Search Results (347)

Toxin–antitoxin (TA) modules represent sophisticated regulatory networks that have evolved from simple plasmid maintenance factors into multifunctional genetic modules orchestrating bacterial stress responses, pathogenesis, and ecological adaptation. This review highlights a compelling correlation between the abundance of toxin–antitoxin (TA) modules and bacterial pathogenicity, as exemplified by Mycobacterium tuberculosis (M.tb), which encodes 118 TA loci—significantly more than the fewer than 10 found in closely related saprophytic species. The clinical significance of TA modules extends beyond traditional stress response roles to encompass antimicrobial persistence, where systems like VapBC and MazEF facilitate dormant subpopulations that survive antibiotic therapy while maintaining chronic infections. Recent discoveries have revealed TA modules as sophisticated bacterial defense mechanisms against bacteriophage infection, with DarTG and ToxIN systems representing novel antiviral immunity components that complement CRISPR-Cas and restriction–modification systems. The immunomodulatory capacity of TA modules demonstrates their role in host–pathogen interactions, where systems such as VapC12 in M.tb promote macrophage polarization toward permissive M2 phenotypes while inducing anti-inflammatory cytokine production. Large-scale genomic analyses reveal that TA modules function as drivers of horizontal gene transfer networks, with their signatures enabling accurate prediction of plasmid community membership and serving as determinants of microbial community structure. The biotechnological applications of TA modules have expanded to include genetic circuit stabilization, biocontainment device construction, and multi-species microbial community engineering, while therapeutic strategies focus on developing multi-target inhibitors against conserved TA protein families as promising approaches for combating drug-resistant bacterial infections. The evolutionary conservation of TA modules across diverse bacterial lineages underscores their fundamental importance as central organizing principles in bacterial adaptation strategies, where their multifunctional nature reflects complex selective pressures operating across environmental niches and host-associated ecosystems. This review provides an integrated perspective on TA modules as dynamic regulatory elements that support bacterial persistence, immune evasion, and ecological versatility, establishing them as genetic elements with truly “many faces and functions” in prokaryotic biology. Full article

This study characterized the microbiota by sequencing the V3-V4 regions of prokaryotic 16S rRNA to investigate the bacterial diversity of fermented fish-entrail sauce (tai-pla or pung-pla) from five provinces in Thailand. Tai-pla samples made from seven different species of fish, three freshwater and four marine, were purchased. Three subsamples from each were analyzed. The samples had salt concentrations ranging from 3 to 13% and pH values ranging from 4.26 to 6.19. The top 35 genera of bacterial taxa by relative abundance were considered in more detail. Lactic acid bacteria (LAB), primarily in the order Lactobacillales (Levilactobacillus, Companilactobacillus, Lactococcus, Latilactobacillus, Weissella, Pediococcus, and Ligilactobacillus), were abundant in several groups of samples, as were halophilic bacteria, including Halanaerobium, Chromohalobacter, and Virgibacillus. Other beneficial bacterial species were frequently detected, including Tetragenococcus halophilus and Tetragenococcus muriaticus. Principal Coordinate Analysis visualization of beta diversity showed distinct bacterial community structures across tai-pla samples prepared with different fish species. Differences between samples may be due to the use of different raw materials, salt concentrations, recipes, processes and fermentation periods. This study provides baseline information on microbial communities and diversity in tai-pla, offering better insights into the production outcomes of traditional products. Further optimization of the fermentation process, such as using beneficial bacterial taxa in starter cultures, may enhance the system of food fermentation, food quality, and flavor control, supporting regulation useful for industrial applications. Full article

The endangered Rhinogobio ventralis, endemic to the upper Yangtze River, is dependent on captive breeding for its conservation. However, this highly stress-sensitive species is exceptionally susceptible to Ichthyophthirius multifiliis, leading to severe pathology and high mortality in culture. Elevated salinity holds potential for managing key aquaculture pathogens, including Ichthyophthirius multifiliis and Saprolegnia spp. However, its potential unintended ecological consequences remain insufficiently understood. This study evaluated the systemic impacts of 5‰ salinity on the culture environment of the endangered species Rhinogobio ventralis, using integrated 16S/18S rRNA gene sequencing and water quality analysis. The results demonstrated that while salinity treatment effectively reduced the environmental molecular signal of harmful eukaryotes such as Ichthyophthirius and Saprolegnia, it also induced significant ecological shifts: (1) aquatic prokaryotic diversity increased, yet the self-purification capacity of the water was compromised, indicated by elevated dissolved oxygen, nitrate nitrogen, and total nitrogen; (2) in the fish intestinal microbiome, a decline in potentially beneficial taxa (e.g., Exiguobacterium) co-occurred with an enrichment of genera containing potentially pathogenic species (e.g., Staphylococcus and Pseudomonas), collectively suggesting a state of dysbiosis; (3) co-occurrence network analysis revealed that the aquatic microbial community developed greater complexity, while the intestinal network became structurally simplified and more antagonistic. These findings reveal that elevating salinity in freshwater aquaculture systems compromises both host microbiome health and aquatic ecosystem functioning. As such, future aquaculture management should integrate supportive measures like probiotic supplementation to maintain overall system stability. Full article

