Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass).

Experimental tests of community assembly mechanisms for host-associated microbiomes in nature are lacking. Asymptomatic foliar fungal endophytes are a major component of the plant microbiome and are increasingly recognized for their impacts on plant performance, including pathogen defense, hormonal manipulation, and drought tolerance. However, it remains unclear whether fungal endophytes preferentially colonize certain host ecotypes or genotypes, reflecting some degree of biotic adaptation in the symbioses, or whether colonization is simply a function of spore type and abundance within the local environment. Whether host ecotype, local environment, or some combination of both controls the pattern of microbiome formation across hosts represents a new dimension to the age-old debate of nature versus nurture. Here, we used a reciprocal transplant design to explore the extent of host specificity and biotic adaptation in the plant microbiome, as evidenced by differential colonization of host genetic types by endophytes. Specifically, replicate plants from three locally-adapted ecotypes of the native grass Panicum virgatum (switchgrass) were transplanted at three geographically distinct field sites (one home and two away) in the Midwestern US. At the end of the growing season, plant leaves were harvested and the fungal microbiome characterized using culture-dependent sequencing techniques. Our results demonstrated that fungal endophyte community structure was determined by local environment (i.e., site), but not by host ecotype. Fungal richness and diversity also strongly differed by site, with lower fungal diversity at a riparian field site, whereas host ecotype had no effect. By contrast, there were significant differences in plant phenotypes across all ecotypes and sites, indicating ecotypic differentiation of host phenotype. Overall, our results indicate that environmental factors are the primary drivers of community structure in the switchgrass fungal microbiome.

Accumulation and potential health risks of cadmium, lead and arsenic in vegetables grown near mining sites in Northern Vietnam.

The effect of environmental pollution on the safety of vegetable crops is a serious global public health issue. This study was conducted to assess heavy metal concentrations in soil, irrigation water, and 21 local vegetable species collected from four sites near mining activities and one control site in Northern Vietnam. Soils from vegetable fields in the mining areas were contaminated with cadmium (Cd), lead (Pb), and arsenic (As), while irrigation water was contaminated with Pb. Average concentrations of Pb and As in fresh vegetable samples collected at the four mining sites exceeded maximum levels (MLs) set by international food standards for Pb (70.6 % of vegetable samples) and As (44.1 % of vegetable samples), while average Cd concentrations in vegetables at all sites were below the MLs of 0.2. The average total target hazard quotient (TTHQ) across all vegetable species sampled was higher than the safety threshold of 1.0, indicating a health risk. Based on the weight of evidence, we find that cultivation of vegetables in the studied mining sites is an important risk contributor for local residents' health.

Plant-soil feedbacks shift from negative to positive with decreasing light in forest understory species.

Net pairwise plant-soil feedbacks (PSF) may be an important factor structuring plant communities, yet the influence of abiotic context on PSF is not yet understood. Abiotic factors such as light availability can alter plant-soil interactions, potentially resulting in strong context dependence of PSF. Here, we present an experiment in which we measured whole-soil net pairwise feedbacks amongst six common forest understory species across a gradient of light availability. Light treatments were imposed throughout both phases (the conditioning phase and the response phase) of the feedback experiment. Across the plant community, PSF shifted from negative at high light availability to weakly positive under low light (P = 0.0 13). Differences in the biomass of plants during the conditioning phase did not fully explain light-imposed differences in feedbacks, indicating that reduced light availability qualitatively changes the nature of PSF rather than simply weakening feedbacks by reducing plant growth. Results indicate that abiotic context can fundamentally alter the role of PSF in structuring plant communities.

Think globally, research locally: paradigms and place in agroecological research.

Conducting science for practical ends implicates scientists, whether they wish it or not, as agents in social-ecological systems, raising ethical, economic, environmental, and political issues. Considering these issues helps scientists to increase the relevance and sustainability of research outcomes. As we rise to the worthy call to connect basic research with food production, scientists have the opportunity to evaluate alternative food production paradigms and consider how our research funds and efforts are best employed. In this contribution, we review some of the problems produced by science conducted in service of industrial agriculture and its associated economic growth paradigm. We discuss whether the new concept of "ecological intensification" can rescue the industrial agriculture/growth paradigm and present an emerging alternative paradigm of decentralized, localized, biodiversity-promoting agriculture for a steady-state economy. This "custom fit" agriculture engages constructively with complex and highly localized ecosystems, and we draw from examples of published work to demonstrate how ecologists can contribute by using approaches that acknowledge local agricultural practices and draw on community participation.

Nitrogen-fixing bacteria, arbuscular mycorrhizal fungi, and the productivity and structure of prairie grassland communities.

