Search

Unprecedented and dramatic transformations are occurring in the Arctic in response to climate change, but academic, public, and political discourse has disproportionately focussed on the most visible and direct aspects of change, including sea ice melt, permafrost thaw, the fate of charismatic megafauna, and the expansion of fisheries. Such narratives disregard the importance of less visible and indirect processes and, in particular, miss the substantive contribution of the shelf seafloor in regulating nutrients and sequestering carbon. Here, we summarise the biogeochemical functioning of the Arctic shelf seafloor before considering how climate change and regional adjustments to human activities may alter its biogeochemical and ecological dynamics, including ecosystem function, carbon burial, or nutrient recycling. We highlight the importance of the Arctic benthic system in mitigating climatic and anthropogenic change and, with a focus on the Barents Sea, offer some observations and our perspectives on future management and policy.

The effectiveness of liquid carbon additions to enhance zinc removal in laboratory-scale short hydraulic residence time (19 h) compost bioreactors receiving synthetic mine water with a high influent zinc concentration (45 mg/L) was investigated. Effective removal of such elevated zinc concentrations could not be sustained by sulfate reduction and/or other attenuation processes without carbon supplementation. Propionic acid addition resulted in improved and sustained performance by promoting the activities of sulfate reducing bacteria, leading to efficient zinc removal (mean 99%) via bacterial sulfate reduction. In contrast, cessation of propionic acid addition led to carbon limitation and the growth of sulfur oxidising bacteria, compromising zinc removal by bacterial sulfate reduction. These research findings demonstrate the potential for modest liquid carbon additions to compost-based passive treatment systems to engineer microbial responses which enhance rates of zinc attenuation in a short hydraulic residence time, enabling remediation of highly polluting mine drainage at sites with limited land availability.

A low-cost approach for enhancing mesophilic (37 °C) anaerobic digestion (AD) of organic waste using a low-temperature (37 °C) pretreatment with different mineral wastes (MW) was investigated. A higher and stable methane production rate, in comparison to MW-free controls, was achieved for 80 days at organic loading rates of 1-2 g VS/L·d, using a feed substrate pretreated with incinerator bottom ash (IBA). The boiler ash and cement-based waste pretreatments also produced high methane production rates but with some process instability. In contrast, an incinerator fly ash pretreatment showed a progressive decrease in methane production rates and poor process stability, leading to reactor failure after 40 days. To avoid process instability and/or reactor failure, two metrics had to be met: (a) a methanogenesis to fermentation ratio higher than 0.6 and (b) a cell-specific methanogenic activity to cell-specific fermentation activity ratio of >1000. The prevalence of Methanofastidiosum together with a mixed community of acetoclastic (Methanosaeta) and hydrogenotrophic (Methanobacterium) methanogens in the stable IBA treatment indicated the importance of Methanofastidiosum as a potential indicator of a healthy and stable reactor.

Previous studies found mineral wastes (MW; incineration bottom ash (IBA), cement based waste (CBW), Fly ash (FA) and boiler ash (BA) are a promising resource for the macro-/micronutrients necessary for anaerobic digestion (AD) processes. The current study used first-order and modified Gompertz models from BMP assays to investigate the effects of integrating MW on the AD of OFMSW at 37 °C. Results from the first-order model showed a 45% increase in the specific growth rate of microorganisms (μ) in the MW- supplemented BMP compared to the control. Gompertz model results indicated that the IBA, CBW, FA and BA BMP amended assays obtained the highest K values (45–54 mL CH4 g VS−1 d−1) than the control (K ∼ 31 mL CH4 g VS−1 d−1), with no significant adverse effects of co-digestion of OFMSW with MW on the length of the lag phase (λ) in BMP assays (λ = 1.89 ± 0.07 days for IBA, CBW and BA amended assays compared to 1.5 ± 0.01 days for the control). However, FA amended assays had a greater λ value (3.66 ± 0.1 days). The MW provided both alkalinity and released several trace elements at concentrations within the optimal ranges for methanogenic archaea.

Rice paddies are major contributors to anthropogenic greenhouse gas emissions via methane (CH4) flux. The accurate quantification of CH4 emissions from rice paddies remains problematic, in part due to uncertainties and omissions in the contribution of microbial aggregates on the soil surface to carbon fluxes. Herein, we comprehensively evaluated the contribution of one form of microbial aggregates, periphytic biofilm (PB), to carbon dioxide (CO2) and CH4 emissions from paddies distributed across three climatic zones, and quantified the pathways that drive net CH4 production as well as CO2 fixation. We found that PB accounted for 7.1%–38.5% of CH4 emissions and 7.2%–12.7% of CO2 fixation in the rice paddies. During their growth phase, PB fixed CO2 and increased the redox potential, which promoted aerobic CH4 oxidation. During the decay phase, PB degradation reduced redox potential and increased soil organic carbon availability, which promoted methanogenic microbial community growth and metabolism and increased CH4 emissions. Overall, PB acted as a biotic converter of atmospheric CO2 to CH4, and aggravated carbon emissions by up to 2,318 kg CO2 equiv ha−1 season−1. Our results provide proof-of-concept evidence for the discrimination of the contributions of surface microbial aggregates (i.e., PB) from soil microbes, and a profound foundation for the estimation and simulation of carbon fluxes in a potential novel approach to the mitigation of CH4 emissions by manipulating PB growth., Graphical abstract, Public summary • Field experiments were conducted in tropical, subtropical, and temperate rice paddies • Periphytic biofilm promoted CO2 fixation and CH4 emission • Periphytic biofilm acted as a biotic converter of atmospheric CO2 to CH4

Mineral wastes (MWs) from municipal solid waste incineration plants and construction demolition sites are rich in minerals, heavy metals and have acid neutralising capacity. This renders such MWs a promising source of bulk and trace elements to enhance and stabilize biogas production in anaerobic processes. However, finding a MW with typical heavy metal concentrations, which promotes anaerobic digestion (AD) without adverse effects on the microbial community of the reactor is of major importance. To investigate the impact of several MW additives (1. incineration bottom ash; 2. fly ash; 3. boiler ash; 4. cement-based waste) as AD co-substrates, six 5 L single stage mesophilic, continuously stirred tank reactors (CSTR) were setup. Two different feeding regimes were employed including: (a) a liquid-recycled feeding method (LRFM); (b) a draw-and-fill feeding method (DFFM). Under the LRFM regime, one gram MW per gram organic waste enhanced process stability (pH), increased methane production (25–45% increase), and yielded (450–520 mL CH4/g VS); DFFM enhanced digestibility to a lesser degree. Illumina HiSeq 16S rRNA community sequencing of reactors showed that the microbial community compositions were unaffected by the presence of MW additives in comparison to unamended controls, but MW amendment accelerated bacterial growth (determined by qPCR). In contrast, different feeding regimes altered the microbial communities; Methanoculleus (hydrogenotrophic) and Methanosaeta (acetoclastic) were the most abundant methanogenic genera in the LRFM reactors, and the more metabolically versatile Methanosarcina genus dominated under DFFM.

