Rachel Simister

Rachel Simister
University of British Columbia - Vancouver | UBC · Department of Microbiology and Immunology

PhD

About

79
Publications
15,244
Reads
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1,542
Citations
Citations since 2016
60 Research Items
1233 Citations
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Introduction
My research interests span the broad field of microbial interactions and ecology, incorporating varied disciplines such as molecular biology, phylogenetics, biogeochemistry and biotechnology. My work is highly interdisciplinary, centring on the analysis of microbial communities from a wide variety of environments and putting these comparisons in a temporal and spatial context. My research focuses on both free-living and host-associated bacteria and archaeal communities, as well as eukaryotic (fungal) microbial communities. My ultimate goal is to understand how microbes interact with their environment and in particular, how biogeochemical variables shape community structure and function.
Additional affiliations
May 2013 - May 2015
Haverford College
Position
  • PostDoc Position
March 2009 - October 2012
University of Auckland
Position
  • PhD

Publications

Publications (79)
Article
Full-text available
Dietary fibers are potent modulators of immune responses that can restrain inflammation in multiple disease contexts. However, dietary fibers encompass a biochemically diverse family of carbohydrates, and it remains unknown how individual fiber sources influence immunity. In a direct comparison of four different high-fiber diets, we demonstrate a p...
Preprint
Dietary fibers are potent modulators of immune responses that can restrain inflammation in multiple disease contexts. However, dietary fibers encompass a biochemically diverse family of carbohydrates, and it remains unknown how different fiber sources influence immunity. In a head-to-head comparison of four different high-fiber diets, we demonstrat...
Preprint
Autoimmune disorders like type 1 diabetes (T1D) are complex diseases caused by numerous factors including both genetic variance and environmental influences. Two such exogenous factors, intestinal microbial composition and enterovirus infection, have been independently associated with T1D onset in both humans and animal models. Since environmental...
Article
Full-text available
Methane produced by methanogenic archaea has an important influence on Earth’s changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochro...
Article
Recent evidence indicates that viral components of the microbiota can contribute to intestinal homeostasis and protection from local inflammatory or infectious insults. However, host-derived mechanisms that regulate the virome remain largely unknown. Here, we use colonization with the model commensal murine norovirus (MNV CR6) to interrogate host-d...
Article
Full-text available
Deposition of ferruginous sediment was widespread during the Archaean and Proterozoic Eons, playing an important role in global biogeochemical cycling. Knowledge of organic matter mineralization in such sediment, however, remains mostly conceptual, as modern ferruginous analogs are largely unstudied. Here we show that in sediment of ferruginous Lak...
Article
Full-text available
Subclinical bacterial infections (biofilms) are strongly implicated in breast augmentation failure due to capsular contracture, and while these infections are generally ascribed to common skin commensals, this remains largely unsubstantiated through robust cultivation independent analyses. To determine capsule biofilm microbial community compositio...
Article
Burial of large quantities of magnetite (Fe(II)Fe(III)2O4) in iron formations (IFs) likely contributed to the protracted oxidation of Earth's surface during the Precambrian Eons. Magnetite can form through a diversity of biological and abiotic pathways and its preservation in IFs may thus be variably interpreted as the result of some combination of...
Article
In previous work, lab‐scale reactors designed to study microbial Fe(II) oxidation rates at low pH were found to have stable rates under a wide range of pH and Fe(II) concentrations. Since the stirred reactor environment eliminates many of the temporal and spatial variations that promote high diversity among microbial populations in nature, we were...
Preprint
Full-text available
Ferruginous sediments were widespread during the Archaean and Proterozoic Eons, but our knowledge about organic matter mineralization remains mostly conceptual, as analogous modern ferruginous sediments are largely unstudied. In sediments of ferruginous Lake Towuti, Indonesia, methanogenesis dominates organic matter mineralization despite abundant...
Article
Full-text available
Ferruginous lacustrine systems, such as Lake Towuti, Indonesia, are characterized by a specific type of phosphorus cycling in which hydrous ferric iron (oxyhydr)oxides trap and precipitate phosphorus to the sediment, which reduces its bioavailability in the water column and thereby restricts primary production. The oceans were also ferruginous duri...
Article
