Josh D. Neufeld
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View article: Effect of temperature on microbial communities in bentonite for use in engineered barrier systems
Effect of temperature on microbial communities in bentonite for use in engineered barrier systems Open
Bentonite is an important component of deep geological repository (DGR) designs, where it will serve as a buffer between used fuel containers (UFCs) and subsurface rock walls of the repository. The potential for microbial activity in bento…
View article: Interface-associated microbial growth in anoxic pressure vessels containing compacted gapfill bentonite
Interface-associated microbial growth in anoxic pressure vessels containing compacted gapfill bentonite Open
Aims Deep geological repositories (DGR) for belowground storage of used nuclear fuel rely on highly compacted bentonite to limit growth of microorganisms, including those that can contribute to microbiologically influenced corrosion, like …
View article: Low water activity limits bentonite-associated microbial growth
Low water activity limits bentonite-associated microbial growth Open
aims This research investigated the impact of water activity on microbial abundance estimates from bentonite under conditions relevant to a deep geological repository for used nuclear fuel. Because previous research tested saturation of be…
View article: Comparative proteomics of biofilm development in <i>Pseudoalteromonas tunicata</i> discovers a distinct family of Ca <sup>2+</sup> -dependent adhesins
Comparative proteomics of biofilm development in <i>Pseudoalteromonas tunicata</i> discovers a distinct family of Ca <sup>2+</sup> -dependent adhesins Open
The marine bacterium, Pseudoalteromonas tunicata , is a useful model for studying biofilm development due to its ability to colonize and form biofilms on a variety of marine and eukaryotic host-associated surfaces. However, the pathways re…
View article: Minimal changes in microbial abundances and diversity over 7 years of emplacement for modules of compacted bentonite exposed to natural groundwater
Minimal changes in microbial abundances and diversity over 7 years of emplacement for modules of compacted bentonite exposed to natural groundwater Open
The multi-national in situ Materials Corrosion Test (MaCoTe), being conducted at the Grimsel Test Site in Switzerland, assesses the stability of bentonite as it may be utilized within deep geological repositories (DGRs), which are proposed…
View article: Microbial community succession of home aquarium biofilters associated with early establishment of comammox <i>Nitrospira</i>
Microbial community succession of home aquarium biofilters associated with early establishment of comammox <i>Nitrospira</i> Open
Nitrification in aquarium biofilters transforms toxic ammonia (NH₃/NH₄+) into less toxic nitrate (NO₃-) via nitrite (NO₂-). Known freshwater aquarium nitrifiers include ammonia- and nitrite-oxidizing bacteria, ammonia-oxidizing archaea (AO…
View article: Validating digital polymerase chain reaction for 16S rRNA gene amplification from low biomass environmental samples
Validating digital polymerase chain reaction for 16S rRNA gene amplification from low biomass environmental samples Open
Digital polymerase chain reaction (dPCR) is a DNA quantification technology that offers absolute quantification of DNA templates. In this study, we optimized and validated a chip-based dPCR EvaGreen assay with commonly used 16S rRNA gene p…
View article: Deep terrestrial indigenous microbial community dominated by Candidatus Frackibacter
Deep terrestrial indigenous microbial community dominated by Candidatus Frackibacter Open
Characterizing deep subsurface microbial communities informs our understanding of Earth’s biogeochemistry as well as the search for life beyond the Earth. Here we characterized microbial communities within the Kidd Creek Observatory subsur…
View article: Arctic tundra soil depth, more than seasonality, determines active layer bacterial community variation down to the permafrost transition
Arctic tundra soil depth, more than seasonality, determines active layer bacterial community variation down to the permafrost transition Open
View article: Comammox <i>Nitrospira</i> among dominant ammonia oxidizers within aquarium biofilter microbial communities
Comammox <i>Nitrospira</i> among dominant ammonia oxidizers within aquarium biofilter microbial communities Open
Nitrification by aquarium biofilters transforms ammonia waste (NH 3 /NH 4 + ) to less toxic nitrate (NO 3 - ) via nitrite (NO 2 - ). Prior to the discovery of complete ammonia-oxidizing (“comammox” or CMX) Nitrospira , previous research re…
View article: Microbial communities change along the 300 km length of the Grand River for extreme high- and low-flow regimes
Microbial communities change along the 300 km length of the Grand River for extreme high- and low-flow regimes Open
The Grand River watershed is the largest catchment in southern Ontario. The river’s northern and southern sections are influenced by agriculture, whereas central regions receive wastewater effluent and urban runoff. To characterize in-rive…
View article: AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods
AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods Open
The analysis and comparison of gene neighborhoods is a powerful approach for exploring microbial genome structure, function, and evolution. Although numerous tools exist for genome visualization and comparison, genome exploration across la…
View article: Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre
Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre Open
View article: Impact of dry density and incomplete saturation on microbial growth in bentonite clay for nuclear waste storage
