Berkeley Lab

Spring Snowmelt Drives Transport and Degradation of Dissolved Organic Matter in a Semi-Arid Floodplain

Berkeley Lab geochemists and hydrologists who study a mountainous watershed near Rifle, CO, discovered that spring snowmelt is essential to the transport of freshly dissolved organic matter (DOM) from the top soil to the part of the Earth’s subsurface that lies above the groundwater table. Because dissolved organic matter undergoes biological humification over the year, these processes involving this deep vadose zone suggest an annual cycle of DOM degradation and transport at this semi-arid floodplain site.

Spring snowmelt transports fresh DOM from top soil into the deeper vadose zone, and then undergoes microbial humification process over the year (see depth and seasonal EEM spectra)

Characterizing the dynamics of dissolved organic matter in semi-arid regions of Earth’s subsurface is challenging. The authors obtained insights into transport and humification processes of DOM using several spectroscopic techniques on depth- and temporally-distributed pore-waters. This methodology can be applied to other subsurface environments for understanding DOM responses and feedbacks to earth system processes.


Scientists studying DOM in surface waters considered it to be the mobile fraction of natural organic matter that falls into or is washed into water bodies. Although it has been extensively studied over many decades, relatively little is known about the dynamics of DOM in the subsurface of semi-arid environments. In order to understand transport and humification processes of DOM within a semi-arid floodplain at Rifle, Colorado, the authors applied fluorescence excitation-emission matrix (EEM) spectroscopy, humification index (HIX) and specific UV absorbance (SUVA) for characterizing depth and seasonal variations of DOM composition. They found that late spring snowmelt leached relatively fresh DOM from plant residue and soil organic matter down into the deeper vadose zone (VZ). More humified DOM is preferentially adsorbed by upper VZ sediments, while non- or less-humified DOM was transported into the deeper VZ. Interestingly, DOM at all depths undergoes rapid biological humification processes as evidenced by the products of microbial by-product-like matter in late spring and early summer, particularly in the deeper VZ, resulting in more humified DOM at the end of year. The finding indicates that DOM transport is dominated by spring snowmelt, and DOM humification is controlled by microbial degradation. It is expected that these relatively simple spectroscopic measurements (e.g., EEM spectroscopy, HIX and SUVA) applied to depth- and temporally-distributed pore-water samples can provide useful insights into transport and humification of DOM in other subsurface environments as well.


Dong, W., J. Wan, T. K. Tokunaga, B. Gilbert, and K. H. Williams (2017). Transport and Humification of Dissolved Organic Matter within a Semi-Arid Floodplain. Journal of Environmental Sciences 57, 24-32, DOI: 10.1016/j.jes.2016.12.011

SFA Research Identifies New Microbial Players in the Global Sulfur Cycle

Sulfate is ubiquitous in the environment, and sulfate reduction – a key control on anaerobic carbon turnover – impacts a number of other processes such as carbon oxidation and sulfide production. Until now, sulfate reduction was believed to be restricted to organisms from select bacterial and archael phyla. But scientists at UC Berkeley have now found this ability to be more widespread. They used genome-resolved metagenomics to discover roles in sulfur cycling for organisms from 16 microbial phyla not previously associated with this process.

DsrAB protein tree showing the diversity of organisms involved in dissimilatory sulfur cycling using the dsr system.
Lineages in blue contain genomes reported in this study. Phylum-level lineages with first report of evidence for sulfur cycling are indicated by blue letters.

Sulfate-reducing bacteria are anaerobic microorganisms essential to sulfur and carbon cycling. Sulfate reduction drives other key processes and produces hydrogen sulfide, an important but potentially toxic gas present in sediments, wetlands, aquifers, the human gut, and the deep-sea. The discovery of novel microbes connected to sulfur cycling is relevant in biogeochemistry, ecosystem science and engineering, and fundamentally reshape our understanding of microbial function and capabilities associated with phylogenetic information.


