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While the importance of plant secondary metabolites to belowground functioning is gaining recognition, the perception remains that secondary metabolites are produced for herbivore defense, whereas their belowground impacts are ecological by-products, or ‘afterlife’ effects. However, plants invest a significant amount of resources into production of secondary metabolites that have minimal effects on herbivore resistance (e.g. condensed tannins and insect herbivores). We show that genetically mediated variation in condensed tannin concentration is correlated with plant nitrogen recovery following a severe defoliation event. We used single-tree mesocosms labeled with 15N to track nitrogen through both the frass and litter cycling pathways. High concentrations of leaf tannins in Populus tremuloides were correlated with 15N recovery from frass within the same growing season and in the following growing season. Likewise, leaf tannin concentrations were also correlated with 15N recovery from the litter of defoliated trees in the growing season following the defoliation event. Conversely, tannins were not well correlated with nitrogen uptake under conditions of nominal herbivory. Our results suggest that tannins may confer benefits in response to herbivore pressure through conserved belowground nitrogen cycling, rather than via defensive properties. Consequently, tannins may be considered as chemical mediators of tolerance rather than resistance.

Biodiversity promotes ecosystem function as a consequence of functional differences among organisms that enable resource partitioning and facilitation. As the need for biodiversity assessments increases in the face of accelerated global change, novel approaches that are rapid, repeatable and scalable are critical, especially in ecosystems for which information about species identity and the number of species is difficult to acquire. Here, we present 'spectral diversity'—a spectroscopic index of the variability of electromagnetic radiation reflected from plants measured in the visible, near-infrared and short-wave infrared regions (400–2,400 nm). Using data collected from the Cedar Creek biodiversity experiment (Minnesota, USA), we provide evidence that the dissimilarity of species' leaf spectra increases with functional dissimilarity and evolutionary divergence time. Spectral diversity at the leaf level explains 51% of total variation in productivity—a proportion comparable to taxonomic (47%), functional (51%) or phylogenetic diversity (48%)—and performs similarly when calculated from high-resolution canopy image spectra. Spectral diversity is an emerging dimension of plant biodiversity that integrates trait variation within and across species even in the absence of taxonomic, functional, phylogenetic or abundance information, and has the potential to transform biodiversity assessment because of its scalability to remote sensing. A new method for measuring plant biodiversity based on spectral reflectance profiles captures variation in productivity comparable to that of taxonomic, functional and phylogenetic diversity.

Plant genotypes can have important community-and ecosystem-level effects. However, whether the extended phenotypes of plants feed back to influence the fitness of causal genotypes through soil processes remains unknown. We investigated whether aspen genotypes create distinct soil microbial communities that could potentially affect plant fitness. Using naturally occurring aspen stands in an old-field system, we set up reciprocal litter transplants among ten genetically distinct aspen clones and tracked decomposition and changes in belowground nutrients and microbial communities for three years. We found that belowground microbial communities became adapted to process specific genotypes of aspen litter to the extent allowable by environment and litter chemistry. Belowground processes were driven by a combination of little quality and prior exposure to specific genotypes of litter. In general, litter from aspen genotypes native to the soil community decomposed more rapidly than did litter from foreign aspen genotypes (i.e. a home-field advantage existed). While homefield advantages have been documented to occur among litters of different species, we show that intraspecific variation can elicit similar, albeit weak, effects within a single species. Because rapid decomposition and nutrient cycling is likely to benefit fast-growing, early-successional species such as aspen, genotype-mediated selection for soil microbial communities may feed back to positively affect plant fitness. In addition, belowground communities exhibited significant shifts in response to leaf litter inputs. When exposed to foreign litter, microbial communities changed to become more similar to the microbial community beneath the foreign litter's origin, indicating that belowground microbial communities are predictable given the genotype of the aboveground aspen clone.

Using two genetic approaches and seven different plant systems, we present findings from a meta-analysis examining the strength of the effects of plant genetic introgression and genotypic diversity across individual, community and ecosystem levels with the goal of synthesizing the patterns to date. We found that (i) the strength of plant genetic effects can be quite high; however, the overall strength of genetic effects on most response variables declined as the levels of organization increased. (ii) Plant genetic effects varied such that introgression had a greater impact on individual phenotypes than extended effects on arthropods or microbes/fungi. By contrast, the greatest effects of genotypic diversity were on arthropods. (iii) Plant genetic effects were greater on above-ground versus below-ground processes, but there was no difference between terrestrial and aquatic environments. (iv) The strength of the effects of intraspecific genotypic diversity tended to be weaker than interspecific genetic introgression. (v) Although genetic effects generally decline across levels of organization, in some cases they do not, suggesting that specific organisms and/or processes may respond more than others to underlying genetic variation. Because patterns in the overall impacts of introgression and genotypic diversity were generally consistent across diverse study systems and consistent with theoretical expectations, these results provide generality for understanding the extended consequences of plant genetic variation across levels of organization, with evolutionary implications.