In freshwater ecosystems, cross-trophic interactions among biological communities underpin ecosystem stability and functionality. In arid and semi-arid rivers, however, hydrological fluctuations, invasive species, and other perturbations exacerbate the complexity of biological processes. To systematically assess the community structure of fish, eukaryotic plankton, and prokaryotic microorganism in the Irtysh River basin, this study employed environmental DNA (eDNA) metabarcoding for monitoring. High-throughput sequencing of taxa within the study area was conducted via eDNA metabarcoding, coupled with random forest and linear mixed models to dissect the effects of community structure. The eDNA approach effectively unraveled spatial patterns of biodiversity and identified taxon-specific diversity hotspots: invasive fish exerted a facilitative effect on algae and suppressed the richness of protozoa, fungi, and heterotrophic microorganisms, yet had minimal impact on the dominant structure of autotrophic microorganisms. These findings provide a scientific basis for basin-scale ecological management, emphasizing the necessity of balancing habitat preservation and invasive-species control to safeguard ecosystem functionality. Full article

Flow cytometry typically reveals two heterotrophic prokaryote (HP) subpopulations when stained with SYBR Green: high nucleic acid (HNA) and low nucleic acid (LNA) cells. Evidence suggests these populations have distinct physiological and ecological roles with implications for mortality. We assessed HP abundance, production, the relative proportion of HNA and LNA, virus-mediated mortality, and the distribution of lytic versus lysogenic strategies within HP host communities across a latitudinal gradient in the North Atlantic during spring. The study area, characterized by dynamic physicochemical conditions consistent with the onset of seasonal stratification, was divided into three regions based on bio-physicochemical properties: Pre-bloom, Bloom, and Oligotrophic. Multivariant analysis showed these regions significantly structured HPs, as well as influenced the relative abundance and production of virus subpopulations (i.e., V1 and V2). Specifically, V1 viruses increased with the potential of encountering HNA hosts, which were elevated in the surface waters of stratified Oligotrophic and Bloom regions. In contrast, V2 abundance and production correlated with LNA cells, more prominent in DEEP samples and in surface waters of the deeper mixed Pre-bloom region. Lysogeny occurred across all regions, with the percentage of lysogens within the HP community, increasing (largely V1-driven) with HP-specific growth rate until reaching a threshold of 0.1 d⁻¹, after which it declined. We discuss the potential ecological underpinnings driving these patterns and implications for carbon flux. Full article

A wadi ecosystem, a wetland characterized by seasonal water flow, is a unique freshwater environment typically found in semi-arid and arid regions. This study investigates the seasonal and spatial dynamics of environmental properties and microbial plankton communities at Wadi Saiysad in Taif City, Saudi Arabia. Using flow cytometry, three distinct picoplankton populations were observed: Synechococcus and heterotrophic prokaryotes classified as low (LNA) or high (HNA) nucleic acid content. Surface freshwater samples were collected from three distinct sites, representing habitats with actively flowing water, biodiverse communities, and human-influenced areas. Interestingly, no significant differences among stations were observed, suggesting that the sampled stretch of Wadi Saiysad receives similar nutrient inputs. Seasonal water temperature reached 24.5 ± 0.57 °C in summer and the pH ranged from neutral to slightly alkaline. Nutrient analyses revealed that Wadi Saiysad is eutrophic and limited by phosphorus. Phytoplankton biomass was dominated by nanoplankton, particularly in summer (46.60 ± 5.33%), while Synechococcus increased significantly with a maximum abundance of 1.32 × 10⁴ cells mL⁻¹ during the cooler months. HNA prokaryotes displayed marked seasonal variation (1.95 × 10⁴–1.78 × 10⁵ cells mL⁻¹) compared to LNA prokaryotes (2.05–8.17 × 10⁴ cells mL⁻¹). This study highlights the urgent need for monitoring and managing the nutrient inputs in Wadi Saiysad to protect its biodiversity and support sustainable use. Full article

