Applied and Environmental Microbiology最新文献

Coastal lagoon project is a common strategy for enhancing flood control capability and ecosystem services, yet its impact on microbiota, especially archaea, remains unclear. Using 16S rRNA gene and transcript sequencing, we compared archaeal diversity, community assembly processes, and potential activity in an artificial lagoon and adjacent seaward waters through monthly sampling over an annual cycle. The lagoon has created a distinct water environment with reduced salinity and turbidity, along with unique dissolved organic matter profiles. The lagoon's influence overrode seasonal variability in archaeal alpha-diversity, yielding overall higher levels within the lagoon. Despite pronounced seasonal shifts-Nitrosopumilaceae dominating in cooler seasons and Poseidoniales prevailing in warmer months-the lagoon's influence on archaeal community composition across taxonomic scales remained evident, particularly in the spatial niche partitioning of Poseidoniales populations. Lagoon archaeal communities exhibited higher turnover rates and accelerated seasonal recurrence compared with those in the seaward zone. Although archaeal community assembly was primarily driven by water-mass effects, selection occasionally exerted a stronger influence in seaward waters. Analyses involving the 50 most abundant zero-radius operational taxonomic units (ZOTUs) revealed that the lagoon project had a stronger and more widespread effect on the distribution of key archaeal taxa than on their potential activity, consistent with the trend observed at the genus level, except for two Nitrosopumilaceae genera: Nitrosopumilus often exhibited lower activity, while Nitrosopelagicus occasionally showed higher activity in the lagoon. Our findings highlight that the lagoon project variably altered archaeal diversity, community assembly, and potential activity, underscoring microbial consequences and potential ecological impacts of nearshore restoration projects.

Importance: Coastal lagoon projects are widely employed to enhance ecosystem services, such as water quality, yet their impacts on microbial communities-particularly archaea-remain poorly understood. This year-long study reveals that artificial lagoon environments significantly reshape archaeal communities by increasing alpha-diversity, accelerating seasonal turnover, and shifting dominant taxa, especially among ammonia-oxidizing archaea and Poseidoniales. Community assembly was primarily governed by water-mass effects introduced through lagoon maintenance, while archaeal potential activity exhibited taxon-specific patterns. These findings uncover critical, previously overlooked microbial consequences of lagoon engineering and emphasize the importance of incorporating microbial dynamics into the planning and evaluation of nearshore restoration projects.

Marine environments are frequently oligotrophic, characterized by low amount of bioassimilable nitrogen sources. At the global scale, the microbial fixation of N₂, or diazotrophy, represents the primary source of fixed nitrogen in pelagic marine ecosystems, playing a key role in supporting primary production and driving the export of organic matter to the deep ocean. However, given the high energetic cost of N₂ fixation, the active release of fixed nitrogen by diazotrophs appears counterintuitive, suggesting the existence of alternative passive release pathways that remain understudied to date. Here, we show that the marine non-cyanobacterial diazotroph Vibrio diazotrophicus is endowed with a prophage belonging to the Myoviridae family, whose expression is induced under anoxic and biofilm-forming conditions. We demonstrate that this prophage can spontaneously excise from the genome of its host and that it forms intact and infective phage particles. Moreover, phage-mediated host cell lysis leads to increased biofilm production compared with a prophage-free derivative mutant and to increased release of dissolved organic carbon and ammonium. Altogether, the results suggest that viruses may play a previously unrecognized role in oceanic ecosystem dynamics by structuring microhabitats suitable for diazotrophy and by contributing to the recycling of (in)organic matter.

Importance: Diazotrophs are key players in ocean functioning by providing fixed nitrogen to ecosystems and fueling primary production. However, from a physiological point of view, the active release of nitrogenous compounds by diazotrophs is paradoxical, since they would invest in an energy-intensive process and supply nutrient to non-sibling cells, with the risk of being outcompeted. Therefore, alternative ways leading to the release of fixed nitrogen must exist. Here, we show that the marine non-cyanobacterial diazotroph Vibrio diazotrophicus possesses one prophage, whose activation leads to cell death, increased biofilm production, and the release of dissolved organic compounds and ammonium. Taken together, our results provide evidence that marine phage-diazotroph interplay leads to the creation of microhabitats suitable for diazotrophy, such as biofilm, and to nutrient cycling, and contributes to better understanding of the role of viruses in marine ecosystems.

