Microbial Degradation Of Hydrocarbons Research Articles

Construction of yeast microbial consortia for petroleum hydrocarbons degradation.

Microbial degradation of petroleum hydrocarbons plays a vital role in mitigating petroleum contamination and heavy oil extraction. In this study, a Saccharomyces cerevisiae capable of degrading hexadecane has been successfully engineered, achieving a maximum degradation rate of up to 20.42%. However, the degradation ability of this strain decreased under various pressure conditions such as high temperature, high osmotic pressure, and acidity conditions. Therefore, a S. cerevisiae with high tolerance to these conditions has been constructed. And then, we constructed an "anti-stress hydrocarbon-degrading" consortium comprising engineered yeast strain SAH03, which degrades hexadecane, and glutathione synthetic yeast YGSH10, which provides stress resistance. This consortium was able to restore the degradation ability of SAH03 under various pressure conditions, particularly exhibiting a significant increase in degradation rate from 5.04% to 17.04% under high osmotic pressure. This study offers a novel approach for improving microbial degradation of petroleum hydrocarbons.

Origin and microbial degradation of thermogenic hydrocarbons within the sandy gas hydrate reservoirs in the Qiongdongnan Basin, northern South China Sea

Large-scale natural gas hydrate accumulations (generally over one billion cubic meters of natural gas) in coarse-grained marine sediments are the most valuable types for commercial exploration and exploitation. The formation of such a gas hydrate deposit generally requires a sufficient natural gas supply such as deeply buried thermogenic gas source. However, the worldwide discovered thermogenic gas hydrate deposits are rare, leaving relatively a poor understanding of their formation and evolution. Based on the geochemical and microbial analyses of eleven hydrate-related gas and five sediment samples from the thermogenic gas hydrate deposits in the Qiongdongnan Basin in northern South China Sea, we systematically investigated the origin and evolution of thermogenic hydrocarbons within sandy gas hydrate reservoirs. Results show that natural gas within high saturated gas hydrate-filled sandy sediments is predominately of thermogenic (the proportion is 57.1–70.5%), characterized by “dry gas” (99.38–99.7% C1, 0.26–0.47% C2 and <0.5% C3+), relatively lower C1/(C2+C3) ratio (187–376), and heavier δ13C–C1 values (−55.0 to −31.3‰). In addition, typical biomarkers (including the alkanes, tricyclic terpanes, hopanes and steranes) generated from mature source rocks were detected in the hydrate-filled fine sand reservoir, as well as the biomarker indicators (including the unresolved complex mixtures (UCMs) hump and the 25-norhopane homologous series) for severe hydrocarbon biodegradation. Furthermore, large amounts of hydrocarbon degrading bacteria (50.5% of bacteria) and methanogenic archaea (34.3% of archaea) were detected within hydrate-filled sandy sediment. Our results indicated that the deeply buried thermogenic source can indeed provide sufficient gas supply for the formation of a large-scale gas hydrate deposit, but thermogenic liquid hydrocarbons within gas hydrate reservoirs are very susceptible to be degraded and consumed by hydrocarbon degrading bacteria. In addition, we also found that the clay components of argillaceous gas hydrate reservoirs can adsorb and store large amounts of in situ immature organic matter, which can significantly obscure or cover up the original geochemical signatures of thermogenic hydrocarbons therein. These findings suggest that the relative contribution of deeply buried thermogenic source for gas hydrate accumulation worldwide may be underestimated, because we have previously ignored the fact that thermogenic hydrocarbons within gas hydrate reservoirs would be significantly consumed by hydrocarbon degrading microbes or diluted by in situ immature sedimentary organic matter. Our findings are highly significant for the evaluation and exploration of thermogenic gas hydrate accumulations worldwide.

Differential degradation of petroleum hydrocarbons by Shewanella putrefaciens under aerobic and anaerobic conditions.

