应用和环境微生物学 (AEM) 发表的论文对 (A) 应用微生物学，包括生物技术、蛋白质工程、生物修复和食品微生物学，(B) 微生物生态学，包括环境、有机体和基因组微生物学，以及 (C) 做出了重大贡献。 ) 跨学科微生物学，包括无脊椎动物微生物学、植物微生物学、水生微生物学和地球微生物学。

The journal 'Applied and Environmental Microbiology' publishes papers in the following areas: (A) Applied Microbiology, including biotechnology, protein engineering, bioremediation, and food microbiology; (B) Microbial Ecology, covering environmental microbiology, organismal microbiology, and genomic microbiology; (C) Interdisciplinary Microbiology, which includes invertebrate microbiology, plant microbiology, aquatic microbiology, and earth microbiology. These studies have made significant contributions to their respective fields.

《Applied and Environmental Microbiology》期刊发表的论文涵盖以下领域：(A) 应用微生物学，包括生物技术、蛋白质工程、生物修复和食品微生物学；(B) 微生物生态学，涉及环境微生物学、有机体微生物学和基因组微生物学；(C) 跨学科微生物学，包括无脊椎动物微生物学、植物微生物学、水生微生物学和地球微生物学。这些研究对相关领域做出了重要贡献。

Applied and Environmental Microbiology

ABSTRACT Soils were incubated for 80 days in a continuously labeled 14 CO 2 atmosphere to measure the amount of labeled C incorporated into the microbial biomass. Microbial assimilation of 14 C differed between soils and accounted for 0.12% to 0.59% of soil organic carbon (SOC). Assuming a terrestrial area of 1.4 × 10 8 km 2 , this represents a potential global sequestration of 0.6 to 4.9 Pg C year −1 . Estimated global C sequestration rates suggest a “missing sink” for carbon of between 2 and 3 Pg C year −1 . To determine whether 14 CO 2 incorporation was mediated by autotrophic microorganisms, the diversity and abundance of CO 2 -fixing bacteria and algae were investigated using clone library sequencing, terminal restriction fragment length polymorphism (T-RFLP), and quantitative PCR (qPCR) of the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) gene ( cbbL ). Phylogenetic analysis showed that the dominant cbbL -containing bacteria were Azospirillum lipoferum , Rhodopseudomonas palustris , Bradyrhizobium japonicum , Ralstonia eutropha , and cbbL -containing chromophytic algae of the genera Xanthophyta and Bacillariophyta . Multivariate analyses of T-RFLP profiles revealed significant differences in cbbL -containing microbial communities between soils. Differences in cbbL gene diversity were shown to be correlated with differences in SOC content. Bacterial and algal cbbL gene abundances were between 10 6 and 10 8 and 10 3 to 10 5 copies g −1 soil, respectively. Bacterial cbbL abundance was shown to be positively correlated with RubisCO activity ( r = 0.853; P &lt; 0.05), and both cbbL abundance and RubisCO activity were significantly related to the synthesis rates of [ 14 C]SOC ( r = 0.967 and 0.946, respectively; P &lt; 0.01). These data offer new insights into the importance of microbial autotrophy in terrestrial C cycling.

Hongzhao Yuan

Tida Ge

Caiyan Chen

Anthony G. O'Donnell

Jinshui Wu

Appl Environ Microbiol

Significant Role for Microbial Autotrophy in the Sequestration of Soil Carbon

Diamines are important monomers for polyamide plastics; they include 1,3-diaminopropane, 1,4-diaminobutane, 1,5-diaminopentane, and 1,6-diaminohexane, among others. With increasing attention on environmental problems and green sustainable development, utilizing renewable raw materials for the synthesis of diamines is crucial for the establishment of a sustainable plastics industry. Recently, high-performance microbial factories, such as Escherichia coli and Corynebacterium glutamicum , have been widely used in the production of diamines.