Impact of dry density and incomplete saturation on microbial growth in bentonite clay for nuclear waste storage Open
Aims Many countries are in the process of designing a deep geological repository (DGR) for long-term storage of used nuclear fuel. For several designs, used fuel containers will be placed belowground, with emplacement tunnels being backfil…
View article: AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods
AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods Open
The analysis and comparison of gene neighborhoods is a powerful approach for exploring microbial genome structure, function, and evolution. Although numerous tools exist for genome visualization and comparison, genome exploration across la…
View article: Nonparametric richness estimators Chao1 and ACE must not be used with amplicon sequence variant data
Nonparametric richness estimators Chao1 and ACE must not be used with amplicon sequence variant data Open
Microbial ecologists use alpha diversity metrics for estimating species richness and evenness from data obtained by high-throughput sequencing of small subunit ribosomal RNA genes. This perspective argues that the nonparametric richness es…
View article: Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats
Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats Open
Methanotrophic bacteria mitigate emissions of the potent greenhouse gas methane (CH4) from a variety of anthropogenic and natural sources, including freshwater lakes, which are large sources of CH4 on a global scale. Despite a dependence o…
View article: Microbial ecology of the deep terrestrial subsurface
Microbial ecology of the deep terrestrial subsurface Open
The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurfac…
View article: Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples
Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples Open
Combining multiple displacement amplification (MDA) with metagenomics enables the analysis of samples with extremely low DNA concentrations, making them suitable for high-throughput sequencing. Although amplification bias and nonspecific a…
View article: Data collection for Tsuji et al., 2023, Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center
Data collection for Tsuji et al., 2023, Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center Open
Supplementary data files associated with Tsuji et al., 2023, "Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center". These files are used by code in a corresponding GitHub repository (https://github.com/jmtsuji/Ca-Chl…
View article: Data collection for Tsuji et al., 2023, Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center
Data collection for Tsuji et al., 2023, Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center Open
Supplementary data files associated with Tsuji et al., 2023, "Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center". These files are used by code in a corresponding GitHub repository (https://github.com/jmtsuji/Ca-Chl…
View article: Unraveling the functional dark matter through global metagenomics
Unraveling the functional dark matter through global metagenomics Open
View article: Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater
Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater Open
The Materials Corrosion Test (MaCoTe) at the Underground Research Laboratory in Grimsel, Switzerland, assesses the microbiology and corrosion behavior of engineered barrier components of a deep geological repository (DGR) for long-term dis…
View article: Characterization of skin- and intestine microbial communities in migrating High Arctic lake whitefish and cisco
Characterization of skin- and intestine microbial communities in migrating High Arctic lake whitefish and cisco Open
At high latitudes, lake whitefish ( Coregonus clupeaformis) and others in the closely related Coregonus species complex (CSC) including cisco ( C. autumnalis and C. sardinella) can be diadromous, seasonally transitioning between freshwater…
View article: Evaluating <i>cpn60</i> for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis
Evaluating <i>cpn60</i> for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis Open
Despite being the most widely used phylogenetic marker for amplicon-based profiling of microbial communities, limited phylogenetic resolution of the 16S rRNA gene limits its use for studies of host-microbe co-evolution. In contrast, the cp…
View article: Environmental Impacts on Skin Microbiomes of Sympatric High Arctic Salmonids
Environmental Impacts on Skin Microbiomes of Sympatric High Arctic Salmonids Open
In the region of King William Island, Nunavut, in the Canadian high Arctic, populations of salmonids including Arctic char (Salvelinus alpinus), cisco (Coregonus autumnalis and C. sardinella) as well as lake whitefish (C. clupeaformis) are…
View article: Characterization of skin- and intestine microbial communities in migrating high Arctic lake whitefish and cisco
Characterization of skin- and intestine microbial communities in migrating high Arctic lake whitefish and cisco Open
At high latitudes, lake whitefish ( Coregonus clupeaformis ) and others in the closely related Coregonus species complex (CSC), including cisco ( C. autumnalis and C. sardinella ), can be diadromous, seasonally transitioning between freshw…
View article: Microbes ‘R’ us
Microbes ‘R’ us Open
‘Once we understand how similar we are, and how deeply the ties between animals and microbes extend, our view of the world will become immeasurably enriched’ (Yong, 2016). Lynn Margulis had one of her grant proposals rejected with a review…
View article: Thousands of small, novel genes predicted in global phage genomes
Thousands of small, novel genes predicted in global phage genomes Open
View article: Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems
Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems Open