Graphical abstract, What follows is a method applicable generically to the analysis of low levels of organic matter that is embedded in either loose fine-grained or solid geological material. Initially, the range of organic compounds that could be detected in a geological sample using conventional pyrolysis chromatography/mass spectrometry was compared to the range that was detected using thermally assisted hydrolysis and methylation-gas chromatography/mass spectrometry (THM-GC/MS). This method was used to validate the synthetic components fitted to X-ray photoelectron spectroscopy (XPS) carbon spectra of the sample. Reciprocally, XPS analysis was able to identify the constituent carbon-carbon, carbon-oxygen and carbon-nitrogen bonds of the functional groups in the compounds identified by THM-GC/MS. The two independently derived outputs from the THM-GC/MS and the XPS techniques mutually validated the identification of organic compounds in our geological samples. We describe in detail the improvements to: • The preparation of geological samples for analysis by XPS. • Measurements of organic material in geological samples using GC/MS. • The use of THM-GC/MS and XPS data used together to characterise low levels of organic material in geological samples.

Understanding anthropogenic radionuclide biogeochemistry and mobility in natural systems is key to improving the management of radioactively contaminated environments and radioactive wastes. Here, we describe the contemporary depth distribution and phase partitioning of 137Cs, Pu, and 241Am in two sediment cores taken from the Irish Sea (Site 1: the Irish Sea Mudpatch; Site 2: the Esk Estuary). Both sites are located ~10 km from the Sellafield nuclear site. Low-level aqueous radioactive waste has been discharged from the Sellafield site into the Irish Sea for >50 y. We compare the depth distribution of the radionuclides at each site to trends in sediment and porewater redox chemistry, using trace element abundance, microbial ecology, and sequential extractions, to better understand the relative importance of sediment biogeochemistry vs. physical controls on radionuclide distribution/post-depositional mobility in the sediments. We highlight that the distribution of 137Cs, Pu, and 241Am at both sites is largely controlled by physical mixing of the sediments, physical transport processes, and sediment accumulation. Interestingly, at the Esk Estuary, microbially-mediated redox processes (considered for Pu) do not appear to offer significant controls on Pu distribution, even over decadal timescales. We also highlight that the Irish Sea Mudpatch likely still acts as a source of historical pollution to other areas in the Irish Sea, despite ever decreasing levels of waste output from the Sellafield site.

Moderately thermophilic (T-max, similar to 55 degrees C) methanogens are identified after extended enrichments from temperate, tropical and low-temperature environments. However, thermophilic methanogens with higher growth temperatures (T-opt >= 60 degrees C) are only reported from high-temperature environments. A microcosm-based approach was used to measure the rate of methane production and methanogen community structure over a range of temperatures and salinities in sediment from a temperate estuary. We report short-term incubations (, Microorganisms, 8 (10)

Understanding the long-term fate, stability, and bioavailability of uranium (U) in the environment is important for the management of nuclear legacy sites and radioactive wastes. Analysis of U behavior at natural analogue sites permits evaluation of U biogeochemistry under conditions more representative of long-term equilibrium. Here, we have used bulk geochemical and microbial community analysis of soils, coupled with X-ray absorption spectroscopy and mu-focus X-ray fluorescence mapping, to gain a mechanistic understanding of the fate of U transported into an organic-rich soil from a pitchblende vein at the UK Needle's Eye Natural Analogue site. U is highly enriched in the Needle's Eye soils (similar to 1600 mg kg(-1)). We show that this enrichment is largely controlled by U(VI) complexation with soil organic matter and not U(VI) bioreduction. Instead, organic-associated U(VI) seems to remain stable under microbially-mediated Fe(III)-reducing conditions. U(IV) (as non-crystalline U(IV)) was only observed at greater depths at the site (>25 cm); the soil here was comparatively mineral-rich, organic-poor, and sulfate-reducing/methanogenic. Furthermore, nanocrystalline UO2, an alternative product of U(VI) reduction in soils, was not observed at the site, and U did not appear to be associated with Fe-bearing minerals. Organicrich soils appear to have the potential to impede U groundwater transport, irrespective of ambient redox conditions. (C) 2020 The Authors. Published by Elsevier Ltd.

The procedures for detecting fossils on Mars can be derived from the methods that are already used in terrestrial paleobiology (Cady et al., 2003). Here fossils preserving regions are visually located, then inspected for morphological features that might imply fossilised biology (Cady and Noffke, 2009; Westall et al., 2015). Morphological evidence of microfossils on its own is not a completely reliable biosignature (García Ruiz et al., 2002). However, evidence of biological activity may be implanted within the molecular and isotopic composition of organic compounds, which can serve as biosignatures (Summons et al., 2008). Thus, combining both morphological with organo-geochemical evidence could strengthen any argument that a given geological feature could be associated with biological activity. The results from the simultaneous morphological and geochemical analysis of geobiological structures on Earth could provide evidence that any comparable structures that may be observed on Mars, are potentially connected to biological activity, and therefore, may be suitable for collection for return to the Earth, for further analysis.As a proof of concept, the distribution of the organic material that is associated with distinctive microtubules in the glassy volcaniclastic shards within tuff, that have been suggested to be putative ichnofossils (Banergee and Muehlenbachs, 2003), these were analysed by us using X-ray photoelectron spectroscopy, nanoSIMS and the Ionoptika J105 time of flight secondary ion mass spectrometer, with an argon gas cluster ion beam. This indicated that nitrogenous organic material occurred in regions of the sample that were rich in microtubule textures and in the surrounding microfractures (Sano et al., 2016). These results demonstrated that the J105 ToF-SIMS combined with XPS and GC/MS analysis is able to match geomorphological features with their organic and inorganic composition at the µm scale, which may be a useful approach for the identification of fossilised life on Mars.References:Banerjee et al., (2003). Geochemistry, Geophysics, Geosystems, 4(4).Cady et al., (2003). Astrobiology, 3(2), pp.351-368.Cady et al., (2009). GSA Today, 19(11).García Ruiz et al., (2002). Astrobiology, 2(3), pp.353-369.Summons et al., (2008) Astrobiology, 90, 1151–1154.Westall, F., et al., (2015). Astrobiology, 15(11), pp.998-1029.Sano, N et al., (2016). J. of Vac Sci & Tech A: 34(4), p.041405

Structures in geological samples are often interpreted as fossilised life; however, such interpretations are equivocal, as abiotic processes can be invoked to explain their presence. Thus, additional lines of chemical evidence are invaluable in confirming or refuting such morphological evidence. Glass shards in tuff from the Ontong Java Plateau (OJP) contain microtubular structures that are in close proximity to functionalised nitrogen substituted aromatic compounds that may be indicative of the chemical remnants of biological activity. The organic composition of the OJP tuff containing microtubular alteration structures was compared with tuff without such features. In addition, organic matter associated with horizons with compacted remnants of woody material buried in the OJP tuff and overlying pelagic calcareous foraminifer sediment were also characterised, to ascertain the provenance of the organic matter found in the OJP tuff. As a further control, the organic material in submarine and terrestrial basalts from other locations were also characterised providing further evidence to support the view that the organic matter in the OJP tuff is authigenic. Carbon-nitrogen chemistry was detected across all OJP tuff samples irrespective of the presence or absence of microtubular features, but was not detected in either the wood material, the overlying pelagic sediments or in the basalts from other locations. The results indicate no direct link between the OJP nitrogenous organic compounds and the presence or absence of microtubular features.