Li Wang

Guohui Li

Yu Deng

Diamine Biosynthesis: Research Progress and Application Prospects

Metformin is commonly used as the first line of medication for the treatment of metabolic syndromes, such as obesity and type 2 diabetes (T2D). Recently, metformin-induced changes in the gut microbiota have been reported; however, the relationship between metformin treatment and the gut microbiota remains unclear. In this study, the composition of the gut microbiota was investigated using a mouse model of high-fat-diet (HFD)-induced obesity with and without metformin treatment. As expected, metformin treatment improved markers of metabolic disorders, including serum glucose levels, body weight, and total cholesterol levels. Moreover, Akkermansia muciniphila (12.44%±5.26%) and Clostridium cocleatum (0.10%±0.09%) abundances increased significantly after metformin treatment of mice on the HFD. The relative abundance of A. muciniphila in the fecal microbiota was also found to increase in brain heart infusion (BHI) medium supplemented with metformin in vitro. In addition to the changes in the microbiota associated with metformin treatment, when other influences were controlled for, a total of 18 KEGG metabolic pathways (including those for sphingolipid and fatty acid metabolism) were significantly upregulated in the gut microbiota during metformin treatment of mice on an HFD. Our results demonstrate that the gut microbiota and their metabolic pathways are influenced by metformin treatment.

Heetae Lee

GwangPyo Ko

Effect of Metformin on Metabolic Improvement and Gut Microbiota

ABSTRACT Quantitative differentiation of live cells in biosolids samples, without the use of culturing-based approaches, is highly critical from a public health risk perspective, as recent studies have shown significant regrowth and reactivation of indicator organisms. Persistence of DNA in the environment after cell death in the range of days to weeks limits the application of DNA-based approaches as a measure of live cell density. Using selective nucleic acid intercalating dyes like ethidium monoazide (EMA) and propidium monoazide (PMA) is one of the alternative approaches to detecting and quantifying viable cells by quantitative PCR. These compounds have the ability to penetrate only into dead cells with compromised membrane integrity and intercalate with DNA via their photoinducible azide groups and in turn inhibit DNA amplification during PCRs. PMA has been successfully used in different studies and microorganisms, but it has not been evaluated sufficiently for complex environmental samples such as biosolids. In this study, experiments were performed with Escherichia coli ATCC 25922 as the model organism and the uidA gene as the target sequence using real-time PCR via the absolute quantification method. Experiments with the known quantities of live and dead cell mixtures showed that PMA treatment inhibits PCR amplification from dead cells with over 99% efficiency. The results also indicated that PMA-modified quantitative PCR could be successfully applied to biosolids when the total suspended solids (TSS) concentration is at or below 2,000 mg·liter −1 .

Bilgin Taskin

Ayse Gul Gozen

Metin Duran

Selective Quantification of Viable Escherichia coli Bacteria in Biosolids by Quantitative PCR with Propidium Monoazide Modification

ABSTRACT Despite a wealth of experimental evidence concerning the efficacy of the biocidal action associated with the TiO 2 photocatalytic reaction, our understanding of the photochemical mechanism of this particular biocidal action remains largely unclear. It is generally accepted that the hydroxyl radical (·OH), which is generated on the surface of UV-illuminated TiO 2 , plays the main role. However, our understanding of the exact mode of action of the hydroxyl radical in killing microorganisms is far from complete, and some studies report that other reactive oxygen species (ROS) (H 2 O 2 and O 2 · − , etc.) also play significant roles. In particular, whether hydroxyl radicals remain bound to the surface or diffuse into the solution bulk is under active debate. In order to examine the exact mode of action of ROS in inactivating the microorganism, we tested and compared the levels of photocatalytic inactivation of MS-2 phage and Escherichia coli as representative species of viruses and bacteria, respectively. To compare photocatalytic microbial inactivation with the photocatalytic chemical degradation reaction, para -chlorobenzoic acid, which rapidly reacts with a hydroxyl radical with a diffusion-limited rate, was used as a probe compound. Two different hydroxyl radical scavengers, tert -butanol and methanol, and an activator of the bulk phase hydroxyl radical generation, Fe 2+ , were used to investigate their effects on the photocatalytic mode of action of the hydroxyl radical in inactivating the microorganism. The results show that the biocidal modes of action of ROS are very different depending on the specific microorganism involved, although the reason for this is not clear. It seems that MS-2 phage is inactivated mainly by the free hydroxyl radical in the solution bulk but that E. coli is inactivated by both the free and the surface-bound hydroxyl radicals. E. coli might also be inactivated by other ROS, such as O 2 · − and H 2 O 2 , according to the present results.

