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Large landscapes exhibit natural heterogeneity. Land management can impose additional variation, altering ecosystem patterns. Habitat characteristics may reflect these management factors, potentially resulting in habitat differences that manifest along jurisdictional boundaries. We characterized the patchwork of habitats across a case study landscape, the Grand Canyon Protected Area-Centered Ecosystem. We asked: how do ecological conditions vary across different types of jurisdictional boundaries on public lands? We hypothesized that differences in fire and grazing, because they respond to differences in management over time, contribute to ecological differences by jurisdiction. We collected plot-scale vegetation and soils data along boundaries between public lands units surrounding the Grand Canyon. We compared locations across boundaries of units managed differently, accounting for vegetation type and elevation differences that pre-date management unit designations. We used generalized mixed effects models to evaluate differences in disturbance and ecology across boundaries. Jurisdictions varied in evidence of grazing and fire. After accounting for these differences, some measured vegetation and soil properties also differed among jurisdictions. The greatest differences were between US Forest Service wilderness and Bureau of Land Management units. For most measured variables, US Forest Service non-wilderness units and National Park Service units were intermediate. In this study, several ecological properties tracked jurisdictional boundaries, forming a predictable patchwork of habitats. These patterns likely reflect site differences that pre-date jurisdictions as well as those resulting from different management histories. Understanding how ecosystem differences manifest at jurisdictional boundaries can inform resource management, conservation, and cross-boundary collaborations.

Soil-borne pathogens structure plant communities, shaping their diversity, and through these effects may mediate plant responses to climate change and disturbance. Little is known, however, about the environmental determinants of plant pathogen communities. Therefore, we explored the impact of climate gradients and anthropogenic disturbance on root-associated pathogens in grasslands. We examined the community structure of two pathogenic groups—fungal pathogens and oomycetes—in undisturbed and anthropogenically disturbed grasslands across a natural precipitation and temperature gradient in the Midwestern USA. In undisturbed grasslands, precipitation and temperature gradients were important predictors of pathogen community richness and composition. Oomycete richness increased with precipitation, while fungal pathogen richness depended on an interaction of precipitation and temperature, with precipitation increasing richness most with higher temperatures. Disturbance altered plant pathogen composition and precipitation and temperature had a reduced effect on pathogen richness and composition in disturbed grasslands. Because pathogens can mediate plant community diversity and structure, the sensitivity of pathogens to disturbance and climate suggests that degradation of the pathogen community may mediate loss, or limit restoration of, native plant diversity in disturbed grasslands, and may modify plant community response to climate change.

Fire alters microbial community composition, and is expected to increase in frequency due to climate change. Testing whether microbes in different ecosystems will respond similarly to increased fire disturbance is difficult though, because fires are often unpredictable and hard to manage. Fire recurrent or pyrophilic ecosystems, however, may be useful models for testing the effects of frequent disturbance on microbes. We hypothesized that across pyrophilic ecosystems, fire would drive similar alterations to fungal communities, including altering seasonal community dynamics. We tested fire's effects on fungal communities in two pyrophilic ecosystems, a longleaf pine savanna and tallgrass prairie. Fire caused similar fungal community shifts, including (i) driving immediate changes that favored taxa able to survive fire and take advantage of post-fire environments and (ii) altering seasonal trajectories due to fire-associated changes to soil nutrient availability. This suggests that fire has predictable effects on fungal community structure and intra-annual community dynamics in pyrophilic ecosystems, and that these changes could significantly alter fungal function. Parallel fire responses in these key microbes may also suggest that recurrent fires drive convergent changes across ecosystems, including less fire-frequented systems that may start burning more often due to climate change.

