Rapid evolution of a coastal marsh ecosystem engineer in response to global change.

There is increasing evidence that global change can alter ecosystems by eliciting rapid evolution of foundational plants capable of shaping vital attributes and processes. Here we describe results of a field-scale exposure experiment and multilocus assays illustrating that elevated CO2 (eCO2) and nitrogen (N) enrichment can result in rapid shifts in genetic and genotypic variation in Phragmites australis, an ecologically dominant plant that acts as an ecosystem engineer in coastal marshes worldwide. Compared to control treatments, genotypic diversity declined over three years of exposure, especially to N enrichment. The magnitude of loss also increased over time under conditions of N enrichment. Comparisons of genotype frequencies revealed that proportional abundances shifted with exposure to eCO2 and N in a manner consistent with expected responses to selection. Comparisons also revealed evidence of tradeoffs that constrained exposure responses, where any particular genotype responded favorably to one factor rather than to different factors or to combinations of factors. These findings challenge the prevailing view that plant-mediated ecosystem outcomes of global change are governed primarily by differences in species responses to shifting environmental pressures and highlight the value of accounting for organismal evolution in predictive models to improve forecasts of ecosystem responses to global change.

Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution.

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host's physiological capacities; however, the identity and functional role(s) of key members of the microbiome ("core microbiome") in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems' capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts' plastic and adaptive responses to environmental change requires (i) recognizing that individual host-microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.

Litter quality, dispersal and invasion drive earthworm community dynamics and forest soil development.

In temperate deciduous forests of eastern USA, most earthworm communities are dominated by invasive species. Their structure and functional group composition have critical impacts on ecological properties and processes. However, the factors determining their community structure are still poorly understood, and little is known regarding their dynamics during forest succession and the mechanisms leading to these changes. Earthworm communities are usually assumed to be stable and driven by vegetation. In contrast, the importance of dispersal and ecological drift is seldom acknowledged. By analyzing a 19-year dataset collected from forest stands in eastern USA, we demonstrated that on a decadal timescale, earthworm community dynamics are shaped by the interplay of selection, dispersal, and ecological drift. We highlighted that forests at different successional stages have distinct earthworm species and functional groups as a result of environmental filtering through leaf litter quality. Specifically, young forests are characterized by soil-feeding species that rely on relatively fresh soil organic matter derived from fast-decomposing litter, whereas old forests are characterized by those feeding on highly processed soil organic matter derived from slow-decomposing litter. In addition, year-to-year species gains and losses are primarily driven by dispersal from regional to local species pools, and by local extinction resulted from competition and ecological drift. We concluded that with continued dispersal of European species and the recent "second wave" of earthworm invasion by Asian species from the surrounding landscape, earthworms at the investigated forests are well-established, and will remain as the major drivers of soil development for the foreseeable future.

Mycorrhizal fungi affect orchid distribution and population dynamics.

Symbioses are ubiquitous in nature and influence individual plants and populations. Orchids have life history stages that depend fully or partially on fungi for carbon and other essential resources. As a result, orchid populations depend on the distribution of orchid mycorrhizal fungi (OMFs). We focused on evidence that local-scale distribution and population dynamics of orchids can be limited by the patchy distribution and abundance of OMFs, after an update of an earlier review confirmed that orchids are rarely limited by OMF distribution at geographic scales. Recent evidence points to a relationship between OMF abundance and orchid density and dormancy, which results in apparent density differences. Orchids were more abundant, less likely to enter dormancy, and more likely to re-emerge when OMF were abundant. We highlight the need for additional studies on OMF quantity, more emphasis on tropical species, and development and application of next-generation sequencing techniques to quantify OMF abundance in substrates and determine their function in association with orchids. Research is also needed to distinguish between OMFs and endophytic fungi and to determine the function of nonmycorrhizal endophytes in orchid roots. These studies will be especially important if we are to link orchids and OMFs in efforts to inform conservation.

Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae).

PREMISE OF THE STUDY: The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated 10 transcriptomes and incorporated existing RNA-seq data to infer a multilocus nuclear phylogeny of the Cypripedioideae and to determine whether a whole-genome duplication event (WGD) correlated with the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families. METHODS: Transcriptome data were used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree. KEY RESULTS: Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny. CONCLUSIONS: Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.

Drivers of vegetative dormancy across herbaceous perennial plant species.

