A footprint of tree-genetics on the biota of the forest floor

Genetic underpinnings of arthropod community distributions in Populus trichocarpa

Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.

Host genotype structures the microbiome of a globally dispersed marine phytoplankton

Microscale interactions between marine phytoplankton and their bacterial microbiomes can influence ecosystem functioning and global biogeochemical cycling through complex exchanges of metabolites and sophisticated ecological processes. Previous investigation of the phytoplankton microbiome has not focused on the role of a host’s underlying genetic background. Through examination of a single phytoplankton species’ microbiome across the global ocean, we found that host genotype strongly influenced microbiome community composition, with associations that potentially persist across generations and ocean basins but assemble rapidly (within days). The long-term association of microbiomes with host genetic background could explain the evolution and maintenance of intricate phytoplankton–bacteria interactions.

Phytoplankton support complex bacterial microbiomes that rely on phytoplankton-derived extracellular compounds and perform functions necessary for algal growth. Recent work has revealed sophisticated interactions and exchanges of molecules between specific phytoplankton–bacteria pairs, but the role of host genotype in regulating those interactions is unknown. Here, we show how phytoplankton microbiomes are shaped by intraspecific genetic variation in the host using global environmental isolates of the model phytoplankton host Thalassiosira rotula and a laboratory common garden experiment. A set of 81 environmental T. rotula genotypes from three ocean basins and eight genetically distinct populations did not reveal a core microbiome. While no single bacterial phylotype was shared across all genotypes, we found strong genotypic influence of T. rotula, with microbiomes associating more strongly with host genetic population than with environmental factors. The microbiome association with host genetic population persisted across different ocean basins, suggesting that microbiomes may be associated with host populations for decades. To isolate the impact of host genotype on microbiomes, a common garden experiment using eight genotypes from three distinct host populations again found that host genotype influenced microbial community composition, suggesting that a process we describe as genotypic filtering, analogous to environmental filtering, shapes phytoplankton microbiomes. In both the environmental and laboratory studies, microbiome variation between genotypes suggests that other factors influenced microbiome composition but did not swamp the dominant signal of host genetic background. The long-term association of microbiomes with specific host genotypes reveals a possible mechanism explaining the evolution and maintenance of complex phytoplankton–bacteria chemical exchanges.

Consistent community genetic effects in the context of strong environmental and temporal variation in Eucalyptus

Provenance translocations of tree species are promoted in forestry, conservation, and restoration in response to global climate change. While this option is driven by adaptive considerations, less is known of the effects translocations can have on dependent communities. We investigated the relative importance and consistency of extended genetic effects in Eucalyptus using two species-E. globulus and E. pauciflora. In E. globulus, the dependent arthropod and pathogen canopy communities were quantified based on the abundance of 49 symptoms from 722 progeny from 13 geographic sub-races across 2 common gardens. For E. pauciflora, 6 symptoms were quantified over 2 years from 238 progeny from 16 provenances across 2 common gardens. Genetic effects significantly influenced communities in both species. However, site and year effects outweighed genetic effects with site explaining approximately 3 times the variation in community traits in E. globulus and site and year explaining approximately 6 times the variation in E. pauciflora. While the genetic effect interaction terms were significant in some community traits, broad trends in community traits associated with variation in home-site latitude for E. globulus and home-site altitude for E. pauciflora were evident. These broad-scale trends were consistent with patterns of adaptive differentiation within each species, suggesting there may be extended consequences of local adaptation. While small in comparison to site and year, the consistency of genetic effects highlights the importance of provenance choice in tree species, such as Eucalyptus, as adaptive divergence among provenances may have significant long-term effects on biotic communities.

Leaf chemical defences and insect herbivory in oak: accounting for canopy position unravels marked genetic relatedness effects

BACKGROUND AND AIMS

Highly controlled experiments document that plant genetic diversity and relatedness can shape herbivore communities and patterns of herbivory. Evidence from the field is, however, scarce and inconsistent. We assessed whether a genetic signal underlying herbivory can be detected in oak woodlands when accounting for variation at smaller (within-tree) and larger (among-stand) scales.