Interpretation of bacteriohopanepolyol (BHP) biomarkers tracing microbiological processes in modern and ancient sediments relies on understanding environmental controls of production and preservation. BHPs from methanotrophs (35-aminoBHPs) were studied in methane-amended aerobic river-sediment incubations at different temperatures. It was found that: 1. With increasing temperature (4-40°C) a tenfold increase in aminopentol (associated with Crenothrix and Methylobacter spp. growth) occurred with only marginal increases in aminotriol and aminotetrol; 2. A further increase in temperature (50°C) saw selection for the thermophile Methylocaldum and mixtures of aminopentol and C-3 methylated aminopentol, again, with no increase in aminotriol and aminotetrol. 3. At 30°C more aminopentol and an aminopentol isomer and unsaturated aminopentol were produced after methanotroph growth and the onset of substrate starvation/oxygen depletion; 4. At 50°C, aminopentol and C-3 methylated aminopentol, only accumulated during growth but were clearly resistant to remineralisation despite cell death. These results have profound implications for the interpretation of aminoBHP distributions and abundances in modern and past environments. For instance, a temperature regulation of aminopentol production but not aminotetrol or aminotriol is consistent with and, corroborative of, observed aminopentol sensitivity to climate warming recorded in a stratigraphic sequence deposited during the Paleocene-Eocene thermal maximum (PETM). This article is protected by copyright. All rights reserved.

The organic matter within rocks contains chemical and isotopic evidence of its provenance, including information on past and extant life. Such information could further the understanding of life on the early Earth and yield evidence of the existence of past life on Mars. However, the collection of geological samples and subsequent transfer to analytical facilities possibly via long-term storage provides ample opportunity for organic contamination from a variety of sources prior to analysis. Erroneous assignment of organic contamination as authentic indigenous organic material is a significant issue in any geological specimen, but is exacerbated in rocks containing trace levels. This investigation evaluated two decontamination methods for geological samples, namely, the recently developed gas cluster ion beam etching, which supersedes monoatomic sputter etching, and ultra violet/ozone cleaning. Decontamination evaluation involved removal of intentionally applied organic contamination applied to basalt which initially possessed only trace levels of indigenous organic material. Pyrolysis-gas chromatography/mass spectrometry, and X-ray photoelectron spectroscopy were used to measure contaminant removal. Both techniques are suitable for removing organic contamination during the preparation of geological samples.

In many nations industrial scale AD of non-agricultural waste materials (such as MSW) has not yet reached its full potential, often constrained by the lack of secure, inexpensive, high quality AD feedstocks, and markets for the resulting digestate material. We tested the output material of a high throughput novel industrial process to define its potential as an AD feedstock (based on quality and consistency). This process, designed to circumvent the constraints of source segregation while still generating segregated waste streams, resulted in the production of a temporally homogenous fibrous material with: an average moisture content of 44.2 (±2.33)%; C:N ratio of ∼32.9:1 (±3.46:1), C:P ratio of ∼228:1 and gross calorific value of 17.4 (±0.29) MJ/kg(DM). This material provided a CH4 yield of between 201 and 297 m3 CH4/tonne(DM) (271–401 m3 CH4/tonne(vs)) comparable to commonly used AD feedstocks. Material contaminant levels were temporally consistent (P > 0.05), (average values being Cd 0.63 (±0.19), Cu 56.3 (±7.45), Crtot 51.4 (±4.41), Hg < 0.3, Ni 28.9 (±5.17), Pb 79.2 (±23.71), Zn 202 (±44.5), total polyaromatic hydrocarbons (PAH) 2.2 (±0.3), and total polychlorinated biphenyls (PCB) (

N and P are the key limiting nutrients considered most important for the stimulation of crude oil degradation but other trace nutrients may also be important. Experimental soil microcosms were setup to investigate crude oil degradation in the context of Ni amendments. Amended Nickel as NiO, NiCl2, or, a porphyrin complex either inhibited, had no effect, or, enhanced aerobic hydrocarbon degradation in an oil-contaminated soil. Biodegradation was significantly (95% confidence) enhanced (70%) with low levels of Ni-Porph (12 mg/kg) relative to an oil-only control; whereas, NiO (200 and 350 mg/kg) significantly inhibited (36 and 87%) biodegradation consistent with oxide particle induced reactive oxygen stress. Microbial community compositions were also significantly affected by Ni. In 16S rRNA sequence libraries, the enriched hydrocarbon degrading genus, Rhodococcus, was partially replaced by a Nocardia sp. in the presence of low levels of NiO (12 and 50 mg/kg). In contrast, the highest relative and absolute Rhodococcus abundances were coincident with the maximal rates of oil degradation observed in the Ni-Porph-amended soils. Growth dependent constitutive requirements for Ni-dependent urease or perhaps Ni-dependent superoxide dismutase enzymes (found in Rhodococcus genomes) provided a mechanistic explanation for stimulation. These results suggest biostimulation technologies, in addition to N and P, should also consider trace nutrients such as Ni tacitly considered adequately supplied and available in a typical soil.

The utilisation of the organic fraction of municipal solid waste as feedstock for bioethanol production could reduce the need for disposal of the ever-increasing amounts of municipal solid waste, especially in developing countries, and fits with the integrated goals of climate change mitigation and transport energy security. Mixed culture fermentation represents a suitable approach to handle the complexity and variability of such waste, avoiding expensive and vulnerable closed-control operational conditions. It is widely accepted that the control of pH in these systems can direct the fermentation process toward a desired fermentation product, however, little empirical evidence has been provided in respect of lignocellulosic waste substrates and different environmental inocula sources. We evaluated ethanol production from the organic fraction of municipal solid waste using five different inocula sources where lignocellulose degradation putatively occurs, namely, compost, woodland soil, rumen, cow faeces and anaerobic granular sludge, when incubated in batch microcosms at either initially neutral or acidic pH and under initially aerobic or anaerobic conditions. Although ethanol was produced by all the inocula tested, their performance was different in response to the imposed experimental conditions. Rumen and anaerobic granular sludge produced significantly the highest ethanol concentrations (∼30 mM) under initially neutral and acidic pH, respectively. A mixed-source community formed by mixing rumen and sludge (R + S) was then tested over a range of initial pH. In contrast to the differences observed for the individual inocula, the maximal ethanol production of the mixed community was not significantly different at initial pH of 5.5 and 7. Consistent with this broader functionality, the microbial community analyses confirmed the R + S community enriched comprised bacterial taxa representative of both original inocula. It was demonstrated that the interaction of initial pH and inocula source dictated ethanologenic activity from the organic fraction of municipal solid waste. Furthermore, the ethanologenic mixed-source community enriched, was comprised of taxa belonging to the two original inocula sources (rumen and sludge) and had a broader functionality. This information is relevant when diverse inocula sources are combined for mix culture fermentation studies as it experimentally demonstrates the benefits of diversity and function assembled from different inocula.