Vegetative dormancy, that is the temporary absence of aboveground growth for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life-history costs of sprouting, and of dormancy. Short-lived and mycoheterotrophic species have higher proportions of dormant plants than long-lived species and species with other nutritional modes. Foliage loss is associated with higher future dormancy levels, suggesting that carbon limitation promotes dormancy. Maximum dormancy duration is shorter under higher precipitation and at higher latitudes, the latter suggesting an important role for competition or herbivory. Study length affects estimates of some demographic parameters. Our results identify life historical and environmental drivers of dormancy. We also highlight the evolutionary importance of the little understood costs of sprouting and growth, latitudinal stress gradients and mixed nutritional modes.

Cosmopolitan Species As Models for Ecophysiological Responses to Global Change: The Common Reed Phragmites australis.

Phragmites australis is a cosmopolitan grass and often the dominant species in the ecosystems it inhabits. Due to high intraspecific diversity and phenotypic plasticity, P. australis has an extensive ecological amplitude and a great capacity to acclimate to adverse environmental conditions; it can therefore offer valuable insights into plant responses to global change. Here we review the ecology and ecophysiology of prominent P. australis lineages and their responses to multiple forms of global change. Key findings of our review are that: (1) P. australis lineages are well-adapted to regions of their phylogeographic origin and therefore respond differently to changes in climatic conditions such as temperature or atmospheric CO2; (2) each lineage consists of populations that may occur in geographically different habitats and contain multiple genotypes; (3) the phenotypic plasticity of functional and fitness-related traits of a genotype determine the responses to global change factors; (4) genotypes with high plasticity to environmental drivers may acclimate or even vastly expand their ranges, genotypes of medium plasticity must acclimate or experience range-shifts, and those with low plasticity may face local extinction; (5) responses to ancillary types of global change, like shifting levels of soil salinity, flooding, and drought, are not consistent within lineages and depend on adaptation of individual genotypes. These patterns suggest that the diverse lineages of P. australis will undergo intense selective pressure in the face of global change such that the distributions and interactions of co-occurring lineages, as well as those of genotypes within-lineages, are very likely to be altered. We propose that the strong latitudinal clines within and between P. australis lineages can be a useful tool for predicting plant responses to climate change in general and present a conceptual framework for using P. australis lineages to predict plant responses to global change and its consequences.

Symbiont abundance can affect host plant population dynamics.

PREMISE OF THE STUDY: Symbioses are almost universal, but little is known about how symbiont abundance can affect host performance. Many orchids undergo vegetative dormancy and frequent and protracted dormancy have been associated with population declines. If mycorrhizal fungi affect host plant performance, those effects are likely to alter patterns of vegetative dormancy. The goal of this study was to determine whether the abundance of mycorrhizal fungi is related to the likelihood of entering dormancy and whether fungal abundance varied with dormancy duration in the federally listed threatened orchid Isotria medeoloides. METHODS: We studied three populations of the threatened North American terrestrial orchid Isotria medeoloides using long-term emergence data and evaluated the relationship between the abundance of associated mycorrhizal fungi (Russulaceae) and orchid dormancy and emergence. Mycorrhizal fungi in soil adjacent to orchids were quantified in two ways. First, ectomycorrhizal (ECM) fungi on adjacent root tips were identified using DNA sequencing to determine their phylogenetic relationship to fungi that are known to form mycorrhizae with I. medeoloides. Second, we extracted DNA from soil samples and used quantitative real-time PCR to estimate the abundance of Russulaceae hyphae adjacent to each orchid. KEY RESULTS: We found that the abundance of Russulaceae, both in the soil and on nearby ECM root tips, was significantly related to orchid prior emergence. Both abundance and prior emergence history were predictive of future emergence. CONCLUSIONS: These results suggest that the abundance of mycorrhizal fungi can influence orchid population dynamics and is an essential component of orchid conservation.

Belowground interactions with aboveground consequences: Invasive earthworms and arbuscular mycorrhizal fungi.

