Biology subjects

Stamps, B. W.

Publications and source records attributed to Stamps, B. W..

7 recordsLinked to original sources

bioRxiv2023

Spatial and Temporal Dynamics at an Actively Silicifying Hydrothermal System

Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park, Wyoming (YNP), actively gushing silicon rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cones outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 {+/-} 0.11 to 4.26 {+/-} 0.07 mM and 189.7 {+/-} 7.2 to 204.7 {+/-} 3.55 M respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation < 32%. A thermal gradient decrease of ~55{degrees}C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34{degrees}C {+/-} 3.38 to 35.06{degrees}C {+/-} 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance changes of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.

microbiology↗

bioRxiv2022

The Composition of Diesel Fuel Influences the Structure of Microbiological Assemblages in Contaminated Fuel Storage Tanks

Microbiological contamination in diesel storage tanks is widespread and under-reported. The contaminating microorganisms can degrade components of the fuel, which contributes to fouling and corrosion. To better understand the connection between the microorganisms that are responsible for this contamination, the composition of affected fuels, and the resulting impact on fuel quality, we conducted a survey of 106 fuel tanks at 17 military bases across the continental United States. Fuel was sampled from each tank and the resident microbial communities were characterized using high throughput sequencing of small subunit ribosomal RNA gene libraries. Fatty acid methyl esters (FAME) and n-alkanes were characterized and quantified using GC-MS to determine their correlation with the presence of microbial taxa. Redundancy Analyses identified which microbial taxa were more prominent in contaminated fuels. Members of the fungal family Trichomaceae were found to be prominent in fuels containing more FAME. Members of the yeast family Debaryomycetaceae were found to be prominent in fuels containing more pentadecanoic and oleic acid methyl esters. These relationships between fungal taxa and fuel components were directly tested in growth experiments with representative isolates of the Trichocomaceae (Paecilomyces AF001) and Debaryomycetaceae (Wickerhamomyces SE3) families. Paecilomyces was capable of growth on linoleic acid methyl ester but unable to grow on pentadecanoic acid methyl ester, while Wickerhamomyces was able to grow on both substrates. Fuel composition may provide some insight into which microorganisms can proliferate but other factors like competition and symbiosis may also drive microbial proliferation, fouling, degradation, and corrosion in diesel fuels. ImportanceBiodiesel, widely used as an additive or extender of ultra-low sulfur diesel, can increase the potential for microorganisms to proliferate in storage tanks. It is important to know how the composition of diesel fuels can influence the growth of organisms linked to fuel degradation and microbiologically influenced corrosion. This research describes how certain populations of fungi and bacteria can prevail in fuels of different composition, which can be helpful in predicting biodegradation and biocorrosion, and formulating fuels less susceptible to the growth of problematic organisms.

microbiology↗

bioRxiv2021

Locating and Quantifying Carbon Steel Corrosion Rates Linked to Fungal B20 Biodiesel Degradation

Fungi that degrade B20 biodiesel in storage tanks have also been linked to microbiologically influenced corrosion (MIC). A member of the filamentous fungal genus Byssochlamys, and a yeast from the genus Wickerhamomyces were isolated from heavily contaminated B20 storage tanks from multiple Air Force bases. Although these taxa were linked to microbiologically influenced corrosion in situ, precise measurement of their corrosion rates and pitting severity on carbon steel was not available. In the experiments described here, we directly link fungal growth on B20 biodiesel to higher corrosion rates and pitting corrosion of carbon steel under controlled conditions. When these fungi were growing solely on B20 biodiesel for carbon and energy, consumption of FAME and n-alkanes was observed. The corrosion rates for both fungi were highest at the interface between the B20 biodiesel and the aqueous medium, where they acidified the medium and produced deeper pits than abiotic controls. Byssochlamys produced the most corrosion of carbon steel and produced the greatest pitting damage. This study characterizes and quantifies the corrosion of carbon steel by fungi that are common in fouled B20 biodiesel through their metabolism of the fuel, providing valuable insight for assessing MIC associated with storage and dispensing B20 biodiesel. IMPORTANCEBiodiesel is widely used across the United States and worldwide, blended with ultralow sulfur diesel in various concentrations. In this study we were able to demonstrate that the filamentous fungi Byssochlamys AF004 and the yeast Wickerhamomyces SE3 were able to degrade fatty acid methyl esters and alkanes in biodiesel causing increases in acidity. Both fungi also accelerated the corrosion of carbon steel, especially at the interface of the fuel and water, where their biofilms were located. This research provides controlled, quantified measurements and the localization of microbiologically influenced corrosion caused by common fungal contaminants in biodiesel fuels.

microbiology↗

bioRxiv2020

A pilot study of the effect of deployment on the gut microbiome and traveler's diarrhea susceptibility

Travelers diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in travelers diarrhea susceptibility. To this end we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to travelers diarrhea. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution towards identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.

microbiology↗

bioRxiv2020

Metagenomic Insights into Microbial Metabolisms of a Sulfur-Influenced Glacial Ecosystem

