Zackary J Jay

• Ph.D.
• Researcher at Montana State University

High-temperature environments (> 70°C) contain diverse and abundant members of the crenarchaeal order Thermoproteales. However, a comprehensive study of the distribution and function of diverse members of this group across different habitat types has not been conducted. Consequently, the goals of this study were to determine the distribution of dif...

The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discove...

The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently develo...

Methane is the second most abundant climate-active gas, and understanding its sources and sinks is an important endeavour in microbiology, biogeochemistry, and climate sciences1,2. For decades, it was thought that methanogenesis, the ability to conserve energy coupled to methane production, was taxonomically restricted to a metabolically specialize...

Methanogenesis mediated by archaea is the main source of methane, a strong greenhouse gas, and thus is critical for understanding Earth’s climate dynamics. Recently, genes encoding diverse methanogenesis pathways have been discovered in metagenome-assembled genomes affiliated with several archaeal phyla1–7. However, all experimental studies on meth...

Thermophilic microbial communities growing in low-oxygen environments often contain early-evolved archaea and bacteria, which hold clues regarding mechanisms of cellular respiration relevant to early life. Here, we conducted replicate metagenomic, metatranscriptomic, microscopic, and geochemical analyses on two hyperthermophilic (82–84 °C) filament...

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use mul...

Over the past decade, environmental metagenomics and polymerase chain reaction-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic Euryarchaeota t...

High-temperature microbial communities contain early evolved archaea and bacteria growing under low levels of oxygen and thus may hold important clues regarding mechanisms of oxygen respiration relevant to the evolutionary history of Earth. Conch and Octopus Springs in Yellowstone National Park, WY (YNP) are highly similar alkaline-chloride springs...

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use mul...

Over the past decade, environmental metagenomics and PCR-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic euryarchaeotes that have long been co...

Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. D...

Methane is the second most abundant climate-active gas and understanding its sources and sinks is a crucial endeavor in microbiology, biogeochemistry, and climate sciences (1,2). For decades, it was thought that methanogenesis, the ability to conserve energy coupled to methane production, was restricted to a taxonomically and metabolically speciali...

Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, “ Candidatus Culexarchaeia”,...

Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated the methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiment...

Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, “ Candidatus Culexarchaeia”,...

The miniaturization of polymerase chain reaction (PCR) using drop-based microfluidics allows for amplification of single nucleic acids in aqueous picoliter-sized drops. Accurate data collection during PCR requires that drops remain stable to coalescence during thermocycling and drop contents are retained. Following systematic testing of known PCR a...

Metagenomic studies have revolutionized our understanding of the metabolic potential of uncultured microorganisms in various ecosystems. However, many of these genomic predictions have yet to be experimentally tested, and the functional expression of genomic potential often remains unaddressed. In order to obtain a more thorough understanding of ce...

The miniaturization of real time quantitative polymerase chain reaction (qPCR) using drop-based microfluidics, or droplet qPCR, allows for quantification of single genomes. The genomes are compartmentalized into aqueous microdroplets, picoliters in volume, separated by an immiscible oil, and stabilized by a surfactant. In droplet qPCR, accurate dat...

Electron bifurcating, [FeFe]-hydrogenases are recently described members of the hydrogenase family and catalyze a combination of exergonic and endergonic electron exchanges between three carriers (2 ferredoxinred- + NAD(P)H + 3H+ = 2 ferredoxinox + NAD(P)+ + 2 H2). A thermodynamic analysis of the bifurcating, [FeFe]-hydrogenase reaction, using elec...

Phylogenetic and geological evidence supports the hypothesis that life on Earth originated in thermal environments and conserved energy through methanogenesis or sulfur reduction. Here we describe two populations of the deeply rooted archaeal phylum Korarchaeota, which were retrieved from the metagenome of a circumneutral, suboxic hot spring that c...

Background: Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habitats using 16S rRNA gene surveys, genome sequences have been available for only three Nanoarchaeota and their hosts. The host...

Hydrogen peroxide (H2O2), superoxide (O2•-), and hydroxyl radicals (OH•) are produced in natural waters via ultraviolet (UV) light-induced reactions between dissolved oxygen (O2) and organic carbon, and further reaction of H2O2 and Fe(II) (i.e., Fenton chemistry). The temporal and spatial dynamics of H2O2 and other dissolved compounds [Fe(II), Fe(I...

Volcanism and post-magmatism contribute significant annual methane (CH4) fluxes to the atmosphere (on par with other natural sources such as forest fire and wild animal emissions) and have been implicated in past climate-change events. The Yellowstone hot spot is one of the largest volcanic systems on Earth and is known to emit CH4 (as well as carb...