Min Cho

Hyenmi Chung

Wonyong Choi

Jeyong Yoon

Different Inactivation Behaviors of MS-2 Phage and Escherichia coli in TiO 2 Photocatalytic Disinfection

ABSTRACT Because of the urgent need for new antibiotics to treat drug-resistant bacterial pathogens, we employed an assay that rapidly screens large quantities of compounds for their ability to interfere with bacterial protein synthesis, in particular, the delivery of amino acids to the ribosome via tRNA and elongation factor Tu (EF-Tu). We have identified a drug lead, named MGC-10, which kills Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), with a MIC of 6 µM, while being harmless to mammalian cells in vitro in that concentration range. The antibacterial activity of MGC-10 was broad against over 50 strains of antibiotic-resistant samples obtained from hospital infections, where MGC-10 inhibited all tested strains of MRSA. Extensive selection and screening with MGC-10 did not yield any resistant strains, indicating it may have universal antibacterial activity against S. aureus . Pharmacokinetics performed in mice suggested that MGC-10 was too toxic for systemic use; however, it appears to have potential as a topical treatment for difficult-to-treat wounds or skin infections by Gram-positive pathogens such as MRSA. In a mouse skin-infection model with MRSA, MGC-10 performed as well or better than the present topical drug of choice, mupirocin. MGC-10 showed little, if any, accumulation in the livers of topically treated mice. These results bode well for the future use of MGC-10 in clinical application as it could be used to treat a broad range of S. aureus skin infections that are resistant to known antibiotics. IMPORTANCE There is a critical need for new antibiotics to treat bacterial infections caused by pathogens resistant to many if not all currently available antibiotics. We describe here the identification of a prospective new antibiotic from high-throughput screening of a chemical library. The screening was designed to detect the inhibition of formation of a complex required for bacterial protein synthesis in all bacteria, the “ternary complex,” comprised of elongation factor Tu (EF-Tu), aminoacyl-tRNA, and GTP. The inhibitory compound, renamed MGC-10, was effective against all Gram-positive bacteria, including a wide variety of methicillin-resistant Staphylococcus aureus (MRSA) strains. Although apparently too toxic for systemic use, the compound was safe and effective for topical use for treating skin infections in a mouse model. No resistance to the compound has been detected thus far, suggesting the potential to develop this compound for topical use to treat infections, especially those caused by pathogens resistant to existing antibiotics.

Wlodek Mandecki

Maxim Chudaev

Wenjuan Ye

Amy Q. Wang

Kenneth J. Wilson

Xin Xu

Jisun Kim

Dane Parker

David Alland

Pradeep Kumar

Barry Li

Jason H. Yang

Barry Kreiswirth

Jose R. Mediavilla

Juan J. Marugan

Mark J. Henderson

Emanuel Goldman

Identification of an antibiotic from an HTS targeting EF-Tu:tRNA interaction: a prospective topical treatment for MRSA skin infections