A mounting body of research suggests that invasive nonnative earthworms substantially alter microbial communities, including arbuscular mycorrhizal fungi (AMF). These changes to AMF can cascade to affect plant communities and vertebrate populations. Despite these research advances, relatively little is known about (1) the mechanisms behind earthworms' effects on AMF and (2) the factors that determine the outcomes of earthworm-AMF interactions (i.e., whether AMF abundance is increased or decreased and subsequent effects on plants). We predict that AMF-mediated effects of nonnative earthworms on ecosystems are nearly universal because (1) AMF are important components of most terrestrial ecosystems, (2) nonnative earthworms have become established in nearly every type of terrestrial ecosystem, and (3) nonnative earthworms, due to their burrowing and feeding behavior, greatly affect AMF with potentially profound concomitant effects on plant communities. We highlight the multiple direct and indirect effects of nonnative earthworms on plants and review what is currently known about the interaction between earthworms and AMF. We also illustrate how the effects of nonnative earthworms on plant-AMF mutualisms can alter the structure and stability of aboveground plant communities, as well as the vertebrate communities relying on these habitats. Integrative studies that assess the interactive effects of earthworms and AMF can provide new insights into the role that belowground ecosystem engineers play in altering aboveground ecological processes. Understanding these processes may improve our ability to predict the structure of plant and animal communities in earthworm-invaded regions and to develop management strategies that limit the numerous undesired impacts of earthworms.

Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes.

A growing body of literature supports microbial symbiosis as a foundational principle for the competitive success of invasive plant species. Further exploration of the relationships between invasive species and their associated microbiomes, as well as the interactions with the microbiomes of native species, can lead to key new insights into invasive success and potentially new and effective control approaches. In this manuscript, we review microbial relationships with plants, outline steps necessary to develop invasive species control strategies that are based on those relationships, and use the invasive plant species Phragmites australis (common reed) as an example of how development of microbial-based control strategies can be enhanced using a collective impact approach. The proposed science agenda, developed by the Collaborative for Microbial Symbiosis and Phragmites Management, contains a foundation of sequential steps and mutually-reinforcing tasks to guide the development of microbial-based control strategies for Phragmites and other invasive species. Just as the science of plant-microbial symbiosis can be transferred for use in other invasive species, so too can the model of collective impact be applied to other avenues of research and management.

Limitations on orchid recruitment: not a simple picture.

Mycorrhizal fungi have substantial potential to influence plant distribution, especially in specialized orchids and mycoheterotrophic plants. However, little is known about environmental factors that influence the distribution of mycorrhizal fungi. Previous studies using seed packets have been unable to distinguish whether germination patterns resulted from the distribution of appropriate edaphic conditions or the distribution of host fungi, as these cannot be separated using seed packets alone. We used a combination of organic amendments, seed packets and molecular assessment of soil fungi required by three terrestrial orchid species to separate direct and indirect effects of fungi and environmental conditions on both seed germination and subsequent protocorm development. We found that locations with abundant mycorrhizal fungi were most likely to support seed germination and greater growth for all three orchids. Organic amendments affected germination primarily by affecting the abundance of appropriate mycorrhizal fungi. However, fungi associated with the three orchid species were affected differently by the organic amendments and by forest successional stage. The results of this study help contextualize the importance of fungal distribution and abundance to the population dynamics of plants with specific mycorrhizal requirements. Such phenomena may also be important for plants with more general mycorrhizal associations.

Evolution of host breadth in broad interactions: mycorrhizal specificity in East Asian and North American rattlesnake plantains (Goodyera spp.) and their fungal hosts.

Host breadth is often assumed to have no evolutionary significance in broad interactions because of the lack of cophylogenetic patterns between interacting species. Nonetheless, the breadth and suite of hosts utilized by one species may have adaptive value, particularly if it underlies a common ecological niche among hosts. Here, we present a preliminary assessment of the evolution of mycorrhizal specificity in 12 closely related orchid species (genera Goodyera and Hetaeria) using DNA-based methods. We mapped specificity onto a plant phylogeny that we estimated to infer the evolutionary history of the mycorrhiza from the plant perspective, and hypothesized that phylogeny would explain a significant portion of the variance in specificity of plants on their host fungi. Sampled plants overwhelmingly associated with genus Ceratobasidium, but also occasionally with some ascomycetes. Ancestral mycorrhizal specificity was narrow in the orchids, and broadened rarely as Goodyera speciated. Statistical tests of phylogenetic inertia suggested some support for specificity varying with increasing phylogenetic distance, though only when the phylogenetic distance between suites of fungi interacting with each plant taxon were taken into account. These patterns suggest a role for phylogenetic conservatism in maintaining suits of fungal hosts among plants. We stress the evolutionary importance of host breadth in these organisms, and suggest that even generalists are likely to be constrained evolutionarily to maintaining associations with their symbionts.

Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas.

