the structure of intraspecific diversity in functional traits, and in turn, how changes in functional traits affect other scales of biological organization such as communities and ecosystems. Because biological invasions frequently involve the admixture of previously isolated lineages as a result of human-aided dispersal, studies of invasive populations can reveal how admixture results in novel genotypes and shifts in functional trait variation within populations. Further, because invasive species can be ecosystem engineers within invaded ecosystems, admixture-induced shifts in the functional traits of invaders can affect the composition of native biodiversity and alter the flow of resources through the system. Thus, invasions represent promising yet under-investigated examples of how the effects of short-term evolutionary changes can cascade across biological scales of diversity. Here, we propose a conceptual framework that admixture between divergent source populations during biological invasions can reorganize the genetic variation underlying key functional traits, leading to shifts in the mean and variance of functional traits within invasive populations. Changes in the mean or variance of key traits can initiate new ecological feedback mechanisms that result in a critical transition from a native ecosystem to a novel invasive ecosystem. We illustrate the application of this framework with reference to a well-studied plant model system in invasion biology and show how a combination of quantitative genetic experiments, functional trait studies, whole ecosystem field studies and modeling can be used to explore the dynamics predicted to trigger these critical transitions.

Soil microbial communities respond differently to three chemically defined polyphenols

High molecular weight polyphenols (e.g. tannins) that enter the soil may affect microbial populations, by serving as substrates for microbial respiration or by selecting for certain microbes. In this study we examined how three phenolic compounds that represent some environmentally widespread tannins or their constituent functional groups were respired by soil microorganisms and how the compounds affected the abundance and diversity of soil bacteria and archaea, including ammonia oxidizers. An acidic, silt loam soil from a pine forest was incubated for two weeks with the monomeric phenol methyl gallate, the small polyphenol epigallocatechin gallate, or the large polyphenol oenothein B. Respiration of the polyphenols during the incubation was measured using the Microresp™ system. After incubation, metabolic diversity was determined by community level physiological profiling (CLPP), and genetic diversity was determined using denaturing gradient gel electrophoresis (DGGE) analysis on DNA extracted from the soil samples. Total microbial populations and ammonia-oxidizing populations were measured using real time quantitative polymerase chain reaction (qPCR). Methyl gallate was respired more efficiently than the higher molecular weight tannins but not as efficiently as glucose. Methyl gallate and epigallocatechin gallate selected for genetically or physiologically unique populations compared to glucose. None of the polyphenols supported microbial growth, and none of the polyphenols affected ammonia-oxidizing bacterial populations or ammonia-oxidizing archaea. Additional studies using both a wider range of polyphenols and a wider range of soils and environments are needed to elucidate the role of polyphenols in determining soil microbiological diversity.

Conspecific plant-soil feedback scales with population size in Lobelia siphilitica (Lobeliaceae)

Plant-soil interactions directly affect plant success in terms of establishment, survival, growth and reproduction. Negative plant-soil feedback on such traits may therefore reduce the density and abundance of plants of a given species at a given site. Furthermore, if conspecific feedback varies among population sites, it could help explain geographic variation in plant population size. We tested for among-site variation in conspecific plant-soil feedback in a greenhouse experiment using seeds and soils from 8 natural populations of Lobelia siphilitica hosting 30-330 plants. The first cohort of seeds was grown on soil collected from each native site, while the second cohort was grown on the soil conditioned by the first. Our goal was to distinguish site-specific effects mediated by biotic and/or abiotic soil properties from those inherent in seed sources. Cohort 1 plants grown from seeds produced in small populations performed better in terms of germination, growth, and survival compared to plants produced in large populations. Plant performance decreased substantially between cohorts, indicating strong negative feedback. Most importantly, the strength of negative feedback scaled linearly (i.e., was less negative) with increasing size of the native plant population, particularly for germination and survival, and was better explained by soil- rather than seed-source effects. Even with a small number of sites, our results suggest that the potential for negative plant-soil feedback varies among populations of L. siphilitica, and that small populations were more susceptible to negative feedback. Conspecific plant-soil feedback may contribute to plant population size variation within a species' native range.

