Subsurface Hydrocarbon Degradation Strategies in Low- and High-Sulfate Coal Seam Communities Identified with Activity-Based Metagenomics

Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled redox gradient. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways were observed but with a predominance of aerobic dioxygenases. The putative low-molecular weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The novel methods used in this study-- subsurface environmental samplers in combination with metagenomic sequencing of both translationally active metagenomes and environmental genomes-- offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox potentials broadening the understanding of degradation strategies for subsurface carbon.

Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition

Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.

Light-scattering properties of microorganisms Desulfuromonas acetoxidans by influence of silver

The article deals with the concentration changes and relative content of bacterial cells of Desulfuromonas acetoxidans in the intervals of sizes 0.2–2.0 µm under the influence of nano silver particles. Correlation between these changes of light-scattering properties of bacterial cells and growth abilities of bacteria Desulfuromonas acetoxidans under inflence of silver nanoparticles and ions has been shown. The purpose of the work was to research the intensity of processes the change of indexes of the antioxidant system the cells of Desulfuromonas acetoxidans at influence of silver nanoparticles and silver nitrate. The influence of various concentrations of silver nanoparticles and silver nitrate on enzymatic activity of catalase and reduced glutathione synthesis by Desulfuromonas аcetoxidans cells under their cultivation with fumarate addition and with absence of sulphur has been determined. Specific catalase activity increased with enhancing of concentration and duration of bacterial cultivation under the addition of this salt. The highest specific catalase activity was determined on the second day of bacterial growth under the influence of all concentration range of investigated metal salt. The reduced glutathione content under silver nitrate and silver nanoparticles exposure varied depending on the cultivation time and metal concentration. The maximum reduced glutathione content has been observed. The result of catalase activity changes and glutathione content changes of sulfur-reducing D. acetoxidans bacteria cell-free extracts and has been investigated under the influence of different concentrations of Ag nanoparticles during four days of cultivation has been investigated.

Combined Use of Diagnostic Fumarate Addition Metabolites and Genes Provides Evidence for Anaerobic Hydrocarbon Biodegradation in Contaminated Groundwater

The widespread use of hydrocarbon-based fuels has led to the contamination of many natural environments due to accidental spills or leaks. While anaerobic microorganisms indigenous to many fuel-contaminated groundwater sites can play a role in site remediation (e.g., monitored natural attenuation, MNA) via hydrocarbon biodegradation, multiple lines of evidence in support of such bioremediation are required. In this study, we investigated two fuel-contaminated groundwater sites for their potential to be managed by MNA. Microbial community composition, biogeochemical indicators, fumarate addition metabolites, and genes diagnostic of both alkane and alkyl-monoaromatic hydrocarbon activation were assessed. Fumarate addition metabolites and catabolic genes were detected for both classes of hydrocarbon biodegradation at both sites, providing strong evidence for in situ anaerobic hydrocarbon biodegradation. However, relevant metabolites and genes did not consistently co-occur within all groundwater samples. Using newly designed mixtures of quantitative polymerase chain reaction (qPCR) primers to target diverse assA and bssA genes, we measured assA gene abundances ranging from 105–108 copies/L, and bssA gene abundances ranging from 105–1010 copies/L at the sites. Overall, this study demonstrates the value of investigating fuel-contaminated sites using both metabolites and genes diagnostic of anaerobic hydrocarbon biodegradation for different classes of hydrocarbons to help assess field sites for management by MNA.

Marine Sediments Harbor Diverse Archaea and Bacteria With Potentials for Anaerobic Hydrocarbon Degradation via Fumarate Addition

Background: Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. Previous gene- and genome-based surveys have detected ubiquitous and novel fumarate-adding enzymes (FAE), but these were neither confirmed as occurring within full degradation pathways nor affiliated with known organisms. The identity and ecological roles of a significant fraction of anaerobic hydrocarbon degraders in marine sediments therefore remains unknown.Results: By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available and newly sequenced metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Deltaproteobacteria that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. The biogeography survey reveals these bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems.Conclusions: Our results expand the knowledge of novel microbial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons, and shed new light on the importance of marine sedimentary archaea in hydrocarbon degradation.