Biological sulfur cycling in polar, low-temperature ecosystems is an understudied phenomenon in part due to difficulty of access and the ephemeral nature of such environments. One such environment where sulfur cycling plays an important role in microbial metabolisms is located at Borup Fiord Pass (BFP) in the Canadian High Arctic. Here, transient springs emerge from the toe of a glacier creating a large proglacial aufeis (spring-derived ices) that are often covered in bright yellow/white sulfur, sulfate, and carbonate mineral precipitates that are accompanied by a strong odor of hydrogen sulfide. Metagenomic sequencing from multiple sample types at sites across the BFP glacial system produced 31 highly complete metagenome assembled genomes (MAGs) that were queried for sulfur-, nitrogen- and carbon-cycling/metabolism genes. Sulfur cycling, especially within the Sox complex of enzymes, was widespread across the isolated MAGs and taxonomically associated with the bacterial classes Alpha-, Beta-, Gamma-, and Epsilon- Proteobacteria. While this does agree with previous research from BFP implicating organisms within the Gamma- and Epsilon- Proteobacteria as the primary classes responsible for sulfur oxidation, our new data suggests putative sulfur oxidation by organisms within Alpha- and Beta- Proteobacterial classes which was not predicted. These findings indicate that in a low-temperature, ephemeral sulfur-based environment such as this, functional redundancy may be a key mechanism that microorganisms use to co-exist whenever energy is limited and/or focused by redox chemistry. ImportanceBorup Fiord Pass is a unique environment characterized by a sulfur-enriched glacial ecosystem, in the low-temperature environment of the Canadian High Arctic. This unique combination makes BFP one of the best analog sites for studying icy, sulfur-rich worlds outside of our own, such as Europa and Mars. The site also allows investigation of sulfur-based microbial metabolisms in cold environments here on Earth. Herein, we report whole genome sequencing data that suggests sulfur cycling metabolisms at BFP are more widely used across bacterial taxa than predicted. From our data, the metabolic capability of sulfur oxidation among multiple community members appears likely due to functional redundancy within their genomes. Functional redundancy, with respect to sulfur-oxidation at BFP, may indicate that this dynamic ecosystem hosts microorganisms that are able to use multiple sulfur electron donors alongside other important metabolic pathways, including those for carbon and nitrogen.

microbiology↗

bioRxiv2018

Linking Fungal and Bacterial Proliferation to Microbiologically Influenced Corrosion in B20 Biodiesel Storage Tanks

Biodiesel is a renewable substitute, or extender, for petroleum diesel that is composed of a mixture of fatty acid methyl esters (FAME) derived from plant and animal fats. Ultra-low sulfur diesel (ULSD) blended with up to 20% FAME can be used interchangeably with ULSD, is compatible with existing infrastructure, but is also more susceptible to biodegradation. Microbial proliferation and fuel degradation in biodiesel blends has not been directly linked in situ to microbiologically influenced corrosion. We, therefore, conducted a yearlong study of B20 storage tanks in operation at two locations, identified the microorganisms responsible for observed fuel fouling and degradation, and measured in situ corrosion. The bacterial populations were more diverse than the fungal populations, and largely unique to each location. The bacterial populations included members of the Acetobacteraceae, Clostridiaceae, and Proteobacteria. The abundant Eukaryotes at both locations consisted of the same taxa, including a filamentous fungus within the family Trichocomaceae, and the Saccharomycetaceae family of yeasts. Increases in the absolute and relative abundances of the Trichocomaceae were correlated with significant, visible fouling and pitting corrosion. This study identified the relationship between recurrent fouling of B20 with increased rates of corrosion, largely at the bottom of the sampled storage tanks.

microbiology↗

bioRxiv2018

The Metabolic Capability and Phylogenetic Diversity of Mono Lake During a Bloom of the Eukaryotic Phototroph Picocystis strain ML

Algal blooms in lakes are often associated with anthropogenic eutrophication; however, they can occur naturally. In Spring of 2016 Mono Lake, a hyperalkaline lake in California, was near the height of a rare bloom of the algae Picocystis strain ML and at the apex of a multi-year long drought. These conditions presented a unique sampling opportunity to investigate microbiological dynamics during an intense natural bloom. We conducted a comprehensive molecular analysis along a depth transect near the center of the lake from surface to 25 m depth during June 2016. Across sampled depths, rRNA gene sequencing revealed that Picocystis associated chloroplast were found at 40-50 % relative abundance, greater than values recorded previously. Despite the presence of the photosynthetic oxygenic algal genus Picocystis, oxygen declined below detectible limits below 15 m depth, corresponding with an increase in microorganisms known to be anaerobic. In contrast to previously sampled years, metagenomic and metatranscriptomic data suggested a loss of sulfate reducing microorganisms throughout the lakes water column. Gene transcripts associated with Photosystem I and II were expressed at both 2 m and 25 m, suggesting that limited oxygen production may occur at extremely low light levels at depth within the lake. Oxygenic photosynthesis under low light conditions, in the absence of potential grazing by the brine shrimp Artemia, may allow for a cryptic redox cycle to occur in an otherwise anoxic setting at depth in the lake with the following effects: enhanced productivity, reduced grazing pressure on Picocystis, and an exacerbation of bloom.\n\nIMPORTANCEMono Lake, California provides habitat to a unique ecological community that is heavily stressed due to recent human water diversions and a period of extended drought. To date, no baseline information exists about Mono Lake to understand how the microbial community responds to drought, bloom, and what genetic functions are lost in the water column. While previously identified anaerobic members of the microbial community disappear from the water column during drought and bloom, sediment samples suggest these microorganisms seek refuge at lake bottom or in the subsurface. Thus, the sediments may represent a type of seed bank which could restore the microbial community as a bloom subsides. Our work also sheds light on the activity of the halotolerant algae Picocystis strain ML during a bloom at Mono Lake, its ability to potentially produce oxygen via photosynthesis even under extreme low-light conditions, and how the remainder of the microbial community responds.

microbiology↗