Biology subjects

Hamilton, T. L.

Publications and source records attributed to Hamilton, T. L..

10 recordsLinked to original sources

bioRxiv2026

From green to red: experimental evidence for pigment-driven snow darkening

Snow algae are major biological drivers of snow darkening in polar and high-alpine environments. However, the direct contribution of algal pigmentation to snow reflectance has remained difficult to quantify because field observations cannot disentangle the effects of pigmentation from variation in biomass, species composition, and snow physical properties. Here, we characterized the optical effects of pigmentation using hyperspectral spectroradiometry to compare green, orange, and red cyst-like cells of a snow-derived Haematococcus isolate while controlling for developmental stage and cell abundance. Cysts became more red with increasing astaxanthin concentrations while chlorophyll-a concentrations remained relatively constant. Relative to green cysts, mean reflectance decreased by approximately 30% in orange cysts and 40% in red cysts. Integrated reflectance across the visible spectrum (350-800 nm) was negatively correlated with astaxanthin concentration. These results provide direct experimental evidence that algal pigmentation alone substantially reduces reflectance after controlling for cell abundance and developmental stage, and indicate that differences in snow physical properties may partly obscure this effect under natural field conditions. Our findings identify astaxanthin accumulation as an intrinsic driver of biological snow darkening and suggest that algal pigmentation, which may vary with species identity and physiological state, should be considered alongside biomass when predicting the radiative effects of snow algal blooms.

microbiology↗

bioRxiv2025

Metabolic diversity of the Ferrovales and potential contributions to iron oxidation

Active and abandoned metal and coal mines generate acidic, metal-laden water that pollutes downstream areas, commonly referred to as acid mine drainage (AMD). AMD is host to microbial communities, including acidophilic iron oxidizers. Microbially-mediated iron oxidation is a desirable (bio)remediation strategy for AMD. Ferrovales are a common Fe-oxidizing bacterial group observed in AMD globally and thus could be an exceptional target for bioremediation strategies. However, Ferrovales are difficult to culture and both phylogenetically and metabolically diverse. To better understand the potential for Ferrovales to contribute to AMD bioremediation, we circumvented limitations in culture-based approaches and analyzed 240 genomes and metagenome assembled genomes from the Ferrovales, including taxa from AMD sites with high iron oxidation rates. The phylogenetic and physiological diversity of this group was greater than previously known and multiple Ferrovales taxa can co-occur. For example, we observed taxa that varied in mobility (based on the presence or absence of flagellar biosynthesis genes) and taxa that encode multiple iron oxidation pathways. We also identified Ferrovales that are likely capable of anoxygenic photosynthesis. Our data suggest that differences in physiology promote niche differentiation along resource axes and co-occurrence of multiple taxa. Its possible that multiple co-occurring iron oxidizing taxa could support a more robust microbial community, resulting in higher iron oxidation rates and more efficient bioremediation. ImportanceAcid mine drainage (AMD) pollutes watersheds worldwide. Microbial communities can be leveraged to improve AMD bioremediation, the use of living things for the remediation of contaminated sites, because they drive biogeochemical processes in these ecosystems. Iron-oxidizing microbial species remove iron from AMD effluent, and the iron oxides sorb other trace metals. These communities vary across sites and differ in how rapidly they oxidize iron. Therefore, it is difficult to effectively use them for bioremediation. Ferrovales are common iron-oxidizing taxa in AMD globally, including in sites with exceptionally high rates of iron oxidation. To examine the potential for Ferrovales to be key components of bioremediation strategies, we examined the genomic content and functional potential of Ferrovales in publicly available metagenomic data sets. Our analysis uncovered several new species of Ferrovales as well as an expanded metabolic potential for this group. Comparative genomics suggests that functional diversity may lead to the co-occurrence of multiple Ferrovales species. The presence of multiple iron-oxidizing taxa with distinct physiology could be beneficial for bioremediation strategies.

microbiology↗

bioRxiv2025

Taxonomy-driven variations in snow algae color modulate albedo and energy balance in a single snow patch