This study investigates the corrosion inhibition behavior of Bacillus subtilis on B30 copper-nickel alloy in seawater, focusing on its biomass components in regulating biomineralization. Results show that B. subtilis formed a protective biofilm and induced the precipitation of a uniform biomineral layer, mainly composed of Ca-Mg carbonates. This layer acted as a physical barrier, resulting in a low corrosion current of (5.85 ± 0.08) × 10⁻⁷ A/cm² and reducing the maximum pit depth from 44.74 to 18.54 µm. Furthermore, the roles of different biomass components, such as bacterial cells, extracellular polymeric substances (EPS), and soluble microbial products (SMPs), were also investigated. It was found that all components could initiate mineralization, but with distinct outcomes: bacterial cells primarily served as structural templates; EPS facilitated the formation of highly crystalline and stable Mg-calcite, providing the most durable protection, while SMPs promoted the formation of well-crystallized calcite with comparatively lower protective efficacy.IMPORTANCECorrosion is a critical issue prevalent across various industries, where traditional corrosion control technologies are often limited by high costs, complex implementation, and potential environmental hazards. Biomineralization, as an emerging green anti-corrosion strategy, is not only environmentally friendly but also enables long-term effective protection, reducing reliance on toxic chemical agents and lowering economic costs. However, due to the complexity of microbial systems, the mechanisms underlying biomineralization are not yet fully understood. In this study, different biomass components-including bacterial cells, extracellular polymeric substances, and secreted metabolites-were isolated from Bacillus subtilis cultures using a series of separation techniques, and their impacts on the mineralization process were systematically evaluated. This work elucidates the corrosion inhibition mechanism of biomineralization and provides valuable insights into the relationship between specific microbial components and biomineral formation, which holds significant implications for developing eco-friendly corrosion inhibition technologies.

The Kuroshio-Oyashio Extension (KOE) region is a highly variable region in the North Pacific Ocean, characterized by strong environmental gradients and multi-scale oceanographic processes. However, the fine-scale impact of these currents and associated water masses on microbial communities remains poorly understood. Here, high-resolution samples from 18 to 24 layers were collected along a transect in the KOE region in 2021, with 16S rRNA gene amplicon sequencing and environmental parameter measurements conducted to investigate the Kuroshio-Oyashio influence on microbial communities. Strong regional and vertical variations in environmental parameters and microbial communities were observed, with main horizontal regional differentiations confined to the upper 500 m. Photoautotrophic and oligotrophic taxa (e.g., SAR11 clade and Cyanobacteria) were enriched in warm, oligotrophic Kuroshio region, whereas the cold nutrient-rich Oyashio and confluence regions supported higher microbial abundance, diversity, and complex microbial interactions. Consistently, heterotrophic bacteria (1.00 × 10⁶-1.17 × 10⁹ cells L⁻¹) were more abundant in the upper 55 m of the Oyashio and confluence regions than in the Kuroshio region. Below the thermocline (~500 m), community composition was primarily structured by depth, indicating a diminishing Kuroshio-Oyashio current influence. Three main water masses (subtropical mode water [STMW], central mode water, and North Pacific intermediate water [NPIW]) with distinct microbial communities were identified, explaining ~11% of microbial variation beyond depth and geography, with biomarker taxa identified (e.g., Actinomarinales for STMW, Nitrosopumilales for NPIW). This study reveals the extent of Kuroshio-Oyashio influence on microbial communities and highlights the integrated impacts of large-scale currents and fine-scale water masses on shaping microbial biogeography in the KOE region.IMPORTANCEThe convergence of the Kuroshio and Oyashio currents shapes high microbial diversity, as well as complex microbial-mediated biogeochemical processes. However, investigations into the microbial distribution patterns in relation to these current systems remain limited in spatial resolution. This study with high-resolution samples reveals the extent of Kuroshio-Oyashio influence on microbial communities and advances the understanding of how multi-scale oceanographic processes influence microbial biogeographical patterns. It provides a fine-scale perspective for exploring microbial distribution and assembly in highly dynamic oceanic environments.

The genus Micromonospora, a key member of the actinomycetes, has demonstrated considerable potential for natural product biosynthesis. In this study, we isolated 15 Micromonospora spp. strains from desert soil and marine sediment samples, eight of which represent four novel species. To explore the biosynthetic capacity of this genus, we performed an integrated analysis of Micromonospora reference genomes. Pan-genomic analysis further unveiled the core biosynthetic characteristics of the genus responsible for producing terpenes and polyketides. Further multi-omics investigation, combining genomic and metabolomic data, uncovered a positive correlation between phylogenetic relationships and biosynthetic potential, alongside a decoupling of metabolic profiles. Notably, metabolomic findings emphasized the dominant influence of culture conditions on the expression of biosynthetic capabilities. Overall, our study provides a comprehensive elucidation of the biosynthetic potential of the genus Micromonospora and highlights the value of investigating novel strains and applying diverse cultivation strategies in natural product discovery.IMPORTANCEOur study provides a comprehensive genomic and metabolomic elucidation of the significant biosynthetic potential within the genus Micromonospora. It reveals a core biosynthetic capacity for terpenes and polyketides that is phylogenetically linked, whereas the resulting natural product repertoire is subject to strong modulation by cultivation conditions. These findings underscore the critical importance of exploring novel species and employing diverse cultivation strategies to unlock the full potential of microbial resources for natural product discovery.

