Applied and Environmental Microbiology最新文献

Limnospira fusiformis, a nutritionally valuable cyanobacterium with significant biomanufacturing potential, faces critical challenges from pathogenic invasions. This study identified Halomonas variabilis 2-9 as the primary pathogen of L. fusiformis cultivation collapse, demonstrating broad-spectrum algicidal activity against multiple cyanobacterial species. Additionally, the algicidal substance produced by H. variabilis 2-9 was purified and identified as toxic dibutyl phthalate. At a concentration of 3 µg/mL, the purified algicidal substance caused 90.6% reduction in Fv/Fm within 24 h and 86% degradation of chlorophyll-a within 120 h. To be specific, Fv/Fm as the maximum photochemical quantum yield of photosystem II is a core indicator reflecting the photosynthetic activity and health status of spirulina. A sudden drop in Fv/Fm of spirulina indicates impaired function of Photosystem II. Therefore, the purified algicidal substance severely damaged the photosynthetic system of L. fusiformis. To mitigate the detrimental effects of H. variabilis 2-9, Bacillus velezensis L4 was isolated from deep-sea sediments. This strain produced an antimicrobial compound (C₃₁H₄₂O₂) that specifically inhibited H. variabilis 2-9 without damaging L. fusiformis. In co-culture experiments, B. velezensis L4 reversed Halomonas-induced algal decay, demonstrating its potential as a biocontrol agent. These findings provide both mechanistic insights into Halomonas-mediated cyanobacterial pathogenesis and a practical solution for sustainable aquaculture management.

Importance: This study identifies H. variabilis 2-9 as a novel cyanobacterial pathogen that produces hazardous compound dibutyl phthalate (DBP), causing severe damage to L. fusiformis and exhibiting broad-spectrum algicidal activity against other cyanobacteria. The discovery of DBP-mediated pathogenesis provides crucial insights into microbial threats to aquaculture systems. Significantly, we demonstrate that B. velezensis L4, isolated from deep-sea environments, serves as an effective biocontrol agent through the production of a selective antimicrobial compound that specifically targets H. variabilis 2-9 without harming L. fusiformis. These findings offer both fundamental understanding of cyanobacterial disease mechanisms and a practical, sustainable solution for algal disease management.

Mannose, a common monosaccharide with primary functions in protein glycosylation and immune regulation, has been widely used in medicine, cosmetics, and food additives, increasing its economic value. In our study, the ppc gene was knocked out in Enterobacter aerogenes IAM1183 to regulate phosphoenolpyruvate carboxylase activity, thereby optimizing hydrogen-producing metabolism. Unexpectedly, the mutant strain exhibited successful production of a substantial amount of polysaccharides with a yield of 6.75 ± 0.20 g∙L^-1, a feature not observed in the original strain. Notably, the four main monosaccharides of the detected polysaccharide were mannose, glucuronic acid, glucose, and galactose, with proportions of 50.28%, 24.15%, 18.35%, and 7.2%, respectively. According to the transcriptional analysis, 481 genes were significantly differentially expressed, 47% of which were metabolism-related, encoding key enzymes of amino acid and carbohydrate metabolism, phosphotransferase system, and exopolysaccharide synthesis. It was speculated that the deletion of ppc not only enhanced the extracellular polysaccharide synthesis pathway but also affected the transport and phosphorylation of carbohydrates in cells, resulting in a distinct polysaccharide production phenotype. In this study, the production of mannose-rich exopolysaccharide (EPS) in E. aerogenes was realized for the first time. The high-mannose content of this EPS endows the mutant strain with significant potential as a candidate for downstream mannose extraction and utilization. Concurrently, this work delineates a pathway to mannose-rich EPS production in E. aerogenes, thereby enhancing the understanding of its metabolic network in this non-model microorganism.

Importance: Mannose is a crucial monosaccharide with diverse applications in multiple industries, yet current production methods have limitations. Our study is of great importance as it represents the first instance of mannose-rich polysaccharides being identified in Enterobacter aerogenes when hydrogen production metabolism is optimized by knocking out the ppc gene. Transcriptomic analysis suggested that the ppc gene knockout affected numerous genes related to metabolism, which is crucial for further exploring the metabolic regulation mechanism of Enterobacter aerogenes. This study reports a novel genetically engineered strain and a systematic methodology for mannose biosynthesis, thereby identifying candidate regulatory nodes within its metabolic network in this non-model microorganism.

