Biology subjects

Walsh, C. M.

Publications and source records attributed to Walsh, C. M..

8 recordsLinked to original sources

bioRxiv2024

Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities

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, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 common sunflower (Helianthus annuus) genotypes from 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen Sclerotinia were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions. ImportanceDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial and fungal communities are driven primarily by site soil and climatic differences, but that genotype can interact with site to influence composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen Sclerotinia sclerotiorum were widespread but significantly affected by site, while a subset were also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial and fungal community assembly, and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.

ecology↗

bioRxiv2022

Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome

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 communities are structured within and across hosts, including how leaf traits shape this variation and how community assembly processes may differ across distinct microbial habitats on a leaf. In this study, we characterize the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces of 66 plants across 24 species grown at a common site using 16S rRNA amplicon sequencing. By comparing leaves that vary in pH and stomatal densities and analyzing the leaf surfaces separately, we were able to test the key factors shaping the phyllosphere across host plant species from diverse geographical origins. We found a surprisingly large shared/core microbiome across species, as well as a strong effect of plant species and native origin in shaping composition. Importantly, we found the lower leaf side, where pH values are generally lower and stomatal densities higher, to have lower taxonomic richness relative to the upper leaf side. While the upper leaf side community appears to be more strongly influenced by dispersal effects, the lower leaf appears to be more strongly influenced by plant host filtering effects, as supported by higher relative abundance of shared core taxa and higher signatures of endemism. This work highlights important differences in community assembly processes across the upper and lower leaf microbiomes and underscores the importance of considering differences among habitats within a host when explaining microbial community assembly and composition.

microbiology↗

bioRxiv2022

A metagenomic investigation of spatial and temporal changes in sewage microbiomes across a university campus

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 approach to investigate changes in wastewater microbial communities across 17 locations in a sewer network, with samples collected from each location over a 3-week period. Fecal-derived bacteria constituted a relatively small fraction of the taxa found in the collected samples, highlighting the importance of environmental sources to the sewage microbiome. The prokaryotic communities were highly variable in composition depending on the location within the sampling network and this spatial variation was most strongly associated with location-specific differences in sewage pH. However, we also observed substantial temporal variation in the composition of the prokaryotic communities at individual locations. This temporal variation was asynchronous across sampling locations, emphasizing the importance of independently considering both spatial and temporal variation when assessing the wastewater microbiome. The spatiotemporal patterns in viral community composition closely tracked those of the prokaryotic communities, allowing us to putatively identify the bacterial hosts of some of the dominant viruses in these systems. Finally, we found that antibiotic resistance gene profiles also exhibit a high degree of spatiotemporal variability with most of these genes unlikely to be derived from fecal bacteria. Together these results emphasize the dynamic nature of the wastewater microbiome, the challenges associated with studying these systems, and the utility of metagenomic approaches for building a multi-faceted understanding of these microbial communities and their functional attributes. ImportanceSewage 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 the sewage microbiome can be highly variable in ways that are often unresolved. We sequenced DNA recovered from wastewater samples collected over a 3-week period at 17 locations in a single sewer system to determine how these communities vary across time and space. Most of the wastewater bacteria, and the antibiotic resistance genes they harbor, were not derived from human feces, but human usage patterns did impact how the amounts and types of bacteria and bacterial genes we found in these systems varied over time. Likewise, the wastewater communities, including both bacteria and their viruses, varied depending on location within the sewage network, highlighting the challenges, and opportunities, in efforts to monitor and understand the sewage microbiome.

microbiology↗

bioRxiv2019

Neutrophils promote CXCR3-dependent itch in the development of atopic dermatitis

Chronic itch remains a highly prevalent disorder with limited treatment options. Most chronic itch diseases are thought to be driven by both the nervous and immune systems, but the fundamental molecular and cellular interactions that trigger the development of itch and the acute-to-chronic itch transition remain unknown. Here, we show that skin-infiltrating neutrophils are key initiators of itch in atopic dermatitis, the most prevalent chronic itch disorder. Neutrophil depletion significantly attenuated itch-evoked scratching in a mouse model of atopic dermatitis. Neutrophils were also required for several key hallmarks of chronic itch, including skin hyperinnervation, enhanced expression of itch signaling molecules, and upregulation of inflammatory cytokines, activity-induced genes, and markers of neuropathic itch. Finally, we demonstrate that neutrophils are required for induction of CXCL10, a ligand of the CXCR3 receptor that promotes itch via activation of sensory neurons, and we find that that CXCR3 antagonism attenuates chronic itch.

immunology↗

bioRxiv2019

Mutations that improve the efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome

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 addressed other mutations in the genome when fitness is limited by an evolving gene. We have adapted Escherichia coli in which an enzymes weak secondary activity has been recruited to serve an essential function. While the gene encoding the \"weak-link\" enzyme amplified in all eight populations, mutations improving the new activity occurred in only one. This beneficial allele quickly swept the amplified array, displacing the parental allele. Most adaptive mutations, however, occurred elsewhere in the genome. We have identified the mechanisms by which three of the classes of mutations increase fitness. These mutations may be detrimental once a new enzyme has evolved, and require reversion or compensation, leading to permanent changes in the genome.