The complexity of crude oil composition, combined with the fluctuating oxygen level in contaminated environments, poses challenges for the bioremediation of oil pollutants, because of compound-specific microbial degradation of petroleum hydrocarbons under certain conditions. As a result, facultative bacteria capable of breaking down petroleum hydrocarbons under both aerobic and anaerobic conditions are presumably effective, however, this hypothesis has not been directly tested. In the current investigation, Shewanella putrefaciens CN32, a facultative anaerobic bacterium, was used to degrade petroleum hydrocarbons aerobically (using O2 as an electron acceptor) and anaerobically (using Fe(III) as an electron acceptor). Under aerobic conditions, CN32 degraded more saturates (65.65 ± 0.01%) than aromatics (43.86 ± 0.03%), with the following order of degradation: dibenzofurans > n-alkanes > biphenyls > fluorenes > naphthalenes > alkylcyclohexanes > dibenzothiophenes > phenanthrenes. In contrast, under anaerobic conditions, CN32 exhibited a higher degradation of aromatics (53.94 ± 0.02%) than saturates (23.36 ± 0.01%), with the following order of degradation: dibenzofurans > fluorenes > biphenyls > naphthalenes > dibenzothiophenes > phenanthrenes > n-alkanes > alkylcyclohexanes. The upregulation of 4-hydroxy-3-polyprenylbenzoate decarboxylase (ubiD), which plays a crucial role in breaking down resistant aromatic compounds, was correlated with the anaerobic degradation of aromatics. At the molecular level, CN32 exhibited a higher efficiency in degrading n-alkanes with low and high carbon numbers relative to those with medium carbon chain lengths. In addition, the degradation of polycyclic aromatic hydrocarbons (PAHs) under both aerobic and anaerobic conditions became increasingly difficult with increased numbers of benzene rings and methyl groups. This study offers a potential solution for the development of targeted remediation of pollutants under oscillating redox conditions.

Systematic Intrinsic Biodegradation Studies of Crude Oil Contaminated Soil of Bdere Community in South-South, Nigeria

Crude oil pollution is a perennial environmental menace that has bedevilled the South-South ecosystem of Nigeria. This study was aimed at using gas chromatography-mass spectrometry (GC-MS) technique to investigate the biodegradation capabilities of nine bacterial cultures on crude oil residues in Bdere area in South-South, Nigeria. These microorganisms include Pseudomonas aeruginosa, Bacillus subtilis, Bacillus cereus, Micrococcus spp, Pseudomonas putida, Clostridium spp, Bacillus spp, Streptococcus spp, and Serratia spp. The results from the microbial-degraded samples were compared with an abiotic control. The findings reveal that the total petroleum hydrocarbon (TPH) in the microbial-treated samples was significantly attenuated compared to the control, confirming the microrganism's ability to degrade crude oil components. The primary degradation pathway involved biological oxidation of the aliphatic hydrocarbons, transforming them to primary alcohols, aldehydes, and fatty acid derivatives. Degradation was also observed across a wide range of short and long-chain alkanes, aromatic hydrocarbons, and polycyclic aromatic hydrocarbons (PAHs). However, some resistant compounds persisted, and certain degradation products inhibited the rate of further biodegradation. The generation of new metabolites and intermediates confirmed the effective microbial remediation. These findings expand our understanding of microbial degradation of hydrocarbons, offering potential strategies for environmental remediation of oil-contaminated sites.

Degrading characteristics of oil‐degrading bacteria and its study of petroleum hydrocarbon metabolites

AbstractExploring the community characteristics of petroleum degrading bacteria and revealing the types of petroleum metabolites produced by degrading bacteria play an important role in solving the problem of oil pollution. In this study, the bacterial suspension was extracted from the sludge of the sewage treatment plant, and the efficient dominant bacteria were enriched and cultured by microbial screening. The optimal environmental conditions and kinetic behavior of microbial degradation of petroleum hydrocarbons in groundwater were discussed, and the metabolites of microbial degradation of petroleum hydrocarbons were analyzed. The results showed that the optimum degradation conditions of the strain were as follows: bacterial suspension inoculum: 2%, pH: 7, temperature: 30°C, initial concentration of contaminated water sample: 500 mg/L. Under these conditions, the microbial petroleum hydrocarbon degradation efficiency was 84.7% and followed the first‐order kinetics; qualitative and quantitative statistical analysis of the metabolites of the microbial degradation of petroleum hydrocarbons by gas chromatography‐time‐of‐flight mass spectrometry was performed. A total of 10 significantly upregulated products and 12 significantly downregulated products were screened, which were significantly different from the metabolites of the control group. Further microbial community analysis showed that Pseudomonas was dominant in the bacterial suspension, more than 99.5%, which was significantly different from the sludge sample, providing data support for the degradation of petroleum hydrocarbons by Pseudomonas. This study has provided a scientific basis for in situ remediation of petroleum pollution in groundwater.

Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica

Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h−1. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.

Species-specific responses of marine bacteria to environmental perturbation

Environmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.

Effects of marine diesel on microbial diversity and activity in high Arctic beach sediments

Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.

Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation.

Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. Cycloclasticus spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including rhd3α, rhd2α, and pahE. However, it remains unknown if the expression of these genes can serve as an indicator for active PAH degradation. Here, we determined transcript-to-gene (TtG) ratios with (reverse transcription) qPCR in cultures of Cycloclasticus pugetii strain PS-1 grown with naphthalene, phenanthrene, a mixture of these PAHs, or alternate substrates (i.e., no PAHs). Mean TtG ratios of 1.99 × 10-2, 1.80 × 10-3, and 3.20 × 10-3 for rhd3α, rhd2α, and pahE, respectively, were measured in the presence or absence of PAHs. The TtG values suggested that marker-gene expression is independent of PAH degradation. Measurement of TtG ratios in Arctic seawater microcosms amended with water-accommodated crude oil fractions, and incubated under in situ temperature conditions (i.e., 1.5°C), only detected Cycloclasticus spp. rhd2α genes and transcripts (mean TtG ratio of 4.15 × 10-1). The other marker genes-rhd3α and pahE-were not detected, suggesting that not all Cycloclasticus spp. carry these genes and a broader yet-to-be-identified repertoire of PAH-degradation genes exists. The results indicate that the expression of PAH marker genes may not correlate with PAH-degradation activity, and transcription data should be interpreted cautiously.

Development of an in vitro method for activation of X-succinate synthases for fumarate hydroalkylation

Anaerobic microbial degradation of hydrocarbons is often initiated through addition of the hydrocarbon to fumarate by enzymes known as X-succinate synthases (XSSs). XSSs use a glycyl radical cofactor, which is installed by an activating enzyme (XSS-AE), to catalyze this carbon-carbon coupling reaction. The activation step, although crucial for catalysis, has not previously been possible invitro because of insolubility of XSS-AEs. Here, we take a genome mining approach to find an XSS-AE, a 4-isopropylbenzylsuccinate synthase (IBSS)-AE (IbsAE) that can be solubly expressed in Escherichia coli. This soluble XSS-AE can activate both IBSS and the well-studied benzylsuccinate synthase (BSS) invitro, allowing us to explore XSSs biochemically. To start, we examine the role of BSS subunits and find that the beta subunit accelerates the rate of hydrocarbon addition. Looking forward, the methodology and insight gathered here can be used more broadly to understand and engineer XSSs as synthetically useful biocatalysts.

The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea.

The geological isolation, lack of freshwater inputs and specific internal water circulations make the Red Sea one of the most extreme-and unique-oceans on the planet. Its high temperature, salinity and oligotrophy, along with the consistent input of hydrocarbons due to its geology (e.g., deep-sea vents) and high oil tankers traffic, create the conditions that can drive and influence the assembly of unique marine (micro)biomes that evolved to cope with these multiple stressors. We hypothesize that mangrove sediments, as a model-specific marine environment of the Red Sea, act as microbial hotspots/reservoirs of such diversity not yet explored and described. To test our hypothesis, we combined oligotrophic media to mimic the Red Sea conditions and hydrocarbons as C-source (i.e., crude oil) with long incubation time to allow the cultivation of slow-growing environmentally (rare or uncommon) relevant bacteria. This approach reveals the vast diversity of taxonomically novel microbial hydrocarbon degraders within a collection of a few hundred isolates. Among these isolates, we characterized a novel species, Nitratireductor thuwali sp. nov., namely, Nit1536T. It is an aerobic, heterotrophic, Gram-stain-negative bacterium with optimum growth at 37°C, 8 pH and 4% NaCl, whose genome and physiological analysis confirmed the adaptation to extreme and oligotrophic conditions of the Red Sea mangrove sediments. For instance, Nit1536T metabolizes different carbon substrates, including straight-chain alkanes and organic acids, and synthesizes compatible solutes to survive in salty mangrove sediments. Our results showed that the Red Sea represent a source of yet unknown novel hydrocarbon degraders adapted to extreme marine conditions, and their discovery and characterization deserve further effort to unlock their biotechnological potential.

