Disturbance reduces the differentiation of mycorrhizal fungal communities in grasslands along a precipitation gradient

Given that mycorrhizal fungi play key roles in shaping plant communities, greater attention should be focused on factors that determine the composition of mycorrhizal fungal communities and their sensitivity to anthropogenic disturbance. We investigate changes in arbuscular mycorrhizal (AM) fungal community composition across a precipitation gradient in North American grasslands as well as changes occurring with varying degrees of site disturbance that have resulted in invasive plant establishment. We find strong differentiation of AM fungal communities in undisturbed remnant grasslands across the precipitation gradient, whereas communities in disturbed grasslands were more homogeneous. These changes in community differentiation with disturbance are consistent with more stringent environmental filtering of AM fungal communities in undisturbed sites that may also be promoted by more rigid functional constraints imposed on AM fungi by the native plant communities in these areas. The AM fungal communities in eastern grasslands were particularly sensitive to anthropogenic disturbance, with disturbed sites having low numbers of AM fungal operational taxonomic units (OTUs) commonly found in undisturbed sites, and also the proliferation of AM fungal OTUs in disturbed sites. This proliferation of AM fungi in eastern disturbed sites coincided with increased soil phosphorus availability and is consistent with evidence suggesting the fungi represented by these OTUs would provide reduced benefits to native plants. The differentiation of AM fungal communities along the precipitation gradient in undisturbed grasslands but not in disturbed sites is consistent with AM fungi aiding plant adaptation to climate, and suggests they may be especially important targets for conservation and restoration in order to help maintain or re-establish diverse grassland plant communities.This work was supported by Strategic Environmental Research and Development Program (SERDP) grant RC-2330 to J. D. BeverNational Science Foundation grant DEB-1556664 to J. D. Beve

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora. However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. IMPORTANCE Arbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over- or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account

Root pathogen diversity and composition varies with climate in undisturbed grasslands, but less so in anthropogenically disturbed grasslands

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

Arbuscular Mycorrhizal Fungi Taxa Show Variable Patterns of Micro-Scale Dispersal in Prairie Restorations

Human land use disturbance is a major contributor to the loss of natural plant communities, and this is particularly true in areas used for agriculture, such as the Midwestern tallgrass prairies of the United States. Previous work has shown that arbuscular mycorrhizal fungi (AMF) additions can increase native plant survival and success in plant community restorations, but the dispersal of AMF in these systems is poorly understood. In this study, we examined the dispersal of AMF taxa inoculated into four tallgrass prairie restorations. At each site, we inoculated native plant species with greenhouse-cultured native AMF taxa or whole soil collected from a nearby unplowed prairie. We monitored AMF dispersal, AMF biomass, plant growth, and plant community composition, at different distances from inoculation. In two sites, we assessed the role of plant hosts in dispersal, by placing known AMF hosts in a “bridge” and “island” pattern on either side of the inoculation points. We found that AMF taxa differ in their dispersal ability, with some taxa spreading to 2-m in the first year and others remaining closer to the inoculation point. We also found evidence that AMF spread altered non-inoculated neighboring plant growth and community composition in certain sites. These results represent the most comprehensive attempt to date to evaluate AMF spread

A motif-based approach to network epidemics

Networks have become an indispensable tool in modelling infectious diseases, with the structure of epidemiologically relevant contacts known to affect both the dynamics of the infection process and the efficacy of intervention strategies. One of the key reasons for this is the presence of clustering in contact networks, which is typically analysed in terms of prevalence of triangles in the network. We present a more general approach, based on the prevalence of different four-motifs, in the context of ODE approximations to network dynamics. This is shown to outperform existing models for a range of small world networks

Security: Collective good or commodity?

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2008 Sage.The state monopoly on the legitimate use of violence in Europe and North America has been central to the development of security as a collective good. Not only has it institutionalized the state as the prime national and international security provider, it has helped to reduce the threat from other actors by either prohibiting or limiting their use of violence. The recent growth of the private security industry appears to undermine this view. Not only are private security firms proliferating at the national level; private military companies are also taking over an increasing range of military functions in both national defence and international interventions. This article seeks to provide an examination of the theoretical and practical implications of the shift from states to markets in the provision of security. Specifically, it discusses how the conceptualization of security as a commodity rather than a collective good affects the meaning and implementation of security in Western democracies.ESR

Primary Care Physicians’ Experience and Confidence with Genetic Testing and Perceived Barriers to Genomic Medicine

Purpose: Genetic testing is progressing towards use of patients’ genomes for personalized medicine. Primary care physicians (PCPs) may use genetic tests to screen and assess risk. However, PCPs’ current preparedness for the expanding integration of genetics into practice is uncharacterized. We examined primary care physicians’ perceptions of and experience with genetic testing. Methods: An anonymous survey was mailed to PCPs across three regional health networks querying opinions of, experience with, confidence in, and perceived barriers to genetic testing. Results: The survey response rate was 37.8%. Respondents believed learning about new genetic advances was important to clinical practice (67.0%). A minority (19.0%) had ordered genetic testing in six months, with cancer risk testing the most frequently ordered. Respondents were not confident in the skills required for using genetic testing in practice. Few respondents felt that they had time to counsel about genetic risk (9.5%) or that most patients could comprehend the concept of risk (27.0%). Conclusions: Primary care physicians had a high opinion of using genetic testing in medicine, but reported little experience or confidence incorporating genetic testing into practice. A majority perceived time constraints and patient comprehension as barriers. These data demonstrate a need for genetics educational resources for physicians and patients

Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm

Citation: Boyles, R. E., Cooper, E. A., Myers, M. T., Brenton, Z., Rauh, B. L., Morris, G. P., & Kresovich, S. (2016). Genome-Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm. Plant Genome, 9(2), 17. doi:10.3835/plantgenome2015.09.0091Grain yield and its primary determinants, grain number and weight, are important traits in cereal crops that have been well studied; however, the genetic basis of and interactions between these traits remain poorly understood. Characterization of grain yield per primary panicle (YPP), grain number per primary panicle (GNP), and 1000-grain weight (TGW) in sorghum [Sorghum bicolor (L.) Moench], a hardy C-4 cereal with a genome size of similar to 730 Mb, was implemented in a diversity panel containing 390 accessions. These accessions were genotyped to obtain 268,830 single-nucleotide polymorphisms (SNPs). Genome-wide association studies (GWAS) were performed to identify loci associated with each grain yield component and understand the genetic interactions between these traits. Genome-wide association studies identified associations across the genome with YPP, GNP, and TGW that were located within previously mapped sorghum QTL for panicle weight, grain yield, and seed size, respectively. There were no significant associations between GNP and TGW that were within 100 kb, much greater than the average linkage disequilibrium (LD) in sorghum. The identification of nonoverlapping loci for grain number and weight suggests these traits may be manipulated independently to increase the grain yield of sorghum. Following GWAS, genomic regions surrounding each associated SNP were mined for candidate genes. Previously published expression data indicated several TGW candidate genes, including an ethylene receptor homolog, were primarily expressed within developing seed tissues to support GWAS. Furthermore, maize (Zea mays L.) homologs of identified TGW candidates were differentially expressed within the seed between small- and large-kernel lines from a segregating maize population