Highly compacted MX80 bentonite has been selected as the engineered buffer and backfill material in several proposed concepts for long-term deep geological storage of nuclear waste. Iron-reducing bacteria reduce Fe (III) to Fe (II) and some are adapted to high temperatures and desiccated environments, in keeping with periods of less habitable conditions within the repository. In one potential UK repository concept, iron from carbon steel canisters may contribute to an iron-rich environment at the clay-canister interface. This could lead to changes in the mineralogy and iron-content of MX80 bentonite due to variation of the redox state and solubility, which in turn could alter the geomechanical properties of the clay. To investigate the potential role of iron-reducing bacteria in this process enrichments were carried out with both commercially available MX80 bentonite powder and compacted MX80 bentonite to identify the presence of an indigenous iron-interacting community in the clay. Throughout these enrichments Fe (II) soluble, Fe (II) total, and pH were measured, and the enrichments were subjected to 16S rRNA community analysis. Concentrations of Fe (II) total peaked at day 28 in all enrichments; however, the concentration was overall higher when accompanied by bacterial growth. Fe (II) soluble remained low throughout. 16S rRNA gene sequencing revealed the presence of several putative iron-interacting bacteria, as well as thermotolerant and spore-forming species. The indigenous community was largely comprised of firmicutes, including iron-reducers and spore-forming bacteria such as Desulfosporosinus. Therefore, MX80 bentonite inherently carries a viable microbial community which could potentially interact with structural iron present within MX80 bentonite or other mineral components, such as a carbon steel waste canister. Various research has shown that microbial activity is unlikely within the bulk bentonite provided high compaction is maintained. The importance of this high compaction is highlighted by the finding here of a viable, robust and functionally diverse community within the clay and activity may be possible anyway at edge sites and interfaces where, locally, swelling pressures might not fully develop.

Earlier investigations have suggested that an extensive deep biosphere with a significant fungal component is present within the sub-oceanic crust. To investigate this further, the organic material in the lithic sections of a sub-oceanic volcaniclastic tuff obtained from the eastern lobe of the Ontong Java Plateau (OJP tuff) were characterised using X-ray photoelectron spectroscopy and thermal hydrolysis and methylation coupled to gas chromatography/mass spectrometry. In the investigation here, the chemical and molecular composition of plant and fungal structural biopolymer standards were characterised using the same techniques and then compared to the organic material from the OJP tuff. This was conducted on untreated material and after hydrous pyrolysis, a process that simulated the physical and thermal decomposition of organic material that occurs during late diagenesis. The characteristics of the organic material in the OJP tuff matched the products of hydrous-pyrolysed chitin. This result suggested that OJP tuff contained organic material that could have been derived from fossilised chitin, implying that the OJP tuff potentially contained the remnants of a microbial community with a fungal component.

Mixed Culture Fermentation is a promising route for bioethanol production from organic wastes. Yet, achieving a stable ethanologenic activity in undefined mixed cultures remains a challenge. This work aimed to retain ethanol production from organic municipal solid waste by microbial communities enriched from sheep rumen and anaerobic sludge mixtures, under low process control (initially aerobic conditions and initial pH ≤ 5.5). To find a stable operating window, sequential inoculum transfer intervals were evaluated (14 and 3-days). Soluble fermentation product profiles and changes in the prokaryotic communities were monitored. The originally inoculated batches always produced high ethanol concentrations (60 mM; 0.070 LEtOH/Kgwaste), equivalent to 1/6 of the current corn grain-based ethanol industrial production process. Fermentative activity and community richness significantly decreased in both transfer times regimes tested. However, the 3-day transfer interval led to a stable community which consistently produced ethanol (30 mM) as its main soluble fermentation product. Originally inoculated and 3-day transferred communities consistently enriched for a solventogenic Clostridium and an acid-tolerant Pseudomonas species. Ethanologenesis, as a dominant catabolic process, is an inherent property of these mixed culture fermentations, and its maintenance across successive transfers is critically dependant on the inoculum transfer time.

Summary This roadmap examines the future of microbiology research and technology in fossil fuel energy recovery. Globally, the human population will be reliant on fossil fuels for energy and chemical feedstocks for at least the medium term. Microbiology is already important in many areas relevant to both upstream and downstream activities in the oil industry. However, the discipline has struggled for recognition in a world dominated by geophysicists and engineers despite widely known but still poorly understood microbially mediated processes e.g. reservoir biodegradation, reservoir souring and control, microbial enhanced oil recovery. The role of microbiology is even less understood in developing industries such as shale gas recovery by fracking or carbon capture by geological storage. In the future, innovative biotechnologies may offer new routes to reduced emissions pathways especially when applied to the vast unconventional heavy oil resources formed, paradoxically, from microbial activities in the geological past. However, despite this potential, recent low oil prices may make industry funding hard to come by and recruitment of microbiologists by the oil and gas industry may not be a high priority. With regards to public funded research and the imperative for cheap secure energy for economic growth in a growing world population, there are signs of inherent conflicts between policies aimed at a low carbon future using renewable technologies and policies which encourage technologies which maximize recovery from our conventional and unconventional fossil fuel assets., A perspective on the potential future roles of microbiology in the fossil fuel sector is presented. This is placed in the context of technical and economic factors that may facilitate or mitigate against the uptake of new technologies.

Summary River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane‐oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4–30°C, pH 6–8, 1–15 g l−1 NaCl), communities were enriched by sequences affiliated with M ethylobacter and M ethylomonas spp. and specifically a M ethylobacter psychrophilus‐related species at 4–21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l−1 selected for putative thermophiles (M ethylocaldum), acidophiles (M ethylosoma) and haloalkaliphiles (M ethylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.

Crude oil-amended microcosms were prepared with inocula from eleven anoxic environments (4 river sediments, 3 lake sediments, and 4 sludges from wastewater treatment reactors) to determine their ability to produce methane from the biodegradation of crude oil. Over incubation periods of up to 1150 days, oil-stimulated methanogenesis and concomitant loss of alkanes occurred in microcosms prepared with five of the inocula whereas six of the inocula did not show oil-stimulated methane production. Bacterial and archaeal communities from microcosms exhibiting high levels of oil-stimulated methanogenesis were distinct from communities where methanogenic crude oil degradation was not detected. Successional changes were consistent with the quantitative enrichment of syntrophic hydrocarbon degrading bacteria and methanogens over time. In conclusion, in oil-impacted environments methanogenic crude oil-degrading microbial consortia are present in relatively low abundance and exhibit slow growth, and while they may be ubiquitously distributed they may not be present at sufficiently high abundance to be detected.

