The oily sludge produced in petroleum exploitation and processing is the main pollution source in the petrochemical industry, causing continuous harm to the surrounding eco-environment. Bioremediation as an effective and sustainable technology has attracted much attention. However, the current studies focus on the microbial degradation of petroleum in oily sludge and rarely report enzymatic degradation. [Objective] This study aims to screen petroleum-degradation enzymes by computer simulation and experimental techniques and improve the degradation effect by adding surfactants and enzyme immobilization. [Methods] Molecular docking was employed to analyze the possibility and mode of binding of target enzymes to common substrates in petroleum and the strongest degrading enzyme was screened out by enzymatic degradation experiments. Furthermore, the degradation conditions of the enzyme screened out were optimized, and the degradation effect on petroleum was further improved by immobilization and addition of surfactants. [Results] A total of five petroleum-degrading enzymes were obtained by molecular docking simulation and experimental verification. Among them,Bacillussubtilis laccase (BsLac) exhibited the highest degradation rate of petroleum, which reached 34.1% at the time point of 72 h. Surfactants improved the degradation of BsLac on petroleum, and sophorolipid showcased the strongest promoting effect, with the highest degradation rate of 46.3% at the sophorolipid concentration of 1 000 mg/L. However, 2,2′-azinoo-bis(3-ethyl-benzothiazoline-6-sulfonic acid) diammonium salt (ABTS) did not present promoting effect on BsLac for petroleum degradation. The BsLac immobilized by peanut shell as the adsorption carrier exhibited the highest petroleum degradation rate (56.3%). [Conclusion] We screened out the strongest petroleum-degrading enzyme by molecular docking and experimental verification. Furthermore, the immobilization of BsLac can improve the degradation performance on petroleum. The findings lay an experimental and theoretical foundation for further exploring the enzymatic degradation of petroleum.

[Objective] To investigate the removal efficiency and mechanism by a strain ofRhodotorula. [Methods] The strain was identified based on the morphological characteristics and the phylogenetic tree based on 26S rRNA gene sequences. Then, the removal effect of the strain on Mn(Ⅱ) was studied at different initial pH and Mn(Ⅱ) concentrations. Finally, the products were characterized by scanning electron microscopy, X-ray diffraction analysis, and X-ray photoelectron spectroscopy. [Results] The isolate was identified asRhodotorula taiwanensis, which could grow well at pH 2.0 and 2 000 mg/L Mn(Ⅱ). The removal rate of Mn(Ⅱ) by the strain reached 98.52% at the initial pH 6.0 and Mn(Ⅱ) concentration of 300 mg/L after 144 h, while higher concentrations (≥500 mg/L) of Mn(Ⅱ) caused toxicity to the cells and weakened the removal effect. The strain could oxidize Mn(Ⅱ) to manganese oxides (mainly amorphous MnO₂, Mn₂O₃, and MnO), which produced layered minerals accumulated on the cell surface. In addition, the process of removing Mn(Ⅱ) by the strain increased the pH of the medium (initial pH 7.0, Mn(Ⅱ) concentration of 100 mg/L) up to 8.4 after 144 h. [Conclusion] R.taiwanensis MF4 isolated in this study can tolerate low pH and high concentrations of Mn(Ⅱ), remove Mn(Ⅱ), and increase medium pH. The findings have a reference value for the end process design in the remediation and treatment of acid mine drainage.

[Objective] To screen the indigenous functional microorganisms in reservoirs and explore their oil recovery mechanisms, we conducted field tests to determine the process and technical feasibility of enhancing crude oil recovery by indigenous microorganisms. [Methods] We collected samples from the Yingdong Oilfield and used oil plates to screen for the target bacteria. Next, we evaluated the environmental adaptability and optimized the culture conditions of the strain. Further, we measured the emulsifying, viscosity-reducing, paraffin-resistant, and hydrocarbon conversion abilities of the isolate to evaluate the oil recovery competence of the strain and explored its oil recovery mechanism. Finally, we carried out the microbial enhanced oil recovery tests in the oilfields. [Results] We isolatedBacillus velezensis B6 from the oil-water sample with an emulsifying activity index (EI24) of 100.00%, a viscosity reduction rate of 97.20%, and a paraffin resistance rate of 86.90%, which indicated that strain B6 had good emulsifying and viscosity-reducing abilities and improved oil recovery potential. Strain B6 could reduce heavy components in crude oil and increase light hydrocarbons to improve crude oil properties and quality. Moreover, we carried out single-well huff and puff and paraffin removal operations in Yingdong Oilfield, Yuejin Oilfield, and Huatugou Oilfield with a total of 62 well-times in the field test, which resulted in a cumulative oil increase of 1 460.36 tons and an average delay of 47 days in the well flushing cycle. The economic benefit was CNY 3.425 million, and the input-output ratio was 1:4. [Conclusion] The laboratory studies and field tests proved that indigenousB.velezensis B6 can significantly improve the oil recovery and well paraffin removal, with great application potential.

