Abstract:环境微生物学是一门研究微生物与其生活环境之间相互作用的科学，主要包括环境中的微生物和微生物在环境中的作用两大研究领域。《微生物学通报》本期推出的“环境微生物学主题刊”报道了研究报告21篇，内容涵盖环境微生物学研究前沿、环境微生物生态学及生物修复、环境微生物资源的发掘与利用、环境微生物生理学及生物制剂、环境污染修复与微生物多样性等领域，希望该主题刊的出版有助于促进我国环境微生物学领域的学术交流，推动我国环境微生物学学科的发展。

Abstract:Since Roche launched the first commercial next-generation DNA sequencer in 2005, high-throughput sequencing-based metagenomic approaches have been widely employed to analyze the composition and functions of microbial communities in various environments, revealing numerous novel species, genes, enzymes, and metabolic processes within environmental microbiomes. The relevant work indicates that uncultured microorganisms play crucial roles in driving biogeochemical cycles and promotes theoretical breakthroughs and technological innovation in areas such as pollutant degradation, environmental remediation, biotechnology, and natural pharmaceutical development. This review comprehensively discusses the applications and progress of metagenomics in environmental microbiome, focusing on four aspects of discovery including new species, functional genes (clusters), metabolic pathways, and Microorganism-Environment-Performance (M-E-P) nexus, and prospects the future research.

Abstract:Lignin is a heterogeneous aromatic biopolymer composed of diverse aromatic monomers linked by various types of chemical bonds, which make the efficient degradation and cost-effective transformation of lignin a formidable global issue. Recent studies have discover unique non-specific redox systems inherent in microorganisms and the metabolic capacity of microorganisms for degrading aromatic compounds, shedding light on lignin valorization. Given that most of lignin-derived aromatic monomers contain methoxy groups, demethylation emerges as a rate-limiting step in the metabolism of these compounds. This review offers an extensive summary of the latest studies about the biological and enzymatic mechanisms of demethylation during the biodegradation of lignin. Meanwhile, by examining exemplary studies on lignin valorization with novel aromatic demethylases, this paper highlights the pivotal role of understanding microbial demethylation mechanisms and mining new demethylases in lignin degradation and transformation.

Abstract:Bacterial surface display is an important biotechnology that involves expressing exogenous target proteins, peptides, or other biomolecules on the surface of bacterial cells to better realize their functions. This technology has been applied in various fields such as biocatalysis, bioremediation, biosensors, and vaccine design. This article first introduces the surface display systems of both Gram-negative and Gram-positive bacteria and summarizes the main host bacteria and anchored proteins currently known. It then reviews the latest research progress in the applications of bacterial surface display in bioremediation. Finally, this paper summarizes the limitations of bacterial surface display in application and makes an outlook on the future research directions, aiming to expand the specific applications of this technology in bioremediation practice.

Abstract:The black soil in northeast China is facing the threat of continuous deterioration. The carbon cycle plays a critical role in the maintenance of soil fertility and productivity in farmland, where microorganisms regulate the carbon balance in soil. This review summarizes the distribution, characteristics, and degradation of black soil. Firstly, it describes the transformation pathways and community composition of carbon-fixing microorganisms in the black soil in farmland. These microorganisms employ six pathways to fix carbon. The high-throughput sequencing with the carbon fixation gene cbbL as the probe reveals that the carbon-fixing microorganisms in the black soil of northeast China mainly belong to Proteobacteria and Cyanobacteria. Secondly, the review discusses the effects of tillage systems, fertilization, straw return, and freezing-thawing on microbial carbon fixation in black soil. Finally, the contributions of carbon-fixing microorganisms to agriculture and the environment are expounded from increasing crop yields, reducing agricultural non-point source pollution, and reducing greenhouse gas emissions. While these microorganisms are crucial for nutrient recovery and crop yield improvement, research remains to be carried out. The protection and utilization of black soil necessitates a deeper understanding of the microbial resources involved in carbon fixation. Interdisciplinary studies should be carried out to reveal the ecological processes and function and structure changes of these microorganisms, and a black soil management scheme focusing on microbial carbon cycling should be formulated for the protection and utilization of black soil.

Abstract:Plant endophytes as indispensable components of plant microcosms are the major part of the plant microbial community. They inhabit plant tissues or tissue gaps, and most of them promote plant growth via different pathways. The plant endophyte community is characterized by diverse species and a complex structure. Beneficial endophytes can promote plant growth, enhance plant resistance, and produce valuable secondary metabolites. By reviewing the articles about the research methods for endophyte resources, we explored the relationship between plant endophytes and host plants, the diversity of endophytes, the research methods for isolation and colonization, and the roles and functioning mechanisms of endophytes in host plants. Furthermore, we make an outlook on the trend of new technologies in the research on plant endophytes, aiming to provide a theoretical reference for the application of plant endophytes.

Abstract:[Background] A large number of black-headed gulls (Chroicocephalus ridibundus) overwinter in Kunming and have close contact with people. Whether their fecal bacteria can be a source of infections or not arouses public concern. [Objective] To explore the potential pathogenic bacteria, antibiotic resistance genes (ARGs), and virulence factors (VFs) in the feces of C. ridibundus. [Methods] Firstly, the bacteria in the feces were isolated and identified, and the antibiotic resistance of some potential pathogens was examined. Secondly, metagenomic sequencing was employed to detect the potential pathogens, ARGs, and VFs in the feces. [Results] Enterococcus faecalis, Aeromonas veronii, and Shigella flexneri were the main potential pathogenic bacteria detected by the isolation method, and Escherichia coli, Escherichia albertii, and Enterococcus faecium were the main potential pathogenic bacteria detected by metagenomic sequencing. These bacteria were frequently detected in the intestines of other animals and humans. Some isolated potential pathogenic bacteria were resistant to few antibiotics. The ARGs and VFs detected through metagenomic sequencing were abundant and had rich sources in addition to potential pathogenic bacteria. However, the ARGs receiving clinical concerns were not detected with high identity and coverage. In addition, some potential pathogenic bacterial genera and ARGs had high associations between the feces and the water in the Dianchi Lake. [Conclusion] No pathogenic bacteria belonging to the risk group II (China) or the ARGs arousing clinical concern were detected in the feces of C. ridibundus. Therefore, we conclude that the bacteria from the feces of C. ridibundus do not pose an infection threat to healthy people.

