Applied and Environmental Microbiology最新文献

Deep-sea ferromanganese nodules are valuable materials for investigating microorganism-mediated geochemical cycling of manganese. While many microbial metabolic pathways are closely associated with manganese reduction, few studies have examined the role of amino acid metabolism in the release of Mn(II) from these nodules. Here, we explored the impact of non-proteinogenic β-alanine metabolism on manganese reduction. Halomonas sp. MNB13 is an indigenous bacterium isolated from a ferromanganese nodule that can reduce Mn oxides and decrease the pH of the environment during Mn(II) release. Comparative transcriptomic analysis unveiled that exposure to MnO₂ significantly upregulated β-alanine metabolism, leading to a reduced intracellular concentration of β-alanine. Exogenous β-alanine decreased the proportion of Mn(IV) without changing the type of Mn residues by promoting MNB13 growth and reshaping the profile of secreted organic acids. β-Alanine elevated energy metabolism in MNB13 and increased catalase activity, mitigating reactive oxygen species generated during Mn(II) release and thereby enhancing bacterial growth. Among the secreted organic acids, levulinate and pantothenate showed altered abundance and were confirmed to promote Mn(II) release following β-alanine supplementation. This study suggests that environmental β-alanine modulates Mn(IV) reduction by promoting bacterial growth and organic acid secretion, offering novel insights into bacteria-mediated Mn(II) release from deep-sea ferromanganese nodules.

Importance: Microorganisms are believed to play a role in the biotic processes of deep-sea ferromanganese nodule formation and biosolubilization. Although most studies have linked microbial metabolism to manganese reduction, the role of microbial amino acid metabolism in the release of Mn(Ⅱ) from ferromanganese nodules into seawater remains underexplored. β-Alanine is a naturally occurring non-proteinogenic β-amino acid widely distributed in the marine environment. However, its role in Mn(Ⅳ) reduction is unclear. This study demonstrated that Mn oxides upregulate β-alanine metabolism in Halomonas sp. MNB13 and external β-alanine significantly enhances Mn(Ⅱ) release from Mn oxides. We showed that ferromanganese nodules induce β-alanine metabolism and lead to the release of pantothenate and levulinate, decreasing the culture pH, reducing Mn(Ⅳ) to Mn(Ⅱ), and resulting in Mn(Ⅱ) release. These findings provide new insights into bacterial non-proteinogenic amino acid metabolism and its role in facilitating the Mn(Ⅱ) release from ferromanganese nodules in deep-sea environments.

Burkholderia gladioli is a critical pathogen causing bacterial panicle blight in rice, severely threatening global rice yield and grain quality. Here, B. gladioli strains were isolated and identified from two rice fields exhibiting markedly different severities of bacterial panicle blight. Although the two strains belong to the same species, they displayed significant differences in phenotype and pathogenicity. Comparative genomic and transcriptomic analyses revealed that natural variation between the strains not only arose from 79 single-nucleotide polymorphisms (SNPs), 12 insertions/deletions (INDELs), and 3 structural variations (SVs) across 27 mutated genes, which may affect protein function and stability, but also coincided with the significant downregulation of genes in multiple virulence-associated pathways, such as two-component systems, bacterial chemotaxis, quorum sensing, and flagellar assembly at the transcriptional level. The combined effects of genetic variation and transcriptional regulation ultimately contributed to the observed differences in pathogenicity. This study uncovers the potential mechanisms by which natural variation in B. gladioli influences pathogenicity, providing a theoretical basis and potential molecular targets for the precise control of rice bacterial panicle blight.

Importance: This study demonstrates that natural variation in Burkholderia gladioli, a major pathogen responsible for bacterial panicle blight in rice, has a significant impact on its pathogenicity and further explores the underlying mechanisms. These findings expand our understanding of how phytopathogens' virulence differentiates conditions of natural variation, and provide potential molecular targets for the development of novel bactericides. The identification of low-virulence strains and their associated gene variations in this study offers both theoretical and practical foundations for ecological disease management and biocontrol of rice bacterial diseases, highlighting their importance for promoting precision agriculture and sustainable development.

Malaria remains a major global health challenge, particularly in developing countries, necessitating innovative control strategies. With rising resistance of Plasmodium to drugs and Anopheles mosquitoes to insecticides, paratransgenesis-using engineered symbiotic bacteria to deliver anti-pathogen molecules-offers a promising alternative. Translating this approach to field applications requires rigorous evaluation under semi-field conditions. We evaluated the environmental stability and transmission dynamics of Serratia AS1-mCherry, a paratransgenesis candidate, in Anopheles stephensi habitats under semi-field conditions in Bandar Abbas, Iran. Serratia AS1 successfully colonized mosquito midguts and ovaries, persisted in larval breeding water for 14 days, and remained stable on sugar-soaked cotton pads for 4-6 days. Transmission routes include transstadial, venereal, and vertical transmission, in addition to adult acquisition from larval habitats (sipping), demonstrating robust colonization and dissemination. Water-based delivery effectively disseminates Serratia AS1 among mosquito populations, highlighting its potential for paratransgenesis-based malaria control. This study establishes the feasibility of using Serratia AS1 with effector molecules in field settings, offering a sustainable strategy for managing vector-borne diseases.