Phylogenetic information shapes our expectations regarding microbial capabilities. In fact, this is the basis of currently used methods that link gene surveys to metabolic predictions of community function. Sulfate Reduction, an important anaerobic metabolism, impacts carbon, nitrogen, and hydrogen transformations in numerous environments across our planet and is known to be restricted to organisms from selected bacterial and archaeal phyla. The authors used genome-resolved metagenomic analyses to determine the metabolic potential of microorganisms from six complex marine and terrestrial environments. By analyzing >4000 genomes, they identified 123 near-complete genomes that encode dissimilatory sulfite reductases involved in sulfate reduction. They discovered roles in sulfur cycling for organisms from 16 microbial phyla not previously known to be associated with this process. Additional findings include some of the earliest-evolved sulfite reductases in bacteria, identification of a novel protein unique to sulfate reducing bacteria, and a key sulfite reductase gene in putatively symbiotic Candidate Phyla Radiation (CPR) bacteria. This study fundamentally reshapes expectations regarding the roles of a remarkable diversity of organisms in the biogeochemical cycle of sulfur.


Anantharaman, K., B. Hausmann, S.P. Jungbluth, R.S. Kantor, A. Lavy, L.A. Warren, M.S. Rappé, M. Pester, A. Loy, B.C. Thomas, and J.F. Banfield (2017). Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. The ISME journal 12, 1715–1728, DOI: 10.1038/s41396-018-0078-0

New Approach to Predict Flow and Transport Processes in Fractured Rock uses Causal Modeling

Scientists and engineers simulate the flow of fluids through permeable media to determine how water, oil, gas or heat can be safely extracted from subsurface fractured-porous rock, or how harmful materials like carbon dioxide could be stored deep underground. Now, a scientist from Lawrence Berkeley National Lab has identified a causal relationship between gases and liquids flowing through fractured-porous media. They observed oscillating liquid and gas fluxes and pressures as the two transitioned back and forth within a subsurface rock fracture.

Evaluation of diagnostic parameters of deterministic chaos and 3-D strange attractor (bottom right) indicating that the system would behave within the boundaries of the attractor.

When both liquid and gas are injected into a rock fracture, the cumulative effect of forward and return pressure waves causes intermittent oscillations of liquid and gas fluxes and pressures within the fracture. The Granger causality test is used to determine whether the measured time series of one of the fluids can be applied to forecast the pressure variations in another fluid. This method could also be used to better understand the causation of other hydrological processes, such as infiltration and evapotranspiration in heterogeneous subsurface media, and climatic processes, for example, relationships between meteorological parameters—temperature, solar radiation, barometric pressure, etc.


Identifying dynamic causal inference involved in flow and transport processes in complex fractured-porous media is generally a challenging task, because nonlinear and chaotic variables may be positively coupled or correlated for some periods of time, but can then become spontaneously decoupled or non-correlated. The author hypothesized that the observed pressure oscillations at both inlet and outlet edges of the fracture result from a superposition of both forward and return waves of pressure propagation through the fracture. He tested the theory by exploring an application of a combination of methods for detecting nonlinear chaotic dynamics behavior (Figure A) along with the multivariate Granger Causality (G-causality) time series test. Based on the G-causality test, the author infers that his hypothesis is correct, and presents a causation loop diagram (Figure B) of the spatial-temporal distribution of gas, liquid, and capillary pressures measured at the inlet and outlet of the fracture. The causal modeling approach can be used for the analysis of other hydrological processes such as infiltration and pumping tests in heterogeneous subsurface media, and climatic processes.


Faybishenko, B. (2017). Detecting dynamic causal inference in nonlinear two-phase fracture flow, Advances in Water Resources 106, 111–120, DOI: 10.1016/j.advwatres.2017.02.011

Microbial “hotspots” and organic rich sediments are key determinants of nitrogen cycling in a floodplain

Figure 1. Simulated and observed nitrate concentrations at different depths in TT wells. Nitrification contributes up to 35% (TT-01), 67% (TT-02), and 48% (TT-03) of nitrate levels in groundwater.

Biogeochemical hot spots are regions with disproportionally high reaction rates relative to the surrounding spatial locations, while hot moments are short periods of time manifesting high reaction rates relative to longer intervening time periods. These hot spots and hot moments together affect ecosystem processes and are considered ‘‘ecosystem control points”. However, relatively few studies have incorporated hot spots and/or hot moments in numerical models to quantify their aggregated effects on biogeochemical processes at floodplain and riverine scales. This study quantifies the occurrence and distribution of nitrogen hot spots and hot moments at a Colorado River floodplain site in Rifle, CO, using a high-resolution, 3-D flow and reactive transport model.