Abstract:[Background] A large amount of Chinese medicine residues is produced every year in China, which not only wastes medicinal materials but also causes environmental pollution. Semipermeable membrane aerobic composting of Chinese medicine residues is an effective method to address the solid waste and realize the regeneration value and sustainable development of Chinese medicine waste resources. [Objective] To explore the composting process and the suitable C/N ratio of Chinese medicine residues for fermentation, and reveal the relationship between functional microorganisms and composting process based on the changes of microbial community structure during the composting process. [Methods] Chinese medicine residues were composted with cow dung as the auxiliary materials, and the 16S rRNA gene high-through sequencing was employed to disclose the succession of microbial community structure during the composting process. The temperature, C/N ratio, moisture content, pH, NH₄⁺-N, total nutrients, and seed germination index were measured, and their relationship with the changes of functional microorganisms was explored. Furthermore, the Chinese medicine residue fertilizer was applied to the seeds of the medicinal plants Isatis indigotica and dandelion, and the seed germination was examined to verify the performance and safety of the fertilizer. [Results] The high-temperature period of Chinese medicine residue composting with a C/N ratio of 25 exceeded 7 days. With the extension of fermentation time, the moisture content significantly decreased and the pH gradually increased. The obtained fertilizer showed the NH₄⁺-N content of 78.8 mg/kg (<400 mg/kg), total nutrient content of 5.48% (>5%), and the germination index (GI) reaching 161.34%, which met the standards of organic fertilizer fermentation. The composting performance of Chinese medicine residues with the C/N ratio of 25 was better than that with the C/N ratios of 20, 30, and 35. During the high-temperature fermentation of the pile, Lysinibacillus and unclassified_f__Rhizobiaceae were the dominant bacteria and Mycothermus and Aspergillus were the dominant fungi. Moreover, the obtained fertilizer promoted the seed germination of I. indigotica and dandelion. [Conclusion] The results of this study not only provide a theoretical basis for further research on the mechanism of microbial compost and different types of Chinese medicine residue compost, but also provide a reference for solving the problem of effective resource utilization of Chinese medicine waste, and expand the application of semi-permeable membrane aerobic compost process in the field of environmental pollution control.

Abstract:[Background] The vertical distribution of bacterial communities impacts the formation and nutrient cycling of paddy soils, while the assembly and functional characteristics of bacterial communities in different soil genetic horizons remain unclear. [Objective] To explore the characteristics and functional differences of bacterial communities in different paddy soil genetic horizons and reveal the driving mechanism of bacterial community assembly in each horizon. [Methods] The reddish clayey paddy soil was excavated and profiled, and soil samples were collected from different soil genetic horizons. The bacteria in each horizon were analyzed by high-throughput sequencing. [Results] The α diversity of the bacterial community in the cultivated horizon (Ap1, 0−19 cm) was significantly higher than that in the other horizons. The β diversity analysis showed that the bacterial community structure was significantly different among different horizons. The relative abundance of Chloroflexi and Acidobacteriota decreased with the increase in soil depth, while that of GAL15 and Desulphurvibrio showed the opposite trend. As the soil horizon deepened, the relative abundance of Methylomirabilota and Nitrospirota first increased and then decreased, while that of Proteobacteria first decreased and then increased. Available phosphorus and soil organic matter significantly improved bacterial diversity in the soil, and soil organic matter, total potassium, and nitric nitrogen were the main environmental factors affecting the bacterial community assembly. The TaxFun2 analysis showed that there were significant differences in bacterial community functions among different soil horizons, with stronger metabolism in Ap1 (0−19 cm), Ap2 (20−30 cm), and BrC (95−112 cm) horizons and weaker metabolism in the Br horizon (31−94 cm). Surface soil and the soil close to the parent material had more unique bacterial taxa than other soil horizons. Both the bacteria taxa with high relative abundance and those with low relative abundance played a role in the bacterial network connectivity, and deterministic processes dominated the bacterial community assembly of the soil profile. [Conclusion] There are significant differences in the structure and function of bacterial communities of the reddish clayey paddy soil profile, and deterministic processes dominate the bacterial community assembly.