In this study, we examined the reflectance, pigment composition, and community composition of three snow algae blooms showing distinct colors in the same snowfield in Glacier National Park (USA). Each color bloom was dominated by a different algae, each exhibiting a unique pigment signature but with astaxanthin as the predominant pigment across all three blooms. The spectral reflectance of red snow algae was consistently lower than that of green algae, while orange algae had intermediate reflectance values. Specifically, red algae reduced reflectance by approximately 55% across the PAR range, while green algae reduced reflectance by 25%. Red algae also demonstrated the highest radiative forcing, double that of green algae, leading to increased energy re-emission into the surrounding environment, which likely contributes to the localized melting of adjacent ice crystals. The high absorbance around 680 nm in cells with high astaxanthin content, such as the orange algae, suggests that semi-automatic detection methods could effectively identify these algae, as their spectral features remain distinct despite the presence of secondary carotenoids. Our data demonstrate the impact of snow algae taxonomic and pigment composition on the radiative balance of snowfields, underscoring taxonomy as a key determinant of bloom color under similar environmental conditions

microbiology↗

bioRxiv2025

Enhancing DNA recovery in low-biomass snow algae samples: a comparative study of extraction methods and their effect on community composition

High-throughput sequencing is a powerful tool for environmental microbiology and can be particularly important for examining community structure and function for organisms that are difficult to culture or environments that are difficult to mimic like snow algae. DNA extraction significantly impacts these analyses, often introducing more variation than PCR or sequencing. Snow algae are widespread on mountain and polar snowfields where they contribute to biogeochemical cycling and accelerate melt. Despite increasing research on snow algae, inconsistencies in DNA extraction remain a major challenge, and no recommended method exists for assessing their community composition and richness. Here, we compared three common extraction methods (DNeasy PowerSoil Pro, DNeasy PowerWater, and phenol-chloroform) alongside ultrasonication in samples with varying snow algae abundance. The extraction method strongly influenced resulting microbial profiles assessed by amplicon sequencing of rRNA genes. Ultrasonication improved DNA yield in low-biomass samples and enhanced the recovery of resilient cells, including mature-phase snow algae likely due to improved cell lysis step. This is the first systematic comparison of DNA extraction methods for snow algae, highlighting how methodological choices affect microbial community analyses. Our findings provide insights to improve standardization, enhancing the reliability of future studies in snow and ice environments.

microbiology↗

bioRxiv2025

Terrestrial Organic Matter Amplifies Methane Emissions Across Sediments of the Mississippi River Headwaters

Terrestrial organic matter (tOM) plays a critical role in aquatic ecosystems, influencing carbon processes and greenhouse gas emissions. Here, we investigate the impact of tOM on methane production in littoral and pelagic sediments from the Mississippi River headwaters using a microcosm approach. Contrary to our expectations, tOM addition universally increased methane production across lentic sediments, with no significant difference between littoral and pelagic zones. Methane production was influenced by select sediment microorganisms, primarily methanogens and lignocellulose degrading bacteria, which responded similarly across different sediment habitats. The study highlights the role of cytochrome-containing methanogens and their syntrophic relationships with fermentative bacteria, emphasizing the significance of microbial community structure in sediment methane dynamics. Our findings suggest that increasing tOM loads to freshwater systems could have broader implications for methane emissions, driven by specific microbial interactions. Author Contribution StatementHMS and TLH conceived the study and obtained the funds. HMS led fieldwork and microcosm set-up. HMS and LAD analyzed gas samples and HMS performed the data analysis and graphical representation of the results. HMS wrote the first draft of the manuscript, and all authors contributed significantly to the preparation of the final draft. Scientific Significance StatementAs human activities and climate change increase the amount of organic material entering lakes and rivers, understanding the effects this has on greenhouse gas emissions is crucial. Our study reveals that adding terrestrial organic matter to freshwater sediments universally boosts methane production, a potent greenhouse gas. Through the exploration of microbial communities responsible for this process, our research highlights how changes in terrestrial organic matter export to aquatic systems could increase methane emissions from sediments. Data Availability StatementAdditional Supporting Information can be found in the online version of this article, including an extended version of methods and supplementary tables. Sequencing data associated with this paper is available on NCBI, BioProject PRJNA1164797.