Process-based, mechanistic investigations of organic matter transformation and diagenesis directly beneath the sediment–water interface (SWI) in Arctic continental shelves are vital as these regions are at greatest risk of future change. This is in part due to disruptions in benthic–pelagic coupling associated with ocean current change and sea ice retreat. Here, we focus on a high-resolution, multi-disciplinary set of measurements that illustrate how microbial processes involved in the degradation of organic matter are directly coupled with inorganic and organic geochemical sediment properties (measured and modelled) as well as the extent/depth of bioturbation. We find direct links between aerobic processes, reactive organic carbon and highest abundances of bacteria and archaea in the uppermost layer (0–4.5 cm depth) followed by dominance of microbes involved in nitrate/nitrite and iron/manganese reduction across the oxic-anoxic redox boundary (approx. 4.5–10.5 cm depth). Sulfate reducers dominate in the deeper (approx. 10.5–33 cm) anoxic sediments which is consistent with the modelled reactive transport framework. Importantly, organic matter reactivity as tracked by organic geochemical parameters ( n -alkanes, n -alkanoic acids, n -alkanols and sterols) changes most dramatically at and directly below the SWI together with sedimentology and biological activity but remained relatively unchanged across deeper changes in sedimentology. This article is part of the theme issue ‘The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning’.

Microbial biodegradation of hydrocarbons in petroleum reservoirs has major consequences in the petroleum value and quality. The identification of microorganisms capable of in-situ degradation of hydrocarbons under the reservoir conditions is crucial to understand microbial roles in hydrocarbon transformation and the impact of oil exploration and production on energy resources. The aim of this study was to profile the metagenome of microbial communities in crude oils and associated formation water from two high temperature and relatively saline oil-production wells, where one has been subjected to water flooding (BA-2) and the other one is considered pristine (BA-1). The microbiome was studied in the fluids using shotgun metagenome sequencing. Distinct microbial compositions were revealed when comparing pristine and water flooded oil wells in contrast to the similar community structures observed between the aqueous and oil fluids from the same well (BA-2). The equal proportion of archaea and bacteria together with the greater anaerobic hydrocarbon degradation potential in the BA-1 pristine but degraded reservoir contrasted with the predominance of bacteria over archaea, aerobic pathways and lower frequency of anaerobic degradation genes in the BA-2 water flooded undegraded well. Our results suggest that Syntrophus, Syntrophomonas, candidatus Atribacteria and Synergistia, in association with mainly acetoclastic methanogenic archaea of the genus Methanothrix, were collectively responsible for the oil biodegradation observed in the pristine petroleum well BA-1. Conversely, the microbial composition of the water flooded oil well BA-2 was mainly dominated by the fast-growing and putatively aerobic opportunists Marinobacter and Marinobacterium. This presumable allochthonous community introduced a greater metabolic versatility, although oil biodegradation has not been detected hitherto perhaps due to in-reservoir unfavorable physicochemical conditions. These findings provide a better understanding of the petroleum reservoir microbiomes and their potential roles in biogeochemical processes occurring in environments with different geological and oil recovery histories.

Anaerobic digestion is widely used for the management of the organic fraction of municipal solid waste and is also predicted to play a vital role in the future of renewable energy production. However, reactor instability due to low acid buffering capacity at high organic loading rates in single stage reactors is a known risk of this technology. Such process instability represents a risk to electricity and heat generation through interruptions to biogas production. Co-digestion and trace element supplementation have each been advocated as strategies to stabilize biogas production, but the relative merits of these strategies have never been assessed. Here we operated a series of anaerobic continuously stirred tank reactors fed with synthetic organic household waste with or without trace element supplementation and with or without wheat straw as co-substrate at gradually increasing loading rates. Stable and high methane yields (450–550 mL/g VS) at higher organic loading rates were only maintained with trace element supplementation, regardless of co-digestion. We conclude that trace element supplementation was hierarchically more important than co-digestion at maintaining stable biogas production.

This study investigated the effects of mineral waste extracts (MWE) on laboratory-scale two-stage anaerobic digesters treating synthetic organic waste. MWE was prepared as aqueous extracts from different ash samples (incineration bottom ash (IBA), fly ash (FA) and boiler ash (BA) taken from a municipal solid waste incineration plant. At 20 days hydraulic retention time, all three MWE stimulated hydrogen production in their respective acidogenic reactor by around 35% (c.f. control acidogenic reactor), whilst no difference was seen in the methane productivity of the linked methanogenic reactors (average 527 ± 45 mL CH4/g VS, including control methanogenic reactor). Following a step reduction in hydraulic retention time from 20 to 10 days and a doubling of the organic loading rate from 2.5 g to 5 g VS/L. d, no significant change was seen in hydrogen production (p > 0.05) in the acidogenic reactor amended with MWE from IBA and BA, or the control acidogenic reactor. However, the acidogenic reactor receiving MWE from FA had 45% lower hydrogen productivity. The step change in hydraulic retention time and organic loading rates led to the failure of most methanogenic reactors (≤100 mL CH4/g VS), however, the one receiving feed containing MWE from IBA showed stable performance without signs of failure, and had higher volumetric methane productivity, albeit at lower methane yields (370 ± 20 mL CH4/g VS). 16S rRNA analysis using the Illumina sequencing platform revealed acidogenesis by Lactobacillaceae in the acidogenic reactor and syntrophic acetate oxidation by Synergistaceae linked to enrichment of the candidatus genus Methanofastidiosum, in the stable methanogenic reactor receiving MWE from IBA.

Soils in tropical and temperate locations are known to be a sink for the genetic potential of anthropogenic-driven acquired antibiotic resistance (AR). In contrast, accumulation of acquired AR is less probable in most Polar soils, providing a platform for characterizing background resistance and establishing a benchmark for assessing AR spread. Here, high-throughput qPCR and geochemistry were used to quantify the abundance and diversity of both antibiotic resistance genes (ARGs) and selected mobile genetic elements (MGEs) across eight soil clusters in the Kongsfjorden region of Svalbard in the High Arctic. Relative ARG levels ranged by over two orders of magnitude (10

A natural Mn oxide (NMO) waste was assessed as an in situ remediation amendment for Pb contaminated sites. The viability of this was investigated using a 10 month lysimeter trial, wherein a historically Pb contaminated soil was amended with a 10% by weight model NMO. The model NMO was found to have a large Pb adsorption capacity (qmax 346±14 mg g(-1)). However, due to the heterogeneous nature of the Pb contamination in the soils (3650.54-9299.79 mg kg(-1)), no treatment related difference in Pb via geochemistry could be detected. To overcome difficulties in traditional geochemical techniques due to pollutant heterogeneity we present a new method for unequivocally proving metal sorption to in situ remediation amendments. The method combines two spectroscopic techniques; namely electron probe microanalysis (EPMA) and X-ray photoelectron spectroscopy (XPS). Using this we showed Pb immobilisation on NMO, which were Pb free prior to their addition to the soils. Amendment of the soil with exogenous Mn oxide had no effect on microbial functioning, nor did it perturb the composition of the dominant phyla. We conclude that NMOs show excellent potential as remediation amendments.

