Jennifer L Macalady

• Ph.D. Soil Science UC Davis
• Professor (Associate) at Pennsylvania State University

High concentrations of harmful metal(loid)s and extreme acidity are persistent environmental concerns in acidic pit lakes. In this study, we examine Cueva de la Mora (CM), a meromictic pit lake in the Iberian Pyrite Belt, Spain, as a model system. Our research aims to explore potential bioremediation strategies to mitigate the impacts of metal(loid...

Cueva de la Mora (CM) is a permanently stratified acidic pit lake in the Iberian Pyrite Belt in southwestern Spain. CM accumulates mine drainage from water-rock interactions with its open cast pit and adjacent mine spoils, leading to high concentrations of metal(loid)s, sulfate, and acidity. This unique environment makes CM a model system for study...

The search for analogs of extraterrestrial microbial life has prompted exhaustive exploration and research of many chemically and physically extreme environments on Earth, including dry desserts, cold arctic environments, hot geothermal systems, volcanic crater lakes or acidic and metal-rich acid mine drainage (AMD) sites. In recent years, acidic p...

Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active g...

Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes...

This work shines light on the role of extracellular polymeric substances (EPS) in the formation and preservation of elemental sulfur biominerals produced by sulfur-oxidizing bacteria. We characterized elemental sulfur particles produced within a Sulfurovum-rich biofilm in the Frasassi Cave System (Italy). The particles adopt spherical and bipyramid...

In previous work, lab‐scale reactors designed to study microbial Fe(II) oxidation rates at low pH were found to have stable rates under a wide range of pH and Fe(II) concentrations. Since the stirred reactor environment eliminates many of the temporal and spatial variations that promote high diversity among microbial populations in nature, we were...

Cueva de la Mora (CM) is an acidic, meromictic pit lake in the Iberian Pyrite Belt characterized by extremely high metal(loid) concentrations and strong gradients in oxygen, metal, and nutrient concentrations. We hypothesized that geochemical variations with depth would result in differences in community composition and in metal resistance strategi...

Cyanobacterial mats were hotspots of biogeochemical cycling during the Precambrian. However, mechanisms that controlled O2 release by these ecosystems are poorly understood. In an analog to Proterozoic coastal ecosystems, the Frasassi sulfidic springs mats, we studied the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis (OP and A...

We examined the geochemistry and bacterial and archaeal community structure in the acidic (pH < 2.4) pit lake at Peña de Hierro, near the headwaters of the Río Tinto. The lake has strong vertical gradients in light, O2, pH, conductivity, and dissolved ions. Bacterial and archaeal communities between 0 and 32 m displayed low species richness and eve...

Chemotrophic microorganisms gain energy for cellular functions by catalyzing oxidation‐reduction (redox) reactions that are out of equilibrium. Calculations of the Gibbs energy (∆Gr) can identify whether a reaction is thermodynamically favorable and quantify the accompanying energy yield at the temperature, pressure, and chemical composition in the...

Elemental sulfur [S(0)] is a central and ecologically important intermediate in the sulfur cycle, which can be used by a wide diversity of microorganisms that gain energy from its oxidation, reduction, or disproportionation. S(0) is formed by oxidation of reduced sulfur species, which can be chemically or microbially mediated. A variety of sulfur-o...

Chemotrophic microorganisms gain energy for cellular functions by catalyzing oxidation-reduction (redox) reactions that are out of equilibrium. Calculations of the Gibbs energy (ΔG r ) can identify whether a reaction is thermodynamically favorable, and the accompanying energy yield at the temperature, pressure, and chemical composition in the syste...

Our understanding or the early record of life on Earth relies on our ability to identify microbial biosignatures in the geological record. Among those, morphological signatures (i.e. microfossils), which often consist in microscopic spheres and filaments preserved in rocks, are particularly difficult to interpret. Recently, we discovered that the r...

Central Italy has been a cradle of geology for centuries. For more than 100 years, studies at the Umbria and Marche Apennines have led to new ideas and a better understanding of the past, such as the Cretaceous-Paleogene (K-Pg) boundary event, or the events across the Eocene-Oligocene transition from a greenhouse to an icehouse world. The Umbria-Ma...

The Iberian Pyrite Belt (IPB) hosts the world’s largest massive sulfide deposit and has been mined from pre-Roman times to the present day for precious (Au, Ag) and base (Cu, Pb, Zn) metals and sulfur. Most of the mines were abandoned during the twentieth century leaving an extensive legacy of waste rock dumps, tailings impoundments, and flooded op...

Elemental sulfur (S(0)) is an important intermediate of the sulfur cycle and is generated by chemical and biological sulfide oxidation. Raman spectromicroscopy can be applied to environmental samples for the detection of S(0), as a practical non-destructive micron-scale method for use on wet material and living cells. Technical advances in filter m...

