Abstract:

Abstract:[Objective] To detail the molecular evolution and ecological adaptation of Pseudoalteromonas arabiensis. [Methods] Illumina HiSeq X Ten and Oxford Nanopore PromethION were used for the whole genome sequencing of Pseudoalteromonas 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 strain Pseudoalteromonas 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.

Abstract:[Objective] Coastal wetland ecosystems, situated at the interface of freshwater and seawater, are characterized by the seepage of groundwater with high Fe²⁺ concentrations into the surface layers of sediments, which forms wetland runoff. This runoff, combined with periodic tidal flooding, creates an oxic-anoxic interface conducive to the bio-oxidation of Fe²⁺ by Fe-oxidizing bacteria. However, there is a lack of comprehensive assessment of Fe-oxidizing bacterial communities in coastal wetland ecosystems. [Methods] We measured the basic environmental parameters such as the oxygen penetration depth in the sediments of five coastal wetland sites in Xisha Wetland Park in Chongming, Shanghai and Dongsha Beach in Zhujiajian Island in Zhoushan, Zhejiang. The community composition and distribution of bacteria and Fe-oxidizing bacteria were comprehensively deciphered by 16S rRNA gene amplicon sequencing. [Results] Dongsha Beach in Zhujiajian Island exhibited deeper oxygen penetration (reaching more than 10 mm) than Xisha Wetland in Chongming. The non-metric multidimensional scaling (NMDS) results indicated that the bacterial community structure was primarily influenced by environmental conditions that varied with geographical location, while the community structure of Fe-oxidizing bacteria was influenced by both the geographical location of the sampling sites and the oxygen penetration depth of the sediments. The dominant bacteria in Xisha Wetland and Dongsha Beach were Cyanobacteria, Gammaproteobacteria, Bacteroidetes, Alphaproteobacteria, and Actinobacteria. The dominant genera of Fe-oxidizing bacteria were Gallionella, Rhodobacter, Lepthothrix, and Sideroxydans. [Conclusion] We studied the Fe-oxidizing bacteria in the sediments of Xisha Wetland in Chongming and Dongsha Beach in Zhujiajian Island and discovered that the composition of Fe-oxidizing bacterial communities was closely linked to the oxygen penetration depth variations caused by different types of wetland sediments.

Abstract:Anabaena azotica, as a photoautotrophic microorganism, has good carbon and nitrogen sequestration abilities. The application of A. azotica could improve soil fertility and reduce the application of chemical fertilizers. However, the mechanism of carbon and nitrogen sequestration in soil by A. azotica and the sequestration efficiency of different strains remain to be studied. Therefore, it is important to screen A. 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 in A. azotica at the single-cell level, this study introduced the carbon and nitrogen sequestration process in soil by A. 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 in A. 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 different A. azotica strains in soil. It provides a theoretical basis for reducing the use of chemical fertilizers and improving soil fertility in agricultural production.

Abstract:[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 of hzsB 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, and Candidatus 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.

Abstract:[Objective] To compare the physicochemical properties and fungal community characteristics between rhizosphere soil and non-rhizosphere soil of Hippophae rhamnoides growing for different years in Pisha sandstone area of Inner Mongolia. [Methods] A total of 12 rhizosphere and non-rhizosphere soil samples were collected from the Pisha sandstone area of Ordos. Chemical methods were used to analyze soil physicochemical properties, and the fungal community composition in soil was analyzed by high-throughput sequencing. The correlations between fungal community characteristics and soil properties were analyzed. [Results] Total nitrogen (TN), available nitrogen (AN), available potassium (AK), organic matter (OM), and electrical conductivity (EC) of rhizosphere soil were higher than those of non-rhizosphere soil (P<0.05). Soil moisture content (SMC) increased as the planting years increased (P<0.05). The fungal richness and diversity in rhizosphere soil were higher than those in non-rhizosphere. Ascomycota and Mortierellomycota were the common dominant phyla in rhizosphere soil and non-rhizosphere soil, and Mortierella, Penicillium, and Aspergillus were the common dominant genera. The key fungal groups in non-rhizosphere soil and rhizosphere soil were Mortierella and Gibberella, respectively. The redundancy analysis showed that OM was a key soil factor affecting the soil fungal distribution. Mortierella was correlated with OM, AN, and total potassium (TK) (P<0.05). Gibberella was correlated with AN, OM, and EC (P<0.05). [Conclusion] The planting of H. rhamnoides in Pisha sandstone area of Inner Mongolia increases the nutrients and fungal richness in the rhizosphere soil, improving the stability of the soil environment. Moreover, the cultivation of H. rhamnoides increases the soil moisture, improving soil and water conservation and contributing to the ecological restoration. This study provides a theoretical basis for biodiversity conservation in the study area as well as for the ecological restoration and sustainable management of H. rhamnoides shrubland.

