The changing influence of host genetics on the leaf fungal microbiome throughout plant development

Host genetics and the environment influence which fungal microbes colonize a plant. A new study in PLOS Biology finds that the relative influence of these factors changes throughout the development of the biofuel crop switchgrass growing in field settings

The Age of the Woolly Rhino from Dream Cave, Derbyshire, UK

The Dream Cave woolly rhinoceros, Coelodonta antiquitatis, is a classic specimen of a cold-stage fossil fauna from central England. The find was illustrated and described by Dean William Buckland in his seminal tome Reliquiae Diluvianae (1823) during the first half of the 19th century, and made a significant contribution to the development of Buckland\u27s views on the origin of extinct and extirpated fossil vertebrates. The report presents the first, albeit indirect, radiometric dates on the specimen, and argues that the animal fell into the cave just before 37,000 years BP, during the middle of Marine Isotope Stage 3 Interstadial (41 - 39 ka BP)

Root-associated bacterial communities as an extended phenotype of the plant

Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. In my research I primarily wanted to test the hypothesis that plants that evolved to live in environments with different challenges also evolved the ability to associate with a unique microbiota as one means of overcoming these challenges. Despite great agronomic interest, genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly-understood. I first used extensive sequencing of ribosomal 16S rRNA genes to characterize bacterial populations from hundreds of roots of different genotypes of the model plant Arabidopsis thaliana grown in two wild (non-native) soils from North Carolina. These results demonstrated that soil type is the major determinant of the membership of the bacterial community in the rhizosphere and the community living inside roots, and that the developmental stage of the plant as well and the plant genotype actually have relatively minor effects on the colonization behavior of major bacterial taxonomies. Because in wild microbial communities bacteria with different genomic content may share a similar 16S rRNA gene, and because of limitations in the 16S sequencing technology, we were limited to statements about bacterial families, and could not say with confidence to which Arabidopsis genotypes individual strains of bacteria associated. This was a major limitation, because the presence or absence of specific bacterial genes may be a strong determinant of potential host genotypes for a given symbiont. Therefore, I developed technological improvements to increase the accuracy and depth of sequencing, while meanwhile culturing individual strains of bacteria from roots and creating a gnotobiotic system for growing plants in direct association with mixtures of cultured strains. Initial results from this system demonstrate that we can culture a wide diversity of root-associated bacteria and can successfully recolonize plants with complex but defined cocktails of bacteria. Experiments to explore microbe-by genotype association in this gnotobiotic system are underway.Doctor of Philosoph

Learning Microbial Interaction Networks from Metagenomic Count Data

Abstract Many microbes associate with higher eukaryotes and impact their vitality. To engineer microbiomes for host benefit, we must understand the rules of community assembly and maintenance that, in large part, demand an understanding of the direct interactions among community members. Toward this end, we have developed a Poisson-multivariate normal hierarchical model to learn direct interactions from the count-based output of standard metagenomics sequencing experiments. Our model controls for confounding predictors at the Poisson layer and captures direct taxon–taxon interactions at the multivariate normal layer using an ℓ1 penalized precision matrix. We show in a synthetic experiment that our method handily outperforms state-of-the-art methods such as SparCC and the graphical lasso (glasso). In a real in planta perturbation experiment of a nine-member bacterial community, we show our model, but not SparCC or glasso, correctly resolves a direct interaction structure among three community members that ..

Modelling of non uniform washcoat in catalytic monolith reactors

For advances in the design of exhaust aftertreatment systems, modelling can be a valuable tool. There have been various efforts in modelling the diesel oxidation catalyst (DOC) with varying degree of complexity. The simplest 1D models discretize the monolithic channel axially and use an effectiveness factor to account for different washcoat geometries. The more complex 1+1D models also resolve the catalyst washcoat which makes them able to better predict efficiency of e.g. layered catalysts. However, the vast majority of these 1+1D models assume the washcoat to be a uniform slab with homogeneous properties. Thus, they cannot identify tangential washcoat variations which have been found to have substantial effects on washcoat diffusivity (1). In this work a new parallel 1+1D reactor model has been developed. Similar to the sectionalizing method presented by Papadias et al (2), the washcoat is sliced into multiple tangential sections based on an evenly distributed angle. The model then solves each section of the washcoat independently – assuming that no mass is transferred between each section. Preliminary results (see figure 1) compare NO light-off simulations using the original 1+1D model and the parallel model using 3 sections. If the washcoat properties for each section are kept constant, then the conversion efficiency of the parallel model is slightly decreased because of the increased diffusive resistance of the thicker corners. However, if including the local porosity of each section (where the corners show a 13% increase in local porosity based on SEM images), the conversion efficiency of the parallel model is significantly higher because of the increased pore diffusivity in the corners. The proposed methodology enables analysis of local washcoat properties. The results are important for high performance modelling towards zero emission vehicles