[Objective] Hydrothermal plumes exchange matter and energy with background seawater during the processes of buoyant rising and non-buoyant lateral migration. Due to the dynamic variability of both hydrothermal activity and ocean currents, the pattern, physico-chemical parameters, and microbial communities of hydrothermal plumes experience spatio-temporal variations. However, due to the lack of long-term monitoring and time-series sampling of hydrothermal plumes, the diversity and spatio-temporal variations of microbial communities, especially archaea, remain unclear. [Methods] From July 2018 to June 2019, a mooring system with two sediment traps (one for collection of hydrothermal plume samples 300 m above seafloor and the other for collection of near-bottom water 40 m above seafloor) and a turbidity sensor (150 m above seafloor) was deployed at 300 m southeast of the active Wocan-1 hydrothermal field for 18 months. We employed 16S rRNA gene high-throughput sequencing to study the diversity and spatio-temporal variations of archaeal communities in the samples on the monthly scale. [Results] The abundance of hydrothermal plume-associated archaea includingThermoplasmata,Methanosarcinia, andMethanobacteria increased when turbidity anomalies were higher. Spatially, the archaeal community structures in the hydrothermal plume and near-bottom water were similar at the phylum and class levels but showed differences at the order level. The relative abundance ofThermoplasmata was generally higher in the plume, whereas ammonia-oxidizing archaea andMethanosarcinia were more abundant in the near-bottom water. [Conclusion] Both the hydrothermal plume and the near-bottom water from 300 m southeast of the Wocan-1 hydrothermal field were affected by hydrothermal fluids, with the plume layer being more significantly affected. The near-bottom layer was affected by re-suspended sediments in addition to hydrothermal fluids. Dynamic changes of hydrothermal contributions and re-suspension of sediments were probably the main factors responsible for the spatial and temporal heterogeneity of archaeal communities. This study gives insights into the structure and spatio-temporal evolution of the archaeal community in the hydrothermal-influenced zone on a monthly scale.

Polycyclic aromatic hydrocarbons (PAHs) are a kind of teratogenic, carcinogenic, and mutagenic organic pollutants. In recent years, the pollution of PAHs in mangrove ecosystems has attracted widespread attention, for which microbial degradation has been recognized as an effective, economical, and multifunctional treatment approach. Researchers have identified a large number of bacteria that utilize PAHs as carbon and energy sources, whereas these bacteria generally suffer from low degradation efficiency, narrow degradation spectra, and poor adaptability to high-salinity environments. In addition, the degradation mechanisms of PAH-degrading bacteria from mangroves remain to be fully explored. [Objective] The present study screened efficient and broad-spectrum PAH-degrading strains in mangrove sediments and explored their degradation efficiency and mechanism, with a view to providing a solid scientific foundation for the innovative research and development of microbial remediation technologies in mangrove ecosystems in the future. [Methods] A new PAH-degrading strain P-9^T was isolated from mangrove sediments collected from Futian, Shenzhen and identified based on the phenotypic and biochemical characteristics and phylogenetic relationship. The genomic DNA of this strain was extracted and sequenced, and the potential of P-9^T in degrading PAHs was investigated by genomic analysis. The degradation ability of P-9^T was measured at different temperatures (25–40 ℃), pH (5.0–9.0), and substrate conditions. Finally, according to the intermediate metabolites detected by high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS), we preliminarily revealed the mechanism of P-9^T in degrading PAHs. [Results] Strain P-9^T was proposed to represent a potential novel species belonging toAquabacter ofXanthobacteraceae and named asAquabacter sediminis P-9^T, which was also the first PAH-degrader identified within this genus. A complete benzoate degradation pathway and key genes encoding dehydrogenase, salicylate hydroxylase, and cytochrome P450 involved in PAHs degradation were found identified in the genome of P-9^T. Strain P-9^T could use naphthalene, phenanthrene, or pyrene as the sole carbon and energy source and grow at 25–40 ℃ and pH 5.0–8.0. In a mineral salt medium (MSM) with phenanthrene (50 mg/L) as the substrate, the degradation efficiency reached 100% after five days. Several metabolites, such as 1-hydroxy-2-naphthoic acid, 1,2-naphthalenediol, catechol, and 1-hydroxy-2-naphthaldehyde were detected, which indicated that strain P-9^T might degrade PAHs via the salicylate pathway. [Conclusion] A.sediminis P-9^T, the first strain ofAquabacter identified to be capable of degrading PAHs could efficiently degrade naphthalene, phenanthrene, and pyrene via the salicylate pathway, with the optimum degradation performance at 37 ℃ and pH 7.0.

