[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 ofCastanea henryi. [Methods] The transparent halo method was employed to isolate PSB from the ectomycorrhizosphere ofC.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 ofC.henryi. Strains LSCh1, LSCh2, and LSCh5 were identified asBurkholderia lata, and strains LSCh3 and LSCh4 were identified asParaburkholderia 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.

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.

[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 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] 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.

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, andBacillota 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 SO₄²⁻ 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.

[Objective] To reveal the dynamic changes of soil microbial community and nutrient cycling process in the artificial grass squares dominated by pioneering plants such asLeymus secalinus andCarex 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 asSphingomonas,Bradyrhizobium,Nitrospira,Solirubrobacter, andNocardioides. Furthermore, the artificial establishment of grass squares enriched theamoCAB gene cluster and thenxrAB 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.

[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 asAcidobacteria,Crenarchaeota, andChloroflexi, were abundant in RL and RS, while those with tolerance to drought and extreme environments, such asGemmatimonadetes,Actinobacteria,Firmicutes,Euryarchaeota, andDeinococcus-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.

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 ofCerasus humilis (Bge.) Sok. introduced for the control of rocky desertification in the karst graben basin with different years were studied. [Results] Planting years ofC.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 wereStreptomyces,Burkholderia-Caballeronia-Paraburkholderia andChitinophaga, and the top three dominant bacterial genera in the fifth year wereStreptomyces,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 ofC.humilis, thereby enhancing the ecological and economic benefits ofC.humilis for the comprehensive control of rocky desertification in the karst graben basin.

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.