Oil biodegradation. Water droplets in oil are microhabitats for microbial life

Imprints of ecological processes in the taxonomic core community: an analysis of naturally replicated microbial communities enclosed in oil

It is widely assumed that a taxonomic core community emerges among microbial communities from similar habitats because similar environments select for the same taxa bearing the same traits. Yet, a core community itself is no indicator of selection because it may also arise from dispersal and neutral drift, i.e. by chance. Here, we hypothesize that a core community produced by either selection or chance processes should be distinguishable. While dispersal and drift should produce core communities with similar relative taxon abundances, especially when the proportional core community, i.e. the sum of the relative abundances of the core taxa, is large, selection may produce variable relative abundances. We analyzed the core community of 16S rRNA gene sequences of 193 microbial communities occurring in tiny water droplets enclosed in heavy oil from the Pitch Lake, Trinidad and Tobago. These communities revealed highly variable relative abundances along with a large proportional core community (68.0 ± 19.9%). A dispersal-drift null model predicted a negative relationship of proportional core community and compositional variability along a range of dispersal probabilities and was largely inconsistent with the observed data, suggesting a major role of selection for shaping the water droplet communities in the Pitch Lake.

Enrichment of microbial consortia for MEOR in crude oil phase of reservoir-produced liquid and their response to environmental disturbance

Developing microbial consortiums is necessary for microbial enhanced oil recovery (MEOR) in heavy crude oil production. The aqueous phase of produced fluid has long been considered an ideal source of microorganisms for MEOR. However, it is recently found that rich microorganisms (including hydrocarbon-degrading bacteria) are present in the crude oil phase, which is completely different from the aqueous phase of produced fluid. So, in this study, the microbial consortia from the crude oil phase of produced fluids derived from four wells were enriched, respectively. The microbial community structure during passage was dynamically tracked, and the response of enriched consortia to successive disturbance of environmental factors was investigated. The results showed the crude oil phase had high microbial diversity, and the original microbial community structure from four wells was significantly different. After ten generations of consecutive enrichment, different genera were observed in the four enriched microbial consortia, namely, Geobacillus, Bacillus, Brevibacillus, Chelativorans, Ureibacillus, and Ornithinicoccus. In addition, two enriched consortia (eG1614 and eP30) exhibited robustness to temperature and oxygen perturbations. These results further suggested that the crude oil phase of produced fluids can serve as a potential microbial source for MEOR.

Adding nanoparticles to improve emulsion efficiency and enhance microbial degradation in Pickering emulsions

Interfacial microbial degradation of alkane in Pickering emulsions stabilized by hydrophobic bacterial cells is a new mechanism for microbial degradation of water-insoluble chemicals, where both water-insoluble chemicals in the oil phase and water-soluble nutrients (such as nitrogen and phosphorus) in the water phase are bio-accessible to living microorganisms anchoring onto the oil-water interfaces. In the present work, super-hydrophobic Mycobacterium sp. (contact angle 168.6°) degradation of tetradecane was set up as a model. Addition of fumed SiO2 particles (Aerosil® R974) as a new strategy was developed to enhance tetradecane degradation where the biodegradation rate (based on the accumulated biomass) increased by approximately 80%. The enhanced effect of SiO2 particles on the tetradecane degradation attributed to the synergistic effect of SiO2 particles on the emulsion efficiency of Pickering emulsions stabilized by bacterial cells and then on the enhancement of interfacial microbial degradation in Pickering emulsions. KEY POINTS: • Interfacial microbial degradation in bacterial cells stabilized Pickering emulsions. • Adding fumed SiO2 particles to enhance microbial degradation of tetradecane. • Correlation relationship between emulsion efficiency and interfacial microbial degradation.

Nitrate Bioreduction under Cr(VI) Stress: Crossroads of Denitrification and Dissimilatory Nitrate Reduction to Ammonium

This study explored the response of NO₃^--N bioreduction to Cr(VI) stress, including reduction efficiency and the pathways involved (denitrification and dissimilatory nitrate reduction to ammonium (DNRA)). Different response patterns of NO₃^--N conversion were proposed under Cr(VI) suppress (0, 0.5, 5, 15, 30, 50, and 80 mg/L) by evaluating Cr(VI) dose dependence, toxicity accumulation, bioelectron behavior, and microbial community structure. Cr(VI) concentrations of >30 mg/L rapidly inhibited NO₃^--N removal and immediately induced DNRA. However, denitrification completely dominated the NO₃^--N reduction pathway at Cr(VI) concentrations of <15 mg/L. Therefore, 30 and 80 mg/L Cr(VI) (R₄ and R₆) were selected to explore the selection of the different NO₃^--N removal pathways. The pathway of NO₃^--N reduction at 30 mg/L Cr(VI) exhibited continuous adaptation, wherein the coexistence of denitrification (51.7%) and DNRA (13.6%) was achieved by regulating the distribution of denitrifiers (37.6%) and DNRA bacteria (32.8%). Comparatively, DNRA gradually replaced denitrification at 80 mg/L Cr(VI). The intracellular Cr(III) accumulation in R₆ was 6.60-fold greater than in R₄, causing more severe oxidant injury and cell death. The activated NO₃^--N reduction pathway depended on the value of nitrite reductase activity/nitrate reductase activity, with 0.84-1.08 associated with DNRA activation and 1.48-1.57 with DNRA predominance. Although Cr(VI) increased microbial community richness and improved community structure stability, the inhibition or death of nitrogen-reducing microorganisms caused by Cr(VI) decreased NO₃^--N reduction efficiency.

Evaluating microbial contaminations of alternative heating oils

Since 2008, European and German legislative initiatives for climate protection and reduced dependency on fossil resources led to the introduction of biofuels as CO2-reduced alternatives in the heating oil sector. In the case of biodiesel, customers were confronted with accelerated microbial contaminations during storage. Since then, other fuel alternatives, like hydrogenated vegetable oils (HVOs), gas-to-liquid (GtL) products, or oxymethylene ether (OME) have been developed. In this study, we use online monitoring of microbial CO2 production and the simulation of onset of microbial contamination to investigate the contamination potential of fuel alternatives during storage. As references, fossil heating oil of German refineries are used. Biodiesel blends with fossil heating oils confirmed the promotion of microbial activity. In stark contrast, OMEs have an antimicrobial effect. The paraffinic Fischer-Tropsch products and biogenic hydrogenation products demonstrate to be at least as resistant to microbial contamination as fossil heating oils despite allowing a diversity of representative microbes. Through mass spectrometry, elemental analysis, and microbial sequencing, we can discuss fuel properties that affect microbial contaminations. In summary, novel, non-fossil heating oils show clear differences in microbial resistance during long-term storage. Designing blends with an intrinsic resistance against microbial contamination and hence reduced activity might be an option.

