Abstract:This short paper describes the aims of this special memorial issue of Acta Microbiologica Sinica for its 70^th anniversary. The special issue harbors 22 papers with a broad fields and topics, and some of those topics are briefly introduced in this short paper.

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Abstract:The year 2023 marks the centenary of the publication of the Bergey's Manual of Determinative Bacteriology. Bergey's Manual of Determinative Bacteriology was created to establish clear criteria for the classification of prokaryotic microorganisms and to initiate a mission to explore the taxonomy of prokaryotic microorganisms. With the innovation and promotion of biology, physics, chemistry, molecular biology, bioinformatics and related research techniques, and the interdisciplinary nature of microbial taxonomy, which is based on phylogenetic relationships and polyphasic taxonomy, the study of the evolution and biology of microbial species and interspecies correlation has led to a rapid increase in the number of newly discovered microbial species and information on their biological characteristics. The Bergey's Manual of Determinative Bacteriology was renamed to Bergey's Manual of Systematics of Archaea and Bacteria in 2015 and made available electronically, allowing for quick updates and a new dynamic in the field of systematic taxonomy of prokaryotic microorganisms. The "Bergey's International Society for Microbial Systematics (BISMiS)" was established in 2009 to enhance the dissemination of systematic microbiological biotechnology and to promote international academic exchange in the field of microbiology. This review provides a comprehensive overview of the history and recent developments of the Bergey's Manual of Determinative Bacteriology and "Bergey's International Society for Microbial Systematics (BISMiS)", as well as an outlook on their future directions.

Abstract:2022 and 2023 mark the 70th anniversary of the Chinese Society of Microbiology and Acta Microbiaogica Sinica, respectively. China's prokaryotic microbial taxonomy research has gone through 70 years from starting from scratch, tracking and imitating to gradually entering the international stage, from following and running to being in the international advanced ranks as a whole, leading international counterparts in some fields, and providing microbial data services for international counterparts. These achievements are the result of the efforts of generations of scholars in the field of prokaryotic microbial taxonomy in China, and the result of the resonance of the same frequency with national development and national rejuvenation. Especially in the past 30 years, China's prokaryotic microbial taxonomy has made remarkable achievements in terms of theory, method innovation and novel species discovery, and its status and influence in the international community have been increasing, and it has gradually become the leading force in the field of international prokaryotic systematic taxonomy. Based on respecting history and being objective and realistic, this review sorts out the development context and achievements of bacteria and archaea taxonomy and related fields in China in the past 70 years, and looks forward to the latest development direction in this field.<

Abstract:Microbial Resources Committee of the Chinese Society for Microbiology was established in 2009, with the aim of promoting the research, protection, sustainable utilization and development of microbial resources, and providing technical support and strategic guidance for their protection and utilization. The committee actively conducts various forms of academic exchanges, talent training, and international cooperation, promotes innovation and development in the field of microbial resources, and advances the development of microbiology in China. With the continuous progress of science and technology and the rapid development of the economy, research and utilization of microbial resources has become one of the important hotspots in the international scientific and technological field. Therefore, the construction and development of the Microbial Resources Committee is of great significance and will further promote the development of microbiology in China, enhance China's academic status and international competitiveness in the field of microbial resources.

Abstract:The budding yeast Saccharomyces cerevisiae has been used by humans in food and beverage fermentation for nearly 10 000 years. It is also a model organism commonly used in genetics, molecular biology, genomics, and synthetic biology research. Ecological, population genetics, and population genomics studies on both wild and domesticated populations of this species conducted globally in recent years have shown that S. cerevisiae distributes ubiquitously in the wild, including in primitive forests, and may prefer habitats such as broad-leaved tree bark, decaying wood, and surrounding soil. The genetic diversity of S. cerevisiae in China is significantly higher than that in other parts of the world, and the oldest lineages of this species have only been found in China, suggesting an out-of-China origin of this species. Ecological adaptation is the main force shaping the population structure of this species, leading to a clear differentiation between the wild and domesticated populations. The domesticated population has further diverged into solid- and liquid-state fermentation groups, each with different domesticated lineages. The genetic diversity of the wild population is significantly higher than that of the domesticated population, and the formation of genetic diversity in the wild population appears to be mainly caused by neutral mutations. The wild and domesticated populations exhibit significant differences in maltose utilization ability, genomic heterozygosity, sporulation rate, and spore viability, indicating that these two populations adopt different life strategies to adapt to their different habitats. The domesticated lineages adapt to specific ecological niches through lineage-specific copy number variation (CNV), gene content and allele distribution variations, horizontal gene transfer, and introgression.