The use of perennial crop species in agricultural systems may increase ecosystem services and sustainability. Because soil microbial communities play a major role in many processes on which ecosystem services and sustainability depend, characterization of soil community structure in novel perennial crop systems is necessary to understand potential shifts in function and crop responses. Here, we characterized soil fungal community composition at two depths (0-10 and 10-30 cm) in replicated, long-term plots containing one of three different cropping systems: a tilled three-crop rotation of annual crops, a novel perennial crop monoculture (Intermediate wheatgrass, which produces the grain Kernza®), and a native prairie reconstruction. The overall fungal community was similar under the perennial monoculture and native vegetation, but both were distinct from those in annual agriculture. The mutualist and saprotrophic community subsets mirrored differences of the overall community, but pathogens were similar among cropping systems. Depth structured overall communities as well as each functional group subset. These results reinforce studies showing strong effects of tillage and sampling depth on soil community structure and suggest plant species diversity may play a weaker role. Similarities in the overall and functional fungal communities between the perennial monoculture and native vegetation suggest Kernza® cropping systems have the potential to mimic reconstructed natural systems.

Pyrogenic savannas with a tree–grassland ‘matrix’ experience frequent fires (i.e. every 1–3 yr). Aboveground responses to frequent fires have been well studied, but responses of fungal litter decomposers, which directly affect fuels, remain poorly known. We hypothesized that each fire reorganizes belowground communities and slows litter decomposition, thereby influencing savanna fuel dynamics. In a pine savanna, we established patches near and away from pines that were either burned or unburned in that year. Within patches, we assessed fungal communities and microbial decomposition of newly deposited litter. Soil variables and plant communities were also assessed as proximate drivers of fungal communities. Fungal communities, but not soil variables or vegetation, differed substantially between burned and unburned patches. Saprotrophic fungi dominated in unburned patches but decreased in richness and relative abundance after fire. Differences in fungal communities with fire were greater in litter than in soils, but unaffected by pine proximity. Litter decomposed more slowly in burned than in unburned patches. Fires drive shifts between fire‐adapted and sensitive fungal taxa in pine savannas. Slower fuel decomposition in accordance with saprotroph declines should enhance fuel accumulation and could impact future fire characteristics. Thus, fire reorganization of fungal communities may enhance persistence of these fire‐adapted ecosystems.

Small mammal disturbances in tallgrass prairies are known to influence a variety of ecosystem properties, including plant establishment, plant diversity, and soil nutrient dynamics. We explored direct and indirect effects of mammalian soil disturbance on a newly established grassland restoration site. In 2016–2017, we measured variation in small mammal soil disturbance, plant cover, and total inorganic nitrogen, all within the same plots. Within our site, interior plots had greater disturbance than plots located near site edges. On average, plots with high soil disturbance in 2016 had high disturbance in 2017, and disturbance in the first year was greater than in the second year. Soil disturbance was associated with an overall decline in grass cover and an increase in forb cover (especially Asteraceae). However, there were no associations between soil disturbance and either inorganic nitrogen or plant species richness/diversity on the new restoration site. Our study supports the important link between prairie plant communities and small mammal soil disturbance, potentially creating heterogeneity that is important for tallgrass prairie restoration and conservation.

Soil factors and host plant identity can both affect the growth and functioning of mycorrhizal fungi. Both components change during primary succession, but it is unknown if their relative importance to mycorrhizas also changes. This research tested how soil type and host plant differences among primary successional stages determine the growth and plant effects of arbuscular mycorrhizal (AM) fungal communities. Mycorrhizal fungal community, plant identity, and soil conditions were manipulated among three stages of a lacustrine sand dune successional series in a fully factorial greenhouse experiment. Late succession AM fungi produced more arbuscules and soil hyphae when grown in late succession soils, although the community was from the same narrow phylogenetic group as those in intermediate succession. AM fungal growth did not differ between host species, and plant growth was similarly unaffected by different AM fungal communities. These results indicate that though ecological filtering and/or adaptation of AM fungi occurs during this primary dune succession, it more strongly reflects matching between fungi and soils, rather than interactions between fungi and host plants. Thus, AM fungal performance during this succession may not depend directly on the sequence of plant community succession.

