Microbial mediation of salinity stress response varies by plant genotype and provenance over time.

Although it is becoming widely appreciated that microbes can enhance plant tolerance to environmental stress, the nature of microbial mediation of exposure responses is not well understood. We addressed this deficit by examining whether microbial mediation of plant responses to elevated salinity is contingent on the environment and factors intrinsic to the host. We evaluated the influence of contrasting environmental conditions relative to host genotype, provenance and evolution by conducting a common-garden experiment utilizing ancestral and descendant cohorts of Schoenoplectus americanus genotypes recovered from two 100+ year coastal marsh seed banks. We compared S. americanus productivity and trait variation as well as associated endophytic microbial communities according to plant genotype, provenance, and age cohort under high and low salinity stress with and without native soil inoculation. The magnitude and direction of microbial mediation of S. americanus responses to elevated salinity varied according to individual genotype, provenance, as well as temporal shifts in genotypic variation and G × E (gene by environment) interactions. Relationships differed between plant traits and the structure of endosphere communities. Our findings indicate that plant-microbe associations and microbial mediation of plant stress are not only context-dependent but also dynamic. Our results additionally suggest that evolution can shape the fate of marsh ecosystems by altering how microbes confer plant tolerance to pressures linked to global change.

Rhizosphere microbial communities reflect genotypic and trait variation in a salt marsh ecosystem engineer.

PREMISE: There is growing recognition that intraspecific genetic variation in plants can influence associated soil microbial communities, but the functional bridges linking plant genotype with microbial community structure are not well understood. This deficit is due in part to a prevailing focus on characterizing relationships between microbial communities and functional trait variation among plant species or across plant communities, rather than within a single species. METHODS: We examined whether and how spatiotemporal variation in salt marsh rhizosphere microbial communities reflect plant provenance (genotypic variation) and associated trait variation within an ecosystem engineer, Spartina alterniflora. We planted S. alterniflora from four genetically distinct source populations in replicate sets of experimental plots across a shoreline in southeastern Louisiana, USA. After 2 years, we measured functional plant traits and profiled microbial communities. RESULTS: Bacterial and fungal α-diversity and richness were significantly higher in winter than in summer and corresponded to plant trait variation associated with provenance. Notably, 20% of the variation in fungal community composition was explained by trait differences while bacterial community structure did not reflect plant provenance or trait variation. However, evidence was found suggesting that bacterial communities are indirectly shaped by the influence of plant provenance on soil physicochemical properties. CONCLUSIONS: This study illustrates that intraspecific genetic and corresponding trait variation in an ecosystem engineer can shape rhizosphere microbial communities, with fungal communities being more responsive than bacteria to the influence of plant provenance and associated trait variation. Our results highlight the potential relevance of plant intraspecific variation in plant-microbe-soil feedbacks shaping naturally depauperate ecosystems like salt marshes.

Ice ages leave genetic diversity 'hotspots' in Europe but not in Eastern North America.

After the last glacial cycle, temperate European trees migrated northward, experiencing genetic bottlenecks and founder effects, which left high haplotype endemism in southern populations and clines in genetic diversity northward. These patterns are thought to be ubiquitous across temperate forests, and are therefore used to anticipate the potential genetic consequences of future warming. We compared existing and new phylogeographic data sets (chloroplast DNA) from 14 woody taxa in Eastern North America (ENA) to data sets from 21 ecologically similar European species to test for common impacts of Quaternary climate swings on genetic diversity across diverse taxa and between continents. Unlike their European counterparts, ENA taxa do not share common southern centres of haplotype endemism and they generally maintain high genetic diversity even at their northern range limits. Differences between the genetic impacts of Quaternary climate cycles across continents suggest refined lessons for managing genetic diversity in today's warming world.

Habitat differences influence genetic impacts of human land use on the American beech (Fagus grandifolia).