evolutionary biology↗

bioRxiv2019

A global survey of mycobacterial diversity in soil

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 growing relevance to public health worldwide. Although soils are often considered an important source of environmentally-acquired NTM infections, the biodiversity and ecological preferences of soil mycobacteria remain largely unexplored across contrasting climates and ecosystem types. Using a culture-independent approach by combining 16S rRNA marker gene sequencing with mycobacterial-specific hsp65 gene sequencing, we analyzed the diversity, distributions, and environmental preferences of soil-dwelling mycobacteria in 143 soil samples collected from across the globe. The surveyed soils harbored highly diverse mycobacterial communities that span the full-extent of the known mycobacterial phylogeny, with most soil mycobacteria belonging to previously undescribed lineages. While the genus Mycobacterium tended to have higher relative abundances in cool, wet, and acidic soil environments, several individual mycobacterial clades had contrasting environmental preferences. We identified the environmental preferences of many mycobacterial clades, including the clinically-relevant M. avium complex that was more commonly detected in wet and acidic soils. However, most of the soil mycobacteria detected were not closely related to known pathogens, calling into question previous assumptions about the general importance of soil as a source of NTM infections. Together this work provides novel insights into the diversity, distributions and ecological preferences of soil mycobacteria, and lays the foundation for future efforts to link mycobacterial phenotypes to their distributions. ImportanceMycobacteria are common inhabitants of soil, and while most members of the bacterial genus are innocuous, some mycobacteria can cause environmentally-acquired infections of humans and other animals. Human infections from nontuberculous mycobacteria (NTM) are increasingly prevalent worldwide, and some areas appear to be hotspots for NTM disease. While exposure to soil is frequently implicated as an important mode of NTM transmission, the diversity, distributions and ecological preferences of soil mycobacteria remain poorly understood. We analyzed 143 soils from across the globe and found that the genus Mycobacterium and lineages within the genus often exhibited predictable preferences for specific environmental conditions. Soils harbor large amounts of previously-undescribed mycobacterial diversity, and lineages that include known pathogens were rarely detected in soil. Together these findings suggest that soil is an unlikely source of many mycobacterial infections. The biogeographical patterns we documented lend insight into the ecology of this important group of soil-dwelling bacteria.

microbiology↗

bioRxiv2019

Optical Metabolic Imaging of Heterogeneous Drug Response in Pancreatic Cancer Patient Organoids

New tools are needed to match pancreatic cancer patients with effective treatments. Patient-derived organoids offer a high-throughput platform to personalize treatments and discover novel therapies. Currently, methods to evaluate drug response in organoids are limited because they cannot be completed in a clinically relevant time frame, only evaluate response at one time point, and most importantly, overlook cellular heterogeneity. In this study, non-invasive optical metabolic imaging (OMI) of cellular heterogeneity in organoids was evaluated as a predictor of clinical treatment response. Organoids were generated from fresh patient tissue samples acquired during surgery and treated with the same drugs as the patient's prescribed adjuvant treatment. OMI measurements of heterogeneity in response to this treatment were compared to later patient response, specifically to the time to recurrence following surgery. OMI was sensitive to patient-specific treatment response in as little as 24 hours. OMI distinguished subpopulations of cells with divergent and dynamic responses to treatment in living organoids without the use of labels or dyes. OMI of organoids agreed with long-term therapeutic response in patients. With these capabilities, OMI could serve as a sensitive high-throughput tool to identify optimal therapies for individual pancreatic cancer patients, and to develop new effective therapies that address cellular heterogeneity in pancreatic cancer.

bioengineering↗

bioRxiv2019

Label-free Method for Classification of T cell Activation

T cells have a range of cytotoxic and immune-modulating functions, depending on activation state and subtype. However, current methods to assess T cell function use exogenous labels that often require cell permeabilization, which is limiting for time-course studies of T cell activation and non-destructive quality control of immunotherapies. Label-free optical imaging is an attractive solution. Here, we use autofluorescence imaging of NAD(P)H and FAD, co-enzymes of metabolism, to quantify optical imaging endpoints in quiescent and activated T cells. Machine learning classification models were developed for label-free, non-destructive determination of T cell activation state. T cells were isolated from the peripheral blood of human donors, and a subset were activated with a tetrameric antibody against CD2/CD3/CD28 surface ligands. NAD(P)H and FAD autofluorescence intensity and lifetime of the T cells were imaged using a multiphoton fluorescence lifetime microscope. Significant differences in autofluorescence imaging end-points were observed between quiescent and activated T cells. Feature selection methods revealed that the contribution of the short NAD(P)H lifetime (1) is the most important feature for classification of activation state, across multiple donors and T cell subsets. Logistic regression models achieved 97-99% accuracy for classification of T cell activation from the autofluorescence imaging endpoints. Additionally, autofluorescence imaging revealed NAD(P)H and FAD autofluorescence differences between CD3+CD8+ and CD3+CD4+ T cells, and random forest models of the autofluorescence imaging endpoints achieved 97+% accuracy for four-group classification of quiescent and activated CD3+CD8+ and CD3+CD4+ T cells. Altogether these results indicate that autofluorescence imaging of NAD(P)H and FAD is a powerful method for label-free, non-destructive determination of T cell activation and subtype, which could have important applications for the treatment of cancer, autoimmune, infectious, and other diseases.

bioengineering↗