Stress-responses of microbes in oil reservoir under high tetracycline exposure and their environmental risks

As the groundwater ecosystem is connected with surface, antibiotics and antibiotic resistance genes (ARGs) in aquatic environments will gradually infiltrate into the deep environment, posing a potential threat to groundwater ecosystem. However, knowledge on the environmental risk of antibiotics and ARGs in groundwater ecosystem and their ecological process still remains unexplored. In this study, lab-scale oil reservoirs under high tetracycline stress were performed to evaluate the dynamics of microbial communities, ARGs and potential functions by using 16S rRNA gene sequencing and metagenomics analysis. Although the presence of antibiotics remarkably reduced the microbial abundance and diversity in a short term, but remain stable or even increased after a long-term incubation. Antibiotic stress caused a greater diversity and abundance of ARGs, and higher numbers of ARGs-related species with the capacity to transfer ARGs to other microbes through horizontal gene transfer. Thus, a much more frequent associations of microbial community at both node- and network-level and a selective pressure on enrichment of antibiotic resistant bacteria related to "anaerobic n-alkane degradation" and "methylotrophic methanogenesis" were observed. It is important to emphasize that high antibiotic stress could also prevent some microbes related to "Sulfate reduction", "Fe(II) oxidation", "Nitrate reduction", and "Xylene and Toluene degradation". This study provides an insight into the long-term stress-responses of microbial communities and functions in oil reservoir under tetracycline exposure, which may help to elucidate the effect of antibiotic stress on biogeochemical cycling with microbial involvement in groundwater ecosystem.

Natural Asphalt Seeps Are Potential Sources for Recalcitrant Oceanic Dissolved Organic Sulfur and Dissolved Black Carbon

Natural oil seepages contribute about one-half of the annual petroleum input to marine systems. Yet, environmental implications and the persistence of water-soluble hydrocarbons from these seeps are vastly unknown. We investigated the release of oil-derived dissolved organic matter (DOM) from natural deep sea asphalt seeps using laboratory incubation experiments. Fresh asphalt samples collected at the Chapopote asphalt volcano in the Southern Gulf of Mexico were incubated aerobically in artificial seawater over 4 weeks. The compositional changes in the water-soluble fraction of asphalt-derived DOM were determined with ultrahigh-resolution mass spectrometry (Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) and by excitation-emission matrix spectroscopy to characterize fluorescent DOM (FDOM) applying parallel factor (PARAFAC) analysis. Highly reduced aliphatic asphalt-derived DOM was readily biodegraded, while aromatic and sulfur-enriched DOM appeared to be less bioavailable and accumulated in the aqueous phase. A quantitative molecular tracer approach revealed the abundance of highly condensed aromatic molecules of thermogenic origin. Our results indicate that natural asphalt and potentially other petroleum seepages can be sources of recalcitrant dissolved organic sulfur and dissolved black carbon to the ocean.

Natural Source Zone Depletion (NSZD) Quantification Techniques: Innovations and Future Directions

Natural source zone depletion (NSZD) is an emerging technique for sustainable and cost-effective bioremediation of light non-aqueous phase liquid (LNAPL) in oil spill sites. Depending on regulatory objectives, NSZD has the potential to be used as either the primary or sole LNAPL management technique. To achieve this goal, NSZD rate (i.e., rate of bulk LNAPL mass depletion) should be quantified accurately and precisely. NSZD has certain characteristic features that have been used as surrogates to quantify the NSZD rates. This review highlights the most recent trends in technology development for NSZD data collection and rate estimation, with a focus on the operational and technical advantages and limitations of the associated techniques. So far, four principal techniques are developed, including concentration gradient (CG), dynamic closed chamber (DCC), CO2 trap and thermal monitoring. Discussions revolving around two techniques, “CO2 trap” and “thermal monitoring”, are expanded due to the particular attention to them in the current industry. The gaps of knowledge relevant to the NSZD monitoring techniques are identified and the issues which merit further research are outlined. It is hoped that this review can provide researchers and practitioners with sufficient information to opt the best practice for the research and application of NSZD for the management of LNAPL impacted sites.

Deep mining decreases the microbial taxonomic and functional diversity of subsurface oil reservoirs

Microbes in subsurface oil reservoirs play important roles in elemental cycles and biogeochemical processes. However, the community assembly pattern of indigenous microbiome and their succession under long-term human activity remain poorly understood. Here we studied the microbial community assembly in underground sandstone cores from 190 to 2050 m in northeast China and their response to long-term oil recovery (10-50 years). Indigenous microbiome in subsurface petroleum reservoirs were dominated by Gammaproteobacteria, Firmicutes, Alphaproteobacteria, Bacteroidetes, and Actinobacteria, which exhibited a higher contribution of homogenizing dispersal assembly and different taxonomy distinct ecological modules when compared with perturbed samples. Specifically, the long-term oil recovery reduced the bacterial taxonomic- and functional-diversity, and increased the community co-occurrence associations in subsurface oil reservoirs. Moreover, distinguished from the perturbed samples, both variation partition analysis and structural equation model revealed that the contents of quartz, NO₃^- and Cl^- significantly structured the α- and β-diversity in indigenous subsurface bacterial communities. These findings first provide the holistic picture of microbiome in the deep oil reservoirs, which demonstrate the significant impact of human activity on microbiome in deep continental subsurface.

Microbial communities in crude oil phase and filter-graded aqueous phase from a Daqing oilfield after polymer flooding

AIMS

The aim was to characterize indigenous microorganisms in oil reservoirs after polymer flooding (RAPF).

METHODS

The microbial communities in the crude oil phase (Oil) and in the filter-graded aqueous phases Aqu0.22 (>0.22 μm) and Aqu0.1 (0.1~0.22 μm) were investigated by 16S rRNA gene high-throughput sequencing.

RESULTS

Indigenous microorganisms related to hydrocarbon degradation prevailed in the three phases of each well. However, obvious differences of bacterial compositions were observed among the three phases of the same well and among the same phase of different wells. The crude oil and Aqu0.22 shared many dominant bacteria. Aqu0.1 contained a unique bacterial community in each well. Most bacteria in Aqu0.1 were affiliated to culturable genera, suggesting that they may adapt to the oil reservoir environment by reduction of cell size. Contrary to the bacterial genera, archaeal genera were similar in the three phases but varied in relative abundances. The observed microbial differences may be driven by specific environmental factors in each oil well.

CONCLUSIONS

The results suggest an application potential of microbial enhanced oil recovery (MEOR) technology in RAPF. The crude oil and Aqu0.1 contain many different functional microorganisms related to hydrocarbon degradation. Both should not be overlooked when investing and exploring the indigenous microorganisms for MEOR.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work facilitates the understanding of microbial community structures in RAPF and provides information for microbial control in oil fields.

