Dr. Wade H Jeffrey

High-altitude hydrothermal systems provide laboratories for understanding microbial adaptation to extreme conditions. Here we investigated thermodynamic controls on metabolic transitions in Lirima hydrothermal system (Chile, 4000 meters above sea level) calculating affinities of competing carbon and sulfur reactions across pools (53–75 °C). Through geochemistry, numerical thermodynamic modeling, and stable isotope analysis, we identify Energetic Convergence Nodes where chemical affinities of competing pathways become equal. Calculations reveal hydrogenotrophic and carboxydotrophic methanogenesis converge with sulfate reduction at 63–64 °C. This corresponds with responses: carbon isotopes shift from −17.2‰ to −27.7‰, sulfur isotopes from −20.5‰ to −9.1‰, and carbon-to-sulfur ratios drop from ~10 to <1, indicating transition from carbon to sulfur-dominated metabolism. Microbial activity collapses at this temperature, while metagenomics validates both pathways. Independent analysis confirms convergence at 63–64 °C, establishing Energetic Convergence Nodes as predictive frameworks for metabolic boundaries with applications for early Earth biogeochemistry and extraterrestrial biosignature detection.
Equal affinities of competing reactions at an energetic convergence node demonstrated a metabolic transition in the high-altitude Lirima hydrothermal system of Chile, according to combined geochemistry, thermodynamic modeling, stable isotope analysis, microbial activity measurements, and metagenomics.

Terrestrial hydrothermal systems provide a window for studying the biogeochemical interactions that occur in hot and gas-rich ecosystems resembling the conditions found in early life on Earth. The biogeochemical dynamics of the Andean hydrothermal systems in the Atacama Desert area are still understudied. Thus, we aimed to characterize the taxonomic composition and genomic potential of nitrogen transformations in a microbial community inhabiting a high-altitude hydrothermal system on the Altiplano Plateau of the Chilean Andes. Specifically, we sampled sediment and microbial mats in three ponds with water temperatures ranging from 42 to 64 °C. We found a high prevalence of photoheterotrophs, with differences in taxonomic composition and gene abundance between the microbial communities found in the sediment and microbial mats. Changes in physicochemical conditions, such as temperature and pH, and the concentrations of CO2, CH4 and Mn accounted for the variability in the microbial community structure. Our results indicated an enrichment of N-related genes associated with nitrate reduction, denitrification, and ammonia assimilation, suggesting a metabolically versatile community using nitrate, nitrite, and gaseous nitrogen species to assimilate ammonia into their biomass. This study contributes to our understanding of the taxonomy and functional microbial dynamics in a high-altitude thermal system, where ammonia assimilation is potentially critical for
biomass formation, and particular environmental conditions favor adaptations to maintain biogeochemical cycles.

We introduce the Global rRNA Universal Metabarcoding Plankton database (GRUMP), which consists of 1194 samples that were collected from 2003–2020 and cover extensive latitudinal and longitudinal transects, as well as depth profiles in all major ocean basins. DNA from unfractionated (>0.2 µm) seawater samples was amplified using the 515Y/926 R universal three-domain rRNA gene primers, simultaneously quantifying the relative abundance of amplicon sequencing variants (ASVs) from bacteria, archaea, eukaryotic nuclear 18S, and eukaryotic plastid 16S. Thus, the ratio between taxa in one sample is directly comparable to the ratio in any other GRUMP sample, regardless of gene copy number differences. This obviates a problem in prior global studies that used size-fractionation and different rRNA gene primers for bacteria, archaea, and eukaryotes, precluding comparisons across size fractions or domains. On average, bacteria contributed 71%, eukaryotes 19%, and archaea 8% to rRNA gene abundance, though eukaryotes contributed 32% at latitudes >40°. GRUMP is publicly available on the Simons Collaborative Marine Atlas Project (CMAP), promoting the global comparison of marine microbial dynamics.

Seagrass beds are important to the health of estuaries around the world, and often these grasses are keystone species for their environments. Water quality conditions controlling light availability such as total suspended solids (TSS), phytoplankton biomass, and the color of the water are important in understanding seagrass health. Six locations from the Pensacola Bay System in Santa Rosa Sound and Big Lagoon with extensive seagrass beds were sampled monthly between May and October 2023. Water quality was measured, and surveys of seagrass beds were conducted at each site. Linear models were developed to attempt to explain K d from water color, phytoplankton biomass, and TSS, as well as their impact on the percent cover of the seagrasses. Seagrass cover increased over the growing season. K d varied between 0.3 /m and 1.8 /m, and across all study sites only color was significantly (p < 0.1) related to light attenuation, although it could not explain much variability (R 2 =0.08). While water depth was significantly related to percent cover of Halodule wrightii and Thalassia testudinum, depth integrated values of light available and factors related to light attenuation explained little variability in percent cover despite significance levels (p < 0.1). Sites in Santa Rosa Sound and Big Lagoon were similar. Larger scale surveys with more opportunistic sampling (e.g. following rain events) in addition to planned collection days, might provide data with clearer relationships to light attenuation and seagrass cover. Surveys that extend to the deepwater edge of the seagrass beds should also be done in the future to provide a clearer picture of the habitat and changes in the beds.

