A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions

Anaerobic hydrocarbon biodegradation by alkylotrophic methanogens in deep oil reservoirs

In subsurface biodegraded oil reservoirs, methanogenic biodegradation of crude oil is a common process. This process was previously assigned to the syntrophy of hydrocarbon-degrading bacteria and methanogenic archaea. Recent studies showed that archaea of the Candidatus Methanoliparum named as alkylotrophic methanogens couple hydrocarbon degradation and methane production in a single archaeon. To assess the geochemical role of Ca. Methanoliparum, we analyzed the chemical and microbial composition and metabolites of 209 samples from 15 subsurface oil reservoirs across China. Gas chromatography-mass spectrometry analysis revealed that 92% of the tested samples were substantially degraded. Molecular analysis showed that 85% of the tested samples contained Ca. Methanoliparum, and 52% of the tested samples harbored multiple alkyl-coenzyme M derivatives, the intercellular metabolites of alkylotrophic archaea. According to metagenomic and metatranscriptomic analyses, Ca. Methanoliparum dominates hydrocarbon degradation in biodegraded samples from the Changqing, Jiangsu, and Shengli (SL) oilfields, and it is persistently present as shown in a 15-year-long sampling effort at the Shengli oilfield. Together, these findings demonstrate that Ca. Methanoliparum is a widely distributed oil degrader in reservoirs of China, suggesting that alkylotrophic methanogenesis by archaea plays a key role in the alteration of oil reservoirs, thereby expanding our understanding of biogeochemical process in the deep biosphere.

Towards facing uncertainties in biofuel supply chain networks: a systematic literature review

Biofuel supply chains (BSCs) face diverse uncertainties that pose serious challenges. This has led to an expanding body of research focused on studying these challenges. Hence, there is a growing need for a comprehensive review that summarizes the current studies, identifies their limitations, and provides essential advancements to support scholars in the field. To overcome these limitations, this research aims to provide insights into managing uncertainties in BSCs. The review utilizes the Systematic Reviews and Meta-Analyses (PRISMA) method, identifying 205 papers for analysis. This study encompasses three key tasks: first, it analyses the general information of the shortlisted papers. Second, it discusses existing methodologies and their limitations in addressing uncertainties. Lastly, it identifies critical research gaps and potential future directions. One notable gap involves the underutilization of machine learning techniques, which show potential for risk identification, resilient planning, demand prediction, and parameter estimations in BSCs but have received limited attention. Another area for investigation is the potential of agent-based simulation, which can contribute to analysing resilient policies, evaluating resilience, predicting parameters, and assessing the impact of emerging technologies on BSC resilience in the twenty-first century. Additionally, the study identifies the omission of various realistic assumptions, such as backward flow, lateral transshipments, and ripple effects in BSC. This study highlights the complexity of managing uncertainties in BSCs and emphasizes the need for further research and attention. It contributes to policymakers' understanding of uncertain sources and suitable approaches while inspiring researchers to address limitations and generate breakthrough ideas in managing BSC uncertainties.

Oil Has a Higher Methanogenic Potential than Coal in an Oil-Bearing Coal Seam

The presence of oil in coal seams from coal-oil symbiosis areas poses a serious threat to the safe and efficient mining of coal. However, the information about the application of microbial technology in oil-bearing coal seams was insufficient. In this study, the biological methanogenic potential of coal and oil samples in an oil-bearing coal seam was analyzed by anaerobic incubation experiments. The results showed that the biological methanogenic efficiency of the coal sample increased from 0.74 to 1.06 from day 20 to day 90, and the biological methanogenic potential of the oil sample was about twice as high as that of the coal sample after 40 days of incubation. The Shannon diversity and observed operational taxonomic unit (OTU) number of oil were lower than those in coal. The major genera in coal were Sedimentibacter, Lysinibacillus, Brevibacillus, etc., and the major genera in oil mainly included Enterobacter, Sporolactobacillus, and Bacillus. The methanogenic archaea in coal mainly belonged to the order Methanobacteriales, Methanocellales, Methanococcales, etc., and the methanogenic archaea in oil mainly belonged to the genera Methanobacterium, Methanobrevibacter, Methanoculleus, and Methanosarcina. In addition, metagenome analysis showed that functional genes belonging to processes such as methane metabolism, microbial metabolism in different environments, and benzoate degradation were in a higher abundance in the oil culture system, while genes belonging to sulfur metabolism, biotin metabolism, and glutathione metabolism were in a higher abundance in the coal culture system. The metabolites specific to coal samples mainly belonged to phenylpropanoids, polyketides, lipids, and lipid-like molecules; meanwhile, the metabolites specific to oil were mainly organic acids and their derivatives. In summary, this study has a reference value for the elimination of oil from coal in oil-bearing coal seams and can be used to separate oil from oil-bearing coal seams and reduce the hazard brought by oil for coal seam mining.