Abstract:[Background] The abundance of airborne microbes in urban environments, as well as their community composition, dispersion and transmission, are influenced by diverse factors such as regional environmental and meteorological conditions, which have profound impacts on the urban environmental security and the health of local residents. [Objective] To investigate the spatiotemporal distribution characteristics of the abundance and community composition of airborne bacteria and fungi in different urban functional zones and administrative districts of Xiamen in Fujian, explore the main influencing factors of the spatiotemporal distribution of airborne microbes, and evaluate the potential risks of pathogens. [Methods] This study employed a large-capacity sampler to collect bioaerosol samples from several urban functional zones of Xiamen in the summer of 2021 and the winter of 2022. Real-time quantitative PCR was employed to study the absolute abundance of airborne bacteria and fungi in different functional zones and administrative districts, and their correlations with environmental factors were analyzed; The composition of bacterial communities in Xiamen Island and Tongan district was analyzed by metagenome sequencing, and the risk of potential pathogens was evaluated. [Results] The bacterial absolute abundance was different between winter and summer (P<0.001), with the that in winter (average 2.17×10⁵ copies/m³) being approximately one order of magnitude higher than that in summer (average 3.18×10⁴ copies/m³). The bacterial absolute abundance was the lowest in the parks and the highest in the industrial areas. The fungal absolute abundance showed no significant difference between the winter and summer, with that in summer (average 4.24×10³ copies/m³) being higher than that in winter (average 8.95×10² copies/m³), and the lowest was observed in the parks. In summer, the absolute abundance of bacteria and fungi were the highest in Tongan district, which was significantly different from those in the other three administrative districts. In winter, Xiamen Island had the lowest average bacterial absolute abundance and the highest fungal absolute abundance, which showed significant differences from those in other three administrative districts of Xiamen. Within different radius ranges of sampling sites, the proportion of green space had a correlation (P<0.01) with bacterial absolute abundance. The bacterial absolute abundance showed significant correlations with environmental factors such as NO₂, PM_2.5, SO₂, temperature, and relative humidity. However, the fungal abundance only showed positive correlations with temperature (P<0.01). The community composition results revealed that the dominant bacteria in Xiamen Island and Tongan did not exist the significant spatiotemporal variation. The absolute abundance of potential pathogens was significantly higher in winter than in summer (P<0.001) and higher in industrial areas than in parks (P<0.05). [Conclusion] The absolute abundance of airborne microbes in Xiamen was at a low level compared with that in other cities in China. The absolute abundance of airborne bacteria and fungi showed significant spatial variations. The airborne bacterial absolute abundance exhibited significantly seasonal differences; The absolute abundance distribution of airborne bacteria and fungi in Xiamen showed closely relations with environmental factors, with the main influencing factors being different. The bacterial community composition showed relatively stable spatiotemporal distribution in Xiamen Island and Tongan, however, the risk of potential pathogens was higher in winter than in summer and higher in industrial areas than in parks.

Abstract:[Background] Zabuye Lake (ZL) is a saline-alkali lake in Xizang, with high concentrations of CO₃²⁻, HCO₃⁻, and Na⁺. There are few studies involving eukaryotic plankton diversity in this lake. [Objective] To clarify the diversity and composition of eukaryotic plankton and the trophic mode of fungi in ZL. [Methods] High-throughput sequencing of the V5–V7 region of the 18S rRNA gene was employed to analyze the community structure and species diversity of eukaryotic plankton in ZL. Spearman correlation coefficients were calculated to measure the correlations of genera with the chemical characteristics of lake water. FUNGuild was used to predict the trophic mode of fungi. [Results] Illumina sequencing yielded 25 genera of eukaryotic plankton belonging to 20 classes, 12 phyla, and 2 kingdoms. The dominant phyla were Aphelidea (0.12%−51.84%), Nucleariidae-Fonticula (0%−91.70%), Ascomycota (1.38%−9.04%), and Basidiomycota (0.20%−10.16%). The common genera included Nuclearia (0%−91.70%), Fusarium (1.38%−4.32%), Paraphelidium (0%−4.57%) and Homalogastra (0%−4.39%). Homalogastra, Protosporangium and Nuclearia showed significantly positive correlations with Na⁺, K⁺, and Ca²⁺ concentrations and total salinity, and they had significantly negative correlations with temperature, total phosphorus, total organic carbon, and pH. The functions of planktonic fungi in each sample site were mostly unknown and saprotrophic fungi (1.38%−5.24%) were present in all the sample sites. [Conclusion] The community structure of eukaryotic plankton in ZL was similar to that in other saline-alkali lakes. The dominant phyla were Ascomycetes and Basidiomycota, with the presence of Aphelidea and Nucleariidae-Fonticula. The community structure was closely related to the salt concentrations of ZL. Most of the planktonic fungi in this lake were saprotrophs.

Abstract:[Background] The microbial community structure of wetland soil will adjust itself according to the environmental changes. Therefore, different wetland environments will shape soil microbial communities with different structures and distribution characteristics. [Objective] To investigate the impacts of land use changes on soil bacteria in in dryland and wetland, we collected soil samples of two land use patterns (0−20 cm) from the wetland and dryland of Xianshan Lake National Wetland Park for analysis. [Methods] High-throughput sequencing was employed to study the composition, α-diversity, and abundance of soil bacterial communities, and the soil physical and chemical factors affecting bacterial community structure were analyzed. [Results] The bacteria in the soil of Xianshan Lake Wetland Park belonged to 147 classes of 49 phyla. The dominant phyla (OTUs>1%) in the dryland soil were Acidobacteria, Proteobacteria, Chloroflexi, Crenarchaeota, Actinobacteria, Cyanobacteria, Gemmatimonadetes, Planctomycetes, and Bacteroidetes, and those in the wetland soil were Proteobacteria, Cyanobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Firmicutes, and Nitrospirae. The dominant genus (OTUs>0.3%) were Candidatus Solibacter, Candidatus Koribacter, Rhodoplanes, Burkholderia, and Mycobacterium in the dryland and Geobacter, Bacteroides, Bradyrhizobium, Dok59, Candidatus Methylomirabilis, and Flavobacterium in the wetland. The dominant OTUs of wetland soil and dryland soil were positively correlated with soil carbon content and negatively correlated with soil water content and pH. The LEfSe results revealed the relationship between soil biomarkers and soil physical and chemical properties in the dryland and wetland. [Conclusion] Land use changes could vitally alter the bacterial community structure in the wetland soil of Xianshan Lake Wetland Park, it can provide theoretical basis for wetland soil protection.