Importance: Malaria remains a major health challenge, especially in developing countries where traditional control methods like insecticides and drugs are becoming less effective due to resistance. This study explores a promising new approach called paratransgenesis, which uses genetically modified bacteria to fight malaria. We tested a bacterium called Serratia AS1, which can live inside mosquitoes and spread through their populations. Our experiments showed that Serratia AS1 can survive in mosquito breeding sites and spread effectively among mosquitoes through multiple routes, such as larval water, sugar sources, and even from parent mosquitoes to their offspring. These findings suggest that Serratia AS1 could be used to deliver anti-malaria molecules to mosquitoes in the wild, offering a sustainable and innovative way to control the disease. This work brings us one step closer to using paratransgenesis as a practical tool to reduce malaria transmission and save lives.

Genomic analysis revealed numerous plasmids in Thermus thermophilus strains isolated from the Senami Hot Spring in Japan. Five plasmids contained putative replication proteins (REP proteins) distinct from the pTT8-type commonly used in T. thermophilus-Escherichia coli shuttle vectors. Among them, two plasmids contained toxin-antitoxin-like tandemly aligned short open reading frames (ORFs) downstream of the putative REP protein. A series of shuttle vectors, pIOK, was constructed by cloning the putative REP protein gene and its flanking regions into an E. coli plasmid (ColE1, hygromycin-resistant). All five vectors were stably maintained in T. thermophilus HB27 in the presence of hygromycin. Among them, two containing the toxin-antitoxin-like module demonstrated greater persistence, exhibiting no plasmid loss after 168 generations of subcultivation without hygromycin. This module also enhanced the persistence of the pTT8-type shuttle vector pSN2, suggesting its broad applicability to the Thermus plasmids for stable maintenance. Quantitative PCR analysis demonstrated that the copy numbers of the pIOK vectors were equal to or greater than threefold those of the chromosomes. The pIOK vectors were compatible with one another and with pSN2. The xylan utilization pathway from Thermus brockianus (13 kbp) was split into two parts, which were cloned into pIOK and pSN2. Wild-type HB27 could not utilize xylan as the sole carbon source, while the double transformant carrying the two plasmids could, indicating the successful reconstitution of the complete xylan utilization pathway from two compatible plasmids. The pIOK vectors and toxin-antitoxin-like module will be invaluable for advancing synthetic biology research in T. thermophilus.IMPORTANCEThe rapid accumulation of genomic data from Thermus thermophilus, which we recently isolated from hot springs in Japan, has revealed the presence of plasmids with novel replication origins. We have developed a series of shuttle vectors, called pIOK, that are compatible with existing pTT8-based shuttle vectors. The effective use of multiple plasmid systems in T. thermophilus was demonstrated by dividing a relatively large (approximately 13 kbp) xylan assimilation pathway and reconstituting it using two compatible plasmids. The toxin-antitoxin-like module, located downstream of the newly identified replication proteins, significantly enhanced persistence, enabling the cultivation of the recombinant strain without the use of antibiotics. The pIOK vectors and the toxin-antitoxin-like module are expected to be valuable tools in the synthetic biology of T. thermophilus.

Predatory myxobacteria play a crucial role as key predators in the soil microbial food web, influencing microbial community structure and functions. However, the mechanisms through which myxobacteria regulate these communities and their associated ecological functions remain inadequately understood. This study aims to investigate the regulatory effects of myxobacterial predation on soil bacterial composition, community dynamics, and ecological functions using a controlled soil microcosm system. The results show that the predatory myxobacterium Corallococcus sp. EGB exhibits strong predatory activity against common agricultural soil bacteria, particularly Acinetobacter lwoffii and Bacillus subtilis. In the microcosm systems, myxobacterial predation significantly altered bacterial community composition, diversity, and carbon metabolism (P < 0.05). In soils with high microbial abundance, myxobacterial predation reduced niche breadth (P < 0.05) and decreased the contribution of stochastic processes to community assembly. Prolonged incubation also increased extracellular enzyme activities and organic carbon mineralization rates (P < 0.05). Additionally, myxobacterial predation disrupted several metabolic pathways and modulated the functional distribution of bacterial communities. These findings highlight the critical role of myxobacteria in shaping soil microbial community dynamics and ecological functions, providing new insights for sustainable soil management and agricultural optimization.IMPORTANCESoil microbial communities drive nutrient cycling and carbon transformation, underpinning soil fertility and ecosystem function. Although microbial interactions are key regulators of soil processes, the ecological roles of predatory myxobacteria in modulating community composition and dynamics remain poorly understood. Here, we provide preliminary evidence that predation by Corallococcus sp. EGB reshapes bacterial community composition, alters functional potential, and influences carbon cycling, particularly in soils with high microbial abundance. By linking microbial predation to community dynamics and soil biogeochemical processes, this study advances understanding of the ecological significance of predatory myxobacteria and underscores their potential role in sustainable soil management.