Natural attenuation of oil in marine environments: A review

Natural attenuation is an important process for oil spill management in marine environments. Natural attenuation affects the fate of oil by physical, chemical, and biological processes, which include evaporation, dispersion, dissolution, photo-oxidation, emulsification, oil particle aggregation, and biodegradation. This review examines the cumulative knowledge regarding these natural attenuation processes as well as their simulation and prediction using modelling approaches. An in-depth discussion is provided on how oil type, microbial community and environmental factors contribute to the biodegradation process. It describes how our understanding of the structure and function of indigenous oil degrading microbial communities in the marine environment has been advanced by the application of next generation sequencing tools. The synergetic and/or antagonist effects of oil spill countermeasures such as the application of chemical dispersants, in-situ burning and nutrient enrichment on natural attenuation were explored. Several knowledge gaps were identified regarding the synergetic and/or antagonistic effects of active response countermeasures on the natural attenuation/biodegradation process. This review highlighted the need for field data on both the effectiveness and potential detrimental effects of oil spill response options to support modelling and decision-making on their selection and application.

Inhibition of sulfate-reducing bacteria with formate

Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally. Ion chromatography revealed very high formate concentrations around 2.37 mM in 21 out of 43 examined droplets. Since these concentrations were unexpectedly high, we performed growth experiments with the three sulfate-reducing type strains Desulfovibrio vulgaris, Desulfobacter curvatus, and Desulfococcus multivorans, and tested the effects of 2.5, 8 or 10 mM formate on sulfate reduction. Experiments demonstrated that 8 or 10 mM formate slowed down the growth rate of D. vulgaris and D. curvatus and the sulfate reduction rate of D. curvatus and D. multivorans. Concerning D. multivorans, increasing formate concentrations delayed the onsets of growth and sulfate reduction, which were even inhibited completely while formate was added constantly. Contrary to previous studies, D. multivorans was the only organism capable of formate consumption. Our study suggests that formate accumulates in the natural environment of the water droplets dispersed in oil and that such levels are very likely inhibiting sulfate-reducing microorganisms.

Indigenous microbial communities in heavy oil show a threshold response to salinity

Microbial degradation influences the quality of oil resources. The environmental factors that shape the composition of oil microbial communities are largely unknown because most samples from oil fields are impacted by anthropogenic oil production, perturbing the native ecosystem with exogenous fluids and microorganisms. We investigated the relationship between formation water geochemistry and microbial community composition in undisturbed oil samples. We isolated 43 microliter-sized water droplets naturally enclosed in the heavy oil of the Pitch Lake, Trinidad and Tobago. The water chemistry and microbial community composition within the same water droplet were determined by ion chromatography and 16S rRNA gene amplicon sequencing, respectively. The results revealed a high variability in ion concentrations and community composition between water droplets. Microbial community composition was mostly affected by the chloride concentration, which ranged from freshwater to brackish-sea water. Remarkably, microbial communities did not respond gradually to increasing chloride concentration but showed a sudden change to less diverse and uneven communities when exceeding a chloride concentration of 57.3 mM. The results reveal a threshold-regulated response of microbial communities to salinity, offering new insights into the microbial ecology of oil reservoirs.

Recent Advances in Multicellular Tumor Spheroid Generation for Drug Screening

Multicellular tumor spheroids (MCTs) have been employed in biomedical fields owing to their advantage in designing a three-dimensional (3D) solid tumor model. For controlling multicellular cancer spheroids, mimicking the tumor extracellular matrix (ECM) microenvironment is important to understand cell-cell and cell-matrix interactions. In drug cytotoxicity assessments, MCTs provide better mimicry of conventional solid tumors that can precisely represent anticancer drug candidates' effects. To generate incubate multicellular spheroids, researchers have developed several 3D multicellular spheroid culture technologies to establish a research background and a platform using tumor modelingvia advanced materials science, and biosensing techniques for drug-screening. In application, drug screening was performed in both invasive and non-invasive manners, according to their impact on the spheroids. Here, we review the trend of 3D spheroid culture technology and culture platforms, and their combination with various biosensing techniques for drug screening in the biomedical field.

Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting

Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO₃^- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.

Are microorganisms everywhere they can be?

Baas-Becking is famously attributed with the conjecture that 'everything is everywhere, but the environment selects'. Although this aphorism is largely challenged by microbial biogeographical data, even weak versions of the claim leave unanswered the question about whether all environments that could theoretically support life contain life. In the last decade, the discovery of thermally sterilized habitable environments disconnected from inhabited regions, and habitats within organisms such as the sterile, but habitable human fetal gut, suggest the existence of a diversity of macroscopic habitable environments apparently devoid of actively metabolizing or reproducing life. Less clear is the status of such environments at the micron scale, for example, between colonies of organisms within rock interstices or on and within other substrates. I discuss recent evidence for these types of environments. These environments have practical uses in: (i) being negative controls for understanding the role of microbial processes in geochemical cycles and geological processes, (ii) yielding insights into the extent to which the biosphere extends into all spaces it theoretically can, (iii) suggesting caution in interpreting the results of life detection instrumentation, and (iv) being useful for establishing the conditions for the origin of life and its prevalence on other planetary bodies.

Disentangling the distinct mechanisms shaping the subsurface oil reservoir bacterial and archaeal communities across northern China

Microbes in surface ecosystem exhibit strong biogeographic patterns, and are less apparent after human management. However, in contrast with the considerable knowledge on the surface ecosystem, the microbial biogeographic patterns in deep subsurface ecosystem under artificial disturbance is poorly understood. Here, we explored the spatial scale-dependence patterns of bacterial and archaeal communities in oil reservoirs under different artificial flooding duration and environmental conditions across northern China. Bacterial and archaeal communities of oil reservoirs exhibited distinct assembly patterns with a stronger distance-decay relationship in archaeal communities than bacterial communities, as different environmental factors linked to the diversity of bacteria and archaea. Specifically, bacterial and archaeal network properties revealed a significant correlation with spatial reservoir isolation by distinct co-occurrence patterns. The co-occurrences of bacterial communities were more complex in high temperature and alkaline pH, while archaeal co-occurrences were more frequent in low temperature and neutral pH. Potential functions in bacterial communities were more connected with chemoheterotrophy, whereas methanogenesis was abundant in archaeal communities, as confirmed by both keystone taxa and main ecological clusters in networks. This revealed that different mechanisms underlain geography and co-occurrence patterns of bacteria and archaea in oil reservoirs, providing a new insight for understanding biogeography and coexistence theory in deep subsurface ecosystem.

