Search Results (127)

Biological control with beneficial bacteria offers a sustainable alternative to synthetic agrochemicals for managing plant pathogens and enhancing plant health. However, bacterial biocontrol agents (BCAs) remain underexploited due to regulatory hurdles (such as complex registration timelines and extensive dossier requirements) and limited strain characterization. Recent advances in omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have strengthened the bioprospecting pipeline by uncovering key microbial traits involved in biocontrol. Genomics enables the identification of biosynthetic gene clusters, antimicrobial pathways, and accurate taxonomy, while comparative genomics reveals genes relevant to plant–microbe interactions. Metagenomics uncovers unculturable microbes and their functional roles, especially in the rhizosphere and extreme environments. Transcriptomics (e.g., RNA-Seq) sheds light on gene regulation during plant-pathogen-bacteria interactions, revealing stress-related and biocontrol pathways. Metabolomics, using tools like Liquid Chromatography–Mass Spectrometry (LC-MS) and Nuclear Magnetic Resonance spectroscopy (NMR), identifies bioactive compounds such as lipopeptides, Volatile Organic Compounds (VOCs), and polyketides. Co-culture experiments and synthetic microbial communities (SynComs) have shown enhanced biocontrol through metabolic synergy. This review highlights how integrating omics tools accelerates the discovery and functional validation of new BCAs. Such strategies support the development of effective microbial products, promoting sustainable agriculture by improving crop resilience, reducing chemical inputs, and enhancing soil health. Looking ahead, the successful application of omics-driven bioprospection of BCAs will require addressing challenges of large-scale production, regulatory harmonization, and their integration into real-world agricultural systems to ensure reliable, sustainable solutions. Full article

Mollusks are among the most ecologically and economically significant invertebrates; yet, their associated microbiomes remain understudied relative to those of other metazoans. This scoping review synthesizes the current literature on the diversity, composition, functional roles, and ecological implications of molluscan microbiomes, with an emphasis on three major groups: gastropods, bivalves, and cephalopods. Drawing on studies from terrestrial, freshwater, and marine systems, we identified the dominant bacterial phyla, including Proteobacteria, Bacteroidetes, and Firmicutes, and explored how microbiota vary across different habitats, diets, tissue types, and host taxonomies. We examined the contribution of molluscan microbiomes to host functions, including digestion, immune modulation, stress responses, and nutrient cycling. Particular attention was given to the role of microbiota in shell formation, pollutant degradation, and adaptation to environmental stressors. The review also evaluated microbial interactions at different developmental stages and under aquaculture conditions. Factors influencing microbiome assembly, such as the host’s genetics, life history traits, and environmental exposure, were mapped using conceptual and graphical tools. Applications of molluscan microbiome research in aquaculture, conservation biology, and environmental biomonitoring are highlighted. However, inconsistencies in the sampling methods, taxonomic focus, and functional annotations limit the generalizability across taxa. We identify key knowledge gaps and propose future directions, including the use of meta-omics, standardized protocols, and experimental validation to deepen insights. By synthesizing emerging findings, this review contributes to a growing framework for understanding mollusk–microbiome interactions and their relevance to host fitness and ecosystem health. It further establishes the importance of mollusks as model systems for advancing microbiome science. Full article

Nitrate reduction serves as a pivotal process in the global nitrogen cycle, playing a crucial role in natural ecosystems and industrial applications. Although the genus Alteromonas is not traditionally regarded as a nitrate reducer, several Alteromonas strains have recently been found to be capable of doing so. However, the evolutionary trajectory of this capability remains undiscovered. In this study, 32 bacterial strains were isolated and cultivated from the tidal flat sediment in Hangzhou Bay and classified into the classes Cytophagia (n = 2), Alphaproteobacteria (n = 2), Gammaproteobacteria (n = 17), Flavobacteriia (n = 5), and Bacilli (n = 6). One nitrate-reducing strain, designated as CYL-A6^T, was identified by polyphasic taxonomy and proposed as a novel Alteromonas species. Genomic analysis reveals that seven Alteromonas genomes encode the dissimilatory nitrate reduction genes narGHI. Evolutionary analysis showed that these three nitrate-reducing genes were present in the early common ancestor of the genus Alteromonas, while gene loss events occurred in the subsequent evolution. With the loss of nitrate-reducing genes in the ancestry nodes, a wide variety of genes related to energy production and conversion, as well as carbohydrate, nucleotide, coenzyme, and inorganic ion metabolism, were gained in those nodes, which enabled Alteromonas members to utilize diverse substrates for increased energy production. This study enhances the understanding of microbial diversity in marine tidal flat sediments, proposes a novel nitrate-reducing species of the genus Alteromonas, and highlights the ecological diversification and ecological niche breadth in the evolution of the microbial metabolic network. Full article

Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon squamiferum and Gigantopelta aegis. Using microscopic, phylogenetic, and metagenomic analyses, this study examines bacterial communities inhabiting the foot and gland tissues of these snails. G. aegis exhibited exceptionally low bacterial diversity (Shannon index 0.14–0.18), primarily Gammaproteobacteria (99.9%), including chemosynthetic sulfur-oxidizing Chromatiales using Calvin–Benson–Bassham cycle and methane-oxidizing Methylococcales in the glands. C. squamiferum hosted significantly more diverse symbionts (Shannon indices 1.32–4.60). Its black variety scales were dominated by Campylobacterota (67.01–80.98%), such as Sulfurovum, which perform sulfur/hydrogen oxidation via the reductive tricarboxylic acid cycle, with both Campylobacterota and Gammaproteobacteria prevalent in the glands. The white-scaled variety of C. squamiferum had less Campylobacterota but a higher diversity of heterotrophic bacteria, including Delta-/Alpha-Proteobacteria, Bacteroidetes, and Firmicutes (classified as Desulfobacterota, Pseudomomonadota, Bacteroidota, and Bacillota in GTDB taxonomy). In C. squamiferum, Gammaproteobacteria, including Chromatiales, Thiotrichales, and a novel order “Endothiobacterales,” were chemosynthetic, capable of oxidizing sulfur, hydrogen, or iron, and utilizing the Calvin–Benson–Bassham cycle for carbon fixation. Heterotrophic Delta- and Alpha-Proteobacteria, Bacteroidetes, and Firmicutes potentially utilize organic matter from protein, starch, collagen, amino acids, thereby contributing to the holobiont community and host nutrition accessibility. The results indicate that host species and intra-species variation, rather than the immediate habitat, might shape the symbiotic microbial communities, crucial for the snails’ adaptation to vent ecosystems. Full article

Microbial contamination is a critical challenge for the pharmaceutical industry, especially in thermosensitive sterile products, and can compromise their quality and safety. The accurate identification of microorganisms is essential to trace sources of contamination and adopt corrective measures. Although MALDI-TOF MS technology has revolutionized this process, its database limitations necessitate the use of complementary methods, such as sequencing 16S rRNA genes, housekeeping genes, and, in some cases, the entire genome. Advances in sequencing have expanded genomic taxonomy, increasing the accuracy of bacterial identification. The integration of these approaches significantly improves the reliability of identification, overcoming the limitations of isolated methods. Full article

Biochar-based fertilizers can improve soil structure and fertility. However, their efficiency is affected by the raw materials of biochar. The effects of biochar-based fertilizers on the soil microenvironment under Fenlong-ridging conditions remain unclear. This study aimed to evaluate the effects of biochar-based fertilizers derived from sugarcane filter mud and rice straw on soil physicochemical properties, microbial communities, and sugarcane yield under Fenlong-ridging in Guangxi’s acidic red soil (Hapludults). A two-year field experiment (2021–2022) was conducted on a clay loam soil classified as Hapludults (USDA Soil Taxonomy) in the same experimental plots using three fertilizer applications—conventional chemical fertilization (CK), straw biochar-based fertilizer (T1), and sugar filter mud biochar-based fertilizer (T2)to determine the responses of soil physicochemical properties and bacterial community diversity to different biochar-based fertilizers and evaluate benefits to the soil environment and sugarcane yield. Soil samples (0–20 cm depth) revealed that T1 and T2 reduced bulk density by 2.31% and increased porosity by 2.00–2.31% versus CK. Notably, T2 exhibited 4.1-fold higher specific surface area than T1, driving stronger soil–bacterial interactions: it enhanced soil moisture (7.17–13.05%) and pH (17.89–24.14% in 2021; 8.68–11.57% in 2022), thereby promoting nutrient availability (N, P, K), organic matter (SOM), and sucrase activity. Microbiome analysis showed T2 enriched Gemmatimonadota and Sphingomonas (beneficial taxa) while suppressing Acidothermus. The results of RDA and Spearman correlation analysis indicated that the bacterial community structure was mainly affected by soil pH, TN, AP, and SOM. Consequently, T2 increased sugarcane yield by 5.63–11.16% over T1 through synergistic soil–microbial improvements. Future studies involving multi-site and long-term experiments are needed to confirm the broader applicability and stability of these findings. This study provides a theoretical basis for the positive regulation of sugar filter mud biochar-based fertilizers in the soil environment, bacterial community structure, and sugarcane yield. Full article