Abstract:Marine sediment is the largest organic carbon reservoir on Earth, and the microorganisms thereof constitute the marine sediment microbiome which are in large quantity, widely distributed, with diversified lineages and versatile metabolic capacities. The organic carbon degradation and mineralization processes mediated by the marine sedimentary microbes not only provide material and energy for life in the sediments, but also participate in carbon cycling processes and have a significant impact on the Earth՚s climate system for long time scales. Organic carbon in sediments is gradually degraded by complex microbial metabolic activities, and its final mineralization process sequentially couples with the depletion of different electron acceptors which forms the corresponding geochemical zones in marine sediment. The study of marine sedimentary microbiome and the associated organic carbon transformation processes is important for our in-depth understanding of elemental cycling processes in sediments and further assessment of their impact on the Earth system. This review provides an overview of the quantity of the marine sediment microbiome, the diversity of microorganisms, their metabolic capacities as well as the major microbial taxa and metabolic mechanisms that forms geochemical zones. Finally, based on the current research status, the future research directions of marine sedimentary microbiome are prospected.

Abstract:Environmental microorganisms are the primary decomposers in nature, and their genetic and metabolic diversity make them crucial for breaking down organic pollutants. With the continuous release of pharmaceuticals into the environment, their potential effects on human health and environmental risks have become a topic of concern. Thus, understanding the biodegradation process of pharmaceuticals in the environment is essential for assessing their environmental fate and developing removal technology for pharmaceutical pollutants. This paper aims to focus on the microbial degradation pathways and molecular mechanisms of frequently occurred pharmaceuticals in the environment. We also summarized the current progresses in the field of microbial pharmaceutical degradation and discussed the potential research directions.

Abstract:Methanogens are widely distributed in anaerobic environments, such as wetlands, paddy fields, animal rumens, oil reservoirs, oceans, and hydrothermal vents. They play critical roles in global carbon cycling, climate change, and clean energy production, making them a hot research topic both domestically and internationally. This article briefly reviews the research progress of methanogens in China, focusing on their resources and taxonomy, physiology and biochemistry, molecular biology, ecological roles, and applications. The future research trends of methanogens are also highlighted.

Abstract:Streptomycetes are well known for their dramatic production capacity of antibiotics, which are widely used in medicine and pharmacy. It is the largest and most diverse branch of the phylum Actinomycetota. After years of in-depth research, streptomycetes have made great progress in the field of systematics, culture-dependent diversity research, and natural product resource exploration. Based on these three aspects, this paper reviews the most recently advances, opportunities and challenges in the related studies on streptomycetes, and also proposes the future directions.

Abstract:Rapid and accurate identification and characterization of microorganisms is essential for the research in environmental science, food quality, and medical diagnostics. Raman spectroscopy has been shown to be a new technique that enables rapid microbial diagnosis, providing microbial fingerprinting information while enabling rapid, non-labeled, non-invasive, and sensitive detection of microorganisms at the single-cell level in both solid and liquid environments. This paper briefly introduced the basic concepts and principles of Raman spectroscopy and focused on a review of the sample handling methods and spectral data processing methods in the application of Raman spectroscopy for microbial detection. Besides, this paper outlined the application of Raman spectroscopy in bacteria, viruses, and fungi, among which the application of Raman in rapid bacterial identification and antibiotic drug sensitivity detection was outlined separately. Finally, this paper described the challenges and prospects of Raman spectroscopy in microbial detection.

Abstract:The livestock digestive tract is colonized by a large number of microbes, which not only affect the digestion and absorption of nutrients, but also play an important role in the regulation of the animal immunity, growth, and development. The study of livestock digestive tract microbiome is a hot research field worldwide, and a series of important achievements have been made. Understanding the structure and function digestive tract microbiome in the animals will lay a theoretical foundation for manipulation and utilization of gut microbes to increase production performance, improve gastrointestinal health, and thus promote a green and healthy livestock industry. In this review, we summarized and analyzed the recent achievements on the structure and function of the digestive tract microbial community in four representative farm animals (cattle, sheep, pigs and chickens). We also discussed future research directions in this field.