Figure 2. Sensitivity of nitrogen to flow reversal and microbial pathways in NRZ and non-NRZ. NRZs produce more nitrogen (approximately 70%) than non-NRZs.

This study was used to assess the interplay between dynamic hydrologic processes and organic matter rich, geochemically reduced sediments (aka “naturally reduced zones”) within the Rifle floodplain and the impact of hot spots and hot moments on nitrogen cycling at the site using a fully-coupled, high-resolution reactive flow and transport simulator. Simulation results indicated that nitrogen hot spots are not simply hydrologically-driven, but occur because of complex fluid mixing, localized reduced zones, and biogeochemical variability. Furthermore, results indicated that chemically reduced sediments of the Rifle floodplain have 70% greater potential for nitrate removal than nonreduced zones.


Although hot spots and hot moments are important for understanding large-scale coupled carbon and nitrogen cycling, relatively few studies have incorporated hot spots and hot moments in numerical models, especially not in a 3D framework, thereby neglecting the potential effects of fluid mixing on the biogeochemistry. In this study, scientists from the Lawrence Berkeley National Laboratory integrated a complex biotic and abiotic reaction network into a high-resolution, three-dimensional subsurface reactive transport model to understand key processes that produce hot spots and hot moments of nitrogen in a floodplain environment. The model was able to capture the significant hydrological and biogeochemical variability observed across the Rifle floodplain site. In particular, simulation results demonstrated that hot and cold moments of nitrogen did not coincide in different wells, in contrast to flow hydrographs. This has important implications for identifying nitrogen hot moments at other contaminated sites and/or mitigating risks associated with the persistence of nitrate in groundwater. Model simulations further demonstrated that nitrogen hot spots are both flow-related and microbially-driven in the Rifle floodplain. Sensitivity analyses results indicated that the naturally reduced zones (NRZs) have a higher potential for nitrate removal than the non-NRZs for identical hydrological conditions. However, flow reversal leads to a reduction in nitrate removal (approximately 95% lower) in non-NRZs whereas the NRZ remains unaffected by the influx of the river water. This study demonstrates that chemolithoautotrophy, the microbial processes responsible for Fe+2 and S-2 oxidation, is primarily responsible for the removal of nitrate in the Rifle floodplain.


Dwivedi, D., Arora, B., Steefel, C. I., Dafflon, B., & Versteeg, R. (2018). Hot spots and hot moments of nitrogen in a riparian corridor. Water Resources Research, 53. DOI: 10.1002/2017WR022346.

New Approach to Characterize Natural Organic Matter in Belowground Sediments

FTIR analysis (top) and pictures (bottom) of three natural organic matter fractions extracted from sediment: water extractable (MQ-SPE), acid-soluble pyrophosphate (PP) extractable (PP-SPE), and acid-insoluble PP extractable (PP >1 kD).

Organic carbon concentrations in sediments more than 1 meter below the land surface are typically 10 to 200 times lower than in surface soils, posing a distinct challenge for characterization. In this SFA study, published in Organic Chemistry, a range of chemical extractions were evaluated for extraction of natural organic matter (NOM) from low-carbon (<0.2%) alluvial sediments and an extraction and purification scheme was developed in order to isolate and characterize different fractions of sediment-associated NOM.


Surface soils typically contain 5-10% levels of organic carbon (OC), but OC concentrations in sediments more than 1 meter below the land surface are often 10 to 200 times lower, and the usual techniques to measure the chemical characteristics of OC in these sediments are not sufficiently sensitive. In this study, a range of chemical extractions were evaluated for extraction of natural organic matter (NOM) from two low-carbon (<0.2%) alluvial sediments. The OC extraction efficiency followed the order pyrophosphate (PP)>NaOH>HCl, hydroxylamine hydrochloride>dithionite, water. A NOM extraction and purification scheme was developed using sequential extraction with water (MQ) and sodium pyrophosphate at pH 10 (PP), combined with purification by dialysis and solid phase extraction in order to isolate different fractions of sediment-associated NOM. Characterization of these pools of NOM for metal content and by Fourier transform infrared spectroscopy (FITR) showed that the water soluble fraction (MQ-SPE) had a higher fraction of aliphatic and carboxylic groups, while the PP-extractable NOM (PP-SPE and PP >1kD) had higher fractions of C=C groups and higher residual metals. This trend from aliphatic to more aromatic is also supported by the specific UV absorbance at 254 nm (SUVA254) (3.5 vs 5.4 for MQ-SPE and PP-SPE, respectively) and electrospray ionization Fourier transform ion cyclotron resonance spectrometry (ESI-FTICR-MS) data which showed a greater abundance of peaks in the low O/C and high H/C region (0-0.4 O/C, 0.8-2.0 H/C) for the MQ-SPE fraction of NOM. Radiocarbon measurements yielded standard radiocarbon ages of 1020, 3095, and 9360 years BP for PP-SPE, PP >1kD, and residual (non-extractable) OC fractions, indicating an increase in NOM stability correlated with greater metal complexation, apparent molecular weight, and aromaticity.


P.M. Fox, P.S. Nico, M.M. Tfaily, K. Heckman, and J.A. Davis (2017), “Characterization of natural organic matter in low-carbon sediments: Extraction and analytical approaches.” Organic Geochemistry, 114, 12-22, DOI:10.1016/j.orggeochem.2017.08.009

First Measurements of Dark Reactive Oxygen Species in a Groundwater Aquifer

Hydrogen peroxide concentrations across the Rifle, CO field site.

Hydrogen peroxide concentrations across the Rifle, CO field site.

Yuan et al. (2017) reports on the first measurement of the presence of hydrogen peroxide concentrations in groundwaters. Hydrogen peroxide and an associated class of compounds called reactive oxygen species have long been known to be important drivers of biogeochemical cycling and contaminant decomposition in surface water (oceans, rivers, and lakes). However, their importance in groundwater was unestablished.

By demonstrating that hydrogen peroxide and therefore the associated group of reactive oxygen species were widely distributed in the groundwaters of our site, the study establishes that they are likely important to the chemistry and function of groundwater systems. The widespread presence of reactive oxygen species may be an explanation for apparent non-equilibrium conditions in some waters as well as organic matter oxidation pathways without other obvious causes. Finally by showing that concentrations tended to be highest at transition zones the work focuses the likely most impactful areas of future investigation.


The commonly held assumption that photodependent processes dominate H2O2 production in natural waters has been recently questioned. This paper demonstrated for the unrecognized and light-independent generation of H2O2 in groundwater of an alluvial aquifer adjacent to the Colorado River near Rifle, CO. In situ detection using a sensitive chemiluminescent method suggests H2O2 concentrations ranging from lower than the detection limit (<1 nM) to 54 nM along the vertical profiles obtained at various locations across the aquifer. Our results also suggest dark formation of H2O2 is more likely to occur in transitional redox environments where reduced elements (e.g., reduced metals and NOM) meet oxygen, such as oxic–anoxic interfaces. A simplified kinetic model involving interactions among iron, reduced NOM, and oxygen was able to reproduce roughly many, but not all, of the features in our detected H2O2 profiles, and therefore there are other minor biological and/or chemical controls on H2O2 steady-state concentrations in such aquifer. Because of its transient nature, the widespread presence of H2O2 in groundwater suggests the existence of a balance between H2O2 sources and sinks, which potentially involves a cascade of various biogeochemically important processes that could have significant impacts on metal/nutrient cycling in groundwater-dependent ecosystems, such as wetlands and springs. More importantly, our results demonstrate that reactive oxygen species are not only widespread in oceanic and atmospheric systems but also in the subsurface domain, possibly the least understood component of biogeochemical cycles.


Yuan, X., P. S. Nico, X. Huang, T. Liu, C. Ulrich, K. H. Williams, and J. A. Davis (2017), Production of hydrogen peroxide in groundwater at Rifle, Colorado, Environ. Sci. Technol., DOI: 10.1021/acs.est.6b04803.

Simple non-electrostatic model successfully predicts long-term uranium mobility

Comparing U(VI) breakthrough curves at a monitoring well location (FSB110D) in the F-Area of the Savannah River Site (SRS) using two model simulations: the electrostatic surface complexation model (SCM) and the best-fit NEM.

Arora et al. (2017) developed a simple non-electrostatic model through a step-by-step calibration procedure to describe U plume behavior at the Savannah River site. This simple model was found to be more numerically-efficient than a complex mechanistic model with electrostatic correction terms in predicting long-term U behavior at the site and by extension other uranium contaminated sites.

Uranium geochemistry has been extremely challenging to describe and predict. Although complex mechanistic models have been used to describe U sorption in field settings, there is significant uncertainty in model predictions due to scarce field data and modeling assumptions concerning mineral assemblage and subsurface heterogeneity. This study demonstrates that a simpler non-electrostatic model is a powerful alternative for describing U plume evolution at the Savannah River Site (SRS) because it can describe U(VI) sorption much more accurately than a constant coefficient (Kd) approach, while being more numerically efficient than a complex model with electrostatic correction terms. This study provides valuable insight into predicting uranium plume persistence from contaminated sites using simple non-electrostatic models.


The aim of this study was to test if a simpler, semi-empirical, non-electrostatic U(VI) sorption model (NEM) could achieve the same predictive performance as a model with electrostatic correction terms in describing pH and U(VI) behavior at multiple locations within the SRS F-Area. Modeling results indicate that the simpler NEM was able to perform as well as the electrostatic surface complexation model especially in simulating uranium breakthrough tails and long-term trends. However, the model simulations differed significantly during the early basin discharge period. Model performance cannot be assessed during this early period due to a lack of field observations (e.g., initial pH of the basin water) that would better constrain the models. In this manner, modeling results highlight the importance of the range of environmental data that are typically used for calibrating the model.


Arora, B., Davis, J. A., Spycher, N. F., Dong, W., & Wainwright, H. M. (2017). Comparison of Electrostatic and Non‐Electrostatic Models for U (VI) Sorption on Aquifer Sediments. Groundwater. doi: 10.1111/gwat.12551

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

Terrain/Satellite view of the study site. Stars indicate sampling locations and the red circle indicates the location of the Gold King Mine.

Published in Environmental Science: Processes & Impacts, this study investigated the fate of heavy metals adsorbed onto riverbed sediments following the August 2015 Gold King Mine Spill in Colorado’s San Juan Mountains. It represents the first biogeochemical study of spill-impacted sediments from the Animas River and revealed mobilization of zinc, arsenic, and molybdenum species accompanying microbe-catalyzed dissolution of metal oxide sorbents.

Concentration changes in aqueous metal cations and anions from the three sediment types across 28-day microcosm incubations. The dashed line in the SO42- panel indicates the time point where exogenous SO42- was added to microcosms to stimulate additional SO42- reduction.


Following the Gold King Mine waste spill, metal contaminants adsorbed onto riverbed sediments along the spill flow path. Differences in sediment mineralogy and adsorbed metals were strongly linked to sampling locations and proximity to the mine. Results suggest that anaerobic microbial metabolisms, stimulated by natural organic carbon pools, will play a significant role in mobilizing adsorbed metal pools following the onset of anoxia in buried riverbed sediments. The site-specific nature of metal release may be linked to different reductive metabolisms, with microbial iron reduction driving dissolution of grain coatings, and alkalinity increases during sulfate reduction offering another mechanism for metal desorption from fluvial sediments. Given the iron and sulfur-rich nature of the Colorado Basin, these complex processes represent a challenge for the tracking of mining-impacted biogeochemistry and associated water quality issues, and emphasize the need for monitoring efforts that account for the dynamic nature of fluvial systems, and their ability to moderate strong spatial and temporal gradients in redox status.

This study provides valuable insight into metal mobility, particularly in mining-impacted watersheds. These results highlight the importance of long-term river water quality monitoring as river sediments undergo sedimentation and burial processes, driving the onset of anoxic conditions which favor metal (re)mobilization.