Despite advances owing to molecular approaches, several hurdles still obstruct the identification of fungi forming orchid mycorrhizas. The Tulasnellaceae exhibit accelerated evolution of the nuclear ribosomal operon, causing most standard primers to fail in polymerase chain reaction (PCR) trials. Insufficient sequences are available from well characterized isolates and fruitbodies. Lastly, taxon-specific PCR primers are needed in order to explore the ecology of the fungi outside of the orchid root. Here, progress in overcoming these hurdles is reported. Broad-spectrum basidiomycete internal transcribed spacer (ITS) primers that do not exclude most known Tulasnellaceae are presented. blast searches and empirical PCR tests support their wide utility within the Basidiomycota. Taxon-specific ITS primers are presented targeted to orchid-associated Tulasnella, and a core component of the Thelephora-Tomentella complex. The efficiency and selectivity of these primer sets are again supported by blast searches and empirical tests. Lastly, ITS DNA sequences are presented from several strains of Epulorhiza, Ceratorhiza, Ceratobasidium, Sistotrema, Thanatephorus and Tulasnella that were originally described in the landmark mycorrhizal studies of Currah and Warcup. Detailed phylogenetic analyses reveal some inconsistencies in species concepts in these taxonomically challenging resupinate basidiomycetes, but also help to place several sequences from environmental samples.

The evolutionary history of mycorrhizal specificity among lady's slipper orchids.

Although coevolution is acknowledged to occur in nature, coevolutionary patterns in symbioses not involving species-to-species relationships are poorly understood. Mycorrhizal plants are thought to be too generalist to coevolve with their symbiotic fungi; yet some plants, including some orchids, exhibit strikingly narrow mycorrhizal specificity. Here, we assess the evolutionary history of mycorrhizal specificity in the lady's slipper orchid genus, Cypripedium. We sampled 90 populations of 15 taxa across three continents, using DNA methods to identify fungal symbionts and quantify mycorrhizal specificity. We assessed phylogenetic relationships among sampled Cypripedium taxa, onto which we mapped mycorrhizal specificity. Cypripedium taxa associated almost exclusively with fungi within family Tulasnellaceae. Ancestral specificity appears to have been narrow, followed by a broadening after the divergence of C. debile. Specificity then narrowed, resulting in strikingly narrow specificity in most of the taxa in this study, with no taxon rewidening to the same extant as basal members of the genus. Sympatric taxa generally associated with different sets of fungi, and most clades of Cypripedium-mycorrhizal fungi were found throughout much of the northern hemisphere, suggesting that these evolutionary patterns in specificity are not the result of biogeographic lack of opportunity to associate with potential partners. Mycorrhizal specificity in genus Cypripedium appears to be an evolvable trait, and associations with particular fungi are phylogenetically conserved.

Orchid-fungus fidelity: a marriage meant to last?

The characteristics of plant-mycorrhizae associations are known to vary in both time and space, but the ecological consequences of variation in the dynamics of plant-fungus interactions are poorly understood. For example, do plants associate with single fungi or multiple fungi simultaneously, and do the associations persist through a plant's lifetime or do plants support a succession of different fungi? We investigated these and other questions related to plant-fungus interactions in Goodyera pubescens, an evergreen terrestrial orchid of the eastern United States, that interacts with closely related fungi in the genus Tulasnella. Unlike the mycorrhizal associations of other plants, orchid-mycorrhizal associations only benefit the orchid, based on current evidence. Many terrestrial orchids have been found to associate with specific groups of fungi. This characteristic could potentially limit orchids to relatively narrow ranges of environmental conditions and may be a contributing factor in the decline of many orchids in the face of changing environmental conditions. We found that G. pubescens protocorms (developing embryos prior to leaf production) and adults associated with only one fungal individual at a time. The orchid-fungus association persists for years, but during a drought period that was associated with the death of many plants, surviving plants were able to switch to new fungal individuals. These results suggest that G. pubescens interacts with the same fungal partner during periods of modest environmental variation but is able to switch to a different fungal partner. We hypothesize that the ability to switch fungi allows G. pubescens to survive more extreme environmental perturbations. However, laboratory experiments suggest that switching fungi has potential costs, as it increases the risk of mortality, especially for smaller individuals. Our findings indicate that it is unlikely that switching fungi is a common way to improve tolerance of less severe environmental fluctuations and disturbances. These findings may have important implications for plant responses to severe climatic events or to more gradual environmental changes such as global warming.