[Objective] Studies have discovered that magnetite could be used as an extracellular electron transfer mediator to increase or decrease the microbial reduction rate of dyes. However, the mechanisms underlying these two distinct results remain to be elucidated. [Methods] In this study, magnetite was synthesized by the hydrothermal method and used for the anaerobic reduction of methyl orange (MO), a typical azo dye, byShewanella oneidensis MR-1. [Results] Magnetite exerted concentration-dependent effects on the degradation of MO. Specifically, low concentrations (20–50 mg/L) of magnetite increased the decolorization efficiency of MO by 4.07%–10.64%, while high concentrations (100–200 mg/L) of magnetite decreased the efficiency by 3.92%–18.35%, compared with the group with only bacteria for degradation. Furthermore, the changes in magnetite concentration affected cell surface morphology, metabolic activity, and electron transfer efficiency rather than the distribution of dyes on the microbial surface in the microbial reduction of MO. Low concentrations of magnetite increased ATP production by 1.08%–7.65% and led to the production of 0.033–0.051 mg/L Fe²⁺, while the high concentrations of magnetite decreased ATP production by 38.74%–60.14% and increased Fe²⁺ concentration to 0.091 mg/L. In addition, exogenous Fe²⁺ showed similar concentration-dependent effects on the anaerobic reduction of MO, i.e., promoting the MO reduction at low concentrations (0.01–0.02 mg/L) and inhibiting the reduction at high concentrations (> 0.05 mg/L). [Conclusion] Low concentrations of magnetite did not affect the bacterial cell morphology and improved the cell metabolic activity. A small amount of dissolved Fe²⁺ in the system favored the reduction of MO by bacteria, whereas high concentrations of magnetite showed an opposite influencing trend. This work enriches our understanding about the effect of magnetite on extracellular electron transfer and its application in the reductive transformation of organic pollutants.

[Objective] To detail the molecular evolution and ecological adaptation ofPseudoalteromonas arabiensis. [Methods] Illumina HiSeq X Ten and Oxford Nanopore PromethION were used for the whole genome sequencing ofPseudoalteromonas arabiensis N1230-9 isolated from the surface seawater of the Pacific Ocean. Bioinformatics tools were used to assemble and annotate the original sequencing data, and the type strainPseudoalteromonas arabiensis JCM 17292 was used for comparative genomic analysis. [Results] The genome of strain N1230-9 consisted of two chromosomes, with a size of 4 627 470 bp and the G+C content of 40.85%, encoding a total of 4 202 proteins. Genome annotation showed that strain N1230-9 carried functional genes contributing to the adaption to the marine environment. These genes were mainly involved in heavy metal resistance, iron-uptake systems, anti-phage defense systems, hydrolytic enzymes, carbohydrate metabolism, and two-component signaling systems. Comparative genomic analysis revealed that strain N1230-9 and strain JCM 17292 possessed unique genes conferring adaption to different ecological niches. These genes were primarily involved in heme uptake, heavy metal resistance, anti-phage defense, two-component signaling, and horizontal gene transfer. [Conclusion] P. arabiensis N1230-9 isolated from surface seawater has evolved unique genes for adaption to its ecological niche.