Abstract:[Background] The knownledge is limited about the effects of Panax notoginseng cultivation in forestland on the physicochemical properties of the soil and the structure and function of the soil microbial community. Studying such effects will be of great significance in guiding the cultivation of P. notoginseng in forestland. [Objective] To analyze the soil microbial communities in the forestland cultivated with P. notoginseng for different years during the rainy and dry seasons, and to elucidate the response patterns of soil microbial communities to the P. notoginseng cultivation process as well as the key influencing factors. [Methods] The natural forestland soil without P. notoginseng cultivation was taken as the control. High-throughput sequencing and biochemical tests were carried out to reveal the dynamics of soil microbial communities in the soil of the forestland with P. notoginseng cultivation. Based on the results, the redundancy analysis was then performed to clarify the drivers of the microbial community changes. [Results] The dominant bacteria and fungi in the soil of the forestland with and without P. notoginseng cultivation were Proteobacteria and Basidiomycota, respectively. The abundance of beneficial microbial phyla and genera showed an increasing trend. The number of unique genera of fungi and bacteria in soil was the lowest in the control, while it was the highest in the forestland with two-year P. notoginseng cultivation. The Chao1 and ACE indexes were the highest in the forestland with three-year P. notoginseng cultivation. The results of the principal coordinate analysis showed that the microbial distribution area in the forestland with P. notoginseng cultivation shifted and shrank with the increase in cultivation years. The soil microbial community composition was more similar among different groups in the dry season than in the rainy season. The redundancy analysis showed that total phosphorus and acid phosphatase were the main soil factors driving the changes of soil microbial communities in the forestland with P. notoginseng cultivation. [Conclusion] P. notoginseng cultivation in the forestland significantly changed the microbial community composition in the soil, and the microbial distribution presented a gradual shift and contraction with the increase in cultivation years. The alternation of rainy and dry seasons accelerated the composition and structure differentiation of the soil microbial communities in the forestland with P. notoginseng cultivation. Total phosphorus and acid phosphatase were the main environmental factors affecting the soil microbial communities.

Abstract:[Background] Carriers influences the effects and costs of microbial fertilizers. [Objective] To screen the vector with strong adsorption ability of Bacillus velezensis PZ-3. [Methods] We carried out adsorption experiments for B. velezensis PZ-3 with biochar, humic acid, biomass ash, organic fertilizer, mushroom bran, and rice husk powder as carriers. The carrier suitable for the target strain was screened by dilution coating-colony counting method, flow cytometry, and maize pot experiment. Then, we investigated the effects of the adsorbed target strain on the microbial diversity in the rhizosphere soil of maize. [Results] The best colonization effect was achieved in the rhizosphere soil of maize after the adsorption of the target strain by humic acid+mushroom bran. The abundance and number of the target strain in the rhizosphere soil of this treatment peaked at 1.28×10⁵ CFU/g, with a relative abundance of 59.15%, on day 7. Compared with the control (original soil), this treatment increased the plant height, stem diameter, and aboveground dry weight of maize by 28.51%, 19.05%, and 48.65%, respectively. Moreover, this treatment increased the relative abundance of Streptomyces and Pseudomonas (P<0.05) and reduced the relative abundance of Paeniclostridium, Lophotrichus, and Gibberella in the rhizosphere soil of maize. [Conclusion] Humic acid combined with mushroom bran had a strong ability to adsorb B. velezensis PZ-3. The combination significantly promoted the growth of maize, increased the relative abundance of plant growth-promoting strains, and reduced the relative abundance of plant pathogenic fungi in the rhizosphere soil of maize.

Abstract:[Background] As the largest inland basin in China, the Tarim Basin is a natural laboratory for studying the responses of bacterial communities to the environment on a local scale. Although researchers have studied the bacterial diversity in the Tarim Basin, few of them have studied the diversity and distribution pattern of bacterial communities in plant habitats of the Tarim Basin. [Objective] This study investigated and analyzed the diversity and distribution pattern of bacterial communities in plant habitats in the Tarim Basin, laying the foundation for subsequent research on bacterial ecology in the region. [Methods] We conducted a large-scale and systematic field survey and sampling of the soil in a plant habitat of the Tarim Basin to analyze the bacterial community structure and diversity. Furthermore, we explored the changes of soil bacterial diversity and community spatial pattern along geographic and climatic gradients on a large scale and the assembly process of phylogenetic groups at the continental level. [Results] The species composition, network structures, and assembly processes of bacterial communities showed significant differences between the plant habitat and the desert habitat. Notably, the soil bacterial communities in the plant habitat showed greater stability and complexity than those in the desert habitat. The null model analysis showed that heterogeneous selection and diffusion limitation were the key ecological processes in the bacterial community assembly. [Conclusion] This study reveals the diversity and driving factors of soil bacterial communities in three habitats of the Tarim Basin. The findings provide data and research basis for understanding the safety and stability of ecosystems in the arid zone in the context of global change and give insights into the fragility and assembly processes of plant habitat ecosystems in arid zones.

