Biology subjects

McAllister, S. M.

Publications and source records attributed to McAllister, S. M..

10 recordsLinked to original sources

bioRxiv2026

MagicLamp: a web server and software toolkit for targeted gene annotation of microbial functions

Genome and metagenome annotation tools designed for large databases are ill-suited to the discovery of specialized, ecologically relevant microbial functions. MagicLamp (https://github.com/Arkadiy-Garber/MagicLamp) is a modular command-line software toolkit that performs targeted functional gene annotation searches using curated collections of hidden Markov models (HMMs), each representing discrete microbial metabolic processes. MagicLamp is also available as a web server: https://midauthorbio.com/#magiclamp. This targeted approach enables sensitive and specific annotation of genes involved in defined microbial processes, allowing MagicLamp to serve as a dedicated repository for the annotation of specialized microbial functions currently overlooked in other databases and software. The server accepts unannotated genome assemblies or GenBank-formatted annotations to perform HMM-based searches against curated model sets with reproducible, model-specific bit-score thresholds. Automated results are returned as tabular summaries and interactive HTML reports containing cross-genome/metagenome comparisons.

bioinformatics↗

bioRxiv2026

Molecular Star Gazing: Development and Validation of an Environmental DNA Assay for the Imperiled Sunflower Sea Star (Pycnopodia helianthoides)

The sunflower sea star (Pycnopodia helianthoides) suffered a catastrophic population decline across its range from 2013 to 2017 due to the devastating Vibrio pectenicida FHCF-3 driven sea star wasting disease (SSWD) pandemic with minimal signs of population recovery. The functional extinction of this apex predator across substantial parts of its range has created a need to identify and track the remaining intact populations. Environmental DNA (eDNA) approaches provide a simple, cost-effective, and non-destructive method for monitoring occurrences, and in some cases abundances, of marine species, consistently outperforming visual occurrence monitoring efforts in sensitivity, speed, and cost. Here, we designed, developed, and validated a P. helianthoides-specific eDNA assay to identify refugia, using both quantitative and digital droplet PCR approaches. We first generated the most comprehensive sea star mitochondrial genome reference database to date (n=93 taxa, n= 15 novel). We then used unikseq and Geneious bioinformatics software to identify the unique nad5 gene region and design a highly specific hydrolysis probe-based PCR assay. We validated the performance of this assay through laboratory, mesocosm, and field testing, demonstrating a highly specific and sensitive assay. In a field application of the new assay across regions in British Columbia, Canada, we found a positive correlation between P. helianthoides eDNA concentrations and biomass density, especially when appropriately accounting for spatiotemporal integration scales (R2=0.67). The eDNA assay provides a rapid and scalable tool for monitoring the sunflower sea star which has been proposed for listing as threatened under the U.S. Endangered Species Act of 1973. Molecular tools like the one presented here enhance management and recovery efforts not only by identification and monitoring of remnant wild populations, but also by helping to assess population level response and recovery following reintroduction efforts.

molecular biology↗

bioRxiv2021

SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

Shotgun sequencing of cultured microbial isolates/individual eukaryotes (whole-genome sequencing) and microbial communities (metagenomics) has become commonplace in biology. Very often, sequenced samples encompass organisms spanning multiple domains of life, necessitating increasingly elaborate software for accurate taxonomic classification of assembled sequences. While many software tools for taxonomic classification exist, SprayNPray offers a quick and user-friendly, semiautomated approach, allowing users to separate contigs by taxonomy (and other metrics) of interest. Easy installation, usage, and intuitive output, which is amenable to visual inspection and/or further computational parsing, will reduce barriers for biologists beginning to analyze genomes and metagenomes. This approach can be used for broad-level overviews, preliminary analyses, or as a supplement to other taxonomic classification or binning software. SprayNPray profiles contigs using multiple metrics, including closest homologs from a user-specified reference database, gene density, read coverage, GC content, tetranucleotide frequency, and codon-usage bias. The output from this software is designed to allow users to spot-check metagenome-assembled genomes, identify, and remove contigs from putative contaminants in isolate assemblies, identify bacteria in eukaryotic assemblies (and vice-versa), and identify possible horizontal gene transfer events.

bioinformatics↗

bioRxiv2019

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms, and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earths crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and the associated surge in publicly-available sequence data has now made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition and utilization in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) that is based on genes related to iron acquisition, storage, and reduction/oxidation. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate the provided datasets with respect to iron-related genes and gene clusters. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenies database will be maintained and continually-updated as new genetic markers are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.

