Search Results (223)

Root nitrogen acquisition is a central belowground process that determines how efficiently plants capture nitrogen from the rhizosphere and influences fertilizer demand and environmental nitrogen losses. Root N transporters, including nitrate, ammonium, amino acid, and peptide transporters, provide the molecular basis for inorganic and organic N uptake. However, root N acquisition is not determined solely by plant transport systems but is also shaped by rhizosphere microbial communities that regulate N mobilization, transformation, and availability. In addition to bacteria and archaea, saprotrophic fungi and mycorrhizal associations contribute to organic matter decomposition, N mineralization, and symbiotic N transfer. Mechanistically, transporter activity may alter rhizosphere N gradients and substrate availability, while root exudates and microbial metabolites can influence microbial recruitment, root physiology, and transporter expression. Evidence from rice NRT1.1B and OsLHT1 suggests that specific N transporter genes can influence rhizosphere microbiome assembly, although direct genetic evidence remains limited to a small number of transporter systems and crop contexts. This review synthesizes current knowledge on root N transporter diversity, rhizosphere microbial N cycling, organic N availability, and transporter–microbiome feedbacks in root-level N acquisition. By integrating plant physiology, soil microbiology, and rhizosphere ecology, this review proposes a conceptual framework in which root N transporters and microbial communities act as interconnected components of belowground N acquisition. Future integration of transporter-informed breeding, microbiome management, and fertilization strategies may improve root N capture while reducing reliance on synthetic N inputs. Full article

Temperature is a state variable that affects all life. While it is known that archaea can grow at 120 °C and many bacteria can grow at over 100 °C, no eukaryote is known to complete a life cycle at above 65 °C. This paper explores why the difference in the maximum temperature of eukaryotes and other kingdoms of life might occur. It finds that chemical and genome structural differences between the domains of life are unlikely to explain the difference in maximum growth temperature, with the exception of the Saccharomycotina, which are different from other fungi, possibly because of their unique ecology. The distribution of inherently disordered proteins (IDPs), however, is significantly correlated with maximum and minimum growth temperature in fungi, and with the range of temperatures over which fungi can grow. I also demonstrate that the range of temperatures over which a species can grow is correlated with its maximum temperature. I postulate that the range is correlated with maximum temperature because all real-world ecologies fluctuate between elevated and average surface temperatures, and the thermodynamics of IDP-based structures in eukaryotes inherently limits the range over which they can operate. Thus, the 65 °C maximum temperature limit for eukaryotes is a result of a combination of thermodynamic properties of their organization and the temperature regime on the modern Earth; I suggest an experimental approach to testing this. Full article

The mosquito-associated virome may modulate host biology and influence vector competence, highlighting the importance of understanding its composition. Here, a metagenomic analysis was conducted to characterize the virome of the sea-rock pool mosquito Aedes mariae across sexes and developmental stages, together with water from its sea-rock pool breeding site in San Felice Circeo (Italy). A total of 51 viral taxa were identified, including viruses associated with bacteria and archaea (39%), plants, algae, fungi, and protists (35%), vertebrates (8%), and invertebrates (18%), including insect-specific viruses such as Mesoniviridae, Baculoviridae, Nudiviridae, Iridoviridae and Totiviridae. Twenty-five percent of the taxa were shared across samples, suggesting acquisition from breeding-site water and persistence across stages during development. Interestingly, the need for host genome filtering highlights the potential sequence similarity between viral and mosquito genomes, which may reflect the presence of endogenous viral elements or historical virus–host interactions. These findings represent the first characterization of the virome of Aedes mariae and highlight the role of aquatic breeding sites in shaping mosquito virome. Finally, we argue the importance of adequate sequencing depth and host genome filtering to capture the diversity of the mosquito virome. Full article