The transition between anaerobic and aerobic conditions represents a fundamental ecological process occurring ubiquitously in both natural ecosystems and engineered wastewater treatment systems. This study investigated the microbial community succession and co-occurrence network dynamics during the transition from anaerobic sludge to aerobic cultivation. High-throughput 16S and 18S rDNA sequencing revealed two distinct succession phases: an initial “aerobic adaptation period” (Day 1) and a subsequent “aerobic stable period” (Day 15). Eukaryotic communities shifted from Cryptomycota to the unassigned eukaryotes dominance, while prokaryotic communities maintained Firmicutes and Proteobacteria as core phyla, with persistent low-abundance archaea indicating functional adaptation. Network analysis highlighted predominant co-occurrence patterns between eukaryotic and prokaryotic communities, suggesting synergistic interactions. These findings provide insights into microbial ecological dynamics during anaerobic-to-aerobic transitions, offering potential applications for optimizing wastewater treatment processes. Full article

Harmful algal blooms (HABs), caused by the dinoflagellate Alexandrium pacificum, are increasingly frequent in the Marlborough Sounds, an important aquaculture region in Aotearoa New Zealand. Alexandrium pacificum produces paralytic shellfish toxins and blooms cause significant economic and ecological disruptions through contamination of edible shellfish. High-throughput sequencing of prokaryotic and eukaryotic communities was used to investigate community dynamics during bloom events across two consecutive summers. Distinct successional shifts were observed, with prokaryotic communities dominated by Rhodobacterales and Flavobacteriales during blooms, and increased abundance of the SAR11 clade (Pelagibacterales) post-bloom. Eukaryotic diversity was dominated by Alexandrium species (Gonyaulacales) during the bloom, and subsequently shifted towards Syndiniales, Gymnodiniales, and Peridiniales as blooms collapsed. Significant correlations indicated potential ecological roles for these taxa in bloom regulation, particularly Syndiniales, which could indicate parasitic interactions. Depth profiles revealed consistent microbial composition throughout the water column, validating depth-integrated sampling strategies for community studies. This research describes changes in the composition of microbial communities during two A. pacificum blooms, suggesting that species interactions (e.g., via parasitism) may play a role shaping bloom dynamics. Further studies incorporating environmental parameters, especially nutrient dynamics linked to anthropogenic activities, are necessary to better understand the drivers of blooms in this important aquaculture region. Full article

The coastal waters of Qinhuangdao are a major hotspot for harmful algal blooms (HABs) in the Bohai Sea, with Noctiluca scintillans being one of the primary algal species responsible for these events. A comprehensive understanding of the microbial community structure and functional responses to N. scintillans bloom events is crucial for elucidating their underlying mechanisms and ecological impacts. This study investigated the microbial community dynamics, metabolic shifts, and the environmental drivers associated with a N. scintillans bloom in the coastal waters of Qinhuangdao, China, using high-throughput sequencing of 16S and 18S rRNA genes, co-occurrence network analysis, and metabolic pathway prediction. The results revealed that the proliferation of autotrophic phytoplankton, such as Minutocellus spp., likely provided a nutritional foundation and favorable conditions for the N. scintillans bloom. The bloom significantly altered the community structures of prokaryotes and microeukaryotes, resulting in significantly lower α-diversity indices in the blooming region (BR) compared to the non-blooming region (NR). Co-occurrence network analyses demonstrated reduced network complexity and stability in the BR, with keystone taxa primarily belonging to Flavobacteriaceae and Rhodobacteraceae. Furthermore, the community structures of both prokaryotes and microeukaryotes correlated with multiple environmental factors, particularly elevated levels of NH₄⁺-N and PO₄³⁻-P. Metabolic predictions indicated enhanced anaerobic respiration, fatty acid degradation, and nitrogen assimilation pathways, suggesting microbial adaptation to bloom-induced localized hypoxia and high organic matter. Notably, ammonia assimilation was upregulated, likely as a detoxification strategy. Additionally, carbon flux was redirected through the methylmalonyl-CoA pathway and pyruvate-malate shuttle to compensate for partial TCA cycle downregulation, maintaining energy balance under oxygen-limited conditions. This study elucidates the interplay between N. scintillans blooms, microbial interactions, and functional adaptations, providing insights for HAB prediction and management in coastal ecosystems. Full article