Abstract:[Background] East Dongting Lake occupies a special geographical location and harbors abundant species resources, including a variety of microorganisms with unique physiological and biochemical characteristics. [Objective] To obtain the bacterial resources with tolerance to heavy metals and polycyclic aromatic hydrocarbons (PAHs) by the culturable methods and clarify their physiological characteristics. [Method] Forty samples were collected from five different regions of East Dongting Lake in January 2022 for the measurement of environmental factors. The bacteria were isolated, microbial strain resources were obtained, and the correlations of bacteria with environmental factors were analyzed. [Results] A total of 253 bacterial strains were isolated, including 210 strains with tolerance to heavy metals and 43 strains with tolerance to PAHs. The strains belonged to 42 genera, which were dominated by Pseudomonas (46.6%), Fictibacillus (7.5%), Pseudarthrobacter (6.7%) and Bacillus (5.1%). After re-screening, 30 strains with strong tolerance to heavy metals and 7 strains with strong tolerance to PAHs were obtained. Specifically, 20, 4, 3 and 3 strains showed tolerance to Mg²⁺, Mn²⁺, Ni²⁺ and Zn²⁺, with the maximum tolerance concentrations (MTCs) of 500, 500, 30 and 25 mmol/L, respectively. 5 and 2 strains had tolerance to naphthalene and phenanthrene, with the MTCs of 0.04 g/mL and 0.02 g/mL, respectively. Two strains of potentially novel species and one strain of potentially novel genus were identified in this study. [Conclusion] The bacterial diversity varied among the samples from five regions, being higher in Yueshan, Yueyanglou, and Junshan than that in Lujiao and Nanhu. The temperature, total dissolved solids, electrical conductivity, and dissolved oxygen had the greatest influences on the composition of bacterial community, while pH and salinity had the least influences. The low number of strains with strong tolerance to heavy metals and PAHs in this study may be associated with the effective pollution control in East Dongting Lake.

Abstract:[Background] Fungi of Botryosphaeriaceae are mostly major pathogens in agriculture and forestry. [Objective] To investigate the microfungi of Ascomycota from Xanthoceras sorbifolium in Changchun and Siping of Jilin province. [Methods] The specimens of microfungi were collected, and their morphology was observed and described in detail. After DNA extraction, the internal transcribed spacer (ITS) rDNA, ribosome large subunit (LSU), and translation elongation factor 1-alpha (tef1-α) of each species were sequenced. Phylogenetic trees were constructed based on maximum likelihood method, maximum parsimony method, and Bayesian inference. [Results] Four species of Botryosphaeriaceae were identified as Botryosphaeria sinensis, Phaeobotryon aplosporum, Phaeobotryon negundinis, and Phaeobotryon rhois, respectively. These four species of ascomycetes were reported on Xanthoceras sorbifolium for the first time. This paper described and illustrated the macroscopic, microscopic, and colony morphological characteristics of the above four new record species in detail. [Conclusion] P. negundinis was identified as a new record in China. B. sinensis, P. aplosporum, and P. rhois were identified as new records in Jilin.

Abstract:[Background] The N-acyl-homoserine lactone synthase AhyⅠ plays a critical role in regulating the production of virulence in Aeromonas hydrophila biofilm. [Objective] To reveal the structure of AhyⅠ, so as to discover effective inhibitors that can disrupt bacterial pathogenicity at the source. [Methods] We constructed the three-dimensional structure of AhyⅠ by employing homology modeling and molecular dynamics simulation with a resolved protein structure as a template. On the basis of previous research results, we selected 214 candidate ligands including two highly effective inhibitors (NOO and MTA) and active components from Chinese herbal medicines to undergo molecular docking with the receptor protein. [Results] Through this process, we identified four potential inhibitors. The minimum inhibitory concentration (MIC), bacterial growth curve, violacein production, biofilm formation, extracellular protease activity, and bacterial swarming and swimming performance showed that artemisinin served as a highly efficient inhibitor of A. hydrophila quorum sensing. [Conclusion] Artemisinin from the Chinese herbal medicine serves the prevention and treatment of infections of waterborne bacteria in the aquaculture industry, holding a promising prospect for the treatment of bacterial infections in the future.

Abstract:[Background] The deterioration of cultural relics in burial environments is closely associated with microorganisms that are recognized as one of the major contributors to the degradation and disappearance of cultural relics. The knowledge is limited regarding anaerobes in the anoxic conditions deep at the Sanxingdui site. [Objective] To investigate the culturable anaerobe diversity in the ivory burial layer of Sanxingdui, explore the factors influencing the distribution of culturable anaerobes, and provide strain resources and theoretical reference for further research on the organic acid and protease production of the anaerobes and the mechanism of ivory degradation. [Methods] Anaerobes were isolated from the ivory burial layer of Sanxingdui using an anaerobic workstation and three isolation media, and the effectiveness of different media for isolating anaerobes was analyzed. The phylogenetic analysis based on 16S rRNA gene sequences was performed to reveal the diversity of culturable anaerobes. Furthermore, the Mantel test was carried out to study the environmental factors influencing the distribution of culturable anaerobes. [Results] A total of 61 strains of anaerobes were isolated from the ivory burial layer of Sanxingdui. Based on the 16S rRNA gene sequences, the strains were assigned into Clostridium, Terrisporobacter, Hathewaya, and Haloimpatiens belonging to Clostridiaceae and Peptostreptococcaceae. Eleven species were identified: Clostridium cibarium, C. beijerinckii, C. magnum, C. nitrophenolicum, C. kogasense, C. intestinale, C. sporogenes, Clostridium sp. (A4d), Terrisporobacter mayombei, Hathewaya massiliensis, and Haloimpatiens massiliensis. Among the three isolation media used, the reinforced Clostridium medium yielded the highest number and the most species of fermentative anaerobes, and the other two media also showed unique isolation effects. Mantel test results indicated significant positive correlations between the distribution characteristics of culturable fermentative anaerobes and the content of Cu and Pb. [Conclusion] The culturable fermentative anaerobes present varied diversity in the ivory burial environment of Sanxingdui, with the highest richness and diversity in pit K8. Multiple isolation media facilitated the isolation of diverse microbial groups. Cu, Pb, and organic matter are the key factors influencing the distribution of culturable fermentative anaerobes in the ivory burial layer of Sanxingdui.