High-throughput sequencing is a powerful tool for environmental microbiology and can be particularly important for examining community structure and function for organisms that are difficult to culture or environments that are difficult to mimic, like snow. Nucleic acid extraction significantly impacts these analyses, often introducing more variation between samples than PCR or sequencing. Snow algae are widespread on mountain and polar snowfields, where they contribute to biogeochemical cycling and accelerate melt. Despite increasing research on snow algae, DNA extraction remains challenging, as the thick, resilient walls of snow algal cysts can limit cell lysis, and differences among extraction methods may therefore affect the estimates of community composition and richness. Here, we compared three common extraction methods (Qiagen DNeasy PowerSoil Pro, Qiagen DNeasy PowerWater, and phenol-chloroform) alongside ultrasonication in samples with varying snow algae abundance. The extraction method strongly influenced the resulting microbial profiles assessed by amplicon sequencing of rRNA genes. Ultrasonication improved DNA yield in low-biomass samples and enhanced the recovery of DNA from resilient cells, including mature-phase snow algae, likely due to improved cell lysis. Our findings provide insights to improve standardization and facilitate comparison among studies in snow and ice environments.IMPORTANCEHigh-throughput sequencing has transformed environmental microbiology, allowing for detailed, culture-independent analyses of microbial communities. However, multiple methodological factors, including DNA extraction, can introduce variability in results, making cross-study comparisons challenging. This research contributes to improving our understanding of snow algae, which play a role in alpine and polar ecosystems by influencing biogeochemical cycles and snow reflectivity. By evaluating common DNA extraction techniques for snow algae, this study helps improve the reliability and reproducibility of sequencing data, supporting broader efforts toward methodological standardization in microbial ecology.

Lignin is one of the most common biopolymers on Earth. In nature, lignin is primarily deconstructed by fungi into mixtures of aromatic compounds that are then assimilated by bacteria and fungi. Industrially, lignin is primarily generated as a byproduct of pulp and paper production and burned for process heat. However, if the appropriate assimilatory pathways were identified, deconstructed lignin could be funneled into value-added products using engineered bacteria. Foundational work has described pathways for assimilation of diverse monomeric aromatic compounds such as protocatechuate, ferulate, and syringate, as well as select dimers including those with β-O-4 and 5-5 interunit linkages. Recent advances have elucidated additional pathways for dimer assimilation, including pathways for new substrates as well as parallel pathways for previously characterized substrates. Comparing these dimer assimilation pathways can illuminate the underlying biochemical logic of assimilation for lignin-associated aromatic dimers and provide opportunities for metabolic engineering to enhance lignin valorization.

Inadequate management of lignocellulosic waste poses a risk of substantial environmental pollution. Enriched microbial communities selected from environmental samples can effectively contribute to lignocellulose degradation. Utilizing a lower diversity but equally effective microbial community can enhance the control and efficiency of industrial operations. However, the mechanisms of cellulose degradation and functional microbial interactions within microbial communities with reduced diversity remain unclear. In this study, high-diversity and low-diversity lignocellulose-degrading communities were constructed using the dilution-to-stimulation and dilution-to-extinction methods. The enzymatic activity, community composition, degradation pathways, key functional microbes, and microbial co-occurrence network during cellulose degradation were analyzed in both high-diversity and low-diversity communities at the DNA and RNA level. Results showed that the low-diversity community exhibited a higher substrate degradation rate than the higher-diversity community. The activity of FPase and CMCase in the low-diversity community was significantly higher. Sphingobacterium, Pseudoxanthomonas, and Devosia were key players in the high-diversity community. Cellulomonas played a significant role in the low-diversity community. Reducing community diversity strengthens the cooperation among functional microbes. This study can guide the design of functional microbial synthetic communities and also can help to expand the ecological understanding of lignocellulosic waste degradation in synthetic microbial systems.IMPORTANCEMicrobial community diversity is pivotal in the degradation of lignocellulose. Nonetheless, reducing microbial diversity does not invariably result in decreased degradation efficiency. The utilization of low-diversity communities offers several advantages in industrial applications. Previous studies on lignocellulose-degrading functional microbial communities with low diversity have predominantly concentrated on community composition, with limited investigation into functionality and microbial interaction mechanisms. In this study, we constructed microbial communities with high and low diversity to investigate their efficiency in lignocellulose degradation and to elucidate the microbial ecological mechanisms. Our findings indicate that communities with low diversity decreased microbial competition and altered the composition of key functional microbes during the lignocellulose degradation process, thereby enhancing the efficiency of lignocellulose degradation. Investigating the microbial ecological mechanisms underlying lignocellulose degradation in both high- and low-diversity microbial communities can aid in the design of synthetic functional microbial communities and significantly contribute to the bioconversion of lignocellulosic waste.

The proliferation of antibiotic resistance genes (ARGs) in environmental microbiomes represents a major and growing threat to public health, creating a critical demand for precise and efficient tools to monitor resistance risk. Current approaches often depend on contig-based quantification or lack comprehensive risk indices, which compromises their accuracy and utility. To address this, we developed MetaRanker (https://github.com/SteamedFish6/MetaRanker), a computational pipeline that assesses resistome risk by integrating the abundance of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs)-calculated directly from sequencing reads-with their genetic co-occurrence on contigs into a unified risk index (RI). This index reflects the potential for horizontal transfer and pathogen emergence. Evaluated using in silico and diverse real-world metagenomes (n = 353), MetaRanker demonstrated superior accuracy and stronger discriminatory power than existing methods. Its optimized compact database (29.6 MB) and alignment strategy reduced runtime by over 50% in comparison to MetaCompare 2.0 under identical hardware configurations (32 CPU cores, 128 GB RAM). Practical applications confirmed that MetaRanker effectively discriminates risk levels across environments (e.g., hospital wastewater versus natural soil) and quantifies risk mitigation through wastewater treatment. As a robust, lightweight, and sequencing-platform-agnostic tool, MetaRanker offers a powerful solution for comprehensive environmental resistome surveillance and evidence-based risk management.IMPORTANCEThe environmental reservoir of antibiotic resistance is a key contributor to the global health crisis of antimicrobial resistance. Effective surveillance and risk assessment of complex microbial communities are essential for prioritizing interventions and safeguarding public health. However, existing methods often provide fragmented or computationally demanding analyses, limiting their practical application for large-scale environmental monitoring. The significance of our work lies in developing MetaRanker, which overcomes these barriers by delivering a fast, accurate, and integrated metric of resistome risk. By simultaneously accounting for the abundance, mobility potential, and pathogenicity linkage of resistance determinants, MetaRanker enables a more realistic threat assessment. This tool empowers researchers and public health officials to track resistance hotspots, evaluate the impact of human activities such as waste disposal, and monitor the effectiveness of mitigation strategies, ultimately supporting data-driven decisions to curb the environmental spread of resistance.