Differences in the arrival timing of plants and soil biota may result in different plant communities through priority effects, potentially affecting the success of native vs. exotic plants, but experimental evidence is largely lacking. We conducted a greenhouse experiment to investigate whether the assembly history of plants and fungal root endophytes could interact to influence plant emergence and biomass. We introduced a grass species and eight fungal species from one of three land-use types (undisturbed, disturbed, or pasture sites in a Florida scrubland) in factorial combinations. We then introduced all plants and fungi from the other land-use types 2 weeks later. Plant emergence was monitored for 6 months, and final plant biomass and fungal species composition assessed. The emergence and growth of the exotic Melinis repens and the native Schizacharyium niveum were affected negatively when introduced early with their "home" fungi, but early introduction of a different plant species or fungi from a different site type eliminated these negative effects, providing evidence for interactive priority effects. Interactive effects of plant and fungal arrival history may be an overlooked determinant of plant community structure and may provide an effective management tool to inhibit biological invasion and aid ecosystem restoration.

Novel associations between plants and pathogens can have serious impacts on managed and natural ecosystems world-wide. The introduction of alien plants increases the potential for biogeographically novel plant-pathogen associations to arise when pathogens are transmitted from native to alien plant species and vice versa. We quantified biogeographically novel associations recorded in New Zealand over the last 150 yr between plant pathogens (fungi, oomycetes and plasmodiophorids) and vascular plants. We examined the extent to which taxonomic similarity, pathogen traits, contact opportunity and sampling effort could explain the number of novel associates for host and pathogen species. Novel associations were common; approximately one-third of surveyed plants and pathogens were recorded with at least one biogeographically novel associate. Native plants had more alien pathogens than vice versa. Taxonomic similarity between the native and alien flora and the total number of recorded associations (a measure of sampling effort) best explained the number of novel associates among species. The frequency of novel associations and the importance of sampling effort as an explanatory variable emphasize the need for effective monitoring and risk assessment tools to mitigate the potential environmental and economic impact of novel pathogen associations.

Plant interactions with soil biota could have a significant impact on plant successional trajectory by benefiting plants in a particular successional stage over others. The influence of soil mutualists such as mycorrhizal fungi is thought to be an important feedback component, yet they have shown benefits to both early and late successional plants that could either retard or accelerate succession. Here we first determine if arbuscular mycorrhizal (AM) fungi differ among three stages of primary sand dune succession and then if they alter growth of plants from particular successional stages. We isolated AM fungal inoculum from early, intermediate or late stages of a primary dune succession and compared them using cloning and sequencing. We then grew eight plant species that dominate within each of these successional stages with each AM fungal inoculum. We measured fungal growth to assess potential AM functional differences and plant growth to determine if AM fungi positively or negatively affect plants. AM fungi isolated from early succession were more phylogenetically diverse relative to intermediate and late succession while late successional fungi consistently produced more soil hyphae and arbuscules. Despite these differences, inocula from different successional stages had similar effects on the growth of all plant species. Host plant biomass was not affected by mycorrhizal inoculation relative to un-inoculated controls. Although mycorrhizal communities differ among primary dune successional stages and formed different fungal structures, these differences did not directly affect the growth of plants from different dune successional stages in our experiment and therefore may be less likely to directly contribute to plant succession in sand dunes.