Biodiversity and biocatalyst activity of culturable hydrocarbonoclastic fungi isolated from Marac-Moruga mud volcano in South Trinidad

Mud volcanoes (MVs) are visible signs of oil and gas reserves present deep beneath land and sea. The Marac MV in Trinidad is the only MV associated with natural hydrocarbon seeps. Petrogenic polyaromatic hydrocarbons (PAHs) in its sediments must undergo biogeochemical cycles of detoxification as they can enter the water table and aquifers threatening ecosystems and biota. Recurrent hydrocarbon seep activity of MVs consolidates the growth of hydrocarbonoclastic fungal communities. Fungi possess advantageous metabolic and ecophysiological features for remediation but are underexplored compared to bacteria. Additionally, indigenous fungi are more efficient at PAH detoxification than commercial/foreign counterparts and remediation strategies remain site-specific. Few studies have focused on hydrocarbonoclastic fungal incidence and potential in MVs, an aspect that has not been explored in Trinidad. This study determined the unique biodiversity of culturable fungi from the Marac MV capable of metabolizing PAHs in vitro and investigated their extracellular peroxidase activity to utilize different substrates ergo their extracellular oxidoreductase activity (> 50% of the strains decolourized of methylene blue dye). Dothideomycetes and Eurotiomycetes (89% combined incidence) were predominantly isolated. ITS rDNA sequence cluster analysis confirmed strain identities. 18 indigenous hydrocarbonoclastic strains not previously reported in the literature and some of which were biosurfactant-producing, were identified. Intra-strain variability was apparent for PAH utilization, oil-tolerance and hydroxylase substrate specificity. Comparatively high levels of extracellular protein were detected for strains that demonstrated low substrate specificity. Halotolerant strains were also recovered which indicated marine-mixed substrata of the MV as a result of deep sea conduits. This work highlighted novel MV fungal strains as potential bioremediators and biocatalysts with a broad industrial applications.

Bioemulsification and Microbial Community Reconstruction in Thermally Processed Crude Oil

Utilization of low-cost, environmental-friendly microbial enhanced oil recovery (MEOR) techniques in thermal recovery-processed oil reservoirs is potentially feasible. However, how exogenous microbes facilitate crude oil recovery in this deep biosphere, especially under mesophilic conditions, is scarcely investigated. In this study, a thermal treatment and a thermal recurrence were processed on crude oil collected from Daqing Oilfield, and then a 30-day incubation of the pretreated crude oil at 37 °C was operated with the addition of two locally isolated hydrocarbon-degrading bacteria, Amycolicicoccus subflavus DQS3-9A1^T and Dietzia sp. DQ12-45-1b, respectively. The pH, surface tension, hydrocarbon profiles, culture-dependent cell densities and taxonomies, and whole and active microbial community compositions were determined. It was found that both A. subflavus DQS3-9A1^T and Dietzia sp. DQ12-45-1b successfully induced culture acidification, crude oil bioemulsification, and residual oil sub-fraction alteration, no matter whether the crude oil was thermally pretreated or not. Endogenous bacteria which could proliferate on double heated crude oil were very few. Compared with A. subflavus, Dietzia sp. was substantially more effective at inducing the proliferation of varied species in one-time heated crude oil. Meanwhile, the effects of Dietzia sp. on crude oil bioemulsification and hydrocarbon profile alteration were not significantly influenced by the ploidy increasing of NaCl contents (from 5 g/L to 50 g/L), but the reconstructed bacterial communities became very simple, in which the Dietzia genus was predominant. Our study provides useful information to understand MEOR trials on thermally processed oil reservoirs, and proves that this strategy could be operated by using the locally available hydrocarbon-degrading microbes in mesophilic conditions with different salinity degrees.

Microbial Degradation Rates of Natural Bitumen

Microorganisms are present in nearly every oil or bitumen sample originating from temperate reservoirs. Nevertheless, it is very difficult to obtain reliable estimates about microbial processes taking place in deep reservoirs, since metabolic rates are rather low and differ strongly during artificially cultivation. Here, we demonstrate the importance and impact of microorganisms entrapped in microscale water droplets for the overall biodegradation process in bitumen. To this end, we measured degradation rates of heavily biodegraded bitumen from the Pitch Lake (Trinidad and Tobago) using the novel technique of reverse stable isotope labeling, allowing precise measurements of comparatively low mineralization rates in the ng range in microcosms under close to natural conditions. Freshly taken bitumen samples were overlain with artificial brackish water and incubated for 945 days. Additionally, three-dimensional distribution of water droplets in bitumen was studied with computed tomography, revealing a water bitumen interface of 1134 cm² per liter bitumen, resulting in an average mineralization rate of 9.4-38.6 mmol CO₂ per liter bitumen and year. Furthermore, a stable and biofilm-forming microbial community established on the bitumen itself, mainly composed of fermenting and sulfate-reducing bacteria. Our results suggest that small water inclusions inside the bitumen substantially increase the bitumen-water interface and might have a major impact on the overall oil degradation process.

Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad

Trinidad and Tobago is the largest producer of oil and natural gas in Central America and the Caribbean. Natural crude oil seeps, in addition to leaking petroleum pipelines, have resulted in chronic contamination of the surrounding terrestrial environments since the time of petroleum discovery, production, and refinement in Trinidad. In this study, we isolated microbes from soils chronically contaminated with crude oil using a culture-dependent approach with enrichment. The sampling of eight such sites located in the southern peninsula of Trinidad revealed a diverse microbial composition and novel oil-degrading filamentous fungi and yeast as single-isolate degraders and naturally occurring consortia, with specific bacterial species not previously reported in the literature. Multiple sequence comparisons and phylogenetic analyses confirmed the identity of the top degraders. The filamentous fungal community based on culturable species was dominated by Ascomycota, and the recovered yeast isolates were affiliated with Basidiomycota (65.23%) and Ascomycota (34.78%) phyla. Enhanced biodegradation of petroleum hydrocarbons is maintained by biocatalysts such as lipases. Five out of seven species demonstrated extracellular lipase activity in vitro. Our findings could provide new insights into microbial resources from chronically contaminated terrestrial environments, and this information will be beneficial to the bioremediation of petroleum contamination and other industrial applications.

Identity and hydrocarbon degradation activity of enriched microorganisms from natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI)

A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100-200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C₈-C₁₇ alkanes and up to 28% degradation of C₁₈-C₃₃ alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.

The Case (or Not) for Life in the Venusian Clouds

The possible detection of the biomarker of phosphine as reported by Greaves et al. in the Venusian atmosphere stirred much excitement in the astrobiology community. While many in the community are adamant that the environmental conditions in the Venusian atmosphere are too extreme for life to exist, others point to the claimed detection of a convincing biomarker, the conjecture that early Venus was doubtlessly habitable, and any Venusian life might have adapted by natural selection to the harsh conditions in the Venusian clouds after the surface became uninhabitable. Here, I first briefly characterize the environmental conditions in the lower Venusian atmosphere and outline what challenges a biosphere would face to thrive there, and how some of these obstacles for life could possibly have been overcome. Then, I discuss the significance of the possible detection of phosphine and what it means (and does not mean) and provide an assessment on whether life may exist in the temperate cloud layer of the Venusian atmosphere or not.