The order Lysobacterales consists of three families (Rhodanobacteraceae, Lysobacteraceae and Marinicellaceae), many members of which are important pathogenic and beneficial bacteria. Previous classifications of members within order Lysobacterales have relied heavily on 16S rRNA gene sequences, leading to taxonomic ambiguities at the familial level. With the advancement of sequencing technologies, an increasing number of whole-genome sequences have been available, providing an opportunity to revisit the taxonomy of families in Lysobacterales. In this study, we revisited the taxonomy of Lysobacterales by focusing on family-level reclassification based on phylogenomic frameworks. A total of 218 genome sequences, including 217 strains from Lysobacterales and 1 from Nevskiales (used as an outgroup), were collected for phylogenetic analysis. Phylogenetic relationships were inferred based on UBCG (up-to-date bacterial core gene) approach using 92 core genes and a concatenated protein phylogeney based on 227 single-copy orthologous proteins. Additionally, genomic similarity metrics, including average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), average amino acid identity (AAI) and core-proteome average amino acid identity (cpAAI), were employed to assess the taxonomy of order Lysobacterales. Our results support the proposal of one novel family and the reassignment of six genera across different families within Lysobacterales, emphasizing the need for a refined family-level taxonomy. In addition, four novel species belonging to the family Lysobacteraceae were also confirmed. This study provides an updated familial framework for Lysobacterales, laying a robust foundation for future detailed taxonomic revisions at the genus and species levels. Full article

The vegetation restoration of contaminated sites plays a critical role in ensuring the sustained stability and functional integrity of natural ecosystems. However, during the natural revegetation process, the variations in habitat conditions, bacterial community structure, and metabolic functions in aged, polluted soil are still unclear. In the present study, we investigated aged, polycyclic aromatic hydrocarbon (PAH)-polluted soils at closed, abandoned oil well sites from the Yellow River Delta. Using gene amplification and real-time qPCR methods, the abundance, taxonomy, and diversity characteristics of indigenous bacterial communities and functional bacteria carrying C12O genes in both vegetated soils and bare soils were investigated. The results show that natural revegetation significantly changes the physicochemical parameters, PAH content, and bacterial community structure of aged, PAH-polluted soils. When comparing the abundance and components of PAH-degrading bacterial communities in vegetated and bare soils, the PAH-degrading potential was revealed to be stimulated by vegetation communities. Through correlation analysis, dual stress from soil salinity and PAH contamination in bacterial communities was revealed to be mediated through alterations in the soil’s physicochemical properties by local vegetation. The network analysis revealed that bacterial communities in vegetated soils have higher network connectivity. These results elucidate the alterations in habitat conditions, bacterial components, and PAH-degrading communities following vegetation restoration, providing critical insights for optimizing ecological rehabilitation strategies in salinized and contaminated ecosystems. Full article

The Oxford Nanopore platform and nanopore sequencing are gaining increasing popularity in modern metagenomic research. However, there is a limited set of dedicated tools for analyzing this type of data. The tools used for nanopore amplicon sequencing data analysis often provide only taxonomy annotation without OTU sequence assembly. Conversely, tools that facilitate OTU assembly are constrained in their analysis to long reads, such as the V1–V9 regions of 16S rRNA for bacterial community studies or the full-length ITS cluster (ITS1–5.8S–ITS2) for fungal community studies. In other cases, researchers propose their own solutions without dedicated tools. In this paper, we present Pike, a novel tool for analyzing Oxford Nanopore amplicon sequencing data. Pike allows analysis without amplicon size limitations and allows de novo assembly of OTU sequences. In our research, we created mock communities of fungi and bacteria, which we then used to demonstrate the efficiency of our algorithm. Furthermore, we validated the algorithm using externally available data. We also compared our approach with similar ones to show its applicability. Full article