Thermophilic microorganisms possess several adaptations to thrive in high temperature, which is reflected as biosynthesis of proteins and thermostable molecules, isolation and culture represent a great methodological challenge, therefore High throughput sequencing enables screening of the whole bacterial genome for functional potential, providing rapid and cost-effective information to guide targeted cultures for the identification and characterization of novel natural products. In this study, we isolated two thermophilic bacterial strains corresponding to Bacillus LB7 and Streptomyces LB8, from the microbial mats in the Atacama Desert. By combining genome mining, targeted cultures and biochemical characterization, we aimed to identify their capacity to synthesize bioactive compounds with antimicrobial properties. Additionally, we determined the capability to produce bioactive compounds under controlled in vitro assays and detected by determining their masses by Thin-Layer Chromatography/Mass Spectrometry (TLC/MS). Overall, both isolates can produce antimicrobial (e.g., Myxalamide C by-product) and antioxidants (e.g. Dihydroxymandelic Acid, Amide biotine and Flavone by-products) compounds. Bacillus LB7 strain possesses a more diverse repertoire with 51.95% of total metabolites unmatched, while Streptomyces LB8 favors mainly antioxidants, but has over 70% of unclassified compounds, highlighting the necessity to study and elucidate the structure of novel compounds. Based on these results, we postulate that the uncultured or rare cultured thermophiles inhabiting high-altitude hydrothermal ecosystems in the Atacama Desert offer a promising opportunity to the study of novel microbial bioactive compounds.

The 2010 Deepwater Horizon (DwH) Oil spill released an enormous volume of oil into the Gulf of Mexico (GoM), prompting the widespread use of chemical dispersants like Corexit ® EC9500A. The ecological consequences of this treatment, especially when combined with natural factors such as sunlight, remain unexplored in the context of marine bacterial communities’ dynamics. To address this knowledge gap, our study employed a unique metaproteomic approach, investigating the combined effects of sunlight, crude Macondo surrogate oil, and Corexit on GoM microbiome across different mesocosms. Exposure to oil and/or Corexit caused a marked change in community composition, with a decrease in taxonomic diversity relative to controls in only 24 hours. Hydrocarbon (HC) degraders, particularly those more tolerant to Corexit and phototoxic properties of crude oil and/or Corexit, proliferated at the expense of more sensitive taxa. Solar radiation exacerbated these effects in most taxa. We demonstrated that sunlight increased the dispersant’s toxicity, impacting on community structure and functioning. These functional changes were primarily directed by oxidative stress with upregulated proteins and enzymes involved in protein turnover, general stress response, DNA replication and repair, chromosome condensation, and cell division. These factors were more abundant in chemically treated conditions, especially in the presence of Corexit compared to controls. Oil treatment significantly enhanced the relative abundance of Alteromonas , an oil-degrading Gammaproteobacteria . In combined oil-Corexit treatments, the majority of identified protein functions were assigned to Alteromonas , with strongly expressed proteins involved in membrane transport, motility, carbon and amino acid metabolism and cellular defense mechanisms. Marinomonas , one of the most active genera in dark conditions, was absent from the light treatment. Numerous metabolic pathways and HC-degrading genes provided insights into bacterial community adaptation to oil spills. Key enzymes of the glyoxylate bypass, enriched in contaminant-containing treatments, were predominantly associated with Rhodobacterales and Alteromonadales. Several proteins related to outer membrane transport, photosynthesis, and nutrient metabolisms were characterized, allowing predictions of the various treatments on biogeochemical cycles. The study also presents novel perspectives for future oil spill clean-up processes.

Petroleum products in the environment can produce significant toxicity through photochemically driven processes. Burning surface oil and photochemical degradation were two mechanisms for oil removal after the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico. After burning, residual oil remains in the environment and may undergo further weathering, a poorly understood fate. Although photochemistry was a major degradation pathway of the DWH oil, its effect on burned oil residue in the environment is under studied. Here, we ignited Macondo surrogate crude oil and allowed it to burn to exhaustion. Water-accommodated fractions (WAFs) of the burn residue were created in full sunlight to determine the effects of photochemical weathering on the burned oil residue. Our findings show that increased dissolved organic carbon concentrations (DOC) for the light unburned and light burned after sunlight exposure positively correlated to decreased microbial growth and production inhibition (i.e. more toxic) when compared to the dark controls. Optical and molecular analytical techniques were used to identify the classes of compounds contributing to the toxicity in the dark and light burned and dark and light unburned WAFs. After light exposure, the optical composition between the light unburned and light burned differed significantly (p < 0.05), revealing key fluorescence signatures commonly identified as crude oil degradation products. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis showed more condensed aromatic, reduced oxygenated compounds present in the light burned than in the light unburned. FT-ICR MS also showed an increase in the percent relative abundance of carboxyl-rich alicyclic molecules (CRAM) like compounds in the light burned compared to light unburned. The increase in CRAM suggests that the composition of the light burned is more photorefractory, i.e., reduced, explaining the residual toxicity observed in microbial activity. Overall, these data indicate burning removes some but not all toxic compounds, leaving behind compounds which retain considerable toxicity. This study shows that burn oil residues are photolabile breaking down further into complex reduced compounds.

Excerpt - The project provided key baseline information about the shallow continental shelf environment in the northeastern Gulf of Mexico. This area is poorly studied compared to other continental shelves such as the South Atlantic Bight. Colonization of benthic invertebrates increased secondary production. This in turn supports higher trophic levels, particularly the commercially important reef fishes such as snapper, triggerfish and sheepshead. Results from this work represent one of the few studies of primary production, biogeochemical cycling, and the implications to fisheries production in the northeastern Gulf of Mexico. With the increasing deployment of artificial reefs in Florida, this provides key information for management of these habitats.