Environmental Microbiology Reports最新文献

Magnetotactic bacteria (MTB) are a diverse group of microorganisms that synthesize intracellular magnetic nanocrystals termed magnetosomes. In this study, a novel marine magnetotactic coccus, designated strain HHB-1, was magnetically enriched from intertidal sediments in Houhai Bay, southern China. Optical microscopy, electron microscopy and elemental analysis revealed that HHB-1 cells are relatively large coccoid-ovoid bacteria (3.9 ± 0.3 μm × 2.8 ± 0.2 μm) containing multiple chains of prismatic magnetite magnetosomes and prominent intracellular Ca/Mg-rich polyphosphate (Ca-Mg-polyP) granules. Whole-genome sequencing and phylogenomic analyses revealed that HHB-1 represents a novel and deeply branching lineage within the order Magnetococcales, exhibiting low average amino acid identity (57.3%–58.7%) with previously reported strains. The magnetosome gene cluster (MGC) of HHB-1 comprises a nearly complete set of mam (magnetosome membrane) genes with conserved gene order and structure, representing the first genomic and MGC characterization of a novel magnetococcus possessing multi-chain magnetosomes. These findings expand our understanding of the diversity, biomineralization strategies and evolutionary history of MTB in marine environments.

Viruses are the most abundant biological entities on Earth and play crucial roles in regulating ecosystem processes and biogeochemical cycling. Proglacial lakes—key components of cryosphere aquatic systems—host diverse microbial communities despite extreme environmental conditions. However, the composition and ecological roles of DNA viral communities in proglacial lake sediments remain poorly understood. In this study, we applied metagenomic and metatranscriptomic approaches to investigate the diversity, function, activity and host interactions of DNA viruses in sediments from Qiangyong proglacial lake on the Tibetan Plateau. We recovered 4039 viral operational taxonomic units (vOTUs), with 76.6% unclassified at the family level, highlighting a vast reservoir of uncharacterized viral lineages. Host prediction linked 1.8% of vOTUs to key microbial taxa involved in carbon, nitrogen and sulphur cycling. We identified a broad array of virus-encoded auxiliary metabolic genes (AMGs) involved in host resource utilization and metabolic transformation. Moreover, 63 AMGs not previously reported in the literature were discovered, significantly expanding the known viral functional gene repertoire. These findings offer new insights into the diversity and ecological potential of sediment-associated DNA viruses in proglacial lakes, and emphasize their possible roles in shaping microbial communities and influencing biogeochemical processes in cold-region ecosystems.

This study evaluated the bioremediation potential of two psychrotolerant strains, Pusillimonas sp. ANT_WB101 and Dietzia sp. ANT_WB102, isolated from an uncontaminated water pond. Comparative analysis indicated affinities with P. gingsengisoli/soli and D. kunjamensis/maris. Both strains demonstrated substantial crude oil degradation efficiency, achieving ≥ 79% under aerobic conditions and ≥ 34% under anaerobic conditions. Genomic analysis identified crucial genes involved in crude oil degradation, including alkane monooxygenase, cytochrome P450, and polyphenol monooxygenase. These strains displayed adaptability to a wide range of environmental factors, such as pH (4–11), salinity (up to 6%–9%), temperature (4°C–37°C), resistance to freeze–thaw cycles, and tolerance to high crude oil concentration. Biosafety evaluations indicated the sensitivity of the strains to various antibiotics, ensuring their suitability and safety for environmental applications. At low temperature, these strains increased microbial activity in environmental samples (1.34 times in biological oxygen demand compared to the control) and showed effective biodegradation (~39%). In conclusion, the study highlights the potential of ANT_WB101 and ANT_WB102 for treating contaminated sites and indicates the possible challenges of using microorganisms not initially adapted to site-specific conditions in bioremediation efforts.