Background: Variability in recanalization success during endovascular treatment for acute ischemic stroke (AIS) has led to increased interests in thrombus composition and associated cellular materials. While evidence suggests that bacteria may influence thrombus characteristics, limited data exist on microbiological profiles of thrombi in stroke patients. Objectives: Characterization of bacterial communities present in thrombi of AIS patients undergoing mechanical thrombectomy, providing insights into microbial contributions to stroke pathogenesis and treatment outcomes. Methods: Thrombi were collected from 20 AIS patients. After extracting metagenome, 16S rDNA sequencing was performed. Bioinformatic analysis included taxonomy and diversity assessments. The presence of bacterial DNA and viable bacteria in thrombi was validated using polymerase chain reaction (PCR) and bacterial culturing followed by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) analysis, respectively. Results: 16S rDNA was amplified in 19/20 thrombi (95%). Analysis identified a diverse microbial community, with Corynebacterium spp. as the most prevalent genus, followed by Staphylococcus spp., Bifidobacterium spp., Methylobacterium spp., and Anaerococcus spp. Alpha diversity analyses (Shannon index: 4.0–6.0 and Simpson index: 0.8–1.0) revealed moderate to high microbial diversity across samples; beta diversity demonstrated distinct clustering, indicating inter-patient variability in microbial profiles. PCR confirmed the presence of DNA specific to dominant bacterial taxa identified through sequencing. Culturing showed the presence of Staphylococcus epidermidis and Enterococcus faecalis in some clots as identified through MALDI analysis. Conclusions: This study shows bacterial communities present in AIS patients’ thrombi, suggesting a potential link between microbial signatures and thrombus characteristics. Full article

Fish is an essential lean protein source worldwide. Unfortunately, fresh fish food products deteriorate rapidly due to microbial spoilage. With consumers’ growing concerns about using chemical preservatives, we propose using natural preservatives as safer alternatives to prevent microbial spoilage. In this study, we used Next-Generation Sequencing (NGS) metagenomics to study microbiomes on catfish fillets at early (day one for all samples), middle (day seven for control store-bought and aquaculture-raised samples, day nine for other treatment store-bought samples, and day eleven for other treatment aquaculture-raised samples), and late (day fifteen for all store-bought, day eleven for control aquaculture-raised samples, and day twenty-seven for other treatment aquaculture-raised samples) points. Store-bought and aquaculture-raised catfish were treated individually with natural preservatives (vinegar, lemon, and grapefruit seed [GSE]). We observed bacterial populations and sequenced 16S NGS libraries of catfish microbes. Vinegar treatment showed the greatest suppression of bacterial growth in both groups, and GSE and lemon treatment had similar levels of suppression in the mid and late points (−4 to −5 Log CFU/g vinegar and −0.1 to −4 Log CFU/g other treatments in aquaculture and −1 to −2 Log CFU/g vinegar and −0.2 to −0.5 Log CFU/g other treatments in store-bought). Aquaculture-raised vinegar treatment samples had similar proportional taxonomy abundance values through storage duration. Pseudomonas, Janthinobacterium, and Camobacteriaceae were the dominant bacteria species in the early point for store-bought fish. Still, Pseudomonas was suppressed by vinegar treatment in the middle point, which allowed for less biased relative abundance compared to other treatments. Chryseobacterium, CK-1C4-19, and Cetobacterium were the dominant bacteria species for early point treatments in aquaculture-raised fish. Still, they remained the predominant bacteria for only aquaculture-raised vinegar samples in the middle and late points, which allowed for a similar relative abundance to fresh catfish. Meanwhile, Pseudomonas in most lemon and GSE samples became the dominant species at a later point. This study provides a better understanding of bacterial spoilage of catfish during storage. Additionally, we showed that natural preservative treatments can effectively extend the shelf-life of fishery products. Full article

A Gram-positive, rod-shaped, and obligate anaerobic bacterial strain OS1-26 was isolated from apple orchard soil in Iksan, South Korea. Interestingly, strain OS1-26 was observed to possess the functional genes involved in biological nitrogen fixation (BNF), including nifH, which was actively transcribed during the anaerobic cultivation with excessive production of extracellular NH₄⁺ despite of presence of other fixed N nutrients. The BNF of strain OS1-26 was distinguished from the other well-known Clostridium diazotrophs, such as C. pasteurianum and C. acetobutylicum. The altruistic N-fixing ability of the strain may play a pivotal role in providing N nutrients to the microbial community and plants in the soil ecosystem. The microorganism grew at 25–35 °C (optimum 30–35 °C) and pH 5.0–8.0 (optimum 6.0–8.0) but was not able to grow in the presence of >0.5% NaCl. The major cellular fatty acids of strain OS1-26 were C_16:0, C_14:0, and the summed feature consisted of C_16:1 ω7c and C_16:1 ω6c (35.63%, 25.29%, and 18.84%, respectively). The 16S rRNA phylogeny indicated that strain OS1-26 is a member of the genus Clostridium, and the closest species are C. aciditolerans, C. nitrophenolicum, and C. thailandense, with 16S rRNA sequence similarities such as 99.71%, 98.52%, and 98.45%, respectively. In spite of the high 16S rRNA sequence similarity, strain OS1-26 showed overall genomic relatedness, such as the average nucleotide identity (ANI), and phenotypical features distinctly different from Clostridium aciditolerans. Although the species taxonomy of strain OS1-26 is undetermined within the genus Clostridium based on overall genomic and phenotypic properties, further studies on the soil bacterial strain would enhance our understanding of its taxonomic identity, ecological roles for the terrestrial soil N cycle, and the potential to be developed as a biological N fertilizer. Full article