Abstract:[Background] The microorganisms in the Taklimakan Desert as a typical extreme habitat with high temperatures and drought demonstrate distinct regional characteristics after undergoing long-term adaptation to the environment. [Objective] To obtain culturable microbial resources in the extreme environment of the Taklimakan Desert and to explore the effects of different diluted media supplemented with norfloxacin on the isolation of microorganisms in this area. [Methods] Different dilutions of Gauze’s medium No. 1, LB medium, and R2A medium were supplemented with norfloxacin at a final concentration of 0.015 µg/mL for the isolation of microorganisms from the Taklimakan Desert. [Results] A total of 246 strains were isolated and identified, which belonged to 221 species, 58 genera, 29 families, 21 orders, 6 classes of 4 phyla. Firmicutes and Actinobacteria were the dominant phyla, Bacilli and Actinomycetia the dominant classes, Bacillales and Streptomycetales the dominant orders, Bacillaceae and Streptomycetaceae the dominant families, and Streptomyces, Bacillus, and Nocardiopsis the dominant genera. Eighty strains with the maximum similarity lower than 98.65% were classified as potential new species, and 2 strains with the maximum similarity lower than 95.00% were classified as potential new genera. A total of 221 isolated strains were tested for drug sensitivity, among which 43 strains represented by Streptomyces showed resistance to norfloxacin. Twenty-five isolates showed moderate resistance to norfloxacin. [Conclusion] Different dilutions of media supplemented with norfloxacin are beneficial for the isolation of microorganisms in the extreme environment of the Taklimakan Desert. With this method, rich microbial resources were isolated, including a number of new species and drug-resistant strains. The findings provide a basis for the subsequent mining of drug-resistant strains and exploring microbial resources in extreme environments.

Abstract:[Background] The synthetic progestin levonorgestrel has attracted wide attention due to its endocrine-disrupting effects. Microorganisms demonstrate extensive potential in pollutant degradation and environmental remediation. However, the characteristics and mechanisms of levonorgestrel degradation by microorganisms remain poorly understood. [Objective] To isolate an efficient levonorgestrel-degrading strain and explore its degradation mechanism for the remediation of levonorgestrel pollution. [Methods] We isolated a strain capable of efficiently degrading levonorgestrel from aquaculture wastewater and identified the strain based on its morphological, physiological, and biochemical characteristics and the 16S rRNA gene sequence. The degradation characteristics of the strain for levonorgestrel were investigated by whole genome analysis, degradation kinetics, and analysis of the degradation product spectrum. [Results] Gordonia sp. H52 was isolated, which had 99.0% homology of the 16S rRNA gene sequence compared with Gordonia cholesterolivorans Chol-3. This strain completely removed 0.5 mg/L levonorgestrel within 18 h. Liquid chromatography-tandem mass spectrometry revealed that Gordonia sp. H52 produced five metabolites during the degradation process of levonorgestrel, primarily through the cleavage of the side chain and hydroxy group. Furthermore, the strain facilitated the removal of various synthetic progestins in water, increasing the removal rates of levonorgestrel from 0% to 91.06%, acetylene norethindrone from 37% to 100%, and gestodene from 0% to 88.87%. [Conclusion] Gordonia sp. H52 demonstrates high degradation efficiency for levonorgestrel. This study provides valuable microbial resources and theoretical references for the treatment and remediation of water contamination caused by synthetic progestins.

Abstract:[Background] As one of the major fungal diseases in cucumber production, powdery mildew occurs widely in the world, resulting in declined cucumber quality and yield and causing serious economic losses. [Objective] To isolate and identify the original strains for biocontrol against cucumber powdery mildew and to verify their biocontrol and plant growth-promoting effects. [Methods] Multiple methods including plate screening, 16S rRNA gene sequencing, phylogenetic analysis, whole genome sequencing, secondary metabolite analysis, and morphological characterization were employed to isolate, identify, and characterize the strains. [Results] An antagonistic bacterium S1 was obtained from the rhizosphere soil of cucumber with Bipolaris maydis as the indicator strain, and its growth-promoting effect on cucumber seedlings and control effect on powdery mildew were examined by pot experiments. The blast result of 16S rRNA gene sequences showed that this strain had a nucleotide identity of 100% compared with Bacillus subtilis KZH-E3. The whole genome sequencing combined with the phylogenetic analysis eventually identified the strain as B. subtilis. The pot experiments in a greenhouse proved that S1 had a significant biocontrol effect on cucumber powdery mildew. [Conclusion] B. subtilis S1 has obvious disease-preventing and growth-promoting effects on cucumber seedlings, having important research significance.

Abstract:[Background] Low temperatures are one of the main factors limiting microbial degradation of straw returned to the field in cold regions. [Objective] To obtain the bacterial strains capable of degrading cellulose at low temperatures to improve the straw reutilization in cold regions. [Methods] The soil samples were collected in winter for strain enrichment with sodium carboxymethyl cellulose (CMC-Na) as the sole carbon source. The pure culture of the strain was obtained by the dilution-plate coating method, and the enzyme production conditions of the strain were optimized by single factor and orthogonal tests. [Results] A cellulose-degrading strain was obtained at 15 ℃ and identified as Duganella sp. The optimal enzyme production conditions of the strain were incubation with the liquid loading volume of 50/100 mL and inoculum volume of 12.5% at 15 ℃ and initial pH 7.0, under which the highest CMC enzyme activity was 398.2 U/mL, 40.45% higher than that before optimization. The degradation rates of filter paper, rice straw, and maize straw by the strain were 19.24%, 9.48%, and 7.30%, respectively, under optimal culture conditions. [Conclusion] This study provides new strain resources for straw degrading microbial resources in cold regions, as well as data reference for subsequent research on low temperature cellulose-degrading strains.