Summary As we transition from fossil fuel reliance to a new energy future, innovative microbial biotechnologies may offer new routes to maximize recovery from conventional and unconventional energy assets; as well as contributing to reduced emission pathways and new technologies for carbon capture and utilization. Here we discuss the role of microbiology in petroleum biotechnologies in relation to addressing UN Sustainable Development Goal 12 (ensure sustainable consumption and production patterns), with a focus on microbially‐mediated energy recovery from unconventionals (heavy oil to methane), shale gas and fracking, bioelectrochemical systems for the production of electricity from fossil fuel resources, and innovations in synthetic biology. Furthermore, using wastes to support a more sustainable approach to fossil fuel extraction processes is considered as we undertake the move towards a more circular global economy., How to access and exploit natural resources sustainably: petroleum biotechnology.

The ability of a Fe-Mn binary oxide waste to adsorb arsenic (As) in a historically contaminated soil was investigated. Initial laboratory sorption experiments indicated that arsenite [As(III)] was oxidized to arsenate [As(V)] by the Mn oxide component, with concurrent As(V) sorption to the Fe oxide. The binary oxide waste had As(III) and As(V) adsorption capacities of 70 mg g‾¹ and 32 mg g‾¹ respectively. X-ray Absorption Near-Edge Structure and Extended X-ray Absorption Fine Structure at the As K-edge confirmed that all binary oxide waste surface complexes were As(V) sorbed by mononuclear bidentate corner-sharing, with 2 Fe at (approx.) 3.27 Ǻ. The ability of the waste to perform this coupled oxidation-sorption reaction in real soils was investigated with a 10% by weight addition of the waste to an industrially As contaminated soil. Electron probe microanalysis showed As accumulation onto the Fe oxide component of the binary oxide waste, which had no As innately. The bioaccessibility of As was also significantly reduced by 7.80% (p < 0.01) with binary oxide waste addition. The results indicate that Fe-Mn binary oxide wastes could provide a potential in situ remediation strategy for As and Pb immobilization in contaminated soils.

Summary Given the cost of conventional fertilizers and increasing demand as a result of increasing population growth, new sources of potassium (K) for plant nutrition need to be considered. Readily soluble nutrients are rapidly lost from well-drained soils, and so it is appropriate to consider silicate minerals that release K slowly during weathering. In this paper, we compare the availability to plants grown in sandy soils of K from microcline (feldspar), biotite (mica) and nepheline syenite (nepheline + microcline) using leek (Allium ampeloprasum var. porrum L.) as a model plant. Pot experiments were carried out under controlled environmental conditions using natural and artificial soil. The performance of the minerals was compared with treatment with KCl and a negative control (no K added). Plant shoot diameter was measured weekly to assess growth rates. After 10 weeks, plant dry mass and soil and plant contents of soluble K were measured to determine offtake; mineralogical changes in biotite-treated soils were assessed. Results for artificial and natural soil differed, reflecting differences in their mineralogy. With no added K, plant growth ceased after 2 weeks. Growth rates were greatest for KCl, followed by biotite; linear growth continued for 5 weeks in the natural soil and for the entire 10 weeks in the artificial soil. Growth rates with nepheline syenite (natural soil) and microcline (both soils) did not differ significantly from the negative control, but for nepheline syenite, leek shoot K content was significantly greater, demonstrating availability of K from this source. X-ray diffraction analysis showed that biotite reacted to form vermiculite.

High concentrations of minerals, heavy metals are often found in mineral wastes (MWs) originated from municipal solid waste incineration plants, so as construction/demolition sites. Such by-products (minerals) often have buffering capacity. The current work provides analysis of total and soluble (dissolved) metal concentrations released by four different MWs (a. cement-based waste, b. incineration (bottom), c. fly and d. boiler ash) supplemented to anaerobic reactors of organic waste at 37 °C. The reactors (continuous stirred tank reactor (CSTR)) were ran for 75 days at hydrolytic retention time of 20 days. Genomic DNA extraction, and qPCR and Illumina HiSeq (16S V4) analyses were conducted to investigate microbial community population and composition in anaerobic digestate samples collected from these reactors. Output data from Illumina sequencing analysis were FastQ files analysed using the QIIME2 pipeline to produce a feature table listing the frequency of each assigned microbial taxa per samples. Additional study was conducted on the microbial data to visualise variations in microbial communities using the STAMP software and phyloseq R package. Detailed interpretation and discussion of the results can be found in the related research article [1].

Fumarate addition has been widely proposed as an initial step in the anaerobic oxidation of both aromatic and aliphatic hydrocarbons. Alkyl and aryl succinates have been reported as metabolites of hydrocarbon degradation in laboratory studies with both pure and enrichment cultures of sulfate-, nitrate-, and iron-reducing bacteria. In addition these compounds have been reported in samples from environments such as hydrocarbon contaminated aquifers where, in addition to the above redox processes, hydrocarbon degradation linked to methanogenesis was observed. Here we report data from anaerobic crude oil degrading microcosms which revealed significant differences between the acid metabolite profiles of crude oil degraded under sulfate-reducing or methanogenic conditions. Under sulfate-reducing conditions fumarate addition and the formation of alkylsuccinate metabolites was the principal mechanism for the anaerobic degradation of n- alkanes and branched chain alkanes. Other than alkyl succinates that represent indigenous metabolites in the sediment inoculum, alkyl succinate metabolites were never detected in sediment microcosms where methane generation was quantitatively linked to n -alkane degradation. This indicates that alternative mechanisms of alkane activation may operate under methanogenic conditions.

Quantitative real-time PCR is a valuable tool for microbial ecologists. To obtain accurate absolute quantification it is essential that PCR efficiency for pure standards is close to amplification efficiency for test samples. Counter to normal expectation that PCR efficiency might be lower in environmental DNA, due to the presence of PCR inhibitors, we report the counterintuitive observation that PCR efficiency of pure standards can be lower than for environmental DNA. This can lead to overestimation of gene abundances if not corrected. SYBR green-based qPCR assays of 16S rRNA genes targeting Bacteria, Syntrophus and Smithella spp., Marinobacter spp., Methanomicrobiales, Methanosarcinaceae, and Methanosaetaceae in samples from methanogenic crude oil biodegradation enrichments were tested. In five out of the six assays, PCR efficiency was lower with pure standards than with environmental DNA samples. We developed a solution to this problem based on amending pure clone standards with a background of non-target environmental 16S rRNA genes which significantly improved PCR efficiency of standards in the qPCR assays that exhibited this phenomenon. Overall this method of qPCR standard preparation achieved a more reliable and robust quantification of 16S rRNA genes. We believe this may be a potentially common issue in microbial ecology that often goes unreported, as intuitively one would not expect standards to have poorer PCR efficiency than samples.