Allelopathic phytochemicals have been linked to invasion success, but their role in the invasion process remains unclear. Toxicity effects demonstrated with lab bioassays may be neutralized in soils, and their role in population expansion can be intertwined with nonallelopathic processes that also influence dispersal and establishment. Here, we use greenhouse experiments to test the soil-based impacts of invasive fine fescue ( Festuca rubra L.) on recruitment in tallgrass prairie. Fescue roots release the growth inhibitor m-tyrosine. Using root washes and fescue-conditioned soils to mimic field potency, we determined allelopathic impacts on recruitment, including intraspecific limitation. We also tested whether nonallelopathic factors (propagule pressure, disturbance, and fertility) influence invasion into constructed fescue and prairie mesocosms, and whether root washes inhibit arbuscular mycorrhizal (AM) fungi. We observed significant negative effects of fescue soils and root washes on germination and seedling survival, including on fescue itself. Mesocosm invasion, however, was determined more by nonallelopathic mechanisms (propagule pressure and rapid growth). In prairie mesocosms, fescue invasion was higher than its own understory, with no effects of disturbance or fertility. Tallgrass species had difficulty establishing in all environments, regardless of propagule pressure. Impacts on AM fungal hyphal length and spore production were insignificant. Our results suggest that nonallelopathic traits may be sufficient to explain fescue invasion, with allelopathy likely emerging as a final "coup de grâce" for recruiting native grasses once dominance has been attained. Allelopathic species, including fine fescue, may thus not necessarily be invasive unless nonallelopathic traits facilitate establishment prior to the accumulation of soil-based toxins.

This is the author's manuscript. The definitive version is available at www.newphytologist.com

This is the peer reviewed version of the following article: BA Sikes, K Cottenie and JN Klironomos. (2009) Plant and fungal identity determines pathogen protection of plant roots by arbuscular mycorrhizas. Journal of Ecology 97: 1274-1280. http://dx.doi.org/10.1111/j.1365-2745.2009.01557.x, which has been published in final form at http://doi.org/10.1111/j.1365-2745.2009.01557.x This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.

While numerous studies have documented patterns of invasion by non-indigenous plant species, few have considered the invasive properties of non-native genotypes of native species. Characteristics associated with specific genotypes, such as tolerance to disturbance, may mistakenly be applied to an entire species in the absence of genetic information, which consequently may affect management decisions. We report here on the incidence and growth of an introduced lineage of Phragmites australis in the Gulf of Mexico coastal zone of Louisiana. P. australis was collected from nine separate locations for inclusion in a series of growth experiments. Chloroplast DNA analysis indicated that specimens collected from four locations in the Mississippi River Delta represented the introduced Eurasian haplotype; the remainder represented the gulf coast haplotype. Three distinct genotypes, or clones, were identified within each haplotype via analysis using amplified fragment length polymorphisms, which also revealed reduced genetic diversity of the gulf coast clones compared to the Eurasian clones. Clones of each haplotype were planted along with three other native macrophytes at similar densities in a restored brackish marsh and monitored for growth. After 14 months, the Eurasian haplotype had spread vegetatively to cover about 82% of the experimental plots, more than four times the coverage (18%) of the gulf coast haplotype. Thus, the use of P. australis plantings for wetland restoration should consider the genetic lineage of plants used since our results indicate the potential of the Eurasian haplotype to grow rapidly at newly restored sites. This rapid growth may limit the establishment of more slowly growing native species.

Mutualisms are important structuring forces in ecological communities, influencing ecosystem functions, diversity, and evolutionary trajectories. New interactions, particularly between native and non-native species, are globally increasing in biotic communities as species introductions accelerate. Positive interactions such as novel mutualisms can affect the fitness of organisms in invaded communities. Non-natives can augment native mutualism networks, replace extinct native partners, or disrupt native mutualisms. Because they are actively forming or newly formed, novel mutualisms offer a unique opportunity to examine in real time the factors governing early mutualism formation and stability, including frequency-dependent processes and those relying on specific traits or functions. These central ecological questions have been inferred from long-formed mutualisms, but novel mutualisms may allow a glimpse of successes and failures in ecological time with insights into the relative importance of these factors as ecological systems shift. To this end, this commentary addresses how novel mutualisms inform our understanding of mutualism formation, stability, the importance of functional traits, and niche vs. neutral processes, using examples across multiple systems. Novel mutualism research thus far has been largely limited in both questions and ecosystems, but if more broadly applied could benefit both theoretical and applied ecology.