METHODS

We tested relationships between tree genetic relatedness, leaf chemical defences and insect herbivory for different canopy layers in 240 trees from 15 pedunculate oak (Quercus robur) forest stands. We partitioned sources of variability in herbivory and defences among stands, individuals and branches.

KEY RESULTS

Leaf defences, insect herbivory and their relationship differed systematically between the upper and the lower tree canopy. When accounting for this canopy effect, the variation explained by tree genetic relatedness rose from 2.8 to 34.1 % for herbivory and from 7.1 to 13.8 % for leaf defences. The effect was driven by markedly stronger relationships in the upper canopy.

CONCLUSIONS

Our findings illustrate that considerable effects of the host plant genotype on levels of leaf chemical defences and associated insect herbivory can be detected in natural tree populations when within-individual variation is properly accounted for.

Local adaptation and rapid evolution of aphids in response to genetic interactions with their cottonwood hosts

Several studies have demonstrated the ecological consequences of genetic variation within a single plant species. For example, these studies show that individual plant genotypes support unique composition of the plants' associated arthropod community. By contrast, fewer studies have explored how plant genetic variation may influence evolutionary dynamics in the plant's associated species. Here, we examine how aphids respond evolutionarily to genetic variation in their host plant. We conducted two experiments to examine local adaptation and rapid evolution of the free‐feeding aphid Chaitophorus populicola across genetic variants of its host plant, Populus angustifolia. To test for local adaptation, we collected tree cuttings and aphid colonies from three sites along an elevation/climate gradient and conducted a reciprocal transplant experiment. In general, home aphids (aphids transplanted onto trees from the same site) produced 1.7–3.4 times as many offspring as foreign aphids (aphids transplanted onto trees from different sites). To test for rapid evolution, we used 4 clonally replicated aphid genotypes and transplanted each onto 5 clonally replicated P. angustifolia genotypes. Each tree genotype started with the same aphid genotype composition. After 21 days (~two aphid generations), aphid genotype composition changed (i.e., aphids evolved) and some tree genotypes supported unique evolutionary trajectories of aphids. These results suggest that plant evolution in response to human perturbation, such as climate change and invasive species, will also result in evolutionary responses in strongly interacting species that could cascade to affect whole communities.

A water availability gradient reveals the deficit level required to affect traits in potted juvenile Eucalyptus globulus

Background and aims

Drought leading to soil water deficit can have severe impacts on plants. Water deficit may lead to plant water stress and affect growth and chemical traits. Plant secondary metabolite (PSM) responses to water deficit vary between compounds and studies, with inconsistent reports of changes to PSM concentrations even within a single species. This disparity may result from experimental water deficit variation among studies, and so multiple water deficit treatments are used to fully assess PSM responses in a single species.

Methods

Juvenile Eucalyptus globulus were grown for 8 weeks at one of ten water deficit levels based on evapotranspiration from control plants (100 %). Treatments ranged from 90 % of control evapotranspiration (mild water deficit) to 0 % of control evapotranspiration (severe water deficit) in 10 % steps. Plant biomass, foliar abscisic acid (ABA) levels, Ψ leaf , leaf C/N, selected terpenes and phenolics were quantified to assess responses to each level of water deficit relative to a control.

Key Results

Withholding ≥30 % water resulted in higher foliar ABA levels and withholding ≥40 % water reduced leaf water content. Ψ leaf became more negative when ≥60 % water was withheld. Plant biomass was lower when ≥80 % water was withheld, and no water for 8 weeks (0 % water) resulted in plant death. The total oil concentration was lower and C/N was higher in dead and desiccated juvenile E. globulus leaves (0 % water). Concentrations of individual phenolic and terpene compounds, along with condensed tannin and total phenolic concentrations, remained stable regardless of water deficit or plant stress level.