Both the gut and the lungs possess a microbiome, a community of commensal bacteria, archaea, fungi, and viruses that perform important housekeeping functions in those organs. The colonic microbiome primarily ferments indigestible dietary fibers into essential short-chain fatty acids, synthesizes essential vitamins, regulates the mucosal immune system, and forms a protective barrier against pathogenic colonization. The lung microbiome maintains respiratory health primarily by regulating mucosal immunity, providing a physical barrier against invading pathogens, and producing beneficial metabolites. Several colonic microbiota metabolites, including the short-chain fatty acids acetate, propionate, and butyrate, together with the tryptophan metabolites indole-3-acetate and indole-3-propionate, secondary bile acids, and the polyamines spermidine and putrescine, are transported to the lungs via the gut–lung axis. These colonic microbiota biomolecules suppress lung inflammation, strengthen immune homeostasis, and reduce the severity of respiratory diseases. In contrast, lung microorganisms and their metabolites can travel to the gut via the gut–lung axis, influencing intestinal immune responses and potentially leading to an imbalance of gut microorganisms or dysbiosis. This means that respiratory diseases may lead to digestive issues, intestinal inflammation and chronic diseases. Here, we have reviewed this crosstalk and its impact on the principal pulmonary diseases: asthma, chronic obstructive pulmonary disease, cystic fibrosis, bronchogenic carcinoma, COVID-19, interstitial lung diseases, pneumonia, and tuberculosis. It is concluded that the gut microbiome plays a significant part in lung health and disease. Diet, tobacco smoking and electronic cigarette vaping all impact both the gut and lung microbiomes. Full article

This study aims to evaluate the blanching process of wasted Undaria pinnatifida as a ruminant feed source by assessing chemical compositions, in vitro nutrient digestibility, rumen fermentation characteristics, greenhouse gas emissions, and rumen microbes. The blanching process was conducted at different temperatures (15 vs. 80 vs. 90 °C) and times (2 vs. 4 min) to assess the chemical and mineral contents. Supplementation levels of U. pinnatifida (0 vs. 0.5 vs. 1 vs. 2%) were observed with the blanching process (non-blanching (NBL) vs. blanching (LOS)). Increasing blanching temperature and time decreased (p < 0.05) dry matter, crude ash, and the mineral contents, including sodium, phosphorus, and arsenic. Moreover, LOS treatment increased (p < 0.01) in vitro dry matter and neutral detergent fiber digestibility, ruminal pH, and the acetate-to-propionate ratio, but reduced (p < 0.01) CH₄ (mL/g NDFD). Additionally, 2% of LOS treatment reduced the abundance of protozoa, fungi, fibrolytic microbes, methanogenic archaea, Methanobrevibacter ruminantium, Methanosarcina barkeri, and Methanosphaera stadtmanae (p < 0.01). Therefore, blanching at 80 °C for 2 min improved the nutritional profile by reducing antinutritional minerals. Subsequent in vitro fermentation suggested that supplementing the diet with 0.5–1% of LOS improved digestibility and altered fermentation, potentially reducing methane yield (per NDFD). Full article

Invasion by Spartina alterniflora has detrimental effects on existing ecosystems. Studies have shown that microorganisms can control plant growth and development. However, the root-associated community structures of bacteria, archaea, and fungi of S. alterniflora have rarely been investigated. Here, we applied metagenomics to reveal the bacterial, archaeal, and fungal communities across four root compartments, including the bulk soil, rhizosphere, rhizoplane, and endosphere. Our findings revealed the variation in different community structures. The bacterial and fungal communities exhibited greater potential environmental flexibility than the archaeal community. The endosphere environment had the simplest microbial networks and highest stability. Additionally, we identified root-exuded metabolites from S. alterniflora, which may influence microbial community assembly. Our results indicate that the rhizoplane plays a crucial role in controlling microbial entry into the root, selectively recruiting beneficial microbes for plant growth and colonization, thereby impacting nutrient cycling and plant health. This study provides insights into microbial diversity and function within the S. alterniflora root zone and suggests potential microbial-based strategies for managing this invasive species. Full article

Exocytosis is a fundamental biological process in all eukaryotes involving the vesicular transport of cellular cargo to the plasma membrane or extracellular space. However, in walled organisms such as plants, fungi, and certain archaea, the rigid cell wall presents a unique barrier to vesicular secretion. The dense, structured matrix of the mature cell wall restricts the passage of macromolecules and vesicles, raising the fundamental question of how vesicle secretion operates in this constrained environment. In the present study, we integrate transmission electron microscopy (TEM), cryo-electron tomography (cryo-ET), and serial section electron tomography (SS-ET) to investigate the structural mechanisms underlying cell wall-related exocytosis. We demonstrate that secretory vesicles do not undergo fusion with the plasma membrane in cell wall-related vesicle secretion in Arabidopsis thaliana (A. thaliana) and Saccharomyces cerevisiae (S. cerevisiae). Furthermore, in the floral nectary of A. thaliana, we identify the details of vesicles inside the multivesicular body (MVB)-like structure in cell wall. Collectively, these results reveal distinct vesicle secretion pathways adapted to the presence of a cell wall, expanding our understanding of how secretory vesicles traverse and deliver cargo beyond the plasma membrane in walled eukaryotic cells. Full article

