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1. Microbial production and consumption of hydrocarbons in the global ocean

   Love, C.R.; Arrington, E.C.; Gosselin, K.M.; Reddy, C.M.; Van Mooy, B.A.S.; Nelson, R.K.; Valentine, D.L. (February 2020, Nature microbiology)

   null (Ed.)

   Seeps, spills and other oil pollution introduce hydrocarbons into the ocean. Marine cyanobacteria also produce hydrocarbons from fatty acids, but little is known about the size and turnover of this cyanobacterial hydrocarbon cycle. We report that cyanobacteria in an oligotrophic gyre mainly produce n-pentadecane and that microbial hydrocarbon production exhibits stratification and diel cycling in the sunlit surface ocean. Using chemical and isotopic tracing we find that pentadecane production mainly occurs in the lower euphotic zone. Using a multifaceted approach, we estimate that the global flux of cyanobacteria-produced pentadecane exceeds total oil input in the ocean by 100- to 500-fold. We show that rapid pentadecane consumption sustains a population of pentadecane-degrading bacteria, and possibly archaea. Our findings characterize a microbial hydrocarbon cycle in the open ocean that dwarfs oil input. We hypothesize that cyanobacterial hydrocarbon production selectively primes the ocean’s microbiome with long-chain alkanes whereas degradation of other petroleum hydrocarbons is controlled by factors including proximity to petroleum seepage. 

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2. Sterane and hopane biomarkers capture microbial transformations of complex hydrocarbons in young hydrothermal Guaymas Basin sediments

   https://doi.org/10.1038/s43247-022-00582-8  

   Mara, Paraskevi; Nelson, Robert K.; Reddy, Christopher M.; Teske, Andreas; Edgcomb, Virginia P. (October 2022, Communications Earth & Environment)

   Abstract In Guaymas Basin, organic-rich hydrothermal sediments produce complex hydrocarbon mixtures including saturated, aromatic and alkylated aromatic compounds. We examined sediments from push cores from Guyamas sites with distinct temperature and geochemistry profiles to gain a better understanding on abiotic and biological hydrocarbon alteration. Here we provide evidence for biodegradation of hopanoids, producing saturated hydrocarbons like drimane and homodrimane as intermediate products. These sesquiterpene by-products are present throughout cooler sediments, but their relative abundance is drastically reduced within hotter hydrothermal sediments, likely due to hydrothermal mobilization. Within the sterane pool we detect a trend toward aromatization of steroidal compounds within hotter sediments. The changes in hopane and sterane biomarker composition at different sites reflect temperature-related differences in geochemical and microbial hydrocarbon alterations. In contrast to traditionally observed microbial biodegradation patterns that may extend over hundreds of meters in subsurface oil reservoirs, Guaymas Basin shows highly compressed changes in surficial sediments. 

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3. Methanogens and Their Syntrophic Partners Dominate Zones of Enhanced Magnetic Susceptibility at a Petroleum Contaminated Site

   https://doi.org/10.3389/feart.2021.598172  

   Beaver, Carol L.; Atekwana, Estella A.; Bekins, Barbara A.; Ntarlagiannis, Dimitrios; Slater, Lee D.; Rossbach, Silvia (March 2021, Frontiers in Earth Science)

   Geophysical investigations documenting enhanced magnetic susceptibility (MS) within the water table fluctuation zone at hydrocarbon contaminated sites suggest that MS can be used as a proxy for investigating microbial mediated iron reduction during intrinsic bioremediation. Here, we investigated the microbial community composition over a 5-year period at a hydrocarbon-contaminated site that exhibited transient elevated MS responses. Our objective was to determine the key microbial populations in zones of elevated MS. We retrieved sediment cores from the petroleum-contaminated site near Bemidji, MN, United States, and performed MS measurements on these cores. We also characterized the microbial community composition by high-throughput 16S rRNA gene amplicon sequencing from samples collected along the complete core length. Our spatial and temporal analysis revealed that the microbial community composition was generally stable throughout the period of investigation. In addition, we observed distinct vertical redox zonations extending from the upper vadose zone into the saturated zone. These distinct redox zonations were concomitant with the dominant microbial metabolic processes as follows: (1) the upper vadose zone was dominated by aerobic microbial populations; (2) the lower vadose zone was dominated by methanotrophic populations, iron reducers and iron oxidizers; (3) the smear zone was dominated by iron reducers; and (4) the free product zone was dominated by syntrophic and methanogenic populations. Although the common notion is that high MS values are caused by high magnetite concentrations that can be biotically formed through the activities of iron-reducing bacteria, here we show that the highest magnetic susceptibilities were measured in the free-phase petroleum zone, where a methanogenic community was predominant. This field study may contribute to the emerging knowledge that methanogens can switch their metabolism from methanogenesis to iron reduction with associated magnetite precipitation in hydrocarbon contaminated sediments. Thus, geophysical methods such as MS may help to identify zones where iron cycling/reduction by methanogens is occurring. 