Phenanthrene Degradation by Photosynthetic Bacterial Consortium Dominated by Fischerella sp.

Microbial degradation of aromatic hydrocarbons is an emerging technology, and it is well recognized for its economic methods, efficiency, and safety; however, its exploration is still scarce and greater emphasis on cyanobacteria-bacterial mutualistic interactions is needed. We evaluated and characterized the phenanthrene biodegradation capacity of consortium dominated by Fischerella sp. under holoxenic conditions with aerobic heterotrophic bacteria and their molecular identification through 16S rRNA Illumina sequencing. Results indicated that our microbial consortium can degrade up to 92% of phenanthrene in five days. Bioinformatic analyses revealed that consortium was dominated by Fischerella sp., however different members of Nostocaceae and Weeksellaceae, as well as several other bacteria, such as Chryseobacterium, and Porphyrobacter, were found to be putatively involved in the biological degradation of phenanthrene. This work contributes to a better understanding of biodegradation of phenanthrene by cyanobacteria and identify the microbial diversity related.

Vertical heterogeneity of hydrocarbon-degrading bacteria in a core sediment sample from the Central Indian Ridge

Hydrocarbons are ubiquitous in marine environments and might fuel hydrocarbon-metabolizing microbes in the ocean. Numerous studies have documented microbial hydrocarbon degradation in water columns and deep-sea surface sediment. However, the degradation potential and biogeochemical cycling of hydrocarbons in subsurface sediments remain largely unknown. In this study, we used two different hydrocarbons, n-hexadecane (HEX) and methylcyclohexane (MCH), to investigate the distribution and diversity of hydrocarbon-consuming bacteria in a core sediment sample from the Central Indian Ridge (CIR), which is adjacent to mid-ridge hydrothermal vents in the Indian Ocean. We observed different vertical profiles of HEX- and MCH-degrading bacteria in the core sediments. Specifically, HEX-degrading bacteria were universally distributed, while MCH-degrading bacteria were found only in the intermediate layers of the core sediments. Changing factors including dissolved oxygen might affect the natural distribution of different hydrocarbon consumers. We found that a novel species of the genus C1-B045 might play a pivotal role in metabolizing MCH in the CIR deep biosphere. Through amino acid identity comparison with published sequences, we determined that C1-B045 harbors two novel classes of cyclohexanone monooxygenases involved in MCH metabolism. This study sheds light on the structure and function of hydrocarbon-consuming microbes in deep biospheres.

Post-Formation of Oil Particle Aggregates: Breakup and Biodegradation.

Spilled oil slicks are likely to break into droplets in the subtidal and intertidal zones of seashores due to wave energy. The nonliving suspended fine particles in coastal ecosystems can interact with the dispersed oil droplets, resulting in the formation of Oil Particle Aggregates (OPAs). Many investigations assumed that these aggregates will settle due to the particles' high density. Recent studies, however, reported that some particles penetrate the oil droplets, which results in further breakup while forming smaller OPAs that remain suspended in the water column. Here, we investigated the interaction of crude oil droplets with intertidal and subtidal sediments, as well as artificial pure kaolinite, in natural seawater. Results showed that the interaction between oil droplets and intertidal sediments was not particularly stable, with an Oil Trapping Efficiency (OTE) < 25%. When using subtidal sediments, OTE reached 56%. With artificial kaolinite, OPA formation and breakup were more significant (OTE reaching up to 67%) and occurred faster (within 12 h). Oil chemistry analysis showed that the biodegradation of oil in seawater (half-life of 485 h) was significantly enhanced with the addition of sediments, with half-lives of 305, 265, and 150 h when adding intertidal sediments, subtidal sediments, and pure kaolinite, respectively. Such results reveal how the sediments' shape and size affect the various oil-sediment interaction mechanisms, and the subsequent impact on the microbial degradation of petroleum hydrocarbons. Future studies should consider investigating the application of fine (several microns) and sharp (elongated-sheeted) sediments as a nondestructive and nontoxic technique for dispersing marine oil spills.