Lentinula edodes (L. edodes) is the largest proportion of edible mushrooms in China. However, the yield is highly susceptible to environmental stress. Factors such as high-temperature stress, low-temperature stress, Trichoderma infection, heavy metal stress, and light exposure all impact the growth status of L. edodes mycelium to varying degrees. Small GTPase is a small molecular switch involved in multiple biological processes of eukaryotes. The main functions of small GTPase in fungi include morphogenesis, secondary metabolism, vesicle trafficking, stress response, and virulence. However, the understanding of small GTPase in L. edodes is minimal. In this study, a total of 34 small GTPase genes in L. edodes were identified and clustered into five subfamilies, namely, Rho, Ras, Arf, Rab, and Ran. The 34 identified genes were phylogenetically analyzed and compared with those of various ascomycetes and basidiomycetes using the genome assembly and annotation databases of L. edodes. The results of expression patterns of 34 small GTPase genes under different biotic and abiotic stresses showed that most of these genes exhibited different degrees of responses to different stresses. The gene function analysis showed that the heat tolerance, resistance to Trichoderma atroviride (T. atroviride) infection, and light sensitivity of the LeRho1 overexpression transformants were significantly higher than those of the control transformants. This study verified that LeRho1 is an important stress-resistant gene in L. edodes and that this gene is distributed in edible fungi. This study verified that LeRho1 is an important stress-resistant gene in L. edodes and that this gene is distributed in edible fungi. Our findings provide a theoretical basis for further research on the stress response mechanism of the small GTPases in large edible fungi.IMPORTANCEThis study verified that LeRho1 is an important stress-resistant gene in L. edodes and that this gene is distributed in edible fungi. Clarifying the function of LeRho1 protein in the heat stress response of L. edodes, and analyzing the differentiation of the structure and function of small GTPase in fungi such as L. edodes, Saccharomyces cerevisiae, and Aspergillus fumigatus, is of great significance for elucidating the heat stress response mechanism of filamentous fungi of Agariales under heat stress and for conducting germplasm innovation for heat-tolerant edible fungi.

Globally, the rise in antibiotic-resistant pathogens has underscored the urgent need for new strategies to discover antimicrobials, with emphasis on microbial producers of secondary metabolites. The influence of pH on bacterial recovery, metabolite expression, and antibacterial activity in isolates from marine sediments was evaluated in this study. Three culture media were used to isolate sediment bacteria across a pH gradient (5.0-8.0), and conventional biochemical methods were employed for putative identification of the bacterial isolates. The agar plug assay was used for primary antibacterial screening, while the disk diffusion assay of the cell-free and sonicated extracts was used for secondary screening after 7 days of submerged fermentation of the isolates at their different culture pH levels. The results revealed the predominance of Bacillus species from the different pH levels, with zones of inhibition ranging from 10.00 ± 1.00 to 47.50 ± 2.50 mm against clinical and environmental isolates. The four Bacillus species-like isolates selected for submerged fermentation showed a pH drift toward alkalinity, except for the culture initiated at pH 7.5, which remained stable. The secondary screening revealed a markedly reduced antibacterial activity for all isolates (≤9 mm) compared to primary screening, with the pH 7.5 isolate retaining the strongest inhibition. The findings suggest that pH stability during fermentation was strongly associated with sustained antibacterial activity, with isolates maintained at near-constant pH retaining significantly higher inhibitory activity than those in cultures whose pH increased during fermentation. This highlights a key consideration for the bioprospecting workflow targeting biosynthetic gene clusters and producers of secondary metabolites.

Importance: Marine environments are important reservoirs of bacteria capable of producing bioactive secondary metabolites; however, many promising antimicrobial producers identified during initial screening fail to retain activity during fermentation. This study demonstrates that pH stability during fermentation, rather than pH value alone, is a key determinant of sustained antibacterial metabolite production in marine sediment-derived Bacillus species. By linking isolation conditions, fermentation physiology, and bioactivity outcomes, the findings provide practical guidance for improving the reliability of marine bioprospecting and antimicrobial discovery pipelines. These insights are particularly relevant for efforts to recover stable antimicrobial producers from complex environmental systems.