Biology subjects

Kent, A. D.

Publications and source records attributed to Kent, A. D..

5 recordsLinked to original sources

bioRxiv2024

Contrasting Rhizosphere Nitrogen Dynamics in Andropogoneae Grasses: Implications for Sustainable Agriculture

Background: Nitrogen (N) fertilization in crop production significantly impacts ecosystems, often disrupting natural plant-microbe-soil interactions and causing environmental pollution. Our research tested the hypothesis that phylogenetically related perennial grasses might preserve rhizosphere management strategies conducive to a sustainable N economy for crops. Method: We analyzed the N cycle in the rhizospheres of 36 Andropogoneae grass species related to maize and sorghum, investigating their impacts on N availability and losses. This assay is supplemented with the collection and comparison of native habitat environment data for ecological inference as well as cross-species genomic and transcriptomic association analyses for candidate gene discovery. Result: Contrary to our hypothesis, all examined annual species, including sorghum and maize, functioned as N "Conservationists," reducing soil nitrification potential and conserving N. In contrast, some perennial species enhanced nitrification and leaching ("Leachers"). Yet a few other species exhibited similar nitrification stimulation effects but limited NO3- losses ("Nitrate Keepers"). We identified significant soil characteristics as influential factors in the eco- evolutionary dynamics of plant rhizospheres, and highlighted the crucial roles of a few transporter genes in soil N management and utilization. Conclusion: These findings serve as valuable guidelines for future breeding efforts for global sustainability.

plant biology↗

bioRxiv2023

Response of soil bacteria to PUREX chemicals suggests biomarker utility and bioremediation potential

Chemicals involved in plutonium uranium reduction extraction (PUREX) have the potential to be released from nuclear reprocessing facilities and accumulate in the environment. In order to understand how soil microbial communities respond to contamination by PUREX chemicals, we carried out a series of microcosm experiments, exposing chemically diverse soils to a range of concentrations of key chemicals used in the PUREX process. We tested 4 PUREX chemicals, and 5 soil types using 16S rRNA amplicon sequencing, determining that responses of microbial communities are dependent on the soil type in which they reside, and that tributyl phosphate exposure appears to generate the most reproducible and detectable shifts in microbial communities. We identified a number of key taxa that are consistently enriched in soils exposed to tributyl phosphate. These key taxa are either in the family Rhizobiaceae or genus Pseudomonas. The relative abundance of these key taxa is concentration dependent, and their abundance remains elevated at least 100 days post initial exposure. Using whole-shotgun metagenomic sequencing, we reconstructed the genomes of these key taxa and find a number of putative phosphotriesterase genes found only in Rhizobiaceae. We find the abundance of phosphotriesterase genes is significantly higher in samples exposed to tributyl phosphate. These phosphotriesterase genes, which degrade tributyl phosphate into dibutyl phosphate and butanol, may serve as effective biomarkers for tributyl phosphate contaminated soil, as well as a method for future bioremediation. ImportanceNuclear materials reprocessing facilities have the capacity to release toxic chemicals during normal operations or accidents. This study examines the ways in which chemicals involved with nuclear materials reprocessing impact microorganisms in the soil. Our intention was to understand the consequences of the release of these chemicals on ecosystems that may surround these reprocessing facilities. We find soil microbial communities change in response to some chemicals but not others, and that tributyl phosphate appears to generate the most reproducible and detectable shifts in microbial communities. Microorganisms in the family Rhizobiaceae increase in abundance in response to the addition of tributyl phosphate, and an examination of the genomes of these microbes suggest they may be able to break down tributyl phosphate to access the phosphosphate present in this chemical. Overall, this work demonstrates that changes in soil microbial communities in response to contamination with chemicals from nuclear materials reprocessing facilities may be predictable, and these responses could be leveraged to remediate contamination.

microbiology↗

bioRxiv2023

Genetic variation exists within Zea mays to influence unsustainable nitrogen cycling microbiome function