Abstract:The temperature and precipitation variations caused by global climate change have profoundly impacted soil microbial communities. Understanding the impacts of the variations on the structure and function of microbial communities over time is crucial for predicting and adapting to future climate changes. [Objective] To explore the variations in the diversity, composition, structure, and succession of bacterial communities in mollisol soil in the context of climate change. [Methods] Based on a long-term soil transplantation experiment platform of Hailun, Fengqiu and Yingtan Agroecosystem Field Experiment Stations of the Chinese Academy of Sciences, we translocated the mollisol soil from a cold-temperate region (Hailun) to a warm-temperate region (Fengqiu) and a mid-subtropical region (Yingtan) to simulate the increasing conditions of temperature and precipitation. We collected 63 mollisol soil samples from Hailun, Fengqiu, and Yingtan during 2005–2011. We employed high-throughput sequencing of the 16S rRNA gene to study the diversity, composition, and structure of soil bacterial communities under different temperature and precipitation conditions. With consideration to the soil physicochemical properties, we analyzed the relationship between environmental factors and microbial community characteristics and calculated the species turnover rate. [Results] After six years of transplantation of the mollisol soil from the cold temperate zone to warm temperate and mid-subtropical zones, significant changes occurred in soil physicochemical properties, including decreases in soil organic matter and total nitrogen, along with a noticeable reduction in aboveground biomass. Moreover, the bacterial diversity in the soil decreased, and significant changes occurred in the community composition and structure. The dominant bacteria included Verrucomicrobia, Proteobacteria, Acidobacteria, and Actinobacteria, among which Verrucomicrobia showed increased relative abundance after the soil transplantation to the warmer area Yingtan. Additionally, climatic factors were highly correlated with microbial community characteristics. The nonmetric multidimensional scaling analysis showed that the bacterial community structure evolved with changes in temperature and precipitation and over time, which was related to the increased microbial species turnover rate. The species turnover rates of bacterial communities varied significantly under different temperature and precipitation conditions, following an increasing trend of Hailun (0.030)[Conclusion] A six-year increase in temperature and precipitation significantly reduced the bacterial diversity, altered the bacterial community composition and structure, and accelerated the species turnover.

Abstract:[Objective] To study the population diversity, spatial distribution characteristics, and correlations with physicochemical factors of yeasts in the Napahai plateau wetland. [Methods] Yeast strains were isolated from the water samples of the Napahai plateau wetland by membrane filtration and plate culture. The strains were identified based on the D1/D2 sequences of the 26S rRNA gene and morphological characteristics. R 4.2.2 and Canoco 5 were used to analyze the yeast diversity and its correlations with physicochemical factors. [Results] A total of 565 yeast strains were isolated from the water bodies in the Napahai plateau wetland and identified as 36 species of 21 genera. The dominant species were Rhodotorula mucilaginosa, Meyerozyma guilliermondii, and Rhodotorula graminis. Total nitrogen was the main physicochemical factor affecting the yeast count, which presented a negative correlation. [Conclusion] The water bodies of Napahai plateau wetland harbor abundant yeast resources which present significant spatial heterogeneity. Human activities and total nitrogen have significant impacts on the yeast count. The yeast community composition in the water bodies of the Napahai plateau wetland is significantly different from that in other plateau freshwater lakes and has unique yeast resources that require further research.