Although the biological fixation of CO2 by chemolithoautotrophs provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs as a carbon and energy source, the relative amounts of autotrophic C in chemotrophic microbial communities are not well-established. The extent and mechanisms of CO2 fixation were evaluated across a compr...

Two haloalkaliphilic bacteria isolated from industrial brine solutions were characterized via molecular, physiological, and in silico metabolic pathway analyses. Genomes from the organisms, designated Halomonas BC1 and BC2, were sequenced; 16S ribosomal subunit-based phylogenetic analysis revealed a high level of similarity to each other and to Hal...

Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentou...

Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and su...

Yellowstone Lake (Yellowstone National Park, WY, USA) is a large high-altitude (2200 m), fresh-water lake, which straddles an extensive caldera and is the center of significant geothermal activity. The primary goal of this interdisciplinary study was to evaluate the microbial populations inhabiting thermal vent communities in Yellowstone Lake using...

Thermoproteales populations (phylum Crenarchaeota) are abundant in high-temperature (>70 °C) environments of Yellowstone National Park (YNP) and are important in mediating biogeochemical cycles of sulfur, arsenic, and carbon. The objectives of this study were to determine specific physiological attributes of the isolate Pyrobaculum yellowstonensis...

Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The obje...

The candidate archaeal phylum 'Aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. The phylogeny and metabolic potential of Aigarchaeota has been deduced from several recent single-cell amplified genomes; however, a detailed description of their metabolic potential and in situ transcriptional activity is abs...

Novel lineages of the phylum Thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. The primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found...

High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal...

Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across the Yellowstone geothermal ecosystem, and to identify met...

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal "filamentous streamer" communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone...

TIGRFAM electron transport gene family counts across six Aquificales streamer communities and results for comparison of low-pH and high-pH sites using White’s non-parametric T-test.

TIGRFAM functional category gene family counts across six Aquificales streamer communities and results for comparison of taxonomically distinct sites (Hydrogenobaculum-dominated, Sulfurihydrogenibium-dominated, Thermocrinis (Aquificaceae)-dominated) using ANOVA.

Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dom...

The Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply rooted and poorly understood archaea, bacteria, and viruses. Microbial communities in high-temperature environments are generally less diverse than soil, marine, sediment, or lake habitats and therefore offer a tremendous o...

Contributions of NSF Research Coordination Network Steering Committee and Working Group members to the Yellowstone Metagenome Community Sequencing Project (DOE_JGI CSP 787081).

Geochemical parameters measured in the bulk aqueous (<0.2 μm) phase in 20 different geothermal systems sampled for metagenome analysis.

List of gene sequences and corresponding accession numbers used to query the assembled environmental sequence data for assessing potential metabolic attributes associated with the predominant phylotypes found within these geothermal sites.

Distribution of direct repeats (DR) in archaeal-dominated sites.

Summary of 16S rRNA gene sequences observed in assembled metagenome sequence data from high-temperature, archaeal-dominated chemotrophic sites in Yellowstone National Park (also, see Figure 4 for phylogenetic tree).

Survey of single-copy genes corresponding to the predominant archaeal populations present in high-temperature geothermal microbial communities of YNP.

Description of predominant sequence assemblies in archaeal-dominated sites, including largest scaffold (kbp), number of scaffolds in cluster, total consensus sequence (Mbp), average G + C content (%), and closest cultured relative of the 16S rRNA gene found within the assembled data.

Geothermal and hydrothermal waters often contain high concentrations of dissolved sulfide, which reacts with oxygen (abiotically or biotically) to yield elemental sulfur and other sulfur species that may support microbial metabolism. The primary goal of this study was to elucidate predominant biogeochemical processes important in sulfur biogeochemi...

YNP metagenome project steering committee and working group members and their respective contributions are listed in Table S1 in Supplementary Material. The Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply rooted and poorly understood archaea, bac-teria, and viruses. Microbia...

Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YN...

Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats in Yellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of cren...

Background/Question/Methods Phototrophic microbial mats that develop in the effluent channels of hot springs in Yellowstone National Park serve as models to investigate how microbial community structures are related to community functions, given their relatively limited diversity and their tractability for studying organismal interactions. It was...

Yellowstone Lake (Yellowstone National Park, WY, USA) is a large, high-altitude, fresh-water lake that straddles the most recent Yellowstone caldera, and is situated on top of significant hydrothermal activity. An interdisciplinary study is underway to evaluate the geochemical and geomicrobiological characteristics of several hydrothermal vent envi...