Conclusions

These juvenile E. globulus became stressed with a moderate reduction in available water, and yet the persistent concentrations of most PSMs in highly stressed or dead plants suggests no PSM re-metabolization and continued ecological roles of foliar PSMs during drought.

Rapid plant evolution in the presence of an introduced species alters community composition

Because introduced species may strongly interact with native species and thus affect their fitness, it is important to examine how these interactions can cascade to have ecological and evolutionary consequences for whole communities. Here, we examine the interactions among introduced Rocky Mountain elk, Cervus canadensis nelsoni, a common native plant, Solidago velutina, and the diverse plant-associated community of arthropods. While introduced species are recognized as one of the biggest threats to native ecosystems, relatively few studies have investigated an evolutionary mechanism by which introduced species alter native communities. Here, we use a common garden design that addresses and supports two hypotheses. First, native S. velutina has rapidly evolved in the presence of introduced elk. We found that plants originating from sites with introduced elk flowered nearly 3 weeks before plants originating from sites without elk. Second, evolution of S. velutina results in a change to the plant-associated arthropod community. We found that plants originating from sites with introduced elk supported an arthropod community that had ~35 % fewer total individuals and a different species composition. Our results show that the impacts of introduced species can have both ecological and evolutionary consequences for strongly interacting species that subsequently cascade to affect a much larger community. Such evolutionary consequences are likely to be long-term and difficult to remediate.

Genetic diversity in aspen and its relation to arthropod abundance

The ecological consequences of biodiversity have become a prominent public issue. Little is known on the effect of genetic diversity on ecosystem services. Here, a diversity experiment was established with European and North American aspen (Populus tremula, P. tremuloides) planted in plots representing either a single deme only or combinations of two, four and eight demes. The goals of this study were to explore the complex inter- and intraspecific genetic diversity of aspen and to then relate three measures for diversity (deme diversity, genetic diversity determined as Shannon index or as expected heterozygosity) to arthropod abundance. Microsatellite and AFLP markers were used to analyze the genetic variation patterns within and between the aspen demes and deme mixtures. Large differences were observed regarding the genetic diversity within demes. An analysis of molecular variance revealed that most of the total genetic diversity was found within demes, but the genetic differentiation among demes was also high. The complex patterns of genetic diversity and differentiation resulted in large differences of the genetic variation within plots. The average diversity increased from plots with only one deme to plots with two, four, and eight demes, respectively and separated plots with and without American aspen. To test whether intra- and interspecific diversity impacts on ecosystem services, arthropod abundance was determined. Increasing genetic diversity of aspen was related to increasing abundance of arthropods. However, the relationship was mainly driven by the presence of American aspen suggesting that species identity overrode the effect of intraspecific variation of European aspen.

Plant genetic identity of foundation tree species and their hybrids affects a litter-dwelling generalist predator

The effects of plant genetics on predators, especially those not living on the plant itself, are rarely studied and poorly understood. Therefore, we investigated the effect of plant hybridization and genotype on litter-dwelling spiders. Using an 18-year-old cottonwood common garden, we recorded agelenid sheet-web density associated with the litter layers of replicated genotypes of three tree cross types: Populus fremontii, Populus angustifolia, and their F1 hybrids. We surveyed 118 trees for agelenid litter webs at two distances from the trees (0-100 and 100-200 cm from trunk) and measured litter depth as a potential mechanism of web density patterns. Five major results emerged: web density within a 1-m radius of P. angustifolia was approximately three times higher than within a 1-m radius of P. fremontii, with F1 hybrids having intermediate densities; web density responded to P. angustifolia and F1 hybrid genotypes as indicated by a significant genotype × distance interaction, with some genotypes exhibiting a strong decline in web density with distance, while others did not; P. angustifolia litter layers were deeper than those of P. fremontii at both distance classes, and litter depth among P. angustifolia genotypes differed up to 300%; cross type and genotype influenced web density via their effects on litter depth, and these effects were influenced by distance; web density was more sensitive to the effects of tree cross type than genotype. By influencing generalist predators, plant hybridization and genotype may indirectly impact trophic interactions such as intraguild predation, possibly affecting trophic cascades and ecosystem processes.