Enhanced carbon emission driven by the interaction between functional microbial community and hydrocarbons: An enlightenment for carbon cycle

Soil microbial communities are usually regarded as one of the key players in the global element cycling. Moreover, an important consequence of oil contamination altering the structure of microbial communities is likely to result in an increased carbon emission. However, understanding of the complex interactions between environmental factors and biological communities is clearly lagging behind. Here it showed that the flux of carbon emissions increased in oil-contaminated soils, up to 13.64 g C·(kg soil)^-1·h^-1. This phenomenon was mainly driven by the enrichment of rare degrading microorganisms (e.g., Methylosinus, Marinobacter, Pseudomonas, Alcanivorax, Yeosuana, Halomonas and Microbulbifer) in the aerobic layer, rather than the anaerobic layer, which is more conducive to methane formation. In addition, petroleum hydrocarbons and environmental factors are equally important in shaping the structure of microbial communities (the ecological stability) and functional traits (e.g., fatty acid metabolism, lipid metabolism and amino acid metabolism) due to the different ecological sensitivities of microorganisms. Thus, it can be believed that the variability of rare hydrocarbon degrading microorganisms is of greater concern than changes in dominant microorganisms in oil-contaminated soil. Undoubtedly, this study could reveal the unique characterization of bacterial communities that mediate carbon emission and provide evidence for understanding the conversion from carbon stores to carbon gas release in oil-contaminated soils.

Application of the Fluorescence-Activating and Absorption-Shifting Tag (FAST) for Flow Cytometry in Methanogenic Archaea

Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans have been biochemically characterized and can be genetically engineered by using a variety of existing molecular tools. The anaerobic lifestyle and autofluorescence of methanogens, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives), which require oxygen for chromophore maturation. Recently, the use of a novel oxygen-independent fluorescent activation and absorption-shifting tag (FAST) was demonstrated with M. maripaludis. Similarly, we now describe the use of the tandem activation and absorption-shifting tag protein 2 (tdFAST2), which fluoresces when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. Expression of tdFAST2 in M. acetivorans and M. maripaludis is noncytotoxic and tdFAST2:HBR-3,5DOM fluorescence is clearly distinguishable from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be distinguished, thereby allowing for the possibility of high-throughput investigations of the characteristic dynamics within single and mixed cultures. IMPORTANCE Methane-producing archaea play an essential role in the global carbon cycle and demonstrate great potential for various biotechnological applications, e.g., biofuel production, carbon dioxide capture, and electrochemical systems. Oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins for studying methanogens. By using tdFAST2:HBR-3,5DOM fluorescence, which functions under anaerobic conditions and is distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of the mixed culture dynamics of methanogens via flow cytometry were made possible. This will further help accelerate the sustainable exploitation of methanogens.

Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide

Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with a lower level of intervention were the most similar to the potential functional core, while the oil fields with a long history of water injection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical transformations in these ecosystems.

Biodegradation of metoprolol in oxic and anoxic hyporheic zone sediments: unexpected effects on microbial communities

Abstract

Metoprolol is widely used as a beta-blocker and considered an emerging contaminant of environmental concern due to pseudo persistence in wastewater effluents that poses a potential ecotoxicological threat to aquatic ecosystems. Microbial removal of metoprolol in the redox-delineated hyporheic zone (HZ) was investigated using streambed sediments supplemented with 15 or 150 μM metoprolol in a laboratory microcosm incubation under oxic and anoxic conditions. Metoprolol disappeared from the aqueous phase under oxic and anoxic conditions within 65 and 72 days, respectively. Metoprolol was refed twice after initial depletion resulting in accelerated disappearance under both conditions. Metoprolol disappearance was marginal in sterile control microcosms with autoclaved sediment. Metoprolol was transformed mainly to metoprolol acid in oxic microcosms, while metoprolol acid and α-hydroxymetoprolol were formed in anoxic microcosms. Transformation products were transient and disappeared within 30 days under both conditions. Effects of metoprolol on the HZ bacterial community were evaluated using DNA- and RNA-based time-resolved amplicon Illumina MiSeq sequencing targeting the 16S rRNA gene and 16S rRNA, respectively, and were prominent on 16S rRNA rather than 16S rRNA gene level suggesting moderate metoprolol-induced activity-level changes. A positive impact of metoprolol on Sphingomonadaceae and Enterobacteriaceae under oxic and anoxic conditions, respectively, was observed. Nitrifiers were impaired by metoprolol under oxic and anoxic conditions. Collectively, our findings revealed high metoprolol biodegradation potentials in the hyporheic zone under contrasting redox conditions associated with changes in the active microbial communities, thus contributing to the attenuation of micropollutants.

Key points

• High biotic oxic and anoxic metoprolol degradation potentials in the hyporheic zone.

• Key metoprolol-associated taxa included Sphingomonadaceae, Enterobacteraceae, and Promicromonosporaceae.

• Negative impact of metoprolol on nitrifiers.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11466-w.