A Gram-positive, aerobic, rod-shaped and spore-forming bacterium strain designation, B190/17, was isolated from an air monitoring sample of a Brazilian immunobiological production facility in 2017. The strain was not identifiable by biochemical methodology VITEK^® 2 or by MALDI-TOF MS with VITEK^® MS RUO and MALDI Biotyper^®. The 16S rRNA gene sequencing results showed 98.51% similarity with Bacillus wudalianchiensis FJAT 27215^T, 98.28% with ‘Bacillus aerolatus’ CX 253^T, 97.96% with Bacillus badius MTCC 1458^T, 97.63% with Bacillus xiapuensis FJAT 46582^T and 97.21% with Bacillus thermotolerans SGZ8^T. Biochemical data showed that the strain was alanine arylamidase-, Ala-Phe-Pro arylamidase-, ELLMAN (cysteine residues)-, leucine arylamidase-, phenyalanine arylamidase- and tyrosine arylamidase-positive. The genomic DNA G+C% content of B190/17 was 41.6 mol%. The phylogenetic, genomic taxonomy and biochemical tests suggested that B190/17 represents a novel species and should be classified as the type strain of a novel Bacillus species. The name Bacillus lumedeiriae sp. nov. was proposed. After characterization, B190/17 was added to the MALDI Biotyper^® database as Bacillus lumedeiriae sp. nov. Full article

As natural predators of bacteria, tailed bacteriophages can be used in biocontrol applications, including antimicrobial therapy. Also, phage lysis is a detrimental factor in technological processes based on bacterial growth and metabolism. The spectrum of bacteria bacteriophages interact with is known as the host range. Phage science produced a vast amount of host range data. However, there has been no attempt to analyse these data from the viewpoint of modern phage and bacterial taxonomy. Here, we performed a meta-analysis of spotting and plaquing host range data obtained on strains of production host species. The main metric of our study was the host range value calculated as a ratio of lysed strains to the number of tested bacterial strains. We found no boundary between narrow and broad host ranges in tailed phages taken as a whole. Family-level groups of strictly lytic bacteriophages had significantly different median plaquing host range values in the range from 0.18 (Drexlerviridae) to 0.70 (Herelleviridae). In Escherichia coli phages, broad host ranges were associated with decreased efficiency of plating. Bacteriophage morphology, genome size, and the number of tRNA-coding genes in phage genomes did not correlate with host range values. From the perspective of bacterial species, median plaquing host ranges varied from 0.04 in bacteriophages infecting Acinetobacter baumannii to 0.73 in Staphylococcus aureus phages. Taken together, our results imply that taxonomy of bacteriophages and their bacterial hosts can be predictive of intraspecies host ranges. Full article

Climate change and soil acidification are critical factors affecting crop production and soil quality. This study comprehensively analyzed the impact of fertilization practices, including conventional (CA), sustainable (SA), and unfertilized (BK), on soil properties, enzyme activities, and gene diversity in paddy fields across seasonal changes. Soil pH was significantly influenced by fertilization, with higher pH in BK and a decrease in pH with increased fertilization. Soil enzyme activities and Biolog EcoPlate™ analysis revealed the lowest activities in September, with the highest in December under different practices. Metagenomic analysis showed the highest genetic richness in CA soil, with seasonal variations influencing genetic diversity. From the perspective of genes in species taxonomy, Sorangium cellulosum and Anaeromyxobacter sp. were the most abundant taxa. Soil genes annotated by CAZy, COG, and GO databases revealed highly similar gene structures among different practices. Moreover, the genetic origins of soil enzymes were linked to specific bacterial contributors. While not all gene’s diversity and abundance were associated with soil enzyme activity, arylsulfatase showed an obvious correlation. Enzyme activities proved more sensitive indicators of microbial activity than gene abundance. This study emphasizes the need for rational fertilization strategies to maintain soil enzyme activities, considering agricultural practices and seasonal variations. Full article