Abstract:[Objective] Loess-paleosol sequence (LPS) is a good carrier recording the changes of Quaternary climate and environment, and the characteristics of soil microorganisms in it indicates important information about the changes of soil environment. Due to the climate difference between loess and paleosoil, the soil microbial community may have different responses in the structural characteristics. The research on this problem, however, is limited. [Methods] In this paper, the loess (RL and JL)-paleosol (RS and JS) sequences in Renjiapo (R) and Jiuzhoutai (J) were selected, and high-throughput sequencing and linear discriminant analysis effect size (LEfSe) were employed to gain insights into the community structure and group differences of soil prokaryotes. Furthermore, functional annotation of prokaryotic taxa (FAPROTAX) was used to predict the community function, and the Mantel test was carried out to identify the environmental factors affecting the community stability of soil prokaryotes. [Results] The carbon and nitrogen in soil showed changes consistent with the magnetic susceptibility and Rb/Sr ratio, the alternative indicators of climate change. The content of carbon and nitrogen was high in the paleosol (RS and JS, especially in RS) and low in the corresponding loess (RL and JL). In the same climate era, Jiuzhoutai was drier and colder than Renjiapo. The paleosol deposition stage in Jiuzhoutai was affected by strong winter monsoon, which ultimately led to the gradual change from the dry-cold to wet-warm climate. In the prokaryotic community, thermophilic or mesophilic bacteria and archaea, such as Acidobacteria, Crenarchaeota, and Chloroflexi, were abundant in RL and RS, while those with tolerance to drought and extreme environments, such as Gemmatimonadetes, Actinobacteria, Firmicutes, Euryarchaeota, and Deinococcus-Thermus, had high abundance in JL and JS. The functional genes related to energy source and nitrogen, manganese, iron, and chlorine cycling had the highest expression levels in RS, while those involved in carbon, hydrogen, and sulfur cycling showed the highest expression levels in RL. The prokaryotic community in Jiuzhoutai had higher species diversity and fewer functional species than that in Renjiapo. Mantel test results indicated that soil organic carbon (SOC), soil water content (SWC), total nitrogen (TN), and nitrate nitrogen (NO₃^--N) were the key environmental factors influencing the stability and functions of the prokaryotic community in Renjiapo, while the influencing factors in Jiuzhoutai were TN, SOC, pH, and ammonium nitrogen (NH₄⁺-N). [Conclusion] During the warm-humid period, the microbial community differentiated into more functional categories and exhibited more vigorous life activities. When the climate was dry and cold, the microbial community completed the main life activities by improving species diversity and jointly maintaining the community survival and stability to adapt to environmental stress. The findings are of great significance for understanding the impacts of climate change on the diversity and functions of soil microorganisms.

Abstract:Soil viruses are the most abundant biological entities on Earth. They play important roles in the regulation of host dynamics and soil ecosystem, including microbial diversity, community composition, and element cycling. However, due to the tremendous complexity of the soil ecosystem, the incredible functions of soil viruses and the underlying functioning mechanisms remain largely unexplored and represent a hot topic and frontier in soil biology, microbial ecology, and environmental science. The recent advances in molecular biotechnology and the widespread application of ecological theories have significantly boosted the research on soil viruses. To provide a comprehensive overview of the state-of-the-art knowledge of soil virology, we conducted a literature review using bibliometric methods. This paper offers an overview of the current status and hotspots in soil virus research, shedding light on the development in this field. Taking into account the characteristics of soil environments, the study presents the future prospects for soil virus research, including the diversity, biological characteristics, environmental factors, mechanisms, and applications of soil viruses. With the interdisciplinary integration and advancements in research technologies, soil virus research is experiencing rapid growth. The noteworthy achievements in nutrient cycling, ecosystem services, and biological regulation through soil virus research can contribute to soil health and carbon neutrality initiatives.

Abstract:[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 including Thermoplasmata, Methanosarcinia, and Methanobacteria 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 of Thermoplasmata was generally higher in the plume, whereas ammonia-oxidizing archaea and Methanosarcinia 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.