The COVID-19 outbreak brought to the fore the importance of airborne transmission in spreading human infectious diseases and highlighted the need for sustainable mitigation strategies. Triethylene glycol (TEG) has been documented as having microbicidal capabilities and has been proposed as one such mitigation strategy. Aerosolized TEG exhibits antimicrobial activity against airborne microorganisms. Grignard Pure Technology was developed to safely aerosolize TEG for decontamination of enclosed spaces. Here, we show that this TEG formulation effectively inactivates airborne microorganisms, resulting in 2 to 4.5 net log reduction in concentration of viable bacteria, viruses, and mycobacteria within 30-60 min at TEG concentration (aerosol + vapor) of ~0.7 mg/m³, which is well within the range considered safe for humans. Our data also demonstrate that aerosolizing both the test organisms and the antimicrobial product provides a more accurate and relevant measure of the product's efficacy for indoor usage than traditional surface-or solution-based disinfection assays. Accurate evaluation of antimicrobial efficacy is a crucial step in adopting novel interventions and tools to control airborne pathogens that pose a public health risk. Our findings argue that testing protocols must match the intended use of any intervention. Given the safety concerns of aerosolizing human pathogens for direct testing of airborne infectious burden, we also advance an approach for selecting suitable surrogate microorganisms based on their phenotypic and biophysical similarity to corresponding pathogenic species.IMPORTANCEDuring the COVID-19 pandemic, personal protective equipment, social distancing, and even vaccinations proved sub-optimal in controlling the spread of COVID-19. Public health practice and the hierarchy of controls emphasize primary prevention, whereby the pathogen is removed or destroyed before exposure to the public. Triethylene glycol (TEG) has the potential to inactivate airborne pathogens and limit their spread. TEG is designated a "safer chemical" by the US EPA and has been used for decades in aerosol deodorizers and theatrical special effects. This study shows that aerosolized TEG is highly effective at eliminating a wide spectrum of viable airborne pathogen surrogates at concentrations well below the threshold of safety concern. Thus, it may afford significant protection against the transmission of infectious agents with pandemic potential.

Microbes are fundamental to ocean ecosystem function, yet they remain understudied across broad spatial and environmental scales in dynamic regions like the Gulf of America/Gulf of Mexico (GOM). We employed DNA metabarcoding to characterize prokaryotes (16S V4-V5) and protists (18S V9) across 51 stations, spanning 16 inshore-offshore transects and three depths. Cluster analysis revealed three clusters corresponding to depth zones that integrated vertical and horizontal sampling: photic zone (inshore near surface-bottom and offshore surface), deep chlorophyll maximum (offshore), and aphotic zone (offshore near bottom). We applied group-specific generalized additive models (GAMs) to log-transformed abundance data of major taxa in the photic zone, identifying key environmental factors that explained 42%-82% of the variation in abundance. SAR11 and SAR86 were positively associated with temperature and dissolved inorganic carbon, while cyanobacterial genera (Prochlorococcus and Synechococcus) were differently impacted by nutrients, salinity, and pH in ways that often followed their expected ecological niches. Representatives of protist parasites (Syndiniales) and grazers (Sagenista) showed group-specific nonlinear associations with salinity, oxygen, nutrients, and temperature. Using GAMs, we expanded the spatial resolution of DNA sampling and predicted surface log abundances at 84 cruise sites lacking amplicon data. Indicator analysis was performed with sequence-level data, revealing several protists that were indicative of more acidic waters and the absence of any significant prokaryote indicators. Our results provide the first basin-scale survey of microbes in the GOM and highlight the need for coordinated omics and environmental sampling to improve predictions of microbial responses to changing conditions.IMPORTANCEMarine microbes are key indicators of environmental change and play central roles in ocean food webs and biogeochemical cycles. Yet, how natural microbial communities respond to shifting environmental conditions remains unclear, particularly in the Gulf of Mexico (GOM), a region shaped by dynamic physical and chemical gradients. Here, we conducted a novel basin-scale DNA metabarcoding survey of prokaryotes and protists in the GOM. We used generalized additive models and indicator analysis to reveal environmental drivers of microbial abundance, from broader taxonomic groups to unique sequences. Our results show group-specific associations with environmental factors such as temperature, nutrients, salinity, and carbonate chemistry parameters and identify several protist taxa associated with distinct ocean conditions. These findings provide a foundation for microbial monitoring in the GOM and shed light on the importance of integrating in situ biological, physical, and chemical data across spatial gradients to inform accurate ecosystem and biogeochemical models.