Abstract:A carefully curated group of microbial strains known as probiotics are "live microorganisms that, when administered in adequate amounts, confer a health benefit on the host". The well-known microbe with prebiotic properties include traditional probiotics:lactic acid bacteria, Saccharomyces, etc., and the next generation probiotics:Faecalibacterium prausnitzii, Bacteroides fragilis, Akkermansia muciniphila, Prevotella copri, etc.. Probiotics and the health of humans are closely related. To regulate the host's health, these bacteria can either trigger the gastrointestinal response through the stomach or can directly affect other organs like the mouth, vagina, and skin. As a result, they are often utilized in food production, agriculture, animal husbandry, and medicine. They are also effective instruments for enhancing host health. In order to provide references for the research on the development and application of probiotics resources, this paper reviewed the development and application of traditional probiotics like lactic acid bacteria and the next-generation of probiotics like Akkermansia muciniphila. It also summarized the potential of these probiotics in food production, disease treatment, and agricultural production, and prospected the development trend of probiotics resource research and application, in order to provide reference for the research on the development and application of new and old probiotics.

Abstract:Microbial diseases can greatly reduce the yield and quality of edible fungi cultivated with the soil-covered mode. Prevention and control of these microbial diseases is kept focused in both research and industrial development of edible fungi. Nevertheless, the drawbacks of regular techniques limit their practical applications to effectively prevent and control microbial diseases. In this review, we summarize recent applications, as well as the pros and cons, of regular biological and non-biological techniques for preventing and controlling microbial diseases in the soil-covered cultivation of edible fungi. We also review recent research progresses on soil microbial community diversity in the soil-covered cultivation of edible fungi. Based on these progresses, we propose a new strategy that applies a synthetic soil microbial community to prevent and control microbial diseases in the soil-covered cultivation of edible fungi. Moreover, the challenges and prospects to constructing and applying a synthetic soil microbial community are present. This review contributes to the efficient prevention and control of microbial diseases in the cultivation of edible fungi and the maintenance of soil health.

Abstract:Seagrasses are aquatic angiosperms which are widely distributed in coastal zones. Seagrass bed ecosystem is one of the three typical marine ecosystems, which performed high level of productivity and significant ecological functions. Seagrass beds have decreased rapidly worldwide since 20^th century, yet present restoration methods did not pay enough attention to the importance and functions of microorganisms. This paper summarized the significant roles of microorganisms in seagrass bed ecosystem within the process of organic mineralization and nutrient flow, and analyzed the biogeochemical cycling among seagrass bed water and sediment. Moreover, this paper proposed the anthropogenic factors that caused the seagrass bed lost and the research methods of these microorganisms. We raised the possible restoration ideas via regulating the microbial diversities and structures affiliated with the seagrass bed ecosystem.

Abstract:Electroactive microorganisms have the unique ability to transfer electrons between intracellular and extracellular environments. Based on a thorough study of the electron transfer mechanism of natural electroactive microorganisms, the structural basis of electron transfer in natural electroactive microorganisms can also be heterologously constructed by synthetic biology methods, which can transform non-electroactive Escherichia coli with clear genetic background into electroactive microorganisms. The engineered electroactive E. coli obtained can be directly applied to fields such as microbial fuel cells, biosensors, and be used as a chassis cell to integrate the corresponding target product synthesis pathway to achieve electric-driven biosynthesis. This review article focuses on the construction of electroactive E. coli by synthetic biology methods, elaborates on the mechanism and structural basis of electron transfer in natural electroactive microorganisms, summarizes the construction strategy, successful cases, and application fields of engineered electroactive E. coli, and looks forward to the future research direction of constructing electroactive E. coli by synthetic biology methods.

Abstract:Actinomycetes are a special group of bacteria that have strong tolerance and can live in extreme environments. With rich species, diverse functions, and strong adaptability, actinomycetes have been widely used in antibiotic production, biological control, and environmental remediation. Actinomycetes can regulate soil microbial community structure, mediate nutrient transformation and plant assimilation, and catalyze organic pollutant degradation and heavy metal redox process.These roles endow actinomycetes with great application potentials in soil improvement, fertility maintenance, and pollutant removal. This paper introduced the diversity and environmental distribution of actinomycetes and summarized the characteristics and mechanisms of actinomycetes in environmental improvement and pollutant removal. Furthermore, we reviewed their application progress in environmental remediation and summarized the advantages and development direction of actinomycetes-based remediation technology.