[Objective] Methane-oxidizing bacteria (MOB) are crucial indicators in the microbial exploration of oil and gas reservoirs, while their diversity and distribution are influenced by geographical location and environmental factors. This study aims to explore the effects of environmental variations on the abundance and distribution of MOB in the soil samples collected from seven representative areas in typical oil and gas reservoirs. [Methods] Soil samples were subjected to real-time fluorescence quantitative PCR (qPCR) forpmoA and sequencing of bacterial 16S rRNA gene andpmoA. The abundance of MOB was compared among different samples, on the basis of which the impacts of environmental factors on the distribution of MOB were analyzed. [Results] The highest water content (approximately 22.8%) was detected in the samples from the Jianghan Basin. The average content of nitrate nitrogen was highest in the Yubei oil field, reaching approximately 31.96 μg/g. The Chunguang oil field showcased the highest concentrations of SO₄²⁻ (6 425.0 mg/g) and Cl⁻ (1 617.0 mg/g). The qPCR results revealed that thepmoA in MOB accounted for only 0.77% of that in total soil bacteria, indicating the low absolute abundance of MOB in the soil. The 16S rRNA gene sequencing identified three type Ⅰ MOB genera (Methylosarcina,Methylocaldum, andMethylococcus) and one type Ⅱ MOB genera (Methylocystis). However, the dominant genera in the MOB had extremely low relative abundance, with the maximum of 0.124%. Sequencing ofpmoA revealed thatMethylocystis andMethylosinus, two genera of type Ⅱ MOB, were dominant. The absolute abundance of MOB showed significant correlations with ammonium nitrogen, pH, particle size, SO₄²⁻, and Cl⁻. The relative abundance of MOB had significant correlations only with particle size, total nitrogen, total phosphorus, and metal ions (Al, Fe, K, Ca, Mg, Mn, Zn, and Cu). The discriminant correlation analysis (DCA) indicated that soil moisture, pH, soil particles<2 μm, total nitrogen, and Ca²⁺ significantly influenced the composition of the functional genepmoA in MOB. [Conclusion] This study analyzed the absolute and relative abundance of MOB in soil samples from seven typical oil and gas reservoirs. The MOB abundance showed significant differences depending on the measurement method used. The 16S rRNA gene sequencing fails to comprehensively reflect the community structure of MOB in the soil samples. Different geographical locations showed variations in MOB communities, and no specific indicator communities were detected for oil and gas reservoirs or background sites on a national scale. The correlation analysis between environmental factors and MOB revealed that the environmental factors had different effects on the absolute and relative abundance of MOB.

[Objective] To further understand the community structure, distribution, and ecological function differentiation mechanism of anammox bacteria in the groundwater of red soil areas. [Methods] We employed physical and chemical tests and high-throughput sequencing to study the microbial community structure, distribution of anammox bacteria, and their influencing factors in the groundwater of Ji'an. [Results] The nitrogen content exceeded the limit at three sites among the 11 groundwater sampling sites, with an over-limit rate of 27.3%. The water quality of only two sites met the requirements of the Standard for Drinking Water Quality (GB 5749—2022), which indicated an over-limit rate of 81.8%. Anammox bacteria presented wide distribution in groundwater, and the abundance ofhzsB gene in the 11 samples ranged from 3.67×10⁴ copies/g to 6.62×10⁸ copies/g. Compared with other habitats, the groundwater in red soil areas showed increased copy number of functional genes of anammox bacteria, which indicated that the environmental characteristics of groundwater were more suitable for the growth and metabolism of anammox bacteria. Four genera of anammox bacteria were detected at each site. Specifically,Candidatus Brocadia,Candidatus Scalindua,Candidatus Jettenia, andCandidatus Kuenenia showed the average abundance of 62.47%, 17.44%, 14.41%, and 5.67%, respectively. The correlation analysis suggested that the gene abundance of anammox bacteria was significantly correlated with ammonia nitrogen, manganese, and chloride, which indicated that the increases in ammonia nitrogen, manganese, and chloride in groundwater may enhance the activity and abundance of anammox bacteria. [Conclusion] The results of this study highlight the importance of anammox bacteria in the geochemical and biological cycling of elements in the groundwater of red soil areas, which will provide basic data for the bioremediation of groundwater pollution in the red soil areas of China.

Anabaena azotica, as a photoautotrophic microorganism, has good carbon and nitrogen sequestration abilities. The application ofA.azotica could improve soil fertility and reduce the application of chemical fertilizers. However, the mechanism of carbon and nitrogen sequestration in soil byA.azotica and the sequestration efficiency of different strains remain to be studied. Therefore, it is important to screenA.azotica strains and probe into the processes of C and N sequestration in soil by the strains at the single-cell level. In view of the complex and dynamic process of element changes inA.azotica at the single-cell level, this study introduced the carbon and nitrogen sequestration process in soil byA.azotica. In addition, we expounded the principle, progress, and difficulties of using nano-secondary ion mass spectrometry combined with stable isotopic probing (NanoSIMS-SIP) and Raman spectroscopy imaging combined with stable isotopic probing (Raman-SIP) to analyze the spatiotemporal distribution of carbon and nitrogen at the single-cell level. This review focuses on the latest technological development and application of single-cell stable isotope technology for quantitative visualization of carbon and nitrogen sequestration inA.azotica. At the same time, future research on the visualization technology is prospected. This review is of great scientific significance for understanding the mechanism of carbon and nitrogen sequestration and the difference in nitrogen fixation efficiency of differentA.azotica strains in soil. It provides a theoretical basis for reducing the use of chemical fertilizers and improving soil fertility in agricultural production.