Due to their complementary roles in meeting plant nutritional needs, arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing bacteria (N(2)-fixers) may have synergistic effects on plant communities. Using greenhouse microcosms, we tested the effects of AMF, N(2)-fixers (symbiotic: rhizobia, and associative: Azospirillum brasilense), and their potential interactions on the productivity, diversity, and species composition of diverse tallgrass prairie communities and on the productivity of Panicum virgatum in monoculture. Our results demonstrate the importance of AMF and N(2)-fixers as drivers of plant community structure and function. In the communities, we found a positive effect of AMF on diversity and productivity, but a negative effect of N(2)-fixers on productivity. Both AMF and N(2)-fixers affected relative abundances of species. AMF shifted the communities from dominance by Elymus canadensis to Sorghastrum nutans, and seven other species increased in abundance with AMF, accounting for the increased diversity. N(2)-fixers led to increases in Astragalus canadensis and Desmanthus illinoense, two legumes that likely benefited from the presence of the appropriate rhizobia symbionts. Sorghastrum nutans declined 44 % in the presence of N(2)-fixers, with the most likely explanation being increased competition from legumes. Panicum monocultures were more productive with AMF, but showed no response to N(2)-fixers, although inference was constrained by low Azospirillum treatment effectivity. We did not find interactions between AMF and N(2)-fixers in communities or Panicum monocultures, indicating that short-term effects of these microbial functional groups are additive.

Resource heterogeneity, soil fertility, and species diversity: effects of clonal species on plant communities.

Spatial heterogeneity in soil resources is widely thought to promote plant species coexistence, and this mechanism figures prominently in resource-ratio models of competition. However, most experimental studies have found that nutrient enhancements depress diversity regardless of whether nutrients are uniformly or heterogeneously applied. This mismatch between theory and empirical pattern is potentially due to an interaction between plant size and the scale of resource heterogeneity. Clonal plants that spread vegetatively via rhizomes or stolons can grow large and may integrate across resource patches, thus reducing the positive effect of small-scale resource heterogeneity on plant species richness. Many rhizomatous clonal species respond strongly to increased soil fertility, and they have been hypothesized to drive the descending arm of the hump-shaped productivity-diversity relationship in grasslands. We tested whether clonals reduce species richness in a grassland community by manipulating nutrient heterogeneity, soil fertility, and the presence of rhizomatous clonal species in a 6-year field experiment. We found strong and consistent negative effects of clonals on species richness. These effects were greatest at high fertility and when soil resources were applied at a scale at which rhizomatous clonals could integrate across resource patches. Thus, we find support for the hypothesis that plant size and resource heterogeneity interact to determine species diversity.

Perturbations alter community convergence, divergence, and formation of multiple community states.

Environmental perturbations (e.g., disturbance, fertilization) commonly shift communities to a new mean state, but much less is known about their effects on the variability (dispersion) of communities around the mean, particularly when perturbations are combined. Community dispersion may increase or decrease (representing a divergence or convergence among communities) if changing environmental conditions alter species interactions or magnify small initial differences that develop during community assembly. We used data from an experimental study of disturbance and fertilization in a low-productivity grassland to test how these two perturbations affect patterns of species composition and abundance. We found that a one-time biomass reduction decreased community dispersion, which persisted over four growing seasons. Conversely, continuous fertilization increased community dispersion and, when combined with disturbance, led to the formation of three distinct community states. These results illustrate that perturbations can have differing effects on community dispersion. Attention to the variance in community responses to perturbations lends insight into how ecological interactions determine community structure, which may be missed when focusing only on mean responses. Furthermore, multiple perturbations may have complex effects on community dispersion, yielding convergence or divergence patterns that are difficult to predict based on analysis of single factors.

Cytochrome c552 mutants: structure and dynamics at the active site probed by multidimensional NMR and vibration echo spectroscopy.

Spectrally resolved infrared stimulated vibrational echo experiments are used to measure the vibrational dephasing of a CO ligand bound to the heme cofactor in two mutated forms of the cytochrome c552 from Hydrogenobacter thermophilus. The first mutant (Ht-M61A) is characterized by a single mutation of Met61 to an Ala (Ht-M61A), while the second variant is doubly modified to have Gln64 replaced by an Asn in addition to the M61A mutation (Ht-M61A/Q64N). Multidimensional NMR experiments determined that the geometry of residue 64 in the two mutants is consistent with a non-hydrogen-bonding and hydrogen-bonding interaction with the CO ligand for Ht-M61A and Ht-M61A/Q64N, respectively. The vibrational echo experiments reveal that the shortest time scale vibrational dephasing of the CO is faster in the Ht-M61A/Q64N mutant than that in Ht-M61A. Longer time scale dynamics, measured as spectral diffusion, are unchanged by the Q64N modification. Frequency-frequency correlation functions (FFCFs) of the CO are extracted from the vibrational echo data to confirm that the dynamical difference induced by the Q64N mutation is primarily an increase in the fast (hundreds of femtoseconds) frequency fluctuations, while the slower (tens of picoseconds) dynamics are nearly unaffected. We conclude that the faster dynamics in Ht-M61A/Q64N are due to the location of Asn64, which is a hydrogen bond donor, above the heme-bound CO. A similar difference in CO ligand dynamics has been observed in the comparison of the CO derivative of myoglobin (MbCO) and its H64V variant, which is caused by the difference in axial residue interactions with the CO ligand. The results suggest a general trend for rapid ligand vibrational dynamics in the presence of a hydrogen bond donor.