Genetic by environment interactions affect plant-soil linkages

The role of plant intraspecific variation in plant–soil linkages is poorly understood, especially in the context of natural environmental variation, but has important implications in evolutionary ecology. We utilized three 18- to 21-year-old common gardens across an elevational gradient, planted with replicates of five Populus angustifolia genotypes each, to address the hypothesis that tree genotype (G), environment (E), and G × E interactions would affect soil carbon and nitrogen dynamics beneath individual trees. We found that soil nitrogen and carbon varied by over 50% and 62%, respectively, across all common garden environments. We found that plant leaf litter (but not root) traits vary by genotype and environment while soil nutrient pools demonstrated genotype, environment, and sometimes G × E interactions, while process rates (net N mineralization and net nitrification) demonstrated G × E interactions. Plasticity in tree growth and litter chemistry was significantly related to the variation in soil nutrient pools and processes across environments, reflecting tight plant–soil linkages. These data overall suggest that plant genetic variation can have differential affects on carbon storage and nitrogen cycling, with implications for understanding the role of genetic variation in plant–soil feedback as well as management plans for conservation and restoration of forest habitats with a changing climate.

Bacterial biofilms in a 'genes-to-ecosystems' context

In ecology, there is an increasing amount of research dedicated to understanding how intraspecific genetic diversity can extend beyond the population level to influence the assembly of communities and the functioning of ecosystems. In this issue of Molecular Ecology, Koh et al. (2012) take this exploration to a new level using bacterial biofilms and protozoan grazers. They show that there is heritable variation in the phenotypes of different variants of biofilms of Serratia marcescens and that these strains display complementarity when combined in a diverse assemblage. Mixtures of variants were significantly more resistant to protozoan grazing than either wild-type or variant biofilms grown in monocultures. While similar biodiversity effects of genotype mixtures have been observed in other systems, Koh et al. (2012) link phenotype variation of the biofilms to a single nucleotide polymorphism in one regulatory gene. Importantly, the authors demonstrate that minimal changes in a genotype can result in substantial shifts in interspecific ecological interactions.

Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse

Recent losses of honey bee colonies have led to increased interest in the microbial communities that are associated with these important pollinators. A critical function that bacteria perform for their honey bee hosts, but one that is poorly understood, is the transformation of worker-collected pollen into bee bread, a nutritious food product that can be stored for long periods in colonies. We used 16S rRNA pyrosequencing to comprehensively characterize in genetically diverse and genetically uniform colonies the active bacterial communities that are found on honey bees, in their digestive tracts, and in bee bread. This method provided insights that have not been revealed by past studies into the content and benefits of honey bee-associated microbial communities. Colony microbiotas differed substantially between sampling environments and were dominated by several anaerobic bacterial genera never before associated with honey bees, but renowned for their use by humans to ferment food. Colonies with genetically diverse populations of workers, a result of the highly promiscuous mating behavior of queens, benefited from greater microbial diversity, reduced pathogen loads, and increased abundance of putatively helpful bacteria, particularly species from the potentially probiotic genus Bifidobacterium. Across all colonies, Bifidobacterium activity was negatively correlated with the activity of genera that include pathogenic microbes; this relationship suggests a possible target for understanding whether microbes provide protective benefits to honey bees. Within-colony diversity shapes microbiotas associated with honey bees in ways that may have important repercussions for colony function and health. Our findings illuminate the importance of honey bee-bacteria symbioses and examine their intersection with nutrition, pathogen load, and genetic diversity, factors that are considered key to understanding honey bee decline.

Hybridization among dominant tree species correlates positively with understory plant diversity

PREMISE OF THE STUDY

Elucidating the factors that determine the abundance and distribution of species remains a central goal of ecology. It is well recognized that genetic differences among individual species can affect the distribution and species interactions of dependent taxa, but the ecological effects of genetic differences on taxa of the same trophic level remain much less understood. Our goal was to test the hypothesis that differences between related overstory tree species and their hybrids can influence the understory plant community in wild settings.

METHODS

We conducted vegetation surveys in a riparian community with the overstory dominated by Populus fremontii, P. angustifolia, and their natural hybrids (referred to as cross types) along the Weber River in north central Utah, USA. Understory diversity and community composition, as well as edaphic properties, were compared under individual trees.

KEY RESULTS

Diversity metrics differ under the three different tree cross types such that a greater species richness, diversity, and cover of understory plants exist under the hybrids compared with either of the parental taxa (30-54%, 40-48%, and 35-74% greater, respectively). The community composition of the understory also varied by cross type, whereby additional understory plant species cluster with hybrids, not with parental species.

CONCLUSIONS

Genetic composition dictated by hybridization in the overstory can play a role in structuring the associated understory plants in natural communities-where a hybridized overstory correlates with a species-rich understory-and thus can have cascading effects on community members of the same trophic level. The underlying mechanism requires further investigation.