Jan P. Amend

University of Southern California | USC · Department of Earth Sciences

This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora . To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron‐oxidizer, providing a unique opportunit...

Biogeochemical sulfur cycling in sulfidic karst systems is largely driven by abiotic and biological sulfide oxidation, but the fate of elemental sulfur (S ⁰ ) that accumulates in these systems is not well understood. The Frasassi Cave system (Italy) is intersected by a sulfidic aquifer that mixes with small quantities of oxygen‐rich meteoric water,...

Deep marine sediments (>1mbsf) harbor~26% of microbial biomass and are the largest reservoir of methane on Earth. Yet, the deep subsurface biosphere and controls on its contribution to methane production remain underexplored. Here, we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying...

A novel, autotrophic, mesophilic bacterium, strain RS19-109 T , was isolated from sulphidic stream sediments in the Frasassi Caves, Italy. The cells of this strain grew chemolithoautotrophically under anaerobic conditions while disproportionating elemental sulphur (S ⁰ ) and thiosulphate, but not sulphite with bicarbonate/CO 2 as a carbon source. A...

Sulfur comproportionation is a heretofore undiscovered microbial catabolism that was predicted based on thermodynamic calculations. Here, we report the isolation of an Acidithiobacillus thiooxidans strain from extremely low pH snottite biofilms in the karst at Frasassi, Italy. The strain grew to cell densities of >10 ⁷ cells mL ⁻¹ in autotrophic su...

Biogeochemical sulfur cycling in sulfidic karst systems is largely driven by abiotic and biological sulfide oxidation, but the fate of elemental sulfur (S ⁰ ) that accumulates in these systems is not well understood. The Frasassi Cave system (Italy) is intersected by a sulfidic aquifer that mixes with small quantities of oxygen-rich meteoric water,...

Introduction Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and...

A novel, autotrophic, mesophilic bacterium, strain RS19-109 T , was isolated from sulfidic stream sediments in the Frasassi Caves, Italy. The cells of this strain grew chemolithoautotrophically under anaerobic conditions while disproportionating elemental sulfur (S ⁰ ) and thiosulfate, but not sulfite with bicarbonate/CO 2 as a carbon source. Autot...

Marine sediments comprise one of the largest microbial habitats and organic carbon sinks on the planet. However, it is unclear how variations in sediment physicochemical properties impact microorganisms on a global scale. Here we investigate patterns in the distribution of microbial cells, organic carbon, and the amounts of power used by microorgan...

Mt. Erebus, Antarctica, is the world’s southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C–65°C) sites on Mt. Erebus: Tr...

Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to...

Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in denitrification, a key process in the global nitrogen cycle. This study identifies a novel Nir domain architecture and expanded diversity in a rarely reported nitric oxide reductase variant (eNOR) in members of the bacterial phylum Chloroflexi. Abstract Denitri...

Chemolithotrophic microorganisms are key primary producers in hydrothermal environments. However, the complex thermal and compositional gradients that frequently describe these settings commonly obfuscate which reactions are fueling such complex ecosystems. Nonetheless, potential sources of microbial energy can be identified by combining analytical...

Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two ce...

Microorganisms are found in nearly every surface and near-surface environment, where they gain energy by catalyzing reactions among a wide variety of chemical compounds. The discovery of new catabolic strategies and microbial habitats can therefore be guided by determining which redox reactions can supply energy under environmentally-relevant condi...

A novel mesophilic, anaerobic, mixotrophic bacterium, with designated strains EPR-M T and HR-1, was isolated from a semi-extinct hydrothermal vent at the East Pacific Rise and from an Fe-mat at Lō'ihi Seamount, respectively. The cells were Gram-negative, pleomorphic rods of about 2.0 µm in length and 0.5 µm in width. Strain EPR-M T grew between 25...

The subsurface is Earth's largest reservoir of biomass. Micro‐organisms are the dominant lifeforms in this habitat, but the nature of their in situ activities remains largely unresolved. At the Deep Mine Microbial Observatory (DeMMO) located in the Sanford Underground Research Facility (SURF) in Lead, South Dakota (USA), we performed in situ electr...

The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view o...

Shallow-sea (<200 m depth) hydrothermal systems have garnered far less attention than their deep-sea or on-land counterparts. However, interdisciplinary research efforts on rock, sediment, water, gas, and biofilm samples collected in the Baia di Levante, Vulcano Island (Italy) have led to major discoveries in geobiology. For example, the archaeal s...