Oil contamination poses significant risks to human health and ecosystems, emphasizing the importance of studying alkane biodegradation. In this study, we found that Rhodococcus erythropolis XP can utilize various alkanes, including C16-C36 n-alkanes and iso-alkane (pristane). The degradation capacity was significant, with over 95% of C20 degraded (500-2,500 mg/L) within 72 h. The bioremediation capacity in oily sludge was determined by a novel Low Pressure Gas Chromatography-Mass Spectrometry methodology especially for rapid analysis (within 12 min) of n-alkanes. Notable biodegradation of C14-C30 alkanes was observed in sludge treated with Rhodococcus erythropolis XP. In addition, metabolic intermediates of C16 and C20 were identified, indicating the presence of both terminal and subterminal pathways in Rhodococcus erythropolis XP. A new Baeyer-Villiger monooxygenase (BVMO_4041) was characterized, which catalyzes a key step in the subterminal pathway of alkane degradation. These results reflect the promise of Rhodococcus erythropolis XP in addressing the pressing need for efficient alkane degradation in contaminated environments.IMPORTANCEOil pollution posed a severe threat to human health and environmental safety due to its chemical stability and prolonged persistence. Although a lot of bacteria have been reported to degrade alkanes, the main components in oil pollution, it is urgent to identify strains that can degrade medium- and long-chain alkanes and to evaluate their performances during bioremediation. In this study, Rhodococcus erythropolis XP has been proved to obtain the almost strongest ability to degrade C16-C36 n-alkanes and branched alkanes (pristane), and to be a promising option for oily sludge bioremediation with newly developed rapid detection technology based on low pressure gas chromatography-mass spectrometry. Meanwhile, the metabolic pathways and a new BVMO_4041 gene encoding Baeyer-Villiger monooxygenase were revealed. Our research provides a promising candidate for both practical bioremediation efforts and microbial research, and enriches the strain and gene resources for oil degradation.

Endosymbiotic interactions have long played fundamental roles in shaping the evolution and diversification of eukaryotes. However, we still have a limited understanding of how ecological processes govern the distribution of endosymbionts that are still segregating in host populations. To contribute to this understanding, here, we use the interactions between Paraburkholderia endosymbionts and their dictyostelid social amoeba hosts as a model system to investigate the role of dispersal, a fundamental ecological process, in shaping the distribution and evolution of endosymbiotic interactions. We first found that patterns of endosymbiont diversification were highly biogeographic, suggesting a significant degree of dispersal limitation. We then experimentally mediated the dispersal of several endosymbiont species into environments with multiple host species and found that each symbiont was able to sustain a high prevalence in each host population. The benefit/detriment of these mediated interactions did not change with increasing phylogenetic distance from what is suspected to be the focal amoeba host species in nature. Taken together, our findings suggest Paraburkholderia endosymbionts are generally pre-adapted to occupy a variety of dictyostelid host environments, and their distribution among host populations is subject to a high degree of dispersal limitation. Overall, our findings have significant implications for our understanding of how ecological processes facilitate and limit the evolution of endosymbiotic interactions.

Importance: Endosymbiotic interactions are ubiquitous in complex eukaryotes, as organelles such as mitochondria and chloroplasts represent the remnants of what were once free-living prokaryotes. However, how ecological processes facilitate the transition from free-living to host-associated is less understood. Selection is the most commonly invoked process to explain this transition: symbionts that are better at infecting hosts and potentially confer some benefit rise in frequency because they are selected for (and otherwise selected against). However, this only describes one fundamental process that can shape the ecology of symbiotic interactions. Here, we present evidence that the importance of dispersal (and its limitations) likely exceeds that of selection in shaping the distribution and frequency of Paraburkholderia endosymbionts in their dictyostelid social amoeba host communities. These findings highlight the need to consider regional ecological processes that operate at a scale beyond the individual when studying ecology and evolution of endosymbiotic interactions.

Within the human gut microbiota, lactic acid bacteria (LAB) play a crucial role in host health by producing lactic acid, which has been shown to shape microbial interactions and support intestinal homeostasis. However, despite their importance, there are limited insights regarding how LAB species interact with the host and other gut commensals. In this study, the investigation of the human gut microbiota of 10,000 healthy adults allowed the identification of Lactococcus lactis and Streptococcus thermophilus as commonly detected food bacteria. Further in silico analyses led to the identification of reference strains of the L. lactis and S. thermophilus species within the human gut, represented by PRL2024 and PRL2025 strains, respectively, which can represent nomadic bacteria. In vitro experiments revealed that both strains are ecologically adapted to survive and interact within the human gastrointestinal tract, while also highlighting their metabolic capacity to utilize a broad range of carbon sources. Specifically, the lactose metabolism was investigated, revealing that S. thermophilus PRL2025, despite high lactic acid output, incompletely metabolizes galactose, whereas L. lactis PRL2024 ensures full galactose utilization with lower acid production.

Importance: The identification and functional characterization of Lactococcus lactis PRL2024 and Streptococcus thermophilus PRL2025 as human-adapted reference strains provide a valuable foundation for further in vivo experimentation. Given their ecological resilience, metabolic versatility, and interaction potential with beneficial gut microbes, these strains represent promising candidates as microbiota-targeted functional foods.