Ecosystem productivity commonly increases asymptotically with plant species diversity, and determining the mechanisms responsible for this well-known pattern is essential to predict potential changes in ecosystem productivity with ongoing species loss. Previous studies attributed the asymptotic diversity-productivity pattern to plant competition and differential resource use (e.g., niche complementarity). Using an analytical model and a series of experiments, we demonstrate theoretically and empirically that host-specific soil microbes can be major determinants of the diversity-productivity relationship in grasslands. In the presence of soil microbes, plant disease decreased with increasing diversity, and productivity increased nearly 500%, primarily because of the strong effect of density-dependent disease on productivity at low diversity. Correspondingly, disease was higher in plants grown in conspecific-trained soils than heterospecific-trained soils (demonstrating host-specificity), and productivity increased and host-specific disease decreased with increasing community diversity, suggesting that disease was the primary cause of reduced productivity in species- poor treatments. In sterilized, microbe-free soils, the increase in productivity with increasing plant species number was markedly lower than the increase measured in the presence of soil microbes, suggesting that niche complementarity was a weaker determinant of the diversity- productivity relationship. Our results demonstrate that soil microbes play an integral role as determinants of the diversity-productivity relationship.

Arbuscular mycorrhizal (AM) fungi are mainly thought to facilitate phosphorus uptake in plants, but they can also perform several other functions that are equally beneficial. Our recent study sheds light on the factors determining one such function, enhanced plant protection from root pathogens. Root infection by the fungal pathogen Fusarium oxysporum was determined by both plant susceptibility and the ability of an AM fungal partner to suppress the pathogen. The non-susceptible plant species (Allium cepa) had limited F. oxysporum infection even without AM fungi. In contrast, the susceptible plant species (Setaria glauca) was heavily infected and only AM fungi in the family Glomeraceae limited pathogen abundance. Plant susceptibility to pathogens was likely determined by contrasting root architectures between plants, with the simple rooted plant (A. cepa) presenting fewer sites for infection. AM fungal colonization, however, was not limited in the same way in part because plants with fewer, simple roots are more mycorrhizal dependent. Protection only by Glomus species also indicates that whatever the mechanism(s) of this function, it responds to AM fungal families differently. While poor at pathogen protection, AM fungal species in the family Gigasporaceae most benefited the growth of the simple rooted plant species. Our research indicates that plant trait differences, such as root architecture can determine how important each mycorrhizal function is to plant growth but the ability to provide these functions differs among AM fungi.

The importance of a spatial context in understanding the ecology and evolution of organisms has become increasingly clear. Although there is a growing awareness of the importance of mycorrhizal fungi in many communities and ecosystems, much of this understanding is based on a spatially homogenized view of these soil fungi. This homogenized approach may limit our understanding of how these organisms interact with plants and other biota in the field. As an attempt to advance a spatial framework for understanding mycorrhizal ecology, we review our current understanding of the spatial structure of communities and populations of ectomycorrhizal and arbuscular mycorrhizal fungi at the scale of landscapes, communities, and individual host root systems. A variety of potential mechanisms such as disturbance, abiotic and biotic dispersal of mycorrhizal propagules, and biotic interactions may be responsible for generating and maintaining this spatial variation of populations and communities, but the links between observed spatial patterns and mechanisms have yet to be formed. Future work assessing the potential functional significance of spatial variation of mycorrhizal fungi for plant communities and ecosystem function, as well as measuring spatial variation in mycorrhizal function, will continue to advance our understanding of the spatial template for mycorrhizal–plant interactions in the field.

This is the peer reviewed version of the following article: BA Sikes (2012) Internalizing Conservation through our own Microbes. Conservation Biology, 26(2): 198. http://dx.doi.org/10.1111/j.1523-1739.2012.01834.x, which has been published in final form at http://doi.org/10.1111/j.1523-1739.2012.01834.x. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.