A combined geochemical, geological and microbiological analysis of an actively biodegrading 24.5 m thick oil column in a Canadian heavy oil reservoir has been carried out. The reservoir properties associated with the cored vertical well are characterised by a 15.75 m thick oil column and an 8.75 m zone of steadily decreasing oil saturation below the oil column, referred to as the oil–water transition zone (OWTZ), grading down into a thin water leg. The oil column exhibits systematic gradients in oil physical properties and hydrocarbon composition and shows variations in biodegradation level throughout the reservoir consistent with the notion that the biodegradation of oil is focussed in a bioreactor zone at the base of the oil column. Through the oil column, the dead oil viscosity measured at 20 °C ranged from 50,000 cP (0.05 McP) at the top of the oil column to 1.4 McP at the oil–OWTZ contact, and continued to increase to 10.5 McP within the OWTZ. The saturated and aromatic hydrocarbons are characterised by systematically decreasing bulk fraction and component concentrations down through the oil column. Different compound classes decreased to levels below their detection limit at different depths within the OWTZ, defining a likely bioreactor extent of over 5 m in depth with, for example, n-alkanes being reduced to their detection limit concentration at the bottom of the oil column/top of the OWTZ, while branched isoprenoid alkanes were not completely degraded until well into the OWTZ. Core samples from the oil column and the lower part of the OWTZ were estimated to contain ca. 104–105 bacterial cells/g, based on qPCR of bacterial 16S rRNA genes, while samples from a narrow interval in the OWTZ immediately below the oil column contained on the order of 106–107 cells/g of sediment. Interestingly, these latter numbers are typical of those observed in active deep subsurface biosphere systems with the notion that microbial activity and abundance in the deep subsurface is elevated at geochemical interfaces. The numbers of organisms are not constant throughout the OWTZ. The highest bacterial abundance and geochemical gradients of, for example, methylphenanthrene biodegradation define a zone near the oil–water contact as likely the most active in terms of biodegradation. The largest bacterial abundances in the upper part of the OWTZ are in line with the trend of bacterial abundance with depth that has emerged from extensive analysis of microbial cells in deep subsurface sediments, implying that in terms of deep biosphere cell abundance, oil reservoirs are similar to other deep subsurface microbial environments. This is puzzling, given the atypical abundance of organic carbon in petroleum reservoirs and may imply a common large scale control on microbial abundance and activity in the deep biosphere, including in oilfields.

Crude oil degradation under sulphate-reducing conditions was investigated in microcosms, amended with North Sea crude oil and inoculated with estuarine sediment from the River Tyne, UK. Linear-alkanes (nC7-nC34) were degraded over a 686 day period in oil-amended microcosms, in contrast alkane degradation was minimal in microcosms which were inhibited with sodium molybdate. Libraries of PCR-amplified 16S rRNA genes were prepared from DNA extracted from oil-amended microcosms at day 176, when the systems were actively sulphate-reducing (17.7 ± 0.9 μmol L−1 SO 4 2 − day−1 g−1 wet sediment) and at day 302, by which point sulphate was depleted. Bacteria from the phyla Chloroflexi, Firmicutes, Proteobacteria (Delta-, Gamma- classes) were enriched in oil-degrading microcosms relative to control microcosms to which no oil was added. Sequences of 16S rRNA genes from conventional sulphate-reducing microorganisms (SRM) such as Desulfotomaculum, Desulfosporomusa, Desulfosporosinus, Desulfovibrio, Desulfobulbus, Desulfobacter and Desulfobacterium, which have previously been implicated in oil degradation in other hydrocarbon-impacted environments, were not dominant in clone libraries prepared from oil-amended microcosms that were actively reducing sulphate at day 176. Instead sequences from Gammaproteobacteria (∼34%), most closely related to Marinobacterium sp. and members of the family Peptostreptococcaceae within the Firmicutes (∼27%), were detected at highest frequency. By day 302, when sulphate was depleted and the majority of n-alkane degradation had already occurred, a shift in community composition was apparent in oil-amended microcosms with sequences from Chloroflexi (family Anaerolineaceae) being most frequently encountered (24%), together with Firmicutes (20%) and the more conventional SRM; Deltaproteobacteria (19%). These data suggest that other groups of organisms in addition to conventional sulphate-reducing microorganisms play a role in the anaerobic degradation of crude oil in some sulphate-containing environments.

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

Libraries of 16S rRNA genes cloned from methanogenic oil degrading microcosms amended with North Sea crude oil and inoculated with estuarine sediment indicated that bacteria from the genera Smithella (Deltaproteobacteria, Syntrophaceace) and Marinobacter sp. (Gammaproteobacteria) were enriched during degradation. Growth yields and doubling times (36 days for both Smithella and Marinobacter) were determined using qPCR and quantitative data on alkanes, which were the predominant hydrocarbons degraded. The growth yield of the Smithella sp. [0.020 g(cell-C)/g(alkane-C)], assuming it utilized all alkanes removed was consistent with yields of bacteria that degrade hydrocarbons and other organic compounds in methanogenic consortia. Over 450 days of incubation predominance and exponential growth of Smithella was coincident with alkane removal and exponential accumulation of methane. This growth is consistent with Smithella's occurrence in near surface anoxic hydrocarbon degrading systems and their complete oxidation of crude oil alkanes to acetate and/or hydrogen in syntrophic partnership with methanogens in such systems. The calculated growth yield of the Marinobacter sp., assuming it grew on alkanes, was [0.0005 g(cell-C)/g(alkane-C)] suggesting that it played a minor role in alkane degradation. The dominant methanogens were hydrogenotrophs (Methanocalculus spp. from the Methanomicrobiales). Enrichment of hydrogen-oxidizing methanogens relative to acetoclastic methanogens was consistent with syntrophic acetate oxidation measured in methanogenic crude oil degrading enrichment cultures. qPCR of the Methanomicrobiales indicated growth characteristics consistent with measured rates of methane production and growth in partnership with Smithella.

The subsurface microbiology of an Athabasca oil sands reservoir in western Canada containing severely biodegraded oil was investigated by combining 16S rRNA gene- and polar lipid-based analyses of reservoir formation water with geochemical analyses of the crude oil and formation water. Biomass was filtered from formation water, DNA was extracted using two different methods, and 16S rRNA gene fragments were amplified with several different primer pairs prior to cloning and sequencing or community fingerprinting by denaturing gradient gel electrophoresis (DGGE). Similar results were obtained irrespective of the DNA extraction method or primers used. Archaeal libraries were dominated by Methanomicrobiales (410 of 414 total sequences formed a dominant phylotype affiliated with a Methanoregula sp.), consistent with the proposed dominant role of CO2-reducing methanogens in crude oil biodegradation. In two bacterial 16S rRNA clone libraries generated with different primer pairs, > 99% and 100% of the sequences were affiliated with Epsilonproteobacteria (n = 382 and 72 total clones respectively). This massive dominance of Epsilonproteobacteria sequences was again obtained in a third library (99% of sequences; n = 96 clones) using a third universal bacterial primer pair (inosine-341f and 1492r). Sequencing of bands from DGGE profiles and intact polar lipid analyses were in accordance with the bacterial clone library results. Epsilonproteobacterial OTUs were affiliated with Sulfuricurvum, Arcobacter and Sulfurospirillum spp. detected in other oil field habitats. The dominant organism revealed by the bacterial libraries (87% of all sequences) is a close relative of Sulfuricurvum kujiense – an organism capable of oxidizing reduced sulfur compounds in crude oil. Geochemical analysis of organic extracts from bitumen at different reservoir depths down to the oil water transition zone of these oil sands indicated active biodegradation of dibenzothiophenes, and stable sulfur isotope ratios for elemental sulfur and sulfate in formation waters were indicative of anaerobic oxidation of sulfur compounds. Microbial desulfurization of crude oil may be an important metabolism for Epsilonproteobacteria indigenous to oil reservoirs with elevated sulfur content and may explain their prevalence in formation waters from highly biodegraded petroleum systems.