Elemental sulfur (S 0) in the environment is frequently interpreted as having been produced by S-cycling bacteria. Several crystalline phases (α-S8, β-S8, and γ-S8 allotropes) of S 0 exist in nature. It was recently discovered that micrometric S 0 spheres encapsulated with carbon can be produced in the absence of any microbial activity through the...

During much of the Proterozoic, large portions of the oceanic margins might have experienced ferro-euxinic conditions, where both dissolved sulfide and ferrous iron were available. Local microoxic conditions close to the redox interface might have enabled sulfur-oxidizing microorganisms to thrive, producing elemental sulfur (S 0) [1]. Chemical oxid...

A significant portion of oil released during the Deepwater Horizon disaster reached the Gulf of Mexico (GOM) seafloor. Predicting the long-term fate of this oil is hindered by a lack of data about the combined influences of pressure, temperature, and sediment composition on microbial hydrocarbon remineralization in deep-sea sediments. To investigat...

Gas chromatography–Mass spectrometry (GC-MS) and quantification methods. (DOCX)

Calculating contamination level. (DOCX)

Depletion (%) of total n-alkane and total PAH of individual samples. (TOC: total organic carbon, Carb: carbonate in the sediments, P: pressure, T: temperature, WD: water depth, SED: sediment fraction, WAF: water fraction). (DOCX)

Depletion of different PAH compound groups to compare the extent of biodegradation as number of rings increases. (C1: methyl, C2: ethyl or dimethyl, C3: trimethyl, C4: tetramethyl; Naph: napthalene, PNT: phenanthrene, Fluo: fluorene, DBT: dibenzothiophene, Py: pyrene, 11H-benzoF: 11H-benzo[b]fluorene, Chy: chrysene). (TIFF)

Change in ratios of C17 n-alkane/pristane and C18 n-alkane/phytane after 18 days. A, sediment fractions (SED) and B, water fractions (WAF). Initial ratios are represented by the black square. Samples are color-coded according to sampling water depths. The dashed arrow represents interpreted direction of increasing biodegradation extent. (TIF)

Background hydrocarbons in un-incubated sediments. (DOCX)

Selected Ion Monitoring method for alkylated PAHs. Each compound group is identified based on a quantitative ion and a confirmation ion m/z (Zeigler et al., 2008; Robbat Jr. and Wilton, 2014*). * Zeigler C., MacNamara K., Wang Z., Robbat Jr. A. Total alkylated polycyclic aromatic hydrocarbon characterization and quantitative comparison of selected...

Summary of experimental and analytical procedures. (TIF)

Depletion in total cyclohexanes (m/z 83) after 18 days. The dashed arrow represents interpreted direction of increasing biodegradation extent. (TIF)

Depletion of total PAHs after 18 days of incubation of oil in water fraction (WAF, triangles). Initial total PAHs are represented by squares. Samples are color-coded according to sampling water depths. The dashed arrow represents interpreted direction of increasing biodegradation extent. (TIF)

Distribution of hopanes and triaromatic sterane compound groups, showing the similarity between day 0 and day 18 samples, to justify the use of C30 hopane and C26-TAS as internal conservative oil biomarker in our study. (DOCX)

Calculation of n-alkane depletion due to off-gassing at 15 Mpa. (DOCX)

Oil hydrocarbons analyzed in this study and their quantitative molecular ion (m/z). (DOCX)

Depletion of different n-alkanes to compare the extent of biodegradation as number of carbon increases. A. Mean and standard errors plot for depletion of each n-alkane for all day-18 samples; B. Boxplot for depletion of each n-alkane for all day-18 samples. (TIFF)

We report extremely low-light-adapted anoxygenic photosynthesis in a thick microbial mat in Magical Blue Hole, Abaco Island, The Bahamas. Sulfur cycling was reduced by iron oxides and organic carbon limitation. The mat grows below the halocline/oxycline at 30 m depth on the walls of the flooded sinkhole. In situ irradiance at the mat surface on a s...

We report the isolation of a pinnacle-forming cyanobacterium isolated from a microbial mat covering the sediment surface at Little Salt Spring—a flooded sinkhole in Florida with a perennially microoxic and sulfidic water column. The draft genome of the isolate encodes all of the enzymatic machinery necessary for both oxygenic and anoxygenic photosy...

Cave minerals deposited in the presence of microbes may host geochemical biosignatures that can be utilized to detect subsurface life on Earth, Mars, or other habitable worlds. The sulfur isotopic composition of gypsum (CaSO4·2H2O) formed in the presence of sulfur-oxidizing microbes in the Frasassi cave system, Italy, was evaluated as a biosignatur...

Little Salt Spring (Sarasota County, FL, USA) is a sinkhole with groundwater vents at ~77 m depth. The entire water column experiences sulfidic (~50 μM) conditions seasonally, resulting in a system poised between oxic and sulfidic conditions. Red pinnacle mats occupy the sediment–water interface in the sunlit upper basin of the sinkhole, and yielde...