Biodegradation of hydrocarbons by Purpureocillium lilacinum and Penicillium chrysogenum from heavy oil sludge and their potential for bioremediation of contaminated soils

Heavy oil sludge as a highly hazardous solid waste poses potential pollution risks to the ecological environment. Microbial degradation of petroleum hydrocarbons is an emerging strategy for controlling the environmental pollution by oil sludge. Two hydrocarbon-degrading fungi, designated HF and HQ, were isolated from heavy oil sludge collected at Tahe Oilfield, Xinjiang, Northwest China. Based on morphological analysis and gene sequencing, HF and HQ were identified as Purpureocillium lilacinum and Penicillium chrysogenum, respectively. When supplemented with a small amount of additional carbon (soluble starch) and nitrogen (yeast extract) sources, HF and HQ were able to biodegrade hydrocarbons in oil sludge. Following fungal treatment (30 days), the relative abundances of various hydrocarbon components changed in distinct patterns based on gas chromatography-mass spectrometry. The mean degradation rate of HF for cycloalkanes, n-alkanes, aromatics, and iso-alkanes was 100.0%, 21.2%, 15.1%, and 14.5%, respectively. HQ showed contrasting effects on hydrocarbon composition, as indicated by the decrease of n-alkanes (1.3%) and the increase of cycloalkanes, aromatics, and iso-alkanes (82.6%, 10.2%, and 11.9%, respectively). Approximately 15.3% and 7.6% of total petroleum hydrocarbons in modified oil sludge were removed by HF and HQ, respectively. The results provide empirical evidence for application of P. lilacinum HF and P. chrysogenum HQ as candidate hydrocarbon degraders in bioremediation of oil sludge-contaminated soils.

Effect of plant root exudate constituents on the degradation of phenanthrene by rhizobacterium Mycolicibacterium gilvum (Mycobacteriaceae, Actinobacteria)

The influence of the major components of plant root exudates, namely, carboxylic acids (succinic acid as an example) and secondary plant phenolic metabolites – flavonoids (rutin as an example), on the microbial degradation of the three-ring polycyclic aromatic hydrocarbon (PAH) phenanthrene by rhizobacterium Mycolicibacterium gilvum was studied. The destructive activity of this microorganism relative to PAH was studied by cultivating it in a liquid mineral medium containing phenanthrene (0.2 g/L), succinic acid (5 g/L), and rutin (0, 0.05, 0.1 or 0.2 mmol/L) at 30°C under aeration on a shaker (130 rpm) for 14 days. The stimulating effect of succinic acid and rutin on the microbial degradation of phenanthrene was revealed. It was found that carboxylate was utilized as the main growth substrate for the microorganism, while flavonol and PAH had little effect on bacterial growth. Rutin had no antimicrobial effect on the microorganisms studied; on the contrary, in combination with succinic acid, it significantly increased the biomass growth. At high concentrations (0.1 and 0.2 mmol/L), rutin inhibited the degradation of phenanthrene by 22 and 56%, respectively. However, at a concentration of 0.05 mmol/L rutin increased phenanthrene degradation by 10%. Thus, the results obtained showed the dependence of the PAH microbial degradation efficiency on the presence, combination, and concentration of the plant root exudate constituents.

The effect of chemical dispersant of the third generation (Finasol OSR 62) on the microbial biodegradation process of Zarzaitine oil in water treatment

The application of chemical dispersants aims to stimulate microbial oil degradation by increasing the bioavailability of oil compounds. Overall, nine microcosms were prepared (three for each treatment) using treated sediment with (i) dispersant (d: 25 ppm), (ii) oil (500 ppm), and (iii) with oil + dispersant (500: 25 ppm), respectively. There are also three control microcosms containing only water and sediment without petroleum. Then, we analyzed bacterial abundance, total hydrocarbon, biological oxygen demand (BOD5), and chemical oxygen demand (COD) in each microcosm. Bacterial response density was significantly affected after 40 days of exposure; it was higher in the control microcosm and d (> 24.103 cell/l) than in the other treatments. The index of total hydrocarbons was equal to 53 mg/kg dw in oil and 56 mg/kg dw in oil + dispersant. The higher BOD5 found in oil and in oil + d shows the increased amount of oxygen consumed, which indicates enhanced bacterial activity. Microcosms treated with dispersant had higher COD than the others, but the dispersant did not stimulate microbial hydrocarbon degradation.