Active Femtoliter Droplet Generation in Microfluidics by Confined Interface Vibration

The precise and effective generation of micron-sized droplets is one of the most common and important issues for droplet-based microfluidics. Active droplet generation makes use of additional energy input in promoting interfacial instabilities for droplet generation. Here, we report a new technique for the active generation of femtoliter droplets in microfluidic systems using confined interfacial vibration (CIV). The CIV is formed at the orifice of a traditional inkjet nozzle first by pushing the liquid out and then pulling it back. Droplets are pinched off during the withdrawal process, and this is different from the current active droplet generation techniques, which only monodirectionally push the liquid out. Droplets with radius ranging from ca. 1 to 28 μm can be actively generated by CIV at an orifice with radius 30 μm, distinguishing from conventional active generation techniques in which the droplets are always comparable or slightly bigger than the orifice. Experimental results showed that the droplet volume can be customized by controlling the intensity of the CIV. The inherent digital nature of the inkjet technique enables easy and precise regulating of the droplet volume, making it seamlessly compatible with the digital microfluidic systems.

Assembly of Multi-Spheroid Cellular Architectures by Programmable Droplet Merging

Artificial multicellular systems are gaining importance in the field of tissue engineering and regenerative medicine. Reconstruction of complex tissue architectures in vitro is nevertheless challenging, and methods permitting controllable and high-throughput fabrication of complex multicellular architectures are needed. Here, a facile and high-throughput method is developed based on a tunable droplet-fusion technique, allowing programmed assembly of multiple cell spheroids into complex multicellular architectures. The droplet-fusion technique allows for construction of various multicellular architectures (double-spheroids, multi-spheroids, hetero-spheroids) in a miniaturized high-density array format. As an example of application, the propagation of Wnt signaling is investigated within hetero-spheroids formed from two fused Wnt-releasing and Wnt-reporter cell spheroids. The developed method provides an approach for miniaturized, high-throughput construction of complex 3D multicellular architectures and can be applied for studying various biological processes including cell signaling, cancer invasion, embryogenesis, and neural development.

Sulfate Alters the Competition Among Microbiome Members of Sediments Chronically Exposed to Asphalt

Sulfate-reducing microorganisms (SRMs) often compete with methanogens for common substrates. Due to thermodynamic reasons, SRMs should outcompete methanogens in the presence of sulfate. However, many studies have documented coexistence of these microbial groups in natural environments, suggesting that thermodynamics alone cannot explain the interactions among them. In this study, we investigated how SRMs compete with the established methanogenic communities in sediment from a long-term, electron acceptor-depleted, asphalt-exposed ecosystem and how they affect the composition of the organic material. We hypothesized that, upon addition of sulfate, SRMs (i) outcompete the methanogenic communities and (ii) markedly contribute to transformations of the organic material. We sampled sediments from the test and proximate control sites under anoxic conditions and incubated them in seawater medium with or without sulfate. Abundance and activity pattern of SRMs and methanogens, as well as the total prokaryotic community, were followed for 6 weeks by using qPCR targeting selected marker genes. Some of these genes were also subjected to amplicon sequencing to assess potential shifts in diversity patterns. Alterations of the organic material in the microcosms were determined by mass spectrometry. Our results indicate that the competition of SRMs with methanogens upon sulfate addition strongly depends on the environment studied and the starting microbiome composition. In the asphalt-free sediments (control), the availability of easily degradable organic material (mainly plant-derived) allows SRMs to use a larger variety of substrates, reducing interspecies competition with methanogens. In contrast, the abundant presence of recalcitrant compounds in the asphalt-exposed sediment was associated with a strong competition between SRMs and methanogens, ultimately detrimental for the latter. Our data underpin the importance of the quality of bioavailable organic materials in anoxic environments as a driver for microbial community structure and function.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

The Astrobiology of Alien Worlds: Known and Unknown Forms of Life

Most definitions of life assume that, at a minimum, life is a physical form of matter distinct from its environment at a lower state of entropy than its surroundings, using energy from the environment for internal maintenance and activity, and capable of autonomous reproduction. These assumptions cover all of life as we know it, though more exotic entities can be envisioned, including organic forms with novel biochemistries, dynamic inorganic matter, and self-replicating machines. The probability that any particular form of life will be found on another planetary body depends on the nature and history of that alien world. So the biospheres would likely be very different on a rocky planet with an ice-covered global ocean, a barren planet devoid of surface liquid, a frigid world with abundant liquid hydrocarbons, on a rogue planet independent of a host star, on a tidally locked planet, on super-Earths, or in long-lived clouds in dense atmospheres. While life at least in microbial form is probably pervasive if rare throughout the Universe, and technologically advanced life is likely much rarer, the chance that an alternative form of life, though not intelligent life, could exist and be detected within our Solar System is a distinct possibility.

Densely Populated Water Droplets in Heavy-Oil Seeps

Most of the microbial degradation in oil reservoirs is believed to take place at the oil-water transition zone (OWTZ). However, a recent study indicates that there is microbial life enclosed in microliter-sized water droplets dispersed in heavy oil of Pitch Lake in Trinidad and Tobago. This life in oil suggests that microbial degradation of oil also takes place in water pockets in the oil-bearing rock of an oil leg independent of the OWTZ. However, it is unknown whether microbial life in water droplets dispersed in oil is a generic property of oil reservoirs rather than an exotic exception. Hence, we took samples from three heavy-oil seeps, Pitch Lake (Trinidad and Tobago), the La Brea Tar Pits (California, USA), and an oil seep on the McKittrick oil field (California, USA). All three tested oil seeps contained dispersed water droplets. Larger droplets between 1 and 10 μl revealed high cell densities of up to 10⁹ cells ml^-1 Testing for ATP content and LIVE/DEAD staining showed that these populations consist of active and viable microbial cells with an average of 60% membrane-intact cells and ATP concentrations comparable to those of other subsurface ecosystems. Microbial community analyses based on 16S rRNA gene amplicon sequencing revealed the presence of known anaerobic oil-degrading microorganisms. Surprisingly, the community analyses showed similarities between all three oil seeps, revealing common OTUs, although the sampling sites were thousands of kilometers apart. Our results indicate that small water inclusions are densely populated microhabitats in heavy oil and possibly a generic trait of degraded-oil reservoirs.IMPORTANCE Our results confirmed that small water droplets in oil are densely populated microhabitats containing active microbial communities. Since these microhabitats occurred in three tested oil seeps which are located thousands of kilometers away from each other, such populated water droplets might be a generic trait of biodegraded oil reservoirs and might be involved in the overall oil degradation process. Microbial degradation might thus also take place in water pockets in the oil-bearing oil legs of the reservoir rock rather than only at the oil-water transition zone.