Community specificity: life and afterlife effects of genes

Community-level genetic specificity results when individual genotypes or populations of the same species support different communities. Our review of the literature shows that genetic specificity exhibits both life and afterlife effects; it is a widespread phenomenon occurring in diverse taxonomic groups, aquatic to terrestrial ecosystems, and species-poor to species-rich systems. Such specificity affects species interactions, evolution, ecosystem processes and leads to community feedbacks on the performance of the individuals expressing the traits. Thus, genetic specificity by communities appears to be fundamentally important, suggesting that specificity is a major driver of the biodiversity and stability of the world's ecosystems.

Divergence in ectomycorrhizal communities with foreign Douglas-fir populations and implications for assisted migration

Assisted migration of forest trees has been widely proposed as a climate change adaptation strategy, but moving tree populations to match anticipated future climates may disrupt the geographically based, coevolved association suggested to exist between host trees and ectomycorrhizal fungal (EMF) communities. We explored this issue by examining the consistency of EMF communities among populations of 40 year-old Douglas-fir (Pseudotsuga menziesii var. menziesii) trees in a common-garden field trial using four provenances from contrasting coastal climates in southwestern British Columbia. Considerable variation in EMF community composition within test sites was found, ranging from 0.38 to 0.65 in the mean similarity index, and the divergence in EMF communities from local populations increased with site productivity. Clinal patterns in colonization success were detected for generalist and specialist EMF species on only the two productive test sites. Host population effects were limited to EMF species abundance rather than species loss, as richness per site averaged 15.0 among provenances and did not differ by transfer extent (up to 450 km), while Shannon's diversity index declined slightly. Large differences in colonization rates of specialist fungi, such as Tomentella stuposa and Clavulina cristata, raise the possibility that EMF communities maladapted to soil conditions contributed to the inferior growth of some host populations on productive sites. The results of the study suggest locally based specificity in host-fungal communities is likely a contributing factor in the outcome of provenance trials, and should be a consideration in analyzing seed-transfer effects and developing strategies for assisted migration.

Plant genotype and nitrogen loading influence seagrass productivity, biochemistry, and plant-herbivore interactions

Genetic variation within and among key species can have significant ecological consequences at the population, community, and ecosystem levels. In order to understand ecological properties of systems based on habitat-forming clonal plants, it is crucial to clarify which traits vary among plant genotypes and how they influence ecological processes, and to assess their relative contribution to ecosystem functioning in comparison to other factors. Here we used a mesocosm experiment to examine the relative influence of genotypic identity and extreme levels of nitrogen loading on traits that affect ecological processes (at the population, community, and ecosystem levels) for Zostera marina, a widespread marine angiosperm that forms monospecific meadows throughout coastal areas in the Northern Hemisphere. We found effects of both genotype and nitrogen addition on many plant characteristics (e.g., aboveground and belowground biomass), and these were generally strong and similar in magnitude, whereas interactive effects were rare. Genotypes also strongly differed in susceptibility to herbivorous isopods, with isopod preference among genotypes generally matching their performance in terms of growth and survival. Chemical rather than structural differences among genotypes drove these differences in seagrass palatability. Nitrogen addition uniformly decreased plant palatability but did not greatly alter the relative preferences of herbivores among genotypes, indicating that genotype effects are strong. Our results highlight that differences in key traits among genotypes of habitat-forming species can have important consequences for the communities and ecosystems that depend on them and that such effects are not overwhelmed by known environmental stressors.