Severe equine asthma (SEA) is a chronic inflammation of airways affecting ~14–20% of adult horses in the Northern Hemisphere. SEA is characterized by a mixed phenotype of T helper cell responses with marked neutrophilia in the bronchoalveolar lavage fluid (BALF) of affected horses. Human studies have demonstrated the impact of gut microbiota in many diseases, including asthma susceptibility and severity. However, the potential role of the gut–lung axis in the development and persistence of SEA remains to be determined. This study aimed to identify key bacterial, archaeal, and fungal microbiota alterations in the feces of horses with severe neutrophilic asthma (n = 4) compared to healthy horses (n = 8). Archaea alpha diversity was lower in the feces of SEA-affected horses, but with high abundance of archaea genus Candidatus Nitrosocosmicus, which impacts hydrogen metabolism in horses with SEA. Other key bacterial and fungi species differences lower in SEA included Blautia and Alternaria, respectively. Blautia is associated with positive metabolic health due to its fibrolytic capabilities. Overall, our findings indicate that horses experiencing severe neutrophilic asthma have an imbalance in the intestinal microbiota that may exacerbate systemic inflammatory responses through the gut–lung axis. Full article

Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery. Full article

The skin microbiome comprises a diverse community of bacteria, fungi, and archaea, all of which play a foundational role in maintaining skin health, immune tolerance, and barrier integrity. Recent advances in cosmetic science focus on the skin microbiome through the incorporation of prebiotics, probiotics and postbiotics in topical skincare formulations. This review critically examines the scientific understanding of the skin microbiome, explores the mechanisms and extractions of key “biotics” ingredients, and evaluates the clinical and regulatory landscape surrounding their use in the cosmetic industry. Despite promising scientific data and early clinical findings, there are notable challenges, including limited robust in vivo evidence, regulatory ambiguity, difficulties in formulation, and inconsistent definition and marketing claims. Regulatory harmonisation and the development of standardised testing protocols are necessary to fill the gap in today’s research and to maximise the benefits of “biotics” in the cosmetic industry. Full article

In nature, a significant number of plant species form symbiotic associations with microorganisms, with arbuscular mycorrhizal fungi (AMF) and endophytic fungi being two prevalent groups of these partners. However, the ability to establish such symbioses with AMF and endophytic fungi is limited to a small fraction of native grass species. Nitrogen is a crucial nutrient for plant growth, yet it is often a limiting factor, underscoring the importance of understanding how plants acquire it. AMF enhance plant growth by improving nitrogen uptake efficiency, but the combined effects of endophytic fungi and AMF on plant physiology and ecology remain underexplored. To address this knowledge gap, in the present study, we conducted an indoor randomized block experiment to investigate the influence of endophytic fungi and AMF infection on the physiological and ecological attributes of Festuca rubra under various nitrogen regimes. The findings indicated that AMF inoculation significantly affected the total carbon content of F. rubra and the total sulfur concentration in its underground tissues across different nitrogen conditions. Additionally, dual colonization by AMF and endophytic fungi had a significant impact on the underground total nitrogen content of the plants. Furthermore, the complex interactions among AMF, endophytic fungi, and nitrogen availability emerged as critical determinants influencing underground total carbon content, transpiration rates, intercellular carbon dioxide concentrations, and the activity of soil extracellular enzymes in F. rubra. The activity of soil extracellular enzymes and pH significantly affected the structure and diversity of rhizosphere bacterial, fungal, and archaeal communities. AMF enhanced the richness of rhizosphere bacterial communities under low-nitrogen conditions, whereas endophytic fungi infection increased bacterial diversity. Soil extracellular enzyme activity and pH were closely related to the community structures and diversities of rhizosphere bacteria, fungi, and archaea. This study clarifies the effects of AMF and endophytic fungi infection on the physiological and ecological characteristics of F. rubra, significantly contributing to our understanding of the synergistic mechanisms governing the interactions among AMF, endophytic fungi, and their host plants. Full article