Mycorrhizal fungal identity and richness determine the diversity and productivity of a tallgrass prairie system.

We investigated the effects of arbuscular mycorrhizal fungal (AMF) species richness and composition on plant community productivity and diversity, and whether AMF mediate plant species coexistence by promoting niche differentiation in phosphorus use. Our experiment manipulated AMF species richness and identity across a range of P conditions in tallgrass prairie mesocosms. We showed that increasing AMF richness promoted plant diversity and productivity, but that this AMF richness effect was small relative to the effects of individual AMF species. We found little support for AMF-facilitated complementarity in P use. Rather, the AMF richness effect appeared to be caused by the inclusion of particular diversity- and productivity-promoting AMF (a sampling effect). Furthermore, the identity of the diversity-promoting fungi changed with P environment, as did the relationship between the diversity-promoting and productivity-promoting benefits of AMF. Our results suggest that plant diversity and productivity are more responsive to AMF identity than to AMF diversity per se, and that AMF identity and P environment can interact in complex ways to alter community-level properties.

Variable responses of old-field perennials to arbuscular mycorrhizal fungi and phosphorus source.

If arbuscular mycorrhizal fungi (AMF) promote phosphorus partitioning of plant hosts, they could provide one mechanism for the maintenance of plant community diversity. We investigated whether AMF improved the ability of old field perennials to grow on a range of phosphorus sources and whether AMF facilitated differential performance of plant species on different phosphorus sources (phosphorus niche partitioning). We manipulated form of phosphorus (control versus different inorganic and organic sources) and AM fungal species (control versus four individual AMF species or an AMF community) for five old field perennials grown in a greenhouse in individual culture. Based on biomass after four months of growth, we found no evidence for phosphorus niche partitioning. Rather, we found that effects of AMF varied from parasitic to mutualistic depending on plant species, AMF species, and phosphorus source (significant Plant x Fungus x Phosphorus interaction). Our results suggest that the degree of AMF benefit to a plant host depends not only on AMF species, plant species, and soil phosphorus availability (as has also been found in other work), but can also depend on the form of soil phosphorus. Thus, the position of any AMF species along the mutualism to parasitism continuum may be a complex function of local conditions, and this has implications for understanding plant competitive balance in the field.

Arbuscular mycorrhizal fungi do not enhance nitrogen acquisition and growth of old-field perennials under low nitrogen supply in glasshouse culture.

Arbuscular mycorrhizal fungi (AMF) are known to promote plant growth when phosphorus is limiting, but the role of AMF in plant growth under nitrogen (N) limiting conditions is unclear. Here, we manipulated N (control vs inorganic and organic forms) and AMF species (control vs four AMF species) for five old-field perennials grown individually in a glasshouse under N-limiting conditions. We found that AMF were at best neutral and that some AMF species depressed growth for some plant species (significant plant-fungus interaction). Native plant species growth was strongly depressed by all but one AMF species; exotic plant species were less sensitive to AMF. We found no evidence of plant N preferences. Both natives and exotics were able to acquire more N with N addition, but only exotics grew more with added N. Our results suggest that AMF do not promote plant N acquisition at low N supply, and our results are consistent with other research showing that AMF can act as a parasitic carbon drain when phosphorus availability is relatively high.

Root foraging for patchy resources in eight herbaceous plant species.

The root foraging strategy of a plant species can be characterized by measuring foraging scale, precision, and rate. Trade-offs among these traits have been predicted to contribute to coexistence of competitors. We tested for trade-offs among root foraging scale (total root mass and length of structural roots), precision (ln-ratio of root lengths in resource-rich and resource-poor patches), and rate (days required for roots to reach a resource-rich patch, or growth rate of roots within a resource-rich patch) in eight co-occurring species. We found that root foraging scale and precision were positively correlated, as were foraging scale and the rate of reaching patches. High relative growth rate of a species did not contribute to greater scale, precision, or rate of root foraging. Introduced species had greater foraging scale, precision, and rate than native species. The positive correlations between foraging scale and foraging precision and rate may give larger species a disproportionate advantage in competition for patchy soil resources, leading to size asymmetric competition below ground.