The molecular basis of quantitative variation in foliar secondary metabolites in Eucalyptus globulus

Eucalyptus is characterized by high foliar concentrations of plant secondary metabolites with marked qualitative and quantitative variation within a single species. Secondary metabolites in eucalypts are important mediators of a diverse community of herbivores. We used a candidate gene approach to investigate genetic associations between 195 single nucleotide polymorphisms (SNPs) from 24 candidate genes and 33 traits related to secondary metabolites in the Tasmanian Blue Gum (Eucalyptus globulus). We discovered 37 significant associations (false discovery rate (FDR) Q < 0.05) across 11 candidate genes and 19 traits. The effects of SNPs on phenotypic variation were within the expected range (0.018 < r(2) < 0.061) for forest trees. Whereas most marker effects were nonadditive, two alleles from two consecutive genes in the methylerythritol phosphate pathway (MEP) showed additive effects. This study successfully links allelic variants to ecologically important phenotypes which can have a large impact on the entire community. It is one of very few studies to identify the genetic variants of a foundation tree that influences ecosystem function.

Effect of poplar genotypes on mycorrhizal infection and secreted enzyme activities in mycorrhizal and non-mycorrhizal roots

The impact of ectomycorrhiza formation on the secretion of exoenzymes by the host plant and the symbiont is unknown. Thirty-eight F(1) individuals from an interspecific Populus deltoides (Bartr.)×Populus trichocarpa (Torr. & A. Gray) controlled cross were inoculated with the ectomycorrhizal fungus Laccaria bicolor. The colonization of poplar roots by L. bicolor dramatically modified their ability to secrete enzymes involved in organic matter breakdown or organic phosphorus mobilization, such as N-acetylglucosaminidase, β-glucuronidase, cellobiohydrolase, β-glucosidase, β-xylosidase, laccase, and acid phosphatase. The expression of genes coding for laccase, N-acetylglucosaminidase, and acid phosphatase was studied in mycorrhizal and non-mycorrhizal root tips. Depending on the genes, their expression was regulated upon symbiosis development. Moreover, it appears that poplar laccases or phosphatases contribute poorly to ectomycorrhiza metabolic activity. Enzymes secreted by poplar roots were added to or substituted by enzymes secreted by L. bicolor. The enzymatic activities expressed in mycorrhizal roots differed significantly between the two parents, while it did not differ in non-mycorrhizal roots. Significant differences were found between poplar genotypes for all enzymatic activities measured on ectomycorrhizas except for laccases activity. In contrast, no significant differences were found between poplar genotypes for enzymatic activities of non-mycorrhizal root tips except for acid phosphatase activity. The level of enzymes secreted by the ectomycorrhizal root tips is under the genetic control of the host. Moreover, poplar heterosis was expressed through the enzymatic activities of the fungal partner.

Recurrent nuclear DNA introgression accompanies chloroplast DNA exchange between two eucalypt species

Numerous studies within plant genera have found geographically structured sharing of chloroplast (cp) DNA among sympatric species, consistent with introgressive hybridization. Current research is aimed at understanding the extent, direction and significance of nuclear (nr) DNA exchange that accompanies putative cpDNA exchange. Eucalyptus is a complex tree genus for which cpDNA sharing has been established between multiple species. Prior phylogeographic analysis has indicated cpDNA introgression into the widespread forest species Eucalyptus globulus from its rare congener E. cordata. In this study, we use AFLP markers to characterize corresponding nrDNA introgression, on both a broad and fine spatial scale. Using 388 samples we examine (i) the fine-scale spatial structure of cp and nrDNA introgression from E. cordata into E. globulus at a site in natural forest and (ii) broad-scale patterns of AFLP marker introgression at six additional mixed populations. We show that while E. globulus and E. cordata retain strongly differentiated nuclear gene pools overall, leakage of nrDNA occurs at mixed populations, with some AFLP markers being transferred to E. globulus recurrently at different sites. On the fine scale, different AFLP fragments show varying distances of introgression into E. globulus, while introgression of cpDNA is extensive. The frequency of E. cordata markers in E. globulus is correlated with spatial proximity to E. cordata, but departs from expectations based on AFLP marker frequency in E. cordata, indicating that selection may be governing the persistence of introgressed fragments in E. globulus.