Iron Compounds in Anaerobic Degradation of Petroleum Hydrocarbons: A Review.

Waste and wastewater containing hydrocarbons are produced worldwide by various oil-based industries, whose activities also contribute to the occurrence of oil spills throughout the globe, causing severe environmental contamination. Anaerobic microorganisms with the ability to biodegrade petroleum hydrocarbons are important in the treatment of contaminated matrices, both in situ in deep subsurfaces, or ex situ in bioreactors. In the latter, part of the energetic value of these compounds can be recovered in the form of biogas. Anaerobic degradation of petroleum hydrocarbons can be improved by various iron compounds, but different iron species exert distinct effects. For example, Fe(III) can be used as an electron acceptor in microbial hydrocarbon degradation, zero-valent iron can donate electrons for enhanced methanogenesis, and conductive iron oxides may facilitate electron transfers in methanogenic processes. Iron compounds can also act as hydrocarbon adsorbents, or be involved in secondary abiotic reactions, overall promoting hydrocarbon biodegradation. These multiple roles of iron are comprehensively reviewed in this paper and linked to key functional microorganisms involved in these processes, to the underlying mechanisms, and to the main influential factors. Recent research progress, future perspectives, and remaining challenges on the application of iron-assisted anaerobic hydrocarbon degradation are highlighted.

Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor.

Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within a linear pathway, a phenomenon termed metabolic division of labor (MDOL). However, little is known about how such metabolic behaviors shape microbial communities. Here, we derive a theoretical framework to define the assembly of a community that degrades an organic compound through MDOL. The framework indicates that to ensure community stability, the strains performing the initial steps should hold a growth advantage (m) over the "private benefit" (n) of the strain performing the last step. The steady-state frequency of the last strain is then determined by the quotient of n and m. Our experiments show that the framework accurately predicts the assembly of our synthetic consortia that degrade naphthalene through MDOL. Our results provide insights for designing and managing stable microbial systems for metabolic pathway optimization.

Promoting Resuscitation of the VBNC Bacteria and Enrichment of Naphthalene-degrading Bacteria from Oil-contaminated Soils with the Rpf4 from Rhodococcus erythropolis KB1

Nowadays, more than 90% of bacteria in nature are in a viable but not culturable (VBNC) state, and they cannot be separated by traditional plate culture methods. However, resuscitation-promoting factors (Rpf) participate in recovery of dormant cells and promoting bacterial growth. The Rpf4 of Rhodococcus erythropolis KB1 is a Rpf like protein of Micrococcus luteus and contained the Rpf domain and LysM domain. In this study, an expression vector for the rpf4 gene was constructed and expressed in Escherichia coli. The recombinant protein Rpf4 was purified by Ni2+-affinity chromatography. The recombinant protein showed a muralytic activity of 549 ± 28.77 U/mg. The purified Rpf4 could increase R. erythropolis KB1 cell proliferation and improve the resuscitation of R. erythropolis cells that were VBNC. The Rpf4 altered the diversity of naphthalene-degrading bacteria enriched from oil-contaminated soils. Based on the high-throughput sequencing, we found that Proteobacteria and Actinobacteria phyla increased from 76.10% and 0.029% to 98.23% and 0.401% after the Rpf4 treatment, while the Bacteroidetes phylum decreased from 22.70% to 0.76%. The genera Enterobacter, Citrobacter, and Acinetobacter increased from 0.0054%, 0.001%, and 0.745% to 19.02%, 6.34% and 2.49%. Some new genera such as Bifidobacterium, Limnobacter, Alloprevotella, Hydrogenophaga, and Nevskia were founded in the treatment group. Meanwhile, 23 naphthalene-degrading bacteria were isolated by adding the Rpf4 protein to the oil-contaminated soil samples. Study on the naphthalene-degrading bacteria will provide a basis for the microbial degradation of naphthalene and other polycyclic aromatic hydrocarbons and discover the wider application value of Rpf.