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4. Burial and Denudation Alter Microbial Life at the Bottom of the Hypo‐Critical Zone

   https://doi.org/10.1029/2022GC010831  

   McIntosh, Jennifer; Kim, Ji‐Hyun; Bailey, Lydia; Osburn, Magdalena; Drake, Henrik; Martini, Anna; Reiners, Peter; Stevenson, Bradley; Ferguson, Grant (June 2023, Geochemistry, Geophysics, Geosystems)

   Abstract How subsurface microbial life changed at the bottom of the kilometers‐deep (hypo) Critical Zone in response to evolving surface conditions over geologic time is an open question. This study investigates the burial and exhumation, biodegradation, and fluid circulation history of hydrocarbon reservoirs across the Colorado Plateau as a window into the hypo‐Critical Zone. Hydrocarbon reservoirs, in the Paradox and Uinta basins, were deeply buried starting ca. 100 to 60 Ma, reaching temperatures >80–140°C, likely sterilizing microbial communities present since the deposition of sediments. High salinities associated with evaporites may have further limited microbial activity. Upward migration of hydrocarbons from shale source rocks into shallower reservoirs during maximum burial set the stage for microbial re‐introduction by creating organic‐rich “hot spots.” Denudation related to the incision of the Colorado River over the past few million years brought reservoirs closer to the surface under cooler temperatures, enhanced deep meteoric water circulation and flushing of saline fluids, and likely re‐inoculated more permeable sediments up to several km depth. Modern‐ to paleo‐hydrocarbon reservoirs show molecular and isotopic evidence of anaerobic oxidation of hydrocarbons coupled to bacterial sulfate reduction in areas with relatively high SO₄‐fluxes. Anaerobic oil biodegradation rates are high enough to explain the removal of at least some portion of postulated “supergiant oil fields” across the Colorado Plateau by microbial activity over the past several million years. Results from this study help constrain the lower limits of the hypo‐Critical Zone and how it evolved over geologic time, in response to changing geologic, hydrologic, and biologic forcings. 

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5. Data report: the DNA event horizon in the Guaymas Basin subsurface biosphere: technical advances and redefined limits in bulk extractions of nucleic acids from deep marine sediments, IODP Expedition 385

   https://doi.org/10.14379/iodp.proc.385.204.2024  

   Ramírez, GA; Mara, P; Beaudoin, D; Bojanova, D; Hinkle, JE; Kingham, B; Edgcomb, VP; Morono, Y; Teske, A (October 2024, Proceedings of the International Ocean Discovery Program Expedition reports)

   We compiled DNA and RNA isolation protocols for sediment bulk extraction and their yields from Guaymas Basin subsurface sediments recovered during International Ocean Discovery Program Expedition 385 and evaluated their sensitivity for metagenomic and amplicon analyses of subsurface microbial communities. Guaymas Basin sediments present a challenge for DNA and RNA recovery due to high concentrations of hydrocarbons, steep thermal gradients, and rapidly declining cell numbers downhole. Metagenomic library construction and sequencing was possible from as little as 0.2 to 0.5 ng DNA/cm3 sediment; polymerase chain reaction (PCR) amplification of 16S rRNA genes required in most cases approximately 1–2 ng DNA/cm3 sediment. At in situ temperatures of 50° to 60°C, decreasing DNA recovery leads to increasingly uncertain hit or miss outcomes and failures for metagenomic and amplicon analyses. DNA concentration profiles show that, even before these hot temperatures are reached, relatively moderate temperatures (near 40°C) have a major effect on microbial abundance and DNA yield. Comparison with cell count profiles shows that hydrothermal influence reduces downhole cell densities by multiple orders of magnitude compared to nonhydrothermal sediments. This effect is also visible at relatively moderate temperatures. RNA recovery is highly sensitive to downhole increasing temperatures and decreasing cell numbers, and was most efficient for microbial communities in cool, relatively shallow subsurface sediments. 

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