Aim Quaking aspen (Populus tremuloides) has the largest natural distribution of any tree native to North America. The primary objectives of this study were to characterize range-wide genetic diversity and genetic structuring in quaking aspen, and to assess the influence of glacial history and rear-edge dynamics. Location North America. Methods Using a sample set representing the full longitudinal and latitudinal extent of the species' distribution, we examined geographical patterns of genetic diversity and structuring using 8 nuclear microsatellite loci in 794 individuals from 30 sampling sites. Results Two major genetic clusters were identified across the range: a south-western cluster and a northern cluster. The south-western cluster, which included two subclusters, was bounded approximately by the Continental Divide to the east and the southern extent of the ice sheet at the Last Glacial Maximum to the north. Subclusters were not detected in the northern cluster, despite its continent-wide distribution. Genetic distance was significantly correlated with geographical distance in the south-western but not the northern cluster, and allelic richness was significantly lower in south-western sampling sites compared with northern sampling sites. Population structuring was low overall, but elevated in the south-western cluster. Main conclusions Aspen populations in the south-western portion of the range are consistent with expectations for a historically stable edge, with low within-population diversity, significant geographical population structuring, and little evidence of northward expansion. Structuring within the south-western cluster may result from distinct gene pools separated during the Pleistocene and reunited following glacial retreat, similar to patterns found in other forest tree species in the western USA. In aspen, populations in the south-western portion of the species range are thought to be at particularly high risk of mortality with climate change. Our findings suggest that these same populations may be disproportionately valuable in terms of both evolutionary potential and conservation value.

We document high rates of triploidy in aspen (Populus tremuloides) across the western USA (up to 69% of genets), and ask whether the incidence of triploidy across the species range corresponds with latitude, glacial history (as has been documented in other species), climate, or regional variance in clone size. Using a combination of microsatellite genotyping, flow cytometry, and cytology, we demonstrate that triploidy is highest in unglaciated, drought-prone regions of North America, where the largest clone sizes have been reported for this species. While we cannot completely rule out a low incidence of undetected aneuploidy, tetraploidy or duplicated loci, our evidence suggests that these phenomena are unlikely to be significant contributors to our observed patterns. We suggest that the distribution of triploid aspen is due to a positive synergy between triploidy and ecological factors driving clonality. Although triploids are expected to have low fertility, they are hypothesized to be an evolutionary link to sexual tetraploidy. Thus, interactions between clonality and polyploidy may be a broadly important component of geographic speciation patterns in perennial plants. Further, cytotypes are expected to show physiological and structural differences which may influence susceptibility to ecological factors such as drought, and we suggest that cytotype may be a significant and previously overlooked factor in recent patterns of high aspen mortality in the southwestern portion of the species range. Finally, triploidy should be carefully considered as a source of variance in genomic and ecological studies of aspen, particularly in western U.S. landscapes.

Cave ecosystems are carbon limited and thus are particularly susceptible to anthropogenic pollution. Yet, how carbon quality and quantity that can modulate the pathways and amount of Mn cycling in caves remains largely unknown. To explore Mn cycling, baseline bacterial, archaeal, and fungal communities associated with Mn(III/IV) oxide deposits were assessed in both relatively ‘pristine’ and anthropogenically impacted caves in the Appalachian Mountains (USA). Cave sites were then amended with various carbon sources that are commonly associated with anthropogenic input to determine whether they stimulate biotic Mn(II) oxidation in situ. Results revealed patterns between sites that had long-term exogenous carbon loading compared to sites that were relatively ‘pristine,’ particularly among Bacteria and Archaea. Carbon treatments that stimulated Mn(II) oxidation at several sites resulted in significant changes to the microbial communities, indicating that anthropogenic input can not only enhance biotic Mn(II) oxidation, but also shape community structure and diversity. Additional carbon sources amended with copper were incubated at various cave sites to test the role that Cu(II) plays in in situ biotic Mn(II) oxidation. Media supplemented with 100 µM Cu(II) inhibited bacterial Mn(II) oxidation but stimulated fungal Mn(II) oxidation, implicating fungal use of multicopper oxidase (MCO) enzymes but bacterial use of superoxide to oxidize Mn(II). In sites with low C:N ratios, the activity of the Mn(II) oxidizing enzyme manganese peroxidase (MnP) appears to be limited (particularly by MnPutilizing Basidiomycetes and/or Zygomycetes).

