Corinne Walsh
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View article: Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities
Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities Open
Associations with soil microorganisms are crucial for plants’ overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, clima…
View article: Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities
Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities Open
Associations with soil microorganisms are crucial for plants’ overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, clima…
View article: Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology
Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology Open
Due to the complex nature of microbiome data, the field of microbial ecology has many current and potential uses for machine learning (ML) modeling. With the increased use of predictive ML models across many disciplines, including microbia…
View article: Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome
Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome Open
Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain uncle…
View article: Can we manipulate the soil microbiome to promote carbon sequestration in croplands?
Can we manipulate the soil microbiome to promote carbon sequestration in croplands? Open
Manipulating the microbiome of cropland soils has the potential to accelerate soil carbon sequestration, but strategies to do so need to be carefully vetted. Here, we highlight the general steps required to develop, implement, and validate…
View article: A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus
A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus Open
Sewage systems harbor extensive microbial diversity, including microbes derived from both human and environmental sources. Studies of the sewage microbiome are useful for monitoring public health and the health of our infrastructure, but t…
View article: Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome
Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome Open
Leaf surface-associated bacterial communities play a significant role in plant health and have therefore been the focus of increasing interest. Despite this, we currently lack a predictive understanding of how leaf-associated bacterial com…
View article: A metagenomic investigation of spatial and temporal changes in sewage microbiomes across a university campus
A metagenomic investigation of spatial and temporal changes in sewage microbiomes across a university campus Open
Wastewater microbial communities are not static and can vary significantly across time and space, but this variation and the factors driving the observed spatiotemporal variation often remain undetermined. We used a shotgun metagenomic app…
View article: Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes
Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes Open
Plants grown in distinct soils typically harbor distinct microbial communities, but the degree of the soil microbiome influence on plant microbiome assembly remains largely undetermined. We also know that the microbes associated with seeds…
View article: Table S2 representative sequences
Table S2 representative sequences Open
Fasta file containing representative sequences for ASVs listed in Table S2
View article: TableS2_metadata
TableS2_metadata Open
Sample Metadata for accompanying Table S2. Details for each Sample ID listed in Table S2.
View article: Table: representative sequences
Table: representative sequences Open
Fasta file containing representative sequences for ASVs listed in Table S2
View article: Table: metadata
Table: metadata Open
Sample Metadata for accompanying Table S2. Details for each Sample ID listed in Table S2.
View article: Table: Bacterial ASVs
Table: Bacterial ASVs Open
Bacterial ASV table in relative abundance. Includes bacterial taxa recovered from wheat seeds, wheat seedlings, and soil slurries. This data was used in analyses for the manuscript titled "Variable influences of soil and seed-associated ba…
View article: TableS2: Bacterial ASV Table
TableS2: Bacterial ASV Table Open
Bacterial ASV table in relative abundance. Includes bacterial taxa recovered from wheat seeds, wheat seedlings, and soil slurries. This data was used in analyses for the manuscript titled "Variable influences of soil and seed-associated ba…
View article: Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome
Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome Open
New enzymes often evolve by gene amplification and divergence. Previous experimental studies have followed the evolutionary trajectory of an amplified gene, but have not considered mutations elsewhere in the genome when fitness is limited …
View article: A Global Survey of Mycobacterial Diversity in Soil
A Global Survey of Mycobacterial Diversity in Soil Open
Mycobacteria are common inhabitants of soil, and while most members of this bacterial group are innocuous, some mycobacteria can cause environmentally acquired infections of humans and other animals. Human infections from nontuberculous my…
View article: Mutations that improve the efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome
Mutations that improve the efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome Open
New enzymes often evolve by amplification and divergence of genes encoding enzymes with a weak ability to provide a new function. Experimental studies to date have followed the evolutionary trajectory of an amplified gene, but have not add…
View article: A global survey of mycobacterial diversity in soil
A global survey of mycobacterial diversity in soil Open
Mycobacterium is a diverse bacterial genus ubiquitous in many soil and aquatic environments. Members of this genus have been associated with human and other animal diseases, including the nontuberculous mycobacteria (NTM), which are of gro…
View article: hsp65_ESV_table.csv.zip
hsp65_ESV_table.csv.zip Open
Data generated for marker gene analysis of a region of the hsp65 gene specifically targeting mycobacteria. For detailed PCR and sequence methods, see Gebert et al 2018. Briefly, a two-step PCR approach was used with mycobacterial-specific …
View article: 16S_OTU_table.txt.zip
16S_OTU_table.txt.zip Open
The V3-V4 hypervariable region of the bacterial 16SrRNA gene was amplified with 341F/805R primers. For detailed sequencing methods, see Delgado-Baquerizo et al 2018. Data were processed using the USEARCH10 pipeline. Unique sequences were i…