Our ability to identify unambiguously microbial biosignatures in the rock record conditions our knowledge and understanding of life on early Earth and on other planets. This task is complicated by the fact that several abiotic processes can produce microscopic objects, called biomorphs, that closely resemble microorganisms. Here we will present a n...

Low-pH Fe(II) oxidation occurs naturally in certain acid mine drainage (AMD) systems and can be incorporated into passive treatments by enhancing the development of terraced iron formations (TIFs). For extremely difficult-to-treat AMD (very low pH, high concentrations of Fe(II) and associated metals), an active treatment bioreactor may be required....

Importance: Acid mine drainage pollutes more than 19,300 km of rivers and streams and 72,000 ha of lakes worldwide (1). Remediation is frequently ineffective and costly, upwards of US$100 billion globally (2, 3, 4) and nearly US$5 billion in Pennsylvania alone (5). Microbial Fe(II) oxidation is more efficient than abiotic Fe(II) oxidation at low p...

Oxygenic and anoxygenic photosynthesis were studied with microsensors in microbial mats found at 9-10 m depth in anoxic and sulfidic water in Little Salt Spring (Florida, USA). The lake sediments were covered with a 1-2 mm thick red mat dominated by filamentous Cyanobacteria, below which Green Sulfur Bacteria (GSB, Chlorobiaceae) were highly abunda...

Importance: This study showed that different microbial communities enriched from two sites maintained distinct microbial community traits inherited from their respective 'seed' materials. Long-term operation (up to 128 d fed-batch enrichment followed by up to 138 d flow-through experiments) of these two systems did not lead to the same, or even mo...

Extremely acidic (pH 0-1.5) Acidithiobacillus-dominated biofilms known as snottites are found in sulfide-rich caves around the world. Given the extreme geochemistry and subsurface location of the biofilms, we hypothesized that snottite Acidithiobacillus populations would be genetically isolated. We therefore investigated biogeographic relationships...

The draft genome sequence of Chlorobium limicola strain Frasassi was assembled from metagenomic sequencing of a green mat in an artificially lighted aquarium inside the Frasassi caves in Italy. The genome is 2.08 Mbp in size and contains the necessary genes for anoxygenic photosynthesis and CO 2 fixation.

Caves are subterranean environments that support life largely in the absence of light. Because caves are completely or almost completely removed from the photosynthetic productivity of the sunlit realm, most cave ecosystems are supported either by inputs of organic matter from the surface or by in situ sources of inorganic chemical energy. The majo...

Mahoney Lake in British Columbia is an extreme meromictic system with unusually high levels of sulfate and sulfide present in the water column. As is common in strongly stratified lakes, Mahoney Lake hosts a dense, sulfide-oxidizing phototrophic microbial community where light reaches the chemocline. Below this “plate,” the euxinic hypolimnion is a...

Gypsum (CaSO4.2H2O) precipitation experiments were carried out at low pH in the presence of the sulfur oxidizing bacterium Acidithiobacillus thiooxidans. The observed Ca isotopic fractionation (expressed as Δ44/40Cas-f = δ44/40Casolid- δ44/40Cafluid) at the end of each experimental time period (∼50 to 60 days) was -1.41 to -1.09‰ in the biotic expe...

Understanding the role of biology in planetary evolution remains an outstanding challenge to geobiologists. Progress towards unraveling this puzzle for Earth is hindered by the scarcity of well-preserved rocks from the Archean (4.0 to 2.5 Gyr ago) and Proterozoic (2.5 to 0.5 Gyr ago) Eons. In addition, the microscopic life that dominated Earth's bi...

Sulfide oxidation forms a critical step in the global sulfur cycle, although this process is notoriously difficult to constrain due to the multiple pathways and highly reactive intermediates involved. Multiple sulfur isotopes (δ34S and δ33S) can provide a powerful tool for unravelling sulfur cycling processes in modern (and ancient) environments, a...

We studied the interaction between phototrophic and chemolithoautotrophic sulphide-oxidizing microorganisms in natural microbial mats forming in sulphidic streams. The structure of these mats varied between two end-members: one characterized by a layer dominated by large sulphur-oxidizing bacteria (SOB; mostly Beggiatoa-like) on top of a cyanobacte...

Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces at sites throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cul...

We report here the draft genome sequence of Rhodococcus qingshengii strain TUHH-12. The ability of this piezotolerant bacterium to grow on crude oil and tetracosane as sole carbon sources at 150 × 105 Pa makes it useful in studies of hydrocarbon degradation under simulated deep-sea conditions.