Plants rely on specialised adaptive mechanisms to enhance resistance against environmental stress. One such mechanism, priming, enables faster and stronger defence responses upon subsequent stress exposure. This study examines whether the non-pathogenic Fusarium oxysporum Fo47 primes flax by colonising roots and activating antioxidant defences. Flax plants primed with Fo47 and those treated with both Fo47 and the pathogenic strain F. oxysporum Foln were analysed for fungal colonisation, PR genes expression and antioxidant systems: enzymatic (ROS metabolism-related genes expression, catalase and superoxide dismutase activity, hydrogen peroxide and superoxide anion levels) and non-enzymatic (phenolic compound content and antioxidant potential). The results demonstrate that Fo47 colonises host tissues, significantly reducing Foln penetration and colonisation, particularly in primed plants. Root-specific suppression of Foln by Fo47 was stronger than systemic suppression in shoots. Fo47 induced early chitinase and NADPH oxidases D transcript accumulation and reduced superoxide anion level in roots, likely triggering defence activation. Notably, Fo47 also activated both enzymatic and non-enzymatic antioxidant systems in shoots, suggesting a systemic priming effect. These findings underscore the potential of non-pathogenic F. oxysporum strains in sustainable plant protection strategies.

The atmosphere is increasingly recognised as a dynamic microbial habitat, yet the mechanisms that enable bacterial survival in air remain underexplored. This mini-review synthesises current knowledge on airborne bacterial diversity, the selective pressures they face and the traits that support survival. Drawing from environmental surveys, laboratory studies and emerging omics data, we highlight how airborne bacteria survive despite extreme conditions including UV radiation, low water activity, oxidative conditions and limited nutrients. Common traits such as DNA repair, pigmentation, antioxidant systems and spore formation are discussed in relation to atmospheric stress. We also review recent evidence of microbial activity and function in air. By integrating ecological patterns with physiological adaptations, this review outlines how specific traits may contribute to survival in the atmosphere and suggests future directions for functional studies in diverse atmospheric environments.

Human lice are obligate bloodsucking ectoparasites harbouring endosymbiotic bacteria essential for their survival. Despite the medical significance of human lice, their endosymbionts remain understudied, and knowledge about their species identity, prevalence and genetic diversity is largely limited. Head, body and pubic louse specimens' collection from infested patients of various origins between 2019 and 2023 enabled molecular screening for distribution and genetic diversity of bacterial endosymbionts through conventional PCR targeting two fragments of 16S-rRNA. A total of 209 louse specimens isolated from infested patients, including 186 head lice, 11 body lice and 12 pubic lice were examined with 77.5%, 41.7% and 94.3% of the specimens found to be infested with Candidatus Riesia pediculicola, Candidatus Riesia pthiripubis and Wolbachia respectively. Inferred phylogenetic analysis of Candidatus Riesia and Wolbachia sequences revealed heterogeneity clustering into four and three clades respectively. No specific correlation was observed between these endosymbionts and lice ecological forms or geographical origin demonstrating that head, body and pubic lice share the same Candidatus Riesia and Wolbachia strains with independent adaptation and co-evolution, except Candidatus Riesia pthiripubis which was identified exclusively in pubic lice. These phylogenetic results were aligned by network analysis. These findings could be helpful in evolutionary and biological control investigations.

Antibiotics revolutionized medicine in the 20th century by drastically reducing mortality from bacterial infections. However, their effectiveness is threatened by the global rise of antimicrobial resistance (AMR), driven by misuse, overuse, and environmental dissemination. This review explores the historical trajectory of antibiotics, the mechanisms of bacterial resistance, and the urgent need for innovation amid a declining antibiotic development pipeline. Herein, we highlight the scientific and economic barriers that have discouraged investment by major pharmaceutical companies and examine emerging strategies to address this crisis. Key advances in microbial bioprospecting, including cultivation improvement techniques and genome mining, are discussed alongside the role of high-throughput sequencing and bioinformatics in unlocking the metabolic potential of uncultivated microorganisms. Particular emphasis is placed on the integration of artificial intelligence and machine learning to accelerate drug discovery, predict antimicrobial activity, and identify resistance genes. Additionally, we present alternative therapeutic strategies beyond traditional antibiotics, such as phage therapy, antimicrobial peptides, quorum sensing inhibitors, synthetic conjugates, and vaccine development. Together, these interdisciplinary approaches offer promising pathways to revitalize the antimicrobial pipeline and address the growing threat of antibiotic resistance.