Abstract:Citrus is the highest yield and largest fruit in China. Citrus canker disease is one of the most destructive bacterial diseases and results in the decrease in citrus production and quality, thereby further leading to great economic losses to the citrus industry and harmful effects for its sustainable development. The pathogen of citrus canker disease is identified as Xanthomonas citri subsp. citri (Xcc). Microbial control of citrus canker disease pathogen has the advantages of safe, eco-friendly, and efficient, and thus has received extensive attention. In this paper, we outlined the characteristic of citrus canker disease and the taxonomy and distribution of Xcc, analyzed the main and auxiliary pathogenesis of Xcc on citrus, reviewed the microbial diversity against citrus canker disease and Xcc, and summarized biocontrol mechanisms of microorganisms mainly including the action of bioactive metabolites and the inducing and activation of plant immune defense system. Finally, we summed up the challenges and possible solutions to microbial control of citrus canker to provide the theoretical basis for citrus industry development.

Abstract:[Objective] Pseudomonas aeruginosa is a Gram-negative bacterium prevalent that is conditionally pathogenic and commonly associated with nosocomial infections. Its quorum sensing signal, 3-oxo-dodecanoyl-homoserine lactone (3OC12-HSL), has been reported as a biomarker for its infection. Here, we aimed to develop a 3OC12-HSL biosensor for facilitating rapid diagnostics of clinical P. aeruginosa infections. [Methods] We constructed a reporter plasmid responsive to 3OC12-HSL and prepared a lyophilized cell-free biosensor based on that plasmid. We characterized the biosensor with 3OC12-HSL concentration gradient, validated its utility by testing clinical samples, and attempted to optimize the preprocessing procedure for clinical samples.[Results] Our cell-free biosensor is sensitive, specific, and capable of diagnosing P. aeruginosa infections in clinical respiratory samples within 60 min.[Conclusion] In this study, we developed a lyophilized cell-free 3OC12-HSL biosensor. By pre-expressing RNase inhibitor, we increased our biosensor's tolerance to body fluid, and further demonstrated its potential to be developed as a rapid diagnostic method for clinical P. aeruginosa infections.

Abstract:[Objective] To obtain the composition spectrum of Helicobacter pylori (HP) GroEL binding proteins and provide new insights into the role of GroEL and its interacting proteins in the pathogenesis of H. pylori. [Methods] Based on the construction of H. pylori GroEL prokaryotic expression recombinant bacteria Escherichia coli BL21(DE3)^{pET-28a(+)-groEL}, the His-tagged GroEL protein was purified and incubated with H. pylori whole-cell protein extract. The complex was captured using Protein G magnetic beads and anti-His tag antibody immunoprecipitation, and the GroEL and its possible binding proteins were identified by mass spectrometry. The proteins were classified according to their main functions, and protein interaction network analysis was performed. [Results] A total of 59 proteins were identified as possible binding partners of GroEL, including 19 metabolic enzymes (7 of which are involved in oxidative stress, such as KatA, GltA, and AhpC; 5 peptidases, such as PepA, RocF, and HtrA; 2 enzymes involved in lipid metabolism; 2 enzymes involved in ATP synthesis; HP17_08079 and 2 urease enzymes), 15 outer membrane proteins (including adhesins BabA, SabA, HapA, and other membrane proteins), 8 transcription and translation-related proteins (such as Tuf and RpoBC), 5 molecular chaperones (such as DnaK and GroES), 3 cytotoxin-related proteins (such as CagA), 3 oxidative stress-related proteins (such as TrxA), 2 signal transduction proteins (TlpB and TlpD), and 4 proteins with unknown functions. Protein interaction analysis revealed that the entire network could form multiple clusters, with GroEL as the central node of the network. The extensive association of outer membrane proteins, particularly the important adhesins BabA, SabA, HapA, with GroEL suggests that GroEL may play an important role in the interaction between H. pylori and host gastric mucosal epithelial cells. [Conclusion] The spectrum of H. pylori GroEL binding proteins is extensive, and the related proteins are involved in H. pylori metabolism, transcription and translation, oxidation-reduction, and adhesion, participating in the survival, colonization, and pathogenic processes. GroEL is expected to become a novel important target for studying H. pylori pathogenicity and developing infection intervention strategies.