Abstract:[Objective] Currently, there are few studies on microorganisms in Antarctic ice cores, and the available studies mostly employ the pure culture and high-throughput sequencing methods, with limited knowledge about the microbial diversity. We studied the microbial community composition of the meltwater at -183 m depth of the Dalk Glacier in eastern Antarctica, aiming to provide a reference for the development of extremophiles in Antarctica. [Methods] we employed the culture, single-cell sorting, and high-throughput sequencing methods to study the microbial community composition in the meltwater at -183 m depth of the Dalk Glacier. [Results] We obtained bacterial isolates belonging to 94 genera, 19 orders of 10 phyla, in which Proteobacteria, Alphaproteobacteria, and Sphingomonas were the dominant phylum, order, and genus, respectively. This result indicated high microbial diversity in the meltwater. The culture, single-cell sorting, and high-throughput sequencing yielded 25 bacterial strains, 24 bacterial strains, and 55 183 sequences (116 operational taxonomic units), respectively. The dominant taxa were different among the three methods. By the culture and single-cell sorting methods, we identified 7 bacterial strains with the 16S rRNA gene identity less than 98.65% compared with their closest relatives in GenBank, of which two strains had the identity less than 95.00% identity. Accordingly, we inferred that there may be two potential new genera and five potential new species. [Conclusion] We studied the microbial diversity in the meltwater of the Dalk Glacier in eastern Antarctica by using the culture, single-cell sorting, and high-throughput sequencing method and discovered rich bacterial species in the meltwater. Each method has its own advantages and limitations. This means that when studying microbial diversity, more comprehensive information about the composition of the microbial community can be obtained by combining different methods. The results of this study can serve as a reference for further research on the genetic resources in Antarctica.

Abstract:[Objective] To isolate efficient phosphorus-solubilizing strains from soils in the permafrost region of the Qinghai-Xizang Plateau and provide strain resources for the activation of unavailable phosphorus in the soil of the Plateau. [Methods] The selective media with organic and inorganic phosphorus were used to isolate phosphorus-solubilizing strains from the soil samples collected in the permafrost region around the Tanggula Pass of the Qinghai-Xizang Plateau by the plate streaking method. The phylogenetic tree was built based on the 16S rRNA gene sequences to identify the strains, and then the phosphorus-solubilizing abilities and stress tolerance of the strains were determined. [Results] Five strains belonging to Pseudomonas were isolated, including three inorganic phosphorus-solubilizing strains (i5, i6, and i9L) and two organic phosphorus-solubilizing strains (Qb and Qo). After 7 days of incubation in shake flasks at 30 ℃, the content of available phosphorus in the supernatants of Qb and Qo was 534.8 mg/L and 723.7 mg/L, respectively, which was significantly higher than that (166.9–210.5 mg/L) in the supernatants of i5, i6, and i9L. The available phosphorus content in the supernatant of Qo was the highest (519.7–683.0 mg/L) among the five isolates under different concentrations of PEG6000. The phosphorus-solubilizing abilities of Qb and Qo were stronger than those of the other strains at 5 ℃ and 10 ℃. [Conclusion] Qo outperformed the other strains in terms of tolerance to low temperature and drought stress, serving the development of microbial fertilizers and vegetation restoration in alpine regions such as the Qinghai-Xizang Plateau.

Abstract:Yuncheng Salt Lake, located in the southwest of Shanxi Province, has a long history and unique climatic and geographical features, harboring rich microbial resources. The soil ecosystem is of great significance for understanding the diversity and functions of bacteria in the saline-alkali soil. [Objective] To explore the diversity of bacteria in the soil and sediment of Yuncheng Salt Lake, analyze its influencing factors, and provide a scientific basis and reference for the sustainable management of saline-alkali soil ecosystems and the mining of pure cultures. [Methods] Eighteen soil samples were collected from six sampling sites of Yuncheng Salt Lake. We measured the soil physicochemical properties and carried out high-throughput sequencing of the 16S rRNA gene to analyze the impact of environmental factors on bacterial diversity. [Results] Pseudomonadota, Bacteroidota, and Bacillota were the dominant bacteria in the soil of Yuncheng Salt Lake. The bacterial diversity and community composition showed significant differences among different sampling sites. The results of canonical correlation analysis indicated that total dissolved solids (TDS), total nitrogen (TN), total carbon (TC), and SO₄^2- had the greatest impacts on soil microbial diversity, followed by Na⁺, Ca²⁺, Cl^-, available phosphorous (A-P), and pH. HCO₃^-, nitrate nitrogen (NO₃^--N), ammonia nitrogen (NH₄⁺-N), K⁺, and Mg²⁺ had mild impacts on the diversity. [Conclusion] The soil microorganisms of Yuncheng Salt Lake had high diversity which was closely related to environmental factors. This study provides comprehensive biological information on the bacterial resources in the soil of Yuncheng Salt Lake, offering a theoretical basis for the exploration and research of bacterial resources in this lake.