Abstract:[Background] Bamboo is considered an excellent source for biorefining for its high cellulose content. However, the complex interactions between lignin and cellulose present an obstacle to the efficient utilization of bamboo. The process of lignin degradation is essential for the efficient utilization of bamboo. [Objective] To screen out the strains that specialize in degrading bamboo lignin and investigate their enzyme activities and effects of lignin degradation. [Methods] A culture medium with lignin as the solo carbon source was used for the primary screening, which was followed by the secondary screening with the media containing aniline blue and Congo red. The activities of enzymes were measured to assess the lignocellulose degradation performance. X-ray diffraction, Fourier-transform infrared spectroscopy, and scanning electron microscopy were employed to study the changes of bamboo appearance and structure after degradation. [Results] A strain XKG6 capable of degrading lignin was isolated from the bamboo forest and identified as Pseudomonas oleovorans. The maximum activities of lactase, lignin peroxidase, manganese peroxidase, filter paper enzyme, and xylanase secreted by the strain reached 1 543.21, 6 229.32, 826.41, 2 602.1, and 1 889.25 U/L, respectively. The strain showed a degradation rate of 14.04% against alkaline lignin on day 7. Fourier transform infrared spectroscopy and scanning electron microscopy showed the significant structural changes in bamboo lignin after treatment with XKG6. [Conclusion] In this study, a bacterial strain with the ability to degrade lignin was screened out. This strain retained much cellulose while degrading bamboo lignin, serving as an alternative strain for the industrial production of lignocellulosic resources.

Abstract:[Background] The lignin in tobacco waste acts as a primary obstacle for environmental microorganisms to degrade lignocellulose in tobacco stems or other straw. Additionally, the nicotine in tobacco stem threatens the survival of most reported lignin-degrading microorganisms. [Objective] To screening the strains with strong degrading effects on tobacco stems, so as to solve the problem of long-term accumulation of tobacco stems which are difficult to degrade and enhance the industrial availability of tobacco stems. [Methods] The aniline blue fading method and the guaiacol assay were employed to screen out the dominant strains capable of degrading lignin from cattle manure. The nicotine tolerance of the strains was tested, and the degradation effects of the strains on tobacco stems were verified. [Results] The lignin-degrading strain YP-2023-9 screened belonged to Enterobacter and showed tolerance to nicotine with the concentration≤0.60%. The strain produced lignin peroxidase and manganese peroxidase, thereby promoting lignin degradation in tobacco stems. The maximum levels of the two enzymes reached 309.68 U/mL on day 5 and 21.76 U/mL on day 1, respectively. Scanning electron microscopy demonstrated that the strain primarily facilitated the degradation of lignin and hemicellulose on the tobacco stem surface, causing evident damage to the cell wall structure of tobacco stems. After incubation at 30 ℃ for 15 days, YP-2023-9 showed a degradation rate of 42.42% against tobacco stems, with the relative degradation rates of 13.17% and 33.12% against hemicellulose and lignin, respectively. [Conclusion] This strain exhibits promising potential for application in the degradation of both tobacco stems and associated waste.

Abstract:[Background] Continuous planting of common crops can lead to the secretion of phenolic acid autotoxic substances in roots, which are the main factors causing soil-borne diseases and continuous cropping obstacles. [Objective] To mine the microorganisms capable of degrading benzoic acid secreted by crop roots, reduce the occurrence of soil-borne diseases, and reserve beneficial microbial resources. [Methods] We used benzoic acid as the sole carbon source in the inorganic salt medium to screen the strain resources of Wuliang Mountain and determined the degradation rate of benzoic acid by high-performance liquid chromatography. The plate confrontation test, tomato seed germination experiment, tomato seedling growth experiment, and pathogen (Fusarium wilt) inoculation experiment with tomato seedlings were carried out to examine the biological activities of the strains. The strains were identified based on morphological, physiological, and biochemical characteristics and 16S rRNA gene sequences. [Results] Four strains of Actinomycetes and three strains of bacteria with phenolic acid-degrading ability were screened from Wuliang Mountain. After culture in shake flasks for 72 h, the strains showed the benzoic acid-degrading rate of 100%, 99.83%, 99.89%, 99.87%, 64.91%, 56.92%, and 49.33%, respectively. Two Actinomycetes strains (YNK-FS0018 and YNK-FS0019) and one bacterial strain (YNK-FB0022) could make good use of benzoic acid. The treatments with the three strains alleviated the inhibitory effect of benzoic acid on tomato seed germination, with the seed germination rates of 73%, 73%, and 97%, the root length of 13.31, 13.04, and 14.56 cm, respectively. Furthermore, the three strains had broad-spectrum resistance to pathogens. YNK-FS0018 and YNK-FS0019 carried PKSII and NRPS, and YNK-FB0022 carried fenD, bioA, yndJ, ysnE, ituC, sboA, and srfAB. The results of pot experiments showed that strain YNK-FS0018 increased the plant height, above ground fresh weight, above ground dry weight, root weight, root length, and stem diameter by 53.40%, 67.50%, 57.50%, 73.50%, 77.28%, and 9.40%, respectively. The increases in the above indicators by YNK-FS0019 were 23.00%, 40.90%, 14.00%, 57.00%, 26.30%, and 16.80%, respectively. The increases by YNK-FB0022 were 24.50%, 44.70%, 26.40%, 75.10%, 98.00%, and 9.00%, respectively. The control effects of three strains on tomato Fusarium wilt were 87.10%, 74.18%, and 80.65%, respectively. YNK-FS0018, YNK-FS0019, and YNK-FB0022 were identified as Streptomyces blastmyceticus (Genbank accession number: OR523286), Streptomyces alboflavus (Genbank accession number: OR523289), and Bacillus halotolerans (Genbank accession number: OR523290), respectively. All the strains had the abilities of solubilizing organic phosphorus and zinc, secreting siderophores, and producing amylase and protease. [Conclusion] The three phenolic acid-degrading bacterial strains have the abilities of solubilizing organic phosphorus and zinc, secreting siderophores, and producing amylase and protease. They can significantly increase the plant height, stem thickness, root length, root weight, above ground fresh weight and above ground dry weight of tomato seedlings. Moreover, they demonstrate strong control effects on tomato Fusarium wilt, serving as the microbial resources for the biocontrol of soil-borne diseases.