Overuse of synthetic nitrogen fertilizers in agroecosystems causes environmental pollution and human harm at a global level. Nitrogenous fertilizers provide a short-lived benefit to crops in the agroecosystem, but stimulate microbially-mediated nitrification and denitrification, processes that result in N pollution, greenhouse gas (GHG) production, and reduced soil fertility. Recent advances in plant microbiome science suggest that plants can modulate the composition and activity of rhizosphere microbial communities. These rhizosphere communities act as an extended phenotype, primed by genetic variation in the plant host. Genetic variation in traits (e.g., plant secondary metabolites, root architecture, immune system, etc.) act as mechanistic selective agents on the composition of the microbiome. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the extended phenotype of rhizosphere soil microbiome composition and function. Specifically, we determined whether plants influence on soil nitrogen cycling activities was altered by plant genetics and thereby allowing it to be incorporated into breeding practices. To capture an extensive amount of genetic diversity within maize we sampled the rhizosphere microbiome of a germplasm chronosequence that included ex-PVP inbreds, hybrids, and teosinte (Z. mays ssp. mexicana and Z. mays ssp. parviglumis). We observed that potential N cycling processes were influenced by plant genetics. Teosinte and some hybrid genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbreds stimulated/did not inhibit these undesirable N-cycling activities. These potential differences translated to functional differences in N2O production, with teosinte plots producing less GHG than maize plots. Furthermore, within these Zea cultivars we found that plant genetics explained a significant amount of variation in the microbiome, particularly among different nitrification and denitrification functional genes within the community. We found that potential nitrification, potential incomplete denitrification, and overall denitrification rates, but not abundance of N-cycling genes of rhizosphere soils were influenced by growth stage and plant genetics. Taken together, these results suggest that crop selection can lead to changes in root phenotypes that could suppress unsustainable N-cycling processes. Reintroducing stress-adapted and "wild" root characteristics into modern germplasm may be a way to manipulate soil microbiomes at both a composition and functional level to improve sustainability.

ecology↗

bioRxiv2022

Pyrophosphate-Mediated Repair of Damaged and Mismatched RNA by a Polymerase Ribozyme

Prior to the emergence of the contemporary biosphere, the first replicating systems are thought to have progressed through an RNA-based stage. Such an evolving world would likely have transferred heritable information during replication using RNA polymerase ribozymes. Though substantial effort has been put forth towards evolving RNA polymerases, many variants suffer from premature termination and low fidelity, resulting in low yields of full-length or active sequences. Replication of longer sequences requires a sufficiently high fidelity to lend an evolutionary advantage to an evolvable system. Here we demonstrate ribozyme-mediated repair of mismatched and damaged RNA sequences. Under conditions of saturating pyrophosphate concentrations, we show that a polymerase ribozyme can repair RNA sequences terminated in a mismatch, a non-extendable 2'-3' cyclic phosphate, or both, to generate a triphosphorylated nucleotide. This repair step increases the fidelity and allows polymerization along an extended template, including the ribozyme itself. This increase of copying fidelity advances the longstanding goal of developing a self-replicating polymerase ribozyme.

biochemistry↗

bioRxiv2022

A modular platform for bioluminescent RNA tracking

A complete understanding of RNA biology requires methods for tracking transcripts in vivo. Common strategies rely on fluorogenic probes that are limited in sensitivity, dynamic range, and depth of interrogation, owing to their need for excitation light and tissue autofluorescence. To overcome these challenges, we developed a bioluminescent platform for serial imaging of RNAs. Small RNA tags were engineered to recruit light-emitting luciferase fragments (termed RNA lanterns) upon transcription. Robust photon production was observed for RNA targets both in cells and in live animals. Importantly, only a single copy of the tag was necessary for sensitive detection, in sharp contrast to fluorescent platforms requiring multiple repeats. Overall, this work provides a foundational platform for visualizing RNA dynamics from the micro to the macro scale.

molecular biology↗