Abstract:[Background] Yuncheng Salt Lake is a high-salt environment with intensive human activities. The community structure and ecological diversity of bacteria in Yuncheng Salt Lake are similar to those in other salt lakes while having their particularities. [Objective] Yuncheng Salt Lake is rich in color and harbors abundant halophilic and salt-tolerant microorganisms. To understand the distribution of bacterial resources in Yuncheng Salt Lake, we measured the bacterial diversity and community structures in different areas of this lake. [Methods] We employed 16S rRNA gene amplicon sequencing to study the community structures of halophiles in different areas of Yuncheng Salt Lake and predicted the potential metabolic functions of the bacteria. [Results] The dominant bacteria varied in different areas of Yuncheng Salt Lake. Specifically, Pseudomonadota, Actinobacteriota, and Bacteroidota were dominant in the central lake, Bacillota in the eastern lake, and Patescibacteria in the western lake. The bacterial diversity in the central lake area with light yellow water was significantly higher than that in the eastern and western lake. However, the bacterial diversity was low in the central lake area with red water. This result indicated that the bacterial distribution was different in the central lake areas with different water colors the metabolic pathway activity of bacteria in the salt lake and strong regional distribution. The microbial metabolism in the east and west lake was more active than that in the lake. [Conclusion] Bacteria show high diversity in Yuncheng Salt Lake. The environment in different of lake influence the community structure of bacteria. This study provides a theoretical basis for the diversity conservation, development, and utilization of the bacterial resources in Yuncheng Salt Lake.

Abstract:As an interdisciplinary subject combined with deep space exploration, astrobiology studies the habitability of extraterrestrial planets by the analogical study of the extreme environments on Earth, the exploration of carrier information of ancient life, and simulation. Notably, suitable environmental conditions are crucial for evaluating the habitability of planets. Recently, a large number of lava landforms suspected of lava tubes have been found on the Moon and planets such as Mars. These giant tube-shaped underground spaces may provide shelters for life to survive in consideration of the relative stable temperature inside and the function of radiation protection. Therefore, the analogical studies based on lava tubes on Earth can provide fundamental clues for exploring the traces of extraterrestrial life. Here, we review the microbial studies about the lava tubes on Earth, the implications of microbial metabolism of trace gas for astrobiology, and the recent progress in astrobiology, aiming to provide ideas for astrobiological research on lava tubes on Earth and other planets.

Abstract: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, Bacillus subtilis 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.

Abstract:[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] Wecollected 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 isolated Bacillus 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 indigenous B. velezensis B6 can significantly improve the oil recovery and well paraffin removal, with great application potential.

Abstract:[Objective] To study the effect of hydrogen peroxide (H₂O₂) treatment on biogas production of vitrinite from coal. [Methods] Shengli lignite collected from Inner Mongolia was used in this study. The methanogenic microbial consortium previously enriched and preserved in our laboratory was used as the inoculum. Coal macerals were separated by floatation, which yielded three samples containing high vitrinite (GJ), medium vitrinite (ZJ), and low vitrinite (DJ). After being characterized, the samples were treated with 10% H₂O₂ for 30 days at a solid-to-liquid ratio of 1:15. Biogas production experiments were conducted with the coal samples before and after treatment. Gas chromatography was employed to analyze the gas composition, and X-ray diffractometry and Fourier transform infrared spectroscopy were employed to study the physical and chemical properties of the coal before and after treatment as well as after gas production.[Results] The coal samples after H₂O₂ treatment showcased reduced vitrinite content and carbon fixation and increased volatile matter. The reaction was more intense in the coal sample with high content of vitrinite, accompanied by increased oxygen content and reduced carbon. Methane yields from untreated coal samples on day 100 followed the order of GJ (174.24 μmol/g coal)＞ZJ (164.31 μmol/g coal)＞DJ (135.52 μmol/g coal). However, the coal samples pretreated with H₂O₂ ceased gas production after day 20, with the gas yields of 39.63, 39.61, and 41.55 μmol/g coal, respectively, representing reductions of 77.26%, 75.89%, and 69.34%, respectively, compared with those from the coal samples without treatment. Furthermore, as vitrinite content increased, the coal samples demonstrated decreased layer spacing (d₀₀₂) of the aromatic ring lamellae, ductility (L_a) of the single-layer lamellae, and stacking degree (L_c) of the lamellae and increased number of aromatic layers (N) after H₂O₂ treatment, which indicated that the crystal nuclei appeared smaller. In addition, H₂O₂ treatment led to increased proportions of aromatic carbons, aromatic moieties, C=O groups, and C=C groups, enhanced aromatic ring condensation, and increased number of oxygen-containing functional groups. [Conclusion] Long-term H₂O₂ treatment reduces organic matter that is readily bioavailable in coal matrix, thereby decreasing gas production.