The Sanniang Bay (SNB) and Dafeng River Estuary (DFR) in the Northern Beibu Gulf, China, are critical habitats for the Indo-Pacific humpback dolphin (Sousa chinensis). However, whether and how the decreased dissolved oxygen (DO) has happened in bottom seawater remains poorly understood. This study investigated DO depletion and microbial community responses using a multidisciplinary approach. High-resolution spatiotemporal sampling (16 stations across four seasons) was combined with functional annotation of prokaryotic taxa (FAPROTAX) to characterize anaerobic metabolic pathways and quantitative PCR (qPCR) targeting dsrA and dsrB genes to quantify sulfate-reducing bacteria. Partial least-squares path modeling (PLS-PM) was employed to statistically link environmental variables (seawater properties and nutrients) to microbial community structure. Results revealed pronounced bottom DO declining to 5.44 and 7.09 mg L⁻¹, a level approaching sub-optimal state (4.0–4.8 mg L⁻¹) in September. Elevated chlorophyll-a (Chl-a) near the SDH coincided with anaerobic microbial enrichment, including sulfate reducers (dsrA/dsrB abundance: SNB > DFR). PLS-PM identified seawater properties (turbidity, DO, pH) and nitrogen as key drivers of anaerobic taxa distribution. Co-occurrence network analysis further demonstrated distinct microbial modules in SNB (phytoplankton-associated denitrifiers) and DFR (autotrophic sulfur oxidizers, nitrogen fixation, and denitrification). These findings highlight how environmental factors drive decreased DO, reshaping microbial networks and threatening coastal ecosystems. This work underscores the need for regulating aquaculture/agricultural runoff to limit eutrophication-driven hypoxia and temporarily restrict human activities in SNB during peak hypoxia (September–October). Full article

Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria, Aspergillus, Blastobotrys, Thermomyces, and Rasamsonia as dominant genera, with prokaryotic communities showing greater richness and diversity than eukaryotic ones. Beta diversity and clustering analyses revealed stable microbial structures during late fermentation stages. Non-targeted metabolomics detected 347 metabolites, including 56 significantly differential compounds enriched in caffeine metabolism and unsaturated fatty acid biosynthesis. Fermentation phases exhibited distinct metabolic patterns, with volatile aroma compounds (2-acetyl-1-pyrroline, 2,5-dimethylpyrazine) and health-beneficial fatty acids (linoleic acid, arachidonic acid) accumulating in later stages. OPLS-DA and KEGG PATHWAY analyses confirmed significant shifts in metabolite profiles relevant to flavor and biofunctionality. RDA revealed strong correlations between microbial taxa, environmental parameters, and representative metabolites. To functionally verify microbial contributions, 17 bacterial and 10 fungal strains were isolated. Six representative strains, mainly Bacillus and Aspergillus, exhibited high enzymatic activity on macromolecules, confirming their roles in polysaccharide and protein degradation. This integrative multi-omics investigation provides mechanistic insights into Pu-erh tea fermentation and offers a scientific basis for microbial community optimization in tea processing. Full article

The intestinal microbiota of fish is predominantly composed of prokaryotic microorganisms, with research historically focused on bacteria. In contrast, the role of microeukaryotic organisms in the fish gut remains largely unexplored. This review synthesizes current knowledge on the diversity, ecology, and potential functions of intestinal microeukaryotes, particularly fungi and protozoans, in teleost fish. Fungi, especially Ascomycota and Basidiomycota phyla members, are consistently identified across species and may contribute to digestion, immune modulation, and microbial homeostasis. Protists, though often viewed as pathogens, also exhibit potential commensal or immunoregulatory roles, including the modulation of bacterial communities through grazing. Other eukaryotic taxa, including metazoan parasites, microalgae, and zooplankton, are commonly found as transient or diet-derived members of the gut ecosystem. While many of these organisms remain poorly characterized, emerging evidence suggests they may play essential roles in host physiology and microbial balance. The review highlights the need for improved detection methodologies, functional studies using gnotobiotic and in vitro models, and multi-kingdom approaches to uncover fish gut microeukaryotes’ ecological and biotechnological potential. Full article