The deep subsurface contains a vast reservoir of microbial life. While recent studies have revealed critical details about this biosphere including the sheer diversity of microbial taxa and their metabolic potential, long-term monitoring of deep subsurface microbial populations is rare, thus limiting our understanding of subsurface microbial popula...

Microbial cells buried in subseafloor sediments comprise a substantial portion of Earth’s biosphere and control global biogeochemical cycles; however, the rate at which they use energy (i.e., power) is virtually unknown. Here, we quantify organic matter degradation and calculate the power utilization of microbial cells throughout Earth’s Quaternary...

A novel, obligately anaerobic bacterium (strain SURF-ANA1 T ) was isolated from deep continental subsurface fluids at a depth of 1500 m below surface in the former Homestake Gold Mine (now Sanford Underground Research Facility, in Lead, South Dakota, USA). Cells of strain SURF-ANA1 T were Gram-negative, helical, non-spore-forming and were 0.25–0.55...

Microbial degradation of organic carbon in marine sediments is a key driver of global element cycles on multiple time scales. However, it is not known to what depth microorganisms alter organic carbon in marine sediments or how microbial rates of organic carbon processing change with depth, and thus time since burial, on a global scale. To better u...

Shallow-sea hydrothermal systems, like their deep-sea and terrestrial counterparts, can serve as relatively accessible portals into the microbial ecology of subsurface environments. In this study, we determined the chemical composition of 47 sediment porewater samples along a transect from a diffuse shallow-sea hydrothermal vent to a non-thermal ba...

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...

Microbial degradation of organic carbon in marine sediments is a key driver of global element cycles on multiple time scales. However, it is not known to what depth microorganisms alter organic carbon in marine sediments or how microbial rates of organic carbon processing change with depth, and thus time since burial, on a global scale. To better u...

In recent decades, the taxonomy of Bacteria and Archaea , and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the averag...

The terrestrial deep subsurface is host to significant and diverse microbial populations. However, these microbial populations remain poorly characterized, partially due to the inherent difficulty of sampling, in situ studies, and isolating of the in situ microbes. Motivated by the ability of microbes to gain energy from redox reactions at mineral...

Recent studies reveal that life in the terrestrial and marine subsurface exists on far less energy flux than is commonly understood from laboratory incubations with isolated organisms. This has profound implications for understanding the development of life on Earth, as well as for the search for life in the universe. Similarly, several recent rese...

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...

Mariprofundus sp. strain EBB-1 was isolated from a pyrrhotite biofilm incubated in seawater from East Boothbay (ME, USA). Strain EBB-1 is an autotrophic member of the class Zetaproteobacteria with the ability to form iron oxide biominerals. Here, we present the 2.88-Mb genome sequence of EBB-1, which contains 2,656 putative protein-coding sequences...

The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy ( ∆ G r 0 ) define the direction and energy yield of a reaction; they do not. ∆ G r 0 is one part of the actual Gibbs energy of a reaction (∆Gr ), with...

Identifying temporal trends in deep subsurface geomicrobiology is challenging as it requires both in-depth knowledge of in situ geochemistry and innovative sampling techniques. Subsurface microbial dynamics can only be understood in the context of accompanying geochemistry, and thus, it is imperative to first characterize available microbial habita...

The present study is innovative in that we have identified previously unknown growth dynamics related to the temporal expression of the growth advantage in stationary phase (GASP) phenotype that allow mutants in long-term stationary-phase cultures to capitalize on the decrease of energy over prolonged incubation periods. By remaining in an active,...

The next NASA-led Mars mission (Mars 2020) will carry a suite of instrumentation dedicated to investigating Martian history and the in situ detection of potential biosignatures. SHERLOC, a deep UV Raman/Fluorescence spectrometer has the ability to detect and map the distribution of many organic compounds, including the aromatic molecules that are f...

Calorimetric measurements of heat flow and total heat prodn. can inform on the energetics of microbial activity. Nanocalorimetry permits such investigations in environments (natural or lab.) where energy supplies are extremely limited and/or very few cells are metabolically active. We will present nanocalorimetry data obtained during incubations of...