Marine fog is a key non-rainfall water source that sustains microbial activity and transports dissolved nutrients inland, influencing early soil development in hyperarid ecosystems. However, the mechanisms through which sustained fog inputs drive soil surface modification and biocrust formation remain poorly understood. This study evaluated the effects of long-term fog augmentation on soil surface development, biocrust dynamics, and associated microbial communities in the Atacama Desert. We implemented a four-year fog addition field experiment with three sampling times (T0, T24, T48) to assess changes in soil physicochemical properties, biocrust composition, and the integrated multi-diversity of archaea, bacteria, fungi and protist. Sustained fog input transformed bare soils into biological soil crusts, particularly lichen- and moss-dominated stages. This transition was accompanied by increases in soil nitrogen, variations in organic matter accumulation, a shift from alkaline to near-neutral pH, and improvements in soil stability and water retention. Multi-diversity increased over time and was positively associated with ecosystem variables linked to water availability, structural stabilization, and decomposition. These functions, integrated into an ecosystem multifunctionality index, also increased under prolonged fog input, revealing a positive relationship between multifunctionality and multi-diversity. Overall, the results demonstrate that sustained fog input strongly enhances early soil surface development and biocrust establishment, highlighting the ecological importance of marine fog in shaping biodiversity and ecosystem functioning in hyperarid landscapes. Full article

This study explores the intestinal microbiota of eight 18-month-old male alpacas from two distinct high-altitude regions in Peru: the Wet Puna (4200 m above sea level) and the Dry Puna (4900 m above sea level). Using 16S rRNA and 18S rRNA metabarcoding, microbial communities of bacteria, archaea, fungi, and protists were analyzed from the first compartment of the stomach (C1) to investigate the diversity, taxonomic composition, and correlations with hematological parameters. Significant differences in microbial diversity and composition were observed between regions, driven by dietary and environmental factors. The Wet Puna exhibited greater alpha diversity in bacterial and fungal communities, while beta diversity highlighted distinct microbial compositions. Key taxa, such as Prevotella ruminicola and Acetitomaculum, were associated with energy metabolism and host adaptation, whereas methanogenic archaea (Methanobrevibacter, Methanosphaera) dominated in the Dry Puna, reflecting adaptations to arid conditions. Correlations between microbial taxa and hematological variables, such as Acetitomaculum with red blood cell count and Eremoplastron with neutrophil percentage, emphasize the complex interplay between microbiota and host physiology. These findings contribute to understanding microbial adaptations in high-altitude livestock and provide practical insights for enhancing alpaca management and conservation strategies through tailored nutritional approaches and sustainable grazing practices. Full article

Microorganisms, as the foundation of deep-sea ecosystems, are crucial for maintaining the structure and stability of polymetallic nodule field environments. To investigate the community structure and distributional patterns of benthic microorganisms in such environments, this study used high-throughput sequencing to analyze the composition, diversity, and environmental correlations of bacteria, archaea, and fungi in the BPC (Beijing Pioneer Hi-tech Development Corporation Ltd., Beijing, China). Furthermore, microbial communities from BPC were compared with those from UK-1 (UK Seabed Resources, Southampton, UK) in terms of community structure and co-occurrence network characteristics. The results revealed that in the BPC, the bacterial communities were dominated by Proteobacteria and Chloroflexi, while Crenarchaeota represented the overwhelmingly dominant group. Fungal communities were primarily composed of Ascomycota and Basidiomycota. Correlation Analysis suggested that water depth, TOC (Total organic carbon), TN (Total nitrogen), and δ¹⁵N emerged as the key environmental drivers of microbial community variation. Comparative analysis showed microbial groups exhibited certain similarities but also some differences at the phylum, class, and order levels, with the differences becoming increasingly pronounced at finer taxonomic resolutions between BPC and UK-1. Co-occurrence network analyses indicated the microbial networks with higher density and node connectivity in the BPC, whereas the UK-1 exhibited greater modularity and clustering coefficients. Microbial interactions were weaker in the UK-1, but its resilience to benthic disturbance was expected to be higher than in the BPC. Full article