Applied and Environmental Microbiology最新文献

In prokaryotes, the energy-dependent protein degradation is controlled, primarily, by two ATP-dependent proteases, Lon and Clp. This study investigates the roles of Escherichia coli (E. coli)-encoded Lon protease in the metabolism of 2,4-dinitrophenol (2,4-DNP), a toxic industrial compound. Enhanced conversion of yellow-colored 2,4-DNP to a reddish-brown product was observed in a strain lacking Lon protease (Δlon). This observation led us to characterize and understand the mechanisms of 2,4-DNP metabolism. UV-visible and LC-MS analyses revealed differences in the conversion products between the wild-type and Δlon. One of the substrates of Lon protease is MarA, a transcription factor, and studies with different mutants followed by trans complementation demonstrated MarA-dependent conversion. The bathochromic shift of spectral peaks suggested reduction processes and possible involvement of nitroreductase enzymes. Indeed, the expression of two genes encoding nitroreductases, nfsA and nfsB, increased with 2,4-DNP and was dependent on MarA. Importantly, the production of the reddish-brown product was lower in strains lacking nfsA or nfsB. Finally, LC-MS analysis identified one of the conversion products of 2,4-DNP to be 4-amino-2-nitrophenol (4,2-ANP). Dose studies with purified 4,2-ANP demonstrated that it did not lower the growth of E. coli (unlike 2,4-DNP) and induced phenotypic antibiotic resistance in an acrB-dependent (like 2,4-DNP) but in a marA-independent (unlike 2,4-DNP) manner. This study revealed how E. coli in the environment converts a toxic compound (2,4-DNP) into a lesser toxic compound (4,2-ANP) and helps survive in the presence of antibiotics. Overall, this study contributes to our understanding of biological responses to nitroaromatics.

Importance: E. coli is one of the common microorganisms in feces-contaminated sewage and often interacts with several pollutants. This study identifies the roles of Lon protease and its substrate MarA in inducing nitroreductases, NfsA and NfsB, in reducing toxic 2,4-DNP to less toxic 4,2-ANP, a novel inducer of phenotypic antibiotic resistance in E. coli. This study sheds light on the roles of E. coli-encoded Lon protease upon exposure to harmful nitroaromatics. Common environmental pollutants can act as a selective pressure, favoring the survival as well as proliferation of bacteria containing antibiotic-resistant genes, which can easily be transferred to other bacteria through horizontal gene transfer. This study offers insights into mitigation methods in E. coli, a well-characterized model. It is possible that such environmental pollution strategies may be translated to other models, such as Pseudomonas, which are commonly used in bioremediation studies.

Minerals are fundamental yet underappreciated drivers of microbial ecology. Traditionally viewed as passive nutrient sources or inert scaffolds, their broader ecological roles remain poorly defined. This study investigates the evolutionary influence of substrates (minerals and rocks) on soil bacterial communities through serial passage evolution experiments. Soil-derived microbial consortia from three distinct locations were exposed to nutritive (olivine, granite, diorite) and non-nutritive (quartz, kaolinite, montmorillonite) substrates under nutrient-rich conditions to isolate substrate-specific effects. Results revealed systemic variations of community structure across all treatments, characterized by elevated Firmicutes/Bacteroidetes ratio and taxonomic changes predominantly driven by rare taxa. These discoveries indicate that, under the influence of substrates, the communities shifted toward ones that preferentially utilize more labile carbon. Crucially, the acute responsiveness of rare taxa to mineral-induced environmental selection suggests that, although abundant taxa appeared to maintain core community functions, the rare biosphere facilitated niche specialization and functional diversification. These findings position minerals as dynamic drivers of microbial ecology and evolution, highlighting the mineralosphere as a critical microhabitat where abiotic properties govern biodiversity, functional redundancy, and evolutionary innovation in soil ecosystems.

Importance: Even under nutrient-rich conditions, non-nutritive and chemically inert minerals, exemplified by quartz, actively reshape microbial community assembly. Through controlled serial-passage experiments, we show that distinct substrates selectively enrich rare biosphere members that expand functional potential and seed adaptation, while dominant taxa sustain core processes. These results reveal that mineral surface properties and physical interfaces, rather than nutrient supply, govern microbial diversification and evolutionary trajectories. Accordingly, the mineralosphere emerges as a dynamic microhabitat where abiotic complexity regulates biodiversity, metabolism, and long-term community succession. This reframes minerals and rocks as active ecological and evolutionary agents, bridging geomicrobiology and evolutionary ecology, with implications for soil health, biogeochemical cycling, and the origin and maintenance of microbial diversity.

Nontuberculous mycobacteria (NTM) are a group of environmental bacteria that encompass nearly 200 described species, some of which can cause chronic pulmonary and extrapulmonary infections in humans. What makes these infections unique is that they are environmentally acquired, yet there remains a limited understanding of how different environments contribute to potential pathogen exposure. Here, we use new and existing marker gene data sets to compare the amounts and types of NTM across three environments known to harbor mycobacteria, surface waters, soil, and household plumbing biofilms, to better understand potential pathogen occurrence in each environment. We used 16S rRNA gene sequencing, in tandem with mycobacterial-specific marker gene sequencing, to characterize variation in the relative abundances of the genus Mycobacterium and specific mycobacterial taxa across the three environments, with a focus on a clinically significant NTM. We found that household plumbing biofilms contained both the highest relative abundance of the genus Mycobacterium (on average, 13.7% of bacteria were members of the genus), as well as the highest occurrence of clinically relevant species detected (Mycobacterium avium and Mycobacterium abscessus), compared to surface waters and soil. Although mycobacteria are ubiquitous across many different environments, mycobacterial diversity is highly variable between environments with clinically relevant species largely restricted to household plumbing biofilms, information that is critical for understanding the ecology and epidemiology of NTM disease.IMPORTANCENontuberculous mycobacteria, or NTM, are a diverse group of bacteria within the genus Mycobacterium that are common in many environments. While most members of the genus pose little threat to human health, a handful of species, namely the Mycobacterium avium complex, M. abscessus, and M. kansasii, can cause severe and prolonged lung infections. These environmentally acquired infections are on the rise in the United States and around the world, yet we still do not have a good understanding of which environment types pose the greatest risk of infection to susceptible populations. Our study used cultivation-independent approaches to identify the specific NTM taxa found in over 1,000 samples from three potentially important environmental reservoirs-surface waters, soils, and household plumbing systems, to determine which of these environments are most likely to harbor NTM of clinical significance. Our results highlight the high degree of variability in the types of NTM taxa detected in different environments (including extensive novel diversity within the genus) and show that household plumbing biofilms are likely the most important reservoir and subsequent route of transmission for clinically significant NTM.

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.

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.

The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.

Bifidobacterium is a key member of the human gut microbiota, and many strains are widely used as probiotics due to their health-promoting properties. Despite growing interest, genetic studies in Bifidobacterium have been relatively limited, primarily due to the lack of available genome editing tools. Recent advances in genomics and CRISPR-Cas systems provide opportunities for targeted genome modification in this genus. In this review, we provide an overview of the occurrence, diversity, and distribution of CRISPR-Cas systems across Bifidobacterium species and examine the editing tools developed and implemented to date. We also highlight practical challenges such as strain variability and low transformation efficiency and introduce future avenues of research such as large-payload insertion and in situ editing. Expanding the genetic toolbox for Bifidobacterium will broaden our understanding of this important genus and enable the development of next-generation probiotics.

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.