Thermogenic hydrocarbons fuel a redox stratified subseafloor microbiome in deep sea cold seep sediments

At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. In this work, we combined geochemical, metagenomic and metabolomic measurements in distinct sediment redox regimes to profile microbial activities within the uppermost 350 cm of a newly discovered cold seep in the NW Atlantic deep sea (2.3 km water depth). Depth-resolved metagenomic profiling revealed compositional and functional differentiation between near-surface sediments (dominated by Proteobacteria) and deeper subsurface layers (dominated by Atribacteria, Chloroflexi, Euryarchaeota and Lokiarchaeota). Metabolic capabilities of community members were inferred from 376 metagenome-assembled genomes spanning 46 phyla (including five novel candidate phyla). In deeper sulfate-reducing and methanogenic sediments, various community members are capable of anaerobically oxidizing short-chain alkanes (alkyl-CoM reductase pathway), longer-chain alkanes (fumarate addition pathway), and aromatic hydrocarbons (fumarate addition and subsequent benzoyl-CoA pathways). Geochemical profiling demonstrated that hydrocarbon substrates are abundant in this location, thermogenic in origin, and subject to biodegradation. The detection of alkyl-/arylalkylsuccinate metabolites, together with carbon isotopic signatures of ethane, propane and carbon dioxide, support that microorganisms are actively degrading hydrocarbons in these sediments. Hydrocarbon oxidation pathways operate alongside other deep seabed metabolisms such as sulfide oxidation, hydrogen oxidation, carbon fixation, fermentation and reductive dehalogenation. Upward migrated thermogenic hydrocarbons thus sustain diverse microbial communities with activities that affect subseafloor biogeochemical processes across the redox spectrum in deep sea cold seeps.

Methanogenic Degradation of Longn-Alkanes Requires Fumarate-Dependent Activation

ABSTRACTMethanogenic degradation ofn-alkanes is prevalent inn-alkane-impacted anoxic oil reservoirs and oil-polluted sites. However, little is known about the initial activation mechanism of the substrate, especiallyn-alkanes with a chain length above C16. Here, a methanogenic C16to C20n-alkane-degrading enrichment culture was established from production water of a low-temperature oil reservoir. At the end of the incubation (364 days), C16to C20(1-methylalkyl)succinates were detected in then-alkane-amended enrichment culture, suggesting that fumarate addition had occurred in the degradation process. This evidence is supported further by the positive amplification of theassAgene encoding the alpha subunit of alkylsuccinate synthase. A phylogenetic analysis shows theseassAamplicons to be affiliated withSmithellaandDesulfatibacillumclades. Together with the high abundance of these clades in the bacterial community, these two species are postulated to be the key players in the degradation of C16to C20n-alkanes in the present study. Our results provide evidence that longn-alkanes are activated via a fumarate addition mechanism under methanogenic conditions.IMPORTANCEMethanogenic hydrocarbon degradation is the major process for oil degradation in subsurface oil reservoirs and is blamed for the formation of heavy oil and oil sands. Addition ofn-alkanes to fumarate yielding alkyl-substituted succinates is a well-characterized anaerobic activation mechanism for hydrocarbons and is the most common activation mechanism in the anaerobic biodegradation ofn-alkanes with chain lengths less than C16. However, the activation mechanism involved in the methanogenic biodegradation ofn-alkanes longer than C16is still uncertain. In this study, we analyzed a methanogenic enrichment culture amended with a mixture of C16to C20n-alkanes. Thesen-alkanes can be activated via fumarate addition by mixed cultures containingSmithellaandDesulfatibacillumspecies under methanogenic conditions. These observations provide a fundamental understanding of long-n-alkane metabolism under methanogenic conditions and have important applications for the remediation of oil-contaminated sites and for energy recovery from oil reservoirs.