A legacy of coal mining in the Appalachians has provided a unique opportunity to study the ecological niches of iron-oxidizing microorganisms. Mine-impacted, anoxic groundwater with high dissolved metal concentrations emerges at springs and seeps associated with iron oxide mounds and deposits. These deposits are colonized by iron oxidizing microorg...

Mahoney Lake represents an extreme meromictic model system and is a valuable site for examining the organisms and processes that sustain photic zone euxinia (PZE). A single population of purple sulfur bacteria (PSB) living in a dense phototrophic plate in the chemocline is responsible for most of the primary production in Mahoney Lake. Here, we pre...

Snottites are extremely acidic (pH 0–2) biofilms that form on the walls and ceilings of hydrogen sulfide-rich caves. Recent work suggests that microbial communities including snottites and related cave wall biofilms accelerate cave formation by oxidizing sulfide to sulfuric acid. Therefore, we used full-cycle rRNA methods and metagenomics to explor...

The Frasassi and Acquasanta Terme cave systems in Italy host isolated lithoautotrophic ecosystems characterized by sulfur-oxidizing biofilms with up to 50% S(0) by mass. The net contributions of microbial taxa in the biofilms to production and consumption of S(0) are poorly understood and have implications for understanding the formation of geologi...

Isoprenoids, a diverse class of compounds synthesized by all three domains of life, comprise many of the biomarker compounds used in paleoenvironmental and paleoecological reconstruction of Earth history. These biomarkers include hopanoids, sterols and archaeal membrane lipids. While changes in hydrocar- bon profiles in anoxic sediments and oilfiel...

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population s...

Halorhabdus utahensis, Natronomonas pharaonis, Haloferax sulfurifontis and Halobaculum gomorrense were grown at salinity values between 10% and 30% NaCl (w/v). The strains represent four haloarchaeal genera and have a range of salinity optima. Analysis of core membrane lipids of each strain using gas chromatography– mass spectrometry (GC–MS) reveal...

Filter-collected production water samples from a methane-rich gas field in the Cook Inlet basin of Alaska were investigated using whole-cell rRNA-targeted fluorescence in situ hybridization (FISH) and 16S rRNA tag pyrosequencing. Both techniques were consistent in determining the microbial community composition, including the archaeal or bacterial...

Inland blue holes of the Bahamas are anchialine ecosystems with distinct fresh and salt water layers, and anoxic or microoxic conditions at depth. Scientific cave diving and geomicrobiology exploration of blue holes are providing a first glimpse of the geochemistry and microbial life in these vertically stratified karst features. We hypothesized th...

Organic biomarkers in marine sedimentary rocks hold important clues about the early history of Earth's surface environment. The chemical relicts of carotenoids from anoxygenic sulfur bacteria are of particular interest to geoscientists because of their potential to signal episodes of marine photic-zone euxinia such as those proposed for extended pe...

Highly acidic (pH 0-1) biofilms, known as 'snottites', form on the walls and ceilings of hydrogen sulfide-rich caves. We investigated the population structure, physiology and biogeochemistry of these biofilms using metagenomics, rRNA methods and lipid geochemistry. Snottites from the Frasassi cave system (Italy) are dominated (>70% of cells) by Aci...

Microbial methane accumulations have been discovered in multiple coal-bearing basins over the past two decades. Such discoveries were originally based on unique biogenic signatures in the stable isotopic composition of methane and carbon dioxide. Basins with microbial methane contain either low-maturity coals with predominantly microbial methane ga...

Lower Red Eyes is an acid mine drainage site in Pennsylvania where low-pH Fe(II) oxidation has created a large, terraced iron mound downstream of an anoxic, acidic, metal-rich spring. Aqueous chemistry, mineral precipitates, microbial communities, and laboratory-based Fe(II) oxidation rates for this site were analyzed in the context of a deposition...

Acid mine drainage (AMD) is a common environmental problem in Pennsylvania that results from the oxidation of sulfide minerals exposed at abandoned coal mines. In these systems, acidophilic microorganisms catalyze the oxidation of ferrous (Fe2+) to ferric iron (Fe3+), which precipitates as iron-hydroxide minerals. To develop and improve low-pH bior...

Two major sources of energy, light and chemical potential, are available to microorganisms. However, energy is not always abundant and is often a limiting factor in microbial survival and replication. The anoxic, terrestrial subsurface offers a unique opportunity to study microorganisms and their potentially novel metabolic strategies that are rele...

Sequences were screened for chimeras using Bellerophon 3.

Sequences were screened for chimeras using Bellerophon 3.

Sequences were screened for chimeras using Bellerophon 3.

Sequences were screened for chimeras using Bellerophon 3.

Sequences were screened for chimeras using Bellerophon 3.

Sequences were screened for chimeras using Bellerophon 3.

Sequences were screened for chimeras using Bellerophon 3.

Sequences were screened for chimeras using Bellerophon 3.

Sequences were screened for chimeras using Bellerophon 3.