鉴定一种针对EF-Tu:tRNA相互作用的HTS抗生素：一种潜在的MRSA皮肤感染局部治疗方法

ABSTRACT This study explored the genomic alterations in Yarrowia lipolytica , a key yeast in industrial biotechnology, under both spontaneous and mutagen-induced conditions. Our findings reveal that spontaneous mutations occur at a rate of approximately 4 × 10 −10 events per base pair per cell division, primarily manifesting as single-nucleotide variations (SNVs) and small insertions and deletions (InDels). Notably, C-to-T/G-to-A transitions and C-to-A/G-to-T transversions dominate the spontaneous SNVs, while 1 bp deletions, likely resulting from template slippage, are the most frequent InDels. Furthermore, chromosomal aneuploidy and rearrangements occur, albeit at a lower frequency. Exposure to ultraviolet (UV) light, methylmethane sulfonate (MMS), and Zeocin significantly enhances the rates of SNVs and alters their mutational spectra in distinct patterns. Notably, Zeocin-induced SNVs are predominantly T-to-A and T-to-G substitutions, often occurring within the 5′-TGT * −3′ motif ( * denotes the mutated base). Additionally, Zeocin exhibits a higher potency in stimulating InDels compared to UV and MMS. Translesion DNA synthesis is implicated as the primary mechanism behind most Zeocin-induced SNVs and some InDels, whereas non-homologous end joining serves as the main pathway for Zeocin-mediated InDels. Intriguingly, the study identifies the gene YALI1_E21053g , encoding a protein kinase, as negatively associated with Zeocin resistance. Overall, our results not only deepened our knowledge about the genome evolution in Y. lipolytica but also provided reference to develop innovative strategies to harness its genetic potential. IMPORTANCE Yarrowia lipolytica exhibits high environmental stress tolerance and lipid metabolism capabilities, making it a microorganism with significant industrial application potential. In this study, we investigated the genomic variation and evolutionary patterns of this yeast under both spontaneous and induced mutation conditions. Our results reveal distinctive mutation spectra induced by different mutagenic conditions and elucidate the underlying genetic mechanisms. We further highlight the roles of non-homologous end joining and translesion synthesis pathways in Zeocin-induced mutations, demonstrating that such treatments can rapidly confer drug resistance to the cells. Overall, our research enhances the understanding of how yeast genomes evolve under various conditions and provides guidance for developing more effective mutagenesis and breeding techniques.

Yuan-Ru Xiong

Yuan-Chun Fang

Min He

Ke-Jing Li

Lei Qi

Yang Sui

Ke Zhang

Xue-Chang Wu

Liang Meng

Ou Li

Dao-Qiong Zheng

Patterns of spontaneous and induced genomic alterations in Yarrowia lipolytica

Yarrowia lipolytica 自发和诱导基因组改变的模式

ABSTRACT Mildiomycin is a representative peptidyl nucleoside antibiotic and was first isolated from Streptoverticillium rimofaciens , which has been used as an important biological agent to control powdery mildew in plants. Despite its importance, the biosynthetic pathways and regulatory mechanisms remain to be fully elucidated. In this study, we identified MilO as a positive pathway-specific regulator of mildiomycin biosynthesis in the heterologous host Streptomyces avermitilis . Gene disruption of milO resulted in almost loss of mildiomycin production, and it was restored to the level comparable to that in the wild-type strain in complemented strain. Overexpression of milO using host native promoter rpsJ p, engineered promotor SP44, and kasO p* led to a 50%, 6.5-fold, and 9.2-fold increase in mildiomycin production compared with the wild-type strain, respectively. Quantitative real-time PCR and electrophoretic mobility shift assay (EMSA) experiments revealed that MilO directly enhances the transcription of the milA gene by 20 folds after 48 h fermentation and indirectly regulates the transcription levels of other genes from milB to milM . Using DNase I footprinting assays, milO was revealed to bind to a 44 bp DNA sequence of the milA promoter region. The binding region consists of three imperfect direct repeats of TGTC(N) 3 CGGT separated by two-nucleotide spacers and each repeat is important to efficient binding to MilO. In addition, we identified two related compounds by overexpressing milO in a structural gene milN -deficient mutant. Taken together, this study indicates that pathway-specific regulator MilO is essential for mildiomycin biosynthesis and provides an effective strategy to improve the production of mildiomycin and its intermediates. IMPORTANCE As an important biological agent to control powdery mildew on plants, mildiomycin has been commercialized and used in various plants. However, its regulatory mechanisms and biosynthetic pathways remain unknown. This study provides new insights into the regulation of mildiomycin biosynthesis through MilO, a LuxR family protein that modulates mildiomycin production by directly enhancing the transcription of milA . The yield of mildiomycin was significantly improved by overexpressing milO in a heterologous host. In addition, the positive regulatory effect of milO helped to discover two related compounds, which provide important clues for the timing of uploading of two amino acid side chains during mildiomycin biosynthesis for the first time. In brief, our findings on transcriptional regulation of mildiomycin biosynthesis by milO will be valuable to further increase the yield of mildiomycin and explore its biosynthetic pathways.

