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1. Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes

   https://doi.org/10.1038/s41396-023-01421-0  

   Zhou, Zhichao; Tran, Patricia Q.; Adams, Alyssa M.; Kieft, Kristopher; Breier, John A.; Fortunato, Caroline S.; Sheik, Cody S.; Huber, Julie A.; Li, Meng; Dick, Gregory J.; et al (January 2023, The ISME Journal)

   Abstract In globally distributed deep-sea hydrothermal vent plumes, microbiomes are shaped by the redox energy landscapes created by reduced hydrothermal vent fluids mixing with oxidized seawater. Plumes can disperse over thousands of kilometers and their characteristics are determined by geochemical sources from vents, e.g., hydrothermal inputs, nutrients, and trace metals. However, the impacts of plume biogeochemistry on the oceans are poorly constrained due to a lack of integrated understanding of microbiomes, population genetics, and geochemistry. Here, we use microbial genomes to understand links between biogeography, evolution, and metabolic connectivity, and elucidate their impacts on biogeochemical cycling in the deep sea. Using data from 36 diverse plume samples from seven ocean basins, we show that sulfur metabolism defines the core microbiome of plumes and drives metabolic connectivity in the microbial community. Sulfur-dominated geochemistry influences energy landscapes and promotes microbial growth, while other energy sources influence local energy landscapes. We further demonstrated the consistency of links among geochemistry, function, and taxonomy. Amongst all microbial metabolisms, sulfur transformations had the highest MW-score, a measure of metabolic connectivity in microbial communities. Additionally, plume microbial populations have low diversity, short migration history, and gene-specific sweep patterns after migrating from background seawater. Selected functions include nutrient uptake, aerobic oxidation, sulfur oxidation for higher energy yields, and stress responses for adaptation. Our findings provide the ecological and evolutionary bases of change in sulfur-driven microbial communities and their population genetics in adaptation to changing geochemical gradients in the oceans. 

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2. Stable isotope values of consumers, producers, and organic matter in the Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, 2019 – ongoing

   https://doi.org/10.6073/pasta/da36c97eccd5461ba32eecce23a53892  

   Rezek, Ryan (January 2024, Environmental Data Initiative)

   {"Abstract":["Wetland food webs have often been characterized as detrital-based ‘brown’ energy pyramids, whereas the relative role of autotrophic (‘green’) vs. microbial (‘brown’) energy sources falls along a continuum set by physical drivers, as well as autochthonous and allochthonous inputs (Moore et al. 2004; Evans-White & Halvorson 2017) that change with ecosystem development (Schmitz et al. 2006). In the Florida Coastal Everglades (FCE), metabolic imbalances, including the collapse of calcareous periphyton mats, begin with a loss of foundation species primary production and legacy organic matter (Gaiser et al. 2006). This process likely enhances heterotrophic microbial productivity (Schulte 2016) and the supply of detrital energy to consumers by changing bioavailable and recalcitrant carbon supplies (Baggett et al. 2013). A shift from complex periphyton communities to transient planktonic communities under elevated P exposure reduces habitat structure and animal refuges but increases ‘green’ energy supplies and edibility (Trexler et al. 2015; Naja et al. 2017). Multiple sites (n=9) within the FCE were selected to document changes in coastal food webs as a result of eutrophication and increasing hydrologic variability. The project began in 2019 and is currently ongoing.\n \n References:\n Baggett, L. P., Heck, K. L., Frankovich, T. A., Armitage, A. R., & Fourqurean, J. W. (2013). Stoichiometry, growth, and fecundity responses to nutrient enrichment by invertebrate grazers in sub-tropical turtle grass (Thalassia testudinum) meadows. Marine biology, 160, 169-180.\n Evans-White, M. A., and H. M. Halvorson. 2017. Comparing the Ecological Stoichiometry in Green and Brown Food Webs – A Review and Meta-analysis of Freshwater Food Webs. Frontiers in Microbiology 8:1184. \n Gaiser, E. E., Childers, D. L., Jones, R. D., Richards, J. H., Scinto, L. J., & Trexler, J. C. (2006). Periphyton responses to eutrophication in the Florida Everglades: cross‐system patterns of structural and compositional change. Limnology and Oceanography, 51(1part2), 617-630.\n Moore, J. C., E. L. Berlow, D. C. Coleman, P. C. Ruiter, Q. Dong, A. Hastings, N. C. Johnson, K. S. McCann, K. Melville, P. J. Morin, K. Nadelhoffer, A. D. Rosemond, D. M. Post, J. L. Sabo, K. M. Scow, M. J. Vanni, and D. H. Wall. 2004. Detritus, trophic dynamics and biodiversity: Detritus, trophic dynamics and biodiversity. Ecology Letters 7:584–600. \n Naja, M., Childers, D. L., & Gaiser, E. E. (2017). Water quality implications of hydrologic restoration alternatives in the Florida Everglades, United States. Restoration Ecology, 25, S48-S58.\n Schmitz, O. J., Kalies, E. L., & Booth, M. G. (2006). Alternative dynamic regimes and trophic control of plant succession. Ecosystems, 9, 659-672.\n Schulte, Nicholas O., "Controls on Benthic Microbial Community Structure and Assembly in a Karstic Coastal Wetland" (2016). FIU Electronic Theses and Dissertations. 2447. 10.25148/etd.FIDC000233\n Trexler, J. C., Gaiser, E. E., Kominoski, J. S., & Sanchez, J. (2015). The role of periphyton mats in consumer community structure and function in calcareous wetlands: lessons from the Everglades. Microbiology of the everglades ecosystem, 155-179."]} 