Changes in communities of syntrophic acetate-oxidizing bacteria (SAOB) and methanogens caused by elevated ammonia levels were quantified in laboratory-scale methanogenic biogas reactors operating at moderate temperature (37°C) using quantitative polymerase chain reaction (qPCR). The experimental reactor was subjected to gradually increasing ammonia levels (0.8-6.9 g NH4 (+) -N l(-1) ), whereas the level of ammonia in the control reactor was kept low (0.65-0.90 g NH4 (+) -N l(-1) ) during the entire period of operation (660 days). Acetate oxidation in the experimental reactor, indicated by increased production of (14) CO2 from acetate labelled in the methyl carbon, occurred when ammonia levels reached 5.5 and 6.9 g NH4 (+) -N l(-1) . Syntrophic acetate oxidizers targeted by newly designed qPCR primers were Thermacetogenium phaeum, Clostridium ultunense, Syntrophaceticus schinkii and Tepidanaerobacter acetatoxydans. The results showed a significant increase in abundance of all these bacteria except T. phaeum in the ammonia-stressed reactor, coincident with the shift to syntrophic acetate oxidation. As the abundance of the bacteria increased, a simultaneous decrease was observed in the abundance of aceticlastic methanogens from the families Methanosaetaceae and Methanosarcinaceae. qPCR analyses of sludge from two additional high ammonia processes, in which methane production from acetate proceeded through syntrophic acetate oxidation (reactor SB) or through aceticlastic degradation (reactor DVX), demonstrated that SAOB were significantly more abundant in the SB reactor than in the DVX reactor.

Clay minerals are abundant in soils and sediments and often contain Fe. Some varieties, such as nontronites, contain as much as 40 wt.% Fe2O3 within their molecular structure. Several studies have shown that various Fe-reducing micro-organisms can use ferric iron in Fe-bearing clay minerals as their terminal electron acceptor, thereby reducing it to ferrous iron. Laboratory experiments have also demonstrated that chemically or bacterially reduced clays can promote the reductive degradation of various organics, including chlorinated pesticides and nitroaromatics. Therefore, Fe-bearing clays may play a crucial role in the natural attenuation of various redox-sensitive contaminants in soils and sediments. Although the organochlorinated pesticide p,p−-DDT is one of the most abundant and recalcitrant sources of contamination in many parts of the world, the impact of reduced Fe-bearing clays on its degradation has never been documented. The purpose of the present study was to evaluate the extent of degradation of p,p−-DDT during the bacterial reduction of Fe(III) in an Fe-rich clay. Microcosm experiments were conducted under anaerobic conditions using nontronite (sample NAu-2) spiked withpp−-DDT and the metal-reducing bacteria Shewanella oneidensis MR-1. Similar experiments were conducted using a sand sample to better ascertain the true impact of the clay vs. the bacteria on the degradation of DDT. Samples were analyzed for DDT and degradation products after 0, 3, and 6 weeks of incubation at 30°C. Results revealed a progressive decrease in p,p−-DDT and increase in p,p−-DDD concentrations in the clay experiments compared to sand and abiotic controls, indicating that Fe-bearing clays may substantially contribute toward the reductive degradation of DDT in soils and sediments. These new findings further demonstrate the impact that clay materials can have on the natural attenuation of pollutants in natural and artificial systems and open new avenues for the passive treatment of contaminated land.

Purpose: Vascular endothelial growth factor (VEGF) signaling is key to tumor angiogenesis and is an important target in the development of anticancer drugs. However, VEGF receptor (VEGFR) expression in human cancers, particularly the relative expression of VEGFR-2 and VEGFR-3 in tumor vasculature versus tumor cells, is poorly defined. Experimental Design: VEGFR-2– and VEGFR-3–specific antibodies were identified and used in the immunohistochemical analysis of human primary cancers and normal tissue. The relative vascular localization of both receptors in colorectal and breast cancers was determined by coimmunofluorescence with vascular markers. Results: VEGFR-2 and VEGFR-3 were expressed on vascular endothelium but not on malignant cells in 13 common human solid tumor types (n > 400, bladder, breast, colorectal, head and neck, liver, lung, skin, ovarian, pancreatic, prostate, renal, stomach, and thyroid). The signal intensity of both receptors was significantly greater in vessels associated with malignant colorectal, lung, and breast than adjacent nontumor tissue. In colorectal cancers, VEGFR-2 was expressed on both intratumoral blood and lymphatic vessels, whereas VEGFR-3 was found predominantly on lymphatic vessels. In breast cancers, both receptors were localized to and upregulated on blood vessels. Conclusions: VEGFR-2 and VEGFR-3 are primarily localized to, and significantly upregulated on, tumor vasculature (blood and/or lymphatic) supporting the majority of solid cancers. The primary clinical mechanism of action of VEGF signaling inhibitors is likely to be through the targeting of tumor vessels rather than tumor cells. The upregulation of VEGFR-3 on tumor blood vessels indicates a potential additional antiangiogenic effect for dual VEGFR-2/VEGFR-3–targeted therapy. Clin Cancer Res; 16(14); 3548–61. ©2010 AACR.

Summary Methanogenic degradation of polycyclic aromatic hydrocarbons (PAHs) has long been considered impossible, but evidence in contaminated near surface environments and biodegrading petroleum reservoirs suggests that this is not necessarily the case. To evaluate the thermodynamic constraints on methanogenic PAH degradation we have estimated the Gibbs free energy values for naphthalene, phenanthrene, anthracene, pyrene and chrysene in the aqueous phase, and used these values to evaluate several possible routes whereby PAHs may be converted to methane. Under standard conditions (25°C, solutes at 1 M concentrations, and gases at 1 atm), methanogenic degradation of these PAHs yields between 209 and 331 kJ mol−1. Per mole of methane produced this is 27–35 kJ mol−1, indicating that PAH-based methanogenesis is exergonic. We evaluated the energetics of three potential PAH degradation routes: oxidation to H2/CO2, complete conversion to acetate, or incomplete oxidation to H2 plus acetate. Depending on the in situ conditions the energetically most favourable pathway for the PAH-degrading organisms is oxidation to H2/CO2 or conversion into acetate. These are not necessarily the pathways that prevail in the environment. This may be because the kinetic theory of optimal length of metabolic pathways suggests that PAH degraders may have evolved towards incomplete oxidation to acetate plus H2 as the optimal pathway.