Abstract:[Objective] To investigate the effects of hydrogen peroxide treatment on the physicochemical properties and biogas production of lignite. [Methods] We carried out orthogonal experiments to optimize the conditions of hydrogen peroxide pretreatment for Shenli No.5 lignite. Lignite was treated under the optimal conditions to obtain coal residues and treatment solutions. The physicochemical properties, including elemental and maceral composition, mineral components, microcrystalline structure, porosity, permeability, surface morphology, organic functional groups, and organic composition in the treatment solution were determined by X-ray diffraction (XRD), scanning electron microscopy (SEM), brunauer-emmett-teller (BET), gas chromatography-mass spectrometry (GC-MS), and high-performance liquid chromatography (HPLC). The physicochemical properties were then compared among the raw coal, treated residue, and treatment solution. [Results] The optimal pretreatment conditions of lignite were treatment with 5.0% hydrogen peroxide at a liquid-to-solid ratio of 30:1 for 20 days, under which the total organic carbon yield in the treatment solution was 105 mg/L. After treatment under these optimal conditions, the treated residue exhibited increased cracks and dents on the surface and loosened surface structures. In addition, the interlayer spacing of the aromatic plains of the coal increased while the aromatic ring structure became more open with smaller crystal nucleus structures. Both porosity and specific surface area increased after the treatment. Compared with that before treatment, the treated residue showcased decreased fixed carbon, carbon, and vitrinite and increased ash, volatile matter, oxygen and hydrogen, and inertinite. The content of functional groups such as O=C-O, C=C, and C=O increased in the treated residue, while that of N-H and C-H reduced. The biogas production of the treatment solution and the treated residue was 39.13% and 94.46%, respectively, lower than that of raw coal. Hydrogen peroxide pretreatment primarily acted on vitrinite, dissolving organic carbon and altering the functional groups of large molecular structures in coal. This altered the aromatic ring structure of coal, causing small molecules to dissolve into the treatment solution under oxidative conditions. The organic compounds in the treatment solution mainly consisted of short-chain fatty acids. After biogas production, the number of low-molecule-weight acids and organic compounds decreased in the treatment solution. The relative abundance of dominant microbial phyla and genera varied significantly among different microcosms. Regarding the archaea for biogas production, the dominant phylum and genus were Halobacteriota and Methanosarcina in the raw coal and Thermoproteota and Bathyarchaeia in the treatment solution, respectively. In terms of the bacteria for biogas production, the dominant phylum and genus were Actinomycetota and Gaiellales in the raw coal and Pseudomonadota and Delftia in the treatment solution, respectively. [Conclusion] The organic carbon dissolved from coal can be utilized by microorganisms for biogas production. However, the removal of organic components by over-oxidation may decrease the biogas production.

Abstract:[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) for pmoA and sequencing of bacterial 16S rRNA gene and pmoA. 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 SO₄^2- (6 425.0 mg/g) and Cl^- (1 617.0 mg/g). The qPCR results revealed that the pmoA 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, and Methylococcus) 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 of pmoA revealed that Methylocystis and Methylosinus, two genera of type II MOB, were dominant. The absolute abundance of MOB showed significant correlations with ammonium nitrogen, pH, particle size, SO₄^2-, 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 gene pmoA 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.