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3. HPLC and 32P ‐radiolabeling method for quantification of microbial adenylate concentrations and turnover rates in seawater

   https://doi.org/10.1002/lom3.10499  

   Lanpher, Kaycie B.; Popendorf, Kimberly J. (July 2022, Limnology and Oceanography: Methods)

   Abstract We optimized a high throughput method to quantify turnover rates of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) in marine microbes from simultaneous measures of the respective stocks and phosphorylation rates. We combined a microbial adenylate extraction method using boiling 20 mM Tris buffer with purification and analysis by high pressure liquid chromatography optimized to quantify these intracellular adenylate concentrations in marine microbes. Additionally, we incorporated radiolabeled phosphate (³²P_i) incubations to quantify phosphorus (P) uptake rates and the phosphorylation rates for these adenylate compounds in microbial cells. With this method, we can directly assess the variations in microbial growth rates, metabolic turnover rates, energy charge, and adenylate storage. We applied and validated this method application with environmental samples from Biscayne Bay, Florida, and quantified adenylate turnover times of 12, 15, and 73 min, for ATP, ADP, and AMP, respectively. Future incorporation of this method into experiments and geographic surveys across marine environments will allow for direct assessments of changes in microbial metabolic activity in relation to other ecological variables. 

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4. Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents

   https://doi.org/10.1128/mSystems.00553-19  

   McAllister, Sean M.; Polson, Shawn W.; Butterfield, David A.; Glazer, Brian T.; Sylvan, Jason B.; Chan, Clara S.; Lloyd, Karen G. (February 2020, mSystems)

   ABSTRACT Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans . However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria , using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ , often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments. IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2 , in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments. 

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5. Chemical Speciation: Defining the Niche of Hot Spring Ammonia-Oxidizing Archaea (Oral Presentation)

   Weeks, Katelyn; Trembath-Reichert, Elizabeth; Robare, Jordyn; Debes, Vincent R; Howells, Alta; Boyer, Grayson; Shock, Everett L (July 2025, Goldschmidt 2025 Conference)

   The availability of chemical energy supplies is fundamental to environmental and planetary habitability. However, the presence of a chemical energy supply does not guarantee the presence of microorganisms capable of consuming it. In this study, chemical energy supplies available in Yellowstone National Park (YNP) hot springs were calculated, and the results indicate that ammonia oxidation, calculated using total dissolved ammonia, is one of the major energy supplies. Nevertheless, known ammonia-oxidizers (AO) are only present in a small fraction of the hot springs tested. Where AO are present, they do not dominate the microbial communities (relative abundances <5%), even in cases where total dissolved ammonia oxidation is the richest energy supply. The AO in YNP hot springs are predominantly ammonia-oxidizing archaea (AOA), which tend to favor environments with low total ammonia (sum of NH3 and NH4+) concentrations, despite the requirement of ammonia (NH3) as a substrate. Hot spring pH and temperature determine the ratio of NH3 to NH4+ and, consequently, NH3 availability to resident AOA. In this study, total ammonia measurements were collected from YNP hot spring samples using ion chromatography in coordination with biological sampling. DNA was extracted from simultaneously collected samples for 16S rRNA gene sequencing and analysis, and for the identification of known AOA. The WORM-portal (https://worm-portal.asu.edu/) was used to speciate the total ammonia measurements into ammonia and ammonium activities. By performing speciation calculations, we identified a potential lower limit for substrate (NH3) availability and a potential upper limit for NH4+ concentrations for the YNP hot spring AOA. Thus, the niche for AOA across YNP hot springs is dictated by the form of the total dissolved ammonia present, not by the energy supply available for total dissolved ammonia oxidation. 

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