Stony coral tissue loss disease (SCTLD) has reduced coral diversity and homogenised benthic communities. Beyond coral loss, SCTLD may disrupt microbiome composition and function, affecting reef recovery. We examined microbiome changes of apparently healthy corals, water, and sediment at three patch reefs in the Lower Florida Keys during three SCTLD stages: before (vulnerable), during (epidemic), and after (endemic) the outbreak. SCTLD significantly altered microbial diversity and functional potential within apparently healthy corals and the surrounding reef environment. In corals, microbial alpha and beta diversity were highest at the vulnerable stage before declining by the endemic stage, indicating lingering impacts of SCTLD on microbial diversity. Network neighbour and betweenness analyses revealed a loss in connectivity in microbial communities in coral and sediments during the endemic stage. Microbial functional prediction indicated an increase in multidrug resistance and sulphur cycling genes in corals in the epidemic stage. Predicted nitrogen fixation genes were enriched in epidemic coral and seawater, and endemic coral and sediments. SCTLD-associated taxa increased in apparently healthy corals, water and sediments during the epidemic stage, with some taxa persisting in the reef environment during the endemic stage. Thus, SCTLD likely has lasting taxonomic and functional microbial disruptions in coral reef ecosystems.

Antimicrobial-resistant bacteria (AMRB) distributed in the environment can cause human refractory infections. Sufficient monitoring of environmental AMRB had not been performed regularly, and a less burdensome and more efficient method for monitoring environmental AMRB was needed. Assuming to monitor AMRB in the environment, we selected 910 AMRB isolates using cefotaxime and ciprofloxacin from Vietnamese environmental water samples and subjected to 16S rRNA sequencing. It indicated that Escherichia coli (36.0%), Citrobacter freundii (21.4%), Acinetobacter baumannii (20.6%), and Klebsiella pneumoniae (19.7%) were dominant. Using E. coli as a model, we further analysed AMRB isolates by phylogenetic analysis and whole-genome sequencing (WGS). The sequenced full-length fimH of the isolates were plotted with the already published fimH sequences on a phylogenetic tree. Considering phylogeny, 14 E. coli strains were subjected to WGS that indicated not only the number and type of ARGs but also the order of ARGs on the plasmid were confirmed in the analysed E. coli isolates. More importantly, 3 of the 14 strains were bla_NDM-5-positive that is, carbapenem-resistant E. coli. These results suggest that our analytical procedure in this study is applicable as a monitoring method to understand in detail genetic characteristics of AMRB isolates in environmental water samples.

Viral-mediated bacterial mortality and the prevalence of lysogeny are two key parameters for understanding the role of viral activity in aquatic ecosystems. The viral production assay is most commonly used to assess these parameters, with lytic and mitomycin C-induced viral production rates prevalently extracted using the linear regression or increment-based (VIPCAL) approach. A literature survey shows that 64% of the 89 viral production studies used the linear regression approach for lytic and 48% employed VIPCAL for lysogenic viral production rates. Our comparative evaluation highlights significant differences between these two approaches of estimating viral production rates. To refine estimations, we enhanced VIPCAL to VIPCAL-SE by incorporating standard error of the means to rigorously identify maxima–minima pairs, accounting for biological and ecological variabilities between replicates. We also included a bacterial net generation time endpoint to reduce estimation bias due to potential secondary infections, particularly relevant in more productive ecosystems. VIPCAL-SE is now available as a part of the viralprod R package and provides an opportunity for further standardisation in the field of aquatic viral ecology.