Natural reforestation after regional forest clearance is a globally common land-use sequence. The genetic recovery of tree populations in these recolonized forests may depend on the biogeographic setting of the landscape, for instance whether they are in the core or in the marginal part of the species' range. Using data from 501 individuals genotyped across 7 microsatellites, we investigated whether regional differences in habitat quality affected the recovery of genetic variation in a wind-pollinated tree species, American beech (Fagus grandifolia) in Massachusetts. We compared populations in forests that were recolonized following agricultural abandonment to those in remnant forests that have only been logged in both central inland and marginal coastal regions. Across all populations in our entire study region, recolonized forests showed limited reduction of genetic diversity as only observed heterozygosity was significantly reduced in these forests (H(O) = 0.520 and 0.590, respectively). Within inland region, this pattern was observed, whereas in the coast, recolonized populations exhibited no reduction in all genetic diversity estimates. However, genetic differentiation among recolonized populations in marginal coastal habitat increased (F(st) logged = 0.072; F(st) secondary = 0.249), with populations showing strong genetic structure, in contrast to inland region. These results indicate that the magnitude of recovery of genetic variation in recolonized populations can vary at different habitats.

Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics.

BACKGROUND: Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes. RESULTS: We successfully sequenced DNA from 64 samples (out of 126) comprised of bulk sediment and seeds, leaf fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10 copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments < 2000 years old, but we were able to successfully amplify DNA from samples up to 4600 years old. DNA sequences matched the taxonomic identity of the macrofossil from which they were extracted 79% of the time. Exceptions suggest that DNA molecules from surrounding nearby sediments may permeate or adhere to macrofossils in sediments. CONCLUSIONS: An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights into the genetic consequences of long-term environmental change. The low DNA copy numbers we found in fossil material and the discovery of multiple sequence variants from single macrofossil extractions highlight the need for careful experimental and laboratory protocols. Further application of these protocols should lead to better understanding of the ecological and evolutionary consequences of environmental change.

Intraspecific variation in landform engineering across a restored salt marsh shoreline.

Ecosystem engineers that modify landforms can be valuable tools for restoring habitat, but their use has frequently resulted in unanticipated outcomes. Departures from expectations might arise because applications discount the possibility that geomorphic processes are influenced by heritable phenotypic variation. We conducted a field-scale common garden experiment to assess whether shoreline erosion reflects intraspecific variation in the landform engineer Spartina alterniflora. Replicated plots on a shoreline denuded by the Deepwater Horizon oil spill were revegetated using plants from four genetically distinct sources: the local population, a nonlocal population, and two nursery stocks. We assessed variation in biomass, tissue nutrients, and functional traits alongside soil shear strength, surface elevation, and shoreline erosion rates over 2 years. We found that productivity, traits, nutrient content, and erosion rates varied according to plant provenance. Erosion reflected traits like root architecture more so than coarser metrics of growth. Erosion was significantly higher in plots with nonlocal plants that exhibited lower productivity, likely due to nitrogen limitation. Our results indicate that restoration practices should account for intraspecific variation in landform engineers and that in situ trials should be performed at sites slated for restoration to evaluate donor source suitability, particularly if introductions might modify local populations.

Plant diversity and litter accumulation mediate the loss of foliar endophyte fungal richness following nutrient addition.

Foliar fungal endophytes are ubiquitous plant symbionts that can affect plant growth and reproduction via their roles in pathogen and stress tolerance, as well as plant hormonal signaling. Despite their importance, we have a limited understanding of how foliar fungal endophytes respond to varying environmental conditions such as nutrient inputs. The responses of foliar fungal endophyte communities to increased nutrient deposition may be mediated by the simultaneous effects on within-host competition as well as the indirect impacts of altered host population size, plant productivity, and plant community diversity and composition. Here, we leveraged a 7-yr experiment manipulating nitrogen, phosphorus, potassium, and micronutrients to investigate how nutrient-induced changes to plant diversity, plant productivity, and plant community composition relate to changes in foliar fungal endophyte diversity and richness in a focal native grass host, Andropogon gerardii. We found limited evidence of direct effects of nutrients on endophyte diversity. Instead, the effects of nutrients on endophyte diversity appeared to be mediated by accumulation of plant litter and plant diversity loss. Specifically, nitrogen addition is associated with a 40% decrease in plant diversity and an 11% decrease in endophyte richness. Although nitrogen, phosphorus, and potassium addition increased aboveground live biomass and decreased relative Andropogon cover, endophyte diversity did not covary with live plant biomass or Andropogon cover. Our results suggest that fungal endophyte diversity within this focal host is determined in part by the diversity of the surrounding plant community and its potential impact on immigrant propagules and dispersal dynamics. Our results suggest that elemental nutrients reduce endophyte diversity indirectly via impacts on the local plant community, not direct response to nutrient addition. Thus, the effects of global change drivers, such as nutrient deposition, on characteristics of host populations and the diversity of their local communities are important for predicting the response of symbiont communities in a changing global environment.