Studies assessing the environmental impacts of oil spills focus primarily on the non-water-soluble components, leaving the fate of the water-soluble fraction (WSF) largely unexplored. We employed untargeted chemical analysis along with biological information to probe the transformation of crude oil WSF in seawater, in the absence of light, in a lab...
Preprint
Full-text available
Recent evidence indicates that viral components of the microbiota can contribute to intestinal homeostasis and protection from local inflammatory or infectious insults. However, host-derived mechanisms that maintain tolerance to the virome remain largely unknown. Here, we use colonization with the model commensal murine norovirus (MNV CR6) to inter...
Preprint
Full-text available
Burial of large quantities of magnetite (Fe(II)Fe(III)2O4) in iron formations (IFs) likely contributed to the protracted oxidation of Earth’s surface during the Precambrian Eons. Magnetite can form through a diversity of biological and abiotic pathways and its preservation in IFs may thus be variably interpreted as the result of some combination of...
Preprint
Full-text available
Ferruginous lacustrine systems, such as Lake Towuti, Indonesia, can experience restricted primary production due to phosphorus trapping by hydrous ferric iron (oxyhydr)oxides that reduce P concentrations in the water column. The oceans were also ferruginous during the Archean, so understanding the dynamics of phosphorus in modern-day ferruginous an...
Article
Full-text available
Electroactive type IV pili, or e‐pili, are used by some microbial species for extracellular electron transfer. Recent studies suggest that e‐pili may be more phylogenetically and structurally diverse than previously assumed. Here, we used updated aromatic density thresholds (≥9.8% aromatic amino acids, ≤22‐aa aromatic gaps, and aromatic amino acids...
Article
Full-text available
Banded iron formation (BIF) deposition was the likely result of oxidation of ferrous iron in seawater by either oxygenic photosynthesis or iron-dependent anoxygenic photosynthesis—photoferrotrophy. BIF deposition, however, remains enigmatic because the photosynthetic biomass produced during iron oxidation is conspicuously absent from BIFs. We have...
Article
Full-text available
Development of Archean paleosols and patterns of Precambrian rock weathering suggest colonization of continents by subaerial microbial mats long before evolution of land plants in the Phanerozoic Eon. Modern analogues for such mats, however, have not been reported, and possible biogeochemical roles of these mats in the past remain largely conceptua...
Preprint
The emergence of oxygenic photosynthesis created a new niche with dramatic potential to transform energy flow through Earth's biosphere. However, more primitive forms of photosynthesis that fix CO2 into biomass using electrons from reduced species like Fe(II) and H2 instead of water would have competed with Earth's early oxygenic biosphere for esse...
Article
Full-text available
The emergence of oxygenic photosynthesis created a new niche with dramatic potential to transform energy flow through Earth's biosphere. However, more primitive forms of photosynthesis that fix CO2 into biomass using electrons from reduced species like Fe(II) and H2 instead of water would have competed with Earth's early oxygenic biosphere for esse...
Preprint
Studies assessing the environmental impacts of oil spills focus primarily on the non-water-soluble components, leaving the fate of the water-soluble fraction (WSF) largely unexplored. In this study, we combined chemical and genomic analyses to examine the degradation of crude oil WSF in seawater in the absence of light in a laboratory experiment. O...
Preprint
Full-text available
Electroactive type IV pili, or e-pili, are used by some microbial species for extracellular electron transfer. Recent studies suggest that e-pili may be more phylogenetically and structurally diverse than previously assumed. Here, we used updated aromatic density thresholds (≥9.8% aromatic amino acids, ≤22-aa aromatic gaps, and aromatic amino acids...
Article
Oil and gas development can result in natural gas migration into shallow groundwater. Methane (CH4), the primary component of natural gas, can subsequently react with solutes and minerals in the aquifer to create byproducts that affect groundwater chemistry. Hydro-biogeochemical processes induced by fugitive gas from leaky oil and gas wells are cur...
Article
Full-text available
Qualitative and quantitative changes of organic and carbonate carbon in sedimentary records are frequently used to reconstruct past environments, paleoproductivity and sediment provenance. Amongst the most commonly used proxies are Total organic carbon (TOC), Mineral carbon (MinC), as well as Hydrogen (HI) and Oxygen Indices (OI) of organic matter...
Article
Full-text available
Ferruginous conditions prevailed in the world’s deep oceans during the Archean and Proterozoic Eons. Sedimentary iron formations deposited at that time may provide an important record of environmental conditions, yet linking the chemistry and mineralogy of these sedimentary rocks to depositional conditions remains a challenge due to a dearth of inf...