ecology↗

bioRxiv2023

Carbonate bedrock may not alleviate DIC limitation of snow algae - a test of hypothesis in the Medicine Bow Mountains, WY, USA

Snow is a critical component of the Earth system. High elevation snow can persist into the melt season and hosts a diverse array of life including snow algae. Due in part to the presence of pigments, snow algae lower albedo and accelerate snow melt which has led to increasing interest in identifying and quantifying the environmental factors that constrain their distribution. Dissolved inorganic carbon (DIC) concentration is low in supraglacial snow on Cascade stratovolcanoes and snow algae primary productivity can be stimulated through DIC addition. Here we asked if CO2 would still be a limiting nutrient for snow hosted on glacially eroded carbonate bedrock (which could provide an additional source of DIC). We assayed snow algae communities for nutrient and DIC limitation on two seasonal snowfields on glacially eroded carbonate bedrock in the Snowy Range of the Medicine Bow Mountains, Wyoming, USA. DIC stimulated snow algae primary productivity in snow with lower DIC concentration despite the presence of carbonate bedrock, which alleviated DIC limitation in the other site. Our results support the hypothesis that increased atmospheric CO2 concentrations may lead to larger and more robust snow algae blooms globally, even for sites with carbonate bedrock.

ecology↗

bioRxiv2022

Distribution and genomic variation of thermophilic cyanobacteria in diverse microbial mats at the upper temperature limits of photosynthesis

Thermophilic cyanobacteria have been extensively studied in Yellowstone National Park (YNP) hot springs, particularly from decades of work on the thick laminated mats of Octopus and Mushroom Springs. However, focused studies of cyanobacteria outside of these two hot springs have been lacking, especially regarding how physical and chemical parameters along with community morphology influence the genomic makeup of these organisms. Here, we used a metagenomic approach to examine cyanobacteria existing at the upper temperature limits of photosynthesis. We examined 15 alkaline hot spring samples across six geographic areas of YNP, all with varying physical and chemical parameters, and community morphology. We recovered 22 metagenome-assembled genomes (MAGs) belonging to thermophilic cyanobacteria, notably an uncultured Synechococcus-like taxon recovered from the upper temperature limit of photosynthesis, 73{degrees}C, in addition to thermophilic Gloeomargarita. Furthermore, we found that three distinct groups of Synechococcus-like MAGs recovered from different temperature ranges vary in their genomic makeup. MAGs from the uncultured very high temperature (up to 73{degrees}C) Synechococcus-like taxon lack key nitrogen metabolism genes and have genes implicated in cellular stress responses that diverge from other Synechococcus-like MAGs. Across all parameters measured, temperature was the primary determinant of taxonomic makeup of recovered cyanobacterial MAGs. However, Fe, community morphology, and biogeography played an additional role in the distribution and abundance of upper temperature limit-adapted Synechococcus-like MAGs.These findings expand our understanding of cyanobacterial diversity in YNP and provide a basis for interrogation of understudied thermophilic cyanobacteria. ImportanceOxygenic photosynthesis arose early in microbial evolution - approx. 2.5-3.5 billion years ago - and entirely reshaped the biological makeup of Earth. However, despite the span of time in which photosynthesis has been refined, it is strictly limited to temperatures below 73{degrees}C, a barrier that many other biological processes have been able to overcome. Furthermore, photosynthesis at temperatures above 56{degrees}C is limited to circumneutral and alkaline pH. Hot springs in Yellowstone National Park (YNP), which have a large diversity in temperatures, pH and geochemistry provide a natural laboratory to study thermophilic microbial mats, and the cyanobacteria within. While cyanobacteria in YNP microbial mats have been studied for decades, a vast majority of work has focused on two springs within the same geyser basin, both containing similar community morphologies. Thus, the drivers of cyanobacterial adaptations to the upper limits of photosynthesis across a variety of environmental parameters have been understudied. Our findings provide new insights into the influence of these parameters on both taxonomic diversity and genomic content of cyanobacteria across a range of hot spring samples.