Abstract:[Objective] To investigate the role of Jingpixian tincture (JPXT) in inducing apoptosis of Trichophyton rubrum and reveal the antifungal mechanism of JPXT. [Methods] Cell counting kit-8 (CCK-8) was used to evaluate the effect of JPXT on the viability of T. rubrum. The reactive oxygen species (ROS) level and mitochondrial membrane potential (MMP) in T. rubrum were measured by flow cytometry. Annexin V-FITC/PI staining was employed to observe the externalization of phosphatidylserine (PS) in T. rubrum. Flow cytometry, FITC-VAD-FMK staining, and an ultraviolet spectrophotometer were employed to determine the apoptosis rate, metacaspase activity, and cytochrome C oxidase activity, respectively. [Results] After JPXT treatment, the viability and MMP of T. rubrum decreased, and the ROS level increased. Furthermore, the JPXT treatment promoted PS externalization, increased the apoptosis rate and metacaspase activity, and decreased the cytochrome C oxidase activity. [Conclusion] JPXT can inhibit T. rubrum by inducing apoptosis.

Abstract:Gray mold is a common disease in the production process of a variety of cash crops, and in the storage and transportation of fruits and vegetables. Streptomyces spp. can produce many secondary metabolites with strong inhibition effects on Botrytis cinerea. [Objective] The present study focused on screening Streptomyces sp. with more efficient functions and provides excellent strains for the research and development of biocontrol agents for gray mold. [Methods] Tube dish method was applied for the selecting culture media and for determining bioactivities of culture broth of strain K2. The antifungal activity of volatile substances against B. cinerea was determined by double dish confrontation. 16S rRNA gene sequence analysis was used for identification of strain K2. High performance liquid chromatography and liquid chromatography-mass spectrometry methods were applied for qualitatively verification of the active components in the culture broth. Volatile components were determined using headspace solid phase micro-extraction gas chromatography-mass spectrometry. [Results] The secondary metabolites produced by strain K2 in culture medium A had strong inhibitory effects on a variety of plant pathogenic fungi such as Valsa mali, Physalospora piricola, Sclerotinia sclerotiorum, Botryosphaeria dothidea and Alternaria alternata. The inhibition rate of volatile substances produced by K2 on B. cinerea reached 100%, and the inhibition effect was correlated with the amount of volatile substances in the culture broth. K2 was identified as Streptomyces lydicus through the 16S rRNA gene sequence (maximum identity of 99%), glutamicin, fengamycin and natamycin were detected in the culture broth with high performance liquid chromatography. A total of 30 volatile substances including olefins, alcohols, esters and alkenes were detected using headspace solid phase micro-extraction gas chromatography and mass spectroscopy, in which 2-methylisoborneol, 1-undecene, p-menth-8-ene and 3-methylene were the major biochemicals. Two substances with fungicidal activity, benzothiazole and β-pinene, were detected as well. [Conclusion] The strain K2 was identified as Streptomyces lydicus and its culture broth had a broad spectrum of bioactivities against different plant pathogens, and its volatile substances also had good inhibitory effects on B. cinerea. As a result, K2 can be used as a high-quality biocontrol agent to develop bio-fungicides for controlling gray mold on some fruit and vegetable crops.

Abstract:[Objective] In this study, we identified possibly critical sites for the higher glucose tolerance and promotion of Bgl2A through three ways, and checked their significance by mutation and characterized the mutants. Further, we investigated the mechanism of the critical sites affecting the glucose tolerance and promotion by molecular docking. Further, Bgl3A (Bgl2A:A22S/V224S), with low glucose tolerance, was rationally engineered to obtain mutants with better application potential. [Methods] Through sequence and structure comparison, statistical coupling analysis, and structural analysis, we selected the residues in the substrate tunnel and near the active center that may indirectly affect the glucose tolerance and promotion for mutations to different type amino acids, then prepared the mutants and tested their enzymatic properties. [Results] Some mutants with higher glucose tolerance and promotion, such as D322I, W325A, W126Y, F172N, C173I and N226V were obtained. Molecular docking showed that these mutations may change the energy of glucose binding to the active center by allosteric effect, thus influence the glucose tolerance and promotion. Based on the above results, corresponding mutants were then made for Bgl3A. Some mutants, such as N226V and F172N, with high glucose tolerance and promotion while considerable activity and stability remained, have higher application potential. [Conclusion] The results demonstrated that in addition to the sites where glucose directly binds to, there are other sites that do not interact directly with glucose can indirectly influence the glucose tolerance and promotion of β-glucosidase through long range effect, which provides a new clue for rational engineering β-glucosidases.