bioinformatics↗

bioRxiv2019

Validating the Cyc2 neutrophilic Fe oxidation pathway using meta-omics of Zetaproteobacteria iron mats at marine hydrothermal vents

Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe-oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans. However, Cyc2 function is not well verified in neutrophilic Fe-oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe-oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions, and in incubations. The putative Fe oxidase gene, cyc2, was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.

microbiology↗

bioRxiv2018

Marine Fe-oxidizing Zetaproteobacteria: Historical, ecological, and genomic perspectives

The Zetaproteobacteria are a class of bacteria typically associated with marine Fe oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal sediments, other marine subsurface environments, steel corrosion biofilms, as well as saline terrestrial aquifers and springs. Isolates from a range of environments all grow by Fe oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe oxidation at the low O2 concentrations common to Fe(II)-rich oxic/anoxic transition zones. Also, Zetaproteobacteria make a variety of biomineral morphologies as a repository for Fe(III) waste, and as attachment structures. To determine the known diversity of the Zetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While some Zetaproteobacteria taxa appear to be cosmopolitan, various habitats enrich for different sets of Zetaproteobacteria. OTU networks show that certain Zetaproteobacteria co-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2, and nitrate availability, based on genomic analyses. Also, a putative Fe oxidation gene has been found in diverse Zetaproteobacteria taxa, suggesting that the Zetaproteobacteria evolved as specialists in Fe oxidation. In all, culture, genomic, and environmental studies suggest that Zetaproteobacteria are widespread, and therefore have a broad influence on marine and saline terrestrial Fe cycling.

microbiology↗

bioRxiv2018

ZetaHunter: a reproducible taxonomic classification tool for tracking the ecology of the Zetaproteobacteria and other poorly-resolved taxa

Like many taxa, the Zetaproteobacteria lack well-defined taxonomic divisions, 32 making it difficult to compare between studies. We designed ZetaHunter to reproducibly 33 assign 16S rRNA gene sequences to previously-described OTUs based on a curated 34 database. While ZetaHunter can use any given database, we include a curated 35 classification of publically-available Zetaproteobacteria.

bioinformatics↗

bioRxiv2018

Fe oxidation by a fused cytochrome-porin common to diverse Fe-oxidizing bacteria

Iron (Fe) oxidation is one of Earths major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron-oxidizers. The genomes of many, diverse iron-oxidizers encode a homolog to an outer-membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron-oxidizer Mariprofundus ferrooxydans PV-1. Cyc2PV-1 is capable of oxidizing iron, and its redox potential is 208 {+/-} 20 mV, consistent with the ability to accept electrons from Fe2+ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. Sequence analysis and modeling reveal the entire Cyc2 family share a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. Based on structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe2+, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron-oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism. ImportanceIron is practically ubiquitous across Earths environments, central to both life and geochemical processes, which depend heavily on the redox state of iron. Although iron oxidation, or "rusting," can occur abiotically at near neutral pH, we find neutrophilic iron-oxidizing bacteria (FeOB) are widespread, including in aquifers, sediments, hydrothermal vents, pipes, and water treatment systems. FeOB produce highly reactive Fe(III) oxyhydroxides that bind a variety of nutrients and toxins, thus these microbes are likely a controlling force in iron and other biogeochemical cycles. There has been mounting evidence that Cyc2 functions as an iron oxidase in neutrophiles, but definitive proof of its function has long eluded us. This work provides conclusive biochemical evidence of iron oxidation by Cyc2 from neutrophiles. Cyc2 is common to a wide variety of iron-oxidizers, including acidophilic and phototrophic iron-oxidizers, suggesting that this fused cytochrome-porin structure is especially well-adapted for iron oxidation.

microbiology↗

bioRxiv2017

A biological source of marine sedimentary iron oxides

The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although reductive biological processes that bridge the iron cycle to other element cycles are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments--resulting in the formation of iron oxides. Here, we show that a major source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, stimulated by burrowing animals in coastal sediments. Zetaproteobacteria were estimated to be a global total of 1026 cells in coastal, bioturbated sediments and would equate to an annual production of approximately 7.9 x 1015 grams of sedimentary iron oxides--twenty-five times larger than the annual flux of iron oxides by rivers. These data suggest that iron-oxidizing Zetaproteobacteria are keystone organisms in marine sedimentary environments given their low numerical abundance; yet exert a profound impact via the production of iron oxides.

microbiology↗

bioRxiv2017

Iroki: automatic customization for phylogenetic trees

Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Irokis utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Irokis source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.

bioinformatics↗