A chemical and microbial characterization of selected mud volcanoes in Trinidad reveals pathogens introduced by surface water and rain water

Terrestrial mud volcanoes are unique structures driven by tectonic pressure and fluids from the deep subsurface. These structures are mainly found in active tectonic zones, such as the area near the Los Bajos Fault in Trinidad. Here we report a chemical and microbiological characterization of three mud volcanoes, which included analyses of multiple liquid and solid samples from the mud volcanoes. Our study confirms previous suggestions that at least some of the mud volcano fluids are a mixture of deeper salt-rich water and surficial/precipitation water. No apparent water quality differences were found between sampling sites north and south of a major geological fault line. Microbiological analyses revealed diverse communities, both aerobic and anaerobic, including sulfate reducers, methanogens, carbon dioxide fixing and denitrifying bacteria. Several identified species were halophilic and likely derived from the deeper salt-rich subsurface water, while we also cultivated pathogenic species from the Vibrionaceae, Enterobacteriaceae, Shewanellaceae, and Clostridiaceae. These microorganisms were likely introduced into the mud volcano fluids both from surface water or shallow ground-water, and perhaps to a more minor degree by rain water. The identified pathogens are a major health concern that needs to be addressed.

Microbial Degradation of Hydrocarbons-Basic Principles for Bioremediation: A Review

Crude oil-derived hydrocarbons constitute the largest group of environmental pollutants worldwide. The number of reports concerning their toxicity and emphasizing the ultimate need to remove them from marine and soil environments confirms the unceasing interest of scientists in this field. Among the various techniques used for clean-up actions, bioremediation seems to be the most acceptable and economically justified. Analysis of recent reports regarding unsuccessful bioremediation attempts indicates that there is a need to highlight the fundamental aspects of hydrocarbon microbiology in a clear and concise manner. Therefore, in this review, we would like to elucidate some crucial, but often overlooked, factors. First, the formation of crude oil and abundance of naturally occurring hydrocarbons is presented and compared with bacterial ability to not only survive but also to utilize such compounds as an attractive energy source. Then, the significance of nutrient limitation on biomass growth is underlined on the example of a specially designed experiment and discussed in context of bioremediation efficiency. Next, the formation of aerobic and anaerobic conditions, as well as the role of surfactants for maintaining appropriate C:N:P ratio during initial stages of biodegradation is explained. Finally, a summary of recent scientific reports focused on the removal of hydrocarbon contaminants using bioaugmentation, biostimulation and introduction of surfactants, as well as biosurfactants, is presented. This review was designed to be a comprehensive source of knowledge regarding the unique aspects of hydrocarbon microbiology that may be useful for planning future biodegradation experiments. In addition, it is a starting point for wider debate regarding the limitations and possible improvements of currently employed bioremediation strategies.

Evidence in the Japan Sea of microdolomite mineralization within gas hydrate microbiomes

Over the past 15 years, massive gas hydrate deposits have been studied extensively in Joetsu Basin, Japan Sea, where they are associated primarily with active gas chimney structures. Our research documents the discovery of spheroidal microdolomite aggregates found in association with other impurities inside of these massive gas hydrates. The microdolomites are often conjoined and show dark internal cores occasionally hosting saline fluid inclusions. Bacteroidetes sp. are concentrated on the inner rims of microdolomite grains, where they degrade complex petroleum-macromolecules present as an impurity within yellow methane hydrate. These oils show increasing biodegradation with depth which is consistent with the microbial activity of Bacteroidetes. Further investigation of these microdolomites and their contents can potentially yield insight into the dynamics and microbial ecology of other hydrate localities. If microdolomites are indeed found to be ubiquitous in both present and fossil hydrate settings, the materials preserved within may provide valuable insights into an unusual microhabitat which could have once fostered ancient life.

Molecular change of dissolved organic matter and patterns of bacterial activity in a stream along a land-use gradient

Fluvial networks are globally relevant for the processing of dissolved organic matter (DOM). To investigate the change in molecular DOM diversity along the river course, high-field FTICR mass spectrometry and NMR spectroscopy of riverine DOM as well as bacterial abundance and activity were measured in a third order stream along a land-use gradient from pristine, agricultural to urban landscapes. DOM composition showed a clear evolution along the river course with an initial decrease of average oxidation and unsaturation followed by an increased relative abundance of CHNO and CHOS compounds introduced by agriculture and waste water, respectively. DOM composition was dominated by rather unsaturated CHO compounds (H/C ≤ 1) in headwaters and by more aliphatic molecules at downstream sites. Oxygenated functional groups shifted from aromatic ethers and hydroxyl groups to aliphatic carboxylic acids and aliphatic hydroxyl groups. This massive dislocation of oxygen significantly increased the diversity of atomic environments in branched aliphatic groups from headwater to downstream DOM. Mass spectra of DOM enabled the detection of compositional relationships to bacterial abundance and activity which was positively related to more aliphatic components (H/C > 1) and negatively related to unsaturated components. FTICR mass and NMR spectra corroborated the initial decline in DOM molecular diversity predicted by the River Continuum Concept (RCC) but demonstrated an anthropogenic increase in the molecular diversity of DOM further downstream. While the high DOM molecular diversity in first order headwater streams was the result of small scale ecosystem plurality, agriculture and waste water treatment introduced many components in the lower reaches. These anthropogenic influences together with massive bacterial oxidation of DOM contributed to a growth of molecular diversity of downstream DOM whose composition and structure differed entirely from those found in pristine headwaters.

Ablation of water drops suspended in asphaltene/heptol solutions due to spontaneous emulsification

Complex molecules from crude oil, such as asphaltenes, can adsorb onto oil/water interfaces. This creates a viscoelastic network that may cause difficulties in oil recovery and oil spills. In addition to stabilization of oil/water emulsions, they may also cause the spontaneous formation of micron-sized droplets. Here, we investigate spontaneous emulsification in the presence of asphaltenes, probing parameters that may affect this phenomenon by observing isolated drops of water immersed in asphaltene/hydrocarbon solutions within a co-flow microfluidic device. The results indicate that the initial internal pressure of the drop strongly influences the rate at which the drop will shrink due to spontaneous emulsification. In addition, the viscoelastic skin formation by the asphaltenes inhibits increases in this pressure that normally accompanies a decrease in drop radius. Understanding this spontaneous emulsification has implications not only for the oil industry, but also to the cosmetics, foods, medical, and pharmaceutical industries.

Systems chemical analytics: introduction to the challenges of chemical complexity analysis

We present concepts of complexity, and complex chemistry in systems subjected to biotic and abiotic transformations, and introduce analytical possibilities to disentangle chemical complexity into its elementary parts as a global integrated approach termed systems chemical analytics.