Fermentation plays a fundamental role in organic carbon degradation on a global scale. However, little is known about how environmental variables influence this process. In a step towards quantifying how temperature and composition influence fermentation, we have calculated the Gibbs energies of 47 fermentation reaction, ΔGr, from 0–150 °C for a br...

Methanogenic archaea are of fundamental applied and environmental relevance. This is largely due to their activities in a wide range of anaerobic environments, generating gaseous reduced carbon that can be utilized as a fuel source. While the bioenergetics of a wide variety of methanogens have been well studied with respect to soluble substrates, a...

The terrestrial deep subsurface is host to significant and diverse microbial populations. However, these microbial populations remain poorly characterized, partially due to the inherent difficulty of sampling, in situ studies, and isolating of the in situ microbes. Motivated by the ability of microbes to gain energy from redox reactions at mineral...

Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the ro...

Hydrothermal vents are some of the most exciting candidates for habitable environments on Ocean Worlds, because they supply reduced chemical substrates that enable the development of diverse biological communities capable of harnessing energy from ambient redox gradients. To characterize the habitability of a hydrothermally active region, it is nec...

Shallow-sea hydrothermal systems are ideal for studying the relative contributions to sedimentary sulfur archives from ambient sulfur-utilizing microbes and from fluxes of hydrothermally derived sulfur. Here we present data from a vent field in Palaeochori Bay, Milos, Greece using a suite of biogeochemical analytical tools that captured both spatia...

Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transit...

The Methanosarcinales , a lineage of cytochrome-containing methanogens, have recently been proposed to participate in direct extracellular electron transfer interactions within syntrophic communities. To shed light on this phenomenon, we applied electrochemical techniques to measure electron uptake from cathodes by Methanosarcina barkeri , which is...

The subsurface biosphere is a massive repository of fixed carbon, harboring approximately 90% of Earth’s microbial biomass. These microbial communities drive transformations central to Earth’s biogeochemical cycles. However, there is still much we do not understand about how complex subterranean microbial communities survive and how they interact w...

Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction betw...

The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane and potentially propane. The number of archaeal clades encoding the MCR complex continues to grow, suggesting that this complex was inh...

The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane and potentially propane. The number of archaeal clades encoding the MCR complex continues to grow, suggesting that this complex was inh...

Violin plots of percentages of specific taxa separated by sample type (B, background; I, intermediate; H, hydrothermal) and depth (color coded as blue for 3–4 cmbsf and black for 9–10 cmbsf). On the y-axis, the violin plots display the distribution of relative percentages of the selected taxa in each sample type. (a–f) Shows taxa whose relative per...

Combined relative abundance of the top 300 ASVs (which included all ASVs considered in Figures 4, 5) as a proportion of the total community. The top 300 ASVs represented over half of the sequences in most samples, and included all ASVs over 1% abundance.

Taxonomic assignment at the family level of sequences from extraction blanks. These taxa were not found or were present in extremely low abundances in sediment samples, and when considered with sourcetracker analysis results, indicated a low level of contamination of samples during the extraction and sequencing process.

Relative abundances of genera at Dorado Outcrop. The x-axis includes all samples, with each replicate individually shown. The y-axis shows all assigned genera over 0.15% abundance. Candidatus Scalindua and Candidatus Nitrosopumilus are abundant in hydrothermal samples.

The abundance of the top 100 ASVs and their taxonomic assignments which showed no distinct pattern between sample types, for Acidobacteria and Actinobacteria (A); Bacteroidetes, Chloroflexi, Gemmatimonadetes, Euryarchaeota, and Ignavibacteria (B); Nitrospinae, Nitrospirae, and Planctomycetes (C); Alphaproteobacteria and Deltaproteobacteria (D); Gam...

Cluster diagram of all samples and replicates based on Bray–Curtis dissimilarity. Replicates are color coded. Shallow samples are from 3 to 4 cm below seafloor. Deep samples are from 9–10 cm below seafloor. Samples more closely positioned and sharing nodes are more similar.

Comparison of Dorado Outcrop communities to communities from other deep sea sediments. Taxa are listed at the phylum level, except for the Proteobacteria, which are listed at the class level. Durbin and Teske separated Archaea and Bacteria clone library percentages, so the Thaumarchaea (MGI), which were 100% of the clones, are displayed as a large...

Proportion of samples assigned at the order level in samples.