Abstract:[Objective] Microbial prospecting for oil and gas, characterized by high resolution, high signal-to-noise ratio, minimal environmental interference, low costs, and short time consumption, garners increasing attention from exploration experts. However, in most cases, microbial prospecting is based on laboratory culture and analysis, which cannot accurately and comprehensively reflect the in-situ dynamic changes of microbiota in oil and gas resources in the geological history. In this study, we compared the microbial community structure and developmental characteristics between the gas-producing zone and the background zone in Hangjinqi Gas Field, aiming to identify the surface microbial anomalies related to oil and gas. [Methods] We conducted the bacterial 16S rRNA gene sequencing for the soil samples collected from Xinzao and Shiguhao areas of Hangjinqi. Furthermore, we compared the microbial diversity, analyzed the impacts of physicochemical parameters on microbial distribution, and identified microbial anomalies. The co-occurrence network analysis was employed to explore the assembly process and functional composition of microbial community in the surface soil above the reservoir.[Results] In the Hangjinqi area, Actinobacteria and Proteobacteria were dominant, accounting for 72.47% of the total microbial abundance. The correlation analysis of environmental factors with microbial abundance showed that the distribution of microorganisms in this area was not significantly correlated with environmental factors. The microbial community structure presented significant differences between the gas-producing area and the background area. The co-occurrence network analysis of the gas-producing area revealed non-randomness and connectivity in the microbial community, indicating deterministic factors play a dominant role in the construction of microbial communities. Modular co-occurrence network analysis revealed the formation of specific functional modules within the microbial community, and different modules possibly served different functions. [Conclusion] By comparing the microbial diversity between the gas-producing and background area of Hangjinqi area, we identified the indicator genera in the gas-producing fields of Xinzao and Shiguhao. Furthermore, the co-occurrence network analysis identified Gemmatimonas, Solirubrobacter, Pseudonocardia, Brevibacillus, Aeromicrobium, and Nocardioides as the key taxa in the gas-producing area, which were associated with the main functional modules of carbon and nitrogen cycling and organic matter degradation, contributing to the degradation of hydrocarbons in the surface soil of the gas-producing area.

Abstract:[Objective] To study the variations of soil fungal diversity in the coal mine residue hills with vegetation restored for different years.[Methods] We selected the soil on the coal mine reside hills of Jiangcang Mine with different planting years (2, 4, and 6 years) as the research object, measured the soil chemical property and enzyme activity, and used high-throughput sequencing methods to measure the soil fungal diversity. [Results] As the duration of restoration increased, significant differences were observed in soil pH, total potassium, and organic matter. The activities of enzymes such as sucrase, urease, catalase, and phosphatase gradually increased, which enhanced the fungal richness and diversity in soil. The variations were more obvious after four years of restoration. The fungi were primarily dominated by Ascomycota and Basidiomycota, with saprophytic fungi accounting for 43.2%–89.7%. Nitrogen content and soil enzyme activity were the key factors influencing fungal diversity in the grasslands of the coal mine area in Jiangcang. [Conclusion] Vegetation restoration can improve the chemical properties and fungal diversity in soil.

Abstract:[Objective] Ectomycorrhizal fungi can shape the bacterial community in the ectomycorrhizosphere, which represents an important way to mobilize and acquire insoluble mineral elements from the soil. This study aims to investigate the composition and phosphate-solubilizing characteristics of the dominant phosphate-solubilizing bacteria (PSB) in the ectomycorrhizosphere of Castanea henryi. [Methods] The transparent halo method was employed to isolate PSB from the ectomycorrhizosphere of C. henryi. The strains were identified by 16S rRNA gene sequencing. The degradation abilities of the strains for tricalcium phosphate (TCP) and apatite were studied by liquid fermentation. A scanning electron microscope and a X-ray diffractometer were used to observe the appearance and crystal structures of the degradation products. [Results] Five highly efficient strains of PSB were isolated from the ectomycorrhizosphere of C. henryi. Strains LSCh1, LSCh2, and LSCh5 were identified as Burkholderia lata, and strains LSCh3 and LSCh4 were identified as Paraburkholderia sp. The degradation abilities of the strains for TCP followed the trend of LSCh3 (556.94 mg/L)＞LSCh2 (206.91 mg/L)＞LSCh1 (170.83 mg/L)＞LSCh5 (55.16 mg/L)＞ LSCh4 (14.21 mg/L). The degradation abilities of the strains for apatite were in a descending order of LSCh2 (51.33 mg/L)＞LSCh1 (43.51 mg/L)＞LSCh3 (40.99 mg/L)＞LSCh5 (1.11 mg/L)＞ LSCh4 (1.00 mg/L). [Conclusion] Strain LSCh3 showed good performance in degrading both TCP and apatite and induced the formation of carbonates. It is a plant growth-promoting bacterium with potential application values in improving the phosphorus nutrients of plants and the quality of soil.