Use of 3D-printed mixers in laboratory reactor design for modelling of heterogeneous catalytic converters

A method for identifying radial concentration maldistribution in synthetic catalyst activity test (SCAT) benches, is presented, where spatially resolved concentration measurements are not available. The developed methodology was successfully tested for an injection-based SCAT. To resolve the radial concentration maldistribution a static mixer was designed, 3D-printed and inserted upstream the test sample. The methodology could also prove the effectiveness of the mixer, which did not only resolve the concentration maldistribution but also avoided causing reaction disturbances. The resulting increased axial dispersion from the turbulence created by the static mixer was evaluated using a 3D CFD model in Ansys Fluent 19. The axial dispersion of the injection-based SCAT bench was compared to a premixed SCAT bench through classical Aris-Taylor calculations. The results from the axial dispersion calculations show that the injection-based design with the use of a static mixer is far superior to the premixed design – both with regards to pulse broadening but also time delay. This is highly desirable for modelling studies towards zero emission exhaust aftertreatment

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments

MT-Toolbox: improved amplicon sequencing using molecule tags

Abstract Background Short oligonucleotides can be used as markers to tag and track DNA sequences. For example, barcoding techniques (i.e. Multiplex Identifiers or Indexing) use short oligonucleotides to distinguish between reads from different DNA samples pooled for high-throughput sequencing. A similar technique called molecule tagging uses the same principles but is applied to individual DNA template molecules. Each template molecule is tagged with a unique oligonucleotide prior to polymerase chain reaction. The resulting amplicon sequences can be traced back to their original templates by their oligonucleotide tag. Consensus building from sequences sharing the same tag enables inference of original template molecules thereby reducing effects of sequencing error and polymerase chain reaction bias. Several independent groups have developed similar protocols for molecule tagging; however, user-friendly software for build consensus sequences from molecule tagged reads is not readily available or is highly specific for a particular protocol. Results MT-Toolbox recognizes oligonucleotide tags in amplicons and infers the correct template sequence. On a set of molecule tagged test reads, MT-Toolbox generates sequences having on average 0.00047 errors per base. MT-Toolbox includes a graphical user interface, command line interface, and options for speed and accuracy maximization. It can be run in serial on a standard personal computer or in parallel on a Load Sharing Facility based cluster system. An optional plugin provides features for common 16S metagenome profiling analysis such as chimera filtering, building operational taxonomic units, contaminant removal, and taxonomy assignments. Conclusions MT-Toolbox provides an accessible, user-friendly environment for analysis of molecule tagged reads thereby reducing technical errors and polymerase chain reaction bias. These improvements reduce noise and allow for greater precision in single amplicon sequencing experiments

Efficient Experimental Approach to Evaluate Mass Transfer Limitations for Monolithic DOCs

The diesel oxidation catalyst (DOC, Pt/γ-Al2O3) was used in a synthetic-gas catalyst test bench to study internal mass transfer limitations during NO oxidation. A simple and fast experimental methodology, by varying the washcoat thickness in monolithic DOCs was developed and the results were evaluated using various experimental time scales. The ratio between the reaction time constant and the washcoat diffusion time constant was useful in identifying temperatures where the DOCs tested transitioned between a kinetically controlled region and an internal mass transfer controlled region. The NO conversion was shown to be significantly limited by internal mass transfer already at 175\ua0\ub0C for an average washcoat thickness of 110\ua0\ub5m

HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing

HASTY, the plant ortholog of human exportin 5, was proposed to export miRNAs from the nucleus to the cytoplasm, whereas this has long been disputed. This study shows that HASTY, rather than acting as a miRNA cargo protein, promotes miRNA biogenesis by stabilizing a complex between DCL1 and Mediator at MIRNA loci, thereby acting as a linker between pri-miRNA transcription and processing.Fil: Cambiagno, Damián Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Giudicatti, Axel Joel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Arce, Agustín Lucas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Gagliardi, Delfina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Li, Lei. Institut Max Planck Fuer Gesellschaft. Institut Fur Entwicklungsbiolobie. Developmental Biology; AlemaniaFil: Yuan, Wei. Institut Max Planck Fuer Gesellschaft. Institut Fur Entwicklungsbiolobie. Developmental Biology; AlemaniaFil: Lundberg, Derek S.. Institut Max Planck Fuer Gesellschaft. Institut Fur Entwicklungsbiolobie. Developmental Biology; AlemaniaFil: Weigel, Detlef. Institut Max Planck Fuer Gesellschaft. Institut Fur Entwicklungsbiolobie. Developmental Biology; AlemaniaFil: Manavella, Pablo Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentin