David L. Valentine

Functional metagenomic profiling of nine biomes

Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.

Adaptations to energy stress dictate the ecology and evolution of the Archaea

The three domains of life on Earth include the two prokaryotic groups, Archaea and Bacteria. The Archaea are distinguished from Bacteriabased on phylogenetic and biochemical differences, but currently there is no unifying ecological principle to differentiate these groups. The ecology of the Archaea is reviewed here in terms of cellular bioenergetics. Adaptation to chronic energy stress is hypothesized to be the crucial factor that distinguishes the Archaea from Bacteria. The biochemical mechanisms that enable archaea to cope with chronic energy stress include low-permeability membranes and specific catabolic pathways. Based on the ecological unity and biochemical adaptations among archaea, I propose the hypothesis that chronic energy stress is the primary selective pressure governing the evolution of the Archaea.

Fate of Dispersants Associated with the Deepwater Horizon Oil Spill

Response actions to the Deepwater Horizon oil spill included the injection of ∼771,000 gallons (2,900,000 L) of chemical dispersant into the flow of oil near the seafloor. Prior to this incident, no deepwater applications of dispersant had been conducted, and thus no data exist on the environmental fate of dispersants in deepwater. We used ultrahigh resolution mass spectrometry and liquid chromatography with tandem mass spectrometry (LC/MS/MS) to identify and quantify one key ingredient of the dispersant, the anionic surfactant DOSS (dioctyl sodium sulfosuccinate), in the Gulf of Mexico deepwater during active flow and again after flow had ceased. Here we show that DOSS was sequestered in deepwater hydrocarbon plumes at 1000-1200 m water depth and did not intermingle with surface dispersant applications. Further, its concentration distribution was consistent with conservative transport and dilution at depth and it persisted up to 300 km from the well, 64 days after deepwater dispersant applications ceased. We conclude that DOSS was selectively associated with the oil and gas phases in the deepwater plume, yet underwent negligible, or slow, rates of biodegradation in the affected waters. These results provide important constraints on accurate modeling of the deepwater plume and critical geochemical contexts for future toxicological studies.

A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico

Methane released during the Deepwater Horizon blowout was degraded by methanotrophic bacteria. Methane was the most abundant hydrocarbon released during the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. Beyond relevancy to this anthropogenic event, this methane release simulates a rapid and relatively short-term natural release from hydrates into deep water. Based on methane and oxygen distributions measured at 207 stations throughout the affected region, we find that within ~120 days from the onset of release ~3.0 × 1010 to 3.9 × 1010 moles of oxygen were respired, primarily by methanotrophs, and left behind a residual microbial community containing methanotrophic bacteria. We suggest that a vigorous deepwater bacterial bloom respired nearly all the released methane within this time, and that by analogy, large-scale releases of methane from hydrate in the deep ocean are likely to be met by a similarly rapid methanotrophic response.

Propane Respiration Jump-Starts Microbial Response to a Deep Oil Spill

Diving into Deep Water The Deepwater Horizon oil spill in the Gulf of Mexico was one of the largest oil spills on record. Its setting at the bottom of the sea floor posed an unanticipated risk as substantial amounts of hydrocarbons leaked into the deepwater column. Three separate cruises identified and sampled deep underwater hydrocarbon plumes that existed in May and June, 2010—before the well head was ultimately sealed. Camilli et al. (p. 201; published online 19 August) used an automated underwater vehicle to assess the dimensions of a stabilized, diffuse underwater plume of oil that was 22 miles long and estimated the daily quantity of oil released from the well, based on the concentration and dimensions of the plume. Hazen et al. (p. 204; published online 26 August) also observed an underwater plume at the same depth and found that hydrocarbon-degrading bacteria were enriched in the plume and were breaking down some parts of the oil. Finally, Valentine et al. (p. 208; published online 16 September) found that natural gas, including propane and ethane, were also present in hydrocarbon plumes. These gases were broken down quickly by bacteria, but primed the system for biodegradation of larger hydrocarbons, including those comprising the leaking crude oil. Differences were observed in dissolved oxygen levels in the plumes (a proxy for bacterial respiration), which may reflect differences in the location of sampling or the aging of the plumes. Hydrocarbon gases were the first compounds that bacteria degraded in deep underwater petroleum plumes. The Deepwater Horizon event resulted in suspension of oil in the Gulf of Mexico water column because the leakage occurred at great depth. The distribution and fate of other abundant hydrocarbon constituents, such as natural gases, are also important in determining the impact of the leakage but are not yet well understood. From 11 to 21 June 2010, we investigated dissolved hydrocarbon gases at depth using chemical and isotopic surveys and on-site biodegradation studies. Propane and ethane were the primary drivers of microbial respiration, accounting for up to 70% of the observed oxygen depletion in fresh plumes. Propane and ethane trapped in the deep water may therefore promote rapid hydrocarbon respiration by low-diversity bacterial blooms, priming bacterial populations for degradation of other hydrocarbons in the aging plume.

Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill

Microbial communities present in the Gulf of Mexico rapidly responded to the Deepwater Horizon oil spill. In deep water plumes, these communities were initially dominated by members of Oceanospirillales, Colwellia, and Cycloclasticus. None of these groups were abundant in surface oil slick samples, and Colwellia was much more abundant in oil-degrading enrichment cultures incubated at 4 °C than at room temperature, suggesting that the colder temperatures at plume depth favored the development of these communities. These groups decreased in abundance after the well was capped in July, but the addition of hydrocarbons in laboratory incubations of deep waters from the Gulf of Mexico stimulated Colwellias growth. Colwellia was the primary organism that incorporated 13C from ethane and propane in stable isotope probing experiments, and given its abundance in environmental samples at the time that ethane and propane oxidation rates were high, it is likely that Colwellia was active in ethane and propane oxidation in situ. Colwellia also incorporated 13C benzene, and Colwellias abundance in crude oil enrichments without natural gas suggests that it has the ability to consume a wide range of hydrocarbon compounds or their degradation products. However, the fact that ethane and propane alone were capable of stimulating the growth of Colwellia, and to a lesser extent, Oceanospirillales, suggests that high natural gas content of this spill may have provided an advantage to these organisms.

Biodiversity and biogeography of phages in modern stromatolites and thrombolites

Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (>97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.

Chemical data quantify Deepwater Horizon hydrocarbon flow rate and environmental distribution

Detailed airborne, surface, and subsurface chemical measurements, primarily obtained in May and June 2010, are used to quantify initial hydrocarbon compositions along different transport pathways (i.e., in deep subsurface plumes, in the initial surface slick, and in the atmosphere) during the Deepwater Horizon oil spill. Atmospheric measurements are consistent with a limited area of surfacing oil, with implications for leaked hydrocarbon mass transport and oil drop size distributions. The chemical data further suggest relatively little variation in leaking hydrocarbon composition over time. Although readily soluble hydrocarbons made up ∼25% of the leaking mixture by mass, subsurface chemical data show these compounds made up ∼69% of the deep plume mass; only ∼31% of the deep plume mass was initially transported in the form of trapped oil droplets. Mass flows along individual transport pathways are also derived from atmospheric and subsurface chemical data. Subsurface hydrocarbon composition, dissolved oxygen, and dispersant data are used to assess release of hydrocarbons from the leaking well. We use the chemical measurements to estimate that (7.8 ± 1.9) × 106 kg of hydrocarbons leaked on June 10, 2010, directly accounting for roughly three-quarters of the total leaked mass on that day. The average environmental release rate of (10.1 ± 2.0) × 106 kg/d derived using atmospheric and subsurface chemical data agrees within uncertainties with the official average leak rate of (10.2 ± 1.0) × 106 kg/d derived using physical and optical methods.

Oil Weathering after the Deepwater Horizon Disaster Led to the Formation of Oxygenated Residues

Following the Deepwater Horizon disaster, the effect of weathering on surface slicks, oil-soaked sands, and oil-covered rocks and boulders was studied for 18 months. With time, oxygen content increased in the hydrocarbon residues. Furthermore, a weathering-dependent increase of an operationally defined oxygenated fraction relative to the saturated and aromatic fractions was observed. This oxygenated fraction made up >50% of the mass of weathered samples, had an average carbon oxidation state of -1.0, and an average molecular formula of (C(5)H(7)O)(n). These oxygenated hydrocarbon residues were devoid of natural radiocarbon, confirming a fossil source and excluding contributions from recent photosynthate. The incorporation of oxygen into the oils hydrocarbons, which we refer to as oxyhydrocarbons, was confirmed from the detection of hydroxyl and carbonyl functional groups and the identification of long chain (C(10)-C(32)) carboxylic acids as well as alcohols. On the basis of the diagnostic ratios of alkanes and polycyclic aromatic hydrocarbons, and the context within which these samples were collected, we hypothesize that biodegradation and photooxidation share responsibility for the accumulation of oxygen in the oil residues. These results reveal that molecular-level transformations of petroleum hydrocarbons lead to increasing amounts of, apparently recalcitrant, oxyhydrocarbons that dominate the solvent-extractable material from oiled samples.

Fallout plume of submerged oil from Deepwater Horizon

Significance Following the sinking of the Deepwater Horizon in the Gulf of Mexico an unprecedented quantity of oil irrupted into the ocean at a depth of 1.5 km. The novelty of this event makes the oil’s subsequent fate in the deep ocean difficult to predict. This work identifies a fallout plume of hydrocarbons from the Macondo Well contaminating the ocean floor over an area of 3,200 km2. Our analysis suggests the oil initially was suspended in deep waters and then settled to the underlying sea floor. The spatial distribution of contamination implicates accelerated settling as an important fate for suspended oil, supports a patchwork mosaic model of oil deposition, and frames ongoing attempts to determine the event’s impact on deep-ocean ecology. The sinking of the Deepwater Horizon in the Gulf of Mexico led to uncontrolled emission of oil to the ocean, with an official government estimate of ∼5.0 million barrels released. Among the pressing uncertainties surrounding this event is the fate of ∼2 million barrels of submerged oil thought to have been trapped in deep-ocean intrusion layers at depths of ∼1,000–1,300 m. Here we use chemical distributions of hydrocarbons in >3,000 sediment samples from 534 locations to describe a footprint of oil deposited on the deep-ocean floor. Using a recalcitrant biomarker of crude oil, 17α(H),21β(H)-hopane (hopane), we have identified a 3,200-km2 region around the Macondo Well contaminated by ∼1.8 ± 1.0 × 106 g of excess hopane. Based on spatial, chemical, oceanographic, and mass balance considerations, we calculate that this contamination represents 4–31% of the oil sequestered in the deep ocean. The pattern of contamination points to deep-ocean intrusion layers as the source and is most consistent with dual modes of deposition: a “bathtub ring” formed from an oil-rich layer of water impinging laterally upon the continental slope (at a depth of ∼900–1,300 m) and a higher-flux “fallout plume” where suspended oil particles sank to underlying sediment (at a depth of ∼1,300–1,700 m). We also suggest that a significant quantity of oil was deposited on the ocean floor outside this area but so far has evaded detection because of its heterogeneous spatial distribution.