Zhiyu Li

Yuli Wang

Chen Lin

Yu Wen

Zixin Deng

Ming Jiang

Xinyi He

Positive regulation of a LuxR family protein, MilO, in mildiomycin biosynthesis

米尔多霉素生物合成中LuxR家族蛋白MilO的正调控作用

ABSTRACT Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing Bacillus velezensis FZB42 and two bacterial strains susceptible to its antibiotics: Xanthomonas euvesicatoria 85-10 and Pseudomonas syringae DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably , X. euvesicatoria shows increased protection against both the cells and supernatants of B. velezensis under wet-dry cycles, while P. syringae cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between P. syringae and B. velezensis , where P. syringae inhibits B. velezensis under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance. IMPORTANCE Our study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by Bacillus velezensis against two susceptible bacterial species: Xanthomonas and Pseudomonas varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.

Yana Beizman-Magen

Tomer Orevi

Nadav Kashtan

Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes

水合条件作为抗生素介导的细菌竞争结果的关键因素

ABSTRACT During the establishment of the symbiosis with legume plants, rhizobia are exposed to hostile physical and chemical microenvironments to which adaptations are required. Stress response proteins including small heat shock proteins (sHSPs) were previously shown to be differentially regulated in bacteroids induced by Rhizobium leguminosarum bv. viciae UPM791 in different hosts. In this work, we undertook a functional analysis of the host-dependent sHSP RLV_1399. A rlv_1399- deleted mutant strain was impaired in the symbiotic performance with peas but not with lentil plants. Expression of rlv_1399 gene was induced under microaerobic conditions in a FnrN-dependent manner consistent with the presence of an anaerobox in its regulatory region. Overexpression of this sHSP improves the viability of bacterial cultures following exposure to hydrogen peroxide and to cationic nodule-specific cysteine-rich (NCR) antimicrobial peptides. Co-purification experiments have identified proteins related to nitrogenase synthesis, stress response, carbon and nitrogen metabolism, and to other relevant cellular functions as potential substrates for RLV_1399 in pea bacteroids. These results, along with the presence of unusually high number of copies of shsp genes in rhizobial genomes, indicate that sHSPs might play a relevant role in the adaptation of the bacteria against stress conditions inside their host. IMPORTANCE The identification and analysis of the mechanisms involved in host-dependent bacterial stress response is important to develop optimal Rhizobium /legume combinations to maximize nitrogen fixation for inoculant development and might have also applications to extend nitrogen fixation to other crops. The data presented in this work indicate that sHSP RLV_1399 is part of the bacterial stress response to face specific stress conditions offered by each legume host. The identification of a wide diversity of sHSP potential targets reveals the potential of this protein to protect essential bacteroid functions. The finding that nitrogenase is the most abundant RLV_1399 substrate suggests that this protein is required to obtain an optimal nitrogen-fixing symbiosis.

Lucía Domingo-Serrano

Claudia Sanchis-López

Carla Alejandre

Joanna Soldek

José Manuel Palacios

Marta Albareda

A microaerobically induced small heat shock protein contributes to Rhizobium leguminosarum / Pisum sativum symbiosis and interacts with a wide range of bacteroid proteins

微需氧诱导的小热休克蛋白有助于Rhizobium leguminosarum / Pisum sativum共生并与广泛的类菌体蛋白相互作用

Abbreviation	Appl Environ Microbiol
Journal Impact	3.85
Quartiles(Global)	MICROBIOLOGY(Q2)

ISSN	0099-2240, 1098-5336
h-index	367

Publication Information	Publisher: American Society for Microbiology，Publishing cycle: Semimonthly，Journal Type: journal，Open Access Journals: No
Basic data	Year of publication: 1976，Proportion of original research papers: 98.45%，Self Citation Rate:2.60%， Gold OA Rate: 24.98%
Average review cycle	网友分享经验：平均1.9个月
Average recruitment ratio	网友分享经验：60%

Applied and Environmental Microbiology

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