Divergent biotic and abiotic filtering of root endosphere and rhizosphere soil fungal communities along ecological gradients.

Plant roots assemble in two distinct microbial compartments: the rhizosphere (microbes in soil surrounding roots) and the endosphere (microbes within roots). Our knowledge of fungal community assembly in these compartments is limited, especially in wetlands. We tested the hypothesis that biotic factors would have direct effects on rhizosphere and endosphere assembly, while abiotic factors would have direct and indirect effects. Using a field study, we examined the influences of salinity, water level and biotic factors on baldcypress (Taxodium distichum) fungal communities. We found that endosphere fungi, unlike rhizosphere fungi, were correlated with host density and canopy cover, suggesting that hosts can impose selective filters on fungi colonizing their roots. Meanwhile, local abiotic conditions strongly influenced both rhizosphere and endosphere diversity in opposite patterns, e.g. highest endosphere diversity (hump-shaped) and lowest rhizosphere diversity (U-shaped) at intermediate salinity levels. These results indicate that the assembly and structure of the root endosphere and rhizosphere within a host can be shaped by different processes. Our results also highlight the importance of assessing how environmental changes affect plant and plant-associated fungal communities in wetland ecosystems where saltwater intrusion and sea level rise are major threats to both plant and fungal communities.

Site-specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales.

The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within-host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.

Effects of nutrient supply, herbivory, and host community on fungal endophyte diversity.

The microbes contained within free-living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across four mesic prairies in the central United States. Composition of fungal endophyte communities differed among sites and among individuals within a site, but was not consistently affected by experimental manipulation of nutrient supply to hosts (A. gerardii) or herbivore reduction via fencing. In contrast, mean fungal diversity was similar among sites but was limited by total plant biomass at the plot scale. Our work demonstrates that distributed experiments motivated by ecological theory are a powerful tool to unravel the multiscale processes governing microbial community composition and diversity.

Persisting responses of salt marsh fungal communities to the Deepwater Horizon oil spill.

The plant microbiome, composed of diverse interacting microorganisms, is thought to undergird host integrity and well-being. Though it is well understood that environmental perturbations like oil pollution can alter the diversity and composition of microbiomes, remarkably little is known about how disturbance alters plant-fungal associations. Using Next-Generation sequencing of the 18S rDNA internal transcribed spacer (ITS1) region, we examined outcomes of enduring oil exposure on aboveground leaf and belowground endophytic root and rhizosphere fungal communities of Spartina alterniflora, a highly valued ecosystem engineer in southeastern Louisiana marshes affected by the 2010 Deepwater Horizon accident. We found that aboveground foliar fungal communities exhibited site-dependent compositional turnover with consequent loss in diversity according to oiling history. Rhizosphere soil communities also exhibited shifts in community composition associated with oiling history, whereas root endophytic communities did not. Oiling did not increase or decrease similarities among aboveground and belowground communities within an individual host, indicating that host plant characteristics exert stronger control than external factors on fungal community composition. These results show that fungal community responses to oiling vary within tissues of the same host plant, and that differences in the local environment, or alternatively, site-specific differences in residual oil constrain the magnitude of exposure responses. Our study offers novel perspectives on how environmental contaminants and perturbations can influence plant microbiomes, highlighting the importance of assessing long-term ecological outcomes of oil pollution to better understand how shifts in microbial communities influence plant performance and ecosystem function. Our findings are relevant to coastal management programs tasked with responding to oil spills and increasing pressures arising from intensifying development and climate change. Understanding how modification of plant-microbiome associations influences plant performance, particularly of ecosystem engineers like S. alterniflora, can help guide efforts to protect and restore at-risk coastal ecosystems.