microbiology↗

bioRxiv2021

Meet me in the middle: median temperatures impact cyanobacteria and photoautotrophy in eruptive Yellowstone hot springs

Geographic isolation can be a main driver of microbial evolution in hot springs while temperature plays a role on local scales. For example, cyanobacteria, particularly high temperature Synechococcus spp., have undergone ecological diversification along temperature gradients in hot spring outflow channels. While water flow, and thus temperature, is largely stable in many hot springs, flow can vary in geysing/eruptive hot springs resulting in large temperature fluctuations (sometimes more than 40{degrees}C). However, the role of large temperature fluctuations in driving diversification of cyanobacteria in eruptive hot springs has not been explored. Here, we examined phototroph community composition and potential photoautotrophic activity in two alkaline eruptive hot springs with similar geochemistry in the Lower Geyser Basin in Yellowstone National Park, WY. We observed distinct cyanobacterial amplicon sequencing variants (ASVs) consistent with allopatry and levels of light-dependent inorganic carbon uptake rates similar to other hot springs, despite large temperature fluctuations. Our data suggests median temperatures may drive phototroph fitness in eruptive hot springs while future studies are necessary to determine the evolutionary consequences of thriving under continuously fluctuating temperatures. We propose that large temperature swings in eruptive hot springs offer unique environments to examine the role of allopatry vs. physical and chemical characteristics of ecosystems in driving cyanobacteria evolution and add to the debate regarding the ecology of thermal adaptation and the potential for narrowing niche breadth with increasing temperature. ImportanceHot spring cyanobacteria have long been model systems for examining ecological diversification as well as characterizing microbial adaptation and evolution to extreme environments. These studies have reported cyanobacterial diversification in hot spring outflow channels that can be defined by distinct temperature ranges. Our study builds on these previous studies by examining cyanobacteria in geysing hot springs. Geysing hot springs result in outflow channel that experience regular and large temperature fluctuations. While community composition is similar between geysing and nongeysing hot spring outflow channels, our data suggests median, rather than high temperature, drive the fitness of cyanobacteria in geysing hot springs. We propose that large temperature swings may result in patterns of ecological diversification that are distinct from more stable outflows.

microbiology↗

bioRxiv2021

Diversity and distribution of sediment bacteria across an ecological and trophic gradient

Can we cluster bacterial sediment communities based on lake size, depth, and trophic status? Or, are bacterial microbial communities an emergent property of their geography, integrating regional physical and climatic conditions? Lakes in Minnesota are uniquely situated to address these questions because of their wide geographic range and variability in size and basin land-use. In this study, we selected twenty lakes with varying morphological and chemical properties across four ecological regions of Minnesota. Our objectives were to (i)) evaluate the diversity and spatial variation of the bacterial community at the sediment-water interface and (ii) determine how lake location and watershed land-use impact aqueous chemistry and influence community structure. Our data indicate that sediment communities from similar depth intervals are more likely to cluster by ecological region rather than any individual lake properties (e.g., trophic status, TP concentration, lake depth). However, composition is tied to a given lake, wherein samples from the same core were more alike than samples at similar depths across lakes. Our results illustrate the diversity within lake sediment microbial communities and provide insight into relationships between taxonomy, physicochemical, and geographic properties of north temperate lakes.

ecology↗

bioRxiv2020

Metagenome assembled genomes of novel taxa from an acid mine drainage environment

ABSTRACTAcid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from16S rRNA gene amplicons but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, KY, USA. The genomes span 11 bacterial phyla and include one Archaea and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies.IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements like carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.View Full Text

microbiology↗