Cliffs harbor unique ecological communities while facing increasing pressure from human disturbances. How abiotic factors such as surface heterogeneity, slope, and aspect interact locally to drive variation in plant communities remains largely unknown. We surveyed the vascular plants, bryophytes, and lichens along 50 vertical transects throughout the Big South Fork National River and Recreation Area (Tennessee, USA) to characterize the vegetative community and to determine which factors influenced the distribution of cliff vegetation. Across all cliff face plots, the dominant lichen genus was Lepraria; the dominant vascular plant was Dennstaedtia punctilobula; and the dominant bryophyte was Dicranum montanum. We found several rare species including Cladonia pocillum, a boreal disjunct lichen; Vittaria appalachiana, Appalachian shoestring fern; and Cynodontium schisti, a rare bryophyte. Vascular plants, bryophytes, and lichens were each influenced by different environmental drivers. West-facing slopes supported high vascular plant diversity, low-angle slopes supported high bryophyte diversity, and faces with high surface heterogeneity supported high lichen diversity. Both plant and lichen communities varied widely by transect within and across sampling areas. Recreational rock climbing did not appear to influence community structure, possibly due to low levels of climbing traffic among our survey transects. Nonetheless, we overlapped our vegetative model with a simple spatial model of potential for rock climbing development to highlight specific areas of concern. Our predictive model of vegetative diversity was moderately accurate (ρ = 0.43), suggesting that surveying each cliff individually may be necessary for conservation efforts. In addition, our work indicated that preserving vegetation along the top of cliff faces should remain a focus of conservation efforts.

It is commonly assumed that microbial communities are structured by “bottom-up” ecological forces, although few experimental manipulations have rigorously tested the mechanisms by which resources structure soil communities. We investigated how plant substrate availability might structure fungal communities and belowground processes along an experimental plant richness gradient in a grassland ecosystem. We hypothesized that variation in total plant-derived substrate inputs, plant functional group diversity, as well as the relative abundance of C4 grasses and legumes would modulate fungal α- and β-diversity and their rates of soil carbon (C) and nitrogen (N) cycling. To test these predictions, we molecularly characterized fungal communities, as well as potential extracellular enzyme activity, net N mineralization, and soil organic matter respiration. We found higher fungal richness was associated with increasing aboveground plant biomass; whereas, fungal β-diversity was explained by contributions from C4 grass and legume relative dominance, plant functional group diversity, as well as plant biomass. Furthermore, aboveground plant biomass consistently shaped the richness and composition of individual fungal trophic modes (i.e., saprotrophs, symbiotrophs, pathotrophs). Finally, variation in extracellular enzyme activity, net N mineralization rates, and soil organic matter respiration was significantly explained by fungal β-diversity when fungi were functionally classified. Via changes in the supply and composition of organic substrates entering soil, our study demonstrates that changes in the plant species richness and functional composition collectively influence fungal communities and rates of soil C and N cycling.

The ecosystem response to wildfire is often linked to fire severity, with potentially large consequences for belowground biogeochemistry and microbial processes. While the impacts of wildfire on belowground processes are generally well documented, it remains unclear how fire affects the fine-scale composition of microbial communities. Here, we investigate the composition of soil bacterial and fungal communities in burned and unburned forests in an attempt to better understand how these diverse communities respond to wildfire. We explored the belowground responses to three wildfires in Linville Gorge, NC, USA. Wildfires generally increased soil carbon content while simultaneously reducing soil respiration. We employed amplicon sequencing to describe soil microbial communities and found that fires decreased both bacterial and fungal diversity. In addition, wildfires resulted in significant shifts in both bacterial and fungal community composition. Bacterial phylum-level distributions in response to fire were mixed without clear patterns, with members of Acidobacteria being representative of both burned and unburned sites. Fungal communities showed consistent increases in Ascomycota dominance and concurrent decreases in Basidiomycota and Zygomycota dominance in response to burning. Indicator species analysis confirmed shift to Ascomycota in burned sites. These shifts in microbial communities may reflect differences in the quality and quantity of soil organic matter following wildfires.