Abstract:[Background] Esters are one of the common components in industrial waste gas. Using microorganisms for the degradation of esters has a promising application prospect and thus deserves research. [Objective] To study the degradation characteristics and pathway of a butyl acetate-degrading strain isolated from the activated sludge of a sewage treatment plant in Zhejiang Province. [Methods] This strain was identified based on the physiological, biochemical, and 16S rRNA gene sequence. The single factor experiments were carried out to analyze the degradation characteristics of the strain for butyl acetate, and the degradation intermediates were detected. [Results] The strain was identified as Acinetobacter modestus HYY-1. It demonstrated strong degradation effect on butyl acetate under alkaline conditions (pH 8.0–10.0). The strain showed high degradation efficiency for butyl acetate at 264.75–1 059.00 mg/L, which nearly reached 100% within 120 h in the case of the highest butyl acetate concentration. The initial inoculation concentration of the strain had little effect on the degradation efficiency, which reached 100% within 120 h in the case of different initial inoculation concentrations. The main intermediates in the degradation of butyl acetate by this strain were n-butanol and acetic acid, and the final products were CO₂ and bacteria biomass. The proportions of the products varied under different initial butyl acetate concentrations. [Conclusion] Strain HYY-1 has the ability to efficiently degrade butyl acetate. Specifically, the strain may degrade butyl acetate by ester bond hydrolases into n-butanol and acetic acid, which were ultimately mineralized into CO₂ and bacteria biomass. This study provides theoretical support for deciphering the biodegradation mechanism of butyl acetate and exploring the bioremediation path of butyl acetate-contaminated environment.

Abstract:[Background] Hydrogen peroxide (H₂O₂), an environmentally friendly disinfectant, is widely used in medical treatment, food safety, industrial bleaching, environmental disinfection and other fields. However, long-term use of H₂O₂ can lead to bacterial tolerance to H₂O₂. [Objective] Through bibliometric analysis, we can gain insights into the current research hotspots and frontiers within the realm of bacterial responses to H₂O₂ stress, thereby predicting the future development trends in this field. [Methods] CiteSpace was used to visually analyze the research papers about bacterial responses to H₂O₂ stress in the last ten years regarding the annual publications, countries, institutions, cited journals, authors, keywords, etc. [Results] A total of 986 SCI research papers that met the requirements were screened out, mainly involving the fields of Microbiology, Biochemistry and Molecular Biology, and Biotechnology and Applied Microbiology. The studies in this field in the last ten years mainly focused on factors affecting the endogenous H₂O₂ production, oxidative stress damage, antioxidant defense systems, signal transduction, and immune regulation. [Conclusion] The available studies in this field mainly focus on the response and regulation of bacterial themselves to H₂O₂. However, few studies report the interactions between different bacteria as well as between bacteria and hosts. The future research directions may include exploring the impact of endogenous H₂O₂ produced by pathogenic bacteria on the hosts and the bacterial adaption mechanism in dealing with host stress responses, which can be used for antibacterial and bactericidal treatment and environmental pollution remediation. This article lays a foundation for deciphering the mechanism of bacterial responses to H₂O₂ stress, preventing and controlling pathogenic bacteria, and revealing bacterial interactions with hosts.

Abstract:[Background] Viable but non-culturable (VBNC) bacteria with adaptive responses to unfavorable environmental conditions have been extensively studied in the medical and food fields. However, environmental scientists have not paid attention to these bacteria until the last decade. Furthermore, few bibliometric studies in environmental sciences have been conducted regarding VBNC state bacteria. [Objective] The study investigated the research status of VBNC state bacteria in environmental sciences and summarized the research hotspots, trends, and shortcomings, aiming to provide references for the research in this field. [Methods] CiteSpace, Bibliometrix (a R package), and VOSviewer were used to statistically and visually analyze 416 available articles on VBNC state bacteria in environmental sciences that were published from 1994 to 2023 in the Web of Science Core Collection. [Results] In the last 30 years, the number of articles on VBNC state bacteria in environmental sciences showed linear growth (R²=0.917). China and the United States led the research in this field. European and American research institutions embraced close cooperation, while Chinese research institutions mainly cooperated domestically and worked independently. Oliver DJ and Yu X were the authors with the highest number of articles in this field. The research hotspots in this field included the inactivation of VBNC state bacteria in the disinfection of drinking water and the resuscitation of VBNC state bacteria in the treatment of pollutants. [Conclusion] The available studies about VBNC state bacteria in environmental sciences have mainly focused on the formation, inactivation, and resuscitation of VBNC state bacteria, while the inactivation and resuscitation methods remain to be improved. How to improve the inactivation efficiency of VBNC state bacteria in drinking water and enhance the resuscitation of VBNC state bacteria during microbial remediation of pollutants deserves further research.