Biology subjects

Cregger, M. A.

Publications and source records attributed to Cregger, M. A..

4 recordsLinked to original sources

bioRxiv2026

RAPID: an interactive R/Shiny platform for end-to-end 16S rRNA and ITS amplicon sequence analysis using DADA2

MotivationAmplicon sequencing of 16S rRNA and internal transcribed spacer (ITS) gene regions is the most widely used approach for characterizing bacterial and fungal communities, respectively. The DADA2 pipeline has become a standard for inferring amplicon sequence variants (ASVs), offering single-nucleotide resolution over traditional OTU clustering. However, executing the full DADA2 workflow requires proficiency in R programming and manual coordination of multiple sequential steps, presenting a substantial barrier for researchers in clinical, environmental, and agricultural sciences who lack computational training. ResultsWe present RAPID (R-based Amplicon Pipeline for Interactive DADA2), a pair of R/Shiny applications providing complete graphical user interfaces for 16S rRNA and ITS amplicon sequence analysis. The 16S application implements a 10-step guided workflow from raw paired-end FASTQ files through quality filtering, error learning, dereplication, paired-read merging, chimera removal, taxonomy assignment (SILVA), phyloseq construction with data transformation (rarefaction, relative abundance, or CLR), interactive visualization (rarefaction curves, alpha diversity, NMDS, PCoA, taxonomic abundance), PERMANOVA, and ANCOM-BC2 differential abundance analysis. The ITS application extends this to an 11-step workflow, adding an automated primer removal step using cutadapt with support for multiple primers and length-variable amplicons, and uses the UNITE database for fungal taxonomy. Both applications feature asynchronous background processing, session persistence, real-time progress monitoring, publication-ready figure export, and comprehensive result downloads. AvailabilityRAPID is freely available at https://github.com/beantkapoor786/RAPID. Both applications can be installed locally on any system with R (version 4.0 or higher) and run as local web applications accessible through a standard browser.

bioinformatics↗

bioRxiv2025

Populus trichocarpa associated microbiomes vary across a natural temperature, elevation and rainfall gradient

Abiotic stresses associated with warming and drought are increasing in frequency and severity due to climate change. However, microbial associations can partially mitigate their adverse effects on plant physiology. We examined the bacterial/archaeal and fungal communities with 16S rRNA and ITS2 gene region amplicon sequencing of bulk soil, rhizosphere soil, and root endosphere samples of Populus trichocarpa trees from 11 sites along a 200 km transect with highly variable precipitation, temperature, and soil conditions over the Cascade Mountains in Washington, USA. Foliar stress response was examined with qRT-PCR and field physiological measurements. Soil conditions were examined with physiochemical sample analysis and site climate conditions were approximated using DAYMET. For each niche sampled, bacterial/archaeal and fungal communities clustered into three distinct micro-climate groups: a high-precipitation, low-stress community on the western side of the range, and two stressed climate communities: a high-elevation community nearer the crest of the pass, and a warmer and drier community along the eastern slope. The differences between these micro-climate communities, though still distinct, were notably diminished within the P. trichocarpa root endosphere, indicating that P. trichocarpa likely has a homogenizing effect on the microbiome under stress, but climate plays a major role in shaping these microbial communities.

ecology↗

bioRxiv2024

Catabolic pathway acquisition by soil pseudomonads readily enables growth with salicyl alcohol but does not affect colonization of Populus roots

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally reproduced one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol into soil isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferred by HGT but is selectively neutral under environmentally-relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting, because the selective benefits are small and negative frequency-dependent.

microbiology↗

bioRxiv2019

One-time Nitrogen Fertilization Shifts Switchgrass Soil Microbiomes within a Context of Larger Spatial and Temporal Variation

Soil microbiome responses to short-term nitrogen (N) inputs within the context of existing spatio-temporal variability remain uncertain. Here, we examined soil bacterial and fungal communities pre/post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha-1 as NH4NO3) for the first time since planting. Soils were collected at two depths, 0-5 and 5-15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions, and soil metagenomic analysis. Baseline assessment prior to fertilization revealed no pre-existing differences in either bacterial or fungal communities across plots. The one-time N fertilization increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12-22 % of the variation in bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. Thus, variability within the field might override the changes induced by N addition. Continued analyses of these trends over time with fertilization and management are needed to understand whether these transient effects change over time.

ecology↗