Drought stress is an important abiotic stress factor restricting crop production. Broomcorn millet (Panicum miliaceum L.) has become an ideal material for analyzing the stress adaptation mechanisms of crops due to its strong stress resistance. However, the functional characteristics of its rhizosphere microorganisms in response to drought remain unclear. In this study, metagenomics and metabolomics techniques were employed to systematically analyze the compositional characteristics of the microbial community, functional properties, and changes in metabolites in the rhizosphere soil of broomcorn millet under drought stress. On this basis, an analysis was conducted in combination with the differences in functional pathways. The results showed that the drought treatment during the flowering stage significantly altered the species composition of the rhizosphere microorganisms of broomcorn millet. Among them, the relative abundances of beneficial microorganisms such as Nitrosospira, Coniochaeta, Diversispora, Gigaspora, Glomus, and Rhizophagus increased significantly. Drought stress significantly affects the metabolic pathways of rhizosphere microorganisms. The relative abundances of genes associated with prokaryotes, glycolysis/gluconeogenesis, and other metabolic process (e.g., ribosome biosynthesis, amino sugar and nucleotide sugar metabolism, and fructose and mannose metabolism) increased significantly. Additionally, the expression levels of functional genes involved in the phosphorus cycle were markedly upregulated. Drought stress also significantly alters the content of specific rhizosphere soil metabolites (e.g., trehalose, proline). Under drought conditions, broomcorn millet may stabilize the rhizosphere microbial community by inducing its restructuring and recruiting beneficial fungal groups. These community-level changes can enhance element cycling efficiency, optimize symbiotic interactions between broomcorn millet and rhizosphere microorganisms, and ultimately improve the crop’s drought adaptability. Furthermore, the soil metabolome (e.g., trehalose and proline) functions as a pivotal interfacial mediator, orchestrating the interaction network between broomcorn millet and rhizosphere microorganisms, thereby enhancing plant stress tolerance. This study sheds new light on the functional traits of rhizosphere microbiota under drought stress and their mechanistic interactions with host plants. Full article

Dehesas are mosaics of open grassland and standalone trees that are diversity reservoirs. However, they have recently faced abandonment and intensification, being replaced by plantations of fast-growing trees or subject to encroachment. Following a change in dehesa communities and structure, a change in soil microbial diversity and functionality in dehesas is expected, but dehesas’ microbial diversity is still a big unknown. In this work, we bring to light the soil prokaryotic taxonomic diversity in dehesa ecosystems and present a first approach to assessing their metabolic diversity through metabarcoding data. For this, we compared three dehesas dominated by different tree species: (i) one dehesa dominated by Quercus ilex; (ii) one dominated by Pinus pinea; and (iii) one dominated by a mixture of Q. ilex and Q. suber. At each dehesa, samples were taken under the canopy and in the open grassland, as well as through two seasons of peak vegetation productivity (autumn and spring). Our results show the following findings: (1) seasonality plays an important role in prokaryotic richness, showing higher values in autumn, and higher evenness in spring; (2) the effect of seasonality on the soil’s prokaryotic diversity is often modulated by the effect of tree species and canopy; (3) taxonomic diversity is driven mainly by the site effects, i.e., the opposite of the metabolic diversity that seemed to be driven by complex interactions among seasons, tree species, and canopies. Full article

Drinking water biofilm ecosystems harbor complex and dynamic prokaryotic and eukaryotic microbial communities. However, little is known about the impact of copper corrosion on microbial community functions in metabolisms and resistance. This study was conducted to evaluate the impact of upstream Cu pipe materials on downstream viable community structures, pathogen populations, and metatranscriptomic responses of the microbial communities in drinking water biofilms. Randomly transcribed cDNA was generated and sequenced from downstream biofilm samples of either unplasticized polyvinylchloride (PVC) or Cu coupons. Diverse viable microbial organisms with enriched pathogen-like organisms and opportunistic pathogens were active in those biofilm samples. Cu-influenced tubing biofilms had a greater upregulation of genes associated with potassium (K) metabolic pathways (i.e., K-homeostasis, K-transporting ATPase, and transcriptional attenuator), and a major component of the cell wall of mycobacteria (mycolic acids) compared to tubing biofilms downstream of PVC. Other upregulated genes on Cu influenced biofilms included those associated with stress responses (various oxidative resistance genes), biofilm formation, and resistance to toxic compounds. Downregulated genes included those associated with membrane proteins responsible for ion interactions with potassium; respiration–electron-donating reactions; RNA metabolism in eukaryotes; nitrogen metabolism; virulence, disease, and defense; and antibiotic resistance genes. When combined with our previous identification of biofilm community differences, our studies reveal how microbial biofilms adapt to Cu plumbing conditions by fine-tuning gene expression, altering metabolic pathways, and optimizing their structural organization. This study offers new insights into how copper pipe materials affect the development and composition of biofilms in premise plumbing. Specifically, it highlights copper’s role in inhibiting the growth of many microbes while also contributing to the resistance of some microbes within the drinking water biofilm community. Full article