Saup, C.M., K.H. Williams, L. Rodriguez-Freire, J. Manuel Cerrato, M.D. Johnston, M.J. Wilkins (2017). Anoxia stimulates microbially catalyzed metal release from Animas River sediments. Environmental Science: Processes & Impacts. doi:10.1039/C7EM00036G

Improved modeling of floodplain nutrient and metal cycling using new multi-omics and isotope fractionation information

Water table peaking event mixes oxygen and nitrate into the anoxic Rifle floodplain aquifer. Naturally reduced zones containing sediments higher in organic matter, iron sulfides, and U(IV) rapidly consume DO and nitrate to maintain anoxic conditions, yielding Fe(II) from FeS oxidation, nitrite from denitrification, and U(VI) from nitrite-promoted U(IV) oxidation. Redox cycling is facilitated by coupled geochemistry, heterotrophy, and chemolithoautotrophy.

The study, published in Environmental Science & Technology, is one of the most comprehensive syntheses of processes and datatypes published to date and links BER’s investments in advanced multi-omics techniques and high-performance computing, representing the first critical stage in building a predictive understanding of natural hydrobiogeochemical processes at floodplain and larger scales.


Three-dimensional variably saturated flow and multicomponent biogeochemical reactive transport modeling is used to better understand the interplay of hydrology, geochemistry, and biology controlling the cycling of carbon, nitrogen, oxygen, iron, sulfur, and uranium in a shallow floodplain of the Colorado River in Rifle, Colorado. In this river-aquifer-vadose zone system, aerobic respiration generally maintains anoxic groundwater below an oxic vadose zone until seasonal snowmelt-driven water table peaking transports dissolved oxygen (DO) and nitrate from the vadose zone into the alluvial aquifer. The response to this perturbation is localized due to distinct physico-biogeochemical environments and relatively long time scales for transport through the floodplain aquifer and vadose zone. Naturally reduced zones (NRZs) containing sediments higher in organic matter, iron sulfides, and non-crystalline U(IV) rapidly consume DO and nitrate to maintain anoxic conditions, yielding Fe(II) from FeS oxidative dissolution, nitrite from denitrification, and U(VI) from nitrite-promoted U(IV) oxidation. Redox cycling is a key factor for sustaining the observed aquifer behaviors despite continuous oxygen influx and the annual hydrologically-induced oxidation event. Depth-dependent activity of fermenters, aerobes, nitrate reducers, sulfate reducers, and chemolithoautotrophs [e.g., oxidizing Fe(II), S compounds, and ammonium] is linked to the presence of DO, which has higher concentrations near the water table.


Yabusaki, S., M. Wilkins, Y. Fang, K. Williams, B. Arora, J. Bargar, H. Beller, N. Bouskill, E. Brodie, J. Christensen, M. Conrad, R. Danczak, E. King, M. Soltanian, N. Spycher, C. Steefel, T. Tokunaga, R. Versteeg, S. Waichler, H. Wainwright (2017).  Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain.  Environmental Science and Technology, 51 (6), 3307-3317,  DOI: 10.1021/acs.est.6b04873

Diverse Microbial Metabolism in Aquifer BGC Hot Spot


Summary of key metabolic pathways expressed by a prominent bacterium (Hydrogenophaga b174) in an NRZ biogeochemical hot spot in the Rifle aquifer. Surprisingly, this bacterium actively catalyzed both heterotrophic and chemolithoautotrophic processes and influenced biogeochemical cycling of several elements, including C, N, and S. Unexpectedly, denitrification played an important role in this metabolism.

Organic matter deposits in alluvial aquifers have been shown to result in the formation of NRZs, which can modulate aquifer redox status and influence the speciation and mobility of metals, significantly affecting groundwater geochemistry. This study (Jewell et al., Frontiers in Microbiology) sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (NRZs) in a shallow alluvial aquifer at the Rifle (CO) site. Overall, the results highlighted the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.


The authors used an anaerobic microcosm experiment in which NRZ sediments served as the sole source of electron donors and microorganisms. Biogeochemical data indicated that the decomposition of native organic matter occurred in different phases, beginning with mineralization of dissolved organic matter (DOM) to CO2 during the first week of incubation, followed by a pulse of acetogenesis that dominated carbon flux after two weeks. The depletion of DOM over time was strongly correlated with increases in expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage (~8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO2 fixation, H2 oxidation, S-compound oxidation, and denitrification. The pulse of acetogenesis appears to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase. Unexpected genes were identified among the most highly expressed (>98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates. Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with recycling of bacterial biomass.