Principal coordinate analysis (PCoA) based on weighted UniFrac analysis of all sediment sample replicates (in red, blue, and black) before sourcetracker with extraction/sequencing blanks (green), as well as the seawater samples (purple). The closer the points are positioned to each other, the more similar the samples are. The further away the sampl...

Class level assignments of major groups in sediments on Dorado Outcrop, based on averages of triplicate samples. Thaumarchaea, Planctomycetes, and Proteobacteria classes dominate in the hydrothermal samples.

ASVs significantly correlated with nitrate or pore fluid manganese concentrations.

Taxonomic assignments and abundances of top 100 most abundant ASVs, which were presenting in Supplementary Figure S5.

Sequence statistics during processing in DADA2.

Alpha diversity measures for each replicate.

Cool hydrothermal systems (CHSs) are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally...

Geothermobacter sp. strain HR-1 was isolated from the Lō‘ihi Seamount vent system in the Pacific Ocean at a depth of 1,000 m. Reported here is its 3.84-Mb genome sequence.

Microbial ecology within oligotrophic marine sediment is poorly understood, yet is critical for understanding geochemical cycles. Here, 16S rRNA sequences from RNA and DNA inform the structure of active and total microbial communities in oligotrophic sediment on the western flank of the Mid-Atlantic Ridge. Sequences identified as Bacillariophyta ch...

Marine sediments constitute one of the most energy-limited habitats on Earth, in which microorganisms persist over extraordinarily long timescales with very slow metabolisms. This habitat provides an ideal environment in which to study the energetic limits of life. However, the bioenergetic factors that can determine whether microorganisms will gro...

The in situ production of necromass and its role as a power source in sustaining heterotrophic microorganisms in natural settings has never been quantified. Here, we quantify the power availability from necromass oxidation to living microorganisms buried in marine sediments over millions of years, first in the oligotrophic South Pacific Gyre (SPG),...

Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubatedin situin the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.

Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic re...

(A) Triplicate heat-flow measurements and (B) heat yields for S. oneidensis MR-1 cultures grown under carbon replete condition. Solid red lines refer to total heat evolved during the respective depleted element conditions. Data presented in Figure 3 is highlighted in bold.

(A) Triplicate heat-flow (solid gray lines) and oxygen concentrations (solid green lines) measurements during growth of S. oneidensis MR-1 under oxygen limiting conditions. (B) Total accumulated heat during growth. Data presented in Figure 1 is highlighted in bold.

(A) Triplicate heat-flow measurements and (B) heat yields for S. oneidensis MR-1 cultures grown under nitrogen replete condition. Solid red lines refer to total heat evolved during the respective depleted element conditions. Data presented in Figure 3 is highlighted in bold.

(A) Triplicate heat-flow measurements and (B) heat yields for S. oneidensis MR-1 cultures grown under phosphorus replete condition. Solid red lines refer to total heat evolved during the respective depleted element conditions. Data presented in Figure 3 is highlighted in bold.

Life may have emerged on early Earth in serpentinizing systems, where ultramafic rocks react with aqueous solutions to generate high levels of dissolved H2 and CH4 and, on meeting seawater, steep redox, ionic, and pH gradients. Most extant life harnesses energy as ion (e.g., H⁺, Na⁺) gradients across membranes, and it seems reasonable to suggest th...

Sulfur cycling is ubiquitous in sedimentary environments, where it plays a major role in mediating carbon remineralization and impacts both local and global redox budgets. Microbial sulfur cycling is dominated by metabolic activity that either produces (e.g., sulfate reduction, disproportionation) or consumes (sulfide oxidation) hydrogen sulfide (H...

We have analyzed the dissolved organic carbon, OC, in ocean basement fluids using Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry (FT-ICR-MS). The compounds identified at the two sites, near the Juan de Fuca and Mid-Atlantic Ridges (North Pond), differ substantially from each other and from seawater. Compared to Juan de Fuca, North Pond...

Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity, and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea Paleoenvi...

Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines, and sampling of deeply-sourced vents and springs. In an effort to understand the ecology of deep terrestrial habi...

This corrects the article DOI: 10.1038/sdata.2017.37.

The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples...

Geothermobacter sp. strain EPR-M was isolated from a hydrothermal vent on the East Pacific Rise and has been shown to participate in the reduction of Fe(III) oxides. Here, we report its 3.73-Mb draft genome sequence.

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Ju...