Oil reservoirs, an exceptional habitat for microorganisms

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Water-containing parts within oil reservoirs extend the zone of biodegradation.

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Biodegradation is controlled by environmental factors.

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Proteobacteria and Euryarchaeota are ubiquitous in oil reservoirs over all temperature ranges.

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Biofilms as microbial adaption in oil reservoirs.

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Viruses as potential control for microbial activity and function.

Microorganisms are present in oil reservoirs around the world where they degrade oil and lead to changes in oil quality. Unfortunately, our knowledge about processes in deep oil reservoirs is limited due to the lack of undisturbed samples. In this review, we discuss the distribution of microorganisms at the oil-water transition zone as well as in water saturated parts of the oil leg and their possible physiological adaptations to abiotic and biotic ecological factors such as temperature, salinity and viruses. We show the importance of studying the water phase within the oil, because small water inclusions and pockets within the oil leg provide an exceptional habitat for microorganisms within a natural oil reservoir and concurrently enlarge the zone of oil biodegradation. Environmental factors such as temperature and salinity control oil biodegradation. Temperature determines the type of microorganisms which are able to inhabit the reservoir. Proteobacteria and Euryarchaeota, are ubiquitous in oil reservoirs over all temperature ranges, whereas some others are tied to specific temperatures. It is proposed that biofilm formation is the dominant way of life within oil reservoirs, enhancing nutrient uptake, syntrophic interactions and protection against environmental stress. Literature shows that viruses are abundant in oil reservoirs and the possible impact on microbial community composition due to control of microbial activity and function is discussed.

A General Approach for Fluid Patterning and Application in Fabricating Microdevices

Engineering the fluid interface such as the gas-liquid interface is of great significance for solvent processing applications including functional material assembly, inkjet printing, and high-performance device fabrication. However, precisely controlling the fluid interface remains a great challenge owing to its flexibility and fluidity. Here, a general method to manipulate the fluid interface for fluid patterning using micropillars in the microchannel is reported. The principle of fluid patterning for immiscible fluid pairs including air, water, and oils is proposed. This understanding enables the preparation of programmable multiphase fluid patterns and assembly of multilayer functional materials to fabricate micro-optoelectronic devices. This general strategy of fluid patterning provides a promising platform to study the fundamental processes occurring on the fluid interface, and benefits applications in many subjects, such as microfluidics, microbiology, chemical analysis and detection, material synthesis and assembly, device fabrication, etc.

Antimicrobial cholic acid derivatives from the Pitch Lake bacterium Bacillus amyloliquefaciens UWI-W23

Six cholic acid derivatives (1-6) were isolated from broth cultures of Bacillus amyloliquefaciens UWI-W23, an isolate from the Trinidad Pitch Lake. The compounds were extracted via solvent extraction and/or XAD resin adsorption and purified using silica gel column chromatography. Their structures were elucidated using 1D, 2D NMR and ESI-MS spectrometry and FT-IR spectrophotometry. One of the compounds, taurodeoxycholate (2) is for the first time being reported from a bacterial source while deoxycholate (4) is for the first time being reported from a Gram-positive bacterium. The other compounds have not been previously isolated from Bacillus spp. viz. cholate (1), taurocholic acid (3); glycodeoxycholic acid (5) and glycocholic acid (6). All six compounds exhibited antimicrobial activity against P. aeruginosa and B. cereus with MICs ranging from 7 to 250 µg/mL. Cholate (1) also showed activity against MRSA (MICs = 125 µg/mL) and glycocholic acid (6) against S. cerevisiae (MICs = 15.6 µg/mL).

Microbial micropatches within microbial hotspots

The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have 'hotspots' of high abundance, and 'coldspots' of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.

Different Diversity and Distribution of Archaeal Community in the Aqueous and Oil Phases of Production Fluid From High-Temperature Petroleum Reservoirs

To get a better knowledge on how archaeal communities differ between the oil and aqueous phases and whether environmental factors promote substantial differences on microbial distributions among production wells, we analyzed archaeal communities in oil and aqueous phases from four high-temperature petroleum reservoirs (55–65°C) by using 16S rRNA gene based 454 pyrosequencing. Obvious dissimilarity of the archaeal composition between aqueous and oil phases in each independent production wells was observed, especially in production wells with higher water cut, and diversity in the oil phase was much higher than that in the corresponding aqueous phase. Statistical analysis further showed that archaeal communities in oil phases from different petroleum reservoirs tended to be more similar, but those in aqueous phases were the opposite. In the high-temperature ecosystems, temperature as an environmental factor could have significantly affected archaeal distribution, and archaeal diversity raised with the increase of temperature (p < 0.05). Our results suggest that to get a comprehensive understanding of petroleum reservoirs microbial information both in aqueous and oil phases should be taken into consideration. The microscopic habitats of oil phase, technically the dispersed minuscule water droplets in the oil could be a better habitat that containing the indigenous microorganisms.

Curvature-Guided Motility of Microalgae in Geometric Confinement

Microorganisms, such as bacteria and microalgae, often live in habitats consisting of a liquid phase and a plethora of interfaces. The precise ways in which these motile microbes behave in their confined environment remain unclear. Using experiments and Brownian dynamics simulations, we study the motility of a single Chlamydomonas microalga in an isolated microhabitat with controlled geometric properties. We demonstrate how the geometry of the habitat controls the cell's navigation in confinement. The probability of finding the cell swimming near the boundary increases with the wall curvature, as seen for both circular and elliptical chambers. The theory, utilizing an asymmetric dumbbell model of the cell and steric wall interactions, captures this curvature-guided navigation quantitatively with no free parameters.

Monitoring Microbial Mineralization Using Reverse Stable Isotope Labeling Analysis by Mid-Infrared Laser Spectroscopy

Assessing the biodegradation of organic compounds is a frequent question in environmental science. Here, we present a sensitive, inexpensive, and simple approach to monitor microbial mineralization using reverse stable isotope labeling analysis (RIL) of dissolved inorganic carbon (DIC). The medium for the biodegradation assay contains regular organic compounds and ¹³C-labeled DIC with ¹³C atom fractions (x(¹³C)_DIC) higher than natural abundance (typically 2-50%). The produced CO₂ (x(¹³C) ≈ 1.11%) gradually dilutes the initial x(¹³C)_DIC allowing to quantify microbial mineralization using mass-balance calculations. For ¹³C-enriched CO₂ samples, a newly developed isotope ratio mid-infrared spectrometer was introduced with a precision of x(¹³C) < 0.006%. As an example for extremely difficult and slowly degradable compounds, CO₂ production was close to the theoretical stoichiometry for anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Furthermore, we could measure the aerobic degradation of dissolved organic carbon (DOC) adsorbed to granular activated carbon in a drinking water production plant, which cannot be labeled with ¹³C. Thus, the RIL approach can be applied to sensitively monitor biodegradation of various organic compounds under anoxic or oxic conditions.