Abstract:Endophytic bacteria in the roots of a healthy plant not only form a symbiotic relationship with the host plant but also promote plant growth and enhance plant uptake of nutrients, being of importance for maintaining terrestrial ecological balance and improving the comprehensive management of karst rocky desertification. [Objective] To explore the endophytic bacterial communities in the roots of host plants and provide a theoretical basis for deeply understanding the interaction mechanisms between host plants and endophytic bacteria. [Methods] The community structures of endophytic bacteria and physicochemical properties of rhizosphere soil of Cerasus humilis (Bge.) Sok. introduced for the control of rocky desertification in the karst graben basin with different years were studied. [Results] Planting years of C. humilis had a direct and significant influence on the rhizosphere soil quality and an indirect effect on the bacterial community in the roots. The endophytic bacterial community was mainly characterized by symbiotic interactions. The top three dominant bacterial genera identified by the co-occurrence network in the first year and third year were Streptomyces, Burkholderia-Caballeronia-Paraburkholderia and Chitinophaga, and the top three dominant bacterial genera in the fifth year were Streptomyces, Chitinophaga and Haliangium, which had biocontrol effects. The endophytic bacterial community was shaped by stochastic ecological drift processes. [Conclusion] The differences of endophytic bacterial communities along the planting year gradient are due to the microbial diversity endowed by stochastic processes. The interactions among endophytic bacteria and the dominant bacteria with biocontrol effects could promote the colonization and growth of C. humilis, thereby enhancing the ecological and economic benefits of C. humilis for the comprehensive control of rocky desertification in the karst graben basin.

Abstract:[Objective] To reveal the dynamic changes of soil microbial community and nutrient cycling process in the artificial grass squares dominated by pioneering plants such as Leymus secalinus and Carex praeclara in the alpine sandy land. [Methods] Metagenomic sequencing and qPCR were performed for the structure analysis, functional gene annotation, and absolute abundance determination of soil microbial communities, which were combined with soil physico-chemical factors for redundancy analysis. [Results] The artificial establishment of grass squares increased the total nitrogen by 20%–68%, available phosphorus by 10%–247%, and organic carbon by 19%–56% in sandy soils. Furthermore, it increased the bacterial and fungal abundance by 17%–81% and 2%–95%, respectively. Specifically, it increased the relative abundance of plant growth-promoting bacteria, such as Sphingomonas, Bradyrhizobium, Nitrospira, Solirubrobacter, and Nocardioides. Furthermore, the artificial establishment of grass squares enriched the amoCAB gene cluster and the nxrAB gene cluster associated with ammonia oxidation and nitrite oxidation in the nitrogen cycle. In addition, a genetic signature for complete ammonia oxidation was identified. [Conclusion] The artificial establishment of grass squares increases the content of soil nutrients and microbial abundance and promotes the nutrient cycling in alpine sandy areas. Moderate grazing can increase the diffusivity of nitrogen sinks and promote the colonization of native pioneer plants in the sandy ecosystem. The findings provide theoretical references for future restoration of sandy ecosystems in similar high-altitude areas.

Abstract:[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, by Shewanella 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.

Abstract:[Objective] To investigate the removal efficiency and mechanism by a strain of Rhodotorula. [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 as Rhodotorula 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.

Abstract: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 to Aquabacter of Xanthobacteraceae and named as Aquabacter 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 of Aquabacter 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.

Abstract:[Objective] Bio-inspired artificial mineral shells are used to protect living bacterial cells. [Methods] Bacterial cells were encapsulated in firm and intact mineral shells, where the limited physical space and substance exchange induced the dormancy of living bacteria to decrease the viability loss during long-term preservation and even in extreme environments. Moreover, acids can erode the shells to reactivate the bacteria. [Results] Compared with the un-mineralization treatment (EcN), the mineralization treatment (EcN@CaCO₃) increased the bacterial viability by a maximum of 262 folds in a 32-day storage experiment and the survival rate by 837, 171, 59.1, and 729.7 folds at pH 2.5, pH 12.0, 80 ℃, and in the presence of an antibiotic, respectively. [Conclusion] We employed biomimetic mineralization to improve the stability of bacterial cells in storage, which can provide a research basis for the application of microorganisms in environmental engineering, food production, and biomedical engineering.