Article
Full-text available
Marine oxygen minimum zones (OMZs) support 30–50% of global fixed-nitrogen (N) loss but comprise only 7% of total ocean volume. This N-loss is driven by canonical denitrification and anaerobic ammonium oxidation (anammox), and the distribution and activity of these two processes vary greatly in space and time. Factors that regulate N-loss processes...
Article
Full-text available
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of spon...
Article
Full-text available
Anoxygenic photosynthesis evolved prior to oxygenic photosynthesis and harnessed energy from sunlight to support biomass production on the early Earth. Models that consider the availability of electron donors predict that anoxygenic photosynthesis using Fe(II), known as photoferrotrophy, would have supported most global primary production before th...
Article
Full-text available
Reactive Fe(III) minerals can influence methane (CH4) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH4 oxidation. The balance between Fe(III) reduction, methanogenesis, and CH4 oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH4 fluxes to the atmosphere, thereby regulating the capac...
Article
Full-text available
Here, we report the draft genome sequence of Chlorobium phaeoferrooxidans , a photoferrotrophic member of the genus Chlorobium in the phylum Chlorobi . This genome sequence provides insight into the metabolic capacity that underpins photoferrotrophy within low-light-adapted pelagic Chlorobi .
Preprint
Reactive Fe(III) minerals can influence methane (CH 4 ) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH 4 oxidation. The balance between Fe(III) reduction, methanogenesis, and methane oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH 4 fluxes to the atmosphere, thereby regulating t...
Article
To investigate the long-term weathering of oil from the Deepwater Horizon (DWH) incident, oil-soaked sand patties were collected from Gulf of Mexico beaches from Florida to Alabama over a three-year period from 2012 to 2014. Analysis of oil residues by gas chromatography with flame ionization detection (GC-FID), thin-layer chromatography with flame...
Article
Full-text available
The Towuti Drilling Project (TDP) is an international research program, whose goal is to understand long-term environmental and climatic change in the tropical western Pacific, the impacts of geological and environmental changes on the biological evolution of aquatic taxa, and the geomicrobiology and biogeochemistry of metal-rich, ultramafic-hosted...
Article
Full-text available
Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities re...
Data
Mapping data Habitat file used for grouping of samples in multivariate analyses (nMDS & adonis).
Data
Tukey multiple betadisper comparisons Tukey multiple comparisons of means for the group based betadisper analysis. 95% family-wise confidence level—diff giving the difference in the observed means, lwr giving the lower end point of the interval, upr giving the upper end point and p adj giving the p-value after adjustment for the multiple comparison...
Data
Hierarchical OTU clustering Dendrograms showing the Bray-Curtis dissimilarity of microbial communities of (A) the complete sample dataset, (B) Callyspongia sp., (C) R. globostellata, (D) seawater, (E) A. cavernosa, (F) Rhaphoxya sp. sponge specimens based on 97%-OTU amplicon subsets.
Data
Rarefaction curves Rarefied 97%-OTU 16S rRNA gene amplicon data for each sample.
Data
Betadisper pairwise comparisons Pairwise comparisons of the group based permutation test for homogeneity of multivariate dispersions. Observed p-value below diagonal, permuted p-value above diagonal.
Article
Deep-sea surface sediments and flocculent material (floc) associated with corals containing oil originating from the Deepwater Horizon (DWH) oil spill were examined to determine the diversity of microbes and the presence of functional genes involved in oil degradation. For all samples, 16 S rRNA clone libraries were constructed to obtain full-lengt...
Poster
Full-text available
Marine sponges host diverse and often specific microbial communities. Recent high-throughput sequencing studies on sponge-associated microbial communities from different geographic regions and habitats have expanded our knowledge about the microbial composition of low- and high-microbial-abundance sponges, and divided their communities into: ’core’...
Article
The characterization of changes in microbial communities is an essential step towards a better understanding of host-microbe associations. It is well established that sponges (phylum Porifera) harbor a diverse and abundant microbial community but it is not known whether these microbial communities change over time. Here, we followed two sponge spec...
Article
Full-text available
Large-scale mortality of marine invertebrates is a major global concern for ocean ecosystems and many sessile, reef-building animals, such as sponges and corals, are experiencing significant declines through temperature-induced disease and bleaching. The health and survival of marine invertebrates is often dependent on intimate symbiotic associatio...