The Adaptability of Life on Earth and the Diversity of Planetary Habitats

The evolutionary adaptability of life to extreme environments is astounding given that all life on Earth is based on the same fundamental biochemistry. The range of some physicochemical parameters on Earth exceeds the ability of life to adapt, but stays within the limits of life for other parameters. Certain environmental conditions such as low water availability in hyperarid deserts on Earth seem to be close to the limit of biological activity. A much wider range of environmental parameters is observed on planetary bodies within our Solar System such as Mars or Titan, and presumably even larger outside of our Solar System. Here we review the adaptability of life as we know it, especially regarding temperature, pressure, and water activity. We use then this knowledge to outline the range of possible habitable environments for alien planets and moons and distinguish between a variety of planetary environment types. Some of these types are present in our Solar System, others are hypothetical. Our schematic categorization of alien habitats is limited to life as we know it, particularly regarding to the use of solvent (water) and energy source (light and chemical compounds).

The microbiology of oil sands tailings: past, present, future

Surface mining of enormous oil sands deposits in northeastern Alberta, Canada since 1967 has contributed greatly to Canada's economy but has also received negative international attention due largely to environmental concerns and challenges. Not only have microbes profoundly affected the composition and behavior of this petroleum resource over geological time, they currently influence the management of semi-solid tailings in oil sands tailings ponds (OSTPs) and tailings reclamation. Historically, microbial impacts on OSTPs were generally discounted, but next-generation sequencing and biogeochemical studies have revealed unexpectedly diverse indigenous communities and expanded our fundamental understanding of anaerobic microbial functions. OSTPs that experienced different processing and management histories have developed distinct microbial communities that influence the behavior and reclamation of the tailings stored therein. In particular, the interactions of Deltaproteobacteria and Firmicutes with methanogenic archaea impact greenhouse gas emissions, sulfur cycling, pore water toxicity, sediment biogeochemistry and densification, water usage and the trajectory of long-term mine waste reclamation. This review summarizes historical data; synthesizes current understanding of microbial diversity and activities in situ and in vitro; predicts microbial effects on tailings remediation and reclamation; and highlights knowledge gaps for future research.

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

BACKGROUND

Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods.

RESULTS

Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments.

CONCLUSIONS

The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.

Towards an integrated understanding of how micro scale processes shape groundwater ecosystem functions

Micro scale processes are expected to have a fundamental role in shaping groundwater ecosystems and yet they remain poorly understood and under-researched. In part, this is due to the fact that sampling is rarely carried out at the scale at which microorganisms, and their grazers and predators, function and thus we lack essential information. While set within a larger scale framework in terms of geochemical features, supply with energy and nutrients, and exchange intensity and dynamics, the micro scale adds variability, by providing heterogeneous zones at the micro scale which enable a wider range of redox reactions. Here we outline how understanding micro scale processes better may lead to improved appreciation of the range of ecosystems functions taking place at all scales. Such processes are relied upon in bioremediation and we demonstrate that ecosystem modelling as well as engineering measures have to take into account, and use, understanding at the micro scale. We discuss the importance of integrating faunal processes and computational appraisals in research, in order to continue to secure sustainable water resources from groundwater.

The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation

One consequence of oil production is the possibility of unplanned accidental oil spills; therefore, it is important to evaluate the potential of indigenous microorganisms (both prokaryotes and eukaryotes) from different oceanic basins to degrade oil. The aim of this study was to characterize the microbial response during the biodegradation process of Brazilian crude oil, both with and without the addition of the dispersant Corexit 9500, using deep-sea water samples from the Amazon equatorial margin basins, Foz do Amazonas and Barreirinhas, in the dark and at low temperatures (4°C). We collected deep-sea samples in the field (about 2570 m below the sea surface), transported the samples back to the laboratory under controlled environmental conditions (5°C in the dark) and subsequently performed two laboratory biodegradation experiments that used metagenomics supported by classical microbiological methods and chemical analysis to elucidate both taxonomic and functional microbial diversity. We also analyzed several physical–chemical and biological parameters related to oil biodegradation. The concomitant depletion of dissolved oxygen levels, oil droplet density characteristic to oil biodegradation, and BTEX concentration with an increase in microbial counts revealed that oil can be degraded by the autochthonous deep-sea microbial communities. Indigenous bacteria (e.g., Alteromonadaceae, Colwelliaceae, and Alcanivoracaceae), archaea (e.g., Halobacteriaceae, Desulfurococcaceae, and Methanobacteriaceae), and eukaryotic microbes (e.g., Microsporidia, Ascomycota, and Basidiomycota) from the Amazonian margin deep-sea water were involved in biodegradation of Brazilian crude oil within less than 48-days in both treatments, with and without dispersant, possibly transforming oil into microbial biomass that may fuel the marine food web.

Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water

BACKGROUND

Oil field produced water (OFPW) is widely produced in large volumes around the world. Transforming the organic matter in OFPW into bioenergy, such as biomethane, is one promising way to sustainability. However, OFPW is difficult to biologically degrade because it contains complex compounds such as naphthenic acids (NAs), or polycyclic aromatic hydrocarbons (PAHs). Although active microbial communities have been found in many oil reservoirs, little is known about how an exotic microbiome, e.g. the one which originates from municipal wastewater treatment plants, would evolve when incubated with OFPW.

RESULTS

In this study, we harvested methanogenic biomass from two sources: a full-scale anaerobic digester (AD) treating oil and gas processing wastewater (named O&G sludge), and from a full-scale AD reactor treating multiple fractions of municipal solid wastes (named MS, short for mixed sludge). Both were incubated in replicate microcosms fed with PAHs, NAs, or OFPW. The results showed that the PAHs, NAs, and OFPW feeds could rapidly alter the methanogenic microbiomes, even after 14 days, while the O&G sludge adapted faster than the mixed sludge in all the incubations. Two rarely reported microorganisms, a hydrogenotrophic methanogen Candidatus methanoregula and a saccharolytic fermenter Kosmotoga, were found to be prevalent in the PAHs and OFPW microcosms, and are likely to play an important role in the syntrophic degradation of PAHs and OFPW, cooperating with methanogens such as Methanoregula, Methanosarcina, or Methanobacterium.

CONCLUSIONS

The dominant phyla varied in certain patterns during the incubations, depending on the biomass source, feed type, and variation in nutrients. The sludge that originated from the oil and gas processing wastewater treatment (O&G) reactor adapted faster than the one from municipal solid waste reactors, almost certainly because the O&G biomass had been "pre-selected" by the environment. This study reveals the importance of biomass selection for other crude oil-waste-related bioengineering studies, such as bioaugmentation and bioremediation.