Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times ( 2 S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.

Recent Advances in Petroleum Microbiology

Large, abrupt, and widespread climate changes with major impacts have occurred repeatedly in the past, when the Earth system was forced across thresholds. Although abrupt climate changes can occur for many reasons, it is conceivable that human forcing of climate change is increasing the probability of large, abrupt events. Were such an event to recur, the economic and ecological impacts could be large and potentially serious. Unpredictability exhibited near climate thresholds in simple models shows that some uncertainty will always be associated with projections. In light of these uncertainties, policy-makers should consider expanding research into abrupt climate change, improving monitoring systems, and taking actions designed to enhance the adaptability and resilience of ecosystems and economies.

/pdf/abrupt-climate-change-5bwhk8ky17.pdf

Abrupt climate change

This review shows that thermodynamic and kinetic constraints largely prevent large-scale methanogenesis in the open ocean water column. One example of open-ocean methanogenesis involves anoxic digestive tracts and fecal pellet microenvironments; methane released during fecal pellet disaggregation results in the mixed-layer methane maximum. However, the bulk of the methane in the ocean is added by coastal runoff, seeps, hydrothermal vents, decomposing hydrates, and mud volcanoes. Since methane is present in the open ocean at nanomolar concentrations, and since the flux to the atmosphere is small, the ultimate fate of ocean methane additions must be oxidation within the ocean. As indicated in the Introduction and highlighted in Table 3, sources of methane to the ocean water column are poorly quantified. There are only a small number of direct water column methane oxidation rates, so sinks are also poorly quantified. We know that methane oxidation rates are sensitive to ambient methane concentrations, but we have no information on reaction kinetics and only one report of the effect of pressure on methane oxidation. Our perspective on methane sources and the extent of methane oxidation has been changed dramatically by new techniques involving gene probes, determination of isotopically depleted biomarkers, and recent 14C-CH4 measurements showing that methane geochemistry in anoxic basins is dominated by seeps providing fossil methane. The role of anaerobic oxidation of methane has changed from a controversial curiosity to a major sink in anoxic basins and sediments. © 2007 American Chemical Society.

/pdf/oceanic-methane-biogeochemistry-12rf80pqzx.pdf

Oceanic methane biogeochemistry.

Anaerobic methanotrophs help regulate Earth’s climate and may have been an important part of the microbial ecosystem on the early Earth. The anaerobic oxidation of methane (AOM) is often thought of as a sulfate-dependent process, despite the fact that other electron acceptors are more energetically favorable. Here, we show that microorganisms from marine methane-seep sediment in the Eel River Basin in California are capable of using manganese (birnessite) and iron (ferrihydrite) to oxidize methane, revealing that marine AOM is coupled, either directly or indirectly, to a larger variety of oxidants than previously thought. Large amounts of manganese and iron are provided to oceans from rivers, indicating that manganese- and iron-dependent AOM have the potential to be globally important.

https://science.sciencemag.org/content/sci/325/5937/184.full.pdf

Manganese- and Iron-Dependent Marine Methane Oxidation

Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 1030 cells) exist in the ‘big five’ habitats: deep oceanic subsurface (4 × 1029), upper oceanic sediment (5 × 1028), deep continental subsurface (3 × 1029), soil (3 × 1029) and oceans (1 × 1029). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20–80% of cells in the subsurface exist as biofilms. Hence, overall, 40–80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life. In this Analysis article, Flemming and Wuertz calculate the total number of bacteria and archaea on Earth and estimate the fraction that lives in biofilms. They propose that biofilms are the most prominent and influential type of microbial life.

Bacteria and archaea on Earth and their abundance in biofilms

Detailed microbial analyses of a glacial outwash aquifer contaminated by crude oil provide insights into the pattern of microbial succession from iron reducing to methanogenic in the anaerobic portion of the contaminant plume We analysed sediments from this area for populations of aerobes, iron reducers, fermenters and methanogens, using the most probable number method On the basis of the microbial data the anaerobic area can be divided into distinct physiological zones dominated by either iron-reducers or a consortium of fermenters and methanogens Chemistry and permeability data show that methanogenic conditions develop first in areas of high hydrocarbon flux Thus, we find methanogens both in high permeability horizons and also where separate-phase crude oil is present in either the saturated or unsaturated zone Microbial numbers peak at the top of the separate-phase oil suggesting that growth is most rapid in locations with access to both hydrocarbons and nutrients infiltrating from the surface

Microbial ecology of a crude oil contaminated aquifer.

https://link.springer.com/content/pdf/10.1007/s100400050002.pdf

Preface – Groundwater and microbial processes

I ncreased concentrations of nitrate in groundwater in agricultural areas, coinciding with increased use of chemical and organic fertilizers, have raised concern because of risks to environmental and human health. At some sites, these problems are mitigated by natural attenuation of nitrate as a result of microbially mediated reactions. Results from U.S. Geological Survey (USGS) research under the National WaterQuality Assessment (NAWQA) program show that reactions of dissolved nitrate with solid aquifer minerals and organic carbon help lower nitrate concentrations in groundwater beneath agricultural fields. However, increased fluxes of nitrate cause ongoing depletion of the finite pool of solid reactants. Consumption of the solid reactants diminishes the capacity of the aquifer to remove nitrate, calling into question the long-term sustainability of these natural attenuation processes.

/pdf/sustainability-of-natural-attenuation-of-nitrate-in-3fz9qgq2y1.pdf

Sustainability of natural attenuation of nitrate in agricultural aquifers

Comparing zero- and first-order approximations to the Monod model

..........................................................................................................................................................

/pdf/fate-and-transport-of-petroleum-hydrocarbons-in-the-42953miida.pdf

Barbara A. Bekins

Papers

Microbial ecology of a crude oil contaminated aquifer.

Preface – Groundwater and microbial processes

Sustainability of natural attenuation of nitrate in agricultural aquifers

Comparing zero- and first-order approximations to the Monod model

Fate and transport of petroleum hydrocarbons in the subsurface near Cass Lake, Minnesota